Items where Subject is "Mathematical and Computer Sciences"

A

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.

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

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

Alphonse, Amal and Caetano, Diogo and Djurdjevac, Ana and Elliott, Charles M. (2023) Function spaces, time derivatives and compactness for evolving families of Banach spaces with applications to PDEs. Journal of Differential Equations, 353 . pp. 268-338.

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.

Arts, Marloes and Garcia Sattorras, Victor and Huang, Chin-Wei and Zuegner, Daniel and Federici, Marco and Clementi, Cecilia and Noé, Frank and Pinsler, Robert and van den Berg, Rianne (2023) Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics. arXiv . (Submitted)

Ayaz, Cihan and Scalfi, Laura and Dalton, Benjamin and Netz, Roland R. (2022) Generalized Langevin equation with a nonlinear potential of mean force and nonlinear memory friction from a hybrid projection scheme. PHYSICAL REVIEW E, 105 . pp. 1-19.

Ayaz, Cihan and Tepper, Lucas and Netz, Roland R. (2022) Markovian embedding of generalized Langevin equations with a nonlinear friction kernel and configuration-dependent mass. Turkish Journal of Physics, 46 (6). pp. 194-205.

B

Bach, V. and Delle Site, L. (2014) On Some Open Problems in Many-Electron Theory. In: Many-Electron Approaches in Physics, Chemistry and Mathematics: A Multidisciplinary View. Mathematical Physics Studies . Springer, pp. 413-417. ISBN 978-3-319-06378-2

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

Banisch, Ralf and Djurdjevac, N. and Schütte, Ch. (2015) Reactive flows and unproductive cycles in irreversible Markov chains. The European Physical Journal Special Topics, 224 (12). pp. 2369-2387. ISSN 1951-6355

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)

Banisch, Ralf and Koltai, Péter and Padberg-Gehle, Kathrin (2019) Network measures of mixing. Chaos: An Interdisciplinary Journal of Nonlinear Science 29, 063125 (2019), 29 . pp. 1-16.

Bardos, Claude and Boutros, Daniel W. and Titi, Edriss (2023) Hoelder regularity of the pressure for weak solutions of the 3D Euler equations in bounded domains. Preprint . pp. 1-35. (Unpublished)

Basaric, Danica and Bella, Peter and Feireisl, Eduard and Oschmann, Florian and Titi, Edriss (2022) On the incompressible limit of a strongly stratified heat conducting fluid. On the incompressible limit of a strongly stratified heat conducting fluid . pp. 1-20. (Unpublished)

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

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) .

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.

Bernhard, S. and Noé, F. (2010) Optimal Identification of Semi-Rigid Domains in Macromolecules from Molecular Dynamics Simulation. PLoS One, 5 . e10491.

Bielow, C. and Gröpl, C. and Kohlbacher, O. and Reinert, K. (2011) Bioinformatics for qualitative and quantitative proteomics. In: Bioinformatics for Omics Data Methods and Protocols. Humana Press, pp. 331-49.

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.

Bittracher, A. and Koltai, P. and Klus, S. and Banisch, R. and Dellnitz, M. and Schütte, Ch. (2018) Transition manifolds of complex metastable systems: Theory and data-driven computation of effective dynamics. Journal of Nonlinear Science, 28 (2). pp. 471-512. ISSN 1432-1467 (online)

Bockmayr, A. and Siebert, H. and Röblitz, S. and Schütte, Ch. and Deuflhard, P. (2014) Advanced mathematical modeling in systems biology. In: MATHEON : mathematics for key technologies. EMS series in industrial and applied mathematics, 1 . EMS Publishing House, Zürich, pp. 22-44. ISBN 978-3-03719-137-8

Boltz, Horst-Holger and Sirbu, Alexei and Stelzer, Nina and de Lanerolle, Primal and Winkelmann, Stefanie and Annibale, Paolo (2022) The impact of membrane protein diffusion on GPCR signaling. Cells, 11 (10).

Botta, N. and Klein, R. and Almgren, A. (1999) Dry Atmosphere Asymptotics. Technical Report. PIK Report, Summary Report No. 55.

