Publications
Jump to: 2020  2019  2018  2017  2016  2015  2014
Number of items: 223.
2020

Delle Site, L. and Klein, R. (2020) Liouvilletype equations for the nparticle distribution functions of an open system. Journal of Mathematical Physics, 61 (8).

Kosari, Ehsan and Rosenau, Matthias and Bedford, Jonathan and Rudolf, Michael and Oncken, Onno (2020) On the relationship between offshore geodetic coverage and slip model uncertainty: Analog megathrust earthquake case studies. Geophysical Research Letters, 47 . pp. 115.

Straube, Arthur V. and Kowalik, Bartosz G. and Netz, Roland R. and Höfling, Felix (2020) Rapid onset of molecular friction in liquids bridging between the atomistic and hydrodynamic pictures. Communications Physics, 3 (126). pp. 111.

Höfling, F. and Dietrich, S. (2020) Finitesize corrections for the static structure factor of a liquid slab with open boundaries. Journal of Chemical Physics, 153 (5). pp. 113.

Hittmeir, Sabine and Klein, Rupert and Li, Jinkai and Titi, Edriss (2020) Global wellposedness for the primitive equations coupled to nonlinear moisture dynamics with phase changes. Nonlinearity, 33 (7). pp. 32063236.

Delle Site, Luigi and Klein, Rupert and Höfling, Felix and Viand, Roya Ebrahimi (2020) Open Systems out of Equilibrium: Theory and Simulation Preprint arXiv:2005.07481. SFB 1114 Preprint in arXiv . pp. 111. (Submitted)

Nüsken, N. and Richter, L. (2020) Solving highdimensional HamiltonJacobiBellman PDEs using neural networks: perspectives from the theory of controlled diffusions and measures on path space. SFB 1114 Preprint in arXiv . pp. 140. (Submitted)

Bittracher, Andreas and Schütte, Christof (2020) A weak characterization of slow variables in stochastic dynamical systems. SFB 1114 Preprint in arXive . pp. 120. ISSN 2005.01631 (Submitted)

Mielke, Alexander and Netz, Roland R. and Zendehroud, Sina (2020) A rigorous derivation and energetics of a wave equation with fractional damping. arXiv . pp. 120. (Submitted)

Haug, Ø. T. and Rosenau, M. and Rudolf, M. and Leever, K. and Oncken, O. (2020) Variations in runout of rock avalanches controlled by fragmentation, not basal friction. EarthArXiv . pp. 111. (Submitted)

Corbi, F. and Bedford, J. and Sandri, L. and Funiciello, F. and Gualandi, A. and Rosenau, M. (2020) Predicting Imminence of Analog Megathrust Earthquakes With Machine Learning: Implications for Monitoring Subduction Zones. Geophysical Research Letters . pp. 110. ISSN 19448007

Heida, M. and Kornhuber, R. and Podlesny, J. (2020) Fractal homogenization of multiscale interface problems. Multiscale Modeling & Simulation, 18 (1). pp. 294314. ISSN 15403459

Banisch, R. and Trstanova, Z. and Bittracher, A. and Klus, S. and Koltai, P. (2020) Diffusion maps tailored to arbitrary nondegenerate Ito processes. SciendeDirect, 48 (1). pp. 242265.
2019

Müller, Annette and Névir, Peter (2019) Using the concept of the Dynamic State Index for a scaledependent analysis of atmospheric blocking. Meteorologische Zeitschrift, 28 (6). pp. 487498.

Duncan, A. and Nüsken, N. and Szpruch, L. (2019) On the geometry of Stein variational gradient descent. SFB 1114 Preprint in arXiv:1912.00894 . (Unpublished)

Garbuno Inigo, A. and Nüsken, N. and Reich, S. (2019) Affine invariant interacting Langevin dynamics for Bayesian inference. SFB 1114 Preprint in arXiv:1912.02859 . pp. 129. (Unpublished)

Hartmann, C. and Neureither, L. and Sharma, U. (2019) Coarsegraining of nonreversible stochastic differential equations: quantitative results and connections to averaging. SIAM J. Math. Anal. . pp. 139. (Submitted)

Leung, T.Y. and Leutbecher, M. and Reich, S. and Shepherd, Th.G. (2019) Atmospheric Predictability: Revisiting the Inherent FiniteTime Barrier. Journal of the Atmospheric Sciences, 76 (12). pp. 38833892. ISSN Online: 15200469 Print: 00224928

Kappler, Julian and Hinrichsen, Victor B. and Netz, Roland R. (2019) NonMarkovian barrier crossing with twotimescale memory is dominated by the faster memory component. The European Physical Journal E, 42 (119). ISSN 12928941

Noé, F. and Olsson, S. and Köhler, J. and Wu, H. (2019) Boltzmann Generators: Sampling Equilibrium States of ManyBody Systems with Deep Learning. Science, 365 (6457). eaaw1147.

Patterson, R. I. A and Renger, M. (2019) Large deviations of jump process fluxes. Math. Phys. Anal. Geom., 22 (21). pp. 132. ISSN 13850172; ESSN: 15729656

Moschner, Johann and Stulberg, Valentina and Fernandes, Rita and Huhmann, Susanne and Leppkes, Jakob and Koksch, Beate (2019) Approaches to Obtaining Fluorinated αAmino Acids. Chem. Rev. 2019, 119 (18). pp. 1071810801.

