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Jump to: Article | Book Section Number of items: 195. ArticleKoltai, Péter and Kunde, Philipp (2024) A Koopman-Takens theorem: Linear least squares prediction of nonlinear time series. Preprint . (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 (Unpublished) Atnip, Jason and Froyland, Gary and Koltai, Péter (2024) An inflated dynamic Laplacian to track the emergence and disappearance of semi-material coherent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 (Unpublished) Quer, Jannes and Ribera Borrell, Enric (2024) Connecting Stochastic Optimal Control and Reinforcement Learning. Submitted Preprint . (Submitted) 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) Delle Site, Luigi and Hartmann, Carsten (2024) Scaling law for the size dependence of a short-ranged quantum gas. Physical Review A, 109 . Delle Site, Luigi and Hartmann, Carsten (2024) Scaling law for the size dependence of a finite-range quantum gas. Physical Review A, 109 (2). 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). 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 . 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). 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. 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) Koronaki, D. Eleni and Evangelou, Nikolaos and Martin-Linares, Cristina P. and Titi, Edriss and Kevrekidis, Ioannis G. (2023) Nonlinear dimensionality reduction then and now: AIMs for dissipative PDEs in the ML era. Preprint . (Unpublished) 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. 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) 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. Majewski, Maciej and Pérez, Adrià and Thölke, Philipp and Doerr, Stefan and Charron, Nicholas E. and Giorgino, Toni and Husic, Brooke E. and Clementi, Cecilia and Noé, Frank and De Fabritiis, Gianni (2023) Machine Learning Coarse-Grained Potentials of Protein Thermodynamics. Nature Communications, 14 . 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) Unanue, Alvaro de Diego and Froyland, Gary and Junge, Oliver and Koltai, Péter (2023) A dynamic p-Laplacian. Preprint . (Unpublished) Maity, Priyanka and Bittracher, Andreas and Koltai, Péter and Schumacher, Jörg (2023) Collective variables between large-scale states in turbulent convection. Physical Review Research, 5 (3). 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) 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. ArXiv . (Unpublished) 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. Richter, Lorenz and Berner, Julius and Liu, Guang-Horng (2023) Improved sampling via learned diffusions. 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. 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). 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 . Chemnitz, Robin and Engel, Maximilian and Koltai, Péter (2023) Continuous-time extensions of discrete-time cocycles. Contemporary Mathematics . (In Press) 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. Bittracher, Andreas and Mollenhauer, Mattes and Koltai, Péter and Schütte, Christof (2023) Optimal Reaction Coordinates: Variational Characterization and Sparse Computation. Multiscale Modeling & Simulation, 21 (2). pp. 449-488. 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. The Journal of Physical Chemistry, 14 . pp. 3970-3979. Engel, Maximilian and Gottwald, Georg A. (2023) Canards in modified equations for Euler discretizations. Preprint to appear in Contemporary Mathematics . (In Press) 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 . Engel, Maximilian and Olicon-Méndez, Guillermo (2023) Noise-induced instabilities in a stochastic Brusselator. Preprint to appear in Contemporary Mathematics . (In Press) Nüsken, Nikolas and Richter, Lorenz (2023) Interpolating Between BSDEs and PINNs: Deep Learning for Elliptic and Parabolic Boundary Value Problems. Journal of Machine Learning, 2 . pp. 31-64. 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. 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. 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). Dibak, Manuel and Klein, Leon and Krämer, Andreas and Noé, Frank (2022) Temperature steerable flows and Boltzmann generators. Physical Review Research, 4 (4). 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). 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) 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. 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 Mollenhauer, Mattes and Klus, Stefan and Schütte, Christof and Koltai, Péter (2022) Kernel autocovariance operators of stationary processes: Estimation and convergence. Journal of Machine Learning Research, 23 (327). pp. 1-34. 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. Zendehroud, Sina and Loche, Philip and Kornhuber, Ralf and Netz, Roland R. (2022) Boundary Conditions on Conical Hydrophobic Inclusions in Lipid Membranes. Preprint . (Unpublished) 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. 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. 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. 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. 