Publications
List of all publications sorted by year
| • | 2026 |
| • | 2025 |
| • | 2024 |
| • | 2023 |
| • | 2022 |
| • | 2021 |
| • | 2020 |
| • | 2019 |
| • | 2018 |
| • | 2017 |
| • | 2016 |
| • | 2015 |
| • | before 2015 |
Link to CKAN data management system (recent datasets)
rdm-cmt.physik.uni-mainz.de/organization/trr-146-multiscale-simulation-methods-for-soft-matter-systems
2026 - Publications
Temperature-driven turbulence in compressible fluid flows
Eduard Feireisl, Mária Lukáčová-Medvid'ová, Bangwei She, Yuhuan Yuan
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2603.28158
Convergence of a finite volume method to weak solutions for the compressible Navier-Stokes-Fourier system
Eduard Feireisl, Mária Lukáčová-Medvid'ová, Bangwei She, Yuhuan Yuan
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2603.20758
Discretizing Group-Convolutional Neural Networks for 3D Geometry in Feature Space
D. Franzen, J.-P. Filling, M. Wand
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2606.09647
Ab initio parametrization of distributed polarizable force fields
F. Post, J.-P. Filling, T. Maitra, F. May, M. Wand, D. Andrienko
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2606.09647
Polymer knots in thin films: Thickness dependence, local effects, and stiffness
M.P. Schmitt, H. Meyer, Peter Virnau
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2605.02644
Markov State Model for the forced unfolding of a small Peptide
M. Oestereich, J. Gauss, G. Diezemann
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2605.15805
From single-chain dynamics to structure formation: Dynamic self-consistent field theory and molecular dynamics of (co)polymer melts across entanglement regimes
A. Foroozani Behbahani, J. Cheraghalizadeh, F. Schmid
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2609.04548
Multi-drawing Pólya urns via labelled random DAGs
C. Mailler, R. Steiner
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2508.20592
Oscillatory approximations and maximum entropy principle for the Euler system of gas dynamics
Eduard Feireisl, Mária Lukáčová-Medvid'ová, Changsheng Yu
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2505.02070
Convergence to the uniform distribution of moderately self-interacting diffusions on compact Riemannian manifolds
S. Holbach, O. Raimond
accepted at Annales de l’Institut Henri Poincaré
Link: https://doi.org/10.48550/arXiv.2307.01538
Learning Effective Hydro-Phoretic Interactions in Active Matter
P. Bera, A.K. Mukhopadhyay, B. Liebchen
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2601.02277
Learning Microstructure in Active Matter
W. Dasgupta, S. Mandal, A.K. Mukhopadhyay, B. Liebchen
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2601.05894
Topological chiral random walker
S. Osat, E. Meyberg, J. Metson, T. Speck
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2602.12020
Organic materials of tomorrow: Horizons of artificial intelligence
Harold Mena, Terence J. Balskovits, Kun-Han Lin, Denis Andrienko
Advanced Materials, Early access (2026)
Link: https://doi.org/10.1002/adma.202523667
Tensor Channel Equivariant Graph Neural Networks for Molecular Polarizability Prediction
J.-P. Filling, D. Franzen, M. Wand
accepted to the 35th International Conference on Artificial Neural Networks (ICANN 2026)
Link: https://doi.org/10.48550/arXiv.2605.16891
Thermodynamics of active matter with internal degrees of freedom
R. Bebon, T. Speck
Commun. Physics 9, 162
Link: https://doi.org/10.1038/s42005-026-02662-z
Automated Decision-Making by Chemical Echolocation in Active Droplets
A.K. Mukhopadhyay, R. Niu, L. Fu, K. Feng, C. Fujta, Q. Zhao, J. Qu, B. Liebchen
Proc. Natl. Acad. Sci. 123, e2526773123 (2026)
Link: https://doi.org/10.1073/pnas.2526773123
Maximal dissipation and well-posedness of the Euler system of gas dynamics
E. Feireisl, A. Jüngel, M. Lukáčová-Medvid'ová
Archive for rational mechanics and analysis 250, 53 (2026)
Link: https://doi.org/10.1007/s00205-026-02205-4
On the fluctuations of the extremal and cluster level sets of branching Brownian motion
Lisa Hartung, Oren Louidor, Tianqi Wu
Probability theory and related fields, early access (2026)
Link: https://doi.org/10.1007/s00440-026-01477-x
Pressure-induced pKa variations influence conformations of pH-sensitive polymers
Ved Mahajan, Varun Mandalaparthy, Nico F.A. van der Vegt
The Journal of Chemical Physics 164, 084907 (2026)
Link: https://doi.org/10.1063/5.0303682
Self-Assembly of Unconventional Triphenylene-Based Frustrated Amphiphile in Solution
H.M. Cezar, G. Berton, T. Lorenzetto, S. Zorzi, C.J.D. Foumthuim, S.M. Szostak, P. Ballester, C. Mondelli, R. Schweins, V. Cristiglio, F. Fabris, R. Lund, A. Scarso, A. Giacometti, M. Cascella
Langmuir 42, 4507-4517 (2026)
Link: https://doi.org/10.1021/acs.langmuir.5c05203
Plasticization as a tool for tuning the dynamics of polymerized ionic liquids: insights from molecular dynamics simulations
Arshid Ahmad, Michael Vogel
Soft Matter 22, 3750-3758 (2026)
Link: https://doi.org/10.1007/d6sm00189k
Determining extended Markov parameterizations for vector-valued generalized Langevin Equations
N. Bockius, M. Braun, K. Hofmann, F. Schmid, M. Hanke
Z. Naturforsch. A 81, 157-171 (2026)
Link: https://doi.org/10.1515/zna-2025-0354
Dynamical scaling of coarse-grained ionic liquid under shear flow
Abbas Gholami, Michael Vogel, Torsten Stuehn, Joseph F. Rudzinski
The Journal of Chemical Physics 164, 184503 (2026)
Link: https://doi.org/10.1063/5.0325186
A Novel Implementation of CCSD Analytic Gradients Using Cholesky Decomposition of the Two-Electron Integrals and Abelian Point-Group Symmetry
Luca Melega, Tommaso Nottoli, Jürgen Gauss, Filippo Lipparini
The Journal of Physical Chemistry A 130, 2097-2111 (2026)
Link: https://doi.org/10.1021/acs.jpca.5c08579
Thermoresponsivity and cononsolvency of a minimal polymer model in mixed solvents
Ved Mahajan, Nico F.A. van der Vegt
The Journal of Chemical Physics 164, 124901 (2026)
Link: https://doi.org/10.1063/5.0325441
Molecular Mechanisms behind Nonmonotonic Surface Tensions of Binary Aqueous n-Diol Mixtures
Evangelia Charvati, Pim J. Dekker, Christian Diddens, Detlef Lohse, Florian Müller-Plathe
The Journal of Physical Chemistry B 130, 2585-2596 (2026)
Link: https://doi.org/10.1021/acs.jpcb.5c06813
A simple, fully-discrete, unconditionally energy-stable method for the two-phase Navier-Stokes Cahn-Hilliard model with arbitrary density ratios
A. Brunk, M.F.P. ten Eikelder
J. Comp. Phys. 548, 114558 (2026)
Link: https://doi.org/10.1016/j.jcp.2025.114558
Nanofriction of Adsorbed Polymer Chains on Rough Surfaces: A Generalized Friction Model
Daniel A. Vega, Friederike Schmid, Andrey Milchev
Macromolecules 59, 7890-7899 (2026)
Link: https://doi.org/10.1021/acs.macromol.6c01472
Mechanistic Insight Into Ionizable Cationic Lipid-Mediated Endosomal Escape via Transient Lipid Complexes
