# Publications for: All SFB 1114 publications

**82**.

## 2017

Junghans, C. and Agarwal, A. and Delle Site, L.
(2017)
*Computational Efficiency and Amdahl's law for the Adaptive Resolution Simulation Technique.*
Computer Physics Communications, 215
.
pp. 20-25.
ISSN 0010-4655

Seshaditya, A. and Ghiringhelli, L. M. and Delle Site, L.
(2017)
*Levy-Lieb-based Monte Carlo study of the dimensionality behaviour of the electronic kinetic functional.*
Computationa, 5
(2).
pp. 1-10.
ISSN 2079-3197

Gerber, S. and Horenko, I.
(2017)
*Toward a direct and scalable identification of reduced models for categorical processes.*
Proceedings of the National Academy of Sciences, 114
(19).
pp. 4863-4868.

Acevedo, W. and de Wiljes, J. and Reich, S.
(2017)
*Second-order accurate ensemble transform particle filters.*
SFB 1114 Preprint
.
(Submitted)

Agarwal, A. and Clementi, C. and Delle Site, L.
(2017)
*Path Integral-GC-AdResS simulation of a large hydrophobic solute in water: A tool to investigate the interplay between local microscopic structures and quantum delocalization of atoms in space.*
Physical Chemistry Chemical Physics, 19
.
pp. 13030-13037.
ISSN 1463-9084

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

Kornhuber, R. and Podlesny, J. and Yserentant, H.
(2017)
*Direct and Iterative Methods for Numerical Homogenization.*
In:
Domain Decomposition Methods in Science and Engineering.
Lecture Notes in Computational Science and Engineering, XXIII
(116).
SpringerLink, pp. 215-225.
ISBN 978-3-319-52389-7

Donati, L. and Hartmann, C. and Keller, B.G.
(2017)
*Girsanov reweighting for path ensembles and Markov state models.*
SFB 1114 Preprint
.
(Submitted)

Gräser, C. and Kies, T.
(2017)
*Discretization Error Estimates for Penalty Formulations of a Linearized Canham-Helfrich Type Energy.*
SFB 1114 Preprint
.

O'Kane, T.J. and Monselesan, D.P. and Risbey, J.S. and Horenko, I. and Franzke, Ch.L.E.
(2017)
*On memory, dimension, and atmospheric teleconnection patterns.*
Math. Clim. Weather Forecast, 3
(1).
pp. 1-27.

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

Dellnitz, M. and Klus, S. and Ziessler, A.
(2017)
*A Set-Oriented Numerical Approach for Dynamical Systems with Parameter Uncertainty.*
SIAM Journal on Applied Dynamical Systems, 16
(1).
pp. 120-138.
ISSN 1536-0040

Krekeler, C. and Delle Site, L.
(2017)
*Towards open boundary molecular dynamics simulation of ionic liquids.*
Physical Chemistry Chemical Physics, 6
(19).
pp. 4701-4709.
ISSN 1463-9076

Horenko, I. and Gerber, S. and O'Kane, T.J. and Risbey, J.S. and Monselesan, D.P.
(2017)
*On inference and validation of causality relations in climate teleconnections.*
In:
Nonlinear and Stochastic Climate Dynamics.
Cambridge University Press, pp. 184-208.
ISBN 9781107118140

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

Pinamonti, G. and Zhao, J. and Condon, D. and Paul, F. and Noé, F. and Turner, D. and Bussi, G.
(2017)
*Predicting the kinetics of RNA oligonucleotides using Markov state models.*
J. Comp. Theory Comput. , 13
.
pp. 926-934.

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

## 2016

Klus, S. and Schütte, Ch.
(2016)
*Towards tensor-based methods for the numerical approximation of the Perron-Frobenius and Koopman operator.*
Journal of Computational Dynamics
.
ISSN 2158-2491

Mielke, A. and Roubícek, T.
(2016)
*Rate-Independent elastoplasticity at finite strain and its numerical approximation.*
Mathematical Models and Methods in Applied Sciences, 26
(12).
pp. 2203-2236.
ISSN 1793-6314

Zhu, J. and Klein, R. and Delle Site, L.
(2016)
*Adaptive Molecular Resolution Approach in Hamiltonian
Form: An Asymptotic Analysis.*
Physical Review E, 94
(043321).

