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

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

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

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

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

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

Agarwal, A. and Delle Site, L. (2015) Path Integral Molecular Dynamics within the Grand Canonical-like Adaptive Resolution Technique: Simulation of Liquid Water. Journal of Chemical Physics, 143 (9). ISSN 0021-9606

Agarwal, A. and 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 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

Agazzi, Andrea and Andreis, Luisa and Patterson, Robert I. A. and Renger, D.R. Michiel (2021) Large deviations for Markov jump processes with uniformly diminishing rates. arXive . pp. 1-19. (Unpublished)

Agazzi, Andrea and Andreis, Luisa and Patterson, Robert I.A. and Renger, D.R. Michiel (2021) LARGE DEVIATIONS FOR MARKOV JUMP PROCESSES WITH UNIFORMLY DIMINISHING RATES. arXive . pp. 1-19. (Unpublished)

Ague, Jay J. and Tassara, Santiago and Holycross, Megan E. and Li, Jei-Li and Cottrell, Elizabeth and Schwarzenbach, Esther M. and Fassoulas, Charalampos and John, Timm (2022) Slab-derived devolatilization fluids oxidized by subducted metasedimentary rocks. Nature Geoscience, 15 . pp. 320-326.

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

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

Alchikh, M. and Conrad, T. O. F. and Hoppe, Ch. and Ma, X. and Broberg, E. and Penttinen, P. and Reiche, J. and Biere, B. and Schweiger, B. and Rath, B. (2019) Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care. Clinical Microbiology and Infection, 25 (3). 380.e9-380.e16. ISSN 1469-0691

Alchikh, Maren and Conrad, T. O. F. and Obermeier, Patrick E. and Ma, Xiaolin and Schweiger, Brunhilde and Opota, Onya and Rath, Barbara A. (2024) Disease Burden and Inpatient Management of Children with Acute Respiratory Viral Infections during the Pre-COVID Era in Germany: A Cost-of-Illness Study. Viruses, 16 (4).

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.

Andreis, Luisa and König, Wolfgang and Patterson, Robert I.A. (2021) A large‐deviations principle for all the cluster sizes of a sparse Erdős–Rényi graph. Random Structures and Algorithms . pp. 1-32.

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

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

Arts, Marloes and Garcia Sattorras, Victor and Huang, Chin-Wei and Zuegner, Daniel and Federici, Marco and Clementi, Cecilia and Noé, Frank and Pinsler, Robert and van den Berg, Rianne (2023) Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics. JCTC - Journal of Chemical Theory and Computation, 19 . pp. 6151-6159.

Atnip, Jason and Froyland, Gary and Koltai, Péter (2024) An inflated dynamic Laplacian to track the emergence and disappearance of semi-material coherent sets. Preprint . (Unpublished)

Ayanbayev, Birzhan and Klebanov, Ilja and Lie, Han Cheng and Sullivan, Timothy Γ-convergence of Onsager-Machlup functionals. Part I: With applications to maximum a posteriori estimation in Bayesian inverse problems. Inverse Problems .

Ayaz, Cihan and Dalton, Benjamin and Netz, Roland R. (2022) Generalized Langevin Equation with a Non-Linear Potential of Mean Force and Non-Linear Friction From a Hybrid Projection Scheme. Preprint . (Unpublished)

Ayaz, Cihan and Tepper, Lucas and Brünig, Florian N. and Daldrop, Jan O. and Netz, Roland R. (2021) Non-Markovian modeling of protein folding. Proceedings of the National Academy of Sciences, 118 (31). pp. 1-7.

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.

Azouz, Nurit P. and Klingler, Andrea M. and Callahan, Victoria and Akhrymuk, Ivan V. and Elez, Katarina and Raich, Lluís and Henry, Brandon M. and Benoit, Justin L. and Benoit, Stefanie W. and Noé, Frank and Kehn-Hall, Kylene and Rothenberg, Marc E. (2021) Alpha 1 Antitrypsin is an Inhibitor of the SARS-CoV-2–Priming Protease TMPRSS2. Pathogens and Immunity, 6 (1). pp. 55-74.

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

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.

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 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

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)

Bardos, Claude and Liu, Xin and Titi, Edriss (2023) Derivation of a generalized quasi-geostrophic approximation for inviscid ows in a channel domain: The fast waves correction. pp. 1-33. (Unpublished)

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

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.

Bartsch, Clemens and John, Volker and Patterson, Robert I. A. (2019) Simulations of an ASA flow crystallizer with a coupled stochastic-deterministic approach. Computers & Chemical Engineering, 124 . pp. 350-363.

Bartscha, Clemens and Wiedmeyer, Viktoria and Lakdawala, Zahra and Patterson, Robert I.A. and Voigt, Andreas and Sundmacher, Kai and John, Volker (2019) Stochastic-deterministic population balance modeling and simulation of a fluidized bed crystallizer experiment. Chemical Engineering Science, 208 . ISSN 115102

Barua, Amlan K. and Chew, Ray and Li, Shuwang and Lowengrub, John and Münch, A. and Wagner, B. (2021) Sharp-interface problem of the Ohta-Kawasaki model 2 for symmetric diblock copolymers. Journal of Computational Physics . pp. 1-34. ISSN 0021-9991 (Submitted)

Barua, Amlan K. and Chew, Ray and Li, Shuwang and Lowengrub, John and Münch, Andreas and Wagner, Barbara (2023) Sharp-interface problem of the Ohta-Kawasaki model for symmetric diblock copolymers. Journal of Computational Physics, 481 .

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)

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

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

Bastian, P. and Blatt, M. and Dedner, A. and Dreier, N.-A. and Engwer, C. and Fritze, R. and Gräser, C. and Grüninger, C. and Kempf, D. and Klöfkorn, R. and Ohlberger, M. and Sander, O. (2021) The Dune framework: Basic concepts and recent developments. Computers & Mathematics with Applications, 81 . pp. 75-112. ISSN 0898-1221

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

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

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 .

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

Becker, Simon and Hartmann, Carsten and Redmann, Martin and Richter, Lorenz (2022) Error bounds for model reduction of feedback-controlled linear stochastic dynamics on Hilbert spaces. Stochastic Processes and their Applications, 149 . pp. 107-141.

Becker, Simon and Hartmann, Carsten and Redmann, Martin and Richter, Lorenz (2019) Feedback control theory & Model order reduction for stochastic equations. ArXive . pp. 1-36. (Submitted)

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

Beinlich, A. and John, T. and Vrijmoed, J.C. and Tominaga, M. and Podladchikov, Y.Y. (2020) Instantaneous rock transformations in the deep crust driven by reactive fluid flow. nature geoscience, 13 . pp. 307-311.

Berg, Mascha and Plöntzke, Julia and Siebert, Heike and Röblitz, Susanna (2021) Modelling Oscillatory Patterns in the Bovine Estrous Cycle with Boolean Delay Equations. Modelling Oscillatory Patterns in the Bovine Estrous Cycle with Boolean Delay Equations .

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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 Klus, Stefan and Hamzi, Boumediene and Koltai, Péter and Schütte, Christof (2020) Dimensionality Reduction of Complex Metastable Systems via Kernel Embeddings of Transition Manifolds. Journal of Nonlinear Science, 31 (3).

