Publications for: All SFB 1114 publications
Junghans, C. and Agarwal, A. and Delle Site, L. (2017) Computational Efficiency and Amdahl's law for the Adaptive Resolution Simulation Technique. Computer Physics Communications, 215 . pp. 20-25. ISSN 0010-4655
Seshaditya, A. and Ghiringhelli, L. M. and Delle Site, L. (2017) Levy-Lieb-based Monte Carlo study of the dimensionality behaviour of the electronic kinetic functional. Computationa, 5 (2). pp. 1-10. ISSN 2079-3197
Gerber, S. and Horenko, I. (2017) Toward a direct and scalable identification of reduced models for categorical processes. Proceedings of the National Academy of Sciences, 114 (19). pp. 4863-4868.
Acevedo, W. and de Wiljes, J. and Reich, S. (2017) Second-order accurate ensemble transform particle filters. SFB 1114 Preprint . (Submitted)
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
Hittmeir, S. and Klein, R. (2017) Asymptotics for moist deep convection I: Refined scalings and self-sustaining updrafts. Theoretical and Computational Fluid Dynamics . ISSN 1432-2250 (Online) (In Press)
Kornhuber, R. and Podlesny, J. and Yserentant, H. (2017) Direct and Iterative Methods for Numerical Homogenization. In: Domain Decomposition Methods in Science and Engineering. Lecture Notes in Computational Science and Engineering, XXIII (116). SpringerLink, pp. 215-225. ISBN 978-3-319-52389-7
Donati, L. and Hartmann, C. and Keller, B.G. (2017) Girsanov reweighting for path ensembles and Markov state models. SFB 1114 Preprint . (Submitted)
Gräser, C. and Kies, T. (2017) Discretization Error Estimates for Penalty Formulations of a Linearized Canham-Helfrich Type Energy. SFB 1114 Preprint .
O'Kane, T.J. and Monselesan, D.P. and Risbey, J.S. and Horenko, I. and Franzke, Ch.L.E. (2017) On memory, dimension, and atmospheric teleconnection patterns. Math. Clim. Weather Forecast, 3 (1). pp. 1-27.
Pipping, E. (2017) Existence of long-time solutions to dynamic problems of viscoelasticity with rate-and-state friction. SFB 1114 Preprint . (Submitted)
Dellnitz, M. and Klus, S. and Ziessler, A. (2017) A Set-Oriented Numerical Approach for Dynamical Systems with Parameter Uncertainty. SIAM Journal on Applied Dynamical Systems, 16 (1). pp. 120-138. ISSN 1536-0040
Krekeler, C. and Delle Site, L. (2017) Towards open boundary molecular dynamics simulation of ionic liquids. Physical Chemistry Chemical Physics, 6 (19). pp. 4701-4709. ISSN 1463-9076
Horenko, I. and Gerber, S. and O'Kane, T.J. and Risbey, J.S. and Monselesan, D.P. (2017) On inference and validation of causality relations in climate teleconnections. In: Nonlinear and Stochastic Climate Dynamics. Cambridge University Press, pp. 184-208. ISBN 9781107118140
Nüske, F. and Wu, H. and Wehmeyer, C. and Clementi, C. and Noé, F. (2017) Markov State Models from short non-Equilibrium Simulations - Analysis and Correction of Estimation Bias. J. Chem. Phys., 146 . 094104.
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. Comp. Theory Comput. , 13 . pp. 926-934.
Winkelmann, S. (2017) Markov Control with Rare State Observation: Average Optimality. Markov Processes and Related Fields, 23 . pp. 1-34. ISSN 1024-2953
Klus, S. and Schütte, Ch. (2016) Towards tensor-based methods for the numerical approximation of the Perron-Frobenius and Koopman operator. Journal of Computational Dynamics . ISSN 2158-2491
Mielke, A. and Roubícek, T. (2016) Rate-Independent elastoplasticity at finite strain and its numerical approximation. Mathematical Models and Methods in Applied Sciences, 26 (12). pp. 2203-2236. ISSN 1793-6314
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).
Banisch, Ralf and Hartmann, C. (2016) A sparse Markov chain approximation of LQ-type stochastic control problems. Math. Control Relat. F., 6 (3). pp. 363-389. ISSN 1064-8275
Kornhuber, R. and Peterseim, D. and Yserentant, H. (2016) An analysis of a class of variational multiscale methods based on subspace decomposition. Mathematics of Computation . ISSN 0025-5718 (In Press)
Hartmann, C. and Schütte, Ch. and Zhang, W. (2016) Model reduction algorithms for optimal control and importance sampling of diffusions. Nonlinearity, 29 (8). pp. 2298-2326. ISSN 0951-7715
Klus, S. and Koltai, Péter and Schütte, Ch. (2016) On the numerical approximation of the Perron-Frobenius and Koopman operator. Journal of Computational Dynamics, 3 (1). pp. 51-79. ISSN 2158-2491
Chustagulprom, N. and Reich, S. and Reinhardt, M. (2016) A HYBRID ENSEMBLE TRANSFORM FILTER FOR HIGH DIMENSIONAL DYNAMICAL SYSTEMS. SIAM/ASA Journal on Uncertainty Quantification, 4 (1). pp. 592-608. ISSN 2166-2525
Klein, R. and Benacchio, T. (2016) A doubly blended model for multiscale atmospheric dynamics. Journal of the Atmospheric Sciences, 73 . pp. 1179-1186. ISSN Online: 1520-0469 Print: 0022-4928
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 . pp. 37-46.