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) 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. 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. 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). 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) 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. 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. 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) 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) 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. Giulietti, P. and Koltai, P. and Vaienti, S. (2021) Targets and holes. Proc. Amer. Math. Soc., 149 . pp. 3293-3306. 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) 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). 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. 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, 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. To appear 2024 in SIAM/ASA Journal on Uncertainty Quantification . (In Press) 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) 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. 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) 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. 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 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) 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). 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. 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) 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 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. 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) 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) 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. 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. 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. 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. 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) 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. 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 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 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) 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. 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. 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. 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) 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 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 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) 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 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) 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) 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 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 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) 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 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) 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) 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 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 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) 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) 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) 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 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 . 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) Schuster, I. and Constantine, P.G. and Sullivan, T.J. (2017) Exact active subspace Metropolis-Hastings, with applications to the Lorenz-96 system. SFB 1114 Preprint in arXiv:1712.02749 . pp. 1-10. (Unpublished) 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 Quer, J. and Lie, H. (2017) Some connections between importance sampling and enhanced sampling methods in molecular dynamics. Journal of Chemical Physics . pp. 1-19. ISSN 0021-9606 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. 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 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. 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. Mazza, E. and Ulbrich, U. and Klein, R. (2017) The Tropical Transition of the October 1996 Medicane in the Western Mediterranean Sea: A Warm Seclusion Event. Monthly Weather Review, 145 . pp. 2575-2595. ISSN Online: 1520-0493 Print: 0027-0644 Gerber, S. and Horenko, I. (2017) Toward a direct and scalable identification of reduced models for categorical processes. Proceedings of the National Academy of Sciences, 114 (19). pp. 4863-4868. Ritschel, C. and Rust, H.W. and Ulbrich, U. (2017) Precipitation extremes on multiple time scales -- Bartlett-Lewis Rectangular Pulse Model and Intensity-Duration-Frequency curves. Hydrol. Earth Syst. Sci. . pp. 1-20. (Submitted) O'Kane, T.J. and Monselesan, D.P. and Risbey, J.S. and Horenko, I. and Franzke, Ch.L.E. (2017) On memory, dimension, and atmospheric teleconnection patterns. Math. Clim. Weather Forecast, 3 (1). pp. 1-27. Quer, J. and Donati, L. and Keller, B.G. and Weber, M. (2017) An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates. SIAM J. Sci. Comput. . pp. 1-19. ISSN 1064-8275 (print) (In Press) Weber, M. and Fackeldey, K. and Schütte, Ch. (2017) Set-free Markov state model building. Journal of Chemical Physics, 146 (12). p. 124133. Hirt, M. and Schielicke, L. and Müller, A. and Névir, P. (2017) Statistical and dynamical analyses of atmospheric blocking with an idealized point vortex model. Tellus A . pp. 1-22. (Submitted) Nüske, F. and Wu, H. and Wehmeyer, C. and Clementi, C. and Noé, F. (2017) Markov State Models from short non-Equilibrium Simulations - Analysis and Correction of Estimation Bias. J. Chem. Phys., 146 . 