Benacchio, T. and Klein, R. (2019) A semiimplicit compressible model for atmospheric flows with seamless access to soundproof and hydrostatic dynamics. Monthly Weather Review, 147 (11). pp. 42214240. ISSN Online: 15200493; Print: 00270644

Pipping, E. (2019) Existence of longtime solutions to dynamic problems of viscoelasticity with rateandstate friction. ZAMM  Journal of Applied Mathematics and Mechanics . ISSN 15214001 (online)

Kowalik, Bartosz G. and Daldrop, Jan O. and Kappler, Julian and Schulz, J.C.F. and Schlaich, Alexander and Netz, Roland R. (2019) Memorykernel extraction for different molecular solutes in solvents of varying viscosity in confinement. PhysRevE (100). 012126.

Delle Site, L. and Klein, R. (2019) Liouvilletype equations for the nparticle distribution functions of an open system. Physical Review Research . (Submitted)

Kebiri, O. and Neureither, L. and Hartmann, C. (2019) Adaptive importance sampling with forwardbackward stochastic differential equations. In: Stochastic Dynamics Out of Equilibrium. IHPStochDyn 2017. Springer Proceedings in Mathematics & Statistics, 282 . Springer, pp. 265281. ISBN 9783030150952

Neureither, L. and Hartmann, C. (2019) Time scales and exponential trends to equilibrium: Gaussian model problems. In: Stochastic Dynamics Out of Equilibrium. IHPStochDyn 2017. Springer Proceedings in Mathematics & Statistics, 282 . Springer, pp. 391410. ISBN 9783030150952

Renger, M. and Zimmer, J. (2019) Orthogonality of fluxes in general nonlinear reaction networks. SFB1114 Preprint 07/2019 in WIAS No. 2609 . pp. 112. (Unpublished)

Hartmann, C. and Kebiri, O. and Neureither, L. and Richter, L. (2019) Variational approach to rare event simulation using leastsquares regression. Chaos, 29 (6). 063107. ISSN 10541500 (print); 10897682 (online)

Heida, M. and Neukamm, S. and Varga, M. (2019) Stochastic homogenization of Λconvex gradient flows. SFB 1114 Preprint in arXiv:1905.02562 . pp. 128. (Unpublished)

Nüsken, N. and Reich, S. and Rozdeba, P.J. (2019) State and parameter estimation from observed signal increments. Entropy, 21 (5). 505. ISSN 10994300

Rosenau, M. and Rudolf, M. and Oncken, O. (2019) Creep on seismogenic faults: Insights from analogue earthquake experiments. SFB 1114 Preprint in EarthArXiv:10.31223/osf.io/24u5h . pp. 125. (Unpublished)

Franchi, B. and Heida, M. and Lorenzani, S. (2019) A Mathematical model for Alzheimer's disease: An approach via stochastic homogenization of the Smoluchowski equation. SFB 1114 Preprint in arXiv:1904.11015 . pp. 143. (Unpublished)

Hartmann, C. and Schütte, Ch. and Zhang, W. (2019) Jarzysnki equality, fluctuation theorems and variance reduction: Mathematical analysis and numerical algorithms. J. Stat. Phys., 175 (6). pp. 12141261. ISSN 00224715; ESSN: 15729613

Heida, M. and Nesenenko, S. (2019) Stochastic homogenization of ratedependent models of monotone type in plasticity. Asymptotic Analysis, 112 (34). pp. 185212. ISSN 09217134

Miron, P. and BeronVera, F.J. and Olascoaga, M.J. and Koltai, P. (2019) Markovchaininspired search for MH370. Chaos: An Interdisciplinary Journal of Nonlinear Science, 29 (4). ISSN 10541500 (print); 10897682 (online)

Paul, F. and Wu, H. and Vossel, M. and de Groot, B.L. and Noé, F. (2019) Identification of kinetic order parameters for nonequilibrium dynamics. J. Chem. Phys., 150 (16). p. 164120. ISSN 00219606, ESSN: 10897690

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 coreset Markov state models. J. Chem. Phys., 150 (15). p. 154123. ISSN 00219606, ESSN: 10897690

Rosenau, M. and Horenko, I. and Corbi, F. and Rudolf, M. and Kornhuber, R. and Oncken, O. (2019) Synchronization of great subduction megathrust earthquakes: Insights from scale model analysis. Journal of Geophysical Research: Solid Earth, 124 (4). pp. 36463661. ISSN 21699356

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 coarsegrained Molecular Dynamics Force Fields. ACS Cent. Sci., 5 (5). pp. 755767. ISSN 23747943, ESSN: 23747951

Keller, B.G. and Aleksic, S. and Donati, L. (2019) Markov State Models in drug design. In: Biomolecular Simulations in Structurebased Drug Discovery. Methods and Principles in Medicinal Chemistry, 75 . WileyInterscience, Weinheim, pp. 6786. ISBN 9783527342655

Kappler, Julian and Noe, Frank and Netz, Roland R. (2019) Cyclization and Relaxation Dynamics of FiniteLength Collapsed SelfAvoiding Polymers. Phys. Rev. Lett., 122 (6). 067801.

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 meanfield particle reservoir. Adv. Th. Simul, 2 (5).