Bittracher, Andreas and 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

Bittracher, Andreas and Mollenhauer, Mattes and Koltai, Péter and Schütte, Christof (2021) Optimal Reaction Coordinates: Variational Characterization and Sparse Computation. ArXiv . pp. 1-36. (Submitted)

Bittracher, Andreas and Moschner, Johann and Koksch, Beate and Netz, Roland R. and Schütte, Christof (2021) Exploring the locking stage of NFGAILS amyloid fibrillation via transition manifold analysis. The European Physical Journal B volume, 94 (195).

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

Bittracher, Andreas and Schütte, Christof (2020) A weak characterization of slow variables in stochastic dynamical systems. Studies in Systems, Decision and Control, 304 . pp. 132-150.

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

Bleich, Amnon and Linnemann, Antje and Benjamin, Jaidi and Bjoern, H. Diem and Conrad, T. O. F. (2023) Enhancing ECG Analysis of Implantable Cardiac Monitor Data: An Efficient Pipeline for Multi-Label Classification. Machine Learning and Knowledge Extraction, 5 (4). ISSN 2504-4990

Blumenthal, Alex and Engel, Maximilian and Neamţu, Alexandra (2023) On the pitchfork bifurcation for the Chafee-Infante equation with additive noise. Probability Theory and Related Fields, 187 . pp. 603-627.

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

Blömker, Dirk and Schillings, Claudia and Wacker, Philipp and Weissmann, Simon (2019) Well posedness and convergence analysis of the ensemble Kalman inversion. Inverse Problems, 35 . pp. 1-33.

Bogdanow, Boris and Gruska, Iris and Mühlberg, Lars and Protze, Jonas and Hohensee, Svea and Vetter, Barbara and Bosse, Jens B. and Lehmann, Martin and Sadeghi, Mohsen and Wiebusch, Lüder and Liu, Fan (2023) Spatially resolved protein map of intact human cytomegalovirus virions. Nature Microbiology, 8 . pp. 1732-1747.

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).

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

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

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

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.

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

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

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.

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

Borrell, Enric Ribera and Quer, Jannes and Richter, Lorenz and Schütte, Christof (2023) Improving control based importance sampling strategies for metastable diffusions via adapted metadynamics. Preprint to appear in SISC 2024 . (In Press)

Bostanci, Inan and Conrad, T. O. F. (2024) Integrating Agent-Based and Compartmental Models for Infectious Disease Modeling: A Novel Hybrid Approach. Journal of Artificial Societies and Social Simulation . (Submitted)

Bouanani, Hafida and Hartmann, Carsten and Kebiri, Omar (2021) Model reduction and uncertainty quantification of multiscale diffusions with parameter uncertainties using nonlinear expectations. arXive . pp. 1-22. (Submitted)

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)

Breiten, T. and Hartmann, Carsten and Neureither, Lara and Sharma, Upanshu (2021) Stochastic gradient descent and fast relaxation to thermodynamic equilibrium: a stochastic control approach. Journal of Mathematical Physics, 62 (12). pp. 1-19.

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

Bryant, Patrick and Kelkar, Atharva and Guljas, Andrea and Clementi, Cecilia and Noé, Frank (2024) Structure prediction of protein-ligand complexes from sequence information with Umol. Nature Communications, 15 .

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

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

Brünig, Florian N. and Geburtig, Otto and von Canal, Alexander and Kappler, Julian and Netz, Roland R. (2022) Time-dependent friction effects on vibrational infrared frequencies and line shapes of liquid water. J. Phys. Chem. B, 126 . pp. 1579-1589.

Bäumer, D. and Hittmeir, S. and Klein, R. (2023) Scaling approaches to quasi-geostrophic theory for moist, precipitating air. J. Atmos. Sci. . pp. 1-18.

Büeler, Dominik and Pfahl, Stephan (2017) Potential Vorticity Diagnostics to Quantify Effects of Latent Heating in Extratropical Cyclones. Part I: Methodology. Journal of the Atmospheric Sciences, 74 (11).

Cao, Chongsheng and Li, Jinkai and Titi, Edriss S. and Wang, Dong (2024) Global well-posedness of the 3D primitive equations with horizontal viscosity and vertical diffusivity II: close to H1 initial data. arXiv (Preprint) . (Unpublished)

Carlson, Shane and Brünig, Florian N. and Loche, Philip and Bonthuis, Douwe Jan and Netz, Roland R. (2020) Exploring the Absorption Spectrum of Simulated Water from MHz to Infrared. The Journal of Physical Chemistry A, 124 (27). pp. 5599-5605. ISSN 1089-5639

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

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.

Charron, Nicholas E. and Musil, Felix and Guljas, Andrea and Chen, Yaoyi and Bonneau, Klara and Pasos-Trejo, Aldo S. and Venturin, Jacopo and Gusew, Daria and Zaporozhets, Iryna and Krämer, Andreas and Templeton, Clark and Kelkar, Atharva and Durumeric, Alexander E.P. and Olsson, Simon and Pérez, Adrià and Majewski, Maciej and Husic, Brooke E. and Patel, Ankit and Fabritiis, Gianni De and Noé, Frank and Clementi, Cecilia (2023) Navigating protein landscapes with a machine-learned transferable coarse-grained model. Preprint . (Unpublished)

Chemnitz, Dennis and Engel, Maximilian (2023) Positive Lyapunov Exponent in the Hopf Normal Form with Additive Noise. Communications in Mathematical Physics, 402 . pp. 1807-1843.

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

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

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

Chen, Shuo and Hin, Remco C. and John, Timm and Bryan, Ben and Nui, Yaoling and Elliott, Tim and Brooker, R. (2019) Molybdenum systematics of subducted crust record reactive fluid flow from underlying slab serpentine dehydration. nature communications . pp. 1-9.

Chen, Yaoyi and Krämer, Andreas and Charron, Nicholas E. and Husic, Brooke E. and Clementi, Cecilia and Noé, Frank (2021) Machine learning implicit solvation for molecular dynamics. The Journal of Chemical Physics, 155 (084101). pp. 1-15.

Chew, R. and Schlutow, M. and Klein, R. (2023) An unstable mode of the stratified atmosphere under the non-traditional Coriolis acceleration. Journal of Fluid Mechanics, 967 .

Chowdhary, Suvrat and Moschner, Johann and Mikolajczak, Dorian J. and Becker, Maximilian and Thünemann, Andreas F. and Kästner, Claudia and Klemczak, Damian and Stegemann, Anne-Katrin and Böttcher, Christoph and Metrangolo, Pierangelo and Netz, Roland R. and Koksch, Beate (2020) The Impact of Halogenated Phenylalanine Derivatives on NFGAIL Amyloid Formation. ChemBioChem, 21 . pp. 3544-3554.

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

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

Coghi, Michele and Nilssen, Torstein and Nüsken, Nikolas and Reich, Sebastian (2023) Rough McKean–Vlasov dynamics for robust ensemble Kalman filtering. The Annals of Applied Probability, 33 (6b). pp. 5693-5752.

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

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

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

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

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

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

Conrad, T. O. F. and Ferrer, Eloi and Mietchen, Daniel and Pusch, Larissa and Stegmüller, Johannes and Schubotz, Moritz (2024) Making Mathematical Research Data FAIR: Pathways to Improved Data Sharing. Nature Scientific Data, 11 (1).

