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Number of items: 221. AAlphonse, 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. 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. 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. 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. 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. Andreis, Luisa and König, Wolfgang and Patterson, Robert I.A. (2021) A large‐deviations principle for all the cluster sizes of a sparse Erdős–Rényi graph. Random Structures and Algorithms . pp. 1-32. Agazzi, Andrea and Andreis, Luisa and Patterson, Robert I.A. and Renger, D.R. Michiel (2021) LARGE DEVIATIONS FOR MARKOV JUMP PROCESSES WITH UNIFORMLY DIMINISHING RATES. arXive . pp. 1-19. (Unpublished) Agazzi, Andrea and Andreis, Luisa and Patterson, Robert I. A. and Renger, D.R. Michiel (2021) Large deviations for Markov jump processes with uniformly diminishing rates. arXive . pp. 1-19. (Unpublished) Andreis, L. and König, W. and Patterson, R. I. A (2019) A large-deviations approach to gelation. SFB 1114 Preprint in arXiv:1901.01876 . pp. 1-22. (Unpublished) Agarwal, A. and Clementi, C. and Delle Site, L. (2017) Path Integral-GC-AdResS simulation of a large hydrophobic solute in water: A tool to investigate the interplay between local microscopic structures and quantum delocalization of atoms in space. Physical Chemistry Chemical Physics, 19 . pp. 13030-13037. ISSN 1463-9084 Albrecht, D. and Winterflood, C. M. and Sadeghi, M. and Tschager, T. and Noé, F. and Ewers, H. (2016) Nanoscopic compartmentalization of membrane protein motion at the axon initial segment. J. Cell Biol., 215 (1). pp. 37-46. Agarwal, A. and Delle Site, L. (2015) Path Integral Molecular Dynamics within the Grand Canonical-like Adaptive Resolution Technique: Simulation of Liquid Water. Journal of Chemical Physics, 143 (9). ISSN 0021-9606 Agarwal, A. and Zhu, J. and Wang, H. and Hartmann, C. and Delle Site, L. (2015) Molecular dynamics in a Grand Ensemble: Bergmann-Lebowitz model and adaptive resolution simulation. New Journal of Physics, 17 (083042). ISSN 1367-2630 BBäumer, D. and Hittmeir, S. and Klein, R. (2023) Scaling approaches to quasi-geostrophic theory for moist, precipitating air. J. Atmos. Sci. . pp. 1-18. 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. 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) Bardos, Claude and Liu, Xin and Titi, Edriss (2023) Derivation of a generalized quasi-geostrophic approximation for inviscid ows in a channel domain: The fast waves correction. pp. 1-33. (Unpublished) Bardos, Claude and Boutros, Daniel W. and Titi, Edriss (2023) Hoelder regularity of the pressure for weak solutions of the 3D Euler equations in bounded domains. Preprint . pp. 1-35. (Unpublished) 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. 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) 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). Brünig, Florian N. and Geburtig, Otto and von Canal, Alexander and Kappler, Julian and Netz, Roland R. (2022) Time-dependent friction effects on vibrational infrared frequencies and line shapes of liquid water. J. Phys. Chem. B, 126 . pp. 1579-1589. Beinlich, A. and John, T. and Vrijmoed, J.C. and Tominaga, M. and Podladchikov, Y.Y. (2020) Instantaneous rock transformations in the deep crust driven by reactive fluid flow. nature geoscience, 13 . pp. 307-311. Bartscha, Clemens and Wiedmeyer, Viktoria and Lakdawala, Zahra and Patterson, Robert I.A. and Voigt, Andreas and Sundmacher, Kai and John, Volker (2019) Stochastic-deterministic population balance modeling and simulation of a fluidized bed crystallizer experiment. Chemical Engineering Science, 208 . ISSN 115102 Bartsch, Clemens and John, Volker and Patterson, Robert I. A. (2019) Simulations of an ASA flow crystallizer with a coupled stochastic-deterministic approach. Computers & Chemical Engineering, 124 . pp. 350-363. Büeler, Dominik and Pfahl, Stephan (2017) Potential Vorticity Diagnostics to Quantify Effects of Latent Heating in Extratropical Cyclones. Part I: Methodology. Journal of the Atmospheric Sciences, 74 (11). Bonetti, E. and Rocca, E. and Rossi, R. and Thomas, M. (2016) A rate-independent gradient system in damage coupled with plasticity via structured strains. ESAIM: Proceedings and Surveys, 54 . pp. 54-69. CCortes-Huerto, Robinson and Praprotnik, Matej and Kremer, Kurt and Delle Site, Luigi (2021) From Adaptive Resolution to Molecular Dynamics of Open Systems. The European Physical Journal B, 94 (189). pp. 1-22. Carlson, Shane and Brünig, Florian N. and Loche, Philip and Bonthuis, Douwe Jan and Netz, Roland R. (2020) Exploring the Absorption Spectrum of Simulated Water from MHz to Infrared. The Journal of Physical Chemistry A, 124 (27). pp. 5599-5605. ISSN 1089-5639 Chen, Shuo and Hin, Remco C. and John, Timm and Bryan, Ben and Nui, Yaoling and Elliott, Tim and Brooker, R. (2019) Molybdenum systematics of subducted crust record reactive fluid flow from underlying slab serpentine dehydration. nature communications . pp. 1-9. Ciccotti, G. and Delle Site, L. (2019) The physics of open systems for the simulation of complex molecular environments in soft matter. Soft Matter, 15 (10). pp. 2114-2124. ISSN 1744-683X, ESSN: 1744-6848 DDelle 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). 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). 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). Djurdjevac, Ana and Kremp, Helena and Perkowski, Nicolas (2022) Weak error analysis for a nonlinear SPDE approximation of the Dean-Kawasaki equation. Unpublished . (Unpublished) Dibak, Manuel and Klein, Leon and Krämer, Andreas and Noé, Frank (2022) Temperature steerable flows and Boltzmann generators. Physical Review Research, 4 (4). 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. 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). Dolores-Tesillos, Edgar and Teubler, Franziska and Pfahl, Stephan (2022) Future changes in North Atlantic winter cyclones in CESM-LE – Part 1: Cyclone intensity, potential vorticity anomalies, and horizontal wind speed. Weather Clim. Dynam., 3 . pp. 429-448. 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. Dörffel, T. and Papke, A. and Klein, R. and Ernst, Natalia and Smolarkiewicz, Piotr K. (2021) Dynamics of tilted atmospheric vortices under asymmetric diabatic heating. Theoretical and Computational Fluid Dynamics . 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). Djurdjevac, A. (2021) Linear Parabolic Problems in Random Moving Domains. ASA Jounal on Uncertainty Quantification, 9 (2). Delle Site, L. and Klein, R. and Höfling, F. and Viand, R. E. (2020) Theory and simulation of open systems out of equilibrium. J. Chem. Phys. (2020);, 153 (10). pp. 1-7. ISSN 101102 Delle Site, L. and Klein, R. (2020) Liouville-type equations for the n-particle distribution functions of an open system. Journal of Mathematical Physics, 61 (8). Delle Site, L. and Praprotnik, M. and Bell, John B. and Klein, R. (2020) "Particle-Continuum Coupling and its Scaling Regimes: Theory and Applications". Advanced Theory and Simulations, 3 (5). Delle Site, L. and Praprotnik, M. and Bell, J. B. and Klein, R. (2020) Particle–Continuum Coupling and its Scaling Regimes: Theory and Applications. Advanced Theory and Simulation, 3, 1900232 (2020), 3 (190023). pp. 1-20. Dibak, Manuel and Fröhner, Christoph and Noé, Frank and Höfling, Felix (2019) Diffusion-influenced reaction rates in the presence of pair interactions. The Journal of Chemical Physics, 151 (16). Delle Site, L. and Krekeler, C. and Whittaker, J. and Agarwal, A. and Klein, R. and Höflling, F. (2019) Molecular dynamics of open systems: construction of a mean-field particle reservoir. Adv. Th. Simul, 2 (5). Dondl, Patrick and Frenzel, Thomas and Mielke, Alexander (2019) A gradient system with a wiggly energy and relaxed EDP-convergence. ESAIM Control Optimisation and Calculus of Variations, 25 (68). pp. 1-45. 