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Number of items: 992.

2017

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

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)

von Larcher, T. and Klein, R. (2017) On identification of self-similar characteristics using the Tensor Train decomposition method with application to channel turbulence flow. Theoretical and Computational Fluid Dynamics . pp. 1-22. ISSN 0935-4964 (Print) 1432-2250 (Online) (Submitted)

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

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 (Unpublished)

Djurdjevac, A. and Elliott, C.M. and Kornhuber, R. and Ranner, Th. (2017) Evolving surface finite element methods for random advection-diffusion equations. arXiv.org . pp. 1-25. (Submitted)

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.

Gerber, S. and Olsson, S. and Noé, F. and Horenko, I. (2017) A scalable approach to the computation of invariant measures for high-dimensional Markovian systems. SFB 1114 Preprint . pp. 1-22. (Unpublished)

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)

Müller, A. and Névir, P. and Klein, R. (2017) Scale Dependent Analytical Investigation of the Dynamic State Index Concerning the Quasi-Geostrophic Theory. Journal of Atmospheric Sciences . pp. 1-38. (Submitted)

Schmidt, B. and Hartmann, C. (2017) WavePacket: A Matlab package for numerical quantum dynamics. II: Open quantum systems, optimal control, and model reduction. Comp. Phys. Comm. . (Submitted)

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 . (In Press)

Benner, P. and Breiten, T. and Hartmann, C. and Schmidt, B. (2017) Model reduction of controlled Fokker-Planck and Liouville-von Neumann equations. SIAM J. Appl. Dyn. Syst. . (Submitted)

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

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. (Submitted)

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 (Submitted)

Mazza, E. and Ulbrich, U. and Klein, R. (2017) The Tropical Transition of the October 1996 Medicane in the Western Mediterranean Sea: A Warm Seclusion Event. Monthly Weather Review, 145 . pp. 2575-2595. ISSN Online: 1520-0493 Print: 0027-0644

Gerber, S. and Horenko, I. (2017) Toward a direct and scalable identification of reduced models for categorical processes. Proceedings of the National Academy of Sciences, 114 (19). pp. 4863-4868.

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.

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

Acevedo, W. and de Wiljes, J. and Reich, S. (2017) Second-order accurate ensemble transform particle filters. SFB 1114 Preprint . (Submitted)

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 (In Press)

Gräser, C. and Kies, T. (2017) Discretization Error Estimates for Penalty Formulations of a Linearized Canham-Helfrich Type Energy. arXiv.com .

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)

Donati, L. and Hartmann, C. and Keller, B.G. (2017) Girsanov reweighting for path ensembles and Markov state models. SFB 1114 Preprint . (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.

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) (Submitted)

Vatansever, B. and Muñoz, A. and Klein, C. L. and Reinert, K. (2017) Development and optimisation of a generic micro LC-ESI-MS method for the qualitative and quantitative determination of 30-mer toxic gliadin peptides in wheat flour for food analysis. Analytical and Bioanalytical Chemistry, 409 (4). pp. 989-997. ISSN 1618-2642

Rath , B. and Conrad, T. O. F. and Myles, P. and Alchikh, M. and Ma, X. and Hoppe, Ch. and Tief, F. and Obermeier, P. and Reiche, J. and Kisler, B. and Schweiger, B. (2017) Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials. Expert Review of Anti-infective Therapy (IERZ), 15 (6). pp. 545-568.

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)

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

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.

Klus, S. and Nüske, F. and Koltai, Péter and Wu, H. and Kevrekidis, Ioannis and Schütte, Ch. and Noé, F. (2017) Data-driven model reduction and transfer operator approximation. J. Nonlin. Sci. . (Submitted)

Schlutow, M. and Klein, R. and Achatz, U. (2017) Finite-amplitude pseudo-incompressible gravity wave trains. Journal of Fluid Mechanics, 826 . pp. 1034-1065.

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.

Sadeghi, M. and Weikl, T. and Noé, F. (2017) Particle-based membrane model for mesoscopic simulation of cellular dynamics. arXiv:1710.06907 . (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. Comp. Theory Comput. , 13 . pp. 926-934.

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).

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.

Rüderich, Stefan 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)

Mardt, A. and Pasquali, L. and Wu, H. and Noé, F. (2017) VAMPnets: Deep learning of molecular kinetics. arXiv:1710.06012 . (Submitted)

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 .

Gokhale, N. and Nikiforakis, N. and Klein, R. (2017) A dimensionally split Cartesian cut cell method for hyperbolic conservation laws. Journal of Computational Physics . (Submitted)

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 . (Submitted)

2016

Jäger, Marten and Schubach, Max and Zemojtel, Tomasz and Reinert, Knut and Church, Deanna M. and Robinson, Peter N. (2016) Alternate-locus aware variant calling in whole genome sequencing. Genome Medicine, 8 (1). ISSN 1756-994X

You, Xintian Arthur and Conrad, T. O. F. (2016) Acfs: accurate circRNA identification and quantification from NGS data. Nature Scientific Reports, 6 . ISSN 2045-2322

Yousef, K. P. and Meixenberger, K. and Smith, M. and Jansen, K. and Bartmeyer, B. and Hamouda, O. and Kücherer, C. and von Kleist, M. (2016) Inferring HIV-1 transmission dynamics in Germany from recently transmitted viruses. Journal of Acquired Immunodeficiency Virus, 73 (3). pp. 356-363. ISSN 1525-4135

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

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

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

Marschall, T. and Reinert, K. and others, (59 authors in total) (2016) Computational pan-genomics: status, promises and challenges. Briefings in Bioinformatics . ISSN 1477-4054 (Online)

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

Mireles, Victor and Conrad, T. O. F. (2016) Decomposing biological systems into reusable modules reveals characteristic module size distributions. n/a . (Submitted)

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

Kornhuber, R. and Peterseim, D. and Yserentant, H. (2016) An analysis of a class of variational multiscale methods based on subspace decomposition. Mathematics of Computation . ISSN 0025-5718 (In Press)

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

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

Smith, M. and Smyth, R.P. and Marquet, R. and von Kleist, M. (2016) MIMEAnTo – Profiling functional RNA in Mutational Interference Mapping Experiments. Bioinformatics . ISSN 1367-4803 (Submitted)

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

Zhang, W. and Hartmann, C. and Schütte, Ch. (2016) Effective dynamics along given reaction coordinates, and reaction rate theory. Faraday discussions . ISSN 1359-6640 (In Press)

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, Péter 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 FILTER FOR HIGH DIMENSIONAL DYNAMICAL SYSTEMS. SIAM/ASA Journal on Uncertainty Quantification, 4 (1). pp. 592-608. ISSN 2166-2525

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

Babushkina, E. and Kornhuber, R. (2016) Adaptive multilevel Monte Carlo methods for stochastic variational inequalities. arXiv:1611.06012 . (Submitted)

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)

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

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 .

Berndt, P. and Klein, R. and Paschereit, O. C. (2016) A Kinetics Model For The Shockless Explosion Combustion.

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.

Bennett, W.P. and Nikiforakis, N. and Klein, R. (2016) A Moving Boundary Flux Stabilization Method for Cartesian Cut-Cell Grids using Directional Operator Splitting. Journal of Computational Physics . (Submitted)

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 . pp. 37-46.

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.

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, 666 . pp. 12-20.

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 /PhysRevE.94.023309. Phys. Rev. E, 94 (2).

Wu, H. and Noé, F. (2016) Spectral learning of dynamic systems from nonequilibrium data. NIPS, 29 . pp. 4179-4187.

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)

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 . ISSN 0928-0987 (In Press)

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.

Youett, J. and Sander, O. and Kornhuber, R. (2016) A globally convergent filter-trust-region method for large deformation contact problems. Preprint 1116, Matheon Berlin . (Submitted)

2015

Enciso, M. and Schütte, Ch. and Delle Site, L. (2015) Influence of pH and sequence in peptide aggregation via molecular simulation. Journal of Chemical Physics, 143 (24). p. 243130. ISSN 0021-9606

Schultz, L. and Zurich, M.-G. and Culot, M. and da Costa, A. and Landry, C. and Bellwon, P. and Kristl, T. and Hörmann, K. and Ruzek, S. and Aiche, S. and Reinert, K. and Bielow, C. and Gosselet, F. and Cecchelli, R. and Huber, C. G. and Schroeder, O. H.-U. and Gramowski-Voss, A. and Weiss, D. G. and Bal-Price, A. (2015) Evaluation of drug-induced neurotoxicity based on metabolomics, proteomics and electrical activity measurements in complementary CNS in vitro models. Toxicology in Vitro, 30 (1). pp. 138-165. ISSN 08872333

Wilmes, Anja and Bielow, Chris and Ranninger, Christina and Bellwon, Patricia and Aschauer, Lydia and Limonciel, Alice and Chassaigne, Hubert and Kristl, Theresa and Aiche, Stephan and Huber, Christian G. and Guillou, Claude and Hewitt, Philipp and Leonard, Martin O. and Dekant, Wolfgang and Bois, Frederic and Jennings, Paul (2015) Mechanism of cisplatin proximal tubule toxicity revealed by integrating transcriptomics, proteomics, metabolomics and biokinetics. Toxicology in Vitro, 30 (1, Part A). pp. 117-127. ISSN 08872333

Grohs, P. and Hardering, H. and Sander, O. (2015) Optimal a priori discretization error bounds for geodesic finite elements. Foundations of Computational Mathematics, 15 (6). pp. 1357-1411. ISSN 1615-3375

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).

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.

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.

Matera, S. and Blomberg, S. and Hoffmann, M. J. and Zetterberg, J. and Gustafson, J. and Lundgren, E. and Reuter, K. (2015) Evidence for the Active Phase of Heterogeneous Catalysts through In Situ Reaction Product Imaging and Multiscale Modeling. ACS Catalysis, 5 (8). pp. 4514-4518.

Erbar, M. and Maas, J. and Renger, M. (2015) From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability, 20 (89).

Wu, H. and Noé, F. (2015) Gaussian Markov transition models of molecular kinetics. J. Chem. Phys., 142 (8). 084104.

Gunkel, M. and Schöneberg, J. and Alkhaldi, W. and Irsen, S. and Noé, F. and Kaupp, U. B. and Al-Amoudi, A. (2015) Higher-order architecture of rhodopsin in intact photoreceptors and its implication for phototransduction kinetics. Structure, 23 . pp. 628-638.

Kuchenbecker, L. and Nienen, M. and Hecht, J. and Neumann, A. U. and Babel, N. and Reinert, K. and Robinson, P. N. (2015) IMSEQ - a fast and error aware approach to immunogenetic sequence analysis. Bioinformatics, 31 (18). pp. 2963-2971. ISSN 1367-4803

Rinne, K.F. and Schulz, J.C.F. and Netz, R.R. (2015) Impact of secondary structure and hydration water on the dielectric spectrum of poly-alanine and possible relation to the debate on slaved versus slaving water. The Journal of Physical Chemistry .

Hartmann, C. and Schütte, Ch. and Weber, M. and Zhang, W. (2015) Importance sampling in path space for diffusion processes. Probab. Theory Rel. Fields . (Submitted)

Horenko, I. and Gerber, S. (2015) Improving clustering by imposing network information. Science Advances, 1 (7). ISSN 2375-2548

Riechelmann, T. and Wacker, U. and Beheng, K.D. and Etling, D. and Raasch, S. (2015) Influence of turbulence on the drop growth in warm clouds, Part II: sensitivity studies with a spectral bin microphysics and a Lagrangian cloud model. Meteorologische Zeitschrift .

Santimano, T.N. and Rosenau, M. and Oncken, O. (2015) Intrinsic versus extrinsic variability of analogue sand-box experiments - Insights from statistical analysis of repeated accretionary sand wedge experiments. Journal of Structural Geology, 75 . pp. 80-100.

Boninsegna, L. and Gobbo, G. and Noé, F. and Clementi, C. (2015) Investigating Molecular Kinetics by Variationally Optimized Diffusion Maps. J. Chem. Theory Comput., 11 . pp. 5947-5960.

Noé, F. and Clementi, C. (2015) Kinetic distance and kinetic maps from molecular dynamics simulation. J. Chem. Theory Comput., 11 . pp. 5002-5011.

Schlegel, F. and Stiller, J. and Bienert, A. and Maas, H.-G and Queck, R. and Bernhofer, C. (2015) Large-Eddy Simulation Study of the Effects on Flow of a Heterogeneous Forest at Sub-tree Resolution. Boundary-Layer Meteorology, 154 . pp. 27-56.

Hu, J. and Reinert, K. (2015) LocalAli: An Evolutionary-based Local Alignment Approach to Identify Functionally Conserved Modules in Multiple Networks. Bioinformatics, 30 (1). pp. 363-372. ISSN 1367-4803

Yousef, K. P. and Streck, A. and Schütte, Ch. and Siebert, H. and Hengge, R. and von Kleist, M. (2015) Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli. BMC Systems Biology, 9 . p. 39. ISSN 1752-0509

Wu, H. (2015) Maximum Margin Clustering for State Decomposition of Metastable Systems. Neurocomputing, 164 . pp. 5-22. ISSN 0925-2312

Stolzenberg, S. and Quick, M. and Zhao, C. and Gotfryd, K. and Khelashvili, G. and Gether, U. and Loland, C. J. and Javitch, J. A. and Noskov, S. and Weinstein, H. and Shi, L. (2015) Mechanism of the Association between Na+Binding and Conformations at the Intracellular Gate in Neurotransmitter:Sodium Symporters. Journal of Biological Chemistry, 290 (22). p. 13992. ISSN 0021-9258

Holtgrewe, M. and Kuchenbecker, L. and Reinert, K. (2015) Methods for the Detection and Assembly of Novel Sequence in High-Throughput Sequencing Data. Bioinformatics, 31 (12). pp. 1904-1912. ISSN 1367-4803

Gräser, C. and Kornhuber, R. and Sack, U. (2015) Nonsmooth Schur-Newton methods for multicomponent Cahn-Hilliard systems. IMA Journal of Numerical Analysis, 35 (2). pp. 652-679. ISSN 0272-4979

Liero, M. and Mielke, A. and Peletier, M. A. and Renger, M. (2015) On microscopic origins of generalized gradient structures. SFB Preprint . (Submitted)

O’Kane, T.J. and Risbey, J.S. and Monselesan, D.P. and Horenko, I. and Franzke, Ch.L.E. (2015) On the dynamics of persistent states and their secular trends in the waveguides of the Southern Hemisphere troposphere. Climate Dynamics . ISSN Print: 0930-7575, Online: 1432-0894

Zhang, W. and Hartmann, C. and von Kleist, M. (2015) Optimal control of Markov jump processes: Asymptotic analysis, algorithms, and application to modelling of chemical reaction systems. SIAM Multiscale Modeling & Simulation . ISSN print: 1540-3459; online: 1540-3467 (Submitted)

Wu, H. and Prinz, J.-H. and Noé, F. (2015) Projected Metastable Markov Processes and Their Estimation with Observable Operator Models. J. Chem. Phys., 143 (14). p. 144101.

Plattner, N. and Noé, F. (2015) Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models. Nat. Commun., 6 . p. 7653.

Scherer, M. K. and Trendelkamp-Schroer, B. and Paul, F. and Pérez-Hernández, G. and Hoffmann, M. and Plattner, N. and Wehmeyer, C. and Prinz, J.-H. and Noé, F. (2015) PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models. J. Chem. Theory Comput., 11 (11). pp. 5525-5542.

Biedermann, J. and Ullrich, A. and Schöneberg, J. and Noé, F. (2015) ReaDDyMM: fast interacting-particle reaction-diffusion simulations using graphical processing units. Biophys. J., 108 . pp. 457-461. ISSN 00063495

Li, S. and Moreno, M. and Bedford, J. and Rosenau, M. and Oncken, O. (2015) Revisiting viscoelastic effects on interseismic deformation and locking degree: A case study of the Peru-North Chile subduction zone. Journal of Geophysical Research-Solid Earth, 120 (6). pp. 4522-4538.

Schror, M. and Mey, A.S.J.S. and Noé, F. and MacPhee, C. (2015) Shedding Light on the Dock-Lock Mechanism in Amyloid Fibril Growth Using Markov State Models. J. Chem. Phys. Lett., 6 . pp. 1076-1081.

Noé, F. (2015) Statistical inefficiency of Markov model count matrices. preprint . (Unpublished)

Billesbølle, C. B. and Krüger, M. B. and Shi, L. and Quick, M. and Li, Z. and Stolzenberg, S. and Kniazeff, J. and Gotfryd, K. and Mortensen, J. S. and Javitch, J. A. and Weinstein, H. and Loland, C.J. and Gether, U. (2015) Substrate-induced Unlocking of the Inner Gate Determines the Catalytic Efficiency of a Neurotransmitter:Sodium Symporter. Journal of Biological Chemistry, 290 (44). p. 26725. ISSN 0021-9258

Becker, N. and Ulbrich, U. and Klein, R. (2015) Systematic large-scale secondary circulations in a regional climate model. Geophysical Research Letters, 42 (10). 4142-4149 .

von Larcher, T. and Beck, A. and Klein, R. and Horenko, I. and Metzner, Ph. and Waidmann, M. and Igdalov, D. and Gassner, G. and Munz , C.-D. (2015) Towards a Framework for the Stochastic Modelling of Subgrid Scale Fluxes for Large Eddy Simulation. Meteorologische Zeitschrift, 24 (3). pp. 313-342.

Akyuz, N. and Georgieva, E. R. and Zhou, Z. and Stolzenberg, S. and Cuendet, M. A. and Khelashvili, G. and Altman, R. B. and Terry, D. S. and Freed, J. H. and Weinstein, H. and Boudker, O. and Blanchard, S. (2015) Transport domain unlocking sets the uptake rate of an aspartate transporter. Nature, 518 (7537). p. 68. ISSN 0028-0836

Schulz, J.C.F. and Miettinen, M.S. and Netz, R.R. (2015) Unfolding and Folding Internal Friction of β‑Hairpins Is Smaller than That of α‑Helices. Journal of Physical Chemistry B, 119 (13). pp. 4565-4574.

Vitalini, F. and Noé, F. and Keller, B. (2015) A basis set for peptides for the variational approach to conformational kinetics. J. Chem. Theory Comput., 11 . pp. 3992-4004.

Vercauteren, N. and Klein, R. (2015) A clustering method to characterize intermittent bursts of turbulence and interaction with submeso motions in the stable boundary layer. Journal of the Atmospheric Sciences, 72 (1). ISSN Online: 1520-0469 Print: 0022-4928

Mielke, A. and Peletier, M. A. and Renger, M. (2015) A generalization of Onsager's reciprocity relations to gradient flows with nonlinear mobility. Journal of Non-Equilibrium Thermodynamics . (Submitted)

Kim, W.K. and Netz, R.R. (2015) The mean shape of transition and first-passage paths. The Journal of Chemical Physics, 143 (224108).

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

Vener, M. V. and Odinokov, A. V. and Wehmeyer, C. and Sebastiani, D. (2015) The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations. The Journal of Chemical Physics, 142 (21). p. 215106. ISSN 0021-9606

2014

Neu, V. and Bielow, C. and Reinert, K. and Huber, C. G. (2014) Ultrahigh-performance liquid chromatography-ultraviolet absorbance detection-high-resolution-mass spectrometry combined with automated data processing for studying the kinetics of oxidative thermal degradation of thyroxine in the solid state. Journal of chromatography A, 1371 . pp. 196-203.

Meixenberger, K. and Yousef, K. P. and Somogyi, S. and Fiedler, S. and Bartmeyer, B. and von Kleist, M. and Kücherer, C. (2014) Characterization of natural polymorphic sites of the HIV-1 integrase before the introduction of HIV-1 integrase inhibitors in Germany. J Int AIDS Soc., 17 (4 Suppl 3). p. 19746.

Schlutow, M. and Becker, E. and Körnich, H. (2014) Positive definite and mass conserving tracer transport in spectral GCMs. Journal of Geophysical Research Atmospheres .

Gräser, C. and Kornhuber, R. and Sack, U. (2014) Numerical simulation of coarsening in binary solder alloys. Computational Materials Science, 93 . pp. 221-233. ISSN 0927-0256

Gräser, C. and Sander, O. (2014) Polyhedral Gauß-Seidel converges. Journal of Numerical Mathematics, 22 (3). pp. 221-254. ISSN 1570-2820

Hauswedell, H. and Singer, J. and Reinert, K. (2014) Lambda: the local aligner for massive biological data. Bioinformatics (Oxford, England), 30 (17). i349-i355.

