# Publications for: All SFB 1114 publications

**232**.

## 2020

Richter, Lorenz and Boustati, Ayman and Nüsken, Nikolas and Ruiz, Francisco J. R. and Akyildiz, Ömer Deniz
(2020)
*VarGrad: A Low-Variance Gradient Estimator for Variational Inference.*
Advances in Neural Information Processing Systems 2020
.
pp. 1-25.
(Submitted)

Hastermann, G. and Reinhardt, M. and Klein, R. and Reich, S.
(2020)
*Balanced data assimilation for highly-oscillatory mechanical systems.*
Communications in Applied Mathematics & Computational Science
.
pp. 1-36.
(Submitted)

Frömberg, Daniela and Höfling, Felix
(2020)
*Generalized master equation for first-passage problems in
partitioned spaces.*
Journal of Physics A
.
pp. 1-23.
(Submitted)

Hittmeir, S. and Klein, R. and Müller, A. and Névir, P.
(2020)
*The Dynamic State Index with Moisture and Phase Changes.*
Mathematics of Climate and Weather Forecasting 2020
.
pp. 1-12.
(Submitted)

Delle Site, Luigi and Klein, Rupert and Höfling, Felix and Viand, Roya Ebrahimi
(2020)
*Theory and simulation of open systems out of equilibrium.*
J. Chem. Phys. (2020);, 153
(10).
pp. 1-7.
ISSN 101102

Müller, Annette and Niedrich, Benjamin and Névir, Peter
(2020)
*Three-dimensional potential vorticity structures for extreme precipitation events on the convective scale.*
Tellus A: Dynamic Meteorology and Oceanography, 72
(1).
pp. 1-20.
ISSN (Print) (Online) Journal homepage: https://www.tandfonline.com/loi/zela20

Delle Site, L. and Klein, R.
(2020)
*Liouville-type equations for the n-particle distribution functions of
an open system.*
Journal of Mathematical Physics, 61
(8).

Froyland, Gary and Koltai, Péter and Stahn, Martin
(2020)
*Computation and Optimal Perturbation of Finite-Time Coherent Sets for Aperiodic Flows Without Trajectory Integration.*
SIAM J. APPLIED DYNAMICAL SYSTEMS, 19
(3).
pp. 1659-1700.

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. 1-15.

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. 1-11.

Höfling, F. and Dietrich, S.
(2020)
*Finite-size corrections for the static structure factor of a liquid slab with open boundaries.*
Journal of Chemical Physics, 153
(5).
pp. 1-13.

Hittmeir, Sabine and Klein, Rupert and Li, Jinkai and Titi, Edriss
(2020)
*Global well-posedness for the primitive equations coupled to nonlinear moisture dynamics with phase changes.*
Nonlinearity, 33
(7).
pp. 3206-3236.

Nüsken, N. and Richter, L.
(2020)
*Solving high-dimensional Hamilton-Jacobi-Bellman PDEs using
neural networks: perspectives from the theory of controlled diffusions and measures on path space.*
SFB 1114 Preprint in arXiv
.
pp. 1-40.
(Submitted)

Bittracher, Andreas and Schütte, Christof
(2020)
*A weak characterization of slow variables in stochastic dynamical systems.*
SFB 1114 Preprint in arXive
.
pp. 1-20.
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. 1-20.
(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. 1-11.
(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. 1-10.
ISSN 1944-8007

Heida, M. and Kornhuber, R. and Podlesny, J.
(2020)
*Fractal homogenization of multiscale interface problems.*
Multiscale Modeling & Simulation, 18
(1).
pp. 294-314.
ISSN 1540-3459

Banisch, R. and Trstanova, Z. and Bittracher, A. and Klus, S. and Koltai, P.
(2020)
*Diffusion maps tailored to arbitrary non-degenerate Ito processes.*
Applied and computational harmonic analysis, 48
(1).
pp. 242-265.
ISSN 1063-5203, 1096-603X

Kaiser, A. and Faranda, D. and Krumscheid, S. and Belušić, D. and Vercauteren, N.
(2020)
*Detecting regime transitions of the nocturnal and Polar near-surface temperature inversion.*
Journal of the Atmospheric Sciences
.
ISSN 0022-4928; eISSN: 1520-0469

Kies, T. and Gräser, C. and Delle Site, L. and Kornhuber, R.
(2020)
*Free energy computation of particles with membrane-mediated interactions via Langevin dynamics.*
arXiv:2009.14713
.
pp. 1-20.
(Submitted)

Mielke, A. and Roubícek, T.
(2020)
*Thermoviscoelasticity in Kelvin-Voigt
rheology at large strains.*
Arch. Rational Mech. Anal., 238
.
pp. 1-45.

## 2019

Müller, Annette and Névir, Peter
(2019)
*Using the concept of the Dynamic State Index for a scale-dependent analysis of atmospheric blocking.*
Meteorologische Zeitschrift, 28
(6).
pp. 487-498.

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. 1-29.
(Unpublished)

Hartmann, C. and Neureither, L. and Sharma, U.
(2019)
*Coarse-graining of non-reversible stochastic differential equations: quantitative results and connections to averaging.*
SIAM J. Math. Anal.
.
pp. 1-39.
(Submitted)

Leung, T.Y. and Leutbecher, M. and Reich, S. and Shepherd, Th.G.
(2019)
*Atmospheric Predictability: Revisiting the Inherent Finite-Time Barrier.*
Journal of the Atmospheric Sciences, 76
(12).
pp. 3883-3892.
ISSN Online: 1520-0469 Print: 0022-4928

Koltai, P. and Lie, Han Cheng and Plonka, M.
(2019)
*Fréchet differentiable drift dependence of Perron--Frobenius and Koopman operators for non-deterministic dynamics.*
https://iopscience.iop.org/article/10.1088/1361-6544/ab1f2a, 32
(11).
pp. 4232-4257.

