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Number of items: 1671. Weimann, K. and Conrad, T. O. F. (2024) FELRec: Efficient Handling of Item Cold-Start With Dynamic Representation Learning in Recommender Systems. International Journal of Data Science and Analytics . (In Press) Doppler, Sabine and Klein, Rupert and Liu, Xin and Titi, Edriss (2024) Local well-posedness of a system coupling compressible atmospheric dynamics and a micro-physics model of moisture in air. Preprint arXiv . (Unpublished) Delle Site, Luigi and Hartmann, Carsten (2024) Computationally feasible bounds for the free energy of nonequilibrium steady states, applied to simple models of heat conduction. Molecular Physics . Rosemeier, Juliane and Haut, Terry and Wingate, Beth (2024) Multilevel Parareal Algorithm with Averaging for Oscillatory Problems. Numerical Algorithms for Scientific Computung, 46 (4). pp. 2709-2736. Huber, Konstantin and John, Timm and Vrijmoed, Johannes C. and Pleuger, Jan and Zhong, Xin (2024) Pulsed fluid release from subducting slabs caused by a scale-invariant dehydration process. Earth and Planetary Science Letters, 644 . Schebek, Maximilian and Invernizzi, Michele and Noé, Frank and Rogal, Jutta (2024) Efficient Mapping of Phase Diagrams with Conditional Boltzmann Generators. Preprint arXiv . (Unpublished) Cao, Chongsheng and Li, Jinkai and Titi, Edriss S. and Wang, Dong (2024) Global well-posedness of the 3D primitive equations with horizontal viscosity and vertical diffusivity II: close to H1 initial data. arXiv (Preprint) . (Unpublished) Bryant, Patrick and Noé, Frank (2024) Improved Protein Complex Prediction with AlphaFold-Multimer by Denoising the MSA Profile. PLOS Computational Biology, 20 (7). Sun, Jingtong and Berner, Julius and Richter, Lorenz and Zeinhofer, Marius and Müller, Johannes and Azizzadenesheli, Kamyar and Anandkumar, Anima (2024) Dynamical Measure Transport and Neural PDE Solvers for Sampling. Preprint arXiv . (Unpublished) Weimann, K. and Conrad, T. O. F. (2024) Federated Learning with Deep Neural Networks: A Privacy-Preserving Approach to Enhanced ECG Classification. IEEE Journal of Biomedical and Health Informatics . (In Press) Bostanci, Inan and Conrad, T. O. F. (2024) Integrating Agent-Based and Compartmental Models for Infectious Disease Modeling: A Novel Hybrid Approach. Journal of Artificial Societies and Social Simulation . (Submitted) Liu, Xin and Titi, Edriss S. and Xin, Zhouping (2024) Asymptotic stability of the equilibrium for the free boundary problem of a compressible atmospheric primitive model with physical vacuum. Preprint . (Unpublished) Delle Site, Luigi and Djurdjevac, Ana (2024) An effective Hamiltonian for the simulation of open quantum molecular systems. Journal of Physics A: Mathematical and Theoretical, 57 (25). Keller, Bettina G. and Bolhuis, Peter G. (2024) Dynamical Reweighting for Biased Rare Event Simulations. Annual Review of Physical Chemistry, 75 (1). pp. 137-162. Conrad, T. O. F. and Ferrer, Eloi and Mietchen, Daniel and Pusch, Larissa and Stegmüller, Johannes and Schubotz, Moritz (2024) Making Mathematical Research Data FAIR: Pathways to Improved Data Sharing. Nature Scientific Data . (In Press) Gaskin, Thomas and Conrad, T. O. F. and Pavliotis, Grigorios A. and Schütte, Ch. (2024) Neural parameter calibration and uncertainty quantification for epidemic forecasting. PLoS ONE . ISSN 1932-6203 (In Press) Chemnitz, Robin and Engel, Maximilian and Olicón-Mendez, Guillermo (2024) Random attractors on countable state spaces. Preprint arXiv . (Unpublished) Bryant, Patrick and Kelkar, Atharva and Guljas, Andrea and Clementi, Cecilia and Noé, Frank (2024) Structure prediction of protein-ligand complexes from sequence information with Umol. Nature Communications, 15 . Winkler, Ludwig and Richter, Lorenz and Opper, Manfred (2024) Bridging discrete and continuous state spaces: Exploring the Ehrenfest process in time-continuous diffusion models. Preprint arXiv . (Unpublished) Fürst, Steffen and Conrad, T. O. F. and Jaeger, Carlo and Wolf, S. (2024) Vahana.jl - A framework (not only) for large-scale agent-based models. Social Simulation Conference 2024 . (In Press) Sherratt, Katharine and Srivastava, Ajitesh and Ainslie, Kylie and Singh, David E. and Cublier, Aymar and Marinescu, Maria Cristina and Carretero, Jesus and Garcia, Alberto Cascajo and Franco, Nicolas and Willem, Lander and Abrams, Steven and Faes, Christel and Beutels, Philippe and Hens, Niel and Müller, Sebastian and Charlton, Billy and Ewert, Ricardo and Paltra, Sydney and Rakow, Christian and Rehmann, Jakob and Conrad, T. O. F. and Schütte, Christof and Nagel, Kai and Abbott, Sam and Grah, Rok and Niehus, Rene and Prasse, Bastian and Sandmann, Frank and Funk, Sebastian (2024) Characterising information gains and losses when collecting multiple epidemic model outputs. Epidemics . Koltai, Péter and Kunde, Philipp (2024) A Koopman-Takens theorem: Linear least squares prediction of nonlinear time series. Preprint . (In Press) Chemnitz, Robin and Engel, Maximilian and Koltai, Péter (2024) Extracting coherent sets in aperiodically driven flows from generators of Mather semigroups. Preprint . (Unpublished) Berner, Julius and Richter, Lorenz and Ullrich, Karen (2024) An optimal control perspective on diffusion-based generative modeling. Preprint arXiv . (Unpublished) Djurdjevac, Ana and Kremp, Helena and Perkowski, Nicolas (2024) Weak error analysis for a nonlinear SPDE approximation of the Dean-Kawasaki equation. Stochastics and Partial Differential Equations: Analysis and Computations . Atnip, Jason and Froyland, Gary and Koltai, Péter (2024) An inflated dynamic Laplacian to track the emergence and disappearance of semi-material coherent sets. Preprint . (Unpublished) Hauswedell, Hannes and Hetzel, Sara and Gottlieb, Simon G and Kretzmer, Helene and Meissner, Alexander and Reinert, Knut and Cowen, Lenore (2024) Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences. Bioinformatics, 40 (3). ISSN 1367-4811 Smit, Matthijs and Vrijmoed, Johannes C. and Scherer, Erik E. and Mezger, Klaus and Kooijman, Ellen and Schmitt-Kielmann, Melanie and Tual, Lorraine and Guilmette, Carl and Ratschbacher, Lothar (2024) Retentiveness of rare earth elements in garnet with implications for garnet Lu-Hf chronology. Journal of Metamorphic Geology . Ghysbrecht, Simon and Keller, Bettina G. (2024) Thermal isomerization rates in retinal analogues using Ab-Initio molecular dynamics. Journal of Computational Chemistry, 45 (16). pp. 1317-1427. Zhao, Yue and Zhang, Wei and Li, Tiejun (2024) EPR-Net: Constructing non-equilibrium potential landscape via a variational force projection formulation. National Science Review . Quer, Jannes and Ribera Borrell, Enric (2024) Connecting Stochastic Optimal Control and Reinforcement Learning. Submitted Preprint . (Submitted) Hartmann, Carsten and Jöster, Annika (2024) Risk-neutral limit of adaptive importance sampling of random stopping times. Submitted to 26th International Symposium on Mathematical Theory of Networks and Systems . (Submitted) Delle Site, Luigi and Hartmann, Carsten (2024) Scaling law for the size dependence of a finite-range quantum gas. Physical Review A, 109 (2). Delle Site, Luigi and Hartmann, Carsten (2024) Scaling law for the size dependence of a short-ranged quantum gas. Physical Review A, 109 . Dolores-Tesillos, Edgar and Pfahl, Stephan (2024) Future changes in North Atlantic winter cyclones in CESM-LE – Part 2: A Lagrangian analysis. Weather and Climate Dynmics, 5 . pp. 163-179. Wu, Hao and Noé, Frank (2024) Reaction coordinate flows for model reduction of molecular kinetics. The Journal of Chemical Physics, 160 (4). Pan, Chenxu and Reinert, Knut and Valencia, Alfonso (2024) A simple refined DNA minimizer operator enables 2-fold faster computation. Bioinformatics, 40 (2). ISSN 1367-4811 Pavliotis, Grigorios A. and Reich, Sebastian and Zanoni, Andrea (2024) Filtered data based estimators for stochastic processes driven by colored noise. Preprint arXiv . (Unpublished) Rentsch, Jakob and Bandstra, Selle and Sezen, Batuhan and Sigrist, Philipp Stephan and Bottanelli, Francesca and Schmerl, Bettina and Shoichet, Sarah and Noé, Frank and Sadeghi, Mohsen and Ewers, Helge (2024) Sub-membrane actin rings compartmentalize the plasma membrane. Journal of Cell Biology (JCB), 223 (4). Sikorski, Alexander and Ribera Borrell, Enric and Weber, Marcus (2024) Learning Koopman eigenfunctions of stochastic diffusions with optimal importance sampling and ISOKANN. Journal of Mathematical Physics, 65 (1). Paltra, Sydney and Conrad, T. O. F. (2024) Clinical Effectiveness of Ritonavir-Boosted Nirmatrelvir—A Literature Review. Advances in Respiratory Medicine, 92 (1). ISSN 2543-6031 Alchikh, Maren and Conrad, T. O. F. and Obermeier, Patrick E. and Ma, Xiaolin and Schweiger, Brunhilde and Opota, Onya and Rath, Barbara A. (2024) Disease Burden and Inpatient Management of Children with Acute Respiratory Viral Infections during the Pre-COVID Era in Germany: A Cost-of-Illness Study. Viruses, 16 (4). Mischau, A. and Ransiek, A. (2024) Gendered Gatekeeping in the Recruitment and Support of (Prospective) PhDs and Postdocs in a Mathematical Cluster of Excellence. International Journey of Gender Science and Technology, 16 (1). pp. 71-99. Guth, Philipp A. and Kaarnioja, Vesa (2024) Generalized dimension truncation error analysis for high-dimensional numerical integration: lognormal setting and beyond. to appear in SIAM Journal on Numerical Analysis . (Submitted) Maier, Kristina and Weiser, Martin and Conrad, T. O. F. (2024) Hybrid PDE-ODE Models for Efficient Simulation of Infection Spread in Epidemiology. arXiv . (Submitted) Werkovits, A. and Hollweger, S. and Niederreiter, M. and Risse, T. and Cartus, J.J. and Sterrer, M. and Matera, S. (2024) Kinetic Trapping of Charge-Transfer Molecules at Metal Interfaces. The Journal of Physical Chemistry C . Eigel, Martin and Gruhlke, Robert and Sommer, David (2024) Less interaction with forward models in Langevin dynamics: Enrichment and Homotopy Martin , Robert , David. arXiv To appear in SIADS . (Submitted) Liu, X. and Klein, R. (2024) On the boundary layer arising from fast internal waves dynamics. (Submitted) Gruhlke, Robert and Nouy, Anthony and Trunschke, Philipp (2024) Optimal sampling for stochastic and natural gradient descent Robert Gruhlke, ,. arXiv . (Submitted) Montefusco, Alberto and Helfmann, Luzie and Okunola, Toluwani and Winkelmann, Stefanie and Schütte, Christof (2024) Partial mean-field model for neurotransmission dynamics. Mathematical Biosciences, 369 . Kaarnioja, Vesa and Rupp, Andreas (2024) Quasi-Monte Carlo and discontinuous Galerkin. arXiv . (Submitted) Guth, Philipp A. and Kaarnioja, Vesa (2024) Uncertainty quantification for random domains using periodic random variables. Numerische Mathematik, 156 . pp. 273-317. Engel, Maximilian and Olicón-Mendez, Guillermo (2023) A singular perturbation analysis for the Brusselator. Preprint . (Submitted) Engel, Maximilian and Piliouras, Georgios (2023) A stochastic variant of replicator dynamics in zero-sum games and its invariant measures. Physica D: Nonlinear Phenomena, 456 . Jong-Bolm, Daniëlle de and Sadeghi, Mohsen and Bogaciu, Cristian A. and Bao, Guobin and Klaehn, Gabriele and Hoff, Merle and Mittelmeier, Lucas and Basmanav, F. Buket and Noé, Frank and Rizzoli, Silvio O. (2023) Protein nanobarcodes enable single-step multiplexed fluorescence imaging. PLOS BIOLOGY, 21 (12). Piro, Vitor C. and Reinert, Knut (2023) ganon2: up-to-date and scalable metagenomics analysis. bioRxiv preprint . Mielke, Alexander (2023) Non-equilibrium steady states as saddle points and EDP-convergence for slow-fast gradient systems. Journal of Mathematical Physics, 64 (12). Ernst, Ariane and Falkenhagen, Undine and Winkelmann, Stefanie (2023) Model reduction for Ca²+ -induced vesicle fusion dynamics. Proceedings in Applied Mathematics and Mechanics, 23 (4). Coghi, Michele and Nilssen, Torstein and Nüsken, Nikolas and Reich, Sebastian (2023) Rough McKean–Vlasov dynamics for robust ensemble Kalman filtering. The Annals of Applied Probability, 33 (6b). pp. 5693-5752. Pacey, George and Pfahl, Stephan and Schielicke, Lisa and Wapler, Kathrin (2023) The climatology and nature of warm-season convective cells in cold-frontal environments over Germany. Natural Hazards Earth System Sciences, 23 (12). pp. 3703-3721. Liero, Matthias and Mielke, Alexander and Savaré, Giuseppe (2023) Fine properties of geodesics and geodesic lambda-convexity for the Hellinger-Kantorovich distance. Archive for Rational Mechanics and Analysis, 247 (112). Giurgiu, Mădălina and Wittstruck, Nadine and Rodriguez-Fos, Elias and Chamorro González, Rocío and Brückner, Lotte and Krienelke-Szymansky, Annabell and Helmsauer, Konstantin and Hartebrodt, Anne and Koche, Richard P. and Haase, Kerstin and Reinert, Knut and Henssen, Anton G. (2023) Decoil: Reconstructing extrachromosomal DNA structural heterogeneity from long-read sequencing data. bioRxiv - The Preprint Server for Biology . Kern, Julian and Wiederhold, Bastian (2023) A Λ-Fleming-Viot type model with intrinsically varying population size. Electronic Journal of Probability . (Submitted) Kern, Julian (2023) Exponential equivalence for misanthrope processes in contact with weak reservoirs and applications to totally asymmetric exclusion processes. Preprint . (Unpublished) Bleich, Amnon and Linnemann, Antje and Benjamin, Jaidi and Bjoern, H. Diem and Conrad, T. O. F. (2023) Enhancing ECG Analysis of Implantable Cardiac Monitor Data: An Efficient Pipeline for Multi-Label Classification. Machine Learning and Knowledge Extraction, 5 (4). ISSN 2504-4990 Charron, Nicholas E. and Musil, Felix and Guljas, Andrea and Chen, Yaoyi and Bonneau, Klara and Pasos-Trejo, Aldo S. and Venturin, Jacopo and Gusew, Daria and Zaporozhets, Iryna and Krämer, Andreas and Templeton, Clark and Kelkar, Atharva and Durumeric, Alexander E.P. and Olsson, Simon and Pérez, Adrià and Majewski, Maciej and Husic, Brooke E. and Patel, Ankit and Fabritiis, Gianni De and Noé, Frank and Clementi, Cecilia (2023) Navigating protein landscapes with a machine-learned transferable coarse-grained model. Preprint . (Unpublished) Koronaki, D. Eleni and Evangelou, Nikolaos and Martin-Linares, Cristina P. and Titi, Edriss and Kevrekidis, Ioannis G. (2023) Nonlinear dimensionality reduction then and now: AIMs for dissipative PDEs in the ML era. Preprint . (Unpublished) Bäumer, D. and Hittmeir, S. and Klein, R. (2023) Scaling approaches to quasi-geostrophic theory for moist, precipitating air. J. Atmos. Sci. . pp. 1-18. Lelièvre, Tony and Pigeon, Thomas and Stoltz, Gabriel and Zhang, Wei (2023) Analyzing multimodal probability measures with autoencoders. To appear in The Journal of Physical Chemistry B . (In Press) Blumenthal, Alex and Engel, Maximilian and Neamţu, Alexandra (2023) On the pitchfork bifurcation for the Chafee-Infante equation with additive noise. Probability Theory and Related Fields, 187 . pp. 603-627. Kern, Julian (2023) Skorokhod topologies: What they are and why we should care. Mathematische Semesterberichte . Borrell, Enric Ribera and Quer, Jannes and Richter, Lorenz and Schütte, Christof (2023) Improving control based importance sampling strategies for metastable diffusions via adapted metadynamics. Preprint to appear in SISC 2024 . (In Press) Weimann, K. and Conrad, T. O. F. (2023) Predicting Coma Recovery After Cardiac Arrest With Residual Neural Networks. Computing in Cardiology (CinC) 2023, 50 . Huysmans, Lucas and Titi, Edriss (2023) Non-Uniqueness and Inadmissibility of the Vanishing Viscosity Limit of the Passive Scalar Transport Equation. arXiv . (Unpublished) Nowatzky, Yannek and Benner, Philipp and Reinert, Knut and Muth, Thilo (2023) Mistle: bringing spectral library predictions to metaproteomics with an efficient search index. Bioinformatics, 39 (6). ISSN 1367-4811 Arts, Marloes and Garcia Sattorras, Victor and Huang, Chin-Wei and Zuegner, Daniel and Federici, Marco and Clementi, Cecilia and Noé, Frank and Pinsler, Robert and van den Berg, Rianne (2023) Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics. JCTC - Journal of Chemical Theory and Computation, 19 . pp. 6151-6159. Majewski, Maciej and Pérez, Adrià and Thölke, Philipp and Doerr, Stefan and Charron, Nicholas E. and Giorgino, Toni and Husic, Brooke E. and Clementi, Cecilia and Noé, Frank and De Fabritiis, Gianni (2023) Machine Learning Coarse-Grained Potentials of Protein Thermodynamics. Nature Communications, 14 . Polzin, Robert and Klebanov, Ilja and Nüsken, Nikolas and Koltai, Péter (2023) Nonnegative matrix factorization for coherent set identification by direct low rank maximum likelihood estimation. arXiv . pp. 1-43. (Unpublished) Unanue, Alvaro de Diego and Froyland, Gary and Junge, Oliver and Koltai, Péter (2023) A dynamic p-Laplacian. Preprint . (Unpublished) Bogdanow, Boris and Gruska, Iris and Mühlberg, Lars and Protze, Jonas and Hohensee, Svea and Vetter, Barbara and Bosse, Jens B. and Lehmann, Martin and Sadeghi, Mohsen and Wiebusch, Lüder and Liu, Fan (2023) Spatially resolved protein map of intact human cytomegalovirus virions. Nature Microbiology, 8 . pp. 1732-1747. Müller, Sebastian and Paltra, Sydney and Rehmann, Jakob and Nagel, Kai and Conrad, T. O. F. (2023) Explicit Modelling of Antibody Levels for Infectious Disease Simulations in the Context of SARS-CoV-2. iScience, 26 (9). ISSN 2589-0042 Ernst, Ariane and Unger, Nathalie and Schütte, Christof and Walter, Alexander M. and Winkelmann, Stefanie (2023) Rate-limiting recovery processes in neurotransmission under sustained stimulation. Mathematical Biosciences, 362 . p. 109023. Maity, Priyanka and Bittracher, Andreas and Koltai, Péter and Schumacher, Jörg (2023) Collective variables between large-scale states in turbulent convection. Physical Review Research, 5 (3). Richter, Lorenz and Sallandt, Leon and Nüsken, Nikolas (2023) From continuous-time formulations to discretization schemes: tensor trains and robust regression for BSDEs and parabolic PDEs. Preprint . (Unpublished) Chew, R. and Schlutow, M. and Klein, R. (2023) An unstable mode of the stratified atmosphere under the non-traditional Coriolis acceleration. Journal of Fluid Mechanics, 967 . Nickl, Richard and Titi, Edriss (2023) On posterior consistency of data assimilation with Gaussian process priors: the 2D Navier-Stokes equations. ArXiv . (Unpublished) Froyland, Gary and Koltai, Péter (2023) Detecting the birth and death of finite-time coherent sets. Communications on Pure and Applied Mathematics, 76 (12). pp. 3642-3684. Richter, Lorenz and Berner, Julius and Liu, Guang-Horng (2023) Improved sampling via learned diffusions. Preprint . (Unpublished) Fradon, Myriam and Kern, Julian and Roelly, Sylvie and Zass, Alexander (2023) Diffusion dynamics for an infinite system of two-type spheres and the associated depletion effect. Preprint submitted to Stochastic Processes and their Applications . (Submitted) Chemnitz, Dennis and Engel, Maximilian (2023) Positive Lyapunov Exponent in the Hopf Normal Form with Additive Noise. Communications in Mathematical Physics, 402 . pp. 1807-1843. Reible, Benedikt M. and Hille, Julian F. and Hartmann, Carsten and Delle Site, Luigi (2023) Finite-size effects and thermodynamic accuracy in many-particle systems. Physical Review Research, 5 (2). Dyhr, Michael C. A. and Sadeghi, Mohsen and Moynova, Ralista and Knappe, Carolin and Burcu Kepsutlu, Çakmak and Werner, Stephan and Schneider, Gerd and McNally, James and Noé, Frank and Ewers, Helge (2023) 3D surface reconstruction of cellular cryo-soft X-ray microscopy tomograms using semisupervised deep learning. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 120 (24). Mehringer, Svenja and Seiler, Enrico and Droop, Felix and Darvish, Mitra and Rahn, René and Vingron, Martin and Reinert, Knut (2023) Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries. Genome Biology, 24 (131). ISSN 1474-760X Kaatz, L. and Schmalholz, Stefan M. and John, T. (2023) Numerical Simulations Reproduce Field Observations Showing Transient Weakening During Shear Zone Formation by Diffusional Hydrogen Influx and H2O Inflow. Geochemistry, Geophysics, Geosystems, 24 (5). Boutros, Daniel W. and Markfelder, Simon and Titi, Edriss (2023) Nonuniqueness of generalised weak solutions to the primitive and Prandtl equations. arXiv . pp. 1-73. (Unpublished) Barua, Amlan K. and Chew, Ray and Li, Shuwang and Lowengrub, John and Münch, Andreas and Wagner, Barbara (2023) Sharp-interface problem of the Ohta-Kawasaki model for symmetric diblock copolymers. Journal of Computational Physics, 481 . Chemnitz, Robin and Engel, Maximilian and Koltai, Péter (2023) Continuous-time extensions of discrete-time cocycles. Contemporary Mathematics . (In Press) Schütte, Christof and Klus, Stefan and Hartmann, Carsten (2023) Overcoming the Timescale Barrier in Molecular Dynamics: Transfer Operators, Variational Principles, and Machine Learning. Acta Numerica, 32 . pp. 517-673. Bittracher, Andreas and Mollenhauer, Mattes and Koltai, Péter and Schütte, Christof (2023) Optimal Reaction Coordinates: Variational Characterization and Sparse Computation. Multiscale Modeling & Simulation, 21 (2). pp. 449-488. Gertler, Charles G. and O’Gorman, Paul A. and Pfahl, Stephan (2023) Moist available potential energy of the mean state of the atmosphere and the thermodynamic potential for warm conveyor belts and convection. Weather Clim. Dynam., 4 . pp. 361-379. Krämer, Andreas and Durumeric, Alexander E.P. and Charron, Nicholas E. and Chen, Yaoyi and Clementi, Cecilia and Noé, Frank (2023) Statistically Optimal Force Aggregation for Coarse-Graining Molecular Dynamics. The Journal of Physical Chemistry, 14 . pp. 3970-3979. Engel, Maximilian and Gottwald, Georg A. (2023) Canards in modified equations for Euler discretizations. Preprint to appear in Contemporary Mathematics . (In Press) Bardos, Claude and Liu, Xin and Titi, Edriss (2023) Derivation of a generalized quasi-geostrophic approximation for inviscid ows in a channel domain: The fast waves correction. pp. 1-33. (Unpublished) Bardos, Claude and Boutros, Daniel W. and Titi, Edriss (2023) Hoelder regularity of the pressure for weak solutions of the 3D Euler equations in bounded domains. Preprint . pp. 1-35. (Unpublished) Durumeric, Alexander E.P. and Charron, Nicholas E. and Templeton, Clark and Musil, Félix and Bonneau, Klara and Pasos-Trejo, Aldo S. and Chen, Yaoyi and Kelkar, Atharva and Noé, Frank and Clementi, Cecilia (2023) Machine learned coarse-grained protein force-fields: Are we there yet? Current Opinion in Structural Biology, 79 . Piro, Vitor C and Renard, Bernhard Y (2023) Contamination detection and microbiome exploration with GRIMER. GigaScience, 12 . ISSN 2047-217X Engel, Maximilian and Olicon-Méndez, Guillermo (2023) Noise-induced instabilities in a stochastic Brusselator. Preprint to appear in Contemporary Mathematics . (In Press) Straube, Arthur V. and Winkelmann, Stefanie and Höfling, Felix (2023) Accurate reduced models for the pH oscillations in the urea-urease reaction confined to giant lipid vesicles. J. Phys. Chem. B, 127 (13). pp. 2955-2967. Mohammadi, Somayeh and PourKarimi, Latif and Droop, Felix and De Mecquenem, Ninon and Leser, Ulf and Reinert, Knut (2023) A mathematical programming approach for resource allocation of data analysis workflows on heterogeneous clusters. The Journal of Supercomputing, 79 (17). pp. 19019-19048. ISSN 0920-8542 Pan, Chenxu and Rahn, René and Heller, David and Reinert, Knut (2023) Linear: a framework to enable existing software to resolve structural variants in long reads with flexible and efficient alignment-free statistical models. Briefings in Bioinformatics, 24 (2). ISSN 1467-5463; Online ISSN 1477-4054 Nüsken, Nikolas and Richter, Lorenz (2023) Interpolating Between BSDEs and PINNs: Deep Learning for Elliptic and Parabolic Boundary Value Problems. Journal of Machine Learning, 2 . pp. 31-64. Zafferi, Andrea and Huber, Konstantin and Peschka, Dirk and Vrijmoed, Johannes and John, Timm and Thomas, Marita (2023) A porous-media model for reactive fluid-rock interaction in a dehydrating rock. Preprint . pp. 1-22. (Unpublished) Alphonse, Amal and Caetano, Diogo and Djurdjevac, Ana and Elliott, Charles M. (2023) Function spaces, time derivatives and compactness for evolving families of Banach spaces with applications to PDEs. Journal of Differential Equations, 353 . pp. 268-338. del Razo, M.J. and Winkelmann, S. and Klein, R. and Höfling, F. (2023) Chemical diffusion master equation: formulations of reaction–diffusion processes on the molecular level. J. Math. Phys., 64 (013304). Köhler, Jonas and Chen, Yaoyi and Krämer, Andreas and Clementi, Cecilia and Noé, Frank (2023) Flow-Matching: Efficient Coarse-Graining of Molecular Dynamics without Forces. J. Chem. Theory Comput., 19 (3). pp. 942-952. Yang, Wangfei and Templeton, Clark and Rosenberger, David and Bittracher, Andreas and Nüske, Feliks and Noé, Frank and Clementi, Cecilia (2023) Slicing and Dicing: Optimal Coarse-Grained Representation to Preserve Molecular Kinetics. ACS Cent. Sci., 9 (2). pp. 186-196. Thies, Arne and Sunkara, Vikram and Ray, Sourav and Wulkow, Hanna and Özgür Celik, M. and Yergöz, Fatih and Schütte, Christof and Stein, Christoph and Weber, Marcus and Winkelmann, Stefanie (2023) Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design. Scientific Reports, 13 (1). p. 607. Wang, Yuwei and Lian, Bin and Zhang, Haohui and Zhong, Yuanke and He, Jie and Wu, Fashuai and Reinert, Knut and Shang, Xuequn and Yang, Hui and Hu, Jialu and Mathelier, Anthony (2023) A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data. Bioinformatics, 39 (1). ISSN 1367-4803 Melnyk, Kateryna and Weimann, K. and Conrad, T. O. F. (2023) Understanding microbiome dynamics via interpretable graph representation learning. Scientific Reports, 13 (2058). ISSN 2045-2322 Mischau, A. (2023) Den Ballast tradierter Zerrbilder in Mathematikschulbüchern endlich abwerfen. Mitteilungen der Deutschen Mathematiker-Vereinigung, 31 (1). Matera, S. and Dortaj, S. (2023) Efficient global sensitivity analysis of kinetic Monte Carlo simulations using Cramérs–von Mises distance. Journal of Chemical Physics . ISSN Online ISSN 1089-7690 Print ISSN 0021-9606 Hanu, Matei and Hesser, Jürgen and Kanschat, Guido and Moviglia, Javier and Schillings, Claudia and Stallkamp, Jan (2023) Ensemble Kalman Inversion for Image Guided Guide Wire Navigation in Vascular Systems. arXiv . (Submitted) Schillings, Claudia and Totzeck, Claudia and Wacker, Philipp (2023) Ensemble-based gradient inference for particle methods in optimization and sampling. SIAM/ASA Journal on Uncertainty Quantification, 11 (3). pp. 757-787. Gelß, P. and Issagali, A. and Kornhuber, R. (2023) Fredholm integral equations for function approximation and the training of neural networks. arXiv . (Submitted) Harikrishnan, A. P. and Ansorge, C. and Klein, R. and Vercauteren, N. (2023) Geometry and organization of coherent structures in stably stratified atmospheric boundary layers. Journal of Fluid Mechanics . (Submitted) Hittmeir, S. and Klein, R. and Li, J. and Titi, Edriss (2023) Global well-posedness for the thermodynamically refined passively transported nonlinear moisture dynamics with phase changes. Journal of Nonlinear Science, 33 (65). ISSN Online: 1432-1467 Print: 0938-8974 Jung, S. and Schwedhelm, J.C. and Schillings, Claudia and Keuper, M. (2023) Happy People--Image Synthesis as Black-Box Optimization Problem in the Discrete Latent Space of Deep Generative Models. arXiv . (Submitted) Mollenhauer, Mattes and Schillings, Claudia (2023) On the concentration of subgaussian vectors and positive quadratic forms in Hilbert spaces. arXiv . (Submitted) Hanu, Matei and Weissmann, Simon (2023) On the ensemble Kalman inversion under inequality constraints. arXiv . (Submitted) Harikrishnan, A. P. and Rodal, M. and Klein, R. and Margerit, D, and Vercauteren, N. (2023) On the motion of hair-pin filaments in the atmospheric boundary layer. Physics of Fluids, 35 (7). Li, Z. and Meunier, D. and Mollenhauer, Mattes and Gretton, A. (2023) Optimal Rates for Regularized Conditional Mean Embedding Learning. Advances in Neural Information Processing Systems (NeurIPS), 36 . (Submitted) Bittracher, Andreas and Mollenhauer, Mattes and Koltai, Péter and Schütte, Ch. (2023) Optimal Reaction Coordinates: Variational Characterization and Sparse Computation. Multiscale Modeling & Simulation, 21 (2). ISSN ISSN (print): 1540-3459 ISSN (online): 1540-3467 Gelß, P. and Matera, S. and Klein, R. and Schmidt, B. (2023) Quantum Dynamics of Coupled Excitons and Phonons in Chain-Like Systems: Tensor Train Approaches and Higher-Order Propagators. J. Chem. Phys. . (Submitted) Grosu, C. and Panosetti, C. and Merz, S. and Jakes, P. and Matera, S. and Eichel, R.A. and Granwehr, J. and Scheurer, C. (2023) Revisiting the storage capacity limit of graphite battery anodes: spontaneous lithium overintercalation at ambient pressure. PRX Energy, 2 . von Kleist, M. and Raharinirina, Alexia and Gubela, Nils and Börnigen, Daniela and Smith, Maureen and Oh, Djin-Ye and Budt, Matthias and Mache, Christin and Schillings, Claudia and Fuchs, Stephan and Dürrwald, Ralf and Wolff, Thorsten and Hoelzer, Martin and Sofia, Paraskevopoulou (2023) SARS-CoV-2 Evolution on a Dynamic Immune Landscape. Biological Sciences . (Submitted) Hirt, M. and Craig, G.C. and Klein, R. (2023) Scale-interactions between the meso- and synoptic scales and the impact of diabatic heating. QJRMS, 149 (753). pp. 1319-1334. Hanu, Matei and Latz, J. and Schillings, Claudia (2023) Subsampling in ensemble Kalman inversion. Inverse Problems, 39 (9). Li, Z. and Meunier, D. and Mollenhauer, M. and Gretton, A. (2023) Towards Optimal Sobolev Norm Rates for the Vector-Valued Regularized Least-Squares Algorithm. arXiv . (Submitted) Riedel, J. and Gelß, P. and Klein, R. and Schmidt, B. (2023) WaveTrain: A Python Package for Numerical Quantum Mechanics of Chain-Like Systems Based on Tensor Trains. J. Chem. Phys. (164801), 158 (16). ISSN 0021-9606 Lai, King Chun and Matera, S. and Scheurer, C. and Reuter, K. (2023) A fuzzy classification framework to identify equivalent atoms in complex materials and molecules. Journal of Chemical Physics, 159 (2). ISSN 0021-9606 Montefusco, Alberto and Schütte, Christof and Winkelmann, Stefanie (2023) A route to the hydrodynamic limit of a reaction-diffusion master equation using gradient structures. Society for Industrial and Applied Mathematic (siam), 83 (2). pp. 836-861. Ayaz, Cihan and Tepper, Lucas and Netz, Roland R. (2022) Markovian embedding of generalized Langevin equations with a nonlinear friction kernel and configuration-dependent mass. Turkish Journal of Physics, 46 (6). pp. 194-205. Panahian Jand, Sara and Nourbakhsh, Zahra and Delle Site, Luigi (2022) Nuclear Quantum Effects in Fullerene-Fullerene Aggregation in Water. Front. Chem., 10 . pp. 1-8. Donati, Luca and Weber, Marcus and Keller, Bettina (2022) A review of Girsanov reweighting and of square root approximation for building molecular Markov state models. J. Math. Phys., 63 (12). pp. 1-22. Brünig, Florian N. and Daldrop, Jan O. and Netz, Roland R. (2022) Pair-Reaction Dynamics in Water: Competition of Memory, Potential Shape, and Inertial Effects. J. Phys. Chem. B, 126 . pp. 1-10. Trung, Minh Nguyen and Kieninger, Stefanie and Fandi, Zeinab and Qiu, Danye and Liu, Guizhen and Mehendale, Neelay K. and Saiardi, Adolfo and Jessen, Henning and Keller, Bettina and Fiedler, Dorothea (2022) Stable Isotopomers of myo-Inositol Uncover a Complex MINPP1-Dependent Inositol Phosphate Network. ACS Cent. Sci., 8 (12). pp. 1683-1694. Gholami, Abbas and Klein, R. and Delle Site, Luigi (2022) Simulation of a Particle Domain in a Continuum, Fluctuating Hydrodynamics Reservoir. Physical Review Letters, 129 (23). Basaric, Danica and Bella, Peter and Feireisl, Eduard and Oschmann, Florian and Titi, Edriss (2022) On the incompressible limit of a strongly stratified heat conducting fluid. On the incompressible limit of a strongly stratified heat conducting fluid . pp. 1-20. (Unpublished) Viennet, Akim and Vercauteren, Nikki and Engel, Maximilian and Faranda, Davide (2022) Guidelines for data-driven approaches to study transitions in multiscale systems: The case of Lyapunov vectors. Chaos, 32 . pp. 1-15. Mardt, Andreas and Hempel, Tim and Clementi, Cecilia and Noé, Frank (2022) Deep learning to decompose macromolecules into independent Markovian domains. nature communications, 13 . Musil, Félix and Zaporozhets, Iryna and Noé, Frank and Clementi, Cecilia and Kapil, Venkat (2022) Quantum dynamics using path integral coarse-graining. The Journal of Chemical Physics, 157 (18). Zendehroud, Sina and Netz, Roland R. and Kappler, Julian (2022) Linear Waves at Viscoelastic Interfaces Between Viscoelastic Media. Physical Review Fluids, 7 . pp. 1-32. Gholami, A. and Klein, R. and Delle Site, L. (2022) Simulation of a particle domain in a continuum/fluctuating hydrodynamics reservoir. Phys. Rev. Lett., 129 (23). Dibak, Manuel and Klein, Leon and Krämer, Andreas and Noé, Frank (2022) Temperature steerable flows and Boltzmann generators. Physical Review Research, 4 (4). Djurdjevac Conrad, Nataša and Köppl, Jonas and Djurdjevac, Ana (2022) Feedback Loops in Opinion Dynamics of Agent-Based Models with Multiplicative Noise. Entropy, 24 (10). pp. 1-23. Reible, Benedikt and Hartmann, Carsten and Delle Site, Luigi (2022) Two-sided Bogoliubov inequality to estimate finite size effects in quantum molecular simulations. Letters in Mathematical Physics, 112 (97). Kieninger, Stefanie and Keller, Bettina (2022) GROMACS Stochastic Dynamics and BAOAB Are Equivalent Configurational Sampling Algorithms. J. Chem. Theory Comput., 18 (10). Kosari, Ehsan and Rosenau, Matthias and Ziegenhagen, Thomas and Oncken, Onno (2022) Upper plate response to a sequential elastic rebound and slab acceleration during laboratory-scale subduction megathrust earthquakes. JGR Solid Earth, 127 (9). pp. 1-16. Lavacchi, Laura and Daldrop, Jan O. and Netz, Roland R. (2022) Non-Arrhenius barrier crossing dynamics of non-equilibrium non-Markovian systems. Europhysics Letters, 139 (5). pp. 1-7. Klimek, Anton and Netz, Roland R. (2022) Optimal non-Markovian composite search algorithms for spatially correlated targets. EPL A Letters Journal Exploring The Frontiers of Physics, 139 . pp. 1-8. Richter, Lorenz and Berner, Julius (2022) Robust SDE-Based Variational Formulations for Solving Linear PDEs via Deep Learning. Preprint arXiv . (Unpublished) Mastella, G. and Corbi, Fabio and Bedford, Jonathan and Funiciello, Francesca and Rosenau, Matthias (2022) Forecasting Surface Velocity Fields Associated With Laboratory Seismic Cycles Using Deep Learning. AGU-Geophysical Research Letters, 49 (15). pp. 1-12. Mikula, Natalia and Dörffel, Tom and Baum, Daniel and Hege, Hans-Christian (2022) An Interactive Approach for Identifying Structure Definitions. Computer Graphics Forum . pp. 1-29. Djurdjevac, Ana and Kremp, Helena and Perkowski, Nicolas (2022) Rough homogenization for Langevin dynamics on fluctuating Helfrich surfaces. Preprint arXiv . (Unpublished) Darvish, Mitra and Seiler, Enrico and Mehringer, Svenja and Rahn, René and Reinert, Knut and Ponty, Yann (2022) Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments. Bioinformatics, 38 (17). pp. 4100-4108. ISSN 1367-4803 Engel, Maximilian and Olicon-Mendez, Guillermo and Unger, Nathalie and Winkelmann, Stefanie (2022) Synchronization and random attractors for reaction jump processes. in Press . pp. 1-39. (In Press) Becker, Simon and Hartmann, Carsten and Redmann, Martin and Richter, Lorenz (2022) Error bounds for model reduction of feedback-controlled linear stochastic dynamics on Hilbert spaces. Stochastic Processes and their Applications, 149 . pp. 107-141. Chew, R. and Benacchio, T. and Hastermann, G. and Klein, R. (2022) A one-step blended soundproof-compressible model with balanced data assimilation: theory and idealised tests. Monthly Weather Review, 150 (9). pp. 2231-2254. ISSN 0027-0644; elSSN: 1520-0493 Zertani, Sascha and John, Timm and Brachmann, Caroline and Vrijmoed, Johannes and Plümper, Oliver (2022) Reactive fluid flow guided by grain-scale equilibrium reactions during eclogitization of dry crustal rocks. Contributions to Mineralogy and Petrology, 177 (61). Ayaz, Cihan and Scalfi, Laura and Dalton, Benjamin and Netz, Roland R. (2022) Generalized Langevin equation with a nonlinear potential of mean force and nonlinear memory friction from a hybrid projection scheme. PHYSICAL REVIEW E, 105 . pp. 1-19. del Razo, Mauricio J. and Frömberg, Daniela and Straube, Arthur V. and Schütte, Christof and Höfling, Felix and Winkelmann, Stefanie (2022) A probabilistic framework for particle-based reaction–diffusion dynamics using classical Fock space representations. Letters in Mathematical Physics, 112 (49). Boltz, Horst-Holger and Sirbu, Alexei and Stelzer, Nina and de Lanerolle, Primal and Winkelmann, Stefanie and Annibale, Paolo (2022) The impact of membrane protein diffusion on GPCR signaling. Cells, 11 (10). Sadeghi, Mohsen (2022) Investigating the entropic nature of membrane-mediated interactions driving the aggregation of peripheral proteins. Soft Matter (18). pp. 3917-3927. Tuncay, E. G. and Erdur, R. C. and Conrad, T. O. F. (2022) Parallel Exchange of Randomized SubGraphs for Optimization of Network Alignment: PERSONA. IEEE Transactions on Computational Biology and Bioinformatics . ISSN 1557-9964 (In Press) Kosari, Ehsan and Rosenau, Matthias and Oncken, Onno (2022) Strain signals governed by frictional-elastoplastic interaction of the upper plate and shallow subduction megathrust interface over seismic cycles. Tectonics . pp. 1-41. ISSN 1944-9194 Meyer, F. and Fritz, A. and Deng, Z.-L. and Koslicki, D. and Gurevich, A. and Robertson, G. and Alser, M. and Antipov, D. and Beghini, F. and Bertrand, D. and Brito, J. J. and Brown, C.T. and Buchmann, J. and Buluç, A. and Chen, B. and Chikhi, R. and Clausen, P. T. and Cristian, A. and Dabrowski, P. W. and Darling, A. E. and Egan, R. and Eskin, E. and Georganas, E. and Goltsman, E. and Gray, M. A. and Hansen, L. H. and Hofmeyr, S. and Huang, P. and Irber, L. and Jia, H. and Jørgensen, T. S. and Kieser, S. D. and Klemetsen, T. and Kola, A. and Kolmogorov, M. and Korobeynikov, A. and Kwan, J. and LaPierre, N. and Lemaitre, C. and Li, C. and Limasset, A. and Malcher-Miranda, F. and Mangul, S. and Marcelino, V. R. and Marchet, C. and Marijon, P. and Meleshko, D. and Mende, D. R. and Milanese, A. and Nagarajan, N. and Nissen, J. and Nurk, S. and Oliker, L. and Paoli, L. and Peterlongo, P. and Piro, V. C. and Porter, J. S. and Rasmussen, S. and Rees, E. R. and Reinert, K. and Renard, B. and Robertsen, E. M. and Rosen, G. L. and Ruscheweyh, H.-J. and Sarwal, V. and Segata, N. and Seiler, E. and Shi, L. and Sun, F. and Sunagawa, S. and Sørensen, S. J. and Thomas, A. and Tong, C. and Trajkovski, M. and Tremblay, J. and Uritskiy, G. and Vicedomini, R. and Wang, Zi. and Wang, Zhe. and Wang, Zho. and Warren, A. and Willassen, N. P. and Yelick, K. and You, R. and Zeller, G. and Zhao, Z. and Zhu, S. and Zhu, J. and Garrido-Oter, R. and Gastmeier, P. and Hacquard, S. and Häußler, S. and Khaledi, A. and Maechler, F. and Mesny, F. and Radutoiu, S. and Schulze-Lefert, P. and Smit, N. and Strowig, T. and Bremges, A. and Sczyrba, A. and McHardy, A. C. (2022) Critical Assessment of Metagenome Interpretation - the second round of challenges. Nature Methods, 19 (4). pp. 429-440. ISSN 1548-7091 Dolores-Tesillos, Edgar and Teubler, Franziska and Pfahl, Stephan (2022) Future changes in North Atlantic winter cyclones in CESM-LE – Part 1: Cyclone intensity, potential vorticity anomalies, and horizontal wind speed. Weather Clim. Dynam., 3 . pp. 429-448. Mollenhauer, Mattes and Klus, Stefan and Schütte, Christof and Koltai, Péter (2022) Kernel autocovariance operators of stationary processes: Estimation and convergence. Journal of Machine Learning Research, 23 (327). pp. 1-34. Obermeier, P. and Heim, A. and Biere, B. and Hage, E. and Alchikh, M. and Conrad, T. O. F. and Schweiger, B. and Rath, B. (2022) Linking digital surveillance and in-depth virology to study clinical patterns of viral respiratory infections in vulnerable patient populations. iScience, 25 (5). ISSN 25890042 Ague, Jay J. and Tassara, Santiago and Holycross, Megan E. and Li, Jei-Li and Cottrell, Elizabeth and Schwarzenbach, Esther M. and Fassoulas, Charalampos and John, Timm (2022) Slab-derived devolatilization ﬂuids oxidized by subducted metasedimentary rocks. Nature Geoscience, 15 . pp. 320-326. Klein, R. and Delle Site, Luigi (2022) Derivation of Liouville-like equations for the n-state probability density of an open system with thermalized particle reservoirs and its link to molecular simulation. Journal of Physics A: Mathematical and Theoretical, 55 . pp. 1-18. Gholami, Jafar and Kamankesh, Mohamad Reza and Mohammadi, Somayeh and Hosseinkhani, Elahe and Abdi, Somayeh (2022) Powerful enhanced Jaya algorithm for efficiently optimizing numerical and engineering problems. Soft Computing . ISSN 1432-7643 Polzin, Robert and Müller, Annette and Rust, Henning W. and Névir, Peter and Koltai, Péter (2022) Direct Bayesian model reduction of smaller scale convective activity conditioned on large-scale dynamics. Nonlinear Processes in Geophysics, 29 (1). pp. 37-52. Mastella, G. and Corbi, Fabio and Funiciello, Francesca and Rosenau, Matthias (2022) Foamquake: a novel analog model mimicking megathrust seismic cycles. JGR Solid Earth . pp. 1-32. (In Press) Brünig, Florian N. and Geburtig, Otto and von Canal, Alexander and Kappler, Julian and Netz, Roland R. (2022) Time-dependent friction effects on vibrational infrared frequencies and line shapes of liquid water. J. Phys. Chem. B, 126 . pp. 1579-1589. Peschka, Dirk and Zafferi, Andrea and Heltai, Luca and Thomas, Marita (2022) Variational Approach to Fluid–Structure Interaction via GENERIC. Journal of Non-Equilibrium Thermodynamics . ISSN 1437-4358 Kosari, Ehsan and Rosenau, Matthias and Ziegenhagen, Thomas and Oncken, Onno (2022) Upper plate dynamic response to a sequential elastic rebound and slab acceleration in laboratory-scale subduction megathrust. Earth and Space Science Open Archive . Zwaan, Frank and Schreurs, Guido and Buiter, Susanne and Ferrer, Oriol and Reitano, Riccardo and Rudolf, Michael and Willingshofer, Ernst (2022) Analogue modelling of basin inversion: a review and future perspectives. Preprint se-2022-8 Solid Earth . (Submitted) Gelß, P. and Klein, R. and Matera, S. and Schmidt, B. (2022) Solving the time-independent Schrödinger equation for chains of coupled excitons and phonons using tensor trains. J. Chem. Phys., 156 (02). 024109. Zendehroud, Sina and Loche, Philip and Kornhuber, Ralf and Netz, Roland R. (2022) Boundary Conditions on Conical Hydrophobic Inclusions in Lipid Membranes. Preprint . (Unpublished) Kiefer, Henrik and Dalton, Benjamin and Bruenig, Florian N. and Netz, Roland R. (2022) Connection between Macroscopic Hydrodynamics and Molecular Friction in Liquids. Preprint . pp. 1-26. (Unpublished) Ayaz, Cihan and Dalton, Benjamin and Netz, Roland R. (2022) Generalized Langevin Equation with a Non-Linear Potential of Mean Force and Non-Linear Friction From a Hybrid Projection Scheme. Preprint . (Unpublished) Winkler, Jörg and Urgese, Gianvito and Ficarra, Elisa and Reinert, Knut (2022) LaRA 2: parallel and vectorized program for sequence–structure alignment of RNA sequences. BMC Bioinformatics, 23 (1). ISSN 1471-2105 Rams, Mona and Conrad, T. O. F. (2022) Sparse dictionary learning allows model-free pseudotime estimation of transcriptomics data. BMC Genomics, 23 (56). ISSN 1471-2105 Ernst, Ariane and Schütte, Christof and Sigrist, Stephan J. and Winkelmann, Stefanie (2022) Variance of filtered signals: Characterization for linear reaction networks and application to neurotransmission dynamics. Mathematical Biosciences, 343 . Weissmann, Simon and Chada, Neil and Schillings, Claudia and Tong, Xin (2022) Adaptive Tikhonov strategies for stochastic ensemble Kalman inversion. Inverse Problems, 38 (4). Chada, Neil and Schillings, Claudia and Tong, Xin and Weissmann, Simon (2022) Consistency analysis of bilevel data-driven learning in inverse problems. Communications in Mathematical Sciences, 20 (1). pp. 123-164. Blömker, Dirk and Schillings, Claudia and Wacker, Philipp and Weissmann, Simon (2022) Continuous time limit of the stochastic ensemble Kalman inversion: Strong convergence analysis. SIAM Journal on Numerical Analysis, 60 (6). pp. 3181-3215. von Lindheim, Johannes and Harikrishnan, A. P. and Dörffel, T. and Klein, R. and Koltai, Péter and Mikula, Natalia and Müller, Annette and Névir, Peter and Pacey, George and Polzin, Robert and Vercauteren, N. (2022) Definition, detection and trackingof persistent structures in atmospheric flows. J. Math. Phys . (Submitted) Delle Site, L. and Klein, R. (2022) Derivation of Liouville-like equation for the n-state probability density of an open system with thermalized particle reservoirs and its link to molecular simulation. J. Physics A:Math. Theor., 55 (15). Thethy, Bhavraj S. and Haghdoost, M.R. and Kirby, R. and Seo, B. and Nadolski, M. and Zenker, C. and Oevermann, M. and Klein, R. and Oberleithner, K. and Edgington-Mitchell, D. (2022) Diffraction of shock waves through a non-quiescent medium. Journal of Fluid Mechanics, 944 . Fischer, Julian and Hopf, Katharina and Kniely, Michael and Mielke, Alexander (2022) Global existence analysis of energy-reaction-diffusion systems. SIAM Journal on Mathematical Analysis. SIAM Journal on Mathematical Analysis, 54 . pp. 220-267. Chew, R. and Schlutow, M. and Klein, R. (2022) Instability of the isothermal, hydrostatic equatorial atmosphere at rest under the full Coriolis acceleration. J. Atmos. Sci. . (Submitted) Mollenhauer, Mattes and Mücke, Nicole and Sullivan, T.J. (2022) Learning linear operators: Infinite-dimensional regression as a well-behaved non-compact inverse problem. arXiv . (Submitted) Haghdoost, M.R. and Thethy, B.S. and Nadolski, M. and Klein, R. and Honnery, D. and Hennington- Mitchell, D. and Seo, B. and Paschereit, O. C. and Oberleithner, K. (2022) Numerical and Experimental Evaluation of Shock Dividers. Shock Waves, 32 . pp. 195-211. Kornhuber, R. and Podlesny, J. and Yserentant, H. (2022) Numerical homogenization of fractal interface problems. ESAIM: M2AN, 56 (4). 