Items where Subject is "Mathematical and Computer Sciences > Mathematics"

Article

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

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.

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

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

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

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 (Unpublished)

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

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

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

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

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

Banisch, 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

Banisch, R. and Trstanova, Z. and Bittracher, A. and Klus, S. and Koltai, P. (2018) Diffusion maps tailored to arbitrary non-degenerate Itô processes. Applied and Computational Harmonic Analysis . ISSN 1063-5203 (In Press)

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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)

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

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

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

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

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

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

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

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

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

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

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

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

Conrad, T. O. F. and Genzel, Martin and Cvetkovic, Nada and Wulkow, Niklas and Vybiral, Jan and Kutyniok, Gitta and Schütte, Ch. (2017) Sparse Proteomics Analysis - a compressed sensing-based approach for feature selection and classification of high-dimensional proteomics mass spectrometry data. BMC Bioinformatics, 18 (160). ISSN 1471-2105

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Fischer, A. and Cordes, F. and Schütte, Ch. (1998) Hybrid Monte Carlo with adaptive temperature in mixed-canonical ensemble: Efficient conformational analysis of RNA. J. Comp. Chem., 19 (15). pp. 1689-1697.

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

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

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

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.

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.

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

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.

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

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

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

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

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

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

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

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

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

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

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

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

Hartmann, 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)

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

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

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

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

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

Horenko, I. (2010) Parameter identification in nonstationary Markov chains with external impact and its application to computational sociology. Multiscale Modeling & Simulation . (Submitted)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Huysmans, Lucas and Titi, Edriss (2023) Non-Uniqueness and Inadmissibility of the Vanishing Viscosity Limit of the Passive Scalar Transport Equation. arXiv . (Unpublished)

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

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

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).

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

Keller, Bettina G. and Bolhuis, Peter G. (2024) Dynamical Reweighting for Biased Rare Event Simulations. Annual Review of Physical Chemistry, 75 (1). pp. 137-162.

Kern, Julian (2023) Exponential equivalence for misanthrope processes in contact with weak reservoirs and applications to totally asymmetric exclusion processes. Preprint . (Unpublished)

Kern, Julian (2023) Skorokhod topologies: What they are and why we should care. Mathematische Semesterberichte .

Kern, Julian and Wiederhold, Bastian (2024) A Λ-Fleming-Viot type model with intrinsically varying population size. Electronic Journal of Probability, 29 (125).

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

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

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

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

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

Klein, R. (1988) Detonation Initiation Due to Shock Wave-Boundary Interactions. Notes on Numerical Fluid Mechanics, 24 . 279-288..

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

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

Klein, R. 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.

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

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

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

Koltai, P. and 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

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

Koltai, Péter and Kunde, Philipp (2024) A Koopman-Takens theorem: Linear least squares prediction of nonlinear time series. Preprint . (In Press)

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

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

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)

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

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

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.

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.

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.

Lelièvre, Tony and Pigeon, Thomas and Stoltz, Gabriel and Zhang, Wei (2023) Analyzing multimodal probability measures with autoencoders. To appear in The Journal of Physical Chemistry B . (In Press)

Liero, Matthias and Mielke, Alexander and Savaré, Giuseppe (2023) Fine properties of geodesics and geodesic lambda-convexity for the Hellinger-Kantorovich distance. Archive for Rational Mechanics and Analysis, 247 (112).

Liu, Xin and Titi, Edriss S. and Xin, Zhouping (2024) Asymptotic stability of the equilibrium for the free boundary problem of a compressible atmospheric primitive model with physical vacuum. Preprint . (Unpublished)

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

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

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).

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 .

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

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

Mardt, Andreas and Hempel, Tim and Clementi, Cecilia and Noé, Frank (2022) Deep learning to decompose macromolecules into independent Markovian domains. nature communications, 13 .

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.

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

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

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

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

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

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

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

Mielke, Alexander (2023) Non-equilibrium steady states as saddle points and EDP-convergence for slow-fast gradient systems. Journal of Mathematical Physics, 64 (12).

Mielke, Alexander and Peletier, Mark A. and Stephan, Artur (2021) EDP-convergence for nonlinear fast–slow reaction systems with detailed balance. Nonlinearity, 34 (8). pp. 5762-5798.

Montefusco, Alberto and Helfmann, Luzie and Okunola, Toluwani and Winkelmann, Stefanie and Schütte, Christof (2024) Partial mean-field model for neurotransmission dynamics. Mathematical Biosciences, 369 .

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

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).