Boutros, Daniel W. and Markfelder, Simon and Titi, Edriss (2023) Nonuniqueness of generalised weak solutions to the primitive and Prandtl equations. arXiv . pp. 1-73. (Unpublished)

Bowman, G. R. and Pande, V. S. and Noé, F. (2014) Introduction and overview of this book. In: An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation. Advances in Experimental Medicine and Biology, 797 . Springer, pp. 1-6.

Boyko, V. and Vercauteren, N. (2020) Multiscale Shear Forcing of Turbulence in the Nocturnal Boundary Layer: A Statistical Analysis. Boundary-Layer Meteorology, 177 (2-3). ISSN Electronic: 1573-1472; Print: 0006-8314

Bruckner, S. and Hüffner, F. and Komusiewicz, Ch. and Niedermeier, R. (2013) Evaluation of ILP-based approaches for partitioning into colorful components. In: Experimental Algorithms. Lecture Notes in Computer Science, 7933 (7933). Springer, Heidelberg, pp. 176-187. ISBN 978-3-642-38526-1 (print) / 978-3-642-38527-8 (online)

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.

Brünig, Florian N. and Daldrop, Jan O. and Netz, Roland R. (2022) Pair-Reaction Dynamics in Water: Competition of Memory, Potential Shape, and Inertial Effects. J. Phys. Chem. B, 126 . pp. 1-10.

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Chemnitz, Dennis and Engel, Maximilian (2022) Positive Lyapunov Exponent in the Hopf Normal Form with Additive Noise. arXive preprint . pp. 1-35. (Unpublished)

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

Ciccotti, G. and Ferrario, M. and Schütte, Ch. (2014) Molecular Dynamics Simulation. MDPI AG, Basel. ISBN 978-3-906980-65-2

Ciccotti, G. and Ferrario, M. and Schütte, Ch. (2018) Molecular Dynamics vs. Stochastic Processes: Are We Heading Anywhere? Entropy (Special Issue), 20 (5). p. 348. ISSN 1099-4300

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Delle Site, L. (2014) Levy-Lieb Principle meets Quantum Monte Carlo. In: Many-Electron Approaches in Physics, Chemistry and Mathematics: A Multidisciplinary View. Mathematical Physics Studies . Springer, pp. 361-375. ISBN 978-3-319-06378-2

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

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

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

Delle Site, L. and Agarwal, A. and Junghans, C. and Wang, H. (2016) Adaptive Resolution Simulation as a Grand Canonical Molecular Dynamics Scheme: Principles, Applications and Perspectives. In: Multiscale Methods in Molecular Biophysics. Series in Computational Biophysics . CRC Press. ISBN 1482225700 (In Press)

Dellnitz, M. and Klus, S. (2016) Sensing and control in symmetric networks. Dynamical Systems. An International Journal . pp. 1-19. (Submitted)

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

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

Dibak, M. and del Razo, M.J. and De Sancho, D. and Schütte, Ch. and Noé, F. (2018) MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations. Journal of Chemical Physics, 148 (214107). ISSN 0021-9606

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

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

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

Djurdjevac, N. and Fuerstenau, D. and Grabundzija, A. and Helfmann, L. and Park, M. and Schier, W. and Schütt, B. and Schütte, Ch. and Weber, M. and Wulkow, N. and Zonker, J. (2018) Mathematical Modeling of the Spreading of Innovations in the Ancient World. eTopoi. Journal for Ancient Studies, 7 . ISSN 2192-2608

Djurdjevac, N. and Helfmann, L. and Zonker, J. and Winkelmann, S. and Schütte, Ch. (2018) Human mobility and innovation spreading in ancient times: a stochastic agent-based simulation approach. EPJ Data Science, 7 (1). p. 24.

Djurdjevac Conrad, Natasa and Köppl, Jonas and Djurdjevac, Ana (2022) Feedback Loops in Opinion Dynamics of Agent-Based Models with Multiplicative Noise. Entropy, 24 (10). pp. 1-23.

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

Donati, Luca and Weber, Marcus and Keller, Bettina (2022) A review of Girsanov reweighting and of square root approximation for building molecular Markov state models. J. Math. Phys., 63 (12). pp. 1-22.