1451- 1481. ISSN 2822-7840 - eISSN: 2804-7214 Guth, Philipp A. and Kaarnioja, Vesa and Kuo, Frances Y. and Sloan, Ian H. (2022) Parabolic PDE-constrained optimal control under uncertainty with entropic risk measure using quasi-Monte Carlo integration. arXiv preprint arXiv:2208.02767 . (Submitted) Klein, R. and Schielicke, L. and Pfahl, S. and Khouider, B. (2022) QG-DL-Ekman: Dynamics of a diabatic layer in the quasi-geostrophic framework. Journal of the Atmospheric Sciences, 79 (3). pp. 887-905. Bresch, D. and Klein, R. and Liu, X. (2022) The Soundproof Model of an Acoustic–internal Waves System with Low Stratification. Journal of Mathematical Fluid Mechanics, 24 (149). ISSN 1422-6928 (Print) 1422-6952 (Online) Brösigke, G. and Jens-Uwe Repke, J.U. and Schomäcker, R. and Matera, S. (2022) The closer the better? Theoretical assessment of the impact of catalytic site separation for bifunctional core–shell catalyst particles. Chemical Engineering Journal, 446 (1). Bresch, D. and Klein, R. and Liu, X. (2022) The soundproof model of an acoustic-internal waves system with low stratification. Journal of Mathematical Fluid Mechanics, 25 (2). ISSN Electronic 1422-6952; Print 1422-6928 Delle Site, Luigi (2021) Investigation of water-mediated intermolecular interactions with the adaptive resolution simulation technique. Journal of Physics: Condensed Matter, 34 (11). pp. 1-15. Breiten, T. and Hartmann, Carsten and Neureither, Lara and Sharma, Upanshu (2021) Stochastic gradient descent and fast relaxation to thermodynamic equilibrium: a stochastic control approach. Journal of Mathematical Physics, 62 (12). pp. 1-19. Eiter, Thomas and Hopf, Katharina and Mielke, Alexander (2021) Leray–Hopf solutions to a viscoelastoplastic fluid model with nonsmooth stress–strain relation. Nonlinear Analysis, 65 . Huber, Konstantin and Vrijmoed, Johannes and John, Timm (2021) Formation of olivine-rich veins by reactive fluid flow in a dehydrating serpentinite. Earth and Space Science Open Archive . pp. 1-18. Vrijmoed, Johannes and Podladchikov, Y.Y. (2021) Thermolab: a thermodynamics laboratory for nonlinear transport processes in open systems. Earth and Space Science Open Archive . Peschka, Dirk and Zafferi, Andrea and Heltai, Luca and Thomas, Marita (2021) Variational approach to fluid-structure interaction via GENERIC. WIAS Preprint . pp. 1-13. (Submitted) Hoffmann, Moritz and Scherer, Martin and Hempel, Tim and Mardt, Andreas and de Silva, Brian and Husic, Brooke E. and Klus, Stefan and Wu, Hao and Kutz, Nathan and Brunton, Steven L (2021) Deeptime: a Python library for machine learning dynamical models from time series data. Mach. Learn.: Sci. Technol. 3 (2022), 3 (015009). pp. 1-28. Iravani, Sahar and Conrad, T. O. F. (2021) An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20 (1). ISSN 1545-4963 Rudolf, Michael and Rosenau, Matthias and Oncken, Onno (2021) The spectrum of slip behaviours of a granular fault gouge analogue governed by rate and state friction. Geochemistry, Geophysics, Geosystems . pp. 1-40. Kostré, Margarita and Schütte, Christof and Noé, Frank and del Razo, Mauricio J. (2021) Coupling Particle-Based Reaction-Diffusion Simulations with Reservoirs Mediated by Reaction-Diffusion PDEs. Sociaty for Industrial and Applied Mathematics, 19 (4). Hartmann, Carsten and Neureither, Lara and Stehlau, Markus (2021) Reachability Analysis of Randomly Perturbed Hamiltonian Systems. IFAC-PapersOnLine, 54 (19). pp. 307-3014. Gholami, Abbas and Klein, R. and Delle Site, Luigi (2021) On the relation between Pressure and Coupling Potential in Adaptive Resolution Simulations of Open Systems in contact with a Reservoir. Advanced Theory and Simulations, 5 . pp. 1-8. Heida, Martin and Kantner, Markus and Stephan, Artur (2021) Consistency and convergence for a family of finite volume discretizations of the Fokker--Planck operator. ESAIM: Mathematical Modelling and Numerical Analysis, 55 . pp. 3017-3042. Neubert, Kerstin and Zuchantke, Eric and Leidenfrost, Robert Maximilian and Wünschiers, Röbbe and Grützke, Josephine and Malorny, Burkhard and Brendebach, Holger and Al Dahouk, Sascha and Homeier, Timo and Hotzel, Helmut and Reinert, Knut and Tomaso, Herbert and Busch, Anne (2021) Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures. BMC Genomics, 22 (1). p. 822. ISSN 1471-2164 Leser, Ulf and Hilbrich, Marcus and Draxl, Claudia and Eisert, Peter and Grunske, Lars and Hostert, Patrick and Kainmüller, Dagmar and Kao, Odej and Kehr, Birte and Kehrer, Timo and Koch, Christoph and Markl, Volker and Meyerhenke, Henning and Rabl, Tilmann and Reinefeld, Alexander and Reinert, Knut and Ritter, Kerstin and Scheuermann, Björn and Schintke, Florian and Schweikardt, Nicole and Weidlich, Matthias (2021) The Collaborative Research Center FONDA. Datenbank-Spektrum, 21 (3). pp. 255-260. ISSN 1618-2162 Dörffel, T. and Papke, A. and Klein, R. and Ernst, Natalia and Smolarkiewicz, Piotr K. (2021) Dynamics of tilted atmospheric vortices under asymmetric diabatic heating. Theoretical and Computational Fluid Dynamics . von Lindheim, Johannes and Harikrishnan, A. P. and Dörffel, T. and Ernst, Natalia and Klein, R. and Koltai, Péter and Müller, Annette and Pacey, George and Polzin, Robert and Vercauteren, N. (2021) Definition, detection and tracking of persistent structures in atmospheric flows. preprint. J. Math. Phys. . pp. 1-64. (In Press) Sadeghi, Mohsen and Noé, Frank (2021) Thermodynamics and kinetics of aggregation of flexible peripheral membrane proteins. The Journal of Physical Chemistry Letters, 12 (43). pp. 10497-10504. Hetzel, Sara and Giesselmann, Pay and Reinert, Knut and Meissner, Alexander and Kretzmer, Helene and Alkan, Can (2021) RLM: fast and simplified extraction of read-level methylation metrics from bisulfite sequencing data. Bioinformatics, 37 (21). pp. 3934-3935. ISSN 1367-4803 Harikrishnan, A. P. and Ansorge, C. and Klein, R. and Vercauteren, N. (2021) Lagrangian hairpins in atmospheric boundary layers. Gallery of Fluid Motion . Hittmeir, S. and Klein, R. and Müller, A. and Névir, P. (2021) The Dynamic State Index with Moisture and Phase Changes. J. Math. Phys, 62 (12). pp. 1-12. Gräser, Carsten and Kornhuber, Ralf and Podlesny, Joscha (2021) NUMERICAL SIMULATION OF MULTISCALE FAULT SYSTEMS WITH RATE- AND STATE-DEPENDENT FRICTION. ArXiv . pp. 1-27. (Unpublished) Jojić, Vida and Čabrilo, Borislav and Bjelić-Čabrilo, Olivera and Jovanović, Vladimir M. and Budinski, Ivana and Vujošević, Mladen and Blagojević, Jelena (2021) Canalization and developmental stability of the yellow-necked mouse (Apodemus flavicollis) mandible and cranium related to age and nematode parasitism. Frontiers in Zoology, 18 (1). ISSN 1742-9994 Hastermann, G. and Reinhardt, M. and Klein, R. and Reich, S. (2021) Balanced data assimilation for highly-oscillatory mechanical systems. Communications in Applied Mathematics & Computational Science, 16 (1). pp. 119-154. Detring, Carola and Müller, Annette and Schielicke, Lisa and Névir, Peter and Rust, Henning W. (2021) Occurrence and transition probabilities of omega and high-over-low blocking in the Euro-Atlantic region. Weather Clim. Dynamics, 2 . pp. 927-952. Straube, Arthur V. and Winkelmann, Stefanie and Schütte, Christof and Höfling, Felix (2021) Stochastic pH Oscillations in a Model of the Urea−Urease Reaction Confined to Lipid Vesicles. J. Phys. Chem. Lett., 12 . pp. 1-6. Bittracher, Andreas and Moschner, Johann and Koksch, Beate and Netz, Roland R. and Schütte, Christof (2021) Exploring the locking stage of NFGAILS amyloid fibrillation via transition manifold analysis. The European Physical Journal B volume, 94 (195). del Razo, Mauricio J. and Dibak, Manuel and Schütte, Christof and Noé, Frank (2021) Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics. The Journal of Chemical Physics, 155 (12). Cortes-Huerto, Robinson and Praprotnik, Matej and Kremer, Kurt and Delle Site, Luigi (2021) From Adaptive Resolution to Molecular Dynamics of Open Systems. The European Physical Journal B, 94 (189). pp. 1-22. Bittracher, Andreas and Mollenhauer, Mattes and Koltai, Péter and Schütte, Christof (2021) Optimal Reaction Coordinates: Variational Characterization and Sparse Computation. ArXiv . pp. 1-36. (Submitted) Sadeghi, Mohsen and Noé, Frank (2021) Hydrodynamic coupling for particle-based solvent-free membrane models. The Journal of Chemical Physics, 155 (11). Maity, Priyanka and Koltai, Péter and Schumacher, Jörg (2021) Large-scale flow in a cubic Rayleigh-B ́enard cell: Long-term turbulence statistics and Markovianity of macrostate transitions. Philosophical Transaction of the Royal Society . pp. 1-13. (In Press) Heida, Martin and Thomas, Marita (2021) GENERIC for dissipative solids with bulk-interface interaction. wias preprint . pp. 1-27. ISSN 2198-5855 (Submitted) Hempel, Tim and Elez, Katarina and Krüger, Nadine and Raich, Lluís and Shrimp, Jonathan H. and Danov, Olga and Jonigk, Danny and Braun, Arnim and Shen, Min and Hall, Matthew D. and Pöhlmann, Stefan and Hoffmann, Markus and Noé, Frank (2021) Synergistic inhibition of SARS-CoV-2 cell entry by otamixaban and covalent protease inhibitors: pre-clinical assessment of pharmacological and molecular properties. Chemical Science, 12 (38). pp. 12600-12609. Chen, Yaoyi and Krämer, Andreas and Charron, Nicholas E. and Husic, Brooke E. and Clementi, Cecilia and Noé, Frank (2021) Machine learning implicit solvation for molecular dynamics. The Journal of Chemical Physics, 155 (084101). pp. 1-15. Stephan, Artur (2021) EDP-convergence for a linear reaction-diffusion system with fast reversible reaction. Calculus of Variations, 60 (226). pp. 1-35. Klus, Stefan and Gelß, Patrick and Nüske, Feliks and Noé, Frank (2021) Symmetric and antisymmetric kernels for machine learning problems in quantum physics and chemistry. Machine Learning: Science and Technologie, 2 . pp. 1-23. Ayaz, Cihan and Tepper, Lucas and Brünig, Florian N. and Daldrop, Jan O. and Netz, Roland R. (2021) Non-Markovian modeling of protein folding. Proceedings of the National Academy of Sciences, 118 (31). pp. 1-7. Hoffmann, Marie and Monaghan, Michael T. and Reinert, Knut (2021) PriSeT: Efficient De Novo Primer Discovery. Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics . pp. 1-12. Müller, Annette and Névir, Peter (2021) On the algebra and groups of incompressible vortex dynamics. Journal of Physics A: Mathematical and Theoretical, 54 . pp. 1-34. Seiler, Enrico and Mehringer, Svenja and Darvish, Mitra and Turc, Etienne and Reinert, Knut (2021) Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences. iScience, 24 (7). p. 102782. ISSN 25890042 Coghi, Michele and Nilssen, Torstein and Nüsken, Nikolas (2021) Rough McKean-Vlasov dynamics for robust ensemble Kalman filtering. arXive . pp. 1-41. (Submitted) Michail, Maria and Rudolf, Michael and Rosenau, Matthias and Riva, Alberto and Gianolla, Piero and Coltorti, Massimo (2021) Shape of plutons in crustal shear zones: A tectono-magmatic guide based on analogue models. Journal of Structural Geology . p. 104417. ISSN 0191-8141 Mielke, Alexander and Peletier, Mark A. and Stephan, Artur (2021) EDP-convergence for nonlinear fast–slow reaction systems with detailed balance. Nonlinearity, 34 (8). pp. 5762-5798. Leung, Tsz Yan and Leutbecher, Martin and Reich, Sebastian and Shepherd, Theodore G. (2021) Forecast verification: relating deterministic and probabilistic metrics. Quarterly Journal of the Royal Meteorological Society . pp. 1-17. ISSN 1477-870X (Submitted) Thomas, Marita and Tornquist, Sven (2021) Discrete approximation of dynamic phase-field fracture in visco-elastic materials. Discrete Contin. Dyn. Syst. Ser. S, 14 . pp. 3865-3924. Herter, Felix and Hege, Hans-Christian and Hadwiger, Markus and Lepper, Verena and Baum, Daniel (2021) Thin-Volume Visualization on Curved Domains. Computer Graphics forum, 40 (3). pp. 147-157. Nüsken, Nikolas and Richter, Lorenz (2021) Solving high-dimensional Hamilton–Jacobi–Bellman PDEs using neural networks: perspectives from the theory of controlled diffusions and measures on path space. Partial Differential Equations and Applications, 2 (48). pp. 1-48. Helfmann, Luzie and Heitzig, Jobst and Koltai, Péter and Kurths, Jürgen and Schütte, Ch. (2021) Statistical analysis of tipping pathways in agent-based models. The European Physical Journal Special Topics . ISSN 1951-6355 Mirahmadi, M. and Schmidt, B. and Friedrich, B. (2021) Quantum dynamics of a planar rotor driven by suddenly switched combined aligning and orienting interactions. New Journal of Physics, 23 (06). 063040. ISSN 1367-2630 Gelß, Patrick and Klus, Stefan and Schuster, Ingmar and Schütte, Christof (2021) Feature space approximation for kernel-based supervised learning. Knowledge-Based Systems, 221 . Rezaei, majid and Netz, Roland R. (2021) Airborne virus transmission via respiratory droplets: Effects of droplet evaporation and sedimentation. ScienceDirect, 55 . ISSN 101471 Jovanovic, Vladimir M. and Sarfert, Melanie and Reyna-Blanco, Carlos S. and Indrischek, Henrike and Valdivia, Dulce I. and Shelest, Ekaterina and Nowick, Katja (2021) Positive Selection in Gene Regulatory Factors Suggests Adaptive Pleiotropic Changes During Human Evolution. Frontiers in Genetics, 12 . ISSN 1664-8021 Niemann, Jan-Hendrik and Klus, Stefan and Schütte, Christof (2021) Data-driven model reduction of agent-based systems using the Koopman generator. PLOS ONE, 16 (5). Giulietti, P. and Koltai, P. and Vaienti, S. (2021) Targets and holes. Proc. Amer. Math. Soc., 149 . pp. 3293-3306. Zafferi, Andrea and Peschka, Dirk and Thomas, Marita (2021) GENERIC framework for reactive fluid flows. Preprint (2841). pp. 1-75. ISSN 2198-5855 (Submitted) Klein, R. and Viand, R. E. and Höfling, Felix and Delle Site, Luigi (2021) Nonequilibrium Induced by Reservoirs: Physico-Mathematical Models and Numerical Tests. Advanced Theory and Simulations, 4 . pp. 1-10. Mielke, Alexander and Montefusco, Alberto and Peletier, Mark A. (2021) Exploring families of energy-dissipation landscapes via tilting: three types of EDP convergence. Continuum Mechanics and Thermodynamics, 33 (2). pp. 611-637. Karra, M. and Friedrich, B. and Schmidt, B. (2021) Quantum dynamics of a polar rotor acted upon by an electric rectangular pulse of variable duration. Molecular Physics, 119 . e1966111. ISSN 0026-8976 Azouz, Nurit P. and Klingler, Andrea M. and Callahan, Victoria and Akhrymuk, Ivan V. and Elez, Katarina and Raich, Lluís and Henry, Brandon M. and Benoit, Justin L. and Benoit, Stefanie W. and Noé, Frank and Kehn-Hall, Kylene and Rothenberg, Marc E. (2021) Alpha 1 Antitrypsin is an Inhibitor of the SARS-CoV-2–Priming Protease TMPRSS2. Pathogens and Immunity, 6 (1). pp. 55-74. Frömberg, Daniela and Höfling, Felix (2021) Generalized master equation for first-passage problems in partitioned spaces. Journal of Physics A: Mathematical and Theoretical, 54 (21). pp. 1-29. Winkelmann, Stefanie and Zonker, J. and Schütte, Christof and Djurdjevac Conrad, Natasa (2021) Mathematical modeling of spatio-temporal population dynamics and application to epidemic spreading. Mathematical Biosciences, 336 . Klein, R. and Schielicke, L. and Pfahl, S. and Khouider, B. (2021) QG-DL: Dynamics of a diabatic layer in the quasi-geostrophic framework. Journal of the Atmospheric Sciences . pp. 1-12. ISSN Online: 1520-0469 Print: 0022-4928 (Submitted) Mielke, Alexander and Netz, Roland R. and Zendehroud, Sina (2021) A rigorous derivation and energetics of a wave equation with fractional damping. Journal Evolution Equations, 21 . pp. 3079-3102. Hassan, Irtaza and Ferraro, Federica and Imhof, Petra (2021) Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide. Molecules 2021, 26 (8). pp. 1-24. Andreis, Luisa and König, Wolfgang and Patterson, Robert I.A. (2021) A large‐deviations principle for all the cluster sizes of a sparse Erdős–Rényi graph. Random Structures and Algorithms . pp. 1-32. Wulkow, Hanna and Conrad, T. O. F. and Djurdjevac Conrad, Natasa and Mueller, Sebastian Alexander and Nagel, Kai and Schütte, Ch. (2021) Prediction of Covid-19 spreading and optimal coordination of counter-measures: From microscopic to macroscopic models to Pareto fronts. PLoS ONE, 16 (4). ISSN 1932-6203 Liang, YongTian and Piao, Chengji and B. Beuschel, Christine and Toppe, David and Kollipara, Laxmikanth and Bogdanow, Boris and Maglione, Marta and Lützkendorf, Janine and See, Jason Chun Kit and Huang, Sheng and Conrad, T. O. F. and Kintscher, Ulrich and Madeo, Frank and Liu, Fan and Sickmann, Albert and Sigrist, Stephan J. (2021) eIF5A hypusination, boosted by dietary spermidine, protects from premature brain aging and mitochondrial dysfunction. Cell Reports, 35 (2). ISSN 2211-1247 Keshavan, Sandeep and Andón, Fernando Torres and Gallud, Audrey and Chen, Wei and Reinert, Knut and Tran, Lang and Fadeel, Bengt (2021) Profiling of Sub-Lethal in Vitro Effects of Multi-Walled Carbon Nanotubes Reveals Changes in Chemokines and Chemokine Receptors. Nanomaterials, 11 (4). p. 883. ISSN 2079-4991 Patterson, Robert I.A. and Renger, D.R. Michiel and Sharma, Upanshu (2021) Variational structures beyond gradient flows: a macroscopic fluctuation-theory perspective. arXive . pp. 1-47. (Unpublished) Chew, R. and Benacchio, T. and Hastermann, G. and Klein, R. (2021) Balanced data assimilation with a blended numerical model. Monthly Weather Review . pp. 1-43. (Submitted) Sikorski, Alexander and Weber, Marcus and Schütte, Christof (2021) The augmented jump chain – a sparse representationof time-dependent Markov jump processes. Advanced Theory and Simulations, 4(4):2000274, 2021, 4 (4). Rodrigues, D.R. and Everschor-Sitte, K. and Gerber, S. and Horenko, I. (2021) A deeper look into natural sciences with physics-based and data-driven measures. iSCIENCE, 24 (3). pp. 1-13. ISSN 102171 Kaatz, Lisa and Zertani, Sascha and Moulas, Evangelos and John, Timm and Labrousse, Loïc and Schmalholz, Stefan M. and Andersen, Torgeir B. (2021) Widening of Hydrous Shear Zones During Incipient Eclogitization of Metastable Dry and Rigid Lower Crust— Holsnøy, Western Norway. Tectonics, 40 (3). pp. 1-19. ISSN 1944-9194 Niemann, Jan-Hendrik and Winkelmann, Stefanie and Wolf, S. and Schütte, Christof (2021) Agent-based modeling: Population limits and large timescales. Chaos: An Interdisciplinary Journal of Nonlinear Science, 31 (3). Gholami, A. and Höfling, Felix and Klein, R. and Delle Site, Luigi (2021) Thermodynamic Relations at the Coupling Boundary in Adaptive Resolution Simulations for Open Systems. Advanced Theory and Simulations, 4 . pp. 1-10. Poppe, S. and Holohan, E.P. and Rudolf, M. and Rosenau, M. and Galland, O. and Delcamp, A. and Kervyn, M. (2021) Mechanical properties of quartz sand and gypsum powder (plaster) mixtures: 25implications for laboratory model analoguesfor the Earth’s upper crust. EartharXiv . pp. 1-55. Miron, P. and Beron-Vera, F.J. and Helfmann, L. and Koltai, P. (2021) Transition paths of marine debris and the stability of the garbage patches. Chaos, 31 . pp. 1-16. Kieninger, S. and Keller, B. (2021) Path probability ratios for Langevin dynamics—Exact and approximate. The Journal of Chemical Physics, 154 . pp. 1-21. Agazzi, Andrea and Andreis, Luisa and Patterson, Robert I.A. and Renger, D.R. Michiel (2021) LARGE DEVIATIONS FOR MARKOV JUMP PROCESSES WITH UNIFORMLY DIMINISHING RATES. arXive . pp. 1-19. (Unpublished) Nüsken, Nikolas and Renger, D.R. Michiel (2021) Stein Variational Gradient Descent:many-particle and long-time asymptotics. arxiv preprint . pp. 1-25. (Submitted) Agazzi, Andrea and Andreis, Luisa and Patterson, Robert I. A. and Renger, D.R. Michiel (2021) Large deviations for Markov jump processes with uniformly diminishing rates. arXive . pp. 1-19. (Unpublished) Nüsken, N. and Renger, M. (2021) Stein Variational Gradient Descent: many-particle and long-time asymptotics. arXive . pp. 1-25. (Unpublished) Richter, Lorenz and Sallandt, Leon and Nüsken, Nikolas (2021) Solving high-dimensional parabolic PDEs using the tensor train format. Proceedings of the 38th International Conferenceon Machine Learning, 139 . pp. 8998-9009. Hartmann, C. and Richter, L. (2021) Nonasymptotic bounds for suboptimal importance sampling. To appear 2024 in SIAM/ASA Journal on Uncertainty Quantification . (In Press) Bouanani, Hafida and Hartmann, Carsten and Kebiri, Omar (2021) Model reduction and uncertainty quantification of multiscale diffusions with parameter uncertainties using nonlinear expectations. arXive . pp. 1-22. (Submitted) Sandiford, Dan and Brune, Sascha and Glerum, Anne and Naliboff, John and Whittaker, Joanne M. (2021) Kinematics of footwall exhumation at oceanic detachment faults: solid-block rotation and apparent unbending. Earth and Space Science Open Archive . Wolf, Silver A and Epping, Lennard and Andreotti, Sandro and Reinert, Knut and Semmler, Torsten and Birol, Inanc (2021) SCORE: Smart Consensus Of RNA Expression—a consensus tool for detecting differentially expressed genes in bacteria. Bioinformatics, 37 (3). pp. 426-428. ISSN 1367-4803 Bittracher, Andreas and Schütte, Christof (2021) A probabilistic algorithm for aggregating vastly undersampled large Markov chains. Physica D, 416 . pp. 1-19. Weimann, K. and Conrad, T. O. F. (2021) Transfer Learning for ECG Classification. Scientific Reports, 11 (5251). ISSN 2045-2322 Cvetkovic, Nada and Conrad, T. O. F. and Lie, Han Cheng (2021) A convergent discretisation method for transition path theory for diffusion processes. Multiscale Modeling & Simulation, 19 (1). ISSN 15403467 Reuten, Raphael and Zendehroud, Sina and Nicolau, Monica and Fleischhauer, Lutz and Laitala, Anu and Kiderlen, Stefanie and Nikodemus, Denise and Wullkopf, Lena and Nielsen, Sebastian Rune and McNeilly, Sarah and Prein, Carina and Rafaeva, Maria and Schoof, Erwin M. and Furtwängler, Benjamin and Porse, Bo T. and Kim, Hyobin and Won, Kyoung Jae and Sudhop, Stefanie and Westarp Zornhagen, Kamilla and Suhr, Frank and Maniati, Eleni and Pearce, Oliver M. T. and Koch, Manuel and Broeng Oddershede, Lene and Van Agtmael, Tom and Madsen, Chris D. and Mayorca-Guiliani, Alejandro E. and Bloch, Wilhelm and Netz, Roland R. and Clausen-Schaumann, Hauke and Erler, Janine T. (2021) Basement membrane stiffness determines metastases formation. Nature Materials, 20 . pp. 892-903. Netz, Roland R. and Eaton, William A. (2021) Estimating computational limits on theoretical descriptions of biological cells. PNAS, 118 . pp. 1-3. ISSN 1091-6490 (online) Nüske, Feliks and Koltai, Péter and Boninsegna, Lorenzo and Clementi, Cecilia (2021) Spectral Properties of Effective Dynamics from Conditional Expectations. Entropy, 23 (134). pp. 1-25. Helfmann, L. and Djurdjevac Conrad, N. and Djurdjevac, A. and Winkelmann, S. and Schütte, Ch. (2021) From interacting agents to density-based modeling with stochastic PDEs. Commun. Appl. Math. Comput. Sci., 16 (1). pp. 1-32. ISSN Online: 2157-5452; Print: 1559-3940 Wulkow, Niklas and Koltai, Péter and Schütte, Ch. (2021) Memory-Based Reduced Modelling and Data-Based Estimation of Opinion Spreading. Journal of Nonlinear Science, 31 . ISSN 1432-1467 (online) Donati, Luca and Weber, Marcus and Keller, Bettina G. (2021) Markov models from the square root approximation of the Fokker–Planck equation: calculating the grid-dependent flux. J. Phys.: Condens. Matter, 33 . pp. 1-15. Bastian, P. and Blatt, M. and Dedner, A. and Dreier, N.-A. and Engwer, C. and Fritze, R. and Gräser, C. and Grüninger, C. and Kempf, D. and Klöfkorn, R. and Ohlberger, M. and Sander, O. (2021) The Dune framework: Basic concepts and recent developments. Computers & Mathematics with Applications, 81 . pp. 75-112. ISSN 0898-1221 Kavokine, Nikita and Netz, Roland R. and Bocquet, Lydéric (2021) Fluids at the Nanoscale: From Continuum to Subcontinuum Transport. Annual Reviews of Fluid Mechanics, 53 . pp. 377-410. Kurbalija Novičić, Zorana and Bodén, Robert and Kozarski, Ksenija and Jelić, Mihailo and Jovanović, Vladimir M. and Cunningham, Janet L. (2021) Lithium influences whole‐organism metabolic rate in Drosophila subobscura. Journal of Neuroscience Research, 99 (1). pp. 407-418. ISSN 0360-4012 Renger, D.R. Michiel and Zimmer, Johannes (2021) Orthogonality of fluxes in general nonlinear reaction networks. DCDS-S 2021, 14 (1). pp. 205-217. (Submitted) Heida, Martin and Neukamm, Stefan and Varga, Mario (2021) Stochastic homogenization of Λ-convex gradient flows. DISCRETE AND CONTINUOUS DYNAMICAL SYSTEMS SERIES S, 14 (1). pp. 427-459. von Lindheim, Johannes and Harikrishnan, A. P. and Dörffel, Tom and Klein, Rupert and Koltai, Péter and Mikula, Natalia and Müller, Annette and Névir, Peter and Pacey, George and Polzin, Robert and Vercauteren, Nikki (2021) Definition, detection and tracking of persistent structures in atmospheric flows. arXiv J. Math. Phys . (Submitted) Leyshon, Thomas and Tonello, Elisa and Schnoerr, David and Siebert, Heike and Stumpf, Michael P.H. (2021) The Design Principles of Discrete Turing Patterning Systems. Journal of Theoretical Biology, 531 . Sechi, Renata and Sikorski, Alexander and Weber, Marcus (2021) Estimation of the Koopman Generator by Newton's Extrapolation. Multiscale Modeling & Simulation, 19 (2). pp. 758-774. Sechi, Renata and Sikorski, Alexander and Weber, Marcus (2021) Estimation of the Koopman generator by Newton’s extrapolation. SIAM Multiscale Modeling & Simulation, 19 (2). pp. 758-774. ISSN print: 1540-3459; online: 1540-3467 Schillings, Claudia and Guth, Philipp A. and Weissmann, Simon (2021) A General Framework for Machine Learning based Optimization Under Uncertainty. . . (Submitted) John, David N. and Stohrer, Livia and Schillings, Claudia and Schick, Michael and Heuveline, Vincent (2021) Hierarchical surrogate-based Approximate Bayesian Computation for an electric motor test bench. . . (Submitted) Osagiede, Edoseghe E. and Rosenau, Matthias and Rotevatn, Atle and Gawthorpe, Robert and Jackson, Christopher A-L and Rudolf, Michael (2021) Influence of zones of pre-existing crustal weakness on strain localization and partitioning during rifting: Insights from analogue modeling using high resolution 3D digital image correlation. EarthArXiv . pp. 1-55. (Submitted) Prieto, M. J. and Mullan, T. and Schlutow, M. and Gottlob, D. M. and Tanase, L. C. and Menzel, D. and Sauer, J. and Usvyat, D. and Schmidt, T. and Freund, H.-J. (2021) Insights into reaction kinetics in confined space: real time observation of water formation under a silica cover. Journal of the American Chemical Society, 143 . pp. 8780-8790. Djurdjevac, A. (2021) Linear Parabolic Problems in Random Moving Domains. ASA Jounal on Uncertainty Quantification, 9 (2). Poppe, S. and Holohan, Eoghan P. and Rudolf, M. and Rosenau, M. and Galland, O. and Delcamp, A. and Kervyn, M. (2021) Mechanical test data of quartz sand, garnet sand, gypsum powder (plaster), kaolin and sand-plaster mixtures used as granular analogue materials in geoscience laboratory experiments. Tectonophysics, 814 . p. 228976. ISSN 0040-1951 Berg, Mascha and Plöntzke, Julia and Siebert, Heike and Röblitz, Susanna (2021) Modelling Oscillatory Patterns in the Bovine Estrous Cycle with Boolean Delay Equations. Modelling Oscillatory Patterns in the Bovine Estrous Cycle with Boolean Delay Equations . Mollenhauer, Mattes and Koltai, Péter (2021) Nonparametric approximation of conditional expectation operators. arXiv . (Unpublished) Kies, T. and Gräser, C. (2021) On differentiability of the membrane-mediated mechanical interaction energy of discrete-continuum membrane-particle models. Interfaces and Free Boundaries . pp. 1-22. ISSN 1463-9963 (In Press) Guth, Philipp A. and Kaarnioja, Vesa and Kuo, Frances Y. and Schillings, Claudia and Sloan, Ian H. (2021) A Quasi-Monte Carlo Method for Optimal Control Under Uncertainty. SIAM/ASA Journal on Uncertainty Quantification, 9 (2). pp. 354-383. Heida, Martin and Neukamm, Stefan and Varga, Mario (2021) STOCHASTIC HOMOGENIZATION OF L-CONVEX GRADIENT FLOWS. Discrete and Continuous Dynamical Systems - S, 14 (1). pp. 1-27. Barua, Amlan K. and Chew, Ray and Li, Shuwang and Lowengrub, John and Münch, A. and Wagner, B. (2021) Sharp-interface problem of the Ohta-Kawasaki model 2 for symmetric diblock copolymers. Journal of Computational Physics . pp. 1-34. ISSN 0021-9991 (Submitted) Haug, Ø. T. and Rosenau, M. and Rudolf, M. and Leever, K. (2021) Short communication: Runout of rock avalanches limited by basal friction but controlled by fragmentation. Earth Surface Dynamics, 9 (3). pp. 665-672. Boyko, V. and Krumscheid, S. and Vercauteren, N. (2021) Statistical learning of non-linear stochastic differential equations from non-stationary time-series using variational clustering. . . (Submitted) Tierno, Pietro and Johansen, Tom H. and Straube, Arthur V. (2021) Thermally active nanoparticle clusters enslaved by engineered domain wall traps. NATURE COMMUNICATIONS, 12 (5813). pp. 1-11. Schmidt, F. and Gagarina, E. and Klein, R. and Achatz, U. (2021) Toward a Numerical Laboratory for Investigations of Gravity Wave–Mean Flow Interactions in the Atmosphere. Monthly Weather Review, 149 (12). pp. 4005-4026. Schmidt, F. and Gagarina, E. and Klein, R. and Achatz, U. (2021) Towards a numerical laboratory for investigations of gravity-wave 2 mean-ow interactions in the atmosphere. Monthly Weather Review MWR-D-21-0126 . pp. 1-75. (Submitted) Koltai, Péter and von Lindheim, Johannes and Neumayer, Sebastian and Steidl, Gabriele (2021) Transfer Operators from Optimal Transport Plans for Coherent Set Detection. Physica D: Nonlinear Phenomena, 426 . pp. 1-34. Gräser, C. and Kienle, D. and Sander, O. (2021) Truncated Nonsmooth Newton Multigrid for phase-field brittle-fracture problems. arXiv:2007.12290 . pp. 1-41. (Submitted) Rodal, M. and Schlutow, M. (2021) Waves in the gas centrifuge: Asymptotic theory and similarities with the atmosphere. Journal of Fluid Mechanics, 928 . Detring, Carola and Müller, Annette and Schielicke, Lisa and Névir, Peter and Rust, Henning W. (2020) Atmospheric blocking types: Frequencies and transitions. European Geosiences Union . pp. 1-33. (Submitted) Bittracher, Andreas and Klus, Stefan and Hamzi, Boumediene and Koltai, Péter and Schütte, Christof (2020) Dimensionality Reduction of Complex Metastable Systems via Kernel Embeddings of Transition Manifolds. Journal of Nonlinear Science, 31 (3). pp. 1-41. ISSN 1432-1467 (online) Bittracher, Andreas and Klus, Stefan and Hamzi, Boumediene and Koltai, Péter and Schütte, Christof (2020) Dimensionality Reduction of Complex Metastable Systems via Kernel Embeddings of Transition Manifolds. Journal of Nonlinear Science, 31 (3). Funiciello, Francesca and Corbi, Fabio and Heuret, Arnauld and Piromallo, Claudia and Rosenau, Matthias (2020) Empirical Analysis of Global-Scale Natural Data and Analogue Seismotectonic Modelling Data to Unravel the Seismic Behaviour of the Subduction Megathrust. Frontiers in Earth Science, 8 . pp. 1-8. ISSN 2296-6463 Ntini, Evgenia and Budach, Stefan and Vang Ørom, Ulf A and Marsico, Annalisa (2020) Predictive modeling of long non-coding RNA chromatin (dis-)association. bioRxiv . Melnyk, Kateryna and Klus, S. and Montavon, Grègoire and Conrad, T. O. F. (2020) Graph Kernel Koopman Embedding for Human Microbiome Analysis. Applied Network Science, 5 (96). ISSN 2364-8228 Boyko, V. and Vercauteren, N. (2020) Multiscale Shear Forcing of Turbulence in the Nocturnal Boundary Layer: A Statistical Analysis. Boundary-Layer Meteorology, 177 (2-3). ISSN Electronic: 1573-1472; Print: 0006-8314 Husic, Brooke E. and Charron, Nicholas E. and Lemm, Dominik and Wang, Jiang and Pérez, Adrià and Majewski, Maciej and Krämer, Andreas and Chen, Yaoyi and Olsson, Simon and de Fabritiis, Gianni and Noé, Frank and Clementi, Cecilia (2020) Coarse graining molecular dynamics with graph neural networks. J. Chem. Phys., 153 (194101). pp. 1-17. Mielke, Alexander and Maas, Jan (2020) Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics, 181 . pp. 2257-2303. Hufsky, Franziska and Lamkiewicz, Kevin and Almeida, Alexandre and Aouacheria, Abdel and Arighi, Cecilia and Bateman, Alex and Baumbach, Jan and Beerenwinkel, Niko and Brandt, Christian and Cacciabue, Marco and Chuguransky, Sara and Drechsel, Oliver and Finn, Robert D and Fritz, Adrian and Fuchs, Stephan and Hattab, Georges and Hauschild, Anne-Christin and Heider, Dominik and Hoffmann, Marie and Hölzer, Martin and Hoops, Stefan and Kaderali, Lars and Kalvari, Ioanna and von Kleist, Max and Kmiecinski, Renó and Kühnert, Denise and Lasso, Gorka and Libin, Pieter and List, Markus and Löchel, Hannah F and Martin, Maria J and Martin, Roman and Matschinske, Julian and McHardy, Alice C and Mendes, Pedro and Mistry, Jaina and Navratil, Vincent and Nawrocki, Eric P and O’Toole, Áine Niamh and Ontiveros-Palacios, Nancy and Petrov, Anton I and Rangel-Pineros, Guillermo and Redaschi, Nicole and Reimering, Susanne and Reinert, Knut and Reyes, Alejandro and Richardson, Lorna and Robertson, David L and Sadegh, Sepideh and Singer, Joshua B and Theys, Kristof and Upton, Chris and Welzel, Marius and Williams, Lowri and Marz, Manja (2020) Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. Briefings in Bioinformatics, 22 (2). pp. 642-663. ISSN 1467-5463 Farshbaf-Shaker, M. Hassan and Thomas, Marita (2020) Analysis of a compressible Stokes-flow with degenerating and singular viscosity. Preprint . pp. 1-45. (Submitted) Richter, Lorenz and Boustati, Ayman and Nüsken, Nikolas and Ruiz, Francisco J. R. and Akyildiz, Ömer Deniz (2020) VarGrad: A Low-Variance Gradient Estimator for Variational Inference. Advances in Neural Information Processing Systems 2020 . pp. 1-25. (Submitted) Mitterwallner, Bernhard G. and Lavacchi, Laura and Netz, Roland R. (2020) Negative friction memory induces persistent motion. Eur Phys J E Soft Matter, 43 (10). Leung, Tsz Yan and Leutbecher, M. and Reich, S. and Shepherd, Th.G. (2020) Impact of the mesoscale range on error growth and the limits to atmospheric predictability. Journal of the Atmospheric Sciences, 77 (11). pp. 3769-3779. ISSN 1520-0469 Schulz, Julius C. F. and Schlaich, Alexander and Heyden, Matthias and Netz, Roland R. and Kappler, Julian (2020) Molecular interpretation of the non-Newtonian viscoelastic behavior of liquid water at high frequencies. Phys. Rev. Fluids, 5 . Chowdhary, Suvrat and Moschner, Johann and Mikolajczak, Dorian J. and Becker, Maximilian and Thünemann, Andreas F. and Kästner, Claudia and Klemczak, Damian and Stegemann, Anne-Katrin and Böttcher, Christoph and Metrangolo, Pierangelo and Netz, Roland R. and Koksch, Beate (2020) The Impact of Halogenated Phenylalanine Derivatives on NFGAIL Amyloid Formation. ChemBioChem, 21 . pp. 3544-3554. Helfmann, Luzie and Ribera Borrell, Enric and Schütte, Christof and Koltai, Péter (2020) Extending Transition Path Theory: Periodically Driven and Finite-Time Dynamics. Journal of Nonlinear Science, 30 . pp. 3321-3366. Helfmann, Luzie and Ribera Borrell, Enric and Schütte, Christof and Koltai, Péter (2020) Extending Transition Path Theory: Periodically Driven and Finite-Time Dynamics. Journal of Nonlinear Science . pp. 1-46. ISSN 1432-1467 (online) Delle Site, L. and Klein, R. and Höfling, F. and Viand, R. E. (2020) Theory and simulation of open systems out of equilibrium. J. Chem. Phys. (2020);, 153 (10). pp. 1-7. ISSN 101102 Lavacchi, Laura and Kappler, Julian and Netz, Roland R. (2020) Barrier crossing in the presence of multi-exponential memory functions with unequal friction amplitudes and memory times. EPL, 131 . pp. 1-8. Müller, Annette and Niedrich, Benjamin and Névir, Peter (2020) Three-dimensional potential vorticity structures for extreme precipitation events on the convective scale. Tellus A: Dynamic Meteorology and Oceanography, 72 (1). pp. 1-20. ISSN (Print) (Online) Journal homepage: https://www.tandfonline.com/loi/zela20 Becker, Simon and Richter, Lorenz (2020) Model order reduction for (stochastic-) delay equations with error bounds. arXive . pp. 1-23. (Submitted) Pieper, Robert and Dadi, Temesgen H. and Pieper, Laura and Vahjen, Wilfried and Franke, André and Reinert, Knut and Zentek, Jürgen (2020) Concentration and chemical form of dietary zinc shape the porcine colon microbiome, its functional capacity and antibiotic resistance gene repertoire. The ISME Journal, 14 (11). pp. 2783-2793. ISSN 1751-7362 Delle Site, L. and Klein, R. (2020) Liouville-type equations for the n-particle distribution functions of an open system. Journal of Mathematical Physics, 61 (8). Franchi, Bruno and Heida, Martin and Lorenzani, Silvia (2020) A Mathematical model for Alzheimer's disease: An approach via stochastic homogenization of the Smoluchowski equation. Communications in Mathematical Sciences, 18 (4). pp. 1105-1134. Froyland, Gary and Koltai, Péter and Stahn, Martin (2020) Computation and Optimal Perturbation of Finite-Time Coherent Sets for Aperiodic Flows Without Trajectory Integration. SIAM J. APPLIED DYNAMICAL SYSTEMS, 19 (3). pp. 1659-1700. KORNHUBER, RALF and PODLESNY, JOSCHA and YSERENTANT, HARRY (2020) NUMERICAL HOMOGENIZATION OF FRACTAL INTERFACE PROBLEMS. arXive . pp. 1-30. (Submitted) Bittracher, Andreas and Schütte, Christof (2020) A weak characterization of slow variables in stochastic dynamical systems. Studies in Systems, Decision and Control, 304 . pp. 132-150. Kosari, Ehsan and Rosenau, Matthias and Bedford, Jonathan and Rudolf, Michael and Oncken, Onno (2020) On the relationship between offshore geodetic coverage and slip model uncertainty: Analog megathrust earthquake case studies. Geophysical Research Letters, 47 . pp. 1-15. Garbuno-Inigo, Alfredo and Nüsken, Nikolas and Reich, Sebastian (2020) Affine Invariant Interacting Langevin Dynamics for Bayesian Inference. SIAM J. APPLIED DYNAMICAL SYSTEMS, 19 (3). pp. 1633-1658. Netz, Roland R. (2020) Mechanisms of Airborne Infection via Evaporating and Sedimenting Droplets Produced by Speaking. Journal Phys. Chem. B, 124 (133). pp. 7093-7101. Schillings, Claudia and Sprungk, Björn and Wacker, Philipp (2020) On the convergence of the Laplace approximation and noise-level-robustness of Laplace-based Monte Carlo methods for Bayesian inverse problems. Numerische Mathematik, 145 . pp. 915-971. Renard, Bernhard Y and Reinert, Knut and Seiler, Enrico and Dadi, Temesgen H and Piro, Vitor C (2020) ganon: precise metagenomics classification against large and up-to-date sets of reference sequences. Bioinformatics, 36 (Supple). i12-i20. ISSN 1367-4803 Straube, Arthur V. and Kowalik, Bartosz G. and Netz, Roland R. and Höfling, Felix (2020) Rapid onset of molecular friction in liquids bridging between the atomistic and hydrodynamic pictures. Communications Physics, 3 (126). pp. 1-11. Klus, Stefan and Nüske, Felix and Hamzi, Boumediene (2020) Kernel-Based Approximation of the Koopman Generator and Schrödinger Operator. entropy, 22 . Sadeghi, Mohsen and Noé, Frank (2020) Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models. Nature Communications, 11 (2951). Horenko, I. (2020) On a Scalable Entropic Breaching of the Overtting Barrier for Small Data Problems in Machine Learning. Neural Computation, 32 (8). pp. 1563-1579. Höfling, F. and Dietrich, S. (2020) Finite-size corrections for the static structure factor of a liquid slab with open boundaries. Journal of Chemical Physics, 153 (5). pp. 1-13. Noé, Frank (2020) Machine Learning for Molecular Dynamics on Long Timescales. Machine Learning Meets Quantum Physics . pp. 331-372. Schönhuth, Alexander and Moeinzadeh, M-Hossein and Yang, Jun and Muzychenko, Evgeny and Gallone, Giuseppe and Heller, David and Reinert, Knut and Haas, Stefan and Vingron, Martin (2020) Ranbow: A fast and accurate method for polyploid haplotype reconstruction. PLOS Computational Biology, 16 (5). e1007843. ISSN 1553-7358 Hittmeir, S. and Klein, R. and Li, J. and Titi, E. (2020) Global well-posedness for the primitive equations coupled to nonlinear moisture dynamics with phase changes. Nonlinearity, 33 (7). pp. 3206-3236. Naliboff, J.B. and Glerum, A. and Brune, S.A. and Péron-Pinvidic, G. and Wrona, T. (2020) Development of 3-D Rift Heterogeneity Through Fault Network Evolution. Geophysical Research Letters, 47 (13). ISSN 0094-8276; ESSN: 1944-8007 Nüsken, N. and Richter, L. (2020) Solving high-dimensional Hamilton-Jacobi-Bellman PDEs using neural networks: perspectives from the theory of controlled diffusions and measures on path space. SFB 1114 Preprint in arXiv . pp. 1-40. (Submitted) Witt, Natalie and Andreotti, Sandro and Busch, Anne and Neubert, Kerstin and Reinert, Knut and Tomaso, Herbert and Meierhofer, David (2020) Rapid and Culture Free Identification of Francisella in Hare Carcasses by High-Resolution Tandem Mass Spectrometry Proteotyping. Frontiers in Microbiology, 11 . ISSN 1664-302X Soucek, Ondrej and Heida, Martin and Malek, Josef (2020) On a thermodynamic framework for developing boundary conditions for Korteweg-type fluids. International Journal of Engineering Science, 154 . pp. 1-28. Juds, Carmen and Schmidt, Johannes and Weller, Michael and Lange, Thorid and Conrad, T. O. F. and Boerner, Hans (2020) Combining Phage Display and Next-generation Sequencing for Materials Sciences: A Case Study on Probing Polypropylene Surfaces. Journal of the American Chemical Society, 142 (24). ISSN 0002-7863 Haug, Ø. T. and Rosenau, M. and Rudolf, M. and Leever, K. and Oncken, O. (2020) Variations in runout of rock avalanches controlled by fragmentation, not basal friction. EarthArXiv . pp. 1-11. Reinert, Knut and Iliopoulos, Costas S and Alzamel, Mai and Pockrandt, Christopher and Xu, Jinbo (2020) GenMap: ultra-fast computation of genome mappability. Bioinformatics, 36 (12). pp. 3687-3692. ISSN 1367-4803 Beinlich, A. and John, T. and Vrijmoed, J.C. and Tominaga, M. and Podladchikov, Y.Y. (2020) Instantaneous rock transformations in the deep crust driven by reactive fluid flow. nature geoscience, 13 . pp. 307-311. Mitterwallner, Bernhard G. and Schreiber, Christoph and Daldrop, Jan O. and Netz, Roland R. and Rädler, Joachim O. (2020) Non- markovian data-driven modeling of single-cell motility. PHYSICAL REVIEW E, 101 . ISSN 032408 Corbi, F. and Bedford, J. and Sandri, L. and Funiciello, F. and Gualandi, A. and Rosenau, M. (2020) Predicting Imminence of Analog Megathrust Earthquakes With Machine Learning: Implications for Monitoring Subduction Zones. Geophysical Research Letters . pp. 1-10. ISSN 1944-8007 Rams, Mona and Conrad, T. O. F. (2020) Dictionary Learning for transcriptomics data reveals type-specific gene modules in a multi-class setting. Information Technology, 62 (3). ISSN 2196-7032 Delle Site, L. and Praprotnik, M. and Bell, John B. and Klein, R. (2020) "Particle-Continuum Coupling and its Scaling Regimes: Theory and Applications". Advanced Theory and Simulations, 3 (5). Koltai, Péter and Weiss, Stephan (2020) Diffusion maps embedding and transition matrix analysis of the large-scale flow structure in turbulent Rayleigh-Bénard convection. Nonlinearity, 33 (4). p. 