Kappler, Julian and Hinrichsen, Victor B. and Netz, Roland R.
(2019)
*Non-Markovian barrier crossing with two-time-scale memory is dominated by the faster memory component.*
The European Physical Journal E, 42
(119).
ISSN 1292-8941

Noé, F. and Olsson, S. and Köhler, J. and Wu, H.
(2019)
*Boltzmann Generators: Sampling Equilibrium States of Many-Body 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. 1-32.
ISSN 1385-0172; ESSN: 1572-9656

Moschner, Johann and Stulberg, Valentina and Fernandes, Rita and Huhmann, Susanne and Leppkes, Jakob and Koksch, Beate
(2019)
*Approaches to Obtaining Fluorinated α-Amino Acids.*
Chem. Rev. 2019, 119
(18).
pp. 10718-10801.

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, 147
(11).
pp. 4221-4240.
ISSN Online: 1520-0493; Print: 0027-0644

Pipping, E.
(2019)
*Existence of long-time solutions to dynamic problems of viscoelasticity with rate-and-state friction.*
ZAMM - Journal of Applied Mathematics and Mechanics
.
ISSN 1521-4001 (online)

Hittmeir, Sabine and Klein, Rupert and Li, Jinkai and Titi, Edriss
(2019)
*"Global well-posedness for the primitive equations coupled to nonlinear moisture dynamics with phase changes" by Hittmeir, Sabine; Klein, Rupert; Li, Jinkai; Titi, Edriss.*
Analysis of PDEs
.
pp. 1-28.
ISSN 1907.11199
(Submitted)

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

Kebiri, O. and Neureither, L. and Hartmann, C.
(2019)
*Adaptive importance sampling with forward-backward stochastic differential equations.*
In:
Stochastic Dynamics Out of Equilibrium. IHPStochDyn 2017.
Springer Proceedings in Mathematics & Statistics, 282
.
Springer, pp. 265-281.
ISBN 978-3-030-15095-2

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. 391-410.
ISBN 978-3-030-15095-2

Renger, M. and Zimmer, J.
(2019)
*Orthogonality of fluxes in general nonlinear reaction networks.*
SFB1114 Preprint 07/2019 in WIAS No. 2609
.
pp. 1-12.
(Unpublished)

Hartmann, C. and Kebiri, O. and Neureither, L. and Richter, L.
(2019)
*Variational approach to rare event simulation using least-squares regression.*
Chaos, 29
(6).
063107.
ISSN 1054-1500 (print); 1089-7682 (online)

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)

Gräser, C. and Kies, T.
(2019)
*Discretization error estimates for penalty formulations of a linearized Canham-Helfrich-type energy.*
IMA Journal of Numerical Analysis, 39
(2).
pp. 626-649.
ISSN 0272-4979

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. 1214-1261.
ISSN 0022-4715; ESSN: 1572-9613

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

Kappler, Julian and Noe, Frank and Netz, Roland R.
(2019)
*Cyclization and Relaxation Dynamics of Finite-Length Collapsed Self-Avoiding 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 mean-field 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 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

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. 1303-1311.
ISSN 0094-8276; ESSN: 1944-8007

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.

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. 294-308.
ISSN 1549-9596, ESSN: 1549-960X

Daldrop, Jan O. and Netz, Roland R.
(2019)
*Mass-Dependent Solvent Friction of a
Hydrophobic Molecule.*
J. Phys. Chem. B
(123).
pp. 8123-8130.

Kieninge, Stefanie and Donati, Luca and Keller, Bettina
(2019)
*Dynamical reweighting methods for Markov models.*
Current Opinion in Structural Biology, 61
.
pp. 124-131.
ISSN 0959-440X

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

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

von Larcher, T. and Klein, R.
(2019)
*Approximating turbulent and non-turbulent events with the Tensor Train decomposition method.*
In:
Turbulent Cascades II.
Springer.
ISBN Print: 978-3-030-12546-2 Electronic: 978-3-030-12547-9

## 2018

Kies, Tobias
(2018)
*Gradient Methods for Membrane-Mediated Particle Interactions.*
PhD Thesis
.
pp. 1-147.

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

Bittracher, Andreas and Banisch, Ralf and Schütte, Christof
(2018)
*Data-driven 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 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

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, 6
(3).
p. 41.
ISSN 2079-3197 (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. 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)

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. 5169-5174.

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

Hartmann, C. and Schütte, Ch. and Weber, M. and Zhang, W.
(2018)
*Importance sampling in path space for diffusion processes with
slow-fast variables.*
Probab. Theory Rel. Fields, 170
(1-2).
pp. 177-228.
ISSN 0178-8051 (print) 1432-2064 (online)

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)

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)

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)

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)

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 Beta-Sheet
Formation and the Mechanism for Fibril Formation.*
J. Am. Chem. Soc. 2018, 140, 244−249, 140
.
pp. 244-249.

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, P. and Schütte, Ch.
(2018)
*A multiscale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics.*
Multiscale Modeling and Simulation: A SIAM Interdisciplinary Journal, 16
(4).
pp. 1455-1485.
ISSN 1540-3459

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 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.

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

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)

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.

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

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 Proceedings of the INdAM-ISIMM Workshop, Rome, Italy, September 2016
(27).
Springer INdAM series, pp. 159-177.

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
.

## 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)