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2024

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).

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 (Unpublished)

Berner, Julius and Richter, Lorenz and Ullrich, Karen (2024) An optimal control perspective on diffusion-based generative modeling. Preprint arXiv . (Unpublished)

Blaskovic, Filip and Conrad, T. O. F. and Klus, Stefan and Djurdjevac Conrad, Natasa (2024) Clustering Time-Snapshots of Temporal Networks: From Synthetic Data to Real-World Applications. arXiv . (Submitted)

Bleich, Amnon and Linnemann, Antje and Diem, Björn and Conrad, T. O. F. (2024) Enhancing ECG Analysis of Implantable Cardiac Monitor Data: An Efficient Pipeline for Multi-Label Classification. arXiv . (Submitted)

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)

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 .

Bryant, Patrick and Noé, Frank (2024) Improved Protein Complex Prediction with AlphaFold-Multimer by Denoising the MSA Profile. PLOS Computational Biology, 20 (7).

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 (Unpublished)

Chemnitz, Robin and Engel, Maximilian and Koltai, Péter (2024) Extracting coherent sets in aperiodically driven flows from generators of Mather semigroups. Preprint . (Unpublished)

Chemnitz, Robin and Engel, Maximilian and Olicón-Mendez, Guillermo (2024) Random attractors on countable state spaces. Preprint arXiv . (Unpublished)

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, 11 (1).

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).

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 .

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 .

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 .

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.

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)

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)

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, 19 (10). ISSN 1932-6203

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.

Gonçalves, Patrícia and Kern, Julian and Xu, Lu (2024) A novel approach to hydrodynamics for long-range generalized exclusion. arXiv . (Unpublished)

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)

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 .

Iravani, Sahar and Conrad, T. O. F. (2024) Towards More Effective Table-to-Text Generation: Assessing In-Context Learning and Self-Evaluation with Open-Source Models. Computational Linguistics . (Submitted)

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.

Kern, Julian and Wiederhold, Bastian (2024) A Λ-Fleming-Viot type model with intrinsically varying population size. Electronic Journal of Probability, 29 (125).

Koltai, Péter and Kunde, Philipp (2024) A Koopman-Takens theorem: Linear least squares prediction of nonlinear time series. Preprint . (In Press)

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)

Maier, Kristina and Weiser, Martin and Conrad, T. O. F. (2024) Hybrid PDE-ODE Models for Efficient Simulation of Infection Spread in Epidemiology. Proceedings of the Royal Society A . (In Press)

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 .

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

Pavliotis, Grigorios A. and Reich, Sebastian and Zanoni, Andrea (2024) Filtered data based estimators for stochastic processes driven by colored noise. Preprint arXiv . (Unpublished)

Polzin, Robert and Klebanov, Ilja and Nüsken, Nikolas and Koltai, Péter (2024) Coherent set identification via direct low rank maximum likelihood estimation. Journal of Nonlinear Science .

Pusch, Larissa and Conrad, T. O. F. (2024) Combining LLMs and Knowledge Graphs to Reduce Hallucinations in Question Answering. Bioinformatics . ISSN 1367-4803 (Submitted)

Quer, Jannes and Ribera Borrell, Enric (2024) Connecting Stochastic Optimal Control and Reinforcement Learning. Submitted Preprint . (Submitted)

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).

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.

Schebek, Maximilian and Invernizzi, Michele and Noé, Frank and Rogal, Jutta (2024) Efficient Mapping of Phase Diagrams with Conditional Boltzmann Generators. Preprint arXiv . (Unpublished)

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, 47 . ISSN 1755-4365

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).

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 .

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) FELRec: Efficient Handling of Item Cold-Start With Dynamic Representation Learning in Recommender Systems. International Journal of Data Science and Analytics, 19 (1).

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, 28 (11). ISSN 2168-2194

Weimann, K. and Conrad, T. O. F. (2024) Self-Supervised Pre-Training with Joint-Embedding Predictive Architecture Boosts ECG Classification Performance. IEEE . (Submitted)

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)

Wu, Hao and Noé, Frank (2024) Reaction coordinate flows for model reduction of molecular kinetics. The Journal of Chemical Physics, 160 (4).

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 .

2023

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.

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.

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)

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)

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 .

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

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.

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.

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)

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)

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.

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)

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.

Chemnitz, Robin and Engel, Maximilian and Koltai, Péter (2023) Continuous-time extensions of discrete-time cocycles. Contemporary Mathematics . (In Press)

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.

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 .

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).

Engel, Maximilian and Gottwald, Georg A. (2023) Canards in modified equations for Euler discretizations. Preprint to appear in Contemporary Mathematics . (In Press)

Engel, Maximilian and Olicon-Méndez, Guillermo (2023) Noise-induced instabilities in a stochastic Brusselator. Preprint to appear in Contemporary Mathematics . (In Press)

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 .

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).

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.

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)

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.

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.

Huysmans, Lucas and Titi, Edriss (2023) Non-Uniqueness and Inadmissibility of the Vanishing Viscosity Limit of the Passive Scalar Transport Equation. arXiv . (Unpublished)

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).

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).

Kern, Julian (2023) Exponential equivalence for misanthrope processes in contact with weak reservoirs and applications to totally asymmetric exclusion processes. Preprint . (Unpublished)

Kern, Julian (2023) Skorokhod topologies: What they are and why we should care. Mathematische Semesterberichte .

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)

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.

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.

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)

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).

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).

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 .

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

Mielke, Alexander (2023) Non-equilibrium steady states as saddle points and EDP-convergence for slow-fast gradient systems. Journal of Mathematical Physics, 64 (12).

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.

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

Nickl, Richard and Titi, Edriss (2023) On posterior consistency of data assimilation with Gaussian process priors: the 2D Navier-Stokes equations. ArXiv . (Unpublished)

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.

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)

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).

Richter, Lorenz and Berner, Julius and Liu, Guang-Horng (2023) Improved sampling via learned diffusions. Preprint . (Unpublished)

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)

Schubotz, Moritz and Ferrer, Eloi and Stegmüller, Johannes and Mietchen, Daniel and Teschke, Olaf and Pusch, Larissa and Conrad, T. O. F. (2023) Bravo MaRDI: A Wikibase Knowledge Graph on Mathematics. In: Proceedings of the 4th Wikidata Workshop 2022 co-located with the 22st International Semantic Web Conference (ISWC2023), Athens, Greece, November 2023. (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.

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.

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.

Unanue, Alvaro de Diego and Froyland, Gary and Junge, Oliver and Koltai, Péter (2023) A dynamic p-Laplacian. Preprint . (Unpublished)

Weimann, K. and Conrad, T. O. F. (2023) Predicting Coma Recovery After Cardiac Arrest With Residual Neural Networks. Computing in Cardiology (CinC) 2023, 50 .

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.

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)

2022

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.

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)

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.

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)

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.

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).

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.

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.