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 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 Delle Site, L. and Ciccotti, G. and Hartmann, C. (2017) Partitioning a macroscopic system into independent subsystems. Journal of Statistical Mechanics: Theory and Experiment, 2017 . pp. 1-13. Dörffel, T. and Papke, A. and Klein, R. and Smolarkiewicz, P. (2017) Intensification of tilted atmospheric vortices by asymmetric diabatic heating. SFB 1114 Preprint in arXiv:1708.07674 . pp. 1-22. (Unpublished) Delle Site, L. and Praprotnik, M. (2017) Molecular systems with open boundaries: Theory and Simulation. Physics Reports, 693 . pp. 1-56. ISSN 0370-1573 Delle Site, L. (2016) Formulation of Liouville's theorem for grand ensemble molecular simulations. Physical Review E, 93 (022130). Delle Site, L. and Agarwal, A. (2016) Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and Application. Computer Physics Communications (206). pp. 26-34. EErnst, 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 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. 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 . Enciso, M. and Schütte, Ch. and Delle Site, L. (2015) Influence of pH and sequence in peptide aggregation via molecular simulation. Journal of Chemical Physics, 143 (24). p. 243130. ISSN 0021-9606 Erbar, M. and Maas, J. and Renger, M. (2015) From large deviations to Wasserstein gradient flows in multiple dimensions. Electronic Communications in Probability, 20 (89). FFradon, 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) Frömberg, Daniela and Höfling, Felix (2021) Generalized master equation for first-passage problems in partitioned spaces. Journal of Physics A: Mathematical and Theoretical, 54 (21). pp. 1-29. Farshbaf-Shaker, M. Hassan and Thomas, Marita (2020) Analysis of a compressible Stokes-flow with degenerating and singular viscosity. Preprint . pp. 1-45. (Submitted) Franchi, Bruno and Heida, Martin and Lorenzani, Silvia (2020) A Mathematical model for Alzheimer's disease: An approach via stochastic homogenization of the Smoluchowski equation. Communications in Mathematical Sciences, 18 (4). pp. 1105-1134. Flegel, Franziska and Heida, Martin (2020) The fractional p-Laplacian emerging from homogenization of the random conductance model with degenerate ergodic weights and unbounded-range jumps. Calculus of Variations and Partial Differential Equations, 59 (8). (Unpublished) Flegel, Franziska and Heida, Martin and Slowik, Martin (2019) Homogenization theory for the random conductance model with degenerate ergodic weights and unbounded-range jumps. Ann. Inst. H. Poincaré Probab. Statist., 55 (3). pp. 1226-1257. Fröhner, Chr. and Noé, F. (2018) Reversible interacting-particle reaction dynamics. J. Phys. Chem. B, 122 (49). pp. 11240-11250. GGertler, Charles G. and O’Gorman, Paul A. and Pfahl, Stephan (2023) Moist available potential energy of the mean state of the atmosphere and the thermodynamic potential for warm conveyor belts and convection. Weather Clim. Dynam., 4 . pp. 361-379. 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). Gholami, Abbas and Klein, R. and Delle Site, Luigi (2021) On the relation between Pressure and Coupling Potential in Adaptive Resolution Simulations of Open Systems in contact with a Reservoir. Advanced Theory and Simulations, 5 . pp. 1-8. Gholami, A. and Höfling, Felix and Klein, R. and Delle Site, Luigi (2021) Thermodynamic Relations at the Coupling Boundary in Adaptive Resolution Simulations for Open Systems. Advanced Theory and Simulations, 4 . pp. 1-10. Gussmann, Pascal and Mielke, Alexander (2020) Linearized elasticity as Mosco-limit of finite elasticity in the presence of cracks. Advances in Calculus of Variations, 13 (1). pp. 1-20. 