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Number of items: 1116. 2019Schmidt, B. and Klein, R. and Cancissu Araujo, L. (2019) WavePacket: A Matlab package for numerical quantum dynamics. III: Quantum-classical simulations and surface hopping trajectories. Preprint available . (Submitted) Gupta, P. and Peter, S. and Jung, M. and Lewin, A. and Hemmrich-Stanisak, G. and Franke, A. and von Kleist, M. and Schütte, Ch. and Einspanier, R. and Sharbati, S. and zur Bruegge, J. (2019) Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections. Sci. Rep., 9 (1571). ISSN 2045-2322 von Larcher, T. and Klein, R. (2019) On identification of self-similar characteristics using the Tensor Train decomposition method with application to channel turbulence flow. Theoretical and Computational Fluid Dynamics, 33 . pp. 1-19. ISSN 0935-4964 (Print) 1432-2250 (Online) Li, Shujuan and Schmidt, B. (2019) Two-Dimensional Water in Graphene Nanocapillaries Simulated with Different Force Fields: Rhombic Versus Square Structures, Proton Ordering, and Phase Transitions. Phys. Chem. Chem. Phys. . (Submitted) Shao, Borong and Bjaanæs, Maria and Helland, Åslaug and Schütte, Ch. and Conrad, T. O. F. (2019) EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma. PLoS ONE, 14 (1). ISSN 1932-6203 Fackeldey, K. and Koltai, P. and Névir, P. and Rust, H.W. and Schild, A and Weber, M. (2019) From Metastable to Coherent Sets – time-discretization schemes. Chaos: An Interdisciplinary Journal of Nonlinear Science, 29 (1). 012101. ISSN 1054-1500 (print); 1089-7682 (online) Rudolf, M. and Rosenau, M. and Ziegenhagen, Th. and Ludwikowski, V. and Schucht, Torsten and Nagel, H. and Oncken, O. (2019) Smart Speed Imaging in Digital Image Correlation: Application to Seismotectonic Scale Modeling. Frontiers in Earth Science, 6 . p. 248. Stange, H. and Brunken, S. and Greiner, D. and Heinemann, M. D. and Barragan Yani, D. A. and Wägele, L. A. and Li, Ch. and Simsek Sanli, E. and Kahnt, M. and Schmidt, S. S. and Bäcker, J.-P. and Kaufmann, Ch. A. and Klaus, M. and Scheer, R. and Genzel, Ch. and Mainz, R. (2019) Stacking fault reduction during annealing in Cu-poor CuInSe2 thin film solar cell absorbers analyzed by in situ XRD and grain growth modeling. Journal of Applied Physics, 125 (3). 035303. ISSN 0021-8979 Andreis, L. and König, W. and Patterson, R. I. A (2019) A large-deviations approach to gelation. SFB 1114 Preprint in arXiv:1901.01876 . pp. 1-22. (Unpublished) 2018Noé, F. and Wu, H. (2018) Boltzmann Generators - Sampling Equilibrium States of Many-Body Systems with Deep Learning. SFB 1114 Preprint in arXiv:1812.01729 . pp. 1-17. (Unpublished) Schulz, R. and von Hansen, Y. and Daldrop, J.O. and Kappler, J. and Noé, F. and Netz, R.R. (2018) Collective hydrogen-bond rearrangement dynamics in liquid water. J. Chem. Phys., 149 (24). -244504. ISSN 0021-9606, ESSN: 1089-7690 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 Mirahmadi, M. and Schmidt, B. and Karra, M. and Friedrich, B. (2018) Dynamics of polar polarizable rotors acted upon by unipolar electromagnetic pulses: From the sudden to the adiabatic regime. J. Chem. Phys., 149 (17). p. 174109. Djurdjevac, A. and Elliott, C.M. and Kornhuber, R. and Ranner, Th. (2018) Evolving surface finite element methods for random advection-diffusion equations. SIAM/ASA Journal on Uncertainty Quantification, 6 (4). pp. 1656-1684. ISSN 2166-2525 Wehmeyer, C. and Scherer, M. K. and Hempel, T. and Husic, B.E. and Olsson, S. and Noé, F. (2018) Introduction to Markov state modeling with the PyEMMA software — v1.0. LiveCoMS, 1 (1). pp. 1-12. ISSN E-ISSN: 2575-6524 (Unpublished) Gräser, C. and Sander, O. (2018) Truncated Nonsmooth Newton Multigrid Methods for Block-Separable Minimization Problems. IMA Journal of Numerical Analysis, dry073 . pp. 1-28. ISSN 0272-4979 Scherer, M. K. and Husic, B.E. and Hoffmann, M. and Paul, F. and Wu, H. and Noé, F. (2018) Variational Selection of Features for Molecular Kinetics. SFB 1114 Preprint in arXiv:1811.11714 . pp. 1-12. (Unpublished) Rahn, René and Budach, Stefan and Costanza, Pascal and Ehrhardt, Marcel and Hancox, Jonny and Reinert, Knut (2018) Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading. Bioinformatics, 34 (20). pp. 3437-3445. ISSN 1367-4803 Donati, L. and Heida, M. and Weber, M. and Keller, B. (2018) Estimation of the infinitesimal generator by square-root approximation. Journal of Physics: Condensed Matter, 30 (42). p. 425201. ISSN 0953-8984, ESSN: 1361-648X Swenson, D.W.H. and Prinz, J.-H. and Noé, F. and Chodera, J. D. and Bolhuis, P.G. (2018) OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics. Journal of Chemical Theory and Computation, Article ASAP . ISSN 1549-9618, ESSN: 15-49-9626 Swenson, D.W.H. and Prinz, J.-H. and Noé, F. and Chodera, J. D. and Bolhuis, P.G. (2018) OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes. Journal of Chemical Theory and Computation, Article ASAP . ISSN 1549-9618, ESSN: 15-49-9626 Müller, A. and Névir, P. and Klein, R. (2018) Scale Dependent Analytical Investigation of the Dynamic State Index Concerning the Quasi-Geostrophic Theory. Mathematics of Climate and Weather Forecasting, 4 (1). pp. 1-22. ISSN 2353-6438 (online) Heida, M. and Patterson, R. I. A and Renger, M. (2018) Topologies and measures on the space of functions of bounded variation taking values in a Banach or metric space. J. Evol. Equ. . pp. 1-42. ISSN Online: 1424-3202 Print: 1424-3199 Dadi, Temesgen Hailemariam and Siragusa, Enrico and Piro, Vitor C and Andrusch, Andreas and Seiler, Enrico and Renard, Bernhard Y and Reinert, Knut (2018) DREAM-Yara: an exact read mapper for very large databases with short update time. Bioinformatics, 34 (17). i766-i772. ISSN 1367-4803 Ma, X. and Conrad, T. O. F. and Alchikh, M. and Reiche, J. and Schweiger, B. and Rath, B. (2018) Can we distinguish respiratory viral infections based on clinical features? A prospective pediatric cohort compared to systematic literature review. Reviews in Medical Virology, 28 (5). ISSN 1099-1654 Renger, M. (2018) Flux large deviations of independent and reacting particle systems, with implications for macroscopic fluctuation theory. J. Stat. Phys., 172 (5). pp. 1261-1326. ISSN 0022-4715 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 Donati, L. and Keller, B. (2018) Girsanov reweighting for metadynamics simulations. Journal of Chemical Physics, 149 (7). 072335. ISSN 0021-9606 del Razo, M.J. and Qian, H. and Noé, F. (2018) Grand canonical diffusion-influenced reactions: a stochastic theory with applications to multiscale reaction-diffusion simulations. J. Chem. Phys., 149 (4). ISSN 0021-9606, ESSN: 1089-7690 Gokhale, N. and Nikiforakis, N. and Klein, R. (2018) A dimensionally split Cartesian cut cell method for hyperbolic conservation laws. Journal of Computational Physics, 364 . pp. 186-208. ISSN 0021-9991 (Submitted) 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. (2018) 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 . ISSN 1469-0691 Koltai, P. and Renger, M. (2018) From Large Deviations to Semidistances of Transport and Mixing: Coherence Analysis for Finite Lagrangian Data. Journal of Nonlinear Science, 28 (5). pp. 1915-1957. ISSN 1432-1467 (online) Renger, M. (2018) Gradient and Generic systems in the space of fluxes, applied to reacting particle systems. SFB 1114 Preprint in arXiv:1806.10461 . pp. 1-29. (Unpublished) Friedrich, B. and Herschbach, D. and Kais, S. and Schmidt, B. (2018) Molecules enhanced by electromagnetic fields. SciTech Europa Quarterly, 27 . pp. 48-49. Schatz, K. and Friedrich, B. and Becker, S. and Schmidt, B. (2018) Symmetric Tops Subject to Combined Electric Fields: Conditional Quasi-Solvability via the Quantum Hamilton-Jacobi Theory. Phys. Rev. A, 97 (5). 053417. Banerjee, T. and Vercauteren, N. and Muste, M. and Yang, D. (2018) Coherent structures in wind shear induced wave-turbulence-vegetation interaction in water bodies. Agricultural and Forest Meteorology, 255 . pp. 57-67. ISSN 0168-1923 Grześkowiak, Łukasz and Martínez-Vallespín, Beatriz and Dadi, Temesgen H and Radloff, Judith and Amasheh, Salah and Heinsen, Femke-Anouska and Franke, Andre and Reinert, Knut and Vahjen, Wilfried and Zentek, Jürgen and Pieper, Robert (2018) Formula Feeding Predisposes Neonatal Piglets to Clostridium difficile Gut Infection. The Journal of Infectious Diseases, 217 (9). pp. 1442-1452. ISSN 0022-1899 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. (2018) Clinical characteristics and disease severity associated with adenovirus infections in infants and children - discovery of a novel adenovirus, HAdV-D80. Clinical Infectious Diseases . (Submitted) Koltai, P. and Lie, Han Cheng and Plonka, M. (2018) Fréchet differentiable drift dependence of Perron--Frobenius and Koopman operators for non-deterministic dynamics. SFB 1114 Preprint in arXiv:1805.06719 . pp. 1-24. (Submitted) Kianfar, Kiavash and Pockrandt, Christopher and Torkamandi, Bahman and Luo, Haochen and Reinert, Knut (2018) Optimum Search Schemes for Approximate String Matching Using Bidirectional FM-Index. bioRxiv, The Preprint Server for Biology . Martinek, T. and Duboué-Dijon, E. and Timr, S. and Mason, Ph. E. and Baxová, K. and Fischer, H. E. and Schmidt, B. and Pluharova, E. and Jungwirth, P. (2018) Calcium Ions in Aqueous Solutions: Accurate Force Field Description Aided by Ab Initio Molecular Dynamics and Neutron Scattering. J. Chem. Phys., 148 (22). p. 222813. Wehmeyer, C. and Noé, F. (2018) Time-lagged autoencoders: Deep learning of slow collective variables for molecular kinetics. The Journal of Chemical Physics, 148 (24). p. 241703. ISSN 0021-9606 Hassan, I. and Donati, L. and Stensitzki, T. and Keller, B. and Heyne, K. and Imhof, P. (2018) The Vibrational Spectrum of the hydrated Alanine-Leucine Peptide in the Amide region from IR experiments and First Principles Calculation. Chem. Phys. Lett. . pp. 1-26. ISSN 0009-2614 Klus, S. and Sahai, T. (2018) A spectral assignment approach for the graph isomorphism problem. Information and Inference: a Journal of the IMA . Kebiri, O. and Neureither, L. and Hartmann, C. (2018) Adaptive importance sampling with forward-backward stochastic differential equations. Proceedings of the Institut Henri Poincaré . (Submitted) 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 . ISSN 0959-2962 Kappler, J. and Noé, F. and Netz, R.R. (2018) Cyclization dynamics of finite-length collapsed self-avoiding polymers. SFB 1114 Preprint 02/2018 . (Unpublished) Marzban, Forough and Conrad, T. O. F. and Marzban, Pouria and Sodoudi, Sahar (2018) Estimation of the Near-Surface Air Temperature during the Day and Nighttime from MODIS in Berlin, Germany. International Journal of Advanced Remote Sensing and GIS, 7 (1). ISSN 2320-0243 Weber, M. (2018) Implications of PCCA+ in Molecular Simulation. Computation, 6 (1). ISSN 2079-3197 (online) Patterson, R. I. A and Renger, M. (2018) Large deviations of reaction fluxes. SFB 1114 Preprint in arXiv:1802.02512 . pp. 1-21. (Unpublished) Schulz, R. and Hansen, Y. von and Daldrop, J.O. and Kappler, J. and Noé, F. and Netz, R.R. (2018) Markov state modeling reveals competing collective hydrogen bond rearrangements in liquid water. SFB 1114 Preprint 02/2018 . (Unpublished) Koltai, P. and Wu, H. and Noé, F. and Schütte, Ch. (2018) Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics. Computation, 6(1) (22). ISSN 2079-3197 (online) 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 . (Submitted) von Kleist, M. and Schütte, Ch. and Zhang, W. (2018) Statistical Analysis of the First Passage Path Ensemble of Jump Processes. Journal of Statistical Physics, 170 (4). pp. 809-843. Neureither, L. and Hartmann, C. (2018) Time scales and exponential trends to equilibrium: Gaussian model problems. Proceedings of the Institut Henri Poincaré . (Submitted) Li, Q. and Bou-Zeid, E. and Vercauteren, N. and Parlange, M. B. (2018) Signatures of air-waves interactions over a large lake. Boundary-Layer Meteorology . pp. 1-24. ISSN 0006-8314 Schmidt, B. and Hartmann, C. (2018) WavePacket: A Matlab package for numerical quantum dynamics. II: Open quantum systems, optimal control, and model reduction. Comp. Phys. Comm., 228 . pp. 229-244. Marschall, T. and Reinert, K. and others, (59 authors in total) (2018) Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics, 19 (1). pp. 118-135. ISSN 1467-5463 (Print), 1477-4054 (Online) Stensitzki, T. and Yang, Y. and Kozich, V. and Ahmed, A.A. and Kössl, F. and Kühn, O. and Heyne, K. (2018) Acceleration of a ground-state reaction by selective femtosecond-infrared-laser-pulse excitation. Nature Chemistry, 10 . pp. 126-131. 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. SFB 1114 Preprint 01/2018 . pp. 1-6. (Unpublished) Gräser, C. and Kies, T. (2018) Discretization error estimates for penalty formulations of a linearized Canham-Helfrich-type energy. IMA Journal of Numerical Analysis, drx071 . pp. 1-24. ISSN 0272-4979 Mielke, A. and Rossi, R. and Savaré, G. (2018) Global existence results for viscoplasticity at finite strain. Archive for Rational Mechanics and Analysis, 227 (1). pp. 423-475. ISSN Print: 0003-9527; Online: 1432-0673 Kappler, J. and Daldrop, J.O. and Brünig, F.N. and Boehle, M.D. and Netz, R.R. (2018) Memory-induced acceleration and slowdown of barrier crossing. J. Chem. Phys., 148 (1). 014903. Sadeghi, M. and Weikl, T. and Noé, F. (2018) Particle-based membrane model for mesoscopic simulation of cellular dynamics. J. Chem. Phys., 148 (4). 044901. 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. Sci. Rep., 8 (1796). ISSN 2045-2322 Klus, S. and Nüske, F. and Koltai, P. and Wu, H. and Kevrekidis, I. and Schütte, Ch. and Noé, F. (2018) Data-driven model reduction and transfer operator approximation. Journal of Nonlinear Science, 28 (1). pp. 1-26. Banisch, R. and Trstanova, Z. and Bittracher, A. and Klus, S. and Koltai, P. (2018) Diffusion maps tailored to arbitrary non-degenerate Itô processes. Applied and Computational Harmonic Analysis . ISSN 1063-5203 (In Press) Engwer, C. and Gräser, C. and Müthing, S. and Sander, O. (2018) Function space bases in the dune-functions module. arXiv:1806.09545 . pp. 1-53. (Submitted) Paul, F. and Noé, F. and Weikl, T. (2018) Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations. J. Phys. Chem. B . von Larcher, T. and Viazzo, S. and Harlander, U. and Vincze, M. and Randriamampianina, A. (2018) Instabilities and small-scale waves within the Stewartson layers of a thermally driven rotating annulus. Journal of Fluid Mechanics, 841 . pp. 380-407. ISSN 0022-1120 Wilhem, J. and Akylas, T.R. and Bölöni, G. and Wei, J. and Ribstein, B. and Klein, R. and Achatz, U. (2018) Interactions between Meso- and Sub-Mesoscale Gravity Waves and their Efficient Representation in Mesoscale-Resolving Models. J. Atmos. Sci. . (Unpublished) Benner, P. and Breiten, T. and Hartmann, C. and Schmidt, B. (2018) Model reduction of controlled Fokker-Planck and Liouville-von Neumann equations. J. Comp. Dyn. . (Submitted) Zhang, W. and Hartmann, C. and von Kleist, M. (2018) Optimal control of Markov jump processes: Asymptotic analysis, algorithms, and application to modelling of chemical reaction systems. Communications in Mathematical Sciences . ISSN 1539-6746 (In Press) Vercauteren, N. and Boyko, V. and Faranda, D. and Stiperski, I. (2018) Scale interactions and anisotropy in stable boundary layers. Quarterly Journal of the Royal Meteorological Society . (Submitted) Vercauteren, N. and Boyko, V. and Kaiser, A. and Belusic, D. (2018) Statistical investigations of flow structures in different regimes of the stable boundary layer. Boundary Layer Meteorology . (Submitted) Mardt, A. and Pasquali, L. and Wu, H. and Noé, F. (2018) VAMPnets: Deep learning of molecular kinetics. Nat. Comm., 9 . p. 5. Kornhuber, R. and Peterseim, D. and Yserentant, H. (2018) An analysis of a class of variational multiscale methods based on subspace decomposition. Mathematics of Computation, 87 (314). pp. 2765-2774. ISSN 1088-6842 (online) Youett, J. and Sander, O. and Kornhuber, R. (2018) A globally convergent filter-trust-region method for large deformation contact problems. SIAM J. Sci. Comput. . ISSN 1064-8275 (In Press) 2017Klus, S. and Schuster, I. and Muandet, K. (2017) Eigendecompositions of Transfer Operators in Reproducing Kernel Hilbert Spaces. SFB 1114 Preprint in SciRate arXiv:1712.01572 . pp. 1-33. (Unpublished) Schuster, I. and Constantine, P.G. and Sullivan, T.J. (2017) Exact active subspace Metropolis-Hastings, with applications to the Lorenz-96 system. SFB 1114 Preprint in arXiv:1712.02749 . pp. 1-10. (Unpublished) 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. Netz, R.R. (2017) Fluctuation-dissipation relation and stationary distribution for an exactly solvable many-particle model far from equilibrium. SFB 1114 Preprint 12/2017 . (Unpublished) Heida, M. and Kornhuber, R. and Podlesny, J. (2017) Fractal homogenization of multiscale interface problems. SFB 1114 Preprint in arXiv . pp. 1-17. (Submitted) Ritter, M. and Rosenau, M. and Oncken, O. (2017) Growing Faults in the Lab: Insights into the Scale Dependence of the Fault Zone Evolution Process. Tectonics, 36 . pp. 1-32. Rudolf, M. and Rosenau, M. and Oncken, O. (2017) Interseismic deformation transients and precursory phenomena: Insights from stick-slip experiments with a granular fault zone. SFB 1114 Preprint in EarthArXiv:10.17605/OSF.IO/6MWRX . pp. 1-26. (Unpublished) Peters, J.H. and Gräser, C. and Klein, R. (2017) Membrane Deformation by N-BAR Proteins: Extraction of membrane geometry and protein diffusion characteristics from MD simulations. SFB 1114 Preprint in arXiv:1712.02666 . pp. 1-12. (Unpublished) Liero, M. and Mielke, A. and Savaré, G. (2017) Optimal Entropy-Transport problems and a new Hellinger-Kantorovich distance between positive measures. Invent. math. . pp. 1-149. ISSN 1432-1297 (online) Vater, S. and Klein, R. (2017) A Semi-Implicit Multiscale Scheme for Shallow Water Flows at Low Froude Number. Communications in Applied Mathematics & Computational Science . pp. 1-27. ISSN 1559-3940 (Submitted) Heida, M. and Neukamm, S. and Varga, M. (2017) Stochastic unfolding and homogenization. SFB 1114 Preprint at WIAS 12/2017 . pp. 1-45. (Unpublished) Rosenau, M. and Horenko, I. and Corbi, F. and Rudolf, M. and Kornhuber, R. and Oncken, O. (2017) Synchronization of great subduction megathrust earthquakes: Insights from scale model analysis. SFB 1114 Preprint in EarthArXiv . pp. 1-35. (Unpublished) Fischer, M. and Ulbrich, U. and Rust, H.W. (2017) A spatial and seasonal climatology of extreme precipitation return-levels: A case study. Spatial Statistics . pp. 1-25. (In Press) Pfeuffer, Julianus and Sachsenberg, Timo and Alka, Oliver and Walzer, Mathias and Fillbrunn, Alexander and Nilse, Lars and Schilling, Oliver and Reinert, Knut and Kohlbacher, Oliver (2017) OpenMS – A platform for reproducible analysis of mass spectrometry data. Journal of Biotechnology, 261 . pp. 142-148. ISSN 01681656 Reinert, Knut and Dadi, Temesgen Hailemariam and Ehrhardt, Marcel and Hauswedell, Hannes and Mehringer, Svenja and Rahn, René and Kim, Jongkyu and Pockrandt, Christopher and Winkler, Jörg and Siragusa, Enrico and Urgese, Gianvito and Weese, David (2017) The SeqAn C++ template library for efficient sequence analysis: A resource for programmers. Journal of Biotechnology, 261 . pp. 157-168. ISSN 01681656 Polthier, L. (2017) Algebraic Multilevel Methods for Markov Chains. SFB 1114 Preprint in arXiv:1711.04332 . pp. 1-19. (Unpublished) Taghvaei, A. and de Wiljes, J. and Mehta, P.G. and Reich, S. (2017) Kalman Filter and Its Modern Extensions for the Continuous-Time Nonlinear Filtering Problem. J. Dyn. Sys., Meas., Control, 140 (3). 030904. Kappler, J. and Shrivastava, S. and Schneider, M.F. and Netz, R.R. (2017) Nonlinear fractional waves at elastic interfaces. Phys. Rev. Fluids, 2 (11). p. 114804. Ritter, M. and Santimano, T.N. and Rosenau, M. and Leever, K. and Oncken, O. (2017) Sandbox rheometry: Coevolution of stress and strain in riedel- and critical wedge-experiments. Tectonophysics, 722 . pp. 400-409. Quer, J. and Lie, H. (2017) Some connections between importance sampling and enhanced sampling methods in molecular dynamics. Journal of Chemical Physics . pp. 1-19. ISSN 0021-9606 Hartmann, C. and Richter, L. and Schütte, Ch. and Zhang, W. (2017) Variational characterization of free energy: theory and algorithms. Entropy (Special Issue), 19 (11). pp. 1-27. ISSN 1099-4300 Hittmeir, S. and Klein, R. (2017) Asymptotics for moist deep convection I: Refined scalings and self-sustaining updrafts. Theoretical and Computational Fluid Dynamics . pp. 1-28. ISSN 0935-4964 (Print) 1432-2250 (Online) Banisch, R. and Trstanova, Z. and Bittracher, A. and Klus, S. and Koltai, P. (2017) Diffusion maps tailored to arbitrary non-degenerate Ito processes. SFB 1114 Preprint in arXiv:1710.03484 . pp. 1-24. (Unpublished) Bennett, W.P. and Nikiforakis, N. and Klein, R. (2017) A Moving Boundary Flux Stabilization Method for Cartesian Cut-Cell Grids using Directional Operator Splitting. Journal of Computational Physics, 368 . p. 333. Paul, F. and Wehmeyer, C. and Abualrous, E. T. and Wu, H. and Crabtree, M. D. and Schöneberg, J. and Clarke, J. and Freund, C. and Weikl, T. and Noé, F. (2017) Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nat. Comm., 8 (1095). Kappler, J. and Netz, R.R. (2017) Pulse propagation at interfaces and their possible relevance for biology. Journal Club for Condensed Matter Physics . Bittracher, A. and Koltai, P. and Klus, S. and Banisch, R. and Dellnitz, M. and Schütte, Ch. (2017) Transition manifolds of complex metastable systems: Theory and data-driven computation of effective dynamics. Journal of Nonlinear Science . pp. 1-42. ISSN 1432-1467 (online) Roehr, Johannes T. and Dieterich, Christoph and Reinert, Knut (2017) Flexbar 3.0 – SIMD and multicore parallelization. Bioinformatics, 33 (18). pp. 2941-2942. ISSN 1367-4803 Koltai, P. and Schütte, Ch. (2017) A multi scale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics. ZIB-Report . ISSN 1438-0064 Hittmeir, S. and Klein, R. and Müller, A. and Névir, P. (2017) The Dynamic State Index with Moisture and Phase Changes. SFB 1114 Preprint . pp. 1-12. (Unpublished) Schlutow, M. and Klein, R. and Achatz, U. (2017) Finite-amplitude gravity waves in the atmosphere: travelling wave solutions. Journal of Fluid Mechanics, 826 . pp. 1034-1065. Hittmeir, S. and Klein, R. and Li, J. and Titi, E. (2017) Global well-posedness for passively transported nonlinear moisture dynamics with phase changes. Nonlinearity, 30 (10). pp. 3676-3718. ISSN 0951-7715 Winkelmann, S. and Schütte, Ch. (2017) Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems. Journal of Chemical Physics, 147 (11). pp. 1-18. Schlaich, A. and Kappler, J. and Netz, R.R. (2017) Hydration Friction in Nanoconfinement: From Bulk via Interfacial to Dry Friction. Nano Lett., 17 (10). pp. 5969-5976. Acevedo, W. and de Wiljes, J. and Reich, S. (2017) Second-order accurate ensemble transform particle filters. SIAM J. Sci. Comput., 39 (5). A1834-A1850. ISSN 1095-7197 (online) Manz, C. and Kobitski, A. and Samanta, A. and Keller, B.G. and Jäschke, A. and Nienhaus, G.U. (2017) Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch. Nat. Chem. Biol., 13 . pp. 1172-1178. Reinhardt, M. and Hastermann, G. and Klein, R. and Reich, S. (2017) Balanced data assimilation for highly-oscillatory mechanical systems. Journal of Nonlinear Science . pp. 1-23. (Submitted) Corbi, F. and Funiciello, F. and Brizzi, S. and Lallemand, S. and Rosenau, M. (2017) Control of asperities size and spacing on seismic behavior of subduction megathrusts. Geophysical Research Letters, 44 (16). pp. 8227-8235. Dörffel, T. and Papke, A. and Klein, R. and Smolarkiewicz, P. (2017) Intensification of tilted atmospheric vortices by asymmetric diabatic heating. SFB 1114 Preprint in arXiv:1708.07674 . pp. 1-22. (Unpublished) Mielke, A. and Patterson, R. I. A and Peletier, M. A. and Renger, M. (2017) Non-equilibrium thermodynamical principles for chemical reactions with mass-action kinetics. SIAM Journal on Applied Mathematics, 77 (4). pp. 1562-1585. ISSN 1095-712X (online) Delle Site, L. and Ciccotti, G. and Hartmann, C. (2017) Partitioning a macroscopic system into independent subsystems. Journal of Statistical Mechanics: Theory and Experiment, 2017 . pp. 1-13. Jayrannejad, Fahrnaz and Conrad, T. O. F. (2017) Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining. Springer Lecture Notes in Artificial Intelligence . Nissen, K.M. and Ulbrich, U. (2017) Increasing frequencies and changing characteristics of heavy precipitation events threatening infrastructure in Europe under climate change. Nat. Hazards Earth Syst. Sci., 17 . pp. 1177-1190. Becker, S. and Mirahmadi, M. and Schmidt, B. and Schatz, K. and Friedrich, B. (2017) Conditional Quasi-Exact Solvability of the Quantum Planar Pendulum and its Anti-Isospectral Hyperbolic Counterpart. Eur. J. Phys. D, 71 (6). p. 149. Junghans, C. and Agarwal, A. and Delle Site, L. (2017) Computational Efficiency and Amdahl's law for the Adaptive Resolution Simulation Technique. Computer Physics Communications, 215 . pp. 20-25. ISSN 0010-4655 Donati, L. and Hartmann, C. and Keller, B.G. (2017) Girsanov reweighting for path ensembles and Markov state models. Journal of Chemical Physics, 146 (24). p. 244112. ISSN 0021-9606 Seshaditya, A. and Ghiringhelli, L. M. and Delle Site, L. (2017) Levy-Lieb-based Monte Carlo study of the dimensionality behaviour of the electronic kinetic functional. Computationa, 5 (2). pp. 1-10. ISSN 2079-3197 Pospisil, L. and Gagliardini, P. and Sawyer, W. and Horenko, I. (2017) On a scalable nonparametric denoising of time series signals. Communications in Applied Mathematics and Computational Science . pp. 1-28. (In Press) Mazza, E. and Ulbrich, U. and Klein, R. (2017) The Tropical Transition of the October 1996 Medicane in the Western Mediterranean Sea: A Warm Seclusion Event. Monthly Weather Review, 145 . pp. 2575-2595. ISSN Online: 1520-0493 Print: 0027-0644 Heida, M. (2017) On Convergences of square-root approximation scheme to Fokker--Planck operator. SFB 1114 Preprint at WIAS 05/2017 . pp. 1-30. (Unpublished) Gerber, S. and Horenko, I. (2017) Toward a direct and scalable identification of reduced models for categorical processes. Proceedings of the National Academy of Sciences, 114 (19). pp. 4863-4868. Rohr, U. and Herrmann, P. and Ilm, K. and Zhang, H. and Lohmann, S. and Reiser, A. and Muranyi, A. and Smith, J. C. and Burock, S. and Osterland, M. and Leith, K. and Singh, S. and Brunhoeber, P. and Bowermaster, R. and Tie, J. and Christie, M. and Wong, H. and Waring, P. and Shanmugam, K. and Gibbs, P. and Stein, U. (2017) Prognostic value of MACC1 and proficient mismatch repair status for recurrence risk prediction in stage II colon cancer patients: the BIOGRID studies. Annals of Oncology, 28 (8). pp. 1869-1875. Gelß, P. and Klus, S. and Matera, S. and Schütte, Ch. (2017) Nearest-neighbor interaction systems in the tensor-train format. Journal of Computational Physics, 341 . pp. 140-162. ISSN 0021-9991 Schmidt, B. and Lorenz, U. (2017) WavePacket: A Matlab package for numerical quantum dynamics. I: Closed quantum systems and discrete variable representations. Comp. Phys. Comm., 213 . pp. 223-234. Schulz, R. and Yamamoto, K. and Klossek, A. and Flesch, R. and Hönzke, S. and Rancan, F. and Vogt, A. and Blume-Peytavi, U. and Hedtrich, S. and Schäfer-Korting, M. and Rühl, E. and Netz, R.R. (2017) Data-based modeling of drug penetration relates human skin barrier function to the interplay of diffusivity and free-energy profiles. PNAS, 114 (14). pp. 3631-3636. ISSN 1091-6490 (online) Shao, Borong and Carlo, Cannistraci and Conrad, T. O. F. (2017) Epithelial Mesenchymal Transition Network-based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data. Genomics and Computational Biology, 3 (3). ISSN 2365-7154 Agarwal, A. and Clementi, C. and Delle Site, L. (2017) Path Integral-GC-AdResS simulation of a large hydrophobic solute in water: A tool to investigate the interplay between local microscopic structures and quantum delocalization of atoms in space. Physical Chemistry Chemical Physics, 19 . pp. 13030-13037. ISSN 1463-9084 Ritschel, C. and Rust, H.W. and Ulbrich, U. (2017) Precipitation extremes on multiple time scales -- Bartlett-Lewis Rectangular Pulse Model and Intensity-Duration-Frequency curves. Hydrol. Earth Syst. Sci. . pp. 1-20. (Submitted) Heida, M. (2017) Stochastic homogenization of rate-independent systems and applications. Continuum Mech. Thermodyn., 29 (3). pp. 853-894. ISSN 1432-0959 (online) 0935-1175 (print) Zhukova, Y. and Hiepen, C. and Knaus, P. and Osterland, M. and Prohaska, S. and Dunlop, J. W. C. and Fratzl, P. and Skorb, E. V. (2017) The role of titanium surface nanotopography on preosteoblast morphology, adhesion and migration. Advanced Healthcare Materials . Dadi, Temesgen Hailemariam and Renard, Bernhard Y. and Wieler, Lothar H. and Semmler, Torsten and Reinert, Knut (2017) SLIMM: species level identification of microorganisms from metagenomes. PeerJ, 5 . e3138. ISSN 2167-8359 Conrad, T. O. F. and Genzel, Martin and Cvetkovic, Nada and Wulkow, Niklas and Vybiral, Jan and Kutyniok, Gitta and Schütte, Ch. (2017) Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data. BMC Bioinformatics, 18 (160). ISSN 1471-2105 Seeber, L. and Conrad, T. O. F. and Hoppe, Ch. and Obermeier, P. and Chen, X. and Karsch, K. and Muehlhans, S. and Tief, F. and Boettcher, S. and Diedrich, S. and Schweiger, B. and Rath , B. (2017) Educating parents about the vaccination status of their children: A user-centered mobile application. Preventive Medicine Reports, 5 . pp. 241-250. Pipping, E. (2017) Existence of long-time solutions to dynamic problems of viscoelasticity with rate-and-state friction. SFB 1114 Preprint . (Submitted) Gussmann, P. and Mielke, A. (2017) Linearized elasticity as Mosco-limit of finite elasticity in the presence of cracks. Adv. Calc. Var. . (Submitted) O'Kane, T.J. and Monselesan, D.P. and Risbey, J.S. and Horenko, I. and Franzke, Ch.L.E. (2017) On memory, dimension, and atmospheric teleconnection patterns. Math. Clim. Weather Forecast, 3 (1). pp. 1-27. Weber, M. and Fackeldey, K. and Schütte, Ch. (2017) Set-free Markov state model building. Journal of Chemical Physics, 146 (12). p. 124133. Banisch, Ralf and Koltai, Péter (2017) Understanding the geometry of transport: diffusion maps for Lagrangian trajectory data unravel coherent sets. Chaos: An Interdisciplinary Journal of Nonlinear Science, 23 (23). ISSN 1054-1500 (print); 1089-7682 (online) (Submitted) Quer, J. and Donati, L. and Keller, B.G. and Weber, M. (2017) An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates. SIAM J. Sci. Comput. . pp. 1-19. ISSN 1064-8275 (print) (In Press) Vatansever, B. and Muñoz, A. and Klein, C. L. and Reinert, K. (2017) Development and optimisation of a generic micro LC-ESI-MS method for the qualitative and quantitative determination of 30-mer toxic gliadin peptides in wheat flour for food analysis. Analytical and Bioanalytical Chemistry, 409 (4). pp. 989-997. ISSN 1618-2642 Flegel, F. and Heida, M. and Slowik, M. (2017) Homogenization theory for the random conductance model with degenerate ergodic weights and unbounded-range jumps. SFB 1114 Preprint in arXiv:1702.02860 . (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. Liero, M. and Mielke, A. and Peletier, M. A. and Renger, M. (2017) On microscopic origins of generalized gradient structures. Discrete and Continuous Dynamical Systems - Series S, 10 (1). Huttary, R. and Goubergrits, L. and Schütte, Ch. and Bernhard, S. (2017) Simulation, Identification and Statistical Variation in Cardiovascular Analysis (SISCA) - a Software Framework for Multi-compartment Lumped Modeling. Computers in Biology and Medicine . ISSN 0010-4825 (In Press) Heida, M. and Schweizer, B. (2017) Stochastic homogenization of plasticity equations. ESAIM: Control, Optimisation and Calculus of Variations . pp. 1-30. (Submitted) Achatz, U. and Ribstein, B. and Senf, F. and Klein, R. (2017) The interaction between synoptic‐scale balanced flow and a finite‐amplitude mesoscale wave field throughout all atmospheric layers: weak and moderately strong stratification. QJRMS, 143 (702). pp. 342-361. Hoffmann, M. J. and Engelmann, F. and Matera, S. (2017) A practical approach to the sensitivity analysis for kinetic Monte Carlo simulation of heterogeneous catalysis. The Journal of Chemical Physics, 146 (044118). ISSN 00219606 Dellnitz, M. and Klus, S. and Ziessler, A. (2017) A Set-Oriented Numerical Approach for Dynamical Systems with Parameter Uncertainty. SIAM Journal on Applied Dynamical Systems, 16 (1). pp. 120-138. ISSN 1536-0040 Audain, Enrique and Uszkoreit, Julian and Sachsenberg, Timo and Pfeuffer, Julianus and Liang, Xiao and Hermjakob, Henning and Sanchez, Aniel and Eisenacher, Martin and Reinert, Knut and Tabb, David L. and Kohlbacher, Oliver and Perez-Riverol, Yasset (2017) In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics. Journal of Proteomics, 150 . pp. 170-182. ISSN 18743919 Krekeler, C. and Delle Site, L. (2017) Towards open boundary molecular dynamics simulation of ionic liquids. Physical Chemistry Chemical Physics, 6 (19). pp. 4701-4709. ISSN 1463-9076 Hartmann, C. and Schütte, Ch. and Weber, M. and Zhang, W. (2017) Importance sampling in path space for diffusion processes with slow-fast variables. Probab. Theory Rel. Fields, 170 (1-2). pp. 177-228. ISSN 1432-2064 (online) Heida, M. and Nesenenko, S. (2017) Stochastic homogenization of rate-dependent models of monotone type in plasticity. SFB 1114 Preprint in arXiv:1701.03505 . pp. 1-26. (Unpublished) Heida, M. and Mielke, A. (2017) Averaging of time-periodic dissipation potentials in rate-independent processes. Discrete and Continuous Dynamical Systems - Series S, 10 (6). pp. 1303-1327. Lorenz, P. and Wolf, F. and Braun, J. and Djurdjevac, N. and Hövel, P. (2017) Capturing the Dynamics of Hashtag-Communities. International Workshop on Complex Networks and their Applications . pp. 401-413. Noé, F. and Clementi, C. (2017) Collective variables for the study of long-time kinetics from molecular trajectories: theory and methods. Curr. Opin. Struct. Biol., 43 . pp. 141-147. Olsson, Simon and Wu, H. and Paul, F. and Clementi, C. and Noé, F. (2017) Combining experimental and simulation data of molecular processes via augmented Markov models. Proc. Natl. Acad. Sci. USA, 114 . pp. 8265-8270. Plattner, N. and Doerr, S. and De Fabritiis, G. and Noé, F. (2017) Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling. Nat. Chem., 9 . pp. 1005-1011. Mielke, A. and Mittnenzweig, M. (2017) Convergence to Equilibrium in Energy-Reaction–Diffusion Systems Using Vector-Valued Functional Inequalities. Journal of Nonlinear Science . pp. 1-42. ISSN 1432-1467 (online) Schlutow, M. and Klein, R. and Achatz, U. (2017) Finite-amplitude pseudo-incompressible gravity wave trains. Journal of Fluid Mechanics, 826 . pp. 1034-1065. Gupta, Pooja and Gramatke, A and Einspanier, R and Schütte, Ch. and von Kleist, M. and Sharbati, J (2017) In silico cytotoxicity assessment on cultured rat intestinal cells deduced from cellular impedance measurements. Toxicology in Vitro, 41 . pp. 179-188. ISSN 08872333 Schöneberg, J. and Lehmann, M. and Ullrich, A. and Posor, Y. and Lo, W.-T. and Lichtner, G. and Schmoranzer, J. and Haucke, V. and Noé, F. (2017) Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nat. Comm., 8 . p. 15873. Winkelmann, S. (2017) Markov Control with Rare State Observation: Average Optimality. Markov Processes and Related Fields, 23 . pp. 1-34. ISSN 1024-2953 Nüske, F. and Wu, H. and Wehmeyer, C. and Clementi, C. and Noé, F. (2017) Markov State Models from short non-Equilibrium Simulations - Analysis and Correction of Estimation Bias. J. Chem. Phys., 146 . 094104. Olsson, Simon and Noé, F. (2017) Mechanistic models of chemical exchange induced relaxation in protein NMR. J. Am. Chem. Soc., 139 . pp. 200-210. Berndt, P. and Klein, R. (2017) Modeling the kinetics of the Shockless Explosion Combustion. Combustion and Flame, 175 . pp. 16-26. Meixenberger, K. and Yousef, K. P. and Smith, M. and Somogyi, S. and Fiedler, S. and Bartmeyer, B. and Hamouda, O. and Bannert, N. and von Kleist, M. and Kücherer, C. (2017) Molecular evolution of HIV-1 integrase during the 20 years prior to the first approval of integrase inhibitors. Virology Journal, 14 . pp. 223-237. Delle Site, L. and Praprotnik, M. (2017) Molecular systems with open boundaries: Theory and Simulation. Physics Reports, 693 . pp. 1-56. ISSN 0370-1573 Kies, T. and Gräser, C. (2017) On differentiability of the membrane-mediated mechanical interaction energy of discrete-continuum membrane-particle models. SFB 1114 Preprint in arXiv:1711.11192 . pp. 1-22. (Submitted) Pinamonti, G. and Zhao, J. and Condon, D. and Paul, F. and Noé, F. and Turner, D. and Bussi, G. (2017) Predicting the kinetics of RNA oligonucleotides using Markov state models. J. Chem. Theory Comput., 13 (2). pp. 926-934. Zhang, W. and Schütte, Ch. (2017) Reliable Approximation of Long Relaxation Timescales in Molecular Dynamics. Entropy, 19 (7). p. 367. Benn, A. and Hiepen, C. and Osterland, M. and Schütte, Ch. and Zwijsen, A. and Knaus, P. (2017) Role of bone morphogenetic proteins in sprouting angiogenesis: differential BMP receptor-dependent signaling pathways balance stalk vs. tip cell competence. FASEB Journal, 31 (11). pp. 4720-4733. Schäpel, J.S. and Wolff, S. and Schulze, P. and Berndt, P. and Klein, R. and Mehrmann, V. and King, R. (2017) State estimation for reactive Euler equation by Kalman Filtering. CEAS Aeronautical Journal, 1 (10). Hirt, M. and Schielicke, L. and Müller, A. and Névir, P. (2017) Statistical and dynamical analyses of atmospheric blocking with an idealized point vortex model. Tellus A . pp. 1-22. (Submitted) Wieczorek, M. and Abualrous, E. T. and Sticht, J. and Alvaro-Benito, M. and Stolzenberg, S. and Noé, F. and Freund, C. (2017) Title: Major Histocompatibility Complex (MHC) class I and MHC class II proteins: Conformational Plasticity in Antigen Presentation. Frontiers Immunology, 8 . p. 292. Rüdrich, S. and Sarich, M. and Schütte, Ch. (2017) Utilizing hitting times for ﬁnding metastable sets in non-reversible Markov chains. Journal of Comp. Dynamics . (In Press) Wu, H. and Nüske, F. and Paul, F. and Klus, S. and Koltai, Péter and Noé, F. (2017) Variational Koopman models: slow collective variables and molecular kinetics from short off-equilibrium simulations. J. Chem. Phys., 146 . p. 154104. Wu, H. and Noé, F. (2017) Variational approach for learning Markov processes from time series data. https://arxiv.org/abs/1707.04659 . Sbailò, L. and Noé, F. (2017) An efficient multi-scale Green's Functions Reaction Dynamics scheme. J. Chem. Phys., 147 . p. 184106. Engwer, C. and Gräser, C. and Müthing, S. and Sander, O. (2017) The interface for functions in the dune-functions module. Archive of Numerical Software, 5 (1). pp. 95-110. ISSN 2197-8263 Abramyan, A. and Stolzenberg, S. and Li, Z. and Loland, C. J. and Noé, F. and Shi, L. (2017) The isomeric preference of an atypical dopamine transporter inhibitor contributes to its selection of the transporter conformation. ACS Chem. Neurosc., 8 . pp. 1735-1746. Yang, J. and Wang, Z.-H. and Li, Q. and Vercauteren, N. and Bou-Zeid, E. and Parlange, M. B. (2017) A novel approach for unraveling the energy balance of water surfaces with a single depth temperature measurement. Limnology and Oceanography, 62 (1). pp. 89-103. ISSN 00243590 Nevo, G. and Vercauteren, N. and Kaiser, A. and Dubrulle, B. and Faranda, D. (2017) A statistical-mechanical approach to study the hydrodynamic stability of stably stratified atmospheric boundary layer. Physical Review Fluids, 2 (8). 084603. 2016Jäger, Marten and Schubach, Max and Zemojtel, Tomasz and Reinert, Knut and Church, Deanna M. and Robinson, Peter N. (2016) Alternate-locus aware variant calling in whole genome sequencing. Genome Medicine, 8 (1). ISSN 1756-994X You, Xintian Arthur and Conrad, T. O. F. (2016) Acfs: accurate circRNA identification and quantification from NGS data. Nature Scientific Reports, 6 . ISSN 2045-2322 Yousef, K. P. and Meixenberger, K. and Smith, M. and Jansen, K. and Bartmeyer, B. and Hamouda, O. and Kücherer, C. and von Kleist, M. (2016) Inferring HIV-1 transmission dynamics in Germany from recently transmitted viruses. Journal of Acquired Immunodeficiency Virus, 73 (3). pp. 356-363. ISSN 1525-4135 Fischer, M. and Rust, H.W. and Ulbrich, U. (2016) Seasonal Cycle in German Daily Precipitation Extremes. Meteorologische Zeitschrift . pp. 1-11. ISSN 0941-2948 (Submitted) Winkelmann, S. and Schütte, Ch. (2016) The spatiotemporal master equation: approximation of reaction-diffusion dynamics via Markov state modeling. Journal of Chemical Physics, 145 (21). p. 214107. Zühlke, Martin and Riebe, Daniel and Beitz, Toralf and Löhmannsröben, Hans-Gerd and Andreotti, Sandro and Reinert, Knut and Zenichowski, Karl and Diener, Marc (2016) High-performance liquid chromatography with electrospray ionization ion mobility spectrometry: Characterization, data management, and applications. Journal of Separation Science, 39 (24). pp. 4756-4764. ISSN 16159306 Smith, M. and Smyth, R.P. and Marquet, R. and von Kleist, M. (2016) MIMEAnTo – Profiling functional RNA in Mutational Interference Mapping Experiments. Bioinformatics, 32 (21). pp. 3369-3370. ISSN 1367-4803 Quer, J. and Weber, M. (2016) Estimating exit rate for rare event dynamical systems by extrapolation. ZIB-Report . pp. 1-19. ISSN 2192-7782 (online) Nielsen, A. (2016) The Monte Carlo computation error of transition probabilities. Statistics & Probability Letters, 118 . pp. 163-170. ISSN 0167-7152 Koltai, P. and Ciccotti, G. and Schütte, Ch. (2016) On metastability and Markov state models for non-stationary molecular dynamics. Journal of Chemical Physics, 145 (17). p. 174103. Mielke, A. and Roubícek, T. (2016) Rate-Independent elastoplasticity at finite strain and its numerical approximation. Mathematical Models and Methods in Applied Sciences, 26 (12). pp. 2203-2236. ISSN 1793-6314 Klus, S. and Schütte, Ch. (2016) Towards tensor-based methods for the numerical approximation of the Perron-Frobenius and Koopman operator. Journal of Computational Dynamics . ISSN 2158-2491 Duwal, S. and von Kleist, M. (2016) Top-down and bottom-up modelling in system pharmacology to understand clinical efficacy : An example with NRTIs of HIV-1. European Journal of Pharmaceutical Sciences, 94 . pp. 72-83. ISSN 0928-0987 Zhu, J. and Klein, R. and Delle Site, L. (2016) Adaptive Molecular Resolution Approach in Hamiltonian Form: An Asymptotic Analysis. Physical Review E, 94 (043321). Djurdjevac, N. and Weber, M. and Schütte, Ch. (2016) Finding dominant structures of nonreversible Markov processes. Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 14 (4). pp. 1319-1340. ISSN 1540-3459 Albrecht, D. and Winterflood, C. M. and Sadeghi, M. and Tschager, T. and Noé, F. and Ewers, H. (2016) Nanoscopic compartmentalization of membrane protein motion at the axon initial segment. J. Cell Biol., 215 (1). pp. 37-46. Banisch, Ralf and Hartmann, C. (2016) A sparse Markov chain approximation of LQ-type stochastic control problems. Math. Control Relat. F., 6 (3). pp. 363-389. ISSN 1064-8275 Röst, Hannes L and Sachsenberg, Timo and Aiche, Stephan and Bielow, Chris and Weisser, Hendrik and Aicheler, Fabian and Andreotti, Sandro and Ehrlich, Hans-Christian and Gutenbrunner, Petra and Kenar, Erhan and Liang, Xiao and Nahnsen, Sven and Nilse, Lars and Pfeuffer, Julianus and Rosenberger, George and Rurik, Marc and Schmitt, Uwe and Veit, Johannes and Walzer, Mathias and Wojnar, David and Wolski, Witold E and Schilling, Oliver and Choudhary, Jyoti S and Malmström, Lars and Aebersold, Ruedi and Reinert, Knut and Kohlbacher, Oliver (2016) OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature Methods, 13 (9). pp. 741-748. ISSN 1548-7091 Dellnitz, M. and Klus, S. (2016) Sensing and control in symmetric networks. Dynamical Systems. An International Journal . pp. 1-19. (Submitted) Lorenzi, J. M. and Matera, S. and Reuter, K. (2016) Synergistic Inhibition of Oxide Formation in Oxidation Catalysis: A First-Principles Kinetic Monte Carlo Study of NO + CO Oxidation at Pd(100). ACS Catalysis, 6 (8). pp. 5191-5197. ISSN 2155-5435 Hartmann, C. and Schütte, Ch. and Zhang, W. (2016) Model reduction algorithms for optimal control and importance sampling of diffusions. Nonlinearity, 29 (8). pp. 2298-2326. ISSN 0951-7715 Liero, M. and Mielke, A. and Savaré, G. (2016) Optimal Transport in Competition with Reaction: The Hellinger--Kantorovich Distance and Geodesic Curves. SIAM J. Math. Anal., 48 (2). pp. 2869-2911. ISSN 1095-7154 (online) Rudolf, M. and Boutelier, D. and Rosenau, M. and Schreurs, G. and Oncken, O. (2016) Rheological benchmark of silicone oils used for analog modeling of short- and long-term lithospheric deformation. Tectonophysics, 684 . pp. 12-22. Bonetti, E. and Rocca, E. and Rossi, R. and Thomas, M. (2016) A rate-independent gradient system in damage coupled with plasticity via structured strains. ESAIM: Proceedings and Surveys, 54 . pp. 54-69. Duwal, S. and Sunkara, V. and von Kleist, M. (2016) Multiscale Systems-Pharmacology Pipeline to Assess the Prophylactic Efficacy of NRTIs Against HIV-1. CPT: Pharmacometrics & Systems Pharmacology, 5 (7). pp. 377-387. ISSN 2163-8306 Zhang, W. and Hartmann, C. and Schütte, Ch. (2016) Effective dynamics along given reaction coordinates, and reaction rate theory. Faraday discussions, 195 . pp. 365-394. ISSN 1359-6640 Bienefeld, Kaspar and Zautke, F. and Gupta, Pooja (2016) A novel method for undisturbed long-term observation of honey bee (Apis mellifera) behavior – illustrated by hygienic behavior towards varroa infestation. Journal of Apicultural Research, 54 (5). 541-547 . ISSN 0021-8839 (print) 2078-6913 (online) Gelß, P. and Matera, S. and Schütte, Ch. (2016) Solving the master equation without kinetic Monte Carlo: tensor train approximations for a CO oxidation model. Journal of Computational Physics, 314 . pp. 489-502. ISSN 0021-9991 Hoppe, C. and Obermeier, P. and Muehlhans, S. and Alchikh, M. and Seeber, L. and Tief, F. and Karsch, K. and Chen, X. and Boettcher, S. and Diedrich, S. and Conrad, T. O. F. and Kisler, B. and Rath , B. (2016) Article: Innovative Digital Tools and Surveillance Systems for the Timely Detection of Adverse Events at the Point of Care: A Proof-of-Concept Study. Drug Safety, 39 (10). pp. 977-988. ISSN 1179-1942 Wu, H. and Paul, F. and Wehmeyer, C. and Noé, F. (2016) Multiensemble Markov models of molecular thermodynamics and kinetics. Proceedings of the National Academy of Sciences, 113 (23). E3221-E3230 . ISSN 0027-8424 Klus, S. and Koltai, P. and Schütte, Ch. (2016) On the numerical approximation of the Perron-Frobenius and Koopman operator. Journal of Computational Dynamics, 3 (1). pp. 51-79. ISSN 2158-2491 Lei, Shulai and Paulus, B. and Li, Shujuan and Schmidt, B. (2016) Curvature-dependent adsorption of water inside and outside armchair carbon nanotubes. J. Comp. Chem., 37 (14). pp. 1313-1320. Spötter, Andreas and Gupta, Pooja and Mayer, Manfred and Reinsch , Norbert and Bienefeld, Kaspar (2016) Genome-Wide Association Study of a Varroa-Specific Defense Behavior in Honeybees (Apis mellifera). Journal of Heredity, 107 (3). pp. 220-227. ISSN 0022-1503 (Print) 1465-7333 (online) Chustagulprom, N. and Reich, S. and Reinhardt, M. (2016) A Hybrid Ensemble Transform Particle Filter for Nonlinear and Spatially Extended Dynamical Systems. SIAM/ASA Journal on Uncertainty Quantification, 4 (1). pp. 592-608. ISSN 2166-2525 Mielke, A. and Peletier, M. A. and Renger, M. (2016) A generalization of Onsager's reciprocity relations to gradient flows with nonlinear mobility. Journal of Non-Equilibrium Thermodynamics, 41 (2). de la Garza, Luis and Veit, Johannes and Szolek, Andras and Röttig, Marc and Aiche, Stephan and Gesing, Sandra and Reinert, Knut and Kohlbacher, Oliver (2016) From the desktop to the grid: scalable bioinformatics via workflow conversion. BMC Bioinformatics, 17 (1). ISSN 1471-2105 Shao, Borong and Conrad, T. O. F. (2016) Epithelial Mesenchymal Transition Regulatory Network-based Feature Selection in Lung Cancer Prognosis Prediction. Lecture Notes in Computer Science (LNCS): Proceeding of IWBBIO 2016, 9656 . Vega del Valle, I. and Schütte, Ch. and Conrad, T. O. F. (2016) Finding metastable states in real-world time series with recurrence networks. Physica A, 445 . Klein, R. and Benacchio, T. (2016) A doubly blended model for multiscale atmospheric dynamics. Journal of the Atmospheric Sciences, 73 . pp. 1179-1186. ISSN Online: 1520-0469 Print: 0022-4928 Tief, F. and Hoppe, Ch. and Seeber, L. and Obermeier, P. and Chen, X. and Karsch, K. and Muehlhans, S. and Adamou, E. and Conrad, T. O. F. and Schweiger, B. and Adam, T. and Rath , B. (2016) An inception cohort study assessing the role of bacterial co-infections in children with influenza and ILI and a clinical decision model for stringent antibiotic use. Antiviral Therapy, 21 (5). pp. 413-424. ISSN 1359-6535 (print); 2040-2058 (online) Canzar, S. and Andreotti, S. and Weese, D. and Reinert, K. and Klau, G. W. (2016) CIDANE: comprehensive isoform discovery and abundance estimation. Genome Biology, 17 (1). ISSN 1474-760X Mielke, A. and Rossi, R. and Savaré, G. (2016) Balanced-Viscosity solutions for multi-rate systems. Journal of Physics: Conference Series, 727 . pp. 1-27. Schreurs, G. and et al, . (2016) Benchmarking analogue models of brittle thrust wedges. J. Struct. Geol. . (In Press) Noé, F. and Banisch, Ralf and Clementi, C. (2016) Commute maps: separating slowly-mixing molecular configurations for kinetic modeling. J. Chem. Theory Comput., 12 . pp. 5620-5630. Stolzenberg, S. and Michino, M. and LeVine, M. and Weinstein, H. and Shi, L. (2016) Computational approaches to detect allosteric pathways in transmembrane molecular machines. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1858 (7). p. 1652. ISSN 00052736 Hallier, M. and Hartmann, C. (2016) Constructing Markov State Models of Reduced Complexity from Agent-Based Simulation Data. Social Simulation Conference 2016 . (Submitted) Lemke, O. and Keller, B.G. (2016) Density-based cluster algorithms for the identification of core sets. Journal of Chemical Physics, 145 (164104). Blatt, M. and Burchardt, A. and Dedner, A. and Engwer, C. and Fahlke, J. and Flemisch, B. and Gersbacher, C. and Gräser, C. and Gruber, F. and Grüninger, C. and Kempf, D. and Klöfkorn, R. and Malkmus, T. and Müthing, S. and Nolte, M. and Piatkowski, M. and Sander, O. (2016) The Distributed and Unified Numerics Environment, Version 2.4. Archive of Numerical Software, 4 (100). pp. 13-29. ISSN 2197-8263 Trendelkamp-Schroer, B. and Noé, F. (2016) Efficient estimation of rare-event kinetics. Phys. Rev. X, 6 . 011009. Obermeier, P. and Muehlhans, S. and Hoppe, Ch. and Karsch, K. and Tief, F. and Seeber, L. and Chen, X. and Conrad, T. O. F. and Boettcher, S. and Diedrich, S. and Rath , B. (2016) Enabling Precision Medicine With Digital Case Classification at the Point-of-Care. EBioMedicine, 4 . pp. 191-196. Rosenau, M. and Leever, K. and Oncken, O. (2016) Experimental tectonics: Convergent plate margins. Earth Sys. Env. Sci. SFB 1114 Preprint . (Submitted) Djurdjevac, N. and Weber, M. and Schütte, Ch. (2016) Finding dominant structures of nonreversible Markov processes. Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 14 (4). pp. 1319-1340. ISSN 1540-3459 Delle Site, L. (2016) Formulation of Liouville's theorem for grand ensemble molecular simulations. Physical Review E, 93 (022130). Ring, S. and Oberhofer, H. and Hille, C. and Matera, S. and Reuter, K. (2016) Function-Space-Based Solution Scheme for the Size-Modified Poisson–Boltzmann Equation in Full-Potential DFT. Journal of Chemical Theory and Computation, 12 (8). pp. 4052-4066. ISSN 1549-9618 Delle Site, L. and Agarwal, A. (2016) Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and Application. Computer Physics Communications (206). pp. 26-34. Doerr, S. and Harvey, M. J. and Noé, F. and De Fabritiis, G. (2016) HTMD: High-Throughput Molecular Dynamics for Molecular Discovery. J. Chem. Theory Comput., 12 . pp. 1845-1852. Pérez-Hernández, G. and Noé, F. (2016) Hierarchical Time-Lagged Independent Component Analysis: Computing Slow Modes and Reaction Coordinates for Large Molecular Systems. J. Chem. Theory Comput., 12 . pp. 6118-6129. Paul, F. and Weikl, T. (2016) How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates. PLOS Computational Biology . Vercauteren, N. and Mahrt, L. and Klein, R. (2016) Investigation of interactions between scales of motion in the stable boundary layer. Quarterly Journal of the Royal Meteorological Society . Wieczorek, M. and Sticht, J. and Stolzenberg, S. and Günther, S. and Wehmeyer, C. and El Habre, Z. and Àlvaro-Benito, M. and Noé, F. and Freund, C. (2016) MHC class II complexes sample intermediate states along the peptide exchange pathway. Nature Communications, 7 . p. 13224. Hallier, M. and Hartmann, C. (2016) A Markov state modelling approach to characterizing the punctuated equilibrium dynamics of stochastic evolutionary games. Games 2016, 5th World Conference of the Game Theory Society, . (Submitted) Vitalini, F. and Noé, F. and Keller, B. (2016) Molecular dynamics simulations data of the twenty encoded amino acids in different force fields. Data in Brief, 7 . pp. 582-590. Kornhuber, R. and Yserentant, H. (2016) Numerical Homogenization of Elliptic Multiscale Problems by Subspace Decomposition. Multiscale Model. Simul., 14 (3). pp. 1017-1036. ISSN print: 1540-3459; online: 1540-3467 Gräser, C. and Kahnt, M. and Kornhuber, R. (2016) Numerical approximation of multi-phase Penrose-Fife systems. Computational Methods in Applied Mathematics, 16 (4). pp. 523-542. ISSN Online: 1609-9389, Print: 1609-4840 Yapp, E.K.Y. and Patterson, R. I. A and Akroyd, J. and Mosbach, S. and Adkins, E.M. and Miller, J.H. and Kraft, M. (2016) Numerical simulation and parametric sensitivity study of optical band gap in a laminar co-flow ethylene diffusion flame. Combustion and Flame, 167 . pp. 320-334. Feireisl, E. and Klein, R. and Novotný, A. and Zatorska, E. (2016) On singular limits arising in the scale analysis of stratified fluid flows. Mathematical Models and Methods in Applied Sciences, World Scientific, 26 (3). pp. 419-443. ISSN Print: 0218-2025 Online: 1793-6314 Pipping, E. and Kornhuber, R. and Rosenau, M. and Oncken, O. (2016) On the efficient and reliable numerical solution of rate-and-state friction problems. Geophysical Journal International, 204 (3). pp. 1858-1866. ISSN Online: 1365-246X Print: 0956-540X Klinkmüller, M. and Schreurs, G. and Rosenau, M. and Kemnitz, H. (2016) Properties of granular analogue materials: A community wide survey. Tectonophysics, 666 . pp. 23-38. Patterson, R. I. A (2016) Properties of the solutions of delocalised coagulation and inception problems with outflow boundaries. Journal of Evolution Equations, 16 . pp. 261-291. Trendelkamp-Schroer, B. and Wu, H. and Noé, F. (2016) Reversible Markov chain estimation using convex-concave programming. arXiv . 1603.01640. Ritter, M. and Leever, K. and Rosenau, M. and Oncken, O. (2016) Scaling the Sand Box - Mechanical (Dis-) Similarities of Granular Materials and Brittle Rock. Journal of Geophysical Research: Solid Earth . (In Press) Dewar, W. and Schoonover, J. and McDougall, T. and Klein, R. (2016) Semicrompressible Ocean Thermodynamics and Boussinesq Energy Conservation. Fluids, 1 (9). Reichel , T. and Schäpel, J.S. and Bobusch, B. and Klein, R. and King, R. and Paschereit, C. O. (2016) Shockless Explosion Combustion: Experimental Investigation of a New Approximate Constant Volume Combustion Process. Journal of Engineering for Gas Turbines and Power, 139 (2). 021504 -021511. ISSN 0742-4795 Peters, J.H. and Klein, R. and Delle Site, L. (2016) Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique. Phys. Rev. E, 94 (2). 023309. Wu, H. and Noé, F. (2016) Spectral learning of dynamic systems from nonequilibrium data. NIPS, 29 . pp. 4179-4187. Wolff, S. and Schäpel, J.S. and Berndt, P. and King, R. (2016) State Estimation for the Homogeneous 1-D Euler Equation by Unscented Kalman Filtering. ASME Proceedings . ISSN ISBN: 978-0-7918-5725-0 Klus, S. and Gelß, P. and Peitz, S. and Schütte, Ch. (2016) Tensor-based dynamic mode decomposition. SIAM Journal on Scientific Computing . ISSN ISSN 1064-8275 (print); 1095-7197 (electronic) (Submitted) Elliott, C.M. and Gräser, C. and Hobbs, G. and Kornhuber, R. and Wolf, M.W. (2016) A Variational Approach to Particles in Lipid Membranes. Archive for Rational Mechanics and Analysis, 222 (2). pp. 1011-1075. ISSN Print: 0003-9527; Online:1432-0673 Nüske, F. and Schneider, R. and Vitalini, F. and Noé, F. (2016) Variational Tensor Approach for Approximating the Rare-Event Kinetics of Macromolecular Systems. J. Chem. Phys., 144 (5). 054105. Lorenzi, Juan M. and Matera, S. and Reuter, K. (2016) A first-principles kinetic Monte Carlo study of NO+ CO oxidation at Pd(100). ACS Catalysis, 6 (8). pp. 5191-5197. ISSN 2155-5435 2015Enciso, M. and Schütte, Ch. and Delle Site, L. (2015) Influence of pH and sequence in peptide aggregation via molecular simulation. Journal of Chemical Physics, 143 (24). p. 243130. ISSN 0021-9606 Schultz, L. and Zurich, M.-G. and Culot, M. and da Costa, A. and Landry, C. and Bellwon, P. and Kristl, T. and Hörmann, K. and Ruzek, S. and Aiche, S. and Reinert, K. and Bielow, C. and Gosselet, F. and Cecchelli, R. and Huber, C. G. and Schroeder, O. H.-U. and Gramowski-Voss, A. and Weiss, D. G. and Bal-Price, A. (2015) Evaluation of drug-induced neurotoxicity based on metabolomics, proteomics and electrical activity measurements in complementary CNS in vitro models. Toxicology in Vitro, 30 (1). pp. 138-165. ISSN 08872333 Wilmes, Anja and Bielow, Chris and Ranninger, Christina and Bellwon, Patricia and Aschauer, Lydia and Limonciel, Alice and Chassaigne, Hubert and Kristl, Theresa and Aiche, Stephan and Huber, Christian G. and Guillou, Claude and Hewitt, Philipp and Leonard, Martin O. and Dekant, Wolfgang and Bois, Frederic and Jennings, Paul (2015) Mechanism of cisplatin proximal tubule toxicity revealed by integrating transcriptomics, proteomics, metabolomics and biokinetics. Toxicology in Vitro, 30 (1, Part A). pp. 117-127. ISSN 08872333 Grohs, P. and Hardering, H. and Sander, O. (2015) Optimal a priori discretization error bounds for geodesic finite elements. Foundations of Computational Mathematics, 15 (6). pp. 1357-1411. ISSN 1615-3375 Trendelkamp-Schroer, B. and Wu, H. and Paul, F. and Noé, F. (2015) Estimation and uncertainty of reversible Markov models. J. Chem. Phys., 143 (17). p. 174101. Gul, Rahim and Bernhard, S. (2015) Parametric uncertainty and global sensitivity analysis in a model of the carotid bifurcation: Identification and ranking of most sensitive model parameters. Mathematical Biosciences, 269 . pp. 104-116. ISSN 0025-5564 Babushkina, E. S. and Bessonov, N. M. and Ataullakhanov, F. I. and Panteleev, M. A. (2015) Continuous modeling of arterial platelet thrombus formation using a spatial adsorption equation. PLoS ONE, 10 (10). ISSN 1932-6203 Stötzel, C. and Röblitz, S. and Siebert, H. (2015) Complementing ODE-Based System Analysis Using Boolean Networks Derived from an Euler-Like Transformation. PLoS ONE, 10 (10). e0140954. ISSN 1932-6203 Kryven, I. and Röblitz, S. and Schütte, Ch. (2015) Solution of the chemical master equation by radial basis functions approximation with interface tracking. BMC Systems Biology, 9 (67). ISSN 1752-0509 Delle Site, L. (2015) Shannon entropy and many-electron correlations: Theoretical concepts, numerical results, and Collins conjecture. International Journal of Quantum Chemistry, 115 (19). pp. 1396-1404. ISSN 1097-461X You, Xintian Arthur (2015) Hastings: An R pipeline for large-scale RNA-Seq data analysis. Technical Report . (Unpublished) Karsch, K. and Obermeier, P. and Seeber, L. and Chen, X. and Tief, F. and Muehlhans, S. and Hoppe, Ch. and Conrad, T. O. F. and Boettcher, S. and Diedrich, S. and Rath , B. (2015) Human Parechovirus Infections Associated with Seizures and Rash: A Syndromic Surveillance Study in Children. The Pediatric Infectious Disease Journal, 34 (10). Schuster, I. and Strathmann, H. and Paige, B. and Sejdinovic, Dino (2015) Kernel Sequential Monte Carlo. SFB 1114 Preprint in arXiv:1510.03105 . (Submitted) Kappler, J. and Netz, R.R. (2015) Multiple surface wave solutions on linear viscoelastic media. EPL, 112 (1). p. 19002. Agarwal, A. and Delle Site, L. (2015) Path Integral Molecular Dynamics within the Grand Canonical-like Adaptive Resolution Technique: Simulation of Liquid Water. Journal of Chemical Physics, 143 (9). ISSN 0021-9606 Wang, H. and Agarwal, A. (2015) Adaptive resolution simulation in equilibrium and beyond. The European Physical Journal Special Topics, 224 (12). pp. 2269-2287. ISSN 1951-6355 Bittracher, Andreas and Hartmann, C. and Junge, O. and Koltai, Péter (2015) Pseudo generators for under-resolved molecular dynamics. The European Physical Journal Special Topics, 224 (12). pp. 2463-2490. ISSN 1951-6355 Bittracher, Andreas and Koltai, Péter and Junge, Oliver (2015) Pseudogenerators of spatial transfer operators. SIAM Journal on Applied Dynamical Systems, 14 (3). pp. 1478-1517. ISSN 1536-0040 Banisch, Ralf and Djurdjevac, N. and Schütte, Ch. (2015) Reactive flows and unproductive cycles in irreversible Markov chains. The European Physical Journal Special Topics, 224 (12). pp. 2369-2387. ISSN 1951-6355 Wang, H. and Agarwal, A. (2015) Reply to comment by R. Klein on “Adaptive resolution simulation in equilibrium and beyond”. The European Physical Journal Special Topics, 224 (12). pp. 2501-2502. ISSN 1951-6355 Hartmann, C. and Delle Site, L. (2015) Scale Bridging in Molecular Simulation. The European Physical Journal Special Topics, 224 (12). pp. 2173-2176. ISSN 1951-6355 Schütte, Ch. and Sarich, M. (2015) A critical appraisal of Markov state models. The European Physical Journal Special Topics, 224 (12). pp. 2445-2462. ISSN 1951-6355 Klein, R. (2015) Comments on "Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations" by K. Kreis, A.C. Fogarty, K. Kremer R. Potestio. The European Physical Journal, 224 (12). pp. 2503-2504. ISSN Online: 1951-6401 Print: 1951-6355 Klein, R. (2015) Comments on "Open Boundary Molecular Dynamics " by R. Delgado-Buscalioni, J. Sablic, and M. Praprotnik. The European Physical Journal, 224 (12). pp. 2509-2510. ISSN Online: 1951-6401 Print: 1951-6355 Agarwal, A. and Zhu, J. and Wang, H. and Hartmann, C. and Delle Site, L. (2015) Molecular dynamics in a Grand Ensemble: Bergmann-Lebowitz model and adaptive resolution simulation. New Journal of Physics, 17 (083042). ISSN 1367-2630 Smyth, R.P. and Despons, L. and Huili, G. and Bernacchi, S. and Hijnen, M. and Mak, J. and Jossinet, F. and Weixi, L. and Paillart, J.-C. and von Kleist, M. and Marquet, R. (2015) Mutational Interference Mapping Experiment (MIME) for studying the relationship between RNA structure and function. Nature Methods, 12 . pp. 866-872. ISSN 1548-7091 Djurdjevac, N. and Banisch, Ralf and Schütte, Ch. (2015) Modularity of Directed Networks: Cycle Decomposition Approach. Journal of Computational Dynamics, 2 (1). pp. 1-24. ISSN 2158-2491 Lenga, Matthias and Conrad, T. O. F. (2015) Non-convex regularization for supervised learning. Technical Report . (Unpublished) Mireles, Victor and Conrad, T. O. F. (2015) Minimum-overlap clusterings and the sparsity of overcomplete decompositions of binary matrices. Procedia Computer Science, 51 . pp. 2967-2971. ISSN 1877-0509 Reinert, K. and Langmead, B. and Weese, D. and Evers, D.J. (2015) Alignment of Next-Generation Sequencing Reads. Annual Review of Genomics and Human Genetics, 16 (1). pp. 133-151. ISSN 1527-8204 Duwal, S. and Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2015) Optimal treatment strategies in the context of 'treatment for prevention' against HIV-1 in resource-poor settings. PLOS Computational Biology, 11 . e1004200. Schütte, Ch. and Wang, H. (2015) Building Markov State Models for Periodically Driven Non-Equilibrium Systems. Journal of Chemical Theory and Computation, 11 (4). pp. 1819-1831. ISSN 1549-9618 Moualeu-Ngangue, D. P. and Röblitz, S. and Ehrig, R. and Deuflhard, P. (2015) Parameter Identification in a Tuberculosis Model for Cameroon. PLoS ONE, 10 (4). e0120607. ISSN 1932-6203 Pipping, E. and Sander, O. and Kornhuber, R. (2015) Variational formulation of rate- and state-dependent friction problems. Zeitschrift für angewandte Mathematik und Mechanik (ZAMM), 95 (4). pp. 377-395. ISSN 0044-2267 Aiche, S. and Sachsenberg, T. and Kenar, E. and Walzer, M. and Wiswedel, B. and Kristl, T. and Boyles, M. and Duschl, A. and Huber, C. G. and Berthold, M. R. and Reinert, K. and Kohlbacher, O. (2015) Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry. PROTEOMICS, 15 (8). pp. 1443-1447. ISSN 16159853 Schütte, Ch. and Sarich, M. (2015) A Critical Appraisal of Markov State Models. SFB 1114 Preprint, 15-18 . ISSN 1438-0064 Shao, Borong and Conrad, T. O. F. (2015) Are NoSQL data stores useful for bioinformatics researchers? "International Journal on Recent and Innovation Trends in Computing and Communication (IJRITCC), 3 (3). pp. 1704-1708. ISSN 2321-8169 Schmidt, B. and Friedrich, B. (2015) Supersymmetry and eigensurface topology of the spherical quantum pendulum. Phys. Rev. A, 91 (02). 022111. Li, Shujuan and Schmidt, B. (2015) Molecular Dynamics Simulations of Proton-Ordered Water Confined in Low-Diameter Carbon Nanotubes. Phys. Chem. Chem. Phys., 17 (11). pp. 7303-7316. Berninger, H. and Kornhuber, R. and Sander, O. (2015) A multidomain discretization of the Richards equation in layered soil. Computational Geosciences, 19 (1). pp. 213-232. ISSN 1420-0597 Banisch, Ralf and Djurdjevac, N. (2015) Cycle-flow–based module detection in directed recurrence networks. EPL (Europhysics Letters) , 108 (6). ISSN 0295-5075 Schütte, Ch. and Nielsen, A. and Weber, M. (2015) Markov state models and molecular alchemy. Molecular Physics, 113 (1). pp. 69-78. ISSN 0026-8976 Delle Site, L. (2015) Levy-Lieb principle: The bridge between the electron density of Density Functional Theory and the wavefunction of Quantum Monte Carlo. Chemical Physics Letters, 619 . pp. 148-151. ISSN 0009-2614 Djurdjevac, A. (2015) Advection-diffusion equations with random coefficients on evolving hypersurfaces. Interfaces and Free Boundaries . (Submitted) Wallmeyer, Leonie and Rams, Mona and Börno, Stefan and Timmermann, Bernd and Hedtrich, Sarah and Conrad, T. O. F. (2015) Analyzing the Influence of Filaggrin on Other Skin Associated Genes in a Filaggrin Deficient Skin Model Using the Core Network Approach. Technical Report . (Unpublished) Noé, F. (2015) Beating the Millisecond Barrier in Molecular Dynamics Simulations. Biophys J., 108 . pp. 228-229. Münch, M. (2015) Brandereignisse in Flüchtlingsunterkünften. BRANDSchutz / Deutsche Feuerwehr-Zeitung . Di Giuseppe, E. and Corbi, F. and Funiciello, F. and Massmeyer, A. and Santimano, T.N. and Rosenau, M. and Davaille, A. (2015) Characterization of Carbopol hydrogel rheology for experimental tectonics and geodynamics, , 642, 29-45, doi:10.1016/j.tecto.2014.12.005. Tectonophysics . pp. 29-45. Klein, R. (2015) Comments on "Adaptive Resolution Simulation in Equilibrium and Beyond" by H. Wang and A. Agarwal. The European Physical Journal, 224 (12). pp. 2497-2499. Benacchio, T. and Klein, R. and Dubos, T. and Voitus, F. (2015) Comments on “A Semihydrostatic Theory of Gravity-Dominated Compressible Flow”. Journal of the Atmospheric Sciences , 72 (7). pp. 2850-2851. ISSN Online: 1520-0469 Print: 0022-4928 Boger, M. and Jägle, F. and Munz , C.-D. and Klein, R. (2015) Coupling of compressible and incompressible flow regions using the multiple pressure variables approach. Mathematical Methods in the Applied Sciences, 38 (3). pp. 458-477. Reubold, T. F. and Faelber, K. and Plattner, N. and Posor, Y. and Branz, K. and Curth, U. and Schlegel, J. and Anand, R. and Manstein, D. and Noé, F. and Haucke, V. and Daumke, O. and Eschenburg, S. (2015) Crystal structure of the dynamin tetramer. Nature, 525 . pp. 404-408. Vitalini, F. and Mey, A.S.J.S. and Noé, F. and Keller, B. (2015) Dynamic Properties of Force Fields. J. Chem. Phys., 142 . 084101. Ullrich, A. and Böhme, M. A. and Schöneberg, J. and Depner, H. and Sigrist, S. J. and Noé, F. (2015) Dynamical organization of Syntaxin-1A at the presynaptic active zone. PLoS Comput. Biol., 11 . e1004407. Matera, S. and Blomberg, S. and Hoffmann, M. J. and Zetterberg, J. and Gustafson, J. and Lundgren, E. and Reuter, K. (2015) Evidence for the Active Phase of Heterogeneous Catalysts through In Situ Reaction Product Imaging and Multiscale Modeling. ACS Catalysis, 5 (8). pp. 4514-4518. Erbar, M. and Maas, J. and Renger, M. (2015) From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability, 20 (89). Wu, H. and Noé, F. (2015) Gaussian Markov transition models of molecular kinetics. J. Chem. Phys., 142 (8). 084104. Gunkel, M. and Schöneberg, J. and Alkhaldi, W. and Irsen, S. and Noé, F. and Kaupp, U. B. and Al-Amoudi, A. (2015) Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics. 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(2014) Variational analysis of the coupling between a geometrically exact Cosserat rod and an elastic continuum. Zeitschrift für Angewandte Mathematik und Physik (ZAMP), 65 (6). pp. 1261-1288. ISSN 0044-2275 (Print) 1420-9039 (Online) Oevermann, M. and Klein, R. (2014) An asymptotic solution approach for elliptic equations with discontinuous coefficients. Journal of Computational Physics, 261 . pp. 230-243. Benacchio, T. and O'Neill, W.P. and Klein, R. (2014) A blended soundproof-to-compressible numerical model for small- to mesoscale atmospheric dynamic. Monthly Weather Review, 142 (12). pp. 4416-4438. ISSN Online:1520-0493; Print: 0027-0644 Plattner, N. and Meuwly, M. (2014) The effect of classical and quantum dynamics on vibrational frequency shifts of H2 in clathrate hydrates. The Journal of Chemical Physics, 140 (2). 024311. ISSN 0021-9606 Vincze, M. and Harlander, U. and von Larcher, T. and Egbers, C. 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Phys. Chem. Lett., 4 (23). pp. 4177-4181. Haack, F. and Fackeldey, K. and Röblitz, S. and Scharkoi, O. and Weber, M. and Schmidt, B. (2013) Adaptive spectral clustering with application to tripeptide conformation analysis. J. Chem. Phys., 139 (19). p. 194110. Paulus, F. and Weiss, M. E. R. and Steinhilber, D. and Nikitin, A. and Schütte, Ch. and Haag, R. (2013) Anionic Ring-Opening Polymerization Simulations for Hyperbranched Polyglycerols with Defined Molecular Weights. Macromolecules, 46 (21). pp. 8458-8466. ISSN 0024-9297 Steijger, T. and Abril, J. F. and Engström, P. G. and Kokocinski, F. and The RGASP Consortium, and Richard, H. and Schulz, M. H. and Weese, D. and Hubbard, T. and Guigó, R. and Harrow, J. and Bertone, P. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nature Methods, 10 (12). pp. 1177-1184. Jouvet, G. and Gräser, C. (2013) An adaptive Newton multigrid method for a model of marine ice sheets. Journal of Computational Physics, 252 . pp. 419-437. ISSN 0021-9991 Wang, H. and Hartmann, C. and Schütte, Ch. (2013) Linear response theory and optimal control for a molecular system under nonequilibrium conditions. Molecular Physics, 111 . pp. 3555-3564. ISSN 0026-8976 Hartmann, C. and Yanao, Tomohiro (2013) The falling cat problem and shape effects in small molecules in a random environment: a case study. Molecular Physics, 111 (22-23). pp. 3534-3545. ISSN 0026-8976 Gräser, C. and Kornhuber, R. and Sack, U. (2013) Time discretizations of anisotropic Allen-Cahn equations. IMA Journal of Numerical Analysis, 33 (4). pp. 1226-1244. ISSN 0272-4979 Andreotti, S. and Reinert, K. and Canzar, S. (2013) The duplication-loss small phylogeny problem: from cherries to trees. Journal of Computational Biology, 20 (9). pp. 643-59. Nikitin, A. and Wulkow, M. and Schütte, Ch. (2013) Modeling of Free Radical Styrene/Divinylbenzene Copolymerization with the Numerical Fractionation Technique. Macromolecular Theory and Simulation, 22 (9). pp. 475-489. Enciso , M. and Schütte, Ch. and Delle Site, L. (2013) pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study. Molecular Physics, 111 (22-23). pp. 3363-3371. ISSN 0026-8976 Pattyn, F. and Perichon, L. and Durand, G. and Favier, L. and Gagliardini, O. and Hindmarsh, R. and Zwinger, T. and Albrecht, T. and Cornford, S. and Docquier, D. and Fuerst, J. and Goldberg, G. and Gudmundsson, G. H. and Humbert, A. and Huetten, M. and Huybrechts, P. and Jouvet, G. and Kleiner, T. and Larour, E. and Martin, D. (2013) Grounding-line migration in plan-view marine ice-sheet models: Results of the ice2sea MISMIP3d intercomparison. Journal of Glaciology, 59 (215). pp. 410-422. ISSN 0022-1430 Gul, Rahim and Bernhard, Stefan (2013) Local sensitivity analysis of cardiovascular system parameters. International Journal of Scientific and Engineering Research (IJSER), 4 (7). pp. 2648-2661. ISSN 2229-5518 Sander, O. and Klapproth, C. and Youett, J. and Kornhuber, R. and Deuflhard, P. (2013) Towards an efficient numerical simulation of complex 3D knee joint motion. Computing and Visualization in Science, 16 (3). pp. 119-138. ISSN 1432-9360 Vercauteren, N. and Destouni, G. and Dahlberg, C.J. and Hylander, K. (2013) Fine-resolved, near-coastal spatiotemporal variation of temperature in response to insolation. Journal of Applied Meteorology and Climatology, 52 (5). pp. 1208-1220. ISSN Online: 1558-8432 Print: 1558-8424 Leichtle, A. and Ceglarek, U. and Weinert, P. and Nakas, C. T. and Nuoffer, J.-M. and Kase, J. and Conrad, T. O. F. and Witzigmann, H. and Thiery, J. and Fiedler, G. M. (2013) Pancreatic carcinoma, pancreatitis, and healthy controls - metabolite models in a three-class diagnostic dilemma. Metabolomics, 9 (3). pp. 677-687. ISSN 1573-3890 Rath, B. A. and Yousef, K. P. and Katzenstein, D. K. and Shafer, R. W. and Schütte, Ch. and von Kleist, M. and Merigan, T. C. (2013) In vitro HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitors & In Silico Phenotypic Analysis. PLoS ONE, 8 (4). e61102. ISSN 1932-6203 Blomberg, S. and Hoffmann, M. and Gustafson, J. and Martin, N. M. and Fernandes, V. R. and Borg, A. and Liu, Z. and Chang, R. and Matera, S. and Reuter, K. and Lundgren, E. (2013) In Situ X-Ray Photoelectron Spectroscopy of Model Catalysts: At the Edge of the Gap. Physical Review Letters, 110 (11). p. 117601. Nahnsen, S. and Bielow, C. and Reinert, K. and Kohlbacher, O. (2013) Tools for Label-free Peptide Quantification. Molecular & Cellular Proteomics, 12 (3). pp. 549-556. ISSN 1535-9476 Zerck, A. and Nordhoff, E. and Lehrach, H. and Reinert, K. (2013) Optimal precursor ion selection for LC-MALDI MS/MS. BMC Bioinformatics, 14 (1). p. 56. ISSN 1471-2105 Neu, V. and Bielow, C. and Gostomski, I. and Wintringer, R. and Braun, R. and Reinert, K. and Schneider, P. and Stuppner, H. and Huber, C. (2013) Rapid and Comprehensive Impurity Profiling of Synthetic Thyroxine by Ultrahigh-Performance Liquid Chromatography–High-Resolution Mass Spectrometry. Analytical Chemistry, 85 (6). pp. 3309-3317. ISSN 0003-2700 Pérez-Hernández, G. and Schmidt, B. (2013) Anisotropy of the Water-Carbon Interaction: Molecular Simulations of Water in Low-Diameter Carbon Nano-Tubes. Phys. Chem. Chem. Phys., 15 (14). pp. 4995-5006. Latorre, J.C. and Pavliotis, G. A. and Kramer, P. R. (2013) Corrections to Einstein's relation for Brownian motion in a tilted periodic potential. J. Stat. Phys., 150 (4). pp. 776-803. ISSN 0022-4715 Siragusa, E. and Weese, D. and Reinert, K. (2013) Fast and accurate read mapping with approximate seeds and multiple backtracking. Oxford Journals, 41 (7). e78. ISSN Print ISSN 0305-1048; Online ISSN 1362-4962 Neu, V. and Bielow, C. and Schneider, P. and Reinert, K. and Stuppner, H. and Huber, C. (2013) Investigation of Reaction Mechanisms of Drug Degradation in the Solid State: A Kinetic Study Implementing Ultrahigh-Performance Liquid Chromatography and High-Resolution Mass Spectrometry for Thermally Stressed Thyroxine. Analytical Chemistry, 85 (4). pp. 2385-2390. ISSN 0003-2700 Rath, B. and von Kleist, M. and Castillo, M. E. and Kolevic, L. and Caballero, P. and Soto-Castellares, G. and Amedee, A. M. and Robinson, J.E. and Katzenstein, D. K. and Van Dyke, R.B. and Oberhelman, R. (2013) Antiviral Resistance and Correlates of Virologic Failure in the first Cohort of HIV-Infected Children Gaining Access to Structured Antiretroviral Therapy in Lima, Peru: A Cross-Sectional Analysis. BMC Infectious Diseases, 13 (1). Sarich, M. and Banisch, Ralf and Hartmann, C. and Schütte, Ch. (2013) Markov State Models for Rare Events in Molecular Dynamics. Entropy (Special Issue), 16 (1). pp. 258-286. ISSN 1099-4300 Benacchio, T. and Bonaventura, L. (2013) Absorbing boundary conditions: a spectral collocation approach. International Journal for Numerical Methods in Fluids, 72 (10.1002/fld.3768). pp. 913-936. ISSN Online: 1097-0363 Gupta, Pooja and Reinsch , Norbert and Spötter, Andreas and Conrad, T. O. F. and Bienefeld, Kaspar (2013) Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera). BMC Genetics, 14 (36). Hartmann, C. and Schäfer-Bung, B. and Thöns-Zueva, A. (2013) Balanced averaging of bilinear systems with applications to stochastic control. SIAM J. Control Optim., 51 (3). pp. 2356-2378. Kantcheva, A. K. and Quick, M. and Shi, L. and Winther, A.