David Noel Zimmer, Friederike Schmid, Giovanni Settanni
Small 22, 32 (2026)
Link: https://doi.org/10.1002/smll.202513399
Beyond Electrostatic Screening: Effect of Ion Pairing on Acid-Base Equilibria in Complex Electrolyte Solutions
Varun Mandalaparthy, Johannes Hunger, Mischa Bonn, Nico F.A. van der Vegt
Journal of Physical Chemistry Letters 17, 511-518 (2026)
Link: https://doi.org/10.1021/acs.jpclett.5c03363
Stress Relaxation in Monodisperse Entangled Polymer Melts: Correlation between Viscoelastic Response and Single-Chain Relaxation via Molecular Dynamics Simulations
Alireza F. Behbahani
Macromolecules 59, 3455-3464 (2026)
Link: https://doi.org/10.1021/acs.macromol.5c03613
Role of a trap in disordered OLED host-guest systems
A. Stankevych, N. Kinaret, A. Zhugayevych, R. Saxena, A. Vakhnin, K.-H. Lin, D. Andrienko, H. Bassler, A. Köhler, A. Kadashchuk
Physical Review Applied 25, 044005 (2026)
Link: https://doi.org/10.1103/pvvg-j94v
Bottom-up synthesis of molecular nanodiamond from nanographene
I. Batatia, J. Liu, X. Yang, R.G. Brouwer, L. Kazak, R. Blinder, L. Cancellara, N.V. Tarakina, Y. Liu, T. Eklund, M. Sinha, S. Koster, S. Bhat, F. Rohmann, A. Tangemann, K.L. Gallo, R. Berger, R. Farla, A. Kubanek, K. Amann-Winkel, M. Wagner, F. Jelezko, K. Müllen, G. Csanyi, R. Cortes-Huerto, Y. Wu, T. Weil
Nature 655, 8121 (2026)
Link: https://doi.org/10.1038/s41586-026-10669-3
Mutual linearity is a generic property of steady-state Markov networks
Robin Bebon, Thomas Speck
Physical Review Letters 136, 137401 (2026)
Link: https://doi.org/10.1103/jcm3-57d8
Direct nonequilibrium molecular dynamics simulation of diffusio-osmotic flow in nanopores
Hossein Eslami, Xinxin Deng
J. Coll. Interf. Sci. 724, 141119 (2026)
Link: https://doi.org/10.1016/j.jcis.2026.141119
Structure-preserving approximation of the non-isothermal Cahn-Hilliard system based on the entropy equation
A. Brunk, D. Höhn, M. Lukáčová-Medvid'ová
Applied Mathematics and Computation, 522, 129987 (2026)
Link: https://doi.org/10.1016/j.amc.2026.129987
A general model for frictional contacts in colloidal systems
Kay Hofmann, Kay-Robert Dormann, Benno Liebchen, Friederike Schmid
Commun. Phys. 9, 139 (2026)
Link: https://doi.org/10.1038/s42005-026-02624-5
Convergence of a hyperbolic thermodynamically compatible finite volume scheme for the Euler equations
Michael Dumbser, Mária Lukáčová-Medvid'ová, Andrea Thomann
Numerische Mathematik 158, 715-747 (2026)
Link: https://doi.org/10.1007/s00211-025-01522-2
Memory effects in contact line friction
Niklas Wolf, Nico F.A. van der Vegt
The Journal of Chemical Physics 164, 141101 (2026)
Link: https://doi.org/10.1063/5.0316994
Hybrid multiscale method for polymer melts: Analysis and simulations
Ranajay Datta, Mária Lukáčová-Medvid'ová, Andreas Schömer, Peter Virnau
ZAMM 106, e70438 (2026)
Link: https://doi.org/10.1002/zamm.70438
A random walk approach to broadcasting on random recursive trees
Ernst Althaus, Lisa Hartung, Rebecca Steiner
J. Theor. Probability 39, 65 (2026)
Link: https://doi.org/10.1007/s10959-026-01519-z
Solving random hyperbolic conservation laws using linear programming
Shaoshuai Chi, Michael Herty, Mária Lukáčová-Medvid'ová, Yizhou Zhou
SIAM J. Sci. Comp. 48, A1184-A1205 (2026)
Link: https://doi.org/10.1137/25M1731654
Analysis of nonlinear poroviscoelastic flows with discontinuous porosities (vol. 36, 7025, 2023)
Markus Bachmayr, Simon Boissereee, Lisa M. Kreusser
Nonlinearity 39, 049501 (2026)
Link: https://doi.org/10.1088/1361-6544/ae543e
Coarse-graining of small molecules in inhomogeneous systems through local-density dependent potentials
Sayan Dutta, Denis Andrienko, Arash Nikoubashman
The Journal of Chemical Physics 164, 134115 (2026)
Link: https://doi.org/10.1063/5.0325129
Tuning the velocity of thermophoretic microswimmers with thermo-sensitive polymer
F. Braun, A.K. Mukhopadhyay, S. Mahmoudi, K. Graff, A. Razavi, C. Schneider, S. Lessnau, B. Liebchen, R. von Klitzing
Soft matter 22, 747-762 (2026)
Link: https://doi.org/10.1039/d5sm01119a
Ring polymer physics and rheology: Challenges and opportunities
C.M. Schroeder, R. Everaers, K. Kremer, M. Kruteva, C.N. Likos, G.B. McKenna, T. O'Connor, J.R. Prakash, D. Richter, R. Robertson-Anderson, M. Rubinstein, K.S. Schweizer, D. Vlassopoulos
J. Rheology 70, 183-216 (2026)
Link: https://doi.org/10.1122/8.0001099
Modelling dissipation in quantum active matter
A.P. Antonov, S. Lee, B. Liebchen, H. Löwen, J. Melles, G. Morigi, Y. Tuchkov, M. te Vrugt
Physical Review A 114, 012201 (2026)
Link: https://doi.org/10.1103/4gyc-3pht
Thermodynamically consistent Continuum Theory for Active Ellipsoidal Particle Suspensions
Ben Gozlen, H., Wang, Y. and M. Oberlack
Intnl. J. Multiphase 202, 105839 (2026)
Link: https://doi.org/10.1016/j.ijmultiphaseflow.2026.105839
From heteropolymer stiffness distributions to effective homopolymers. I. Theoretical modeling and computational verification
Yannick Witzky, Friederike Schmid, Arash Nikoubashman
The Journal of Chemical Physics 163, 164907 (2026)
Link: https://doi.org/10.1063/5.0276010
From heteropolymer stiffness distributions to effective homopolymers. II. Conformational analysis of intrinsically disordered proteins
Yannick Witzky, Friederike Schmid, Arash Nikoubashman
The Journal of Chemical Physics 163, 164908 (2026)
Link: https://doi.org/10.1063/5.0287110
Accurate coarse-graining of conjugated organic molecules in melts and thin films using density-dependent potentials
Sayan Dutta, Maria C. Lesniewski, Muhammad Nawaz, Will G. Noid, Denis Andrienko, Arash Nikoubashman
J. Chem. Theory Comput. 22, 3697-3708 (2026)
Link: https://doi.org/10.1021/acs.jctc.6c00079
Real-Time Modeling of Skyrmion Dynamics in Arbitrary 2D Spatially Dependent Pinning Potential Landscapes
S.F. Fröhlich, T. Sparmann, M.A. Brems, J. Rothörl, F. Kammerbauer, K. Raab, K. Sachin, M. Kläui, P. Virnau
Comm. Phys. 9, 243 (2026)
Link: https://doi.org/10.1038/s42005-026-02766-6
Impact of currents on non-equilibrium coexistence in chemically driven mixtures
Ellen Meyberg, Joshua F. Robinson, Thomas Speck
The Journal of Chemical Physics 165, 044118 (2026)
Link: https://doi.org/10.1063/5.0336459
Chemical potentials of hydrogen-bonded aqueous mixtures from adaptive resolution simulations and Kirkwood-Buff theory
Maria Duena-Herrera, Mauricio Sevilla, Diego Veloza-Diaz, Luis A. Baptista, Nancy C. Forero-Martinez, Robinson Cortes-Huerto
The Journal of Chemical Physics 164, 164502 (2026)
Link: https://doi.org/10.1063/5.0326808
Reconstruction of spin structures from topological charge distributions via generative neural network systems
Kyra H.M. Klos, Jan Disselhoff, Michael Wand, Karin Everschor-Sitte, Friederike Schmid
The Journal of Chemical Physics 164, 194113 (2026)
Link: https://doi.org/10.1063/5.0323442
Consistency and convergence of flux-corrected finite element methods for nonlinear hyperbolic problems
Kuzmin, D., Lukáčová-Medvid'ová, M., Öffner, P.