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. HHuysmans, Lucas and Titi, Edriss (2023) Non-Uniqueness and Inadmissibility of the Vanishing Viscosity Limit of the Passive Scalar Transport Equation. arXiv . (Unpublished) Huber, Konstantin and Vrijmoed, Johannes and John, Timm (2021) Formation of olivine-rich veins by reactive fluid flow in a dehydrating serpentinite. Earth and Space Science Open Archive . pp. 1-18. Heida, Martin and Kantner, Markus and Stephan, Artur (2021) Consistency and convergence for a family of finite volume discretizations of the Fokker--Planck operator. ESAIM: Mathematical Modelling and Numerical Analysis, 55 . pp. 3017-3042. Harikrishnan, A. P. and Ansorge, C. and Klein, R. and Vercauteren, N. (2021) Lagrangian hairpins in atmospheric boundary layers. Gallery of Fluid Motion . Hittmeir, S. and Klein, R. and Müller, A. and Névir, P. (2021) The Dynamic State Index with Moisture and Phase Changes. J. Math. Phys, 62 (12). pp. 1-12. Heida, Martin and Thomas, Marita (2021) GENERIC for dissipative solids with bulk-interface interaction. wias preprint . pp. 1-27. ISSN 2198-5855 (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. Herter, Felix and Hege, Hans-Christian and Hadwiger, Markus and Lepper, Verena and Baum, Daniel (2021) Thin-Volume Visualization on Curved Domains. Computer Graphics forum, 40 (3). pp. 147-157. Helfmann, L. and Djurdjevac Conrad, N. and Djurdjevac, A. and Winkelmann, S. and Schütte, Ch. (2021) From interacting agents to density-based modeling with stochastic PDEs. Commun. Appl. Math. Comput. Sci., 16 (1). pp. 1-32. ISSN Online: 2157-5452; Print: 1559-3940 Heida, Martin and Neukamm, Stefan and Varga, Mario (2021) STOCHASTIC HOMOGENIZATION OF L-CONVEX GRADIENT FLOWS. Discrete and Continuous Dynamical Systems - S, 14 (1). pp. 1-27. 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. Höfling, F. and Dietrich, S. (2020) Finite-size corrections for the static structure factor of a liquid slab with open boundaries. Journal of Chemical Physics, 153 (5). pp. 1-13. 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. Heida, M. and Kornhuber, R. and Podlesny, J. (2020) Fractal homogenization of multiscale interface problems. Multiscale Modeling & Simulation, 18 (1). pp. 294-314. ISSN 1540-3459 Heida, Martin and Patterson, Robert I. A. and Renger, Michiel D.R. (2019) Topologies and measures on the space of functions of bounded variation taking values in a Banach or metric space. Journal of Evolution Equations, 19 (1). pp. 111-152. 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) Heida, M. and Nesenenko, S. (2019) Stochastic homogenization of rate-dependent models of monotone type in plasticity. Asymptotic Analysis, 112 (3-4). pp. 185-212. ISSN 0921-7134 Heydecker, Daniel and Patterson, Robert I. A. (2019) Bilinear Coagulation Equations. SFB1114 Preprint in arxiv:1902.07686 . (Unpublished) Hoffmann, M. and Fröhner, Chr. and Noé, F. (2019) ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics. PLoS Computational Biology, 15 (2). e1006830. ISSN 1553-7358 Hoffmann, M. and Fröhner, Chr. and Noé, F. (2019) Reactive SINDy: Discovering governing reactions from concentration data. J. Chem. Phys., 150 (2). 025101. ISSN 0021-9606, ESSN: 1089-7690 Heida, M. (2018) Convergences of the squareroot approximation scheme to the Fokker–Planck operator. Mathematical Models and Methods in Applied Sciences, 28 (13). pp. 2599-2635. ISSN 0218-2025, ESSN: 1793-6314 Heida, Martin and Röger, Matthias (2018) Large deviation principle for a stochastic Allen--Cahn equation. Journal of Theoretical Probability 31(1), 31 (1). pp. 1-18. (Submitted) Heida, Martin and Schweizer, Ben (2018) Stochastic homogenization of plasticity equations. ESAIM: Control, Optimisation and Calculus of Variations, 24 (1). 