# Publications for: All SFB 1114 publications

**141**.

## 2018

Kebiri, O. and Neureither, L. and Hartmann, C.
(2018)
*Adaptive importance sampling with forward-backward stochastic differential equations.*
Proceedings of the Institut Henri Poincaré
.
(Submitted)

Kebiri, O. and Neureither, L. and Hartmann, C.
(2018)
*Singularly perturbed forward-backward stochastic differential equations: application to the optimal control of bilinear systems.*
Computation
.
(Submitted)

Neureither, L. and Hartmann, C.
(2018)
*Time scales and exponential trends to equilibrium: Gaussian model problems.*
Proceedings of the Institut Henri Poincaré
.
(Submitted)

Patterson, R. I. A and Renger, M.
(2018)
*Large deviations of reaction fluxes.*
SFB 1114 Preprint in arXiv:1802.02512
.
pp. 1-21.
(Unpublished)

Weber, M.
(2018)
*Implications of PCCA+ in Molecular Simulation.*
Computation, 6
(1).
ISSN 2079-3197 (online)

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
.
ISSN 1088-6842 (online)

Gerber, S. and Olsson, S. and Noé, F. and Horenko, I.
(2018)
*A scalable approach to the computation of invariant measures for high-dimensional Markovian systems.*
Sci. Rep., 8
(1796).
ISSN 2045-2322

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

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.

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 ground-state reaction by selective femtosecond-infrared-laser-pulse excitation.*
Nature Chemistry, 10
.
pp. 126-131.

Klus, S. and Nüske, F. and Koltai, P. and Wu, H. and Kevrekidis, I. and Schütte, Ch. and Noé, F.
(2018)
*Data-driven model reduction and transfer operator approximation.*
Journal of Nonlinear Science, 28
(1).
pp. 1-26.

Koltai, Péter and Wu, H. and Noé, F. and Schütte, Ch.
(2018)
*Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics.*
Computing
.
(Submitted)

## 2017

Fackeldey, K. and Koltai, P. and Névir, P. and Rust, H.W. and Schild, A and Weber, M.
(2017)
*From Metastable to Coherent Sets – time-discretization schemes.*
SFB 1114 Preprint
.
pp. 1-13.
(Unpublished)

Fischer, M. and Ulbrich, U. and Rust, H.W.
(2017)
*A spatial and seasonal climatology of extreme precipitation return-levels: A case study.*
Spatial Statistics
.
pp. 1-25.
(In Press)

Hassan, I. and Donati, L. and Stensitzki, T. and Keller, B. and Heyne, K. and Imhof, P.
(2017)
*The Vibrational Spectrum of the hydrated Alanine-Leucine Peptide in the Amide region from IR experiments and First Principles Calculation.*
SFB 1114 Preprint
.
pp. 1-26.
(Submitted)

Heida, M. and Kornhuber, R. and Podlesny, J.
(2017)
*Fractal homogenization of multiscale interface problems.*
SFB 1114 Preprint in arXiv
.
pp. 1-17.
(Submitted)

Heida, M. and Neukamm, S. and Varga, M.
(2017)
*Stochastic unfolding and homogenization.*
SFB 1114 Preprint at WIAS 12/2017
.
pp. 1-45.
(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. 1-33.
(Unpublished)

Liero, M. and Mielke, A. and Savaré, G.
(2017)
*Optimal Entropy-Transport problems and a new Hellinger-Kantorovich distance between positive measures.*
Invent. math.
.
pp. 1-149.
ISSN 1432-1297 (online)

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)

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. 1-32.

Rosenau, M. and Horenko, I. and Corbi, F. and Rudolf, M. and Kornhuber, R. and Oncken, O.
(2017)
*Synchronization of great subduction megathrust earthquakes: Insights from scale model analysis.*
SFB 1114 Preprint in EarthArXiv
.
pp. 1-35.
(Unpublished)

Rudolf, M. and Rosenau, M. and Oncken, O.
(2017)
*Interseismic deformation transients and precursory phenomena: Insights from stick-slip experiments with a granular fault zone.*
SFB 1114 Preprint in EarthArXiv:10.17605/OSF.IO/6MWRX
.
pp. 1-26.
(Unpublished)

Schuster, I. and Constantine, P.G. and Sullivan, T.J.
(2017)
*Exact active subspace Metropolis-Hastings, with applications to the Lorenz-96 system.*
SFB 1114 Preprint in arXiv:1712.02749
.
pp. 1-10.
(Unpublished)

Vater, S. and Klein, R.
(2017)
*A Semi-Implicit Multiscale Scheme for Shallow Water Flows at
Low Froude Number.*
Communications in Applied Mathematics & Computational Science
.
pp. 1-27.
ISSN 1559-3940
(Submitted)

Hartmann, C. and Richter, L. and Schütte, Ch. and Zhang, W.
(2017)
*Variational characterization of free energy: theory and algorithms.*
Entropy (Special Issue), 19
(11).
pp. 1-27.
ISSN 1099-4300

Polthier, L.
(2017)
*Algebraic Multilevel Methods for Markov Chains.*
SFB 1114 Preprint
.
pp. 1-19.
(Submitted)

Quer, J. and Lie, H.
(2017)
*Some connections between importance sampling and enhanced sampling methods in molecular dynamics.*
Journal of Chemical Physics
.
pp. 1-19.
ISSN 0021-9606

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 wedge-experiments.*
Tectonophysics, 722
.
pp. 400-409.

