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Number of items: 447. 2023Bäumer, D. and Hittmeir, S. and Klein, R. (2023) Scaling approaches to quasi-geostrophic theory for moist, precipitating air. J. Atmos. Sci. . pp. 1-18. (Submitted) 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. Arxive . pp. 1-43. (Unpublished) Chew, R. and Schlutow, M. and Klein, R. (2023) An unstable mode of the stratified atmosphere under the non-traditional Coriolis acceleration.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 . Nickl, Richard and Titi, Edriss (2023) On posterior consistency of data assimilation with Gaussian process priors: the 2D Navier-Stokes equations. ArXive . (Unpublished) Huysmans, Lucas and Titi, Edriss (2023) NON-UNIQUENESS & INADMISSIBILITY OF THE VANISHING VISCOSITY LIMIT OF THE PASSIVE SCALAR TRANSPORT EQUATION. Arxive . pp. 1-49. (Unpublished) Reible, Benedikt M. and Hille, Julian F. and Hartmann, Carsten and Delle Site, Luigi (2023) Finite-size effects and thermodynamic accuracy in many-particle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). 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 (Unpublished) Barua, Amlan K. and Chew, Ray and Li, Shuwang and Lowengrub, John and Münch, Andreas and Wagner, Barbara (2023) Sharp-interface problem of the Ohta-Kawasaki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 . 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. 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 (Unpublished) Bardos, Claude and Boutros, Daniel W. and Titi, Edriss (2023) Hoelder regularity of the pressure for weak solutions of the 3D Euler equations in bounded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 (Unpublished) Durumeric, Alexander E.P. and Charron, Nicholas E. and Templeton, Clark and Musil, Félix and Bonneau, Klara and Pasos-Trejo, Aldo S. and Chen, Yaoyi and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 . 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. Zafferi, Andrea and Huber, Konstantin and Peschka, Dirk and Vrijmoed, Johannes and John, Timm and Thomas, Marita (2023) A porous-media model for reactive fluid-rock interaction in a dehydrating rock. Preprint . pp. 1-22. (Unpublished) Engel, Maximilian and Piliouras, Georgios (2023) A stochastic variant of replicator dynamics in zero-sum games and its invariant measures. arXive . pp. 1-19. (Submitted) Krämer, Andreas and Durumeric, Alexander E.P. and Charron, Nicholas E. and Chen, Yaoyi and Clementi, Cecilia and Noé, Frank (2023) Statistically Optimal Force Aggregation for Coarse-Graining Molecular Dynamics. arXiv . (Submitted) Arts, Marloes and Garcia Sattorras, Victor and Huang, Chin-Wei and Zuegner, Daniel and Federici, Marco and Clementi, Cecilia and Noé, Frank and Pinsler, Robert and van den Berg, Rianne (2023) Two for One: Diffusion Models and Force Fields for Coarse-Grained Molecular Dynamics. arXiv . (Submitted) 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. Köhler, Jonas and Chen, Yaoyi and Krämer, Andreas and Clementi, Cecilia and Noé, Frank (2023) Flow-Matching: Efficient Coarse-Graining of Molecular Dynamics without Forces. J. Chem. Theory Comput., 19 (3). pp. 942-952. del Razo, M.J. and Winkelmann, S. and Klein, R. and Höfling, F. (2023) Chemical diffusion master equation: formulations of reaction–diffusion processes on the molecular level. J. Math. Phys., 64 (013304). Yang, Wangfei and Templeton, Clark and Rosenberger, David and Bittracher, Andreas and Nüske, Feliks and Noé, Frank and Clementi, Cecilia (2023) Slicing and Dicing: Optimal Coarse-Grained Representation to Preserve Molecular Kinetics. ACS Cent. Sci., 9 (2). pp. 186-196. 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). pp. 1-12. 2022Chemnitz, Dennis and Engel, Maximilian (2022) Positive Lyapunov Exponent in the Hopf Normal Form with Additive Noise. arXive preprint . pp. 1-35. (Unpublished) Ayaz, Cihan and Tepper, Lucas and Netz, Roland R. (2022) Markovian embedding of generalized Langevin equations with a nonlinear friction kernel and configuration-dependent mass. Turkish Journal of Physics, 46 (6). pp. 194-205. 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. 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. Majewski, Maciej and Pérez, Adrià and Thölke, Philipp and Doerr, S. and Charron, Nicholas E. and Giorgino, Toni and Husic, Brooke E. and Clementi, Cecilia and Noé, Frank and De Fabritis, Gianni (2022) Machine Learning Coarse-Grained Potentials of Protein Thermodynamics. arXiv . pp. 1-31. (Submitted) 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. 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. Gholami, Abbas and Klein, Rupert and Delle Site, Luigi (2022) Simulation of a Particle Domain in a Continuum, Fluctuating Hydrodynamics Reservoir. Physical Review Letters, 129 (23). 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) 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. Musil, Félix and Zaporozhets, Iryna and Noé, Frank and Clementi, Cecilia and Kapil, Venkat (2022) Quantum dynamics using path integral coarse-graining. The Journal of Chemical Physics, 157 (18). Zendehroud, Sina and Netz, Roland R. and Kappler, Julian (2022) Linear Waves at Viscoelastic Interfaces Between Viscoelastic Media. Physical Review Fluids, 7 . pp. 1-32. Djurdjevac Conrad, Natasa and Köppl, Jonas and Djurdjevac, Ana (2022) Feedback Loops in Opinion Dynamics of Agent-Based Models with Multiplicative Noise. Entropy, 24 (10). pp. 1-23. Reible, Benedikt and Hartmann, Carsten and Delle Site, Luigi (2022) Two-sided Bogoliubov inequality to estimate finite size effects in quantum molecular simulations. Letters in Mathmeaical Physics, 112 (97). pp. 1-17. Kieninger, Stefanie and Keller, Bettina (2022) GROMACS Stochastic Dynamics and BAOAB Are Equivalent Configurational Sampling Algorithms. J. Chem. Theory Comput., 18 (10). Lavacchi, Laura and Daldrop, Jan O. and Netz, Roland R. (2022) Non-Arrhenius barrier crossing dynamics of non-equilibrium non-Markovian systems. Europhysics Letters, 139 (5). pp. 1-7. Klimek, Anton and Netz, Roland R. (2022) Optimal non-Markovian composite search algorithms for spatially correlated targets. EPL A Letters Journal Exploring The Frontiers of Physics, 139 . pp. 1-8. Mastella, G. and Corbi, Fabio and Bedford, Jonathan and Funiciello, Francesca and Rosenau, Matthias (2022) Forecasting Surface Velocity Fields Associated With Laboratory Seismic Cycles Using Deep Learning. AGU-Geophysical Research Letters, 49 (15). pp. 1-12. Engel, Maximilian and Olicon-Mendez, Guillermo and Unger, Nathalie and Winkelmann, Stefanie (2022) Synchronization and random attractors for reaction jump processes. arXive preprint . pp. 1-39. (Submitted) Chew, R. and Benacchio, T. and Hastermann, G. and Klein, R. (2022) A one-step blended soundproof-compressible model with balanced data assimilation: theory and idealised tests. Monthly Weather Review, 150 (9). pp. 2231-2254. ISSN 0027-0644; elSSN: 1520-0493 Ayaz, Cihan and Scalfi, Laura and Dalton, Benjamin and Netz, Roland R. (2022) Generalized Langevin equation with a nonlinear potential of mean force and nonlinear memory friction from a hybrid projection scheme. PHYSICAL REVIEW E, 105 . pp. 1-19. del Razo, Mauricio J. and Frömberg, Daniela and Straube, Arthur V. and Schütte, Christof and Höfling, Felix and Winkelmann, Stefanie (2022) A probabilistic framework for particle-based reaction–diffusion dynamics using classical Fock space representations. Letters in Mathematical Physics, 112 (49). pp. 1-59. 