Durumeric, Alexander E.P. and Charron, Nicholas E. and Templeton, Clark and Musil, Félix and Bonneau, Klara and Pasos-Trejo, Aldo S. and Chen, Yaoyi and Kelkar, Atharva and Noé, Frank and Clementi, Cecilia (2023) Machine learned coarse-grained protein force-fields: Are we there yet? Current Opinion in Structural Biology, 79 .

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

del Razo, M.J. and Winkelmann, S. and Klein, R. and Höfling, F. (2023) Chemical diffusion master equation: formulations of reaction–diffusion processes on the molecular level. J. Math. Phys., 64 (013304).

del Razo, Mauricio J. and Frömberg, Daniela and Straube, Arthur V. and Schütte, Christof and Höfling, Felix and Winkelmann, Stefanie (2022) A probabilistic framework for particle-based reaction–diffusion dynamics using classical Fock space representations. Letters in Mathematical Physics, 112 (49). pp. 1-59.

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

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

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.

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

Engel, Maximilian and Olicon-Mendez, Guillermo and Unger, Nathalie and Winkelmann, Stefanie (2022) Synchronization and random attractors for reaction jump processes. arXive preprint . pp. 1-39. (Submitted)

Engel, Maximilian and Piliouras, Georgios (2023) A stochastic variant of replicator dynamics in zero-sum games and its invariant measures. arXive . pp. 1-19. (Submitted)

Ernst, Ariane and Schütte, Christof and Sigrist, Stephan J. and Winkelmann, Stefanie (2022) Variance of filtered signals: Characterization for linear reaction networks and application to neurotransmission dynamics. Mathematical Biosciences, 343 .

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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.

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

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).

Froyland, Gary and Koltai, Péter and Stahn, Martin (2020) Computation and Optimal Perturbation of Finite-Time Coherent Sets for Aperiodic Flows Without Trajectory Integration. SIAM J. APPLIED DYNAMICAL SYSTEMS, 19 (3). pp. 1659-1700.

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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

Gholami, Abbas and Klein, Rupert and Delle Site, Luigi (2022) Simulation of a Particle Domain in a Continuum, Fluctuating Hydrodynamics Reservoir. Physical Review Letters, 129 (23).

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

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

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

Gupta, P. and Peter, S. and Jung, M. and Lewin, A. and Hemmrich-Stanisak, G. and Franke, A. and von Kleist, M. and Schütte, Ch. and Einspanier, R. and Sharbati, S. and zur Bruegge, J. (2019) Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections. Sci. Rep., 9 (1571). ISSN 2045-2322

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Hartmann, C. and Banisch, Ralf and Sarich, M. and Badowski, T. and Schütte, Ch. (2014) Characterization of Rare Events in Molecular Dynamics. In: Molecular Dynamics Simulation. MDPI AG, Basel, pp. 222-249. ISBN 978-3-906980-65-2

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

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.

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

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)

Huysmans, Lucas and Titi, Edriss (2023) NON-UNIQUENESS & INADMISSIBILITY OF THE VANISHING VISCOSITY LIMIT OF THE PASSIVE SCALAR TRANSPORT EQUATION. Arxive . pp. 1-49. (Unpublished)

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

J

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

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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

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.

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.

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

Klein, Rupert and Delle Site, Luigi (2022) Derivation of Liouville-like equations for the n-state probability density of an open system with thermalized particle reservoirs and its link to molecular simulation. Journal of Physics A: Mathematical and Theoretical, 55 . pp. 1-18.

Klus, S. and Gelß, P. and Peitz, S. and Schütte, Ch. (2018) Tensor-based dynamic mode decomposition. Nonlinearity, 31 (7). pp. 3359-3380. ISSN 0951-7715

Klus, S. and Nüske, F. and Koltai, P. and Wu, H. and Kevrekidis, I. and Schütte, Ch. and Noé, F. (2018) Data-driven model reduction and transfer operator approximation. Journal of Nonlinear Science, 28 (1). pp. 1-26.