Berg, M. and Accardi, A. and Paulus, B. and Schmidt, B. (2014) Rotationally Adiabatic Pair Interactions of para- and ortho-Hydrogen with the Halogen Molecules F2, Cl2 and Br2. J. Chem. Phys., 141 (7). 074303.

Walzer, M. and Pernas, L. E. and Nasso, S. and Bittremieux, W. and Nahnsen, S. and Kelchtermans, P. and Pichler, P. and van den Toorn, H. W. P. and Staes, A. and Vandenbussche, J. and Mazanek, M. and Taus, T. and Scheltema, R. A. and Kelstrup, C. D. and Gatto, L. and van Breukelen, B. and Aiche, S. and Valkenborg, D. and Laukens, K. and Lilley, K. S. and Olsen, J. V. and Heck, A. J. R. and Mechtler, K. and Aebersold, R. and Gevaert, K. and Vizcaino, J. A. and Hermjakob, H. and Kohlbacher, O. and Martens, L. (2014) qcML: An Exchange Format for Quality Control Metrics from Mass Spectrometry Experiments. Molecular & Cellular Proteomics, 13 (8). pp. 1905-1913. ISSN 1535-9476

Muehlhans, S. and von Kleist, M. and Gretchuka, T and Martin, T. and Fegeler, U. and Maurer, W. and Namazova-Baranova, L. and Gaedicke, G. and Baranov, A. and Rath , B. (2014) Awareness and Utilization of Standards and Pathways for the Reporting of Adverse Events Following Immunization among Pediatricians in Russia and Germany. Pediatric Drugs, 16 (4). pp. 31-330. ISSN 1174-5878 (Print) 1179-2019 (Online)

Rahn, R. and Weese, D. and Reinert, K. (2014) Journaled string tree--a scalable data structure for analyzing thousands of similar genomes on your laptop. Bioinformatics . ISSN Online ISSN 1460-2059 - Print ISSN 1367-4803

Trappe, K. and Emde, A.-K. and Ehrlich, H.-C. and Reinert, K. (2014) Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone. Bioinformatics, 30 (24). pp. 3484-3490. ISSN 1367-4803

Hoffmann, M. J. and Matera, S. and Reuter, K. (2014) kmos: A lattice kinetic Monte Carlo framework. Computer Physics Communications, 185 (7). pp. 2138-2150.

Pluharova, E. and Baer, M. and Mundy, Ch. and Schmidt, B. and Jungwirth, P. (2014) Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics. J. Phys. Chem. Lett., 5 (13). pp. 2235-2240.

Schmidt, B. and Friedrich, B. (2014) Supersymmetry and eigensurface topology of the planar quantum pendulum. Front. Physics, 2 . p. 37.

Sarich, M. and Djurdjevac, N. and Bruckner, S. and Conrad, T. O. F. and Schütte, Ch. (2014) Modularity revisited: A novel dynamics-based concept for decomposing complex networks. Journal of Computational Dynamics, 1 (1). pp. 191-212. ISSN 2158-2491

Kornhuber, R. and Schwab, C. and Wolf, M.W. (2014) Multilevel Monte Carlo finite element methods for stochastic elliptic variational inequalities. SIAM Journal on Numerical Analysis, 52 (3). pp. 1243-1268. ISSN 0036-1429

Manz, J. and Schild, A and Schmidt, B. and Yonggang, Y (2014) Maximum tunneling velocities in symmetric double well potentials. Chem. Phys., 442 . pp. 9-17.

Katchanov, J. and von Kleist, M. and Arasteh, K. and Stocker, H. (2014) “Time-to-Amphotericin B” in Cryptococcal Meningitis in a European Low-Prevalence Setting: Analysis of Diagnostic Delays. QJM: An International Journal of Medicine, 107 (10). pp. 799-803. ISSN 1460-2393

Kehr, B. and Trappe, K. and Holtgrewe, M. and Reinert, K. (2014) Genome alignment with graph data structures: a comparison. BMC Bioinformatics, 15 . ISSN 1471-2105

Dommert, F. and Wendler, K. and Qiao, B. and Delle Site, L. (2014) Generic force fields for ionic liquids. Journal of Molecular Liquids, 192 . pp. 32-37. ISSN 0167-7322

Chen, X. and Yousef, K. P. and Duwe, S. and Karsch, K. and Grover, S. and Wählisch, S. and Obermeier, P. and Tief, F. and Muehlhans, S. and Seeber, L. and von Kleist, M. and Schweiger, B. and Rath , B. (2014) Quantitative influenza follow-up testing (QIFT) - a novel biomarker for the monitoring of disease activity at the point-of-care. PLoS ONE, 9 (3). ISSN 1932-6203

Wang, H. and Schütte, Ch. and Ciccotti, G. and Delle Site, L. (2014) Exploring the conformational dynamics of alanine dipeptide in solution subjected to an external electric field: A nonequilibrium molecular dynamics simulation. Journal of Chemical Theory and Computation, 10 (4). pp. 1376-1386. ISSN 1549-9618

Parsa, A. M. and Kozhan, I. and Wulkow, M. and Hutchinson, R. A. (2014) Modeling of Functional Group Distribution in Copolymerization: A Comparison of Deterministic and Stochastic Approaches. Macromolecular Theory and Simulations, 23 (3). pp. 207-217. ISSN 10221344

Wandelt, S. and Deng, D. and Gerdjikov, S. and Mishra, S. and Mitankin, P. and Patil, M. and Siragusa, E. and Tiskin, A. and Wang, W. and Wang, J. and Leser, U. (2014) State-of-the-art in String Similarity Search and Join. SIGMOD Record, 43 (1).

Hu, J. and Kehr, B. and Reinert, K. (2014) NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. Bioinformatics, 30 (4). pp. 540-548. ISSN 1367-4803

Latorre, J.C. and Kramer, P. R. and Pavliotis, G. A. (2014) Numerical methods for computing effective transport properties of flashing Brownian motors. Journal of Computational Physics, 257 (Part A). pp. 57-82. ISSN 0021-9991

Zhu, J. and Zhang, P. and Wang, H. and Delle Site, L. (2014) Is there a third order phase transition for supercritical fluids? The Journal of Chemical Physics, 140 (1). 014502. ISSN 00219606

Delle Site, L. (2014) What is a Multiscale Problem in Molecular Dynamics? Entropy (Special Issue), 16 (1). pp. 23-40. ISSN 1099-4300

Berninger, H. and Loisel, S. and Sander, O. (2014) The 2-Lagrange multiplier method applied to nonlinear transmission problems for the Richards equation in heterogeneous soil with cross points. SIAM J. Sci. Comput., 36 (5). A2166-A2198. ISSN 1064-8275

Yelash, L. and Müller, A. and Lukacova-Medvidova, M. and Giraldo, F.X. and Wirth, V. (2014) Adaptive discontinuous evolution Galerkin method for dry atmospheric flow. Journal of Computational Physics, 268C . 106 -133. ISSN 0021-9991

Zhang, W. and Wang, H. and Hartmann, C. and Weber, M. and Schütte, Ch. (2014) Applications of the cross-entropy method to importance sampling and optimal control of diffusions. SIAM J. Sci. Comput., 36 (6). A2654-A2672. ISSN 1064-8275

Meixenberger, K. and Hauser, A. and Jansen, K. and Yousef, K. P. and Fiedler, S. and von Kleist, M. and Norley, S. and Somogyi, S. and Hamouda, O. and Bannert, N. and Bartmeyer, B. and Kücherer, C. (2014) Assessment of ambiguous base calls in HIV-1 pol population sequences as a biomarker to identify recent infections in HIV-1 incidence studies. Journal of Clinical Microbiology, 52 (8). pp. 2977-2983. ISSN 0095-1137

Vincze, M. and Borchert, S. and Achatz, U. and von Larcher, T. and Baumann, M. and Hertel, C. and Remmler, S. and Beck, T. and Alexandrov, K. and Egbers, C. and Froehlich, J. and Heuveline , V. and Hickel, S. and Harlander, U. (2014) Benchmarking in a rotating annulus: a comparative experimental and numerical study of baroclinic wave dynamics. Meteorologische Zeitschrift .

Agarwal, A. and Wang, H. and Schütte, Ch. and Delle Site, L. (2014) Chemical potential of liquids and mixtures via Adaptive Resolution Simulation. Journal of Chemical Physics, 141 (3). ISSN 0021-9606

Ziemer, C. and Wacker, U. (2014) A Comparative Study of B , Γ and Log Normal Distributions in a Three Moment Parameterization for Drop Sedimentation. Atmosphere, 5 (3). pp. 484-517.

Ziemer, C. and Wacker, U. (2014) A Comparative Study of B-, Γ- and Log-Normal Distributions in a Three-Moment Parameterization for Drop Sedimentation. Atmosphere, 5 (3). pp. 484-517. ISSN 2073-4433

Keller, B. and Kobitski, A. and Jäschke, A. and Nienhaus, G.U. and Noé, F. (2014) Complex RNA folding kinetics revealed by single molecule FRET and hidden Markov models. J. Am. Chem. Soc., 136 . pp. 4534-4543.

Kabbe, G. and Wehmeyer, C. and Sebastiani, D. (2014) A Coupled Molecular Dynamics/Kinetic Monte Carlo Approach for Protonation Dynamics in Extended Systems. Journal of Chemical Theory and Computation, 10 (10). p. 4221. ISSN 1549-9618

de Wiljes, J. and Putzig, L. and Horenko, I. (2014) Discrete nonhomogeneous and nonstationary logistic and Markov regression models for spatiotemporal data with unresolved external influences. Communications in Applied Mathematics & Computational Science, 9 . pp. 1-46. ISSN 1559-3940

von Rudorff, G. F. and Wehmeyer, C. and Sebastiani, D. (2014) Efficient implementation and application of the artificial bee colony algorithm to low-dimensional optimization problems. Computer Physics Communications, 185 (6). p. 1639. ISSN 00104655

Schöneberg, J. and Heck, M. and Hofmann, K. P. and Noé, F. (2014) Explicit Spatio-temporal Simulation of Receptor-G Protein Coupling in Rod Cell Disk Membranes. Biophys. J., 107 . pp. 1042-1053. ISSN 00063495

van der Velde, Y. and Vercauteren, N. and Jaramillo, F. and Dekker, S.C. and Destouni, G. and Lyon, S.W. (2014) Exploring hydroclimatic change disparity via the Budyko framework. Hydrological Processes, 28 (13). pp. 4110-4118. ISSN 1099-1085

Schulz, M. H. and Weese, D. and Holtgrewe, M. and Dimitrova, V. and Niu, S. and Reinert, K. and Richard, H. (2014) Fiona: a parallel and automatic strategy for read error correction. Bioinformatics, 30 (17). i356-i363.

Vetter, A. and Sander, O. and Duda, G. and Weinkamer, R. (2014) Healing of a mechano-responsive material. Europhysics Letters (EPL), 104 (6). pp. 1-6. ISSN 0295-5075

Siewert, C. and Bordás, R. and Wacker, U. and Beheng, K.D. and Kunnen, R. P. J. and Meinke, M. and Schröder, W. and Thévenin, D. (2014) Influence of turbulence on the drop growth in warm clouds, Part I: comparison of numerically and experimentally determined collision kernels. Meteorologische Zeitschrift, 23 (4). 397 -410.

Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2014) Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1. Communications in Mathematical Sciences, 12 (5). pp. 859-877. ISSN 1539-6746

Chodera, J. D. and Noé, F. (2014) Markov state models of biomolecular conformational dynamics. Curr. Opin. Struct. Biol., 25 . pp. 135-144.

Lie, Han Cheng and Schütte, Ch. and Hartmann, C. (2014) Martingale-based gradient descent algorithm for estimating free energy values of diffusions. SIAM J. Sci. Comput. . ISSN 1064-8275 (Submitted)

Jasor, G. and Wacker, U. and Beheng, K.D. and Polifke, W. (2014) Modeling artifacts in the simulation of the sedimentation of raindrops with a Quadrature Method of Moments. Meteorologische Zeitschrift, 23 (4). pp. 369-385.

Jouvet, G. and Funk, M. (2014) Modelling the trajectory of the corpses of mountaineers who disappeared in 1926 on Aletschgletscher, Switzerland. Journal of Glaciology, 60 (220). pp. 255-261. ISSN 0022-1430

von Larcher, T. and Dörnbrack, A. (2014) Numerical simulations of baroclinic driven flows in a thermally driven rotating annulus using the immersed boundary method. Meteorologische Zeitschrift . ISSN 0941-2948

Muraschko, J and Fruman, M. D. and Achatz, U. and Hickel, S. and Toledo, Y. (2014) On the application of WKB theory for the simulation of the weakly nonlinear dynamics of gravity waves. Quarterly Journal of the Royal Meteorological Society .

Hartmann, C. and Latorre, J.C. and Pavliotis, G. A. and Zhang, W. (2014) Optimal control of multiscale systems using reduced-order models. J. Computational Dynamics, 1 (2). pp. 279-306. ISSN 2158-2505

Wu, H. and Noé, F. (2014) Optimal estimation of free energies and stationary densities from multiple biased simulations. SIAM Multiscale Model. Simul., 12 . pp. 25-54.

Koltai, Péter and Volf, Alexander (2014) Optimizing the stable behavior of parameter-dependent dynamical systems --- maximal domains of attraction, minimal absorption times. Journal of Computational Dynamics, 1 (2). pp. 339-356. ISSN 2158-2491

Matera, S. and Maestri, M. and Cuoci, A. and Reuter, K. (2014) Predictive-Quality Surface Reaction Chemistry in Real Reactor Models: Integrating First-Principles Kinetic Monte Carlo Simulations into Computational Fluid Dynamics. ACS Catalysis, 4 (11). pp. 4081-4092.

Ziemer, C. and Jasor, G. and Wacker, U. and Beheng, K.D. and Polifke, W. (2014) Quantitative comparison of presumed number density and quadrature moment methods for the parameterisation of drop sedimentation. Meteorologische Zeitschrift, 23 (4). pp. 411-423.

Accardi, A. and Schmidt, B. (2014) Quantum effects on translation and rotation of molecular chlorine in solid para-hydrogen. (Unpublished)

Vollmer, J. and Papke, A. and Rohloff, M. (2014) Ripening and Focusing of Aggregate Size Distributions with Overall Volume Growth. Frontiers in Physics, 2 (18).

Vercauteren, N. and Lyon, S.W. and Destouni, G. (2014) Seasonal influence of insolation on fine-resolved air temperature variation and snowmelt. Journal of Applied Meteorology and Climatology, 53 (2). pp. 323-332. ISSN Online: 1558-8432 Print: 1558-8424

Bobusch, B. and Berndt, P. and Paschereit, O. C. and Klein, R. (2014) Shockless explosion combustion: An innovative way of efficient constant volume combustion in gas turbines. Combustion Science and Technology, 186 (10-11). pp. 1680-1689.

Bauer, M. and Baumann, M. and Scheck, L. and Gassmann, A. and Heuveline , V. and Jones, S. (2014) Simulation of tropical-cyclone-like vortices in shallow-water ICON-hex using goal-oriented r-adaptivity. Theoretical and Computational Fluid Dynamics, 28 (1). pp. 107-128. ISSN Print: 0935-4964 Online:1432-2250

Schöneberg, J. and Ullrich, Alexander and Noé, F. (2014) Simulation tools for particle-based reaction-diffusion dynamics in continuous space. BMC Biophysics, 7 . p. 11.

Hédin, F. and Plattner, N. and Doll, J. D. and Meuwly, M. (2014) Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules. Journal of Chemical Theory and Computation, 10 (10). pp. 4284-4296. ISSN 1549-9618

Remmler, S. and Hickel, S. (2014) Spectral eddy viscosity of stratified turbulence. Journal of Fluid Mechanics . (In Press)

Prinz, J.-H. and Chodera, J. D. and Noé, F. (2014) Spectral rate theory for two-state kinetics. Phys Rev X, 4 . 011020.

Wu, H. and Mey, A.S.J.S. and Rosta, E. and Noé, F. (2014) Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states. J. Chem. Phys., 141 (21). p. 214106.

Schmidt, B. and Friedrich, B. (2014) Topology of surfaces for molecular Stark energy, alignment and orientation generated by combined permanent and induced electric dipole interactions. J. Chem. Phys., 140 (6). 064317.

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

Queck, R. and Bernhofer, C. and Bienert, A. and Eipper, T. and Goldberg, V. and Harmansa, S. and Hildebrand, V. and Maas, H.-G and Schlegel, F. and Stiller, J. (2014) TurbEFA: an interdisciplinary effort to investigate the turbulent flow across a forest clearing. Meteorologische Zeitschrift, 1 .

Berninger, H. and Ohlberger, M. and Sander, O. and Smetana, K. (2014) Unsaturated subsurface flow with surface water and nonlinear in- and outflow conditions. Mathematical Models and Methods in Applied Sciences, 24 (5). pp. 901-936. ISSN 1793-6314

Nüske, F. and Keller, B. and Pérez-Hernández, G. and Mey, A.S.J.S. and Noé, F. (2014) Variational Approach to Molecular Kinetics. J. Chem. Theory Comput., 10 . pp. 1739-1752.

Sander, O. and Schiela, A. (2014) Variational analysis of the coupling between a geometrically exact Cosserat rod and an elastic continuum. Zeitschrift für Angewandte Mathematik und Physik (ZAMP), 65 (6). pp. 1261-1288. ISSN 0044-2275 (Print) 1420-9039 (Online)

Oevermann, M. and Klein, R. (2014) An asymptotic solution approach for elliptic equations with discontinuous coefficients. Journal of Computational Physics, 261 . pp. 230-243.

Benacchio, T. and O'Neill, W.P. and Klein, R. (2014) A blended soundproof-to-compressible numerical model for small- to mesoscale atmospheric dynamic. Monthly Weather Review, 142 (12). pp. 4416-4438. ISSN Online:1520-0493; Print: 0027-0644

Plattner, N. and Meuwly, M. (2014) The effect of classical and quantum dynamics on vibrational frequency shifts of H2 in clathrate hydrates. The Journal of Chemical Physics, 140 (2). 024311. ISSN 0021-9606

Vincze, M. and Harlander, U. and von Larcher, T. and Egbers, C. (2014) An experimental study of regime transitions in a differentially heated baroclinic annulus with flat and sloping bottom topographies. Nonlinear Processes in Geophysics, 21 . pp. 237-250.

O'Neill, W.P. and Klein, R. (2014) A moist pseudo-incompressible model. Atmospheric Research, 142 (1). pp. 133-141.

Gerber, S. and Oevermann, M. (2014) A two dimensional Euler–Lagrangian model of wood gasification in a charcoal bed – Part I: model description and base scenario. Science Direct, 115 . pp. 385-400.

Mey, A.S.J.S. and Wu, H. and Noé, F. (2014) xTRAM: Estimating equilibrium expectations from time-correlated simulation data at multiple thermodynamic states. Phys. Rev. X, 4 (4). 041018.

2013

Hartmann, C. and Banisch, Ralf and Sarich, M. and Badowski, T. and Schütte, Ch. (2013) Characterization of Rare Events in Molecular Dynamics. Entropy (Special Issue), 16 (1). pp. 350-376. ISSN 1099-4300

Delle Site, L. (2013) Multidisziplinarität in Deutschland: Mehrwert oder Beschränkung? Physik Journal (12). p. 17.

Pluharova, E. and Marsalek, O. and Schmidt, B. and Jungwirth, P. (2013) Ab Initio Molecular Dynamics Approach to Quantitative Description of Ion Pairing in Water. J. Phys. Chem. Lett., 4 (23). pp. 4177-4181.

Haack, F. and Fackeldey, K. and Röblitz, S. and Scharkoi, O. and Weber, M. and Schmidt, B. (2013) Adaptive spectral clustering with application to tripeptide conformation analysis. J. Chem. Phys., 139 (19). p. 194110.

Paulus, F. and Weiss, M. E. R. and Steinhilber, D. and Nikitin, A. and Schütte, Ch. and Haag, R. (2013) Anionic Ring-Opening Polymerization Simulations for Hyperbranched Polyglycerols with Defined Molecular Weights. Macromolecules, 46 (21). pp. 8458-8466. ISSN 0024-9297

Steijger, T. and Abril, J. F. and Engström, P. G. and Kokocinski, F. and The RGASP Consortium, and Richard, H. and Schulz, M. H. and Weese, D. and Hubbard, T. and Guigó, R. and Harrow, J. and Bertone, P. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nature Methods, 10 (12). pp. 1177-1184.