J. Num. Math. 34, 1-20 (2026)
Link: https://doi.org/10.1515/jnma-2024-0123
2025 - Publications
The second fluctuation-dissipation theorem for the generalized Langevin equation
M. Hanke
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2507.17350
A note on relations between convexity and concavity of thermodynamic functions
Mária Lukáčová-Medvid'ová, Ferdinand Thein, Gerald Warnecke, Yuhuan Yuan
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2510.24440
Discerning Performance Bottlenecks of State-of-the-Art Narrow Bandgap Organic Solar Cells
A. Shukla, M. Pranav, G. He, Terence J. Blaskovits, D. Mascione, Y. Cao, Y. Gong, D.B. Riley, J.A. Steele, E. Solano, A. Ehm, M.S. Shadabroo, A. Armin, S. Shoaee, D.R.T. Zahn, Y. Li, L. Meng, F. Lang, D. Andrienko, D. Neher
Adv. Energy Materials 15, 32 (2025)
Link: https://doi.org/10.1002/aenm.202502398
Influence of topology on rheological properties of polymer ring melts
Ranajay Datta, Peter Virnau
The Journal of Chemical Physics 162, 094902 (2025)
Link: https://doi.org/10.1063/5.0250414
Analysis and discretization of the Ohta-Kawasaki equation with forcing and degenerate mobility
Aaron Brunk, Marvin Fritz
Partial differential equations and applications 6, 54 (2025)
Link: https://doi.org/10.1007/s42985-025-00362-x
Relating thermodynamic quantities of convex-hard-body fluids to the body's shape
T. Franosch, C. De Michele, R. Schilling
Physical Review Research 7, 023260 (2025)
Link: https://doi.org/10.1103/5shk-zjsc
Knots in polymer molecules under Poiseuille flow
M.P. Schmitt, A. Milchev
Foundations 5, 28 (2025)
Link: https://doi.org/10.3390/foundations5030028
Proton First: Rationalizing a Proton Transfer in a Protein-Fragment Complex
H. Vatheuer, J. Paulus, L. Johannknecht, G. Keller, R.M. Ziora, L.S. Stelzl, P. Czodrowski
CHEMMEDCHEM 20, 202500244 (2025)
Link: https://doi.org/10.1002/cmdc.202500244
Realizing Quantitative Quasiparticle Modeling of Skyrmion Dynamics in Arbitrary Potentials
M.A. Brems, T. Sparmann, S.M. Fröhlich, L.-C. Dany, J. Rothörl, F. Kammerbauer, E.M. Jefremovas, O. Farago, M. Kläui, P. Virnau
Physical Review Letters 134, 046701 (2025)
Link: https://doi.org/10.1103/PhysRevLett.134.046701
Beyond Core-Shell Micellar Structures: Complex Structures in Simple Surfactant
Henrique Musseli Cezar, Victoria Ariel Bjørnestad, Sylvain Prevost, Reidar Lund, Michele Cascella
Small structures 6, 2400553 (2025)
Link: https://doi.org/10.1002/sstr.202400553
Pure-blue single-layer organic light-emitting diodes based on trap-free hyperfluorescence
O. Sachnik, N. Kinaret, R. Saxena, M. Manz, W. Liu, J.T. Baskovits, D. Andrienko, J.J. Michels, P.W.M. Blom, G.-J.A.H. Wetzelaer
Nature Materials 24, 1742-1748 (2025)
Link: https://doi.org/10.1038/s41563-025-02294-8
A kinetic model to simulate charge flow through an electro-chemical half-cell
D. Veloza-Diaz, F. Schmid, R. Cortes-Huerto, P. Ballone, N.C. Forero-Martinez
The Journal of Chemical Physics 163, 164113 (2025)
Link: https://doi.org/10.1063/5.0295632
Sequence determinants of protein phase separation and recognition by protein phase-separated condensates through molecular dynamics and active learning
A. Changiarath, A. Arya, V.A. Xenidis, J. Padeken, L.S. Stelzl
Faraday Discussions 256, 235-254 (2025)
Link: https://doi.org/10.1039/d4fd00099d
From 1 to infinity: The log-correction for the maximum of variable speed branching Brownian motio
Alexander Alban, Anton Bovier, Annabell Gros, Lisa Hartung
Electronic J. of Probability 30, 1-46 (2025)
Link: https://doi.org/10.1214/25-EJP1287
Product of Experts with LLMs: Boosting Performance on ARC Is a Matter of Perspective
Daniel Franzen, Jan Disselhoff, David Hartmann
ICML 2025, ICML Vol. 267, 17657-17671 (2025)
Link: https://icml.cc/virtual/2025/poster/44610
AMEP: The active matter evaluation package for Python
Lukas Hecht, Kay-Robert Dormann, Kai Luca Spanheimer, Mahdieh Ebrahimi, Malte Cordts, Suvendu Mandal, Artitra K. Mikhopadhyay, Benno Liebchen
Comp. Phys. Commm. 309, 109483 (2025)
Link: https://doi.org/10.1016/j.cpc.2024.109483
Can Dynamic Helical Polymers be Reduced to Linear Chains of Spins? Non-Local Effects from Polymer Self-Avoidance
Keerti Chauhan, Marcus Müller, Kostas Ch. Daoulas
Macromolecules 58, 5408-5420 (2025)
Link: https://doi.org/10.1021/acs.macromol.4c03197
Viscosity calculations with hybrid particle-field molecular dynamics simulations
Simon A.W. Alberti, Evangelia Charvati, Giuseppe Milano, Florian Müller-Plathe
The Journal of Physical Chemistry B 129, 8473-8484 (2025)
Link: https://doi.org/10.1021/acs.jpcb.5c03244
Analysis and structure-preserving approximation of a Cahn-Hilliard-Forchheimer system with solution-dependent mass and volume source
Aaron Brunk, Marvin Fritz
ESAIM 59, 2991-3020 (2025)
Link: https://doi.org/10.1051/m2an/2025081
Matching correlations matters: Modeling friction in a hydrophobic folding transition
Niklas Wolf, Madhusmitha Tripathy, Nico F.A. van der Vegt
The Journal of Chemical Physics 163, 124901 (2025)
Link: https://doi.org/10.1063/5.0289081
Negative drag force on beating flagellar-shaped bodies in active fluids
Timo Knippenberg, Robin Bebon, Thomas Speck, Clemens Bechinger
Physical Review Letters 135, 118301 (2025)
Link: https://doi.org/10.1103/3xbk-sxhh
Density fluctuations, solvation thermodynamics, and coexistence curves in grand canonical molecular dynamics simulations
Mauricio Sevilla, Luis A. Baptista, Kurt Kremer, Robinson Cortes-Huerto
The Journal of Chemical Physics 162, 080901 (2025)
Link: https://doi.org/10.1063/5.0243895
Simulation Insights into the Assembly of Polyplexes for RNA Deliver
Jonas Lehnen, Jorge Moreno Herrero, Heinrich Haas, Friederike Schmid, Giovanni Settanni
Biomacromolecules 26, 8465-8474 (2025)
Link: https://doi.org/10.1021/acs.biomac.5c01219
A generic model for pH-sensitive collapse of hydrophobic polymers
Varun Mandalaparthy, Nico F.A. van der Vegt
Phys. Chem. Chem. Phys. 27, 6984-6993 (2025)
Link: https://doi.org/10.1039/d4cp04756g
Simulation Study of the Water Ordering Effect of the β-(1,3)-Glucan Callose Biopolymer
Robinson Cortes-Huerto, Nancy C. Forero-Martinez, Pietro Ballone
Biomacromolecules 26, 1748-1760 (2025)
Link: https://doi.org/10.1021/acs.biomac.4c01524
Cross-correlations in the fluctuation-dissipation relation influence barrier-crossing d
Niklas Wolf, Viktor Klippenstein, Nico F. A. van der Vegt
The Journal of Chemical Physics 162, 054113 (2025)
Link: https://doi.org/10.1063/5.0246295
Micelle Forming Linear-Dendritic Block Copolymers: A Theoretical Comparison between Random Hyperbranched and Precise Dendrimer Polymer Architectures
Marios Giannakou, Oleg V. Borisov, Friederike Schmid
Macromolecules 58, 5872-5882 (2025)
Link: https://doi.org/10.1021/acs.macromol.5c00615
Continuum–Particle Coupling for Polymer Simulations
S. Norouzi, R. Furge, H. Eslami, F. Müller-Plathe
J. Chem. Theory Comput. 21, 358-373 (2025)
Link: https://doi.org/10.1021/acs.jctc.4c01332
Determination of aqueous solubility of NaCl in molecular dynamics simulation using the Kirkwood-Buff method
Abishek Chattopadhyay, Varun Mandalaparthy, Nico F. A. van der Vegt
The Journal of Chemical Physics 162, 174116 (2025)
Link: https://doi.org/10.1063/5.0264104
Structure and dynamics of ionic liquids under shear flow
Abbas Gholami, Sebastian Kloth, Zhen-Hao Xu, Kurt Kremer, Michael Vogel, Torsten Stuehn, Joseph F. Rudzinski
The Journal of Chemical Physics 163, 074502 (2025)
Link: https://doi.org/10.1063/5.0279946
Decoupling of water and ion dynamics in nanophase-segrated mixtures of an ionic liquid and water studied by NMR experiments and MD simulations
Elisa Steinrücken, Sebastian Kloth, Michael Vogel
J. Phys. D 58, 295302 (2025)
Link: https://doi.org/10.1088/1361-6463/adeabb
Cholesky decomposition of two-electron integrals required for the computation of magnetizabilities using gauge-including atomic orbitals
S. Burger, S. Stopkowiccz, J. Gauss
The Journal of Physical Chemistry A 161, 024117 (2025)
Link: https://doi.org/10.1021/acs.jpca.4c07421
Active adaptolates featuring motility-induced percolating structures with an adaptive packing geometry
Aritra K. Mukhopadhyay, Peter Schmelcher, Benno Liebchen
Comm. Phys. 8, 343 (2025)
Link: https://doi.org/10.1038/s42005-025-02265-0
Decoding dynamics in global assessments of teaching. An introduction to
global assessments for State Space Grids
Niklas Litzenberger, Andreas Pysik, Sebastian Wurster
Frontiers in Education 10, 1625133 (2025)
Link: https://doi.org/10.3389/feduc.2025.1625133
Comparative molecular dynamics simulation studies of simple and polymerized ionic liquids
Ahmad, Arshid and Köster, Robin and Kloth, Sebastian and Vogel, Michael
Soft Matter 21, 5231-5241 (2025)
Link: https://doi.org/10.1039/d5sm00307e
Steady inhomogeneous shear flows as mechanical phase transitions
Thomas Speck
Physical Review E 111, 015430 (2025)
Link: https://doi.org/10.1103/PhysRevE.111.015430
Thermodynamics of Active Matter: Tracking Dissipation across Scales
Robin Bebon, Joshua F. Robinson, Thomas Speck
Physical Review X 15, 021050 (2025)
Link: https://doi.org/10.1103/PhysRevX.15.021050
Error analysis for a second order approximation of a viscoelastic phase separation model
Brunk, A., Egger, H., Habrich, O., Lukáčová-Medvid'ová, M.