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

Banisch, R. and Trstanova, Z. and Bittracher, A. and Klus, S. and Koltai, P.
(2017)
*Diffusion maps tailored to arbitrary non-degenerate Ito processes.*
SFB 1114 Preprint in arXiv:1710.03484
.
pp. 1-24.
(Unpublished)

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 data-driven computation of effective dynamics.*
Journal of Nonlinear Science
.
pp. 1-42.
ISSN 1432-1467 (online)

Hittmeir, S. and Klein, R.
(2017)
*Asymptotics for moist deep convection I: Refined scalings and self-sustaining updrafts.*
Theoretical and Computational Fluid Dynamics
.
pp. 1-28.
ISSN 0935-4964 (Print) 1432-2250 (Online)

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).

von Larcher, T. and Klein, R.
(2017)
*On identification of self-similar characteristics using the Tensor Train decomposition method with application to channel turbulence flow.*
Theoretical and Computational Fluid Dynamics
.
pp. 1-22.
ISSN 0935-4964 (Print) 1432-2250 (Online)
(Submitted)

Acevedo, W. and de Wiljes, J. and Reich, S.
(2017)
*Second-order accurate ensemble transform particle filters.*
SIAM J. Sci. Comput., 39
(5).
A1834-A1850.
ISSN 1095-7197 (online)

Hittmeir, S. and Klein, R. and Li, J. and Titi, E.
(2017)
*Global well-posedness for passively transported nonlinear moisture dynamics with phase changes.*
Nonlinearity, 30
(10).
pp. 3676-3718.
ISSN 0951-7715

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. 1-12.
(Unpublished)

Koltai, P. and Renger, M.
(2017)
*From large deviations to transport semidistances: coherence analysis for finite Lagrangian data.*
SFB 1114 Preprint in arXiv:1709.02352
.
pp. 1-34.
(Unpublished)

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.

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. 8227-8235.

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.

Donati, L. and Heida, M. and Weber, M. and Keller, B.
(2017)
*Estimation of the infinitesimal generator by square-root approximation.*
SFB 1114 Preprint im WIAS
(2416).
pp. 1-34.
(Unpublished)

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)

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)

Müller, A. and Névir, P. and Klein, R.
(2017)
*Scale Dependent Analytical Investigation of the Dynamic State Index Concerning the Quasi-Geostrophic Theory.*
SFB 1114 Preprint
.
pp. 1-38.
(Unpublished)

Reinhardt, M. and Hastermann, G. and Klein, R. and Reich, S.
(2017)
*Balanced data assimilation for highly-oscillatory mechanical systems.*
Journal of Nonlinear Science
.
pp. 1-23.
(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. 1177-1190.

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 0021-9606

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

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

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. 1-28.
(In Press)

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.

Heida, M.
(2017)
*On Convergences of square-root approximation scheme to Fokker--Planck operator.*
SFB 1114 Preprint at WIAS 05/2017
.
pp. 1-30.
(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

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)

Ritschel, C. and Rust, H.W. and Ulbrich, U.
(2017)
*Precipitation extremes on multiple time scales -- Bartlett-Lewis Rectangular Pulse Model and Intensity-Duration-Frequency curves.*
Hydrol. Earth Syst. Sci.
.
pp. 1-20.
(Submitted)

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. 217-225.
ISBN 978-3-319-52389-7

Gussmann, P. and Mielke, A.
(2017)
*Linearized elasticity as Mosco-limit 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. 1-27.

Pipping, E.
(2017)
*Existence of long-time solutions to dynamic problems of viscoelasticity with rate-and-state friction.*
SFB 1114 Preprint
.
(Submitted)

Quer, J. and Donati, L. and Keller, B.G. and Weber, M.
(2017)
*An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates.*
SIAM J. Sci. Comput.
.
pp. 1-19.
ISSN 1064-8275 (print)
(In Press)

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

Flegel, F. and Heida, M. and Slowik, M.
(2017)
*Homogenization theory for the random conductance model with degenerate ergodic weights and unbounded-range 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. 1-30.
(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).

Renger, M.
(2017)
*Flux large deviations of independent and reacting particle systems, with implications for macroscopic fluctuation theory.*
SFB 1114 Preprint in WIAS Preprint No. 2375
.
pp. 1-33.
(Submitted)

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

Hartmann, C. and Schütte, Ch. and Weber, M. and Zhang, W.
(2017)
*Importance sampling in path space for diffusion processes with
slow-fast variables.*
Probab. Theory Rel. Fields
.
pp. 1-52.
ISSN 1432-2064 (online)

Heida, M. and Nesenenko, S.
(2017)
*Stochastic homogenization of rate-dependent models of monotone type in plasticity.*
SFB 1114 Preprint in arXiv:1701.03505
.
pp. 1-26.
(Unpublished)

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

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.