Jouvet, G. and Gräser, C. (2013) An adaptive Newton multigrid method for a model of marine ice sheets. Journal of Computational Physics, 252 . pp. 419-437. ISSN 0021-9991

Wang, H. and Hartmann, C. and Schütte, Ch. (2013) Linear response theory and optimal control for a molecular system under nonequilibrium conditions. Molecular Physics, 111 . pp. 3555-3564. ISSN 0026-8976

Hartmann, C. and Yanao, Tomohiro (2013) The falling cat problem and shape effects in small molecules in a random environment: a case study. Molecular Physics, 111 (22-23). pp. 3534-3545. ISSN 0026-8976

Gräser, C. and Kornhuber, R. and Sack, U. (2013) Time discretizations of anisotropic Allen-Cahn equations. IMA Journal of Numerical Analysis, 33 (4). pp. 1226-1244. ISSN 0272-4979

Andreotti, S. and Reinert, K. and Canzar, S. (2013) The duplication-loss small phylogeny problem: from cherries to trees. Journal of Computational Biology, 20 (9). pp. 643-59.

Nikitin, A. and Wulkow, M. and Schütte, Ch. (2013) Modeling of Free Radical Styrene/Divinylbenzene Copolymerization with the Numerical Fractionation Technique. Macromolecular Theory and Simulation, 22 (9). pp. 475-489.

Enciso , M. and Schütte, Ch. and Delle Site, L. (2013) pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study. Molecular Physics, 111 (22-23). pp. 3363-3371. ISSN 0026-8976

Pattyn, F. and Perichon, L. and Durand, G. and Favier, L. and Gagliardini, O. and Hindmarsh, R. and Zwinger, T. and Albrecht, T. and Cornford, S. and Docquier, D. and Fuerst, J. and Goldberg, G. and Gudmundsson, G. H. and Humbert, A. and Huetten, M. and Huybrechts, P. and Jouvet, G. and Kleiner, T. and Larour, E. and Martin, D. (2013) Grounding-line migration in plan-view marine ice-sheet models: Results of the ice2sea MISMIP3d intercomparison. Journal of Glaciology, 59 (215). pp. 410-422. ISSN 0022-1430

Gul, Rahim and Bernhard, Stefan (2013) Local sensitivity analysis of cardiovascular system parameters. International Journal of Scientific and Engineering Research (IJSER), 4 (7). pp. 2648-2661. ISSN 2229-5518

Sander, O. and Klapproth, C. and Youett, J. and Kornhuber, R. and Deuflhard, P. (2013) Towards an efficient numerical simulation of complex 3D knee joint motion. Computing and Visualization in Science, 16 (3). pp. 119-138. ISSN 1432-9360

Vercauteren, N. and Destouni, G. and Dahlberg, C.J. and Hylander, K. (2013) Fine-resolved, near-coastal spatiotemporal variation of temperature in response to insolation. Journal of Applied Meteorology and Climatology, 52 (5). pp. 1208-1220. ISSN Online: 1558-8432 Print: 1558-8424

Leichtle, A. and Ceglarek, U. and Weinert, P. and Nakas, C. T. and Nuoffer, J.-M. and Kase, J. and Conrad, T. O. F. and Witzigmann, H. and Thiery, J. and Fiedler, G. M. (2013) Pancreatic carcinoma, pancreatitis, and healthy controls - metabolite models in a three-class diagnostic dilemma. Metabolomics, 9 (3). pp. 677-687. ISSN 1573-3890

Rath, B. A. and Yousef, K. P. and Katzenstein, D. K. and Shafer, R. W. and Schütte, Ch. and von Kleist, M. and Merigan, T. C. (2013) In vitro HIV-1 Evolution in Response to Triple Reverse Transcriptase Inhibitors & In Silico Phenotypic Analysis. PLoS ONE, 8 (4). e61102. ISSN 1932-6203

Blomberg, S. and Hoffmann, M. and Gustafson, J. and Martin, N. M. and Fernandes, V. R. and Borg, A. and Liu, Z. and Chang, R. and Matera, S. and Reuter, K. and Lundgren, E. (2013) In Situ X-Ray Photoelectron Spectroscopy of Model Catalysts: At the Edge of the Gap. Physical Review Letters, 110 (11). p. 117601.

Nahnsen, S. and Bielow, C. and Reinert, K. and Kohlbacher, O. (2013) Tools for Label-free Peptide Quantification. Molecular & Cellular Proteomics, 12 (3). pp. 549-556. ISSN 1535-9476

Zerck, A. and Nordhoff, E. and Lehrach, H. and Reinert, K. (2013) Optimal precursor ion selection for LC-MALDI MS/MS. BMC Bioinformatics, 14 (1). p. 56. ISSN 1471-2105

Neu, V. and Bielow, C. and Gostomski, I. and Wintringer, R. and Braun, R. and Reinert, K. and Schneider, P. and Stuppner, H. and Huber, C. (2013) Rapid and Comprehensive Impurity Profiling of Synthetic Thyroxine by Ultrahigh-Performance Liquid Chromatography–High-Resolution Mass Spectrometry. Analytical Chemistry, 85 (6). pp. 3309-3317. ISSN 0003-2700

Pérez-Hernández, G. and Schmidt, B. (2013) Anisotropy of the Water-Carbon Interaction: Molecular Simulations of Water in Low-Diameter Carbon Nano-Tubes. Phys. Chem. Chem. Phys., 15 (14). pp. 4995-5006.

Latorre, J.C. and Pavliotis, G. A. and Kramer, P. R. (2013) Corrections to Einstein's relation for Brownian motion in a tilted periodic potential. J. Stat. Phys., 150 (4). pp. 776-803. ISSN 0022-4715

Siragusa, E. and Weese, D. and Reinert, K. (2013) Fast and accurate read mapping with approximate seeds and multiple backtracking. Oxford Journals, 41 (7). e78. ISSN Print ISSN 0305-1048; Online ISSN 1362-4962

Neu, V. and Bielow, C. and Schneider, P. and Reinert, K. and Stuppner, H. and Huber, C. (2013) Investigation of Reaction Mechanisms of Drug Degradation in the Solid State: A Kinetic Study Implementing Ultrahigh-Performance Liquid Chromatography and High-Resolution Mass Spectrometry for Thermally Stressed Thyroxine. Analytical Chemistry, 85 (4). pp. 2385-2390. ISSN 0003-2700

Rath, B. and von Kleist, M. and Castillo, M. E. and Kolevic, L. and Caballero, P. and Soto-Castellares, G. and Amedee, A. M. and Robinson, J.E. and Katzenstein, D. K. and Van Dyke, R.B. and Oberhelman, R. (2013) Antiviral Resistance and Correlates of Virologic Failure in the first Cohort of HIV-Infected Children Gaining Access to Structured Antiretroviral Therapy in Lima, Peru: A Cross-Sectional Analysis. BMC Infectious Diseases, 13 (1).

Sarich, M. and Banisch, Ralf and Hartmann, C. and Schütte, Ch. (2013) Markov State Models for Rare Events in Molecular Dynamics. Entropy (Special Issue), 16 (1). pp. 258-286. ISSN 1099-4300

Benacchio, T. and Bonaventura, L. (2013) Absorbing boundary conditions: a spectral collocation approach. International Journal for Numerical Methods in Fluids, 72 (10.1002/fld.3768). pp. 913-936. ISSN Online: 1097-0363

Gupta, Pooja and Reinsch , Norbert and Spötter, Andreas and Conrad, T. O. F. and Bienefeld, Kaspar (2013) Accuracy of the unified approach in maternally influenced traits - illustrated by a simulation study in the honey bee (Apis mellifera). BMC Genetics, 14 (36).

Hartmann, C. and Schäfer-Bung, B. and Thöns-Zueva, A. (2013) Balanced averaging of bilinear systems with applications to stochastic control. SIAM J. Control Optim., 51 (3). pp. 2356-2378.

Kantcheva, A. K. and Quick, M. and Shi, L. and Winther, A.-M. L. and Stolzenberg, S. and Weinstein, H. and Javitch, J. A. and Nissen, P. (2013) Chloride binding site of neurotransmitter sodium symporters. Proceedings of the National Academy of Sciences, 110 (21). p. 8489. ISSN 0027-8424

Wolf, S and Hinkel, J., and Hallier, M. and Bisaro, A. and Lincke, D. and Ionescu, C. and Klein, R.J.T. (2013) Clarifying vulnerability definitions and assessments using formalisation. International Journal of Climate Change Strategies and Management, 5 (1). ISSN 1756-8692

Kumar, B. and Schumacher, J. and Shaw, R.A. (2013) Cloud microphysical effects of turbulent mixing and entrainment. Theoretical and Computational Fluid Dynamics , 27 (3-4). pp. 361-376. ISSN Print: 0935-4964; Online: 1432-2250

Müller, A. and Behrens, J. and Giraldo, F.X. and Wirth, V. (2013) Comparison between adaptive and uniform discontinuous Galerkin simulations in dry 2D bubble experiments. Journal of Computational Physics, 235 . pp. 371-393.

Remmler, S. and Fruman, M. D. and Hickel, S. (2013) Direct numerical simulation of a breaking inertia-gravity wave. Journal of Fluid Mechanics, 722 . pp. 424-436.

Lindner, Benjamin and Yi, Zheng and Prinz, J.-H. and Smith, J. C. and Noé, F. (2013) Dynamic Neutron Scattering from Conformational Dynamics I: Theory and Markov models. J. Chem. Phys., 139 . p. 175101.

Yi, Zheng and Lindner, Benjamin and Prinz, J.-H. and Noé, F. and Smith, J. C. (2013) Dynamic Neutron Scattering from Conformational Dynamics II: Application using Molecular Dynamics Simulation and Markov modeling. J. Chem. Phys., 139 . p. 175102.

Trendelkamp-Schroer, B. and Noé, F. (2013) Efficient Bayesian estimation of Markov model transition matrices with given stationary distribution. J. Phys. Chem., 138 . p. 164113.

Delle Site, L. and Ghiringhelli, L. M. and Ceperley, D.M. (2013) Electronic Energy Functionals: Levy-Lieb principle within the Ground State Path Integral Quantum Monte Carlo. International Journal of Quantum Chemistry, 113 . p. 155.

Bordás, R. and Roloff, CH. and Thévenin, D. and Shaw, R.A. (2013) Experimental determination of droplet collision rates in turbulence. New Journal of Physics, 15 (045010 ).

Bruckner, S. and Kayser, B. and Conrad, T. O. F. (2013) Finding Modules in Networks with Non-modular Regions. Lecture Notes in Computer Science (Proceedings of SEA 2013), 7933 . pp. 188-199. ISSN 0302-9743

Wang, H. and Hartmann, C. and Schütte, Ch. and Delle Site, L. (2013) Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique. Phys. Rev. X, 3 . 011018.

Braack, M. and Taschenberger, N. (2013) Hierarchical a posteriori residual based error estimators for bilinear finite elements. Int. J. Numer. Anal. Model., 10 (2). pp. 466-480. (Submitted)

Pérez-Hernández, G. and Paul, F. and Giorgino, T. and de Fabritiis, G. and Noé, F. (2013) Identification of slow molecular order parameters for Markov model construction. J. Chem. Phys., 139 . 015102.

Peuker, Sebastian and Cukkemane, Abhishek and Held, M. and Noé, F. and Kaupp, Benjamin and Seifert, Reinhard (2013) Kinetics of ligand-receptor interaction reveals an induced-fit mode of binding in a cyclic nucleotide-activated protein. Biophys. J., 104 . pp. 63-74.

Winkelmann, S. and Schütte, Ch. and von Kleist, M. (2013) Markov Control Processes with Rare State Observation: Sensitivity Analysis with Respect to Optimal Treatment Strategies against HIV-1. International Journal of Biomathematics and Biostatistics, 2 (1). ISSN 0973-7340

Banisch, Ralf and Hartmann, C. (2013) Meshless discretization of LQ-type stochastic control problems. arXiv preprint, arXiv: . (Unpublished)

Kanda, M. and Inagaki, A. and Miyamoto, T. and Gryschka, M. and Raasch, S. (2013) A New Aerodynamic Parameterization for Real Urban Surfaces. Boundary-Layer Meteorology, 148 . pp. 357-377.

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

Hardering, H. (2013) Numerical approximation of capillary surfaces in a negative gravitational field. Interfaces and Free Boundaries, 15 (3). pp. 263-280. ISSN 1463-9971

Kunnen, R. P. J. and Siewert, C. and Meinke, M. and Schröder, W. and Beheng, K.D. (2013) Numerically determined geometric collision kernels in spatially evolving isotropic turbulence relevant for droplets in clouds. Atmospheric Research, 127 . pp. 8-21. ISSN 0169-8095

Siewert, C. and Kunnen, R. P. J. and Meinke, M. and Schröder, W. (2013) Orientation Statistics and Settling Velocity of Ellipsoids in Decaying Turbulence. Atmospheric Research . (In Press)

Plattner, N. and Doll, J. D. and Meuwly, M. (2013) Overcoming the Rare Event Sampling Problem in Biological Systems with Infinite Swapping. Journal of Chemical Theory and Computation, 9 (9). pp. 4215-4224. ISSN 1549-9618

Noé, F. and Wu, H. and Prinz, J.-H. and Plattner, N. (2013) Projected and Hidden Markov Models for calculating kinetics and metastable states of complex molecules. J. Chem. Phys., 139 . p. 184114.

Schöneberg, J. and Noé, F. (2013) ReaDDy - a software for particle based reaction diffusion dynamics in crowded cellular environments. PLoS ONE, 8 . e74261. ISSN 1932-6203

Scheck, L. and Jones, S. and Heuveline , V. (2013) Singular Vectors for barotropic, hurricane-like vortices in horizontal shear: Structure and perturbation growth mechanisms. Journal of the Atmospheric Sciences . ISSN Online: 1520-0469 Print: 0022-4928 (Submitted)

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.

2012

Doll, J. D. and Plattner, N. and Freeman, D. L. and Liu, Y. and Dupuis, P. (2012) Rare-event sampling: Occupation-based performance measures for parallel tempering and infinite swapping Monte Carlo methods. The Journal of Chemical Physics, 137 (20). p. 204112. ISSN 00219606

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

Pluharova, E. and Marsalek, O. and Schmidt, B. and Jungwirth, P. (2012) Peptide salt bridge stability: From gas phase via microhydration to bulk water simulations. J. Chem. Phys., 137 (18). p. 185101.

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

Matera, S. and Reuter, K. (2012) When atomic-scale resolution is not enough: Spatial effects on in situ model catalyst studies. Journal of Catalysis, 295 . pp. 261-268.

Lee, M. W. and Plattner, N. and Meuwly, M. (2012) Structure, spectroscopy and dynamics of layered H2O and CO2 ices. Physical Chemistry Chemical Physics, 14 (44). pp. 15464-15474. ISSN 1463-9076

Sarich, M. and Schütte, Ch. (2012) Approximating Selected Non-dominant Timescales by Markov State Models. Comm. Math. Sci., 10 (3). pp. 1001-1013.

Weese, D. and Holtgrewe, M. and Reinert, K. (2012) RazerS 3: Faster, fully sensitive read mapping. Bioinformatics, 28 (20). pp. 2592-2599.

Pérez-Hernández, G. and González-Vázquez, J. and González, L. (2012) IR Spectrum of FHF–and FDF–Revisited Using a Spectral Method in Four Dimensions. The Journal of Physical Chemistry A, 116 (46). pp. 11361-11369. ISSN 1089-5639

Wang, H. and Schütte, Ch. and Zhang, P. (2012) Error Estimate of Short-Range Force Calculation in the Inhomogeneous Molecular Systems. Phys. Rev. E, 86 (02). 026704.

Schütte, Ch. and Winkelmann, S. and Hartmann, C. (2012) Optimal control of molecular dynamics using Markov state models. Math. Program. (Series B), 134 (1). pp. 259-282.

Leichtle, A. and Nuoffer, J.-M. and Ceglarek, U. and Kase, J. and Conrad, T. O. F. and Witzigmann, H. and Thiery, J. and Fiedler, G. M. (2012) Serum amino acid profiles and their alterations in colorectal cancer. Metabolomics . ISSN 1573-3890

Wang, H. and Zhang, P. and Schütte, Ch. (2012) On the Numerical Accuracy of Ewald, Smooth Particle Mesh Ewald, and Staggered Mesh Ewald Methods for Correlated Molecular Systems. J. Chem. Theo. Comp., 8 (9). pp. 3243-3256.

Buchholz, M. and Goletz, Ch.-M. and Grossmann, F. and Schmidt, B. and Heyda, J. and Jungwirth, P. (2012) Semiclassical Hybrid Approach to Condensed Phase Molecular Dynamics: Application to the I2Kr17 Cluster. J. Phys. Chem. A, 116 (46). pp. 11199-11210.

Aiche, S. and Reinert, K. and Schütte, Ch. and Hildebrand, D. and Schlüter, H. and Conrad, T. O. F. (2012) Inferring Proteolytic Processes from Mass Spectrometry Time Series Data Using Degradation Graphs. PLoS ONE, 7 (7). e40656. ISSN 1932-6203

Junker, J. and Bielow, C. and Bertsch, A. and Sturm, M. and Reinert, K. and Kohlbacher, O. (2012) TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data. J. Proteome Res., 11 (7). pp. 3914-3920. ISSN 1535-3893

Sander, O. (2012) Geodesic finite elements on simplicial grids. International Journal for Numerical Methods in Engeneering, 92 (12). pp. 999-1025. ISSN Online: 1097-0207

Weiss, M. E. R. and Paulus, F. and Steinhilber, D. and Nikitin, A. and Haag, R. and Schütte, Ch. (2012) Estimating Kinetic Parameters for the Spontaneous Polymerization of Glycidol at Elevated Temperatures. MACROMOLECULAR THEORY and SIMULATIONS, 21 (7). pp. 470-481.

Djurdjevac, N. and Bruckner, S. and Conrad, T. O. F. and Schütte, Ch. (2012) Random Walks on Complex Modular Networks. Journal of Numerical Analysis, Industrial and Applied Mathematics, 6 (1-2). pp. 29-50. ISSN 1790–8140

Higgins, C. W. and Froidevaux, M. and Simeonov, V. and Vercauteren, N. and Barry, C. and Parlange, M. B. (2012) The Effect of Scale on the Applicability of Taylor's Frozen Turbulence Hypothesis in the Atmospheric Boundary Layer. Boundary-Layer Meteorology, 143 (2). 379 -391. ISSN Print: 0006-8314 Online: 1573-1472

Andreotti, S. and Klau, G. W. and Reinert, K. (2012) Antilope - A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) , 9 (2). pp. 385-394.

Plattner, N. and Meuwly, M. (2012) Quantifying the Importance of Protein Conformation on Ligand Migration in Myoglobin. Biophysical Journal, 102 (2). pp. 333-341. ISSN 00063495

Emde, A.-K. and Schulz, M. H. and Weese, D. and Sun, R. and Vingron, M. and Kalscheuer, V. M. and Haas, S. A. and Reinert, K. (2012) Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS. Bioinformatics, 28 (5). pp. 619-627.

Fritsch, S. and Poblete, S. and Junghans, C. and Ciccotti, G. and Delle Site, L. and Kremer, K. (2012) Adaptive Resolution Molecular Dynamics Simulation Through Coupling to an Internal Particle Reservoir. Physical Review Letters, 108 . p. 170602.

Wang, H. and Schütte, Ch. and Delle Site, L. (2012) Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion. J. Chem. Theo. Comp., 8 (8). pp. 2878-2887.

Metzner, Ph. and Putzig, L. and Horenko, I. (2012) Analysis of persistent non-stationary time series and applications. Communications in Applied Mathematics and Computational Science, 7 (2). pp. 175-229.

Donadio, D. and Ghiringhelli, L. M. and Delle Site, L. (2012) Autocatalytic and cooperatively-stabilized dissociation of water on a stepped platinum surface. Journal of the American Chemical Society, 134 . pp. 19217-19222.

Münch, M. (2012) Brände mit Beteiligung von Wärmedämmverbundsystemen. AIZ - Das Immobilienmagazin . pp. 52-55.

Held, M. and Noé, F. (2012) Calculating kinetics and pathways of protein–ligand association. Eur. J. Cell Biol., 91 . pp. 357-364.

Brdar, S. and Dedner, A. and Klöfkorn, R. (2012) Compact and stable Discontinuous Galerkin methods for convection-diffusion problems. SIAM Journal of Scientific Computation, 34 (1). 263-282 . ISSN Print: 1064-8275 Online: 1095-7197

Brdar, S. and Baldauf, M. and Dedner, A. and Klöfkorn, R. (2012) Comparison of dynamical cores for NWP models. Theoretical and Computational Fluid Dynamics . ISSN 0935-4964 (In Press)

Mukherjee, B. and Delle Site, L. and Kremer, K. and Peter, C. (2012) Derivation of Coarse Grained Models for Multiscale Simulation of Liquid Crystalline Phase Transitions. Journal of Physical Chemistry B, 116 . 8474.