Dibak, Manuel and Klein, Leon and Krämer, Andreas and Noé, Frank (2022) Temperature steerable flows and Boltzmann generators. Physical Review Research, 4 (4).

Djurdjevac, Ana and Kremp, Helena and Perkowski, Nicolas (2022) Rough homogenization for Langevin dynamics on fluctuating Helfrich surfaces. Preprint arXiv . (Unpublished)

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.

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.

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.

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)

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 .

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.

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)

Kieninger, Stefanie and Keller, Bettina (2022) GROMACS Stochastic Dynamics and BAOAB Are Equivalent Configurational Sampling Algorithms. J. Chem. Theory Comput., 18 (10).

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.

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

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 .

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.

Mardt, Andreas and Hempel, Tim and Clementi, Cecilia and Noé, Frank (2022) Deep learning to decompose macromolecules into independent Markovian domains. nature communications, 13 .

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.

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)

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.

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).

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

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.

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

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

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).

Richter, Lorenz and Berner, Julius (2022) Robust SDE-Based Variational Formulations for Solving Linear PDEs via Deep Learning. Preprint arXiv . (Unpublished)

Sadeghi, Mohsen (2022) Investigating the entropic nature of membrane-mediated interactions driving the aggregation of peripheral proteins. Soft Matter (18). pp. 3917-3927.

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.

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)

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.

Zendehroud, Sina and Loche, Philip and Kornhuber, Ralf and Netz, Roland R. (2022) Boundary Conditions on Conical Hydrophobic Inclusions in Lipid Membranes. Preprint . (Unpublished)

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.

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).

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)

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).

2021

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)

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)

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.

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.

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.

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)

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

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 .

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)

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).

Bittracher, Andreas and Schütte, Christof (2021) A probabilistic algorithm for aggregating vastly undersampled large Markov chains. Physica D, 416 . pp. 1-19.

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)

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.

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.

Coghi, Michele and Nilssen, Torstein and Nüsken, Nikolas (2021) Rough McKean-Vlasov dynamics for robust ensemble Kalman filtering. arXive . pp. 1-41. (Submitted)

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.

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

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.

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.

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.

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 .

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.

Gelß, Patrick and Klus, Stefan and Schuster, Ingmar and Schütte, Christof (2021) Feature space approximation for kernel-based supervised learning. Knowledge-Based Systems, 221 .

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)

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)

Hartmann, C. and Richter, L. (2021) Nonasymptotic bounds for suboptimal importance sampling. To appear 2024 in SIAM/ASA Journal on Uncertainty Quantification . (In Press)

Hartmann, Carsten and Neureither, Lara and Stehlau, Markus (2021) Reachability Analysis of Randomly Perturbed Hamiltonian Systems. IFAC-PapersOnLine, 54 (19). pp. 307-3014.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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

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.

Kieninger, S. and Keller, B. (2021) Path probability ratios for Langevin dynamics—Exact and approximate. The Journal of Chemical Physics, 154 . pp. 1-21.

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)

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.

Kornhuber, R. and Sander, O. and Schiela, A. and Weiser, M. (2021) Wear Testing of Knee Implants. In: German Success Stories in Industrial Mathematics. Springer, pp. 85-90. ISBN Print 978-3-030-81454-0; Online 978-3-030-81455-7

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).

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)

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 .

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

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 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.

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.

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.

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.

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)

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).

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).

Nüsken, N. and Renger, M. (2021) Stein Variational Gradient Descent: many-particle and long-time asymptotics. arXive . pp. 1-25. (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)

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.

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)

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)

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)

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.

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

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)

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.

Rezaei, majid and Netz, Roland R. (2021) Airborne virus transmission via respiratory droplets: Effects of droplet evaporation and sedimentation. ScienceDirect, 55 . ISSN 101471

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.

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

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.

Sadeghi, Mohsen and Noé, Frank (2021) Hydrodynamic coupling for particle-based solvent-free membrane models. The Journal of Chemical Physics, 155 (11).

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.

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 .

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.

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).

Stephan, Artur (2021) EDP-convergence for a linear reaction-diffusion system with fast reversible reaction. Calculus of Variations, 60 (226). pp. 1-35.

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.

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.

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.

Vrijmoed, Johannes and Podladchikov, Y.Y. (2021) Thermolab: a thermodynamics laboratory for nonlinear transport processes in open systems. Earth and Space Science Open Archive .

Weimann, K. and Conrad, T. O. F. (2021) Transfer Learning for ECG Classification. Scientific Reports, 11 (5251). ISSN 2045-2322

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 .

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

Zafferi, Andrea and Peschka, Dirk and Thomas, Marita (2021) GENERIC framework for reactive fluid flows. Preprint (2841). pp. 1-75. ISSN 2198-5855 (Submitted)

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).

2020

Becker, Simon and Richter, Lorenz (2020) Model order reduction for (stochastic-) delay equations with error bounds. arXive . pp. 1-23. (Submitted)

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.

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).

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.

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

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.

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

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)

Farshbaf-Shaker, M. Hassan and Thomas, Marita (2020) Analysis of a compressible Stokes-flow with degenerating and singular viscosity. Preprint . pp. 1-45. (Submitted)

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)

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.

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

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.

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).

Gräser, C. and Alathur Srinivasan, P. A. (2020) Error bounds for PDE-regularized learning. arXiv:2003.06524 . pp. 1-20. (Submitted)

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.

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

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.

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

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.

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.

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.

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.

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

KORNHUBER, RALF and PODLESNY, JOSCHA and YSERENTANT, HARRY (2020) NUMERICAL HOMOGENIZATION OF FRACTAL INTERFACE PROBLEMS. arXive . pp. 1-30. (Submitted)

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

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)

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).

Klus, Stefan and Nüske, Felix and Hamzi, Boumediene (2020) Kernel-Based Approximation of the Koopman Generator and Schrödinger Operator. entropy, 22 .

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.

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.

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

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.

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

Mielke, A. and Roubícek, T. (2020) Thermoviscoelasticity in Kelvin-Voigt rheology at large strains. Arch. Rational Mech. Anal., 238 . pp. 1-45.

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.

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.

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).

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

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

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

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

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.

Noé, Frank (2020) Machine Learning for Molecular Dynamics on Long Timescales. Machine Learning Meets Quantum Physics . pp. 331-372.

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.

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)

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.

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)

Sadeghi, Mohsen and Noé, Frank (2020) Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models. Nature Communications, 11 (2951).

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 .

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.

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.

Winkelmann, Stefanie and Schütte, Christof (2020) Stochastic Dynamics in Computational Biology. Springer International Publishing.

2019

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

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.

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.

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

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)

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.

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.

Daldrop, Jan O. and Netz, Roland R. (2019) Mass-Dependent Solvent Friction of a Hydrophobic Molecule. J. Phys. Chem. B (123). pp. 8123-8130.

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).

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.

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.

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

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

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

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)

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.