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.

Corbi, F. and Bedford, J. and Sandri, L. and Funiciello, F. and Gualandi, A. and Rosenau, M. (2020) Predicting Imminence of Analog Megathrust Earthquakes With Machine Learning: Implications for Monitoring Subduction Zones. Geophysical Research Letters . pp. 1-10. ISSN 1944-8007

Cortes-Huerto, Robinson and Praprotnik, Matej and Kremer, Kurt and Delle Site, Luigi (2021) From Adaptive Resolution to Molecular Dynamics of Open Systems. The European Physical Journal B, 94 (189). pp. 1-22.

Cvetkovic, Nada and Conrad, T. O. F. and Lie, Han Cheng (2021) A convergent discretisation method for transition path theory for diffusion processes. Multiscale Modeling & Simulation, 19 (1). ISSN 15403467

Daldrop, J.O. and Kappler, J. and Brünig, F.N. and Netz, R.R. (2018) Butane dihedral angle dynamics in water is dominated by internal friction. PNAS, 20 (115). pp. 5169-5174. ISSN 1091-6490 (online)

Daldrop, J.O. and Kowalik, B.G. and Netz, R.R. (2017) External Potential Modifies Friction of Molecular Solutes in Water. Phys. Rev. X, 7 (4). 041065.

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

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

Delle Site, Luigi (2021) Investigation of water-mediated intermolecular interactions with the adaptive resolution simulation technique. Journal of Physics: Condensed Matter, 34 (11). pp. 1-15.

Delle Site, Luigi and Djurdjevac, Ana (2024) An effective Hamiltonian for the simulation of open quantum molecular systems. Journal of Physics A: Mathematical and Theoretical, 57 (25).

Delle Site, Luigi and Hartmann, Carsten (2024) Computationally feasible bounds for the free energy of nonequilibrium steady states, applied to simple models of heat conduction. Molecular Physics .

Delle Site, Luigi and Hartmann, Carsten (2024) Scaling law for the size dependence of a finite-range quantum gas. Physical Review A, 109 (2).

Delle Site, Luigi and Hartmann, Carsten (2024) Scaling law for the size dependence of a short-ranged quantum gas. Physical Review A, 109 .

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

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

Detring, Carola and Müller, Annette and Schielicke, Lisa and Névir, Peter and Rust, Henning W. (2020) Atmospheric blocking types: Frequencies and transitions. European Geosiences Union . pp. 1-33. (Submitted)

Detring, Carola and Müller, Annette and Schielicke, Lisa and Névir, Peter and Rust, Henning W. (2021) Occurrence and transition probabilities of omega and high-over-low blocking in the Euro-Atlantic region. Weather Clim. Dynamics, 2 . pp. 927-952.

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

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)

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

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

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.

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

Dibak, Manuel and Fröhner, Christoph and Noé, Frank and Höfling, Felix (2019) Diffusion-influenced reaction rates in the presence of pair interactions. The Journal of Chemical Physics, 151 (16).

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

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

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

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

Djurdjevac, A. and Elliott, C.M. and Kornhuber, R. and Ranner, Th. (2018) Evolving surface finite element methods for random advection-diffusion equations. SIAM/ASA Journal on Uncertainty Quantification, 6 (4). pp. 1656-1684. ISSN 2166-2525

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

Djurdjevac, Ana and Kremp, Helena and Perkowski, Nicolas (2024) Weak error analysis for a nonlinear SPDE approximation of the Dean-Kawasaki equation. Stochastics and Partial Differential Equations: Analysis and Computations .

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

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

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

Dolores-Tesillos, Edgar and Pfahl, Stephan (2024) Future changes in North Atlantic winter cyclones in CESM-LE – Part 2: A Lagrangian analysis. Weather and Climate Dynmics, 5 . pp. 163-179.

Dolores-Tesillos, Edgar and Teubler, Franziska and Pfahl, Stephan (2022) Future changes in North Atlantic winter cyclones in CESM-LE – Part 1: Cyclone intensity, potential vorticity anomalies, and horizontal wind speed. Weather Clim. Dynam., 3 . pp. 429-448.

Donati, L. and Heida, M. and Weber, M. and Keller, B. (2018) Estimation of the infinitesimal generator by square-root approximation. Journal of Physics: Condensed Matter, 30 (42). p. 425201. ISSN 0953-8984, ESSN: 1361-648X

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

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.

Donati, Luca and Weber, Marcus and Keller, Bettina G. (2021) Markov models from the square root approximation of the Fokker–Planck equation: calculating the grid-dependent flux. J. Phys.: Condens. Matter, 33 . pp. 1-15.

Dondl, Patrick and Frenzel, Thomas and Mielke, Alexander (2019) A gradient system with a wiggly energy and relaxed EDP-convergence. ESAIM Control Optimisation and Calculus of Variations, 25 (68). pp. 1-45.

Doppler, Sabine and Klein, Rupert and Liu, Xin and Titi, Edriss (2024) Local well-posedness of a system coupling compressible atmospheric dynamics and a micro-physics model of moisture in air. Preprint arXiv . (Unpublished)

Durumeric, Aleksander E.P. and Chen, Yaoyi and Noé, Frank and Clementi, Cecilia Learning data efficient coarse-grained molecular dynamics from forces and noise. Preprint arXiv . (Unpublished)

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 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.

Dyhr, Michael C. A. and Sadeghi, Mohsen and Moynova, Ralista and Knappe, Carolin and Burcu Kepsutlu, Çakmak and Werner, Stephan and Schneider, Gerd and McNally, James and Noé, Frank and Ewers, Helge (2023) 3D surface reconstruction of cellular cryo-soft X-ray microscopy tomograms using semisupervised deep learning. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 120 (24).

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

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.

Eiter, Thomas and Hopf, Katharina and Mielke, Alexander (2021) Leray–Hopf solutions to a viscoelastoplastic fluid model with nonsmooth stress–strain relation. Nonlinear Analysis, 65 .

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

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

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

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

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

Engel, Maximilian and Olicón-Mendez, Guillermo (2023) A singular perturbation analysis for the Brusselator. Preprint . (Submitted)

Engel, Maximilian and Piliouras, Georgios (2023) A stochastic variant of replicator dynamics in zero-sum games and its invariant measures. Physica D: Nonlinear Phenomena, 456 .

Engwer, C. and Gräser, C. and Müthing, S. and Sander, O. (2018) Function space bases in the dune-functions module. arXiv:1806.09545 . pp. 1-53. (Submitted)

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

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

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

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

Ernst, Ariane and Falkenhagen, Undine and Winkelmann, Stefanie (2023) Model reduction for Ca²+ -induced vesicle fusion dynamics. Proceedings in Applied Mathematics and Mechanics, 23 (4).

Ernst, Ariane and 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 .

Ernst, Ariane and Unger, Nathalie and Schütte, Christof and Walter, Alexander M. and Winkelmann, Stefanie (2023) Rate-limiting recovery processes in neurotransmission under sustained stimulation. Mathematical Biosciences, 362 . p. 109023.

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

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

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

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

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

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

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

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

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

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.

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.

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.