Spötter, Andreas and Gupta, Pooja and Nürnberg, G. and Reinsch , Norbert and Bienefeld, Kaspar (2012) Development of a 44K SNP assay focussing on the analysis of a varroa-specific defence behaviour in honey bees (Apis mellifera carnica). Molecular Ecology Resources, 12 . pp. 323-332.

Remmler, S. and Hickel, S. (2012) Direct and large-eddy simulation of stratified turbulence. International Journal of Heat and Fluid Flow, 35 . pp. 13-24. ISSN 0142-727X

Senne, M. and Trendelkamp-Schroer, B. and Mey, A.S.J.S. and Schütte, Ch. and Noé, F. (2012) EMMA - A software package for Markov model building and analysis. Journal of Chemical Theory and Computation, 8 . pp. 2223-2238.

Sander, O. and Schiela, A. (2012) Energy minimizers of the coupling of a Cosserat rod to an elastic continuum. Mathematical Modelling, 7 (1). pp. 1118-1123.

Djurdjevac, N. and Sarich, M. and Schütte, Ch. (2012) Estimating the eigenvalue error of Markov State Models. Multiscale Modeling & Simulation, 10 (1). pp. 61-81.

Kumar, B. and Janetzko , F. and Schumacher, J. and Shaw, R.A. (2012) Extreme responses of a coupled scalar–particle system during turbulent mixing. New Journal of Physics, 14 115020 .

Wehmeyer, C. and Falk von Rudorff, G. and Wolf, S. and Kabbe, G. and Schärf, D. and Kühne, T. D. and Sebastiani, D. (2012) Foraging on the potential energy surface: A swarm intelligence-based optimizer for molecular geometry. The Journal of Chemical Physics, 137 (19). p. 194110. ISSN 00219606

Dommert, F. and Wendler, K. and Berger, R. and Delle Site, L. and Holm, C. (2012) Force fields for studying structure and dynamics of imidazolium based ionic liquids - a critical review of recent developments. ChemPhysChem, 13 . p. 1625.

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

2011

Jouvet, G. and Huss, M. and Funk, M. and Blatter, H. (2011) Modelling the retreat of Grosser Aletschgletscher, Switzerland, in a changing climate. Journal of Glaciology, 57 (206). pp. 1033-1045. ISSN 0022-1430

Berninger, H. and Kornhuber, R. and Sander, O. (2011) Fast and robust numerical solution of the Richards equation in homogeneous soil. SIAM Journal on Numerical Analysis, 49 (6). pp. 2576-2597. ISSN 0036-1429

Plattner, N. and Doll, J. D. and Dupuis, P. and Wang, H. and Liu, Y. and Gubernatis, J. E. (2011) An infinite swapping approach to the rare-event sampling problem. The Journal of Chemical Physics, 135 (13). p. 134111. ISSN 00219606

Kehr, B. and Weese, D. and Reinert, K. (2011) STELLAR: fast and exact local alignments. BMC Bioinformatics, 12 (S9). S15. ISSN 1471-2105

Fischer, M. and Lorenz, U. and Schmidt, B. and Schmidt, R. (2011) Fragmentation due to centrifugal forces in the photodissociation of H2+ in intense laser fields. Phys. Rev. A, 84 (3). 033422.

Vercauteren, N. and Huwald, H. and Bou-Zeid, E. and Selker, J. S. and Lemmin, U. and Parlange, M. B. and Lunati, I. (2011) Evolution of Superficial Lake Water Temperature Profile Under Diurnal Radiative Forcing. Water Resources Research, 47 (9).

Berninger, H. and Kornhuber, R. and Sander, O. (2011) Heterogeneous domain decomposition of surface and porous media flow. AIP Conference Proceedings, 1389 . pp. 2025-2028. ISSN 0094-243X

Schäfer-Bung, B. and Hartmann, C. and Schmidt, B. and Schütte, Ch. (2011) Dimension reduction by balanced truncation: Application to light-induced control of open quantum systems. J. Chem. Phys., 135 (1). 014112.

Böcker, S. and Kehr, B. and Rasche, F. (2011) Determination of Glycan Structure from Tandem Mass Spectra. IEEE/ACM Transactions on Computational Biology and Bioinformatics , 8 (4). pp. 976-986. ISSN 1545-4963

Bielow, C. and Aiche, S. and Andreotti, S. and Reinert, K. (2011) MSSimulator: Simulation of Mass Spectrometry Data. Journal of Proteome Research, 10 (7). pp. 2922-2929.

Holtgrewe, M. and Emde, A.-K. and Weese, D. and Reinert, K. (2011) A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping. BMC Bioinformatics, 12 (120). ISSN 1471-2105

Schütte, Ch. and Noé, F. and Lu, Jianfeng and Sarich, M. and Vanden-Eijnden, E. (2011) Markov State Models Based on Milestoning. J. Chem. Phys., 134 (20). p. 204105.

Prinz, J.-H. and Wu, H. and Sarich, M. and Keller, B. and Senne, M. and Held, M. and Chodera, J. D. and Schütte, Ch. and Noé, F. (2011) Markov models of molecular kinetics: Generation and Validation. J. Chem. Phys., 134 . p. 174105.

Ullrich, Alexander and Rohrschneider, Markus and Scheuermann, Gerik and Stadler, Peter F. and Flamm, Christoph (2011) In Silico Evolution of Early Metabolism. Artificial Life, 17 (2). pp. 87-108. ISSN 1064-5462

Zou, Q. and Veeser, A. and Kornhuber, R. and Gräser, C. (2011) Hierarchical error estimates for the energy functional in obstacle problems. Numerische Mathematik, 117 (4). pp. 653-677. ISSN 0029-599X

Ruprecht, D. and Klein, R. (2011) A Model for Nonlinear Interactions of Internal Gravity Waves with Saturated Regions. Meteorologische Zeitschrift, 20 (2). pp. 243-252.

Hartmann, C. and Latorre, J.C. (2011) Computing free energy differences using conditioned diffusions. AIP Conf. Proc., 1332 (1). pp. 218-220.

von Kleist, M. and Menz, S. and Stocker, H. and Arasteh, K. and Huisinga, W. and Schütte, Ch. (2011) HIV Quasispecies Dynamics during Pro-active Treatment Switching: Impact on Multi-Drug Resistance and Resistance Archiving in Latent Reservoirs. Plos One, 6 (3). e18204.

Vetter, A. and Liu, Y. and Witt, F. and Manjubala, I. and Sander, O. and Rao Epari, D. and Fratzl, P. and Duda, G. and Weinkamer, R. (2011) The mechanical heterogeneity of the hard callus influences local tissue strains during bone healing. Journal of Biomechanics, 44 (3). pp. 517-523. ISSN 0021-9290

Owschimikow, N. and Schmidt, B. and Schwentner, N. (2011) Laser-induced alignment and anti-alignment of rotationally excited molecules. Phys. Chem. Chem. Phys., 13 (19). pp. 8671-8680.

Held, M. and Metzner, Ph. and Prinz, J.-H. and Noé, F. (2011) Mechanisms of Protein-Ligand association and its modulation by protein mutations. Biophys. J., 100 (3). pp. 701-710.

Owinoh, A.Z. and Stevens, B. and Klein, R. (2011) Multiscale Asymptotics Analysis for the Mesoscale Dynamics of Cloud-Topped Boundary Layers. Journal of the Atmospheric Sciences, 68 (2). pp. 379-402. ISSN Online 1520-0469, Print 0022-4928

Matera, S. and Meskine, H. and Reuter, K. (2011) Adlayer inhomogeneity without lateral interactions: Rationalizing correlation effects in CO oxidation at RuO2(110) with first-principles kinetic Monte Carlo. The Journal of Chemical Physics, 134 (6). 064713.

Walter, J. and Hartmann, C. and Maddocks, J. (2011) Ambient space formulations and statistical mechanics of holonomically constrained Langevin systems. Eur. Phys. J. Special Topics, 200 (1). pp. 153-181.

Jouvet, G. and Rappaz, J. (2011) Analysis and finite element approximation of a nonlinear stationary stokes problem arising in glaciology. Advances in Numerical Analysis, 2011 (Articl). ISSN 1687-9562

Keller, B. and Hünenberger, Philippe and van Gunsteren, Wilfred (2011) An Analysis of the Validity of Markov State Models for Emulating the Dynamics of Classical Molecular Systems and Ensembles. J. Chem. Theo. Comput., 7 . pp. 1032-1044.

Schiffmann, C and Sebastiani, D (2011) Artificial Bee Colony Optimization of Capping Potentials for Hybrid Quantum Mechanical/Molecular Mechanical Calculations. Journal of Chemical Theory and Computation, 7 (5). p. 1307. ISSN 1549-9618

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 .

2010

Assmann, M. and Sanz, C. S. and Pérez-Hernández, G. and Worth, G. A. and González, L. (2010) Excited state dynamics of a model asymmetric molecular rotor: A five-dimensional study on 2-cyclopentylidene-tetrahydrofuran. Chemical Physics, 377 (1-3). pp. 86-95. ISSN 03010104

Holtgrewe, M. (2010) Mason – A Read Simulator for Second Generation Sequencing Data. Technical Report FU Berlin .

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

Matera, S. and Reuter, K. (2010) Transport limitations and bistability for in situ CO oxidation at RuO 2(110): First-principles based multiscale modeling. Physical Review B, 82 (8). 085446.

Flamm, Christoph and Ullrich, Alexander and Hofacker, L. Ivo and Stadler, Peter F. (2010) Evolution of Metabolic Networks: A Computational Framework. Journal of Systems Chemistry, 1 (4).

Pérez-Hernández, G. and González, L. (2010) Mechanistic insight into light-driven molecular rotors: a conformational search in chiral overcrowded alkenes by a pseudo-random approach. Physical Chemistry Chemical Physics, 12 (38). pp. 12279-12289. ISSN 1463-9076

Assmann, M. and Pérez-Hernández, G. and González, L. (2010) On the Light-Driven Isomerization of a Model Asymmetric Molecular Rotor: Conformations and Conical Intersections of 2-Cyclopentylidene-tetrahydrofuran. The Journal of Physical Chemistry A, 114 (34). pp. 9342-9348. ISSN 1089-5639

Owschimikow, N. and Königsmann, F. and Maurer, J. and Giese, Ph. and Ott, A. and Schmidt, B. and Schwentner, N. (2010) Cross sections for rotational decoherence of perturbed nitrogen measured via decay of laser-induced alignment. J. Chem. Phys., 133 (4). 044311.

Plattner, N. and Lee, M. W. and Meuwly, M. (2010) Structural and spectroscopic characterization of mixed planetary ices. Faraday discussions, 147 . 217-230; discussion 251. ISSN 1359-6640

Plattner, N. and Doll, J. D. and Meuwly, M. (2010) Spatial averaging for small molecule diffusion in condensed phase environments. The Journal of Chemical Physics, 133 (4). 044506. ISSN 00219606

Marsalek, O. and Uhlig, F. and Frigato, T. and Schmidt, B. and Jungwirth, P. (2010) Dynamics of Electron Localization in Warm vs. Cold Water Clusters. Phys. Rev. Lett., 105 (4). 043002.

Hüser, D. and Gogol-Döring, A. and Lutter, T. and Weger, S. and Winter, K. and Hammer, E.-M. and Cathomen, T. and Reinert, K. and Heilbronn, R. (2010) Integration Preferences of Wildtype AAV-2 for Consensus Rep-Binding Sites at Numerous Loci in the Human Genome. PLoS Pathogens, 6 (7). e1000985. ISSN 1553-7374

Pilari, S. and Huisinga, W. (2010) Lumping of Physiologically-Based Pharmacokinetic Models and a Mechanistic Derivation of Classical Compartmental Models. Journal of Pharmacokinetics and Pharmacodynamics, 37 (4). pp. 365-405.

Pérez-Hernández, G. and Pelzer, A. and González, L. and Seideman, T. (2010) Biologically inspired molecular machines driven by light. Optimal control of a unidirectional rotor. New Journal of Physics, 12 (7). 075007. ISSN 1367-2630

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

Diederichs, E. and Juditski, A. and Spokoiny, V. and Schütte, Ch. (2010) Sparse Non-Gaussian Component Analysis. IEEE Transactions on Information Theory, 56 (6). pp. 3033-3047. ISSN 0018-9448

Keller, B. and Gattin, Z. and van Gunsteren, W. F. (2010) What stabilizes the 3_14-helix in beta^3-peptides? A conformational analysis using molecular simulation. PROTEINS: Structure, Function, and Bioinformatics, 78 (7). pp. 1677-1690.

Holtgrewe, M. and Sanders, P. and Schulz, C. (2010) Engineering a scalable high quality graph partitioner. 2010 IEEE International Symposium on Parallel & Distributed Processing (IPDPS) . pp. 1-12. ISSN 1530-2075

von Kleist, M. and Menz, S. and Huisinga, W. (2010) Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV. Plos Computational Biology, 6 (3). e1000720.

Bielow, C. and Ruzek, S. and Huber, C. and Reinert, K. (2010) Optimal Decharging and Clustering of Charge Ladders Generated in ESI−MS. J. Proteome Res., 9 (5). pp. 2688-2695. ISSN 1535-3893

Xavier , D. and Keller, B. and van Gunsteren, W. F. (2010) Comparing geometric and kinetic cluster algorithms for molecular simulation data. J. Chem. Phys., 132 (7). 074110.

Horenko, I. and Schütte, Ch. (2010) On metastable conformational analysis of non-equilibrium biomolecular time series. Multiscale Modeling & Simulation, 8 (2). pp. 701-716. ISSN 15403467

Emde, A.-K. and Grunert, M. and Weese, D. and Reinert, K. and Sperling, S. R. (2010) MicroRazerS: Rapid alignment of small RNA reads. Bioinformatics, 26 (1). pp. 123-124. ISSN 1367-4803

Sander, O. and Schmidt, L. and Ehrig, R. and Heller, M. and Taylor, B. and Kornhuber, R. (2010) Numerical determination of the medio-lateral force distribution in an ovine stifle joint. Biomedizinische Technik/Biomedical Engineering: Proceedings of BMT, Rostock, 55 (s1). ISSN 0013-558

Forster, R. and Kornhuber, R. (2010) A polynomial chaos approach to stochastic variational inequalities. Journal of Numerical Mathematics, 18 (4). pp. 235-255. ISSN 1570-2820

Devanathan, R. and Venkatnathan, A. and Rousseau, R. and Dupuis, M. and Frigato, T. and Gu, W. and Helms, V. (2010) Atomistic Simulation of Water Percolation and Proton Hopping in Nafion Fuel Cell Membrane. J. Phys. Chem. B, 114 (43). pp. 13681-13690.

Hartmann, C. and Vulcanov, V.-M. and Schütte, Ch. (2010) Balanced Truncation of Second Order Systems: a Hamiltonian approach. Multiscale Model. Simul., 8 (4). pp. 1348-1367.

Münch, M. (2010) Brandschutzaufklärung mit mathematischen Simulationsprogrammen: Wie Mathematik hilft, Ihr Leben zu retten! Schadenprisma - Zeitschrift für Schadenverhütung und Schadenforschung der öffentlichen Versicherer, 4 . pp. 16-19.

Zhu, H. and Blom, M. and Compagnon, I. and Rijs, A. M. and Roy, S. and von Helden, G. and Schmidt, B. (2010) Conformations and Vibrational Spectra of a Model Tripeptide: Change of Secondary Structure upon Micro-Solvation. Phys. Chem. Chem. Phys., 12 (14). 3415 -3425.

Queck, R. and Bernhofer, C. (2010) Constructing wind profiles in forests from limited measurements of wind and vegetation structure. Agricultural and Forest Meteorology .

Spötter, Andreas and Gupta, Pooja and Reinsch , Norbert and Zautke, F. and Bienefeld, Kaspar (2010) Development of a SNP-Assay for varroa tolerance in the honey bee. Apidologie, 41 (6). p. 685. ISSN 0044-8435 (Print) 1297-9678 (Online)

Qu, Z.-W. and Zhu, H. (2010) Do Anionic Titanium Dioxide Nano-Clusters Reach Bulk Band Gap? A Density Functional Theory Study. J. Comp. Chem., 31 (10). pp. 2038-2045.

Baumann, M. and Heuveline , V. (2010) Evaluation of Different Strategies for Goal Oriented Adaptivity in CFD - Part I: The Stationary Case. Preprint Series of the Engineering Mathematics and Computing Lab, 2010-05 .

Bordás, R. and Hagemeier, T. and Thévenin, D. (2010) Experimental Investigation of Droplet-Droplet Interactions. 23rd European Conference on Liquid Atomization and Spray Systems . 198.1-198.6. ISSN 978-80-7399-997-1

Münch, M. (2010) Fast and correct computation. A comprehensive test concept to proof the new FDS-ScaRC technique. 11th International Symposium on Fire Protection . 11 p.. ISSN 978-3-00-03966-2

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

Latorre, J.C. and Hartmann, C. and Schütte, Ch. (2010) Free energy computation by controlled Langevin processes. Procedia Computer Science, 1 (1). pp. 1591-1600.

Pilari, S. and Preusse, C. and Huisinga, W. (2010) Gestational Influences on the Pharmacokinetics of Gestagenic Drugs: A Combined In Silico, In Vitro and In Vivo Analysis. European Journal of Pharmaceutical Sciences . (Submitted)

Achatz, U. and Klein, R. and Senf, F. (2010) Gravity waves, scale asymptotics, and the pseudo-incompressible equations. Journal of Fluid Mechanics, 663 . pp. 120-147.

Schütte, Ch. and Wulkow, M. (2010) A Hybrid Galerkin–Monte-Carlo Approach to Higher-Dimensional Population Balances in Polymerization Kinetics. Macromol. React. Eng., 4 (9-10). pp. 562-577.

Marsalek, O. and Frigato, T. and VandeVondele, J. and Bradforth, P. E. and Schmidt, B. and Schütte, Ch. and Jungwirth, P. (2010) Hydrogen Forms in Water by Proton Transfer to a Distorted Electron. J. Phys. Chem. B, 114 (2). pp. 915-920.

Kenfack, A. and Marquardt, F. and Paramonov, G. K. and Barth, I. and Lasser, C. and Paulus, B. (2010) Initial-state dependence of coupled electronic and nuclear fluxes in molecules. Phys. Rev. A, 81 (5). 052502.

Bastian, G and Vogelsang, A and Schiffmann, C (2010) Isotopic Superlattices for Perfect Phonon Reflection. Journal of Electronic Materials, 39 (9). p. 1769. ISSN 0361-5235

Jebens, .S. and Knoth, O. and Arnold, M. and Weiner, R. (2010) Linearly implicit peer methods for the compressible Euler equations. Applied Numerical Mathematics . (Submitted)

Wu, H. and Noé, F. (2010) Maximum a posteriori estimation for Markov chains based on Gaussian Markov random fields. Procedia Computer Science, 1 (1). pp. 1665-1673.

Ruprecht, D. and Klein, R. and Majda, A. J. (2010) Modulation of Internal Gravity Waves in a Multiscale Model for Deep Convection on Mesoscales. Journal.of the Atmospheric Sciences, 67 (8). pp. 2504-2519. ISSN Online 1520-0469, Print 0022-4928

Schlegel, M. and Knoth, O. and Arnold, M. and Wolke, R (2010) Numerical solution of multiscale problems in atmospheric modeling. Applied Numerical Mathematics . (Submitted)

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

Sarich, M. and Noé, F. and Schütte, Ch. (2010) On the Approximation Quality of Markov State Models. Multiscale Model. Simul., 8 (4). pp. 1154-1177.

Horenko, I. (2010) On the identification of non-stationary factor models and their application to atmospherical data analysis. J. Atm. Sci., 67 (5). pp. 1559-1574.

Hartmann, C. and Schütte, Ch. and Ciccotti, G. (2010) On the linear response of mechanical systems with constraints. J. Chem. Phys., 132 (11). p. 111103.

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

2009

Véron, N. and Bauer, H. and Weiße, A. Y. and Lüder, G. and Werber, M. and Herrmann, B. G. (2009) Retention of gene products in syncytial spermatids promotes non-Mendelian inheritance as revealed by the t complex responder. Genes & Development, 23 (23). 2705-2710 .

Noé, F. and Schütte, Ch. and Vanden-Eijnden, E. and Reich, L. and Weikl, T. (2009) Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations. Proc. Natl. Acad. Sci. USA, 106 (45). pp. 19011-19016.