153 -176. Hittmeir, S. and Klein, R. (2018) Asymptotics for moist deep convection I: Refined scalings and self-sustaining updrafts. Theoretical and Computational Fluid Dynamics, 32 (2). pp. 137-164. ISSN 0935-4964 (Print) 1432-2250 (Online) Heida, M. and Neukamm, S. and Varga, M. (2017) Stochastic unfolding and homogenization. SFB 1114 Preprint at WIAS 12/2017 . pp. 1-45. (Unpublished) 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 Heida, M. (2017) Stochastic homogenization of rate-independent systems and applications. Continuum Mech. Thermodyn., 29 (3). pp. 853-894. ISSN 1432-0959 (online) 0935-1175 (print) Heida, M. and Mielke, A. (2017) Averaging of time-periodic dissipation potentials in rate-independent processes. Discrete and Continuous Dynamical Systems - Series S, 10 (6). pp. 1303-1327. Hartmann, C. and Delle Site, L. (2015) Scale Bridging in Molecular Simulation. The European Physical Journal Special Topics, 224 (12). pp. 2173-2176. ISSN 1951-6355 JJunghans, C. and Agarwal, A. and Delle Site, L. (2017) Computational Efficiency and Amdahl's law for the Adaptive Resolution Simulation Technique. Computer Physics Communications, 215 . pp. 20-25. ISSN 0010-4655 KKern, Julian and Wiederhold, Bastian (2023) A Λ-Fleming-Viot type model with intrinsically varying population size. Electronic Journal of Probability . (Submitted) 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 . 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). Klimek, Anton and Netz, Roland R. (2022) Optimal non-Markovian composite search algorithms for spatially correlated targets. EPL A Letters Journal Exploring The Frontiers of Physics, 139 . pp. 1-8. 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. Kiefer, Henrik and Dalton, Benjamin and Bruenig, Florian N. and Netz, Roland R. (2022) Connection between Macroscopic Hydrodynamics and Molecular Friction in Liquids. Preprint . pp. 1-26. (Unpublished) Klein, R. and Schielicke, L. and Pfahl, S. and Khouider, B. (2022) QG-DL-Ekman: Dynamics of a diabatic layer in the quasi-geostrophic framework. Journal of the Atmospheric Sciences, 79 (3). pp. 887-905. 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). Klein, R. and Viand, R. E. and Höfling, Felix and Delle Site, Luigi (2021) Nonequilibrium Induced by Reservoirs: Physico-Mathematical Models and Numerical Tests. Advanced Theory and Simulations, 4 . pp. 1-10. Klein, R. and Schielicke, L. and Pfahl, S. and Khouider, B. (2021) QG-DL: Dynamics of a diabatic layer in the quasi-geostrophic framework. Journal of the Atmospheric Sciences . pp. 1-12. ISSN Online: 1520-0469 Print: 0022-4928 (Submitted) Kaatz, Lisa and Zertani, Sascha and Moulas, Evangelos and John, Timm and Labrousse, Loïc and Schmalholz, Stefan M. and Andersen, Torgeir B. (2021) Widening of Hydrous Shear Zones During Incipient Eclogitization of Metastable Dry and Rigid Lower Crust— Holsnøy, Western Norway. Tectonics, 40 (3). pp. 1-19. ISSN 1944-9194 Kavokine, Nikita and Netz, Roland R. and Bocquet, Lydéric (2021) Fluids at the Nanoscale: From Continuum to Subcontinuum Transport. Annual Reviews of Fluid Mechanics, 53 . pp. 377-410. Kowalik, Bartosz G. and Daldrop, Jan O. and Kappler, Julian and Schulz, J.C.F. and Schlaich, Alexander and Netz, Roland R. (2019) Memory-kernel extraction for different molecular solutes in solvents of varying viscosity in confinement. PhysRevE (100). 012126. Krekeler, C. and Agarwal, A. and Junghans, C. and Praprotnik, M. and Delle Site, L. (2018) Adaptive Resolution Molecular Dynamics Technique: Down to the Essential. J. Chem. Phys., 149 . 