Heydecker, Daniel and Patterson, Robert I. A. (2019) Bilinear Coagulation Equations. SFB1114 Preprint in arxiv:1902.07686 . (Unpublished)

Iravani, Sahar and Conrad, T. O. F. (2019) Deep Learning for Proteomics Data for Feature Selection and Classification. Lecture Notes in Computer Science, 11713 .

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

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 .

Kebiri, Omar and Neureither, Lara and Hartmann, Carsten (2019) Adaptive importance sampling with forward-backward stochastic differential equations. In: Stochastic Dynamics Out of Equilibrium. Springer Proceedings in Mathematics & Statistics, 282 . Springer International Publishing, pp. 265-281. ISBN 978-3-030-15095-2

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.

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).

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.

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.

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.

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.

Neureither, L. and Hartmann, C. (2019) Time scales and exponential trends to equilibrium: Gaussian model problems. In: Stochastic Dynamics Out of Equilibrium. IHPStochDyn 2017. Springer Proceedings in Mathematics & Statistics, 282 . Springer, pp. 391-410. ISBN 978-3-030-15095-2

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

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)

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

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.

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)

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

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

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

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

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

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).

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)

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

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

2018

Bjørstad, P. E. and Brenner, S. C. and Halpern, L. and Kim, H. H. and Kornhuber, R. and Rahman, T. and Widlund, O. B., eds. (2018) Domain Decomposition Methods in Science and Engineering XXIV. Lecture Notes in Computational Science and Engineering, 125 . Springer International Publishing. ISBN 978-3-319-93872-1

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)

Bittracher, Andreas and Banisch, Ralf and Schütte, Christof (2018) Data-driven computation of molecular reaction coordinates. J. Chem. Phys., 149 (154103).

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

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)

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

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

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

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.

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

Donati, Luca and Keller, Bettina G. (2018) Girsanov reweighting for metadynamics simulations. J. Chem. Phys. 149, 149 . pp. 1-16.

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)

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

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)

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)

Heida, Martin and Schweizer, Ben (2018) Stochastic homogenization of plasticity equations. ESAIM: Control, Optimisation and Calculus of Variations, 24 (1). 153 -176.

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.

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.

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)

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

Kies, Tobias (2018) Gradient Methods for Membrane-Mediated Particle Interactions. PhD Thesis . pp. 1-147.

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

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).

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

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

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)

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

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.

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)

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

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

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

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)

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)

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

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

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.

Weber, M. (2018) Implications of PCCA+ in Molecular Simulation. Computation, 6 (1). ISSN 2079-3197 (online)

2017

Blömker, Dirk and Schillings, Claudia and Wacker, Philipp (2017) A strongly convergent numerical scheme from EnKF continuum analysis. ... . (Submitted)

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).

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

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.

Djurdjevac, A. (2017) Advection-diffusion equations with random coefficients on evolving hypersurfaces. Interfaces and Free Boundaries, 19 (4). pp. 525-552. ISSN 1463-9963

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

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

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)

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 .

Kornhuber, R. and Podlesny, J. and Yserentant, H. (2017) Direct and Iterative Methods for Numerical Homogenization. In: Domain Decomposition Methods in Science and Engineering. Lecture Notes in Computational Science and Engineering, XXIII (116). SpringerLink, pp. 217-225. ISBN 978-3-319-52389-7

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

Mielke, A. (2017) Three examples concerning the interaction of dry friction and oscillations. In: Trends on Application of Mathematics to Mechanics. Springer Proceedings of the INdAM-ISIMM Workshop, Rome, Italy, September 2016 (27). Springer INdAM series, pp. 159-177.

Polthier, L. (2017) Algebraic Multilevel Methods for Markov Chains. SFB 1114 Preprint in arXiv:1711.04332 . pp. 1-19. (Unpublished)

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.

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.

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)

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.

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

2016

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

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

Delle Site, L. (2016) Formulation of Liouville's theorem for grand ensemble molecular simulations. Physical Review E, 93 (022130).

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

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

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

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

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.

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.

Rams, Mona (2016) A new approach for biomarker detection using fusion networks. Masters thesis, Freie Universität Berlin.

Schillings, Claudia and Stuart, Andrew M. (2016) Analysis of the ensemble Kalman filter for inverse problems. arXiv .

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 .

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

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)

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 .

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

2015

Deckelnick, K. and Elliott, C.M. and Kornhuber, R. and Sethian, J. A., eds. (2015) Geometric partial differential equations: Surface and bulk processes. Oberwolfach Reports, 12 (4). European Mathematical Society - Publishing House, Zürich, Switzerland.

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

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

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

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

Banisch, Ralf and Djurdjevac, N. (2015) Cycle-flow–based module detection in directed recurrence networks. EPL (Europhysics Letters) , 108 (6). ISSN 0295-5075

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

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

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

Deuflhard, P. and Röblitz, S. (2015) A Guide to Numerical Modelling in Systems Biology. Texts in Computational Science and Engineering, 12 . Springer International Publishing, Basel. ISBN 978-3-319-20058-3 (print) / 978-3-319-20059-0 (online)

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

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.

Ehrig, R. and Dierkes, T. and Schäfer, S. and Röblitz, S. and Tronci, E. and Mancini, T. and Salvo, I. and Alimguzhin, V. and Mari, F. and Melatti, I. and Massini, A. and Krüger, T. H. C. and Egli, M. and Ille, F. and Leeners, B. (2015) An integrative approach for model driven computation of treatments in reproductive medicine. In: BIOMAT - Proceedings of the 15th International Symposium on Mathematical and Computational Biology, 07.11.2015 - 11.11.2015, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India - USA.

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

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

Gräser, C. (2015) A note on Poincaré- and Friedrichs-type inequalities. arXiv:1512.02842 . (Submitted)

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

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

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).

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

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

Ozdoba, Christopher (2015) Ensemble Machine Learning Techniques for Analyzing Large Biological Datasets Using the SAP In-Memory Database HANA. Masters thesis, Freie Universität Berlin.

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

Plöntzke, J. and Berg, M. and Stötzel, C. and Röblitz, S. (2015) A systems biology approach to bovine fertility and metabolism: Introduction of a glucose insulin model. In: BIOMAT - Proceedings of the 15th International Symposium on Mathematical and Computational Biology, 07.11.2015 - 11.11.2015, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India - USA.

Schütte, Ch. and Sarich, M. (2015) A Critical Appraisal of Markov State Models. SFB 1114 Preprint, 15-18 . ISSN 1438-0064

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

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

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

Stötzel, C. and Ehrig, R. and Boer, H.M.T. and Plöntzke, J. and Röblitz, S. (2015) Exploration of different wave patterns in a model of the bovine estrous cycle by Fourier analysis. In: BIOMAT - Proceedings of the 14th International Symposium on Mathematical and Computational Biology, 02.11.2014 - 08.11.2014, Bedlewo - Poland.