Banisch, Ralf and Hartmann, C.
(2016)
*A sparse Markov chain approximation of LQ-type stochastic control problems.*
Math. Control Relat. F., 6
(3).
pp. 363-389.
ISSN 1064-8275

Kornhuber, R. and Peterseim, D. and Yserentant, H.
(2016)
*An analysis of a class of variational multiscale methods based on subspace decomposition.*
Mathematics of Computation
.
ISSN 0025-5718
(In Press)

Hartmann, C. and Schütte, Ch. and Zhang, W.
(2016)
*Model reduction algorithms for optimal control and importance sampling of diffusions.*
Nonlinearity, 29
(8).
pp. 2298-2326.
ISSN 0951-7715

Klus, S. and Koltai, Péter and Schütte, Ch.
(2016)
*On the numerical approximation of the Perron-Frobenius and Koopman operator.*
Journal of Computational Dynamics, 3
(1).
pp. 51-79.
ISSN 2158-2491

Chustagulprom, N. and Reich, S. and Reinhardt, M.
(2016)
*A HYBRID ENSEMBLE TRANSFORM FILTER FOR HIGH DIMENSIONAL DYNAMICAL SYSTEMS.*
SIAM/ASA Journal on Uncertainty Quantification, 4
(1).
pp. 592-608.
ISSN 2166-2525

Klein, R. and Benacchio, T.
(2016)
*A doubly blended model for multiscale atmospheric dynamics.*
Journal of the Atmospheric Sciences, 73
.
pp. 1179-1186.
ISSN Online: 1520-0469 Print: 0022-4928

Albrecht, D. and Winterflood, C. M. and Sadeghi, M. and Tschager, T. and Noé, F. and Ewers, H.
(2016)
*Nanoscopic compartmentalization of membrane protein motion at the axon initial segment.*
J. Cell Biol., 215
.
pp. 37-46.

Delle Site, L.
(2016)
*Formulation of Liouville's theorem for grand ensemble molecular simulations.*
Physical Review E, 93
(022130).

Delle Site, L. and Agarwal, A.
(2016)
*Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and Application.*
Computer Physics Communications
(206).
pp. 26-34.

Elliott, C.M. and Gräser, C. and Hobbs, G. and Kornhuber, R. and Wolf, M.W.
(2016)
*A Variational Approach to Particles in Lipid Membranes.*
Archive for Rational Mechanics and Analysis, 222
(2).
pp. 1011-1075.
ISSN Print: 0003-9527; Online:1432-0673

Feireisl, E. and Klein, R. and Novotný, A. and Zatorska, E.
(2016)
*On singular limits arising in the scale analysis of stratified fluid flows.*
Mathematical Models and Methods in Applied Sciences, World Scientific, 26
(3).
pp. 419-443.
ISSN Print: 0218-2025 Online: 1793-6314

Hittmeir, S. and Klein, R. and Li, J. and Titi, E.
(2016)
*GLOBAL WELL-POSEDNESS FOR PASSIVELY TRANSPORTED NONLINEAR MOISTURE DYNAMICS WITH PHASE CHANGES.*
Nonlinearity
.
(Submitted)

Klinkmüller, M. and Schreurs, G. and Rosenau, M. and Kemnitz, H.
(2016)
*Properties of granular analogue materials: A community wide survey.*
Tectonophysics, 666
.
pp. 23-38.

Klus, S. and Gelß, P. and Peitz, S. and Schütte, Ch.
(2016)
*Tensor-based dynamic mode decomposition.*
SIAM Journal on Scientific Computing
.
ISSN ISSN 1064-8275 (print); 1095-7197 (electronic)
(Submitted)

Kornhuber, R. and Yserentant, H.
(2016)
*Numerical Homogenization of Elliptic Multiscale
Problems by Subspace Decomposition.*
Multiscale Model. Simul., 14
(3).
pp. 1017-1036.
ISSN print: 1540-3459; online: 1540-3467

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

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

Patterson, R. I. A
(2016)
*Properties of the solutions of delocalised coagulation and inception problems with outflow boundaries.*
Journal of Evolution Equations
.
(Submitted)

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

Peters, J.H. and Klein, R. and Delle Site, L.
(2016)
*Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique
/PhysRevE.94.023309.*
Phys. Rev. E, 94
(2).