Heydecker, Daniel and Patterson, Robert I. A. (2019) Bilinear Coagulation Equations. SFB1114 Preprint in arxiv:1902.07686 . (Unpublished)

Hoffmann, M. and Fröhner, Chr. and Noé, F. (2019) ReaDDy 2: Fast and flexible software framework for interactingparticle reaction dynamics. PLoS Computational Biology, 15 (2). e1006830. ISSN 15537358

Kühnlein, C. and Deconinck, W. and Klein, R. and Malardel, S. and Piotrowski, Z. and Smolarkiewicz, P.K. and Szmelter, J. and Wedi, N. (2019) FVM 1.0: a nonhydrostatic finitevolume dynamical core for the IFS. Geosci. Model Dev., 12 (2). pp. 651676. ISSN 1991959X, ESSN: 19919603

von Larcher, T. and Klein, R. (2019) On identification of selfsimilar characteristics using the Tensor Train decomposition method with application to channel turbulence flow. Theoretical and Computational Fluid Dynamics, 33 . pp. 119. ISSN 09354964 (Print) 14322250 (Online)

Andreis, L. and König, W. and Patterson, R. I. A (2019) A largedeviations approach to gelation. SFB 1114 Preprint in arXiv:1901.01876 . pp. 122. (Unpublished)

Ciccotti, G. and Delle Site, L. (2019) The physics of open systems for the simulation of complex molecular environments in soft matter. Soft Matter, 15 (10). pp. 21142124. ISSN 1744683X, ESSN: 17446848

Corbi, F. and Sandri, L. and Bedford, J. and Funiciello, F. and Brizzi, S. and Rosenau, M. and Lallemand, S. (2019) Machine Learning Can Predict the Timing and Size of Analog Earthquakes. Geophysical Research Letters, 46 (3). pp. 13031311. ISSN 00948276; ESSN: 19448007

Fackeldey, K. and Koltai, P. and Névir, P. and Rust, H.W. and Schild, A and Weber, M. (2019) From Metastable to Coherent Sets – timediscretization schemes. Chaos: An Interdisciplinary Journal of Nonlinear Science, 29 (1). 012101. ISSN 10541500 (print); 10897682 (online)

Hoffmann, M. and Fröhner, Chr. and Noé, F. (2019) Reactive SINDy: Discovering governing reactions from concentration data. J. Chem. Phys., 150 (2). 025101. ISSN 00219606, ESSN: 10897690

Rudolf, M. and Rosenau, M. and Ziegenhagen, Th. and Ludwikowski, V. and Schucht, Torsten and Nagel, H. and Oncken, O. (2019) Smart Speed Imaging in Digital Image Correlation: Application to Seismotectonic Scale Modeling. Frontiers in Earth Science, 6 . p. 248.

Witek, J. and Wang, S. and Schroeder, B. and Lingwood, R. and Dounas, A. and Roth, H.J. and Fouché, M. and Blatter, M. and Lemke, O. and Keller, B. and Riniker, S. (2019) Rationalization of the Membrane Permeability Differences in a Series of Analogue Cyclic Decapeptides. J. Chem. Inf. Model., 59 (1). pp. 294308. ISSN 15499596, ESSN: 1549960X

Daldrop, Jan O. and Netz, Roland R. (2019) MassDependent Solvent Friction of a Hydrophobic Molecule. J. Phys. Chem. B (123). pp. 81238130.

Klus, S. and Bittracher, A. and Schuster, I. and Schütte, Ch. (2019) A kernelbased approach to molecular conformation analysis. Journal of Chemical Physics MMMK, 149 (244109).

Straube, Arthur V. and Kowalik, Bartosz G. and Netz, Roland R. and Höfling, Felix (2019) Emergence of molecular friction in liquids: bridging between the atomistic and hydrodynamic pictures. Emergence of molecular friction in liquids: bridging between the atomistic . (Submitted)

Vercauteren, N. and Boyko, V. and Faranda, D. and Stiperski, I. (2019) Scale interactions and anisotropy in stable boundary layers. Quarterly Journal of the Royal Meteorological Society . ISSN 1477870X

Vercauteren, N. and Boyko, V. and Kaiser, A. and Belusic, D. (2019) Statistical investigations of flow structures in different regimes of the stable boundary layer. Boundary Layer Meteorology, 172 . pp. 122. ISSN Print: 00068314; Online: 15731472

von Larcher, T. and Klein, R. (2019) Approximating turbulent and nonturbulent events with the Tensor Train decomposition method. In: Turbulent Cascades II. Springer. ISBN Print: 9783030125462 Electronic: 9783030125479
2018

Schulz, R. and von Hansen, Y. and Daldrop, J.O. and Kappler, J. and Noé, F. and Netz, R.R. (2018) Collective hydrogenbond rearrangement dynamics in liquid water. J. Chem. Phys., 149 (24). 244504. ISSN 00219606, ESSN: 10897690

Vater, S. and Klein, R. (2018) A SemiImplicit Multiscale Scheme for Shallow Water Flows at Low Froude Number. Communications in Applied Mathematics & Computational Science, 13 (2). pp. 303336. ISSN 15593940

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. 112. (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 00219606, ESSN: 10897690

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. 112. ISSN EISSN: 25756524

Bittracher, Andreas and Banisch, Ralf and Schütte, Christof (2018) Datadriven computation of molecular reaction coordinates. J. Chem. Phys., 149 (154103).