1723. ISSN 0951-7715 Noé, Frank and Tkatchenko, Alexandre and Müller, Klaus-Robert and Clementi, Cecilia (2020) Machine Learning for Molecular Simulation. Annual Review of Physical Chemistry, 71 . pp. 361-390. Netz, Roland R. (2020) Approach to equilibrium and nonequilibrium stationary distributions of interacting many-particle systems that are coupled to different heat baths. Phys. Rev. E, 101 . ISSN 022120 Heida, M. and Kornhuber, R. and Podlesny, J. (2020) Fractal homogenization of multiscale interface problems. Multiscale Modeling & Simulation, 18 (1). pp. 294-314. ISSN 1540-3459 Gerber, S. and Pospisil, L. and Navandar, M. and Horenko, I. (2020) Low-cost scalable discretization, prediction and feature selection for complex systems. Science Advances, 6 (5). Pfeuffer, Julianus and Sachsenberg, Timo and Dijkstra, Tjeerd M. H. and Serang, Oliver and Reinert, Knut and Kohlbacher, Oliver (2020) EPIFANY: A Method for Efficient High-Confidence Protein Inference. Journal of Proteome Research, 19 (3). pp. 1060-1072. ISSN 1535-3893 Kieninge, Stefanie and Donati, Luca and Keller, Bettina (2020) Dynamical reweighting methods for Markov models. Current Opinion in Structural Biology, 61 . pp. 124-131. ISSN 0959-440X Gussmann, Pascal and Mielke, Alexander (2020) Linearized elasticity as Mosco-limit of finite elasticity in the presence of cracks. Advances in Calculus of Variations, 13 (1). pp. 1-20. Banisch, R. and Trstanova, Z. and Bittracher, A. and Klus, S. and Koltai, P. (2020) Diffusion maps tailored to arbitrary non-degenerate Ito processes. Applied and computational harmonic analysis, 48 (1). pp. 242-265. ISSN 1063-5203, 1096-603X Hartmann, C. and Neureither, L. and Sharma, U. (2020) Coarse-graining of non-reversible stochastic differential equations: quantitative results and connections to averaging. SIAM Journal on Mathematical Analysis, 52 (3). pp. 2689-2733. Hartmann, Carsten and Neureither, Lara and Sharma, Upanshu (2020) Coarse-graining of non-reversible stochasticdifferential equations: quantitative results and connections to averaging. SIAM Journal on Numerical Analysis, 52 (3). pp. 2689-2733. ISSN 0036-1429 Mielke, Alexander and Stephan, Artur (2020) Coarse-graining via EDP-convergence for linear fast-slow reaction systems. Mathematical Models and Methods in Applied Sciences, 30 (9). pp. 1765-1807. Klus, Stefan (2020) Data-driven analysis of complex dynamical systems. Refubium . pp. 1-174. Klus, Stefan and Nüske, Feliks and Peitz, Sebastian and Niemann, Jan-Hendrik and Clementi, Cecilia and Schütte, Christof (2020) Data-driven approximation of the Koopman generator: Model reduction, system identification, and control. Physica D: Nonlinear Phenomena, 406 (132416). Mardt, Andreas and Pasquali, Luca and Noé, F. and Wu, Hao (2020) Deep learning Markov and Koopman models with physical constraints. Proceedings of Machine Learning Research, 107 . pp. 451-475. Kaiser, A. and Faranda, D. and Krumscheid, S. and Belušić, D. and Vercauteren, N. (2020) Detecting regime transitions of the nocturnal and Polar near-surface temperature inversion. Journal of the Atmospheric Sciences . ISSN 0022-4928; eISSN: 1520-0469 Haghdoost, M.R. and Edgington-Mitchell, D. and Nadolski, M. and Klein, R. and Oberleithner, K. (2020) Dynamic Evolution of a Transient Supersonic Trailing Jet Induced by a Strong Incident Shock Wave. Phys. Rev. Fluids, 5 (7). Guth, Philipp A. and Schillings, Claudia and Weissmann, Simon (2020) Ensemble Kalman filter for neural network based one-shot inversion. . . (Submitted) Guth, Philipp A. and Schillings, Claudia and Weissmann, Simon (2020) Ensemble Kalman filter for neural network-based one-shot inversion. ArXiv . (Submitted) Gräser, C. and Alathur Srinivasan, P. A. (2020) Error bounds for PDE-regularized learning. arXiv:2003.06524 . pp. 1-20. (Submitted) Carlson, Shane and Brünig, Florian N. and Loche, Philip and Bonthuis, Douwe Jan and Netz, Roland R. (2020) Exploring the Absorption Spectrum of Simulated Water from MHz to Infrared. The Journal of Physical Chemistry A, 124 (27). pp. 5599-5605. ISSN 1089-5639 Henneke, F. and Lin, L. and Vorwerk, C. and Draxl, C. and Klein, R. and Yang, C. (2020) Fast Optical Absorption Spectra Calculations for Periodic Solid State Systems. Communications in Applied Mathematics and Computational Science, 15 (1). pp. 89-113. Hammerschmidt, M. and Döpking, S. and Matera, S. (2020) Field Heterogeneities and Their Impact on Photocatalysis: Combining Optical and Kinetic Monte Carlo Simulations on the Nanoscale. J. Phys. Chem. C 2020, 124, 5, 3177–3187 Publication Date:January 8, 2020 https://doi.org/10.1021/acs.jpcc.9b11469 Copyright © 2020 . Kies, T. and Gräser, C. and Delle Site, L. and Kornhuber, R. (2020) Free energy computation of particles with membrane-mediated interactions via Langevin dynamics. arXiv:2009.14713 . pp. 1-20. (Submitted) Schlutow, M. and Wahlén, E. (2020) Generalized modulation theory for nonlinear gravity waves in a compressible atmosphere. Mathematics of Climate and Weather Forecasting, 6 (1). pp. 97-112. ISSN 2353-6438 (online) Ray, Sourav and Sunkara, Vikram and Schütte, Christof and Weber, Markus (2020) How to calculate pH-dependent binding rates for receptor-ligand systems based on thermodynamic simulations with different binding motifs. Molecular Simulation, 46 (18). pp. 1443-1452. Ray, Sourav and Sunkara, Vikram and Schütte, Christof and Weber, Marcus (2020) How to calculate pH-dependent binding rates for receptor–ligand systems based on thermodynamic simulations with different binding motifs. Molecular Simulation, 46 (18). pp. 1443-1452. Benner, P. and Breiten, T. and Hartmann, C. and Schmidt, B. (2020) Model reduction of controlled Fokker-Planck and Liouville-von Neumann equations. J. Comp. Dyn., 7 (1). pp. 1-33. Bachmayr, m: and Djurdjevac, A. (2020) Multilevel Representations of Isotropic Gaussian Random Fields on the Sphere. : . (Submitted) Schlutow, M. and Voelker, G.S. (2020) On strongly nonlinear gravity waves in a vertically sheared atmosphere. Mathematics of Climate and Weather Forecasting, 6 (1). pp. 63-74. Schillings, Claudia and Sprungk, Björn and Wacker, Philipp (2020) On the convergence of the Laplace approximation and noise-level-robustness of Laplace-based Monte Carlo methods for Bayesian inverse problems. Numerische Mathematik, 145 (1). pp. 915-971. Viand, R. E. and Höfling, F. and Klein, R. and Delle Site, L. (2020) Open Systems out of Equilibrium: Theory and Simulation. J. Chem. Phys., 153 (10). Delle Site, L. and Praprotnik, M. and Bell, John B. and Klein, R. (2020) Particle-Continuum Coupling and its Scaling Regimes: Theory and Applications. Advanced Theory and Applications . Delle Site, L. and Praprotnik, M. and Bell, J. B. and Klein, R. (2020) Particle–Continuum Coupling and its Scaling Regimes: Theory and Applications. Advanced Theory and Simulation, 3, 1900232 (2020), 3 (190023). pp. 1-20. Möller, Jan and Isbilir, Ali and Sungkaworn, Titiwat and Osberg, Brendan and Karathanasis, Christos and Sunkara, Vikram and Grushevskyi, Eugene O. and Bock, Andreas and Annibale, Paolo and Heileman, Mike and Schütte, Christof and Lohse, Martin J. (2020) Single molecule mu-opioid receptor membrane-dynamics reveal agonist-specific dimer formation with super-resolved precision. Nature chemical biology (16). pp. 946-954. Mollenhauer, Mattes and Schuster, Ingmar and Klus, Stefan and Schütte, Christof (2020) Singular Value Decomposition of Operators on Reproducing Kernel Hilbert Spaces. Advances in Dynamics, Optimization and Computation . pp. 109-131. Mielke, A. and Roubícek, T. (2020) Thermoviscoelasticity in Kelvin-Voigt rheology at large strains. Arch. Rational Mech. Anal., 238 . pp. 1-45. Nagy, E. and Ransiek, A. and Schäfer, M. and Lux, A. and Bergmann, M. and Jahn, T. and Marg, O. and Theiler, L. (2020) Transfer as a reciprocal process: How to foster receptivity to results of transdisciplinary research. Environmental Science and Policy, 104 . pp. 148-160. Bellingeri, C. and Djurdjevac, A. and Friz, P.K. and Tapia, N. (2020) Transport and continuity equations with (very) rough noise. . . (Submitted) Ernst, Oliver and Nobile, Fabio and Schillings, Claudia and Sullivan, Tim (2020) Uncertainty quantification. Oberwolfach Reports, 16 (1). pp. 695-772. Stevens, B. and Acquistapace, C. and Hansen, A. and Heinze, R. and Klinger, C. and Klocke, D. and Rybka, H. and Schubotz, W. and Windmiller, J. and Adamidis, P. and Arka, I. and Barlakas, V. and Biercamp, J. and Brueck, M. and Brune, S.A. and Buehler, U. and Burkhardt, U. and Cioni, G. and Costa-Suròs, M. and Crewell, S. and Crüger, T. and Deneke, H. and Friederichs, P. and Henken, C.C. and Hohenegger, C. and Jacob, M. and Jakub, F. and Kalthoff, N. and Köhler, M. and van Laar, T.W. and Li, P. and Löhnert, U. and Macke, A and Madenach, N. and Mayer, B. and Nam, C. and Naumann, A.K. and Peters, K. and Poll, S. and Quaas, J. and Röber, N. and Rochetin, N. and Scheck, L. and Schemann, V. and Schnitt, S. and Senf, F. and Shapkalijevski, M. and Simmer, C. and Singh, S. and Sourdeval, O. and Spickermann, D. and Strandgren, J. and Tessiot, O. and Vercauteren, N. and Vial, J. and Voigt, A. and Zängl, G. and Seifert, A. (2020) The added value of large-eddy and storm-resolving models for simulating clouds and precipitation. Journal of the Meteorological Society of Japan, 98 . pp. 395-435. ISSN Online: 2186-9057 Print: 0026-1165 Church, L. and Djurdjevac, A. and Elliott, C.M. (2020) A domain mapping approach for elliptic equations posed on random bulk and surface domains. Numerische Mathematik, 146 . pp. 1-49. ISSN Electronic: 0945-3245; Print: 0029-599X Flegel, Franziska and Heida, Martin (2020) The fractional p-Laplacian emerging from homogenization of the random conductance model with degenerate ergodic weights and unbounded-range jumps. Calculus of Variations and Partial Differential Equations, 59 (8). (Unpublished) Müller, Annette and Névir, Peter (2019) Using the concept of the Dynamic State Index for a scale-dependent analysis of atmospheric blocking. Meteorologische Zeitschrift, 28 (6). pp. 487-498. Becker, Simon and Hartmann, Carsten and Redmann, Martin and Richter, Lorenz (2019) Feedback control theory & Model order reduction for stochastic equations. ArXive . pp. 1-36. (Submitted) Klus, Stefan and Husic, Brooke E. and Mollenhauer, Mattes and Noé, Frank (2019) Kernel methods for detecting coherent structures in dynamical data. Chaos, 29 (12). Garbuno Inigo, A. and Nüsken, N. and Reich, S. (2019) Affine invariant interacting Langevin dynamics for Bayesian inference. SFB 1114 Preprint in arXiv:1912.02859 . pp. 1-29. (Unpublished) Duncan, A. and Nüsken, N. and Szpruch, L. (2019) On the geometry of Stein variational gradient descent. SFB 1114 Preprint in arXiv:1912.00894 . (Unpublished) Loche, Philip and Ayaz, Cihan and Schlaich, Alexander and Uematsu, Yuki and Netz, Roland R. (2019) Giant Axial Dielectric Response in Water-Filled Nanotubes and Effective Electrostatic Ion–Ion Interactions from a Tensorial Dielectric Model. J. Phys. Chem. B, 123 (50). pp. 10850-10857. Bartscha, Clemens and Wiedmeyer, Viktoria and Lakdawala, Zahra and Patterson, Robert I.A. and Voigt, Andreas and Sundmacher, Kai and John, Volker (2019) Stochastic-deterministic population balance modeling and simulation of a fluidized bed crystallizer experiment. Chemical Engineering Science, 208 . ISSN 115102 Whittaker, John and Delle Site, Luigi (2019) Investigation of the hydration shell of a membrane in an open system molecular dynamics simulation. Phys. Rev. Research, 1 (3). Schneide, Ch. and Stahn, Martin and Pandey, A. and Junge, Oliver and Koltai, Péter and Padberg-Gehle, Kathrin and Schumacher, Jörg (2019) Lagrangian coherent sets in turbulent Rayleigh-Bénard convection. Physical Review E, 100 (053103). Leung, T.Y. and Leutbecher, M. and Reich, S. and Shepherd, Th.G. (2019) Atmospheric Predictability: Revisiting the Inherent Finite-Time Barrier. Journal of the Atmospheric Sciences, 76 (12). pp. 3883-3892. ISSN Online: 1520-0469 Print: 0022-4928 Vater, S. and Beisiegel, N. and Behrens, J. (2019) A limiter‐based well‐balanced discontinuous Galerkin method for shallow‐water flows with wetting and drying: Triangular grids. International Journal for Numerical Methods in Fluids, 91 (8). pp. 395-418. Dibak, Manuel and Fröhner, Christoph and Noé, Frank and Höfling, Felix (2019) Diffusion-influenced reaction rates in the presence of pair interactions. The Journal of Chemical Physics, 151 (16). Chen, Shuo and Hin, Remco C. and John, Timm and Bryan, Ben and Nui, Yaoling and Elliott, Tim and Brooker, R. (2019) Molybdenum systematics of subducted crust record reactive fluid flow from underlying slab serpentine dehydration. nature communications . pp. 1-9. Koltai, P. and Lie, Han Cheng and Plonka, M. (2019) Fréchet differentiable drift dependence of Perron--Frobenius and Koopman operators for non-deterministic dynamics. Nonlinearity, 32 (11). pp. 4232-4257. ISSN 0951-7715 Heida, Martin and Patterson, Robert I. A. and Renger, Michiel D.R. (2019) Topologies and measures on the space of functions of bounded variation taking values in a Banach or metric space. Journal of Evolution Equations, 19 (1). pp. 111-152. Kappler, Julian and Hinrichsen, Victor B. and Netz, Roland R. (2019) Non-Markovian barrier crossing with two-time-scale memory is dominated by the faster memory component. The European Physical Journal E, 42 (119). ISSN 1292-8941 Patterson, Robert I. A. and Renger, Michiel D.R. (2019) Large deviations of jump process fluxes. Math. Phys. Anal. Geom., 22 (21). pp. 1-32. ISSN 1385-0172; ESSN: 1572-9656 Schulz, Robert and Yamamoto, Kenji and Klossek, André and Rancan, Fiorenza and Vogt, Annika and Schütte, Christof and Rühl, Eckart and Netz, Roland R. (2019) Modeling of Drug Diffusion Based on Concentration Profiles in Healthy and Damaged Human Skin. Biophysical Journal, 117 (5). pp. 998-1008. ISSN 00063495 Noé, F. and Olsson, S. and Köhler, J. and Wu, H. (2019) Boltzmann Generators: Sampling Equilibrium States of Many-Body Systems with Deep Learning. Science, 365 (6457). eaaw1147. Iravani, Sahar and Conrad, T. O. F. (2019) Deep Learning for Proteomics Data for Feature Selection and Classification. Lecture Notes in Computer Science, 11713 . Zhang, W. and Klus, S. and Conrad, T. O. F. and Schütte, Ch. (2019) Learning chemical reaction networks from trajectory data. SIAM Journal on Applied Dynamical Systems, 18 (4). ISSN 1536-0040 Nüsken, N. and Reich, S. (2019) Note on Interacting Langevin Diffusions: Gradient Structure and Ensemble Kalman Sampler by Garbuno-Inigo, Hoffmann, Li and Stuart. arXive . pp. 1-6. (Submitted) Moschner, Johann and Stulberg, Valentina and Fernandes, Rita and Huhmann, Susanne and Leppkes, Jakob and Koksch, Beate (2019) Approaches to Obtaining Fluorinated α-Amino Acids. Chem. Rev. 2019, 119 (18). pp. 10718-10801. Klus, S. and Schuster, I. and Muandet, K. (2019) Eigendecompositions of Transfer Operators in Reproducing Kernel Hilbert Spaces. Journal of Nonlinear Science, 30 . pp. 283-315. Wu, Ho and Noé, Frank (2019) Variational approach for learning Markov processes from time series data. Journal of Nonlinear Science, 30 . pp. 23-66. ISSN 1432-1467 (online) Ulrich, T. and Vater, S. and Madden, E. H. and Behrens, J. and van Dinther, Y. and van Zelst, I. and Fielding, E. J. and Liang, C. and Gabriel, A.-A. (2019) Coupled, Physics-Based Modeling Reveals Earthquake Displacements are Critical to the 2018 Palu, Sulawesi Tsunami. Pure and Applied Geophysics, 176 . pp. 4069-4109. ISSN 0033-4553 (Print) 1420-9136 (Online) Pipping, E. (2019) Existence of long-time solutions to dynamic problems of viscoelasticity with rate-and-state friction. ZAMM - Journal of Applied Mathematics and Mechanics . ISSN 1521-4001 (online) Flegel, Franziska and Heida, Martin and Slowik, Martin (2019) Homogenization theory for the random conductance model with degenerate ergodic weights and unbounded-range jumps. Ann. Inst. H. Poincaré Probab. Statist., 55 (3). pp. 1226-1257. Schlutow, M. (2019) Modulational stability of nonlinear saturated gravity waves. Journal of the Atmospheric Sciences . Benacchio, T. and Klein, R. (2019) A semi-implicit compressible model for atmospheric flows with seamless access to soundproof and hydrostatic dynamics. Monthly Weather Review, 147 (11). pp. 4221-4240. ISSN Online: 1520-0493; Print: 0027-0644 Nüske, Feliks and Boninsegna, Lorenzo and Clementi, Cecilia (2019) Coarse-graining molecular systems by spectral matching. J. Chem. Phys., 151 . pp. 1-10. ISSN 0021-9606, ESSN: 1089-7690 Blömker, Dirk and Schillings, Claudia and Wacker, Philipp and Weissmann, Simon (2019) Well posedness and convergence analysis of the ensemble Kalman inversion. Inverse Problems, 35 . pp. 1-33. Schmidt, B. and Klein, R. and Cancissu Araujo, L. (2019) WavePacket: A Matlab package for numerical quantum dynamics. III: Quantum-classical simulations and surface hopping trajectories. J. Comp. Chem., 40 (30). pp. 2677-2688. Hittmeir, S. and Klein, R. and Li, J. and Titi, E. (2019) "Global well-posedness for the primitive equations coupled to nonlinear moisture dynamics with phase changes" by Hittmeir, Sabine; Klein, Rupert; Li, Jinkai; Titi, Edriss. Analysis of PDEs . pp. 1-28. ISSN 1907.11199 (Submitted) Li, Shujuan and Schmidt, B. (2019) Replica exchange MD simulations of Two-Dimensional Water in Graphene Nanocapillaries: Rhombic Versus Square Structures, Proton Ordering, and Phase Transitions. Phys. Chem. Chem. Phys., 21 (32). pp. 17640-17654. Seiler, Enrico and Trappe, Kathrin and Renard, Bernhard Y. (2019) Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation. PLOS Computational Biology, 15 (7). e1007208. ISSN 1553-7358 Kowalik, Bartosz G. and Daldrop, Jan O. and Kappler, Julian and Schulz, J.C.F. and Schlaich, Alexander and Netz, Roland R. (2019) Memory-kernel extraction for different molecular solutes in solvents of varying viscosity in confinement. PhysRevE (100). 012126. Renger, M. and Zimmer, J. (2019) Orthogonality of fluxes in general nonlinear reaction networks. SFB1114 Preprint 07/2019 in WIAS No. 2609 . pp. 1-12. (Unpublished) Wilson, Laurence O. W. and Hetzel, Sara and Pockrandt, Christopher and Reinert, Knut and Bauer, Denis C. (2019) VARSCOT: variant-aware detection and scoring enables sensitive and personalized off-target detection for CRISPR-Cas9. BMC Biotechnology, 19 (1). ISSN 1472-6750 Banisch, Ralf and Koltai, Péter and Padberg-Gehle, Kathrin (2019) Network measures of mixing. Chaos: An Interdisciplinary Journal of Nonlinear Science 29, 063125 (2019), 29 . pp. 1-16. Banisch, Ralf and Koltai, Péter and Padberg-Gehle, Kathrin (2019) Network measures of mixing. Chaos 29, 29 . pp. 1-15. Hartmann, Carsten and Kebiri, Omar and Neureither, Lara and Richter, Lorenz (2019) Variational approach to rare event simulation using least-squares regression. Chaos, 29 (6). ISSN 1054-1500 (print); 1089-7682 (online) Bartsch, Clemens and John, Volker and Patterson, Robert I. A. (2019) Simulations of an ASA flow crystallizer with a coupled stochastic-deterministic approach. Computers & Chemical Engineering, 124 . pp. 350-363. Rosenau, M. and Rudolf, M. and Oncken, O. (2019) Creep on seismogenic faults: Insights from analogue earthquake experiments. SFB 1114 Preprint in EarthArXiv:10.31223/osf.io/24u5h . pp. 1-25. (Unpublished) Nüsken, N. and Reich, S. and Rozdeba, P.J. (2019) State and parameter estimation from observed signal increments. Entropy, 21 (5). -505. ISSN 1099-4300 Wang, J. and Olsson, S. and Wehmeyer, C. and Perez, A. and Charron, N.E. and de Fabritiis, G. and Noé, F. and Clementi, C. (2019) Machine Learning of coarse-grained Molecular Dynamics Force Fields. ACS Cent. Sci., 5 (5). pp. 755-767. ISSN 2374-7943, ESSN: 2374-7951 Gräser, C. and Kies, T. (2019) Discretization error estimates for penalty formulations of a linearized Canham-Helfrich-type energy. IMA Journal of Numerical Analysis, 39 (2). pp. 626-649. ISSN 0272-4979 Paul, F. and Wu, H. and Vossel, M. and de Groot, B.L. and Noé, F. (2019) Identification of kinetic order parameters for non-equilibrium dynamics. J. Chem. Phys., 150 (16). p. 164120. ISSN 0021-9606, ESSN: 1089-7690 Hartmann, C. and Schütte, Ch. and Zhang, W. (2019) Jarzysnki equality, fluctuation theorems and variance reduction: Mathematical analysis and numerical algorithms. J. Stat. Phys., 175 (6). pp. 1214-1261. ISSN 0022-4715; ESSN: 1572-9613 Miron, P. and Beron-Vera, F.J. and Olascoaga, M.J. and Koltai, P. (2019) Markov-chain-inspired search for MH370. Chaos: An Interdisciplinary Journal of Nonlinear Science, 29 (4). ISSN 1054-1500 (print); 1089-7682 (online) Heida, M. and Nesenenko, S. (2019) Stochastic homogenization of rate-dependent models of monotone type in plasticity. Asymptotic Analysis, 112 (3-4). pp. 185-212. ISSN 0921-7134 Pinamonti, G. and Paul, F. and Noé, F. and Rodriguez, A. and Bussi, G. (2019) The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models. J. Chem. Phys., 150 (15). p. 154123. ISSN 0021-9606, ESSN: 1089-7690 Rosenau, M. and Horenko, I. and Corbi, F. and Rudolf, M. and Kornhuber, R. and Oncken, O. (2019) Synchronization of great subduction megathrust earthquakes: Insights from scale model analysis. Journal of Geophysical Research: Solid Earth, 124 (4). pp. 3646-3661. ISSN 2169-9356 Alchikh, M. and Conrad, T. O. F. and Hoppe, Ch. and Ma, X. and Broberg, E. and Penttinen, P. and Reiche, J. and Biere, B. and Schweiger, B. and Rath, B. (2019) Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care. Clinical Microbiology and Infection, 25 (3). 380.e9-380.e16. ISSN 1469-0691 Kappler, Julian and Noé, Frank and Netz, Roland R. (2019) Cyclization and Relaxation Dynamics of Finite-Length Collapsed Self-Avoiding Polymers. Physical Review Letters, 122 . Gupta, P. and Peter, S. and Jung, M. and Lewin, A. and Hemmrich-Stanisak, G. and Franke, A. and von Kleist, M. and Schütte, Ch. and Einspanier, R. and Sharbati, S. and zur Bruegge, J. (2019) Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections. Sci. Rep., 9 (1571). ISSN 2045-2322 Heydecker, Daniel and Patterson, Robert I. A. (2019) Bilinear Coagulation Equations. SFB1114 Preprint in arxiv:1902.07686 . (Unpublished) Kühnlein, C. and Deconinck, W. and Klein, R. and Malardel, S. and Piotrowski, Z. and Smolarkiewicz, P.K. and Szmelter, J. and Wedi, N. (2019) FVM 1.0: a nonhydrostatic finite-volume dynamical core for the IFS. Geosci. Model Dev., 12 (2). pp. 651-676. ISSN 1991-959X, ESSN: 1991-9603 Delle Site, L. and Krekeler, C. and Whittaker, J. and Agarwal, A. and Klein, R. and Höflling, F. (2019) Molecular dynamics of open systems: construction of a mean-field particle reservoir. Adv. Th. Simul, 2 (5). von Larcher, T. and Klein, R. (2019) On identification of self-similar characteristics using the Tensor Train decomposition method with application to channel turbulence flow. Theoretical and Computational Fluid Dynamics, 33 . pp. 1-19. ISSN 0935-4964 (Print) 1432-2250 (Online) Hoffmann, M. and Fröhner, Chr. and Noé, F. (2019) ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics. PLoS Computational Biology, 15 (2). e1006830. ISSN 1553-7358 Shao, Borong and Bjaanæs, Maria and Helland, Åslaug and Schütte, Ch. and Conrad, T. O. F. (2019) EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma. PLoS ONE, 14 (1). ISSN 1932-6203 Fackeldey, K. and Koltai, P. and Névir, P. and Rust, H.W. and Schild, A and Weber, M. (2019) From Metastable to Coherent Sets – time-discretization schemes. Chaos: An Interdisciplinary Journal of Nonlinear Science, 29 (1). 012101. ISSN 1054-1500 (print); 1089-7682 (online) Corbi, F. and Sandri, L. and Bedford, J. and Funiciello, F. and Brizzi, S. and Rosenau, M. and Lallemand, S. (2019) Machine Learning Can Predict the Timing and Size of Analog Earthquakes. Geophysical Research Letters, 46 (3). pp. 1303-1311. ISSN 0094-8276; ESSN: 1944-8007 Witek, J. and Wang, S. and Schroeder, B. and Lingwood, R. and Dounas, A. and Roth, H.-J. and Fouché, M. and Blatter, M. and Lemke, O. and Keller, B. and Riniker, S. (2019) Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides. J. Chem. Inf. Model., 59 (1). pp. 294-308. ISSN 1549-9596, ESSN: 1549-960X Hoffmann, M. and Fröhner, Chr. and Noé, F. (2019) Reactive SINDy: Discovering governing reactions from concentration data. J. Chem. Phys., 150 (2). 025101. ISSN 0021-9606, ESSN: 1089-7690 Rudolf, M. and Rosenau, M. and Ziegenhagen, Th. and Ludwikowski, V. and Schucht, Torsten and Nagel, H. and Oncken, O. (2019) Smart Speed Imaging in Digital Image Correlation: Application to Seismotectonic Scale Modeling. Frontiers in Earth Science, 6 . p. 248. Stange, H. and Brunken, S. and Greiner, D. and Heinemann, M. D. and Barragan Yani, D. A. and Wägele, L. A. and Li, Ch. and Simsek Sanli, E. and Kahnt, M. and Schmidt, S. S. and Bäcker, J.-P. and Kaufmann, Ch. A. and Klaus, M. and Scheer, R. and Genzel, Ch. and Mainz, R. (2019) Stacking fault reduction during annealing in Cu-poor CuInSe2 thin film solar cell absorbers analyzed by in situ XRD and grain growth modeling. Journal of Applied Physics, 125 (3). 035303. ISSN 0021-8979 Gräser, Carsten and Sander, Oliver (2019) Truncated Nonsmooth Newton Multigrid Methods for Block-Separable Minimization Problems. IMA Journal of Numerical Analysis, 39 (1). pp. 454-481. ISSN 0272-4979 Dondl, Patrick and Frenzel, Thomas and Mielke, Alexander (2019) A gradient system with a wiggly energy and relaxed EDP-convergence. ESAIM Control Optimisation and Calculus of Variations, 25 (68). pp. 1-45. Andreis, L. and König, W. and Patterson, R. I. A (2019) A large-deviations approach to gelation. SFB 1114 Preprint in arXiv:1901.01876 . pp. 1-22. (Unpublished) Ciccotti, G. and Delle Site, L. (2019) The physics of open systems for the simulation of complex molecular environments in soft matter. Soft Matter, 15 (10). pp. 2114-2124. ISSN 1744-683X, ESSN: 1744-6848 Zhou, J. and Matera, S. and Pfaff, S. and Blomberg, S. and Lundgren, E. and Zetterberg, J. (2019) Combining Planar Laser-Induced Fluorescence with Stagnation Point Flows for Small Single-Crystal Model Catalysts: CO Oxidation on a Pd. Catalysts (9). Hittmeir, S. and Klein, R. and Li, J. and Titi, E. (2019) Global well-posedness for the primitive equations coupled to nonlinear moisture dynamics with phase changes. . . (Submitted) Peschka, D. and Thomas, M. and Ahnert, T. and Münch, A. and Wagner, B. (2019) Gradient structures for flows of concentrated suspensions. Topics in Applied Analysis and Optimisation . pp. 295-318. Pütz, C. and Schlutow, M. and Klein, R. (2019) Initiation of ray tracing models: Evolution of small-amplitude gravity wave packets in non-uniform background. Theoretical and Computational Fluid Dynamics, 33 (5). pp. 509-535. ISSN Elektronisch: 1432-2250; Print: 0935-4964 Daldrop, Jan O. and Netz, Roland R. (2019) Mass-Dependent Solvent Friction of a Hydrophobic Molecule. J. Phys. Chem. B (123). pp. 8123-8130. Chada, Neil and Schillings, Claudia and Weissmann, Simon (2019) On the incorporation of box-constraints for ensemble Kalman inversion. Foundations of Data Science, 1 (4). pp. 433-456. Oesting, Marco and Schlather, Martin and Schillings, Claudia (2019) Sampling sup‐normalized spectral functions for Brown–Resnick processes. Stat, 8 (1). Vercauteren, N. and Boyko, V. and Faranda, D. and Stiperski, I. (2019) Scale interactions and anisotropy in stable boundary layers. Quarterly Journal of the Royal Meteorological Society . ISSN 1477-870X Lux, A. and Schäfer, M. and Bergmann, M. and Jahn, T. and Marg, O. and Nagy, E. and Ransiek, A. and Theiler, L. (2019) Societal effects of transdisciplinary sustainability research – How can they be strengthened during the research process? Environmental Science & Policy, 101 . pp. 183-191. Schlutow, M. and Wahlén, E. and Birken, P. (2019) Spectral stability of nonlinear gravity waves in the atmosphere. Mathematics of Climate and Weather Forecasting, 5 (1). pp. 12-33. ISSN 2353-6438 Vercauteren, N. and Boyko, V. and Kaiser, A. and Belusic, D. (2019) Statistical investigations of flow structures in different regimes of the stable boundary layer. Boundary Layer Meteorology, 172 . pp. 1-22. ISSN Print: 0006-8314; Online: 1573-1472 Youett, J. and Sander, O. and Kornhuber, R. (2019) A globally convergent filter-trust-region method for large deformation contact problems. SIAM J. Sci. Comput., 41 (1). B114-B138. ISSN 1064-8275 Kühnlein, C. and Deconinck, W. and Klein, R. and Malardel, S. and Piotrowski, Z. and Smolarkiewicz, P. and Szmelter, J. and Wedi, N. (2019) A nonhydrostatic finite-volume dynamical core for the IFS. Geoscientific Model Development, 12 (2). pp. 651-676. Guth, Philipp A. and Kaarnioja, Vesa and Kuo, Frances Y. and Schillings, Claudia and Sloan, Ian H. (2019) A quasi-Monte Carlo method for an optimal control problem under uncertainty. ArXiv . Klus, Stefan and Bittracher, Andreas and Schuster, Ingmar and Schütte, Christof (2018) A kernel-based approach to molecular conformation analysis. Journal of Chemical Physics, 149 (244109). Marchenko, A. and Gagliardini, P. and Horenko, I. (2018) Toward a computationally-tractable maximum entropy principle for non-stationary financial time series. SIAM Journal of Financial Mathematics, 9 (4). pp. 1249-1285. ISSN 1945-497X Schulz, R. and von Hansen, Y. and Daldrop, J.O. and Kappler, J. and Noé, F. and Netz, R.R. (2018) Collective hydrogen-bond rearrangement dynamics in liquid water. J. Chem. Phys., 149 (24). -244504. ISSN 0021-9606, ESSN: 1089-7690 Kies, Tobias (2018) Gradient Methods for Membrane-Mediated Particle Interactions. PhD Thesis . pp. 1-147. Mireles, Victor and Conrad, T. O. F. (2018) Reusable building blocks in biological systems. Journal of the Royal Society Interface, 15 (149). ISSN 1742-5662 Vater, S. and Klein, R. (2018) A Semi-Implicit Multiscale Scheme for Shallow Water Flows at Low Froude Number. Communications in Applied Mathematics & Computational Science, 13 (2). pp. 303-336. ISSN 1559-3940 Gokhale, N. and Nikiforakis, N. and Klein, R. (2018) A dimensionally split Cartesian cut cell method for the compressible Navier-Stokes equations. Journal of Computational Physics, 375 . pp. 1205-1219. Mirahmadi, M. and Schmidt, B. and Karra, M. and Friedrich, B. (2018) Dynamics of polar polarizable rotors acted upon by unipolar electromagnetic pulses: From the sudden to the adiabatic regime. J. Chem. Phys., 149 (17). p. 174109. Djurdjevac, A. and Elliott, C.M. and Kornhuber, R. and Ranner, Th. (2018) Evolving surface finite element methods for random advection-diffusion equations. SIAM/ASA Journal on Uncertainty Quantification, 6 (4). pp. 1656-1684. ISSN 2166-2525 Wehmeyer, C. and Scherer, M. K. and Hempel, T. and Husic, B.E. and Olsson, S. and Noé, F. (2018) Introduction to Markov state modeling with the PyEMMA software — v1.0. LiveCoMS, 1 (1). pp. 1-12. ISSN E-ISSN: 2575-6524 Shadrack Jabes, B. and Delle Site, L. (2018) Nanoscale domains in Ionic Liquids: A statistical mechanics definition for molecular dynamics studies. J. Chem. Phys., 149 (18). p. 184502. ISSN 0021-9606, ESSN: 1089-7690 Scherer, M. K. and Husic, B.E. and Hoffmann, M. and Paul, F. and Wu, H. and Noé, F. (2018) Variational Selection of Features for Molecular Kinetics. SFB 1114 Preprint in arXiv:1811.11714 . pp. 1-12. (Unpublished) Bittracher, Andreas and Banisch, Ralf and Schütte, Christof (2018) Data-driven computation of molecular reaction coordinates. J. Chem. Phys., 149 (154103). Rahn, René and Budach, Stefan and Costanza, Pascal and Ehrhardt, Marcel and Hancox, Jonny and Reinert, Knut (2018) Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading. Bioinformatics, 34 (20). pp. 3437-3445. ISSN 1367-4803 Donati, L. and Heida, M. and Weber, M. and Keller, B. (2018) Estimation of the infinitesimal generator by square-root approximation. Journal of Physics: Condensed Matter, 30 (42). p. 425201. ISSN 0953-8984, ESSN: 1361-648X Swenson, D.W.H. and Prinz, J.-H. and Noé, F. and Chodera, J. D. and Bolhuis, P.G. (2018) OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics. Journal of Chemical Theory and Computation, Article ASAP . ISSN 1549-9618, ESSN: 15-49-9626 Swenson, D.W.H. and Prinz, J.-H. and Noé, F. and Chodera, J. D. and Bolhuis, P.G. (2018) OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes. Journal of Chemical Theory and Computation, Article ASAP . ISSN 1549-9618, ESSN: 15-49-9626 Müller, A. and Névir, P. and Klein, R. (2018) Scale Dependent Analytical Investigation of the Dynamic State Index Concerning the Quasi-Geostrophic Theory. Mathematics of Climate and Weather Forecasting, 4 (1). pp. 1-22. ISSN 2353-6438 (online) Dadi, Temesgen Hailemariam and Siragusa, Enrico and Piro, Vitor C and Andrusch, Andreas and Seiler, Enrico and Renard, Bernhard Y and Reinert, Knut (2018) DREAM-Yara: an exact read mapper for very large databases with short update time. Bioinformatics, 34 (17). i766-i772. ISSN 1367-4803 Ma, X. and Conrad, T. O. F. and Alchikh, M. and Reiche, J. and Schweiger, B. and Rath, B. (2018) Can we distinguish respiratory viral infections based on clinical features? A prospective pediatric cohort compared to systematic literature review. Reviews in Medical Virology, 28 (5). ISSN 1099-1654 Heida, M. (2018) Convergences of the squareroot approximation scheme to the Fokker–Planck operator. Mathematical Models and Methods in Applied Sciences, 28 (13). pp. 2599-2635. ISSN 0218-2025, ESSN: 1793-6314 Renger, M. (2018) Flux large deviations of independent and reacting particle systems, with implications for macroscopic fluctuation theory. J. Stat. Phys., 172 (5). pp. 1261-1326. ISSN 0022-4715 Bennett, W.P. and Nikiforakis, N. and Klein, R. (2018) A Moving Boundary Flux Stabilization Method for Cartesian Cut-Cell Grids using Directional Operator Splitting. Journal of Computational Physics, 368 . pp. 333-358. Fröhner, Chr. and Noé, F. (2018) Reversible interacting-particle reaction dynamics. J. Phys. Chem. B, 122 (49). pp. 11240-11250. Donati, Luca and Keller, Bettina G. (2018) Girsanov reweighting for metadynamics simulations. J. Chem. Phys. 149, 149 . pp. 1-16. Djurdjevac, N. and Helfmann, L. and Zonker, J. and Winkelmann, S. and Schütte, Ch. (2018) Human mobility and innovation spreading in ancient times: a stochastic agent-based simulation approach. EPJ Data Science, 7 (1). p. 24. Kornhuber, R. and Youett, E. (2018) Adaptive Multilevel Monte Carlo Methods for Stochastic Variational Inequalities. SIAM Journal on Numerical Analysis, 56 (4). pp. 1987-2007. ISSN 0036-1429 Krekeler, C. and Agarwal, A. and Junghans, C. and Praprotnik, M. and Delle Site, L. (2018) Adaptive Resolution Molecular Dynamics Technique: Down to the Essential. J. Chem. Phys., 149 . 024104. ISSN 0021-9606, ESSN: 1089-7690 Donati, L. and Keller, B. (2018) Girsanov reweighting for metadynamics simulations. Journal of Chemical Physics, 149 (7). 072335. ISSN 0021-9606 del Razo, M.J. and Qian, H. and Noé, F. (2018) Grand canonical diffusion-influenced reactions: a stochastic theory with applications to multiscale reaction-diffusion simulations. J. Chem. Phys., 149 (4). 044102. ISSN 0021-9606, ESSN: 1089-7690 Gokhale, N. and Nikiforakis, N. and Klein, R. (2018) A dimensionally split Cartesian cut cell method for hyperbolic conservation laws. Journal of Computational Physics, 364 . pp. 186-208. ISSN 0021-9991 Duwal, S. and Dickinson, L. and Khoo, S. and von Kleist, M. (2018) Hybrid stochastic framework predicts efficacy of prophylaxis against HIV: An example with different dolutegravir regimen. PLoS Computational Biology, 14 . e1006155. ISSN 1553-7358 Ciccotti, G. and Ferrario, M. and Schütte, Ch. (2018) Molecular Dynamics vs. Stochastic Processes: Are We Heading Anywhere? Entropy (Special Issue), 20 (5). p. 348. ISSN 1099-4300 Klus, S. and Gelß, P. and Peitz, S. and Schütte, Ch. (2018) Tensor-based dynamic mode decomposition. Nonlinearity, 31 (7). pp. 3359-3380. ISSN 0951-7715 Kork, F. and Spies, C. and Conrad, T. O. F. and Weiss, B. and Roenneberg, T. and Wernecke, K.-D. and Balzer, F. (2018) Associations of postoperative mortality with the time of day, week and year. Anaesthesia, 73 (6). pp. 711-718. ISSN 0959-2962 Koltai, P. and Renger, M. (2018) From Large Deviations to Semidistances of Transport and Mixing: Coherence Analysis for Finite Lagrangian Data. Journal of Nonlinear Science, 28 (5). pp. 1915-1957. ISSN 1432-1467 (online) Renger, M. (2018) Gradient and Generic systems in the space of fluxes, applied to reacting particle systems. SFB 1114 Preprint in arXiv:1806.10461 . pp. 1-29. (Unpublished) Dibak, M. and del Razo, M.J. and De Sancho, D. and Schütte, Ch. and Noé, F. (2018) MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations. Journal of Chemical Physics, 148 (214107). ISSN 0021-9606 Friedrich, B. and Herschbach, D. and Kais, S. and Schmidt, B. (2018) Molecules enhanced by electromagnetic fields. SciTech Europa Quarterly, 27 . pp. 48-49. Kebiri, O. and Neureither, L. and Hartmann, C. (2018) Singularly perturbed forward-backward stochastic differential equations: application to the optimal control of bilinear systems. Computation, 6 (3). p. 41. ISSN 2079-3197 (online) Shadrack Jabes, B. and Klein, R. and Delle Site, L. (2018) Structural Locality and Early Stage of Aggregation of Micelles in Water: An Adaptive Resolution Molecular Dynamics Study. Advanced Theory & Simulations, 1 (6). Schatz, K. and Friedrich, B. and Becker, S. and Schmidt, B. (2018) Symmetric Tops Subject to Combined Electric Fields: Conditional Quasi-Solvability via the Quantum Hamilton-Jacobi Theory. Phys. Rev. A, 97 (5). 053417. Banerjee, T. and Vercauteren, N. and Muste, M. and Yang, D. (2018) Coherent structures in wind shear induced wave-turbulence-vegetation interaction in water bodies. Agricultural and Forest Meteorology, 255 . pp. 57-67. ISSN 0168-1923 Daldrop, J.O. and Kappler, J. and Brünig, F.N. and Netz, R.R. (2018) Butane dihedral angle dynamics in water is dominated by internal friction. PNAS, 20 (115). pp. 5169-5174. ISSN 1091-6490 (online) Zhang, W. and Hartmann, C. and von Kleist, M. (2018) Optimal control of Markov jump processes: Asymptotic analysis, algorithms, and application to modelling of chemical reaction systems. Communications in Mathematical Sciences, 16 (2). pp. 293-331. ISSN 1539-6746 Netz, Roland R. (2018) Fluctuation-dissipation relation and stationary distribution of an exactly solvable many-particle model for active biomatter far from equilibrium. J. Chem. Phys., 148 . ISSN 0021-9606, ESSN: 1089-7690 Lazzaroni, Guiliano and Rossi, Riccarda and Thomas, Marita and Toader, Rodica (2018) Rate-independent damage in thermoviscoelastic materials with inertia. J Dyn Diff Equat, 30 . pp. 1311-1364. Grześkowiak, Łukasz and Martínez-Vallespín, Beatriz and Dadi, Temesgen H and Radloff, Judith and Amasheh, Salah and Heinsen, Femke-Anouska and Franke, Andre and Reinert, Knut and Vahjen, Wilfried and Zentek, Jürgen and Pieper, Robert (2018) Formula Feeding Predisposes Neonatal Piglets to Clostridium difficile Gut Infection. The Journal of Infectious Diseases, 217 (9). pp. 1442-1452. ISSN 0022-1899 Kianfar, Kiavash and Pockrandt, Christopher and Torkamandi, Bahman and Luo, Haochen and Reinert, Knut (2018) Optimum Search Schemes for Approximate String Matching Using Bidirectional FM-Index. bioRxiv, The Preprint Server for Biology . Bittracher, A. and Koltai, P. and Klus, S. and Banisch, R. and Dellnitz, M. and Schütte, Ch. (2018) Transition manifolds of complex metastable systems: Theory and data-driven computation of effective dynamics. Journal of Nonlinear Science, 28 (2). pp. 471-512. ISSN 1432-1467 (online) Busch, Anne and Thomas, Prasad and Zuchantke, Eric and Brendebach, Holger and Neubert, Kerstin and Gruetzke, Josephine and Al Dahouk, Sascha and Peters, Martin and Hotzel, Helmut and Neubauer, Heinrich and Tomaso, Herbert (2018) Revisiting Francisella tularensis subsp. holarctica, Causative Agent of Tularemia in Germany With Bioinformatics: New Insights in Genome Structure, DNA Methylation and Comparative Phylogenetic Analysis. Frontiers in Microbiology, 9 . ISSN 1664-302X Martinek, T. and Duboué-Dijon, E. and Timr, S. and Mason, Ph. E. and Baxová, K. and Fischer, H. E. and Schmidt, B. and Pluharova, E. and Jungwirth, P. (2018) Calcium Ions in Aqueous Solutions: Accurate Force Field Description Aided by Ab Initio Molecular Dynamics and Neutron Scattering. J. Chem. Phys., 148 (22). p. 222813. Smyth, R.P. and Smith, M. R. and Jousset, A-C. and Despons, L. and Laumond, G. and Decoville, T. and Cattenoz, P. and Moog, C. and Jossinet, F. and Mougel, M. and Paillart, J.-C. and von Kleist, M. and Marquet, R. (2018) In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV - 1 genomic RNA production and packaging. Nucleic Acids Research, 46 (9). e57. Heida, Martin and Röger, Matthias (2018) Large deviation principle for a stochastic Allen--Cahn equation. Journal of Theoretical Probability 31(1), 31 (1). pp. 1-18. (Submitted) Wehmeyer, C. and Noé, F. (2018) Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics. The Journal of Chemical Physics, 148 (24). p. 241703. ISSN 0021-9606 Hassan, I. and Donati, L. and Stensitzki, T. and Keller, B. and Heyne, K. and Imhof, P. (2018) The Vibrational Spectrum of the hydrated Alanine-Leucine Peptide in the Amide region from IR experiments and First Principles Calculation. Chem. Phys. Lett. . pp. 1-26. ISSN 0009-2614 Klus, S. and Sahai, T. (2018) A spectral assignment approach for the graph isomorphism problem. Information and Inference: a Journal of the IMA, 7 (4). pp. 689-706. Kappler, J. and Noé, F. and Netz, R.R. (2018) Cyclization dynamics of finite-length collapsed self-avoiding polymers. SFB 1114 Preprint 02/2018 . (Unpublished) Marzban, Forough and Conrad, T. O. F. and Marzban, Pouria and Sodoudi, Sahar (2018) Estimation of the Near-Surface Air Temperature during the Day and Nighttime from MODIS in Berlin, Germany. International Journal of Advanced Remote Sensing and GIS, 7 (1). ISSN 2320-0243 Weber, M. (2018) Implications of PCCA+ in Molecular Simulation. Computation, 6 (1). ISSN 2079-3197 (online) Hartmann, C. and Schütte, Ch. and Weber, M. and Zhang, W. (2018) Importance sampling in path space for diffusion processes with slow-fast variables. Probab. Theory Rel. Fields, 170 (1-2). pp. 177-228. ISSN 0178-8051 (print) 1432-2064 (online) Schulz, R. and Hansen, Y. von and Daldrop, J.O. and Kappler, J. and Noé, F. and Netz, R.R. (2018) Markov state modeling reveals competing collective hydrogen bond rearrangements in liquid water. SFB 1114 Preprint 02/2018 . (Unpublished) Koltai, P. and Wu, H. and Noé, F. and Schütte, Ch. (2018) Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics. Computation, 6(1) (22). ISSN 2079-3197 (online) von Kleist, M. and Schütte, Ch. and Zhang, W. (2018) Statistical Analysis of the First Passage Path Ensemble of Jump Processes. Journal of Statistical Physics, 170 (4). pp. 809-843. Li, Q. and Bou-Zeid, E. and Vercauteren, N. and Parlange, M. B. (2018) Signatures of air-waves interactions over a large lake. Boundary-Layer Meteorology . pp. 1-24. ISSN 0006-8314 Heida, Martin and Schweizer, Ben (2018) Stochastic homogenization of plasticity equations. ESAIM: Control, Optimisation and Calculus of Variations, 24 (1). 153 -176. Schmidt, B. and Hartmann, C. (2018) WavePacket: A Matlab package for numerical quantum dynamics. II: Open quantum systems, optimal control, and model reduction. Comp. Phys. Comm., 228 . pp. 229-244. Marschall, T. and Reinert, K. and others, (59 authors in total) (2018) Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics, 19 (1). pp. 118-135. ISSN 1467-5463 (Print), 1477-4054 (Online) Stensitzki, T. and Yang, Y. and Kozich, V. and Ahmed, A.A. and Kössl, F. and Kühn, O. and Heyne, K. (2018) Acceleration of a ground-state reaction by selective femtosecond-infrared-laser-pulse excitation. Nature Chemistry, 10 . pp. 126-131. Mielke, A. and Rossi, R. and Savaré, G. (2018) Global existence results for viscoplasticity at finite strain. Archive for Rational Mechanics and Analysis, 227 (1). pp. 423-475. ISSN Print: 0003-9527; Online: 1432-0673 Kappler, J. and Daldrop, J.O. and Brünig, F.N. and Boehle, M.D. and Netz, R.R. (2018) Memory-induced acceleration and slowdown of barrier crossing. J. Chem. Phys., 148 (1). 014903. Sadeghi, M. and Weikl, T. and Noé, F. (2018) Particle-based membrane model for mesoscopic simulation of cellular dynamics. J. Chem. Phys., 148 (4). 