024104. ISSN 0021-9606, ESSN: 1089-7690 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) Kappler, J. and Shrivastava, S. and Schneider, M.F. and Netz, R.R. (2017) Nonlinear fractional waves at elastic interfaces. Phys. Rev. Fluids, 2 (11). p. 114804. Kappler, J. and Netz, R.R. (2017) Pulse propagation at interfaces and their possible relevance for biology. Journal Club for Condensed Matter Physics . Kappler, J. and Netz, R.R. (2015) Multiple surface wave solutions on linear viscoelastic media. EPL, 112 (1). p. 19002. Klein, R. (2015) Comments on "Open Boundary Molecular Dynamics " by R. Delgado-Buscalioni, J. Sablic, and M. Praprotnik. The European Physical Journal, 224 (12). pp. 2509-2510. ISSN Online: 1951-6401 Print: 1951-6355 Klein, R. (2015) Comments on "Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations" by K. Kreis, A.C. Fogarty, K. Kremer R. Potestio. The European Physical Journal, 224 (12). pp. 2503-2504. ISSN Online: 1951-6401 Print: 1951-6355 Klein, R. (2015) Comments on "Adaptive Resolution Simulation in Equilibrium and Beyond" by H. Wang and A. Agarwal. The European Physical Journal, 224 (12). pp. 2497-2499. LLavacchi, 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. Loche, Philip and Ayaz, Cihan and Schlaich, Alexander and Uematsu, Yuki and Netz, Roland R. (2019) Giant Axial Dielectric Response in Water-Filled Nanotubes and Effective Electrostatic Ion–Ion Interactions from a Tensorial Dielectric Model. J. Phys. Chem. B, 123 (50). pp. 10850-10857. Liero, M. and Mielke, A. and Savaré, G. (2018) Optimal Entropy-Transport problems and a new Hellinger-Kantorovich distance between positive measures. Inventiones mathematicae, 211 . pp. 969-1117. ISSN 1432-1297 (online) Liero, M. and Mielke, A. and Peletier, M. A. and Renger, M. (2017) On microscopic origins of generalized gradient structures. Discrete and Continuous Dynamical Systems - Series S, 10 (1). Liero, M. and Mielke, A. and Savaré, G. (2016) Optimal Transport in Competition with Reaction: The Hellinger--Kantorovich Distance and Geodesic Curves. SIAM J. Math. Anal., 48 (2). pp. 2869-2911. ISSN 1095-7154 (online) MMontefusco, 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. Mardt, Andreas and Hempel, Tim and Clementi, Cecilia and Noé, Frank (2022) Deep learning to decompose macromolecules into independent Markovian domains. nature communications, 13 . 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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) Mielke, A. and Rossi, R. and Savaré, G. (2018) Global existence results for viscoplasticity at finite strain. Archive for Rational Mechanics and Analysis, 227 (1). pp. 423-475. ISSN Print: 0003-9527; Online: 1432-0673 Mielke, A. and Mittnenzweig, M. (2018) Convergence to Equilibrium in Energy-Reaction–Diffusion Systems Using Vector-Valued Functional Inequalities. Journal of Nonlinear Science . pp. 1-42. ISSN 1432-1467 (online) Mielke, Alexander and Mittnenzweig, Markus (2018) Convergence to Equilibrium in Energy-Reaction–Diffusion Systems Using Vector-Valued Functional Inequalities. Journal of Nonlinear Science, 28 . pp. 765-806. ISSN 1432-1467 (online) Mielke, A. and Patterson, R. I. A and Peletier, M. A. and Renger, M. (2017) Non-equilibrium thermodynamical principles for chemical reactions with mass-action kinetics. SIAM Journal on Applied Mathematics, 77 (4). pp. 1562-1585. ISSN 1095-712X (online) 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 Mielke, A. (2017) Three examples concerning the interaction of dry friction and oscillations. In: Trends on Application of Mathematics to Mechanics. Springer Proceedings of the INdAM-ISIMM Workshop, Rome, Italy, September 2016 (27). Springer INdAM series, pp. 159-177. Mielke, A. and Peletier, M. A. and Renger, M. (2016) A generalization of Onsager's reciprocity relations to gradient flows with nonlinear mobility. Journal of Non-Equilibrium Thermodynamics, 41 (2). Mielke, A. and Rossi, R. and Savaré, G. (2016) Balanced-Viscosity solutions for multi-rate systems. Journal of Physics: Conference Series, 727 . pp. 1-27. NNiemann, 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). Nüsken, N. and Renger, M. (2021) Stein Variational Gradient Descent: many-particle and long-time asymptotics. arXive . pp. 1-25. (Unpublished) Netz, Roland R. (2020) Mechanisms of Airborne Infection via Evaporating and Sedimenting Droplets Produced by Speaking. Journal Phys. Chem. B, 124 (133). pp. 