Donati, L. and Heida, M. and Weber, M. and Keller, B. (2018) Estimation of the infinitesimal generator by squareroot approximation. Journal of Physics: Condensed Matter, 30 (42). p. 425201. ISSN 09538984, ESSN: 1361648X

Müller, A. and Névir, P. and Klein, R. (2018) Scale Dependent Analytical Investigation of the Dynamic State Index Concerning the QuasiGeostrophic Theory. Mathematics of Climate and Weather Forecasting, 4 (1). pp. 122. ISSN 23536438 (online)

Peschka, D. and Thomas, M. and Ahnert, T. and Münch, A. and Wagner, B. (2018) Gradient structures for flows of concentrated suspensions. SFB 1114 Preprint at WIAS 10/2018 . (Unpublished)

Swenson, D.W.H. and Prinz, J.H. and Noé, F. and Chodera, J. D. and Bolhuis, P.G. (2018) OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics. Journal of Chemical Theory and Computation, Article ASAP . ISSN 15499618, ESSN: 15499626

Swenson, D.W.H. and Prinz, J.H. and Noé, F. and Chodera, J. D. and Bolhuis, P.G. (2018) OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes. Journal of Chemical Theory and Computation, Article ASAP . ISSN 15499618, ESSN: 15499626

Heida, M. and Patterson, R. I. A and Renger, M. (2018) Topologies and measures on the space of functions of bounded variation taking values in a Banach or metric space. J. Evol. Equ. . pp. 142. ISSN Online: 14243202 Print: 14243199

Heida, M. (2018) Convergences of the squareroot approximation scheme to the Fokker–Planck operator. Mathematical Models and Methods in Applied Sciences, 28 (13). pp. 25992635. ISSN 02182025, ESSN: 17936314

Renger, M. (2018) Flux large deviations of independent and reacting particle systems, with implications for macroscopic fluctuation theory. J. Stat. Phys., 172 (5). pp. 12611326. ISSN 00224715

Fröhner, Chr. and Noé, F. (2018) Reversible interactingparticle reaction dynamics. J. Phys. Chem. B, 122 (49). pp. 1124011250.

Donati, L. and Keller, B. (2018) Girsanov reweighting for metadynamics simulations. Journal of Chemical Physics, 149 (7). 072335. ISSN 00219606

Kornhuber, R. and Youett, E. (2018) Adaptive Multilevel Monte Carlo Methods for Stochastic Variational Inequalities. SIAM Journal on Numerical Analysis, 56 (4). pp. 19872007. ISSN 00361429

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 00219606, ESSN: 10897690

del Razo, M.J. and Qian, H. and Noé, F. (2018) Grand canonical diffusioninfluenced reactions: a stochastic theory with applications to multiscale reactiondiffusion simulations. J. Chem. Phys., 149 (4). 044102. ISSN 00219606, ESSN: 10897690

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 reactiondiffusion simulations. Journal of Chemical Physics, 148 (214107). ISSN 00219606

Kebiri, O. and Neureither, L. and Hartmann, C. (2018) Singularly perturbed forwardbackward stochastic differential equations: application to the optimal control of bilinear systems. Computation, 6 (3). p. 41. ISSN 20793197 (online)

Koltai, P. and Renger, M. (2018) From Large Deviations to Semidistances of Transport and Mixing: Coherence Analysis for Finite Lagrangian Data. Journal of Nonlinear Science, 28 (5). pp. 19151957. ISSN 14321467 (online)

Renger, M. (2018) Gradient and Generic systems in the space of fluxes, applied to reacting particle systems. SFB 1114 Preprint in arXiv:1806.10461 . pp. 129. (Unpublished)

Daldrop, J.O. and Kappler, J. and Brünig, F.N. and Netz, R.R. (2018) Butane dihedral angle dynamics in water is dominated by internal friction. https://www.pnas.org/content/pnas/115/20/5169.full.pdf, 20 (115). pp. 51695174.

Koltai, P. and Lie, Han Cheng and Plonka, M. (2018) Fréchet differentiable drift dependence of PerronFrobenius and Koopman operators for nondeterministic dynamics. SFB 1114 Preprint in arXiv:1805.06719 . pp. 124. (Submitted)

Hassan, I. and Donati, L. and Stensitzki, T. and Keller, B. and Heyne, K. and Imhof, P. (2018) The Vibrational Spectrum of the hydrated AlanineLeucine Peptide in the Amide region from IR experiments and First Principles Calculation. Chem. Phys. Lett. . pp. 126. ISSN 00092614

Hartmann, C. and Schütte, Ch. and Weber, M. and Zhang, W. (2018) Importance sampling in path space for diffusion processes with slowfast variables. Probab. Theory Rel. Fields, 170 (12). pp. 177228. ISSN 01788051 (print) 14322064 (online)

Kappler, J. and Noé, F. and Netz, R.R. (2018) Cyclization dynamics of finitelength collapsed selfavoiding polymers. SFB 1114 Preprint 02/2018 . (Unpublished)

Koltai, P. and Wu, H. and Noé, F. and Schütte, Ch. (2018) Optimal datadriven estimation of generalized Markov state models for nonequilibrium dynamics. Computation, 6(1) (22). ISSN 20793197 (online)

Schulz, R. and Hansen, Y. von and Daldrop, J.O. and Kappler, J. and Noé, F. and Netz, R.R. (2018) Markov state modeling reveals competing collective hydrogen bond rearrangements in liquid water. SFB 1114 Preprint 02/2018 . (Unpublished)

Weber, M. (2018) Implications of PCCA+ in Molecular Simulation. Computation, 6 (1). ISSN 20793197 (online)

Gerber, S. and Olsson, S. and Noé, F. and Horenko, I. (2018) A scalable approach to the computation of invariant measures for highdimensional Markovian systems. Sci. Rep., 8 (1796). ISSN 20452322

Kappler, J. and Daldrop, J.O. and Brünig, F.N. and Boehle, M.D. and Netz, R.R. (2018) Memoryinduced acceleration and slowdown of barrier crossing. J. Chem. Phys., 148 (1). 014903.