Klein, R. and Bates, K.R. and Nikiforakis, N. (2009) Well Balanced Compressible Cut-Cell Simulation of Atmospheric Flow. Philosophical Transaction of the Royal Society, 367 (1907). 4559-4575 . ISSN Online: 1471-2962

Matera, S. and Reuter, K. (2009) First-Principles Approach to Heat and Mass Transfer Effects in Model Catalyst Studies. Catalysis letters, 133 (1-2). pp. 156-159. ISSN 1011-372X

Doll, J. D. and Gubernatis, J. E. and Plattner, N. and Meuwly, M. and Dupuis, P. and Wang, H. (2009) A spatial averaging approach to rare-event sampling. The Journal of Chemical Physics, 131 (10). p. 104107. ISSN 00219606

Meskine, H. and Matera, S. and Scheffler, M. and Reuter, K. and Metiu, H. (2009) Examination of the concept of degree of rate control by first-principles kinetic Monte Carlo simulations. Surface Science, 603 (10). pp. 1724-1730.

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

Splettstößer, T. and Noé, F. and Oda, T. and Smith, J. C. (2009) Nucleotide-dependence of G-actin conformation from multiple molecular dynamics simulations and observation of a putatively polymerisation-competent superclosed state. Proteins, 76 . pp. 353-364.

Oevermann, M. and Scharfenberg , C. and Klein, R. (2009) A sharp interface finite volume method for elliptic equations on Cartesian grids. Journal of Computational Physics, 228 (14). pp. 5184-5206.

Weese, D. and Emde, A.-K. and Rausch, T. and Döring, A. and Reinert, K. (2009) RazerS - Fast Read Mapping with Sensitivity Control. Genome Research, 19 (9). pp. 1646-1654.

Schütte, Ch. and Jahnke, T. (2009) Towards Effective Dynamics in Complex Systems by Markov Kernel Approximation. Mathematical Modelling and Numerical Analysis (ESAIM), 43 (4). pp. 721-742.

Klein, R. (2009) Asymptotics, structure, and integration of sound-proof atmospheric flow equations. Theoretical and Computational Fluid Dynamics, 23 (3). pp. 161-195. ISSN 0935-4964 (Print) 1432-2250 (Online)

Jebens, S. and Knoth, O. and Weiner, R. (2009) Explicit Two-Step Peer Methods for the Compressible Euler Equations. Monthly Weather Review, 137 (7). pp. 2380-2392.

Vercauteren, N. and Bou-Zeid, E. and Huwald, H. and Parlange, M. B. and Brutsaert, W. (2009) Estimation of wet surface evaporation from sensible heat flux measurements. Water Resources Research, 45 (6).

Strenziok, R. and Hinz, S. and Wolf, C. and Conrad, T. O. F. and Krause, H. and Miller, K. and Schrader, M. (2009) Surface-enhanced laser desorption/ionization time-of-flight mass spectrometry: serum protein profiling in seminoma patients. World J of Urology, 28 (2). pp. 193-197.

Schütte, Ch. and Noé, F. and Meerbach, E. and Metzner, Ph. and Hartmann, C. (2009) Conformation Dynamics. Proceedings of the 6th International Congress on Industrial and Applied Mathematics, I. Jeltsch and G. Wanner (eds.), . pp. 297-335.

Plattner, N. and Meuwly, M. (2009) Higher order multipole moments for molecular dynamics simulations. Journal of Molecular Modeling, 15 (6). pp. 687-694. ISSN 1610-2940

Fiedler, G. M. and Leichtle, A. and Kase, J. and Baumann, S. and Ceglarek, U. and Felix, K. and Conrad, T. O. F. and Witzigmann, H. and Weimann, A. and Schütte, Ch. and Hauss, J. and Büchler, M. and Thiery, J. (2009) Serum Peptidome Profiling Revealed Platelet Factor 4 as a Potential Discriminating Peptide Associated With Pancreatic Cancer. Clinical Cancer Research, 15 (11). pp. 3812-3819. ISSN 1078-0432

Audusse, E. and Klein, R. and Owinoh, A.Z. (2009) Conservative Discretization of Coriolis Force. Journal of Computational Physics, 228 (8). pp. 2934-2950.

Zerck, A. and Nordhoff, E. and Reseman, A. and Mirgorodskaya, E. and Suckau, D. and Reinert, K. and Lehrach, H. and Gobom, J. (2009) An iterative strategy for precursor ion selection for LC-MS/MS based shotgun proteomics. Journal of Proteome Research .

Hartmann, C. and Schütte, Ch. and Kalibaeva, G. and Di Pierro, M. and Ciccotti, G. (2009) Fast Simulation of Polymer Chains. J. Chem. Phys., 130 . p. 144101.

Schlegel, M. and Knoth, O. and Arnold, M. and Wolke, R (2009) Multirate Runge-Kutta schemes for advection equations. Journal of Computational and Applied Mathematics, 226 (2). pp. 345-357. ISSN 0377-0427

von Kleist, M. and Huisinga, W. (2009) Pharmacokinetic–pharmacodynamic relationship of NRTIs and its connection to viral escape: An example based on zidovudine. European Journal of Pharmaceutical Sciences, 36 . pp. 532-543.

Gassner, G.J. and Lörcher, F. and Munz, C.-D. and Hesthaven, J.-S. (2009) Polymorphic nodal elements and their application in discontinuous Galerkin methods. Journal of Computational Physics, 228 (5). 1573-1590 .

Gräser, C. and Kornhuber, R. (2009) Nonsmooth Newton methods for set-valued saddle point problems. SIAM Journal on Numerical Analysis, 47 (2). pp. 1251-1273. ISSN 0036-1429

Metzner, Ph. and Schütte, Ch. and Vanden-Eijnden, E. (2009) Transition Path Theory for Markov Jump Processes. Mult. Mod. Sim., 7 (3). pp. 1192-1219.

Mellado, J.- P. and Stevens, B. and Schmidt, H. and Peters, N. (2009) Analysis of latent heat effects in the cloud-top mixing layer. Quarterly Journal of the Royal Meteorological Society, 135 (641). pp. 963-978.

Belaschk, H.C. and Münch, M. (2009) Anwendung von massiv paralleler Berechnung mit Grafikkarten GPGPU) für CFD-Methoden im Brandschutz. Bauphysik Volume 31 Issue 4, Pages 216 - 226, 31 (4). pp. 216-226.

Devereux, M. and Plattner, N. and Meuwly, M. (2009) Application of Multipolar Charge Models and Molecular Dynamics Simulations to Study Stark Shifts in Inhomogeneous Electric Fields†. The Journal of Physical Chemistry A, 113 (47). pp. 13199-13209. ISSN 1089-5639

Münch, M. (2009) Brandsimulationsprogramme - Chancen und Risiken. schadenprisma, Zeitschrift für Schadenverhütung und Schadenforschung der öffentlichen Versicherer, 2 . pp. 14-18.

Mellado, J.- P. and Schmidt, H. and Stevens, B. and Peters, N. (2009) Buoyancy reversal in the cloud-top mixing layer. (Submitted)

Gräfe, Ch. and Nordmeier, V. and Schütte, Ch. (2009) Computerspiel zum Thema Moleküldynamik für Schüler der 7.-10. Klasse, Experimentelles Protyping zur Entwicklung eines Lernspiels. Jahrestagung 2008 der GDCP (Gesellschaft für Didaktik der Chemie und Physik), 1 . pp. 77-79. ISSN 978-3-643-10010-8

Giorgetta, M. and Hundertmark, T. and Korn, P. and Reich, S. and Restelli, M. (2009) Conservative Space and Time Regularizations for the ICON Model. Reports on Earth System Science, 67 . pp. 1-32. ISSN 1614-1199

Dumbser, M. and Gassner, G. and Munz , C.-D. (2009) Discontinuous Galerkin-Verfahren für zeitabhängige Advektions-Diffusions-Gleichungen. Jahresbericht der DMV, 111 (3). pp. 87-123.

Metzner, Ph. and Noé, F. and Schütte, Ch. (2009) Estimating the Sampling Error: Distribution of Transition Matrices and Functions of Transition Matrices for Given Trajectory Data. Phys. Rev. E, 80 (2). 021106.

Queck, R. and Bienert, A. (2009) Estimation of PBL model parameters from high resolution vegetation scans. Geophysical Research Abstracts, 11 (EGU2009-10888).

Schatzmann, M. and Leitl, B. (2009) Evaluation of Numerical Flow and Dispersion Models for Applications in Industrial and Urban Areas. Chemical Engineering & Technology, 32 (2). 241 -246.

Swart, A. and Manders, A. and Harlander, U. and Maas, U. and Leo , R. M. (2009) Experimental observation of strong mixing due to internal wave focusing over sloping terrain. Dynamics of Atmospheres and Oceans, 50 (1). pp. 16-34.

Bauer, R. A. and Rother, K. and Moor, P. and Reinert, K. and Steinke, T. and Bujnicki, J. M. and Preissner, R. (2009) Fast Structural Alignment of Biomolecules Using a Hash Table, N-Grams and String Descriptors. Algorithms and Molecular Sciences, 2 (2). pp. 692-709. ISSN 1999-4893

Gerisch, A. and Lang, J. and Podhaisky, H. and Weiner, R. (2009) High-order linearly implicit two-step peer-finite element method for time-dependent PDEs. Applied Numerical Mathematics, 59 (3-4). 624-638 . ISSN 0168-9274

Stenke, A. and Dameris, M. and Grewe, V. and Garny, H. (2009) Implications of Lagrangian transport for simulations with a coupled chemistry-climate model. Atmospheric Chemistry and Physics, 9 . pp. 5489-5504.

Harlander, U. and Ridderinkhof, H. and Schouten, M.W. and de Ruijter, W. P. M (2009) Long-term observations of transport, eddies, and Rossby waves in the Mozambique Channel. JOURNAL OF GEOPHYSICAL RESEARCH, 114 (C02003). 15pp.

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

Papke, A. (2009) Mindestens 17 müssen es sein. Junge Wissenschaft, 84 . pp. 24-31.

Kube, S. and Lasser, C. and Weber, M. (2009) Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics. J. Comp. Phys., 228 (6). pp. 1947-1962.

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

Wensch, J. and Knoth, O. and Galant, A. (2009) Multirate infinitesimal step methods for atmospheric flow simulation. BIT - Numerical Mathematics, 49 (2). pp. 449-473. ISSN 0006-3835 (Print) 1572-9125 (Online)

Schmidt, H. and Mellado, J.- P. and Peters, N. and Kerstein, A.R. and Stevens, B. (2009) Numerical study of buoyancy reversal in stably stratified flows. Geophysical Research Abstracts, 11 . (Submitted)

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

Horenko, I. (2009) On robust estimation of low-frequency variability trends in discrete Markovian sequences of atmospherical circulation patterns. The Journal of Atmospherical Sciences, 66 (7). 2059-2072 .

Horenko, I. (2009) On structure-preserving persistent clustering of multivariate time series. Journal of Computational Physics . (Submitted)

Pingen, G. and Waidmann, M. and Evgrafov, A. and Maute, K. (2009) A Parametric Level-Set Approach for Topology Optimization of Flow Domains. Structural and Multidisciplinary Optimization . ISSN 1615-147X (Print) 1615-1488 (Online)

Dolaptchiev, S. and Klein, R. (2009) Planetary geostrophic equations for the atmosphere with evolution of the barotropic flow. Dynamics of Atmospheres and Oceans Volume, 46 (1-4). pp. 46-61.

Leibscher, M. and Schmidt, B. (2009) Quantum dynamics of a plane pendulum. Phys. Rev. A, 80 (1). 012510.

Altmann, C. and Gassner, G. and Lörcher, F. and Munz , C.-D. (2009) A Space-Time Expansion Discontinuous Galerkin Scheme With Local Time Stepping for the Ideal and Viscous MHD Equations. IEEE Transactions on Plasma Science, 37 (4). 513 -519 .

Vater, S. and Klein, R. (2009) Stability of a Cartesian grid projection method for zero Froude number shallow water flows. Numerische Mathematik, 113 (1). pp. 123-161.

Owschimikow, N. and Schwentner, N. and Schmidt, B. (2009) State Selection in Non-Resonantly Excited Wave Packets by Tuning from Non-Adiabatic to Adiabatic Interaction. Phys. Rev. A, 80 (5). 053409.

Schulz-Trieglaff, O. and Machtejevas, E. and Reinert, K. and Schlueter, H. and Thiemann, J. and Unger, K. (2009) Statistical Quality Assessment and Outlier Detection for Liquid Chromatography-Mass Spectrometry Experiments. BioDataMining, 2 (4).

Franzke, Ch. and Horenko, I. and Majda, A. J. and Klein, R. (2009) Systematic Metastable Atmospheric Regime Identification in an AGCM. J. Atm. Sci., 66 (7). pp. 1997-2012.

Zhu, H. and Röder, B. and May, V. (2009) Time and frequency resolved spontaneous emission from supramolecular pheophorbide-a complexes: A mixed quantum classical computation. Chem. Phys., 362 (1-2). pp. 19-26.

Qu, Z.-W. and Zhu, H. and May, V. and Schinke, R. (2009) Time-Dependent Density Functional Theory Study of the Electronic Excitation Spectra of Chlorophyllide a and Pheophorbide a in Solvents. J. Phys. Chem. B, 113 (14). pp. 4817-4825.

Löbig, S. and Dörnbrack, A. and Fröhlich, J. and Hertel, C. and Kühnlein, C. and Lang, J. (2009) Towards Large-Eddy Simulation on moving grids. PAMM · Proc. Appl. Math. Mech., 9 . 445 -446.

Ionescu, C. and Klein, R.J.T. and Hinkel, J., and Kavi Kumar, K.S., and Klein, R. (2009) Towards a formal framework for vulnerability to climate change. Environmental Modeling and Assessment, 14 (1). pp. 1-16. ISSN 1420-2026 (Print) 1573-2967 (Online)

Barth, I. and Lasser, C. (2009) Trigonometric pulse envelopes for laser-induced quantum dynamics. J. Phys. B: At. Mol. Opt. Phys., 42 (23). p. 235101.

Hickel, S. and von Terzi, D.A. and Fröhlich, J. (2009) An adaptive local deconvolution method for general curvilinear coordinate systems. Springer Proceedings Physics - Advances in Turbulence XII, 132 (11). pp. 783-786.

Rausch, T. and Koren, S. and Denisov, G. and Weese, D. and Emde, A.-K. and Döring, A. and Reinert, K. (2009) A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads. Bioinformatics, 25 (9). pp. 1118-1124.

Kilian, S. and Münch, M. (2009) A new generalized domain decomposition strategy for the efficient parallel solution of the FDS-pressure equation. Part I: Theory, Concept and Implementation. ZIB-Report, 09-19 . 30 pages. ISSN 1438-0064

Schmidt, H. and Oevermann, M. and Bastiaans, R.J.M. and Kerstein, A.R. (2009) A priori Tabulation of Turbulent Flame Speeds via a Combination of a Stochastic Mixing Model and Flamelet Generated Manifolds, Extended to Incorporate Strain Effects. ZIB Report, 09-09 . ISSN 1438-0064

Moeck, J. and Oevermann, M. and Klein, R. and Paschereit, O. C. and Schmidt, H. (2009) A two-way coupling for modeling thermoacoustic instabilities in a flat flame Rijke tube. Proceedings of the Combustion Institute, 32 (1). pp. 1199-1207.

2008

Plattner, N. and Bandi, T. and Doll, J. D. and Freeman, D. and Meuwly, M. (2008) MD simulations using distributed multipole electrostatics: Structural and spectroscopic properties of CO- and methane-containing clathrates. Molecular Physics, 106 (12). pp. 1675-1684. ISSN 0026-8976

Letzel, O. and Krane, M. and Raasch, S. (2008) High resolution urban large-eddy simulation studies from street canyon to neighbourhood scale. Atmospheric Environment, 42 (38). 8770-8784 .

Bou-Zeid, E. and Vercauteren, N. and Parlange, M. B. and Meneveau, C. (2008) Scale dependence of subgrid-scale model coefficients: An a priori study. Physics of Fluid, 20 (115106).

Matute, R. A. and Contreras, R. and Pérez-Hernández, G. and González, L. (2008) The Chromophore Structure of the Cyanobacterial Phytochrome Cph1 As Predicted by Time-Dependent Density Functional Theory. The Journal of Physical Chemistry B, 112 (51). pp. 16253-16256. ISSN 1520-6106

Pérez-Hernández, G. and González, L. and Serrano-Andrés, L. (2008) Rydberg or Valence? The Long-Standing Question in the UV Absorption Spectrum of 1,1′-Bicyclohexylidene. ChemPhysChem, 9 (17). p. 2544. ISSN 14394235

Carqué, G. and Schmidt, H. and Stevens, B. and Klein, R. (2008) Plausibility Check of an Asymptotic Column Model for Deep Convective Clouds. ZIB-Report, 08 (44).

Kornhuber, R. and Yserentant, H. (2008) Multigrid methods for discrete elliptic problems on triangular surfaces. Computing and Visualization in Science, 11 (4-6). pp. 251-257. ISSN 1432-9360

Vercauteren, N. and Bou-Zeid, E. and Parlange, M. B. and Lemmin, U. and Huwald, H. and Selker, J. S. and Meneveau, C. (2008) Subgrid-Scale Dynamics of Water Vapour, Heat, and Momentum over a Lake. Boundary-Layer Meteorology, 128 (2). pp. 205-228. ISSN Print: 0006-8314 Online: 1573-1472

Barth, I. and Manz, J. and Pérez-Hernández, G. and Sebald, P. (2008) Towards Toroidal Hydrogen Bonds. Zeitschrift für Physikalische Chemie, 222 (8-9). pp. 1311-1331. ISSN 0942-9352

Schäfer-Bung, B. and Nest , M. (2008) Correlated Dynamics of Electrons with Reduced 2-Electron Density Matrices. Phys. Rev. A, 78 (1). 012512.

Münch, M. and Klein, R. (2008) Critical numerical aspects for field model applications. EUSAS Journal (4). pp. 41-54.

Abida, R. and Bocquet, M. and Vercauteren, N. and Isnard, O. (2008) Design of a monitoring network over France in case of a radiological accidental release. Atmospheric Environment, 42 (21). pp. 5205-5219. ISSN 1352-2310

Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Ohlberger, M. and Sander, O. (2008) A generic grid interface for parallel and adaptive scientific computing. Part I: Abstract framework. Computing, 82 (2-3). pp. 103-119. ISSN 0010-485X

Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Kornhuber, R. and Ohlberger, M. and Sander, O. (2008) A generic grid interface for parallel and adaptive scientific computing. Part II: Implementation and tests in DUNE. Computing, 82 (2-3). pp. 121-138. ISSN 0010-485X

Rausch, T. and Thomas, A. and Camp, N. J. and Facelli, L. A. (2008) A parallel genetic algorithm to discover patterns in genetic markers that indicate predisposition to multifactorial disease. Comput. Biol. Med., 38 . pp. 826-836.

Plattner, N. and Meuwly, M. (2008) Atomistic Simulations of CO Vibrations in Ices Relevant to Astrochemistry. ChemPhysChem, 9 (9). pp. 1271-1277. ISSN 14394235

Plattner, N. and Meuwly, M. (2008) The Role of Higher CO-Multipole Moments in Understanding the Dynamics of Photodissociated Carbonmonoxide in Myoglobin. Biophysical Journal, 94 (7). pp. 2505-2515. ISSN 00063495

Strenziok, R. and Hinz, S. and Wolf, C. and Conrad, T. O. F. and Krause, H. and Lingnau, A. and Lein, M. and Miller, K. and Schrader, M. (2008) Serum proteomic profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry in testicular germ cell cancer patients. European Urology Supplements, 7 (3). p. 83.

Schäfer-Bung, B. (2008) The interplay of wave packet dephasing, optimization efficiency, and target state population in optimally controlled isotope selective photoionization. Chem. Phys., 343 . pp. 340-346.

Carqué, G. and Owinoh, A.Z. and Klein, R. and Majda, A. J. (2008) Asymptotic Scale Analysis of Precipitating Clouds. ZIB-Report, 08-03 . ISSN 1438-0064

Münch, M. (2008) MOLOCH - Ein Strömungsverfahren für inkompressible Strömungen - Technische Referenz. PIK-Report (109).

Kornhuber, R. and Krause, R. and Sander, O. and Deuflhard, P. and Ertel, S. (2008) A monotone multigrid solver for two body contact problems in biomechanics. Computing and Visualization in Science, 11 (1). pp. 3-15. ISSN 1432-9360

Frigato, T. and VandeVondele, J. and Schmidt, B. and Schütte, Ch. and Jungwirth, P. (2008) Ab Initio Molecular Dynamics Simulation of a Medium-Sized Water Cluster Anion: From an Interior to a Surface Located Excess Electron via a Delocalized State. J. Phys. Chem. A, 112 (27). pp. 6125-6133.