-M. L. and Stolzenberg, S. and Weinstein, H. and Javitch, J. A. and Nissen, P. (2013) Chloride binding site of neurotransmitter sodium symporters. Proceedings of the National Academy of Sciences, 110 (21). p. 8489. ISSN 0027-8424 Wolf, S and Hinkel, J., and Hallier, M. and Bisaro, A. and Lincke, D. and Ionescu, C. and Klein, R.J.T. (2013) Clarifying vulnerability definitions and assessments using formalisation. International Journal of Climate Change Strategies and Management, 5 (1). ISSN 1756-8692 Kumar, B. and Schumacher, J. and Shaw, R.A. (2013) Cloud microphysical effects of turbulent mixing and entrainment. Theoretical and Computational Fluid Dynamics , 27 (3-4). pp. 361-376. ISSN Print: 0935-4964; Online: 1432-2250 Müller, A. and Behrens, J. and Giraldo, F.X. and Wirth, V. (2013) Comparison between adaptive and uniform discontinuous Galerkin simulations in dry 2D bubble experiments. Journal of Computational Physics, 235 . pp. 371-393. Remmler, S. and Fruman, M. D. and Hickel, S. (2013) Direct numerical simulation of a breaking inertia-gravity wave. Journal of Fluid Mechanics, 722 . pp. 424-436. Lindner, Benjamin and Yi, Zheng and Prinz, J.-H. and Smith, J. C. and Noé, F. (2013) Dynamic Neutron Scattering from Conformational Dynamics I: Theory and Markov models. J. Chem. Phys., 139 . p. 175101. Yi, Zheng and Lindner, Benjamin and Prinz, J.-H. and Noé, F. and Smith, J. C. (2013) Dynamic Neutron Scattering from Conformational Dynamics II: Application using Molecular Dynamics Simulation and Markov modeling. J. Chem. Phys., 139 . p. 175102. Trendelkamp-Schroer, B. and Noé, F. (2013) Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution. J. Phys. Chem., 138 . p. 164113. Delle Site, L. and Ghiringhelli, L. M. and Ceperley, D.M. (2013) Electronic Energy Functionals: Levy-Lieb principle within the Ground State Path Integral Quantum Monte Carlo. International Journal of Quantum Chemistry, 113 . p. 155. Bordás, R. and Roloff, CH. and Thévenin, D. and Shaw, R.A. (2013) Experimental determination of droplet collision rates in turbulence. New Journal of Physics, 15 (045010 ). Bruckner, S. and Kayser, B. and Conrad, T. O. F. (2013) Finding Modules in Networks with Non-modular Regions. Lecture Notes in Computer Science (Proceedings of SEA 2013), 7933 . pp. 188-199. ISSN 0302-9743 Wang, H. and Hartmann, C. and Schütte, Ch. and Delle Site, L. (2013) Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique. Phys. Rev. X, 3 . 011018. Braack, M. and Taschenberger, N. (2013) Hierarchical a posteriori residual based error estimators for bilinear finite elements. Int. J. Numer. Anal. Model., 10 (2). pp. 466-480. (Submitted) Pérez-Hernández, G. and Paul, F. and Giorgino, T. and de Fabritiis, G. and Noé, F. (2013) Identification of slow molecular order parameters for Markov model construction. J. Chem. Phys., 139 . 015102. Peuker, Sebastian and Cukkemane, Abhishek and Held, M. and Noé, F. and Kaupp, Benjamin and Seifert, Reinhard (2013) Kinetics of ligand-receptor interaction reveals an induced-fit mode of binding in a cyclic nucleotide-activated protein. Biophys. J., 104 . pp. 63-74. Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2013) Markov Control Processes with Rare State Observation: Sensitivity Analysis with Respect to Optimal Treatment Strategies against HIV-1. International Journal of Biomathematics and Biostatistics, 2 (1). ISSN 0973-7340 Banisch, Ralf and Hartmann, C. (2013) Meshless discretization of LQ-type stochastic control problems. arXiv preprint, arXiv: . (Unpublished) Kanda, M. and Inagaki, A. and Miyamoto, T. and Gryschka, M. and Raasch, S. (2013) A New Aerodynamic Parameterization for Real Urban Surfaces. Boundary-Layer Meteorology, 148 . pp. 357-377. Gräser, C. (2013) Nonsmooth Schur-Newton methods for nonsmooth saddle point problems. Preprint 1004, Matheon Berlin . Hardering, H. (2013) Numerical approximation of capillary surfaces in a negative gravitational field. Interfaces and Free Boundaries, 15 (3). pp. 263-280. ISSN 1463-9971 Kunnen, R. P. J. and Siewert, C. and Meinke, M. and Schröder, W. and Beheng, K.D. (2013) Numerically determined geometric collision kernels in spatially evolving isotropic turbulence relevant for droplets in clouds. Atmospheric Research, 127 . pp. 8-21. ISSN 0169-8095 Siewert, C. and Kunnen, R. P. J. and Meinke, M. and Schröder, W. (2013) Orientation Statistics and Settling Velocity of Ellipsoids in Decaying Turbulence. Atmospheric Research . (In Press) Plattner, N. and Doll, J. D. and Meuwly, M. (2013) Overcoming the Rare Event Sampling Problem in Biological Systems with Infinite Swapping. Journal of Chemical Theory and Computation, 9 (9). pp. 4215-4224. ISSN 1549-9618 Noé, F. and Wu, H. and Prinz, J.-H. and Plattner, N. (2013) Projected and Hidden Markov Models for calculating kinetics and metastable states of complex molecules. J. Chem. Phys., 139 . p. 184114. Schöneberg, J. and Noé, F. (2013) ReaDDy - a software for particle based reaction diffusion dynamics in crowded cellular environments. PLoS ONE, 8 . e74261. ISSN 1932-6203 Scheck, L. and Jones, S. and Heuveline , V. (2013) Singular Vectors for barotropic, hurricane-like vortices in horizontal shear: Structure and perturbation growth mechanisms. Journal of the Atmospheric Sciences . ISSN Online: 1520-0469 Print: 0022-4928 (Submitted) Posor, Y. and Eichhorn-Gruenig, M. and Puchkov, D. and Schöneberg, J. and Ullrich, A. and Lampe, A. and Müller, R. and Zarbakhsh, S. and Gulluni, F. and Hirsch, E. and Krauss, M. and Schultz, C. and Schmoranzer, J. and Noé, F. and Haucke, V. (2013) Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate. Nature, 499 . pp. 233-237. Lie, Han Cheng and Fackeldey, Konstantin and Weber, Marcus (2013) A Square Root Approximation of Transition Rates for a Markov State Model. SIAM Journal on Matrix Analysis and Applications, 34 (2). p. 738. ISSN 0895-4798 Steger, Katrin and Bollmann, Stefan and Noé, F. and Doose, S. (2013) Systematic evaluation of fluorescence correlation spectroscopy data analysis on the nanosecond time scale. Phys. Chem. Chem. Phys., 15 . pp. 10435-10445. Rath , B. and Tief, F. and Karsch, K. and Muehlhans, S. and Obermeier, P. and Adamou, E. and Chen, X. and Seeber, L. and Peiser, Ch. and Hoppe, Ch. and von Kleist, M. and Conrad, T. O. F. and Schweiger, B. (2013) Towards a personalized approach to managing of influenza infections in infants and children - food for thought and a note on oseltamivir. Infectious Disorders - Drug Targets, 13 (1). pp. 25-33. ISSN 2212-3989 Münch, M. and Kaiser, G. (2013) Verbrennungsdynamik, Rauchgastoxizität und ihre Folgen. Eine kleine Argumentationshilfe für die Brandschutzaufklärung. schadenprisma, 1 . pp. 4-8. Wehmeyer, C. and Schrader, M. and Andrienko, D. and Sebastiani, D. (2013) Water-Free Proton Conduction in Hexakis(p-Phosphonatophenyl)benzene Nanochannels. The Journal of Physical Chemistry C, 117 (23). p. 12366. ISSN 1932-7447 de Wiljes, J. and Majda, A.J. and Horenko, I. (2013) An adaptive Markov Chain Monte Carlo approach to time series clustering of processes with regime transition behavior. SIAM Multiscale Modeling & Simulation, 11 (2). pp. 415-441. ISSN print: 1540-3459; online: 1540-3467 Baldauf, M. and Brdar, S. (2013) An analytic solution for linear gravity waves in a channel as a test for numerical models using the non-hydrostatic, compressible Euler equations. Quarterly Journal of the Royal Meteorological Society . Rieper, F. and Hickel, S. and Achatz, U. (2013) A conservative integration of the pseudo-incompressible equations with implicit turbulence parameterization. Monthly Weather Review , 141 (3). pp. 861-886. ISSN Online: 1520-0493; Print: 0027-0644 von Larcher, T. and Fournier, A. and Hollerbach, R. (2013) The influence of a sloping bottom endwall on the linear stability in the thermally driven baroclinic annulus with a free surface. Theoretical and Computational Fluid Dynamics , 27 (3-4). pp. 433-451. ISSN Print: 0935-4964; Online: 1432-2250 Dolaptchiev, S. and Klein, R. (2013) A multi-scale model for the planetary and synoptic motions in the atmosphere. J. Atmos. Sci., 70 (9). pp. 2963-2981. ISSN Online:1520-0469; Print: 0022-4928 Jouvet, G. and Bueler, E. and Gräser, C. and Kornhuber, R. (2013) A nonsmooth Newton multigrid method for a hybrid, shallow model of marine ice sheets. Recent Advances in Scientific Computing and Applications, 586 . pp. 208-217. ISSN 0271-4132 Enciso , M. and Schütte, Ch. and Delle Site, L. (2013) pH-dependent coarse-grained model of peptides. Soft Matter, 9 (26). pp. 6118-6127. Papke, A. and Battiato, I. (2013) A reduced complexity model for dynamic similarity in obstructed shear flows. Geophysical Research Letters, 40 (15). pp. 3888-3892. Noé, F. and Nüske, F. (2013) A variational approach to modeling slow processes in stochastic dynamical systems. SIAM Multiscale Model. Simul., 11 . pp. 635-655. 2012Doll, J. D. and Plattner, N. and Freeman, D. L. and Liu, Y. and Dupuis, P. (2012) Rare-event sampling: Occupation-based performance measures for parallel tempering and infinite swapping Monte Carlo methods. The Journal of Chemical Physics, 137 (20). p. 204112. ISSN 00219606 Youett, J. and Sander, O. (2012) A dissipative discretization for large deformation frictionless dynamic contact problems. MATHEON Preprint #1184 . Pluharova, E. and Marsalek, O. and Schmidt, B. and Jungwirth, P. (2012) Peptide salt bridge stability: From gas phase via microhydration to bulk water simulations. J. Chem. Phys., 137 (18). p. 185101. Hartmann, C. and Schütte, Ch. (2012) Efficient rare event simulation by optimal nonequilibrium forcing. J. Stat. Mech. Theor. Exp., 2012 . P11004. Matera, S. and Reuter, K. (2012) When atomic-scale resolution is not enough: Spatial effects on in situ model catalyst studies. Journal of Catalysis, 295 . pp. 261-268. Lee, M. W. and Plattner, N. and Meuwly, M. (2012) Structure, spectroscopy and dynamics of layered H2O and CO2 ices. Physical Chemistry Chemical Physics, 14 (44). pp. 15464-15474. ISSN 1463-9076 Sarich, M. and Schütte, Ch. (2012) Approximating Selected Non-dominant Timescales by Markov State Models. Comm. Math. Sci., 10 (3). pp. 1001-1013. Weese, D. and Holtgrewe, M. and Reinert, K. (2012) RazerS 3: Faster, fully sensitive read mapping. Bioinformatics, 28 (20). pp. 2592-2599. Pérez-Hernández, G. and González-Vázquez, J. and González, L. (2012) IR Spectrum of FHF–and FDF–Revisited Using a Spectral Method in Four Dimensions. The Journal of Physical Chemistry A, 116 (46). pp. 11361-11369. ISSN 1089-5639 Wang, H. and Schütte, Ch. and Zhang, P. (2012) Error Estimate of Short-Range Force Calculation in the Inhomogeneous Molecular Systems. Phys. Rev. E, 86 (02). 026704. Schütte, Ch. and Winkelmann, S. and Hartmann, C. (2012) Optimal control of molecular dynamics using Markov state models. Math. Program. (Series B), 134 (1). pp. 259-282. Leichtle, A. and Nuoffer, J.-M. and Ceglarek, U. and Kase, J. and Conrad, T. O. F. and Witzigmann, H. and Thiery, J. and Fiedler, G. M. (2012) Serum amino acid profiles and their alterations in colorectal cancer. Metabolomics . ISSN 1573-3890 Wang, H. and Zhang, P. and Schütte, Ch. (2012) On the Numerical Accuracy of Ewald, Smooth Particle Mesh Ewald, and Staggered Mesh Ewald Methods for Correlated Molecular Systems. J. Chem. Theo. Comp., 8 (9). pp. 3243-3256. Buchholz, M. and Goletz, Ch.-M. and Grossmann, F. and Schmidt, B. and Heyda, J. and Jungwirth, P. (2012) Semiclassical Hybrid Approach to Condensed Phase Molecular Dynamics: Application to the I2Kr17 Cluster. J. Phys. Chem. A, 116 (46). pp. 11199-11210. Aiche, S. and Reinert, K. and Schütte, Ch. and Hildebrand, D. and Schlüter, H. and Conrad, T. O. F. (2012) Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs. PLoS ONE, 7 (7). e40656. ISSN 1932-6203 Junker, J. and Bielow, C. and Bertsch, A. and Sturm, M. and Reinert, K. and Kohlbacher, O. (2012) TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data. J. Proteome Res., 11 (7). pp. 3914-3920. ISSN 1535-3893 Sander, O. (2012) Geodesic finite elements on simplicial grids. International Journal for Numerical Methods in Engeneering, 92 (12). pp. 999-1025. ISSN Online: 1097-0207 Weiss, M. E. R. and Paulus, F. and Steinhilber, D. and Nikitin, A. and Haag, R. and Schütte, Ch. (2012) Estimating Kinetic Parameters for the Spontaneous Polymerization of Glycidol at Elevated Temperatures. MACROMOLECULAR THEORY and SIMULATIONS, 21 (7). pp. 470-481. Djurdjevac, N. and Bruckner, S. and Conrad, T. O. F. and Schütte, Ch. (2012) Random Walks on Complex Modular Networks. Journal of Numerical Analysis, Industrial and Applied Mathematics, 6 (1-2). pp. 29-50. ISSN 1790–8140 Higgins, C. W. and Froidevaux, M. and Simeonov, V. and Vercauteren, N. and Barry, C. and Parlange, M. B. (2012) The Effect of Scale on the Applicability of Taylor's Frozen Turbulence Hypothesis in the Atmospheric Boundary Layer. Boundary-Layer Meteorology, 143 (2). 379 -391. ISSN Print: 0006-8314 Online: 1573-1472 Andreotti, S. and Klau, G. W. and Reinert, K. (2012) Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) , 9 (2). pp. 385-394. Plattner, N. and Meuwly, M. (2012) Quantifying the Importance of Protein Conformation on Ligand Migration in Myoglobin. Biophysical Journal, 102 (2). pp. 333-341. ISSN 00063495 Emde, A.-K. and Schulz, M. H. and Weese, D. and Sun, R. and Vingron, M. and Kalscheuer, V. M. and Haas, S. A. and Reinert, K. (2012) Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics, 28 (5). pp. 619-627. Fritsch, S. and Poblete, S. and Junghans, C. and Ciccotti, G. and Delle Site, L. and Kremer, K. (2012) Adaptive Resolution Molecular Dynamics Simulation Through Coupling to an Internal Particle Reservoir. Physical Review Letters, 108 . p. 170602. Wang, H. and Schütte, Ch. and Delle Site, L. (2012) Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion. J. Chem. Theo. Comp., 8 (8). pp. 2878-2887. Metzner, Ph. and Putzig, L. and Horenko, I. (2012) Analysis of persistent non-stationary time series and applications. Communications in Applied Mathematics and Computational Science, 7 (2). pp. 175-229. Donadio, D. and Ghiringhelli, L. M. and Delle Site, L. (2012) Autocatalytic and cooperatively-stabilized dissociation of water on a stepped platinum surface. Journal of the American Chemical Society, 134 . pp. 19217-19222. Münch, M. (2012) Brände mit Beteiligung von Wärmedämmverbundsystemen. AIZ - Das Immobilienmagazin . pp. 52-55. Held, M. and Noé, F. (2012) Calculating kinetics and pathways of protein–ligand association. Eur. J. Cell Biol., 91 . pp. 357-364. Brdar, S. and Dedner, A. and Klöfkorn, R. (2012) Compact and stable Discontinuous Galerkin methods for convection-diffusion problems. SIAM Journal of Scientific Computation, 34 (1). 263-282 . ISSN Print: 1064-8275 Online: 1095-7197 Brdar, S. and Baldauf, M. and Dedner, A. and Klöfkorn, R. (2012) Comparison of dynamical cores for NWP models. Theoretical and Computational Fluid Dynamics . ISSN 0935-4964 (In Press) Mukherjee, B. and Delle Site, L. and Kremer, K. and Peter, C. (2012) Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions. Journal of Physical Chemistry B, 116 . 8474. Spötter, Andreas and Gupta, Pooja and Nürnberg, G. and Reinsch , Norbert and Bienefeld, Kaspar (2012) Development of a 44K SNP assay focussing on the analysis of a varroa-specific defence behaviour in honey bees (Apis mellifera carnica). Molecular Ecology Resources, 12 . pp. 323-332. Remmler, S. and Hickel, S. (2012) Direct and large-eddy simulation of stratified turbulence. International Journal of Heat and Fluid Flow, 35 . pp. 13-24. ISSN 0142-727X Senne, M. and Trendelkamp-Schroer, B. and Mey, A.S.J.S. and Schütte, Ch. and Noé, F. (2012) EMMA - A software package for Markov model building and analysis. Journal of Chemical Theory and Computation, 8 . pp. 2223-2238. Sander, O. and Schiela, A. (2012) Energy minimizers of the coupling of a Cosserat rod to an elastic continuum. Mathematical Modelling, 7 (1). pp. 1118-1123. Djurdjevac, N. and Sarich, M. and Schütte, Ch. (2012) Estimating the eigenvalue error of Markov State Models. Multiscale Modeling & Simulation, 10 (1). pp. 61-81. Kumar, B. and Janetzko , F. and Schumacher, J. and Shaw, R.A. (2012) Extreme responses of a coupled scalar–particle system during turbulent mixing. New Journal of Physics, 14 115020 . Wehmeyer, C. and Falk von Rudorff, G. and Wolf, S. and Kabbe, G. and Schärf, D. and Kühne, T. D. and Sebastiani, D. (2012) Foraging on the potential energy surface: A swarm intelligence-based optimizer for molecular geometry. The Journal of Chemical Physics, 137 (19). p. 194110. ISSN 00219606 Dommert, F. and Wendler, K. and Berger, R. and Delle Site, L. and Holm, C. (2012) Force fields for studying structure and dynamics of imidazolium based ionic liquids - a critical review of recent developments. ChemPhysChem, 13 . p. 1625. Braack, M. and Lang, J. and Taschenberger, N. (2012) Hierarchical a posteriori residual based error estimators for bilinear finite elements. Comput. Meth. Appl. Mech. Eng. . (Submitted) Menz, S. and Latorre, J.C. and Schütte, Ch. and Huisinga, W. (2012) Hybrid Stochastic–Deterministic Solution of the Chemical Master Equation. SIAM Interdisciplinary Journal Multiscale Modeling and Simulation (MMS), 10 (4). pp. 1232-1262. Wendler, K. and Dommert, F. and Zhao, Y.Y. and Berger, R. and Holm, C. and Delle Site, L. (2012) Ionic Liquids studied across different Scales: A Computational Perspective. Faraday Discussions, 154 . pp. 111-132. Münch, M. and Kaiser, G. (2012) Kinderwagen und andere Brandlasten in Treppenhäusern. Der feine Unterschied zwischen richtig und rechtmäßig. Das Grundeigentum, Recht und Praxis, 17 . pp. 1144-1148. Sadiq, S. K. and Noé, F. and de Fabritiis, G. (2012) Kinetic characterization of the critical step in HIV-1 protease maturation. Proc. Natl. Acad. Sci. USA, 109 . pp. 20449-20454. Mukherji, D. and van der Vegt, N.F.A. and Kremer, K. and Delle Site, L. (2012) Kirkwood-Buff analysis of liquid mixtures in an open boundary simulation. Journal of Chemical Theory and Computation, 8 . pp. 375-379. Letzel, M.O. and Helmke, C. and Ng, E. and An, X. and Lai, A. and Raasch, S. (2012) LES case study on pedestrian level ventilation in two neighbourhoods in Hong Kong. Meteorologische Zeitschrift, 21 (6). pp. 575-589. Schlegel, F. and Stiller, J. and Bienert, A. and Maas, H.-G and Queck, R. and Bernhofer, C. (2012) Large-Eddy Simulation of inhomogeneous canopy flows using high resolution terrestrial laser scanning data. Boundary-Layer Meteorology, 142 . pp. 223-243. ISSN 0006-8314 (Print) 1573-1472 (Online) Keller, B. and Prinz, J.-H. and Noé, F. (2012) Markov models and dynamical fingerprints: unraveling the complexity of molecular kinetics. Chem. Phys., 396 . pp. 92-107. Bordás, R. and John, V. and Schmeyer, E. and Thévenin, D. (2012) Measurement and Simulation of a Droplet Population in a Turbulent Flow Field. Computers and Fluids . (Submitted) Kühnlein, C. and Smolarkiewicz, P. and Dörnbrack, A. (2012) Modelling atmospheric flows with adaptive moving meshes. Journal of Computational Physics, 231 (7). pp. 2741-2763. ISSN 0021-9991 Held, M. and Imhof, P. and Keller, B. and Noé, F. (2012) Modulation of a ligand’s energy landscape and kinetics by the chemical environment. J. Phys. Chem. B, 116 . pp. 13597-13607. Paeschke, E. and Marschalik, P. and Owinoh, A.Z. and Klein, R. (2012) Motion and structure of atmospheric mesoscale baroclinic vortices: dry air and weak environmental shear. Journal of Fluid Mechanics, 701 . pp. 137-170. John, V. and Thein, F. (2012) On the efficiency and robustness of the core routine of the quadrature method of moments (QMOM). Chemical Engineering Science, 75 . pp. 327-333. Dupuis, P. and Yufei, L. and Plattner, N. and Doll, J. D. (2012) On the infinite swapping limit for parallel tempering. Multiscale Modeling & Simulation, 10 (3). pp. 986-1022. Ziemer, C. and Wacker, U. (2012) Parameterisation of the Sedimentation of Raindrops with Finite Maximum Diameter. Monthly Weather Review, 140 (5). 1589 -1602. ISSN Online: 1520-0493 Print : 0027-0644 Ziemer, C. and Wacker, U. (2012) Parameterization of the Sedimentation of Raindrops with Finite Maximum Diameter. Monthly Weather Review , 140 (5). 1589 -1602. ISSN Online: 1520-0493 Print: 0027-0644 Bruckner, S. and Hüffner, F. and Komusiewicz, Ch. and Niedermeier, R. and Thiel, S. and Uhlmann, J. (2012) Partitioning into colorful components by minimum edge deletions. Lecture Notes in Computer Science, 7354 . pp. 56-69. Duwal, S. and Schütte, Ch. and von Kleist, M. (2012) Pharmacokinetics and Pharmacodynamics of the Reverse Transcriptase Inhibitor Tenofovir & Prophylactic Efficacy against HIV-1 Infection. PLoS One, 7 (7). e40382. von Kleist, M. and Metzner, Ph. and Marquet, R. and Schütte, Ch. (2012) Polymerase Inhibition by Nucleoside Analogs: Cellular- and Kinetic Parameters of Efficacy, Susceptibility and Resistance Selection. Plos Computational Biology, 8 (1). e1002359. Potestio, R. and Delle Site, L. (2012) Quantum Locality and Equilibrium Properties in Low-temperature Parahydrogen: A Multiscale Simulation Study. Journal of Chemical Physics, 136 . 054101. Keller, B. and Prinz, J.-H. and Noé, F. (2012) Resolving the apparent gap in complexity between simulated and measured kinetics of biomolecules. From Computational Biophysics to Systems Biology (CBSB11) Proceedings, IAS Series, 8 . pp. 61-64. Assêncio, D.C. and Teran, J.M. (2012) A Second Order Virtual Node Algorithm for Stokes Flow Problems with Interfacial Forces and Discontinuous Material Properties. Journal of Computational Physics . (Submitted) Meerbach, E. and Latorre, J.C. and Schütte, Ch. (2012) Sequential Change Point Detection in Molecular Dynamics Trajectories. Multicale Model. Sim., 10 (4). pp. 1263-1291. Wendler, K. and Brehm, M. and Malberg, F. and Kirchner, B. and Delle Site, L. (2012) Short time dynamics of ionic liquids in AIMD based power spectra. Journal of Chemical Theory and Computation, 8 . p. 1570. Gupta, Pooja and Conrad, T. O. F. and Spötter, Andreas and Reinsch, Norbert and Bienefeld, Kaspar (2012) Simulating a base population in honey bee for molecular genetic studies. Genetics Selection Evolution, 44 . p. 14. Mukhopadhyay, A. and Jasor, G. and Polifke, W. (2012) Simulation of Pure Sedimentation of Raindrops using Quadrature Method of Moments. J. Atmospheric Research, 106 . pp. 61-70. Kupfer, S. and Pérez-Hernández, G. and González, L. (2012) Singlet oxygen generation versus O–O homolysis in phenyl-substituted anthracene endoperoxides investigated by RASPT2, CASPT2, CC2, and TD-DFT methods. Theoretical Chemistry Accounts, 131 (12). ISSN 1432-881X Jouvet, G. and Bueler, E. (2012) Steady, shallow ice sheets as obstacle problems: Well-posedness and finite element approximation. SIAM J. Appl. Math., 72 (4). pp. 1292-1314. ISSN 0036-1399 Stolzenberg, S. and Khelashvili, G. and Weinstein, H. (2012) Structural Intermediates in a Model of the Substrate Translocation Path of the Bacterial Glutamate Transporter Homologue GltPh. The Journal of Physical Chemistry B, 116 (18). p. 5372. ISSN 1520-6106 Faelber, K. and Held, M. and Gao, S. and Posor, Y. and Haucke, V. and Noé, F. and Daumke, O. (2012) Structural insights into dynamin-mediated membrane fission. Structure, 20 . 1621-1628. Klein, R. and Pauluis, O. (2012) Thermodynamic Consistency of a Pseudo-Incompressible Approximation for General Equations of State. Journal of the Atmospheric Sciences, 69 (3 ). pp. 961-968. ISSN Online: 1520-0469; Print : 0022-4928 Rieper, F. and Achatz, U. and Klein, R. (2012) Validation of an extended non-linear WKB theory: 1D and 2D case. Journal of Fluid Mechanics . (Submitted) Leyendecker, S. and Hartmann, C. and Koch, M. (2012) Variational collision integrator for polymer chains. J. Comput. Phys, 231 (10). pp. 3896-3911. Leyendecker, S. and Hartmann, C. and Koch, M. and Johnson, G. and Ortiz, M. (2012) Variational collision integrators in forward dynamics and optimal control. Proceedings of the 7th International Conference Croatian Society of Mechanics (7ICCSM2012) . Rath, B. and von Kleist, M. and Tief, F. and Karsch, K. and Tuerk, E. and Muehlhans, S. and Louis, F. and Skopnik, H. and Schweiger, B. and Duwe, S. (2012) Virus Load Kinetics and Resistance Development during Oseltamivir Treatment in Infants and Children Infected with Influenza A(H1N1)2009 and Influenza B Viruses. Pediatr. Infect. Dis. J., 31 (9). pp. 899-905. Park, S.B. and Baik, J.J. and Raasch, S. and Letzel, M.O. (2012) A large-eddy simulation study of thermal effects on turbulent flow and dispersion in and above a street canyon. J. Appl. Meteor. Climatol., 51 (5). pp. 829-841. ISSN Online: 1558-8432 Print: 1558-8424 Riechelmann, T. and Noh, Y . and Raasch, S. (2012) A new method for large-eddy simulations of clouds with Lagrangian droplets including the effects of turbulent collision. New Journal of Physics, 14 (065008). Vetter, A. and Witt, F. and Sander, O. and Duda, G. and Weinkamer, E. (2012) The spatio-temporal arrangement of different tissues during bone healing as a result of simple mechanobiological rules. Biomechanics and Modeling in Mechanobiology, 11 (1-2). pp. 147-160. ISSN 1617-7959 2011Jouvet, G. and Huss, M. and Funk, M. and Blatter, H. (2011) Modelling the retreat of Grosser Aletschgletscher, Switzerland, in a changing climate. Journal of Glaciology, 57 (206). pp. 1033-1045. ISSN 0022-1430 Berninger, H. and Kornhuber, R. and Sander, O. (2011) Fast and robust numerical solution of the Richards equation in homogeneous soil. SIAM Journal on Numerical Analysis, 49 (6). pp. 2576-2597. ISSN 0036-1429 Plattner, N. and Doll, J. D. and Dupuis, P. and Wang, H. and Liu, Y. and Gubernatis, J. E. (2011) An infinite swapping approach to the rare-event sampling problem. The Journal of Chemical Physics, 135 (13). p. 134111. ISSN 00219606 Kehr, B. and Weese, D. and Reinert, K. (2011) STELLAR: fast and exact local alignments. BMC Bioinformatics, 12 (S9). S15. ISSN 1471-2105 Fischer, M. and Lorenz, U. and Schmidt, B. and Schmidt, R. (2011) Fragmentation due to centrifugal forces in the photodissociation of H2+ in intense laser fields. Phys. Rev. A, 84 (3). 