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). Kosari, Ehsan and Rosenau, Matthias and Oncken, Onno (2022) Strain signals governed by frictional-elastoplastic interaction of the upper plate and shallow subduction megathrust interface over seismic cycles. Tectonics . pp. 1-41. ISSN 1944-9194 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. Klein, Rupert and Delle Site, Luigi (2022) Derivation of Liouville-like equations for the n-state probability density of an open system with thermalized particle reservoirs and its link to molecular simulation. Journal of Physics A: Mathematical and Theoretical, 55 . pp. 1-18. Polzin, Robert and Müller, Annette and Rust, Henning W. and Névir, Peter and Koltai, Péter (2022) Direct Bayesian model reduction of smaller scale convective activity conditioned on large-scale dynamics. Nonlinear Processes in Geophysics, 29 (1). pp. 37-52. 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. Mastella, G. and Corbi, Fabio and Funiciello, Francesca and Rosenau, Matthias (2022) Foamquake: a novel analog model mimicking megathrust seismic cycles. JGR Solid Earth . pp. 1-32. (In Press) 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 Kosari, Ehsan and Rosenau, Matthias and Ziegenhagen, Thomas and Oncken, Onno (2022) Upper plate dynamic response to a sequential elastic rebound and slab acceleration in laboratory-scale subduction megathrust. Earth and Space Science Open Archive . Zwaan, Frank and Schreurs, Guido and Buiter, Susanne and Ferrer, Oriol and Reitano, Riccardo and Rudolf, Michael and Willingshofer, Ernst (2022) Analogue modelling of basin inversion: a review and future perspectives. Preprint se-2022-8 Solid Earth . (Submitted) Coghi, Michele and Nilssen, Torstein and Nüsken, Nikolas and Reich, Sebastian (2022) Rough McKean–Vlasov dynamics for robust ensemble Kalman filtering. arxive . pp. 1-44. (In Press) 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) Kiefer, Henrik and Dalton, Benjamin and Bruenig, Florian N. and Netz, Roland R. (2022) Connection between Macroscopic Hydrodynamics and Molecular Friction in Liquids. Preprint . pp. 1-26. (Unpublished) Zendehroud, Sina and Loche, Philip and Kornhuber, Ralf and Netz, Roland R. (2022) Boundary Conditions on Conical Hydrophobic Inclusions in Lipid Membranes. Preprint . (Unpublished) Montefusco, Alberto and Schütte, Christof and Winkelmann, Stefanie (2022) A route to the hydrodynamic limit of a reaction-diffusion master equation using gradient structures. arXiv . (Submitted) 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 . Klein, R. and Schielicke, L. and Pfahl, S. and Khouider, B. (2022) QG-DL-Ekman: Dynamics of a diabatic layer in the quasi-geostrophic framework. Journal of the Atmospheric Sciences, 79 (3). pp. 887-905. Schütte, Christof and Klus, Stefan and Hartmann, Carsten (2022) Overcoming the Timescale Barrier in Molecular Dynamics: Transfer Operators, Variational Principles, and Machine Learning. ZIB . (Submitted) 2021Delle 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. 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. 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 . 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. 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) Vrijmoed, Johannes and Podladchikov, Y.Y. (2021) Thermolab: a thermodynamics laboratory for nonlinear transport processes in open systems. Earth and Space Science Open Archive . 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. Mikula, Natalia and Dörffel, T. and Baum, Daniel and Hege, Hans-Christian (2021) An Interactive Approach for Identifying Structure Definitions. arXive . pp. 1-29. (Submitted) Nüsken, Nikolas and Richter, Lorenz (2021) Interpolating between BSDEs and PINNs: deep learning for elliptic and parabolic boundary value problems. ArXive . pp. 1-25. (Submitted) 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. Kostré, Margarita and Schütte, Christof and Noé, Frank and del Razo, Mauricio J. (2021) Coupling Particle-Based Reaction-Diffusion Simulations with Reservoirs Mediated by Reaction-Diffusion PDEs. Sociaty for Industrial and Applied Mathematics, 19 (4). Hartmann, Carsten and Neureither, Lara and Stehlau, Markus (2021) Reachability Analysis of Randomly Perturbed Hamiltonian Systems. IFAC-PapersOnLine, 54 (19). pp. 307-3014. Reible, Benedikt and Hartmann, Carsten and Delle Site, Luigi (2021) Two-sided Bogoliubov inequality for quantum systems. arXiv . pp. 1-15. Gholami, Abbas and Klein, R. and Delle Site, Luigi (2021) On the relation between Pressure and Coupling Potential in Adaptive Resolution Simulations of Open Systems in contact with a Reservoir. Advanced Theory and Simulations, 5 . pp. 1-8. 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. Dörffel, T. and Papke, A. and Klein, R. and Ernst, Natalia and Smolarkiewicz, Piotr K. (2021) Dynamics of tilted atmospheric vortices under asymmetric diabatic heating. Theoretical and Computational Fluid Dynamics . von Lindheim, Johannes and Harikrishnan, A. P. and Dörffel, T. and Ernst, Natalia and Klein, R. and Koltai, Péter and Müller, Annette and Pacey, George and Polzin, Robert and Vercauteren, N. (2021) Definition, detection and tracking of persistent structures in atmospheric flows. preprint. J. Math. Phys. . pp. 1-64. (In Press) Harikrishnan, A. P. and Ansorge, C. and Klein, R. and Vercauteren, N. (2021) Lagrangian hairpins in atmospheric boundary layers. Gallery of Fluid Motion . Hittmeir, S. and Klein, R. and Müller, A. and Névir, P. (2021) The Dynamic State Index with Moisture and Phase Changes. J. Math. Phys, 62 (12). pp. 1-12. 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) Hastermann, G. and Reinhardt, M. and Klein, R. and Reich, S. (2021) Balanced data assimilation for highly-oscillatory mechanical systems. Communications in Applied Mathematics & Computational Science, 16 (1). pp. 119-154. 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. 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. 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). del Razo, Mauricio J. and Dibak, Manuel and Schütte, Christof and Noé, Frank (2021) Multiscale molecular kinetics by coupling Markov state models and reaction-diffusion dynamics. The Journal of Chemical Physics, 155 (12). 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. 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) Maity, Priyanka and Koltai, Péter and Schumacher, Jörg (2021) Large-scale flow in a cubic Rayleigh-B ́enard cell: Long-term turbulence statistics and Markovianity of macrostate transitions. Philosophical Transaction of the Royal Society . pp. 1-13. (In Press) Heida, Martin and Thomas, Marita (2021) GENERIC for dissipative solids with bulk-interface interaction. wias preprint . pp. 1-27. ISSN 2198-5855 (Submitted) 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. Stephan, Artur (2021) EDP-convergence for a linear reaction-diffusion system with fast reversible reaction. Calculus of Variations, 60 (226). pp. 1-35. Klus, Stefan and Gelß, Patrick and Nüske, Feliks and Noé, Frank (2021) Symmetric and antisymmetric kernels for machine learning problems in quantum physics and chemistry. Machine Learning: Science and Technologie, 2 . pp. 1-23. 