Münch, M. and Klein, R. (2008) Anforderungen an numerische Berechnungen der Brand- und Rauchausbreitung im Vorbeugenden Brandschutz. vfdb-Zeitschrift Forschung, Technik und Management im Brandschutz, Jg. 57 (3). pp. 145-151. ISSN 0042-1804

Horenko, I. (2008) Automated Generation of Reduced Stochastic Weather Models I: Simultaneous Dimension and Model Reduction for Time Series Analysis. Multiscale Modeling & Simulation, 6 (4). p. 1125. ISSN 15403467

Horenko, I. and Klein, R. and Dolaptchiev, S. and Schütte, Ch. (2008) Automated Generation of Reduced Stochastic Weather Models I: Simultaneous Dimension and Model reduction for Time Series Analysis. Mult. Mod. Sim., 6 (4). pp. 1125-1145.

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

Schulz-Trieglaff, O. and Hussong, R. and Gröpl, C. and Hildebrandt, A. and Hildebrandt, A. and Huber, Ch. and Reinert, K. (2008) Computational Quantification of Peptides from LC-MS data. Journal of Computational Biology, 15 (7). pp. 685-704.

Lange, E. and Tautenhahn, R. and Neumann, S. and Gröpl, C. (2008) Critical assessment of alignment procedures for LC-MS proteomics and metabolomic measurements. BMC Bioinformatics, 9 (375).

Warren, R. and de la Nava Santos, S. and Arnell, N.W. and Bane, M. and Barker, T. and Barton, C. and Ford, R. and Füssel, H.-M. and Hankin, Robin K.S. and Klein, R. and Linstead, C. and Kohlera, J. and Mitchella, T.D. and Osborna, T.J. and Pan, H. and Raper, S.C.B. and Riley, G. and Schellnhuber, H.J. and Winne, S. and Anderson, D. (2008) Development and illustrative outputs of the Community Integrated Assessment System (CIAS), a multi-institutional modular integrated assessment approach for modelling climate change. Environmental Modelling & Software, 23 (5). 592-610 .

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

Gassner, G. and Lörcher, F. and Munz , C.-D. (2008) A Discontinuous Galerkin Scheme based on a Space-Time Expansion II. Viscous Flow Equations in Multi Dimensions. Journal of Scientific Computing, 34 (3). pp. 260-286. ISSN 0885-7474 (Print) 1573-7691 (Online)

Craig, G.C. and Dörnbrack, A. (2008) Entrainment in Cumulus Clouds: What resolution is cloud resolving? J. Atmos. Sci., 65 . pp. 3978-3988. ISSN Online 1520-0469 Print 0022-4928

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

Bauer, M. and Klau, G. W. and Reinert, K. (2008) An Exact Mathematical Programming Approach to Multiple RNA Sequence-Structure Alignment. Algorithmic Operations Research .

John, V. and Schmeyer, E. (2008) Finite element methods for time-dependent convection-diffusion-reaction equations with small diffusion. Computer methods in applied mechanics and engineering, 198 (3). pp. 475-494. ISSN 0045-7825

Kadioglu, S.Y. and Minion, M.L. and Klein, R. (2008) A Fourth-Order Auxiliary Variable Projection Method for Zero-Mach Number Gas Dynamics. Journal of Computational Physics , 227 (3). 2012-2043 .

Ullrich, Alexander and Flamm, Christoph (2008) Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe. Computational Methods in Systems Biology, 5307 . pp. 28-43.

Bodirsky, M. and Gröpl, C. and Kang, M. (2008) Generating unlabeled connected cubic planar graphs uniformly at random. Random Structures and Algorithms, 32 (2). pp. 157-180.

von Larcher, T. and Futterer, B. and Egbers, C. and Hollerbach, R. and Chossat, P. and Beltrame, P. and Tuckerman, L. and Feudel, F. (2008) GeoFlow - European Microgravity Experiments on Thermal Convection in Rotating Spherical Shells under influence of Central Force Field. Journal of The Japan Society of Microgravity Application, 25 (3).

von Larcher, T. and Futterer, B. and Egbers, C. (2008) GeoFlow: On the status of experimental preparation of spherical gap flow experiments with central force field on International Space Station (ISS). Journal of Physics: Conference Series, 137 (012025). p. 6.

Oevermann, M. and Schmidt, H. and Kerstein, A.R. (2008) HCCI combustion modeling using detailed chemistry coupled to LEM-based advection. Combustion and Flame, 155 . pp. 370-379.

Teleaga, , I. and Lang, J. (2008) Higher-order linearly implicit one-step methods for three-dimensional incompressible Navier-Strokes equations. Studia Babes-Bolyai Matematica, 53 . pp. 109-121.

Tomm, S. and von Terzi, D.A. and Fröhlich, J. (2008) Interaction of the filter and spatial discretisation operators for Large-Eddy Simulation using the Approximate Deconvolution Model. PAMM, 8 . pp. 10605-10606.

Oevermann, M. and Schmidt, H. and Kerstein, A.R. (2008) Investigation of autoignition under thermal stratification using linear eddy modeling. Combustion and Flame Volume, 155 (3). 370-379 .

Schulz-Trieglaff, O. and Pfeifer, N. and Gröpl, C. and Kohlbacher, O. and Reinert, K. (2008) LC-MSsim - a simulation software for liquid chromatography mass spectrometry data. BMC Bioinformatics, 9 (423).

Horenko, I. and Schütte, Ch. (2008) Likelihood-Based Estimation of Multidimensional Langevin Models and its Application to Biomolecular Dynamics. Mult. Mod. Sim., 7 (2). pp. 731-773.

Horenko, I. and Dittmer, E. and Lankas, F. and Maddocks, J. and Metzner, Ph. and Schütte, Ch. (2008) Macroscopic Dynamics of Complex Metastable Systems: Theory, Algorithms, and Application to B-DNA. J. Appl. Dyn. Syst., 7 (2). pp. 532-560.

Horenko, I. and Dolaptchiev, S. and Eliseev, A. and Mokhov, I. and Klein, R. (2008) Metastable Decomposition of High-Dimensional Meteorological Data with Gaps. Journal of the Atmospheric Sciences, 65 (11). pp. 3479-3496.

Pincus, R. and Stevens, B. (2008) Monte Carlo spectral integration: A consistent approximation for radiative transfer in large eddy simulations. Journal of Advancesin Modeling Earth Systems, 1 . p. 9.

Doyle, J.D. and Grubišić, V. and Brown, W.O.J. and De Wekker, S.F.J. and Dörnbrack, A. and Jiang, Q. and Mayor, S.D. and Weissman, M. (2008) Observations and Numerical Simulations of Subrotor Vortices during T-REX. J. Atmos. Sci., 66 (5). ISSN Online 1520-0469 Print 0022-4928

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

Horenko, I. (2008) On robust estimation of low-frequency variability trends in discrete Markovian sequences of atmospheric circulation patterns. J. Atm. Sci. . (In Press)

Petoukhov, V. and Eliseev, A. and Klein, R. and Oesterle, H. (2008) On the statistics of the free-troposphere synoptic component. Part I: An evaluation of skewnesses and estimation of the third-order moments contribution to the synoptic-scale dynamics and meridional fluxes of heat and humidity. Tellus, 60 (1). pp. 11-31.

Sturm, M. and Andreas, B. and Gröpl, C. and Hussong, R. and Lange, E. and Pfeifer, N. and Schulz-Trieglaff, O. and Zerck, A. and Reinert, K. and Kohlbacher, O. (2008) OpenMS - An open-source software framework for mass spectrometry. BMC Bioinformatics, 9 (163).

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

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

Rausch, T. and Emde, A.-K. and Reinert, K. (2008) Robust consensus computation. BMC Bioinformatics, 9 (Suppl 10). P4.

Rausch, T. and Emde, A.-K. and Weese, D. and Notredame, C. and Reinert, K. (2008) Segment-based multiple sequence alignment. Bioinformatics, 24 (16). i187-192.

Döring, A. and Weese, D. and Rausch, T. and Reinert, K. (2008) SeqAn -- An efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9 (1). p. 11.

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

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

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

Noé, F. and Daidone, I. and Smith, J. C. and Di Nola, A. and Amadei, A. (2008) Solvent Electrostriction Driven Peptide Folding revealed by Quasi-Gaussian Entropy Theory and Molecular Dynamics Simulation. J. Phys. Chem. B, 112 . pp. 11155-11163.

Baldauf, M. (2008) Stability analysis for linear discretisations of the advection equation with Runge–Kutta time integration. Journal of Computational Physics, 227 (13). pp. 6638-6659.

Schulz-Trieglaff, O. and Machtejevas, E. and Reinert, K. and Schlueter, H. and Thiemann, J. and Unger, K. (2008) Statistical Quality Assessment and Outlier Detection for Liquid Chromatography-Mass Spectrometry Experiments. BioDataMining . accepted for publication. (In Press)

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

Schmidt, H. and Oevermann, M. and Bastiaans, R.J.M. and Kerstein, A.R. (2008) Tabulation of turbulent burning rates via a combination of a stochastic mixing model and tabulated chemistry. ZIB Report, 08 (2).

Futterer, B. and Gellert, M. and von Larcher, T. and Egbers, C. (2008) Thermal convection in rotating spherical shells: An experimental and numerical approach within GeoFlow. Acta Astronautica, 62 (4). pp. 300-307.

Schmidt, H. and Mellado, J.- P. and Peters, N. and Stevens, B. (2008) Towards modular front tracking for Stratocumulus clouds considering unsteady entrainment processes. Geophysical Research Abstracts, 10 .

Noé, F. and Fischer, S. (2008) Transition Networks for Modeling the Kinetics of Conformational Change in Macromolecules. Curr. Opin. Struct. Biol., 18 . pp. 154-162.

Ruprecht, D. and Schaedle, A. and Schmidt, F. and Zschiedrich, L. (2008) Transparent Boundary Conditions for Time-dependent Problems. SIAM J. Sci. Comput., 30 (5). pp. 2358-2385. ISSN 1064-8275

Mellado, J.- P. and Stevens, B. and Schmidt, H. and Peters, N. (2008) Two-fluid formulation of the cloud-top mixing layer for direct numerical simulation. Theoretical and Computational Fluid Dynamics . (Submitted)

Klein, R. (2008) An Unified Approach to Meteorological Modelling Based on Multiple-Scales Asymptotics. Advances in Geosciences, 15 . pp. 23-33.

Papke, A. (2008) Wie viele Zahlen müssen es sein? Die Junge Wissenschaft, 79 . pp. 46-51.

Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Kornhuber, R. and Ohlberger, M. and Sander, O. (2008) A generic grid interface for parallel and adaptive scientific computing. II: Implementation and tests in DUNE. Computing, 82 (2-3). pp. 121-138.

2007

Metzner, Ph. and Horenko, I. and Schütte, Ch. (2007) Generator Estimation of Markov Jump Processes Based on Incomplete Observations Nonequidistant in Time. Phys. Rev. E, 76 (06). 066702.

von Kleist, M. and Huisinga, W. (2007) Physiologically Based Pharmacokinetic Modelling: A Sub-Compartmentalized Model of Tissue Distribution. J. Pharmacokin. Pharmacodyn., 34 (6). pp. 789-806.

Metzner, Ph. and Dittmer, E. and Jahnke, T. and Schütte, Ch. (2007) Generator Estimation of Markov Jump Processes. J. Comp. Phys., 227 (1). pp. 353-375.

Bauer, M. and Klau, G. W. and Reinert, K. (2007) Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization. BMC Bioinformatics, 8 (1). p. 271.

Noé, F. and Horenko, I. and Schütte, Ch. and Smith, J. C. (2007) Hierarchical Analysis of Conformational Dynamics in Biomolecules: Transition Networks of Metastable States. J. Chem. Phys., 126 (15). p. 155102.

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

Lorenz, S. and Diederichs, E. and Telgmann, R. and Schütte, Ch. (2007) Discrimination of Dynamical System Models for Biological and Chemical Processes. J. Comp. Chem., 28 (8). pp. 1384-1399.

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

Pingen, G. and Waidmann, M. and Evgrafov, A. and Maute, K. (2007) Application of a Parametric Level-Set Approach to Topology Optimization of Fluids with the Navier–Stokes and Lattice Boltzmann Equations. 7th World Congress on Structural and Multidisciplinary Optimization .

Mellado, J.- P. and Stevens, B. and Schmidt, H. and Peters, N. (2007) Buoyancy-reversal in cloud-top mixing layers. Quarterly journal of the royal meteorological society . pp. 1-21.

Lasser, C. and Swart, T. and Teufel, St. (2007) Construction and validation of a rigorous surface hopping algorithm for conical crossings. Comm. Math. Sci., 5 (4). pp. 789-814.

Horenko, I. and Hartmann, C. and Schütte, Ch. and Noé, F. (2007) Data-based Parameter Estimation of Generalized Multidimensional Langevin Processes. Phys. Rev. E, 76 (01). 016706.

Lörcher, F. and Gassner, G. and Munz , C.-D. (2007) A Discontinuous Galerkin Scheme Based on a Space–Time Expansion. I. Inviscid Compressible Flow in One Space Dimension. Journal of Scientific Computing, 32 (2). pp. 175-199. ISSN 0885-7474 (Print) 1573-7691 (Online)

Gu, W. and Frigato, T. and Straatsma, T. P. and Helms, V. (2007) Dynamic Protonation Equilibrium of Solvated Acetic Acid. Angew. Chem. Int. Ed., 46 (16). pp. 2939-2943.

Bodirsky, M. and Gröpl, C. and Kang, M. (2007) Generating labeled planar graphs uniformly at random. Theoretical Computer Science, 379 (3). pp. 377-386.

Lange, E. and Gröpl, C. and Schulz-Trieglaff, O. and Leinenbach, A. and Huber, Ch. and Reinert, K. (2007) A Geometric Approach for the Alignment of Liquid Chromatography-Mass Spectrometry Data. Oxford Journals, 23 (13). i273-i281. ISSN 1460-2059 (online), 1367-4803 (print)

Fischer, A. and Waldhausen, S. and Horenko, I. and Meerbach, E. and Schütte, Ch. (2007) Identification of Biomolecular Conformations from Incomplete Torsion Angle Observations by Hidden Markov Models. J. Comp. Chem., 28 (15). pp. 2453-2464.

Klau, G. W. and Rahmann, S. and Schliep, A. and Vingron, M. and Reinert, K. (2007) Integer Linear Programming Approaches for Non-unique Probe Selection. Discrete Applied Mathematics, 155 . pp. 840-856.

Christen, M. and Keller, B. and van Gunsteren, W. F. (2007) Local elevation on the dihedral angles to improve the J-values. Journal of Biomolecular NMR, 39 . pp. 265-273.

Lang, J. and Verwer, J. (2007) On Global Error Estimation and Control for Initial Value Problems. SIAM J. Sci. Comp., 29 (4). pp. 1460-1475. ISSN 1064-8275 (print) 1095-7197 (online)

Debrabant, K. and Lang, J. (2007) On Global Error Estimation and Control for Parabolic Equations, Report No. 2512. Appl. Num. Math. . (Submitted)

Keller, B. and Christen, M. and Oostenbrink, C. and van Gunsteren, W. F. (2007) On using oscillating time-dependent restraints in MD simulation. Journal Of Biomolecular NMR, 37 . pp. 1-14.

Noé, F. and Oswald, M. and Reinelt, G. (2007) Optimization in Graphs with Limited Information on the Edge Weights. Operations Research Proceedings 2007. Editors: J. Kalcsics and S. Nickel . pp. 435-440.

Noé, F. and Smith, J. C. (2007) Transition Networks: a unifying theme for molecular simulation and computer science. Mathematical Modeling of Biological Systems I, A. Deutsch, L. Brusch, H. Byrne, G. de Vries and H.-P. Herzel (Eds) . pp. 125-144.

Bodirsky, M. and Gröpl, C. and Johannsen, D. and Kang, M. (2007) A direct decomposition of 3-connected planar graphs. Séminaire Lotharingien de Combinatoire, B54Ak . 15 pages.

Bastian, P. and Blatt, M. and Dedner, A. and Engwer, C. and Klöfkorn, R. and Ohlberger, M. and Sander, O. (2007) A generic grid interface for parallel and adaptive scientific computing. I: Abstract framework. Computing, 82 (2-3). pp. 103-119.

Noé, F. and Smith, J. C. and Schütte, Ch. (2007) A network-based approach to biomolecular dynamics. From Computational Biophysics to Systems Biology (CBSB07). Editors: U. H. E. Hansmann, J. Meinke, S. Mohanty and O. Zimmermann, NIC Se .

2006

Schäfer-Bung, B. and Bonačić-Koutecký, V. and Sauer, F. and Weber, S. and Wöste, L. and Lindinger, A. (2006) Isotope selective photoionization of NaK by optimal control: Theory and experiment. J. Chem. Phys., 125 (21). 214310-1-214310-8.

Oevermann, M. and Klein, R. (2006) A cartesian grid finite volume method for the solution of the Poisson equation with variable coefficients and embedded interfaces. Journal of Computational Physics, 219 (2). 749-769 .

Schäfer-Bung, B. and Mitrić, R. and Bonačić-Koutecký, V. (2006) Photostabilization of ultracold Rb2 molecules by optimal control. J. Phys. B, 39 (19). S1043-S1053.

Bastian, P. and Blatt, M. and Engwer, C. and Dedner, A. and Klöfkorn, R. and Kuttanikkad, S. P. and Ohlberger, M. and Sander, O. (2006) The Distributed and Unified Numerics Environment (DUNE). Proc. of the 19th Symposium on Simulation Technique .

Bernhard, S. (2006) Transient integral boundary layer method to calculate the translesional pressure drop and the fractional flow reserve in myocardial bridges. BioMedical Engineering OnLine, 5 (42).

Kornhuber, R. and Krause, R. (2006) Robust multigrid methods for vector-valued Allen-Cahn equations with logarithmic free energy. Computing and Visualization in Science, 9 (2). pp. 103-116. ISSN 1432-9360

Krause, R. and Sander, O. (2006) Automatic construction of boundary parametrizations for geometric multigrid solvers. Computing and Visualization in Science, 9 (1). pp. 11-22. ISSN 1432-9360

Bonačić-Koutecký, V. and Mitrić, R. and Bürgel, Ch. and Schäfer-Bung, B. (2006) Cluster Properties in the regime in which each atom counts. Comput. Mater. Sci., 35 (3). pp. 151-157.

Oevermann, M. and Klein, R. (2006) A cartesian grid finite volume method for the solution of the Poisson equation with variable coefficients and embedded interfaces. JCP .

Gebauer, S. and Kornhuber, R. and Yserentant, H. (2006) Hierarchical decomposition of domains with fractures. Mathematics of Computation, 75 (253). pp. 73-90. ISSN 00255718

Caselles, V. and Igual, L. and Sander, O. (2006) An axiomatic approach to scalar data interpolation on surfaces. Numerische Mathematik, 102 (3). pp. 383-411. ISSN 0029-599X

Imhof, P. and Noé, F. (2006) AM1/d Parameters for Magnesium in Metalloenzymes. J. Chem. Theo. Comput., 2 . pp. 1050-1056.

Mayr, B. M. and Kohlbacher, O. and Reinert, K. and Gröpl, C. and Lange, E. and Klein, C. L. and Huber, Ch. (2006) Absolute Myoglobin Quantitation in Serum by Combining Two-Dimensional Liquid Chromatography-Electrospray Ionization Mass Spectrometry and Novel Data Analysis Algorithms. Journal of Proteome Research, 5 . pp. 414-421.

Wolski, W. E. and Farrow, M. and Emde, A.-K. and Maciej, L. and Lehrach, H. and Reinert, K. (2006) Analytical model of peptide mass cluster centres with applications. Proteome Science, 4 (18). doi:10.1186/1477-5956.

Horenko, I. and Dittmer, E. and Fischer, A. and Schütte, Ch. (2006) Automated Model Reduction for Complex Systems exhibiting Metastability. Mult. Mod. Sim., 5 (3). pp. 802-827.

Conrad, T. O. F. and Leichtle, A. and Hagehülsmann, A. and Diederichs, E. and Baumann, S. and Thiery, J. and Schütte, Ch. (2006) Beating the Noise: New Statistical Methods for Detecting Signals in MALDI-TOF Spectra Below Noise Level. Lecture Notes in Computer Science, 4216 . pp. 119-128.

Althaus, E. and Caprara, A. and Lenhof, H.-P. and Reinert, K. (2006) A Branch-and-Cut Algorithm for Multiple Sequence Alignment. Mathematical Programming (105). pp. 387-425.