033422. Vercauteren, N. and Huwald, H. and Bou-Zeid, E. and Selker, J. S. and Lemmin, U. and Parlange, M. B. and Lunati, I. (2011) Evolution of Superficial Lake Water Temperature Profile Under Diurnal Radiative Forcing. Water Resources Research, 47 (9). Berninger, H. and Kornhuber, R. and Sander, O. (2011) Heterogeneous domain decomposition of surface and porous media flow. AIP Conference Proceedings, 1389 . pp. 2025-2028. ISSN 0094-243X Schäfer-Bung, B. and Hartmann, C. and Schmidt, B. and Schütte, Ch. (2011) Dimension reduction by balanced truncation: Application to light-induced control of open quantum systems. J. Chem. Phys., 135 (1). 014112. Böcker, S. and Kehr, B. and Rasche, F. (2011) Determination of Glycan Structure from Tandem Mass Spectra. IEEE/ACM Transactions on Computational Biology and Bioinformatics , 8 (4). pp. 976-986. ISSN 1545-4963 Bielow, C. and Aiche, S. and Andreotti, S. and Reinert, K. (2011) MSSimulator: Simulation of Mass Spectrometry Data. Journal of Proteome Research, 10 (7). pp. 2922-2929. Holtgrewe, M. and Emde, A.-K. and Weese, D. and Reinert, K. (2011) A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping. BMC Bioinformatics, 12 (120). ISSN 1471-2105 Schütte, Ch. and Noé, F. and Lu, Jianfeng and Sarich, M. and Vanden-Eijnden, E. (2011) Markov State Models Based on Milestoning. J. Chem. Phys., 134 (20). p. 204105. Prinz, J.-H. and Wu, H. and Sarich, M. and Keller, B. and Senne, M. and Held, M. and Chodera, J. D. and Schütte, Ch. and Noé, F. (2011) Markov models of molecular kinetics: Generation and Validation. J. Chem. Phys., 134 . p. 174105. Ullrich, Alexander and Rohrschneider, Markus and Scheuermann, Gerik and Stadler, Peter F. and Flamm, Christoph (2011) In Silico Evolution of Early Metabolism. Artificial Life, 17 (2). pp. 87-108. ISSN 1064-5462 Zou, Q. and Veeser, A. and Kornhuber, R. and Gräser, C. (2011) Hierarchical error estimates for the energy functional in obstacle problems. Numerische Mathematik, 117 (4). pp. 653-677. ISSN 0029-599X Ruprecht, D. and Klein, R. (2011) A Model for Nonlinear Interactions of Internal Gravity Waves with Saturated Regions. Meteorologische Zeitschrift, 20 (2). pp. 243-252. Hartmann, C. and Latorre, J.C. (2011) Computing free energy differences using conditioned diffusions. AIP Conf. Proc., 1332 (1). pp. 218-220. von Kleist, M. and Menz, S. and Stocker, H. and Arasteh, K. and Huisinga, W. and Schütte, Ch. (2011) HIV Quasispecies Dynamics during Pro-active Treatment Switching: Impact on Multi-Drug Resistance and Resistance Archiving in Latent Reservoirs. Plos One, 6 (3). e18204. Vetter, A. and Liu, Y. and Witt, F. and Manjubala, I. and Sander, O. and Rao Epari, D. and Fratzl, P. and Duda, G. and Weinkamer, R. (2011) The mechanical heterogeneity of the hard callus influences local tissue strains during bone healing. Journal of Biomechanics, 44 (3). pp. 517-523. ISSN 0021-9290 Owschimikow, N. and Schmidt, B. and Schwentner, N. (2011) Laser-induced alignment and anti-alignment of rotationally excited molecules. Phys. Chem. Chem. Phys., 13 (19). pp. 8671-8680. Held, M. and Metzner, Ph. and Prinz, J.-H. and Noé, F. (2011) Mechanisms of Protein-Ligand association and its modulation by protein mutations. Biophys. J., 100 (3). pp. 701-710. Owinoh, A.Z. and Stevens, B. and Klein, R. (2011) Multiscale Asymptotics Analysis for the Mesoscale Dynamics of Cloud-Topped Boundary Layers. Journal of the Atmospheric Sciences, 68 (2). pp. 379-402. ISSN Online 1520-0469, Print 0022-4928 Matera, S. and Meskine, H. and Reuter, K. (2011) Adlayer inhomogeneity without lateral interactions: Rationalizing correlation effects in CO oxidation at RuO2(110) with first-principles kinetic Monte Carlo. The Journal of Chemical Physics, 134 (6). 064713. Walter, J. and Hartmann, C. and Maddocks, J. (2011) Ambient space formulations and statistical mechanics of holonomically constrained Langevin systems. Eur. Phys. J. Special Topics, 200 (1). pp. 153-181. Jouvet, G. and Rappaz, J. (2011) Analysis and finite element approximation of a nonlinear stationary stokes problem arising in glaciology. Advances in Numerical Analysis, 2011 (Articl). ISSN 1687-9562 Keller, B. and Hünenberger, Philippe and van Gunsteren, Wilfred (2011) An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles. J. Chem. Theo. Comput., 7 . pp. 1032-1044. Schiffmann, C and Sebastiani, D (2011) Artificial Bee Colony Optimization of Capping Potentials for Hybrid Quantum Mechanical/Molecular Mechanical Calculations. Journal of Chemical Theory and Computation, 7 (5). p. 1307. ISSN 1549-9618 Hartmann, C. (2011) Balanced model reduction of partially-observed Langevin processes: an averaging principle. Math. Comput. Model. Dyn. Syst., 17 (5). pp. 463-490. Wu, H. and Noé, F. (2011) Bayesian framework for modeling diffusion processes with nonlinear drift based on nonlinear and incomplete observations. Phys. Rev. E, 83 (3). 036705. Faelber, Katja and Posor, York and Held, M. and Roske, Yvette and Schulze, Dennis and Haucke, Volker and Noé, F. and Daumke, Oliver (2011) Crystal structure of nucleotide-free dynamin. Nature, 477 . pp. 556-560. Bordás, R. and Hagemeier, T. and Wunderlich, B. and Thévenin, D. (2011) Droplet Collisions and Interaction with the Turbulent Flow within a Two-Phase Wind Tunnel. Physics of Fluids, 23 (8). ISSN 1070-6631 (print) 1089-7666 (online) Braack, M. and Burman, E. and Taschenberger, N. (2011) Duality based a posteriori error estimation for quasi periodic solutions using time averages. SIAM J. Scientific Computing, 33 (10.1137/100809519). pp. 2199-2216. ISSN print: 1064-8275; online: 1095-7197 Han, D. S. and Golebiewska, U. and Stolzenberg, S. and Scarlata, S. F. and Weinstein, H. (2011) A Dynamic Model of Membrane-Bound Phospholipase C 2 Activation by G Subunits. Molecular Pharmacology, 80 (3). p. 434. ISSN 0026-895X Noé, F. and Doose, S. and Daidone, I. and Löllmann, M. and Chodera, J. D. and Sauer, M. and Smith, J. C. (2011) Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proc. Natl. Acad. Sci. USA, 108 . pp. 4822-4827. Chodera, J. D. and Swope, W. D. and Noé, F. and Prinz, J.-H. and Shirts, M. R. and Pande, V. S. (2011) Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures. J. Chem. Phys., 134 (24). p. 244107. Prinz, J.-H. and Held, M. and Smith, J. C. and Noé, F. (2011) Efficient Computation, Sensitivity and Error Analysis of Committor Probabilities for Complex Dynamical Processes. Multiscale Model. Simul., 9 . pp. 545-567. Kornhuber, R. and Zou, Q. (2011) Efficient and reliable hierarchical error estimates for the discretization error of elliptic obstacle problems. Mathematics of Computation, 80 . pp. 69-88. ISSN 0025-5718 Dedner, A. and Klöfkorn, R. (2011) A Generic Stabilization Approach for Higher Order Discontinuous Galerkin Methods for Convection Dominated Problems. J. Sci. Comput. . (Submitted) Schiffmann, C and Sebastiani, D (2011) Hydrogen bond networks: Structure and dynamics via first-principles spectroscopy. physica status solidi (b), 249 (2). p. 368. ISSN 03701972 Bresch, D. and Klein, R. and Lucas, C. (2011) Multiscale analyses for the Shallow Water equations. Computational Science and High Performance Computing IV, 115/20 . pp. 149-164. ISSN 1612-2909 (Print) 1060-0824 (Online) Hartmann, C. and Latorre, J.C. and Ciccotti, G. (2011) On two possible definitions of the free energy for collective variables. Eur. Phys. J. Special Topics, 200 (1). pp. 73-89. Prinz, J.-H. and Chodera, J. D. and Pande, V. S. and Swope, W. D. and Smith, J. C. and Noé, F. (2011) Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. J. Chem. Phys., 134 (24). p. 244108. Hertwig, D. and Leitl, B. and Schatzmann, M. (2011) Organized turbulent structures –- Link between experimental data and LES. Journal of Wind Engineering and Industrial Aerodynamics, 99 (4). pp. 296-307. ISSN 01676105 Harlander, U. and Wentzel, J. and Alexandrov, K. and Wang, Y. and Egbers, C. (2011) PIV- and LDV-measurements of baroclinic wave interactions in a thermally driven rotating annulus. Experiments in Fluids . (Submitted) Harlander, U. and von Larcher, T. and Wang, Y. and Egbers, C. (2011) PIV- and LDV-measurements of baroclinic wave interactions in a thermally driven rotating annulus. Experiments in Fluids, 51 (1). pp. 37-49. Sander, O. (2011) The PSurface library. Computing and Visualization in Science, 14 (8). pp. 353-370. ISSN 1432-9360 Jebens, .S. and Knoth, O. and Weiner, R. (2011) Partially Implicit PeerMethods for the Compressible Euler Equations. Journal of Computational Physics . (Submitted) Prinz, J.-H. and Keller, B. and Noé, F. (2011) Probing molecular kinetics with Markov models: Metastable states, transition pathways and spectroscopic observables. Phys. Chem. Chem. Phys., 13 . pp. 16912-16927. Frank, M. and von Kleist, M. and Kunz, A. and Harms, G. and Schütte, Ch. and Kloft, Ch. (2011) Quantifying the impact of nevirapine-based prophylaxis strategies to prevent mother-to-child transmission of HIV-1: A combined pharmacokinetic, pharmaco- and viral dynamic analysis to predict clinical outcomes. Antimicrob. Agents Chemother., 55 (12). pp. 5529-5540. Vater, S. and Klein, R. and Knio, O.M. (2011) A Scale-selective Multilevel Method for Long-Wave Linear Acoustics. Acta Geophysica, 59 (6). pp. 1076-1108. Assêncio, D.C. and Teran, J.M. (2011) A Second Order Virtual Node Algorithm for Stokes Flow Problems with Interfacial Forces and Irregular Domains. Journal of Computational Physics . (Submitted) Ullrich, Alexander and Flamm, Christoph (2011) A Sequence-to-Function Map for Ribozyme-catalyzed Metabolisms. Advances in Artificial Life, 5778 . p. 481. ISSN 978-3-642-21313-7 Ihrig, A C and Schiffmann, C and Sebastiani, D (2011) Specific quantum mechanical/molecular mechanical capping-potentials for biomolecular functional groups. The Journal of Chemical Physics, 135 (21). p. 214107. ISSN 00219606 Splettstößer, T. and Holmes, K. C. and Noé, F. and Smith, J. C. (2011) Structural modeling and molecular dynamics simulation of the actin filament. Proteins, 79 . pp. 2033-2043. Latorre, J.C. and Metzner, Ph. and Hartmann, C. and Schütte, Ch. (2011) A Structure-preserving numerical discretization of reversible diffusions. Commun. Math. Sci., 9 (4). pp. 1051-1072. Bienert, A. and Pech, K. and Maas, H.-G (2011) Verfahren zur Registrierung von Laserscannerdaten in Waldbeständen. Schweizerische Zeitschrift für Forstwesen, 162 (6). pp. 178-185. Queck, R. and Bienert, A. and Maas, H.-G and Hermansa, S. and Goldberg, V. and Bernhofer, C. (2011) Wind fields in heterogeneous conifer canopies: parameterisation of momentum absorption using high-resolution 3D vegetation scans. European Journal of Forest Research, 130 . ISSN 1612-4669 (Print) 1612-4677 (Online) Wu, H. and Noé, F. (2011) A flat Dirichlet process switching model for Bayesian estimation of hybrid systems. Procedia Computer Science, 4 . pp. 1393-1402. Benacchio, T. and Bonaventura, L. (2011) A spectral collocation method for the one dimensional shallow water equations on semi-infinite domain. MOX–Report, 34 . 2010Assmann, M. and Sanz, C. S. and Pérez-Hernández, G. and Worth, G. A. and González, L. (2010) Excited state dynamics of a model asymmetric molecular rotor: A five-dimensional study on 2-cyclopentylidene-tetrahydrofuran. Chemical Physics, 377 (1-3). pp. 86-95. ISSN 03010104 Holtgrewe, M. (2010) Mason – A Read Simulator for Second Generation Sequencing Data. Technical Report FU Berlin . Metzner, Ph. and Weber, M. and Schütte, Ch. (2010) Observation Uncertainty in Reversible Markov Chains. Phys. Rev. E, 82 (3). 031114. Matera, S. and Reuter, K. (2010) Transport limitations and bistability for in situ CO oxidation at RuO 2(110): First-principles based multiscale modeling. Physical Review B, 82 (8). 085446. Flamm, Christoph and Ullrich, Alexander and Hofacker, L. Ivo and Stadler, Peter F. (2010) Evolution of Metabolic Networks: A Computational Framework. Journal of Systems Chemistry, 1 (4). Pérez-Hernández, G. and González, L. (2010) Mechanistic insight into light-driven molecular rotors: a conformational search in chiral overcrowded alkenes by a pseudo-random approach. Physical Chemistry Chemical Physics, 12 (38). pp. 12279-12289. ISSN 1463-9076 Assmann, M. and Pérez-Hernández, G. and González, L. (2010) On the Light-Driven Isomerization of a Model Asymmetric Molecular Rotor: Conformations and Conical Intersections of 2-Cyclopentylidene-tetrahydrofuran. The Journal of Physical Chemistry A, 114 (34). pp. 9342-9348. ISSN 1089-5639 Owschimikow, N. and Königsmann, F. and Maurer, J. and Giese, Ph. and Ott, A. and Schmidt, B. and Schwentner, N. (2010) Cross sections for rotational decoherence of perturbed nitrogen measured via decay of laser-induced alignment. J. Chem. Phys., 133 (4). 044311. Plattner, N. and Lee, M. W. and Meuwly, M. (2010) Structural and spectroscopic characterization of mixed planetary ices. Faraday discussions, 147 . 217-230; discussion 251. ISSN 1359-6640 Plattner, N. and Doll, J. D. and Meuwly, M. (2010) Spatial averaging for small molecule diffusion in condensed phase environments. The Journal of Chemical Physics, 133 (4). 044506. ISSN 00219606 Marsalek, O. and Uhlig, F. and Frigato, T. and Schmidt, B. and Jungwirth, P. (2010) Dynamics of Electron Localization in Warm vs. Cold Water Clusters. Phys. Rev. Lett., 105 (4). 043002. Hüser, D. and Gogol-Döring, A. and Lutter, T. and Weger, S. and Winter, K. and Hammer, E.-M. and Cathomen, T. and Reinert, K. and Heilbronn, R. (2010) Integration Preferences of Wildtype AAV-2 for Consensus Rep-Binding Sites at Numerous Loci in the Human Genome. PLoS Pathogens, 6 (7). e1000985. ISSN 1553-7374 Pilari, S. and Huisinga, W. (2010) Lumping of Physiologically-Based Pharmacokinetic Models and a Mechanistic Derivation of Classical Compartmental Models. Journal of Pharmacokinetics and Pharmacodynamics, 37 (4). pp. 365-405. Pérez-Hernández, G. and Pelzer, A. and González, L. and Seideman, T. (2010) Biologically inspired molecular machines driven by light. Optimal control of a unidirectional rotor. New Journal of Physics, 12 (7). 075007. ISSN 1367-2630 Sander, O. (2010) Geodesic finite elements for Cosserat rods. International Journal for Numerical Methods in Engineering, 82 (13). pp. 1645-1670. ISSN 1097-0207 Diederichs, E. and Juditski, A. and Spokoiny, V. and Schütte, Ch. (2010) Sparse Non-Gaussian Component Analysis. IEEE Transactions on Information Theory, 56 (6). pp. 3033-3047. ISSN 0018-9448 Keller, B. and Gattin, Z. and van Gunsteren, W. F. (2010) What stabilizes the 3_14-helix in beta^3-peptides? A conformational analysis using molecular simulation. PROTEINS: Structure, Function, and Bioinformatics, 78 (7). pp. 1677-1690. Holtgrewe, M. and Sanders, P. and Schulz, C. (2010) Engineering a scalable high quality graph partitioner. 2010 IEEE International Symposium on Parallel & Distributed Processing (IPDPS) . pp. 1-12. ISSN 1530-2075 von Kleist, M. and Menz, S. and Huisinga, W. (2010) Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV. Plos Computational Biology, 6 (3). e1000720. Bielow, C. and Ruzek, S. and Huber, C. and Reinert, K. (2010) Optimal Decharging and Clustering of Charge Ladders Generated in ESI−MS. J. Proteome Res., 9 (5). pp. 2688-2695. ISSN 1535-3893 Xavier , D. and Keller, B. and van Gunsteren, W. F. (2010) Comparing geometric and kinetic cluster algorithms for molecular simulation data. J. Chem. Phys., 132 (7). 074110. Horenko, I. and Schütte, Ch. (2010) On metastable conformational analysis of non-equilibrium biomolecular time series. Multiscale Modeling & Simulation, 8 (2). pp. 701-716. ISSN 15403467 Emde, A.-K. and Grunert, M. and Weese, D. and Reinert, K. and Sperling, S. R. (2010) MicroRazerS: Rapid alignment of small RNA reads. Bioinformatics, 26 (1). pp. 123-124. ISSN 1367-4803 Sander, O. and Schmidt, L. and Ehrig, R. and Heller, M. and Taylor, B. and Kornhuber, R. (2010) Numerical determination of the medio-lateral force distribution in an ovine stifle joint. Biomedizinische Technik/Biomedical Engineering: Proceedings of BMT, Rostock, 55 (s1). ISSN 0013-558 Forster, R. and Kornhuber, R. (2010) A polynomial chaos approach to stochastic variational inequalities. Journal of Numerical Mathematics, 18 (4). pp. 235-255. ISSN 1570-2820 Devanathan, R. and Venkatnathan, A. and Rousseau, R. and Dupuis, M. and Frigato, T. and Gu, W. and Helms, V. (2010) Atomistic Simulation of Water Percolation and Proton Hopping in Nafion Fuel Cell Membrane. J. Phys. Chem. B, 114 (43). pp. 13681-13690. Hartmann, C. and Vulcanov, V.-M. and Schütte, Ch. (2010) Balanced Truncation of Second Order Systems: a Hamiltonian approach. Multiscale Model. Simul., 8 (4). pp. 1348-1367. Münch, M. (2010) Brandschutzaufklärung mit mathematischen Simulationsprogrammen: Wie Mathematik hilft, Ihr Leben zu retten! Schadenprisma - Zeitschrift für Schadenverhütung und Schadenforschung der öffentlichen Versicherer, 4 . pp. 16-19. Zhu, H. and Blom, M. and Compagnon, I. and Rijs, A. M. and Roy, S. and von Helden, G. and Schmidt, B. (2010) Conformations and Vibrational Spectra of a Model Tripeptide: Change of Secondary Structure upon Micro-Solvation. Phys. Chem. Chem. Phys., 12 (14). 3415 -3425. Queck, R. and Bernhofer, C. (2010) Constructing wind profiles in forests from limited measurements of wind and vegetation structure. Agricultural and Forest Meteorology . Spötter, Andreas and Gupta, Pooja and Reinsch , Norbert and Zautke, F. and Bienefeld, Kaspar (2010) Development of a SNP-Assay for varroa tolerance in the honey bee. Apidologie, 41 (6). p. 685. ISSN 0044-8435 (Print) 1297-9678 (Online) Qu, Z.-W. and Zhu, H. (2010) Do Anionic Titanium Dioxide Nano-Clusters Reach Bulk Band Gap? A Density Functional Theory Study. J. Comp. Chem., 31 (10). pp. 2038-2045. Baumann, M. and Heuveline , V. (2010) Evaluation of Different Strategies for Goal Oriented Adaptivity in CFD - Part I: The Stationary Case. Preprint Series of the Engineering Mathematics and Computing Lab, 2010-05 . Bordás, R. and Hagemeier, T. and Thévenin, D. (2010) Experimental Investigation of Droplet-Droplet Interactions. 23rd European Conference on Liquid Atomization and Spray Systems . 198.1-198.6. ISSN 978-80-7399-997-1 Münch, M. (2010) Fast and correct computation. A comprehensive test concept to proof the new FDS-ScaRC technique. 11th International Symposium on Fire Protection . 11 p.. ISSN 978-3-00-03966-2 Horenko, I. (2010) Finite Element Approach to Clustering of Multidimensional Time Series. J. Sci. Comp., 32 (1). pp. 62-83. Latorre, J.C. and Hartmann, C. and Schütte, Ch. (2010) Free energy computation by controlled Langevin processes. Procedia Computer Science, 1 (1). pp. 1591-1600. Pilari, S. and Preusse, C. and Huisinga, W. (2010) Gestational Influences on the Pharmacokinetics of Gestagenic Drugs: A Combined In Silico, In Vitro and In Vivo Analysis. European Journal of Pharmaceutical Sciences . (Submitted) Achatz, U. and Klein, R. and Senf, F. (2010) Gravity waves, scale asymptotics, and the pseudo-incompressible equations. Journal of Fluid Mechanics, 663 . pp. 120-147. Schütte, Ch. and Wulkow, M. (2010) A Hybrid Galerkin–Monte-Carlo Approach to Higher-Dimensional Population Balances in Polymerization Kinetics. Macromol. React. Eng., 4 (9-10). pp. 562-577. Marsalek, O. and Frigato, T. and VandeVondele, J. and Bradforth, P. E. and Schmidt, B. and Schütte, Ch. and Jungwirth, P. (2010) Hydrogen Forms in Water by Proton Transfer to a Distorted Electron. J. Phys. Chem. B, 114 (2). pp. 915-920. Kenfack, A. and Marquardt, F. and Paramonov, G. K. and Barth, I. and Lasser, C. and Paulus, B. (2010) Initial-state dependence of coupled electronic and nuclear fluxes in molecules. Phys. Rev. A, 81 (5). 052502. Bastian, G and Vogelsang, A and Schiffmann, C (2010) Isotopic Superlattices for Perfect Phonon Reflection. Journal of Electronic Materials, 39 (9). p. 1769. ISSN 0361-5235 Jebens, .S. and Knoth, O. and Arnold, M. and Weiner, R. (2010) Linearly implicit peer methods for the compressible Euler equations. Applied Numerical Mathematics . (Submitted) Wu, H. and Noé, F. (2010) Maximum a posteriori estimation for Markov chains based on Gaussian Markov random fields. Procedia Computer Science, 1 (1). pp. 1665-1673. Ruprecht, D. and Klein, R. and Majda, A. J. (2010) Modulation of Internal Gravity Waves in a Multiscale Model for Deep Convection on Mesoscales. Journal.of the Atmospheric Sciences, 67 (8). pp. 2504-2519. ISSN Online 1520-0469, Print 0022-4928 Schlegel, M. and Knoth, O. and Arnold, M. and Wolke, R (2010) Numerical solution of multiscale problems in atmospheric modeling. Applied Numerical Mathematics . (Submitted) Horenko, I. (2010) On Clustering of Non-stationary Meteorological Time Series. Dyn. of Atm. and Oc., 49 (2-3). pp. 164-187. Sarich, M. and Noé, F. and Schütte, Ch. (2010) On the Approximation Quality of Markov State Models. Multiscale Model. Simul., 8 (4). pp. 1154-1177. Horenko, I. (2010) On the identification of non-stationary factor models and their application to atmospherical data analysis. J. Atm. Sci., 67 (5). pp. 1559-1574. Hartmann, C. and Schütte, Ch. and Ciccotti, G. (2010) On the linear response of mechanical systems with constraints. J. Chem. Phys., 132 (11). p. 111103. Sarich, M. and Schütte, Ch. and Vanden-Eijnden, E. (2010) Optimal Fuzzy Aggregation of Networks. Multiscale Modeling and Simulation, 8 (4). pp. 1535-1561. Bernhard, S. and Noé, F. (2010) Optimal Identification of Semi-Rigid Domains in Macromolecules from Molecular Dynamics Simulation. PLoS One, 5 . e10491. Horenko, I. (2010) Parameter identification in nonstationary Markov chains with external impact and its application to computational sociology. Multiscale Modeling & Simulation . (Submitted) Bienert, A. and Stiel, B. and Queck, R. and Maas, H.-G (2010) Photogrammetrische Bestimmung von statischen und dynamischen Verformungsstrukturen an Einzelbäumen. Allgemeine Vermessungs-Nachrichten, 5 . 190-197.. Menz, St. and Matthiesen, R. and Dehmel, Ch. and Barembruch, C. and Hengge, R. and Huisinga, W. (2010) Precise Switching of Flagellar Gene Expression in Escherichia Coli by the FlgM–FliA Regulatory Network. PLoS Computational Biology . (Submitted) Wu, H. and Noé, F. (2010) Probability Distance Based Compression of Hidden Markov Models. Multiscale Model. Simul., 8 . pp. 1838-1861. Chodera, J. D. and Noé, F. (2010) Probability distributions of molecular observables computed from Markov models. II: Uncertainties in observables and their time-evolution. J. Chem. Phys, 133 (10). p. 105102. de Souza, L.G.M. and Janiga, G and John, V. and Thévenin, D. (2010) Reconstruction of a distribution from a finite number of moments with an adaptive spline-based algorithm. Chemical Engineering Science, 65 (9). pp. 2741-2750. Klein, R. and Achatz, U. and Bresch, D. and Knio, O.M. and Smolarkiewicz, P. (2010) Regime of Validity of Sound-Proof Atmospheric Flow Models. Journal of the Atmospheric Sciences, 67 (10). pp. 3226-3237. ISSN Online: 1520-0469 Print: 0022-4928 Klein, R. (2010) Scale-Dependent Asymptotic Models for Atmospheric Flows. Annual Review of Fluid Mechanics, 42 . pp. 249-274. Schiffmann, C and Appert-Rolland, C and Santen, L (2010) Shock dynamics of two-lane driven lattice gases. Journal of Statistical Mechanics: Theory and Experiment, 2010 (06). P06002. ISSN 1742-5468 Birn, M. and Holtgrewe, M. and Sanders, P. and Singler, J. (2010) Simple and Fast Nearest Neighbor Search. 2010 Proceedings of the Twelfth Workshop on Algorithm Engineering and Experiments (ALENEX) . pp. 43-54. Berninger, H. and Sander, O. (2010) Substructuring of a Signorini-type problem and Robin's method for the Richards equation in heterogeneous soil. Computing and Visualization in Science, 13 (5). pp. 187-205. ISSN 1432-9360 Rohrschneider, Markus and Ullrich, Alexander and Kerren, Andreas and Stadler, Peter F. and Scheuermann, Gerik (2010) Visual Network Analysis of Dynamic Metabolic Pathways. Advances in visual computing . pp. 316-327. ISSN 3-642-17288-1 Bienert, A. and Queck, R. and Schmidt, A. and Bernhofer, C. and Maas, H.-G (2010) Voxel space analysis of terrestrial laser scans in forests for wind field modelling. International Archives of Photogrammetry.Remote Sensing and Spatial Information Sciences, 38 (5). pp. 92-97. Dedner, A. and Klöfkorn, R. and Nolte, M. and Ohlberger, M. (2010) A generic interface for parallel and adaptive discretization schemes: Abstraction principles and the DUNE-FEM module. Computing, 90 (3-4). pp. 165-196. Huang, W. and Kamenski, L. and Lang, J. (2010) A new anisotropic mesh adaption method based upon hierarchical a posteriori error estimates. J. Comput. Phys., 229 . pp. 2179-2198. Münch, M. and Kilian, S. (2010) A new generalized domain decomposition strategy for the efficient parallel solution of the FDS-pressure equation, Part II: Verification and Validation. ZIB-Report, ZR_09-20 . 40p.. ISSN 1438-0064 Moeck, J. and Scharfenberg , C. and Paschereit, O. C. and Klein, R. (2010) A zero-Mach solver and reduced order acoustic representations for modeling and control of combustion instabilities. Active Flow Control II, Notes on Numerical Fluid Mechanics and Multidisciplinary Design,, 108/2010 . pp. 291-306. ISSN 978-3-642-11734-3 2009Véron, N. and Bauer, H. and Weiße, A. Y. and Lüder, G. and Werber, M. and Herrmann, B. G. (2009) Retention of gene products in syncytial spermatids promotes non-Mendelian inheritance as revealed by the t complex responder. Genes & Development, 23 (23). 