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. Müller, Annette and Névir, Peter (2021) On the algebra and groups of incompressible vortex dynamics. Journal of Physics A: Mathematical and Theoretical, 54 . pp. 1-34. Coghi, Michele and Nilssen, Torstein and Nüsken, Nikolas (2021) Rough McKean-Vlasov dynamics for robust ensemble Kalman filtering. arXive . pp. 1-41. (Submitted) 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 Leung, Tsz Yan and Leutbecher, Martin and Reich, Sebastian and Shepherd, Theodore G. (2021) Forecast verification: relating deterministic and probabilistic metrics. Quarterly Journal of the Royal Meteorological Society . pp. 1-17. ISSN 1477-870X (Submitted) 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. 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. Bittracher, Andreas and Mollenhauer, Mattes and Koltai, Péter and Schütte, Christof (2021) Variational Characterization and Identification of Reaction Coordinates in Stochastic Systems. arXive . pp. 1-33. (Unpublished) 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. Gelß, Patrick and Klus, Stefan and Schuster, Ingmar and Schütte, Christof (2021) Feature space approximation for kernel-based supervised learning. Knowledge-Based Systems, 221 . Rezaei, majid and Netz, Roland R. (2021) Airborne virus transmission via respiratory droplets: Effects of droplet evaporation and sedimentation. ScienceDirect, 55 . ISSN 101471 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). Giulietti, P. and Koltai, P. and Vaienti, S. (2021) Targets and holes. Proc. Amer. Math. Soc., 149 . pp. 3293-3306. Zafferi, Andrea and Peschka, Dirk and Thomas, Marita (2021) GENERIC framework for reactive fluid flows. Preprint (2841). pp. 1-75. ISSN 2198-5855 (Submitted) Klein, R. and Viand, R. E. and Höfling, Felix and Delle Site, Luigi (2021) Nonequilibrium Induced by Reservoirs: Physico-Mathematical Models and Numerical Tests. Advanced Theory and Simulations, 4 . pp. 1-10. 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. Frömberg, Daniela and Höfling, Felix (2021) Generalized master equation for first-passage problems in partitioned spaces. Journal of Physics A, 54 (21). pp. 1-29. Winkelmann, Stefanie and Zonker, J. and Schütte, Christof and Djurdjevac Conrad, Natasa (2021) Mathematical modeling of spatio-temporal population dynamics and application to epidemic spreading. Mathematical Biosciences, 336 . Klein, R. and Schielicke, L. and Pfahl, S. and Khouider, B. (2021) QG-DL: Dynamics of a diabatic layer in the quasi-geostrophic framework. Journal of the Atmospheric Sciences . pp. 1-12. ISSN Online: 1520-0469 Print: 0022-4928 (Submitted) 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. 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. 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. Froyland, Gary and Koltai, Péter (2021) Detecting the birth and death of finite-time coherent sets. arXiv . pp. 1-44. (Submitted) Patterson, Robert I.A. and Renger, D.R. Michiel and Sharma, Upanshu (2021) Variational structures beyond gradient flows: a macroscopic fluctuation-theory perspective. arXive . pp. 1-47. (Unpublished) Chew, R. and Benacchio, T. and Hastermann, G. and Klein, R. (2021) Balanced data assimilation with a blended numerical model. Monthly Weather Review . pp. 1-43. (Submitted) 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 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). Kaatz, Lisa and Zertani, Sascha and Moulas, Evangelos and John, Timm and Labrousse, Loïc and Schmalholz, Stefan M. and Andersen, Torgeir B. (2021) Widening of Hydrous Shear Zones During Incipient Eclogitization of Metastable Dry and Rigid Lower Crust— Holsnøy, Western Norway. Tectonics, 40 (3). pp. 1-19. ISSN 1944-9194 Niemann, Jan-Hendrik and Winkelmann, Stefanie and Wolf, S. and Schütte, Christof (2021) Agent-based modeling: Population limits and large timescales. Choas, 31 (3). Gholami, A. and Höfling, Felix and Klein, R. and Delle Site, Luigi (2021) Thermodynamic Relations at the Coupling Boundary in Adaptive Resolution Simulations for Open Systems. Advanced Theory and Simulations, 4 . pp. 1-10. 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. Miron, P. and Beron-Vera, F.J. and Helfmann, L. and Koltai, P. (2021) Transition paths of marine debris and the stability of the garbage patches. Chaos, 31 . pp. 1-16. Kieninger, S. and Keller, B. (2021) Path probability ratios for Langevin dynamics—Exact and approximate. The Journal of Chemical Physics, 154 . pp. 1-21. 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) Nüsken, Nikolas and Renger, D.R. Michiel (2021) Stein Variational Gradient Descent:many-particle and long-time asymptotics. arxiv preprint . pp. 1-25. (Submitted) 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) Nüsken, N. and Renger, M. (2021) Stein Variational Gradient Descent: many-particle and long-time asymptotics. arXive . pp. 1-25. (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. Hartmann, C. and Richter, L. (2021) Nonasymptotic bounds for suboptimal importance sampling. arXive . pp. 1-26. (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) 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 . Bittracher, Andreas and Schütte, Christof (2021) A probabilistic algorithm for aggregating vastly undersampled large Markov chains. Physica D, 416 . pp. 1-19. 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) Reuten, Raphael and Zendehroud, Sina and Nicolau, Monica and Fleischhauer, Lutz and Laitala, Anu and Kiderlen, Stefanie and Nikodemus, Denise and Wullkopf, Lena and Nielsen, Sebastian Rune and McNeilly, Sarah and Prein, Carina and Rafaeva, Maria and Schoof, Erwin M. and Furtwängler, Benjamin and Porse, Bo T. and Kim, Hyobin and Won, Kyoung Jae and Sudhop, Stefanie and Westarp Zornhagen, Kamilla and Suhr, Frank and Maniati, Eleni and Pearce, Oliver M. T. and Koch, Manuel and Broeng Oddershede, Lene and Van Agtmael, Tom and Madsen, Chris D. and Mayorca-Guiliani, Alejandro E. and Bloch, Wilhelm and Netz, Roland R. and Clausen-Schaumann, Hauke and Erler, Janine T. (2021) Basement membrane stiffness determines metastases formation. Nature Materials, 20 . pp. 892-903. Nüske, Feliks and Koltai, Péter and Boninsegna, Lorenzo and Clementi, Cecilia (2021) Spectral Properties of Effective Dynamics from Conditional Expectations. Entropy, 23 (134). pp. 1-25. Helfmann, L. and Djurdjevac Conrad, N. and Djurdjevac, A. and Winkelmann, S. and Schütte, Ch. (2021) From interacting agents to density-based modeling with stochastic PDEs. Commun. Appl. Math. Comput. Sci., 16 (1). pp. 1-32. ISSN Online: 2157-5452; Print: 1559-3940 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. Kavokine, Nikita and Netz, Roland R. and Bocquet, Lydéric (2021) Fluids at the Nanoscale: From Continuum to Subcontinuum Transport. Annual Reviews of Fluid Mechanics, 53 . pp. 377-410. Renger, D.R. Michiel and Zimmer, Johannes (2021) Orthogonality of fluxes in general nonlinear reaction networks. DCDS-S 2021, 14 (1). pp. 205-217. (Submitted) 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) Djurdjevac, A. (2021) Linear Parabolic Problems in Random Moving Domains. ASA Jounal on Uncertainty Quantification, 9 (2). Haug, Ø. T. and Rosenau, M. and Rudolf, M. and Leever, K. (2021) Short communication: Runout of rock avalanches limited by basal friction but controlled by fragmentation. Earth Surface Dynamics, 9 (3). pp. 665-672. Heida, Martin and Neukamm, Stefan and Varga, Mario (2021) STOCHASTIC HOMOGENIZATION OF L-CONVEX GRADIENT FLOWS. Discrete and Continuous Dynamical Systems - S, 14 (1). pp. 1-27. Kies, T. and Gräser, C. (2021) On differentiability of the membrane-mediated mechanical interaction energy of discrete-continuum membrane-particle models. Interfaces and Free Boundaries . pp. 1-22. ISSN 1463-9963 (In Press) Koltai, Péter and von Lindheim, Johannes and Neumayer, Sebastian and Steidl, Gabriele (2021) Transfer Operators from Optimal Transport Plans for Coherent Set Detection. Physica D: Nonlinear Phenomena, 426 . pp. 1-34. 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) 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 Schmidt, F. and Gagarina, E. and Klein, R. and Achatz, U. (2021) Towards a numerical laboratory for investigations of gravity-wave 2 mean-ow interactions in the atmosphere. Monthly Weather Review MWR-D-21-0126 . pp. 1-75. (Submitted) Sechi, Renata and Sikorski, Alexander and Weber, Marcus (2021) Estimation of the Koopman generator by Newton’s extrapolation. SIAM Multiscale Modeling & Simulation, 19 (2). pp. 758-774. ISSN print: 1540-3459; online: 1540-3467 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. 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. 2020Detring, 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) 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). pp. 1-41. ISSN 1432-1467 (online) 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). 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 Harikrishnan, A. P. and Ansorge, C. and Klein, R. and Vercauteren, N. (2020) The curious nature of hairpin vortices. Gallery of Fluid Motion. In: 73th Annual Meeting of the APS Division of Fluid Dynamics, November 22, 2020 — November 24, 2020, Chicago, IL Virtual. 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. Mielke, Alexander and Maas, Jan (2020) Modeling of chemical reaction systems with detailed balance using gradient structures. Journal of Statistical Physics, 181 . pp. 2257-2303. Farshbaf-Shaker, M. Hassan and Thomas, Marita (2020) Analysis of a compressible Stokes-flow with degenerating and singular viscosity. Preprint . pp. 1-45. (Submitted) 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) Mitterwallner, Bernhard G. and Lavacchi, Laura and Netz, Roland R. (2020) Negative friction memory induces persistent motion. Eur Phys J E Soft Matter, 43 (10). Leung, Tsz Yan and Leutbecher, M. and Reich, S. and Shepherd, Th.G. (2020) Impact of the mesoscale range on error growth and the limits to atmospheric predictability. Journal of the Atmospheric Sciences, 77 (11). pp. 3769-3779. ISSN 1520-0469 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 . 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. Delle Site, L. and Klein, R. and Höfling, F. and Viand, R. E. (2020) Theory and simulation of open systems out of equilibrium. J. Chem. Phys. (2020);, 153 (10). pp. 1-7. ISSN 101102 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 . pp. 1-46. ISSN 1432-1467 (online) 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. Lavacchi, Laura and Kappler, Julian and Netz, Roland R. (2020) Barrier crossing in the presence of multi-exponential memory functions with unequal friction amplitudes and memory times. EPL, 131 . pp. 1-8. 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 Becker, Simon and Richter, Lorenz (2020) Model order reduction for (stochastic-) delay equations with error bounds. arXive . pp. 1-23. (Submitted) Delle Site, L. and Klein, R. (2020) Liouville-type equations for the n-particle distribution functions of an open system. Journal of Mathematical Physics, 61 (8). 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. Froyland, Gary and Koltai, Péter and Stahn, Martin (2020) Computation and Optimal Perturbation of Finite-Time Coherent Sets for Aperiodic Flows Without Trajectory Integration. SIAM J. APPLIED DYNAMICAL SYSTEMS, 19 (3). pp. 1659-1700. KORNHUBER, RALF and PODLESNY, JOSCHA and YSERENTANT, HARRY (2020) NUMERICAL HOMOGENIZATION OF FRACTAL INTERFACE PROBLEMS. arXive . pp. 1-30. (Submitted) 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. Kosari, Ehsan and Rosenau, Matthias and Bedford, Jonathan and Rudolf, Michael and Oncken, Onno (2020) On the relationship between offshore geodetic coverage and slip model uncertainty: Analog megathrust earthquake case studies. Geophysical Research Letters, 47 . pp. 1-15. 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. 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. Schillings, Claudia and Sprungk, Björn and Wacker, Philipp (2020) On the convergence of the Laplace approximation and noise-level-robustness of Laplace-based Monte Carlo methods for Bayesian inverse problems. Numerische Mathematik, 145 . pp. 915-971. 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. Klus, Stefan and Nüske, Felix and Hamzi, Boumediene (2020) Kernel-Based Approximation of the Koopman Generator and Schrödinger Operator. entropy, 22 . Sadeghi, Mohsen and Noé, Frank (2020) Large-scale simulation of biomembranes incorporating realistic kinetics into coarse-grained models. Nature Communications, 11 (2951). 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. 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. Noé, Frank (2020) Machine Learning for Molecular Dynamics on Long Timescales. Machine Learning Meets Quantum Physics . pp. 331-372. Hittmeir, S. and Klein, R. and Li, J. and Titi, E. (2020) Global well-posedness for the primitive equations coupled to nonlinear moisture dynamics with phase changes. Nonlinearity, 33 (7). pp. 3206-3236. 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 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) 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. 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. Mollenhauer, Mattes and Klus, Stefan and Schütte, Christof and Koltai, Péter (2020) Kernel autocovariance operators of stationary processes: Estimation and convergence. arXive . pp. 1-36. (Unpublished) 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. 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 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 Delle Site, L. and Praprotnik, M. and Bell, John B. and Klein, R. (2020) "Particle-Continuum Coupling and its Scaling Regimes: Theory and Applications". Advanced Theory and Simulations, 3 (5). Noé, Frank and Tkatchenko, Alexandre and Müller, Klaus-Robert and Clementi, Cecilia (2020) Machine Learning for Molecular Simulation. Annual Review of Physical Chemistry, 71 . pp. 361-390. 