Klus, S. and Sahai, T. (2018) A spectral assignment approach for the graph isomorphism problem. Information and Inference: a Journal of the IMA, 7 (4). pp. 689-706.

Klus, Stefan and Bittracher, Andreas and Schuster, Ingmar and Schütte, Christof (2018) A kernel-based approach to molecular conformation analysis. Journal of Chemical Physics, 149 (244109).

Koltai, P. and Schütte, Ch. (2017) A multi scale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics. ZIB-Report . ISSN 1438-0064

Koltai, P. and Schütte, Ch. (2018) A multiscale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics. Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 16 (4). pp. 1455-1485. ISSN 1540-3459

Koltai, P. and Wu, H. and Noé, F. and Schütte, Ch. (2018) Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics. Computation, 6(1) (22). ISSN 2079-3197 (online)

Koreuber, M. and Mischau, A. (2020) Mathematik: Geschlechterforschung in disziplinären Zwischenräumen. In: Handbuch Interdisziplinäre Geschlechterforschung. Geschlecht und Gesellschaft, 65 (5). Springer VS, Wiesbaden, pp. 1-19. ISBN ISSN: 2512-0883

Kosari, Ehsan and Rosenau, Matthias and Ziegenhagen, Thomas and Oncken, Onno (2022) Upper plate response to a sequential elastic rebound and slab acceleration during laboratory-scale subduction megathrust earthquakes. JGR Solid Earth, 127 (9). pp. 1-16.

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

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

Krämer, Andreas and Durumeric, Alexander E.P. and Charron, Nicholas E. and Chen, Yaoyi and Clementi, Cecilia and Noé, Frank (2023) Statistically Optimal Force Aggregation for Coarse-Graining Molecular Dynamics. arXiv . (Submitted)

Köhler, Jonas and Chen, Yaoyi and Krämer, Andreas and Clementi, Cecilia and Noé, Frank (2023) Flow-Matching: Efficient Coarse-Graining of Molecular Dynamics without Forces. J. Chem. Theory Comput., 19 (3). pp. 942-952.

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Langfeld, B. and Mischau, A. (2015) MathematikerInnen und PhysikerInnen an Hochschulen: Repairing or Redesigning the Leaky Pipeline? In: Akademische Wissenskulturen und soziale Praxis. Geschlechterforschung zu natur-, technik- und geisteswissenschaftlichen Fächern im Vergleich. Sektionsreihe Forum Frauen- und Geschlechterforschung (42). Westfälisches Dampfboot, pp. 37-59. ISBN 978-3-89691-242-8

Lavacchi, Laura and Daldrop, Jan O. and Netz, Roland R. (2022) Non-Arrhenius barrier crossing dynamics of non-equilibrium non-Markovian systems. Europhysics Letters, 139 (5). pp. 1-7.

Leyshon, Thomas and Tonello, Elisa and Schnoerr, David and Siebert, Heike and Stumpf, Michael P.H. (2021) The Design Principles of Discrete Turing Patterning Systems. Journal of Theoretical Biology, 531 .

Love, Michael I. (2013) Statistical analysis of high-throughput sequencing count data. PhD thesis, Freie Universität Berlin.

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Majewski, Maciej and Pérez, Adrià and Thölke, Philipp and Doerr, S. and Charron, Nicholas E. and Giorgino, Toni and Husic, Brooke E. and Clementi, Cecilia and Noé, Frank and De Fabritis, Gianni (2022) Machine Learning Coarse-Grained Potentials of Protein Thermodynamics. arXiv . pp. 1-31. (Submitted)

Mardt, A. and Pasquali, L. and Wu, H. and Noé, F. (2018) VAMPnets: Deep learning of molecular kinetics. Nat. Comm., 9 . p. 5.

Mastella, G. and Corbi, Fabio and Bedford, Jonathan and Funiciello, Francesca and Rosenau, Matthias (2022) Forecasting Surface Velocity Fields Associated With Laboratory Seismic Cycles Using Deep Learning. AGU-Geophysical Research Letters, 49 (15). pp. 1-12.

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

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.

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

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.