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

You, Xintian Arthur (2015) Hastings: An R pipeline for large-scale RNA-Seq data analysis. Technical Report . (Unpublished)

2014

Bach, V. and Delle Site, L., eds. (2014) Many-Electron Approaches in Physics, Chemistry and Mathematics. Mathematical Physics Studies . Springer, Heidelberg. ISBN 978-3-319-06378-2

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

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

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

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

Gräser, C. and Sander, O. (2014) Truncated nonsmooth Newton multigrid methods for simplex-constrained minimization problems. Preprint 384, IGPM Aachen . (Submitted)

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

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

Jouvet, G. and Rappaz, J. (2014) Numerical analysis and simulation of the dynamics of mountain glaciers. In: Modeling, Simulation and Optimization for Science and Technology. Computational Methods in Applied Sciences (34). Springer Netherlands, pp. 83-92. ISBN 978-94-017-9053-6

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

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

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)

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

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)

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

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

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

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

2013

Berninger, H. and Kornhuber, R. and Sander, O. (2013) Heterogeneous substructuring methods for coupled surface and subsurface flow. In: Domain Decomposition Methods in Science and Engineering XX. Lecture Notes in Computational Science and Engineering, 91 . Springer Berlin Heidelberg, pp. 427-434. ISBN 978-3-642-35274-4

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

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

Gräser, C. (2013) Nonsmooth Schur-Newton methods for nonsmooth saddle point problems. Preprint 1004, Matheon Berlin .

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

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

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).

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

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

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.

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

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

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

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

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

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

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

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

Sander, O. (2013) Coupling geometrically exact cosserat rods and linear elastic continua. In: Domain Decomposition Methods in Science and Engineering XX. Lecture Notes in Computational Science and Engineering, 91 . Springer Berlin Heidelberg, pp. 443-450. ISBN 978-3-642-35274-4

Sander, O. (2013) Geodesic finite elements in spaces of zero curvature. In: Numerical Mathematics and Advanced Applications 2011. Proceedings of ENUMATH 2011, the 9th European Conference on Numerical Mathematics and Advanced Applications, Leicester, September 2011 . Springer Berlin Heidelberg, pp. 449-457. ISBN 978-3-642-33133-6

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

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

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

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.

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

2012

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

Bastian, P. and Berninger, H. and Dedner, A. and Engwer, C. and Henning, P. and Kornhuber, R. and Kröner, D. and Ohlberger, M. and Sander, O. and Schiffler, G. and Shokina, N. and Smetana, K. (2012) Adaptive modelling of coupled hydrological processes with application in water management. In: Progress in Industrial Mathematics at ECMI 2010. Mathematics in Industry: The European Consortium for Mathematics in Industry (17). Springer Berlin Heidelberg, pp. 561-567. ISBN 978-3-642-25100-9

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

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.

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.

Hartmann, C. and Schütte, Ch. (2012) Efficient rare event simulation by optimal nonequilibrium forcing. J. Stat. Mech. Theor. Exp., 2012 . P11004.

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

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

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.

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

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.

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

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

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

Youett, J. and Sander, O. (2012) A dissipative discretization for large deformation frictionless dynamic contact problems. MATHEON Preprint #1184 .

2011

Berninger, H. and Kornhuber, R. and Sander, O. (2011) Convergence behaviour of Dirichlet-Neumann and Robin methods for a nonlinear transmission problem. In: Domain Decomposition Methods in Science and Engineering XIX. Lecture Notes in Computational Science and Engineering, 78 . Springer Berlin Heidelberg, pp. 87-98. ISBN 978-3-642-11303-1

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

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

Dziuk, G. and Elliott, C.M. and Huisken, G. and Kornhuber, R. (2011) Geometric partial differential equations: Theory, numerics and applications. Oberwolfach Reports, 8 (4). European Mathematical Society.

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

Hartmann, C. (2011) Balanced model reduction of partially-observed Langevin processes: an averaging principle. Math. Comput. Model. Dyn. Syst., 17 (5). pp. 463-490.

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.

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

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

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

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

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.

Sander, O. (2011) The PSurface library. Computing and Visualization in Science, 14 (8). pp. 353-370. ISSN 1432-9360

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

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

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

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

2010

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

Bastian, P. and Buse, G. and Sander, O. (2010) Infrastructure for the Coupling of Dune Grids. In: Numerical Mathematics and Advanced Applications 2009: Proceedings of ENUMATH 2009. Springer Berlin Heidelberg, pp. 107-114. ISBN 978-3-642-11794-7

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

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

Djurdjevac, N. and Sarich, M. and Schütte, Ch. (2010) On Markov State Models for Metastable Processes. In: ICM 2010.

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

Gräser, C. and Kornhuber, R. and Sack, U. (2010) On hierarchical error estimators for time-discretized phase field models. In: Numerical Mathematics and Advanced Applications 2009: Proceedings of ENUMATH 2009. Springer Berlin Heidelberg, pp. 397-405. ISBN 978-3-642-11794-7

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.

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.

Horenko, I. (2010) Finite Element Approach to Clustering of Multidimensional Time Series. J. Sci. Comp., 32 (1). pp. 62-83.

Horenko, I. (2010) On Clustering of Non-stationary Meteorological Time Series. Dyn. of Atm. and Oc., 49 (2-3). pp. 164-187.

Kornhuber, R. (2010) Mathematik hilft heilen. In: Wissenschaftsstadt Berlin. Berliner Wirtschaftsgespräche e.V., p. 123.

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.

Metzner, Ph. and Weber, M. and Schütte, Ch. (2010) Observation Uncertainty in Reversible Markov Chains. Phys. Rev. E, 82 (3). 031114.

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

Sander, O. (2010) Geodesic finite elements for Cosserat rods. International Journal for Numerical Methods in Engineering, 82 (13). pp. 1645-1670. ISSN 1097-0207

Sarich, M. and Schütte, Ch. and Vanden-Eijnden, E. (2010) Optimal Fuzzy Aggregation of Networks. Multiscale Modeling and Simulation, 8 (4). pp. 1535-1561.

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

2009

Bercovier, M. and Gander, M. and Kornhuber, R. and Widlund, O., eds. (2009) Domain decomposition methods in science and engineering XVIII. Lecture Notes in Computational Science and Engineering, 70 . Springer Berlin Heidelberg. ISBN 978-3-642-02676-8

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.

Berninger, H. (2009) Non-overlapping domain decomposition for the Richards equation via superposition operators. In: Domain Decomposition Methods in Science and Engineering XVIII. Lecture Notes in Computational Science and Engineering, 70 . Springer Berlin Heidelberg, pp. 169-176. ISBN 978-3-642-02676-8

Dittmer, E. (2009) Hidden Markov Models with Time-Continuous Output Behavior. PhD thesis, FU Berlin.

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

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.