Pipping, E. and Kornhuber, R. and Rosenau, M. and Oncken, O.
(2016)
*On the efficient and reliable numerical solution of rate-and-state friction problems.*
Geophysical Journal International, 204
(3).
pp. 1858-1866.
ISSN Online: 1365-246X Print: 0956-540X

Ritter, M. and Leever, K. and Rosenau, M. and Oncken, O.
(2016)
*Scaling the Sand Box - Mechanical (Dis-) Similarities of Granular Materials and Brittle Rock.*
Journal of Geophysical Research: Solid Earth
.
(In Press)

Rosenau, M. and Leever, K. and Oncken, O.
(2016)
*Experimental tectonics: Convergent plate margins.*
Earth Sys. Env. Sci. SFB 1114 Preprint
.
(Submitted)

Rudolf, M. and Boutelier, D. and Rosenau, M. and Schreurs, G. and Oncken, O.
(2016)
*Rheological benchmark of silicone oils used for analog modeling of short- and long-term lithospheric deformation.*
Tectonophysics, 666
.
pp. 12-20.

Schreurs, G. and et al, .
(2016)
*Benchmarking analogue models of brittle thrust wedges.*
J. Struct. Geol.
.
(In Press)

Vitalini, F. and Noé, F. and Keller, B.
(2016)
*Molecular dynamics simulations data of the twenty encoded amino acids in different force fields.*
Data in Brief, 7
.
pp. 582-590.

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

Yapp, E.K.Y. and Patterson, R. I. A and Akroyd, J. and Mosbach, S. and Adkins, E.M. and Miller, J.H. and Kraft, M.
(2016)
*Simulation and parametric sensitivity study of optical band gap in a laminar co-flow ethylene diffusion flame.*
Combustion and Flame
.
(Submitted)

## 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

Agarwal, A. and Delle Site, L.
(2015)
*Path Integral Molecular Dynamics within the Grand
Canonical-like Adaptive Resolution Technique: Simulation of
Liquid Water.*
Journal of Chemical Physics, 143
(9).
ISSN 0021-9606

Banisch, Ralf and Djurdjevac, N. and Schütte, Ch.
(2015)
*Reactive flows and unproductive cycles in irreversible Markov chains.*
The European Physical Journal Special Topics, 224
(12).
pp. 2369-2387.
ISSN 1951-6355

Bittracher, Andreas and Hartmann, C. and Junge, O. and Koltai, Péter
(2015)
*Pseudo generators for under-resolved molecular dynamics.*
The European Physical Journal Special Topics, 224
(12).
pp. 2463-2490.
ISSN 1951-6355

Hartmann, C. and Delle Site, L.
(2015)
*Scale Bridging in Molecular Simulation.*
The European Physical Journal Special Topics, 224
(12).
pp. 2173-2176.
ISSN 1951-6355

Klein, R.
(2015)
*Comments on "Open Boundary Molecular Dynamics " by R. Delgado-Buscalioni, J. Sablic, and M.
Praprotnik.*
The European Physical Journal, 224
(12).
pp. 2509-2510.
ISSN Online: 1951-6401 Print: 1951-6355

Klein, R.
(2015)
*Comments on "Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations" by K. Kreis, A.C. Fogarty, K. Kremer R. Potestio.*
The European Physical Journal, 224
(12).
pp. 2503-2504.
ISSN Online: 1951-6401 Print: 1951-6355

Agarwal, A. and Zhu, J. and Wang, H. and Hartmann, C. and Delle Site, L.
(2015)
*Molecular dynamics in a Grand Ensemble: Bergmann-Lebowitz model and adaptive resolution simulation.*
New Journal of Physics, 17
(083042).
ISSN 1367-2630

Schütte, Ch. and Sarich, M.
(2015)
*A Critical Appraisal of Markov State Models.*
SFB 1114 Preprint, 15-18
.
ISSN 1438-0064

Di Giuseppe, E. and Corbi, F. and Funiciello, F. and Massmeyer, A. and Santimano, T.N. and Rosenau, M. and Davaille, A.
(2015)
*Characterization of Carbopol hydrogel rheology for experimental tectonics and geodynamics, , 642, 29-45, doi:10.1016/j.tecto.2014.12.005.*
Tectonophysics
.
pp. 29-45.

Djurdjevac, A.
(2015)
*Advection-diffusion equations with random coefficients
on evolving hypersurfaces.*
Interfaces and Free Boundaries
.
(Unpublished)

Erbar, M. and Maas, J. and Renger, M.
(2015)
*From large deviations to Wasserstein gradient flows in multiple dimensions.*
Electronic Communications in Probability, 20
(89).