Numer. Math. 157, 1449–1489 (2025)
Link: https://doi.org/10.1007/s00211-025-01488-1
Structural pores not required: Antimicrobial peptides induce ion permeabilization of lipid membranes through transient water channels
Rosenov Koynarev, V., Nader, M. L., Cezar, H. M., Narayanan, T., Porcar, L., Cascella, M., Lund, R.
Proceedings of the National Academy of Sciences of the United States of America, 122(44), e2517944122 (2025)
Link: https://doi.org/10.1073/pnas.2517944122
Continuum Modeling and Numerical Simulation of Active Suspensions in Curved Channels
H. Ben Gozlen, Y. Wang, and M. Oberlack
Theor. Comput. Fluid Dyn. 39, 32 (2025)
Link: https://doi.org/10.1007/s00162-025-00752-2
Ternary Microphase Diagram of SBM Triblock Terpolymer Morphologies in Spherical Confinement
M. Trömer, E.M. Zirdehi, Y. Post, A. Nikoubashman, A.H. Gröschel
Journal of Polymer Science 63, 4424-4435 (2025)
Link: https://doi.org/10.1002/pol.20250090
Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates
E. Zippo, D. Dormann, T. Speck, L.S. Stelzl
Nature Communications 16, 4649 (2025)
Link: https://doi.org/10.1038/s41467-025-59676-4
Error analysis of the Monte Carlo method for compressible magnetohydrodynamics
E. Feireisl, M. Lukáčová-Medvid'ová, B. She, Y. Yuan
Mathetmatical Models Methods Applied Science 35 (2025), no. 9, 2047–2097 (2025)
Link: https://doi.org/10.1142/S0218202525500332
A posteriori error control for the Allan-Cahn equation with variable mobility
A. Brunk, J. Giesselmann, M. Lukáčová-Medvid'ová
SIAM J. Num. Anal. 63, 1540-1560 (2025)
Link: https://doi.org/10.1137/24M1646406
Convergence Analysis of the Monte Carlo Method for the Random Navier–Stokes–Fourier System
M. Lukáčová-Medvid'ová, B. She, Y. Yuan
SIAM J. Numer. Anal. 63, no. 3, 1254–1280 (2025)
Link: https://doi.org/10.1137/23M1563232
Penalty method for the Navier–Stokes–Fourier system with Dirichlet boundary conditions: convergence and error estimates
M. Lukáčová-Medvid'ová, B. She, Y. Yuan
Numer. Math. 157, no. 3, 1079–1132 (2025)
Link: https://doi.org/10.1007/s00211-025-01468-5
What is a limit of structure-preserving numerical methods for compressible flows? Numerical mathematics and advanced applications
M. Lukáčová-Medvid'ová, B. She, Y. Yuan
ENUMATH 2023. Vol. 1, 17–33, Lect. Notes Comput. Sci. Eng., 153, Springer, Cham (2025)
Link: https://doi.org/10.1007/978-3-031-86173-4_2
Direct Molecular Polarizability Prediction with SO(3)-Equivariant Local Frame GNNs
J.-P. Filling, M. Wand, D. Andrienko, F. Post
Workshop on Machine Learning and the Physical Sciences at NeurIPS 2025
Link: https://ml4physicalsciences.github.io/2025/files/NeurIPS_ML4PS_2025_38.pdf
Convergence and error estimates of a penalization finite volume method for the compressible Navier-Stokes system
M. Lukáčová-Medvid'ová, B. She, Y. Yuan
IMA J. Numer. Anal. 45, no. 2, 1054–1101 (2025)
Link: https://doi.org/10.1093/imanum/drae024
Conditional regularity for the compressible Navier-Stokes equations with potential temperature transport
M. Lukáčová-Medvid'ová, A. Schömer
J. Differential Equations 423, 1–40 (2025)
Link: https://doi.org/10.1016/j.jde.2024.12.028
A mixture theory formulation for active suspensions
H. Ben Gozlen, Y. Wang, and M. Oberlack
Proc. Appl. Math. Mech. 24, e202400166 (2025)
Link: https://doi.org/10.1002/pamm.202400166
2024 - Publications
Estimatable variation neural networks and their application to scalar hyperbolic conservation laws
Mária Lukáčová-Medvid'ová, Simon Schneider
Arxiv preprint
Link: https://doi.org/10.48550/arXiv.2409.08909
A second-order structure-preserving discretization for the Cahn-Hilliard/Allen-Cahn system with cross-kinetic couplin
Aaron Brunk, Herbert Egger, Oliver Habrich
Applied Numerical Mathematics 206, 12-28 (2024)
Link: https://doi.org/10.1016/j.apnum.2024.07.016
Machine-learning-based detection of spin structures
Isaac Labrie-Boulay, Thomas B. Winkler, Daniel Franzen, Alena Romanova, Hans Fangohr, Mathias Kläui
Physical Review Applied 21, 014014 (2024)
Link: https://doi.org/10.1103/PhysRevApplied.21.014014
Self-assembly of model three- and four-patch colloidal particles in two dimensions
Ali Gharibi, Hossein Eslami, Florian Müller-Plathe
J. Chem. Theory Comput. 20, 6858-6869 (2024)
Link: https://doi.org/10.1021/acs.jctc.4c00540
Metadynamics Simulations of Three-Dimensional Nanocrystals Self-Assembled from Triblock Janus Nanoparticles: Implications for Light Filtering
Hossein Eslami, Florian Müller-Plathe
ACS Applied Nano Materials 7, 18045-18055 (2024)
Link: https://doi.org/10.1021/acsanm.4c03858
Cholesky Decomposition in Spin-Free Dirac-Coulomb Coupled-Cluster Calculation
Tereza Uhlírová, Davide Cianchino, Tommaso Nottoli, Filippo Lipparini, Jürgen Gauss
The Journal of Physical Chemistry A 128, 8292-8303 (2024)
Link: https://doi.org/10.1021/acs.jpca.4c04353
Maxima of a random model of the Riemann zeta function over intervals of varying length
Louis-Pierre Arguin, Guillaume Dubach, Lisa Hartung
Annales de L'Institut Henri Poincaré - Probabilités et statistiques 60, 588-611 (2024)
Link: https://doi.org/10.1214/22-AIHP1323
Effect of simple shear on knotted polymer coils and globules
Andrey Milchev, Maurice P. Schmitt, Peter Virnau
The Journal of Chemical Physics 161, 224905 (2024)
Link: https://doi.org/10.1063/5.0236904
Polynomial approximation of symmetric functions
Markus Bachmayr, Genevieve Dusson, Christoph Ortner, Jack Thomas
Mathematics of Computation 93, 811-839 (2024)
Link: https://doi.org/10.1090/mcom/3868
Cholesky Decomposition-Based Implementation of Relativistic Two-Component Coupled-Cluster Methods for Medium-Sized Molecules
Chaoqun Zhang, Filippo Lipparini, Stella Stopkowicz, Jürgen Gauss, Lan Cheng
J. Chem. Theory Comput. 20, 787-798 (2024)
Link: https://doi.org/10.1021/acs.jctc.3c01236
Dependencies between effective parameters in coarse-grained models for phase separation of DNA-based fluids
Soumen De Karmakar, Thomas Speck
The Journal of Chemical Physics 161, 234907 (2024)
Link: https://doi.org/10.1063/5.0232651
Relaxation Dynamics of Entangled Linear Polymer Melts via Molecular Dynamics Simulation
Alireza Behbahani, Friederike Schmid
Macromolecules 58, 767-786 (2024)
Link: https://doi.org/10.1021/acs.macromol.4c02168
How boundary interactions dominate emergent driving of inertial passive probes in active matter
Jeanine Shea, Gerhard Jung, Friederike Schmid
J. Phys. A 57,, 235006 (2024)
Link: https://doi.org/10.1088/1751-8121/ad4ad7
Force renormalization for probes immersed in an active bath
Jeanine Shea, Gerhard Jung, Friederike Schmid
Soft matter 20, 1767-1785 (2024)
Link: https://doi.org/10.1039/d3sm01387a
Collective Hall current in chiral active fluids: Coupling of phase and mass transport through traveling bands
Frank Siebers, Robin Bebon, Ashreya Jayaram, Thomas Speck
PNAS 121, e2320256121 (2024)
Link: https://doi.org/10.1073/pnas.2320256121
Gesture recognition with Brownian reservoir computing using geometrically confined skyrmion dynamics
G. Beneke, T.B. Winkler, K. Raab, M.A. Brems, F. Kammerbauer, P. Gerhards, K. Knobloch, S. Krishnia, J.H. Mentink, M. Kläui
Nature Communications 15, 8103 (2024)
Link: https://doi.org/10.1038/s41467-024-52345-y
Adaptive resolution force probe simulations: Coarse graining in the ideal gas approximation
Marco Oestereich, Jürgen Gauss, Gregor Diezemann
The Journal of Chemical Physics 161, 154903 (2024)
Link: https://doi.org/10.1063/5.0228198
Self-Assembly Pathways of Triblock Janus Particles into 3D Open Lattices
Hossein Eslami, Florian Müller-Plathe
Small 20, 2306337(2024)
Link: https://doi.org/10.1002/smll.202306337
An implicit-explicit solver for a two-fluid single-temperature model
Lukáčová-Medvid'ová, M., Peshkov, I., and Thomann, A.