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.
Elliott, C.M. and Gräser, C. and Hobbs, G. and Kornhuber, R. and Wolf, M.W. (2016) A Variational Approach to Particles in Lipid Membranes. Archive for Rational Mechanics and Analysis, 222 (2). pp. 1011-1075. ISSN Print: 0003-9527; Online:1432-0673
Feireisl, E. and Klein, R. and Novotný, A. and Zatorska, E. (2016) On singular limits arising in the scale analysis of stratified fluid flows. Mathematical Models and Methods in Applied Sciences, World Scientific, 26 (3). pp. 419-443. ISSN Print: 0218-2025 Online: 1793-6314
Hittmeir, S. and Klein, R. and Li, J. and Titi, E. (2016) GLOBAL WELL-POSEDNESS FOR PASSIVELY TRANSPORTED NONLINEAR MOISTURE DYNAMICS WITH PHASE CHANGES. Nonlinearity . (Submitted)
Klinkmüller, M. and Schreurs, G. and Rosenau, M. and Kemnitz, H. (2016) Properties of granular analogue materials: A community wide survey. Tectonophysics, 666 . pp. 23-38.
Klus, S. and Gelß, P. and Peitz, S. and Schütte, Ch. (2016) Tensor-based dynamic mode decomposition. SIAM Journal on Scientific Computing . ISSN ISSN 1064-8275 (print); 1095-7197 (electronic) (Submitted)
Kornhuber, R. and Yserentant, H. (2016) Numerical Homogenization of Elliptic Multiscale Problems by Subspace Decomposition. Multiscale Model. Simul., 14 (3). pp. 1017-1036. ISSN print: 1540-3459; online: 1540-3467
Lemke, O. and Keller, B.G. (2016) Density-based cluster algorithms for the identification of core sets. Journal of Chemical Physics, 145 (164104).
Nüske, F. and Schneider, R. and Vitalini, F. and Noé, F. (2016) Variational Tensor Approach for Approximating the Rare-Event Kinetics of Macromolecular Systems. J. Chem. Phys., 144 (5). 054105.
Patterson, R. I. A (2016) Properties of the solutions of delocalised coagulation and inception problems with outflow boundaries. Journal of Evolution Equations . (Submitted)
Paul, F. and Weikl, T. (2016) How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates. PLOS Computational Biology .
Peters, J.H. and Klein, R. and Delle Site, L. (2016) Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique /PhysRevE.94.023309. Phys. Rev. E, 94 (2).
Pipping, E. and Kornhuber, R. and Rosenau, M. and Oncken, O. (2016) On the efficient and reliable numerical solution of rate-and-state friction problems. Geophysical Journal International, 204 (3). pp. 1858-1866. ISSN Online: 1365-246X Print: 0956-540X
Ritter, M. and Leever, K. and Rosenau, M. and Oncken, O. (2016) Scaling the Sand Box - Mechanical (Dis-) Similarities of Granular Materials and Brittle Rock. Journal of Geophysical Research: Solid Earth . (In Press)
Rosenau, M. and Leever, K. and Oncken, O. (2016) Experimental tectonics: Convergent plate margins. Earth Sys. Env. Sci. SFB 1114 Preprint . (Submitted)
Rudolf, M. and Boutelier, D. and Rosenau, M. and Schreurs, G. and Oncken, O. (2016) Rheological benchmark of silicone oils used for analog modeling of short- and long-term lithospheric deformation. Tectonophysics, 666 . pp. 12-20.
Schreurs, G. and et al, . (2016) Benchmarking analogue models of brittle thrust wedges. J. Struct. Geol. . (In Press)
Vitalini, F. and Noé, F. and Keller, B. (2016) Molecular dynamics simulations data of the twenty encoded amino acids in different force fields. Data in Brief, 7 . pp. 582-590.
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. (In Press)
Yapp, E.K.Y. and Patterson, R. I. A and Akroyd, J. and Mosbach, S. and Adkins, E.M. and Miller, J.H. and Kraft, M. (2016) Simulation and parametric sensitivity study of optical band gap in a laminar co-flow ethylene diffusion flame. Combustion and Flame . (Submitted)
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
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
Banisch, Ralf and Djurdjevac, N. and Schütte, Ch. (2015) Reactive flows and unproductive cycles in irreversible Markov chains. The European Physical Journal Special Topics, 224 (12). pp. 2369-2387. ISSN 1951-6355
Bittracher, Andreas and Hartmann, C. and Junge, O. and Koltai, Péter (2015) Pseudo generators for under-resolved molecular dynamics. The European Physical Journal Special Topics, 224 (12). pp. 2463-2490. ISSN 1951-6355
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
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
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
Schütte, Ch. and Sarich, M. (2015) A Critical Appraisal of Markov State Models. SFB 1114 Preprint, 15-18 . ISSN 1438-0064
Di Giuseppe, E. and Corbi, F. and Funiciello, F. and Massmeyer, A. and Santimano, T.N. and Rosenau, M. and Davaille, A. (2015) Characterization of Carbopol hydrogel rheology for experimental tectonics and geodynamics, , 642, 29-45, doi:10.1016/j.tecto.2014.12.005. Tectonophysics . pp. 29-45.