Fischer, Julian and Hopf, Katharina and Kniely, Michael and Mielke, Alexander (2022) Global existence analysis of energy-reaction-diffusion systems. SIAM Journal on Mathematical Analysis. SIAM Journal on Mathematical Analysis, 54 . pp. 220-267.

Flegel, Franziska and Heida, Martin (2020) The fractional p-Laplacian emerging from homogenization of the random conductance model with degenerate ergodic weights and unbounded-range jumps. Calculus of Variations and Partial Differential Equations, 59 (8). (Unpublished)

Flegel, Franziska and Heida, Martin and Slowik, Martin (2019) Homogenization theory for the random conductance model with degenerate ergodic weights and unbounded-range jumps. Ann. Inst. H. Poincaré Probab. Statist., 55 (3). pp. 1226-1257.

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

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

Fradon, Myriam and Kern, Julian and Roelly, Sylvie and Zass, Alexander (2023) Diffusion dynamics for an infinite system of two-type spheres and the associated depletion effect. Preprint submitted to Stochastic Processes and their Applications . (Submitted)

Franchi, Bruno and Heida, Martin and Lorenzani, Silvia (2020) A Mathematical model for Alzheimer's disease: An approach via stochastic homogenization of the Smoluchowski equation. Communications in Mathematical Sciences, 18 (4). pp. 1105-1134.

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.

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.

Froyland, Gary and Koltai, Péter (2023) Detecting the birth and death of finite-time coherent sets. Communications on Pure and Applied Mathematics, 76 (12). pp. 3642-3684.

Frömberg, Daniela and Höfling, Felix (2021) Generalized master equation for first-passage problems in partitioned spaces. Journal of Physics A: Mathematical and Theoretical, 54 (21). pp. 1-29.

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.

Funiciello, Francesca and Corbi, Fabio and Heuret, Arnauld and Piromallo, Claudia and Rosenau, Matthias (2020) Empirical Analysis of Global-Scale Natural Data and Analogue Seismotectonic Modelling Data to Unravel the Seismic Behaviour of the Subduction Megathrust. Frontiers in Earth Science, 8 . pp. 1-8. ISSN 2296-6463

Fürst, Steffen and Conrad, T. O. F. and Jaeger, Carlo and Wolf, S. (2024) Vahana.jl - A framework (not only) for large-scale agent-based models. Social Simulation Conference 2024 . (In Press)

Galama, Maaike M. and Wu, Hao and Krämer, Andreas and Sadeghi, Mohsen and Noé, Frank (0001) Stochastic Approximation to MBAR and TRAM: Batchwise Free Energy Estimation. Journal of Chemical Theory and Computation (JCTC), 19 (3). pp. 758-766.

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

Garbuno-Inigo, Alfredo and Nüsken, Nikolas and Reich, Sebastian (2020) Affine Invariant Interacting Langevin Dynamics for Bayesian Inference. SIAM J. APPLIED DYNAMICAL SYSTEMS, 19 (3). pp. 1633-1658.

Gaskin, Thomas and Conrad, T. O. F. and Pavliotis, Grigorios A. and Schütte, Ch. (2024) Neural parameter calibration and uncertainty quantification for epidemic forecasting. PLoS ONE, 19 (10). ISSN 1932-6203

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

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

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

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

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.

Gerber, S. and Olsson, S. and Noé, F. and Horenko, I. (2018) A scalable approach to the computation of invariant measures for high-dimensional Markovian systems. Scientific Reports, 8 (1796). ISSN 2045-2322

Gerber, S. and Pospisil, L. and Navandar, M. and Horenko, I. (2020) Low-cost scalable discretization, prediction and feature selection for complex systems. Science Advances, 6 (5).

Gertler, Charles G. and O’Gorman, Paul A. and Pfahl, Stephan (2023) Moist available potential energy of the mean state of the atmosphere and the thermodynamic potential for warm conveyor belts and convection. Weather Clim. Dynam., 4 . pp. 361-379.

Ghysbrecht, Simon and Keller, Bettina G. (2024) Thermal isomerization rates in retinal analogues using Ab-Initio molecular dynamics. Journal of Computational Chemistry, 45 (16). pp. 1317-1427.

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.

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

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

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

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

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

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

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

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

Gräser, C. and Kienle, D. and Sander, O. (2021) Truncated Nonsmooth Newton Multigrid for phase-field brittle-fracture problems. arXiv:2007.12290 . pp. 1-41. (Submitted)

Gräser, C. and Kies, T. (2019) Discretization error estimates for penalty formulations of a linearized Canham-Helfrich-type energy. IMA Journal of Numerical Analysis, 39 (2). pp. 626-649. ISSN 0272-4979

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

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

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

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

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

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

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

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

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

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

Gräser, Carsten and Kornhuber, Ralf and Podlesny, Joscha (2021) NUMERICAL SIMULATION OF MULTISCALE FAULT SYSTEMS WITH RATE- AND STATE-DEPENDENT FRICTION. ArXiv . pp. 1-27. (Unpublished)

Gräser, Carsten and Sander, Oliver (2019) Truncated Nonsmooth Newton Multigrid Methods for Block-Separable Minimization Problems. IMA Journal of Numerical Analysis, 39 (1). pp. 454-481. ISSN 0272-4979

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.

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

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

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.

Gussmann, Pascal and Mielke, Alexander (2020) Linearized elasticity as Mosco-limit of finite elasticity in the presence of cracks. Advances in Calculus of Variations, 13 (1). pp. 1-20.

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

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

Hartmann, C. and Delle Site, L. (2015) Scale Bridging in Molecular Simulation. The European Physical Journal Special Topics, 224 (12). pp. 2173-2176. ISSN 1951-6355

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

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

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

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

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

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

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

Hartmann, C. and 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.

Hartmann, C. and Neureither, L. and Sharma, U. (2020) Coarse-graining of non-reversible stochastic differential equations: quantitative results and connections to averaging. SIAM Journal on Mathematical Analysis, 52 (3). pp. 2689-2733.

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

Hartmann, C. and Richter, L. and Schütte, Ch. and Zhang, W. (2017) Variational characterization of free energy: theory and algorithms. Entropy (Special Issue), 19 (11). pp. 1-27. ISSN 1099-4300

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

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

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

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

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

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

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

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

Hartmann, C. and Schütte, Ch. and Weber, M. and Zhang, W. (2018) Importance sampling in path space for diffusion processes with slow-fast variables. Probab. Theory Rel. Fields, 170 (1-2). pp. 177-228. ISSN 0178-8051 (print) 1432-2064 (online)

Hartmann, C. and Schütte, Ch. and Zhang, W. (2019) Jarzysnki equality, fluctuation theorems and variance reduction: Mathematical analysis and numerical algorithms. J. Stat. Phys., 175 (6). pp. 1214-1261. ISSN 0022-4715; ESSN: 1572-9613

Hartmann, 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

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.