Mielke, A. and Rossi, R. and Savaré, G. (2018) Global existence results for viscoplasticity at finite strain. Archive for Rational Mechanics and Analysis, 227 (1). pp. 423475. ISSN Print: 00039527; Online: 14320673

Sadeghi, M. and Weikl, T. and Noé, F. (2018) Particlebased 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: 10897690

Stensitzki, T. and Yang, Y. and Kozich, V. and Ahmed, A.A. and Kössl, F. and Kühn, O. and Heyne, K. (2018) Acceleration of a groundstate reaction by selective femtosecondinfraredlaserpulse excitation. Nature Chemistry, 10 . pp. 126131.

Hittmeir, S. and Klein, R. (2018) Asymptotics for moist deep convection I: Refined scalings and selfsustaining updrafts. Theoretical and Computational Fluid Dynamics, 32 (2). pp. 137164. ISSN 09354964 (Print) 14322250 (Online)

Hoffmann, Waldemar and Folmert, Kristin and Moschner, Johann and Xing Huang, Xing Huang and von Berlepsch, Hans and Koksch, Beate and Bowers, Michael T. and von Helden, Gert and Pagel, Kevin (2018) NFGAIL Amyloid Oligomers: The Onset of BetaSheet Formation and the Mechanism for Fibril Formation. J. Am. Chem. Soc. 2018, 140, 244−249, 140 . pp. 244249.

Klus, S. and Nüske, F. and Koltai, P. and Wu, H. and Kevrekidis, I. and Schütte, Ch. and Noé, F. (2018) Datadriven model reduction and transfer operator approximation. Journal of Nonlinear Science, 28 (1). pp. 126.

Koltai, P. and Schütte, Ch. (2018) A multiscale perturbation expansion approach for Markov state modeling of nonstationary molecular dynamics. Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 16 (4). pp. 14551485. ISSN 15403459

Kornhuber, R. and Peterseim, D. and Yserentant, H. (2018) An analysis of a class of variational multiscale methods based on subspace decomposition. Mathematics of Computation, 87 (314). pp. 27652774. ISSN 10886842 (online)

Paul, F. and Noé, F. and Weikl, T. (2018) Identifying ConformationalSelection and InducedFit Aspects in the BindingInduced Folding of PMI from Markov State Modeling of Atomistic Simulations. J. Phys. Chem. B .
2017

Daldrop, J.O. and Kowalik, B.G. and Netz, R.R. (2017) External Potential Modifies Friction of Molecular Solutes in Water. Phys. Rev. X, 7 (4). 041065.

Fischer, M. and Ulbrich, U. and Rust, H.W. (2017) A spatial and seasonal climatology of extreme precipitation returnlevels: A case study. Spatial Statistics . pp. 125. (In Press)

Heida, M. and Neukamm, S. and Varga, M. (2017) Stochastic unfolding and homogenization. SFB 1114 Preprint at WIAS 12/2017 . pp. 145. (Unpublished)

Klus, S. and Schuster, I. and Muandet, K. (2017) Eigendecompositions of Transfer Operators in Reproducing Kernel Hilbert Spaces. SFB 1114 Preprint in SciRate arXiv:1712.01572 . pp. 133. (Unpublished)

Liero, M. and Mielke, A. and Savaré, G. (2017) Optimal EntropyTransport problems and a new HellingerKantorovich distance between positive measures. Invent. math. . pp. 1149. ISSN 14321297 (online)

Netz, R.R. (2017) Fluctuationdissipation relation and stationary distribution for an exactly solvable manyparticle model far from equilibrium. SFB 1114 Preprint 12/2017 . (Unpublished)

Peters, J.H. and Gräser, C. and Klein, R. (2017) Membrane Deformation by NBAR Proteins: Extraction of membrane geometry and protein diffusion characteristics from MD simulations. SFB 1114 Preprint in arXiv:1712.02666 . pp. 112. (Unpublished)

Ritter, M. and Rosenau, M. and Oncken, O. (2017) Growing Faults in the Lab: Insights into the Scale Dependence of the Fault Zone Evolution Process. Tectonics, 36 . pp. 132.

Rudolf, M. and Rosenau, M. and Oncken, O. (2017) Interseismic deformation transients and precursory phenomena: Insights from stickslip experiments with a granular fault zone. SFB 1114 Preprint in EarthArXiv:10.17605/OSF.IO/6MWRX . pp. 126. (Unpublished)

Schuster, I. and Constantine, P.G. and Sullivan, T.J. (2017) Exact active subspace MetropolisHastings, with applications to the Lorenz96 system. SFB 1114 Preprint in arXiv:1712.02749 . pp. 110. (Unpublished)

Hartmann, C. and Richter, L. and Schütte, Ch. and Zhang, W. (2017) Variational characterization of free energy: theory and algorithms. Entropy (Special Issue), 19 (11). pp. 127. ISSN 10994300

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.

Polthier, L. (2017) Algebraic Multilevel Methods for Markov Chains. SFB 1114 Preprint in arXiv:1711.04332 . pp. 119. (Unpublished)

Quer, J. and Lie, H. (2017) Some connections between importance sampling and enhanced sampling methods in molecular dynamics. Journal of Chemical Physics . pp. 119. ISSN 00219606

Ritter, M. and Santimano, T.N. and Rosenau, M. and Leever, K. and Oncken, O. (2017) Sandbox rheometry: Coevolution of stress and strain in riedel and critical wedgeexperiments. Tectonophysics, 722 . pp. 400409.

Sbailò, L. and Noé, F. (2017) An efficient multiscale Green's Functions Reaction Dynamics scheme. J. Chem. Phys., 147 . p. 184106. ISSN 00219606, ESSN: 10897690

Taghvaei, A. and de Wiljes, J. and Mehta, P.G. and Reich, S. (2017) Kalman Filter and Its Modern Extensions for the ContinuousTime Nonlinear Filtering Problem. J. Dyn. Sys., Meas., Control, 140 (3). 030904.