7093-7101. OOlsson, 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. PPacey, 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. Peschka, Dirk and Zafferi, Andrea and Heltai, Luca and Thomas, Marita (2022) Variational Approach to Fluid–Structure Interaction via GENERIC. Journal of Non-Equilibrium Thermodynamics . ISSN 1437-4358 Peschka, Dirk and Zafferi, Andrea and Heltai, Luca and Thomas, Marita (2021) Variational approach to fluid-structure interaction via GENERIC. WIAS Preprint . pp. 1-13. (Submitted) Patterson, Robert I.A. and Renger, D.R. Michiel and Sharma, Upanshu (2021) Variational structures beyond gradient flows: a macroscopic fluctuation-theory perspective. arXive . pp. 1-47. (Unpublished) Patterson, Robert I. A. and Renger, Michiel D.R. (2019) Large deviations of jump process fluxes. Math. Phys. Anal. Geom., 22 (21). pp. 1-32. ISSN 1385-0172; ESSN: 1572-9656 Paul, F. and Wu, H. and Vossel, M. and de Groot, B.L. and Noé, F. (2019) Identification of kinetic order parameters for non-equilibrium dynamics. J. Chem. Phys., 150 (16). p. 164120. ISSN 0021-9606, ESSN: 1089-7690 Pinamonti, G. and Paul, F. and Noé, F. and Rodriguez, A. and Bussi, G. (2019) The mechanism of RNA base fraying: Molecular dynamics simulations analyzed with core-set Markov state models. J. Chem. Phys., 150 (15). p. 154123. ISSN 0021-9606, ESSN: 1089-7690 Peschka, D. and Thomas, M. and Ahnert, T. and Münch, A. and Wagner, B. (2019) Gradient structures for flows of concentrated suspensions. Topics in Applied Analysis and Optimisation . pp. 295-318. Peters, J.H. and Gräser, C. and Klein, R. (2017) Membrane Deformation by N-BAR Proteins: Extraction of membrane geometry and protein diffusion characteristics from MD simulations. SFB 1114 Preprint in arXiv:1712.02666 . pp. 1-12. (Unpublished) 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). Pinamonti, G. and Zhao, J. and Condon, D. and Paul, F. and Noé, F. and Turner, D. and Bussi, G. (2017) Predicting the kinetics of RNA oligonucleotides using Markov state models. J. Chem. Theory Comput., 13 (2). pp. 926-934. Peters, J.H. and Klein, R. and Delle Site, L. (2016) Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique. Phys. Rev. E, 94 (2). 023309. RRentsch, 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). (In Press) 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). 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). Rezaei, majid and Netz, Roland R. (2021) Airborne virus transmission via respiratory droplets: Effects of droplet evaporation and sedimentation. ScienceDirect, 55 . 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(2019) Modeling of Drug Diffusion Based on Concentration Profiles in Healthy and Damaged Human Skin. Biophysical Journal, 117 (5). pp. 998-1008. ISSN 00063495 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 Scherer, M. K. and Husic, B.E. and Hoffmann, M. and Paul, F. and Wu, H. and Noé, F. (2018) Variational Selection of Features for Molecular Kinetics. SFB 1114 Preprint in arXiv:1811.11714 . pp. 1-12. (Unpublished) Shadrack Jabes, B. and Delle Site, L. (2018) Nanoscale domains in Ionic Liquids: A statistical mechanics definition for molecular dynamics studies. J. Chem. Phys., 149 (18). p. 184502. ISSN 0021-9606, ESSN: 1089-7690 Sadeghi, M. and Weikl, T. and Noé, F. (2018) Particle-based membrane model for mesoscopic simulation of cellular dynamics. J. Chem. Phys., 148 (4). 