Journal of Computational Physics, 498, 112696, (2024)
Link: https://doi.org/10.1016/j.jcp.2023.112696
New High-Order Numerical Methods for Hyperbolic Systems of Nonlinear PDEs with Uncertainties
Chertock, A., Herty, M., Iskhakov, A. S., Janajra, S., Kurganov, A., and Lukáčová-Medvid’ová, M.
Communications on Applied Mathematics and Computation, 1-34, (2024)
Link: https://doi.org/10.1007/s42967-024-00392-z
Convergence of Numerical Methods for the Navier–Stokes–Fourier System Driven by Uncertain Initial/Boundary Data
Feireisl, E., Lukáčová-Medvid’ová, M., She, B., and Yuan, Y.
Foundations of Computational Mathematics, 1-53, (2024)
Link: https://doi.org/10.1007/s10208-024-09666-7
Stochastic modeling of stationary scalar Gaussian processes in continuous time from autocorrelation data
Hanke, M.
Adv Comput Math 50, 60 (2024)
Link: https://doi.org/10.1007/s10444-024-10150-7
Transferable local density-dependent friction in tert-butanol/water mixtures
Mathes, M., Klippenstein, V., van der Vegt, N.
The Journal of Chemical Physics 160, 184504 (2024)
Link: https://doi.org/10.1063/5.0205020
Differential Capacitance of Ionic Liquid Confined between Metallic Interfaces
Samuel Ntim, Marialore Sulpizi
The Journal of Physical Chemistry B 128, 1936-1942 (2024)
Link: https://doi.org/10.1021/acs.jpcb.3c08042
A space-time adaptive low-rank method for high-dimensional parabolic partial differential equation
Markus Bachmayr, Manfred Faldum
J. Complexity 82, 101839 (2024)
Link: https://doi.org/10.1016/j.jco.2024.101839
On existence, uniqueness and stability of solutions to Cahn-Hilliard/Allen-Cahn systems with cross-kinetic coupling
A. Brunk, H. Egger, T.D. Oyedeji, Y.Yan, B.-X. Yu
Nonlinear Analysis 77, 104051 (2024)
Link: https://doi.org/10.1016/j.nonrwa.2023.104051
Phase coexistence in Hamiltonian hybrid particle-field theory using a multi-Gaussian approach
Samirah Sen, Henrique Musseli Cezar, Morgen Ledum, Xinmeng Li, Michele Cascella
The Journal of Physical Chemistry B 128, 11739-11747 (2024)
Link: https://doi.org/10.1021/acs.jpcb.4c05525
Finite-field Cholesky decomposed coupled-cluster techniques (ff-CD-CC): theory and application to pressure broadening of Mg by a He atmosphere and a strong magnetic field
Simon Blaschke, Marios-Petros Kitsaras, Stella Stopkowicz
Phys. Chem. Chem. Phys. 26, 28828-28848 (2024)
Link: https://doi.org/10.1039/d4cp03103b
Topological comparison of flexible and semiflexible chains in polymer
melts with θ-chains
Maurice P. Schmitt, Sarah Wettermann, Dostas Ch. Daoulas, Hendrik Meyer, Peter Virnau
The Journal of Chemical Physics 161, 144904 (2024)
Link: https://doi.org/10.1063/5.0228826
Efficient approximate screening techniques for integrals over London atomic orbital
Simon Blaschke, Stella Stopkowicz, Ansgar Pausch
The Journal of Chemical Physics 161, 024117 (2024)
Link: https://doi.org/10.1063/5.0217246
A Gauss-Newton method for iterative optimization of memory kernels for generalized Langevin thermostats in coarse-grained molecular dynamics simulations
Viktor Klippenstein, Niklas Wolf, Nico F.A. van der Vegt
The Journal of Chemical Physics 160, 204115 (2024)
Link: https://doi.org/10.1063/5.0203832
Learning Force Field Parameters from Differentiable Particle-Field Molecular Dynamics
Manuel Carrer, Henrique Musseli Cezar, Sigbjørn Løland Bore, Morten Ledum, Michele Cascella
J. Chem. Inform. Modelling 64, 5510-5520 (2024)
Link: https://doi.org/10.1021/acs.jcim.4c00564
Ionizable Cationic Lipids and Helper Lipids Synergistically Contribute to RNA Packing and Protection in Lipid-Based Nanomaterials
David Noel Zimmer, Friederike Schmid, Giovanni Settanni
The Journal of Physical Chemistry B 128, 10165-10177 (2024)
Link: https://doi.org/10.1021/acs.jpcb.4c05057
Structural basis of p53 inactivation by cavity-creating cancer mutations and its implications for the development of mutant p53 reactivators
Dimitrios-Ilias Balourdas, Anja M. Markl, Andreas Krämer, Giovanni Settanni, Andreas C. Jörger
Cell Death and Disease 15, 408 (2024)
Link: https://doi.org/10.1038/s41419-024-06739-x
Interactions of adsorbing cosolutes with hydrophobic hydration shells
Saminath Bharadwaj, Madhusmita Tripathy, Nico F. A. van der Vegt
The Journal of Chemical Physics 160, 164902 (2024)
Link: https://doi.org/10.1063/5.0207075
Predicting molecular ordering in deposited molecular films
C. Scherer, N. Kinaret, K.-H. Lin, M. N. Qiasrani, F. Post, F. May, D. Andrienko
Adv. Energy Mater. 14, 2403124 (2024)
Link: https://doi.org/10.1002/aenm.202403124
Strong stretching theory of polydisperse curved polymer brushes
Marios Giannakou, Oleg V. Borisov, Friederike Schmid
The Journal of Chemical Physics 161, 014903 (2024)
Link: https://doi.org/10.1063/5.0213524
Skyrmion flow in periodically modulated channels
Klaus Raab, Maurice Schmitt, Maarten A. Brems, Jan Rothörl, Fabian Kammerbauer, Sachin Krishnia, Mathias Kläui, Peter Virnau
Physical Review E 110, L042601 (2024)
Link: https://doi.org/10.1103/PhysRevE.110.L042601
Structure-Preserving Approximation of the Cahn-Hilliard-Biot System
Aaron Brunk, Marvin Fritz
Numerical methods for partial differential equations 41, 323159 (2024)
Link: https://doi.org/10.1002/num.23159
2023 - Publications
Multilevel representations of isotropic Gaussian random fields on the sphere
Markus Bachmayr, Ana Djurdjevac
IMA J. Numerical Analysis 43, 1970-2000 (2023)
Link: https://doi.org/10.1093/imanum/drac034
Growth and aging in a few phase-separating active matter system
Florian Dittrich, Jiarul Midya, Peter Virnau, Subir K. Das
Physical Review E 108, 024609 (2023)
Link: https://doi.org/10.1103/PhysRevE.108.024609
Branching Brownian Motion with Self-Repulsion
Anton Bovier, Lisa Hartung
Annales Henri Poincaré 24, 931-956 (2023)
Link: https://doi.org/10.1007/s00023-022-01223-8
Can polymer helicity affect topological chirality of polymer knots?