Bittracher, A. and Koltai, P. and Klus, S. and Banisch, R. and Dellnitz, M. and Schütte, Ch. (2017) Transition manifolds of complex metastable systems: Theory and datadriven computation of effective dynamics. Journal of Nonlinear Science . pp. 142. ISSN 14321467 (online)

Kappler, J. and Netz, R.R. (2017) Pulse propagation at interfaces and their possible relevance for biology. Journal Club for Condensed Matter Physics .

Paul, F. and Wehmeyer, C. and Abualrous, E. T. and Wu, H. and Crabtree, M. D. and Schöneberg, J. and Clarke, J. and Freund, C. and Weikl, T. and Noé, F. (2017) Proteinpeptide association kinetics beyond the seconds timescale from atomistic simulations. Nat. Comm., 8 (1095).

Acevedo, W. and de Wiljes, J. and Reich, S. (2017) Secondorder accurate ensemble transform particle filters. SIAM J. Sci. Comput., 39 (5). A1834A1850. ISSN 10957197 (online)

Hittmeir, S. and Klein, R. and Li, J. and Titi, E. (2017) Global wellposedness for passively transported nonlinear moisture dynamics with phase changes. Nonlinearity, 30 (10). pp. 36763718. ISSN 09517715

Hittmeir, S. and Klein, R. and Müller, A. and Névir, P. (2017) The Dynamic State Index with Moisture and Phase Changes. SFB 1114 Preprint . pp. 112. (Unpublished)

Manz, C. and Kobitski, A. and Samanta, A. and Keller, B.G. and Jäschke, A. and Nienhaus, G.U. (2017) Singlemolecule FRET reveals the energy landscape of the fulllength SAMI riboswitch. Nat. Chem. Biol., 13 . pp. 11721178.

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. 59695976.

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. 118.

Corbi, F. and Funiciello, F. and Brizzi, S. and Lallemand, S. and Rosenau, M. (2017) Control of asperities size and spacing on seismic behavior of subduction megathrusts. Geophysical Research Letters, 44 (16). pp. 82278235.

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. 113.

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. 122. (Unpublished)

Mielke, A. and Patterson, R. I. A and Peletier, M. A. and Renger, M. (2017) Nonequilibrium thermodynamical principles for chemical reactions with massaction kinetics. SIAM Journal on Applied Mathematics, 77 (4). pp. 15621585. ISSN 1095712X (online)

Reinhardt, M. and Hastermann, G. and Klein, R. and Reich, S. (2017) Balanced data assimilation for highlyoscillatory mechanical systems. Journal of Nonlinear Science . pp. 123. (Submitted)

Nissen, K.M. and Ulbrich, U. (2017) Increasing frequencies and changing characteristics of heavy precipitation events threatening infrastructure in Europe under climate change. Nat. Hazards Earth Syst. Sci., 17 . pp. 11771190.

Delle Site, L. and Praprotnik, M. (2017) Molecular systems with open boundaries: Theory and Simulation. Physics Reports, 693 . pp. 156. ISSN 03701573

Donati, L. and Hartmann, C. and Keller, B.G. (2017) Girsanov reweighting for path ensembles and Markov state models. Journal of Chemical Physics, 146 (24). p. 244112. ISSN 00219606

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. 2025. ISSN 00104655

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. 25752595. ISSN Online: 15200493 Print: 00270644

Pospisil, L. and Gagliardini, P. and Sawyer, W. and Horenko, I. (2017) On a scalable nonparametric denoising of time series signals. Communications in Applied Mathematics and Computational Science . pp. 128. (In Press)

Seshaditya, A. and Ghiringhelli, L. M. and Delle Site, L. (2017) LevyLiebbased Monte Carlo study of the dimensionality behaviour of the electronic kinetic functional. Computationa, 5 (2). pp. 110. ISSN 20793197

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. 48634868.

Agarwal, A. and Clementi, C. and Delle Site, L. (2017) Path IntegralGCAdResS 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. 1303013037. ISSN 14639084

Heida, M. (2017) Stochastic homogenization of rateindependent systems and applications. Continuum Mech. Thermodyn., 29 (3). pp. 853894. ISSN 14320959 (online) 09351175 (print)

Ritschel, C. and Rust, H.W. and Ulbrich, U. (2017) Precipitation extremes on multiple time scales  BartlettLewis Rectangular Pulse Model and IntensityDurationFrequency curves. Hydrol. Earth Syst. Sci. . pp. 120. (Submitted)

Schulz, R. and Yamamoto, K. and Klossek, A. and Flesch, R. and Hönzke, S. and Rancan, F. and Vogt, A. and BlumePeytavi, U. and Hedtrich, S. and SchäferKorting, M. and Rühl, E. and Netz, R.R. (2017) Databased modeling of drug penetration relates human skin barrier function to the interplay of diffusivity and freeenergy profiles. PNAS, 114 (14). pp. 36313636. ISSN 10916490 (online)

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. 217225. ISBN 9783319523897

Gussmann, P. and Mielke, A. (2017) Linearized elasticity as Moscolimit of finite elasticity in the presence of cracks. Adv. Calc. Var. . (Submitted)

O'Kane, T.J. and Monselesan, D.P. and Risbey, J.S. and Horenko, I. and Franzke, Ch.L.E. (2017) On memory, dimension, and atmospheric teleconnection patterns. Math. Clim. Weather Forecast, 3 (1). pp. 127.