044901. Shadrack Jabes, B. and Krekeler, C. and Klein, R. and Delle Site, L. (2018) Probing Spatial Locality in Ionic Liquids with the Grand Canonical Adaptive Resolution Molecular Dynamics Technique. The Journal of Chemical Physics, 148 (19). ISSN online: 1089-7690 Gerber, S. and Olsson, S. and Noé, F. and Horenko, I. (2018) A scalable approach to the computation of invariant measures for high-dimensional Markovian systems. Scientific Reports, 8 (1796). ISSN 2045-2322 Döpking, S. and Plaisance, C.P. and Strobusch, D. and Reuter, K. and Scheurer, C. and Matera, S. (2018) Addressing Global Uncertainty and Sensitivity in First-Principles Based Microkinetic Models by an Adaptive Sparse Grid Approach. AIP The Journal of Chemical Physics, 148 (3). Hittmeir, S. and Klein, R. (2018) Asymptotics for moist deep convection I: Refined scalings and self-sustaining updrafts. Theoretical and Computational Fluid Dynamics, 32 (2). pp. 137-164. ISSN 0935-4964 (Print) 1432-2250 (Online) Hajian, Soheil and Hintermüller, Michael and Schillings, Claudia and Strogtes, Michael (2018) A Bayesian approach to parameter identification in gas networks. Preprint : Weierstraß-Institut für Angewandte Analysis und Stochastik, 2537 . Langfeldt, B. and Mischau, A. (2018) Change and Persistence of Gender Disparities in Academic Careers of Mathematicians and Physicists in Germany. International Journal of Gender, Science and Technology, 10 (1). ISSN 2040-0748 Mielke, Alexander and Mittnenzweig, Markus (2018) Convergence to Equilibrium in Energy-Reaction–Diffusion Systems Using Vector-Valued Functional Inequalities. Journal of Nonlinear Science, 28 . pp. 765-806. ISSN 1432-1467 (online) Mielke, A. and Mittnenzweig, M. (2018) Convergence to Equilibrium in Energy-Reaction–Diffusion Systems Using Vector-Valued Functional Inequalities. Journal of Nonlinear Science . pp. 1-42. ISSN 1432-1467 (online) Klus, S. and Nüske, F. and Koltai, P. and Wu, H. and Kevrekidis, I. and Schütte, Ch. and Noé, F. (2018) Data-driven model reduction and transfer operator approximation. Journal of Nonlinear Science, 28 (1). pp. 1-26. Banisch, R. and Trstanova, Z. and Bittracher, A. and Klus, S. and Koltai, P. (2018) Diffusion maps tailored to arbitrary non-degenerate Itô processes. Applied and Computational Harmonic Analysis . ISSN 1063-5203 (In Press) Kienle, D. and Gräser, C. and Sander, O. and Keip, M.-A. (2018) Efficient and reliable phase‐field simulation of brittle fracture using a nonsmooth multigrid solution scheme. PAMM. Special Issue: 89th Annual Meeting of the International Association of Applied Mathematics and Mechanics (GAMM), 18 (1). e201800126. ISSN 1617-7061 Sutton, J.E. and Lorenzi, J. M. and Krogel, J.T. and Xiong, Q. and Pannala, S. and Matera, S. and Savara, A. (2018) Electrons to Reactors Multiscale Modeling: Catalytic CO Oxidation over RuO2. ACS Catalysis, 8 (6). pp. 5002-5016. Nguyen van yen, N. and Waidmann, M. and Klein, R. and Farge, M. (2018) Energy dissipation caused by boundary layer instability at vanishing viscosity. Journal of Fluid Mechanics, 849 . pp. 676-717. Engwer, C. and Gräser, C. and Müthing, S. and Sander, O. (2018) Function space bases in the dune-functions module. arXiv:1806.09545 . pp. 1-53. (Submitted) Paul, F. and Noé, F. and Weikl, T. (2018) Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations. J. Phys. Chem. B . von Larcher, T. and Viazzo, S. and Harlander, U. and Vincze, M. and Randriamampianina, A. (2018) Instabilities and small-scale waves within the Stewartson layers of a thermally driven rotating annulus. Journal of Fluid Mechanics, 841 . pp. 380-407. ISSN 0022-1120 Wilhelm, J. and Akylas, T.R. and Bölöni, G. and Wei, J. and Ribstein, B. and Klein, R. and Achatz, U. (2018) The Interaction between Meso- and Sub-mesoscale Gravity Waves. Journal of the Atmospheric Sciences, 75 (7). pp. 2257-2280. ISSN 0022-4928 Wilhem, J. and Akylas, T.R. and Bölöni, G. and Wei, J. and Ribstein, B. and Klein, R. and Achatz, U. (2018) Interactions between Meso- and Sub-Mesoscale Gravity Waves and their Efficient Representation in Mesoscale-Resolving Models. J. Atmos. Sci. . (Unpublished) Hiptmair, R. and Scarabosio, L. and Schillings, Claudia and Schwab, Ch. (2018) Large deformation shape uncertainty quantification in acoustic scattering. Advances in Computational Mathematics, 44 . pp. 1475-1518. Becker, N. and Névir, P. and Klein, R. (2018) Large-scale secondary circulations in a limited area model - the impact of lateral boundaries and resolution. Tellus A: Dynamic Meteorology and Oceanography, 70 (1). Djurdjevac, N. and Fuerstenau, D. and Grabundzija, A. and Helfmann, L. and Park, M. and Schier, W. and Schütt, B. and Schütte, Ch. and Weber, M. and Wulkow, N. and Zonker, J. (2018) Mathematical Modeling of the Spreading of Innovations in the Ancient World. eTopoi. Journal for Ancient Studies, 7 . ISSN 2192-2608 Hoffmann, Waldemar and Folmert, Kristin and Moschner, Johann and Xing Huang, Xing Huang and von Berlepsch, Hans and Koksch, Beate and Bowers, Michael T. and von Helden, Gert and Pagel, Kevin (2018) NFGAIL Amyloid Oligomers: The Onset of Beta-Sheet Formation and the Mechanism for Fibril Formation. J. Am. Chem. Soc. 2018, 140, 244−249, 140 . pp. 244-249. Pospisil, L. and Gagliardini, P. and Sawyer, W. and Horenko, I. (2018) On a scalable nonparametric denoising of time series signals. Communications in Applied Mathematics and Computational Science, 13 (1). pp. 107-138. Liero, M. and Mielke, A. and Savaré, G. (2018) Optimal Entropy-Transport problems and a new Hellinger-Kantorovich distance between positive measures. Inventiones mathematicae, 211 . pp. 969-1117. ISSN 1432-1297 (online) Mardt, A. and Pasquali, L. and Wu, H. and Noé, F. (2018) VAMPnets: Deep learning of molecular kinetics. Nat. Comm., 9 . p. 5. Kornhuber, R. and Peterseim, D. and Yserentant, H. (2018) An analysis of a class of variational multiscale methods based on subspace decomposition. Mathematics of Computation, 87 (314). pp. 2765-2774. ISSN 1088-6842 (online) Koltai, P. and Schütte, Ch. (2018) A multiscale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics. Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 16 (4). pp. 1455-1485. ISSN 1540-3459 Blömker, Dirk and Schillings, Claudia and Wacker, Philipp (2018) A strongly convergent numerical scheme from ensemble Kalman inversion. SIAM Journal on Numerical Analysis, 56 (4). Daldrop, J.O. and Kowalik, B.G. and Netz, R.R. (2017) External Potential Modifies Friction of Molecular Solutes in Water. Phys. Rev. X, 7 (4). 041065. Schuster, I. and Constantine, P.G. and Sullivan, T.J. (2017) Exact active subspace Metropolis-Hastings, with applications to the Lorenz-96 system. SFB 1114 Preprint in arXiv:1712.02749 . pp. 1-10. (Unpublished) Netz, R.R. (2017) Fluctuation-dissipation relation and stationary distribution for an exactly solvable many-particle model far from equilibrium. SFB 1114 Preprint 12/2017 . (Unpublished) Ritter, M. and Rosenau, M. and Oncken, O. (2017) Growing Faults in the Lab: Insights into the Scale Dependence of the Fault Zone Evolution Process. Tectonics, 36 . pp. 1-32. Rudolf, M. and Rosenau, M. and Oncken, O. (2017) Interseismic deformation transients and precursory phenomena: Insights from stick-slip experiments with a granular fault zone. SFB 1114 Preprint in EarthArXiv:10.17605/OSF.IO/6MWRX . pp. 1-26. Peters, J.H. and Gräser, C. and Klein, R. (2017) Membrane Deformation by N-BAR Proteins: Extraction of membrane geometry and protein diffusion characteristics from MD simulations. SFB 1114 Preprint in arXiv:1712.02666 . pp. 1-12. (Unpublished) Heida, M. and Neukamm, S. and Varga, M. (2017) Stochastic unfolding and homogenization. SFB 1114 Preprint at WIAS 12/2017 . pp. 1-45. (Unpublished) Fischer, M. and Ulbrich, U. and Rust, H.W. (2017) A spatial and seasonal climatology of extreme precipitation return-levels: A case study. Spatial Statistics . pp. 1-25. (In Press) Pfeuffer, Julianus and Sachsenberg, Timo and Alka, Oliver and Walzer, Mathias and Fillbrunn, Alexander and Nilse, Lars and Schilling, Oliver and Reinert, Knut and Kohlbacher, Oliver (2017) OpenMS – A platform for reproducible analysis of mass spectrometry data. Journal of Biotechnology, 261 . pp. 142-148. ISSN 01681656 Reinert, Knut and Dadi, Temesgen Hailemariam and Ehrhardt, Marcel and Hauswedell, Hannes and Mehringer, Svenja and Rahn, René and Kim, Jongkyu and Pockrandt, Christopher and Winkler, Jörg and Siragusa, Enrico and Urgese, Gianvito and Weese, David (2017) The SeqAn C++ template library for efficient sequence analysis: A resource for programmers. Journal of Biotechnology, 261 . pp. 157-168. ISSN 01681656 Büeler, Dominik and Pfahl, Stephan (2017) Potential Vorticity Diagnostics to Quantify Effects of Latent Heating in Extratropical Cyclones. Part I: Methodology. Journal of the Atmospheric Sciences, 74 (11). Polthier, L. (2017) Algebraic Multilevel Methods for Markov Chains. SFB 1114 Preprint in arXiv:1711.04332 . pp. 1-19. (Unpublished) Taghvaei, A. and de Wiljes, J. and Mehta, P.G. and Reich, S. (2017) Kalman Filter and Its Modern Extensions for the Continuous-Time Nonlinear Filtering Problem. J. Dyn. Sys., Meas., Control, 140 (3). 030904. Kappler, J. and Shrivastava, S. and Schneider, M.F. and Netz, R.R. (2017) Nonlinear fractional waves at elastic interfaces. Phys. Rev. Fluids, 2 (11). p. 114804. Ritter, M. and Santimano, T.N. and Rosenau, M. and Leever, K. and Oncken, O. (2017) Sandbox rheometry: Coevolution of stress and strain in riedel- and critical wedge-experiments. Tectonophysics, 722 . pp. 400-409. Quer, J. and Lie, H. (2017) Some connections between importance sampling and enhanced sampling methods in molecular dynamics. Journal of Chemical Physics . pp. 1-19. ISSN 0021-9606 Hartmann, C. and Richter, L. and Schütte, Ch. and Zhang, W. (2017) Variational characterization of free energy: theory and algorithms. Entropy (Special Issue), 19 (11). pp. 1-27. ISSN 1099-4300 Sbailò, L. and Noé, F. (2017) An efficient multi-scale Green's Functions Reaction Dynamics scheme. J. Chem. Phys., 147 . p. 184106. ISSN 0021-9606, ESSN: 1089-7690 Paul, F. and Wehmeyer, C. and Abualrous, E. T. and Wu, H. and Crabtree, M. D. and Schöneberg, J. and Clarke, J. and Freund, C. and Weikl, T. and Noé, F. (2017) Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nat. Comm., 8 (1095). Kappler, J. and Netz, R.R. (2017) Pulse propagation at interfaces and their possible relevance for biology. Journal Club for Condensed Matter Physics . Bittracher, A. and Koltai, P. and Klus, S. and Banisch, R. and Dellnitz, M. and Schütte, Ch. (2017) Transition manifolds of complex metastable systems: Theory and data-driven computation of effective dynamics. Journal of Nonlinear Science . pp. 1-42. ISSN 1432-1467 (online) Roehr, Johannes T. and Dieterich, Christoph and Reinert, Knut (2017) Flexbar 3.0 – SIMD and multicore parallelization. Bioinformatics, 33 (18). pp. 2941-2942. ISSN 1367-4803 Koltai, P. and Schütte, Ch. (2017) A multi scale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics. ZIB-Report . ISSN 1438-0064 Schlutow, M. and Klein, R. and Achatz, U. (2017) Finite-amplitude gravity waves in the atmosphere: travelling wave solutions. Journal of Fluid Mechanics, 826 . pp. 1034-1065. Hittmeir, S. and Klein, R. and Li, J. and Titi, E. (2017) Global well-posedness for passively transported nonlinear moisture dynamics with phase changes. Nonlinearity, 30 (10). pp. 3676-3718. ISSN 0951-7715 Winkelmann, S. and Schütte, Ch. (2017) Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems. Journal of Chemical Physics, 147 (11). pp. 1-18. Schlaich, A. and Kappler, J. and Netz, R.R. (2017) Hydration Friction in Nanoconfinement: From Bulk via Interfacial to Dry Friction. Nano Lett., 17 (10). pp. 5969-5976. Acevedo, W. and de Wiljes, J. and Reich, S. (2017) Second-order accurate ensemble transform particle filters. SIAM J. Sci. Comput., 39 (5). A1834-A1850. ISSN 1095-7197 (online) Manz, C. and Kobitski, A. and Samanta, A. and Keller, B.G. and Jäschke, A. and Nienhaus, G.U. (2017) Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch. Nat. Chem. Biol., 13 . pp. 1172-1178. Corbi, F. and Funiciello, F. and Brizzi, S. and Lallemand, S. and Rosenau, M. (2017) Control of asperities size and spacing on seismic behavior of subduction megathrusts. Geophysical Research Letters, 44 (16). pp. 8227-8235. Dörffel, T. and Papke, A. and Klein, R. and Smolarkiewicz, P. (2017) Intensification of tilted atmospheric vortices by asymmetric diabatic heating. SFB 1114 Preprint in arXiv:1708.07674 . pp. 1-22. (Unpublished) Mielke, A. and Patterson, R. I. A and Peletier, M. A. and Renger, M. (2017) Non-equilibrium thermodynamical principles for chemical reactions with mass-action kinetics. SIAM Journal on Applied Mathematics, 77 (4). pp. 1562-1585. ISSN 1095-712X (online) Delle Site, L. and Ciccotti, G. and Hartmann, C. (2017) Partitioning a macroscopic system into independent subsystems. Journal of Statistical Mechanics: Theory and Experiment, 2017 . pp. 1-13. Jayrannejad, Fahrnaz and Conrad, T. O. F. (2017) Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining. Springer Lecture Notes in Artificial Intelligence . Nissen, K.M. and Ulbrich, U. (2017) Increasing frequencies and changing characteristics of heavy precipitation events threatening infrastructure in Europe under climate change. Nat. Hazards Earth Syst. Sci., 17 . pp. 1177-1190. Becker, S. and Mirahmadi, M. and Schmidt, B. and Schatz, K. and Friedrich, B. (2017) Conditional Quasi-Exact Solvability of the Quantum Planar Pendulum and its Anti-Isospectral Hyperbolic Counterpart. Eur. J. Phys. D, 71 (6). p. 149. Junghans, C. and Agarwal, A. and Delle Site, L. (2017) Computational Efficiency and Amdahl's law for the Adaptive Resolution Simulation Technique. Computer Physics Communications, 215 . pp. 20-25. ISSN 0010-4655 Donati, L. and Hartmann, C. and Keller, B.G. (2017) Girsanov reweighting for path ensembles and Markov state models. Journal of Chemical Physics, 146 (24). p. 244112. ISSN 0021-9606 Seshaditya, A. and Ghiringhelli, L. M. and Delle Site, L. (2017) Levy-Lieb-based Monte Carlo study of the dimensionality behaviour of the electronic kinetic functional. Computationa, 5 (2). pp. 1-10. ISSN 2079-3197 Delle Site, L. and Praprotnik, M. (2017) Molecular systems with open boundaries: Theory and Simulation. Physics Reports, 693 . pp. 1-56. ISSN 0370-1573 Mazza, E. and Ulbrich, U. and Klein, R. (2017) The Tropical Transition of the October 1996 Medicane in the Western Mediterranean Sea: A Warm Seclusion Event. Monthly Weather Review, 145 . pp. 2575-2595. ISSN Online: 1520-0493 Print: 0027-0644 Gerber, S. and Horenko, I. (2017) Toward a direct and scalable identification of reduced models for categorical processes. Proceedings of the National Academy of Sciences, 114 (19). pp. 4863-4868. Rohr, U. and Herrmann, P. and Ilm, K. and Zhang, H. and Lohmann, S. and Reiser, A. and Muranyi, A. and Smith, J. C. and Burock, S. and Osterland, M. and Leith, K. and Singh, S. and Brunhoeber, P. and Bowermaster, R. and Tie, J. and Christie, M. and Wong, H. and Waring, P. and Shanmugam, K. and Gibbs, P. and Stein, U. (2017) Prognostic value of MACC1 and proficient mismatch repair status for recurrence risk prediction in stage II colon cancer patients: the BIOGRID studies. Annals of Oncology, 28 (8). pp. 1869-1875. Gelß, P. and Klus, S. and Matera, S. and Schütte, Ch. (2017) Nearest-neighbor interaction systems in the tensor-train format. Journal of Computational Physics, 341 . pp. 140-162. ISSN 0021-9991 Schmidt, B. and Lorenz, U. (2017) WavePacket: A Matlab package for numerical quantum dynamics. I: Closed quantum systems and discrete variable representations. Comp. Phys. Comm., 213 . pp. 223-234. Schulz, R. and Yamamoto, K. and Klossek, A. and Flesch, R. and Hönzke, S. and Rancan, F. and Vogt, A. and Blume-Peytavi, U. and Hedtrich, S. and Schäfer-Korting, M. and Rühl, E. and Netz, R.R. (2017) Data-based modeling of drug penetration relates human skin barrier function to the interplay of diffusivity and free-energy profiles. PNAS, 114 (14). pp. 3631-3636. ISSN 1091-6490 (online) Shao, Borong and Carlo, Cannistraci and Conrad, T. O. F. (2017) Epithelial Mesenchymal Transition Network-based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data. Genomics and Computational Biology, 3 (3). ISSN 2365-7154 Agarwal, A. and Clementi, C. and Delle Site, L. (2017) Path Integral-GC-AdResS simulation of a large hydrophobic solute in water: A tool to investigate the interplay between local microscopic structures and quantum delocalization of atoms in space. Physical Chemistry Chemical Physics, 19 . pp. 13030-13037. ISSN 1463-9084 Ritschel, C. and Rust, H.W. and Ulbrich, U. (2017) Precipitation extremes on multiple time scales -- Bartlett-Lewis Rectangular Pulse Model and Intensity-Duration-Frequency curves. Hydrol. Earth Syst. Sci. . pp. 1-20. (Submitted) Heida, M. (2017) Stochastic homogenization of rate-independent systems and applications. Continuum Mech. Thermodyn., 29 (3). pp. 853-894. ISSN 1432-0959 (online) 0935-1175 (print) Zhukova, Y. and Hiepen, C. and Knaus, P. and Osterland, M. and Prohaska, S. and Dunlop, J. W. C. and Fratzl, P. and Skorb, E. V. (2017) The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration. Advanced Healthcare Materials . Dadi, Temesgen Hailemariam and Renard, Bernhard Y. and Wieler, Lothar H. and Semmler, Torsten and Reinert, Knut (2017) SLIMM: species level identification of microorganisms from metagenomes. PeerJ, 5 . e3138. ISSN 2167-8359 Conrad, T. O. F. and Genzel, Martin and Cvetkovic, Nada and Wulkow, Niklas and Vybiral, Jan and Kutyniok, Gitta and Schütte, Ch. (2017) Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data. BMC Bioinformatics, 18 (160). ISSN 1471-2105 Seeber, L. and Conrad, T. O. F. and Hoppe, Ch. and Obermeier, P. and Chen, X. and Karsch, K. and Muehlhans, S. and Tief, F. and Boettcher, S. and Diedrich, S. and Schweiger, B. and Rath , B. (2017) Educating parents about the vaccination status of their children: A user-centered mobile application. Preventive Medicine Reports, 5 . pp. 241-250. O'Kane, T.J. and Monselesan, D.P. and Risbey, J.S. and Horenko, I. and Franzke, Ch.L.E. (2017) On memory, dimension, and atmospheric teleconnection patterns. Math. Clim. Weather Forecast, 3 (1). pp. 1-27. Weber, M. and Fackeldey, K. and Schütte, Ch. (2017) Set-free Markov state model building. Journal of Chemical Physics, 146 (12). p. 124133. Banisch, Ralf and Koltai, Péter (2017) Understanding the geometry of transport: diffusion maps for Lagrangian trajectory data unravel coherent sets. Chaos: An Interdisciplinary Journal of Nonlinear Science, 23 (23). ISSN 1054-1500 (print); 1089-7682 (online) (Submitted) Quer, J. and Donati, L. and Keller, B.G. and Weber, M. (2017) An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates. SIAM J. Sci. Comput. . pp. 1-19. ISSN 1064-8275 (print) (In Press) Vatansever, B. and Muñoz, A. and Klein, C. L. and Reinert, K. (2017) Development and optimisation of a generic micro LC-ESI-MS method for the qualitative and quantitative determination of 30-mer toxic gliadin peptides in wheat flour for food analysis. Analytical and Bioanalytical Chemistry, 409 (4). pp. 989-997. ISSN 1618-2642 Rath , B. and Conrad, T. O. F. and Myles, P. and Alchikh, M. and Ma, X. and Hoppe, Ch. and Tief, F. and Obermeier, P. and Reiche, J. and Kisler, B. and Schweiger, B. (2017) Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials. Expert Review of Anti-infective Therapy (IERZ), 15 (6). pp. 545-568. Liero, M. and Mielke, A. and Peletier, M. A. and Renger, M. (2017) On microscopic origins of generalized gradient structures. Discrete and Continuous Dynamical Systems - Series S, 10 (1). Huttary, R. and Goubergrits, L. and Schütte, Ch. and Bernhard, S. (2017) Simulation, Identification and Statistical Variation in Cardiovascular Analysis (SISCA) - a Software Framework for Multi-compartment Lumped Modeling. Computers in Biology and Medicine . ISSN 0010-4825 (In Press) Achatz, U. and Ribstein, B. and Senf, F. and Klein, R. (2017) The interaction between synoptic‐scale balanced flow and a finite‐amplitude mesoscale wave field throughout all atmospheric layers: weak and moderately strong stratification. QJRMS, 143 (702). pp. 342-361. Hoffmann, M. J. and Engelmann, F. and Matera, S. (2017) A practical approach to the sensitivity analysis for kinetic Monte Carlo simulation of heterogeneous catalysis. The Journal of Chemical Physics, 146 (044118). ISSN 00219606 Dellnitz, M. and Klus, S. and Ziessler, A. (2017) A Set-Oriented Numerical Approach for Dynamical Systems with Parameter Uncertainty. SIAM Journal on Applied Dynamical Systems, 16 (1). pp. 120-138. ISSN 1536-0040 Audain, Enrique and Uszkoreit, Julian and Sachsenberg, Timo and Pfeuffer, Julianus and Liang, Xiao and Hermjakob, Henning and Sanchez, Aniel and Eisenacher, Martin and Reinert, Knut and Tabb, David L. and Kohlbacher, Oliver and Perez-Riverol, Yasset (2017) In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics. Journal of Proteomics, 150 . pp. 170-182. ISSN 18743919 Krekeler, C. and Delle Site, L. (2017) Towards open boundary molecular dynamics simulation of ionic liquids. Physical Chemistry Chemical Physics, 6 (19). pp. 4701-4709. ISSN 1463-9076 Djurdjevac, A. (2017) Advection-diffusion equations with random coefficients on evolving hypersurfaces. Interfaces and Free Boundaries, 19 (4). pp. 525-552. ISSN 1463-9963 Heida, M. and Mielke, A. (2017) Averaging of time-periodic dissipation potentials in rate-independent processes. Discrete and Continuous Dynamical Systems - Series S, 10 (6). pp. 1303-1327. Lorenz, P. and Wolf, F. and Braun, J. and Djurdjevac, N. and Hövel, P. (2017) Capturing the Dynamics of Hashtag-Communities. International Workshop on Complex Networks and their Applications . pp. 401-413. Noé, F. and Clementi, C. (2017) Collective variables for the study of long-time kinetics from molecular trajectories: theory and methods. Curr. Opin. Struct. Biol., 43 . pp. 141-147. Olsson, Simon and Wu, H. and Paul, F. and Clementi, C. and Noé, F. (2017) Combining experimental and simulation data of molecular processes via augmented Markov models. Proc. Natl. Acad. Sci. USA, 114 . pp. 8265-8270. Plattner, N. and Doerr, S. and De Fabritiis, G. and Noé, F. (2017) Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling. Nat. Chem., 9 . pp. 1005-1011. Schillings, Claudia and Stuart, Andrew M. (2017) Convergence Analysis of the Ensemble Kalman Filter for Inverse Problems: the Noisy Case. ArXiv . Schillings, Claudia and Stuart, Andrew M. (2017) Convergence analysis of ensemble Kalman inversion: the linear, noisy case. arXiv . (Submitted) Jeschke, A. and Pedersen, G.K. and Vater, S. and Behrens, J. (2017) Depth‐averaged non‐hydrostatic extension for shallow water equations with quadratic vertical pressure profile: equivalence to Boussinesq‐type equations. International Journal for Numerical Methods in Fluids, 84 (109710). pp. 569-583. ISSN 1097-0363 Gupta, Pooja and Gramatke, A and Einspanier, R and Schütte, Ch. and von Kleist, M. and Sharbati, J (2017) In silico cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements. Toxicology in Vitro, 41 . pp. 179-188. ISSN 08872333 Schöneberg, J. and Lehmann, M. and Ullrich, A. and Posor, Y. and Lo, W.-T. and Lichtner, G. and Schmoranzer, J. and Haucke, V. and Noé, F. (2017) Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nat. Comm., 8 . p. 15873. Winkelmann, S. (2017) Markov Control with Rare State Observation: Average Optimality. Markov Processes and Related Fields, 23 . pp. 1-34. ISSN 1024-2953 Nüske, F. and Wu, H. and Wehmeyer, C. and Clementi, C. and Noé, F. (2017) Markov State Models from short non-Equilibrium Simulations - Analysis and Correction of Estimation Bias. J. Chem. Phys., 146 . 094104. Olsson, Simon and Noé, F. (2017) Mechanistic models of chemical exchange induced relaxation in protein NMR. J. Am. Chem. Soc., 139 . pp. 200-210. Berndt, P. and Klein, R. (2017) Modeling the kinetics of the Shockless Explosion Combustion. Combustion and Flame, 175 . pp. 16-26. Meixenberger, K. and Yousef, K. P. and Smith, M. and Somogyi, S. and Fiedler, S. and Bartmeyer, B. and Hamouda, O. and Bannert, N. and von Kleist, M. and Kücherer, C. (2017) Molecular evolution of HIV-1 integrase during the 20 years prior to the first approval of integrase inhibitors. Virology Journal, 14 . pp. 223-237. Pinamonti, G. and Zhao, J. and Condon, D. and Paul, F. and Noé, F. and Turner, D. and Bussi, G. (2017) Predicting the kinetics of RNA oligonucleotides using Markov state models. J. Chem. Theory Comput., 13 (2). pp. 926-934. Liu, Dishi and Litvinenko, Alexander and Schillings, Claudia and Schulz, Volker (2017) Quantification of airfoil geometry-induced aerodynamic uncertainties---comparison of approaches. SIAM/ASA Journal on Uncertainty Quantification, 5 (1). Zhang, W. and Schütte, Ch. (2017) Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics. Entropy, 19 (7). p. 367. Benn, A. and Hiepen, C. and Osterland, M. and Schütte, Ch. and Zwijsen, A. and Knaus, P. (2017) Role of bone morphogenetic proteins in sprouting angiogenesis: differential BMP receptor-dependent signaling pathways balance stalk vs. tip cell competence. FASEB Journal, 31 (11). pp. 4720-4733. Schäpel, J.S. and Wolff, S. and Schulze, P. and Berndt, P. and Klein, R. and Mehrmann, V. and King, R. (2017) State estimation for reactive Euler equation by Kalman Filtering. CEAS Aeronautical Journal, 1 (10). pp. 261-270. ISSN 1869-5582 Hirt, M. and Schielicke, L. and Müller, A. and Névir, P. (2017) Statistical and dynamical analyses of atmospheric blocking with an idealized point vortex model. Tellus A . pp. 1-22. (Submitted) Wieczorek, M. and Abualrous, E. T. and Sticht, J. and Alvaro-Benito, M. and Stolzenberg, S. and Noé, F. and Freund, C. (2017) Title: Major Histocompatibility Complex (MHC) class I and MHC class II proteins: Conformational Plasticity in Antigen Presentation. Frontiers Immunology, 8 . p. 292. Rüdrich, S. and Sarich, M. and Schütte, Ch. (2017) Utilizing hitting times for ﬁnding metastable sets in non-reversible Markov chains. Journal of Comp. Dynamics . (In Press) Wu, H. and Nüske, F. and Paul, F. and Klus, S. and Koltai, Péter and Noé, F. (2017) Variational Koopman models: slow collective variables and molecular kinetics from short off-equilibrium simulations. J. Chem. Phys., 146 . p. 154104. Engwer, C. and Gräser, C. and Müthing, S. and Sander, O. (2017) The interface for functions in the dune-functions module. Archive of Numerical Software, 5 (1). pp. 95-110. ISSN 2197-8263 Abramyan, A. and Stolzenberg, S. and Li, Z. and Loland, C. J. and Noé, F. and Shi, L. (2017) The isomeric preference of an atypical dopamine transporter inhibitor contributes to its selection of the transporter conformation. ACS Chem. Neurosc., 8 . pp. 1735-1746. Yang, J. and Wang, Z.-H. and Li, Q. and Vercauteren, N. and Bou-Zeid, E. and Parlange, M. B. (2017) A novel approach for unraveling the energy balance of water surfaces with a single depth temperature measurement. Limnology and Oceanography, 62 (1). pp. 89-103. ISSN 00243590 Nevo, G. and Vercauteren, N. and Kaiser, A. and Dubrulle, B. and Faranda, D. (2017) A statistical-mechanical approach to study the hydrodynamic stability of stably stratified atmospheric boundary layer. Physical Review Fluids, 2 (8). 084603. Blömker, Dirk and Schillings, Claudia and Wacker, Philipp (2017) A strongly convergent numerical scheme from EnKF continuum analysis. ... . (Submitted) Jäger, Marten and Schubach, Max and Zemojtel, Tomasz and Reinert, Knut and Church, Deanna M. and Robinson, Peter N. (2016) Alternate-locus aware variant calling in whole genome sequencing. Genome Medicine, 8 (1). ISSN 1756-994X You, Xintian Arthur and Conrad, T. O. F. (2016) Acfs: accurate circRNA identification and quantification from NGS data. Nature Scientific Reports, 6 . ISSN 2045-2322 Yousef, K. P. and Meixenberger, K. and Smith, M. and Jansen, K. and Bartmeyer, B. and Hamouda, O. and Kücherer, C. and von Kleist, M. (2016) Inferring HIV-1 transmission dynamics in Germany from recently transmitted viruses. Journal of Acquired Immunodeficiency Virus, 73 (3). pp. 356-363. ISSN 1525-4135 Fischer, M. and Rust, H.W. and Ulbrich, U. (2016) Seasonal Cycle in German Daily Precipitation Extremes. Meteorologische Zeitschrift . pp. 1-11. ISSN 0941-2948 (Submitted) Winkelmann, S. and Schütte, Ch. (2016) The spatiotemporal master equation: approximation of reaction-diffusion dynamics via Markov state modeling. Journal of Chemical Physics, 145 (21). p. 214107. Zühlke, Martin and Riebe, Daniel and Beitz, Toralf and Löhmannsröben, Hans-Gerd and Andreotti, Sandro and Reinert, Knut and Zenichowski, Karl and Diener, Marc (2016) High-performance liquid chromatography with electrospray ionization ion mobility spectrometry: Characterization, data management, and applications. Journal of Separation Science, 39 (24). pp. 4756-4764. ISSN 16159306 Smith, M. and Smyth, R.P. and Marquet, R. and von Kleist, M. (2016) MIMEAnTo – Profiling functional RNA in Mutational Interference Mapping Experiments. Bioinformatics, 32 (21). pp. 3369-3370. ISSN 1367-4803 Quer, J. and Weber, M. (2016) Estimating exit rate for rare event dynamical systems by extrapolation. ZIB-Report . pp. 1-19. ISSN 2192-7782 (online) Nielsen, A. (2016) The Monte Carlo computation error of transition probabilities. Statistics & Probability Letters, 118 . pp. 163-170. ISSN 0167-7152 Koltai, P. and Ciccotti, G. and Schütte, Ch. (2016) On metastability and Markov state models for non-stationary molecular dynamics. Journal of Chemical Physics, 145 (17). p. 174103. Mielke, A. and Roubícek, T. (2016) Rate-Independent elastoplasticity at finite strain and its numerical approximation. Mathematical Models and Methods in Applied Sciences, 26 (12). pp. 2203-2236. ISSN 1793-6314 Klus, S. and Schütte, Ch. (2016) Towards tensor-based methods for the numerical approximation of the Perron-Frobenius and Koopman operator. Journal of Computational Dynamics . ISSN 2158-2491 Duwal, S. and von Kleist, M. (2016) Top-down and bottom-up modelling in system pharmacology to understand clinical efficacy : An example with NRTIs of HIV-1. European Journal of Pharmaceutical Sciences, 94 . pp. 72-83. ISSN 0928-0987 Zhu, J. and Klein, R. and Delle Site, L. (2016) Adaptive Molecular Resolution Approach in Hamiltonian Form: An Asymptotic Analysis. Physical Review E, 94 (043321). Djurdjevac, N. and Weber, M. and Schütte, Ch. (2016) Finding dominant structures of nonreversible Markov processes. Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 14 (4). pp. 1319-1340. ISSN 1540-3459 Albrecht, D. and Winterflood, C. M. and Sadeghi, M. and Tschager, T. and Noé, F. and Ewers, H. (2016) Nanoscopic compartmentalization of membrane protein motion at the axon initial segment. J. Cell Biol., 215 (1). pp. 37-46. Banisch, Ralf and Hartmann, C. (2016) A sparse Markov chain approximation of LQ-type stochastic control problems. Math. Control Relat. F., 6 (3). pp. 363-389. ISSN 1064-8275 Röst, Hannes L and Sachsenberg, Timo and Aiche, Stephan and Bielow, Chris and Weisser, Hendrik and Aicheler, Fabian and Andreotti, Sandro and Ehrlich, Hans-Christian and Gutenbrunner, Petra and Kenar, Erhan and Liang, Xiao and Nahnsen, Sven and Nilse, Lars and Pfeuffer, Julianus and Rosenberger, George and Rurik, Marc and Schmitt, Uwe and Veit, Johannes and Walzer, Mathias and Wojnar, David and Wolski, Witold E and Schilling, Oliver and Choudhary, Jyoti S and Malmström, Lars and Aebersold, Ruedi and Reinert, Knut and Kohlbacher, Oliver (2016) OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature Methods, 13 (9). pp. 741-748. ISSN 1548-7091 Dellnitz, M. and Klus, S. (2016) Sensing and control in symmetric networks. Dynamical Systems. An International Journal . pp. 1-19. (Submitted) Lorenzi, J. M. and Matera, S. and Reuter, K. (2016) Synergistic Inhibition of Oxide Formation in Oxidation Catalysis: A First-Principles Kinetic Monte Carlo Study of NO + CO Oxidation at Pd(100). ACS Catalysis, 6 (8). pp. 5191-5197. ISSN 2155-5435 Hartmann, C. and Schütte, Ch. and Zhang, W. (2016) Model reduction algorithms for optimal control and importance sampling of diffusions. Nonlinearity, 29 (8). pp. 2298-2326. ISSN 0951-7715 Liero, M. and Mielke, A. and Savaré, G. (2016) Optimal Transport in Competition with Reaction: The Hellinger--Kantorovich Distance and Geodesic Curves. SIAM J. Math. Anal., 48 (2). pp. 2869-2911. ISSN 1095-7154 (online) Rudolf, M. and Boutelier, D. and Rosenau, M. and Schreurs, G. and Oncken, O. (2016) Rheological benchmark of silicone oils used for analog modeling of short- and long-term lithospheric deformation. Tectonophysics, 684 . pp. 12-22. Bonetti, E. and Rocca, E. and Rossi, R. and Thomas, M. (2016) A rate-independent gradient system in damage coupled with plasticity via structured strains. ESAIM: Proceedings and Surveys, 54 . pp. 54-69. Duwal, S. and Sunkara, V. and von Kleist, M. (2016) Multiscale Systems-Pharmacology Pipeline to Assess the Prophylactic Efficacy of NRTIs Against HIV-1. CPT: Pharmacometrics & Systems Pharmacology, 5 (7). pp. 377-387. ISSN 2163-8306 Zhang, W. and Hartmann, C. and Schütte, Ch. (2016) Effective dynamics along given reaction coordinates, and reaction rate theory. Faraday discussions, 195 . pp. 365-394. ISSN 1359-6640 Bienefeld, Kaspar and Zautke, F. and Gupta, Pooja (2016) A novel method for undisturbed long-term observation of honey bee (Apis mellifera) behavior – illustrated by hygienic behavior towards varroa infestation. Journal of Apicultural Research, 54 (5). 541-547 . ISSN 0021-8839 (print) 2078-6913 (online) Gelß, P. and Matera, S. and Schütte, Ch. (2016) Solving the master equation without kinetic Monte Carlo: tensor train approximations for a CO oxidation model. Journal of Computational Physics, 314 . pp. 489-502. ISSN 0021-9991 Hoppe, C. and Obermeier, P. and Muehlhans, S. and Alchikh, M. and Seeber, L. and Tief, F. and Karsch, K. and Chen, X. and Boettcher, S. and Diedrich, S. and Conrad, T. O. F. and Kisler, B. and Rath , B. (2016) Article: Innovative Digital Tools and Surveillance Systems for the Timely Detection of Adverse Events at the Point of Care: A Proof-of-Concept Study. Drug Safety, 39 (10). pp. 977-988. ISSN 1179-1942 Wu, H. and Paul, F. and Wehmeyer, C. and Noé, F. (2016) Multiensemble Markov models of molecular thermodynamics and kinetics. Proceedings of the National Academy of Sciences, 113 (23). E3221-E3230 . ISSN 0027-8424 Klus, S. and Koltai, P. and Schütte, Ch. (2016) On the numerical approximation of the Perron-Frobenius and Koopman operator. Journal of Computational Dynamics, 3 (1). pp. 51-79. ISSN 2158-2491 Lei, Shulai and Paulus, B. and Li, Shujuan and Schmidt, B. (2016) Curvature-dependent adsorption of water inside and outside armchair carbon nanotubes. J. Comp. Chem., 37 (14). pp. 1313-1320. Spötter, Andreas and Gupta, Pooja and Mayer, Manfred and Reinsch , Norbert and Bienefeld, Kaspar (2016) Genome-Wide Association Study of a Varroa-Specific Defense Behavior in Honeybees (Apis mellifera). Journal of Heredity, 107 (3). pp. 220-227. ISSN 0022-1503 (Print) 1465-7333 (online) Chustagulprom, N. and Reich, S. and Reinhardt, M. (2016) A Hybrid Ensemble Transform Particle Filter for Nonlinear and Spatially Extended Dynamical Systems. SIAM/ASA Journal on Uncertainty Quantification, 4 (1). pp. 592-608. ISSN 2166-2525 Mielke, A. and Peletier, M. A. and Renger, M. (2016) A generalization of Onsager's reciprocity relations to gradient flows with nonlinear mobility. Journal of Non-Equilibrium Thermodynamics, 41 (2). de la Garza, Luis and Veit, Johannes and Szolek, Andras and Röttig, Marc and Aiche, Stephan and Gesing, Sandra and Reinert, Knut and Kohlbacher, Oliver (2016) From the desktop to the grid: scalable bioinformatics via workflow conversion. BMC Bioinformatics, 17 (1). ISSN 1471-2105 Shao, Borong and Conrad, T. O. F. (2016) Epithelial Mesenchymal Transition Regulatory Network-based Feature Selection in Lung Cancer Prognosis Prediction. Lecture Notes in Computer Science (LNCS): Proceeding of IWBBIO 2016, 9656 . Vega del Valle, I. and Schütte, Ch. and Conrad, T. O. F. (2016) Finding metastable states in real-world time series with recurrence networks. Physica A, 445 . Klein, R. and Benacchio, T. (2016) A doubly blended model for multiscale atmospheric dynamics. Journal of the Atmospheric Sciences, 73 . pp. 1179-1186. ISSN Online: 1520-0469 Print: 0022-4928 Tief, F. and Hoppe, Ch. and Seeber, L. and Obermeier, P. and Chen, X. and Karsch, K. and Muehlhans, S. and Adamou, E. and Conrad, T. O. F. and Schweiger, B. and Adam, T. and Rath , B. (2016) An inception cohort study assessing the role of bacterial co-infections in children with influenza and ILI and a clinical decision model for stringent antibiotic use. Antiviral Therapy, 21 (5). pp. 413-424. ISSN 1359-6535 (print); 2040-2058 (online) Canzar, S. and Andreotti, S. and Weese, D. and Reinert, K. and Klau, G. W. (2016) CIDANE: comprehensive isoform discovery and abundance estimation. Genome Biology, 17 (1). ISSN 1474-760X Schillings, Claudia and Stuart, Andrew M. (2016) Analysis of the ensemble Kalman filter for inverse problems. arXiv . Mielke, A. and Rossi, R. and Savaré, G. (2016) Balanced-Viscosity solutions for multi-rate systems. Journal of Physics: Conference Series, 727 . pp. 1-27. Schreurs, G. and et al, . (2016) Benchmarking analogue models of brittle thrust wedges. J. Struct. Geol. . (In Press) Noé, F. and Banisch, Ralf and Clementi, C. (2016) Commute maps: separating slowly-mixing molecular configurations for kinetic modeling. J. Chem. Theory Comput., 12 . pp. 5620-5630. Stolzenberg, S. and Michino, M. and LeVine, M. and Weinstein, H. and Shi, L. (2016) Computational approaches to detect allosteric pathways in transmembrane molecular machines. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1858 (7). p. 1652. ISSN 00052736 Hallier, M. and Hartmann, C. (2016) Constructing Markov State Models of Reduced Complexity from Agent-Based Simulation Data. Social Simulation Conference 2016 . (Submitted) Lemke, O. and Keller, B.G. (2016) Density-based cluster algorithms for the identification of core sets. Journal of Chemical Physics, 145 (164104). Ransiek, A. and Wundrak, R. (2016) Dialogue and Narration. International Journal of Cross-Cultural Studies and Environmental Communication, 5 (1). pp. 41-51. Blatt, M. and Burchardt, A. and Dedner, A. and Engwer, C. and Fahlke, J. and Flemisch, B. and Gersbacher, C. and Gräser, C. and Gruber, F. and Grüninger, C. and Kempf, D. and Klöfkorn, R. and Malkmus, T. and Müthing, S. and Nolte, M. and Piatkowski, M. and Sander, O. (2016) The Distributed and Unified Numerics Environment, Version 2.4. Archive of Numerical Software, 4 (100). pp. 13-29. ISSN 2197-8263 Trendelkamp-Schroer, B. and Noé, F. (2016) Efficient estimation of rare-event kinetics. Phys. Rev. X, 6 . 011009. Obermeier, P. and Muehlhans, S. and Hoppe, Ch. and Karsch, K. and Tief, F. and Seeber, L. and Chen, X. and Conrad, T. O. F. and Boettcher, S. and Diedrich, S. and Rath , B. (2016) Enabling Precision Medicine With Digital Case Classification at the Point-of-Care. EBioMedicine, 4 . pp. 191-196. Drähne, U. and Goseberg, N. and Vater, S. and Beisiegel, N. and Behrens, J. (2016) An Experimental and Numerical Study of Long Wave Run-Up on a Plane Beach. J. Mar. Sci. Eng., 4 (1). ISSN EISSN 2077-1312 Rosenau, M. and Leever, K. and Oncken, O. (2016) Experimental tectonics: Convergent plate margins. Earth Sys. Env. Sci. SFB 1114 Preprint . (Submitted) Djurdjevac, N. and Weber, M. and Schütte, Ch. (2016) Finding dominant structures of nonreversible Markov processes. Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 14 (4). pp. 1319-1340. ISSN 1540-3459 Delle Site, L. (2016) Formulation of Liouville's theorem for grand ensemble molecular simulations. Physical Review E, 93 (022130). Ring, S. and Oberhofer, H. and Hille, C. and Matera, S. and Reuter, K. (2016) Function-Space-Based Solution Scheme for the Size-Modified Poisson–Boltzmann Equation in Full-Potential DFT. Journal of Chemical Theory and Computation, 12 (8). pp. 4052-4066. ISSN 1549-9618 Delle Site, L. and Agarwal, A. (2016) Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and Application. Computer Physics Communications (206). pp. 26-34. Doerr, S. and Harvey, M. J. and Noé, F. and De Fabritiis, G. (2016) HTMD: High-Throughput Molecular Dynamics for Molecular Discovery. J. Chem. Theory Comput., 12 . pp. 1845-1852. Pérez-Hernández, G. and Noé, F. (2016) Hierarchical Time-Lagged Independent Component Analysis: Computing Slow Modes and Reaction Coordinates for Large Molecular Systems. J. Chem. Theory Comput., 12 . pp. 6118-6129. Paul, F. and Weikl, T. (2016) How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates. PLOS Computational Biology . Vercauteren, N. and Mahrt, L. and Klein, R. (2016) Investigation of interactions between scales of motion in the stable boundary layer. Quarterly Journal of the Royal Meteorological Society . Wieczorek, M. and Sticht, J. and Stolzenberg, S. and Günther, S. and Wehmeyer, C. and El Habre, Z. and Àlvaro-Benito, M. and Noé, F. and Freund, C. (2016) MHC class II complexes sample intermediate states along the peptide exchange pathway. Nature Communications, 7 . p. 13224. Hallier, M. and Hartmann, C. (2016) A Markov state modelling approach to characterizing the punctuated equilibrium dynamics of stochastic evolutionary games. Games 2016, 5th World Conference of the Game Theory Society, . (Submitted) Vitalini, F. and Noé, F. and Keller, B. (2016) Molecular dynamics simulations data of the twenty encoded amino acids in different force fields. Data in Brief, 7 . pp. 582-590. Kornhuber, R. and Yserentant, H. (2016) Numerical Homogenization of Elliptic Multiscale Problems by Subspace Decomposition. Multiscale Model. Simul., 14 (3). pp. 1017-1036. ISSN print: 1540-3459; online: 1540-3467 Gräser, C. and Kahnt, M. and Kornhuber, R. (2016) Numerical approximation of multi-phase Penrose-Fife systems. Computational Methods in Applied Mathematics, 16 (4). pp. 523-542. ISSN Online: 1609-9389, Print: 1609-4840 Yapp, E.K.Y. and Patterson, R. I. A and Akroyd, J. and Mosbach, S. and Adkins, E.M. and Miller, J.H. and Kraft, M. (2016) Numerical simulation and parametric sensitivity study of optical band gap in a laminar co-flow ethylene diffusion flame. Combustion and Flame, 167 . pp. 320-334. Feireisl, E. and Klein, R. and Novotný, A. and Zatorska, E. (2016) On singular limits arising in the scale analysis of stratified fluid flows. Mathematical Models and Methods in Applied Sciences, World Scientific, 26 (3). pp. 419-443. ISSN Print: 0218-2025 Online: 1793-6314 Pipping, E. and Kornhuber, R. and Rosenau, M. and Oncken, O. (2016) On the efficient and reliable numerical solution of rate-and-state friction problems. Geophysical Journal International, 204 (3). pp. 1858-1866. ISSN Online: 1365-246X Print: 0956-540X Klinkmüller, M. and Schreurs, G. and Rosenau, M. and Kemnitz, H. (2016) Properties of granular analogue materials: A community wide survey. Tectonophysics, 666 . pp. 23-38. Patterson, R. I. A (2016) Properties of the solutions of delocalised coagulation and inception problems with outflow boundaries. Journal of Evolution Equations, 16 . pp. 261-291. Trendelkamp-Schroer, B. and Wu, H. and Noé, F. (2016) Reversible Markov chain estimation using convex-concave programming. arXiv . 1603.01640. Schillings, Claudia and Schwab, Christoph (2016) Scaling limits in computational Bayesian inversion. ESAIM: Mathematical Modelling and Numerical Analysis, 50 (6). pp. 1825-1856. ISSN 2822-7840; eISSN = 2804-7214 Ritter, M. and Leever, K. and Rosenau, M. and Oncken, O. (2016) Scaling the Sand Box - Mechanical (Dis-) Similarities of Granular Materials and Brittle Rock. Journal of Geophysical Research: Solid Earth . (In Press) Dewar, W. and Schoonover, J. and McDougall, T. and Klein, R. (2016) Semicrompressible Ocean Thermodynamics and Boussinesq Energy Conservation. Fluids, 1 (9). Reichel , T. and Schäpel, J.S. and Bobusch, B. and Klein, R. and King, R. and Paschereit, C. O. (2016) Shockless Explosion Combustion: Experimental Investigation of a New Approximate Constant Volume Combustion Process. Journal of Engineering for Gas Turbines and Power, 139 (2). 021504 -021511. ISSN 0742-4795 Peters, J.H. and Klein, R. and Delle Site, L. (2016) Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique. Phys. Rev. E, 94 (2). 023309. Wu, H. and Noé, F. (2016) Spectral learning of dynamic systems from nonequilibrium data. NIPS, 29 . pp. 4179-4187. Wolff, S. and Schäpel, J.S. and Berndt, P. and King, R. (2016) State Estimation for the Homogeneous 1-D Euler Equation by Unscented Kalman Filtering. ASME Proceedings . ISSN ISBN: 978-0-7918-5725-0 Klus, S. and Gelß, P. and Peitz, S. and Schütte, Ch. (2016) Tensor-based dynamic mode decomposition. SIAM Journal on Scientific Computing . ISSN ISSN 1064-8275 (print); 1095-7197 (electronic) (Submitted) Elliott, C.M. and Gräser, C. and Hobbs, G. and Kornhuber, R. and Wolf, M.W. (2016) A Variational Approach to Particles in Lipid Membranes. Archive for Rational Mechanics and Analysis, 222 (2). pp. 1011-1075. ISSN Print: 0003-9527; Online:1432-0673 Nüske, F. and Schneider, R. and Vitalini, F. and Noé, F. (2016) Variational Tensor Approach for Approximating the Rare-Event Kinetics of Macromolecular Systems. J. Chem. Phys., 144 (5). 