Noé, F. and Oswald, M. and Reinelt, G. and Smith, J. C. and Fischer, S. (2006) Computing Best Transition Pathways in High-Dimensional Dynamical Systems. Multisc. Model. Sim., 5 . pp. 393-419.

Metzner, Ph. and Schütte, Ch. and Vanden-Eijnden, E. (2006) Illustration of Transition Path Theory on a Collection of Simple Examples. J. Chem. Phys., 125 (8). 084110.

Futterer, B. and Gellert, M. and Huschto, M. and von Larcher, T. and Egbers, C. (2006) Microgravity Science on International Space Station (ISS): The Geoflow Experiment. Forum der Forschung, 10. Jahrgang (19). pp. 113-118. ISSN 0947-6989

Deuflhard, P. and Ertel, S. and Kornhuber, R. and Krause, R. and Sander, O. (2006) Patient-specific simulation of dynamic stress distribution in the human knee. Journal of Biomechanics, 39 . p. 47. ISSN 0021-9290

Becker, T. and Fischer, S. and Noé, F. and Tournier, A. and Ullmann, M. and Kurkal, V. and Smith, J. C. (2006) Physical and functional aspects of protein dynamics. Soft Condensed Matter Physics in Molecular and Cell Biology, Poon & Andelman (Eds) .

Klein, R. and Majda, A. J. (2006) Systematic Multiscale Models for Deep Convection on Mesoscales. Theoretical and Computational Fluid Dynamics, 20 (5-6). pp. 525-551. ISSN 0935-4964 (Print) 1432-2250 (Online)

Kiljunen, T. and Schmidt, B. and Schwentner, N. (2006) Time-Dependent Alignment of Molecules Trapped in Octahedral Crystal Fields. J. Chem. Phys., 124 (16). p. 164502.

Noé, F. and Krachtus, D. and Smith, J. C. and Fischer, S. (2006) Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins. J. Chem. Theo. Comput., 2 . pp. 840-857.

Waidmann, M. and Waidmann, C. and Saile, D. and Grillmayer, G. (2006) Use of new developments on attitude control sensors for the microsatellite Flying Laptop. Proceedings of the 57th IAC/IAF/IAA, Valencia, Spain .

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

2005

Bernhard, S. (2005) Oscillatory flow in a tube with time-dependent wall deformation and its application to Myocardial Bridges. ESAIM: Proc., 14 . pp. 25-40.

Horenko, I. and Lorenz, S. and Schütte, Ch. and Huisinga, W. (2005) Adaptive Approach for Non-Linear Sensitivity Analysis of Reaction Kinetics. J. Comp. Chem., 26 (9). pp. 941-948.

Lorenz, K. and Jahnke, T. and Lubich, Ch. (2005) Adiabatic Integrators for Highly Oscillatory Second-Order Linear Differential Equations with Time-Varying Eigendecomposition. BIT Num. Math., 45 (1). pp. 91-115.

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

Antony, J. and von Helden, G. and Meijer, G. and Schmidt, B. (2005) Anharmonic Midinfrared Vibrational Spectra of Benzoic Acid Monomer and Dimer. J. Chem. Phys., 123 (1). 014305.

Noé, F. and Ille, F. and Smith, J. C. and Fischer, S. (2005) Automated Computation of Low-Energy Pathways for Complex Rearrangements in Proteins: Application to the conformational switch of Ras p21. Proteins, 59 . pp. 534-544.

Wolski, W. E. and Lalowski, M. and Jungblut, P. and Reinert, K. (2005) Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants. BMC Bioinformatics, 6 (203). http://www.biomedcentral.com/1471-2105/6/203.

Hartmann, C. and Schütte, Ch. (2005) A Constrained Hybrid Monte-Carlo Algorithm and the Problem of Calculating the Free Energy in Several Variables. Z. Angew. Math. Mech., 85 (10). pp. 700-710.

von Larcher, T. and Egbers, C. (2005) Dynamics of baroclinic wave pattern in transition zones between different flow regimes. Journal of Physics: Conference Series, 14 . pp. 162-167.

Owinoh, A.Z. and Hunt, J. and Orr, A. and Clark, P. and Klein, R. and Fernando, H. and Nieuwstadt, F. (2005) Effects Of Changing Surface Heat Flux On Atmospheric Boundary-Layer Flow Over Flat Terrain. Boundary Layer Meterology, 116 (2). pp. 331-361.

Meerbach, E. and Schütte, Ch. and Fischer, A. (2005) Eigenvalue Bounds on Restrictions of Reversible Nearly Uncoupled Markov Chains. Lin. Alg. Appl., 398 . pp. 141-160.

von Larcher, T. and Egbers, C. (2005) Experiments on transitions of baroclinic waves in a differentially heated rotating annulus. Nonlinear Processes in Geophysics, 12 . pp. 1033-1041. ISSN 1023-5809 (Print); 1607-7946 (Online)

Schmidt, H. and Klein, R. (2005) Flexible flame structure modelling in a flame front tracking scheme. Analysis and Numerics for Conservation Laws . pp. 405-427. ISSN 978-3-540-24834-7 (Print) 978-3-540-27907-5 (Online)

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

Kiljunen, T. and Schmidt, B. and Schwentner, N. (2005) Intense-Field Alignment of Molecules Confined in Octahedral Field. Phys. Rev. Lett., 94 (12). p. 123003.

Klein, R. (2005) Multiple spacial scales in engineering and atmospheric low Mach number flows. ESAIM: Mathematical Modelling and Numerical Analysis (M2AN), 39 . pp. 537-559. ISSN 0764-583X

Antony, J. and Schmidt, B. and Schütte, Ch. (2005) Nonadiabatic Effects on Peptide Vibrational Dynamics Induced by Conformational Changes. J. Chem. Phys., 122 (1). 014309.

Gonzalez, L. and Manz, J. and Schmidt, B. and Shibl, M. F. (2005) Optical resolution of oriented enantiomers via photodissociation: Quantum simulations for H2POSD. Phys. Chem. Chem. Phys., 7 (24). pp. 4096-4101.

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

Schatzmann, M. and Britter, R. (2005) Quality assurance and improvement of micro-scale meteorological models. International Journal of Environment and Pollution . (Submitted)

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

Klein, C. L. and Kohlbacher, O. and Reinert, K. (2005) Reference methods and materials in standardisation and quality assurance (abstract). FEBS Journal, 272 (Supplement 1). pp. 490-504.

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

Wolski, E. and Lalowski, M. and Martus, P. and Giavalisco, P. and Gobom, J. and Sickmann, A. and Lehrach, H. and Reinert, K. (2005) Transformation and other factors of the peptide mass spectormetry pairwise peaklist comparison process. BMC Bioinformatics, 6 (285). http://www.biomedcentral.com/1471-2105/6/285.

2004

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

Schäfer-Bung, B. and Mitrić, R. and Bonačić-Koutecký, V. and Bartelt, A. and Lupulescu, C. and Lindinger, A. and Vajda, Š. and Weber, S. and Wöste, L. (2004) Optimal control of ionization processes in NaK; comparison between theory and experiment. J. Phys. Chem. A, 108 (19). pp. 4175-4179.

Schütte, Ch. and Walter, J. and Hartmann, C. and Huisinga, W. (2004) An Averaging Principle for Fast Degrees of Freedom Exhibiting Long-Term Correlations. Multiscale Model. Simul., 2 (3). pp. 501-526.

Walter, J. and Schütte, Ch. and Pavliotis, G. A. and Stuart, A. (2004) Averaging of Stochastic Differential Equations: Kurtz's Theorem Revisited. preprint .

Kohlbacher, O. and Reinert, K. (2004) Differenzielle Proteomanalyse -- Experimentelle Methoden, Algorithmische Herausforderungen. it -- Information technology, 46 . pp. 31-38.

Preis, R. and Dellnitz, M. and Hessel, M. and Schütte, Ch. and Meerbach, E. (2004) Dominant Paths Between Almost Invariant Sets of Dynamical Systems. preprint .

Helling, Ch. and Klein, R. and Woitke, P. and Nowak, U. and Sedlmayr, E. (2004) Dust in brown dwarfs. IV. Dust formation and driven turbulence on mesoscopic scales. Astronomy and astrophysics, 423 (2). pp. 657-675. ISSN 0004-6361

Horenko, I. and Weiser, M. and Schmidt, B. and Schütte, Ch. (2004) Fully Adaptive Propagation of the Quantum-Classical Liouville Equation. J. Chem. Phys., 120 (19). pp. 8913-8923.

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

Klein, R. and Mikusky, E. and Owinoh, A.Z. (2004) Multiple Scales Asymptotics for Atmospheric Flows. Proceedings of the 4th European Conference on Mathematics .

Ronen, S. and Nachtigallova, D. and Schmidt, B. and Jungwirth, P. (2004) Non-Adiabatic Chemical Reaction Triggered by Electron Photodetachment: An ab initio Quantum Dynamical Study. Phys. Rev. Lett., 93 (4). 048301.

Gröpl, C. and Prömel, H.-J. and Srivastav, A. (2004) Ordered binary decision diagrams and the Shannon effect. Discrete Applied Mathematics, 142 . pp. 67-85.

Huisinga, W. and Meyn, S. and Schütte, Ch. (2004) Phase Transitions and Metastability in Markovian and Molecular Systems. Ann. Appl. Prob., 14 (1). pp. 419-458.

Kiljunen, T. and Bargheer, M. and Gühr, M. and Schwentner, N. and Schmidt, B. (2004) Photodynamics and Ground State Librational States of ClF Molecule in solid Ar. Comparison of experiment and theory. Phys. Chem. Chem. Phys., 6 (11). pp. 2932-2939.

Fujimura, Y. and Gonzalez, L. and Kröner, D. and Manz, J. and Mehdaoui, I. and Schmidt, B. (2004) Quantum Ignition of Intramolecular Rotation by Means of IR+UV Laser Pulses. Chem. Phys. Lett., 386 (4-6). pp. 248-253.

Korolkov, M. V. and Schmidt, B. (2004) Quantum Molecular Dynamics Driven by Short and Intense Light Pulses: Towards the Limits of the Floquet Picture. Comp. Phys. Comm., 161 (1-2). pp. 1-17.

Botta, N. and Klein, R. and Langenberg, S. and Lützenkirchen, S. (2004) Well Balanced Finite Volume Methods for Nearly Hydrostatic Flows. Journal of Computational Physics, 196 (2). pp. 539-565.

Istrail, S. and Sutton, G. G. and Florea, L. and Mobarry, C. M. and Lippert, R. and Walenz, B. and Shatkay, H. and Dew, Ian and Miller, J. R. and Flanigan, M. J. and Edwards, N. J. and Bolanos, R. and Fasulo, D. and Halldorsson, B. V. and Hannenhalli, S. and Turner, R. J. and Yooseph, S. and Lu, Fu and Nusskern, D. R. and Shue, B. C. and Zheng, X. H. and Zhong, F. and Delcher, A. L. and Huson, D. H. and Kravitz, S. A. and Mouchard, L. and Reinert, K. and Remington, K. A. and Clark, A. G. and Waterman, M. S. and Eichler, E. E. and Adams, M. D. and Hunkapillar, M. W. and Myers, E. W. and Venter, J. C. (2004) Whole-genome shotgun assembly and comparison of human genome assemblies. Proceedings of the national academy of science (PNAS), 101 (7). pp. 1916-1921.

Klein, R. (2004) An applied mathematical view of meteorological modeling. Applied Mathematics Entering the 21st century; Invited talks from the ICIAM 2003 Congress., 116 . pp. 177-219.

Audusse, E. and Bouchut, F. and Bristeau, M.O. and Klein, R. and Perthame, B. (2004) A fast and stable well-balanced scheme with hydrostatic reconstruction for shallow water flows. Journal of Scientific Computation, 25 (6). pp. 2050-2065.

2003

Krah, A. and Schmidt, F. and Becher, D. and Schmid, M. and Albrecht, D. and Rack, A. and Büttner, K. and Jungblut, P. (2003) Analysis of Automatically Generated Peptide Mass Fingerprints of Cellular Proteins and Antigens from Helicobacter pylori 26695 Separated by Two-dimensional Electrophoresis. Molecular & Cellular Proteomics, 2 (12). pp. 1271-1283.

Frömmel, C. and Gille, Ch. and Goede, A. and Gröpl, C. and Hougardy, S. and Nierhoff, T. and Preissner, R. and Thimm, M. (2003) Accelerating screening of 3D protein data with a graph theoretical approach. Bioinformatics, 19 (18). pp. 2442-2447.

Munz , C.-D. and Roller , S. and Klein, R. and Geratz, K. J. (2003) The extension of incompressible flow solvers to the weakly compressible regime. Computers & fluids , 32 (2). 173-196 (31 ref.). ISSN 0045-7930

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

Noé, F. and Schwarzl, S. and Fischer, S. and Smith, J. C. (2003) Computational tools for analysing structural changes in proteins in solution. Applied Bioinformatics, 2 . pp. 11-17.

Cockburn, B. (2003) Discontinuous Galerkin methods. ZAMM - Zeitschrift für Angewandte Mathematik und Mechanik, 83 (11). 731 -754.

Huisinga, W. and Schütte, Ch. and Stuart, A. M. (2003) Extracting Macroscopic Stochastic Dynamics: Model Problems. Comm. Pure Appl. Math., 56 (2). pp. 234-269.

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

Wohlmuth, B. and Krause, R. (2003) Monotone methods on non-matching grids for non-linear contact problems. SIAM J. Sci. Comput., 25 (1). pp. 324-347. ISSN 1064-8275

Becker, T. and Fischer, S. and Noé, F. and Ullmann, M. and Tournier, A. and Smith, J. C. (2003) Protein Dynamics: Glass Transition and Mechanical Function. Advances in Solid State Physics, 43 . pp. 677-694.

Majda, A.J. and Klein, R. (2003) Systematic Multiscale Models for the Tropics. Journal of Atmospheric Sciences, 60 . pp. 393-408.

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

Schmidt, H. and Klein, R. (2003) A generalized level-set/in-cell-reconstruction method for accelerating turbulent premixed flames. Combustion Theory and Modelling, 7 (2). 243-267(25).

2002

Krause, R. and Wohlmuth, B. (2002) A Dirichlet-Neumann type algorithm for contact problems with friction. Computing and Visualization in Science, 5 (3). pp. 139-148. ISSN 1432-9360

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

Mural, Richard and Adams, M. D. and Reinert, K. (2002) A Comparison of Whole-Genome Shotgun-Derived Mouse Chromosome 16 and the Human Genome. Science, 296 . pp. 1661-1671.

Huson, D. H. and Reinert, K. and Myers, E. W. (2002) The Greedy Path-Merging Algorithm for Sequence Assembly. Journal of the ACM, 49 (5). pp. 603-615.

Horenko, I. and Schmidt, B. and Schütte, Ch. (2002) Multidimensional Classical Liouville Dynamics with Quantum Initial Conditions. J. Chem. Phys., 117 (10). pp. 4643-4650.

Klein, R. (2002) Numerical Methods for High and Low Speed Combustion Simulations. Numerical Methods for High and Low Speed Combustion Simulations. PDE's in models of superfluidity, superconductivity and reactive flows, Nato S (569). pp. 491-506.

Roeselova, M. and Mucha, M. and Schmidt, B. and Jungwirth, P. (2002) Quantum dynamics and spectroscopy of photodetachment in Cl-...H2O and Cl-...D2O complexes. J. Phys. Chem. A, 106 (51). pp. 12229-12241.

Horenko, I. and Salzmann, Ch. and Schmidt, B. and Schütte, Ch. (2002) Quantum-Classical Liouville Approach to Molecular Dynamics: Surface Hopping Gaussian Phase-Space Packets. J. Chem. Phys., 117 (24). pp. 11075-11088.

Bailey, J. A. and Gu, Z. and Clark, R. A. and Reinert, K. and Samonte, R. V. and Schwartz, S. S. and Adams, M. D. and Myers, E. W. and Li, P. and Eichler, E. E. (2002) Recent Segmental Duplications in the Human Genome. Science, 297 . pp. 1003-1007.

Korolkov, M. V. and Schmidt, B. (2002) Spin-Orbit Induced Association under Ultrafast Laser Pulse Control. Chem. Phys. Lett., 361 (5-6). pp. 432-438.

Gröpl, C. and Hougardy, S. and Nierhoff, T. and Prömel, H.-J. (2002) Steiner trees in uniformly quasi-bipartite graphs. Information Processing Letters, 83 . pp. 195-200.

Manz, J. and Proppe, B. and Schmidt, B. (2002) Time-Resolved Dual Fluorescence of 1-Phenylpyrrole in Acetonitrile: Molecular Dynamics Symulations of Solvent Response to Twisted Intramolecular Charge Transfer. Phys. Chem. Chem. Phys., 4 (10). pp. 1876-1881.

Berghof, V. and Martins, M. and Schmidt, B. and Schwentner, N. (2002) Vibrational Overtones and Rotational Structures of HCl in Rare Gas Matrices. J. Chem. Phys., 116 (21). pp. 9364-9373.

2001

Kornhuber, R. and Krause, R. (2001) Adaptive multigrid methods for Signorini's problem in linear elasticity. Computing and Visualization in Science, 4 (1). pp. 9-20. ISSN 1432-9360

Krause, R. and Wohlmuth, B. (2001) Domain decomposition methods on nonmatching grids and some applications to linear elasticity problems. Zeitschrift für angewandte Mathematik und Mechanik (ZAMM), 81 (Suppl.). pp. 21-24. ISSN 0044-2267

Kober, C. and Müller-Hannemann, M. (2001) A case study in hexahedral mesh generation: Simulation of the human mandible. Engineering with Computers, 17 (3). pp. 249-260. ISSN 0177-0667

Schäfer-Bung, B. and Engels, B. and Taylor, T. and Neumark, P. and Botschwina, P. and Perić, M. (2001) Measurement and theoretical simulation of the HCCO- anion photoelectron spectrum. J. Chem. Phys., 115 (4). pp. 1777-1788.

Klein, R. and Botta, N. and Schneider, T. and Munz, C.D. and Roller, S. and Meister, A. and Hoffmann, L. and Sonar, T. (2001) Asymptotic adaptive methods for multi-scale problems in fluid mechanics. Journal of Engineering Mathematics, 39 (1). pp. 261-343. ISSN 0022-0833 (Print) 1573-2703 (Online)

Helling, Ch. and Oevermann, M. and Lüttke, M. J. H. and Klein, R. (2001) Dust in Brown Dwarfs I. Dust formation under turbulent conditions on microscopic scales. Astronomy & Astrophysics, - (), 376 . pp. 194-212.

Gröpl, C. and Prömel, H.-J. and Srivastav, A. (2001) On the Evolution of the Worst-Case OBDD Size. Information Processing Letters, 77 . pp. 1-7.

Chaban, G. and Gerber, R. B. and Korolkov, M. V. and Manz, J. and Niv, M. Y. and Schmidt, B. (2001) Photodissociation Dynamics of Molecular Fluorine in an Argon Matrix Induced by Ultrashort Laser Pulses. J. Phys. Chem. A, 105 (12). pp. 2770-2782.

Slavicek, P. and Roeselova, M. and Jungwirth, P. and Schmidt, B. (2001) Preference of Cluster Isomers as a Result of Quantum Delocalization: Potential Energy Surfaces and Intermolecular Vibrational States of Ne...HBr, Ne...HI, and HI(Ar)n (n=1-6). J. Chem. Phys., 114 (4). pp. 1539-1548.

Venter, J. C. and Adams, M. D. and Myers, E. W. and Reinert, K. and et al, . (2001) The Sequence of the Human Genome. Science, 291 (5507). pp. 1304-1351.

Horenko, I. and Schmidt, B. and Schütte, Ch. (2001) A Theoretical Model for Molecules Interacting with Intense Laser Pulses: The Floquet-based Quantum-Classical Liouville Equation. J. Chem. Phys., 115 (13). pp. 5733-5743.

Schmidt, H. and Klein, R. (2001) Towards a Generalized Level-Set/In-Cell Reconstruction Approach for Accelerating Turbulent Premixed Flames.

Wohlmuth, B. and Krause, R. (2001) A multigrid method based on the unconstrained product space for Mortar finite element discretizations. SIAM Journal on Numerical Analysis, 39 (1). pp. 192-213. ISSN 0036-1429

2000

Knio, O.M. and Klein, R. (2000) Improved Thin Tube Methods for Slender Vortex Simulations. Journal of Computational Physics, 162 (1). 68-82(15).