Quer, J. and Donati, L. and Keller, B.G. and Weber, M. (2017) An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates. SIAM J. Sci. Comput. . pp. 119. ISSN 10648275 (print) (In Press)

Weber, M. and Fackeldey, K. and Schütte, Ch. (2017) Setfree Markov state model building. Journal of Chemical Physics, 146 (12). p. 124133.

Flegel, F. and Heida, M. and Slowik, M. (2017) Homogenization theory for the random conductance model with degenerate ergodic weights and unboundedrange jumps. SFB 1114 Preprint in arXiv:1702.02860 . (Unpublished)

Heida, M. and Schweizer, B. (2017) Stochastic homogenization of plasticity equations. ESAIM: Control, Optimisation and Calculus of Variations . pp. 130. (Submitted)

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).

Krekeler, C. and Delle Site, L. (2017) Towards open boundary molecular dynamics simulation of ionic liquids. Physical Chemistry Chemical Physics, 6 (19). pp. 47014709. ISSN 14639076

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. 184208. ISBN 9781107118140

Heida, M. and Mielke, A. (2017) Averaging of timeperiodic dissipation potentials in rateindependent processes. Discrete and Continuous Dynamical Systems  Series S, 10 (6). pp. 13031327.

Hirt, M. and Schielicke, L. and Müller, A. and Névir, P. (2017) Statistical and dynamical analyses of atmospheric blocking with an idealized point vortex model. Tellus A . pp. 122. (Submitted)

Kies, T. and Gräser, C. (2017) On differentiability of the membranemediated mechanical interaction energy of discretecontinuum membraneparticle models. SFB 1114 Preprint in arXiv:1711.11192 . pp. 122. (Submitted)

Mielke, A. (2017) Three examples concerning the interaction of dry friction and oscillations. In: Trends on Application of Mathematics to Mechanics. Springer INdAM series. (In Press)

Mielke, A. and Mittnenzweig, M. (2017) Convergence to Equilibrium in EnergyReaction–Diffusion Systems Using VectorValued Functional Inequalities. Journal of Nonlinear Science . pp. 142. ISSN 14321467 (online)

Nüske, F. and Wu, H. and Wehmeyer, C. and Clementi, C. and Noé, F. (2017) Markov State Models from short nonEquilibrium Simulations  Analysis and Correction of Estimation Bias. J. Chem. Phys., 146 . 094104.

Olsson, Simon and Wu, H. and Paul, F. and Clementi, C. and Noé, F. (2017) Combining experimental and simulation data of molecular processes via augmented Markov models. Proc. Natl. Acad. Sci. USA, 114 . pp. 82658270.

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. 926934.

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) Lipidmediated PXBAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nat. Comm., 8 . p. 15873.

Winkelmann, S. (2017) Markov Control with Rare State Observation: Average Optimality. Markov Processes and Related Fields, 23 . pp. 134. ISSN 10242953

Wu, H. and Noé, F. (2017) Variational approach for learning Markov processes from time series data. https://arxiv.org/abs/1707.04659 .
2016

Fischer, M. and Rust, H.W. and Ulbrich, U. (2016) Seasonal Cycle in German Daily Precipitation Extremes. Meteorologische Zeitschrift . pp. 111. ISSN 09412948 (Submitted)

Winkelmann, S. and Schütte, Ch. (2016) The spatiotemporal master equation: approximation of reactiondiffusion dynamics via Markov state modeling. Journal of Chemical Physics, 145 (21). p. 214107.

Klus, S. and Schütte, Ch. (2016) Towards tensorbased methods for the numerical approximation of the PerronFrobenius and Koopman operator. Journal of Computational Dynamics . ISSN 21582491

Koltai, P. and Ciccotti, G. and Schütte, Ch. (2016) On metastability and Markov state models for nonstationary molecular dynamics. Journal of Chemical Physics, 145 (17). p. 174103.

Mielke, A. and Roubícek, T. (2016) RateIndependent elastoplasticity at finite strain and its numerical approximation. Mathematical Models and Methods in Applied Sciences, 26 (12). pp. 22032236. ISSN 17936314

Quer, J. and Weber, M. (2016) Estimating exit rate for rare event dynamical systems by extrapolation. ZIBReport . pp. 119. ISSN 21927782 (online)

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. 3746.

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 LQtype stochastic control problems. Math. Control Relat. F., 6 (3). pp. 363389. ISSN 10648275

Bonetti, E. and Rocca, E. and Rossi, R. and Thomas, M. (2016) A rateindependent gradient system in damage coupled with plasticity via structured strains. ESAIM: Proceedings and Surveys, 54 . pp. 5469.

Hartmann, C. and Schütte, Ch. and Zhang, W. (2016) Model reduction algorithms for optimal control and importance sampling of diffusions. Nonlinearity, 29 (8). pp. 22982326. ISSN 09517715

Liero, M. and Mielke, A. and Savaré, G. (2016) Optimal Transport in Competition with Reaction: The HellingerKantorovich Distance and Geodesic Curves. SIAM J. Math. Anal., 48 (2). pp. 28692911. ISSN 10957154 (online)

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 longterm lithospheric deformation. Tectonophysics, 684 . pp. 1222.