054105. Lorenzi, Juan M. and Matera, S. and Reuter, K. (2016) A first-principles kinetic Monte Carlo study of NO+ CO oxidation at Pd(100). ACS Catalysis, 6 (8). pp. 5191-5197. ISSN 2155-5435 Enciso, M. and Schütte, Ch. and Delle Site, L. (2015) Influence of pH and sequence in peptide aggregation via molecular simulation. Journal of Chemical Physics, 143 (24). p. 243130. ISSN 0021-9606 Schultz, L. and Zurich, M.-G. and Culot, M. and da Costa, A. and Landry, C. and Bellwon, P. and Kristl, T. and Hörmann, K. and Ruzek, S. and Aiche, S. and Reinert, K. and Bielow, C. and Gosselet, F. and Cecchelli, R. and Huber, C. G. and Schroeder, O. H.-U. and Gramowski-Voss, A. and Weiss, D. G. and Bal-Price, A. (2015) Evaluation of drug-induced neurotoxicity based on metabolomics, proteomics and electrical activity measurements in complementary CNS in vitro models. Toxicology in Vitro, 30 (1). pp. 138-165. ISSN 08872333 Wilmes, Anja and Bielow, Chris and Ranninger, Christina and Bellwon, Patricia and Aschauer, Lydia and Limonciel, Alice and Chassaigne, Hubert and Kristl, Theresa and Aiche, Stephan and Huber, Christian G. and Guillou, Claude and Hewitt, Philipp and Leonard, Martin O. and Dekant, Wolfgang and Bois, Frederic and Jennings, Paul (2015) Mechanism of cisplatin proximal tubule toxicity revealed by integrating transcriptomics, proteomics, metabolomics and biokinetics. Toxicology in Vitro, 30 (1, Part A). pp. 117-127. ISSN 08872333 Grohs, P. and Hardering, H. and Sander, O. (2015) Optimal a priori discretization error bounds for geodesic finite elements. Foundations of Computational Mathematics, 15 (6). pp. 1357-1411. ISSN 1615-3375 Trendelkamp-Schroer, B. and Wu, H. and Paul, F. and Noé, F. (2015) Estimation and uncertainty of reversible Markov models. J. Chem. Phys., 143 (17). p. 174101. Gul, Rahim and Bernhard, S. (2015) Parametric uncertainty and global sensitivity analysis in a model of the carotid bifurcation: Identification and ranking of most sensitive model parameters. Mathematical Biosciences, 269 . pp. 104-116. ISSN 0025-5564 Babushkina, E. S. and Bessonov, N. M. and Ataullakhanov, F. I. and Panteleev, M. A. (2015) Continuous modeling of arterial platelet thrombus formation using a spatial adsorption equation. PLoS ONE, 10 (10). ISSN 1932-6203 Stötzel, C. and Röblitz, S. and Siebert, H. (2015) Complementing ODE-Based System Analysis Using Boolean Networks Derived from an Euler-Like Transformation. PLoS ONE, 10 (10). e0140954. ISSN 1932-6203 Kryven, I. and Röblitz, S. and Schütte, Ch. (2015) Solution of the chemical master equation by radial basis functions approximation with interface tracking. BMC Systems Biology, 9 (67). ISSN 1752-0509 Delle Site, L. (2015) Shannon entropy and many-electron correlations: Theoretical concepts, numerical results, and Collins conjecture. International Journal of Quantum Chemistry, 115 (19). pp. 1396-1404. ISSN 1097-461X You, Xintian Arthur (2015) Hastings: An R pipeline for large-scale RNA-Seq data analysis. Technical Report . (Unpublished) Karsch, K. and Obermeier, P. and Seeber, L. and Chen, X. and Tief, F. and Muehlhans, S. and Hoppe, Ch. and Conrad, T. O. F. and Boettcher, S. and Diedrich, S. and Rath , B. (2015) Human Parechovirus Infections Associated with Seizures and Rash: A Syndromic Surveillance Study in Children. The Pediatric Infectious Disease Journal, 34 (10). Schuster, I. and Strathmann, H. and Paige, B. and Sejdinovic, Dino (2015) Kernel Sequential Monte Carlo. SFB 1114 Preprint in arXiv:1510.03105 . (Submitted) Kappler, J. and Netz, R.R. (2015) Multiple surface wave solutions on linear viscoelastic media. EPL, 112 (1). p. 19002. Agarwal, A. and Delle Site, L. (2015) Path Integral Molecular Dynamics within the Grand Canonical-like Adaptive Resolution Technique: Simulation of Liquid Water. Journal of Chemical Physics, 143 (9). ISSN 0021-9606 Wang, H. and Agarwal, A. (2015) Adaptive resolution simulation in equilibrium and beyond. The European Physical Journal Special Topics, 224 (12). pp. 2269-2287. ISSN 1951-6355 Bittracher, Andreas and Hartmann, C. and Junge, O. and Koltai, Péter (2015) Pseudo generators for under-resolved molecular dynamics. The European Physical Journal Special Topics, 224 (12). pp. 2463-2490. ISSN 1951-6355 Bittracher, Andreas and Koltai, Péter and Junge, Oliver (2015) Pseudogenerators of spatial transfer operators. SIAM Journal on Applied Dynamical Systems, 14 (3). pp. 1478-1517. ISSN 1536-0040 Banisch, Ralf and Djurdjevac, N. and Schütte, Ch. (2015) Reactive flows and unproductive cycles in irreversible Markov chains. The European Physical Journal Special Topics, 224 (12). pp. 2369-2387. ISSN 1951-6355 Wang, H. and Agarwal, A. (2015) Reply to comment by R. Klein on “Adaptive resolution simulation in equilibrium and beyond”. The European Physical Journal Special Topics, 224 (12). pp. 2501-2502. ISSN 1951-6355 Hartmann, C. and Delle Site, L. (2015) Scale Bridging in Molecular Simulation. The European Physical Journal Special Topics, 224 (12). pp. 2173-2176. ISSN 1951-6355 Schütte, Ch. and Sarich, M. (2015) A critical appraisal of Markov state models. The European Physical Journal Special Topics, 224 (12). pp. 2445-2462. ISSN 1951-6355 Klein, R. (2015) Comments on "Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations" by K. Kreis, A.C. Fogarty, K. Kremer R. Potestio. The European Physical Journal, 224 (12). pp. 2503-2504. ISSN Online: 1951-6401 Print: 1951-6355 Klein, R. (2015) Comments on "Open Boundary Molecular Dynamics " by R. Delgado-Buscalioni, J. Sablic, and M. Praprotnik. The European Physical Journal, 224 (12). pp. 2509-2510. ISSN Online: 1951-6401 Print: 1951-6355 Agarwal, A. and Zhu, J. and Wang, H. and Hartmann, C. and Delle Site, L. (2015) Molecular dynamics in a Grand Ensemble: Bergmann-Lebowitz model and adaptive resolution simulation. New Journal of Physics, 17 (083042). ISSN 1367-2630 Smyth, R.P. and Despons, L. and Huili, G. and Bernacchi, S. and Hijnen, M. and Mak, J. and Jossinet, F. and Weixi, L. and Paillart, J.-C. and von Kleist, M. and Marquet, R. (2015) Mutational Interference Mapping Experiment (MIME) for studying the relationship between RNA structure and function. Nature Methods, 12 . pp. 866-872. ISSN 1548-7091 Djurdjevac, N. and Banisch, Ralf and Schütte, Ch. (2015) Modularity of Directed Networks: Cycle Decomposition Approach. Journal of Computational Dynamics, 2 (1). pp. 1-24. ISSN 2158-2491 Mireles, Victor and Conrad, T. O. F. (2015) Minimum-overlap clusterings and the sparsity of overcomplete decompositions of binary matrices. Procedia Computer Science, 51 . pp. 2967-2971. ISSN 1877-0509 Reinert, K. and Langmead, B. and Weese, D. and Evers, D.J. (2015) Alignment of Next-Generation Sequencing Reads. Annual Review of Genomics and Human Genetics, 16 (1). pp. 133-151. ISSN 1527-8204 Duwal, S. and Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2015) Optimal treatment strategies in the context of 'treatment for prevention' against HIV-1 in resource-poor settings. PLOS Computational Biology, 11 . e1004200. Schütte, Ch. and Wang, H. (2015) Building Markov State Models for Periodically Driven Non-Equilibrium Systems. Journal of Chemical Theory and Computation, 11 (4). pp. 1819-1831. ISSN 1549-9618 Moualeu-Ngangue, D. P. and Röblitz, S. and Ehrig, R. and Deuflhard, P. (2015) Parameter Identification in a Tuberculosis Model for Cameroon. PLoS ONE, 10 (4). e0120607. ISSN 1932-6203 Pipping, E. and Sander, O. and Kornhuber, R. (2015) Variational formulation of rate- and state-dependent friction problems. Zeitschrift für angewandte Mathematik und Mechanik (ZAMM), 95 (4). pp. 377-395. ISSN 0044-2267 Aiche, S. and Sachsenberg, T. and Kenar, E. and Walzer, M. and Wiswedel, B. and Kristl, T. and Boyles, M. and Duschl, A. and Huber, C. G. and Berthold, M. R. and Reinert, K. and Kohlbacher, O. (2015) Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry. PROTEOMICS, 15 (8). pp. 1443-1447. ISSN 16159853 Schütte, Ch. and Sarich, M. (2015) A Critical Appraisal of Markov State Models. SFB 1114 Preprint, 15-18 . ISSN 1438-0064 Shao, Borong and Conrad, T. O. F. (2015) Are NoSQL data stores useful for bioinformatics researchers? "International Journal on Recent and Innovation Trends in Computing and Communication (IJRITCC), 3 (3). pp. 1704-1708. ISSN 2321-8169 Schmidt, B. and Friedrich, B. (2015) Supersymmetry and eigensurface topology of the spherical quantum pendulum. Phys. Rev. A, 91 (02). 022111. Li, Shujuan and Schmidt, B. (2015) Molecular Dynamics Simulations of Proton-Ordered Water Confined in Low-Diameter Carbon Nanotubes. Phys. Chem. Chem. Phys., 17 (11). pp. 7303-7316. Berninger, H. and Kornhuber, R. and Sander, O. (2015) A multidomain discretization of the Richards equation in layered soil. Computational Geosciences, 19 (1). pp. 213-232. ISSN 1420-0597 Banisch, Ralf and Djurdjevac, N. (2015) Cycle-flow–based module detection in directed recurrence networks. EPL (Europhysics Letters) , 108 (6). ISSN 0295-5075 Schütte, Ch. and Nielsen, A. and Weber, M. (2015) Markov state models and molecular alchemy. Molecular Physics, 113 (1). pp. 69-78. ISSN 0026-8976 Delle Site, L. (2015) Levy-Lieb principle: The bridge between the electron density of Density Functional Theory and the wavefunction of Quantum Monte Carlo. Chemical Physics Letters, 619 . pp. 148-151. ISSN 0009-2614 Noé, F. (2015) Beating the Millisecond Barrier in Molecular Dynamics Simulations. Biophys J., 108 . pp. 228-229. Münch, M. (2015) Brandereignisse in Flüchtlingsunterkünften. BRANDSchutz / Deutsche Feuerwehr-Zeitung . Di Giuseppe, E. and Corbi, F. and Funiciello, F. and Massmeyer, A. and Santimano, T.N. and Rosenau, M. and Davaille, A. (2015) Characterization of Carbopol hydrogel rheology for experimental tectonics and geodynamics, , 642, 29-45, doi:10.1016/j.tecto.2014.12.005. Tectonophysics . pp. 29-45. Klein, R. (2015) Comments on "Adaptive Resolution Simulation in Equilibrium and Beyond" by H. Wang and A. Agarwal. The European Physical Journal, 224 (12). pp. 2497-2499. Benacchio, T. and Klein, R. and Dubos, T. and Voitus, F. (2015) Comments on “A Semihydrostatic Theory of Gravity-Dominated Compressible Flow”. Journal of the Atmospheric Sciences , 72 (7). pp. 2850-2851. ISSN Online: 1520-0469 Print: 0022-4928 Boger, M. and Jägle, F. and Munz , C.-D. and Klein, R. (2015) Coupling of compressible and incompressible flow regions using the multiple pressure variables approach. Mathematical Methods in the Applied Sciences, 38 (3). pp. 458-477. Reubold, T. F. and Faelber, K. and Plattner, N. and Posor, Y. and Branz, K. and Curth, U. and Schlegel, J. and Anand, R. and Manstein, D. and Noé, F. and Haucke, V. and Daumke, O. and Eschenburg, S. (2015) Crystal structure of the dynamin tetramer. Nature, 525 . pp. 404-408. Langfeldt, B. and Mischau, A. (2015) Die akademische Laufbahn in der Mathematik und Physik. Eine Analyse fach- und geschlechterbezogener Unterschiede bei der Umsetzung von Karrierewissen. Beiträge zur Hochschulforschung, 37 . pp. 80-99. ISSN 0171-645X Vitalini, F. and Mey, A.S.J.S. and Noé, F. and Keller, B. (2015) Dynamic Properties of Force Fields. J. Chem. Phys., 142 . 084101. Ullrich, A. and Böhme, M. A. and Schöneberg, J. and Depner, H. and Sigrist, S. J. and Noé, F. (2015) Dynamical organization of Syntaxin-1A at the presynaptic active zone. PLoS Comput. Biol., 11 . e1004407. Schillings, Claudia and Sunnåker, Mikael and Stelling, Jörg and Schwab, Christoph (2015) Efficient characterization of parametric uncertainty of complex (bio) chemical networks. PLOS Computational Biology . Matera, S. and Blomberg, S. and Hoffmann, M. J. and Zetterberg, J. and Gustafson, J. and Lundgren, E. and Reuter, K. (2015) Evidence for the Active Phase of Heterogeneous Catalysts through In Situ Reaction Product Imaging and Multiscale Modeling. ACS Catalysis, 5 (8). pp. 4514-4518. Erbar, M. and Maas, J. and Renger, M. (2015) From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability, 20 (89). Wu, H. and Noé, F. (2015) Gaussian Markov transition models of molecular kinetics. J. Chem. Phys., 142 (8). 084104. Gunkel, M. and Schöneberg, J. and Alkhaldi, W. and Irsen, S. and Noé, F. and Kaupp, U. B. and Al-Amoudi, A. (2015) Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics. Structure, 23 . pp. 628-638. Kuchenbecker, L. and Nienen, M. and Hecht, J. and Neumann, A. U. and Babel, N. and Reinert, K. and Robinson, P. N. (2015) IMSEQ - a fast and error aware approach to immunogenetic sequence analysis. Bioinformatics, 31 (18). pp. 2963-2971. ISSN 1367-4803 Rinne, K.F. and Schulz, J.C.F. and Netz, R.R. (2015) Impact of secondary structure and hydration water on the dielectric spectrum of poly-alanine and possible relation to the debate on slaved versus slaving water. J. Chem. Phys., 142 (215104). Horenko, I. and Gerber, S. (2015) Improving clustering by imposing network information. Science Advances, 1 (7). ISSN 2375-2548 Riechelmann, T. and Wacker, U. and Beheng, K.D. and Etling, D. and Raasch, S. (2015) Influence of turbulence on the drop growth in warm clouds, Part II: sensitivity studies with a spectral bin microphysics and a Lagrangian cloud model. Meteorologische Zeitschrift . Santimano, T.N. and Rosenau, M. and Oncken, O. (2015) Intrinsic versus extrinsic variability of analogue sand-box experiments - Insights from statistical analysis of repeated accretionary sand wedge experiments. Journal of Structural Geology, 75 . pp. 80-100. Boninsegna, L. and Gobbo, G. and Noé, F. and Clementi, C. (2015) Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps. J. Chem. Theory Comput., 11 . pp. 5947-5960. Noé, F. and Clementi, C. (2015) Kinetic distance and kinetic maps from molecular dynamics simulation. J. Chem. Theory Comput., 11 . pp. 5002-5011. Schlegel, F. and Stiller, J. and Bienert, A. and Maas, H.-G and Queck, R. and Bernhofer, C. (2015) Large-Eddy Simulation Study of the Effects on Flow of a Heterogeneous Forest at Sub-tree Resolution. Boundary-Layer Meteorology, 154 . pp. 27-56. Hu, J. and Reinert, K. (2015) LocalAli: An Evolutionary-based Local Alignment Approach to Identify Functionally Conserved Modules in Multiple Networks. Bioinformatics, 30 (1). pp. 363-372. ISSN 1367-4803 Yousef, K. P. and Streck, A. and Schütte, Ch. and Siebert, H. and Hengge, R. and von Kleist, M. (2015) Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli. BMC Systems Biology, 9 . p. 39. ISSN 1752-0509 Wu, H. (2015) Maximum Margin Clustering for State Decomposition of Metastable Systems. Neurocomputing, 164 . pp. 5-22. ISSN 0925-2312 Stolzenberg, S. and Quick, M. and Zhao, C. and Gotfryd, K. and Khelashvili, G. and Gether, U. and Loland, C. J. and Javitch, J. A. and Noskov, S. and Weinstein, H. and Shi, L. (2015) Mechanism of the Association between Na+Binding and Conformations at the Intracellular Gate in Neurotransmitter:Sodium Symporters. Journal of Biological Chemistry, 290 (22). p. 13992. ISSN 0021-9258 Holtgrewe, M. and Kuchenbecker, L. and Reinert, K. (2015) Methods for the Detection and Assembly of Novel Sequence in High-Throughput Sequencing Data. Bioinformatics, 31 (12). pp. 1904-1912. ISSN 1367-4803 Gräser, C. and Kornhuber, R. and Sack, U. (2015) Nonsmooth Schur-Newton methods for multicomponent Cahn-Hilliard systems. IMA Journal of Numerical Analysis, 35 (2). pp. 652-679. ISSN 0272-4979 O’Kane, T.J. and Risbey, J.S. and Monselesan, D.P. and Horenko, I. and Franzke, Ch.L.E. (2015) On the dynamics of persistent states and their secular trends in the waveguides of the Southern Hemisphere troposphere. Climate Dynamics . ISSN Print: 0930-7575, Online: 1432-0894 Wu, H. and Prinz, J.-H. and Noé, F. (2015) Projected Metastable Markov Processes and Their Estimation with Observable Operator Models. J. Chem. Phys., 143 (14). p. 144101. Plattner, N. and Noé, F. (2015) Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models. Nat. Commun., 6 . p. 7653. Scherer, M. K. and Trendelkamp-Schroer, B. and Paul, F. and Pérez-Hernández, G. and Hoffmann, M. and Plattner, N. and Wehmeyer, C. and Prinz, J.-H. and Noé, F. (2015) PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models. J. Chem. Theory Comput., 11 (11). pp. 5525-5542. Biedermann, J. and Ullrich, A. and Schöneberg, J. and Noé, F. (2015) ReaDDyMM: fast interacting-particle reaction-diffusion simulations using graphical processing units. Biophys. J., 108 . pp. 457-461. ISSN 00063495 Li, S. and Moreno, M. and Bedford, J. and Rosenau, M. and Oncken, O. (2015) Revisiting viscoelastic effects on interseismic deformation and locking degree: A case study of the Peru-North Chile subduction zone. Journal of Geophysical Research-Solid Earth, 120 (6). pp. 4522-4538. Schror, M. and Mey, A.S.J.S. and Noé, F. and MacPhee, C. (2015) Shedding Light on the Dock-Lock Mechanism in Amyloid Fibril Growth Using Markov State Models. J. Chem. Phys. Lett., 6 . pp. 1076-1081. Noé, F. (2015) Statistical inefficiency of Markov model count matrices. preprint . (Unpublished) Billesbølle, C. B. and Krüger, M. B. and Shi, L. and Quick, M. and Li, Z. and Stolzenberg, S. and Kniazeff, J. and Gotfryd, K. and Mortensen, J. S. and Javitch, J. A. and Weinstein, H. and Loland, C.J. and Gether, U. (2015) Substrate-induced Unlocking of the Inner Gate Determines the Catalytic Efficiency of a Neurotransmitter:Sodium Symporter. Journal of Biological Chemistry, 290 (44). p. 26725. ISSN 0021-9258 Becker, N. and Ulbrich, U. and Klein, R. (2015) Systematic large-scale secondary circulations in a regional climate model. Geophysical Research Letters, 42 (10). 4142-4149 . von Larcher, T. and Beck, A. and Klein, R. and Horenko, I. and Metzner, Ph. and Waidmann, M. and Igdalov, D. and Gassner, G. and Munz , C.-D. (2015) Towards a Framework for the Stochastic Modelling of Subgrid Scale Fluxes for Large Eddy Simulation. Meteorologische Zeitschrift, 24 (3). pp. 313-342. Akyuz, N. and Georgieva, E. R. and Zhou, Z. and Stolzenberg, S. and Cuendet, M. A. and Khelashvili, G. and Altman, R. B. and Terry, D. S. and Freed, J. H. and Weinstein, H. and Boudker, O. and Blanchard, S. (2015) Transport domain unlocking sets the uptake rate of an aspartate transporter. Nature, 518 (7537). p. 68. ISSN 0028-0836 Schulz, J.C.F. and Miettinen, M.S. and Netz, R.R. (2015) Unfolding and Folding Internal Friction of β‑Hairpins Is Smaller than That of α‑Helices. Journal of Physical Chemistry B, 119 (13). pp. 4565-4574. Vitalini, F. and Noé, F. and Keller, B. (2015) A basis set for peptides for the variational approach to conformational kinetics. J. Chem. Theory Comput., 11 . pp. 3992-4004. Vercauteren, N. and Klein, R. (2015) A clustering method to characterize intermittent bursts of turbulence and interaction with submeso motions in the stable boundary layer. Journal of the Atmospheric Sciences, 72 (1). ISSN Online: 1520-0469 Print: 0022-4928 Vater, S. and Beisiegel, N. and Behrens, J. (2015) A limiter-based well-balanced discontinuous Galerkin method for shallow-water flows with wetting and drying: One-dimensional case. Advances in Water Resources, 85 . pp. 1-13. ISSN 0309-1708 Kim, W.K. and Netz, R.R. (2015) The mean shape of transition and first-passage paths. J. Chem. Phys., 143 (224108). Gräser, C. (2015) A note on Poincaré- and Friedrichs-type inequalities. arXiv:1512.02842 . (Submitted) Vener, M. V. and Odinokov, A. V. and Wehmeyer, C. and Sebastiani, D. (2015) The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations. The Journal of Chemical Physics, 142 (21). p. 215106. ISSN 0021-9606 Wu, H. and Mey, A.S.J.S. and Rosta, E. and Noé, F. (2014) Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states. J. Chem. Phys., 141 (21). p. 214106. Neu, V. and Bielow, C. and Reinert, K. and Huber, C. G. (2014) Ultrahigh-performance liquid chromatography-ultraviolet absorbance detection-high-resolution-mass spectrometry combined with automated data processing for studying the kinetics of oxidative thermal degradation of thyroxine in the solid state. Journal of chromatography A, 1371 . pp. 196-203. Meixenberger, K. and Yousef, K. P. and Somogyi, S. and Fiedler, S. and Bartmeyer, B. and von Kleist, M. and Kücherer, C. (2014) Characterization of natural polymorphic sites of the HIV-1 integrase before the introduction of HIV-1 integrase inhibitors in Germany. J Int AIDS Soc., 17 (4 Suppl 3). p. 19746. Schlutow, M. and Becker, E. and Körnich, H. (2014) Positive definite and mass conserving tracer transport in spectral GCMs. Journal of Geophysical Research Atmospheres . Gräser, C. and Kornhuber, R. and Sack, U. (2014) Numerical simulation of coarsening in binary solder alloys. Computational Materials Science, 93 . pp. 221-233. ISSN 0927-0256 Gräser, C. and Sander, O. (2014) Polyhedral Gauß-Seidel converges. Journal of Numerical Mathematics, 22 (3). pp. 221-254. ISSN 1570-2820 Mey, A.S.J.S. and Wu, H. and Noé, F. (2014) xTRAM: Estimating equilibrium expectations from time-correlated simulation data at multiple thermodynamic states. Phys. Rev. X, 4 (4). 041018. Hauswedell, H. and Singer, J. and Reinert, K. (2014) Lambda: the local aligner for massive biological data. Bioinformatics (Oxford, England), 30 (17). i349-i355. Berg, M. and Accardi, A. and Paulus, B. and Schmidt, B. (2014) Rotationally Adiabatic Pair Interactions of para- and ortho-Hydrogen with the Halogen Molecules F2, Cl2 and Br2. J. Chem. Phys., 141 (7). 074303. Walzer, M. and Pernas, L. E. and Nasso, S. and Bittremieux, W. and Nahnsen, S. and Kelchtermans, P. and Pichler, P. and van den Toorn, H. W. P. and Staes, A. and Vandenbussche, J. and Mazanek, M. and Taus, T. and Scheltema, R. A. and Kelstrup, C. D. and Gatto, L. and van Breukelen, B. and Aiche, S. and Valkenborg, D. and Laukens, K. and Lilley, K. S. and Olsen, J. V. and Heck, A. J. R. and Mechtler, K. and Aebersold, R. and Gevaert, K. and Vizcaino, J. A. and Hermjakob, H. and Kohlbacher, O. and Martens, L. (2014) qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments. Molecular & Cellular Proteomics, 13 (8). pp. 1905-1913. ISSN 1535-9476 Muehlhans, S. and von Kleist, M. and Gretchuka, T and Martin, T. and Fegeler, U. and Maurer, W. and Namazova-Baranova, L. and Gaedicke, G. and Baranov, A. and Rath , B. (2014) Awareness and Utilization of Standards and Pathways for the Reporting of Adverse Events Following Immunization among Pediatricians in Russia and Germany. Pediatric Drugs, 16 (4). pp. 31-330. ISSN 1174-5878 (Print) 1179-2019 (Online) Rahn, R. and Weese, D. and Reinert, K. (2014) Journaled string tree--a scalable data structure for analyzing thousands of similar genomes on your laptop. Bioinformatics . ISSN Online ISSN 1460-2059 - Print ISSN 1367-4803 Trappe, K. and Emde, A.-K. and Ehrlich, H.-C. and Reinert, K. (2014) Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone. Bioinformatics, 30 (24). pp. 3484-3490. ISSN 1367-4803 Hoffmann, M. J. and Matera, S. and Reuter, K. (2014) kmos: A lattice kinetic Monte Carlo framework. Computer Physics Communications, 185 (7). pp. 2138-2150. Pluharova, E. and Baer, M. and Mundy, Ch. and Schmidt, B. and Jungwirth, P. (2014) Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics. J. Phys. Chem. Lett., 5 (13). pp. 2235-2240. Schmidt, B. and Friedrich, B. (2014) Supersymmetry and eigensurface topology of the planar quantum pendulum. Front. Physics, 2 . p. 37. Sarich, M. and Djurdjevac, N. and Bruckner, S. and Conrad, T. O. F. and Schütte, Ch. (2014) Modularity revisited: A novel dynamics-based concept for decomposing complex networks. Journal of Computational Dynamics, 1 (1). pp. 191-212. ISSN 2158-2491 Kornhuber, R. and Schwab, C. and Wolf, M.W. (2014) Multilevel Monte Carlo finite element methods for stochastic elliptic variational inequalities. SIAM Journal on Numerical Analysis, 52 (3). pp. 1243-1268. ISSN 0036-1429 Manz, J. and Schild, A and Schmidt, B. and Yonggang, Y (2014) Maximum tunneling velocities in symmetric double well potentials. Chem. Phys., 442 . pp. 9-17. Katchanov, J. and von Kleist, M. and Arasteh, K. and Stocker, H. (2014) “Time-to-Amphotericin B” in Cryptococcal Meningitis in a European Low-Prevalence Setting: Analysis of Diagnostic Delays. QJM: An International Journal of Medicine, 107 (10). pp. 799-803. ISSN 1460-2393 Kehr, B. and Trappe, K. and Holtgrewe, M. and Reinert, K. (2014) Genome alignment with graph data structures: a comparison. BMC Bioinformatics, 15 . ISSN 1471-2105 Dommert, F. and Wendler, K. and Qiao, B. and Delle Site, L. (2014) Generic force fields for ionic liquids. Journal of Molecular Liquids, 192 . pp. 32-37. ISSN 0167-7322 Chen, X. and Yousef, K. P. and Duwe, S. and Karsch, K. and Grover, S. and Wählisch, S. and Obermeier, P. and Tief, F. and Muehlhans, S. and Seeber, L. and von Kleist, M. and Schweiger, B. and Rath , B. (2014) Quantitative influenza follow-up testing (QIFT) - a novel biomarker for the monitoring of disease activity at the point-of-care. PLoS ONE, 9 (3). ISSN 1932-6203 Wang, H. and Schütte, Ch. and Ciccotti, G. and Delle Site, L. (2014) Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation. Journal of Chemical Theory and Computation, 10 (4). pp. 1376-1386. ISSN 1549-9618 Parsa, A. M. and Kozhan, I. and Wulkow, M. and Hutchinson, R. A. (2014) Modeling of Functional Group Distribution in Copolymerization: A Comparison of Deterministic and Stochastic Approaches. Macromolecular Theory and Simulations, 23 (3). pp. 207-217. ISSN 10221344 Wandelt, S. and Deng, D. and Gerdjikov, S. and Mishra, S. and Mitankin, P. and Patil, M. and Siragusa, E. and Tiskin, A. and Wang, W. and Wang, J. and Leser, U. (2014) State-of-the-art in String Similarity Search and Join. SIGMOD Record, 43 (1). Hu, J. and Kehr, B. and Reinert, K. (2014) NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. Bioinformatics, 30 (4). pp. 540-548. ISSN 1367-4803 Latorre, J.C. and Kramer, P. R. and Pavliotis, G. A. (2014) Numerical methods for computing effective transport properties of flashing Brownian motors. Journal of Computational Physics, 257 (Part A). pp. 57-82. ISSN 0021-9991 Zhu, J. and Zhang, P. and Wang, H. and Delle Site, L. (2014) Is there a third order phase transition for supercritical fluids? The Journal of Chemical Physics, 140 (1). 014502. ISSN 00219606 Delle Site, L. (2014) What is a Multiscale Problem in Molecular Dynamics? Entropy (Special Issue), 16 (1). pp. 23-40. ISSN 1099-4300 Berninger, H. and Loisel, S. and Sander, O. (2014) The 2-Lagrange multiplier method applied to nonlinear transmission problems for the Richards equation in heterogeneous soil with cross points. SIAM J. Sci. Comput., 36 (5). A2166-A2198. ISSN 1064-8275 Yelash, L. and Müller, A. and Lukacova-Medvidova, M. and Giraldo, F.X. and Wirth, V. (2014) Adaptive discontinuous evolution Galerkin method for dry atmospheric flow. Journal of Computational Physics, 268C . 106 -133. ISSN 0021-9991 Zhang, W. and Wang, H. and Hartmann, C. and Weber, M. and Schütte, Ch. (2014) Applications of the cross-entropy method to importance sampling and optimal control of diffusions. SIAM J. Sci. Comput., 36 (6). A2654-A2672. ISSN 1064-8275 Meixenberger, K. and Hauser, A. and Jansen, K. and Yousef, K. P. and Fiedler, S. and von Kleist, M. and Norley, S. and Somogyi, S. and Hamouda, O. and Bannert, N. and Bartmeyer, B. and Kücherer, C. (2014) Assessment of ambiguous base calls in HIV-1 pol population sequences as a biomarker to identify recent infections in HIV-1 incidence studies. Journal of Clinical Microbiology, 52 (8). pp. 2977-2983. ISSN 0095-1137 Vincze, M. and Borchert, S. and Achatz, U. and von Larcher, T. and Baumann, M. and Hertel, C. and Remmler, S. and Beck, T. and Alexandrov, K. and Egbers, C. and Froehlich, J. and Heuveline , V. and Hickel, S. and Harlander, U. (2014) Benchmarking in a rotating annulus: a comparative experimental and numerical study of baroclinic wave dynamics. Meteorologische Zeitschrift . Agarwal, A. and Wang, H. and Schütte, Ch. and Delle Site, L. (2014) Chemical potential of liquids and mixtures via Adaptive Resolution Simulation. Journal of Chemical Physics, 141 (3). ISSN 0021-9606 Ziemer, C. and Wacker, U. (2014) A Comparative Study of B , Γ and Log Normal Distributions in a Three Moment Parameterization for Drop Sedimentation. Atmosphere, 5 (3). pp. 484-517. Ziemer, C. and Wacker, U. (2014) A Comparative Study of B-, Γ- and Log-Normal Distributions in a Three-Moment Parameterization for Drop Sedimentation. Atmosphere, 5 (3). pp. 484-517. ISSN 2073-4433 Keller, B. and Kobitski, A. and Jäschke, A. and Nienhaus, G.U. and Noé, F. (2014) Complex RNA folding kinetics revealed by single molecule FRET and hidden Markov models. J. Am. Chem. Soc., 136 . pp. 4534-4543. Kabbe, G. and Wehmeyer, C. and Sebastiani, D. (2014) A Coupled Molecular Dynamics/Kinetic Monte Carlo Approach for Protonation Dynamics in Extended Systems. Journal of Chemical Theory and Computation, 10 (10). p. 4221. ISSN 1549-9618 de Wiljes, J. and Putzig, L. and Horenko, I. (2014) Discrete nonhomogeneous and nonstationary logistic and Markov regression models for spatiotemporal data with unresolved external influences. Communications in Applied Mathematics & Computational Science, 9 . pp. 1-46. ISSN 1559-3940 von Rudorff, G. F. and Wehmeyer, C. and Sebastiani, D. (2014) Efficient implementation and application of the artificial bee colony algorithm to low-dimensional optimization problems. Computer Physics Communications, 185 (6). p. 1639. ISSN 00104655 Schöneberg, J. and Heck, M. and Hofmann, K. P. and Noé, F. (2014) Explicit Spatio-temporal Simulation of Receptor-G Protein Coupling in Rod Cell Disk Membranes. Biophys. J., 107 . pp. 1042-1053. ISSN 00063495 van der Velde, Y. and Vercauteren, N. and Jaramillo, F. and Dekker, S.C. and Destouni, G. and Lyon, S.W. (2014) Exploring hydroclimatic change disparity via the Budyko framework. Hydrological Processes, 28 (13). pp. 4110-4118. ISSN 1099-1085 Schulz, M. H. and Weese, D. and Holtgrewe, M. and Dimitrova, V. and Niu, S. and Reinert, K. and Richard, H. (2014) Fiona: a parallel and automatic strategy for read error correction. Bioinformatics, 30 (17). i356-i363. Vetter, A. and Sander, O. and Duda, G. and Weinkamer, R. (2014) Healing of a mechano-responsive material. Europhysics Letters (EPL), 104 (6). pp. 1-6. ISSN 0295-5075 Siewert, C. and Bordás, R. and Wacker, U. and Beheng, K.D. and Kunnen, R. P. J. and Meinke, M. and Schröder, W. and Thévenin, D. (2014) Influence of turbulence on the drop growth in warm clouds, Part I: comparison of numerically and experimentally determined collision kernels. Meteorologische Zeitschrift, 23 (4). 397 -410. Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2014) Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1. Communications in Mathematical Sciences, 12 (5). pp. 859-877. ISSN 1539-6746 Chodera, J. D. and Noé, F. (2014) Markov state models of biomolecular conformational dynamics. Curr. Opin. Struct. Biol., 25 . pp. 135-144. Lie, Han Cheng and Schütte, Ch. and Hartmann, C. (2014) Martingale-based gradient descent algorithm for estimating free energy values of diffusions. SIAM J. Sci. Comput. . ISSN 1064-8275 (Submitted) Jasor, G. and Wacker, U. and Beheng, K.D. and Polifke, W. (2014) Modeling artifacts in the simulation of the sedimentation of raindrops with a Quadrature Method of Moments. Meteorologische Zeitschrift, 23 (4). pp. 369-385. Jouvet, G. and Funk, M. (2014) Modelling the trajectory of the corpses of mountaineers who disappeared in 1926 on Aletschgletscher, Switzerland. Journal of Glaciology, 60 (220). pp. 255-261. ISSN 0022-1430 von Larcher, T. and Dörnbrack, A. (2014) Numerical simulations of baroclinic driven flows in a thermally driven rotating annulus using the immersed boundary method. Meteorologische Zeitschrift . ISSN 0941-2948 Muraschko, J and Fruman, M. D. and Achatz, U. and Hickel, S. and Toledo, Y. (2014) On the application of WKB theory for the simulation of the weakly nonlinear dynamics of gravity waves. Quarterly Journal of the Royal Meteorological Society . Schillings, Claudia and Schulz, Volker (2014) On the influence of robustness measures on shape optimization with stochastic uncertainties. Optimization and Engineering, 16 . pp. 347-386. ISSN 1573-2924; Print 1389-4420 Hartmann, C. and Latorre, J.C. and Pavliotis, G. A. and Zhang, W. (2014) Optimal control of multiscale systems using reduced-order models. J. Computational Dynamics, 1 (2). pp. 279-306. ISSN 2158-2505 Wu, H. and Noé, F. (2014) Optimal estimation of free energies and stationary densities from multiple biased simulations. SIAM Multiscale Model. Simul., 12 . pp. 25-54. Koltai, Péter and Volf, Alexander (2014) Optimizing the stable behavior of parameter-dependent dynamical systems --- maximal domains of attraction, minimal absorption times. Journal of Computational Dynamics, 1 (2). pp. 339-356. ISSN 2158-2491 Matera, S. and Maestri, M. and Cuoci, A. and Reuter, K. (2014) Predictive-Quality Surface Reaction Chemistry in Real Reactor Models: Integrating First-Principles Kinetic Monte Carlo Simulations into Computational Fluid Dynamics. ACS Catalysis, 4 (11). pp. 4081-4092. Ziemer, C. and Jasor, G. and Wacker, U. and Beheng, K.D. and Polifke, W. (2014) Quantitative comparison of presumed number density and quadrature moment methods for the parameterisation of drop sedimentation. Meteorologische Zeitschrift, 23 (4). pp. 411-423. Accardi, A. and Schmidt, B. (2014) Quantum effects on translation and rotation of molecular chlorine in solid para-hydrogen. (Unpublished) Vollmer, J. and Papke, A. and Rohloff, M. (2014) Ripening and Focusing of Aggregate Size Distributions with Overall Volume Growth. Frontiers in Physics, 2 (18). Vercauteren, N. and Lyon, S.W. and Destouni, G. (2014) Seasonal influence of insolation on fine-resolved air temperature variation and snowmelt. Journal of Applied Meteorology and Climatology, 53 (2). pp. 323-332. ISSN Online: 1558-8432 Print: 1558-8424 Bobusch, B. and Berndt, P. and Paschereit, O. C. and Klein, R. (2014) Shockless explosion combustion: An innovative way of efficient constant volume combustion in gas turbines. Combustion Science and Technology, 186 (10-11). pp. 1680-1689. Bauer, M. and Baumann, M. and Scheck, L. and Gassmann, A. and Heuveline , V. and Jones, S. (2014) Simulation of tropical-cyclone-like vortices in shallow-water ICON-hex using goal-oriented r-adaptivity. Theoretical and Computational Fluid Dynamics, 28 (1). pp. 107-128. ISSN Print: 0935-4964 Online:1432-2250 Schöneberg, J. and Ullrich, Alexander and Noé, F. (2014) Simulation tools for particle-based reaction-diffusion dynamics in continuous space. BMC Biophysics, 7 . p. 11. Schillings, Claudia and Schwab, Christoph (2014) Sparsity in Bayesian inversion of parametric operator equations. Inverse Problems, 30 (6). Hédin, F. and Plattner, N. and Doll, J. D. and Meuwly, M. (2014) Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules. Journal of Chemical Theory and Computation, 10 (10). pp. 4284-4296. ISSN 1549-9618 Remmler, S. and Hickel, S. (2014) Spectral eddy viscosity of stratified turbulence. Journal of Fluid Mechanics . (In Press) Prinz, J.-H. and Chodera, J. D. and Noé, F. (2014) Spectral rate theory for two-state kinetics. Phys Rev X, 4 . 011020. Schmidt, B. and Friedrich, B. (2014) Topology of surfaces for molecular Stark energy, alignment and orientation generated by combined permanent and induced electric dipole interactions. J. Chem. Phys., 140 (6). 064317. Gräser, C. and Sander, O. (2014) Truncated nonsmooth Newton multigrid methods for simplex-constrained minimization problems. Preprint 384, IGPM Aachen . (Submitted) Queck, R. and Bernhofer, C. and Bienert, A. and Eipper, T. and Goldberg, V. and Harmansa, S. and Hildebrand, V. and Maas, H.-G and Schlegel, F. and Stiller, J. (2014) TurbEFA: an interdisciplinary effort to investigate the turbulent flow across a forest clearing. Meteorologische Zeitschrift, 1 . Berninger, H. and Ohlberger, M. and Sander, O. and Smetana, K. (2014) Unsaturated subsurface flow with surface water and nonlinear in- and outflow conditions. Mathematical Models and Methods in Applied Sciences, 24 (5). pp. 901-936. ISSN 1793-6314 Nüske, F. and Keller, B. and Pérez-Hernández, G. and Mey, A.S.J.S. and Noé, F. (2014) Variational Approach to Molecular Kinetics. J. Chem. Theory Comput., 10 . pp. 1739-1752. Sander, O. and Schiela, A. (2014) Variational analysis of the coupling between a geometrically exact Cosserat rod and an elastic continuum. Zeitschrift für Angewandte Mathematik und Physik (ZAMP), 65 (6). pp. 1261-1288. ISSN 0044-2275 (Print) 1420-9039 (Online) Oevermann, M. and Klein, R. (2014) An asymptotic solution approach for elliptic equations with discontinuous coefficients. Journal of Computational Physics, 261 . pp. 230-243. Benacchio, T. and O'Neill, W.P. and Klein, R. (2014) A blended soundproof-to-compressible numerical model for small- to mesoscale atmospheric dynamic. Monthly Weather Review, 142 (12). pp. 4416-4438. ISSN Online:1520-0493; Print: 0027-0644 Plattner, N. and Meuwly, M. (2014) The effect of classical and quantum dynamics on vibrational frequency shifts of H2 in clathrate hydrates. The Journal of Chemical Physics, 140 (2). 024311. ISSN 0021-9606 Vincze, M. and Harlander, U. and von Larcher, T. and Egbers, C. (2014) An experimental study of regime transitions in a differentially heated baroclinic annulus with flat and sloping bottom topographies. Nonlinear Processes in Geophysics, 21 . pp. 237-250. O'Neill, W.P. and Klein, R. (2014) A moist pseudo-incompressible model. Atmospheric Research, 142 (1). pp. 133-141. Gerber, S. and Oevermann, M. (2014) A two dimensional Euler–Lagrangian model of wood gasification in a charcoal bed – Part I: model description and base scenario. Science Direct, 115 . pp. 385-400. Hartmann, C. and Banisch, Ralf and Sarich, M. and Badowski, T. and Schütte, Ch. (2013) Characterization of Rare Events in Molecular Dynamics. Entropy (Special Issue), 16 (1). pp. 350-376. ISSN 1099-4300 Delle Site, L. (2013) Multidisziplinarität in Deutschland: Mehrwert oder Beschränkung? Physik Journal (12). p. 17. Pluharova, E. and Marsalek, O. and Schmidt, B. and Jungwirth, P. (2013) Ab Initio Molecular Dynamics Approach to Quantitative Description of Ion Pairing in Water. J. Phys. Chem. Lett., 4 (23). pp. 4177-4181. Haack, F. and Fackeldey, K. and Röblitz, S. and Scharkoi, O. and Weber, M. and Schmidt, B. (2013) Adaptive spectral clustering with application to tripeptide conformation analysis. J. Chem. Phys., 139 (19). p. 194110. Paulus, F. and Weiss, M. E. R. and Steinhilber, D. and Nikitin, A. and Schütte, Ch. and Haag, R. (2013) Anionic Ring-Opening Polymerization Simulations for Hyperbranched Polyglycerols with Defined Molecular Weights. Macromolecules, 46 (21). pp. 8458-8466. ISSN 0024-9297 Steijger, T. and Abril, J. F. and Engström, P. G. and Kokocinski, F. and The RGASP Consortium and Richard, H. and Schulz, M. H. and Weese, D. and Hubbard, T. and Guigó, R. and Harrow, J. and Bertone, P. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nature Methods, 10 (12). pp. 1177-1184. Jouvet, G. and Gräser, C. (2013) An adaptive Newton multigrid method for a model of marine ice sheets. Journal of Computational Physics, 252 . pp. 419-437. ISSN 0021-9991 Wang, H. and Hartmann, C. and Schütte, Ch. (2013) Linear response theory and optimal control for a molecular system under nonequilibrium conditions. Molecular Physics, 111 . pp. 3555-3564. ISSN 0026-8976 Hartmann, C. and Yanao, Tomohiro (2013) The falling cat problem and shape effects in small molecules in a random environment: a case study. Molecular Physics, 111 (22-23). pp. 3534-3545. ISSN 0026-8976 Gräser, C. and Kornhuber, R. and Sack, U. (2013) Time discretizations of anisotropic Allen-Cahn equations. IMA Journal of Numerical Analysis, 33 (4). pp. 1226-1244. ISSN 0272-4979 Andreotti, S. and Reinert, K. and Canzar, S. (2013) The duplication-loss small phylogeny problem: from cherries to trees. Journal of Computational Biology, 20 (9). pp. 643-59. Nikitin, A. and Wulkow, M. and Schütte, Ch. (2013) Modeling of Free Radical Styrene/Divinylbenzene Copolymerization with the Numerical Fractionation Technique. Macromolecular Theory and Simulation, 22 (9). pp. 475-489. Enciso , M. and Schütte, Ch. and Delle Site, L. (2013) pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study. Molecular Physics, 111 (22-23). pp. 3363-3371. ISSN 0026-8976 Pattyn, F. and Perichon, L. and Durand, G. and Favier, L. and Gagliardini, O. and Hindmarsh, R. and Zwinger, T. and Albrecht, T. and Cornford, S. and Docquier, D. and Fuerst, J. and Goldberg, G. and Gudmundsson, G. H. and Humbert, A. and Huetten, M. and Huybrechts, P. and Jouvet, G. and Kleiner, T. and Larour, E. and Martin, D. (2013) Grounding-line migration in plan-view marine ice-sheet models: Results of the ice2sea MISMIP3d intercomparison. Journal of Glaciology, 59 (215). pp. 410-422. ISSN 0022-1430 Gul, Rahim and Bernhard, Stefan (2013) Local sensitivity analysis of cardiovascular system parameters. International Journal of Scientific and Engineering Research (IJSER), 4 (7). pp. 2648-2661. ISSN 2229-5518 Sander, O. and Klapproth, C. and Youett, J. and Kornhuber, R. and Deuflhard, P. (2013) Towards an efficient numerical simulation of complex 3D knee joint motion. Computing and Visualization in Science, 16 (3). pp. 119-138. ISSN 1432-9360 Vercauteren, N. and Destouni, G. and Dahlberg, C.J. and Hylander, K. (2013) Fine-resolved, near-coastal spatiotemporal variation of temperature in response to insolation. Journal of Applied Meteorology and Climatology, 52 (5). pp. 1208-1220. ISSN Online: 1558-8432 Print: 1558-8424 Leichtle, A. and Ceglarek, U. and Weinert, P. and Nakas, C. T. and Nuoffer, J.-M. and Kase, J. and Conrad, T. O. F. and Witzigmann, H. and Thiery, J. and Fiedler, G. M. (2013) Pancreatic carcinoma, pancreatitis, and healthy controls - metabolite models in a three-class diagnostic dilemma. Metabolomics, 9 (3). pp. 677-687. ISSN 1573-3890 Rath, B. A. and Yousef, K. P. and Katzenstein, D. K. and Shafer, R. W. and Schütte, Ch. and von Kleist, M. and Merigan, T. C. (2013) In vitro HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitors & In Silico Phenotypic Analysis. PLoS ONE, 8 (4). e61102. ISSN 1932-6203 Blomberg, S. and Hoffmann, M. and Gustafson, J. and Martin, N. M. and Fernandes, V. R. and Borg, A. and Liu, Z. and Chang, R. and Matera, S. and Reuter, K. and Lundgren, E. (2013) In Situ X-Ray Photoelectron Spectroscopy of Model Catalysts: At the Edge of the Gap. Physical Review Letters, 110 (11). p. 117601. Nahnsen, S. and Bielow, C. and Reinert, K. and Kohlbacher, O. (2013) Tools for Label-free Peptide Quantification. Molecular & Cellular Proteomics, 12 (3). pp. 549-556. ISSN 1535-9476 Zerck, A. and Nordhoff, E. and Lehrach, H. and Reinert, K. (2013) Optimal precursor ion selection for LC-MALDI MS/MS. BMC Bioinformatics, 14 (1). p. 56. ISSN 1471-2105 Neu, V. and Bielow, C. and Gostomski, I. and Wintringer, R. and Braun, R. and Reinert, K. and Schneider, P. and Stuppner, H. and Huber, C. (2013) Rapid and Comprehensive Impurity Profiling of Synthetic Thyroxine by Ultrahigh-Performance Liquid Chromatography–High-Resolution Mass Spectrometry. Analytical Chemistry, 85 (6). pp. 3309-3317. ISSN 0003-2700 Pérez-Hernández, G. and Schmidt, B. (2013) Anisotropy of the Water-Carbon Interaction: Molecular Simulations of Water in Low-Diameter Carbon Nano-Tubes. Phys. Chem. Chem. Phys., 15 (14). pp. 4995-5006. Latorre, J.C. and Pavliotis, G. A. and Kramer, P. R. (2013) Corrections to Einstein's relation for Brownian motion in a tilted periodic potential. J. Stat. Phys., 150 (4). pp. 776-803. ISSN 0022-4715 Siragusa, E. and Weese, D. and Reinert, K. (2013) Fast and accurate read mapping with approximate seeds and multiple backtracking. Oxford Journals, 41 (7). e78. ISSN Print ISSN 0305-1048; Online ISSN 1362-4962 Neu, V. and Bielow, C. and Schneider, P. and Reinert, K. and Stuppner, H. and Huber, C. (2013) Investigation of Reaction Mechanisms of Drug Degradation in the Solid State: A Kinetic Study Implementing Ultrahigh-Performance Liquid Chromatography and High-Resolution Mass Spectrometry for Thermally Stressed Thyroxine. Analytical Chemistry, 85 (4). pp. 2385-2390. ISSN 0003-2700 Rath, B. and von Kleist, M. and Castillo, M. E. and Kolevic, L. and Caballero, P. and Soto-Castellares, G. and Amedee, A. M. and Robinson, J.E. and Katzenstein, D. K. and Van Dyke, R.B. and Oberhelman, R. (2013) Antiviral Resistance and Correlates of Virologic Failure in the first Cohort of HIV-Infected Children Gaining Access to Structured Antiretroviral Therapy in Lima, Peru: A Cross-Sectional Analysis. BMC Infectious Diseases, 13 (1). Sarich, M. and Banisch, Ralf and Hartmann, C. and Schütte, Ch. (2013) Markov State Models for Rare Events in Molecular Dynamics. Entropy (Special Issue), 16 (1). pp. 258-286. ISSN 1099-4300 Benacchio, T. and Bonaventura, L. (2013) Absorbing boundary conditions: a spectral collocation approach. International Journal for Numerical Methods in Fluids, 72 (10.1002/fld.3768). pp. 913-936. ISSN Online: 1097-0363 Gupta, Pooja and Reinsch , Norbert and Spötter, Andreas and Conrad, T. O. F. and Bienefeld, Kaspar (2013) Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera). BMC Genetics, 14 (36). Hartmann, C. and Schäfer-Bung, B. and Thöns-Zueva, A. (2013) Balanced averaging of bilinear systems with applications to stochastic control. SIAM J. Control Optim., 51 (3). pp. 2356-2378. Kantcheva, A. K. and Quick, M. and Shi, L. and Winther, A.