2705-2710 . Noé, F. and Schütte, Ch. and Vanden-Eijnden, E. and Reich, L. and Weikl, T. (2009) Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations. Proc. Natl. Acad. Sci. USA, 106 (45). pp. 19011-19016. Klein, R. and Bates, K.R. and Nikiforakis, N. (2009) Well Balanced Compressible Cut-Cell Simulation of Atmospheric Flow. Philosophical Transaction of the Royal Society, 367 (1907). 4559-4575 . ISSN Online: 1471-2962 Matera, S. and Reuter, K. (2009) First-Principles Approach to Heat and Mass Transfer Effects in Model Catalyst Studies. Catalysis letters, 133 (1-2). pp. 156-159. ISSN 1011-372X Doll, J. D. and Gubernatis, J. E. and Plattner, N. and Meuwly, M. and Dupuis, P. and Wang, H. (2009) A spatial averaging approach to rare-event sampling. The Journal of Chemical Physics, 131 (10). p. 104107. ISSN 00219606 Meskine, H. and Matera, S. and Scheffler, M. and Reuter, K. and Metiu, H. (2009) Examination of the concept of degree of rate control by first-principles kinetic Monte Carlo simulations. Surface Science, 603 (10). pp. 1724-1730. Gräser, C. and Sander, O. (2009) The dune-subgrid module and some applications. Computing, 86 (4). pp. 269-290. ISSN 0010-485X Splettstößer, T. and Noé, F. and Oda, T. and Smith, J. C. (2009) Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerisation-competent superclosed state. Proteins, 76 . pp. 353-364. Oevermann, M. and Scharfenberg , C. and Klein, R. (2009) A sharp interface finite volume method for elliptic equations on Cartesian grids. Journal of Computational Physics, 228 (14). pp. 5184-5206. Weese, D. and Emde, A.-K. and Rausch, T. and Döring, A. and Reinert, K. (2009) RazerS - Fast Read Mapping with Sensitivity Control. Genome Research, 19 (9). pp. 1646-1654. Schütte, Ch. and Jahnke, T. (2009) Towards Effective Dynamics in Complex Systems by Markov Kernel Approximation. Mathematical Modelling and Numerical Analysis (ESAIM), 43 (4). pp. 721-742. Klein, R. (2009) Asymptotics, structure, and integration of sound-proof atmospheric flow equations. Theoretical and Computational Fluid Dynamics, 23 (3). pp. 161-195. ISSN 0935-4964 (Print) 1432-2250 (Online) Jebens, S. and Knoth, O. and Weiner, R. (2009) Explicit Two-Step Peer Methods for the Compressible Euler Equations. Monthly Weather Review, 137 (7). pp. 2380-2392. Vercauteren, N. and Bou-Zeid, E. and Huwald, H. and Parlange, M. B. and Brutsaert, W. (2009) Estimation of wet surface evaporation from sensible heat flux measurements. Water Resources Research, 45 (6). Strenziok, R. and Hinz, S. and Wolf, C. and Conrad, T. O. F. and Krause, H. and Miller, K. and Schrader, M. (2009) Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry: serum protein profiling in seminoma patients. World J of Urology, 28 (2). pp. 193-197. Schütte, Ch. and Noé, F. and Meerbach, E. and Metzner, Ph. and Hartmann, C. (2009) Conformation Dynamics. Proceedings of the 6th International Congress on Industrial and Applied Mathematics, I. Jeltsch and G. Wanner (eds.), . pp. 297-335. Plattner, N. and Meuwly, M. (2009) Higher order multipole moments for molecular dynamics simulations. Journal of Molecular Modeling, 15 (6). pp. 687-694. ISSN 1610-2940 Fiedler, G. M. and Leichtle, A. and Kase, J. and Baumann, S. and Ceglarek, U. and Felix, K. and Conrad, T. O. F. and Witzigmann, H. and Weimann, A. and Schütte, Ch. and Hauss, J. and Büchler, M. and Thiery, J. (2009) Serum Peptidome Profiling Revealed Platelet Factor 4 as a Potential Discriminating Peptide Associated With Pancreatic Cancer. Clinical Cancer Research, 15 (11). pp. 3812-3819. ISSN 1078-0432 Audusse, E. and Klein, R. and Owinoh, A.Z. (2009) Conservative Discretization of Coriolis Force. Journal of Computational Physics, 228 (8). pp. 2934-2950. Zerck, A. and Nordhoff, E. and Reseman, A. and Mirgorodskaya, E. and Suckau, D. and Reinert, K. and Lehrach, H. and Gobom, J. (2009) An iterative strategy for precursor ion selection for LC-MS/MS based shotgun proteomics. Journal of Proteome Research . Hartmann, C. and Schütte, Ch. and Kalibaeva, G. and Di Pierro, M. and Ciccotti, G. (2009) Fast Simulation of Polymer Chains. J. Chem. Phys., 130 . p. 144101. Schlegel, M. and Knoth, O. and Arnold, M. and Wolke, R (2009) Multirate Runge-Kutta schemes for advection equations. Journal of Computational and Applied Mathematics, 226 (2). pp. 345-357. ISSN 0377-0427 von Kleist, M. and Huisinga, W. (2009) Pharmacokinetic–pharmacodynamic relationship of NRTIs and its connection to viral escape: An example based on zidovudine. European Journal of Pharmaceutical Sciences, 36 . pp. 532-543. Gassner, G.J. and Lörcher, F. and Munz, C.-D. and Hesthaven, J.-S. (2009) Polymorphic nodal elements and their application in discontinuous Galerkin methods. Journal of Computational Physics, 228 (5). 1573-1590 . Gräser, C. and Kornhuber, R. (2009) Nonsmooth Newton methods for set-valued saddle point problems. SIAM Journal on Numerical Analysis, 47 (2). pp. 1251-1273. ISSN 0036-1429 Metzner, Ph. and Schütte, Ch. and Vanden-Eijnden, E. (2009) Transition Path Theory for Markov Jump Processes. Mult. Mod. Sim., 7 (3). pp. 1192-1219. Mellado, J.- P. and Stevens, B. and Schmidt, H. and Peters, N. (2009) Analysis of latent heat effects in the cloud-top mixing layer. Quarterly Journal of the Royal Meteorological Society, 135 (641). pp. 963-978. Belaschk, H.C. and Münch, M. (2009) Anwendung von massiv paralleler Berechnung mit Grafikkarten GPGPU) für CFD-Methoden im Brandschutz. Bauphysik Volume 31 Issue 4, Pages 216 - 226, 31 (4). pp. 216-226. Devereux, M. and Plattner, N. and Meuwly, M. (2009) Application of Multipolar Charge Models and Molecular Dynamics Simulations to Study Stark Shifts in Inhomogeneous Electric Fields†. The Journal of Physical Chemistry A, 113 (47). pp. 13199-13209. ISSN 1089-5639 Münch, M. (2009) Brandsimulationsprogramme - Chancen und Risiken. schadenprisma, Zeitschrift für Schadenverhütung und Schadenforschung der öffentlichen Versicherer, 2 . pp. 14-18. Mellado, J.- P. and Schmidt, H. and Stevens, B. and Peters, N. (2009) Buoyancy reversal in the cloud-top mixing layer. (Submitted) Gräfe, Ch. and Nordmeier, V. and Schütte, Ch. (2009) Computerspiel zum Thema Moleküldynamik für Schüler der 7.-10. Klasse, Experimentelles Protyping zur Entwicklung eines Lernspiels. Jahrestagung 2008 der GDCP (Gesellschaft für Didaktik der Chemie und Physik), 1 . pp. 77-79. ISSN 978-3-643-10010-8 Giorgetta, M. and Hundertmark, T. and Korn, P. and Reich, S. and Restelli, M. (2009) Conservative Space and Time Regularizations for the ICON Model. Reports on Earth System Science, 67 . pp. 1-32. ISSN 1614-1199 Dumbser, M. and Gassner, G. and Munz , C.-D. (2009) Discontinuous Galerkin-Verfahren für zeitabhängige Advektions-Diffusions-Gleichungen. Jahresbericht der DMV, 111 (3). pp. 87-123. Metzner, Ph. and Noé, F. and Schütte, Ch. (2009) Estimating the Sampling Error: Distribution of Transition Matrices and Functions of Transition Matrices for Given Trajectory Data. Phys. Rev. E, 80 (2). 021106. Queck, R. and Bienert, A. (2009) Estimation of PBL model parameters from high resolution vegetation scans. Geophysical Research Abstracts, 11 (EGU2009-10888). Schatzmann, M. and Leitl, B. (2009) Evaluation of Numerical Flow and Dispersion Models for Applications in Industrial and Urban Areas. Chemical Engineering & Technology, 32 (2). 241 -246. Swart, A. and Manders, A. and Harlander, U. and Maas, U. and Leo , R. M. (2009) Experimental observation of strong mixing due to internal wave focusing over sloping terrain. Dynamics of Atmospheres and Oceans, 50 (1). pp. 16-34. Bauer, R. A. and Rother, K. and Moor, P. and Reinert, K. and Steinke, T. and Bujnicki, J. M. and Preissner, R. (2009) Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors. Algorithms and Molecular Sciences, 2 (2). pp. 692-709. ISSN 1999-4893 Gerisch, A. and Lang, J. and Podhaisky, H. and Weiner, R. (2009) High-order linearly implicit two-step peer-finite element method for time-dependent PDEs. Applied Numerical Mathematics, 59 (3-4). 624-638 . ISSN 0168-9274 Stenke, A. and Dameris, M. and Grewe, V. and Garny, H. (2009) Implications of Lagrangian transport for simulations with a coupled chemistry-climate model. Atmospheric Chemistry and Physics, 9 . pp. 5489-5504. Harlander, U. and Ridderinkhof, H. and Schouten, M.W. and de Ruijter, W. P. M (2009) Long-term observations of transport, eddies, and Rossby waves in the Mozambique Channel. JOURNAL OF GEOPHYSICAL RESEARCH, 114 (C02003). 15pp. Swart, T. and Rousse, V. (2009) A Mathematical Justification for the Herman-Kluk Propagator. Comm. Math. Phys., 286 (2). pp. 725-750. Papke, A. (2009) Mindestens 17 müssen es sein. Junge Wissenschaft, 84 . pp. 24-31. Kube, S. and Lasser, C. and Weber, M. (2009) Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics. J. Comp. Phys., 228 (6). pp. 1947-1962. Gräser, C. and Kornhuber, R. (2009) Multigrid methods for obstacle problems. Journal of Computational Mathematics, 27 (1). pp. 1-44. ISSN 0254-9409 Wensch, J. and Knoth, O. and Galant, A. (2009) Multirate infinitesimal step methods for atmospheric flow simulation. BIT - Numerical Mathematics, 49 (2). pp. 449-473. ISSN 0006-3835 (Print) 1572-9125 (Online) Schmidt, H. and Mellado, J.- P. and Peters, N. and Kerstein, A.R. and Stevens, B. (2009) Numerical study of buoyancy reversal in stably stratified flows. Geophysical Research Abstracts, 11 . (Submitted) Horenko, I. (2009) On metastable conformational analysis of non-equilibrium biomolecular time series. MMS . (Submitted) Horenko, I. (2009) On robust estimation of low-frequency variability trends in discrete Markovian sequences of atmospherical circulation patterns. The Journal of Atmospherical Sciences, 66 (7). 2059-2072 . Horenko, I. (2009) On structure-preserving persistent clustering of multivariate time series. Journal of Computational Physics . (Submitted) Pingen, G. and Waidmann, M. and Evgrafov, A. and Maute, K. (2009) A Parametric Level-Set Approach for Topology Optimization of Flow Domains. Structural and Multidisciplinary Optimization . ISSN 1615-147X (Print) 1615-1488 (Online) Dolaptchiev, S. and Klein, R. (2009) Planetary geostrophic equations for the atmosphere with evolution of the barotropic flow. Dynamics of Atmospheres and Oceans Volume, 46 (1-4). pp. 46-61. Leibscher, M. and Schmidt, B. (2009) Quantum dynamics of a plane pendulum. Phys. Rev. A, 80 (1). 012510. Altmann, C. and Gassner, G. and Lörcher, F. and Munz , C.-D. (2009) A Space-Time Expansion Discontinuous Galerkin Scheme With Local Time Stepping for the Ideal and Viscous MHD Equations. IEEE Transactions on Plasma Science, 37 (4). 513 -519 . Vater, S. and Klein, R. (2009) Stability of a Cartesian grid projection method for zero Froude number shallow water flows. Numerische Mathematik, 113 (1). pp. 123-161. Owschimikow, N. and Schwentner, N. and Schmidt, B. (2009) State Selection in Non-Resonantly Excited Wave Packets by Tuning from Non-Adiabatic to Adiabatic Interaction. Phys. Rev. A, 80 (5). 053409. Schulz-Trieglaff, O. and Machtejevas, E. and Reinert, K. and Schlueter, H. and Thiemann, J. and Unger, K. (2009) Statistical Quality Assessment and Outlier Detection for Liquid Chromatography-Mass Spectrometry Experiments. BioDataMining, 2 (4). Franzke, Ch. and Horenko, I. and Majda, A. J. and Klein, R. (2009) Systematic Metastable Atmospheric Regime Identification in an AGCM. J. Atm. Sci., 66 (7). pp. 1997-2012. Zhu, H. and Röder, B. and May, V. (2009) Time and frequency resolved spontaneous emission from supramolecular pheophorbide-a complexes: A mixed quantum classical computation. Chem. Phys., 362 (1-2). pp. 19-26. Qu, Z.-W. and Zhu, H. and May, V. and Schinke, R. (2009) Time-Dependent Density Functional Theory Study of the Electronic Excitation Spectra of Chlorophyllide a and Pheophorbide a in Solvents. J. Phys. Chem. B, 113 (14). pp. 4817-4825. Löbig, S. and Dörnbrack, A. and Fröhlich, J. and Hertel, C. and Kühnlein, C. and Lang, J. (2009) Towards Large-Eddy Simulation on moving grids. PAMM · Proc. Appl. Math. Mech., 9 . 445 -446. Ionescu, C. and Klein, R.J.T. and Hinkel, J., and Kavi Kumar, K.S., and Klein, R. (2009) Towards a formal framework for vulnerability to climate change. Environmental Modeling and Assessment, 14 (1). pp. 1-16. ISSN 1420-2026 (Print) 1573-2967 (Online) Barth, I. and Lasser, C. (2009) Trigonometric pulse envelopes for laser-induced quantum dynamics. J. Phys. B: At. Mol. Opt. Phys., 42 (23). p. 235101. Hickel, S. and von Terzi, D.A. and Fröhlich, J. (2009) An adaptive local deconvolution method for general curvilinear coordinate systems. Springer Proceedings Physics - Advances in Turbulence XII, 132 (11). pp. 783-786. Rausch, T. and Koren, S. and Denisov, G. and Weese, D. and Emde, A.-K. and Döring, A. and Reinert, K. (2009) A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics, 25 (9). pp. 1118-1124. Kilian, S. and Münch, M. (2009) A new generalized domain decomposition strategy for the efﬁcient parallel solution of the FDS-pressure equation. Part I: Theory, Concept and Implementation. ZIB-Report, 09-19 . 30 pages. ISSN 1438-0064 Schmidt, H. and Oevermann, M. and Bastiaans, R.J.M. and Kerstein, A.R. (2009) A priori Tabulation of Turbulent Flame Speeds via a Combination of a Stochastic Mixing Model and Flamelet Generated Manifolds, Extended to Incorporate Strain Effects. ZIB Report, 09-09 . ISSN 1438-0064 Moeck, J. and Oevermann, M. and Klein, R. and Paschereit, O. C. and Schmidt, H. (2009) A two-way coupling for modeling thermoacoustic instabilities in a flat flame Rijke tube. Proceedings of the Combustion Institute, 32 (1). pp. 1199-1207. 2008Plattner, N. and Bandi, T. and Doll, J. D. and Freeman, D. and Meuwly, M. (2008) MD simulations using distributed multipole electrostatics: Structural and spectroscopic properties of CO- and methane-containing clathrates. Molecular Physics, 106 (12). pp. 1675-1684. ISSN 0026-8976 Letzel, O. and Krane, M. and Raasch, S. (2008) High resolution urban large-eddy simulation studies from street canyon to neighbourhood scale. Atmospheric Environment, 42 (38). 8770-8784 . Bou-Zeid, E. and Vercauteren, N. and Parlange, M. B. and Meneveau, C. (2008) Scale dependence of subgrid-scale model coefficients: An a priori study. Physics of Fluid, 20 (115106). Matute, R. A. and Contreras, R. and Pérez-Hernández, G. and González, L. (2008) The Chromophore Structure of the Cyanobacterial Phytochrome Cph1 As Predicted by Time-Dependent Density Functional Theory. The Journal of Physical Chemistry B, 112 (51). pp. 16253-16256. ISSN 1520-6106 Pérez-Hernández, G. and González, L. and Serrano-Andrés, L. (2008) Rydberg or Valence? The Long-Standing Question in the UV Absorption Spectrum of 1,1′-Bicyclohexylidene. ChemPhysChem, 9 (17). p. 2544. ISSN 14394235 Carqué, G. and Schmidt, H. and Stevens, B. and Klein, R. (2008) Plausibility Check of an Asymptotic Column Model for Deep Convective Clouds. ZIB-Report, 08 (44). Kornhuber, R. and Yserentant, H. (2008) Multigrid methods for discrete elliptic problems on triangular surfaces. Computing and Visualization in Science, 11 (4-6). pp. 251-257. ISSN 1432-9360 Vercauteren, N. and Bou-Zeid, E. and Parlange, M. B. and Lemmin, U. and Huwald, H. and Selker, J. S. and Meneveau, C. (2008) Subgrid-Scale Dynamics of Water Vapour, Heat, and Momentum over a Lake. Boundary-Layer Meteorology, 128 (2). pp. 205-228. ISSN Print: 0006-8314 Online: 1573-1472 Barth, I. and Manz, J. and Pérez-Hernández, G. and Sebald, P. (2008) Towards Toroidal Hydrogen Bonds. Zeitschrift für Physikalische Chemie, 222 (8-9). pp. 1311-1331. ISSN 0942-9352 Schäfer-Bung, B. and Nest , M. (2008) Correlated Dynamics of Electrons with Reduced 2-Electron Density Matrices. Phys. Rev. A, 78 (1). 012512. Münch, M. and Klein, R. (2008) Critical numerical aspects for field model applications. EUSAS Journal (4). pp. 41-54. Abida, R. and Bocquet, M. and Vercauteren, N. and Isnard, O. (2008) Design of a monitoring network over France in case of a radiological accidental release. Atmospheric Environment, 42 (21). pp. 5205-5219. ISSN 1352-2310 Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Ohlberger, M. and Sander, O. (2008) A generic grid interface for parallel and adaptive scientific computing. Part I: Abstract framework. Computing, 82 (2-3). pp. 103-119. ISSN 0010-485X Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Kornhuber, R. and Ohlberger, M. and Sander, O. (2008) A generic grid interface for parallel and adaptive scientific computing. Part II: Implementation and tests in DUNE. Computing, 82 (2-3). pp. 121-138. ISSN 0010-485X Rausch, T. and Thomas, A. and Camp, N. J. and Facelli, L. A. (2008) A parallel genetic algorithm to discover patterns in genetic markers that indicate predisposition to multifactorial disease. Comput. Biol. Med., 38 . pp. 826-836. Plattner, N. and Meuwly, M. (2008) Atomistic Simulations of CO Vibrations in Ices Relevant to Astrochemistry. ChemPhysChem, 9 (9). pp. 1271-1277. ISSN 14394235 Plattner, N. and Meuwly, M. (2008) The Role of Higher CO-Multipole Moments in Understanding the Dynamics of Photodissociated Carbonmonoxide in Myoglobin. Biophysical Journal, 94 (7). pp. 2505-2515. ISSN 00063495 Strenziok, R. and Hinz, S. and Wolf, C. and Conrad, T. O. F. and Krause, H. and Lingnau, A. and Lein, M. and Miller, K. and Schrader, M. (2008) Serum proteomic profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry in testicular germ cell cancer patients. European Urology Supplements, 7 (3). p. 83. Schäfer-Bung, B. (2008) The interplay of wave packet dephasing, optimization efficiency, and target state population in optimally controlled isotope selective photoionization. Chem. Phys., 343 . pp. 340-346. Carqué, G. and Owinoh, A.Z. and Klein, R. and Majda, A. J. (2008) Asymptotic Scale Analysis of Precipitating Clouds. ZIB-Report, 08-03 . ISSN 1438-0064 Münch, M. (2008) MOLOCH - Ein Strömungsverfahren für inkompressible Strömungen - Technische Referenz. PIK-Report (109). Kornhuber, R. and Krause, R. and Sander, O. and Deuflhard, P. and Ertel, S. (2008) A monotone multigrid solver for two body contact problems in biomechanics. Computing and Visualization in Science, 11 (1). pp. 3-15. ISSN 1432-9360 Frigato, T. and VandeVondele, J. and Schmidt, B. and Schütte, Ch. and Jungwirth, P. (2008) Ab Initio Molecular Dynamics Simulation of a Medium-Sized Water Cluster Anion: From an Interior to a Surface Located Excess Electron via a Delocalized State. J. Phys. Chem. A, 112 (27). pp. 6125-6133. Münch, M. and Klein, R. (2008) Anforderungen an numerische Berechnungen der Brand- und Rauchausbreitung im Vorbeugenden Brandschutz. vfdb-Zeitschrift Forschung, Technik und Management im Brandschutz, Jg. 57 (3). pp. 145-151. ISSN 0042-1804 Horenko, I. (2008) Automated Generation of Reduced Stochastic Weather Models I: Simultaneous Dimension and Model Reduction for Time Series Analysis. Multiscale Modeling & Simulation, 6 (4). p. 1125. ISSN 15403467 Horenko, I. and Klein, R. and Dolaptchiev, S. and Schütte, Ch. (2008) Automated Generation of Reduced Stochastic Weather Models I: Simultaneous Dimension and Model reduction for Time Series Analysis. Mult. Mod. Sim., 6 (4). pp. 1125-1145. Hartmann, C. and Schütte, Ch. (2008) Balancing of partially-observed stochastic differential equations. 47th IEEE Conference on Decision and Control . pp. 4867-4872. Schulz-Trieglaff, O. and Hussong, R. and Gröpl, C. and Hildebrandt, A. and Hildebrandt, A. and Huber, Ch. and Reinert, K. (2008) Computational Quantification of Peptides from LC-MS data. Journal of Computational Biology, 15 (7). pp. 685-704. Lange, E. and Tautenhahn, R. and Neumann, S. and Gröpl, C. (2008) Critical assessment of alignment procedures for LC-MS proteomics and metabolomic measurements. BMC Bioinformatics, 9 (375). Warren, R. and de la Nava Santos, S. and Arnell, N.W. and Bane, M. and Barker, T. and Barton, C. and Ford, R. and Füssel, H.-M. and Hankin, Robin K.S. and Klein, R. and Linstead, C. and Kohlera, J. and Mitchella, T.D. and Osborna, T.J. and Pan, H. and Raper, S.C.B. and Riley, G. and Schellnhuber, H.J. and Winne, S. and Anderson, D. (2008) Development and illustrative outputs of the Community Integrated Assessment System (CIAS), a multi-institutional modular integrated assessment approach for modelling climate change. Environmental Modelling & Software, 23 (5). 592-610 . Horenko, I. and Schütte, Ch. (2008) Dimension Reduction for Time Series with Hidden Phase Transitions and Economic Applications. Adv. Data Anal. Class., submitted . (Submitted) Gassner, G. and Lörcher, F. and Munz , C.-D. (2008) A Discontinuous Galerkin Scheme based on a Space-Time Expansion II. Viscous Flow Equations in Multi Dimensions. Journal of Scientific Computing, 34 (3). pp. 260-286. ISSN 0885-7474 (Print) 1573-7691 (Online) Craig, G.C. and Dörnbrack, A. (2008) Entrainment in Cumulus Clouds: What resolution is cloud resolving? J. Atmos. Sci., 65 . pp. 3978-3988. ISSN Online 1520-0469 Print 0022-4928 Hartmann, C. (2008) An Ergodic Sampling Scheme for Constrained Hamiltonian Systems with Applications to Molecular Dynamics. J. Stat. Phys., 130 (4). pp. 687-712. Bauer, M. and Klau, G. W. and Reinert, K. (2008) An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment. Algorithmic Operations Research . John, V. and Schmeyer, E. (2008) Finite element methods for time-dependent convection-diffusion-reaction equations with small diffusion. Computer methods in applied mechanics and engineering, 198 (3). pp. 475-494. ISSN 0045-7825 Kadioglu, S.Y. and Minion, M.L. and Klein, R. (2008) A Fourth-Order Auxiliary Variable Projection Method for Zero-Mach Number Gas Dynamics. Journal of Computational Physics , 227 (3). 2012-2043 . Ullrich, Alexander and Flamm, Christoph (2008) Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe. Computational Methods in Systems Biology, 5307 . pp. 28-43. Bodirsky, M. and Gröpl, C. and Kang, M. (2008) Generating unlabeled connected cubic planar graphs uniformly at random. Random Structures and Algorithms, 32 (2). pp. 157-180. von Larcher, T. and Futterer, B. and Egbers, C. and Hollerbach, R. and Chossat, P. and Beltrame, P. and Tuckerman, L. and Feudel, F. (2008) GeoFlow - European Microgravity Experiments on Thermal Convection in Rotating Spherical Shells under influence of Central Force Field. Journal of The Japan Society of Microgravity Application, 25 (3). von Larcher, T. and Futterer, B. and Egbers, C. (2008) GeoFlow: On the status of experimental preparation of spherical gap flow experiments with central force field on International Space Station (ISS). Journal of Physics: Conference Series, 137 (012025). p. 6. Oevermann, M. and Schmidt, H. and Kerstein, A.R. (2008) HCCI combustion modeling using detailed chemistry coupled to LEM-based advection. Combustion and Flame, 155 . pp. 370-379. Teleaga, , I. and Lang, J. (2008) Higher-order linearly implicit one-step methods for three-dimensional incompressible Navier-Strokes equations. Studia Babes-Bolyai Matematica, 53 . pp. 109-121. Tomm, S. and von Terzi, D.A. and Fröhlich, J. (2008) Interaction of the filter and spatial discretisation operators for Large-Eddy Simulation using the Approximate Deconvolution Model. PAMM, 8 . pp. 10605-10606. Oevermann, M. and Schmidt, H. and Kerstein, A.R. (2008) Investigation of autoignition under thermal stratification using linear eddy modeling. Combustion and Flame Volume, 155 (3). 370-379 . Schulz-Trieglaff, O. and Pfeifer, N. and Gröpl, C. and Kohlbacher, O. and Reinert, K. (2008) LC-MSsim - a simulation software for liquid chromatography mass spectrometry data. BMC Bioinformatics, 9 (423). Horenko, I. and Schütte, Ch. (2008) Likelihood-Based Estimation of Multidimensional Langevin Models and its Application to Biomolecular Dynamics. Mult. Mod. Sim., 7 (2). pp. 731-773. Horenko, I. and Dittmer, E. and Lankas, F. and Maddocks, J. and Metzner, Ph. and Schütte, Ch. (2008) Macroscopic Dynamics of Complex Metastable Systems: Theory, Algorithms, and Application to B-DNA. J. Appl. Dyn. Syst., 7 (2). pp. 532-560. Horenko, I. and Dolaptchiev, S. and Eliseev, A. and Mokhov, I. and Klein, R. (2008) Metastable Decomposition of High-Dimensional Meteorological Data with Gaps. Journal of the Atmospheric Sciences, 65 (11). pp. 3479-3496. Pincus, R. and Stevens, B. (2008) Monte Carlo spectral integration: A consistent approximation for radiative transfer in large eddy simulations. Journal of Advancesin Modeling Earth Systems, 1 . p. 9. Doyle, J.D. and Grubišić, V. and Brown, W.O.J. and De Wekker, S.F.J. and Dörnbrack, A. and Jiang, Q. and Mayor, S.D. and Weissman, M. (2008) Observations and Numerical Simulations of Subrotor Vortices during T-REX. J. Atmos. Sci., 66 (5). ISSN Online 1520-0469 Print 0022-4928 Horenko, I. (2008) On Simultaneous Data-Based Dimension Reduction and Hidden Phase Identification. J. Atm. Sci, 65 (6). pp. 1941-1954. Horenko, I. (2008) On robust estimation of low-frequency variability trends in discrete Markovian sequences of atmospheric circulation patterns. J. Atm. Sci. . (In Press) Petoukhov, V. and Eliseev, A. and Klein, R. and Oesterle, H. (2008) On the statistics of the free-troposphere synoptic component. Part I: An evaluation of skewnesses and estimation of the third-order moments contribution to the synoptic-scale dynamics and meridional fluxes of heat and humidity. Tellus, 60 (1). pp. 11-31. Sturm, M. and Andreas, B. and Gröpl, C. and Hussong, R. and Lange, E. and Pfeifer, N. and Schulz-Trieglaff, O. and Zerck, A. and Reinert, K. and Kohlbacher, O. (2008) OpenMS - An open-source software framework for mass spectrometry. BMC Bioinformatics, 9 (163). Noé, F. (2008) Probability Distributions of Molecular Observables computed from Markov Models. J. Chem. Phys., 128 . p. 244103. Fermanian Kammerer, C. and Lasser, C. (2008) Propagation through Generic Level Crossings: A Surface Hopping Semigroup. J. Math. Anal., 40 (1). pp. 103-133. Rausch, T. and Emde, A.