Yani Zhao, Jan Rothörl, Pol Besenius, Peter Virnau, Kostas Ch. Daoulas
ACS Macro Letters 12, 234-240 (2023)
Link: https://doi.org/10.1021/acsmacrolett.2c00600
Thermodynamics, statistical mechanics and the vanishing pore width limit of confined fluids
W. Dong, T. Franosch, R. Schilling
Comm. Physics 6, 161 (2023)
Link: https://doi.org/10.1038/s42005-023-01255-4
Stability, Speed, and Constraints for Structural Coarse-Graining in VOTCA
Marvin P. Bernhardt, Martin Hanke, Nico F.A. van der Vegt
J. Chem. Theory Comput. 19, 580-595 (2023)
Link: https://doi.org/10.1021/acs.jctc.2c00665
A DZ white dwarf with a 30 MG magnetic field}
M.A. Hollands, S. Stopkowicz, M.-P. Kitsaras, F. Hampe, S. Blaschke, J.J. Hermes
Monthly Notices of the Royal Astonomical Society 520, 3560-3575 (2023)
Link: https://doi.org/10.1093/mnras/stad143
An ab initio method on large sized molecular aggregate system: Predicting absorption spectra of crystalline organic semiconducting films
Wenlan Liu, Denis Andrienko
The Journal of Chemical Physics 158, 094108 (2023)
Link: https://doi.org/10.1063/5.0138748
Another Torture Track for Quantum Chemistry: Reinvestigation of the Benzaldehyde Amidation by Nitrogen-Atom Transfer from Platinum(II) and Palladium(II) Metallonitrenes
H. Verplancke, M. Diefenbach, J.N. Lienert, M. Ugandi, M.-P. Kitsaras, M. Röhmelt, S. Stopkowicz, M.C. Holthausen
Israel J. Chemistry 63, e292399960 (2023)
Link: https://doi.org/10.1002/ijch.202300060
The speed of invasion in an advancing population
Anton Bovier, Lisa Hartung
J. Mathematical Biology 87, 56 (2023)
Link: https://doi.org/10.1007/s00285-023-01989-3
300-Times-Increased Diffusive Skyrmion Dynamics and Effective Pinning Reduction by Periodic Field Excitation
R. Gruber, M.A. Brems, J. Rothörl, T. Sparmann, M. Schmitt, I. Kononenko, F. Kammerbauer, M.-A. Syskaki, O. Farago, P. Virnau, M. Kläui
Advanced Materials 35, 2208922 (2023)
Link: https://doi.org/10.1002/adma.202208922
Local characteristic decomposition based central-upwind scheme
Alina Chertock, Shaoshuao Chu, Michael Herty, Alexander Kurganov, Mária Lukáčová-Medvid'ová
J. Comp. Phys. 473, 111718
Link: https://doi.org/10.1016/j.jcp.2022.111718
Perspective on unconventional computing using magnetic skyrmions
O. Lee, R. Msiska, M.A. Brems, M. Kläui, H. Kurebayashi, K. Everschor-Sitte
Applied Physics Letters 122, 260501 (2023)
Link: https://doi.org/10.1063/5.0148469
Micelle kinetics of photoswitchable surfactants: Self-assembly pathways and relaxation mechanisms
V.A. Bjørnestad, X. Li, C. Tribet, R. Lund, M. Cascella
J. Coll. Interf. Sci. 646, 883-899 (2023)
Link: https://doi.org/10.1016/j.jcis.2023.05.057
Constructing coarse-grained skyrmion potentials from experimental data with Iterative Boltzmann Inversion
Y. Ge, J. Rothörl, M.A. Brems, N. Kerber, R. Gruber, T. Dohi, M. Kläui, P. Virnau
Comm. Phys. 6, 30 (2023)
Link: https://doi.org/10.1038/s42005-023-01145-9
Electronic coarse-graining of long conjugated molecules: Case study of non-fullerene acceptors
Andriy Zhugyevych, Kun-Han Lin, Denis Andrienko
The Journal of Chemical Physics 159, 024107 (2023)
Link: https://doi.org/10.1063/5.0155488
Viscosity of flexible and semiflexible ring melts: Molecular origins and flow-induced segregation
Ranajay Datta, Fabian Berressem, Friederike Schmid, Arash Nikoubashman, Peter Virnau
Macromolecules 56, 7247-7255 (2023)
Link: https://doi.org/10.1021/acs.macromol.3c01046
Influence of ionic conditions on knotting in a coarse-grained model
Sarah Wettermann, Ranajay Datta, Peter Virnau
Frontiers in Chemistry 10, 1096014 (2023)
Link: https://doi.org/10.3389/fchem.2022.1096014
Cholesky decomposition of two-electron integrals in quantum-chemical calculations with perturbative or finite magnetic fields using gauge-including atomic orbitals
Jürgen Gauss, Simon Blaschke, Sophia Burger, Tommaso Nottoli, Filippo Lipparini, Stella Stopkowicz
Molecular Physics 121, 11-12 (2023)
Link: https://doi.org/10.1080/00268976.2022.2101562
HylleraasMD: A Domain Decomposition-Based Hybrid Particle-Field Software for Multiscale Simulations of Soft Matter
Morten Ledum, Samirah Sen, Xinmeng Li, Manuel Carrer, Yu Feng, Michele Cascella, Sibjørn Løland Bore
J. Chem. Theory Comput. 19, 2939-2952 (2023)
Link: https://doi.org/10.1021/acs.jctc.3c00134
On uniqueness and stable estimation of multiple parameters in the Cahn-Hilliard equation
Aaron Brunk, Herbert Egger, Oliver Habrich
Inverse Problems 39, 065002 (2023)
Link: https://doi.org/0.1088/1361-6420/acca44
Self-Solidifying Active Droplets Showing Memory-Induced Chiralit
Kai Feng, Jose C.U. Marcos, Aritra K. Mukhopadhyay, Ran Niu, Qiang Zhao, Jinping Qu, Benno Liebchen
Adv. Scie. 10, 27 (2023)
Link: https://doi.org/10.1002/advs.202300866
SANS Spectra with PLUMED: Implementation and Application to Metainference
Henrique M. Cezar, Michele Cascella
J. Chem. Information Modelling 63, 4979-4985 (2023)
Link: https://doi.org/10.1021/acs.jcim.3c00724
Structural ensembles of disordered proteins from hierarchical chain growth and simulatio
Lisa M. Pietrek, Lukas Stelzl, Gerhard Hummer
Current Opinion in Structural Biology 78, 102501 (2023)
Link: https://doi.org/0.1016/j.sbi.2022.102501
Code modernization strategies for short-range non-bonded molecular dynamics simulations
James Vance, Zhen-Hao Xu, Nikita Tretyakov, Torsten Stuehn, Markus Rampp, Sebastian Eible, Christoph Junghans, Andre Brinkmann
Comp. Phys. Comm. 290, 108760 (2023)
Link: https://doi.org/10.1016/j.cpc.2023.108760
Stability of Branched Tubular Membrane Structures
Maike Jung, Gerhard Jung, Friederike Schmid
Physical Review Letters 130, 148401 (2023)
Link: https://doi.org/10.1103/PhysRevLett.130.148401
Soft Matter under Pressure: Pushing Particle-Field Molecular Dynamics to the Isobaric Ensemble
Samirah Sen, Morten Ledum, Sigbjørn Løland Bore, Michele Cascella
Journal of Chemical Information and Modeling 63, 2207-2217 (2023)
Link: https://doi.org/10.1021/acs.jcim.3c00186
On the equivalence of the hybrid particle-field and Gaussian core models
Morten Ledum, Samirah Sen, Sigbjørn Løland Bore, Michele Cascella
The Journal of Chemical Physics 158, 1194902 (2023)
Link: https://doi.org/10.1063/5.0145142
Error estimates of a finite volume method for the compressible Navier–Stokes–Fourier system
Danica Basarić, Hana Mizerová, Bangwei She, Yuhuan Yuan
Math.Comp. 92, 2543–2574 (2023)
Link: https://doi.org/10.1090/mcom/3852
Compressible Navier-Stokes equations with potential temperature transport: stability of the strong solution and nu-merical error estimates
M. Lukáčová-Medvid'ová, A. Schömer
Journal of Mathematical Fluid Mechanics 25, 1 (2023)
Link: https://doi.org/10.1007/s00021-022-00733-z