Montefusco, Alberto and Schütte, Christof and Winkelmann, Stefanie (2022) A route to the hydrodynamic limit of a reaction-diffusion master equation using gradient structures. arXiv . (Submitted)

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

Musil, Félix and Zaporozhets, Iryna and Noé, Frank and Clementi, Cecilia and Kapil, Venkat (2022) Quantum dynamics using path integral coarse-graining. The Journal of Chemical Physics, 157 (18).

Möller, Jan and Isbilir, Ali and Sungkaworn, Titiwat and Osberg, Brendan and Karathanasis, Christos and Sunkara, Vikram and Grushevskyi, Eugene O. and Bock, Andreas and Annibale, Paolo and Heileman, Mike and Schütte, Christof and Lohse, Martin J. (2020) Single molecule mu-opioid receptor membrane-dynamics reveal agonist-specific dimer formation with super-resolved precision. Nature chemical biology (16). pp. 946-954.

Münch, M. (1996) Einsatz von CFD bei der Modellierung natürlicher Brände - Ein Vergleich zwischen Simulationsrechnung und Experiment. Masters thesis, Technische Universität Braunschweig.

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Niemann, Jan-Hendrik and Winkelmann, Stefanie and Wolf, S. and Schütte, Christof (2021) Agent-based modeling: Population limits and large timescales. Choas, 31 (3).

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

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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.

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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.

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 .

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.

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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.

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.

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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.

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Panahian Jand, Sara and Nourbakhsh, Zahra and Delle Site, Luigi (2022) Nuclear Quantum Effects in Fullerene-Fullerene Aggregation in Water. Front. Chem., 10 . pp. 1-8.

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Paul, F. and Noé, F. and Weikl, T. (2018) Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations. J. Phys. Chem. B .

Paul, F. and Wehmeyer, C. and Abualrous, E. T. and Wu, H. and Crabtree, M. D. and Schöneberg, J. and Clarke, J. and Freund, C. and Weikl, T. and Noé, F. (2017) Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nat. Comm., 8 (1095).

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

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.

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)

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.

Pinamonti, G. and Zhao, J. and Condon, D. and Paul, F. and Noé, F. and Turner, D. and Bussi, G. (2017) Predicting the kinetics of RNA oligonucleotides using Markov state models. J. Chem. Theory Comput., 13 (2). pp. 926-934.

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.

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

Prinz, J.-H. and Chodera, J. D. and Noé, F. (2014) Estimation and Validation of Markov Models. In: An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation. Advances in Experimental Medicine and Biology , 797 . Springer, pp. 45-60.

Prinz, J.-H. (2012) Advanced estimation methods for Markov models of dynamical systems. PhD thesis, FU Berlin.

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

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.

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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.

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.

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.

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

Ray, Sourav and Sunkara, Vikram and Schütte, Christof and Weber, Markus (2020) How to calculate pH-dependent binding rates for receptor-ligand systems based on thermodynamic simulations with different binding motifs. Molecular Simulation, 46 (18). pp. 1443-1452.

Reible, Benedikt and Hartmann, Carsten and Delle Site, Luigi (2022) Two-sided Bogoliubov inequality to estimate finite size effects in quantum molecular simulations. Letters in Mathmeaical Physics, 112 (97). pp. 1-17.

Reible, Benedikt M. and Hille, Julian F. and Hartmann, Carsten and Delle Site, Luigi (2023) Finite-size effects and thermodynamic accuracy in many-particle systems. Physical Review Research, 5 (2).

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

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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.

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

Sarich, M. and Banisch, Ralf and Hartmann, C. and Schütte, Ch. (2014) Markov State Models for Rare Events in Molecular Dynamics. In: Molecular Dynamics Simulation. MDPI AG, Basel, pp. 250-279. ISBN 978-3-906980-65-2

Sarich, M. and Prinz, J.-H. and Schütte, Ch. (2014) Markov Model Theory. In: An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation. Advances in Experimental Medicine and Biology, 797 (797). Springer, Dordrecht, Heidelberg, New York, London, pp. 23-44. ISBN 978-94-007-7605-0

Sbailò, L. and Noé, F. (2017) An efficient multi-scale Green's Functions Reaction Dynamics scheme. J. Chem. Phys., 147 . p. 184106. ISSN 0021-9606, ESSN: 1089-7690

Schaller, Christoph (2013) STORMicroscopy: A Mathematical Analysis. Masters thesis, FU Berlin.