-M. L. and Stolzenberg, S. and Weinstein, H. and Javitch, J. A. and Nissen, P. (2013) Chloride binding site of neurotransmitter sodium symporters. Proceedings of the National Academy of Sciences, 110 (21). p. 8489. ISSN 0027-8424 Wolf, S and Hinkel, J., and Hallier, M. and Bisaro, A. and Lincke, D. and Ionescu, C. and Klein, R.J.T. (2013) Clarifying vulnerability definitions and assessments using formalisation. International Journal of Climate Change Strategies and Management, 5 (1). ISSN 1756-8692 Kumar, B. and Schumacher, J. and Shaw, R.A. (2013) Cloud microphysical effects of turbulent mixing and entrainment. Theoretical and Computational Fluid Dynamics , 27 (3-4). pp. 361-376. ISSN Print: 0935-4964; Online: 1432-2250 Müller, A. and Behrens, J. and Giraldo, F.X. and Wirth, V. (2013) Comparison between adaptive and uniform discontinuous Galerkin simulations in dry 2D bubble experiments. Journal of Computational Physics, 235 . pp. 371-393. Remmler, S. and Fruman, M. D. and Hickel, S. (2013) Direct numerical simulation of a breaking inertia-gravity wave. Journal of Fluid Mechanics, 722 . pp. 424-436. Lindner, Benjamin and Yi, Zheng and Prinz, J.-H. and Smith, J. C. and Noé, F. (2013) Dynamic Neutron Scattering from Conformational Dynamics I: Theory and Markov models. J. Chem. Phys., 139 . p. 175101. Yi, Zheng and Lindner, Benjamin and Prinz, J.-H. and Noé, F. and Smith, J. C. (2013) Dynamic Neutron Scattering from Conformational Dynamics II: Application using Molecular Dynamics Simulation and Markov modeling. J. Chem. Phys., 139 . p. 175102. Trendelkamp-Schroer, B. and Noé, F. (2013) Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution. J. Phys. Chem., 138 . p. 164113. Delle Site, L. and Ghiringhelli, L. M. and Ceperley, D.M. (2013) Electronic Energy Functionals: Levy-Lieb principle within the Ground State Path Integral Quantum Monte Carlo. International Journal of Quantum Chemistry, 113 . p. 155. Bordás, R. and Roloff, CH. and Thévenin, D. and Shaw, R.A. (2013) Experimental determination of droplet collision rates in turbulence. New Journal of Physics, 15 (045010 ). Bruckner, S. and Kayser, B. and Conrad, T. O. F. (2013) Finding Modules in Networks with Non-modular Regions. Lecture Notes in Computer Science (Proceedings of SEA 2013), 7933 . pp. 188-199. ISSN 0302-9743 Wang, H. and Hartmann, C. and Schütte, Ch. and Delle Site, L. (2013) Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique. Phys. Rev. X, 3 . 011018. Braack, M. and Taschenberger, N. (2013) Hierarchical a posteriori residual based error estimators for bilinear finite elements. Int. J. Numer. Anal. Model., 10 (2). pp. 466-480. (Submitted) Pérez-Hernández, G. and Paul, F. and Giorgino, T. and de Fabritiis, G. and Noé, F. (2013) Identification of slow molecular order parameters for Markov model construction. J. Chem. Phys., 139 . 015102. Peuker, Sebastian and Cukkemane, Abhishek and Held, M. and Noé, F. and Kaupp, Benjamin and Seifert, Reinhard (2013) Kinetics of ligand-receptor interaction reveals an induced-fit mode of binding in a cyclic nucleotide-activated protein. Biophys. J., 104 . pp. 63-74. Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2013) Markov Control Processes with Rare State Observation: Sensitivity Analysis with Respect to Optimal Treatment Strategies against HIV-1. International Journal of Biomathematics and Biostatistics, 2 (1). ISSN 0973-7340 Banisch, Ralf and Hartmann, C. (2013) Meshless discretization of LQ-type stochastic control problems. arXiv preprint, arXiv: . (Unpublished) Kanda, M. and Inagaki, A. and Miyamoto, T. and Gryschka, M. and Raasch, S. (2013) A New Aerodynamic Parameterization for Real Urban Surfaces. Boundary-Layer Meteorology, 148 . pp. 357-377. Gräser, C. (2013) Nonsmooth Schur-Newton methods for nonsmooth saddle point problems. Preprint 1004, Matheon Berlin . Hardering, H. (2013) Numerical approximation of capillary surfaces in a negative gravitational field. Interfaces and Free Boundaries, 15 (3). pp. 263-280. ISSN 1463-9971 Kunnen, R. P. J. and Siewert, C. and Meinke, M. and Schröder, W. and Beheng, K.D. (2013) Numerically determined geometric collision kernels in spatially evolving isotropic turbulence relevant for droplets in clouds. Atmospheric Research, 127 . pp. 8-21. ISSN 0169-8095 Siewert, C. and Kunnen, R. P. J. and Meinke, M. and Schröder, W. (2013) Orientation Statistics and Settling Velocity of Ellipsoids in Decaying Turbulence. Atmospheric Research . (In Press) Plattner, N. and Doll, J. D. and Meuwly, M. (2013) Overcoming the Rare Event Sampling Problem in Biological Systems with Infinite Swapping. Journal of Chemical Theory and Computation, 9 (9). pp. 4215-4224. ISSN 1549-9618 Noé, F. and Wu, H. and Prinz, J.-H. and Plattner, N. (2013) Projected and Hidden Markov Models for calculating kinetics and metastable states of complex molecules. J. Chem. Phys., 139 . p. 184114. Schöneberg, J. and Noé, F. (2013) ReaDDy - a software for particle based reaction diffusion dynamics in crowded cellular environments. PLoS ONE, 8 . e74261. ISSN 1932-6203 Scheck, L. and Jones, S. and Heuveline , V. (2013) Singular Vectors for barotropic, hurricane-like vortices in horizontal shear: Structure and perturbation growth mechanisms. Journal of the Atmospheric Sciences . ISSN Online: 1520-0469 Print: 0022-4928 (Submitted) Schillings, Claudia and Schwab, Christoph (2013) Sparse, adaptive Smolyak quadratures for Bayesian inverse problems. Inverse Problems, 29 (6). Posor, Y. and Eichhorn-Gruenig, M. and Puchkov, D. and Schöneberg, J. and Ullrich, A. and Lampe, A. and Müller, R. and Zarbakhsh, S. and Gulluni, F. and Hirsch, E. and Krauss, M. and Schultz, C. and Schmoranzer, J. and Noé, F. and Haucke, V. (2013) Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate. Nature, 499 . pp. 233-237. Lie, Han Cheng and Fackeldey, Konstantin and Weber, Marcus (2013) A Square Root Approximation of Transition Rates for a Markov State Model. SIAM Journal on Matrix Analysis and Applications, 34 (2). p. 738. ISSN 0895-4798 Steger, Katrin and Bollmann, Stefan and Noé, F. and Doose, S. (2013) Systematic evaluation of fluorescence correlation spectroscopy data analysis on the nanosecond time scale. Phys. Chem. Chem. Phys., 15 . pp. 10435-10445. Rath , B. and Tief, F. and Karsch, K. and Muehlhans, S. and Obermeier, P. and Adamou, E. and Chen, X. and Seeber, L. and Peiser, Ch. and Hoppe, Ch. and von Kleist, M. and Conrad, T. O. F. and Schweiger, B. (2013) Towards a personalized approach to managing of influenza infections in infants and children - food for thought and a note on oseltamivir. Infectious Disorders - Drug Targets, 13 (1). pp. 25-33. ISSN 2212-3989 Münch, M. and Kaiser, G. (2013) Verbrennungsdynamik, Rauchgastoxizität und ihre Folgen. Eine kleine Argumentationshilfe für die Brandschutzaufklärung. schadenprisma, 1 . pp. 4-8. Wehmeyer, C. and Schrader, M. and Andrienko, D. and Sebastiani, D. (2013) Water-Free Proton Conduction in Hexakis(p-Phosphonatophenyl)benzene Nanochannels. The Journal of Physical Chemistry C, 117 (23). p. 12366. ISSN 1932-7447 Mischau, A. (2013) Wo ein Wille, da ein Weg? Die Integration von Gender(kompetenz) in die Lehramtsausbildung von Mathematik. Wissenschaftlerinnen-Rundbrief, 15 (2). pp. 7-10. ISSN ISBN: 987-3-929968-45-3 de Wiljes, J. and Majda, A.J. and Horenko, I. (2013) An adaptive Markov Chain Monte Carlo approach to time series clustering of processes with regime transition behavior. SIAM Multiscale Modeling & Simulation, 11 (2). pp. 415-441. ISSN print: 1540-3459; online: 1540-3467 Baldauf, M. and Brdar, S. (2013) An analytic solution for linear gravity waves in a channel as a test for numerical models using the non-hydrostatic, compressible Euler equations. Quarterly Journal of the Royal Meteorological Society . Rieper, F. and Hickel, S. and Achatz, U. (2013) A conservative integration of the pseudo-incompressible equations with implicit turbulence parameterization. Monthly Weather Review , 141 (3). pp. 861-886. ISSN Online: 1520-0493; Print: 0027-0644 von Larcher, T. and Fournier, A. and Hollerbach, R. (2013) The influence of a sloping bottom endwall on the linear stability in the thermally driven baroclinic annulus with a free surface. Theoretical and Computational Fluid Dynamics , 27 (3-4). pp. 433-451. ISSN Print: 0935-4964; Online: 1432-2250 Dolaptchiev, S. and Klein, R. (2013) A multi-scale model for the planetary and synoptic motions in the atmosphere. J. Atmos. Sci., 70 (9). pp. 2963-2981. ISSN Online:1520-0469; Print: 0022-4928 Jouvet, G. and Bueler, E. and Gräser, C. and Kornhuber, R. (2013) A nonsmooth Newton multigrid method for a hybrid, shallow model of marine ice sheets. Recent Advances in Scientific Computing and Applications, 586 . pp. 208-217. ISSN 0271-4132 Schillings, Claudia and Schwab, Christoph (2013) A note on sparse, adaptive Smolyak quadratures for Bayesian inverse problems. SAM Research Report, 06 . Enciso , M. and Schütte, Ch. and Delle Site, L. (2013) pH-dependent coarse-grained model of peptides. Soft Matter, 9 (26). pp. 6118-6127. Papke, A. and Battiato, I. (2013) A reduced complexity model for dynamic similarity in obstructed shear flows. Geophysical Research Letters, 40 (15). pp. 3888-3892. Noé, F. and Nüske, F. (2013) A variational approach to modeling slow processes in stochastic dynamical systems. SIAM Multiscale Model. Simul., 11 . pp. 635-655. Doll, J. D. and Plattner, N. and Freeman, D. L. and Liu, Y. and Dupuis, P. (2012) Rare-event sampling: Occupation-based performance measures for parallel tempering and infinite swapping Monte Carlo methods. The Journal of Chemical Physics, 137 (20). p. 204112. ISSN 00219606 Youett, J. and Sander, O. (2012) A dissipative discretization for large deformation frictionless dynamic contact problems. MATHEON Preprint #1184 . Pluharova, E. and Marsalek, O. and Schmidt, B. and Jungwirth, P. (2012) Peptide salt bridge stability: From gas phase via microhydration to bulk water simulations. J. Chem. Phys., 137 (18). p. 185101. Hartmann, C. and Schütte, Ch. (2012) Efficient rare event simulation by optimal nonequilibrium forcing. J. Stat. Mech. Theor. Exp., 2012 . P11004. Matera, S. and Reuter, K. (2012) When atomic-scale resolution is not enough: Spatial effects on in situ model catalyst studies. Journal of Catalysis, 295 . pp. 261-268. Lee, M. W. and Plattner, N. and Meuwly, M. (2012) Structure, spectroscopy and dynamics of layered H2O and CO2 ices. Physical Chemistry Chemical Physics, 14 (44). pp. 15464-15474. ISSN 1463-9076 Sarich, M. and Schütte, Ch. (2012) Approximating Selected Non-dominant Timescales by Markov State Models. Comm. Math. Sci., 10 (3). pp. 1001-1013. Weese, D. and Holtgrewe, M. and Reinert, K. (2012) RazerS 3: Faster, fully sensitive read mapping. Bioinformatics, 28 (20). pp. 2592-2599. Pérez-Hernández, G. and González-Vázquez, J. and González, L. (2012) IR Spectrum of FHF–and FDF–Revisited Using a Spectral Method in Four Dimensions. The Journal of Physical Chemistry A, 116 (46). pp. 11361-11369. ISSN 1089-5639 Wang, H. and Schütte, Ch. and Zhang, P. (2012) Error Estimate of Short-Range Force Calculation in the Inhomogeneous Molecular Systems. Phys. Rev. E, 86 (02). 026704. Schütte, Ch. and Winkelmann, S. and Hartmann, C. (2012) Optimal control of molecular dynamics using Markov state models. Math. Program. (Series B), 134 (1). pp. 259-282. Leichtle, A. and Nuoffer, J.-M. and Ceglarek, U. and Kase, J. and Conrad, T. O. F. and Witzigmann, H. and Thiery, J. and Fiedler, G. M. (2012) Serum amino acid profiles and their alterations in colorectal cancer. Metabolomics . ISSN 1573-3890 Wang, H. and Zhang, P. and Schütte, Ch. (2012) On the Numerical Accuracy of Ewald, Smooth Particle Mesh Ewald, and Staggered Mesh Ewald Methods for Correlated Molecular Systems. J. Chem. Theo. Comp., 8 (9). pp. 3243-3256. Buchholz, M. and Goletz, Ch.-M. and Grossmann, F. and Schmidt, B. and Heyda, J. and Jungwirth, P. (2012) Semiclassical Hybrid Approach to Condensed Phase Molecular Dynamics: Application to the I2Kr17 Cluster. J. Phys. Chem. A, 116 (46). pp. 11199-11210. Aiche, S. and Reinert, K. and Schütte, Ch. and Hildebrand, D. and Schlüter, H. and Conrad, T. O. F. (2012) Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs. PLoS ONE, 7 (7). e40656. ISSN 1932-6203 Junker, J. and Bielow, C. and Bertsch, A. and Sturm, M. and Reinert, K. and Kohlbacher, O. (2012) TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data. J. Proteome Res., 11 (7). pp. 3914-3920. ISSN 1535-3893 Sander, O. (2012) Geodesic finite elements on simplicial grids. International Journal for Numerical Methods in Engeneering, 92 (12). pp. 999-1025. ISSN Online: 1097-0207 Weiss, M. E. R. and Paulus, F. and Steinhilber, D. and Nikitin, A. and Haag, R. and Schütte, Ch. (2012) Estimating Kinetic Parameters for the Spontaneous Polymerization of Glycidol at Elevated Temperatures. MACROMOLECULAR THEORY and SIMULATIONS, 21 (7). pp. 470-481. Djurdjevac, N. and Bruckner, S. and Conrad, T. O. F. and Schütte, Ch. (2012) Random Walks on Complex Modular Networks. Journal of Numerical Analysis, Industrial and Applied Mathematics, 6 (1-2). pp. 29-50. ISSN 1790–8140 Higgins, C. W. and Froidevaux, M. and Simeonov, V. and Vercauteren, N. and Barry, C. and Parlange, M. B. (2012) The Effect of Scale on the Applicability of Taylor's Frozen Turbulence Hypothesis in the Atmospheric Boundary Layer. Boundary-Layer Meteorology, 143 (2). 379 -391. ISSN Print: 0006-8314 Online: 1573-1472 Andreotti, S. and Klau, G. W. and Reinert, K. (2012) Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) , 9 (2). pp. 385-394. Plattner, N. and Meuwly, M. (2012) Quantifying the Importance of Protein Conformation on Ligand Migration in Myoglobin. Biophysical Journal, 102 (2). pp. 333-341. ISSN 00063495 Emde, A.-K. and Schulz, M. H. and Weese, D. and Sun, R. and Vingron, M. and Kalscheuer, V. M. and Haas, S. A. and Reinert, K. (2012) Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics, 28 (5). pp. 619-627. Fritsch, S. and Poblete, S. and Junghans, C. and Ciccotti, G. and Delle Site, L. and Kremer, K. (2012) Adaptive Resolution Molecular Dynamics Simulation Through Coupling to an Internal Particle Reservoir. Physical Review Letters, 108 . p. 170602. Wang, H. and Schütte, Ch. and Delle Site, L. (2012) Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion. J. Chem. Theo. Comp., 8 (8). pp. 2878-2887. Metzner, Ph. and Putzig, L. and Horenko, I. (2012) Analysis of persistent non-stationary time series and applications. Communications in Applied Mathematics and Computational Science, 7 (2). pp. 175-229. Donadio, D. and Ghiringhelli, L. M. and Delle Site, L. (2012) Autocatalytic and cooperatively-stabilized dissociation of water on a stepped platinum surface. Journal of the American Chemical Society, 134 . pp. 19217-19222. Münch, M. (2012) Brände mit Beteiligung von Wärmedämmverbundsystemen. AIZ - Das Immobilienmagazin . pp. 52-55. Held, M. and Noé, F. (2012) Calculating kinetics and pathways of protein–ligand association. Eur. J. Cell Biol., 91 . pp. 357-364. Brdar, S. and Dedner, A. and Klöfkorn, R. (2012) Compact and stable Discontinuous Galerkin methods for convection-diffusion problems. SIAM Journal of Scientific Computation, 34 (1). 263-282 . ISSN Print: 1064-8275 Online: 1095-7197 Brdar, S. and Baldauf, M. and Dedner, A. and Klöfkorn, R. (2012) Comparison of dynamical cores for NWP models. Theoretical and Computational Fluid Dynamics . ISSN 0935-4964 (In Press) Mukherjee, B. and Delle Site, L. and Kremer, K. and Peter, C. (2012) Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions. Journal of Physical Chemistry B, 116 . 8474. Spötter, Andreas and Gupta, Pooja and Nürnberg, G. and Reinsch , Norbert and Bienefeld, Kaspar (2012) Development of a 44K SNP assay focussing on the analysis of a varroa-specific defence behaviour in honey bees (Apis mellifera carnica). Molecular Ecology Resources, 12 . pp. 323-332. Remmler, S. and Hickel, S. (2012) Direct and large-eddy simulation of stratified turbulence. International Journal of Heat and Fluid Flow, 35 . pp. 13-24. ISSN 0142-727X Senne, M. and Trendelkamp-Schroer, B. and Mey, A.S.J.S. and Schütte, Ch. and Noé, F. (2012) EMMA - A software package for Markov model building and analysis. Journal of Chemical Theory and Computation, 8 . pp. 2223-2238. Sander, O. and Schiela, A. (2012) Energy minimizers of the coupling of a Cosserat rod to an elastic continuum. Mathematical Modelling, 7 (1). pp. 1118-1123. Djurdjevac, N. and Sarich, M. and Schütte, Ch. (2012) Estimating the eigenvalue error of Markov State Models. Multiscale Modeling & Simulation, 10 (1). pp. 61-81. Kumar, B. and Janetzko , F. and Schumacher, J. and Shaw, R.A. (2012) Extreme responses of a coupled scalar–particle system during turbulent mixing. New Journal of Physics, 14 115020 . Wehmeyer, C. and Falk von Rudorff, G. and Wolf, S. and Kabbe, G. and Schärf, D. and Kühne, T. D. and Sebastiani, D. (2012) Foraging on the potential energy surface: A swarm intelligence-based optimizer for molecular geometry. The Journal of Chemical Physics, 137 (19). p. 194110. ISSN 00219606 Dommert, F. and Wendler, K. and Berger, R. and Delle Site, L. and Holm, C. (2012) Force fields for studying structure and dynamics of imidazolium based ionic liquids - a critical review of recent developments. ChemPhysChem, 13 . p. 1625. Mischau, A. (2012) Genderkompetenz in der Lehramtsausbildung Mathematik: Möglichkeiten der Integration und Vermittlung. Wissenschaftlerinnen-Rundbrief, 1 . pp. 19-22. ISSN ISBN: 978-3-929968-42-2 Mischau, A. and Grabarz, K. and Langfeldt, B. and Reith, F. (2012) Geschlechterdisparitäten in Berufs- und Karriereverläufen von MathematikerInnen und PhysikerInnen. IFFOnZeit, Onlinezeitschrift des Interdisziplinären Zentrums für Frauen- und Geschlechterforschung (IFF), 2 . pp. 67-75. ISSN 1868-7156 Braack, M. and Lang, J. and Taschenberger, N. (2012) Hierarchical a posteriori residual based error estimators for bilinear finite elements. Comput. Meth. Appl. Mech. Eng. . (Submitted) Menz, S. and Latorre, J.C. and Schütte, Ch. and Huisinga, W. (2012) Hybrid Stochastic–Deterministic Solution of the Chemical Master Equation. SIAM Interdisciplinary Journal Multiscale Modeling and Simulation (MMS), 10 (4). pp. 1232-1262. Wendler, K. and Dommert, F. and Zhao, Y.Y. and Berger, R. and Holm, C. and Delle Site, L. (2012) Ionic Liquids studied across different Scales: A Computational Perspective. Faraday Discussions, 154 . pp. 111-132. Münch, M. and Kaiser, G. (2012) Kinderwagen und andere Brandlasten in Treppenhäusern. Der feine Unterschied zwischen richtig und rechtmäßig. Das Grundeigentum, Recht und Praxis, 17 . pp. 1144-1148. Sadiq, S. K. and Noé, F. and de Fabritiis, G. (2012) Kinetic characterization of the critical step in HIV-1 protease maturation. Proc. Natl. Acad. Sci. USA, 109 . pp. 20449-20454. Mukherji, D. and van der Vegt, N.F.A. and Kremer, K. and Delle Site, L. (2012) Kirkwood-Buff analysis of liquid mixtures in an open boundary simulation. Journal of Chemical Theory and Computation, 8 . pp. 375-379. Letzel, M.O. and Helmke, C. and Ng, E. and An, X. and Lai, A. and Raasch, S. (2012) LES case study on pedestrian level ventilation in two neighbourhoods in Hong Kong. Meteorologische Zeitschrift, 21 (6). pp. 575-589. Schlegel, F. and Stiller, J. and Bienert, A. and Maas, H.-G and Queck, R. and Bernhofer, C. (2012) Large-Eddy Simulation of inhomogeneous canopy flows using high resolution terrestrial laser scanning data. Boundary-Layer Meteorology, 142 . pp. 223-243. ISSN 0006-8314 (Print) 1573-1472 (Online) Keller, B. and Prinz, J.-H. and Noé, F. (2012) Markov models and dynamical fingerprints: unraveling the complexity of molecular kinetics. Chem. Phys., 396 . pp. 92-107. Bordás, R. and John, V. and Schmeyer, E. and Thévenin, D. (2012) Measurement and Simulation of a Droplet Population in a Turbulent Flow Field. Computers and Fluids . (Submitted) Kühnlein, C. and Smolarkiewicz, P. and Dörnbrack, A. (2012) Modelling atmospheric flows with adaptive moving meshes. Journal of Computational Physics, 231 (7). pp. 2741-2763. ISSN 0021-9991 Held, M. and Imhof, P. and Keller, B. and Noé, F. (2012) Modulation of a ligand’s energy landscape and kinetics by the chemical environment. J. Phys. Chem. B, 116 . pp. 13597-13607. Paeschke, E. and Marschalik, P. and Owinoh, A.Z. and Klein, R. (2012) Motion and structure of atmospheric mesoscale baroclinic vortices: dry air and weak environmental shear. Journal of Fluid Mechanics, 701 . pp. 137-170. John, V. and Thein, F. (2012) On the efficiency and robustness of the core routine of the quadrature method of moments (QMOM). Chemical Engineering Science, 75 . pp. 327-333. Dupuis, P. and Yufei, L. and Plattner, N. and Doll, J. D. (2012) On the infinite swapping limit for parallel tempering. Multiscale Modeling & Simulation, 10 (3). pp. 986-1022. Ziemer, C. and Wacker, U. (2012) Parameterisation of the Sedimentation of Raindrops with Finite Maximum Diameter. Monthly Weather Review, 140 (5). 1589 -1602. ISSN Online: 1520-0493 Print : 0027-0644 Ziemer, C. and Wacker, U. (2012) Parameterization of the Sedimentation of Raindrops with Finite Maximum Diameter. Monthly Weather Review , 140 (5). 1589 -1602. ISSN Online: 1520-0493 Print: 0027-0644 Bruckner, S. and Hüffner, F. and Komusiewicz, Ch. and Niedermeier, R. and Thiel, S. and Uhlmann, J. (2012) Partitioning into colorful components by minimum edge deletions. Lecture Notes in Computer Science, 7354 . pp. 56-69. Duwal, S. and Schütte, Ch. and von Kleist, M. (2012) Pharmacokinetics and Pharmacodynamics of the Reverse Transcriptase Inhibitor Tenofovir & Prophylactic Efficacy against HIV-1 Infection. PLoS One, 7 (7). e40382. von Kleist, M. and Metzner, Ph. and Marquet, R. and Schütte, Ch. (2012) Polymerase Inhibition by Nucleoside Analogs: Cellular- and Kinetic Parameters of Efficacy, Susceptibility and Resistance Selection. Plos Computational Biology, 8 (1). e1002359. Schillings, Claudia and Schulz, Volker (2012) Problem Formulations and Treatment of Uncertainties in Aerodynamic Design. AIAA Journal, 47 (3). Potestio, R. and Delle Site, L. (2012) Quantum Locality and Equilibrium Properties in Low-temperature Parahydrogen: A Multiscale Simulation Study. Journal of Chemical Physics, 136 . 054101. Keller, B. and Prinz, J.-H. and Noé, F. (2012) Resolving the apparent gap in complexity between simulated and measured kinetics of biomolecules. From Computational Biophysics to Systems Biology (CBSB11) Proceedings, IAS Series, 8 . pp. 61-64. Assêncio, D.C. and Teran, J.M. (2012) A Second Order Virtual Node Algorithm for Stokes Flow Problems with Interfacial Forces and Discontinuous Material Properties. Journal of Computational Physics . (Submitted) Meerbach, E. and Latorre, J.C. and Schütte, Ch. (2012) Sequential Change Point Detection in Molecular Dynamics Trajectories. Multicale Model. Sim., 10 (4). pp. 1263-1291. Wendler, K. and Brehm, M. and Malberg, F. and Kirchner, B. and Delle Site, L. (2012) Short time dynamics of ionic liquids in AIMD based power spectra. Journal of Chemical Theory and Computation, 8 . p. 1570. Gupta, Pooja and Conrad, T. O. F. and Spötter, Andreas and Reinsch, Norbert and Bienefeld, Kaspar (2012) Simulating a base population in honey bee for molecular genetic studies. Genetics Selection Evolution, 44 . p. 14. Mukhopadhyay, A. and Jasor, G. and Polifke, W. (2012) Simulation of Pure Sedimentation of Raindrops using Quadrature Method of Moments. J. Atmospheric Research, 106 . pp. 61-70. Kupfer, S. and Pérez-Hernández, G. and González, L. (2012) Singlet oxygen generation versus O–O homolysis in phenyl-substituted anthracene endoperoxides investigated by RASPT2, CASPT2, CC2, and TD-DFT methods. Theoretical Chemistry Accounts, 131 (12). ISSN 1432-881X Schwab, Christoph and Schillings, Claudia (2012) Sparse, adaptive Smolyak algorithms for Bayesian inverse problems. Research Report No. 2012-37 . Jouvet, G. and Bueler, E. (2012) Steady, shallow ice sheets as obstacle problems: Well-posedness and finite element approximation. SIAM J. Appl. Math., 72 (4). pp. 1292-1314. ISSN 0036-1399 Stolzenberg, S. and Khelashvili, G. and Weinstein, H. (2012) Structural Intermediates in a Model of the Substrate Translocation Path of the Bacterial Glutamate Transporter Homologue GltPh. The Journal of Physical Chemistry B, 116 (18). p. 5372. ISSN 1520-6106 Faelber, K. and Held, M. and Gao, S. and Posor, Y. and Haucke, V. and Noé, F. and Daumke, O. (2012) Structural insights into dynamin-mediated membrane fission. Structure, 20 . 1621-1628. Klein, R. and Pauluis, O. (2012) Thermodynamic Consistency of a Pseudo-Incompressible Approximation for General Equations of State. Journal of the Atmospheric Sciences, 69 (3 ). pp. 961-968. ISSN Online: 1520-0469; Print : 0022-4928 Rieper, F. and Achatz, U. and Klein, R. (2012) Validation of an extended non-linear WKB theory: 1D and 2D case. Journal of Fluid Mechanics . (Submitted) Leyendecker, S. and Hartmann, C. and Koch, M. (2012) Variational collision integrator for polymer chains. J. Comput. Phys, 231 (10). pp. 3896-3911. Leyendecker, S. and Hartmann, C. and Koch, M. and Johnson, G. and Ortiz, M. (2012) Variational collision integrators in forward dynamics and optimal control. Proceedings of the 7th International Conference Croatian Society of Mechanics (7ICCSM2012) . Rath, B. and von Kleist, M. and Tief, F. and Karsch, K. and Tuerk, E. and Muehlhans, S. and Louis, F. and Skopnik, H. and Schweiger, B. and Duwe, S. (2012) Virus Load Kinetics and Resistance Development during Oseltamivir Treatment in Infants and Children Infected with Influenza A(H1N1)2009 and Influenza B Viruses. Pediatr. Infect. Dis. J., 31 (9). pp. 899-905. Park, S.B. and Baik, J.J. and Raasch, S. and Letzel, M.O. (2012) A large-eddy simulation study of thermal effects on turbulent flow and dispersion in and above a street canyon. J. Appl. Meteor. Climatol., 51 (5). pp. 829-841. ISSN Online: 1558-8432 Print: 1558-8424 Riechelmann, T. and Noh, Y . and Raasch, S. (2012) A new method for large-eddy simulations of clouds with Lagrangian droplets including the effects of turbulent collision. New Journal of Physics, 14 (065008). Vetter, A. and Witt, F. and Sander, O. and Duda, G. and Weinkamer, E. (2012) The spatio-temporal arrangement of different tissues during bone healing as a result of simple mechanobiological rules. Biomechanics and Modeling in Mechanobiology, 11 (1-2). pp. 147-160. ISSN 1617-7959 Jouvet, G. and Huss, M. and Funk, M. and Blatter, H. (2011) Modelling the retreat of Grosser Aletschgletscher, Switzerland, in a changing climate. Journal of Glaciology, 57 (206). pp. 1033-1045. ISSN 0022-1430 Berninger, H. and Kornhuber, R. and Sander, O. (2011) Fast and robust numerical solution of the Richards equation in homogeneous soil. SIAM Journal on Numerical Analysis, 49 (6). pp. 2576-2597. ISSN 0036-1429 Plattner, N. and Doll, J. D. and Dupuis, P. and Wang, H. and Liu, Y. and Gubernatis, J. E. (2011) An infinite swapping approach to the rare-event sampling problem. The Journal of Chemical Physics, 135 (13). p. 134111. ISSN 00219606 Kehr, B. and Weese, D. and Reinert, K. (2011) STELLAR: fast and exact local alignments. BMC Bioinformatics, 12 (S9). S15. ISSN 1471-2105 Fischer, M. and Lorenz, U. and Schmidt, B. and Schmidt, R. (2011) Fragmentation due to centrifugal forces in the photodissociation of H2+ in intense laser fields. Phys. Rev. A, 84 (3). 033422. Vercauteren, N. and Huwald, H. and Bou-Zeid, E. and Selker, J. S. and Lemmin, U. and Parlange, M. B. and Lunati, I. (2011) Evolution of Superficial Lake Water Temperature Profile Under Diurnal Radiative Forcing. Water Resources Research, 47 (9). Berninger, H. and Kornhuber, R. and Sander, O. (2011) Heterogeneous domain decomposition of surface and porous media flow. AIP Conference Proceedings, 1389 . pp. 2025-2028. ISSN 0094-243X Schäfer-Bung, B. and Hartmann, C. and Schmidt, B. and Schütte, Ch. (2011) Dimension reduction by balanced truncation: Application to light-induced control of open quantum systems. J. Chem. Phys., 135 (1). 014112. Böcker, S. and Kehr, B. and Rasche, F. (2011) Determination of Glycan Structure from Tandem Mass Spectra. IEEE/ACM Transactions on Computational Biology and Bioinformatics , 8 (4). pp. 976-986. ISSN 1545-4963 Bielow, C. and Aiche, S. and Andreotti, S. and Reinert, K. (2011) MSSimulator: Simulation of Mass Spectrometry Data. Journal of Proteome Research, 10 (7). pp. 2922-2929. Holtgrewe, M. and Emde, A.-K. and Weese, D. and Reinert, K. (2011) A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping. BMC Bioinformatics, 12 (120). ISSN 1471-2105 Schütte, Ch. and Noé, F. and Lu, Jianfeng and Sarich, M. and Vanden-Eijnden, E. (2011) Markov State Models Based on Milestoning. J. Chem. Phys., 134 (20). p. 204105. Prinz, J.-H. and Wu, H. and Sarich, M. and Keller, B. and Senne, M. and Held, M. and Chodera, J. D. and Schütte, Ch. and Noé, F. (2011) Markov models of molecular kinetics: Generation and Validation. J. Chem. Phys., 134 . p. 174105. Ullrich, Alexander and Rohrschneider, Markus and Scheuermann, Gerik and Stadler, Peter F. and Flamm, Christoph (2011) In Silico Evolution of Early Metabolism. Artificial Life, 17 (2). pp. 87-108. ISSN 1064-5462 Zou, Q. and Veeser, A. and Kornhuber, R. and Gräser, C. (2011) Hierarchical error estimates for the energy functional in obstacle problems. Numerische Mathematik, 117 (4). pp. 653-677. ISSN 0029-599X Ruprecht, D. and Klein, R. (2011) A Model for Nonlinear Interactions of Internal Gravity Waves with Saturated Regions. Meteorologische Zeitschrift, 20 (2). pp. 243-252. Hartmann, C. and Latorre, J.C. (2011) Computing free energy differences using conditioned diffusions. AIP Conf. Proc., 1332 (1). pp. 218-220. von Kleist, M. and Menz, S. and Stocker, H. and Arasteh, K. and Huisinga, W. and Schütte, Ch. (2011) HIV Quasispecies Dynamics during Pro-active Treatment Switching: Impact on Multi-Drug Resistance and Resistance Archiving in Latent Reservoirs. Plos One, 6 (3). e18204. Vetter, A. and Liu, Y. and Witt, F. and Manjubala, I. and Sander, O. and Rao Epari, D. and Fratzl, P. and Duda, G. and Weinkamer, R. (2011) The mechanical heterogeneity of the hard callus influences local tissue strains during bone healing. Journal of Biomechanics, 44 (3). pp. 517-523. ISSN 0021-9290 Owschimikow, N. and Schmidt, B. and Schwentner, N. (2011) Laser-induced alignment and anti-alignment of rotationally excited molecules. Phys. Chem. Chem. Phys., 13 (19). pp. 8671-8680. Held, M. and Metzner, Ph. and Prinz, J.-H. and Noé, F. (2011) Mechanisms of Protein-Ligand association and its modulation by protein mutations. Biophys. J., 100 (3). pp. 701-710. Owinoh, A.Z. and Stevens, B. and Klein, R. (2011) Multiscale Asymptotics Analysis for the Mesoscale Dynamics of Cloud-Topped Boundary Layers. Journal of the Atmospheric Sciences, 68 (2). pp. 379-402. ISSN Online 1520-0469, Print 0022-4928 Matera, S. and Meskine, H. and Reuter, K. (2011) Adlayer inhomogeneity without lateral interactions: Rationalizing correlation effects in CO oxidation at RuO2(110) with first-principles kinetic Monte Carlo. The Journal of Chemical Physics, 134 (6). 064713. Walter, J. and Hartmann, C. and Maddocks, J. (2011) Ambient space formulations and statistical mechanics of holonomically constrained Langevin systems. Eur. Phys. J. Special Topics, 200 (1). pp. 153-181. Jouvet, G. and Rappaz, J. (2011) Analysis and finite element approximation of a nonlinear stationary stokes problem arising in glaciology. Advances in Numerical Analysis, 2011 (Articl). ISSN 1687-9562 Keller, B. and Hünenberger, Philippe and van Gunsteren, Wilfred (2011) An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles. J. Chem. Theo. Comput., 7 . pp. 1032-1044. Schiffmann, C and Sebastiani, D (2011) Artificial Bee Colony Optimization of Capping Potentials for Hybrid Quantum Mechanical/Molecular Mechanical Calculations. Journal of Chemical Theory and Computation, 7 (5). p. 1307. ISSN 1549-9618 Mischau, A. and Mehlmann, S. and Wöllmann, T. (2011) Auf dem Weg zu genderkompetenten LehrerInnen im Unterrichtsfach Mathematik. Journal Netzwerk Frauen- und Geschlechterforschung NRW, 27 . pp. 29-39. ISSN 1617-2493 Hartmann, C. (2011) Balanced model reduction of partially-observed Langevin processes: an averaging principle. Math. Comput. Model. Dyn. Syst., 17 (5). pp. 463-490. Wu, H. and Noé, F. (2011) Bayesian framework for modeling diffusion processes with nonlinear drift based on nonlinear and incomplete observations. Phys. Rev. E, 83 (3). 036705. Faelber, Katja and Posor, York and Held, M. and Roske, Yvette and Schulze, Dennis and Haucke, Volker and Noé, F. and Daumke, Oliver (2011) Crystal structure of nucleotide-free dynamin. Nature, 477 . pp. 556-560. Bordás, R. and Hagemeier, T. and Wunderlich, B. and Thévenin, D. (2011) Droplet Collisions and Interaction with the Turbulent Flow within a Two-Phase Wind Tunnel. Physics of Fluids, 23 (8). ISSN 1070-6631 (print) 1089-7666 (online) Braack, M. and Burman, E. and Taschenberger, N. (2011) Duality based a posteriori error estimation for quasi periodic solutions using time averages. SIAM J. Scientific Computing, 33 (10.1137/100809519). pp. 2199-2216. ISSN print: 1064-8275; online: 1095-7197 Han, D. S. and Golebiewska, U. and Stolzenberg, S. and Scarlata, S. F. and Weinstein, H. (2011) A Dynamic Model of Membrane-Bound Phospholipase C 2 Activation by G Subunits. Molecular Pharmacology, 80 (3). p. 434. ISSN 0026-895X Noé, F. and Doose, S. and Daidone, I. and Löllmann, M. and Chodera, J. D. and Sauer, M. and Smith, J. C. (2011) Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proc. Natl. Acad. Sci. USA, 108 . pp. 4822-4827. Chodera, J. D. and Swope, W. D. and Noé, F. and Prinz, J.-H. and Shirts, M. R. and Pande, V. S. (2011) Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures. J. Chem. Phys., 134 (24). p. 244107. Prinz, J.-H. and Held, M. and Smith, J. C. and Noé, F. (2011) Efficient Computation, Sensitivity and Error Analysis of Committor Probabilities for Complex Dynamical Processes. Multiscale Model. Simul., 9 . pp. 545-567. Kornhuber, R. and Zou, Q. (2011) Efficient and reliable hierarchical error estimates for the discretization error of elliptic obstacle problems. Mathematics of Computation, 80 . pp. 69-88. ISSN 0025-5718 Mischau, A. and Langfeldt, B. (2011) Genderkompetenz als Bestandteil der Lehramtsausbildung im Fach Mathematik – zu innovativ für deutsche Hochschulen? Zeitschrift für Hochschulentwicklung, 3 . pp. 311-324. ISSN 2219-6994 Mischau, A. and Langfeldt, B. (2011) Genderkompetenz als Bestandteil der Lehramtsausbildung im Fach Mathematik – zu innovativ für deutsche Hochschulen? Zeitschrift für Hochschulentwicklung, 3 . pp. 311-324. ISSN 2219-6994 Mischau, A. and Mehlmann, S. (2011) Genderkompetenz für angehende Mathematiklehrkräfte. Konzeption einer Lehrveranstaltung für Lehramtsstudierende des Unterrichtsfachs Mathematik. Soziale Technik. Zeitschrift für sozial- und umweltverträgliche Technikgestaltung, 3 . pp. 17-19. ISSN 1022-6893 Dedner, A. and Klöfkorn, R. (2011) A Generic Stabilization Approach for Higher Order Discontinuous Galerkin Methods for Convection Dominated Problems. J. Sci. Comput. . (Submitted) Schiffmann, C and Sebastiani, D (2011) Hydrogen bond networks: Structure and dynamics via first-principles spectroscopy. physica status solidi (b), 249 (2). p. 368. ISSN 03701972 Bresch, D. and Klein, R. and Lucas, C. (2011) Multiscale analyses for the Shallow Water equations. Computational Science and High Performance Computing IV, 115/20 . pp. 149-164. ISSN 1612-2909 (Print) 1060-0824 (Online) Hartmann, C. and Latorre, J.C. and Ciccotti, G. (2011) On two possible definitions of the free energy for collective variables. Eur. Phys. J. Special Topics, 200 (1). pp. 73-89. Prinz, J.-H. and Chodera, J. D. and Pande, V. S. and Swope, W. D. and Smith, J. C. and Noé, F. (2011) Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. J. Chem. Phys., 134 (24). p. 244108. Hertwig, D. and Leitl, B. and Schatzmann, M. (2011) Organized turbulent structures –- Link between experimental data and LES. Journal of Wind Engineering and Industrial Aerodynamics, 99 (4). pp. 296-307. ISSN 01676105 Harlander, U. and Wentzel, J. and Alexandrov, K. and Wang, Y. and Egbers, C. (2011) PIV- and LDV-measurements of baroclinic wave interactions in a thermally driven rotating annulus. Experiments in Fluids . (Submitted) Harlander, U. and von Larcher, T. and Wang, Y. and Egbers, C. (2011) PIV- and LDV-measurements of baroclinic wave interactions in a thermally driven rotating annulus. Experiments in Fluids, 51 (1). pp. 37-49. Sander, O. (2011) The PSurface library. Computing and Visualization in Science, 14 (8). pp. 353-370. ISSN 1432-9360 Jebens, .S. and Knoth, O. and Weiner, R. (2011) Partially Implicit PeerMethods for the Compressible Euler Equations. Journal of Computational Physics . (Submitted) Prinz, J.-H. and Keller, B. and Noé, F. (2011) Probing molecular kinetics with Markov models: Metastable states, transition pathways and spectroscopic observables. Phys. Chem. Chem. Phys., 13 . pp. 16912-16927. Frank, M. and von Kleist, M. and Kunz, A. and Harms, G. and Schütte, Ch. and Kloft, Ch. (2011) Quantifying the impact of nevirapine-based prophylaxis strategies to prevent mother-to-child transmission of HIV-1: A combined pharmacokinetic, pharmaco- and viral dynamic analysis to predict clinical outcomes. Antimicrob. Agents Chemother., 55 (12). pp. 5529-5540. Vater, S. and Klein, R. and Knio, O.M. (2011) A Scale-selective Multilevel Method for Long-Wave Linear Acoustics. Acta Geophysica, 59 (6). pp. 1076-1108. Assêncio, D.C. and Teran, J.M. (2011) A Second Order Virtual Node Algorithm for Stokes Flow Problems with Interfacial Forces and Irregular Domains. Journal of Computational Physics . (Submitted) Ullrich, Alexander and Flamm, Christoph (2011) A Sequence-to-Function Map for Ribozyme-catalyzed Metabolisms. Advances in Artificial Life, 5778 . p. 481. ISSN 978-3-642-21313-7 Ihrig, A C and Schiffmann, C and Sebastiani, D (2011) Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups. The Journal of Chemical Physics, 135 (21). p. 214107. ISSN 00219606 Splettstößer, T. and Holmes, K. C. and Noé, F. and Smith, J. C. (2011) Structural modeling and molecular dynamics simulation of the actin filament. Proteins, 79 . pp. 2033-2043. Latorre, J.C. and Metzner, Ph. and Hartmann, C. and Schütte, Ch. (2011) A Structure-preserving numerical discretization of reversible diffusions. Commun. Math. Sci., 9 (4). pp. 1051-1072. Bienert, A. and Pech, K. and Maas, H.-G (2011) Verfahren zur Registrierung von Laserscannerdaten in Waldbeständen. Schweizerische Zeitschrift für Forstwesen, 162 (6). pp. 178-185. Queck, R. and Bienert, A. and Maas, H.-G and Hermansa, S. and Goldberg, V. and Bernhofer, C. (2011) Wind fields in heterogeneous conifer canopies: parameterisation of momentum absorption using high-resolution 3D vegetation scans. European Journal of Forest Research, 130 . ISSN 1612-4669 (Print) 1612-4677 (Online) Wu, H. and Noé, F. (2011) A flat Dirichlet process switching model for Bayesian estimation of hybrid systems. Procedia Computer Science, 4 . pp. 1393-1402. Benacchio, T. and Bonaventura, L. (2011) A spectral collocation method for the one dimensional shallow water equations on semi-infinite domain. MOX–Report, 34 . Assmann, M. and Sanz, C. S. and Pérez-Hernández, G. and Worth, G. A. and González, L. (2010) Excited state dynamics of a model asymmetric molecular rotor: A five-dimensional study on 2-cyclopentylidene-tetrahydrofuran. Chemical Physics, 377 (1-3). pp. 86-95. ISSN 03010104 Holtgrewe, M. (2010) Mason – A Read Simulator for Second Generation Sequencing Data. Technical Report FU Berlin . Metzner, Ph. and Weber, M. and Schütte, Ch. (2010) Observation Uncertainty in Reversible Markov Chains. Phys. Rev. E, 82 (3). 031114. Matera, S. and Reuter, K. (2010) Transport limitations and bistability for in situ CO oxidation at RuO 2(110): First-principles based multiscale modeling. Physical Review B, 82 (8). 085446. Flamm, Christoph and Ullrich, Alexander and Hofacker, L. Ivo and Stadler, Peter F. (2010) Evolution of Metabolic Networks: A Computational Framework. Journal of Systems Chemistry, 1 (4). Pérez-Hernández, G. and González, L. (2010) Mechanistic insight into light-driven molecular rotors: a conformational search in chiral overcrowded alkenes by a pseudo-random approach. Physical Chemistry Chemical Physics, 12 (38). pp. 12279-12289. ISSN 1463-9076 Assmann, M. and Pérez-Hernández, G. and González, L. (2010) On the Light-Driven Isomerization of a Model Asymmetric Molecular Rotor: Conformations and Conical Intersections of 2-Cyclopentylidene-tetrahydrofuran. The Journal of Physical Chemistry A, 114 (34). pp. 9342-9348. ISSN 1089-5639 Owschimikow, N. and Königsmann, F. and Maurer, J. and Giese, Ph. and Ott, A. and Schmidt, B. and Schwentner, N. (2010) Cross sections for rotational decoherence of perturbed nitrogen measured via decay of laser-induced alignment. J. Chem. Phys., 133 (4). 044311. Plattner, N. and Lee, M. W. and Meuwly, M. (2010) Structural and spectroscopic characterization of mixed planetary ices. Faraday discussions, 147 . 217-230; discussion 251. ISSN 1359-6640 Plattner, N. and Doll, J. D. and Meuwly, M. (2010) Spatial averaging for small molecule diffusion in condensed phase environments. The Journal of Chemical Physics, 133 (4). 044506. ISSN 00219606 Marsalek, O. and Uhlig, F. and Frigato, T. and Schmidt, B. and Jungwirth, P. (2010) Dynamics of Electron Localization in Warm vs. Cold Water Clusters. Phys. Rev. Lett., 105 (4). 043002. Hüser, D. and Gogol-Döring, A. and Lutter, T. and Weger, S. and Winter, K. and Hammer, E.-M. and Cathomen, T. and Reinert, K. and Heilbronn, R. (2010) Integration Preferences of Wildtype AAV-2 for Consensus Rep-Binding Sites at Numerous Loci in the Human Genome. PLoS Pathogens, 6 (7). e1000985. ISSN 1553-7374 Pilari, S. and Huisinga, W. (2010) Lumping of Physiologically-Based Pharmacokinetic Models and a Mechanistic Derivation of Classical Compartmental Models. Journal of Pharmacokinetics and Pharmacodynamics, 37 (4). pp. 365-405. Pérez-Hernández, G. and Pelzer, A. and González, L. and Seideman, T. (2010) Biologically inspired molecular machines driven by light. Optimal control of a unidirectional rotor. New Journal of Physics, 12 (7). 075007. ISSN 1367-2630 Sander, O. (2010) Geodesic finite elements for Cosserat rods. International Journal for Numerical Methods in Engineering, 82 (13). pp. 1645-1670. ISSN 1097-0207 Diederichs, E. and Juditski, A. and Spokoiny, V. and Schütte, Ch. (2010) Sparse Non-Gaussian Component Analysis. IEEE Transactions on Information Theory, 56 (6). pp. 3033-3047. ISSN 0018-9448 Keller, B. and Gattin, Z. and van Gunsteren, W. F. (2010) What stabilizes the 3_14-helix in beta^3-peptides? A conformational analysis using molecular simulation. PROTEINS: Structure, Function, and Bioinformatics, 78 (7). pp. 1677-1690. Holtgrewe, M. and Sanders, P. and Schulz, C. (2010) Engineering a scalable high quality graph partitioner. 2010 IEEE International Symposium on Parallel & Distributed Processing (IPDPS) . pp. 1-12. ISSN 1530-2075 von Kleist, M. and Menz, S. and Huisinga, W. (2010) Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV. Plos Computational Biology, 6 (3). e1000720. Bielow, C. and Ruzek, S. and Huber, C. and Reinert, K. (2010) Optimal Decharging and Clustering of Charge Ladders Generated in ESI−MS. J. Proteome Res., 9 (5). pp. 2688-2695. ISSN 1535-3893 Xavier , D. and Keller, B. and van Gunsteren, W. F. (2010) Comparing geometric and kinetic cluster algorithms for molecular simulation data. J. Chem. Phys., 132 (7). 074110. Horenko, I. and Schütte, Ch. (2010) On metastable conformational analysis of non-equilibrium biomolecular time series. Multiscale Modeling & Simulation, 8 (2). pp. 701-716. ISSN 15403467 Emde, A.