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

Gräser, C. and Kornhuber, R. (2009) Multigrid methods for obstacle problems. Journal of Computational Mathematics, 27 (1). pp. 1-44. ISSN 0254-9409

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

Gräser, C. and Sack, U. and Kornhuber, R. (2009) Truncated nonsmooth Newton multigrid methods for convex minimization problems. In: Domain Decomposition Methods in Science and Engineering XVIII. Lecture Notes in Computational Science and Engineering, 70 . Springer Berlin Heidelberg, pp. 129-136. ISBN 978-3-642-02676-8

Gräser, C. and Sander, O. (2009) The dune-subgrid module and some applications. Computing, 86 (4). pp. 269-290. ISSN 0010-485X

Hartmann, C. (2009) Balancing of dissipative Hamiltonian systems. In: Proceedings of MATHMOD 2009; I. Troch, F. Breitenecker (eds.); ARGESIM Report no. 35.

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.

Horenko, I. (2009) On metastable conformational analysis of non-equilibrium biomolecular time series. MMS . (Submitted)

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)

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.

Meerbach, E. (2009) Off- and Online Detection of Dynamical Phases in Time Series. PhD thesis, Free University of Berlin.

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.

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.

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.

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.

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.

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.

Swart, T. and Rousse, V. (2009) A Mathematical Justification for the Herman-Kluk Propagator. Comm. Math. Phys., 286 (2). pp. 725-750.

2008

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

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

Conrad, T. O. F. and Reinert, K. and Kohlbacher, O. (2008) Bioinformatics Support for Mass Spectrometry Quality Control. In: Proteomics Sample Preparation. Wiley-Vch, p. 485.

Fermanian Kammerer, C. and Lasser, C. (2008) Propagation through Generic Level Crossings: A Surface Hopping Semigroup. J. Math. Anal., 40 (1). pp. 103-133.

Fermanian Kammerer, C. and Lasser, C. (2008) Single switch surface hopping for molecular dynamics with transitions. J. Chem. Phys., 128 (14). p. 144102.

Fischbach, M. (2008) Methods for modeling metastable conformational dynamics from trajectory data. Masters thesis, FU Berlin.

Forster, R. and Kornhuber, R. and Mautner, K. and Sander, O. (2008) Fast and reliable pricing of American options with local volatility. In: Domain Decomposition Methods in Science and Engineering XVII. Lecture Notes in Computational Science and Engineering, 60 . Springer Berlin Heidelberg, pp. 383-390. ISBN 978-3-540-75198-4

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.

Gräser, C. (2008) Globalization of nonsmooth Newton methods for optimal control problems. In: Numerical Mathematics and Advanced Applications. Proceedings of ENUMATH 2007, the 7th European Conference on Numerical Mathematics and Advanced Applications, Graz, Austria, September 2007 . Springer Berlin Heidelberg, pp. 605-612. ISBN 978-3-540-69776-3

Hartmann, C. and Schütte, Ch. (2008) Balancing of partially-observed stochastic differential equations. 47th IEEE Conference on Decision and Control . pp. 4867-4872.

Hartmann, C. (2008) An Ergodic Sampling Scheme for Constrained Hamiltonian Systems with Applications to Molecular Dynamics. J. Stat. Phys., 130 (4). pp. 687-712.

Hartmann, C. (2008) Structure-preserving model reduction of partially observed differential equations: molecular dynamics and beyond. Oberwolfach Reports, 5 (2). pp. 1111-1115.

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. (2008) On Simultaneous Data-Based Dimension Reduction and Hidden Phase Identification. J. Atm. Sci, 65 (6). pp. 1941-1954.

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.

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.

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 Schütte, Ch. (2008) Dimension Reduction for Time Series with Hidden Phase Transitions and Economic Applications. Adv. Data Anal. Class., submitted . (Submitted)

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.

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

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

Lasser, C. and Swart, T. (2008) Single switch surface hopping for a model of pyrazine. J. Chem.Phys., 129 (03). 034302.

Meerbach, E. and Schütte, Ch. (2008) Sequential Change Point Detection in Molecular Dynamics Trajectories. Journal of Multivariate Analysis, submitted .

Noé, F. (2008) Probability Distributions of Molecular Observables computed from Markov Models. J. Chem. Phys., 128 . p. 244103.

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.

Sakalli, I. (2008) Parallelization Strategies for a Brownian Dynamics Algorithm. Other thesis, FU Berlin.

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.

2007

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.

Gräser, C. and Kornhuber, R. (2007) On preconditioned Uzawa-type iterations for a saddle point problem with inequality constraints. In: Domain Decomposition Methods in Science and Engineering XVI. Lecture Notes in Computational Science and Engineering, 55 . Springer Berlin Heidelberg, pp. 91-102. ISBN 978-3-540-34468-1

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.

Hartmann, C. (2007) Model Reduction in Classical Molecular Dynamics. PhD thesis, Freie Universität Berlin.

Hartmann, C. and Schütte, Ch. (2007) Comment on Two Distinct Notions of Free Energy. Physica D, 228 (1). pp. 59-63.

Held, M. (2007) Conformational Studies of UDP-N-Acetyl-Glucosamine in Environments of Increasing Complexity. Masters thesis, FU Berlin.

Held, M. and Meerbach, E. and Hinderlich, S. and Reutter, W. and Schütte, Ch. (2007) Conformational Studies of UDP-GlcNAc in Environments of Increasing Complexity. In: From Computational Biophysics to Systems Biology.

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.

Jahnke, T. and Huisinga, W. (2007) Solving the Chemical Master Equation for Monomolecular Reaction Systems Analytically. J. Math. Biol., 54 (1). pp. 1-26.

Kiljunen, T. and Schmidt, B. (2007) Alignment and Orientation of Molecules in Matrices. In: Analysis and Control of Ultrafast Photoinduced Reactions. Series in Chemical Physics, 87 . Springer, Berlin, pp. 337-352.

Kornhuber, R. and Gräser, C. (2007) On preconditioned Uzawa-type iterations for a saddle point problem with inequality constraints. In: Decomposition Methods in Science and Engineering XVI. LNCSE (55). Springer, pp. 91-102. ISBN 978-3-540-34469-8

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.

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.

Meerbach, E. and Schütte, Ch. and Horenko, I. and Schmidt, B. (2007) Metastable Conformational Structure and Dynamics: Peptides between Gas Phase and Aqueous Solution. In: Analysis and Control of Ultrafast Photoinduced Reactions. Series in Chemical Physics, 87 . Springer, Berlin, pp. 796-806.

Metzner, Ph. (2007) Transition Path Theory for Markov Processes. PhD thesis, Free University of Berlin.

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.

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.

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 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.

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 .

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.

von Kleist, M. and Kloft, Ch. and Huisinga, W. (2007) Combining Systems Biology with Physiologically Based Pharmacokinetics to Support the Understanding of Drug Effects. In: Proceedings of the 2nd Foundations of Systems Biology in Engineering Conference, FOSBE 2007, 09.-12.09.2007, Stuttgart, Germany.