Computational approaches to lipid-based nucleic acid delivery systems
Giovanni Settanni
Eur. Phys. J. E 46, 127 (2023)
Link: https://doi.org/10.1140/epje/s10189-023-00385-5
Modeling of minimal systems based on ATP-Zn coordination for chemically fueled self-assembly
Emma Rossi, Alberta Ferrarini, Marialore Sulpizi
Physical Chemistry Chemical Physics 25, 6102-6111 (2023)
Link: https://doi.org/10.1039/d2cp05516c
Chilling alcohol on the computer: isothermal compressibility and the formation of hydrogen-bond clusters in liquid propan-1-ol
Luis A. Baptista, Mauricio Sevilla, Manfred Wagner, Kurt Kremer, Robinson Cortes-Huerto
Eur. Phys. J. E 46, 117 (2023)
Link: https://doi.org/10.1140/epje/s10189-023-00380-w
Anions and Cations Affect Amino Acid Dissociation Equilibria via Distinct Mechanisms
Varun Mandalaparthy, Madhusmita Tripathy, Nico F.A. van der Vegt
Journal of Physical Chemistry Letters 14, 9250-9256 (2023)
Link: https://doi.org/10.1021/acs.jpclett.3c02062
Finite-size excess-entropy scaling for simple liquids
Mauricio Sevilla, Atreyee Banerjee, Robinson Cortes-Huerto
The Journal of Chemical Physics 158, 204502 (2023)
Link: https://doi.org/10.1063/5.0142912
A novel coupled-cluster singles and doubles implementation that combines the exploitation of point-group symmetry and Cholesky decomposition of the two-electron integrals
Tommaso Nottoli, Jürgen Gauss, Filippo Lipparini
The Journal of Chemical Physics 159, 231101 (2023)
Link: https://doi.org/10.1063/5.0175956
Effective dynamics and fluctuations of a trapped probe moving in a fluid of active hard discs
Ashreya Jayaram, Thomas Speck
EPL 143, 17005 (2023)
Link: https://doi.org/10.1209/0295-5075/acdf1a
Exploiting compositional disorder in collectives of light-driven circle walkers
Frank Siebers, Ashreya Jayaram, Peter Blümler, Thomas Speck
Science Advances 9, eadf5443 (2023)
Link: https://doi.org/10.1126/sciadv.adf5443
Existence and weak-strong uniqueness for global weak solutions for the viscoelastic phase separation model in three space dimensions
Aaron Brunk
Discrete and continuous dynamics systems 43, 2120-2136 (2023)
Link: https://doi.org/10.3934/dcds.2023004
Monitoring the Charge-Carrier-Occupied Density of States in Disordered
Organic Semiconductors under Nonequilibrium Conditions Using Thermally
Stimulated Luminescence Spectroscopy
Andrei Stankevych, Rishabh Saxena, Alexander Vakhnin, Falk May, Naomi Kinaret, Denis Andrienko, Jan Genoe, Heinz Bässler, Anna Köhler, Andreh Kadashchuk
Physical Review Applied 19, 054007 (2023)
Link: https://doi.org/10.1103/PhysRevApplied.19.054007
Convergence of a stochastic collocation finite volume method for the compressible Navier–Stokes system.
E. Feireisl, M. Lukáčová-Medviďová
The Annals of Applied Probability, 33(6A), 4936-4963 (2023)
Link: https://doi.org/10.1214/23-AAP1937
Solvation Behavior of Elastin-like Polypeptides in Divalent Metal Salt Solutions
Yani Zhao, Swaminath Bharadwaj, Ryan L. Myers, Halil Okur, Pho T. Bui, Mengrui Cao, Lauren K. Welch, Tinglu Wang, Paul S. Cremer, Nico F.A. van der Vegt
Journal of Physical Chemistry Letters 14, 10113-10118 (2023)
Link: https://doi.org/10.1021/acs.jpclett.3c02476
Self-Solidifying Active Droplets Showing Memory-Induced Chirality
K. Feng, J.C. Ureña Marcos, A.K. Mukhopadhyay, R. Niu, Q. Zhao, J. Qu, B. Liebchen
Adv. Science 10, 2300866 (2023)
Link: https://doi.org/10.1002/advs.202300866
Solvation Behavior of Elastin-like Polypeptides in Divalent Metal Salt Solutions
Yani Zhao, Swaminath Bharadwaj, Ryan L. Myers, Halil Okur, Pho T. Bui, Mengrui Cao, Lauren K. Welch, Tinglu Wang, Paul S. Cremer, Nico F.A. van der Vegt
Journal of Physical Chemistry Letters 14, 10113-10118 (2023)
Link: https://doi.org/10.1021/acs.jpclett.3c02476
On the convergence of residual distribution schemes for the compressible Euler equations via dissipative weak solutions
Abgrall, R., Lukáčová-Medvid’ová, M. and Öffner, P.
Mathematical Models and Methods in Applied Sciences, 33(01), 139-173, (2023)
Link: https://doi.org/10.1142/S0218202523500057
Convergence of discontinuous Galerkin schemes for the Euler equations via dissipative weak solutions
Lukáčová-Medvid’ová, M. and Öffner, P.
Applied Mathematics and Computation, 436, 127508, (2023)
Link: https://doi.org/10.1016/j.amc.2022.127508
Statistical solutions for the Navier–Stokes–Fourier system
Feireisl, E., and Lukáčová-Medvid’ová, M.
Stochastics and Partial Differential Equations: Analysis and Computations, 1-25, (2023)
Link: https://doi.org/10.1007/s40072-023-00298-6
A second-order fully-balanced structure-preserving variational discretization scheme for the Cahn–Hilliard–Navier–Stokes system
Brunk, A., Egger, H., Habrich, O., and Lukáčová-Medviďová, M.
Mathematical Models and Methods in Applied Sciences, 33(12), 2587-2627, (2023)
Link: https://doi.org/10.1142/S0218202523500562
Stability and discretization error analysis for the Cahn–Hilliard system via relative energy estimates
Brunk, A., Egger, H., Habrich, O., and Lukáčová-Medviďová, M.
ESAIM: Mathematical Modelling and Numerical Analysis, 57(3), (2023)
Link: https://doi.org/10.1051/m2an/2023017
Relative energy and weak–strong uniqueness of a two-phase viscoelastic phase separation model
Aaron Brunk and Mária Lukáčová-Medviďová
ZAMM Z. Angew. Math. Mech. 103(7), Paper No. e202100240, 25 pp, (2023)
Link: https://doi.org/10.1002/zamm.202100240
Error estimates of a finite volume method for the compressible Navier–Stokes–Fourier system
Danica Basarić, Mária Lukáčová-Medviďová, Hana Mizerová, Bangwei She and Yuhuan Yuan
Math. Comp. 92 (2023), 2543-2574, (2023)
Link: https://doi.org/10.1090/mcom/3852
An all Mach number finite volume method for isentropic two-phase flow
Lukáčová-Medvid’ová, M., Puppo, G. and Thomann, A.
Journal of Numerical Mathematics, 31(3), 175-204, (2023)
Link: https://doi.org/10.1515/jnma-2022-0015
Dynamical coarse-grained models of molecular liquids and their ideal and non-ideal mixtures
Madhusmita Tripathy, Viktor Klippenstein and Nico van der Vegt
The Journal of Chemical Physics 2023, 159(9), (2023)
Link: https://doi.org/10.1063/5.0163097
Bottom-Up Informed and Iteratively Optimized Coarse-Grained Non-Markovian Water Models with Accurate Dynamics
Viktor Klippenstein and Nico van der Vegt
J. Chem. Theory Comput. 2023, 19(4), 1099-1110, (2023)
Link: https://doi.org/10.1021/acs.jctc.2c00871
Toward a structural identification of metastable molecular conformations
Simon Lemcke, Jörn H. Appeldorn, Michael Wand, Thomas Speck
The Journal of Chemical Physics 21 September 2023; 159 (11): 114105, (2023)
Link: https://doi.org/10.1063/5.0164145
Stabilizing α-Helicity of a Polypeptide in Aqueous Urea: Dipole Orientation or Hydrogen Bonding?