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.

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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.

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

Schütte, Ch. and Conrad, T. O. F. (2014) Showcase 3: Information-based medicine. In: MATHEON : mathematics for key technologies. EMS Series in Industrial and Applied Mathematics, 1 . EMS Publishing House, Zürich, pp. 66-67. ISBN 978-3-03719-137-8

Schütte, Ch. and Deuflhard, P. (2014) Life sciences. In: MATHEON : mathematics for key technologies. EMS series in industrial and applied mathematics, 1 . EMS Publishing House, Zürich, pp. 1-6. ISBN 978-3-03719-137-8

Schütte, Ch. and Deuflhard, P. and Noé, F. and Weber, M. (2014) Design of functional molecules. In: MATHEON : mathematics for key technologies. EMS series in industrial and applied mathematics, 1 . EMS Publishing House, Zürich, pp. 49-65. ISBN 978-3-03719-137-8

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

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

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

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.

Schütte, Christof and Klus, Stefan and Hartmann, Carsten (2022) Overcoming the Timescale Barrier in Molecular Dynamics: Transfer Operators, Variational Principles, and Machine Learning. ZIB . (Submitted)

Seibert, Johannes (2010) Investigation of the reaction-diffusion processes of rod cell disc membrane photoactivation with single-particle resolution. Masters thesis, FU Berlin.

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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.

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)

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Trung, Minh Nguyen and Kieninger, Stefanie and Fandi, Zeinab and Qiu, Danye and Liu, Guizhen and Mehendale, Neelay K. and Saiardi, Adolfo and Jessen, Henning and Keller, Bettina and Fiedler, Dorothea (2022) Stable Isotopomers of myo-Inositol Uncover a Complex MINPP1-Dependent Inositol Phosphate Network. ACS Cent. Sci., 8 (12). pp. 1683-1694.

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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.

Ullrich, Alexander (2011) Computational Studies on the Evolution of Metabolism. PhD thesis, Universität Leipzig.

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.

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

Ullrich, Alexander and Forst, Christian V. (2009) k-PathA: k-shortest Path Algorithm. In: High Performance Computational Systems Biology (HiBi 2009), September 2009, Trento, Italy.

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

Ulrich, T. and Vater, S. and Madden, E. H. and Behrens, J. and van Dinther, Y. and van Zelst, I. and Fielding, E. J. and Liang, C. and Gabriel, A.-A. (2019) Coupled, Physics-Based Modeling Reveals Earthquake Displacements are Critical to the 2018 Palu, Sulawesi Tsunami. Pure and Applied Geophysics, 176 . pp. 4069-4109. ISSN 0033-4553 (Print) 1420-9136 (Online)

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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.

von Larcher, T. and Viazzo, S. and Harlander, U. and Vincze, M. and Randriamampianina, A. (2018) Instabilities and small-scale waves within the Stewartson layers of a thermally driven rotating annulus. Journal of Fluid Mechanics, 841 . pp. 380-407. ISSN 0022-1120

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Waidmann, M. (2017) Towards a Strictly Conservative Hybrid Level-Set Volume-of-Fluid Finite Volume Method for Zero Mach Number Two-Phase Flow. PhD thesis, Freie Universität Berlin.

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

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

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

Weese, D. (2013) Indices and Applications in High-Throughput Sequencing. PhD thesis, Freie Universität Berlin.

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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.

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Winkelmann, Stefanie and Schütte, Christof Stochastic Dynamics in Computational Biology. Springer.

Winkelmann, Stefanie and Zonker, J. and Schütte, Christof and Djurdjevac Conrad, Natasa (2021) Mathematical modeling of spatio-temporal population dynamics and application to epidemic spreading. Mathematical Biosciences, 336 .

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

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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.

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

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.

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

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.

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, Ho and Noé, Frank (2019) Variational approach for learning Markov processes from time series data. Journal of Nonlinear Science, 30 . pp. 23-66. ISSN 1432-1467 (online)

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