2006

Barth, I. and Gonzalez, L. and Lasser, C. and Manz, J. and Rozgonyi, T. (2006) Laser control of nuclear and electron dynamics: bond selective photodissociation and electron circulation. In: Coherent Control of Molecules. Collaborative Computational Project (6). Daresbury Laboratory, pp. 18-27.

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 .

Bornemann, F. A. and Lasser, C. and Swart, T. (2006) Energy Level Crossings in Molecular Dynamics. In: Analysis, Modeling and Simulation of Multiscale Problems. Springer, Berlin, pp. 577-594.

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

Cohen, D. and Jahnke, T. and Lorenz, K. and Lubich, Ch. (2006) Numerical Integrators for Highly Oscillatory Hamiltonian Systems: A Review. In: Analysis, Modeling and Simulation of Multiscale Problems.

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.

Dellnitz, M. and Molo, M. and Metzner, Ph. and Preis, R. and Schütte, Ch. (2006) Graph Algorithms for Dynamical Systems. In: Analysis, Modeling and Simulation of Multiscale Problems.

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

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

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.

Horenko, I. and Hartmann, C. (2006) Blind Model Reduction for High-Dimensional Time-Dependent Data. Technical Report. Freie Universität Berlin. (Unpublished)

Horenko, I. and Schmidt-Ehrenberg, J. and Schütte, Ch. (2006) Set-Oriented Dimension Reduction: Localizing Principal Component Analysis via Hidden Markov Models. In: Computational Life Sciences II.

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

Lorenz, S. (2006) The model-data-overlap: A new approach to parameter estimation, model validation, selection and discrimination. PhD thesis, Free University of Berlin.

Meerbach, E. and Dittmer, E. and Horenko, I. and Schütte, Ch. (2006) Multiscale Modelling in Molecular Dynamics: Biomolecular Conformations as Metastable States. In: Computer Simulations in Condensed Matter: Systems: From Materials to Chemical Biology. Volume I.

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.

Sander, O. (2006) A fast solver for finite deformation contact problems. Preprint A-06-02 . (Unpublished)

Telgmann, R. and von Kleist, M. and Huisinga, W. (2006) Software Supported Modelling in Pharmacokinetics. In: Computational Life Sciences II.

Walter, J. (2006) Averaging for Diffusive Fast-Slow Systems with Metastability in the Fast Variable. PhD thesis, Free University of Berlin.

Walter, J. and Schütte, Ch. (2006) Conditional Averaging for Diffusive Fast-Slow Systems: A Sketch for Derivation. In: Analysis, Modeling and Simulation of Multiscale Problems.

Weiße, A. Y. and Horenko, I. and Huisinga, W. (2006) Adaptive Approach for Modelling Variability in Pharmacokinetics. In: Computational Life Sciences II.

2005

Kornhuber, R. and Hoppe, R. and Périaux, J. and Pironneau, O. and Widlund, O. and Xu, J., eds. (2005) Domain decomposition methods in science and engineering. Lecture Notes in Computational Science and Engineering, 40 . Springer, Berlin. ISBN 978-3-540-22523-2

Chipot, C. and Elber, R. and Laaksonen, A. and Leimkuhler, B. and Mark, A. and Schlick, T. and Schütte, Ch. and Skeel, R., eds. (2005) New Algorithms for Macromolecular Simulation. Lecture Notes in Computational Science and Engineering, 49 . Springer.

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.

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.

Dellnitz, M. and Neumann, M. and Schütte, Ch. (2005) Special Issue on Matrices and Mathematical Biology. Lin. Alg. Appl., 398 . pp. 1-245.

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.

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.

Hartmann, C. and Schütte, Ch. (2005) A Geometric Approach to Constrained Molecular Dynamics and Free Energy. Comm. Math. Sci., 3 (1). pp. 1-20.

Horenko, I. and Dittmer, E. and Schütte, Ch. (2005) Reduced Stochastic Models for Complex Molecular Systems. Comp. Vis. Sci., 9 (2). pp. 89-102.

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.

Huisinga, W. and Schmidt, Bernd (2005) Metastability and Dominant Eigenvalues of Transfer Operators. In: New Algorithms for Macromolecular Simulation.

Kiljunen, T. and Schmidt, B. and Schwentner, N. (2005) Aligning and Orienting Molecules Trapped in Octahedral Crystal Fields. Phys. Rev. A, 72 (5). 053415.

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.

Krause, R. and Sander, O. (2005) Fast solving of contact problems on complicated geometries. In: Domain Decomposition Methods in Science and Engineering XIII. Lecture Notes in Computational Science and Engineering, 40 . Springer, Berlin, pp. 495-502. ISBN 978-3-540-22523-2

Lasser, C. and Teufel, St. (2005) Propagation through conical crossings: An asymptotic semigroup. Comm. Pure Appl. Math., 58 (9). pp. 1188-1230.

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.

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.

Rack, A. (2005) Prediction of Post-translational Modifications of Proteins from 2-DE/MS Data. Masters thesis, Freie Universität Berlin.

Schütte, Ch. and Forster, R. and Meerbach, E. and Fischer, A. (2005) Uncoupling-Coupling Techniques for Metastable Dynamical Systems. In: Domain Decomposition Methods in Science and Engineering.

2004

Conrad, T. O. F. (2004) Metabolic Pathways. Other thesis, Monash University Melbourne.

Conrad, T. O. F. (2004) New Approaches for Visualizing and Analyzing Metabolic Pathways. Proceedings of the Second Australian Undergraduate Students’ Computing Conference .

Deuflhard, P. and Schütte, Ch. (2004) Molecular Conformation Dynamics and Computational Drug Design. In: Applied Mathematics Entering the 21st Century.

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.

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.

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.

Jahnke, T. (2004) A Long-Time-Step Method for Quantum-Classical Molecular Dynamics. SIAM J. Sci. Comp., 25 (6). pp. 2145-2164.

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.

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.

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 .

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.

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 .

2003

Berninger, H. and Werner, Dirk (2003) Lipschitz spaces and M-ideals. Extracta Mathematicae, 18 (1). pp. 33-56. ISSN 0213-8743

Conrad, T. O. F. (2003) Berechnung von freien Energie Flächen am Beispiel des Alanin-Dipeptides. Other thesis, Freie Universität Berlin.

Fermanian Kammerer, C. and Lasser, C. (2003) Wigner measures and codimension two crossings. J. Math. Phys., 44 (2). pp. 507-557.

Fischer, A. (2003) An Uncoupling-Coupling Method for Markov Chain Monte Carlo Simulations with an Application to Biomolecules. PhD thesis, Free University of Berlin.

Horenko, I. and Weiser, M. (2003) Adaptive Integration of Molecular Dynamics. J. Comp. Chem., 24 (15). pp. 1921-1929.

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.