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

Hartmann, Carsten and Jöster, Annika (2024) Risk-neutral limit of adaptive importance sampling of random stopping times. Submitted to 26th International Symposium on Mathematical Theory of Networks and Systems . (Submitted)

Hartmann, Carsten and Kebiri, Omar and Neureither, Lara and Richter, Lorenz (2019) Variational approach to rare event simulation using least-squares regression. Chaos, 29 (6). ISSN 1054-1500 (print); 1089-7682 (online)

Hartmann, Carsten and Neureither, Lara and Sharma, Upanshu (2020) Coarse-graining of non-reversible stochasticdifferential equations: quantitative results and connections to averaging. SIAM Journal on Numerical Analysis, 52 (3). pp. 2689-2733. ISSN 0036-1429

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

Hassan, Irtaza and Ferraro, Federica and Imhof, Petra (2021) Effect of the Hydration Shell on the Carbonyl Vibration in the Ala-Leu-Ala-Leu Peptide. Molecules 2021, 26 (8). pp. 1-24.

Haug, Ø. T. and Rosenau, M. and Rudolf, M. and Leever, K. (2021) Short communication: Runout of rock avalanches limited by basal friction but controlled by fragmentation. Earth Surface Dynamics, 9 (3). pp. 665-672.

Haug, Ø. T. and Rosenau, M. and Rudolf, M. and Leever, K. and Oncken, O. (2020) Variations in runout of rock avalanches controlled by fragmentation, not basal friction. EarthArXiv . pp. 1-11.

Heida, M. and Kornhuber, R. and Podlesny, J. (2020) Fractal homogenization of multiscale interface problems. Multiscale Modeling & Simulation, 18 (1). pp. 294-314. ISSN 1540-3459

Heida, Martin and Kantner, Markus and Stephan, Artur (2021) Consistency and convergence for a family of finite volume discretizations of the Fokker--Planck operator. ESAIM: Mathematical Modelling and Numerical Analysis, 55 . pp. 3017-3042.

Heida, Martin and Neukamm, Stefan and Varga, Mario (2021) STOCHASTIC HOMOGENIZATION OF L-CONVEX GRADIENT FLOWS. Discrete and Continuous Dynamical Systems - S, 14 (1). pp. 1-27.

Heida, Martin and Neukamm, Stefan and Varga, Mario (2021) Stochastic homogenization of Λ-convex gradient flows. DISCRETE AND CONTINUOUS DYNAMICAL SYSTEMS SERIES S, 14 (1). pp. 427-459.

Heida, Martin and Patterson, Robert I. A. and Renger, Michiel D.R. (2019) Topologies and measures on the space of functions of bounded variation taking values in a Banach or metric space. Journal of Evolution Equations, 19 (1). pp. 111-152.

Heida, Martin and Röger, Matthias (2018) Large deviation principle for a stochastic Allen--Cahn equation. Journal of Theoretical Probability 31(1), 31 (1). pp. 1-18. (Submitted)

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

Heida, Martin and Thomas, Marita (2021) GENERIC for dissipative solids with bulk-interface interaction. wias preprint . pp. 1-27. ISSN 2198-5855 (Submitted)

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

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

Helfmann, Luzie and Ribera Borrell, Enric and Schütte, Christof and Koltai, Péter (2020) Extending Transition Path Theory: Periodically Driven and Finite-Time Dynamics. Journal of Nonlinear Science, 30 . pp. 3321-3366.

Hempel, Tim and Elez, Katarina and Krüger, Nadine and Raich, Lluís and Shrimp, Jonathan H. and Danov, Olga and Jonigk, Danny and Braun, Arnim and Shen, Min and Hall, Matthew D. and Pöhlmann, Stefan and Hoffmann, Markus and Noé, Frank (2021) Synergistic inhibition of SARS-CoV-2 cell entry by otamixaban and covalent protease inhibitors: pre-clinical assessment of pharmacological and molecular properties. Chemical Science, 12 (38). pp. 12600-12609.

Herter, Felix and Hege, Hans-Christian and Hadwiger, Markus and Lepper, Verena and Baum, Daniel (2021) Thin-Volume Visualization on Curved Domains. Computer Graphics forum, 40 (3). pp. 147-157.

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

Hoffmann, Moritz and Scherer, Martin and Hempel, Tim and Mardt, Andreas and de Silva, Brian and Husic, Brooke E. and Klus, Stefan and Wu, Hao and Kutz, Nathan and Brunton, Steven L (2021) Deeptime: a Python library for machine learning dynamical models from time series data. Mach. Learn.: Sci. Technol. 3 (2022), 3 (015009). pp. 1-28.

Hoffmann, Waldemar and Folmert, Kristin and Moschner, Johann and Xing Huang, Xing Huang and von Berlepsch, Hans and Koksch, Beate and Bowers, Michael T. and von Helden, Gert and Pagel, Kevin (2018) NFGAIL Amyloid Oligomers: The Onset of Beta-Sheet Formation and the Mechanism for Fibril Formation. J. Am. Chem. Soc. 2018, 140, 244−249, 140 . pp. 244-249.

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

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

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

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

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

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

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

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

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

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

Horenko, I. (2020) On a Scalable Entropic Breaching of the Overtting Barrier for Small Data Problems in Machine Learning. Neural Computation, 32 (8). pp. 1563-1579.

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

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

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

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

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.

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.

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

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

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.

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

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

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

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

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.

Huber, Konstantin and John, Timm and Vrijmoed, Johannes C. and Pleuger, Jan and Zhong, Xin (2024) Pulsed fluid release from subducting slabs caused by a scale-invariant dehydration process. Earth and Planetary Science Letters, 644 .

Huber, Konstantin and Vrijmoed, Johannes and John, Timm (2021) Formation of olivine-rich veins by reactive fluid flow in a dehydrating serpentinite. Earth and Space Science Open Archive . pp. 1-18.

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

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.

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

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

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

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

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.

Husic, Brooke E. and Charron, Nicholas E. and Lemm, Dominik and Wang, Jiang and Pérez, Adrià and Majewski, Maciej and Krämer, Andreas and Chen, Yaoyi and Olsson, Simon and de Fabritiis, Gianni and Noé, Frank and Clementi, Cecilia (2020) Coarse graining molecular dynamics with graph neural networks. J. Chem. Phys., 153 (194101). pp. 1-17.

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 and Inadmissibility of the Vanishing Viscosity Limit of the Passive Scalar Transport Equation. arXiv . (Unpublished)

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

Höfling, F. and Dietrich, S. (2020) Finite-size corrections for the static structure factor of a liquid slab with open boundaries. Journal of Chemical Physics, 153 (5). pp. 1-13.

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

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

Iravani, Sahar and Conrad, T. O. F. (2021) An Interpretable Deep Learning Approach for Biomarker Detection in LC-MS Proteomics Data. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20 (1). ISSN 1545-4963

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

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

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

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 .

Jong-Bolm, Daniëlle de and Sadeghi, Mohsen and Bogaciu, Cristian A. and Bao, Guobin and Klaehn, Gabriele and Hoff, Merle and Mittelmeier, Lucas and Basmanav, F. Buket and Noé, Frank and Rizzoli, Silvio O. (2023) Protein nanobarcodes enable single-step multiplexed fluorescence imaging. PLOS BIOLOGY, 21 (12).