Zhang, W. and Hartmann, C. and Schütte, Ch. (2016) Effective dynamics along given reaction coordinates, and reaction rate theory. Faraday discussions, 195 . pp. 365394. ISSN 13596640

Klus, S. and Koltai, P. and Schütte, Ch. (2016) On the numerical approximation of the PerronFrobenius and Koopman operator. Journal of Computational Dynamics, 3 (1). pp. 5179. ISSN 21582491

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). E3221E3230 . ISSN 00278424

Chustagulprom, N. and Reich, S. and Reinhardt, M. (2016) A Hybrid Ensemble Transform Particle Filter for Nonlinear and Spatially Extended Dynamical Systems. SIAM/ASA Journal on Uncertainty Quantification, 4 (1). pp. 592608. ISSN 21662525

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 NonEquilibrium Thermodynamics, 41 (2).

Klein, R. and Benacchio, T. (2016) A doubly blended model for multiscale atmospheric dynamics. Journal of the Atmospheric Sciences, 73 . pp. 11791186. ISSN Online: 15200469 Print: 00224928

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) GrandCanonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and Application. Computer Physics Communications (206). pp. 2634.

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. 419443. ISSN Print: 02182025 Online: 17936314

Klus, S. and Gelß, P. and Peitz, S. and Schütte, Ch. (2016) Tensorbased dynamic mode decomposition. SIAM Journal on Scientific Computing . ISSN ISSN 10648275 (print); 10957197 (electronic) (Submitted)

Kornhuber, R. and Yserentant, H. (2016) Numerical Homogenization of Elliptic Multiscale Problems by Subspace Decomposition. Multiscale Model. Simul., 14 (3). pp. 10171036. ISSN print: 15403459; online: 15403467

Lemke, O. and Keller, B.G. (2016) Densitybased cluster algorithms for the identification of core sets. Journal of Chemical Physics, 145 (164104).

Mielke, A. and Rossi, R. and Savaré, G. (2016) BalancedViscosity solutions for multirate systems. Journal of Physics: Conference Series, 727 . pp. 127.

Nüske, F. and Schneider, R. and Vitalini, F. and Noé, F. (2016) Variational Tensor Approach for Approximating the RareEvent Kinetics of Macromolecular Systems. J. Chem. Phys., 144 (5). 054105.

Paul, F. and Weikl, T. (2016) How to Distinguish Conformational Selection and Induced Fit Based on Chemical Relaxation Rates. PLOS Computational Biology .

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.

Pipping, E. and Kornhuber, R. and Rosenau, M. and Oncken, O. (2016) On the efficient and reliable numerical solution of rateandstate friction problems. Geophysical Journal International, 204 (3). pp. 18581866. ISSN Online: 1365246X Print: 0956540X

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. 582590.
2015

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 00219606

TrendelkampSchroer, 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.

Kappler, J. and Netz, R.R. (2015) Multiple surface wave solutions on linear viscoelastic media. EPL, 112 (1). p. 19002.

Schuster, I. and Strathmann, H. and Paige, B. and Sejdinovic, Dino (2015) Kernel Sequential Monte Carlo. SFB 1114 Preprint in arXiv:1510.03105 . (Submitted)

Agarwal, A. and Delle Site, L. (2015) Path Integral Molecular Dynamics within the Grand Canonicallike Adaptive Resolution Technique: Simulation of Liquid Water. Journal of Chemical Physics, 143 (9). ISSN 00219606

Bittracher, Andreas and Hartmann, C. and Junge, O. and Koltai, Péter (2015) Pseudo generators for underresolved molecular dynamics. The European Physical Journal Special Topics, 224 (12). pp. 24632490. ISSN 19516355

Hartmann, C. and Delle Site, L. (2015) Scale Bridging in Molecular Simulation. The European Physical Journal Special Topics, 224 (12). pp. 21732176. ISSN 19516355

Klein, R. (2015) Comments on "Open Boundary Molecular Dynamics " by R. DelgadoBuscalioni, J. Sablic, and M. Praprotnik. The European Physical Journal, 224 (12). pp. 25092510. ISSN Online: 19516401 Print: 19516355

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. 25032504. ISSN Online: 19516401 Print: 19516355

Agarwal, A. and Zhu, J. and Wang, H. and Hartmann, C. and Delle Site, L. (2015) Molecular dynamics in a Grand Ensemble: BergmannLebowitz model and adaptive resolution simulation. New Journal of Physics, 17 (083042). ISSN 13672630

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).

Horenko, I. and Gerber, S. (2015) Improving clustering by imposing network information. Science Advances, 1 (7). ISSN 23752548

Kim, W.K. and Netz, R.R. (2015) The mean shape of transition and firstpassage paths. J. Chem. Phys., 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. 24972499.

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: 09307575, Online: 14320894

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 polyalanine and possible relation to the debate on slaved versus slaving water. J. Chem. Phys., 142 (215104).

Scherer, M. K. and TrendelkampSchroer, B. and Paul, F. and PérezHernández, 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. 55255542.

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. 45654574.

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.
2014

Wu, H. and Mey, A.S.J.S. and Rosta, E. and Noé, F. (2014) Statistically optimal analysis of statediscretized trajectory data from multiple thermodynamic states. J. Chem. Phys., 141 (21). p. 214106.

Mey, A.S.J.S. and Wu, H. and Noé, F. (2014) xTRAM: Estimating equilibrium expectations from timecorrelated simulation data at multiple thermodynamic states. Phys. Rev. X, 4 (4). 041018.

Hartmann, C. and Latorre, J.C. and Pavliotis, G. A. and Zhang, W. (2014) Optimal control of multiscale systems using reducedorder models. J. Computational Dynamics, 1 (2). pp. 279306. ISSN 21582505

Lie, Han Cheng and Schütte, Ch. and Hartmann, C. (2014) Martingalebased gradient descent algorithm for estimating free energy values of diffusions. SIAM J. Sci. Comput. . ISSN 10648275 (Submitted)