Kornhuber, R. and Krause, R. (2003) On multigrid methods for vector-valued Allen-Cahn equations. In: Proceedings of the fourteenth international conference on domain decomposition methods. National Autonomous University of Mexico (UNAM), Mexico City, Cocoyoc, Mexico, pp. 307-314. ISBN 970-32-0859-2

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.

Sander, O. and Caselles, V. and Bertalmio, M. (2003) Axiomatic scalar data interpolation on manifolds. In: International Conference on Image Processing (ICIP) 2003. Proceedings. IEEE, Barcelona, Spain, pp. 681-684. ISBN 0-7803-7750-8

Schütte, Ch. and Huisinga, W. (2003) Biomolecular Conformations can be Identified as Metastable Sets of Molecular Dynamics. In: Special Volume: Computational Chemistry.

Schütte, Ch. and Huisinga, W. and Meyn, S. (2003) Metastability of Diffusion Processes. In: Nonlinear Stochastic Dynamics.

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

2002

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.

Fischer, A. and Schütte, Ch. and Deuflhard, P. and Cordes, F. (2002) Hierarchical Uncoupling-Coupling of Metastable Conformations. In: Computational Methods for Macromolecules: Challenges and Applications.

Gebauer, S. and Neunhäuserer, L. and Kornhuber, R. and Ochs, S. and Hinkelmann, R. and Helmig, R. (2002) Equidimensional modelling of flow and transport processes in fractured porous systems I. In: Computational Methods in Water Resources. Proceedings of the XIVth International Conference on Computational Methods in Water Resources (CMWR XIV). Computational Methods in Water Resources (CMWR XIV), Delft, pp. 335-342. ISBN 978-0-444-50975-8

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.

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.

Kornhuber, R. (2002) On constrained Newton linearization and multigrid for variational inequalities. Numerische Mathematik, 91 (4). pp. 699-721. ISSN 0029-599X

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.

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

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.

Neunhäuserer, L. and Gebauer, S. and Ochs, S. and Hinkelmann, R. and Kornhuber, R. and Helmig, R. (2002) Equidimensional modelling of flow and transport processes in fractured porous systems II. In: Computational Methods in Water Resources. Proceedings of the XIVth International Conference on Computational Methods in Water Resources (CMWR XIV). Computational Methods in Water Resources (CMWR XIV), Delft, pp. 343-350. ISBN 978-0-444-50975-8

Ochs, S. and Hinkelmann, R. and Neunhäuserer, L. and Süß, M. and Helmig, R. and Gebauer, S. and Kornhuber, R. (2002) Adaptive methods for the equidimensional modelling of flow and transport processes in fractured aquifers. In: 5th International Conference on Hydroscience and Engineering, ICHE2002, Advances in Hydro-Science and -Engineering., Sept. 17-21, 2002, Warschau.

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.

2001

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.

Erdmann, B. and Kober, C. and Lang, J. and Deuflhard, P. and Zeilhofer, H.-F. and Sader, R. (2001) Efficient and reliable finite element methods for simulation of the human mandible. In: Proceedings of Medicine Meets Mathematics. Kloster Banz/Staffelstein. Report ZIB 01-14, 2001. (Submitted)

Hartmann, C. and Schmidt, H.-J. (2001) A WKB approximation for the nonlinear Schrödinger-Newton equations. Technical Report. Universität Osnabrück. (Unpublished)

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.

Huisinga, W. (2001) Metastability of Markovian Systems A transfer operator based approach in application to molecular dynamics. PhD thesis, Free University of Berlin.

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

Kober, C. and Sader, R. and Zeilhofer, H.-F. and Prohaska, S. and Zachow, S. and Deuflhard, P. (2001) Anisotrope Materialmodellierung für den menschlichen Unterkiefer. In: Tagungsband des Workshops "Die Methode der Finiten Elemente in der Biomedizin, Biomechanik und angrenzenden Gebieten". Universitätsklinikum/Universitätsrechenzentrum, Ulm. ISBN 978-3980618342

Kornhuber, R. (2001) Nonlinear multigrid techniques. In: Theory and Numerics of Differential Equations. Durham 2000. Universitext . Springer Berlin Heidelberg, pp. 179-229. ISBN 978-3-642-07533-9

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

Müller-Hannemann, M. and Kober, C. and Sader, R. and Zeilhofer, H.-F. (2001) Anisotropic validation of hexahedral meshes for composite materials in biomechanics. In: Proceedings of the 10th International Meshing Roundtable. International Meshing Roundtable, Newport Beach, CA, pp. 249-260.

Schütte, Ch. and Huisinga, W. and Deuflhard, P. (2001) Transfer Operator Approach to Conformational Dynamics in Biomolecular Systems. In: Ergodic Theory, Analysis, and Efficient Simulation of Dynamical Systems.

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.

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

2000

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.

Fischer, A. (2000) An Uncoupling-Coupling Technique for Markov Chain Monte Carlo Methods. preprint .

Galliat, T. and Huisinga, W. and Deuflhard, P. (2000) Self-Organizing Maps Combined with Eigenmode Analysis for Automated Cluster Identification. In: Neural Computation.

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.

Huisinga, W. (2000) The Essential Spectral Radius and Asymptotic Properties of Transfer Operators. preprint .

Kober, C. (2000) Composite material with shape memory alloy fibers. In: Communications of the Bexbach Colloquium on Science 2000. Shaker, Aachen. ISBN 978-3-8322-1517-0

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)

Krause, R. and Wohlmuth, B. (2000) Multigrid methods for Mortar finite elements. In: Multigrid Methods VI. Proceedings of the Sixth European Multigrid Conference Held in Gent, Belgium, September 27–30. Springer Berlin Heidelberg, pp. 136-142. ISBN 978-3-540-67157-2

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

Neunhäuserer, L. and Gebauer, S. and Hinkelmann, R. and Kornhuber, R. and Helmig, R. (2000) Mehrgittermethoden und adaptive Diskretisierungsverfahren zur Simulation von Strömungs- und Transportprozessen in Kluftaquiferen. In: 3. Workshop Kluft-Aquifere "Gekoppelte Prozesse in Geosystemen". Institut für Strömungsmechanik und Elektronisches Rechnen im Bauwesen, Hannover, pp. 241-255.

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.

Schütte, Ch. and Cordes, F. (2000) On Dynamical Transitions between Conformational Ensembles. In: Molecular Dynamics on Parallel Computers.

Schütte, Ch. and Huisinga, W. (2000) Biomolecular Conformations as Metastable Sets of Markov Chains. In: Proceedings of the 38th Annual Allerton Conference on Communication, Control, and Computing, Monticello, Illinoins/USA.

Schütte, Ch. and Huisinga, W. (2000) On Conformational Dynamics induced by Langevin Processes. In: Equadiff 99.

1999

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.

Bornemann, F. A. and Schütte, Ch. (1999) Adaptive Accuracy Control for Car-Parrinello Simulations. Num. Math., 83 (2). pp. 179-186.

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.