Hirt, M. and Schielicke, L. and Müller, A. and Névir, P.
(2017)
*Statistical and dynamical analyses of atmospheric blocking with an idealized point vortex model.*
Tellus A
.
pp. 1-22.
(Submitted)

Kappler, J. and Daldrop, J.O. and Brünig, F.N. and Boehle, M.D. and Netz, R.R.
(2017)
*Memory-induced acceleration and slowdown of barrier crossing.*
J. Chem. Phys., 148
(1).
014903.
(In Press)

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 Energy-Reaction–Diffusion Systems Using Vector-Valued Functional Inequalities.*
Journal of Nonlinear Science
.
pp. 1-42.
ISSN 1432-1467 (online)

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

Olsson, Simon and Wu, H. and Paul, F. and Clementi, C. and Noé, F.
(2017)
*Combining experimental and simulation data of molecular processes via augmented Markov models.*
Proc. Natl. Acad. Sci. USA, 114
.
pp. 8265-8270.

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.

Sbailò, L. and Noé, F.
(2017)
*An efficient multi-scale Green's Functions Reaction Dynamics scheme.*
J. Chem. Phys., 147
.
p. 184106.

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.

Winkelmann, S.
(2017)
*Markov Control with Rare State Observation: Average Optimality.*
Markov Processes and Related Fields, 23
.
pp. 1-34.
ISSN 1024-2953

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

von Larcher, T. and Klein, R.
(2017)
*Approximating turbulent and non-turbulent events with the Tensor Train decomposition method.*
In:
Turbulence in the Complex Conditions.
Springer.
(Submitted)

## 2016

Fischer, M. and Rust, H.W. and Ulbrich, U.
(2016)
*Seasonal Cycle in German Daily Precipitation Extremes.*
Meteorologische Zeitschrift
.
pp. 1-11.
ISSN 0941-2948
(Submitted)

Heida, M. and Patterson, R. I. A and Renger, M.
(2016)
*The space of bounded variation with infinite-dimensional codomain.*
SFB 1114 Preprint in WIAS Preprint No. 2353
.
pp. 1-31.
(Submitted)

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.

Babushkina, E. and Kornhuber, R.
(2016)
*Adaptive multilevel Monte Carlo methods for stochastic variational inequalities.*
SFB 1114 Preprint in arXiv:1611.06012
.
(Submitted)

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

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

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

Quer, J. and Weber, M.
(2016)
*Estimating exit rate for rare event dynamical systems by extrapolation.*
ZIB-Report
.
pp. 1-19.
ISSN 2192-7782 (online)

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.

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

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.

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

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)

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, 684
.
pp. 12-22.

Zhang, W. and Hartmann, C. and Schütte, Ch.
(2016)
*Effective dynamics along given reaction coordinates, and reaction rate theory.*
Faraday discussions, 195
.
pp. 365-394.
ISSN 1359-6640

Klus, S. and Koltai, P. 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

Wu, H. and Paul, F. and Wehmeyer, C. and Noé, F.
(2016)
*Multiensemble Markov models of molecular thermodynamics and kinetics.*
Proceedings of the National Academy of Sciences, 113
(23).
E3221-E3230 .
ISSN 0027-8424

Chustagulprom, N. and Reich, S. and Reinhardt, M.
(2016)
*A Hybrid Ensemble Transform Particle Filter for Nonlinear and Spatially Extended Dynamical Systems.*
SIAM/ASA Journal on Uncertainty Quantification, 4
(1).
pp. 592-608.
ISSN 2166-2525

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).

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

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.

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

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).

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.

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

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

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

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.

## 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 0021-9606

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.

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
Canonical-like Adaptive Resolution Technique: Simulation of
Liquid Water.*
Journal of Chemical Physics, 143
(9).
ISSN 0021-9606

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

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 2375-2548

Kim, W.K. and Netz, R.R.
(2015)
*The mean shape of transition and first-passage 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. 2497-2499.

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.*
J. Chem. Phys., 142
(215104).

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.

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 state-discretized trajectory data from multiple thermodynamic states.*
J. Chem. Phys., 141
(21).
p. 214106.

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

Hartmann, C. and Latorre, J.C. and Pavliotis, G. A. and Zhang, W.
(2014)
*Optimal control of multiscale systems using reduced-order models.*
J. Computational Dynamics, 1
(2).
pp. 279-306.
ISSN 2158-2505

Lie, Han Cheng and Schütte, Ch. and Hartmann, C.
(2014)
*Martingale-based gradient descent algorithm for estimating free energy values of diffusions.*
SIAM J. Sci. Comput.
.
ISSN 1064-8275
(Submitted)