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

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

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

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)

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

Richter, Lorenz and Berner, Julius (2022) Robust SDE-Based Variational Formulations for Solving Linear PDEs via Deep Learning. Preprint arXiv . (Unpublished)

Richter, Lorenz and Berner, Julius and Liu, Guang-Horng (2023) Improved sampling via learned diffusions. Preprint . (Unpublished)

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)

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

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

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

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

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

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

Sadeghi, Mohsen and Noé, Frank (2021) Thermodynamics and kinetics of aggregation of flexible peripheral membrane proteins. The Journal of Physical Chemistry Letters, 12 (43). pp. 10497-10504.

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

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

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

Schlutow, M. (2019) Modulational stability of nonlinear saturated gravity waves. Journal of the Atmospheric Sciences .

Schlutow, M. and Wahlén, E. and Birken, P. (2019) Spectral stability of nonlinear gravity waves in the atmosphere. Mathematics of Climate and Weather Forecasting, 5 (1). pp. 12-33. ISSN 2353-6438

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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).

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

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

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.

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

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

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.

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

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

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 .

Winkler, Ludwig and Richter, Lorenz and Opper, Manfred (2024) Bridging discrete and continuous state spaces: Exploring the Ehrenfest process in time-continuous diffusion models. Preprint arXiv . (Unpublished)

Wu, Hao and Noé, Frank (2024) Reaction coordinate flows for model reduction of molecular kinetics. The Journal of Chemical Physics, 160 (4).

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.

Zertani, Sascha and John, Timm and Brachmann, Caroline and Vrijmoed, Johannes and Plümper, Oliver (2022) Reactive fluid flow guided by grain-scale equilibrium reactions during eclogitization of dry crustal rocks. Contributions to Mineralogy and Petrology, 177 (61).

Zhang, W. and Klus, S. and Conrad, T. O. F. and Schütte, Ch. (2019) Learning chemical reaction networks from trajectory data. SIAM Journal on Applied Dynamical Systems, 18 (4). ISSN 1536-0040

Zhao, Yue and Zhang, Wei and Li, Tiejun (2024) EPR-Net: Constructing non-equilibrium potential landscape via a variational force projection formulation. National Science Review .

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

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

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

Book Section

UNSPECIFIED UNSPECIFIED In: UNSPECIFIED, (ed.) UNSPECIFIED UNSPECIFIED.

Berninger, H. and Kornhuber, R. and Sander, O. (2007) On nonlinear Dirichlet-Neumann Algorithms for jumping nonlinearities. In: Domain Decomposition Methods in Science and Engineering XVI. In: Domain Decomposition Methods in Science and Engineering XVI. LNCSE, 55 . Springer, pp. 489-496. ISBN 978-3-540-34469-8

Brdar, S. and Dedner, A. and Klöfkorn, R. (2012) CDG Method for Navier-Stokes Equations. In: Hyperbolic Problems - Theory, Numerics and Applications. World Scientific Publishing Co Pte Ltd, pp. 320-327. ISBN 9789814417068

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

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

Kiljunen, T. and Schmidt, B. (2007) Alignment and Orientation of Molecules in Matrices. In: Analysis and Control of Ultrafast Photoinduced Reactions. Series in Chemical Physics, 87 . Springer, Berlin, pp. 337-352.

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

Kornhuber, R. and Gräser, C. (2007) On preconditioned Uzawa-type iterations for a saddle point problem with inequality constraints. In: Decomposition Methods in Science and Engineering XVI. LNCSE (55). Springer, pp. 91-102. ISBN 978-3-540-34469-8

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

Monograph

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

Conference or Workshop Item

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

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

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

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

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

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

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

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

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

Jasor, G. and Wacker, U. and Beheng, K.D. and Polifke, W. (2011) Application of Quadrature Method of Moments for Sedimentation and Coagulation of Raindrops. In: International Metstroem Conference, Juni 2011, Berlin.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Weiße, A. Y. and Horenko, I. and Huisinga, W. (2006) Adaptive Approach for Modelling Variability in Pharmacokinetics. In: Computational Life Sciences II.

von Kleist, M. and Kloft, Ch. and Huisinga, W. (2007) Combining Systems Biology with Physiologically Based Pharmacokinetics to Support the Understanding of Drug Effects. In: Proceedings of the 2nd Foundations of Systems Biology in Engineering Conference, FOSBE 2007, 09.-12.09.2007, Stuttgart, Germany.

Book

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

Thesis

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

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

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

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

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

Lorenz, S. (2006) The model-data-overlap: A new approach to parameter estimation, model validation, selection and discrimination. PhD thesis, Free University of Berlin.

Meerbach, E. (2009) Off- and Online Detection of Dynamical Phases in Time Series. PhD thesis, Free University of Berlin.

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

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

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

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

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