Hartmann, C. and Schütte, Ch. and Weber, M. and Zhang, W.
(2015)
*Importance sampling in path space for diffusion processes.*
Probab. Theory Rel. Fields
.
(Submitted)

Horenko, I. and Gerber, S.
(2015)
*Improving clustering by imposing network information.*
Science Advances, 1
(7).
ISSN 2375-2548

Kim, W.K. and Netz, R.R.
(2015)
*The mean shape of transition and first-passage paths.*
The Journal of Chemical Physics, 143
(224108).

Klein, R.
(2015)
*Comments on "Adaptive Resolution Simulation in Equilibrium
and Beyond" by H. Wang and A. Agarwal.*
The European Physical Journal, 224
(12).
pp. 2497-2499.

Li, S. and Moreno, M. and Bedford, J. and Rosenau, M. and Oncken, O.
(2015)
*Revisiting viscoelastic effects on interseismic deformation and locking degree: A case study of the Peru-North Chile subduction zone.*
Journal of Geophysical Research-Solid Earth, 120
(6).
pp. 4522-4538.

Liero, M. and Mielke, A. and Peletier, M. A. and Renger, M.
(2015)
*On microscopic origins of generalized gradient structures.*
SFB Preprint
.
(Submitted)

Mazza, E. and Ulbrich, U. and Klein, R.
(2015)
*A Characterization of the Meteorological Environment Associated with the Tropical Transition of a Medicane in the Western Mediterranean Sea.*
SFB1114-Preprint
.
(Submitted)

Mielke, A. and Patterson, R. I. A and Peletier, M. A. and Renger, M.
(2015)
*Non-equilibrium thermodynamical principles for chemical reactions with mass-action kinetics.*
WIAS Preprint No. 2165
.
(Submitted)

Mielke, A. and Peletier, M. A. and Renger, M.
(2015)
*A generalization of Onsager's reciprocity relations to gradient flows with nonlinear mobility.*
Journal of Non-Equilibrium Thermodynamics
.
(Submitted)

O’Kane, T.J. and Risbey, J.S. and Monselesan, D.P. and Horenko, I. and Franzke, Ch.L.E.
(2015)
*On the dynamics of persistent states and their secular trends in the waveguides of the Southern Hemisphere troposphere.*
Climate Dynamics
.
ISSN Print: 0930-7575, Online: 1432-0894

Rinne, K.F. and Schulz, J.C.F. and Netz, R.R.
(2015)
*Impact of secondary structure and hydration water on the dielectric spectrum of poly-alanine and possible relation to the debate on slaved versus slaving water.*
The Journal of Physical Chemistry
.

Santimano, T.N. and Rosenau, M. and Oncken, O.
(2015)
*Intrinsic versus extrinsic variability of analogue sand-box experiments - Insights from statistical analysis of repeated accretionary sand wedge experiments.*
Journal of Structural Geology, 75
.
pp. 80-100.

Scherer, M. K. and Trendelkamp-Schroer, B. and Paul, F. and Pérez-Hernández, G. and Hoffmann, M. and Plattner, N. and Wehmeyer, C. and Prinz, J.-H. and Noé, F.
(2015)
*PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models.*
J. Chem. Theory Comput., 11
(11).
pp. 5525-5542.

Schulz, J.C.F. and Miettinen, M.S. and Netz, R.R.
(2015)
*Unfolding and Folding Internal Friction of β‑Hairpins Is Smaller than That of α‑Helices.*
Journal of Physical Chemistry B, 119
(13).
pp. 4565-4574.

Trendelkamp-Schroer, B. and Wu, H. and Paul, F. and Noé, F.
(2015)
*Estimation and uncertainty of reversible Markov models.*
J. Chem. Phys., 143
(17).
p. 174101.

Vitalini, F. and Noé, F. and Keller, B.
(2015)
*A basis set for peptides for the variational approach to conformational kinetics.*
J. Chem. Theory Comput., 11
.
pp. 3992-4004.

Wu, H. and Prinz, J.-H. and Noé, F.
(2015)
*Projected Metastable Markov Processes and Their Estimation with Observable Operator Models.*
J. Chem. Phys., 143
(14).
p. 144101.

Wu, H. and Noé, F.
(2015)
*Gaussian Markov transition models of molecular kinetics.*
J. Chem. Phys., 142
(8).
084104.

## 2014

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

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

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

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