094104. Olsson, Simon and Wu, H. and Paul, F. and Clementi, C. and Noé, F. (2017) Combining experimental and simulation data of molecular processes via augmented Markov models. Proc. Natl. Acad. Sci. USA, 114 . pp. 8265-8270. Fischer, M. and Rust, H.W. and Ulbrich, U. (2016) Seasonal Cycle in German Daily Precipitation Extremes. Meteorologische Zeitschrift . pp. 1-11. ISSN 0941-2948 (Submitted) Koltai, P. and Ciccotti, G. and Schütte, Ch. (2016) On metastability and Markov state models for non-stationary molecular dynamics. Journal of Chemical Physics, 145 (17). p. 174103. Quer, J. and Weber, M. (2016) Estimating exit rate for rare event dynamical systems by extrapolation. ZIB-Report . pp. 1-19. ISSN 2192-7782 (online) 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 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 Zhang, W. and Hartmann, C. and Schütte, Ch. (2016) Effective dynamics along given reaction coordinates, and reaction rate theory. Faraday discussions, 195 . pp. 365-394. ISSN 1359-6640 Wu, H. and Paul, F. and Wehmeyer, C. and Noé, F. (2016) Multiensemble Markov models of molecular thermodynamics and kinetics. Proceedings of the National Academy of Sciences, 113 (23). E3221-E3230 . ISSN 0027-8424 Chustagulprom, N. and Reich, S. and Reinhardt, M. (2016) A Hybrid Ensemble Transform Particle Filter for Nonlinear and Spatially Extended Dynamical Systems. SIAM/ASA Journal on Uncertainty Quantification, 4 (1). pp. 592-608. ISSN 2166-2525 Klein, R. and Benacchio, T. (2016) A doubly blended model for multiscale atmospheric dynamics. Journal of the Atmospheric Sciences, 73 . pp. 1179-1186. ISSN Online: 1520-0469 Print: 0022-4928 Feireisl, E. and Klein, R. and Novotný, A. and Zatorska, E. (2016) On singular limits arising in the scale analysis of stratified fluid flows. Mathematical Models and Methods in Applied Sciences, World Scientific, 26 (3). pp. 419-443. ISSN Print: 0218-2025 Online: 1793-6314 Nüske, F. and Schneider, R. and Vitalini, F. and Noé, F. (2016) Variational Tensor Approach for Approximating the Rare-Event Kinetics of Macromolecular Systems. J. Chem. Phys., 144 (5). 054105. Paul, F. and Weikl, T. (2016) How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates. PLOS Computational Biology . Vitalini, F. and Noé, F. and Keller, B. (2016) Molecular dynamics simulations data of the twenty encoded amino acids in different force fields. Data in Brief, 7 . pp. 582-590. Trendelkamp-Schroer, B. and Wu, H. and Paul, F. and Noé, F. (2015) Estimation and uncertainty of reversible Markov models. J. Chem. Phys., 143 (17). p. 174101. 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 Horenko, I. and Gerber, S. (2015) Improving clustering by imposing network information. Science Advances, 1 (7). ISSN 2375-2548 O’Kane, T.J. and Risbey, J.S. and Monselesan, D.P. and Horenko, I. and Franzke, Ch.L.E. (2015) On the dynamics of persistent states and their secular trends in the waveguides of the Southern Hemisphere troposphere. Climate Dynamics . ISSN Print: 0930-7575, Online: 1432-0894 Scherer, M. K. and Trendelkamp-Schroer, B. and Paul, F. and Pérez-Hernández, G. and Hoffmann, M. and Plattner, N. and Wehmeyer, C. and Prinz, J.-H. and Noé, F. (2015) PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models. J. Chem. Theory Comput., 11 (11). pp. 5525-5542. Wu, H. and Prinz, J.-H. and Noé, F. (2015) Projected Metastable Markov Processes and Their Estimation with Observable Operator Models. J. Chem. Phys., 143 (14). p. 144101. Wu, H. and Noé, F. (2015) Gaussian Markov transition models of molecular kinetics. J. Chem. Phys., 142 (8). 084104. Wu, H. and Mey, A.S.J.S. and Rosta, E. and Noé, F. (2014) Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states. J. Chem. Phys., 141 (21). p. 214106. Mey, A.S.J.S. and Wu, H. and Noé, F. (2014) xTRAM: Estimating equilibrium expectations from time-correlated simulation data at multiple thermodynamic states. Phys. Rev. X, 4 (4). 041018. Hartmann, C. and Latorre, J.C. and Pavliotis, G. A. and Zhang, W. (2014) Optimal control of multiscale systems using reduced-order models. J. Computational Dynamics, 1 (2). pp. 279-306. ISSN 2158-2505 Lie, Han Cheng and Schütte, Ch. and Hartmann, C. (2014) Martingale-based gradient descent algorithm for estimating free energy values of diffusions. SIAM J. Sci. Comput. . ISSN 1064-8275 (Submitted) 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. Book SectionKebiri, 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 Horenko, I. and Gerber, S. and O'Kane, T.J. and Risbey, J.S. and Monselesan, D.P. (2017) On inference and validation of causality relations in climate teleconnections. In: Nonlinear and Stochastic Climate Dynamics. Cambridge University Press, pp. 184-208. ISBN 9781107118140 |