-K. and Reinert, K. (2008) Robust consensus computation. BMC Bioinformatics, 9 (Suppl 10). P4. Rausch, T. and Emde, A.-K. and Weese, D. and Notredame, C. and Reinert, K. (2008) Segment-based multiple sequence alignment. Bioinformatics, 24 (16). i187-192. Döring, A. and Weese, D. and Rausch, T. and Reinert, K. (2008) SeqAn -- An efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9 (1). p. 11. Meerbach, E. and Schütte, Ch. (2008) Sequential Change Point Detection in Molecular Dynamics Trajectories. Journal of Multivariate Analysis, submitted . Lasser, C. and Swart, T. (2008) Single switch surface hopping for a model of pyrazine. J. Chem.Phys., 129 (03). 034302. Fermanian Kammerer, C. and Lasser, C. (2008) Single switch surface hopping for molecular dynamics with transitions. J. Chem. Phys., 128 (14). p. 144102. Noé, F. and Daidone, I. and Smith, J. C. and Di Nola, A. and Amadei, A. (2008) Solvent Electrostriction Driven Peptide Folding revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation. J. Phys. Chem. B, 112 . pp. 11155-11163. Baldauf, M. (2008) Stability analysis for linear discretisations of the advection equation with Runge–Kutta time integration. Journal of Computational Physics, 227 (13). pp. 6638-6659. Schulz-Trieglaff, O. and Machtejevas, E. and Reinert, K. and Schlueter, H. and Thiemann, J. and Unger, K. (2008) Statistical Quality Assessment and Outlier Detection for Liquid Chromatography-Mass Spectrometry Experiments. BioDataMining . accepted for publication. (In Press) Hartmann, C. (2008) Structure-preserving model reduction of partially observed differential equations: molecular dynamics and beyond. Oberwolfach Reports, 5 (2). pp. 1111-1115. Schmidt, H. and Oevermann, M. and Bastiaans, R.J.M. and Kerstein, A.R. (2008) Tabulation of turbulent burning rates via a combination of a stochastic mixing model and tabulated chemistry. ZIB Report, 08 (2). Futterer, B. and Gellert, M. and von Larcher, T. and Egbers, C. (2008) Thermal convection in rotating spherical shells: An experimental and numerical approach within GeoFlow. Acta Astronautica, 62 (4). pp. 300-307. Schmidt, H. and Mellado, J.- P. and Peters, N. and Stevens, B. (2008) Towards modular front tracking for Stratocumulus clouds considering unsteady entrainment processes. Geophysical Research Abstracts, 10 . Noé, F. and Fischer, S. (2008) Transition Networks for Modeling the Kinetics of Conformational Change in Macromolecules. Curr. Opin. Struct. Biol., 18 . pp. 154-162. Ruprecht, D. and Schaedle, A. and Schmidt, F. and Zschiedrich, L. (2008) Transparent Boundary Conditions for Time-dependent Problems. SIAM J. Sci. Comput., 30 (5). pp. 2358-2385. ISSN 1064-8275 Mellado, J.- P. and Stevens, B. and Schmidt, H. and Peters, N. (2008) Two-fluid formulation of the cloud-top mixing layer for direct numerical simulation. Theoretical and Computational Fluid Dynamics . (Submitted) Klein, R. (2008) An Unified Approach to Meteorological Modelling Based on Multiple-Scales Asymptotics. Advances in Geosciences, 15 . pp. 23-33. Papke, A. (2008) Wie viele Zahlen müssen es sein? Die Junge Wissenschaft, 79 . pp. 46-51. Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Kornhuber, R. and Ohlberger, M. and Sander, O. (2008) A generic grid interface for parallel and adaptive scientific computing. II: Implementation and tests in DUNE. Computing, 82 (2-3). pp. 121-138. 2007Metzner, Ph. and Horenko, I. and Schütte, Ch. (2007) Generator Estimation of Markov Jump Processes Based on Incomplete Observations Nonequidistant in Time. Phys. Rev. E, 76 (06). 066702. von Kleist, M. and Huisinga, W. (2007) Physiologically Based Pharmacokinetic Modelling: A Sub-Compartmentalized Model of Tissue Distribution. J. Pharmacokin. Pharmacodyn., 34 (6). pp. 789-806. Metzner, Ph. and Dittmer, E. and Jahnke, T. and Schütte, Ch. (2007) Generator Estimation of Markov Jump Processes. J. Comp. Phys., 227 (1). pp. 353-375. Bauer, M. and Klau, G. W. and Reinert, K. (2007) Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics, 8 (1). p. 271. Noé, F. and Horenko, I. and Schütte, Ch. and Smith, J. C. (2007) Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States. J. Chem. Phys., 126 (15). p. 155102. Hartmann, C. and Schütte, Ch. (2007) Comment on Two Distinct Notions of Free Energy. Physica D, 228 (1). pp. 59-63. Lorenz, S. and Diederichs, E. and Telgmann, R. and Schütte, Ch. (2007) Discrimination of Dynamical System Models for Biological and Chemical Processes. J. Comp. Chem., 28 (8). pp. 1384-1399. Jahnke, T. and Huisinga, W. (2007) Solving the Chemical Master Equation for Monomolecular Reaction Systems Analytically. J. Math. Biol., 54 (1). pp. 1-26. Pingen, G. and Waidmann, M. and Evgrafov, A. and Maute, K. (2007) Application of a Parametric Level-Set Approach to Topology Optimization of Fluids with the Navier–Stokes and Lattice Boltzmann Equations. 7th World Congress on Structural and Multidisciplinary Optimization . Mellado, J.- P. and Stevens, B. and Schmidt, H. and Peters, N. (2007) Buoyancy-reversal in cloud-top mixing layers. Quarterly journal of the royal meteorological society . pp. 1-21. Lasser, C. and Swart, T. and Teufel, St. (2007) Construction and validation of a rigorous surface hopping algorithm for conical crossings. Comm. Math. Sci., 5 (4). pp. 789-814. Horenko, I. and Hartmann, C. and Schütte, Ch. and Noé, F. (2007) Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes. Phys. Rev. E, 76 (01). 016706. Lörcher, F. and Gassner, G. and Munz , C.-D. (2007) A Discontinuous Galerkin Scheme Based on a Space–Time Expansion. I. Inviscid Compressible Flow in One Space Dimension. Journal of Scientific Computing, 32 (2). pp. 175-199. ISSN 0885-7474 (Print) 1573-7691 (Online) Gu, W. and Frigato, T. and Straatsma, T. P. and Helms, V. (2007) Dynamic Protonation Equilibrium of Solvated Acetic Acid. Angew. Chem. Int. Ed., 46 (16). pp. 2939-2943. Bodirsky, M. and Gröpl, C. and Kang, M. (2007) Generating labeled planar graphs uniformly at random. Theoretical Computer Science, 379 (3). pp. 377-386. Lange, E. and Gröpl, C. and Schulz-Trieglaff, O. and Leinenbach, A. and Huber, Ch. and Reinert, K. (2007) A Geometric Approach for the Alignment of Liquid Chromatography-Mass Spectrometry Data. Oxford Journals, 23 (13). i273-i281. ISSN 1460-2059 (online), 1367-4803 (print) Fischer, A. and Waldhausen, S. and Horenko, I. and Meerbach, E. and Schütte, Ch. (2007) Identification of Biomolecular Conformations from Incomplete Torsion Angle Observations by Hidden Markov Models. J. Comp. Chem., 28 (15). pp. 2453-2464. Klau, G. W. and Rahmann, S. and Schliep, A. and Vingron, M. and Reinert, K. (2007) Integer Linear Programming Approaches for Non-unique Probe Selection. Discrete Applied Mathematics, 155 . pp. 840-856. Christen, M. and Keller, B. and van Gunsteren, W. F. (2007) Local elevation on the dihedral angles to improve the J-values. Journal of Biomolecular NMR, 39 . pp. 265-273. Lang, J. and Verwer, J. (2007) On Global Error Estimation and Control for Initial Value Problems. SIAM J. Sci. Comp., 29 (4). pp. 1460-1475. ISSN 1064-8275 (print) 1095-7197 (online) Debrabant, K. and Lang, J. (2007) On Global Error Estimation and Control for Parabolic Equations, Report No. 2512. Appl. Num. Math. . (Submitted) Keller, B. and Christen, M. and Oostenbrink, C. and van Gunsteren, W. F. (2007) On using oscillating time-dependent restraints in MD simulation. Journal Of Biomolecular NMR, 37 . pp. 1-14. Noé, F. and Oswald, M. and Reinelt, G. (2007) Optimization in Graphs with Limited Information on the Edge Weights. Operations Research Proceedings 2007. Editors: J. Kalcsics and S. Nickel . pp. 435-440. Noé, F. and Smith, J. C. (2007) Transition Networks: a unifying theme for molecular simulation and computer science. Mathematical Modeling of Biological Systems I, A. Deutsch, L. Brusch, H. Byrne, G. de Vries and H.-P. Herzel (Eds) . pp. 125-144. Bodirsky, M. and Gröpl, C. and Johannsen, D. and Kang, M. (2007) A direct decomposition of 3-connected planar graphs. Séminaire Lotharingien de Combinatoire, B54Ak . 15 pages. Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Ohlberger, M. and Sander, O. (2007) A generic grid interface for parallel and adaptive scientific computing. I: Abstract framework. Computing, 82 (2-3). pp. 103-119. Noé, F. and Smith, J. C. and Schütte, Ch. (2007) A network-based approach to biomolecular dynamics. From Computational Biophysics to Systems Biology (CBSB07). Editors: U. H. E. Hansmann, J. Meinke, S. Mohanty and O. Zimmermann, NIC Se . 2006Schäfer-Bung, B. and Bonačić-Koutecký, V. and Sauer, F. and Weber, S. and Wöste, L. and Lindinger, A. (2006) Isotope selective photoionization of NaK by optimal control: Theory and experiment. J. Chem. Phys., 125 (21). 214310-1-214310-8. Oevermann, M. and Klein, R. (2006) A cartesian grid finite volume method for the solution of the Poisson equation with variable coefficients and embedded interfaces. Journal of Computational Physics, 219 (2). 749-769 . Schäfer-Bung, B. and Mitrić, R. and Bonačić-Koutecký, V. (2006) Photostabilization of ultracold Rb2 molecules by optimal control. J. Phys. B, 39 (19). S1043-S1053. Bastian, P. and Blatt, M. and Engwer, C. and Dedner, A. and Klöfkorn, R. and Kuttanikkad, S. P. and Ohlberger, M. and Sander, O. (2006) The Distributed and Unified Numerics Environment (DUNE). Proc. of the 19th Symposium on Simulation Technique . Bernhard, S. (2006) Transient integral boundary layer method to calculate the translesional pressure drop and the fractional flow reserve in myocardial bridges. BioMedical Engineering OnLine, 5 (42). Kornhuber, R. and Krause, R. (2006) Robust multigrid methods for vector-valued Allen-Cahn equations with logarithmic free energy. Computing and Visualization in Science, 9 (2). pp. 103-116. ISSN 1432-9360 Krause, R. and Sander, O. (2006) Automatic construction of boundary parametrizations for geometric multigrid solvers. Computing and Visualization in Science, 9 (1). pp. 11-22. ISSN 1432-9360 Bonačić-Koutecký, V. and Mitrić, R. and Bürgel, Ch. and Schäfer-Bung, B. (2006) Cluster Properties in the regime in which each atom counts. Comput. Mater. Sci., 35 (3). pp. 151-157. Oevermann, M. and Klein, R. (2006) A cartesian grid finite volume method for the solution of the Poisson equation with variable coefficients and embedded interfaces. JCP . Gebauer, S. and Kornhuber, R. and Yserentant, H. (2006) Hierarchical decomposition of domains with fractures. Mathematics of Computation, 75 (253). pp. 73-90. ISSN 00255718 Caselles, V. and Igual, L. and Sander, O. (2006) An axiomatic approach to scalar data interpolation on surfaces. Numerische Mathematik, 102 (3). pp. 383-411. ISSN 0029-599X Imhof, P. and Noé, F. (2006) AM1/d Parameters for Magnesium in Metalloenzymes. J. Chem. Theo. Comput., 2 . pp. 1050-1056. Mayr, B. M. and Kohlbacher, O. and Reinert, K. and Gröpl, C. and Lange, E. and Klein, C. L. and Huber, Ch. (2006) Absolute Myoglobin Quantitation in Serum by Combining Two-Dimensional Liquid Chromatography-Electrospray Ionization Mass Spectrometry and Novel Data Analysis Algorithms. Journal of Proteome Research, 5 . pp. 414-421. Wolski, W. E. and Farrow, M. and Emde, A.-K. and Maciej, L. and Lehrach, H. and Reinert, K. (2006) Analytical model of peptide mass cluster centres with applications. Proteome Science, 4 (18). doi:10.1186/1477-5956. Horenko, I. and Dittmer, E. and Fischer, A. and Schütte, Ch. (2006) Automated Model Reduction for Complex Systems exhibiting Metastability. Mult. Mod. Sim., 5 (3). pp. 802-827. Conrad, T. O. F. and Leichtle, A. and Hagehülsmann, A. and Diederichs, E. and Baumann, S. and Thiery, J. and Schütte, Ch. (2006) Beating the Noise: New Statistical Methods for Detecting Signals in MALDI-TOF Spectra Below Noise Level. Lecture Notes in Computer Science, 4216 . pp. 119-128. Althaus, E. and Caprara, A. and Lenhof, H.-P. and Reinert, K. (2006) A Branch-and-Cut Algorithm for Multiple Sequence Alignment. Mathematical Programming (105). pp. 387-425. Noé, F. and Oswald, M. and Reinelt, G. and Smith, J. C. and Fischer, S. (2006) Computing Best Transition Pathways in High-Dimensional Dynamical Systems. Multisc. Model. Sim., 5 . pp. 393-419. Metzner, Ph. and Schütte, Ch. and Vanden-Eijnden, E. (2006) Illustration of Transition Path Theory on a Collection of Simple Examples. J. Chem. Phys., 125 (8). 084110. Futterer, B. and Gellert, M. and Huschto, M. and von Larcher, T. and Egbers, C. (2006) Microgravity Science on International Space Station (ISS): The Geoflow Experiment. Forum der Forschung, 10. Jahrgang (19). pp. 113-118. ISSN 0947-6989 Deuflhard, P. and Ertel, S. and Kornhuber, R. and Krause, R. and Sander, O. (2006) Patient-specific simulation of dynamic stress distribution in the human knee. Journal of Biomechanics, 39 . p. 47. ISSN 0021-9290 Becker, T. and Fischer, S. and Noé, F. and Tournier, A. and Ullmann, M. and Kurkal, V. and Smith, J. C. (2006) Physical and functional aspects of protein dynamics. Soft Condensed Matter Physics in Molecular and Cell Biology, Poon & Andelman (Eds) . Klein, R. and Majda, A. J. (2006) Systematic Multiscale Models for Deep Convection on Mesoscales. Theoretical and Computational Fluid Dynamics, 20 (5-6). pp. 525-551. ISSN 0935-4964 (Print) 1432-2250 (Online) Kiljunen, T. and Schmidt, B. and Schwentner, N. (2006) Time-Dependent Alignment of Molecules Trapped in Octahedral Crystal Fields. J. Chem. Phys., 124 (16). p. 164502. Noé, F. and Krachtus, D. and Smith, J. C. and Fischer, S. (2006) Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins. J. Chem. Theo. Comput., 2 . pp. 840-857. Waidmann, M. and Waidmann, C. and Saile, D. and Grillmayer, G. (2006) Use of new developments on attitude control sensors for the microsatellite Flying Laptop. Proceedings of the 57th IAC/IAF/IAA, Valencia, Spain . Sander, O. (2006) A fast solver for finite deformation contact problems. Preprint A-06-02 . (Unpublished) 2005Bernhard, S. (2005) Oscillatory flow in a tube with time-dependent wall deformation and its application to Myocardial Bridges. ESAIM: Proc., 14 . pp. 25-40. Horenko, I. and Lorenz, S. and Schütte, Ch. and Huisinga, W. (2005) Adaptive Approach for Non-Linear Sensitivity Analysis of Reaction Kinetics. J. Comp. Chem., 26 (9). pp. 941-948. Lorenz, K. and Jahnke, T. and Lubich, Ch. (2005) Adiabatic Integrators for Highly Oscillatory Second-Order Linear Differential Equations with Time-Varying Eigendecomposition. BIT Num. Math., 45 (1). pp. 91-115. Kiljunen, T. and Schmidt, B. and Schwentner, N. (2005) Aligning and Orienting Molecules Trapped in Octahedral Crystal Fields. Phys. Rev. A, 72 (5). 053415. Antony, J. and von Helden, G. and Meijer, G. and Schmidt, B. (2005) Anharmonic Midinfrared Vibrational Spectra of Benzoic Acid Monomer and Dimer. J. Chem. Phys., 123 (1). 014305. Noé, F. and Ille, F. and Smith, J. C. and Fischer, S. (2005) Automated Computation of Low-Energy Pathways for Complex Rearrangements in Proteins: Application to the conformational switch of Ras p21. Proteins, 59 . pp. 534-544. Wolski, W. E. and Lalowski, M. and Jungblut, P. and Reinert, K. (2005) Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants. BMC Bioinformatics, 6 (203). http://www.biomedcentral.com/1471-2105/6/203. Hartmann, C. and Schütte, Ch. (2005) A Constrained Hybrid Monte-Carlo Algorithm and the Problem of Calculating the Free Energy in Several Variables. Z. Angew. Math. Mech., 85 (10). pp. 700-710. von Larcher, T. and Egbers, C. (2005) Dynamics of baroclinic wave pattern in transition zones between different flow regimes. Journal of Physics: Conference Series, 14 . pp. 162-167. Owinoh, A.Z. and Hunt, J. and Orr, A. and Clark, P. and Klein, R. and Fernando, H. and Nieuwstadt, F. (2005) Effects Of Changing Surface Heat Flux On Atmospheric Boundary-Layer Flow Over Flat Terrain. Boundary Layer Meterology, 116 (2). pp. 331-361. Meerbach, E. and Schütte, Ch. and Fischer, A. (2005) Eigenvalue Bounds on Restrictions of Reversible Nearly Uncoupled Markov Chains. Lin. Alg. Appl., 398 . pp. 141-160. von Larcher, T. and Egbers, C. (2005) Experiments on transitions of baroclinic waves in a differentially heated rotating annulus. Nonlinear Processes in Geophysics, 12 . pp. 1033-1041. ISSN 1023-5809 (Print); 1607-7946 (Online) Schmidt, H. and Klein, R. (2005) Flexible flame structure modelling in a flame front tracking scheme. Analysis and Numerics for Conservation Laws . pp. 405-427. ISSN 978-3-540-24834-7 (Print) 978-3-540-27907-5 (Online) Hartmann, C. and Schütte, Ch. (2005) A Geometric Approach to Constrained Molecular Dynamics and Free Energy. Comm. Math. Sci., 3 (1). pp. 1-20. Kiljunen, T. and Schmidt, B. and Schwentner, N. (2005) Intense-Field Alignment of Molecules Confined in Octahedral Field. Phys. Rev. Lett., 94 (12). p. 123003. Klein, R. (2005) Multiple spacial scales in engineering and atmospheric low Mach number flows. ESAIM: Mathematical Modelling and Numerical Analysis (M2AN), 39 . pp. 537-559. ISSN 0764-583X Antony, J. and Schmidt, B. and Schütte, Ch. (2005) Nonadiabatic Effects on Peptide Vibrational Dynamics Induced by Conformational Changes. J. Chem. Phys., 122 (1). 014309. Gonzalez, L. and Manz, J. and Schmidt, B. and Shibl, M. F. (2005) Optical resolution of oriented enantiomers via photodissociation: Quantum simulations for H2POSD. Phys. Chem. Chem. Phys., 7 (24). pp. 4096-4101. Lasser, C. and Teufel, St. (2005) Propagation through conical crossings: An asymptotic semigroup. Comm. Pure Appl. Math., 58 (9). pp. 1188-1230. Schatzmann, M. and Britter, R. (2005) Quality assurance and improvement of micro-scale meteorological models. International Journal of Environment and Pollution . (Submitted) Horenko, I. and Dittmer, E. and Schütte, Ch. (2005) Reduced Stochastic Models for Complex Molecular Systems. Comp. Vis. Sci., 9 (2). pp. 89-102. Klein, C. L. and Kohlbacher, O. and Reinert, K. (2005) Reference methods and materials in standardisation and quality assurance (abstract). FEBS Journal, 272 (Supplement 1). pp. 490-504. Dellnitz, M. and Neumann, M. and Schütte, Ch. (2005) Special Issue on Matrices and Mathematical Biology. Lin. Alg. Appl., 398 . pp. 1-245. Wolski, E. and Lalowski, M. and Martus, P. and Giavalisco, P. and Gobom, J. and Sickmann, A. and Lehrach, H. and Reinert, K. (2005) Transformation and other factors of the peptide mass spectormetry pairwise peaklist comparison process. BMC Bioinformatics, 6 (285). http://www.biomedcentral.com/1471-2105/6/285. 2004Conrad, T. O. F. (2004) New Approaches for Visualizing and Analyzing Metabolic Pathways. Proceedings of the Second Australian Undergraduate Students’ Computing Conference . Schäfer-Bung, B. and Mitrić, R. and Bonačić-Koutecký, V. and Bartelt, A. and Lupulescu, C. and Lindinger, A. and Vajda, Š. and Weber, S. and Wöste, L. (2004) Optimal control of ionization processes in NaK; comparison between theory and experiment. J. Phys. Chem. A, 108 (19). pp. 4175-4179. Schütte, Ch. and Walter, J. and Hartmann, C. and Huisinga, W. (2004) An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations. Multiscale Model. Simul., 2 (3). pp. 501-526. Walter, J. and Schütte, Ch. and Pavliotis, G. A. and Stuart, A. (2004) Averaging of Stochastic Differential Equations: Kurtz's Theorem Revisited. preprint . Kohlbacher, O. and Reinert, K. (2004) Differenzielle Proteomanalyse -- Experimentelle Methoden, Algorithmische Herausforderungen. it -- Information technology, 46 . pp. 31-38. Preis, R. and Dellnitz, M. and Hessel, M. and Schütte, Ch. and Meerbach, E. (2004) Dominant Paths Between Almost Invariant Sets of Dynamical Systems. preprint . Helling, Ch. and Klein, R. and Woitke, P. and Nowak, U. and Sedlmayr, E. (2004) Dust in brown dwarfs. IV. Dust formation and driven turbulence on mesoscopic scales. Astronomy and astrophysics, 423 (2). pp. 657-675. ISSN 0004-6361 Horenko, I. and Weiser, M. and Schmidt, B. and Schütte, Ch. (2004) Fully Adaptive Propagation of the Quantum-Classical Liouville Equation. J. Chem. Phys., 120 (19). pp. 8913-8923. Jahnke, T. (2004) A Long-Time-Step Method for Quantum-Classical Molecular Dynamics. SIAM J. Sci. Comp., 25 (6). pp. 2145-2164. Klein, R. and Mikusky, E. and Owinoh, A.Z. (2004) Multiple Scales Asymptotics for Atmospheric Flows. Proceedings of the 4th European Conference on Mathematics . Ronen, S. and Nachtigallova, D. and Schmidt, B. and Jungwirth, P. (2004) Non-Adiabatic Chemical Reaction Triggered by Electron Photodetachment: An ab initio Quantum Dynamical Study. Phys. Rev. Lett., 93 (4). 048301. Gröpl, C. and Prömel, H.-J. and Srivastav, A. (2004) Ordered binary decision diagrams and the Shannon effect. Discrete Applied Mathematics, 142 . pp. 67-85. Huisinga, W. and Meyn, S. and Schütte, Ch. (2004) Phase Transitions and Metastability in Markovian and Molecular Systems. Ann. Appl. Prob., 14 (1). pp. 419-458. Kiljunen, T. and Bargheer, M. and Gühr, M. and Schwentner, N. and Schmidt, B. (2004) Photodynamics and Ground State Librational States of ClF Molecule in solid Ar. Comparison of experiment and theory. Phys. Chem. Chem. Phys., 6 (11). pp. 2932-2939. Fujimura, Y. and Gonzalez, L. and Kröner, D. and Manz, J. and Mehdaoui, I. and Schmidt, B. (2004) Quantum Ignition of Intramolecular Rotation by Means of IR+UV Laser Pulses. Chem. Phys. Lett., 386 (4-6). pp. 248-253. Korolkov, M. V. and Schmidt, B. (2004) Quantum Molecular Dynamics Driven by Short and Intense Light Pulses: Towards the Limits of the Floquet Picture. Comp. Phys. Comm., 161 (1-2). pp. 1-17. Botta, N. and Klein, R. and Langenberg, S. and Lützenkirchen, S. (2004) Well Balanced Finite Volume Methods for Nearly Hydrostatic Flows. Journal of Computational Physics, 196 (2). pp. 539-565. Istrail, S. and Sutton, G. G. and Florea, L. and Mobarry, C. M. and Lippert, R. and Walenz, B. and Shatkay, H. and Dew, Ian and Miller, J. R. and Flanigan, M. J. and Edwards, N. J. and Bolanos, R. and Fasulo, D. and Halldorsson, B. V. and Hannenhalli, S. and Turner, R. J. and Yooseph, S. and Lu, Fu and Nusskern, D. R. and Shue, B. C. and Zheng, X. H. and Zhong, F. and Delcher, A. L. and Huson, D. H. and Kravitz, S. A. and Mouchard, L. and Reinert, K. and Remington, K. A. and Clark, A. G. and Waterman, M. S. and Eichler, E. E. and Adams, M. D. and Hunkapillar, M. W. and Myers, E. W. and Venter, J. C. (2004) Whole-genome shotgun assembly and comparison of human genome assemblies. Proceedings of the national academy of science (PNAS), 101 (7). pp. 1916-1921. Klein, R. (2004) An applied mathematical view of meteorological modeling. Applied Mathematics Entering the 21st century; Invited talks from the ICIAM 2003 Congress., 116 . pp. 177-219. Audusse, E. and Bouchut, F. and Bristeau, M.O. and Klein, R. and Perthame, B. (2004) A fast and stable well-balanced scheme with hydrostatic reconstruction for shallow water flows. Journal of Scientific Computation, 25 (6). pp. 2050-2065. 2003Krah, A. and Schmidt, F. and Becher, D. and Schmid, M. and Albrecht, D. and Rack, A. and Büttner, K. and Jungblut, P. (2003) Analysis of Automatically Generated Peptide Mass Fingerprints of Cellular Proteins and Antigens from Helicobacter pylori 26695 Separated by Two-dimensional Electrophoresis. Molecular & Cellular Proteomics, 2 (12). pp. 1271-1283. Frömmel, C. and Gille, Ch. and Goede, A. and Gröpl, C. and Hougardy, S. and Nierhoff, T. and Preissner, R. and Thimm, M. (2003) Accelerating screening of 3D protein data with a graph theoretical approach. Bioinformatics, 19 (18). pp. 2442-2447. Munz , C.-D. and Roller , S. and Klein, R. and Geratz, K. J. (2003) The extension of incompressible flow solvers to the weakly compressible regime. Computers & fluids , 32 (2). 173-196 (31 ref.). ISSN 0045-7930 Horenko, I. and Weiser, M. (2003) Adaptive Integration of Molecular Dynamics. J. Comp. Chem., 24 (15). pp. 1921-1929. Noé, F. and Schwarzl, S. and Fischer, S. and Smith, J. C. (2003) Computational tools for analysing structural changes in proteins in solution. Applied Bioinformatics, 2 . pp. 11-17. Cockburn, B. (2003) Discontinuous Galerkin methods. ZAMM - Zeitschrift für Angewandte Mathematik und Mechanik, 83 (11). 731 -754. Huisinga, W. and Schütte, Ch. and Stuart, A. M. (2003) Extracting Macroscopic Stochastic Dynamics: Model Problems. Comm. Pure Appl. Math., 56 (2). pp. 234-269. Berninger, H. and Werner, Dirk (2003) Lipschitz spaces and M-ideals. Extracta Mathematicae, 18 (1). pp. 33-56. ISSN 0213-8743 Wohlmuth, B. and Krause, R. (2003) Monotone methods on non-matching grids for non-linear contact problems. SIAM J. Sci. Comput., 25 (1). pp. 324-347. ISSN 1064-8275 Becker, T. and Fischer, S. and Noé, F. and Ullmann, M. and Tournier, A. and Smith, J. C. (2003) Protein Dynamics: Glass Transition and Mechanical Function. Advances in Solid State Physics, 43 . pp. 677-694. Majda, A.J. and Klein, R. (2003) Systematic Multiscale Models for the Tropics. Journal of Atmospheric Sciences, 60 . pp. 393-408. Fermanian Kammerer, C. and Lasser, C. (2003) Wigner measures and codimension two crossings. J. Math. Phys., 44 (2). pp. 507-557. Schmidt, H. and Klein, R. (2003) A generalized level-set/in-cell-reconstruction method for accelerating turbulent premixed flames. Combustion Theory and Modelling, 7 (2). 243-267(25). 