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

Jouvet, G. and Bueler, E. and Gräser, C. and Kornhuber, R. (2013) A nonsmooth Newton multigrid method for a hybrid, shallow model of marine ice sheets. Recent Advances in Scientific Computing and Applications, 586 . pp. 208-217. ISSN 0271-4132

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

Jouvet, G. and 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

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

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

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

Juds, Carmen and Schmidt, Johannes and Weller, Michael and Lange, Thorid and Conrad, T. O. F. and Boerner, Hans (2020) Combining Phage Display and Next-generation Sequencing for Materials Sciences: A Case Study on Probing Polypropylene Surfaces. Journal of the American Chemical Society, 142 (24). ISSN 0002-7863

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

Kaatz, L. and Schmalholz, Stefan M. and John, T. (2023) Numerical Simulations Reproduce Field Observations Showing Transient Weakening During Shear Zone Formation by Diffusional Hydrogen Influx and H2O Inflow. Geochemistry, Geophysics, Geosystems, 24 (5).

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

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

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

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

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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.

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

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

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

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

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

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.

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

Michail, Maria and Rudolf, Michael and Rosenau, Matthias and Riva, Alberto and Gianolla, Piero and Coltorti, Massimo (2021) Shape of plutons in crustal shear zones: A tectono-magmatic guide based on analogue models. Journal of Structural Geology . p. 104417. ISSN 0191-8141

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Mielke, A. and Mittnenzweig, M. (2018) Convergence to Equilibrium in Energy-Reaction–Diffusion Systems Using Vector-Valued Functional Inequalities. Journal of Nonlinear Science . pp. 1-42. ISSN 1432-1467 (online)

Mielke, A. and Rossi, R. and Savaré, G. (2016) Balanced-Viscosity solutions for multi-rate systems. Journal of Physics: Conference Series, 727 . pp. 1-27.

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Mielke, Alexander and Montefusco, Alberto and Peletier, Mark A. (2021) Exploring families of energy-dissipation landscapes via tilting: three types of EDP convergence. Continuum Mechanics and Thermodynamics, 33 (2). pp. 611-637.

Mielke, Alexander and Netz, Roland R. and Zendehroud, Sina (2021) A rigorous derivation and energetics of a wave equation with fractional damping. Journal Evolution Equations, 21 . pp. 3079-3102.

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Mielke, Alexander and Stephan, Artur (2020) Coarse-graining via EDP-convergence for linear fast-slow reaction systems. Mathematical Models and Methods in Applied Sciences, 30 (9). pp. 1765-1807.

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Mitterwallner, Bernhard G. and Schreiber, Christoph and Daldrop, Jan O. and Netz, Roland R. and Rädler, Joachim O. (2020) Non- markovian data-driven modeling of single-cell motility. PHYSICAL REVIEW E, 101 . ISSN 032408

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Montefusco, Alberto and Schütte, Christof and Winkelmann, Stefanie (2023) A route to the hydrodynamic limit of a reaction-diffusion master equation using gradient structures. Society for Industrial and Applied Mathematic (siam), 83 (2). pp. 836-861.

Moschner, Johann and Stulberg, Valentina and Fernandes, Rita and Huhmann, Susanne and Leppkes, Jakob and Koksch, Beate (2019) Approaches to Obtaining Fluorinated α-Amino Acids. Chem. Rev. 2019, 119 (18). pp. 10718-10801.

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Müller, Annette and Niedrich, Benjamin and Névir, Peter (2020) Three-dimensional potential vorticity structures for extreme precipitation events on the convective scale. Tellus A: Dynamic Meteorology and Oceanography, 72 (1). pp. 1-20. ISSN (Print) (Online) Journal homepage: https://www.tandfonline.com/loi/zela20

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Müller, Annette and Névir, Peter (2019) Using the concept of the Dynamic State Index for a scale-dependent analysis of atmospheric blocking. Meteorologische Zeitschrift, 28 (6). pp. 487-498.

Müller, Sebastian and Paltra, Sydney and Rehmann, Jakob and Nagel, Kai and Conrad, T. O. F. (2023) Explicit Modelling of Antibody Levels for Infectious Disease Simulations in the Context of SARS-CoV-2. iScience, 26 (9). ISSN 2589-0042

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Naliboff, J.B. and Glerum, A. and Brune, S.A. and Péron-Pinvidic, G. and Wrona, T. (2020) Development of 3-D Rift Heterogeneity Through Fault Network Evolution. Geophysical Research Letters, 47 (13). ISSN 0094-8276; ESSN: 1944-8007

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

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

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

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

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

Netz, Roland R. (2020) Approach to equilibrium and nonequilibrium stationary distributions of interacting many-particle systems that are coupled to different heat baths. Phys. Rev. E, 101 . ISSN 022120

Netz, Roland R. (2018) Fluctuation-dissipation relation and stationary distribution of an exactly solvable many-particle model for active biomatter far from equilibrium. J. Chem. Phys., 148 . ISSN 0021-9606, ESSN: 1089-7690

Netz, Roland R. (2020) Mechanisms of Airborne Infection via Evaporating and Sedimenting Droplets Produced by Speaking. Journal Phys. Chem. B, 124 (133). pp. 7093-7101.

Netz, Roland R. and Eaton, William A. (2021) Estimating computational limits on theoretical descriptions of biological cells. PNAS, 118 . pp. 1-3. ISSN 1091-6490 (online)

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

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

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

Niemann, Jan-Hendrik and Klus, Stefan and Schütte, Christof (2021) Data-driven model reduction of agent-based systems using the Koopman generator. PLOS ONE, 16 (5).

Niemann, Jan-Hendrik and Winkelmann, Stefanie and Wolf, S. and Schütte, Christof (2021) Agent-based modeling: Population limits and large timescales. Chaos: An Interdisciplinary Journal of Nonlinear Science, 31 (3).

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.

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

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

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

Noé, Frank and Klein, Leon Transferable Boltzmann Generators. Preprint arXiv . (Unpublished)

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

Nüsken, N. and Richter, L. (2020) Solving high-dimensional Hamilton-Jacobi-Bellman PDEs using neural networks: perspectives from the theory of controlled diffusions and measures on path space. SFB 1114 Preprint in arXiv . pp. 1-40. (Submitted)

Nüsken, Nikolas and Renger, D.R. Michiel (2021) Stein Variational Gradient Descent:many-particle and long-time asymptotics. arxiv preprint . pp. 1-25. (Submitted)

Nüsken, Nikolas and Richter, Lorenz (2021) Solving high-dimensional Hamilton–Jacobi–Bellman PDEs using neural networks: perspectives from the theory of controlled diffusions and measures on path space. Partial Differential Equations and Applications, 2 (48). pp. 1-48.

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.

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Osagiede, Edoseghe E. and Rosenau, Matthias and Rotevatn, Atle and Gawthorpe, Robert and Jackson, Christopher A-L and Rudolf, Michael (2021) Influence of zones of pre-existing crustal weakness on strain localization and partitioning during rifting: Insights from analogue modeling using high resolution 3D digital image correlation. EarthArXiv . pp. 1-55. (Submitted)

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

Pacey, George and Pfahl, Stephan and Schielicke, Lisa and Wapler, Kathrin (2023) The climatology and nature of warm-season convective cells in cold-frontal environments over Germany. Natural Hazards Earth System Sciences, 23 (12). pp. 3703-3721.

Paltra, Sydney and Conrad, T. O. F. (2024) Clinical Effectiveness of Ritonavir-Boosted Nirmatrelvir—A Literature Review. Advances in Respiratory Medicine, 92 (1). ISSN 2543-6031

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.