-K. and Grunert, M. and Weese, D. and Reinert, K. and Sperling, S. R. (2010) MicroRazerS: Rapid alignment of small RNA reads. Bioinformatics, 26 (1). pp. 123-124. ISSN 1367-4803 Sander, O. and Schmidt, L. and Ehrig, R. and Heller, M. and Taylor, B. and Kornhuber, R. (2010) Numerical determination of the medio-lateral force distribution in an ovine stifle joint. Biomedizinische Technik/Biomedical Engineering: Proceedings of BMT, Rostock, 55 (s1). ISSN 0013-558 Forster, R. and Kornhuber, R. (2010) A polynomial chaos approach to stochastic variational inequalities. Journal of Numerical Mathematics, 18 (4). pp. 235-255. ISSN 1570-2820 Devanathan, R. and Venkatnathan, A. and Rousseau, R. and Dupuis, M. and Frigato, T. and Gu, W. and Helms, V. (2010) Atomistic Simulation of Water Percolation and Proton Hopping in Nafion Fuel Cell Membrane. J. Phys. Chem. B, 114 (43). pp. 13681-13690. Hartmann, C. and Vulcanov, V.-M. and Schütte, Ch. (2010) Balanced Truncation of Second Order Systems: a Hamiltonian approach. Multiscale Model. Simul., 8 (4). pp. 1348-1367. Münch, M. (2010) Brandschutzaufklärung mit mathematischen Simulationsprogrammen: Wie Mathematik hilft, Ihr Leben zu retten! Schadenprisma - Zeitschrift für Schadenverhütung und Schadenforschung der öffentlichen Versicherer, 4 . pp. 16-19. Zhu, H. and Blom, M. and Compagnon, I. and Rijs, A. M. and Roy, S. and von Helden, G. and Schmidt, B. (2010) Conformations and Vibrational Spectra of a Model Tripeptide: Change of Secondary Structure upon Micro-Solvation. Phys. Chem. Chem. Phys., 12 (14). 3415 -3425. Queck, R. and Bernhofer, C. (2010) Constructing wind profiles in forests from limited measurements of wind and vegetation structure. Agricultural and Forest Meteorology . Spötter, Andreas and Gupta, Pooja and Reinsch , Norbert and Zautke, F. and Bienefeld, Kaspar (2010) Development of a SNP-Assay for varroa tolerance in the honey bee. Apidologie, 41 (6). p. 685. ISSN 0044-8435 (Print) 1297-9678 (Online) Qu, Z.-W. and Zhu, H. (2010) Do Anionic Titanium Dioxide Nano-Clusters Reach Bulk Band Gap? A Density Functional Theory Study. J. Comp. Chem., 31 (10). pp. 2038-2045. Baumann, M. and Heuveline , V. (2010) Evaluation of Different Strategies for Goal Oriented Adaptivity in CFD - Part I: The Stationary Case. Preprint Series of the Engineering Mathematics and Computing Lab, 2010-05 . Bordás, R. and Hagemeier, T. and Thévenin, D. (2010) Experimental Investigation of Droplet-Droplet Interactions. 23rd European Conference on Liquid Atomization and Spray Systems . 198.1-198.6. ISSN 978-80-7399-997-1 Münch, M. (2010) Fast and correct computation. A comprehensive test concept to proof the new FDS-ScaRC technique. 11th International Symposium on Fire Protection . 11 p.. ISSN 978-3-00-03966-2 Horenko, I. (2010) Finite Element Approach to Clustering of Multidimensional Time Series. J. Sci. Comp., 32 (1). pp. 62-83. Latorre, J.C. and Hartmann, C. and Schütte, Ch. (2010) Free energy computation by controlled Langevin processes. Procedia Computer Science, 1 (1). pp. 1591-1600. Pilari, S. and Preusse, C. and Huisinga, W. (2010) Gestational Influences on the Pharmacokinetics of Gestagenic Drugs: A Combined In Silico, In Vitro and In Vivo Analysis. European Journal of Pharmaceutical Sciences . (Submitted) Achatz, U. and Klein, R. and Senf, F. (2010) Gravity waves, scale asymptotics, and the pseudo-incompressible equations. Journal of Fluid Mechanics, 663 . pp. 120-147. Schütte, Ch. and Wulkow, M. (2010) A Hybrid Galerkin–Monte-Carlo Approach to Higher-Dimensional Population Balances in Polymerization Kinetics. Macromol. React. Eng., 4 (9-10). pp. 562-577. Marsalek, O. and Frigato, T. and VandeVondele, J. and Bradforth, P. E. and Schmidt, B. and Schütte, Ch. and Jungwirth, P. (2010) Hydrogen Forms in Water by Proton Transfer to a Distorted Electron. J. Phys. Chem. B, 114 (2). pp. 915-920. Kenfack, A. and Marquardt, F. and Paramonov, G. K. and Barth, I. and Lasser, C. and Paulus, B. (2010) Initial-state dependence of coupled electronic and nuclear fluxes in molecules. Phys. Rev. A, 81 (5). 052502. Bastian, G and Vogelsang, A and Schiffmann, C (2010) Isotopic Superlattices for Perfect Phonon Reflection. Journal of Electronic Materials, 39 (9). p. 1769. ISSN 0361-5235 Jebens, .S. and Knoth, O. and Arnold, M. and Weiner, R. (2010) Linearly implicit peer methods for the compressible Euler equations. Applied Numerical Mathematics . (Submitted) Wu, H. and Noé, F. (2010) Maximum a posteriori estimation for Markov chains based on Gaussian Markov random fields. Procedia Computer Science, 1 (1). pp. 1665-1673. Ruprecht, D. and Klein, R. and Majda, A. J. (2010) Modulation of Internal Gravity Waves in a Multiscale Model for Deep Convection on Mesoscales. Journal.of the Atmospheric Sciences, 67 (8). pp. 2504-2519. ISSN Online 1520-0469, Print 0022-4928 Schlegel, M. and Knoth, O. and Arnold, M. and Wolke, R (2010) Numerical solution of multiscale problems in atmospheric modeling. Applied Numerical Mathematics . (Submitted) Horenko, I. (2010) On Clustering of Non-stationary Meteorological Time Series. Dyn. of Atm. and Oc., 49 (2-3). pp. 164-187. Sarich, M. and Noé, F. and Schütte, Ch. (2010) On the Approximation Quality of Markov State Models. Multiscale Model. Simul., 8 (4). pp. 1154-1177. Horenko, I. (2010) On the identification of non-stationary factor models and their application to atmospherical data analysis. J. Atm. Sci., 67 (5). pp. 1559-1574. Hartmann, C. and Schütte, Ch. and Ciccotti, G. (2010) On the linear response of mechanical systems with constraints. J. Chem. Phys., 132 (11). p. 111103. Borzì, Alfio and Schulz, Volker H. and Schillings, Claudia and von Winckel, Gregory (2010) On the treatment of distributed uncertainties in PDE‐constrained optimization. GAMM-Mitteilungen, 33 (2). pp. 230-246. Sarich, M. and Schütte, Ch. and Vanden-Eijnden, E. (2010) Optimal Fuzzy Aggregation of Networks. Multiscale Modeling and Simulation, 8 (4). pp. 1535-1561. Bernhard, S. and Noé, F. (2010) Optimal Identification of Semi-Rigid Domains in Macromolecules from Molecular Dynamics Simulation. PLoS One, 5 . e10491. Horenko, I. (2010) Parameter identification in nonstationary Markov chains with external impact and its application to computational sociology. Multiscale Modeling & Simulation . (Submitted) Bienert, A. and Stiel, B. and Queck, R. and Maas, H.-G (2010) Photogrammetrische Bestimmung von statischen und dynamischen Verformungsstrukturen an Einzelbäumen. Allgemeine Vermessungs-Nachrichten, 5 . 190-197.. Menz, St. and Matthiesen, R. and Dehmel, Ch. and Barembruch, C. and Hengge, R. and Huisinga, W. (2010) Precise Switching of Flagellar Gene Expression in Escherichia Coli by the FlgM–FliA Regulatory Network. PLoS Computational Biology . (Submitted) Wu, H. and Noé, F. (2010) Probability Distance Based Compression of Hidden Markov Models. Multiscale Model. Simul., 8 . pp. 1838-1861. Chodera, J. D. and Noé, F. (2010) Probability distributions of molecular observables computed from Markov models. II: Uncertainties in observables and their time-evolution. J. Chem. Phys, 133 (10). p. 105102. de Souza, L.G.M. and Janiga, G and John, V. and Thévenin, D. (2010) Reconstruction of a distribution from a finite number of moments with an adaptive spline-based algorithm. Chemical Engineering Science, 65 (9). pp. 2741-2750. Klein, R. and Achatz, U. and Bresch, D. and Knio, O.M. and Smolarkiewicz, P. (2010) Regime of Validity of Sound-Proof Atmospheric Flow Models. Journal of the Atmospheric Sciences, 67 (10). pp. 3226-3237. ISSN Online: 1520-0469 Print: 0022-4928 Klein, R. (2010) Scale-Dependent Asymptotic Models for Atmospheric Flows. Annual Review of Fluid Mechanics, 42 . pp. 249-274. Schiffmann, C and Appert-Rolland, C and Santen, L (2010) Shock dynamics of two-lane driven lattice gases. Journal of Statistical Mechanics: Theory and Experiment, 2010 (06). P06002. ISSN 1742-5468 Birn, M. and Holtgrewe, M. and Sanders, P. and Singler, J. (2010) Simple and Fast Nearest Neighbor Search. 2010 Proceedings of the Twelfth Workshop on Algorithm Engineering and Experiments (ALENEX) . pp. 43-54. Berninger, H. and Sander, O. (2010) Substructuring of a Signorini-type problem and Robin's method for the Richards equation in heterogeneous soil. Computing and Visualization in Science, 13 (5). pp. 187-205. ISSN 1432-9360 Rohrschneider, Markus and Ullrich, Alexander and Kerren, Andreas and Stadler, Peter F. and Scheuermann, Gerik (2010) Visual Network Analysis of Dynamic Metabolic Pathways. Advances in visual computing . pp. 316-327. ISSN 3-642-17288-1 Bienert, A. and Queck, R. and Schmidt, A. and Bernhofer, C. and Maas, H.-G (2010) Voxel space analysis of terrestrial laser scans in forests for wind field modelling. International Archives of Photogrammetry.Remote Sensing and Spatial Information Sciences, 38 (5). pp. 92-97. Dedner, A. and Klöfkorn, R. and Nolte, M. and Ohlberger, M. (2010) A generic interface for parallel and adaptive discretization schemes: Abstraction principles and the DUNE-FEM module. Computing, 90 (3-4). pp. 165-196. Huang, W. and Kamenski, L. and Lang, J. (2010) A new anisotropic mesh adaption method based upon hierarchical a posteriori error estimates. J. Comput. Phys., 229 . pp. 2179-2198. Münch, M. and Kilian, S. (2010) A new generalized domain decomposition strategy for the efficient parallel solution of the FDS-pressure equation, Part II: Verification and Validation. ZIB-Report, ZR_09-20 . 40p.. ISSN 1438-0064 Moeck, J. and Scharfenberg , C. and Paschereit, O. C. and Klein, R. (2010) A zero-Mach solver and reduced order acoustic representations for modeling and control of combustion instabilities. Active Flow Control II, Notes on Numerical Fluid Mechanics and Multidisciplinary Design,, 108/2010 . pp. 291-306. ISSN 978-3-642-11734-3 Véron, N. and Bauer, H. and Weiße, A. Y. and Lüder, G. and Werber, M. and Herrmann, B. G. (2009) Retention of gene products in syncytial spermatids promotes non-Mendelian inheritance as revealed by the t complex responder. Genes & Development, 23 (23). 2705-2710 . Noé, F. and Schütte, Ch. and Vanden-Eijnden, E. and Reich, L. and Weikl, T. (2009) Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations. Proc. Natl. Acad. Sci. USA, 106 (45). pp. 19011-19016. Klein, R. and Bates, K.R. and Nikiforakis, N. (2009) Well Balanced Compressible Cut-Cell Simulation of Atmospheric Flow. Philosophical Transaction of the Royal Society, 367 (1907). 4559-4575 . ISSN Online: 1471-2962 Matera, S. and Reuter, K. (2009) First-Principles Approach to Heat and Mass Transfer Effects in Model Catalyst Studies. Catalysis letters, 133 (1-2). pp. 156-159. ISSN 1011-372X Doll, J. D. and Gubernatis, J. E. and Plattner, N. and Meuwly, M. and Dupuis, P. and Wang, H. (2009) A spatial averaging approach to rare-event sampling. The Journal of Chemical Physics, 131 (10). p. 104107. ISSN 00219606 Meskine, H. and Matera, S. and Scheffler, M. and Reuter, K. and Metiu, H. (2009) Examination of the concept of degree of rate control by first-principles kinetic Monte Carlo simulations. Surface Science, 603 (10). pp. 1724-1730. Gräser, C. and Sander, O. (2009) The dune-subgrid module and some applications. Computing, 86 (4). pp. 269-290. ISSN 0010-485X Splettstößer, T. and Noé, F. and Oda, T. and Smith, J. C. (2009) Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerisation-competent superclosed state. Proteins, 76 . pp. 353-364. Oevermann, M. and Scharfenberg , C. and Klein, R. (2009) A sharp interface finite volume method for elliptic equations on Cartesian grids. Journal of Computational Physics, 228 (14). pp. 5184-5206. Weese, D. and Emde, A.-K. and Rausch, T. and Döring, A. and Reinert, K. (2009) RazerS - Fast Read Mapping with Sensitivity Control. Genome Research, 19 (9). pp. 1646-1654. Schütte, Ch. and Jahnke, T. (2009) Towards Effective Dynamics in Complex Systems by Markov Kernel Approximation. Mathematical Modelling and Numerical Analysis (ESAIM), 43 (4). pp. 721-742. Klein, R. (2009) Asymptotics, structure, and integration of sound-proof atmospheric flow equations. Theoretical and Computational Fluid Dynamics, 23 (3). pp. 161-195. ISSN 0935-4964 (Print) 1432-2250 (Online) Jebens, S. and Knoth, O. and Weiner, R. (2009) Explicit Two-Step Peer Methods for the Compressible Euler Equations. Monthly Weather Review, 137 (7). pp. 2380-2392. Vercauteren, N. and Bou-Zeid, E. and Huwald, H. and Parlange, M. B. and Brutsaert, W. (2009) Estimation of wet surface evaporation from sensible heat flux measurements. Water Resources Research, 45 (6). Strenziok, R. and Hinz, S. and Wolf, C. and Conrad, T. O. F. and Krause, H. and Miller, K. and Schrader, M. (2009) Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry: serum protein profiling in seminoma patients. World J of Urology, 28 (2). pp. 193-197. Schütte, Ch. and Noé, F. and Meerbach, E. and Metzner, Ph. and Hartmann, C. (2009) Conformation Dynamics. Proceedings of the 6th International Congress on Industrial and Applied Mathematics, I. Jeltsch and G. Wanner (eds.), . pp. 297-335. Plattner, N. and Meuwly, M. (2009) Higher order multipole moments for molecular dynamics simulations. Journal of Molecular Modeling, 15 (6). pp. 687-694. ISSN 1610-2940 Fiedler, G. M. and Leichtle, A. and Kase, J. and Baumann, S. and Ceglarek, U. and Felix, K. and Conrad, T. O. F. and Witzigmann, H. and Weimann, A. and Schütte, Ch. and Hauss, J. and Büchler, M. and Thiery, J. (2009) Serum Peptidome Profiling Revealed Platelet Factor 4 as a Potential Discriminating Peptide Associated With Pancreatic Cancer. Clinical Cancer Research, 15 (11). pp. 3812-3819. ISSN 1078-0432 Audusse, E. and Klein, R. and Owinoh, A.Z. (2009) Conservative Discretization of Coriolis Force. Journal of Computational Physics, 228 (8). pp. 2934-2950. Zerck, A. and Nordhoff, E. and Reseman, A. and Mirgorodskaya, E. and Suckau, D. and Reinert, K. and Lehrach, H. and Gobom, J. (2009) An iterative strategy for precursor ion selection for LC-MS/MS based shotgun proteomics. Journal of Proteome Research . Hartmann, C. and Schütte, Ch. and Kalibaeva, G. and Di Pierro, M. and Ciccotti, G. (2009) Fast Simulation of Polymer Chains. J. Chem. Phys., 130 . p. 144101. Schlegel, M. and Knoth, O. and Arnold, M. and Wolke, R (2009) Multirate Runge-Kutta schemes for advection equations. Journal of Computational and Applied Mathematics, 226 (2). pp. 345-357. ISSN 0377-0427 von Kleist, M. and Huisinga, W. (2009) Pharmacokinetic–pharmacodynamic relationship of NRTIs and its connection to viral escape: An example based on zidovudine. European Journal of Pharmaceutical Sciences, 36 . pp. 532-543. Gassner, G.J. and Lörcher, F. and Munz, C.-D. and Hesthaven, J.-S. (2009) Polymorphic nodal elements and their application in discontinuous Galerkin methods. Journal of Computational Physics, 228 (5). 1573-1590 . Gräser, C. and Kornhuber, R. (2009) Nonsmooth Newton methods for set-valued saddle point problems. SIAM Journal on Numerical Analysis, 47 (2). pp. 1251-1273. ISSN 0036-1429 Metzner, Ph. and Schütte, Ch. and Vanden-Eijnden, E. (2009) Transition Path Theory for Markov Jump Processes. Mult. Mod. Sim., 7 (3). pp. 1192-1219. Mellado, J.- P. and Stevens, B. and Schmidt, H. and Peters, N. (2009) Analysis of latent heat effects in the cloud-top mixing layer. Quarterly Journal of the Royal Meteorological Society, 135 (641). pp. 963-978. Belaschk, H.C. and Münch, M. (2009) Anwendung von massiv paralleler Berechnung mit Grafikkarten GPGPU) für CFD-Methoden im Brandschutz. Bauphysik Volume 31 Issue 4, Pages 216 - 226, 31 (4). pp. 216-226. Devereux, M. and Plattner, N. and Meuwly, M. (2009) Application of Multipolar Charge Models and Molecular Dynamics Simulations to Study Stark Shifts in Inhomogeneous Electric Fields†. The Journal of Physical Chemistry A, 113 (47). pp. 13199-13209. ISSN 1089-5639 Münch, M. (2009) Brandsimulationsprogramme - Chancen und Risiken. schadenprisma, Zeitschrift für Schadenverhütung und Schadenforschung der öffentlichen Versicherer, 2 . pp. 14-18. Mellado, J.- P. and Schmidt, H. and Stevens, B. and Peters, N. (2009) Buoyancy reversal in the cloud-top mixing layer. (Submitted) Gräfe, Ch. and Nordmeier, V. and Schütte, Ch. (2009) Computerspiel zum Thema Moleküldynamik für Schüler der 7.-10. Klasse, Experimentelles Protyping zur Entwicklung eines Lernspiels. Jahrestagung 2008 der GDCP (Gesellschaft für Didaktik der Chemie und Physik), 1 . pp. 77-79. ISSN 978-3-643-10010-8 Giorgetta, M. and Hundertmark, T. and Korn, P. and Reich, S. and Restelli, M. (2009) Conservative Space and Time Regularizations for the ICON Model. Reports on Earth System Science, 67 . pp. 1-32. ISSN 1614-1199 Dumbser, M. and Gassner, G. and Munz , C.-D. (2009) Discontinuous Galerkin-Verfahren für zeitabhängige Advektions-Diffusions-Gleichungen. Jahresbericht der DMV, 111 (3). pp. 87-123. Metzner, Ph. and Noé, F. and Schütte, Ch. (2009) Estimating the Sampling Error: Distribution of Transition Matrices and Functions of Transition Matrices for Given Trajectory Data. Phys. Rev. E, 80 (2). 021106. Queck, R. and Bienert, A. (2009) Estimation of PBL model parameters from high resolution vegetation scans. Geophysical Research Abstracts, 11 (EGU2009-10888). Schatzmann, M. and Leitl, B. (2009) Evaluation of Numerical Flow and Dispersion Models for Applications in Industrial and Urban Areas. Chemical Engineering & Technology, 32 (2). 241 -246. Swart, A. and Manders, A. and Harlander, U. and Maas, U. and Leo , R. M. (2009) Experimental observation of strong mixing due to internal wave focusing over sloping terrain. Dynamics of Atmospheres and Oceans, 50 (1). pp. 16-34. Bauer, R. A. and Rother, K. and Moor, P. and Reinert, K. and Steinke, T. and Bujnicki, J. M. and Preissner, R. (2009) Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors. Algorithms and Molecular Sciences, 2 (2). pp. 692-709. ISSN 1999-4893 Gerisch, A. and Lang, J. and Podhaisky, H. and Weiner, R. (2009) High-order linearly implicit two-step peer-finite element method for time-dependent PDEs. Applied Numerical Mathematics, 59 (3-4). 624-638 . ISSN 0168-9274 Stenke, A. and Dameris, M. and Grewe, V. and Garny, H. (2009) Implications of Lagrangian transport for simulations with a coupled chemistry-climate model. Atmospheric Chemistry and Physics, 9 . pp. 5489-5504. Harlander, U. and Ridderinkhof, H. and Schouten, M.W. and de Ruijter, W. P. M (2009) Long-term observations of transport, eddies, and Rossby waves in the Mozambique Channel. JOURNAL OF GEOPHYSICAL RESEARCH, 114 (C02003). 15pp. Swart, T. and Rousse, V. (2009) A Mathematical Justification for the Herman-Kluk Propagator. Comm. Math. Phys., 286 (2). pp. 725-750. Papke, A. (2009) Mindestens 17 müssen es sein. Junge Wissenschaft, 84 . pp. 24-31. Kube, S. and Lasser, C. and Weber, M. (2009) Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics. J. Comp. Phys., 228 (6). pp. 1947-1962. Gräser, C. and Kornhuber, R. (2009) Multigrid methods for obstacle problems. Journal of Computational Mathematics, 27 (1). pp. 1-44. ISSN 0254-9409 Wensch, J. and Knoth, O. and Galant, A. (2009) Multirate infinitesimal step methods for atmospheric flow simulation. BIT - Numerical Mathematics, 49 (2). pp. 449-473. ISSN 0006-3835 (Print) 1572-9125 (Online) Schmidt, H. and Mellado, J.- P. and Peters, N. and Kerstein, A.R. and Stevens, B. (2009) Numerical study of buoyancy reversal in stably stratified flows. Geophysical Research Abstracts, 11 . (Submitted) Horenko, I. (2009) On metastable conformational analysis of non-equilibrium biomolecular time series. MMS . (Submitted) Horenko, I. (2009) On robust estimation of low-frequency variability trends in discrete Markovian sequences of atmospherical circulation patterns. The Journal of Atmospherical Sciences, 66 (7). 2059-2072 . Horenko, I. (2009) On structure-preserving persistent clustering of multivariate time series. Journal of Computational Physics . (Submitted) Pingen, G. and Waidmann, M. and Evgrafov, A. and Maute, K. (2009) A Parametric Level-Set Approach for Topology Optimization of Flow Domains. Structural and Multidisciplinary Optimization . ISSN 1615-147X (Print) 1615-1488 (Online) Dolaptchiev, S. and Klein, R. (2009) Planetary geostrophic equations for the atmosphere with evolution of the barotropic flow. Dynamics of Atmospheres and Oceans Volume, 46 (1-4). pp. 46-61. Leibscher, M. and Schmidt, B. (2009) Quantum dynamics of a plane pendulum. Phys. Rev. A, 80 (1). 012510. Altmann, C. and Gassner, G. and Lörcher, F. and Munz , C.-D. (2009) A Space-Time Expansion Discontinuous Galerkin Scheme With Local Time Stepping for the Ideal and Viscous MHD Equations. IEEE Transactions on Plasma Science, 37 (4). 513 -519 . Vater, S. and Klein, R. (2009) Stability of a Cartesian grid projection method for zero Froude number shallow water flows. Numerische Mathematik, 113 (1). pp. 123-161. Owschimikow, N. and Schwentner, N. and Schmidt, B. (2009) State Selection in Non-Resonantly Excited Wave Packets by Tuning from Non-Adiabatic to Adiabatic Interaction. Phys. Rev. A, 80 (5). 053409. Schulz-Trieglaff, O. and Machtejevas, E. and Reinert, K. and Schlueter, H. and Thiemann, J. and Unger, K. (2009) Statistical Quality Assessment and Outlier Detection for Liquid Chromatography-Mass Spectrometry Experiments. BioDataMining, 2 (4). Franzke, Ch. and Horenko, I. and Majda, A. J. and Klein, R. (2009) Systematic Metastable Atmospheric Regime Identification in an AGCM. J. Atm. Sci., 66 (7). pp. 1997-2012. Zhu, H. and Röder, B. and May, V. (2009) Time and frequency resolved spontaneous emission from supramolecular pheophorbide-a complexes: A mixed quantum classical computation. Chem. Phys., 362 (1-2). pp. 19-26. Qu, Z.-W. and Zhu, H. and May, V. and Schinke, R. (2009) Time-Dependent Density Functional Theory Study of the Electronic Excitation Spectra of Chlorophyllide a and Pheophorbide a in Solvents. J. Phys. Chem. B, 113 (14). pp. 4817-4825. Löbig, S. and Dörnbrack, A. and Fröhlich, J. and Hertel, C. and Kühnlein, C. and Lang, J. (2009) Towards Large-Eddy Simulation on moving grids. PAMM · Proc. Appl. Math. Mech., 9 . 445 -446. Ionescu, C. and Klein, R.J.T. and Hinkel, J., and Kavi Kumar, K.S., and Klein, R. (2009) Towards a formal framework for vulnerability to climate change. Environmental Modeling and Assessment, 14 (1). pp. 1-16. ISSN 1420-2026 (Print) 1573-2967 (Online) Barth, I. and Lasser, C. (2009) Trigonometric pulse envelopes for laser-induced quantum dynamics. J. Phys. B: At. Mol. Opt. Phys., 42 (23). p. 235101. Hickel, S. and von Terzi, D.A. and Fröhlich, J. (2009) An adaptive local deconvolution method for general curvilinear coordinate systems. Springer Proceedings Physics - Advances in Turbulence XII, 132 (11). pp. 783-786. Rausch, T. and Koren, S. and Denisov, G. and Weese, D. and Emde, A.-K. and Döring, A. and Reinert, K. (2009) A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics, 25 (9). pp. 1118-1124. Kilian, S. and Münch, M. (2009) A new generalized domain decomposition strategy for the efﬁcient parallel solution of the FDS-pressure equation. Part I: Theory, Concept and Implementation. ZIB-Report, 09-19 . 30 pages. ISSN 1438-0064 Schmidt, H. and Oevermann, M. and Bastiaans, R.J.M. and Kerstein, A.R. (2009) A priori Tabulation of Turbulent Flame Speeds via a Combination of a Stochastic Mixing Model and Flamelet Generated Manifolds, Extended to Incorporate Strain Effects. ZIB Report, 09-09 . ISSN 1438-0064 Moeck, J. and Oevermann, M. and Klein, R. and Paschereit, O. C. and Schmidt, H. (2009) A two-way coupling for modeling thermoacoustic instabilities in a flat flame Rijke tube. Proceedings of the Combustion Institute, 32 (1). pp. 1199-1207. Plattner, N. and Bandi, T. and Doll, J. D. and Freeman, D. and Meuwly, M. (2008) MD simulations using distributed multipole electrostatics: Structural and spectroscopic properties of CO- and methane-containing clathrates. Molecular Physics, 106 (12). pp. 1675-1684. ISSN 0026-8976 Letzel, O. and Krane, M. and Raasch, S. (2008) High resolution urban large-eddy simulation studies from street canyon to neighbourhood scale. Atmospheric Environment, 42 (38). 8770-8784 . Bou-Zeid, E. and Vercauteren, N. and Parlange, M. B. and Meneveau, C. (2008) Scale dependence of subgrid-scale model coefficients: An a priori study. Physics of Fluid, 20 (115106). Matute, R. A. and Contreras, R. and Pérez-Hernández, G. and González, L. (2008) The Chromophore Structure of the Cyanobacterial Phytochrome Cph1 As Predicted by Time-Dependent Density Functional Theory. The Journal of Physical Chemistry B, 112 (51). pp. 16253-16256. ISSN 1520-6106 Pérez-Hernández, G. and González, L. and Serrano-Andrés, L. (2008) Rydberg or Valence? The Long-Standing Question in the UV Absorption Spectrum of 1,1′-Bicyclohexylidene. ChemPhysChem, 9 (17). p. 2544. ISSN 14394235 Carqué, G. and Schmidt, H. and Stevens, B. and Klein, R. (2008) Plausibility Check of an Asymptotic Column Model for Deep Convective Clouds. ZIB-Report, 08 (44). Kornhuber, R. and Yserentant, H. (2008) Multigrid methods for discrete elliptic problems on triangular surfaces. Computing and Visualization in Science, 11 (4-6). pp. 251-257. ISSN 1432-9360 Vercauteren, N. and Bou-Zeid, E. and Parlange, M. B. and Lemmin, U. and Huwald, H. and Selker, J. S. and Meneveau, C. (2008) Subgrid-Scale Dynamics of Water Vapour, Heat, and Momentum over a Lake. Boundary-Layer Meteorology, 128 (2). pp. 205-228. ISSN Print: 0006-8314 Online: 1573-1472 Barth, I. and Manz, J. and Pérez-Hernández, G. and Sebald, P. (2008) Towards Toroidal Hydrogen Bonds. Zeitschrift für Physikalische Chemie, 222 (8-9). pp. 1311-1331. ISSN 0942-9352 Schäfer-Bung, B. and Nest , M. (2008) Correlated Dynamics of Electrons with Reduced 2-Electron Density Matrices. Phys. Rev. A, 78 (1). 012512. Münch, M. and Klein, R. (2008) Critical numerical aspects for field model applications. EUSAS Journal (4). pp. 41-54. Abida, R. and Bocquet, M. and Vercauteren, N. and Isnard, O. (2008) Design of a monitoring network over France in case of a radiological accidental release. Atmospheric Environment, 42 (21). pp. 5205-5219. ISSN 1352-2310 Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Ohlberger, M. and Sander, O. (2008) A generic grid interface for parallel and adaptive scientific computing. Part I: Abstract framework. Computing, 82 (2-3). pp. 103-119. ISSN 0010-485X Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Kornhuber, R. and Ohlberger, M. and Sander, O. (2008) A generic grid interface for parallel and adaptive scientific computing. Part II: Implementation and tests in DUNE. Computing, 82 (2-3). pp. 121-138. ISSN 0010-485X Rausch, T. and Thomas, A. and Camp, N. J. and Facelli, L. A. (2008) A parallel genetic algorithm to discover patterns in genetic markers that indicate predisposition to multifactorial disease. Comput. Biol. Med., 38 . pp. 826-836. Plattner, N. and Meuwly, M. (2008) Atomistic Simulations of CO Vibrations in Ices Relevant to Astrochemistry. ChemPhysChem, 9 (9). pp. 1271-1277. ISSN 14394235 Plattner, N. and Meuwly, M. (2008) The Role of Higher CO-Multipole Moments in Understanding the Dynamics of Photodissociated Carbonmonoxide in Myoglobin. Biophysical Journal, 94 (7). pp. 2505-2515. ISSN 00063495 Strenziok, R. and Hinz, S. and Wolf, C. and Conrad, T. O. F. and Krause, H. and Lingnau, A. and Lein, M. and Miller, K. and Schrader, M. (2008) Serum proteomic profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry in testicular germ cell cancer patients. European Urology Supplements, 7 (3). p. 83. Schäfer-Bung, B. (2008) The interplay of wave packet dephasing, optimization efficiency, and target state population in optimally controlled isotope selective photoionization. Chem. Phys., 343 . pp. 340-346. Carqué, G. and Owinoh, A.Z. and Klein, R. and Majda, A. J. (2008) Asymptotic Scale Analysis of Precipitating Clouds. ZIB-Report, 08-03 . ISSN 1438-0064 Münch, M. (2008) MOLOCH - Ein Strömungsverfahren für inkompressible Strömungen - Technische Referenz. PIK-Report (109). Kornhuber, R. and Krause, R. and Sander, O. and Deuflhard, P. and Ertel, S. (2008) A monotone multigrid solver for two body contact problems in biomechanics. Computing and Visualization in Science, 11 (1). pp. 3-15. ISSN 1432-9360 Frigato, T. and VandeVondele, J. and Schmidt, B. and Schütte, Ch. and Jungwirth, P. (2008) Ab Initio Molecular Dynamics Simulation of a Medium-Sized Water Cluster Anion: From an Interior to a Surface Located Excess Electron via a Delocalized State. J. Phys. Chem. A, 112 (27). pp. 6125-6133. Münch, M. and Klein, R. (2008) Anforderungen an numerische Berechnungen der Brand- und Rauchausbreitung im Vorbeugenden Brandschutz. vfdb-Zeitschrift Forschung, Technik und Management im Brandschutz, Jg. 57 (3). pp. 145-151. ISSN 0042-1804 Horenko, I. (2008) Automated Generation of Reduced Stochastic Weather Models I: Simultaneous Dimension and Model Reduction for Time Series Analysis. Multiscale Modeling & Simulation, 6 (4). p. 1125. ISSN 15403467 Horenko, I. and Klein, R. and Dolaptchiev, S. and Schütte, Ch. (2008) Automated Generation of Reduced Stochastic Weather Models I: Simultaneous Dimension and Model reduction for Time Series Analysis. Mult. Mod. Sim., 6 (4). pp. 1125-1145. Hartmann, C. and Schütte, Ch. (2008) Balancing of partially-observed stochastic differential equations. 47th IEEE Conference on Decision and Control . pp. 4867-4872. Schulz-Trieglaff, O. and Hussong, R. and Gröpl, C. and Hildebrandt, A. and Hildebrandt, A. and Huber, Ch. and Reinert, K. (2008) Computational Quantification of Peptides from LC-MS data. Journal of Computational Biology, 15 (7). pp. 685-704. Lange, E. and Tautenhahn, R. and Neumann, S. and Gröpl, C. (2008) Critical assessment of alignment procedures for LC-MS proteomics and metabolomic measurements. BMC Bioinformatics, 9 (375). Warren, R. and de la Nava Santos, S. and Arnell, N.W. and Bane, M. and Barker, T. and Barton, C. and Ford, R. and Füssel, H.-M. and Hankin, Robin K.S. and Klein, R. and Linstead, C. and Kohlera, J. and Mitchella, T.D. and Osborna, T.J. and Pan, H. and Raper, S.C.B. and Riley, G. and Schellnhuber, H.J. and Winne, S. and Anderson, D. (2008) Development and illustrative outputs of the Community Integrated Assessment System (CIAS), a multi-institutional modular integrated assessment approach for modelling climate change. Environmental Modelling & Software, 23 (5). 592-610 . Horenko, I. and Schütte, Ch. (2008) Dimension Reduction for Time Series with Hidden Phase Transitions and Economic Applications. Adv. Data Anal. Class., submitted . (Submitted) Gassner, G. and Lörcher, F. and Munz , C.-D. (2008) A Discontinuous Galerkin Scheme based on a Space-Time Expansion II. Viscous Flow Equations in Multi Dimensions. Journal of Scientific Computing, 34 (3). pp. 260-286. ISSN 0885-7474 (Print) 1573-7691 (Online) Craig, G.C. and Dörnbrack, A. (2008) Entrainment in Cumulus Clouds: What resolution is cloud resolving? J. Atmos. Sci., 65 . pp. 3978-3988. ISSN Online 1520-0469 Print 0022-4928 Hartmann, C. (2008) An Ergodic Sampling Scheme for Constrained Hamiltonian Systems with Applications to Molecular Dynamics. J. Stat. Phys., 130 (4). pp. 687-712. Bauer, M. and Klau, G. W. and Reinert, K. (2008) An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment. Algorithmic Operations Research . John, V. and Schmeyer, E. (2008) Finite element methods for time-dependent convection-diffusion-reaction equations with small diffusion. Computer methods in applied mechanics and engineering, 198 (3). pp. 475-494. ISSN 0045-7825 Kadioglu, S.Y. and Minion, M.L. and Klein, R. (2008) A Fourth-Order Auxiliary Variable Projection Method for Zero-Mach Number Gas Dynamics. Journal of Computational Physics , 227 (3). 2012-2043 . Ullrich, Alexander and Flamm, Christoph (2008) Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe. Computational Methods in Systems Biology, 5307 . pp. 28-43. Bodirsky, M. and Gröpl, C. and Kang, M. (2008) Generating unlabeled connected cubic planar graphs uniformly at random. Random Structures and Algorithms, 32 (2). pp. 157-180. von Larcher, T. and Futterer, B. and Egbers, C. and Hollerbach, R. and Chossat, P. and Beltrame, P. and Tuckerman, L. and Feudel, F. (2008) GeoFlow - European Microgravity Experiments on Thermal Convection in Rotating Spherical Shells under influence of Central Force Field. Journal of The Japan Society of Microgravity Application, 25 (3). von Larcher, T. and Futterer, B. and Egbers, C. (2008) GeoFlow: On the status of experimental preparation of spherical gap flow experiments with central force field on International Space Station (ISS). Journal of Physics: Conference Series, 137 (012025). p. 6. Oevermann, M. and Schmidt, H. and Kerstein, A.R. (2008) HCCI combustion modeling using detailed chemistry coupled to LEM-based advection. Combustion and Flame, 155 . pp. 370-379. Teleaga, , I. and Lang, J. (2008) Higher-order linearly implicit one-step methods for three-dimensional incompressible Navier-Strokes equations. Studia Babes-Bolyai Matematica, 53 . pp. 109-121. Tomm, S. and von Terzi, D.A. and Fröhlich, J. (2008) Interaction of the filter and spatial discretisation operators for Large-Eddy Simulation using the Approximate Deconvolution Model. PAMM, 8 . pp. 10605-10606. Oevermann, M. and Schmidt, H. and Kerstein, A.R. (2008) Investigation of autoignition under thermal stratification using linear eddy modeling. Combustion and Flame Volume, 155 (3). 370-379 . Schulz-Trieglaff, O. and Pfeifer, N. and Gröpl, C. and Kohlbacher, O. and Reinert, K. (2008) LC-MSsim - a simulation software for liquid chromatography mass spectrometry data. BMC Bioinformatics, 9 (423). Horenko, I. and Schütte, Ch. (2008) Likelihood-Based Estimation of Multidimensional Langevin Models and its Application to Biomolecular Dynamics. Mult. Mod. Sim., 7 (2). pp. 731-773. Horenko, I. and Dittmer, E. and Lankas, F. and Maddocks, J. and Metzner, Ph. and Schütte, Ch. (2008) Macroscopic Dynamics of Complex Metastable Systems: Theory, Algorithms, and Application to B-DNA. J. Appl. Dyn. Syst., 7 (2). pp. 532-560. Horenko, I. and Dolaptchiev, S. and Eliseev, A. and Mokhov, I. and Klein, R. (2008) Metastable Decomposition of High-Dimensional Meteorological Data with Gaps. Journal of the Atmospheric Sciences, 65 (11). pp. 3479-3496. Pincus, R. and Stevens, B. (2008) Monte Carlo spectral integration: A consistent approximation for radiative transfer in large eddy simulations. Journal of Advancesin Modeling Earth Systems, 1 . p. 9. Doyle, J.D. and Grubišić, V. and Brown, W.O.J. and De Wekker, S.F.J. and Dörnbrack, A. and Jiang, Q. and Mayor, S.D. and Weissman, M. (2008) Observations and Numerical Simulations of Subrotor Vortices during T-REX. J. Atmos. Sci., 66 (5). ISSN Online 1520-0469 Print 0022-4928 Horenko, I. (2008) On Simultaneous Data-Based Dimension Reduction and Hidden Phase Identification. J. Atm. Sci, 65 (6). pp. 1941-1954. Horenko, I. (2008) On robust estimation of low-frequency variability trends in discrete Markovian sequences of atmospheric circulation patterns. J. Atm. Sci. . (In Press) Petoukhov, V. and Eliseev, A. and Klein, R. and Oesterle, H. (2008) On the statistics of the free-troposphere synoptic component. Part I: An evaluation of skewnesses and estimation of the third-order moments contribution to the synoptic-scale dynamics and meridional fluxes of heat and humidity. Tellus, 60 (1). pp. 11-31. Sturm, M. and Andreas, B. and Gröpl, C. and Hussong, R. and Lange, E. and Pfeifer, N. and Schulz-Trieglaff, O. and Zerck, A. and Reinert, K. and Kohlbacher, O. (2008) OpenMS - An open-source software framework for mass spectrometry. BMC Bioinformatics, 9 (163). Noé, F. (2008) Probability Distributions of Molecular Observables computed from Markov Models. J. Chem. Phys., 128 . p. 244103. Fermanian Kammerer, C. and Lasser, C. (2008) Propagation through Generic Level Crossings: A Surface Hopping Semigroup. J. Math. Anal., 40 (1). pp. 103-133. Rausch, T. and Emde, A.-K. and Reinert, K. (2008) Robust consensus computation. BMC Bioinformatics, 9 (Suppl 10). P4. Rausch, T. and Emde, A.-K. and Weese, D. and Notredame, C. and Reinert, K. (2008) Segment-based multiple sequence alignment. Bioinformatics, 24 (16). i187-192. Döring, A. and Weese, D. and Rausch, T. and Reinert, K. (2008) SeqAn -- An efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9 (1). p. 11. Meerbach, E. and Schütte, Ch. (2008) Sequential Change Point Detection in Molecular Dynamics Trajectories. Journal of Multivariate Analysis, submitted . Lasser, C. and Swart, T. (2008) Single switch surface hopping for a model of pyrazine. J. Chem.Phys., 129 (03). 034302. Fermanian Kammerer, C. and Lasser, C. (2008) Single switch surface hopping for molecular dynamics with transitions. J. Chem. Phys., 128 (14). p. 144102. Noé, F. and Daidone, I. and Smith, J. C. and Di Nola, A. and Amadei, A. (2008) Solvent Electrostriction Driven Peptide Folding revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation. J. Phys. Chem. B, 112 . pp. 11155-11163. Baldauf, M. (2008) Stability analysis for linear discretisations of the advection equation with Runge–Kutta time integration. Journal of Computational Physics, 227 (13). pp. 6638-6659. Schulz-Trieglaff, O. and Machtejevas, E. and Reinert, K. and Schlueter, H. and Thiemann, J. and Unger, K. (2008) Statistical Quality Assessment and Outlier Detection for Liquid Chromatography-Mass Spectrometry Experiments. BioDataMining . accepted for publication. (In Press) Hartmann, C. (2008) Structure-preserving model reduction of partially observed differential equations: molecular dynamics and beyond. Oberwolfach Reports, 5 (2). pp. 1111-1115. Schmidt, H. and Oevermann, M. and Bastiaans, R.J.M. and Kerstein, A.R. (2008) Tabulation of turbulent burning rates via a combination of a stochastic mixing model and tabulated chemistry. ZIB Report, 08 (2). Futterer, B. and Gellert, M. and von Larcher, T. and Egbers, C. (2008) Thermal convection in rotating spherical shells: An experimental and numerical approach within GeoFlow. Acta Astronautica, 62 (4). pp. 300-307. Schmidt, H. and Mellado, J.- P. and Peters, N. and Stevens, B. (2008) Towards modular front tracking for Stratocumulus clouds considering unsteady entrainment processes. Geophysical Research Abstracts, 10 . Noé, F. and Fischer, S. (2008) Transition Networks for Modeling the Kinetics of Conformational Change in Macromolecules. Curr. Opin. Struct. Biol., 18 . pp. 154-162. Ruprecht, D. and Schaedle, A. and Schmidt, F. and Zschiedrich, L. (2008) Transparent Boundary Conditions for Time-dependent Problems. SIAM J. Sci. Comput., 30 (5). pp. 2358-2385. ISSN 1064-8275 Mellado, J.- P. and Stevens, B. and Schmidt, H. and Peters, N. (2008) Two-fluid formulation of the cloud-top mixing layer for direct numerical simulation. Theoretical and Computational Fluid Dynamics . (Submitted) Klein, R. (2008) An Unified Approach to Meteorological Modelling Based on Multiple-Scales Asymptotics. Advances in Geosciences, 15 . pp. 23-33. Papke, A. (2008) Wie viele Zahlen müssen es sein? Die Junge Wissenschaft, 79 . pp. 46-51. Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Kornhuber, R. and Ohlberger, M. and Sander, O. (2008) A generic grid interface for parallel and adaptive scientific computing. II: Implementation and tests in DUNE. Computing, 82 (2-3). pp. 121-138. Metzner, Ph. and Horenko, I. and Schütte, Ch. (2007) Generator Estimation of Markov Jump Processes Based on Incomplete Observations Nonequidistant in Time. Phys. Rev. E, 76 (06). 066702. von Kleist, M. and Huisinga, W. (2007) Physiologically Based Pharmacokinetic Modelling: A Sub-Compartmentalized Model of Tissue Distribution. J. Pharmacokin. Pharmacodyn., 34 (6). pp. 789-806. Metzner, Ph. and Dittmer, E. and Jahnke, T. and Schütte, Ch. (2007) Generator Estimation of Markov Jump Processes. J. Comp. Phys., 227 (1). pp. 353-375. Bauer, M. and Klau, G. W. and Reinert, K. (2007) Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics, 8 (1). p. 271. Noé, F. and Horenko, I. and Schütte, Ch. and Smith, J. C. (2007) Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States. J. Chem. Phys., 126 (15). p. 155102. Hartmann, C. and Schütte, Ch. (2007) Comment on Two Distinct Notions of Free Energy. Physica D, 228 (1). pp. 59-63. Lorenz, S. and Diederichs, E. and Telgmann, R. and Schütte, Ch. (2007) Discrimination of Dynamical System Models for Biological and Chemical Processes. J. Comp. Chem., 28 (8). pp. 1384-1399. Jahnke, T. and Huisinga, W. (2007) Solving the Chemical Master Equation for Monomolecular Reaction Systems Analytically. J. Math. Biol., 54 (1). pp. 1-26. Pingen, G. and Waidmann, M. and Evgrafov, A. and Maute, K. (2007) Application of a Parametric Level-Set Approach to Topology Optimization of Fluids with the Navier–Stokes and Lattice Boltzmann Equations. 7th World Congress on Structural and Multidisciplinary Optimization . Mellado, J.- P. and Stevens, B. and Schmidt, H. and Peters, N. (2007) Buoyancy-reversal in cloud-top mixing layers. Quarterly journal of the royal meteorological society . pp. 1-21. Lasser, C. and Swart, T. and Teufel, St. (2007) Construction and validation of a rigorous surface hopping algorithm for conical crossings. Comm. Math. Sci., 5 (4). pp. 789-814. Horenko, I. and Hartmann, C. and Schütte, Ch. and Noé, F. (2007) Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes. Phys. Rev. E, 76 (01). 016706. Lörcher, F. and Gassner, G. and Munz , C.-D. (2007) A Discontinuous Galerkin Scheme Based on a Space–Time Expansion. I. Inviscid Compressible Flow in One Space Dimension. Journal of Scientific Computing, 32 (2). pp. 175-199. ISSN 0885-7474 (Print) 1573-7691 (Online) Gu, W. and Frigato, T. and Straatsma, T. P. and Helms, V. (2007) Dynamic Protonation Equilibrium of Solvated Acetic Acid. Angew. Chem. Int. Ed., 46 (16). pp. 2939-2943. Bodirsky, M. and Gröpl, C. and Kang, M. (2007) Generating labeled planar graphs uniformly at random. Theoretical Computer Science, 379 (3). pp. 377-386. Lange, E. and Gröpl, C. and Schulz-Trieglaff, O. and Leinenbach, A. and Huber, Ch. and Reinert, K. (2007) A Geometric Approach for the Alignment of Liquid Chromatography-Mass Spectrometry Data. Oxford Journals, 23 (13). i273-i281. ISSN 1460-2059 (online), 1367-4803 (print) Fischer, A. and Waldhausen, S. and Horenko, I. and Meerbach, E. and Schütte, Ch. (2007) Identification of Biomolecular Conformations from Incomplete Torsion Angle Observations by Hidden Markov Models. J. Comp. Chem., 28 (15). pp. 2453-2464. Klau, G. W. and Rahmann, S. and Schliep, A. and Vingron, M. and Reinert, K. (2007) Integer Linear Programming Approaches for Non-unique Probe Selection. Discrete Applied Mathematics, 155 . pp. 840-856. Christen, M. and Keller, B. and van Gunsteren, W. F. (2007) Local elevation on the dihedral angles to improve the J-values. Journal of Biomolecular NMR, 39 . pp. 265-273. Lang, J. and Verwer, J. (2007) On Global Error Estimation and Control for Initial Value Problems. SIAM J. Sci. Comp., 29 (4). pp. 1460-1475. ISSN 1064-8275 (print) 1095-7197 (online) Debrabant, K. and Lang, J. (2007) On Global Error Estimation and Control for Parabolic Equations, Report No. 2512. Appl. Num. Math. . (Submitted) Keller, B. and Christen, M. and Oostenbrink, C. and van Gunsteren, W. F. (2007) On using oscillating time-dependent restraints in MD simulation. Journal Of Biomolecular NMR, 37 . pp. 1-14. Noé, F. and Oswald, M. and Reinelt, G. (2007) Optimization in Graphs with Limited Information on the Edge Weights. Operations Research Proceedings 2007. Editors: J. Kalcsics and S. Nickel . pp. 435-440. Noé, F. and Smith, J. C. (2007) Transition Networks: a unifying theme for molecular simulation and computer science. Mathematical Modeling of Biological Systems I, A. Deutsch, L. Brusch, H. Byrne, G. de Vries and H.-P. Herzel (Eds) . pp. 125-144. Bodirsky, M. and Gröpl, C. and Johannsen, D. and Kang, M. (2007) A direct decomposition of 3-connected planar graphs. Séminaire Lotharingien de Combinatoire, B54Ak . 15 pages. Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Ohlberger, M. and Sander, O. (2007) A generic grid interface for parallel and adaptive scientific computing. I: Abstract framework. Computing, 82 (2-3). pp. 103-119. Noé, F. and Smith, J. C. and Schütte, Ch. (2007) A network-based approach to biomolecular dynamics. From Computational Biophysics to Systems Biology (CBSB07). Editors: U. H. E. Hansmann, J. Meinke, S. Mohanty and O. Zimmermann, NIC Se . Schäfer-Bung, B. and Bonačić-Koutecký, V. and Sauer, F. and Weber, S. and Wöste, L. and Lindinger, A. (2006) Isotope selective photoionization of NaK by optimal control: Theory and experiment. J. Chem. Phys., 125 (21). 