Klein, R. (2000) Asymptotic Analyses for Atmospheric Flows and the Construction of Asymptotically Adaptive Numerical Methods. ZAMM ·Zeitschrift für angewandte Mathematik und Mechanik, 80 (11-12). pp. 765-785. ISSN 0044-2267

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

Kober, C. and Sader, R. and Thiele, H. and Bauer, H.-J. and Zeilhofer, H.-F. and Hoffmann, K.-H. (2000) FEM simulations versus biomechnical experiments concerning the human mandible: a comparision of the results of a frontal and a molar biting study. Preprint A-21-2000 . (Unpublished)

UNSPECIFIED (2000) The Genome Sequence of Drosophila melanogaster. Science, 287 (5461). pp. 2185-2195.

Deuflhard, P. and Huisinga, W. and Fischer, A. and Schütte, Ch. (2000) Identification of Almost Invariant Aggregates in Reversible Nearly Uncoupled Markov Chains. Lin. Alg. Appl., 315 (1-3). pp. 39-59.

Reinert, K. and Stoye, J. and Will, T. (2000) An Iterative Methods for Faster Sum-of-Pairs Multiple Sequence Alignment. BIOINFORMATICS, 16 (9). pp. 808-814.

Klein, R. and Münch, M. (2000) Models and Criteria for Prediction of Deflagration to Detonation Transition (DDT) in Hydrogen-Air-Steam Systems under Severe Accident Conditions. Numerical Techniques , 9, Reihe Energietechnik / Energy Technology. . pp. 83-102.

Klein, R. and Rehm, W. (2000) Models and Criteria for Prediction of Deflagration-to- Detonation Transition (DDT) in Hydrogen-Air-Steam Systems under Severe Accident Conditions. Schriften des Forschungszentrums Jülich, Energy Technology Series, 9 . ISSN ISBN 3-89336-258-4

Krause, R. and Wohlmuth, B. (2000) Nonconforming decomposition methods: Techniques for linear elasticity. East-West Journal of Numerical Mathematics, 8 (3). pp. 177-206. ISSN 1569-3953; 0928-0200

Kececioglu, J. D. and Lenhof, H.-P. and Mehlhorn, K. and Reinert, K. and Vingron, M. (2000) A Polyhedral Approach to Sequence Alignment Problems. Discrete Applied Mathematics, 104 . pp. 143-186.

Lermen, M. and Reinert, K. (2000) The Practical Use of the A* Algorithm for Exact Multiple Sequence Alignment. Journal of Computational Biology . pp. 655-671.

Gerber, R. B. and Korolkov, M. V. and Manz, J. and Niv, M. Y. and Schmidt, B. (2000) A Reflection Principle for the Control of Molecular Photodissociation in Solids: Model Simulation for F2 in Ar. Chem. Phys. Lett., 327 (1-2). pp. 76-84.

Schmidt, B. and Zdanska, P. (2000) Solution of the Time-Dependent Schrödinger Equation for Highly Symmetric Potentials. Comp. Phys. Comm., 127 (2-3). pp. 290-308.

Breitung, W. and Chan, C. and Dorofeev, S.B. and Eder, A. and Gelfand, B.E. and Heitsch, M. and Klein, R. and Malliakos, A. and Shepherd, J.E. and Studer, E. and Thibault, P. (2000) State of Art Report on Flame Acceleration and DDT in Nuclear Reactor Safety. OECD .

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

Myers, E. W. and Sutton, G. G. and Delcher, A. L. and Dew, D. P. and Flanigan, M. J. and Kravitz, S. A. and Mobarry, C. M. and Reinert, K. and Remington, K. A. and Anson, E. L. and Bolanos, R. and Chou, H.-H. and Jordan, C. M. and Halpern, A. L. and Lonardi, S. and Beasly, E. M. and Brandon, R. C. and Chen, L. and Dunn, P. J. and Lai, Z. and Liang, Y. and Nusskern, D. R. and Zhan, M. and Zhang, Q. and Zheng, X. H. and Rubin, G. M. and Adams, M. D. and Venter, J. C. (2000) A Whole-Genome Assembly of Drosophila. Science, 287 (5461). pp. 2196-2203.

1999

Reinecke , M. and Hillebrandt , W. and Niemeyer , J.C. and Klein, R. and Gröbl, A. (1999) A new model for deflagration fronts in reactive fluids. Astronomy and Astrophysics, 347 (1999A&A...347..724R). 724-733 . ISSN 0004-6361 (Print) 1432-0746 (Online)

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

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

Backhaus, P. and Schmidt, B. and Dantus, M. (1999) Control of Photoassociation Yield: A Quantum Dynamical Study of the Mercury System to Explore the Role of Pulse Duration from Nanoseconds to Femtoseconds. Chem. Phys. Lett., 306 (1-2). pp. 18-24.

Schütte, Ch. and Fischer, A. and Huisinga, W. and Deuflhard, P. (1999) A Direct Approach to Conformational Dynamics based on Hybrid Monte Carlo. J. Comp. Phys, 151 (1). pp. 146-168.

Schneider, T. and Botta, N. and Geratz, K. J. and Klein, R. (1999) Extension of finite volume compressible flow solvers to multidimensional, variable density zero Mach number flows. J. Comput. Phys., 155 . pp. 248-286.

Huisinga, W. and Pesce, L. and Kosloff, R. and Saalfrank, P. (1999) Faber and Newton Polynomial Integrators for Open-System Density Matrix Propagation. J. Chem. Phys., 110 (12). pp. 5538-5547.

Huisinga, W. and Best, Ch. and Roitzsch, R. and Schütte, Ch. and Cordes, F. (1999) From Simulation Data to Conformational Ensembles: Structure and Dynamics based Methods. J. Comp. Chem., 20 (16). pp. 1760-1774.

Fischer, A. and Cordes, F. and Schütte, Ch. (1999) Hybrid Monte Carlo with adaptive temperature choice: Efficient conformational analysis of RNA. Comp. Phys. Comm., 121 . pp. 37-39.

Worlikar, A.S. and Aniruddha, S. and Knio, O.M. and Klein, R. (1999) Numerical Study of the Effective Impedance of a Thermoacoustic Stack. Acta Acustica united with Acustica, 85 (4,). pp. 480-494. ISSN 1610-1928

Bornemann, F. A. and Schütte, Ch. (1999) On the Singular Limit of the Quantum-Classical Molecular Dynamics Model. J. Appl. Math., 59 (4). pp. 1208-1224.

Zdanska, P. and Schmidt, B. and Jungwirth, P. (1999) Photolysis of Hydrogen Chloride Embedded in the First Argon Solvation Shell: Rotational Control and Quantum Dynamics of Photofragments. J. Chem. Phys., 110 (13). pp. 6246-6256.

Schmidt, B. (1999) Quantum Dynamics of HF Photodissociation in Icosahedral Ar12HF Clusters: Rotational Control of the Hydrogen Atom Cage Exit. Chem. Phys. Lett., 301 (3-4). pp. 207-216.

Lenhof, H.-P. and Morgenstern, B. and Reinert, K. (1999) An exact solution for the segment-to-segment multiple sequence alignment problem. BIOINFORMATICS, 15 (3). pp. 203-210.

1998

Berkenbosch, A. and Kaasschieter, E. and Klein, R. (1998) Detonation capturing for stiff combustion chemistry. Combustion Theory and Modelling, 2 (3). 313-348(36).

Worlikar, A.S. and Knio, O.M. and Klein, R. (1998) Numerical Simulation of a Thermoacoustic Refrigerator II. Stratified Flow around the Stack. Journal of Computational Physics, 144 (2). 299-324(26).

Knio, O.M. and Ting, L. and Klein, R. (1998) Interaction of a Slender Vortex Filament with a Rigid Sphere: Dynamics and far-fi eld 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.

1997

Smiljanovski, V. and Moser, V. and Klein, R. (1997) A Capturing/Tracking Hybrid Scheme for Deflagration Discontinuities. Combustion Theory and Modelling, 1 (2). 183-215 .

Backhaus, P. and Schmidt, B. (1997) Femtosecond Quantum Dynamics of Photoassociation Reactions: The Exciplex Formation of Mercury. Chem. Phys., 217 (2-3). pp. 131-143.

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

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

Korolkov, M. V. and Schmidt, B. (1997) Infrared Picosecond Laser Control of Acceleration of Neutral Atoms: Model Simulations for the Collision Pair O + H. Chem. Phys. Lett., 272 (1-2). pp. 96-102.

Worlikar, A.S. and Knio, O.M. and Klein, R. (1997) Numerical Simulation of a Thermo-Acoustic Refrigerator. Vortex Flows and Related Numerical Methods II .

Manz, J. and Saalfrank, P. and Schmidt, B. (1997) Quantum Dynamical Aspects of Rotationally and Vibrationally Mediated Photochemistry in Matrices and at Surfaces: HCl/DCl in Ar, and NH3/ND3 at Cu(111). J. Chem. Soc. Faraday Trans., 93 (5). pp. 957-967.

Jungwirth, P. and Schmidt, B. (1997) Quantum dynamics following electron photodetachment in the I-Ar2 complex: How Good Are New Separable and Non-Separable Simulation Methods? Chem. Phys. Lett., 275 (3-4). pp. 127-136.

Jungwirth, P. and Schmidt, B. and Moiseyev, N. (1997) Vibrationally Resolved Spectra from Short Time Quantum Molecular Dynamics by the Filter-Diagonalization Method. Chem. Phys. Lett., 280 (3-4). pp. 177-184.

1996

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

Meißner, B. and Schmidt, B. and Berry, R. S. (1996) Cluster Growth From the Gas Phase: Associative Collisions of Small Alkali Halide Aggregates. Z. Phys. Chem., 195 . pp. 237-251.

Nettesheim, P. and Bornemann, F. A. and Schmidt, B. and Schütte, Ch. (1996) An Explicit and Symplectic Integrator for Quantum-Classical Molecular Dynamics. Chem. Phys. Lett., 256 (6). pp. 581-588.

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

Finger, K. and Daniel, Ch. and Saalfrank, P. and Schmidt, B. (1996) Nonadiabatic Effects in the Photodissociation and Electronic Spectroscopy of HMn(CO)3(dab): Quantum Wave Packet Dynamics Based on ab-initio Potentials. J. Phys. Chem., 100 (9). pp. 3368-3376.

Bornemann, F. A. and Nettesheim, P. and Schütte, Ch. (1996) Quantum-classical molecular dynamics as an approximation to full quantum dynamics. J. Chem. Phys., 105 (3). pp. 1074-1083.

Klein, R. and Knio, O.M. and Ting, L. (1996) Representation of Core Dynamics in Slender Vortex Filament Simulations,. Physics of Fluids, 8 (9). 2415{-2425,.

Korolkov, M. V. and Paramonov, G. K. and Schmidt, B. (1996) State-Selective Control For Vibrational Excitation and Dissociation of Diatomic Molecules With Shaped Ultrashort Laser Pulses. J. Chem. Phys., 105 (5). pp. 1862-1879.

Schmidt, B. and Jungwirth, P. (1996) Vibrational Line Shifts of Hydrogen Halides in a Rare Gas Environment: HF/DF and HCl/DCl in Ar Matrices and Clusters. Chem. Phys. Lett., 259 (1-2). pp. 62-688.

Korolkov, M. V. and Manz, J. and Paramonov, G. K. and Schmidt, B. (1996) Vibrationally State Selective Photoassociation by Infrared Picosecond Laser Pulses: Model Simulations for O + H → OH(ν). Chem. Phys. Lett., 260 (5-6). pp. 604-610.

Bornemann, F. A. and Erdmann, B. and Kornhuber, R. (1996) A posteriori error estimates for elliptic problems in two and three space dimensions. SIAM Journal on Numerical Analysis, 33 (3). pp. 1188-1204. ISSN 0036-1429

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

1995

Klein, R. and Ting, L. (1995) Theoretical and Experimental Studies of Slender Vortex Filaments. Applied Mathematics Letters, 8 (2). pp. 45-50.

Klein, R. (1995) Analysis of Accelerating Detonation Using Large Activation Energy Asymptotics. Journal de physique. IV , 5 (4). pp. 443-457. ISSN 1155-4339

Klein, R. and Knio, O.M. (1995) Asymptotic Vorticity Structure and Numerical Simulation of Slender Vortex Filaments. Journal of Fluid Mechanics, 284 . pp. 275-321. ISSN 0022-1120

Schütte, Ch. and Zumbusch, M. D. G and Brinkmann, R. (1995) Dynamics of Erbium-doped Waveguide Lasers: Modelling, Reliable Simulation, and Comparison with Experiments. preprint .

Manz, J. and Proppe, B. and Schmidt, B. (1995) From Torsional Spectra to Hamiltonians and Dynamics: Effects of Coupled Bright and Dark States of 9-(N-Carbazolyl) Anthracene. Z. Phys. D, 34 (2). pp. 111-118.

Klein, R. (1995) The Level-Set Approach to Premixed Turbulent Combustion in the Flamelet Regime: Theory and Numerical Implementation. Euroconference "Premixed Turbulent Combustion: Introduction to the State of the Art" .

Klein, R. (1995) Semi-Implicit Extension of a Godunov-Type Scheme Based on Low Mach Number Asymptotics I: One-dimensional Flow,. Journal of Computational Physics, 121 (2). pp. 213-237. ISSN 0021-9991

Klein, R. and Majda, A. J. and Damodaran, K. (1995) Simplied Equations for the Interaction of Nearly Parallel 3-D Vortex Filaments,. Journal of Fluid Mechanics, 288 . 201-248 . ISSN 0022-1120

Schütte, Ch. (1995) Smoothed Molecular Dynamics for Thermally Embedded Systems. preprint . (Unpublished)

Schütte, Ch. and Dinand, M. (1995) Theoretical Modeling of Relaxation Oscillations in Er-Doped Wave-Guide Lasers. J. Lightw. Techn., 13 (1). pp. 14-23.

1994

Hoppe, R. H. W. and Kornhuber, R. (1994) Adaptive multilevel methods for obstacle problems. SIAM Journal on Numerical Analysis, 31 (2). pp. 301-323. ISSN 0036-1429

Buck, U. and Schmidt, B. (1994) Frequency Shifts in Infrared Spectra of Ethylene Clusters. J. Chem. Phys., 101 (7). pp. 6365-6366.

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

Manz, J. and Paramonov, G. K. and Polasek, M. and Schütte, Ch. (1994) Overtone State-Selective Isomerization by a Series of Picosecond Infrared Laser Pulses - Model Simulations for Be2H3D. Isr. J. Chem., 34 (1). pp. 115-125.

Schmidt, B. and Gerber, R. B. (1994) Reactive Collisions as a Signature for Meltinglike Transitions in Clusters. Phys. Rev. Lett., 72 (15). pp. 2490-2493.

Schmidt, B. and Gerber, R. B. (1994) Solvation Effects on Association Reactions in Microclusters: Classical Trajectory Study of H+Cl(Ar)n. J. Chem. Phys., 101 (1). pp. 343-355.

Klein, R. and Breitbach, H. and Geratz, K. J. and Senger, W. (1994) Surface erosion by high-speed combustion waves. Symposium (International) on Combustion, 25 (1). 95-102 .

Bdzil, J.B. and Klein, R. (1994) Weakly Nonlinear Dynamics of Near-CJ Detonation Waves, Combustion in High-Speed Flows. Combustion in High-Speed Flows, J. Buckmaster et al. (eds), . pp. 513-540. ISSN 978-0-7923-2806-3 (ISBN)

1993

Klein, R. and Stewart, D.S., (1993) The Relation between Curvature, Rate-State Dependence and Detonation Velocity. SIAM Journal on Applied Mathematics, 53 (5). 1401-1435 .

Erdmann, B. and Frei, M. and Hoppe, R. H. W. and Kornhuber, R. and Wiest, U. (1993) Adaptive finite element methods for variational inequalities. East-West Journal of Numerical Mathematics, 1 . pp. 165-197. ISSN 1569-3953; 0928-0200

Bornemann, F. A. and Erdmann, B. and Kornhuber, R. (1993) Adaptive multilevel methods in three space dimensions. International Journal for Numerical Methods in Engineering, 36 (18). pp. 3187-3203. ISSN 1097-0207

Klein, R. and Majda, A. J. (1993) An Asymptotic Theory for the Nonlinear Instability of Anti- Parallel Pairs of Vortex Filaments. Physics of Fluids A, 5 . pp. 369-379. ISSN 0899-8213

Buck, U. and Schmidt, B. (1993) A Perturbation Approach to Predict the Infrared Spectra of Small Molecular Clusters Applied to Methanol. J. Chem. Phys., 98 (12). pp. 9410-9424.

Schütte, Ch. (1993) A Quasiresonant Smoothing Algorithm for the Fast Analysis of Selective Vibrational Excitation. Impact of Computing in Sci. Eng., 5 (3). pp. 176-200.

Kornhuber, R. and Roitzsch, R. (1993) Self-adaptive finite-element simulation of bipolar, strongly reverse-biased pn-junctions. International Journal for Numerical Methods in Biomedical Engineering, 9 (3). pp. 243-250. ISSN 2040-7947

Buck, U. and Schmidt, B. and Siebers, J. G. (1993) Structural Transitions and Thermally Averaged Infrared Spectra of Small Methanol Clusters. J. Chem. Phys., 99 (12). pp. 9428-9437.

Buck, U. and Hobein, M. and Schmidt, B. (1993) Structure and Photodissociation Spectra of Mixed Ethene-Acetone Clusters. J. Chem. Phys., 98 (12). pp. 9425-9431.

1992

Klein, R. and Majda, A. J. and McLaughlin, R.M. (1992) Asymptotic Equations for the Stretching of Vortex Filaments by a Background Flow Field. Physics of Fluids A, 4 . pp. 2271-2281. ISSN 0899-8213

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

Klein, R. and Ting, L. (1992) Vortex Filaments with Axial Core Structure Variation. Appl. Math. Lett., 5 . pp. 99-103.

1991

Klein, R. and Majda, A. J. (1991) Self-Stretching of a Perturbed Vortex Filament I: The Asymptotic Equation for Deviations from a Straight Line. Physica D, 49 (3). pp. 323-352.

Klein, R. (1991) On the Dynamics of Weakly Curved Detonations. Institute for Mathematics and Its Applications, 35 . ISSN 0940-6573

Klein, R. (1991) On the Dynamics of Weakly Curved Detonations. IMA-Volumes in Mathematics and its Applications, 35 . ISSN 978-0-387-97583-2

1990

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

Klein, R. and Ting, L. (1990) Far field velocity potential induced by a rapidly decaying vorticity distribution. Zeitschrift für Angewandte Mathematik und Physik (ZAMP), 41 (3). pp. 395-418. ISSN 0044-2275 (Print) 1420-9039 (Online)

Buck, U. and Schmidt, B. (1990) Calculation of Vibrational Line Shifts for Molecular Dimers. J. Mol. Liqu., 46 . pp. 181-196.

Hoppe, R. H. W. and Kornhuber, R. (1990) Multi-grid solution of two coupled Stefan equations arising in induction heating of large steel slabs. International Journal for Numerical Methods in Engineering, 30 (4). pp. 779-801. ISSN 1097-0207

Klein, R. and Munz , C.-D. and Schmidt, L. (1990) A Numerical Study of Interfacial Instabilities at High Mach Numbers. Notes on Numerical Fluid Mechanics, 29,, 29 . 242-251.

Kornhuber, R. and Roitzsch, R. (1990) On adaptive grid refinement in the presence of internal or boundary layers. IMPACT of Computing in Science and Engineering, 2 (1). pp. 40-72. ISSN 0899-8248

Ahlrichs, R. and Brode, St. and Buck, U. and deKieviet, M. and Lauenstein, Ch. and Rudolph, A. and Schmidt, B. (1990) The Structure of C2H4 Clusters from Theoretical Interaction Potentials and Vibrational Predissociation Data. Z. Phys. D, 15 (4). pp. 341-351.

Maly, R.R. and Koenig, G. and Klein, R. and Peters, N. (1990) Theoretical and Experimental Investigation of Knock Induced Surface Destruction. SAE transactions, 99 (1), no3, pp. (1). 99-137 (62 ref.). ISSN 0096-736X

1989

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

Aziz, R. A. and Buck, U. and Jonsson, H. and Ruiz-Suarez, J. C. and Schmidt, B. and Scoles, G. and Slaman, M. J. and Xu, J. (1989) Two- and Three-Body Forces in the Interaction of He Atoms with Xe Overlayers Adsorbed on (0001) Graphite. J. Chem. Phys., 91 (10). pp. 6477-6493.

1988

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

Klein, R. and Peters, N. (1988) Cumulative Eff ects 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.

This list was generated on Thu Nov 23 06:22:49 2017 CET.