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 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 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). Kieninge, Stefanie and Donati, Luca and Keller, Bettina (2020) Dynamical reweighting methods for Markov models. Current Opinion in Structural Biology, 61 . pp. 124-131. ISSN 0959-440X 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. Banisch, R. and Trstanova, Z. and Bittracher, A. and Klus, S. and Koltai, P. (2020) Diffusion maps tailored to arbitrary non-degenerate Ito processes. Applied and computational harmonic analysis, 48 (1). pp. 242-265. ISSN 1063-5203, 1096-603X 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 Delle Site, L. and Praprotnik, M. and Bell, J. B. and Klein, R. (2020) Particle–Continuum Coupling and its Scaling Regimes: Theory and Applications. Advanced Theory and Simulation, 3, 1900232 (2020), 3 (190023). pp. 1-20. 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) Hartmann, C. and Neureither, L. and Sharma, U. (2020) Coarse-graining of non-reversible stochastic differential equations: quantitative results and connections to averaging. SIAM Journal on Mathematical Analysis, 52 (3). pp. 2689-2733. Hartmann, Carsten and Neureither, Lara and Sharma, Upanshu (2020) Coarse-graining of non-reversible stochasticdifferential equations: quantitative results and connections to averaging. SIAM Journal on Numerical Analysis, 52 (3). pp. 2689-2733. ISSN 0036-1429 Kaiser, A. and Faranda, D. and Krumscheid, S. and Belušić, D. and Vercauteren, N. (2020) Detecting regime transitions of the nocturnal and Polar near-surface temperature inversion. Journal of the Atmospheric Sciences . ISSN 0022-4928; eISSN: 1520-0469 Kies, T. and Gräser, C. and Delle Site, L. and Kornhuber, R. (2020) Free energy computation of particles with membrane-mediated interactions via Langevin dynamics. arXiv:2009.14713 . pp. 1-20. (Submitted) Klus, Stefan (2020) Data-driven analysis of complex dynamical systems. Refubium . pp. 1-174. Klus, Stefan and Nüske, Feliks and Peitz, Sebastian and Niemann, Jan-Hendrik and Clementi, Cecilia and Schütte, Christof (2020) Data-driven approximation of the Koopman generator: Model reduction, system identification, and control. Physica D: Nonlinear Phenomena, 406 (132416). Mardt, Andreas and Pasquali, Luca and Noé, F. and Wu, Hao (2020) Deep learning Markov and Koopman models with physical constraints. Proceedings of Machine Learning Research, 107 . pp. 451-475. Mielke, A. and Roubícek, T. (2020) Thermoviscoelasticity in Kelvin-Voigt rheology at large strains. Arch. Rational Mech. Anal., 238 . pp. 1-45. Mielke, Alexander and 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. Mollenhauer, Mattes and Schuster, Ingmar and Klus, Stefan and Schütte, Christof (2020) Singular Value Decomposition of Operators on Reproducing Kernel Hilbert Spaces. Advances in Dynamics, Optimization and Computation . pp. 109-131. 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. Winkelmann, Stefanie and Schütte, Christof (2020) Stochastic Dynamics in Computational Biology. Buchreihe: Frontiers in Applied Dynamical Systems: Reviews and Tutorials . 2019Müller, 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. 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) Klus, Stefan and Husic, Brooke E. and Mollenhauer, Mattes and Noé, Frank (2019) Kernel methods for detecting coherent structures in dynamical data. Chaos, 29 (12). Duncan, A. and Nüsken, N. and Szpruch, L. (2019) On the geometry of Stein variational gradient descent. SFB 1114 Preprint in arXiv:1912.00894 . (Unpublished) Garbuno Inigo, A. and Nüsken, N. and Reich, S. (2019) Affine invariant interacting Langevin dynamics for Bayesian inference. SFB 1114 Preprint in arXiv:1912.02859 . pp. 1-29. (Unpublished) Loche, Philip and Ayaz, Cihan and Schlaich, Alexander and Uematsu, Yuki and Netz, Roland R. (2019) Giant Axial Dielectric Response in Water-Filled Nanotubes and Effective Electrostatic Ion–Ion Interactions from a Tensorial Dielectric Model. J. Phys. Chem. B, 123 (50). pp. 10850-10857. 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 Whittaker, John and Delle Site, Luigi (2019) Investigation of the hydration shell of a membrane in an open system molecular dynamics simulation. Phys. Rev. Research, 1 (3). Leung, T.Y. and Leutbecher, M. and Reich, S. and Shepherd, Th.G. (2019) Atmospheric Predictability: Revisiting the Inherent Finite-Time Barrier. Journal of the Atmospheric Sciences, 76 (12). pp. 3883-3892. ISSN Online: 1520-0469 Print: 0022-4928 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). 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. Koltai, P. and Lie, Han Cheng and Plonka, M. (2019) Fréchet differentiable drift dependence of Perron--Frobenius and Koopman operators for non-deterministic dynamics. Nonlinearity, 32 (11). pp. 4232-4257. ISSN 0951-7715 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. Kappler, Julian and Hinrichsen, Victor B. and Netz, Roland R. (2019) Non-Markovian barrier crossing with two-time-scale memory is dominated by the faster memory component. The European Physical Journal E, 42 (119). ISSN 1292-8941 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 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 Noé, F. and Olsson, S. and Köhler, J. and Wu, H. (2019) Boltzmann Generators: Sampling Equilibrium States of Many-Body Systems with Deep Learning. Science, 365 (6457). eaaw1147. Nüsken, N. and Reich, S. (2019) Note on Interacting Langevin Diffusions: Gradient Structure and Ensemble Kalman Sampler by Garbuno-Inigo, Hoffmann, Li and Stuart. arXive . pp. 1-6. (Submitted) 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. Klus, S. and Schuster, I. and Muandet, K. (2019) Eigendecompositions of Transfer Operators in Reproducing Kernel Hilbert Spaces. Journal of Nonlinear Science, 30 . pp. 283-315. Wu, Ho and Noé, Frank (2019) Variational approach for learning Markov processes from time series data. Journal of Nonlinear Science, 30 . pp. 23-66. ISSN 1432-1467 (online) Benacchio, T. and Klein, R. (2019) A semi-implicit compressible model for atmospheric flows with seamless access to soundproof and hydrostatic dynamics. Monthly Weather Review, 147 (11). pp. 4221-4240. ISSN Online: 1520-0493; Print: 0027-0644 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. 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) 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. Nüske, Feliks and Boninsegna, Lorenzo and Clementi, Cecilia (2019) Coarse-graining molecular systems by spectral matching. J. Chem. Phys., 151 . pp. 1-10. ISSN 0021-9606, ESSN: 1089-7690 Hittmeir, S. and Klein, R. and Li, J. and Titi, E. (2019) "Global well-posedness for the primitive equations coupled to nonlinear moisture dynamics with phase changes" by Hittmeir, Sabine; Klein, Rupert; Li, Jinkai; Titi, Edriss. Analysis of PDEs . pp. 1-28. ISSN 1907.11199 (Submitted) Kowalik, Bartosz G. and Daldrop, Jan O. and Kappler, Julian and Schulz, J.C.F. and Schlaich, Alexander and Netz, Roland R. (2019) Memory-kernel extraction for different molecular solutes in solvents of varying viscosity in confinement. PhysRevE (100). 