214310-1-214310-8. Oevermann, M. and Klein, R. (2006) A cartesian grid finite volume method for the solution of the Poisson equation with variable coefficients and embedded interfaces. Journal of Computational Physics, 219 (2). 749-769 . Schäfer-Bung, B. and Mitrić, R. and Bonačić-Koutecký, V. (2006) Photostabilization of ultracold Rb2 molecules by optimal control. J. Phys. B, 39 (19). S1043-S1053. Bastian, P. and Blatt, M. and Engwer, C. and Dedner, A. and Klöfkorn, R. and Kuttanikkad, S. P. and Ohlberger, M. and Sander, O. (2006) The Distributed and Unified Numerics Environment (DUNE). Proc. of the 19th Symposium on Simulation Technique . Bernhard, S. (2006) Transient integral boundary layer method to calculate the translesional pressure drop and the fractional flow reserve in myocardial bridges. BioMedical Engineering OnLine, 5 (42). Kornhuber, R. and Krause, R. (2006) Robust multigrid methods for vector-valued Allen-Cahn equations with logarithmic free energy. Computing and Visualization in Science, 9 (2). pp. 103-116. ISSN 1432-9360 Krause, R. and Sander, O. (2006) Automatic construction of boundary parametrizations for geometric multigrid solvers. Computing and Visualization in Science, 9 (1). pp. 11-22. ISSN 1432-9360 Bonačić-Koutecký, V. and Mitrić, R. and Bürgel, Ch. and Schäfer-Bung, B. (2006) Cluster Properties in the regime in which each atom counts. Comput. Mater. Sci., 35 (3). pp. 151-157. Oevermann, M. and Klein, R. (2006) A cartesian grid finite volume method for the solution of the Poisson equation with variable coefficients and embedded interfaces. JCP . Gebauer, S. and Kornhuber, R. and Yserentant, H. (2006) Hierarchical decomposition of domains with fractures. Mathematics of Computation, 75 (253). pp. 73-90. ISSN 00255718 Caselles, V. and Igual, L. and Sander, O. (2006) An axiomatic approach to scalar data interpolation on surfaces. Numerische Mathematik, 102 (3). pp. 383-411. ISSN 0029-599X Imhof, P. and Noé, F. (2006) AM1/d Parameters for Magnesium in Metalloenzymes. J. Chem. Theo. Comput., 2 . pp. 1050-1056. Mayr, B. M. and Kohlbacher, O. and Reinert, K. and Gröpl, C. and Lange, E. and Klein, C. L. and Huber, Ch. (2006) Absolute Myoglobin Quantitation in Serum by Combining Two-Dimensional Liquid Chromatography-Electrospray Ionization Mass Spectrometry and Novel Data Analysis Algorithms. Journal of Proteome Research, 5 . pp. 414-421. Wolski, W. E. and Farrow, M. and Emde, A.-K. and Maciej, L. and Lehrach, H. and Reinert, K. (2006) Analytical model of peptide mass cluster centres with applications. Proteome Science, 4 (18). doi:10.1186/1477-5956. Horenko, I. and Dittmer, E. and Fischer, A. and Schütte, Ch. (2006) Automated Model Reduction for Complex Systems exhibiting Metastability. Mult. Mod. Sim., 5 (3). pp. 802-827. Conrad, T. O. F. and Leichtle, A. and Hagehülsmann, A. and Diederichs, E. and Baumann, S. and Thiery, J. and Schütte, Ch. (2006) Beating the Noise: New Statistical Methods for Detecting Signals in MALDI-TOF Spectra Below Noise Level. Lecture Notes in Computer Science, 4216 . pp. 119-128. Althaus, E. and Caprara, A. and Lenhof, H.-P. and Reinert, K. (2006) A Branch-and-Cut Algorithm for Multiple Sequence Alignment. Mathematical Programming (105). pp. 387-425. Noé, F. and Oswald, M. and Reinelt, G. and Smith, J. C. and Fischer, S. (2006) Computing Best Transition Pathways in High-Dimensional Dynamical Systems. Multisc. Model. Sim., 5 . pp. 393-419. Metzner, Ph. and Schütte, Ch. and Vanden-Eijnden, E. (2006) Illustration of Transition Path Theory on a Collection of Simple Examples. J. Chem. Phys., 125 (8). 084110. Futterer, B. and Gellert, M. and Huschto, M. and von Larcher, T. and Egbers, C. (2006) Microgravity Science on International Space Station (ISS): The Geoflow Experiment. Forum der Forschung, 10. Jahrgang (19). pp. 113-118. ISSN 0947-6989 Deuflhard, P. and Ertel, S. and Kornhuber, R. and Krause, R. and Sander, O. (2006) Patient-specific simulation of dynamic stress distribution in the human knee. Journal of Biomechanics, 39 . p. 47. ISSN 0021-9290 Becker, T. and Fischer, S. and Noé, F. and Tournier, A. and Ullmann, M. and Kurkal, V. and Smith, J. C. (2006) Physical and functional aspects of protein dynamics. Soft Condensed Matter Physics in Molecular and Cell Biology, Poon & Andelman (Eds) . Klein, R. and Majda, A. J. (2006) Systematic Multiscale Models for Deep Convection on Mesoscales. Theoretical and Computational Fluid Dynamics, 20 (5-6). pp. 525-551. ISSN 0935-4964 (Print) 1432-2250 (Online) Kiljunen, T. and Schmidt, B. and Schwentner, N. (2006) Time-Dependent Alignment of Molecules Trapped in Octahedral Crystal Fields. J. Chem. Phys., 124 (16). p. 164502. Noé, F. and Krachtus, D. and Smith, J. C. and Fischer, S. (2006) Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins. J. Chem. Theo. Comput., 2 . pp. 840-857. Waidmann, M. and Waidmann, C. and Saile, D. and Grillmayer, G. (2006) Use of new developments on attitude control sensors for the microsatellite Flying Laptop. Proceedings of the 57th IAC/IAF/IAA, Valencia, Spain . Sander, O. (2006) A fast solver for finite deformation contact problems. Preprint A-06-02 . (Unpublished) Bernhard, S. (2005) Oscillatory flow in a tube with time-dependent wall deformation and its application to Myocardial Bridges. ESAIM: Proc., 14 . pp. 25-40. Horenko, I. and Lorenz, S. and Schütte, Ch. and Huisinga, W. (2005) Adaptive Approach for Non-Linear Sensitivity Analysis of Reaction Kinetics. J. Comp. Chem., 26 (9). pp. 941-948. Lorenz, K. and Jahnke, T. and Lubich, Ch. (2005) Adiabatic Integrators for Highly Oscillatory Second-Order Linear Differential Equations with Time-Varying Eigendecomposition. BIT Num. Math., 45 (1). pp. 91-115. Kiljunen, T. and Schmidt, B. and Schwentner, N. (2005) Aligning and Orienting Molecules Trapped in Octahedral Crystal Fields. Phys. Rev. A, 72 (5). 053415. Antony, J. and von Helden, G. and Meijer, G. and Schmidt, B. (2005) Anharmonic Midinfrared Vibrational Spectra of Benzoic Acid Monomer and Dimer. J. Chem. Phys., 123 (1). 014305. Noé, F. and Ille, F. and Smith, J. C. and Fischer, S. (2005) Automated Computation of Low-Energy Pathways for Complex Rearrangements in Proteins: Application to the conformational switch of Ras p21. Proteins, 59 . pp. 534-544. Wolski, W. E. and Lalowski, M. and Jungblut, P. and Reinert, K. (2005) Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants. BMC Bioinformatics, 6 (203). http://www.biomedcentral.com/1471-2105/6/203. Hartmann, C. and Schütte, Ch. (2005) A Constrained Hybrid Monte-Carlo Algorithm and the Problem of Calculating the Free Energy in Several Variables. Z. Angew. Math. Mech., 85 (10). pp. 700-710. von Larcher, T. and Egbers, C. (2005) Dynamics of baroclinic wave pattern in transition zones between different flow regimes. Journal of Physics: Conference Series, 14 . pp. 162-167. Owinoh, A.Z. and Hunt, J. and Orr, A. and Clark, P. and Klein, R. and Fernando, H. and Nieuwstadt, F. (2005) Effects Of Changing Surface Heat Flux On Atmospheric Boundary-Layer Flow Over Flat Terrain. Boundary Layer Meterology, 116 (2). pp. 331-361. Meerbach, E. and Schütte, Ch. and Fischer, A. (2005) Eigenvalue Bounds on Restrictions of Reversible Nearly Uncoupled Markov Chains. Lin. Alg. Appl., 398 . pp. 141-160. von Larcher, T. and Egbers, C. (2005) Experiments on transitions of baroclinic waves in a differentially heated rotating annulus. Nonlinear Processes in Geophysics, 12 . pp. 1033-1041. ISSN 1023-5809 (Print); 1607-7946 (Online) Schmidt, H. and Klein, R. (2005) Flexible flame structure modelling in a flame front tracking scheme. Analysis and Numerics for Conservation Laws . pp. 405-427. ISSN 978-3-540-24834-7 (Print) 978-3-540-27907-5 (Online) Hartmann, C. and Schütte, Ch. (2005) A Geometric Approach to Constrained Molecular Dynamics and Free Energy. Comm. Math. Sci., 3 (1). pp. 1-20. Kiljunen, T. and Schmidt, B. and Schwentner, N. (2005) Intense-Field Alignment of Molecules Confined in Octahedral Field. Phys. Rev. Lett., 94 (12). p. 123003. Klein, R. (2005) Multiple spacial scales in engineering and atmospheric low Mach number flows. ESAIM: Mathematical Modelling and Numerical Analysis (M2AN), 39 . pp. 537-559. ISSN 0764-583X Antony, J. and Schmidt, B. and Schütte, Ch. (2005) Nonadiabatic Effects on Peptide Vibrational Dynamics Induced by Conformational Changes. J. Chem. Phys., 122 (1). 014309. Gonzalez, L. and Manz, J. and Schmidt, B. and Shibl, M. F. (2005) Optical resolution of oriented enantiomers via photodissociation: Quantum simulations for H2POSD. Phys. Chem. Chem. Phys., 7 (24). pp. 4096-4101. Lasser, C. and Teufel, St. (2005) Propagation through conical crossings: An asymptotic semigroup. Comm. Pure Appl. Math., 58 (9). pp. 1188-1230. Schatzmann, M. and Britter, R. (2005) Quality assurance and improvement of micro-scale meteorological models. International Journal of Environment and Pollution . (Submitted) Horenko, I. and Dittmer, E. and Schütte, Ch. (2005) Reduced Stochastic Models for Complex Molecular Systems. Comp. Vis. Sci., 9 (2). pp. 89-102. Klein, C. L. and Kohlbacher, O. and Reinert, K. (2005) Reference methods and materials in standardisation and quality assurance (abstract). FEBS Journal, 272 (Supplement 1). pp. 490-504. Dellnitz, M. and Neumann, M. and Schütte, Ch. (2005) Special Issue on Matrices and Mathematical Biology. Lin. Alg. Appl., 398 . pp. 1-245. Wolski, E. and Lalowski, M. and Martus, P. and Giavalisco, P. and Gobom, J. and Sickmann, A. and Lehrach, H. and Reinert, K. (2005) Transformation and other factors of the peptide mass spectormetry pairwise peaklist comparison process. BMC Bioinformatics, 6 (285). http://www.biomedcentral.com/1471-2105/6/285. Conrad, T. O. F. (2004) New Approaches for Visualizing and Analyzing Metabolic Pathways. Proceedings of the Second Australian Undergraduate Students’ Computing Conference . Schäfer-Bung, B. and Mitrić, R. and Bonačić-Koutecký, V. and Bartelt, A. and Lupulescu, C. and Lindinger, A. and Vajda, Š. and Weber, S. and Wöste, L. (2004) Optimal control of ionization processes in NaK; comparison between theory and experiment. J. Phys. Chem. A, 108 (19). pp. 4175-4179. Schütte, Ch. and Walter, J. and Hartmann, C. and Huisinga, W. (2004) An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations. Multiscale Model. Simul., 2 (3). pp. 501-526. Walter, J. and Schütte, Ch. and Pavliotis, G. A. and Stuart, A. (2004) Averaging of Stochastic Differential Equations: Kurtz's Theorem Revisited. preprint . Kohlbacher, O. and Reinert, K. (2004) Differenzielle Proteomanalyse -- Experimentelle Methoden, Algorithmische Herausforderungen. it -- Information technology, 46 . pp. 31-38. Preis, R. and Dellnitz, M. and Hessel, M. and Schütte, Ch. and Meerbach, E. (2004) Dominant Paths Between Almost Invariant Sets of Dynamical Systems. preprint . Helling, Ch. and Klein, R. and Woitke, P. and Nowak, U. and Sedlmayr, E. (2004) Dust in brown dwarfs. IV. Dust formation and driven turbulence on mesoscopic scales. Astronomy and astrophysics, 423 (2). pp. 657-675. ISSN 0004-6361 Horenko, I. and Weiser, M. and Schmidt, B. and Schütte, Ch. (2004) Fully Adaptive Propagation of the Quantum-Classical Liouville Equation. J. Chem. Phys., 120 (19). pp. 8913-8923. Jahnke, T. (2004) A Long-Time-Step Method for Quantum-Classical Molecular Dynamics. SIAM J. Sci. Comp., 25 (6). pp. 2145-2164. Klein, R. and Mikusky, E. and Owinoh, A.Z. (2004) Multiple Scales Asymptotics for Atmospheric Flows. Proceedings of the 4th European Conference on Mathematics . Ronen, S. and Nachtigallova, D. and Schmidt, B. and Jungwirth, P. (2004) Non-Adiabatic Chemical Reaction Triggered by Electron Photodetachment: An ab initio Quantum Dynamical Study. Phys. Rev. Lett., 93 (4). 048301. Gröpl, C. and Prömel, H.-J. and Srivastav, A. (2004) Ordered binary decision diagrams and the Shannon effect. Discrete Applied Mathematics, 142 . pp. 67-85. Huisinga, W. and Meyn, S. and Schütte, Ch. (2004) Phase Transitions and Metastability in Markovian and Molecular Systems. Ann. Appl. Prob., 14 (1). pp. 419-458. Kiljunen, T. and Bargheer, M. and Gühr, M. and Schwentner, N. and Schmidt, B. (2004) Photodynamics and Ground State Librational States of ClF Molecule in solid Ar. Comparison of experiment and theory. Phys. Chem. Chem. Phys., 6 (11). pp. 2932-2939. Fujimura, Y. and Gonzalez, L. and Kröner, D. and Manz, J. and Mehdaoui, I. and Schmidt, B. (2004) Quantum Ignition of Intramolecular Rotation by Means of IR+UV Laser Pulses. Chem. Phys. Lett., 386 (4-6). pp. 248-253. Korolkov, M. V. and Schmidt, B. (2004) Quantum Molecular Dynamics Driven by Short and Intense Light Pulses: Towards the Limits of the Floquet Picture. Comp. Phys. Comm., 161 (1-2). pp. 1-17. Botta, N. and Klein, R. and Langenberg, S. and Lützenkirchen, S. (2004) Well Balanced Finite Volume Methods for Nearly Hydrostatic Flows. Journal of Computational Physics, 196 (2). pp. 539-565. Istrail, S. and Sutton, G. G. and Florea, L. and Mobarry, C. M. and Lippert, R. and Walenz, B. and Shatkay, H. and Dew, Ian and Miller, J. R. and Flanigan, M. J. and Edwards, N. J. and Bolanos, R. and Fasulo, D. and Halldorsson, B. V. and Hannenhalli, S. and Turner, R. J. and Yooseph, S. and Lu, Fu and Nusskern, D. R. and Shue, B. C. and Zheng, X. H. and Zhong, F. and Delcher, A. L. and Huson, D. H. and Kravitz, S. A. and Mouchard, L. and Reinert, K. and Remington, K. A. and Clark, A. G. and Waterman, M. S. and Eichler, E. E. and Adams, M. D. and Hunkapillar, M. W. and Myers, E. W. and Venter, J. C. (2004) Whole-genome shotgun assembly and comparison of human genome assemblies. Proceedings of the national academy of science (PNAS), 101 (7). pp. 1916-1921. Klein, R. (2004) An applied mathematical view of meteorological modeling. Applied Mathematics Entering the 21st century; Invited talks from the ICIAM 2003 Congress., 116 . pp. 177-219. Audusse, E. and Bouchut, F. and Bristeau, M.O. and Klein, R. and Perthame, B. (2004) A fast and stable well-balanced scheme with hydrostatic reconstruction for shallow water flows. Journal of Scientific Computation, 25 (6). pp. 2050-2065. Krah, A. and Schmidt, F. and Becher, D. and Schmid, M. and Albrecht, D. and Rack, A. and Büttner, K. and Jungblut, P. (2003) Analysis of Automatically Generated Peptide Mass Fingerprints of Cellular Proteins and Antigens from Helicobacter pylori 26695 Separated by Two-dimensional Electrophoresis. Molecular & Cellular Proteomics, 2 (12). pp. 1271-1283. Frömmel, C. and Gille, Ch. and Goede, A. and Gröpl, C. and Hougardy, S. and Nierhoff, T. and Preissner, R. and Thimm, M. (2003) Accelerating screening of 3D protein data with a graph theoretical approach. Bioinformatics, 19 (18). pp. 2442-2447. Munz , C.-D. and Roller , S. and Klein, R. and Geratz, K. J. (2003) The extension of incompressible flow solvers to the weakly compressible regime. Computers & fluids , 32 (2). 173-196 (31 ref.). ISSN 0045-7930 Horenko, I. and Weiser, M. (2003) Adaptive Integration of Molecular Dynamics. J. Comp. Chem., 24 (15). pp. 1921-1929. Noé, F. and Schwarzl, S. and Fischer, S. and Smith, J. C. (2003) Computational tools for analysing structural changes in proteins in solution. Applied Bioinformatics, 2 . pp. 11-17. Cockburn, B. (2003) Discontinuous Galerkin methods. ZAMM - Zeitschrift für Angewandte Mathematik und Mechanik, 83 (11). 731 -754. Huisinga, W. and Schütte, Ch. and Stuart, A. M. (2003) Extracting Macroscopic Stochastic Dynamics: Model Problems. Comm. Pure Appl. Math., 56 (2). pp. 234-269. Berninger, H. and Werner, Dirk (2003) Lipschitz spaces and M-ideals. Extracta Mathematicae, 18 (1). pp. 33-56. ISSN 0213-8743 Wohlmuth, B. and Krause, R. (2003) Monotone methods on non-matching grids for non-linear contact problems. SIAM J. Sci. Comput., 25 (1). pp. 324-347. ISSN 1064-8275 Becker, T. and Fischer, S. and Noé, F. and Ullmann, M. and Tournier, A. and Smith, J. C. (2003) Protein Dynamics: Glass Transition and Mechanical Function. Advances in Solid State Physics, 43 . pp. 677-694. Majda, A.J. and Klein, R. (2003) Systematic Multiscale Models for the Tropics. Journal of Atmospheric Sciences, 60 . pp. 393-408. Fermanian Kammerer, C. and Lasser, C. (2003) Wigner measures and codimension two crossings. J. Math. Phys., 44 (2). pp. 507-557. Schmidt, H. and Klein, R. (2003) A generalized level-set/in-cell-reconstruction method for accelerating turbulent premixed flames. Combustion Theory and Modelling, 7 (2). 243-267(25). Krause, R. and Wohlmuth, B. (2002) A Dirichlet-Neumann type algorithm for contact problems with friction. Computing and Visualization in Science, 5 (3). pp. 139-148. ISSN 1432-9360 Kornhuber, R. (2002) On constrained Newton linearization and multigrid for variational inequalities. Numerische Mathematik, 91 (4). pp. 699-721. ISSN 0029-599X Mural, Richard and Adams, M. D. and Reinert, K. (2002) A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome. Science, 296 . pp. 1661-1671. Huson, D. H. and Reinert, K. and Myers, E. W. (2002) The Greedy Path-Merging Algorithm for Sequence Assembly. Journal of the ACM, 49 (5). pp. 603-615. Horenko, I. and Schmidt, B. and Schütte, Ch. (2002) Multidimensional Classical Liouville Dynamics with Quantum Initial Conditions. J. Chem. Phys., 117 (10). pp. 4643-4650. Klein, R. (2002) Numerical Methods for High and Low Speed Combustion Simulations. Numerical Methods for High and Low Speed Combustion Simulations. PDE's in models of superfluidity, superconductivity and reactive flows, Nato S (569). pp. 491-506. Roeselova, M. and Mucha, M. and Schmidt, B. and Jungwirth, P. (2002) Quantum dynamics and spectroscopy of photodetachment in Cl-...H2O and Cl-...D2O complexes. J. Phys. Chem. A, 106 (51). pp. 12229-12241. Horenko, I. and Salzmann, Ch. and Schmidt, B. and Schütte, Ch. (2002) Quantum-Classical Liouville Approach to Molecular Dynamics: Surface Hopping Gaussian Phase-Space Packets. J. Chem. Phys., 117 (24). pp. 11075-11088. Bailey, J. A. and Gu, Z. and Clark, R. A. and Reinert, K. and Samonte, R. V. and Schwartz, S. S. and Adams, M. D. and Myers, E. W. and Li, P. and Eichler, E. E. (2002) Recent Segmental Duplications in the Human Genome. Science, 297 . pp. 1003-1007. Korolkov, M. V. and Schmidt, B. (2002) Spin-Orbit Induced Association under Ultrafast Laser Pulse Control. Chem. Phys. Lett., 361 (5-6). pp. 432-438. Gröpl, C. and Hougardy, S. and Nierhoff, T. and Prömel, H.-J. (2002) Steiner trees in uniformly quasi-bipartite graphs. Information Processing Letters, 83 . pp. 195-200. Manz, J. and Proppe, B. and Schmidt, B. (2002) Time-Resolved Dual Fluorescence of 1-Phenylpyrrole in Acetonitrile: Molecular Dynamics Symulations of Solvent Response to Twisted Intramolecular Charge Transfer. Phys. Chem. Chem. Phys., 4 (10). pp. 1876-1881. Berghof, V. and Martins, M. and Schmidt, B. and Schwentner, N. (2002) Vibrational Overtones and Rotational Structures of HCl in Rare Gas Matrices. J. Chem. Phys., 116 (21). pp. 9364-9373. Kornhuber, R. and Krause, R. (2001) Adaptive multigrid methods for Signorini's problem in linear elasticity. Computing and Visualization in Science, 4 (1). pp. 9-20. ISSN 1432-9360 Krause, R. and Wohlmuth, B. (2001) Domain decomposition methods on nonmatching grids and some applications to linear elasticity problems. Zeitschrift für angewandte Mathematik und Mechanik (ZAMM), 81 (Suppl.). pp. 21-24. ISSN 0044-2267 Kober, C. and Müller-Hannemann, M. (2001) A case study in hexahedral mesh generation: Simulation of the human mandible. Engineering with Computers, 17 (3). pp. 249-260. ISSN 0177-0667 Schäfer-Bung, B. and Engels, B. and Taylor, T. and Neumark, P. and Botschwina, P. and Perić, M. (2001) Measurement and theoretical simulation of the HCCO- anion photoelectron spectrum. J. Chem. Phys., 115 (4). pp. 1777-1788. Klein, R. and Botta, N. and Schneider, T. and Munz, C.D. and Roller, S. and Meister, A. and Hoffmann, L. and Sonar, T. (2001) Asymptotic adaptive methods for multi-scale problems in fluid mechanics. Journal of Engineering Mathematics, 39 (1). pp. 261-343. ISSN 0022-0833 (Print) 1573-2703 (Online) Helling, Ch. and Oevermann, M. and Lüttke, M. J. H. and Klein, R. (2001) Dust in Brown Dwarfs I. Dust formation under turbulent conditions on microscopic scales. Astronomy & Astrophysics, - (), 376 . pp. 194-212. Gröpl, C. and Prömel, H.-J. and Srivastav, A. (2001) On the Evolution of the Worst-Case OBDD Size. Information Processing Letters, 77 . pp. 1-7. Chaban, G. and Gerber, R. B. and Korolkov, M. V. and Manz, J. and Niv, M. Y. and Schmidt, B. (2001) Photodissociation Dynamics of Molecular Fluorine in an Argon Matrix Induced by Ultrashort Laser Pulses. J. Phys. Chem. A, 105 (12). pp. 2770-2782. Slavicek, P. and Roeselova, M. and Jungwirth, P. and Schmidt, B. (2001) Preference of Cluster Isomers as a Result of Quantum Delocalization: Potential Energy Surfaces and Intermolecular Vibrational States of Ne...HBr, Ne...HI, and HI(Ar)n (n=1-6). J. Chem. Phys., 114 (4). pp. 1539-1548. Venter, J. C. and Adams, M. D. and Myers, E. W. and Reinert, K. and et al, . (2001) The Sequence of the Human Genome. Science, 291 (5507). pp. 1304-1351. Horenko, I. and Schmidt, B. and Schütte, Ch. (2001) A Theoretical Model for Molecules Interacting with Intense Laser Pulses: The Floquet-based Quantum-Classical Liouville Equation. J. Chem. Phys., 115 (13). pp. 5733-5743. Schmidt, H. and Klein, R. (2001) Towards a Generalized Level-Set/In-Cell Reconstruction Approach for Accelerating Turbulent Premixed Flames. Wohlmuth, B. and Krause, R. (2001) A multigrid method based on the unconstrained product space for Mortar finite element discretizations. SIAM Journal on Numerical Analysis, 39 (1). pp. 192-213. ISSN 0036-1429 Knio, O.M. and Klein, R. (2000) Improved Thin Tube Methods for Slender Vortex Simulations. Journal of Computational Physics, 162 (1). 68-82(15). Klein, R. (2000) Asymptotic Analyses for Atmospheric Flows and the Construction of Asymptotically Adaptive Numerical Methods. ZAMM ·Zeitschrift für angewandte Mathematik und Mechanik, 80 (11-12). pp. 765-785. ISSN 0044-2267 Huisinga, W. (2000) The Essential Spectral Radius and Asymptotic Properties of Transfer Operators. preprint . Kober, C. and Sader, R. and Thiele, H. and Bauer, H.-J. and Zeilhofer, H.-F. and Hoffmann, K.-H. (2000) FEM simulations versus biomechnical experiments concerning the human mandible: a comparision of the results of a frontal and a molar biting study. Preprint A-21-2000 . (Unpublished) UNSPECIFIED (2000) The Genome Sequence of Drosophila melanogaster. Science, 287 (5461). pp. 2185-2195. Deuflhard, P. and Huisinga, W. and Fischer, A. and Schütte, Ch. (2000) Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains. Lin. Alg. Appl., 315 (1-3). pp. 39-59. Reinert, K. and Stoye, J. and Will, T. (2000) An Iterative Methods for Faster Sum-of-Pairs Multiple Sequence Alignment. BIOINFORMATICS, 16 (9). pp. 808-814. Klein, R. and Münch, M. (2000) Models and Criteria for Prediction of Deflagration to Detonation Transition (DDT) in Hydrogen-Air-Steam Systems under Severe Accident Conditions. Numerical Techniques , 9, Reihe Energietechnik / Energy Technology. . pp. 83-102. Klein, R. and Rehm, W. (2000) Models and Criteria for Prediction of Deflagration-to- Detonation Transition (DDT) in Hydrogen-Air-Steam Systems under Severe Accident Conditions. Schriften des Forschungszentrums Jülich, Energy Technology Series, 9 . ISSN ISBN 3-89336-258-4 Krause, R. and Wohlmuth, B. (2000) Nonconforming decomposition methods: Techniques for linear elasticity. East-West Journal of Numerical Mathematics, 8 (3). pp. 177-206. ISSN 1569-3953; 0928-0200 Kececioglu, J. D. and Lenhof, H.-P. and Mehlhorn, K. and Reinert, K. and Vingron, M. (2000) A Polyhedral Approach to Sequence Alignment Problems. Discrete Applied Mathematics, 104 . pp. 143-186. Lermen, M. and Reinert, K. (2000) The Practical Use of the A* Algorithm for Exact Multiple Sequence Alignment. Journal of Computational Biology . pp. 655-671. Gerber, R. B. and Korolkov, M. V. and Manz, J. and Niv, M. Y. and Schmidt, B. (2000) A Reflection Principle for the Control of Molecular Photodissociation in Solids: Model Simulation for F2 in Ar. Chem. Phys. Lett., 327 (1-2). pp. 76-84. Schmidt, B. and Zdanska, P. (2000) Solution of the Time-Dependent Schrödinger Equation for Highly Symmetric Potentials. Comp. Phys. Comm., 127 (2-3). pp. 290-308. Breitung, W. and Chan, C. and Dorofeev, S.B. and Eder, A. and Gelfand, B.E. and Heitsch, M. and Klein, R. and Malliakos, A. and Shepherd, J.E. and Studer, E. and Thibault, P. (2000) State of Art Report on Flame Acceleration and DDT in Nuclear Reactor Safety. OECD . Fischer, A. (2000) An Uncoupling-Coupling Technique for Markov Chain Monte Carlo Methods. preprint . Myers, E. W. and Sutton, G. G. and Delcher, A. L. and Dew, D. P. and Flanigan, M. J. and Kravitz, S. A. and Mobarry, C. M. and Reinert, K. and Remington, K. A. and Anson, E. L. and Bolanos, R. and Chou, H.-H. and Jordan, C. M. and Halpern, A. L. and Lonardi, S. and Beasly, E. M. and Brandon, R. C. and Chen, L. and Dunn, P. J. and Lai, Z. and Liang, Y. and Nusskern, D. R. and Zhan, M. and Zhang, Q. and Zheng, X. H. and Rubin, G. M. and Adams, M. D. and Venter, J. C. (2000) A Whole-Genome Assembly of Drosophila. Science, 287 (5461). pp. 2196-2203. Reinecke , M. and Hillebrandt , W. and Niemeyer , J.C. and Klein, R. and Gröbl, A. (1999) A new model for deflagration fronts in reactive fluids. Astronomy and Astrophysics, 347 (1999A&A...347..724R). 724-733 . ISSN 0004-6361 (Print) 1432-0746 (Online) Bornemann, F. A. and Schütte, Ch. (1999) Adaptive Accuracy Control for Car-Parrinello Simulations. Num. Math., 83 (2). pp. 179-186. Schütte, Ch. (1999) Conformational Dynamics: Modelling, Theory, Algorithm, and Application to Biomolecules. preprint . Backhaus, P. and Schmidt, B. and Dantus, M. (1999) Control of Photoassociation Yield: A Quantum Dynamical Study of the Mercury System to Explore the Role of Pulse Duration from Nanoseconds to Femtoseconds. Chem. Phys. Lett., 306 (1-2). pp. 18-24. Schütte, Ch. and Fischer, A. and Huisinga, W. and Deuflhard, P. (1999) A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo. J. Comp. Phys, 151 (1). pp. 146-168. Schneider, T. and Botta, N. and Geratz, K. J. and Klein, R. (1999) Extension of finite volume compressible flow solvers to multidimensional, variable density zero Mach number flows. J. Comput. Phys., 155 . pp. 248-286. Huisinga, W. and Pesce, L. and Kosloff, R. and Saalfrank, P. (1999) Faber and Newton Polynomial Integrators for Open-System Density Matrix Propagation. J. Chem. Phys., 110 (12). pp. 5538-5547. Huisinga, W. and Best, Ch. and Roitzsch, R. and Schütte, Ch. and Cordes, F. (1999) From Simulation Data to Conformational Ensembles: Structure and Dynamics based Methods. J. Comp. Chem., 20 (16). pp. 1760-1774. Fischer, A. and Cordes, F. and Schütte, Ch. (1999) Hybrid Monte Carlo with adaptive temperature choice: Efficient conformational analysis of RNA. Comp. Phys. Comm., 121 . pp. 37-39. Worlikar, A.S. and Aniruddha, S. and Knio, O.M. and Klein, R. (1999) Numerical Study of the Effective Impedance of a Thermoacoustic Stack. Acta Acustica united with Acustica, 85 (4,). pp. 480-494. ISSN 1610-1928 Bornemann, F. A. and Schütte, Ch. (1999) On the Singular Limit of the Quantum-Classical Molecular Dynamics Model. J. Appl. Math., 59 (4). pp. 1208-1224. Zdanska, P. and Schmidt, B. and Jungwirth, P. (1999) Photolysis of Hydrogen Chloride Embedded in the First Argon Solvation Shell: Rotational Control and Quantum Dynamics of Photofragments. J. Chem. Phys., 110 (13). pp. 6246-6256. Schmidt, B. (1999) Quantum Dynamics of HF Photodissociation in Icosahedral Ar12HF Clusters: Rotational Control of the Hydrogen Atom Cage Exit. Chem. Phys. Lett., 301 (3-4). pp. 207-216. Lenhof, H.-P. and Morgenstern, B. and Reinert, K. (1999) An exact solution for the segment-to-segment multiple sequence alignment problem. BIOINFORMATICS, 15 (3). pp. 203-210. Berkenbosch, A. and Kaasschieter, E. and Klein, R. (1998) Detonation capturing for stiff combustion chemistry. Combustion Theory and Modelling, 2 (3). 313-348(36). Worlikar, A.S. and Knio, O.M. and Klein, R. (1998) Numerical Simulation of a Thermoacoustic Refrigerator II. Stratified Flow around the Stack. Journal of Computational Physics, 144 (2). 299-324(26). Knio, O.M. and Ting, L. and Klein, R. (1998) Interaction of a Slender Vortex Filament with a Rigid Sphere: Dynamics and far-field noise. J. Acoustical Soc. of America, 103 (1). 83 -98. ISSN 0001-4966 (print) Backhaus, P. and Manz, J. and Schmidt, B. (1998) Effect of Rotations and Shape Resonances on Photoassociation and Photoacceleration by Ultrashort Infrared Laser Pulses. J. Phys. Chem. A, 102 (23). pp. 4118-4128. Fischer, A. and Cordes, F. and Schütte, Ch. (1998) Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble: Efficient conformational analysis of RNA. J. Comp. Chem., 19 (15). pp. 1689-1697. Ring, S. and Schmidt, B. and Baumgärtel, H. (1998) Ionization of Rydberg Atoms in THz-Laser Fields at the Transition from Low to High Scaled Frequencies. Eur. Phys. J. D, 3 (2). pp. 155-158. Jungwirth, P. and Zdanska, P. and Schmidt, B. (1998) Librational control of photochemical reactions in small clusters. J. Phys. Chem. A, 102 (37). pp. 7241-7244. Lenhof, H.-P. and Reinert, K. and Vingron, M. (1998) A Polyhedral Approach to RNA Sequence Structure Alignment. Journal of Computational Biology, 5 (3). pp. 517-530. Nettesheim, P. (1998) Second Order Transitions in Quantum-Classical Molecular Dynamics. preprint . Korolkov, M. V. and Schmidt, B. (1998) Vibrationally State-Selective Laser Pulse Control of Electronic Branching in OH (X 2Pi/A 2Sigma+) Photoassociation. Chem. Phys., 237 (1-2). pp. 123-138. Bornemann, F. A. and Schütte, Ch. (1998) A mathematical investigation of the Car-Parrinello Method. Num. Math., 78 (3). pp. 359-376. Smiljanovski, V. and Moser, V. and Klein, R. (1997) A Capturing/Tracking Hybrid Scheme for Deflagration Discontinuities. Combustion Theory and Modelling, 1 (2). 183-215 . Backhaus, P. and Schmidt, B. (1997) Femtosecond Quantum Dynamics of Photoassociation Reactions: The Exciplex Formation of Mercury. Chem. Phys., 217 (2-3). pp. 131-143. Schütte, Ch. and Bornemann, F. A. (1997) Homogenization Approach to Smoothed Molecular Dynamics. Nonlinear Analysis, 30 (3). pp. 1805-1814. Bornemann, F. A. and Schütte, Ch. (1997) Homogenization of Hamiltonian Systems with a Strong Constraining Potential. Physica D, 102 (1-2). pp. 57-77. Korolkov, M. V. and Schmidt, B. (1997) Infrared Picosecond Laser Control of Acceleration of Neutral Atoms: Model Simulations for the Collision Pair O + H. Chem. Phys. Lett., 272 (1-2). pp. 96-102. Worlikar, A.S. and Knio, O.M. and Klein, R. (1997) Numerical Simulation of a Thermo-Acoustic Refrigerator. Vortex Flows and Related Numerical Methods II . Manz, J. and Saalfrank, P. and Schmidt, B. (1997) Quantum Dynamical Aspects of Rotationally and Vibrationally Mediated Photochemistry in Matrices and at Surfaces: HCl/DCl in Ar, and NH3/ND3 at Cu(111). J. Chem. Soc. Faraday Trans., 93 (5). pp. 957-967. Jungwirth, P. and Schmidt, B. (1997) Quantum dynamics following electron photodetachment in the I-Ar2 complex: How Good Are New Separable and Non-Separable Simulation Methods? Chem. Phys. Lett., 275 (3-4). pp. 127-136. Jungwirth, P. and Schmidt, B. and Moiseyev, N. (1997) Vibrationally Resolved Spectra from Short Time Quantum Molecular Dynamics by the Filter-Diagonalization Method. Chem. Phys. Lett., 280 (3-4). pp. 177-184. Nettesheim, P. and Huisinga, W. and Schütte, Ch. (1996) Chebyshev-Approximation for Wavepacket-Dynamics: better than expected. preprint . Meißner, B. and Schmidt, B. and Berry, R. S. (1996) Cluster Growth From the Gas Phase: Associative Collisions of Small Alkali Halide Aggregates. Z. Phys. Chem., 195 . pp. 237-251. Nettesheim, P. and Bornemann, F. A. and Schmidt, B. and Schütte, Ch. (1996) An Explicit and Symplectic Integrator for Quantum-Classical Molecular Dynamics. Chem. Phys. Lett., 256 (6). pp. 581-588. Kornhuber, R. (1996) Monotone multigrid methods for elliptic variational inequalities II. Numerische Mathematik, 72 (4). pp. 481-499. ISSN 0029-599X Finger, K. and Daniel, Ch. and Saalfrank, P. and Schmidt, B. (1996) Nonadiabatic Effects in the Photodissociation and Electronic Spectroscopy of HMn(CO)3(dab): Quantum Wave Packet Dynamics Based on ab-initio Potentials. J. Phys. Chem., 100 (9). pp. 3368-3376. Bornemann, F. A. and Nettesheim, P. and Schütte, Ch. (1996) Quantum-classical molecular dynamics as an approximation to full quantum dynamics. J. Chem. Phys., 105 (3). pp. 1074-1083. Klein, R. and Knio, O.M. and Ting, L. (1996) Representation of Core Dynamics in Slender Vortex Filament Simulations,. Physics of Fluids, 8 (9). 2415{-2425,. Korolkov, M. V. and Paramonov, G. K. and Schmidt, B. (1996) State-Selective Control For Vibrational Excitation and Dissociation of Diatomic Molecules With Shaped Ultrashort Laser Pulses. J. Chem. Phys., 105 (5). pp. 1862-1879. Schmidt, B. and Jungwirth, P. (1996) Vibrational Line Shifts of Hydrogen Halides in a Rare Gas Environment: HF/DF and HCl/DCl in Ar Matrices and Clusters. Chem. Phys. Lett., 259 (1-2). pp. 62-688. Korolkov, M. V. and Manz, J. and Paramonov, G. K. and Schmidt, B. (1996) Vibrationally State Selective Photoassociation by Infrared Picosecond Laser Pulses: Model Simulations for O + H → OH(ν). Chem. Phys. Lett., 260 (5-6). pp. 604-610. Bornemann, F. A. and Erdmann, B. and Kornhuber, R. (1996) A posteriori error estimates for elliptic problems in two and three space dimensions. SIAM Journal on Numerical Analysis, 33 (3). pp. 1188-1204. ISSN 0036-1429 Kornhuber, R. (1996) A posteriori error estimates for elliptic variational inequalities. Computers & Mathematics with Applications, 31 (8). pp. 49-60. ISSN 0898-1221 Klein, R. and Ting, L. (1995) Theoretical and Experimental Studies of Slender Vortex Filaments. Applied Mathematics Letters, 8 (2). pp. 45-50. Klein, R. (1995) Analysis of Accelerating Detonation Using Large Activation Energy Asymptotics. Journal de physique. IV , 5 (4). pp. 443-457. ISSN 1155-4339 Klein, R. and Knio, O.M. (1995) Asymptotic Vorticity Structure and Numerical Simulation of Slender Vortex Filaments. Journal of Fluid Mechanics, 284 . pp. 275-321. ISSN 0022-1120 Schütte, Ch. and Zumbusch, M. D. G and Brinkmann, R. (1995) Dynamics of Erbium-doped Waveguide Lasers: Modelling, Reliable Simulation, and Comparison with Experiments. preprint . Manz, J. and Proppe, B. and Schmidt, B. (1995) From Torsional Spectra to Hamiltonians and Dynamics: Effects of Coupled Bright and Dark States of 9-(N-Carbazolyl) Anthracene. Z. Phys. D, 34 (2). pp. 111-118. Klein, R. (1995) The Level-Set Approach to Premixed Turbulent Combustion in the Flamelet Regime: Theory and Numerical Implementation. Euroconference "Premixed Turbulent Combustion: Introduction to the State of the Art" . Klein, R. (1995) Semi-Implicit Extension of a Godunov-Type Scheme Based on Low Mach Number Asymptotics I: One-dimensional Flow,. Journal of Computational Physics, 121 (2). pp. 213-237. ISSN 0021-9991 Klein, R. and Majda, A. J. and Damodaran, K. (1995) Simplied Equations for the Interaction of Nearly Parallel 3-D Vortex Filaments,. Journal of Fluid Mechanics, 288 . 201-248 . ISSN 0022-1120 Schütte, Ch. (1995) Smoothed Molecular Dynamics for Thermally Embedded Systems. preprint . (Unpublished) Schütte, Ch. and Dinand, M. (1995) Theoretical Modeling of Relaxation Oscillations in Er-Doped Wave-Guide Lasers. J. Lightw. Techn., 13 (1). pp. 14-23. Hoppe, R. H. W. and Kornhuber, R. (1994) Adaptive multilevel methods for obstacle problems. SIAM Journal on Numerical Analysis, 31 (2). pp. 301-323. ISSN 0036-1429 Buck, U. and Schmidt, B. (1994) Frequency Shifts in Infrared Spectra of Ethylene Clusters. J. Chem. Phys., 101 (7). pp. 6365-6366. Kornhuber, R. (1994) Monotone multigrid methods for elliptic variational inequalities I. Numerische Mathematik, 69 (2). pp. 167-184. ISSN 0029-599X Manz, J. and Paramonov, G. K. and Polasek, M. and Schütte, Ch. (1994) Overtone State-Selective Isomerization by a Series of Picosecond Infrared Laser Pulses - Model Simulations for Be2H3D. Isr. J. Chem., 34 (1). pp. 115-125. Schmidt, B. and Gerber, R. B. (1994) Reactive Collisions as a Signature for Meltinglike Transitions in Clusters. Phys. Rev. Lett., 72 (15). pp. 2490-2493. Schmidt, B. and Gerber, R. B. (1994) Solvation Effects on Association Reactions in Microclusters: Classical Trajectory Study of H+Cl(Ar)n. J. Chem. Phys., 101 (1). pp. 343-355. Klein, R. and Breitbach, H. and Geratz, K. J. and Senger, W. (1994) Surface erosion by high-speed combustion waves. Symposium (International) on Combustion, 25 (1). 95-102 . Bdzil, J.B. and Klein, R. (1994) Weakly Nonlinear Dynamics of Near-CJ Detonation Waves, Combustion in High-Speed Flows. Combustion in High-Speed Flows, J. Buckmaster et al. (eds), . pp. 513-540. ISSN 978-0-7923-2806-3 (ISBN) Klein, R. and Stewart, D.S., (1993) The Relation between Curvature, Rate-State Dependence and Detonation Velocity. SIAM Journal on Applied Mathematics, 53 (5). 1401-1435 . Erdmann, B. and Frei, M. and Hoppe, R. H. W. and Kornhuber, R. and Wiest, U. (1993) Adaptive finite element methods for variational inequalities. East-West Journal of Numerical Mathematics, 1 . pp. 165-197. ISSN 1569-3953; 0928-0200 Bornemann, F. A. and Erdmann, B. and Kornhuber, R. (1993) Adaptive multilevel methods in three space dimensions. International Journal for Numerical Methods in Engineering, 36 (18). pp. 3187-3203. ISSN 1097-0207 Klein, R. and Majda, A. J. (1993) An Asymptotic Theory for the Nonlinear Instability of Anti- Parallel Pairs of Vortex Filaments. Physics of Fluids A, 5 . pp. 369-379. ISSN 0899-8213 Buck, U. and Schmidt, B. (1993) A Perturbation Approach to Predict the Infrared Spectra of Small Molecular Clusters Applied to Methanol. J. Chem. Phys., 98 (12). pp. 9410-9424. Schütte, Ch. (1993) A Quasiresonant Smoothing Algorithm for the Fast Analysis of Selective Vibrational Excitation. Impact of Computing in Sci. Eng., 5 (3). pp. 176-200. Kornhuber, R. and Roitzsch, R. (1993) Self-adaptive finite-element simulation of bipolar, strongly reverse-biased pn-junctions. International Journal for Numerical Methods in Biomedical Engineering, 9 (3). pp. 243-250. ISSN 2040-7947 Buck, U. and Schmidt, B. and Siebers, J. G. (1993) Structural Transitions and Thermally Averaged Infrared Spectra of Small Methanol Clusters. J. Chem. Phys., 99 (12). pp. 9428-9437. Buck, U. and Hobein, M. and Schmidt, B. (1993) Structure and Photodissociation Spectra of Mixed Ethene-Acetone Clusters. J. Chem. Phys., 98 (12). pp. 9425-9431. Klein, R. and Majda, A. J. and McLaughlin, R.M. (1992) Asymptotic Equations for the Stretching of Vortex Filaments by a Background Flow Field. Physics of Fluids A, 4 . pp. 2271-2281. ISSN 0899-8213 Schütte, Ch. and Wulkow, M. (1992) Quantum Theory with Discrete Spectra and Countable Systems of Differential Equations - A Numerical Treatment of Raman Spectroscopy. preprint . Klein, R. and Ting, L. (1992) Vortex Filaments with Axial Core Structure Variation. Appl. Math. Lett., 5 . pp. 99-103. Klein, R. and Majda, A. J. (1991) Self-Stretching of a Perturbed Vortex Filament I: The Asymptotic Equation for Deviations from a Straight Line. Physica D, 49 (3). pp. 323-352. Klein, R. (1991) On the Dynamics of Weakly Curved Detonations. Institute for Mathematics and Its Applications, 35 . ISSN 0940-6573 Klein, R. (1991) On the Dynamics of Weakly Curved Detonations. IMA-Volumes in Mathematics and its Applications, 35 . ISSN 978-0-387-97583-2 Roitzsch, R. and Kornhuber, R. (1990) BOXES - a program to generate triangulations from a rectangular domain description. ZIB-Report, TR-90- . ISSN 1438-0064 Klein, R. and Ting, L. (1990) Far field velocity potential induced by a rapidly decaying vorticity distribution. Zeitschrift für Angewandte Mathematik und Physik (ZAMP), 41 (3). pp. 395-418. ISSN 0044-2275 (Print) 1420-9039 (Online) Buck, U. and Schmidt, B. (1990) Calculation of Vibrational Line Shifts for Molecular Dimers. J. Mol. Liqu., 46 . pp. 181-196. Hoppe, R. H. W. and Kornhuber, R. (1990) Multi-grid solution of two coupled Stefan equations arising in induction heating of large steel slabs. International Journal for Numerical Methods in Engineering, 30 (4). pp. 779-801. ISSN 1097-0207 Klein, R. and Munz , C.-D. and Schmidt, L. (1990) A Numerical Study of Interfacial Instabilities at High Mach Numbers. Notes on Numerical Fluid Mechanics, 29,, 29 . 242-251. Kornhuber, R. and Roitzsch, R. (1990) On adaptive grid refinement in the presence of internal or boundary layers. IMPACT of Computing in Science and Engineering, 2 (1). pp. 40-72. ISSN 0899-8248 Ahlrichs, R. and Brode, St. and Buck, U. and deKieviet, M. and Lauenstein, Ch. and Rudolph, A. and Schmidt, B. (1990) The Structure of C2H4 Clusters from Theoretical Interaction Potentials and Vibrational Predissociation Data. Z. Phys. D, 15 (4). pp. 341-351. Maly, R.R. and Koenig, G. and Klein, R. and Peters, N. (1990) Theoretical and Experimental Investigation of Knock Induced Surface Destruction. SAE transactions, 99 (1), no3, pp. (1). 99-137 (62 ref.). ISSN 0096-736X Kornhuber, R. and Roitzsch, R. (1989) Adaptive Finite-Element-Methoden für konvektionsdominierte Randwertprobleme bei partiellen Differentialgleichungen. ZIB-Report . ISSN 1438-0064 Aziz, R. A. and Buck, U. and Jonsson, H. and Ruiz-Suarez, J. C. and Schmidt, B. and Scoles, G. and Slaman, M. J. and Xu, J. (1989) Two- and Three-Body Forces in the Interaction of He Atoms with Xe Overlayers Adsorbed on (0001) Graphite. J. Chem. Phys., 91 (10). pp. 6477-6493. Kornhuber, R. (1988) Convergent extensions of grid-functions. Mathematische Nachrichten, 139 (1). pp. 63-75. ISSN 1522-2616 Klein, R. and Peters, N. (1988) Cumulative Effects of Weak Pressure Waves During the Induction Period of a Thermal Explosion in a Closed Cylinder. J. Fluid Mech., 187 . pp. 197-230. Klein, R. (1988) Detonation Initiation Due to Shock Wave-Boundary Interactions. Notes on Numerical Fluid Mechanics, 24 . 279-288.. Kornhuber, R. (1988) Local change of coordinates for grid-functions on regions with curved boundary. Mathematische Nachrichten, 139 (1). pp. 45-61. ISSN 1522-2616 Liuti, G. and Pirani, F. and Buck, U. and Schmidt, B. (1988) Methane-Rare Gas Interaction Potentials from Scattering Experiments. Chem. Phys., 126 (1). pp. 1-6. Klein, R. (1988) Shock Initiated Ignition in an L-shaped Duct: Two Aspects of its Numerical Simulation. Notes on Numerical Fluid Mechanics, 20 . pp. 138-145. Kornhuber, R. (1973) Vereinfachung eines Computermodells. MNU - Der mathematische und naturwissenschaftliche Unterricht, 26 (3). p. 176. ISSN 0025-5866 Galama, Maaike M. and Wu, Hao and Krämer, Andreas and Sadeghi, Mohsen and Noé, Frank (0001) Stochastic Approximation to MBAR and TRAM: Batchwise Free Energy Estimation. Journal of Chemical Theory and Computation (JCTC), 19 (3). pp. 758-766. Sunkara, V. and von Kleist, M. Coupling cellular phenotype and mechanics to understand extracellular matrix formation and homeostasis in osteoarthritis. IFAC-PapersOnLine, 49 (26). pp. 38-43. Sloan, Ian H. and Kaarnioja, Vesa Doubling the rate – improved error bounds for orthogonal projection in Hilbert spaces. arXiv . (Submitted) Kornhuber, Ralf Fredholm integral equations for function approximation and the training of neural networks. (Submitted) Baumann, M. and Heuveline , V. and et al, . Hiflow3 - A Flexible and Hardware-Aware Parallel Finite Element Package. Parallel/High-Performance Object-Oriented Scientific Computing (POOSC'10) . (Submitted) Durumeric, Aleksander E.P. and Chen, Yaoyi and Noé, Frank and Clementi, Cecilia Learning data efficient coarse-grained molecular dynamics from forces and noise. Preprint arXiv . (Unpublished) Scheck, L. and Jones, S. and Juckes, . The Resonant Interaction of a Tropical Cyclone and a Tropopause Front in a Barotropic Model - Part I: Zonally-oriented front. Journal of Atmospheric Sciences . (Submitted) Scheck, L. and Jones, S. and Juckes, . The Resonant Interaction of a Tropical Cyclone and a Tropopause Front in a Barotropic Model - Part II: Frontal waves. Journal of Atmospheric Sciences . (In Press) Noé, Frank and Klein, Leon Transferable Boltzmann Generators. Preprint arXiv . (Unpublished) Ayanbayev, Birzhan and Klebanov, Ilja and Lie, Han Cheng and Sullivan, Timothy Γ-convergence of Onsager-Machlup functionals. Part I: With applications to maximum a posteriori estimation in Bayesian inverse problems. Inverse Problems . Achatz, U. and Ribstein, B. and Senf, F. and Klein, R. The interaction between synoptic-scale balanced flow and a finite-amplitude mesoscale wave field throughout all atmospheric layers: weak and moderately strong stratification. Quarterly Journal of the Royal Meteorological Society . (In Press) |