Patterson, Robert I. A. and Renger, Michiel D.R. (2019) Large deviations of jump process fluxes. Math. Phys. Anal. Geom., 22 (21). pp. 1-32. ISSN 1385-0172; ESSN: 1572-9656

Patterson, Robert I.A. and Renger, D.R. Michiel and Sharma, Upanshu (2021) Variational structures beyond gradient flows: a macroscopic fluctuation-theory perspective. arXive . pp. 1-47. (Unpublished)

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

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

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

Peschka, D. and Thomas, M. and Ahnert, T. and Münch, A. and Wagner, B. (2019) Gradient structures for flows of concentrated suspensions. Topics in Applied Analysis and Optimisation . pp. 295-318.

Peschka, Dirk and Zafferi, Andrea and Heltai, Luca and Thomas, Marita (2022) Variational Approach to Fluid–Structure Interaction via GENERIC. Journal of Non-Equilibrium Thermodynamics . ISSN 1437-4358

Peschka, Dirk and Zafferi, Andrea and Heltai, Luca and Thomas, Marita (2021) Variational approach to fluid-structure interaction via GENERIC. WIAS Preprint . pp. 1-13. (Submitted)

Pipping, E. (2019) Existence of long-time solutions to dynamic problems of viscoelasticity with rate-and-state friction. ZAMM - Journal of Applied Mathematics and Mechanics . ISSN 1521-4001 (online)

Pipping, E. and Sander, O. and Kornhuber, R. (2015) Variational formulation of rate- and state-dependent friction problems. Zeitschrift für angewandte Mathematik und Mechanik (ZAMM), 95 (4). pp. 377-395. ISSN 0044-2267

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

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

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

Polzin, Robert and Klebanov, Ilja and Nüsken, Nikolas and Koltai, Péter (2023) Nonnegative matrix factorization for coherent set identification by direct low rank maximum likelihood estimation. arXiv . pp. 1-43. (Unpublished)

Poppe, S. and Holohan, E.P. and Rudolf, M. and Rosenau, M. and Galland, O. and Delcamp, A. and Kervyn, M. (2021) Mechanical properties of quartz sand and gypsum powder (plaster) mixtures: 25implications for laboratory model analoguesfor the Earth’s upper crust. EartharXiv . pp. 1-55.

Poppe, S. and Holohan, Eoghan P. and Rudolf, M. and Rosenau, M. and Galland, O. and Delcamp, A. and Kervyn, M. (2021) Mechanical test data of quartz sand, garnet sand, gypsum powder (plaster), kaolin and sand-plaster mixtures used as granular analogue materials in geoscience laboratory experiments. Tectonophysics, 814 . p. 228976. ISSN 0040-1951

Pospisil, L. and Gagliardini, P. and Sawyer, W. and Horenko, I. (2018) On a scalable nonparametric denoising of time series signals. Communications in Applied Mathematics and Computational Science, 13 (1). pp. 107-138.

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 .

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

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

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

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

Rams, Mona and Conrad, T. O. F. (2022) Sparse dictionary learning allows model-free pseudotime estimation of transcriptomics data. BMC Genomics, 23 (56). ISSN 1471-2105

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.

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

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

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

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).

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Rentsch, Jakob and Bandstra, Selle and Sezen, Batuhan and Sigrist, Philipp Stephan and Bottanelli, Francesca and Schmerl, Bettina and Shoichet, Sarah and Noé, Frank and Sadeghi, Mohsen and Ewers, Helge (2024) Sub-membrane actin rings compartmentalize the plasma membrane. Journal of Cell Biology (JCB), 223 (4).

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Richter, Lorenz and Boustati, Ayman and Nüsken, Nikolas and Ruiz, Francisco J. R. and Akyildiz, Ömer Deniz (2020) VarGrad: A Low-Variance Gradient Estimator for Variational Inference. Advances in Neural Information Processing Systems 2020 . pp. 1-25. (Submitted)

Richter, Lorenz and Sallandt, Leon and Nüsken, Nikolas (2023) From continuous-time formulations to discretization schemes: tensor trains and robust regression for BSDEs and parabolic PDEs. Preprint . (Unpublished)

Richter, Lorenz and Sallandt, Leon and Nüsken, Nikolas (2021) Solving high-dimensional parabolic PDEs using the tensor train format. Proceedings of the 38th International Conferenceon Machine Learning, 139 . pp. 8998-9009.

Rodrigues, D.R. and Everschor-Sitte, K. and Gerber, S. and Horenko, I. (2021) A deeper look into natural sciences with physics-based and data-driven measures. iSCIENCE, 24 (3). pp. 1-13. ISSN 102171

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.

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Rosemeier, Juliane and Haut, Terry and Wingate, Beth (2024) Multilevel Parareal Algorithm with Averaging for Oscillatory Problems. Numerical Algorithms for Scientific Computung, 46 (4). pp. 2709-2736.

Rosenau, M. and Horenko, I. and Corbi, F. and Rudolf, M. and Kornhuber, R. and Oncken, O. (2019) Synchronization of great subduction megathrust earthquakes: Insights from scale model analysis. Journal of Geophysical Research: Solid Earth, 124 (4). pp. 3646-3661. ISSN 2169-9356

Rudolf, M. and Rosenau, M. and Oncken, O. (2017) Interseismic deformation transients and precursory phenomena: Insights from stick-slip experiments with a granular fault zone. SFB 1114 Preprint in EarthArXiv:10.17605/OSF.IO/6MWRX . pp. 1-26.

Rudolf, Michael and Rosenau, Matthias and Oncken, Onno (2021) The spectrum of slip behaviours of a granular fault gouge analogue governed by rate and state friction. Geochemistry, Geophysics, Geosystems . pp. 1-40.

Rüdrich, S. and Sarich, M. and Schütte, Ch. (2017) Utilizing hitting times for finding metastable sets in non-reversible Markov chains. Journal of Comp. Dynamics . (In Press)

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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)

Sandiford, Dan and Brune, Sascha and Glerum, Anne and Naliboff, John and Whittaker, Joanne M. (2021) Kinematics of footwall exhumation at oceanic detachment faults: solid-block rotation and apparent unbending. Earth and Space Science Open Archive .

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

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

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

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

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

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

Schiffmann, C and Sebastiani, D (2011) Hydrogen bond networks: Structure and dynamics via first-principles spectroscopy. physica status solidi (b), 249 (2). p. 368. ISSN 03701972

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

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.

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

Schulz, Julius C. F. and Schlaich, Alexander and Heyden, Matthias and Netz, Roland R. and Kappler, Julian (2020) Molecular interpretation of the non-Newtonian viscoelastic behavior of liquid water at high frequencies. Phys. Rev. Fluids, 5 .

Schulz, Robert and Yamamoto, Kenji and Klossek, André and Rancan, Fiorenza and Vogt, Annika and Schütte, Christof and Rühl, Eckart and Netz, Roland R. (2019) Modeling of Drug Diffusion Based on Concentration Profiles in Healthy and Damaged Human Skin. Biophysical Journal, 117 (5). pp. 998-1008. ISSN 00063495

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

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

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

Schütte, Ch. and Sarich, M. (2015) A critical appraisal of Markov state models. The European Physical Journal Special Topics, 224 (12). pp. 2445-2462. ISSN 1951-6355

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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.