012126. Kebiri, Omar and Neureither, Lara and Hartmann, Carsten (2019) Adaptive importance sampling with forward-backward stochastic differential equations. In: Stochastic Dynamics Out of Equilibrium. Springer Proceedings in Mathematics & Statistics, 282 . Springer International Publishing, pp. 265-281. ISBN 978-3-030-15095-2 Neureither, L. and Hartmann, C. (2019) Time scales and exponential trends to equilibrium: Gaussian model problems. In: Stochastic Dynamics Out of Equilibrium. IHPStochDyn 2017. Springer Proceedings in Mathematics & Statistics, 282 . Springer, pp. 391-410. ISBN 978-3-030-15095-2 Renger, M. and Zimmer, J. (2019) Orthogonality of fluxes in general nonlinear reaction networks. SFB1114 Preprint 07/2019 in WIAS No. 2609 . pp. 1-12. (Unpublished) 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. Banisch, Ralf and Koltai, Péter and Padberg-Gehle, Kathrin (2019) Network measures of mixing. Chaos 29, 29 . pp. 1-15. 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) 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. Nüsken, N. and Reich, S. and Rozdeba, P.J. (2019) State and parameter estimation from observed signal increments. Entropy, 21 (5). -505. ISSN 1099-4300 Rosenau, M. and Rudolf, M. and Oncken, O. (2019) Creep on seismogenic faults: Insights from analogue earthquake experiments. SFB 1114 Preprint in EarthArXiv:10.31223/osf.io/24u5h . pp. 1-25. (Unpublished) 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 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 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 Heida, M. and Nesenenko, S. (2019) Stochastic homogenization of rate-dependent models of monotone type in plasticity. Asymptotic Analysis, 112 (3-4). pp. 185-212. ISSN 0921-7134 Miron, P. and Beron-Vera, F.J. and Olascoaga, M.J. and Koltai, P. (2019) Markov-chain-inspired search for MH370. Chaos: An Interdisciplinary Journal of Nonlinear Science, 29 (4). ISSN 1054-1500 (print); 1089-7682 (online) Paul, F. and Wu, H. and Vossel, M. and de Groot, B.L. and Noé, F. (2019) Identification of kinetic order parameters for non-equilibrium dynamics. J. Chem. Phys., 150 (16). p. 164120. ISSN 0021-9606, ESSN: 1089-7690 Pinamonti, G. and Paul, F. and Noé, F. and Rodriguez, A. and Bussi, G. (2019) The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models. J. Chem. Phys., 150 (15). p. 154123. ISSN 0021-9606, ESSN: 1089-7690 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 Keller, B.G. and Aleksic, S. and Donati, L. (2019) Markov State Models in drug design. In: Biomolecular Simulations in Structure-based Drug Discovery. Methods and Principles in Medicinal Chemistry, 75 . Wiley-Interscience, Weinheim, pp. 67-86. ISBN 978-3-527-34265-5 Kappler, Julian and Noé, Frank and Netz, Roland R. (2019) Cyclization and Relaxation Dynamics of Finite-Length Collapsed Self-Avoiding Polymers. Physical Review Letters, 122 . Delle Site, L. and Krekeler, C. and Whittaker, J. and Agarwal, A. and Klein, R. and Höflling, F. (2019) Molecular dynamics of open systems: construction of a mean-field particle reservoir. Adv. Th. Simul, 2 (5). Heydecker, Daniel and Patterson, Robert I. A. (2019) Bilinear Coagulation Equations. SFB1114 Preprint in arxiv:1902.07686 . (Unpublished) Hoffmann, M. and Fröhner, Chr. and Noé, F. (2019) ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics. PLoS Computational Biology, 15 (2). e1006830. ISSN 1553-7358 Kühnlein, C. and Deconinck, W. and Klein, R. and Malardel, S. and Piotrowski, Z. and Smolarkiewicz, P.K. and Szmelter, J. and Wedi, N. (2019) FVM 1.0: a nonhydrostatic finite-volume dynamical core for the IFS. Geosci. Model Dev., 12 (2). pp. 651-676. ISSN 1991-959X, ESSN: 1991-9603 von Larcher, T. and Klein, R. (2019) On identification of self-similar characteristics using the Tensor Train decomposition method with application to channel turbulence flow. Theoretical and Computational Fluid Dynamics, 33 . pp. 1-19. ISSN 0935-4964 (Print) 1432-2250 (Online) Andreis, L. and König, W. and Patterson, R. I. A (2019) A large-deviations approach to gelation. SFB 1114 Preprint in arXiv:1901.01876 . pp. 1-22. (Unpublished) Ciccotti, G. and Delle Site, L. (2019) The physics of open systems for the simulation of complex molecular environments in soft matter. Soft Matter, 15 (10). pp. 2114-2124. ISSN 1744-683X, ESSN: 1744-6848 Corbi, F. and Sandri, L. and Bedford, J. and Funiciello, F. and Brizzi, S. and Rosenau, M. and Lallemand, S. (2019) Machine Learning Can Predict the Timing and Size of Analog Earthquakes. Geophysical Research Letters, 46 (3). pp. 1303-1311. ISSN 0094-8276; ESSN: 1944-8007 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. Fackeldey, K. and Koltai, P. and Névir, P. and Rust, H.W. and Schild, A and Weber, M. (2019) From Metastable to Coherent Sets – time-discretization schemes. Chaos: An Interdisciplinary Journal of Nonlinear Science, 29 (1). 012101. ISSN 1054-1500 (print); 1089-7682 (online) 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 Hoffmann, M. and Fröhner, Chr. and Noé, F. (2019) Reactive SINDy: Discovering governing reactions from concentration data. J. Chem. Phys., 150 (2). 025101. ISSN 0021-9606, ESSN: 1089-7690 Rudolf, M. and Rosenau, M. and Ziegenhagen, Th. and Ludwikowski, V. and Schucht, Torsten and Nagel, H. and Oncken, O. (2019) Smart Speed Imaging in Digital Image Correlation: Application to Seismotectonic Scale Modeling. Frontiers in Earth Science, 6 . p. 248. Witek, J. and Wang, S. and Schroeder, B. and Lingwood, R. and Dounas, A. and Roth, H.-J. and Fouché, M. and Blatter, M. and Lemke, O. and Keller, B. and Riniker, S. (2019) Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides. J. Chem. Inf. Model., 59 (1). pp. 294-308. ISSN 1549-9596, ESSN: 1549-960X Daldrop, Jan O. and Netz, Roland R. (2019) Mass-Dependent Solvent Friction of a Hydrophobic Molecule. J. Phys. Chem. B (123). pp. 8123-8130. 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. Vercauteren, N. and Boyko, V. and Faranda, D. and Stiperski, I. (2019) Scale interactions and anisotropy in stable boundary layers. Quarterly Journal of the Royal Meteorological Society . ISSN 1477-870X Vercauteren, N. and Boyko, V. and Kaiser, A. and Belusic, D. (2019) Statistical investigations of flow structures in different regimes of the stable boundary layer. Boundary Layer Meteorology, 172 . pp. 1-22. ISSN Print: 0006-8314; Online: 1573-1472 von Larcher, T. and Klein, R. (2019) Approximating turbulent and non-turbulent events with the Tensor Train decomposition method. In: Turbulent Cascades II. Springer. ISBN Print: 978-3-030-12546-2 Electronic: 978-3-030-12547-9 2018Klus, Stefan and Bittracher, Andreas and Schuster, Ingmar and Schütte, Christof (2018) A kernel-based approach to molecular conformation analysis. Journal of Chemical Physics, 149 (244109). Marchenko, A. and Gagliardini, P. and Horenko, I. (2018) Toward a computationally-tractable maximum entropy principle for non-stationary financial time series. SIAM Journal of Financial Mathematics, 9 (4). pp. 1249-1285. ISSN 1945-497X Kies, Tobias (2018) Gradient Methods for Membrane-Mediated Particle Interactions. PhD Thesis . pp. 1-147. Schulz, R. and von Hansen, Y. and Daldrop, J.O. and Kappler, J. and Noé, F. and Netz, R.R. (2018) Collective hydrogen-bond rearrangement dynamics in liquid water. J. Chem. Phys., 149 (24). -244504. ISSN 0021-9606, ESSN: 1089-7690 Vater, S. and Klein, R. (2018) A Semi-Implicit Multiscale Scheme for Shallow Water Flows at Low Froude Number. Communications in Applied Mathematics & Computational Science, 13 (2). pp. 303-336. ISSN 1559-3940 Scherer, M. K. and Husic, B.E. and Hoffmann, M. and Paul, F. and Wu, H. and Noé, F. (2018) Variational Selection of Features for Molecular Kinetics. SFB 1114 Preprint in arXiv:1811.11714 . pp. 1-12. (Unpublished) Shadrack Jabes, B. and Delle Site, L. (2018) Nanoscale domains in Ionic Liquids: A statistical mechanics definition for molecular dynamics studies. J. Chem. Phys., 149 (18). p. 184502. ISSN 0021-9606, ESSN: 1089-7690 Wehmeyer, C. and Scherer, M. K. and Hempel, T. and Husic, B.E. and Olsson, S. and Noé, F. (2018) Introduction to Markov state modeling with the PyEMMA software — v1.0. LiveCoMS, 1 (1). pp. 1-12. ISSN E-ISSN: 2575-6524 Bittracher, Andreas and Banisch, Ralf and Schütte, Christof (2018) Data-driven computation of molecular reaction coordinates. J. Chem. Phys., 149 (154103). 