044901. Shadrack Jabes, B. and Krekeler, C. and Klein, R. and Delle Site, L. (2018) Probing Spatial Locality in Ionic Liquids with the Grand Canonical Adaptive Resolution Molecular Dynamics Technique. The Journal of Chemical Physics, 148 (19). ISSN online: 1089-7690 Sbailò, L. and Noé, F. (2017) An efficient multi-scale Green's Functions Reaction Dynamics scheme. J. Chem. Phys., 147 . p. 184106. ISSN 0021-9606, ESSN: 1089-7690 Schlaich, A. and Kappler, J. and Netz, R.R. (2017) Hydration Friction in Nanoconfinement: From Bulk via Interfacial to Dry Friction. Nano Lett., 17 (10). pp. 5969-5976. Seshaditya, A. and Ghiringhelli, L. M. and Delle Site, L. (2017) Levy-Lieb-based Monte Carlo study of the dimensionality behaviour of the electronic kinetic functional. Computationa, 5 (2). pp. 1-10. ISSN 2079-3197 Schulz, R. and Yamamoto, K. and Klossek, A. and Flesch, R. and Hönzke, S. and Rancan, F. and Vogt, A. and Blume-Peytavi, U. and Hedtrich, S. and Schäfer-Korting, M. and Rühl, E. and Netz, R.R. (2017) Data-based modeling of drug penetration relates human skin barrier function to the interplay of diffusivity and free-energy profiles. PNAS, 114 (14). pp. 3631-3636. ISSN 1091-6490 (online) Schöneberg, J. and Lehmann, M. and Ullrich, A. and Posor, Y. and Lo, W.-T. and Lichtner, G. and Schmoranzer, J. and Haucke, V. and Noé, F. (2017) Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nat. Comm., 8 . p. 15873. 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. TThies, Arne and Sunkara, Vikram and Ray, Sourav and Wulkow, Hanna and Özgür Celik, M. and Yergöz, Fatih and Schütte, Christof and Stein, Christoph and Weber, Marcus and Winkelmann, Stefanie (2023) Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design. Scientific Reports, 13 (1). p. 607. Thomas, Marita and Tornquist, Sven (2021) Discrete approximation of dynamic phase-field fracture in visco-elastic materials. Discrete Contin. Dyn. Syst. Ser. S, 14 . pp. 3865-3924. Tierno, Pietro and Johansen, Tom H. and Straube, Arthur V. (2021) Thermally active nanoparticle clusters enslaved by engineered domain wall traps. NATURE COMMUNICATIONS, 12 (5813). pp. 1-11. 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. VVrijmoed, Johannes and Podladchikov, Y.Y. (2021) Thermolab: a thermodynamics laboratory for nonlinear transport processes in open systems. Earth and Space Science Open Archive . WWinkelmann, 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 . Winkelmann, Stefanie and Schütte, Christof (2020) Stochastic Dynamics in Computational Biology. Springer International Publishing. Whittaker, John and Delle Site, Luigi (2019) Investigation of the hydration shell of a membrane in an open system molecular dynamics simulation. Phys. Rev. Research, 1 (3). 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 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 Winkelmann, S. and Schütte, Ch. (2017) Hybrid models for chemical reaction networks: Multiscale theory and application to gene regulatory systems. Journal of Chemical Physics, 147 (11). pp. 1-18. Winkelmann, S. (2017) Markov Control with Rare State Observation: Average Optimality. Markov Processes and Related Fields, 23 . pp. 1-34. ISSN 1024-2953 Winkelmann, S. and Schütte, Ch. (2016) The spatiotemporal master equation: approximation of reaction-diffusion dynamics via Markov state modeling. Journal of Chemical Physics, 145 (21). p. 214107. 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 ZZafferi, Andrea and Huber, Konstantin and Peschka, Dirk and Vrijmoed, Johannes and John, Timm and Thomas, Marita (2023) A porous-media model for reactive fluid-rock interaction in a dehydrating rock. Preprint . pp. 1-22. (Unpublished) Zendehroud, Sina and Netz, Roland R. and Kappler, Julian (2022) Linear Waves at Viscoelastic Interfaces Between Viscoelastic Media. Physical Review Fluids, 7 . pp. 1-32. 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). Zendehroud, Sina and Loche, Philip and Kornhuber, Ralf and Netz, Roland R. (2022) Boundary Conditions on Conical Hydrophobic Inclusions in Lipid Membranes. Preprint . (Unpublished) Zafferi, Andrea and Peschka, Dirk and Thomas, Marita (2021) GENERIC framework for reactive fluid flows. Preprint (2841). pp. 1-75. ISSN 2198-5855 (Submitted) Zhu, J. and Klein, R. and Delle Site, L. (2016) Adaptive Molecular Resolution Approach in Hamiltonian Form: An Asymptotic Analysis. Physical Review E, 94 (043321). |