Djurdjevac, A. (2015) Advection-diffusion equations with random coefficients on evolving hypersurfaces. Interfaces and Free Boundaries . (Unpublished)
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).
Hartmann, C. and Schütte, Ch. and Weber, M. and Zhang, W. (2015) Importance sampling in path space for diffusion processes. Probab. Theory Rel. Fields . (Submitted)
Horenko, I. and Gerber, S. (2015) Improving clustering by imposing network information. Science Advances, 1 (7). ISSN 2375-2548
Kim, W.K. and Netz, R.R. (2015) The mean shape of transition and first-passage paths. The Journal of Chemical Physics, 143 (224108).
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.
Li, S. and Moreno, M. and Bedford, J. and Rosenau, M. and Oncken, O. (2015) Revisiting viscoelastic effects on interseismic deformation and locking degree: A case study of the Peru-North Chile subduction zone. Journal of Geophysical Research-Solid Earth, 120 (6). pp. 4522-4538.
Liero, M. and Mielke, A. and Peletier, M. A. and Renger, M. (2015) On microscopic origins of generalized gradient structures. SFB Preprint . (Submitted)
Mazza, E. and Ulbrich, U. and Klein, R. (2015) A Characterization of the Meteorological Environment Associated with the Tropical Transition of a Medicane in the Western Mediterranean Sea. SFB1114-Preprint . (Submitted)
Mielke, A. and Patterson, R. I. A and Peletier, M. A. and Renger, M. (2015) Non-equilibrium thermodynamical principles for chemical reactions with mass-action kinetics. WIAS Preprint No. 2165 . (Submitted)
Mielke, A. and Peletier, M. A. and Renger, M. (2015) A generalization of Onsager's reciprocity relations to gradient flows with nonlinear mobility. Journal of Non-Equilibrium Thermodynamics . (Submitted)
O’Kane, T.J. and Risbey, J.S. and Monselesan, D.P. and Horenko, I. and Franzke, Ch.L.E. (2015) On the dynamics of persistent states and their secular trends in the waveguides of the Southern Hemisphere troposphere. Climate Dynamics . ISSN Print: 0930-7575, Online: 1432-0894
Rinne, K.F. and Schulz, J.C.F. and Netz, R.R. (2015) Impact of secondary structure and hydration water on the dielectric spectrum of poly-alanine and possible relation to the debate on slaved versus slaving water. The Journal of Physical Chemistry .
Santimano, T.N. and Rosenau, M. and Oncken, O. (2015) Intrinsic versus extrinsic variability of analogue sand-box experiments - Insights from statistical analysis of repeated accretionary sand wedge experiments. Journal of Structural Geology, 75 . pp. 80-100.
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.
Schulz, J.C.F. and Miettinen, M.S. and Netz, R.R. (2015) Unfolding and Folding Internal Friction of β‑Hairpins Is Smaller than That of α‑Helices. Journal of Physical Chemistry B, 119 (13). pp. 4565-4574.
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.
Vitalini, F. and Noé, F. and Keller, B. (2015) A basis set for peptides for the variational approach to conformational kinetics. J. Chem. Theory Comput., 11 . pp. 3992-4004.
Wu, H. and Prinz, J.-H. and Noé, F. (2015) Projected Metastable Markov Processes and Their Estimation with Observable Operator Models. J. Chem. Phys., 143 (14). p. 144101.
Wu, H. and Noé, F. (2015) Gaussian Markov transition models of molecular kinetics. J. Chem. Phys., 142 (8). 084104.
Hartmann, C. and Latorre, J.C. and Pavliotis, G. A. and Zhang, W. (2014) Optimal control of multiscale systems using reduced-order models. J. Computational Dynamics, 1 (2). pp. 279-306. ISSN 2158-2505
Lie, Han Cheng and Schütte, Ch. and Hartmann, C. (2014) Martingale-based gradient descent algorithm for estimating free energy values of diffusions. SIAM J. Sci. Comput. . ISSN 1064-8275 (Submitted)
Mey, A.S.J.S. and Wu, H. and Noé, F. (2014) xTRAM: Estimating equilibrium expectations from time-correlated simulation data at multiple thermodynamic states. Phys. Rev. X, 4 (4). 041018.
Wu, H. and Mey, A.S.J.S. and Rosta, E. and Noé, F. (2014) Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states. J. Chem. Phys., 141 (21). p. 214106.