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 Müller, A. and Névir, P. and Klein, R. (2018) Scale Dependent Analytical Investigation of the Dynamic State Index Concerning the Quasi-Geostrophic Theory. Mathematics of Climate and Weather Forecasting, 4 (1). pp. 1-22. ISSN 2353-6438 (online) Swenson, D.W.H. and Prinz, J.-H. and Noé, F. and Chodera, J. D. and Bolhuis, P.G. (2018) OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics. Journal of Chemical Theory and Computation, Article ASAP . ISSN 1549-9618, ESSN: 15-49-9626 Swenson, D.W.H. and Prinz, J.-H. and Noé, F. and Chodera, J. D. and Bolhuis, P.G. (2018) OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes. Journal of Chemical Theory and Computation, Article ASAP . ISSN 1549-9618, ESSN: 15-49-9626 Heida, M. (2018) Convergences of the squareroot approximation scheme to the Fokker–Planck operator. Mathematical Models and Methods in Applied Sciences, 28 (13). pp. 2599-2635. ISSN 0218-2025, ESSN: 1793-6314 Renger, M. (2018) Flux large deviations of independent and reacting particle systems, with implications for macroscopic fluctuation theory. J. Stat. Phys., 172 (5). pp. 1261-1326. ISSN 0022-4715 Fröhner, Chr. and Noé, F. (2018) Reversible interacting-particle reaction dynamics. J. Phys. Chem. B, 122 (49). pp. 11240-11250. Donati, Luca and Keller, Bettina G. (2018) Girsanov reweighting for metadynamics simulations. J. Chem. Phys. 149, 149 . pp. 1-16. Donati, L. and Keller, B. (2018) Girsanov reweighting for metadynamics simulations. Journal of Chemical Physics, 149 (7). 072335. ISSN 0021-9606 Kornhuber, R. and Youett, E. (2018) Adaptive Multilevel Monte Carlo Methods for Stochastic Variational Inequalities. SIAM Journal on Numerical Analysis, 56 (4). pp. 1987-2007. ISSN 0036-1429 Krekeler, C. and Agarwal, A. and Junghans, C. and Praprotnik, M. and Delle Site, L. (2018) Adaptive Resolution Molecular Dynamics Technique: Down to the Essential. J. Chem. Phys., 149 . 024104. ISSN 0021-9606, ESSN: 1089-7690 del Razo, M.J. and Qian, H. and Noé, F. (2018) Grand canonical diffusion-influenced reactions: a stochastic theory with applications to multiscale reaction-diffusion simulations. J. Chem. Phys., 149 (4). 044102. ISSN 0021-9606, ESSN: 1089-7690 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 Kebiri, O. and Neureither, L. and Hartmann, C. (2018) Singularly perturbed forward-backward stochastic differential equations: application to the optimal control of bilinear systems. Computation, 6 (3). p. 41. ISSN 2079-3197 (online) Koltai, P. and Renger, M. (2018) From Large Deviations to Semidistances of Transport and Mixing: Coherence Analysis for Finite Lagrangian Data. Journal of Nonlinear Science, 28 (5). pp. 1915-1957. ISSN 1432-1467 (online) Renger, M. (2018) Gradient and Generic systems in the space of fluxes, applied to reacting particle systems. SFB 1114 Preprint in arXiv:1806.10461 . pp. 1-29. (Unpublished) 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) Lazzaroni, Guiliano and Rossi, Riccarda and Thomas, Marita and Toader, Rodica (2018) Rate-independent damage in thermoviscoelastic materials with inertia. J Dyn Diff Equat, 30 . pp. 1311-1364. 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 Hassan, I. and Donati, L. and Stensitzki, T. and Keller, B. and Heyne, K. and Imhof, P. (2018) The Vibrational Spectrum of the hydrated Alanine-Leucine Peptide in the Amide region from IR experiments and First Principles Calculation. Chem. Phys. Lett. . pp. 1-26. ISSN 0009-2614 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) 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) Kappler, J. and Noé, F. and Netz, R.R. (2018) Cyclization dynamics of finite-length collapsed self-avoiding polymers. SFB 1114 Preprint 02/2018 . (Unpublished) Koltai, P. and Wu, H. and Noé, F. and Schütte, Ch. (2018) Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics. Computation, 6(1) (22). ISSN 2079-3197 (online) Weber, M. (2018) Implications of PCCA+ in Molecular Simulation. Computation, 6 (1). ISSN 2079-3197 (online) Heida, Martin and Schweizer, Ben (2018) Stochastic homogenization of plasticity equations. ESAIM: Control, Optimisation and Calculus of Variations, 24 (1). 153 -176. 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 Kappler, J. and Daldrop, J.O. and Brünig, F.N. and Boehle, M.D. and Netz, R.R. (2018) Memory-induced acceleration and slowdown of barrier crossing. J. Chem. Phys., 148 (1). 014903. Mielke, A. and Rossi, R. and Savaré, G. (2018) Global existence results for viscoplasticity at finite strain. Archive for Rational Mechanics and Analysis, 227 (1). pp. 423-475. ISSN Print: 0003-9527; Online: 1432-0673 Sadeghi, M. and Weikl, T. and Noé, F. (2018) Particle-based membrane model for mesoscopic simulation of cellular dynamics. J. Chem. Phys., 148 (4). 044901. Shadrack Jabes, B. and Krekeler, C. and Klein, R. and Delle Site, L. (2018) Probing Spatial Locality in Ionic Liquids with the Grand Canonical Adaptive Resolution Molecular Dynamics Technique. The Journal of Chemical Physics, 148 (19). ISSN online: 1089-7690 Stensitzki, T. and Yang, Y. and Kozich, V. and Ahmed, A.A. and Kössl, F. and Kühn, O. and Heyne, K. (2018) Acceleration of a ground-state reaction by selective femtosecond-infrared-laser-pulse excitation. Nature Chemistry, 10 . pp. 126-131. Hittmeir, S. and Klein, R. (2018) Asymptotics for moist deep convection I: Refined scalings and self-sustaining updrafts. Theoretical and Computational Fluid Dynamics, 32 (2). pp. 137-164. ISSN 0935-4964 (Print) 1432-2250 (Online) 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. Klus, S. and Nüske, F. and Koltai, P. and Wu, H. and Kevrekidis, I. and Schütte, Ch. and Noé, F. (2018) Data-driven model reduction and transfer operator approximation. Journal of Nonlinear Science, 28 (1). pp. 1-26. Koltai, P. and Schütte, Ch. (2018) A multiscale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics. Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 16 (4). pp. 1455-1485. ISSN 1540-3459 Kornhuber, R. and Peterseim, D. and Yserentant, H. (2018) An analysis of a class of variational multiscale methods based on subspace decomposition. Mathematics of Computation, 87 (314). pp. 2765-2774. ISSN 1088-6842 (online) Liero, M. and Mielke, A. and Savaré, G. (2018) Optimal Entropy-Transport problems and a new Hellinger-Kantorovich distance between positive measures. Inventiones mathematicae, 211 . pp. 969-1117. ISSN 1432-1297 (online) Mielke, A. and Mittnenzweig, M. (2018) Convergence to Equilibrium in Energy-Reaction–Diffusion Systems Using Vector-Valued Functional Inequalities. Journal of Nonlinear Science . pp. 1-42. ISSN 1432-1467 (online) Mielke, Alexander and Mittnenzweig, Markus (2018) Convergence to Equilibrium in Energy-Reaction–Diffusion Systems Using Vector-Valued Functional Inequalities. Journal of Nonlinear Science, 28 . pp. 765-806. ISSN 1432-1467 (online) Paul, F. and Noé, F. and Weikl, T. (2018) Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced Folding of PMI from Markov State Modeling of Atomistic Simulations. J. Phys. Chem. B . 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. 2017Daldrop, 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. Fischer, M. and Ulbrich, U. and Rust, H.W. (2017) A spatial and seasonal climatology of extreme precipitation return-levels: A case study. Spatial Statistics . pp. 1-25. (In Press) Heida, M. and Neukamm, S. and Varga, M. (2017) Stochastic unfolding and homogenization. SFB 1114 Preprint at WIAS 12/2017 . pp. 1-45. (Unpublished) Netz, R.R. (2017) Fluctuation-dissipation relation and stationary distribution for an exactly solvable many-particle model far from equilibrium. SFB 1114 Preprint 12/2017 . (Unpublished) Peters, J.H. and Gräser, C. and Klein, R. (2017) Membrane Deformation by N-BAR Proteins: Extraction of membrane geometry and protein diffusion characteristics from MD simulations. SFB 1114 Preprint in arXiv:1712.02666 . pp. 1-12. (Unpublished) Ritter, M. and Rosenau, M. and Oncken, O. (2017) Growing Faults in the Lab: Insights into the Scale Dependence of the Fault Zone Evolution Process. Tectonics, 36 . pp. 1-32. Rudolf, M. and Rosenau, M. and Oncken, O. (2017) Interseismic deformation transients and precursory phenomena: Insights from stick-slip experiments with a granular fault zone. SFB 1114 Preprint in EarthArXiv:10.17605/OSF.IO/6MWRX . pp. 1-26. Schuster, I. and Constantine, P.G. and Sullivan, T.J. (2017) Exact active subspace Metropolis-Hastings, with applications to the Lorenz-96 system. 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ISSN 0021-9606 Ritter, M. and Santimano, T.N. and Rosenau, M. and Leever, K. and Oncken, O. (2017) Sandbox rheometry: Coevolution of stress and strain in riedel- and critical wedge-experiments. Tectonophysics, 722 . pp. 400-409. Sbailò, L. and Noé, F. (2017) An efficient multi-scale Green's Functions Reaction Dynamics scheme. J. Chem. Phys., 147 . p. 184106. ISSN 0021-9606, ESSN: 1089-7690 Taghvaei, A. and de Wiljes, J. and Mehta, P.G. and Reich, S. (2017) Kalman Filter and Its Modern Extensions for the Continuous-Time Nonlinear Filtering Problem. J. Dyn. Sys., Meas., Control, 140 (3). 030904. Bittracher, A. and Koltai, P. and Klus, S. and Banisch, R. and Dellnitz, M. and Schütte, Ch. (2017) Transition manifolds of complex metastable systems: Theory and data-driven computation of effective dynamics. Journal of Nonlinear Science . pp. 1-42. ISSN 1432-1467 (online) Kappler, J. and Netz, R.R. (2017) Pulse propagation at interfaces and their possible relevance for biology. Journal Club for Condensed Matter Physics . Paul, F. and Wehmeyer, C. and Abualrous, E. T. and Wu, H. and Crabtree, M. D. and Schöneberg, J. and Clarke, J. and Freund, C. and Weikl, T. and Noé, F. (2017) Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nat. Comm., 8 (1095). Acevedo, W. and de Wiljes, J. and Reich, S. (2017) Second-order accurate ensemble transform particle filters. SIAM J. Sci. Comput., 39 (5). A1834-A1850. ISSN 1095-7197 (online) Hittmeir, S. and Klein, R. and Li, J. and Titi, E. (2017) Global well-posedness for passively transported nonlinear moisture dynamics with phase changes. Nonlinearity, 30 (10). pp. 3676-3718. ISSN 0951-7715 Manz, C. and Kobitski, A. and Samanta, A. and Keller, B.G. and Jäschke, A. and Nienhaus, G.U. (2017) Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch. Nat. Chem. Biol., 13 . pp. 1172-1178. Schlaich, A. and Kappler, J. and Netz, R.R. (2017) Hydration Friction in Nanoconfinement: From Bulk via Interfacial to Dry Friction. Nano Lett., 17 (10). pp. 5969-5976. Winkelmann, S. and Schütte, Ch. (2017) Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems. Journal of Chemical Physics, 147 (11). pp. 1-18. Corbi, F. and Funiciello, F. and Brizzi, S. and Lallemand, S. and Rosenau, M. (2017) Control of asperities size and spacing on seismic behavior of subduction megathrusts. Geophysical Research Letters, 44 (16). pp. 8227-8235. Delle Site, L. and Ciccotti, G. and Hartmann, C. (2017) Partitioning a macroscopic system into independent subsystems. Journal of Statistical Mechanics: Theory and Experiment, 2017 . pp. 1-13. Dörffel, T. and Papke, A. and Klein, R. and Smolarkiewicz, P. (2017) Intensification of tilted atmospheric vortices by asymmetric diabatic heating. SFB 1114 Preprint in arXiv:1708.07674 . pp. 1-22. (Unpublished) Mielke, A. and Patterson, R. I. A and Peletier, M. A. and Renger, M. (2017) Non-equilibrium thermodynamical principles for chemical reactions with mass-action kinetics. SIAM Journal on Applied Mathematics, 77 (4). pp. 1562-1585. ISSN 1095-712X (online) Nissen, K.M. and Ulbrich, U. (2017) Increasing frequencies and changing characteristics of heavy precipitation events threatening infrastructure in Europe under climate change. Nat. Hazards Earth Syst. Sci., 17 . pp. 1177-1190. Delle Site, L. and Praprotnik, M. (2017) Molecular systems with open boundaries: Theory and Simulation. Physics Reports, 693 . pp. 1-56. ISSN 0370-1573 Donati, L. and Hartmann, C. and Keller, B.G. (2017) Girsanov reweighting for path ensembles and Markov state models. Journal of Chemical Physics, 146 (24). p. 244112. ISSN 0021-9606 Junghans, C. and Agarwal, A. and Delle Site, L. (2017) Computational Efficiency and Amdahl's law for the Adaptive Resolution Simulation Technique. Computer Physics Communications, 215 . pp. 20-25. ISSN 0010-4655 Mazza, E. and Ulbrich, U. and Klein, R. (2017) The Tropical Transition of the October 1996 Medicane in the Western Mediterranean Sea: A Warm Seclusion Event. Monthly Weather Review, 145 . pp. 2575-2595. ISSN Online: 1520-0493 Print: 0027-0644 Seshaditya, A. and Ghiringhelli, L. M. and Delle Site, L. (2017) Levy-Lieb-based Monte Carlo study of the dimensionality behaviour of the electronic kinetic functional. Computationa, 5 (2). pp. 1-10. ISSN 2079-3197 Gerber, S. and Horenko, I. (2017) Toward a direct and scalable identification of reduced models for categorical processes. Proceedings of the National Academy of Sciences, 114 (19). pp. 4863-4868. Agarwal, A. and Clementi, C. and Delle Site, L. (2017) Path Integral-GC-AdResS simulation of a large hydrophobic solute in water: A tool to investigate the interplay between local microscopic structures and quantum delocalization of atoms in space. Physical Chemistry Chemical Physics, 19 . pp. 13030-13037. 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