2002Krause, R. and Wohlmuth, B. (2002) A Dirichlet-Neumann type algorithm for contact problems with friction. Computing and Visualization in Science, 5 (3). pp. 139-148. ISSN 1432-9360 Kornhuber, R. (2002) On constrained Newton linearization and multigrid for variational inequalities. Numerische Mathematik, 91 (4). pp. 699-721. ISSN 0029-599X Mural, Richard and Adams, M. D. and Reinert, K. (2002) A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome. Science, 296 . pp. 1661-1671. Huson, D. H. and Reinert, K. and Myers, E. W. (2002) The Greedy Path-Merging Algorithm for Sequence Assembly. Journal of the ACM, 49 (5). pp. 603-615. Horenko, I. and Schmidt, B. and Schütte, Ch. (2002) Multidimensional Classical Liouville Dynamics with Quantum Initial Conditions. J. Chem. Phys., 117 (10). pp. 4643-4650. Klein, R. (2002) Numerical Methods for High and Low Speed Combustion Simulations. Numerical Methods for High and Low Speed Combustion Simulations. PDE's in models of superfluidity, superconductivity and reactive flows, Nato S (569). pp. 491-506. Roeselova, M. and Mucha, M. and Schmidt, B. and Jungwirth, P. (2002) Quantum dynamics and spectroscopy of photodetachment in Cl-...H2O and Cl-...D2O complexes. J. Phys. Chem. A, 106 (51). pp. 12229-12241. Horenko, I. and Salzmann, Ch. and Schmidt, B. and Schütte, Ch. (2002) Quantum-Classical Liouville Approach to Molecular Dynamics: Surface Hopping Gaussian Phase-Space Packets. J. Chem. Phys., 117 (24). pp. 11075-11088. Bailey, J. A. and Gu, Z. and Clark, R. A. and Reinert, K. and Samonte, R. V. and Schwartz, S. S. and Adams, M. D. and Myers, E. W. and Li, P. and Eichler, E. E. (2002) Recent Segmental Duplications in the Human Genome. Science, 297 . pp. 1003-1007. Korolkov, M. V. and Schmidt, B. (2002) Spin-Orbit Induced Association under Ultrafast Laser Pulse Control. Chem. Phys. Lett., 361 (5-6). pp. 432-438. Gröpl, C. and Hougardy, S. and Nierhoff, T. and Prömel, H.-J. (2002) Steiner trees in uniformly quasi-bipartite graphs. Information Processing Letters, 83 . pp. 195-200. Manz, J. and Proppe, B. and Schmidt, B. (2002) Time-Resolved Dual Fluorescence of 1-Phenylpyrrole in Acetonitrile: Molecular Dynamics Symulations of Solvent Response to Twisted Intramolecular Charge Transfer. Phys. Chem. Chem. Phys., 4 (10). pp. 1876-1881. Berghof, V. and Martins, M. and Schmidt, B. and Schwentner, N. (2002) Vibrational Overtones and Rotational Structures of HCl in Rare Gas Matrices. J. Chem. Phys., 116 (21). pp. 9364-9373. 2001Kornhuber, R. and Krause, R. (2001) Adaptive multigrid methods for Signorini's problem in linear elasticity. Computing and Visualization in Science, 4 (1). pp. 9-20. ISSN 1432-9360 Krause, R. and Wohlmuth, B. (2001) Domain decomposition methods on nonmatching grids and some applications to linear elasticity problems. Zeitschrift für angewandte Mathematik und Mechanik (ZAMM), 81 (Suppl.). pp. 21-24. ISSN 0044-2267 Kober, C. and Müller-Hannemann, M. (2001) A case study in hexahedral mesh generation: Simulation of the human mandible. Engineering with Computers, 17 (3). pp. 249-260. ISSN 0177-0667 Schäfer-Bung, B. and Engels, B. and Taylor, T. and Neumark, P. and Botschwina, P. and Perić, M. (2001) Measurement and theoretical simulation of the HCCO- anion photoelectron spectrum. J. Chem. Phys., 115 (4). pp. 1777-1788. Klein, R. and Botta, N. and Schneider, T. and Munz, C.D. and Roller, S. and Meister, A. and Hoffmann, L. and Sonar, T. (2001) Asymptotic adaptive methods for multi-scale problems in fluid mechanics. Journal of Engineering Mathematics, 39 (1). pp. 261-343. ISSN 0022-0833 (Print) 1573-2703 (Online) Helling, Ch. and Oevermann, M. and Lüttke, M. J. H. and Klein, R. (2001) Dust in Brown Dwarfs I. Dust formation under turbulent conditions on microscopic scales. Astronomy & Astrophysics, - (), 376 . pp. 194-212. Gröpl, C. and Prömel, H.-J. and Srivastav, A. (2001) On the Evolution of the Worst-Case OBDD Size. Information Processing Letters, 77 . pp. 1-7. Chaban, G. and Gerber, R. B. and Korolkov, M. V. and Manz, J. and Niv, M. Y. and Schmidt, B. (2001) Photodissociation Dynamics of Molecular Fluorine in an Argon Matrix Induced by Ultrashort Laser Pulses. J. Phys. Chem. A, 105 (12). pp. 2770-2782. Slavicek, P. and Roeselova, M. and Jungwirth, P. and Schmidt, B. (2001) Preference of Cluster Isomers as a Result of Quantum Delocalization: Potential Energy Surfaces and Intermolecular Vibrational States of Ne...HBr, Ne...HI, and HI(Ar)n (n=1-6). J. Chem. Phys., 114 (4). pp. 1539-1548. Venter, J. C. and Adams, M. D. and Myers, E. W. and Reinert, K. and et al, . (2001) The Sequence of the Human Genome. Science, 291 (5507). pp. 1304-1351. Horenko, I. and Schmidt, B. and Schütte, Ch. (2001) A Theoretical Model for Molecules Interacting with Intense Laser Pulses: The Floquet-based Quantum-Classical Liouville Equation. J. Chem. Phys., 115 (13). pp. 5733-5743. Schmidt, H. and Klein, R. (2001) Towards a Generalized Level-Set/In-Cell Reconstruction Approach for Accelerating Turbulent Premixed Flames. Wohlmuth, B. and Krause, R. (2001) A multigrid method based on the unconstrained product space for Mortar finite element discretizations. SIAM Journal on Numerical Analysis, 39 (1). pp. 192-213. ISSN 0036-1429 2000Knio, O.M. and Klein, R. (2000) Improved Thin Tube Methods for Slender Vortex Simulations. Journal of Computational Physics, 162 (1). 68-82(15). Klein, R. (2000) Asymptotic Analyses for Atmospheric Flows and the Construction of Asymptotically Adaptive Numerical Methods. ZAMM ·Zeitschrift für angewandte Mathematik und Mechanik, 80 (11-12). pp. 765-785. ISSN 0044-2267 Huisinga, W. (2000) The Essential Spectral Radius and Asymptotic Properties of Transfer Operators. preprint . Kober, C. and Sader, R. and Thiele, H. and Bauer, H.-J. and Zeilhofer, H.-F. and Hoffmann, K.-H. (2000) FEM simulations versus biomechnical experiments concerning the human mandible: a comparision of the results of a frontal and a molar biting study. Preprint A-21-2000 . (Unpublished) UNSPECIFIED (2000) The Genome Sequence of Drosophila melanogaster. Science, 287 (5461). pp. 2185-2195. Deuflhard, P. and Huisinga, W. and Fischer, A. and Schütte, Ch. (2000) Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains. Lin. Alg. Appl., 315 (1-3). pp. 39-59. Reinert, K. and Stoye, J. and Will, T. (2000) An Iterative Methods for Faster Sum-of-Pairs Multiple Sequence Alignment. BIOINFORMATICS, 16 (9). pp. 808-814. Klein, R. and Münch, M. (2000) Models and Criteria for Prediction of Deflagration to Detonation Transition (DDT) in Hydrogen-Air-Steam Systems under Severe Accident Conditions. Numerical Techniques , 9, Reihe Energietechnik / Energy Technology. . pp. 83-102. Klein, R. and Rehm, W. (2000) Models and Criteria for Prediction of Deflagration-to- Detonation Transition (DDT) in Hydrogen-Air-Steam Systems under Severe Accident Conditions. Schriften des Forschungszentrums Jülich, Energy Technology Series, 9 . ISSN ISBN 3-89336-258-4 Krause, R. and Wohlmuth, B. (2000) Nonconforming decomposition methods: Techniques for linear elasticity. East-West Journal of Numerical Mathematics, 8 (3). pp. 177-206. ISSN 1569-3953; 0928-0200 Kececioglu, J. D. and Lenhof, H.-P. and Mehlhorn, K. and Reinert, K. and Vingron, M. (2000) A Polyhedral Approach to Sequence Alignment Problems. Discrete Applied Mathematics, 104 . pp. 143-186. Lermen, M. and Reinert, K. (2000) The Practical Use of the A* Algorithm for Exact Multiple Sequence Alignment. Journal of Computational Biology . pp. 655-671. Gerber, R. B. and Korolkov, M. V. and Manz, J. and Niv, M. Y. and Schmidt, B. (2000) A Reflection Principle for the Control of Molecular Photodissociation in Solids: Model Simulation for F2 in Ar. Chem. Phys. Lett., 327 (1-2). pp. 76-84. Schmidt, B. and Zdanska, P. (2000) Solution of the Time-Dependent Schrödinger Equation for Highly Symmetric Potentials. Comp. Phys. Comm., 127 (2-3). pp. 290-308. Breitung, W. and Chan, C. and Dorofeev, S.B. and Eder, A. and Gelfand, B.E. and Heitsch, M. and Klein, R. and Malliakos, A. and Shepherd, J.E. and Studer, E. and Thibault, P. (2000) State of Art Report on Flame Acceleration and DDT in Nuclear Reactor Safety. OECD . Fischer, A. (2000) An Uncoupling-Coupling Technique for Markov Chain Monte Carlo Methods. preprint . Myers, E. W. and Sutton, G. G. and Delcher, A. L. and Dew, D. P. and Flanigan, M. J. and Kravitz, S. A. and Mobarry, C. M. and Reinert, K. and Remington, K. A. and Anson, E. L. and Bolanos, R. and Chou, H.-H. and Jordan, C. M. and Halpern, A. L. and Lonardi, S. and Beasly, E. M. and Brandon, R. C. and Chen, L. and Dunn, P. J. and Lai, Z. and Liang, Y. and Nusskern, D. R. and Zhan, M. and Zhang, Q. and Zheng, X. H. and Rubin, G. M. and Adams, M. D. and Venter, J. C. (2000) A Whole-Genome Assembly of Drosophila. Science, 287 (5461). pp. 2196-2203. 1999Reinecke , M. and Hillebrandt , W. and Niemeyer , J.C. and Klein, R. and Gröbl, A. (1999) A new model for deflagration fronts in reactive fluids. Astronomy and Astrophysics, 347 (1999A&A...347..724R). 724-733 . ISSN 0004-6361 (Print) 1432-0746 (Online) Bornemann, F. A. and Schütte, Ch. (1999) Adaptive Accuracy Control for Car-Parrinello Simulations. Num. Math., 83 (2). pp. 179-186. Schütte, Ch. (1999) Conformational Dynamics: Modelling, Theory, Algorithm, and Application to Biomolecules. preprint . Backhaus, P. and Schmidt, B. and Dantus, M. (1999) Control of Photoassociation Yield: A Quantum Dynamical Study of the Mercury System to Explore the Role of Pulse Duration from Nanoseconds to Femtoseconds. Chem. Phys. Lett., 306 (1-2). pp. 18-24. Schütte, Ch. and Fischer, A. and Huisinga, W. and Deuflhard, P. (1999) A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo. J. Comp. Phys, 151 (1). pp. 146-168. Schneider, T. and Botta, N. and Geratz, K. J. and Klein, R. (1999) Extension of finite volume compressible flow solvers to multidimensional, variable density zero Mach number flows. J. Comput. Phys., 155 . pp. 248-286. Huisinga, W. and Pesce, L. and Kosloff, R. and Saalfrank, P. (1999) Faber and Newton Polynomial Integrators for Open-System Density Matrix Propagation. J. Chem. Phys., 110 (12). pp. 5538-5547. Huisinga, W. and Best, Ch. and Roitzsch, R. and Schütte, Ch. and Cordes, F. (1999) From Simulation Data to Conformational Ensembles: Structure and Dynamics based Methods. J. Comp. Chem., 20 (16). pp. 1760-1774. Fischer, A. and Cordes, F. and Schütte, Ch. (1999) Hybrid Monte Carlo with adaptive temperature choice: Efficient conformational analysis of RNA. Comp. Phys. Comm., 121 . pp. 37-39. Worlikar, A.S. and Aniruddha, S. and Knio, O.M. and Klein, R. (1999) Numerical Study of the Effective Impedance of a Thermoacoustic Stack. Acta Acustica united with Acustica, 85 (4,). pp. 480-494. ISSN 1610-1928 Bornemann, F. A. and Schütte, Ch. (1999) On the Singular Limit of the Quantum-Classical Molecular Dynamics Model. J. Appl. Math., 59 (4). pp. 1208-1224. Zdanska, P. and Schmidt, B. and Jungwirth, P. (1999) Photolysis of Hydrogen Chloride Embedded in the First Argon Solvation Shell: Rotational Control and Quantum Dynamics of Photofragments. J. Chem. Phys., 110 (13). pp. 6246-6256. Schmidt, B. (1999) Quantum Dynamics of HF Photodissociation in Icosahedral Ar12HF Clusters: Rotational Control of the Hydrogen Atom Cage Exit. Chem. Phys. Lett., 301 (3-4). pp. 207-216. Lenhof, H.-P. and Morgenstern, B. and Reinert, K. (1999) An exact solution for the segment-to-segment multiple sequence alignment problem. BIOINFORMATICS, 15 (3). pp. 203-210. 1998Berkenbosch, A. and Kaasschieter, E. and Klein, R. (1998) Detonation capturing for stiff combustion chemistry. Combustion Theory and Modelling, 2 (3). 313-348(36). Worlikar, A.S. and Knio, O.M. and Klein, R. (1998) Numerical Simulation of a Thermoacoustic Refrigerator II. Stratified Flow around the Stack. Journal of Computational Physics, 144 (2). 299-324(26). Knio, O.M. and Ting, L. and Klein, R. (1998) Interaction of a Slender Vortex Filament with a Rigid Sphere: Dynamics and far-field noise. J. Acoustical Soc. of America, 103 (1). 83 -98. ISSN 0001-4966 (print) Backhaus, P. and Manz, J. and Schmidt, B. (1998) Effect of Rotations and Shape Resonances on Photoassociation and Photoacceleration by Ultrashort Infrared Laser Pulses. J. Phys. Chem. A, 102 (23). pp. 4118-4128. Fischer, A. and Cordes, F. and Schütte, Ch. (1998) Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble: Efficient conformational analysis of RNA. J. Comp. Chem., 19 (15). pp. 1689-1697. Ring, S. and Schmidt, B. and Baumgärtel, H. (1998) Ionization of Rydberg Atoms in THz-Laser Fields at the Transition from Low to High Scaled Frequencies. Eur. Phys. J. D, 3 (2). pp. 155-158. Jungwirth, P. and Zdanska, P. and Schmidt, B. (1998) Librational control of photochemical reactions in small clusters. J. Phys. Chem. A, 102 (37). pp. 7241-7244. Lenhof, H.-P. and Reinert, K. and Vingron, M. (1998) A Polyhedral Approach to RNA Sequence Structure Alignment. Journal of Computational Biology, 5 (3). pp. 517-530. Nettesheim, P. (1998) Second Order Transitions in Quantum-Classical Molecular Dynamics. preprint . Korolkov, M. V. and Schmidt, B. (1998) Vibrationally State-Selective Laser Pulse Control of Electronic Branching in OH (X 2Pi/A 2Sigma+) Photoassociation. Chem. Phys., 237 (1-2). pp. 123-138. Bornemann, F. A. and Schütte, Ch. (1998) A mathematical investigation of the Car-Parrinello Method. Num. Math., 78 (3). pp. 359-376. 1997Smiljanovski, V. and Moser, V. and Klein, R. (1997) A Capturing/Tracking Hybrid Scheme for Deflagration Discontinuities. Combustion Theory and Modelling, 1 (2). 183-215 . Backhaus, P. and Schmidt, B. (1997) Femtosecond Quantum Dynamics of Photoassociation Reactions: The Exciplex Formation of Mercury. Chem. Phys., 217 (2-3). pp. 131-143. Schütte, Ch. and Bornemann, F. A. (1997) Homogenization Approach to Smoothed Molecular Dynamics. Nonlinear Analysis, 30 (3). pp. 1805-1814. Bornemann, F. A. and Schütte, Ch. (1997) Homogenization of Hamiltonian Systems with a Strong Constraining Potential. Physica D, 102 (1-2). pp. 57-77. Korolkov, M. V. and Schmidt, B. (1997) Infrared Picosecond Laser Control of Acceleration of Neutral Atoms: Model Simulations for the Collision Pair O + H. Chem. Phys. Lett., 272 (1-2). pp. 96-102. Worlikar, A.S. and Knio, O.M. and Klein, R. (1997) Numerical Simulation of a Thermo-Acoustic Refrigerator. Vortex Flows and Related Numerical Methods II . Manz, J. and Saalfrank, P. and Schmidt, B. (1997) Quantum Dynamical Aspects of Rotationally and Vibrationally Mediated Photochemistry in Matrices and at Surfaces: HCl/DCl in Ar, and NH3/ND3 at Cu(111). J. Chem. Soc. Faraday Trans., 93 (5). pp. 957-967. Jungwirth, P. and Schmidt, B. (1997) Quantum dynamics following electron photodetachment in the I-Ar2 complex: How Good Are New Separable and Non-Separable Simulation Methods? Chem. Phys. Lett., 275 (3-4). pp. 127-136. Jungwirth, P. and Schmidt, B. and Moiseyev, N. (1997) Vibrationally Resolved Spectra from Short Time Quantum Molecular Dynamics by the Filter-Diagonalization Method. Chem. Phys. Lett., 280 (3-4). pp. 177-184. 1996Nettesheim, P. and Huisinga, W. and Schütte, Ch. (1996) Chebyshev-Approximation for Wavepacket-Dynamics: better than expected. preprint . Meißner, B. and Schmidt, B. and Berry, R. S. (1996) Cluster Growth From the Gas Phase: Associative Collisions of Small Alkali Halide Aggregates. Z. Phys. Chem., 195 . pp. 237-251. Nettesheim, P. and Bornemann, F. A. and Schmidt, B. and Schütte, Ch. (1996) An Explicit and Symplectic Integrator for Quantum-Classical Molecular Dynamics. Chem. Phys. Lett., 256 (6). pp. 581-588. Kornhuber, R. (1996) Monotone multigrid methods for elliptic variational inequalities II. Numerische Mathematik, 72 (4). pp. 481-499. ISSN 0029-599X Finger, K. and Daniel, Ch. and Saalfrank, P. and Schmidt, B. (1996) Nonadiabatic Effects in the Photodissociation and Electronic Spectroscopy of HMn(CO)3(dab): Quantum Wave Packet Dynamics Based on ab-initio Potentials. J. Phys. Chem., 100 (9). pp. 3368-3376. Bornemann, F. A. and Nettesheim, P. and Schütte, Ch. (1996) Quantum-classical molecular dynamics as an approximation to full quantum dynamics. J. Chem. Phys., 105 (3). pp. 1074-1083. Klein, R. and Knio, O.M. and Ting, L. (1996) Representation of Core Dynamics in Slender Vortex Filament Simulations,. Physics of Fluids, 8 (9). 2415{-2425,. Korolkov, M. V. and Paramonov, G. K. and Schmidt, B. (1996) State-Selective Control For Vibrational Excitation and Dissociation of Diatomic Molecules With Shaped Ultrashort Laser Pulses. J. Chem. Phys., 105 (5). pp. 1862-1879. Schmidt, B. and Jungwirth, P. (1996) Vibrational Line Shifts of Hydrogen Halides in a Rare Gas Environment: HF/DF and HCl/DCl in Ar Matrices and Clusters. Chem. Phys. Lett., 259 (1-2). pp. 62-688. Korolkov, M. V. and Manz, J. and Paramonov, G. K. and Schmidt, B. (1996) Vibrationally State Selective Photoassociation by Infrared Picosecond Laser Pulses: Model Simulations for O + H → OH(ν). Chem. Phys. Lett., 260 (5-6). pp. 604-610. Bornemann, F. A. and Erdmann, B. and Kornhuber, R. (1996) A posteriori error estimates for elliptic problems in two and three space dimensions. SIAM Journal on Numerical Analysis, 33 (3). pp. 1188-1204. ISSN 0036-1429 Kornhuber, R. (1996) A posteriori error estimates for elliptic variational inequalities. Computers & Mathematics with Applications, 31 (8). pp. 49-60. ISSN 0898-1221 1995Klein, R. and Ting, L. (1995) Theoretical and Experimental Studies of Slender Vortex Filaments. Applied Mathematics Letters, 8 (2). pp. 45-50. Klein, R. (1995) Analysis of Accelerating Detonation Using Large Activation Energy Asymptotics. Journal de physique. IV , 5 (4). pp. 443-457. ISSN 1155-4339 Klein, R. and Knio, O.M. (1995) Asymptotic Vorticity Structure and Numerical Simulation of Slender Vortex Filaments. Journal of Fluid Mechanics, 284 . pp. 275-321. ISSN 0022-1120 Schütte, Ch. and Zumbusch, M. D. G and Brinkmann, R. (1995) Dynamics of Erbium-doped Waveguide Lasers: Modelling, Reliable Simulation, and Comparison with Experiments. preprint . Manz, J. and Proppe, B. and Schmidt, B. (1995) From Torsional Spectra to Hamiltonians and Dynamics: Effects of Coupled Bright and Dark States of 9-(N-Carbazolyl) Anthracene. Z. Phys. D, 34 (2). pp. 111-118. Klein, R. (1995) The Level-Set Approach to Premixed Turbulent Combustion in the Flamelet Regime: Theory and Numerical Implementation. Euroconference "Premixed Turbulent Combustion: Introduction to the State of the Art" . Klein, R. (1995) Semi-Implicit Extension of a Godunov-Type Scheme Based on Low Mach Number Asymptotics I: One-dimensional Flow,. Journal of Computational Physics, 121 (2). pp. 213-237. ISSN 0021-9991 Klein, R. and Majda, A. J. and Damodaran, K. (1995) Simplied Equations for the Interaction of Nearly Parallel 3-D Vortex Filaments,. Journal of Fluid Mechanics, 288 . 201-248 . ISSN 0022-1120 Schütte, Ch. (1995) Smoothed Molecular Dynamics for Thermally Embedded Systems. preprint . (Unpublished) Schütte, Ch. and Dinand, M. (1995) Theoretical Modeling of Relaxation Oscillations in Er-Doped Wave-Guide Lasers. J. Lightw. Techn., 13 (1). pp. 14-23. 1994Hoppe, R. H. W. and Kornhuber, R. (1994) Adaptive multilevel methods for obstacle problems. SIAM Journal on Numerical Analysis, 31 (2). pp. 301-323. ISSN 0036-1429 Buck, U. and Schmidt, B. (1994) Frequency Shifts in Infrared Spectra of Ethylene Clusters. J. Chem. Phys., 101 (7). pp. 6365-6366. Kornhuber, R. (1994) Monotone multigrid methods for elliptic variational inequalities I. Numerische Mathematik, 69 (2). pp. 167-184. ISSN 0029-599X Manz, J. and Paramonov, G. K. and Polasek, M. and Schütte, Ch. (1994) Overtone State-Selective Isomerization by a Series of Picosecond Infrared Laser Pulses - Model Simulations for Be2H3D. Isr. J. Chem., 34 (1). pp. 115-125. Schmidt, B. and Gerber, R. B. (1994) Reactive Collisions as a Signature for Meltinglike Transitions in Clusters. Phys. Rev. Lett., 72 (15). pp. 2490-2493. Schmidt, B. and Gerber, R. B. (1994) Solvation Effects on Association Reactions in Microclusters: Classical Trajectory Study of H+Cl(Ar)n. J. Chem. Phys., 101 (1). pp. 343-355. Klein, R. and Breitbach, H. and Geratz, K. J. and Senger, W. (1994) Surface erosion by high-speed combustion waves. Symposium (International) on Combustion, 25 (1). 95-102 . Bdzil, J.B. and Klein, R. (1994) Weakly Nonlinear Dynamics of Near-CJ Detonation Waves, Combustion in High-Speed Flows. Combustion in High-Speed Flows, J. Buckmaster et al. (eds), . pp. 513-540. ISSN 978-0-7923-2806-3 (ISBN) 1993Klein, R. and Stewart, D.S., (1993) The Relation between Curvature, Rate-State Dependence and Detonation Velocity. SIAM Journal on Applied Mathematics, 53 (5). 1401-1435 . Erdmann, B. and Frei, M. and Hoppe, R. H. W. and Kornhuber, R. and Wiest, U. (1993) Adaptive finite element methods for variational inequalities. East-West Journal of Numerical Mathematics, 1 . pp. 165-197. ISSN 1569-3953; 0928-0200 Bornemann, F. A. and Erdmann, B. and Kornhuber, R. (1993) Adaptive multilevel methods in three space dimensions. International Journal for Numerical Methods in Engineering, 36 (18). pp. 3187-3203. ISSN 1097-0207 Klein, R. and Majda, A. J. (1993) An Asymptotic Theory for the Nonlinear Instability of Anti- Parallel Pairs of Vortex Filaments. Physics of Fluids A, 5 . pp. 369-379. ISSN 0899-8213 Buck, U. and Schmidt, B. (1993) A Perturbation Approach to Predict the Infrared Spectra of Small Molecular Clusters Applied to Methanol. J. Chem. Phys., 98 (12). pp. 9410-9424. Schütte, Ch. (1993) A Quasiresonant Smoothing Algorithm for the Fast Analysis of Selective Vibrational Excitation. Impact of Computing in Sci. Eng., 5 (3). pp. 176-200. Kornhuber, R. and Roitzsch, R. (1993) Self-adaptive finite-element simulation of bipolar, strongly reverse-biased pn-junctions. International Journal for Numerical Methods in Biomedical Engineering, 9 (3). pp. 243-250. ISSN 2040-7947 Buck, U. and Schmidt, B. and Siebers, J. G. (1993) Structural Transitions and Thermally Averaged Infrared Spectra of Small Methanol Clusters. J. Chem. Phys., 99 (12). pp. 9428-9437. Buck, U. and Hobein, M. and Schmidt, B. (1993) Structure and Photodissociation Spectra of Mixed Ethene-Acetone Clusters. J. Chem. Phys., 98 (12). pp. 9425-9431. 1992Klein, R. and Majda, A. J. and McLaughlin, R.M. (1992) Asymptotic Equations for the Stretching of Vortex Filaments by a Background Flow Field. Physics of Fluids A, 4 . pp. 2271-2281. ISSN 0899-8213 Schütte, Ch. and Wulkow, M. (1992) Quantum Theory with Discrete Spectra and Countable Systems of Differential Equations - A Numerical Treatment of Raman Spectroscopy. preprint . Klein, R. and Ting, L. (1992) Vortex Filaments with Axial Core Structure Variation. Appl. Math. Lett., 5 . pp. 99-103. 1991Klein, R. and Majda, A. J. (1991) Self-Stretching of a Perturbed Vortex Filament I: The Asymptotic Equation for Deviations from a Straight Line. Physica D, 49 (3). pp. 323-352. Klein, R. (1991) On the Dynamics of Weakly Curved Detonations. Institute for Mathematics and Its Applications, 35 . ISSN 0940-6573 Klein, R. (1991) On the Dynamics of Weakly Curved Detonations. IMA-Volumes in Mathematics and its Applications, 35 . ISSN 978-0-387-97583-2 1990Roitzsch, R. and Kornhuber, R. (1990) BOXES - a program to generate triangulations from a rectangular domain description. ZIB-Report, TR-90- . ISSN 1438-0064 Klein, R. and Ting, L. (1990) Far field velocity potential induced by a rapidly decaying vorticity distribution. Zeitschrift für Angewandte Mathematik und Physik (ZAMP), 41 (3). pp. 395-418. ISSN 0044-2275 (Print) 1420-9039 (Online) Buck, U. and Schmidt, B. (1990) Calculation of Vibrational Line Shifts for Molecular Dimers. J. Mol. Liqu., 46 . pp. 181-196. Hoppe, R. H. W. and Kornhuber, R. (1990) Multi-grid solution of two coupled Stefan equations arising in induction heating of large steel slabs. International Journal for Numerical Methods in Engineering, 30 (4). pp. 779-801. ISSN 1097-0207 Klein, R. and Munz , C.-D. and Schmidt, L. (1990) A Numerical Study of Interfacial Instabilities at High Mach Numbers. Notes on Numerical Fluid Mechanics, 29,, 29 . 242-251. Kornhuber, R. and Roitzsch, R. (1990) On adaptive grid refinement in the presence of internal or boundary layers. IMPACT of Computing in Science and Engineering, 2 (1). pp. 40-72. ISSN 0899-8248 Ahlrichs, R. and Brode, St. and Buck, U. and deKieviet, M. and Lauenstein, Ch. and Rudolph, A. and Schmidt, B. (1990) The Structure of C2H4 Clusters from Theoretical Interaction Potentials and Vibrational Predissociation Data. Z. Phys. D, 15 (4). pp. 341-351. Maly, R.R. and Koenig, G. and Klein, R. and Peters, N. (1990) Theoretical and Experimental Investigation of Knock Induced Surface Destruction. SAE transactions, 99 (1), no3, pp. (1). 99-137 (62 ref.). ISSN 0096-736X 1989Kornhuber, R. and Roitzsch, R. (1989) Adaptive Finite-Element-Methoden für konvektionsdominierte Randwertprobleme bei partiellen Differentialgleichungen. ZIB-Report . ISSN 1438-0064 Aziz, R. A. and Buck, U. and Jonsson, H. and Ruiz-Suarez, J. C. and Schmidt, B. and Scoles, G. and Slaman, M. J. and Xu, J. (1989) Two- and Three-Body Forces in the Interaction of He Atoms with Xe Overlayers Adsorbed on (0001) Graphite. J. Chem. Phys., 91 (10). pp. 6477-6493. 1988Kornhuber, R. (1988) Convergent extensions of grid-functions. Mathematische Nachrichten, 139 (1). pp. 63-75. ISSN 1522-2616 Klein, R. and Peters, N. (1988) Cumulative Effects of Weak Pressure Waves During the Induction Period of a Thermal Explosion in a Closed Cylinder. J. Fluid Mech., 187 . pp. 197-230. Klein, R. (1988) Detonation Initiation Due to Shock Wave-Boundary Interactions. Notes on Numerical Fluid Mechanics, 24 . 279-288.. Kornhuber, R. (1988) Local change of coordinates for grid-functions on regions with curved boundary. Mathematische Nachrichten, 139 (1). pp. 45-61. ISSN 1522-2616 Liuti, G. and Pirani, F. and Buck, U. and Schmidt, B. (1988) Methane-Rare Gas Interaction Potentials from Scattering Experiments. Chem. Phys., 126 (1). pp. 1-6. Klein, R. (1988) Shock Initiated Ignition in an L-shaped Duct: Two Aspects of its Numerical Simulation. Notes on Numerical Fluid Mechanics, 20 . pp. 138-145. 1973Kornhuber, R. (1973) Vereinfachung eines Computermodells. MNU - Der mathematische und naturwissenschaftliche Unterricht, 26 (3). p. 176. ISSN 0025-5866 |