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 .

Schütte, Christof and Klus, Stefan and Hartmann, Carsten (2023) Overcoming the Timescale Barrier in Molecular Dynamics: Transfer Operators, Variational Principles, and Machine Learning. Acta Numerica, 32 . pp. 517-673.

Sechi, Renata and Sikorski, Alexander and Weber, Marcus (2021) Estimation of the Koopman Generator by Newton's Extrapolation. Multiscale Modeling & Simulation, 19 (2). pp. 758-774.

Seeber, L. and Conrad, T. O. F. and Hoppe, Ch. and Obermeier, P. and Chen, X. and Karsch, K. and Muehlhans, S. and Tief, F. and Boettcher, S. and Diedrich, S. and Schweiger, B. and Rath , B. (2017) Educating parents about the vaccination status of their children: A user-centered mobile application. Preventive Medicine Reports, 5 . pp. 241-250.

Shao, Borong and Carlo, Cannistraci and Conrad, T. O. F. (2017) Epithelial Mesenchymal Transition Network-based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data. Genomics and Computational Biology, 3 (3). ISSN 2365-7154

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

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 .

Shao, Borong and Bjaanæs, Maria and Helland, Åslaug and Schütte, Ch. and Conrad, T. O. F. (2019) EMT network-based feature selection improves prognosis prediction in lung adenocarcinoma. PLoS ONE, 14 (1). ISSN 1932-6203

Sherratt, Katharine and Srivastava, Ajitesh and Ainslie, Kylie and Singh, David E. and Cublier, Aymar and Marinescu, Maria Cristina and Carretero, Jesus and Garcia, Alberto Cascajo and Franco, Nicolas and Willem, Lander and Abrams, Steven and Faes, Christel and Beutels, Philippe and Hens, Niel and Müller, Sebastian and Charlton, Billy and Ewert, Ricardo and Paltra, Sydney and Rakow, Christian and Rehmann, Jakob and Conrad, T. O. F. and Schütte, Christof and Nagel, Kai and Abbott, Sam and Grah, Rok and Niehus, Rene and Prasse, Bastian and Sandmann, Frank and Funk, Sebastian (2024) Characterising information gains and losses when collecting multiple epidemic model outputs. Epidemics, 47 . ISSN 1755-4365

Sikorski, Alexander and Ribera Borrell, Enric and Weber, Marcus (2024) Learning Koopman eigenfunctions of stochastic diffusions with optimal importance sampling and ISOKANN. Journal of Mathematical Physics, 65 (1).

Sikorski, Alexander and Weber, Marcus and Schütte, Christof (2021) The augmented jump chain – a sparse representationof time-dependent Markov jump processes. Advanced Theory and Simulations, 4(4):2000274, 2021, 4 (4).

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.

Smit, Matthijs and Vrijmoed, Johannes C. and Scherer, Erik E. and Mezger, Klaus and Kooijman, Ellen and Schmitt-Kielmann, Melanie and Tual, Lorraine and Guilmette, Carl and Ratschbacher, Lothar (2024) Retentiveness of rare earth elements in garnet with implications for garnet Lu-Hf chronology. Journal of Metamorphic Geology .

Soucek, Ondrej and Heida, Martin and Malek, Josef (2020) On a thermodynamic framework for developing boundary conditions for Korteweg-type fluids. International Journal of Engineering Science, 154 . pp. 1-28.

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.

Stange, H. and Brunken, S. and Greiner, D. and Heinemann, M. D. and Barragan Yani, D. A. and Wägele, L. A. and Li, Ch. and Simsek Sanli, E. and Kahnt, M. and Schmidt, S. S. and Bäcker, J.-P. and Kaufmann, Ch. A. and Klaus, M. and Scheer, R. and Genzel, Ch. and Mainz, R. (2019) Stacking fault reduction during annealing in Cu-poor CuInSe2 thin film solar cell absorbers analyzed by in situ XRD and grain growth modeling. Journal of Applied Physics, 125 (3). 035303. ISSN 0021-8979

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

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

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

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

Straube, Arthur V. and Kowalik, Bartosz G. and Netz, Roland R. and Höfling, Felix (2020) Rapid onset of molecular friction in liquids bridging between the atomistic and hydrodynamic pictures. Communications Physics, 3 (126). pp. 1-11.

Straube, Arthur V. and Winkelmann, Stefanie and Höfling, Felix (2023) Accurate reduced models for the pH oscillations in the urea-urease reaction confined to giant lipid vesicles. J. Phys. Chem. B, 127 (13). pp. 2955-2967.

Straube, Arthur V. and Winkelmann, Stefanie and Schütte, Christof and Höfling, Felix (2021) Stochastic pH Oscillations in a Model of the Urea−Urease Reaction Confined to Lipid Vesicles. J. Phys. Chem. Lett., 12 . pp. 1-6.

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.

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.

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

Stötzel, C. and Röblitz, S. and Siebert, H. (2015) Complementing ODE-Based System Analysis Using Boolean Networks Derived from an Euler-Like Transformation. PLoS ONE, 10 (10). e0140954. ISSN 1932-6203

Sun, Jingtong and Berner, Julius and Richter, Lorenz and Zeinhofer, Marius and Müller, Johannes and Azizzadenesheli, Kamyar and Anandkumar, Anima (2024) Dynamical Measure Transport and Neural PDE Solvers for Sampling. Preprint arXiv . (Unpublished)

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

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

Thies, Arne and Sunkara, Vikram and Ray, Sourav and Wulkow, Hanna and Özgür Celik, M. and Yergöz, Fatih and Schütte, Christof and Stein, Christoph and Weber, Marcus and Winkelmann, Stefanie (2023) Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design. Scientific Reports, 13 (1). p. 607.

Thomas, Marita and Tornquist, Sven (2021) Discrete approximation of dynamic phase-field fracture in visco-elastic materials. Discrete Contin. Dyn. Syst. Ser. S, 14 . pp. 3865-3924.

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)

Tierno, Pietro and Johansen, Tom H. and Straube, Arthur V. (2021) Thermally active nanoparticle clusters enslaved by engineered domain wall traps. NATURE COMMUNICATIONS, 12 (5813). pp. 1-11.

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

Tuncay, E. G. and Erdur, R. C. and Conrad, T. O. F. (2022) Parallel Exchange of Randomized SubGraphs for Optimization of Network Alignment: PERSONA. IEEE Transactions on Computational Biology and Bioinformatics . ISSN 1557-9964 (In Press)

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

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 .

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

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

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

Viennet, Akim and Vercauteren, Nikki and Engel, Maximilian and Faranda, Davide (2022) Guidelines for data-driven approaches to study transitions in multiscale systems: The case of Lyapunov vectors. Chaos, 32 . pp. 1-15.

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

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

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

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

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

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

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

Wang, J. and Olsson, S. and Wehmeyer, C. and Perez, A. and Charron, N.E. and de Fabritiis, G. and Noé, F. and Clementi, C. (2019) Machine Learning of coarse-grained Molecular Dynamics Force Fields. ACS Cent. Sci., 5 (5). pp. 755-767. ISSN 2374-7943, ESSN: 2374-7951

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This list was generated on Thu Nov 7 20:12:05 2024 CET.