Deuflhard, P. and Dellnitz, M. and Junge, O. and Schütte, Ch. (1999) Computation of Essential Molecular Dynamics by Subdivision Techniques. In: Computational Molecular Dynamics: Challenges, Methods, Ideas.

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.

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.

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.

Kornhuber, R. (1999) Monotone iterations for elliptic variational inequalities. In: Free boundary problems: theory and applications. Research notes in mathematics (409). Chapman & Hall/CRC, Boca Raton, London, New York, Washington, D.C., pp. 335-343. ISBN 1-58488-018-X

Nettesheim, P. and Reich, S. (1999) Symplectic Multiple-Time-Stepping Integrators for Quantum-Classical Molecular Dynamics. In: Computational Molecular Dynamics: Challenges, Methods, Ideas.

Nettesheim, P. and Schütte, Ch. (1999) Numerical Integrators for Quantum-Classical Molecular Dynamics. In: Computational Molecular Dynamics: Challenges, Methods, Ideas.

Schütte, Ch. (1999) Conformational Dynamics: Modelling, Theory, Algorithm, and Application to Biomolecules. preprint .

Schütte, Ch. (1999) Partial Wigner transforms and the quantum-classical Liouville equation. Other thesis, UNSPECIFIED.

Schütte, Ch. and Bornemann, F. A. (1999) Approximation Properties and Limits of the Quantum-Classical Molecular Dynamics Model. In: Computational Molecular Dynamics: Challenges, Methods, Ideas.

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.

Schütte, Ch. and Nettesheim, P. (1999) Nonadiabatic Effects in Quantum-Classical Molecular Dynamics. In: Scientific Computing in Chemical Engineering II.

1998

Bornemann, F. A. and Schütte, Ch. (1998) A mathematical investigation of the Car-Parrinello Method. Num. Math., 78 (3). pp. 359-376.

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.

Kornhuber, R. (1998) On robust multigrid methods for non-smooth variational problems. In: Multigrid methods 5: Proceedings of the Fifth European Multigrid Conference held in Stuttgart, Germany, October 1.4, 1996. Lecture Notes in Computational Science and Engineering (3). Springer Berlin Heidelberg, pp. 173-188. ISBN 978-3-540-63133-0

Nettesheim, P. (1998) Second Order Transitions in Quantum-Classical Molecular Dynamics. preprint .

1997

Bornemann, F. A. and Schütte, Ch. (1997) Homogenization of Hamiltonian Systems with a Strong Constraining Potential. Physica D, 102 (1-2). pp. 57-77.

Kornhuber, R. (1997) Adaptive monotone multigrid methods for nonlinear variational problems. Advances in Numerical Mathematics . Vieweg+Teubner Verlag, Stuttgart. ISBN 3519027224

Kornhuber, R. (1997) Adaptive monotone multigrid methods for some non-smooth optimization problems. In: Domain decomposition methods in science and engineering: 8th international conference, Bejing, P.R. China. John Wiley & Sons, pp. 177-191. ISBN 047196560X

Schütte, Ch. and Bornemann, F. A. (1997) Homogenization Approach to Smoothed Molecular Dynamics. Nonlinear Analysis, 30 (3). pp. 1805-1814.

1996

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

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.

Kornhuber, R. (1996) Monotone multigrid methods for elliptic variational inequalities II. Numerische Mathematik, 72 (4). pp. 481-499. ISSN 0029-599X

Kornhuber, R. (1996) A posteriori error estimates for elliptic variational inequalities. Computers & Mathematics with Applications, 31 (8). pp. 49-60. ISSN 0898-1221

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.

Nettesheim, P. and Huisinga, W. and Schütte, Ch. (1996) Chebyshev-Approximation for Wavepacket-Dynamics: better than expected. preprint .

1995

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.

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 .

1994

Erdmann, B. and Hoppe, R. H. W. and Kornhuber, R. (1994) Adaptive multilevel-methods for obstacle problems in three space dimensions. In: Adaptive Methods - Algorithms, Theory and Applications. Notes on Numerical Fluid Mechanics (NNFM), 46 . Vieweg+Teubner Verlag, pp. 120-141. ISBN 978-3-528-07646-7

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

Kornhuber, R. (1994) Monotone multigrid methods for elliptic variational inequalities I. Numerische Mathematik, 69 (2). pp. 167-184. ISSN 0029-599X

Kornhuber, R. and Yserentant, H. (1994) Multilevel methods for elliptic problems on domains not resolved by the coarse grid. In: Domain Decomposition Methods in Scientific and Engineering Computing. Contemporary Mathematics, 180 . American Mathematical Society, Providence, Rhode Island, pp. 49-60. ISBN 0-8218-5171-3

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.

1993

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

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

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

Kornhuber, R. and Wittum, G. (1993) Discretization and preconditioning of convection diffusion equations. In: Incomplete Decomposition (ILU) - Algorithms, Theory, and Applications. Notes on Numerical Fluid Mechanics (41). Springer Vieweg, pp. 67-77. ISBN 978-3-528-07641-2

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.

1992

Schütte, Ch. and Wulkow, M. (1992) Quantum Theory with Discrete Spectra and Countable Systems of Differential Equations - A Numerical Treatment of Raman Spectroscopy. preprint .

1991

Kornhuber, R. and Roitzsch, R. (1991) Self adaptive computation of the breakdown voltage of planar pn-junctions with multistep field plates. In: Proc. 4th International Conference on Simulation of Semiconductor Devices and Processes. Hartung-Gorre Verlag, Zürich, pp. 535-543. ISBN 3-89191-476-8

1990

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

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

Roitzsch, R. and Kornhuber, R. (1990) BOXES - a program to generate triangulations from a rectangular domain description. ZIB-Report, TR-90- . ISSN 1438-0064

1989

Hoppe, R. H. W. and Kornhuber, R. (1989) Numerical simulation of induction heating processes by multi-grid techniques. In: Numerical methods in Thermal Problems. Pineridge Press, Swansea, pp. 1142-1152.

Kornhuber, R. and Roitzsch, R. (1989) Adaptive Finite-Element-Methoden für konvektionsdominierte Randwertprobleme bei partiellen Differentialgleichungen. ZIB-Report . ISSN 1438-0064

1988

Hoppe, R. H. W. and Kornhuber, R. (1988) Multi-grid solution of the two-phase Stefan problem. In: Multigrid Methods: Theory, Applications and Supercomputing. Lecture Notes in Pure and Applied Mathematics (110). Marcel Dekker Inc., pp. 267-297. ISBN 0824779797, 978-0824779795

Kornhuber, R. (1988) Convergent extensions of grid-functions. Mathematische Nachrichten, 139 (1). pp. 63-75. ISSN 1522-2616

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

1973

Kornhuber, R. (1973) Vereinfachung eines Computermodells. MNU - Der mathematische und naturwissenschaftliche Unterricht, 26 (3). p. 176. ISSN 0025-5866

0001

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.