# Publications for: All SFB 1114 publications

**191**.

## 2019

Delle Site, L. and Klein, R.
(2019)
*Liouville-type equations for the n-particle distribution functions of
an open system.*
Physical Review Research
.
(Submitted)

Heida, M. and Neukamm, S. and Varga, M.
(2019)
*Stochastic homogenization of Λ-convex gradient flows.*
SFB 1114 Preprint in arXiv:1905.02562
.
pp. 1-28.
(Unpublished)

Nüsken, N. and Reich, S. and Rozdeba, P.J.
(2019)
*State and parameter estimation from observed signal increments.*
Entropy, 21
(5).
-505.
ISSN 1099-4300

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. 1-25.
(Unpublished)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. 1-43.
(Unpublished)

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

Miron, P. and Beron-Vera, F.J. and Olascoaga, M.J. and Koltai, P.
(2019)
*Markov-chain-inspired search for MH370.*
Chaos: An Interdisciplinary Journal of Nonlinear Science, 29
(4).
ISSN 1054-1500 (print); 1089-7682 (online)

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

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. 3646-3661.
ISSN 2169-9356

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

Keller, B.G. and Aleksic, S. and Donati, L.
(2019)
*Markov State Models in drug design.*
In:
Biomolecular Simulations in Structure-based Drug Discovery.
Methods and Principles in Medicinal Chemistry, 75
.
Wiley-Interscience, Weinheim, pp. 67-86.
ISBN 978-3-527-34265-5

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
.
(Submitted)

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

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 finite-volume dynamical core for the IFS.*
Geosci. Model Dev., 12
(2).
pp. 651-676.
ISSN 1991-959X, ESSN: 1991-9603

von Larcher, T. and Klein, R.
(2019)
*On identification of self-similar characteristics using the Tensor Train decomposition method with application to channel turbulence flow.*
Theoretical and Computational Fluid Dynamics, 33
.
pp. 1-19.
ISSN 0935-4964 (Print) 1432-2250 (Online)

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)

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

Fackeldey, K. and Koltai, P. and Névir, P. and Rust, H.W. and Schild, A and Weber, M.
(2019)
*From Metastable to Coherent Sets – time-discretization schemes.*
Chaos: An Interdisciplinary Journal of Nonlinear Science, 29
(1).
012101.
ISSN 1054-1500 (print); 1089-7682 (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 0021-9606, ESSN: 1089-7690

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.

Benacchio, T. and Klein, R.
(2019)
*A semi-implicit compressible model for atmospheric flows with seamless access to soundproof and hydrostatic dynamics.*
Monthly Weather Review
.
pp. 1-49.
ISSN Online: 1520-0493; Print: 0027-0644
(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 1477-870X

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. 1-22.
ISSN Print: 0006-8314; Online: 1573-1472

## 2018

Noé, F. and Wu, H.
(2018)
*Boltzmann Generators - Sampling Equilibrium States of Many-Body Systems with Deep Learning.*
SFB 1114 Preprint in arXiv:1812.01729
.
pp. 1-17.
(Unpublished)

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

Vater, S. and Klein, R.
(2018)
*A Semi-Implicit Multiscale Scheme for Shallow Water Flows at
Low Froude Number.*
Communications in Applied Mathematics & Computational Science, 13
(2).
pp. 303-336.
ISSN 1559-3940

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

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

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

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)

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 1549-9618, ESSN: 15-49-9626

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 1549-9618, ESSN: 15-49-9626

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. 1-42.
ISSN Online: 1424-3202 Print: 1424-3199

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

Renger, M.
(2018)
*Flux large deviations of independent and reacting particle systems, with implications for macroscopic fluctuation theory.*
J. Stat. Phys., 172
(5).
pp. 1261-1326.
ISSN 0022-4715

Fröhner, Chr. and Noé, F.
(2018)
*Reversible interacting-particle reaction dynamics.*
J. Phys. Chem. B, 122
(49).
pp. 11240-11250.

Donati, L. and Keller, B.
(2018)
*Girsanov reweighting for metadynamics simulations.*
Journal of Chemical Physics, 149
(7).
072335.
ISSN 0021-9606

Kornhuber, R. and Youett, E.
(2018)
*Adaptive Multilevel Monte Carlo Methods for Stochastic Variational Inequalities.*
SIAM Journal on Numerical Analysis, 56
(4).
pp. 1987-2007.
ISSN 0036-1429

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

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

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)

Renger, M.
(2018)
*Gradient and Generic systems in the space of fluxes, applied to reacting particle systems.*
SFB 1114 Preprint in arXiv:1806.10461
.
pp. 1-29.
(Unpublished)

Koltai, P. and Lie, Han Cheng and Plonka, M.
(2018)
*Fréchet differentiable drift dependence of Perron--Frobenius and Koopman operators for non-deterministic dynamics.*
SFB 1114 Preprint in arXiv:1805.06719
.
pp. 1-24.
(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 Alanine-Leucine Peptide in the Amide region from IR experiments and First Principles Calculation.*
Chem. Phys. Lett.
.
pp. 1-26.
ISSN 0009-2614

Kappler, J. and Noé, F. and Netz, R.R.
(2018)
*Cyclization dynamics of finite-length collapsed self-avoiding polymers.*
SFB 1114 Preprint 02/2018
.
(Unpublished)

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)

Koltai, P. and Wu, H. and Noé, F. and Schütte, Ch.
(2018)
*Optimal data-driven estimation of generalized Markov state models for non-equilibrium dynamics.*
Computation, 6(1)
(22).
ISSN 2079-3197 (online)

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)

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 2079-3197 (online)

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.*
SFB 1114 Preprint 01/2018
.
pp. 1-6.
(Unpublished)

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

Kappler, J. and Daldrop, J.O. and Brünig, F.N. and Boehle, M.D. and Netz, R.R.
(2018)
*Memory-induced 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. 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.

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

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.

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)

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.

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. 2765-2774.
ISSN 1088-6842 (online)

Paul, F. and Noé, F. and Weikl, T.
(2018)
*Identifying Conformational-Selection and Induced-Fit Aspects in the Binding-Induced 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 return-levels: A case study.*
Spatial Statistics
.
pp. 1-25.
(In Press)

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)

Netz, R.R.
(2017)
*Fluctuation-dissipation relation and stationary distribution for an exactly solvable many-particle model far from equilibrium.*
SFB 1114 Preprint 12/2017
.
(Unpublished)

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.

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)

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

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. 1-19.
(Unpublished)

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.

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

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)

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)
*Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations.*
Nat. Comm., 8
(1095).

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)

Manz, C. and Kobitski, A. and Samanta, A. and Keller, B.G. and Jäschke, A. and Nienhaus, G.U.
(2017)
*Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch.*
Nat. Chem. Biol., 13
.
pp. 1172-1178.

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.

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.

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)

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.

Delle Site, L. and Praprotnik, M.
(2017)
*Molecular systems with open boundaries: Theory and Simulation.*
Physics Reports, 693
.
pp. 1-56.
ISSN 0370-1573

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.

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)

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)

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).

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, 170
(1-2).
pp. 177-228.
ISSN 1432-2064 (online)

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)

Kies, T. and Gräser, C.
(2017)
*On differentiability of the membrane-mediated mechanical interaction energy of discrete-continuum membrane-particle models.*
SFB 1114 Preprint in arXiv:1711.11192
.
pp. 1-22.
(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 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.

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)

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.

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.*
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 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.

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
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)