Luis A. Baptista, Yani Zhao, Kurt Kremer, Debashish Mukherji, and Robinson Cortes-Huerto
ACS Macro Letters 2023, 12, 841–847, (2023)
Link: https://doi.org/10.1021/acsmacrolett.3c00223
Enhanced Sampling Methods for Molecular Dynamics Simulations
Jérôme Hénin, Tony Lelièvre, Michael R. Shirts, Omar Valsson, and Lucie Delemotte
Living Journal of Computational Molecular Science, 4(1), 1583, (2023)
Link: https://doi.org/10.33011/livecoms.4.1.1583
Sampling rare event energy landscapes via birth-death augmented dynamics
Benjamin Pampel, Simon Holbach, Lisa Hartung, and Omar Valsson
Physical Review E 107, 024141 (2023)
Link: https://doi.org/10.1103/PhysRevE.107.024141
Molecular Structure and Dynamics in Wet Gecko beta-Keratin
H. Eslami, F. Müller-Plathe
ACS Biomaterials Sc. Engineering 9, 257 (2023)
Link: https://doi.org/10.1021/acsbiomaterials.2c01022
Molecular dynamics simulations of electrified interfaces including the metal polarisation
Samuel Ntim, Marialore Sulpizi
Physical Chemistry Chemical Physics 25, 22619-22625 (2023)
Link: https://doi.org/10.1039/d3cp01472j
2022 - Publications
Refined Large Deviation Principle for Branching Brownian Motion Conditioned to Have a Low Maximum
Yanjia Bai, Lisa Hartung
ALEA - Latin American Journal of Probability and Mathematical Statistics 19, 8590880 (2022)
Link: https://doi.org/10.30757/ALEA.v19-34
Asymptotic properties of a class of linearly implicit schemes for weakly compressible Euler equations
V. Kucera, M. Lukáčová-Medvid'ová, S. Nölle, J. Schütz
Numerische Mathematik 150, 79-103 (2022)
Link: https://doi.org/10.1007/s00211-021-01240-5
Approximating viscosity solutions of the Euler system
E. Feireisl, M. Lukáčová-Medvid'ová, S. Scheiner, B. Whe
Mathematics of Computation 91, 2129-2164 (2022)
Link: https://doi.org/10.1090/mcom/3738
Data-based stochastic modeling reveals sources of activity bursts in single-cell TGF-β signaling
Niklas Kolbe, Lorenz Hexemer, Lukas-Malte Bammert, Alexander Löwer, Mária Lukáčová-Medvid'ová, Stefan Legewie
PLOS Comp. Biology 18, 31010266 (2022)
Link: https://doi.org/10.1371/journal.pcbi.1010266
Small-to-large length scale transition of TMAO interaction with hydrophobic solutes
Angelina Folberth, Swaminath Bharadwaj, Nico F.A. van der Vegt
Phys. Chem. Chem. Phys. 24, 2080-2087 (2022)
Link: https://doi.org/10.1039/d1cp05167a
Computation of NMR shieldings at the CASSCF level using gauge-including atomic orbitals and Cholesky decomposition
T. Nottoli, S. Burger, S. Stopkowicz, J. Gauss, F. Lipparini
The Journal of Chemical Physics 157, 084122 (2022)
Link: https://doi.org/10.1063/5.0101838
Cononsolvency of thermoresponsive polymers: where we are now and where we are going
S. Bharadwaj, B.-J. Niebuur, K. Nothdurft, W. Richtering, N.F.A. van der Vegt, C.M. Papadakis
Soft Matter 18, 2884-2909 (2022)
Link: https://doi.org/10.1039/d2sm00146b
Open-circuit voltage of organic solar cells: interfacial roughness makes the difference
C. Pölking, J. Benduhn, D. Spoltore, M. Schwarze, S. Roland, F. Piersimoni, D. Neher, K. Leo, K. Vandewal, D. Andrienko
Comm. Phys. 5, 307 (2022)
Link: https://doi.org/10.1038/s42005-022-01084-x
Error Estimates of the Godunov Method for the Multidimensional Compressible Euler System
Mária Lukáčová-Medvid'ová, Bangwei She, Yuhuan Yuan
J. Scientific Computing 91, 71 (2022)
Link: https://doi.org/10.1007/s10915-022-01843-6
Particle number conservation and block structures in matrix product states
Markus Bachmayr, Michael Götte, Max Pfeffer
CALCOLO 59, 24 (2022)
Link: https://doi.org/10.1007/s10092-022-00462-9
Lower degree of dissociation of pyruvic acid at water surfaces than in bulk
Dominika Lesnicki, Veronika Wank, Jenee D. Cyran, Ellen H.G. Backus, Marialore Sulpizi
Physical Chemistry Chemical Physics 24, 13510-13513 (2022)
Link: https://doi.org/10.1039/d2cp01293f
Substrate spectrum of PPM1D in the cellular response to DNA
double-strand breaks
Justus F. Gräf, Ivan Mikicic, Xiaofei Ping, Claudia Scalera, Katharina Mayr, Lukas S. Stelzl, Petera Beli, Sebastian A. Wagner
iScience 25, 104892 (2022)
Link: https://doi.org/10.1016/j.isci.2022.104892
Knot formation of dsDNA pushed inside a nannochannel
Jan Rothörl, Sarah Wettermann, Peter Virnau, Ankiet Bhattacharya
Scientific Reports 12, 5342 (2022)
Link: https://doi.org/10.1038/s41598-022-09242-5
Temporally Coherent Backmapping of Molecular Trajectories From Coarse-Grained to Atomistic Resolution
Kirill Shmilovich, Marc Stieffenhofer, Nichalas E. Charron, Moritz Hoffmann
The Journal of Physical Chemistry A 126, 9124-9139 (2022)
Link: https://doi.org/10.1021/acs.jpca.2c07716
Solvation shell thermodynamics of extended hydrophobic solutes in mixed solvents
Madhusmita Tripathy, Swaminath Bharadwaj, Nico F.A. van der Vegt
The Journal of Chemical Physics 156, 164901 (2022)
Link: https://doi.org/10.1063/5.0090646
A Relation between the Formation of a Hydrogen-Bond Network and a Time-Scale Separation of Translation and Rotation in Molecular Liquids
Manuel Becher, Robin Horstmann, Sebastian Kloth, Ernst A. Rössler, Michael Vogel
Journal of Physical Chemistry Letters 13, 4556-4562 (2022)
Link: https://doi.org/10.1021/acs.jpclett.2c00821
Structural and Dynamical Properties of Liquids in Confinements: A Review of Molecular Dynamics Simulation Studies
R. Horstmann, L. Hecht, S. Kloth, M. Vogel
Soft Matter 18, 2373-2382 (2022)
Link: https://doi.org/10.1021/acs.langmuir.2c00521
Finite-size scaling and thermodynamics of model supercooled liquids: long-range concentration fluctuations and the role of attractive interactions
Atreyee Banerjee, Mauricio Sevilla, Joseph F. Rudzinski, Robinson Cortes-Huerto
Soft Matter 18, 2373-2382 (2022)
Link: https://doi.org/10.1039/d2sm00089j
pH-Dependent Behavior of Ionizable Cationic Lipids in mRNA-Carrying Lipoplexes Investigated by Molecular Dynamics Simulations
Giovanni Settanni, Wolfgang Brill, Heinrich Haas, Friederike Schmid
Macromolecular rapid communications 43, 2100683 (2022)
Link: https://doi.org/10.1002/marc.202100683
Editorial: Multiscale simulation methods for soft matter systems
Friederike Schmid
J. Phys.: Cond. Matter 34, 160401 (2022)
Link: https://doi.org/10.1088/1361-648X/ac5071
Critical behavior of active Brownian particles: Connection to field theories
Thomas Speck
Physical Review E 105, 064601 (2022)
Link: https://doi.org/10.1103/PhysRevE.105.064601
Connecting density fluctuations and Kirkwood-Buff integrals for finite-size systems
Mauricio Sevilla, Robinson Cortes-Huerto
The Journal of Chemical Physics 156, 044502 (2022)
Link: https://doi.org/10.1063/5.0076744
A deterministic two-phase model for an active suspension with non-spherical active particles using the Eulerian spatial averaging theory
B. Deußen, Y. Wang, M. Oberlack
Phys. Fluids 34, 023302 (2022)
Link: https://doi.org/10.1063/5.0077735
Single-chain and condensed-state behavior of hnRNPA1 from molecular simulations
D.J. Bauer, L.S. Stelzl, A. Nikoubashman
The Journal of Chemical Physics 165, 044118 (2022)
Link: https://doi.org/10.1063/5.0105540
An adaptive stochastic Galerkin method based on multilevel expansions of random fields: Convergence and optimality
Markus Bachmayr, Igor Voulis
Esaim - Mathematical modelling and numerical analysis 56, 12955-1992 (2022)
Link: https://doi.org/10.1051/m2an/2022062
Benchmarking coarse-grained models of organic semiconductors via deep backmapping
Marc Stieffenhofer, Christoph Scherer, Falk May, Tristan Bereau, Denis Andrienko
Frontiers in Chemistry 10, 982757 (2022)
Link: https://doi.org/10.3389/fchem.2022.982757
Nonadditive ion effects on the coil-globule equilibrium of PNIPAM: a computer simulation study
Yani Zhao, Saminath Bharadwaj, Nico F.A. van der Vegt
Phys. Chem. Chem. Phys. 24, 10346-10355 (2022)
Link: https://doi.org/10.1039/d2cp00057a
Slow liquid dynamics near solid surfaces: Insights from site-resolved studies of ionic liquids in silica confinement
Robin Köster, Michael Vogel
The Journal of Chemical Physics 156, 074501 (2022)
Link: https://doi.org/10.1063/5.0079722
AlphaFold predicts the most complex protein knot and composite protein knots
Brems, Maarten A. and Runkel, Robert and Yeates, Todd O. and Virnau, Peter
Protein Science 31, e4380 (2022)
Link: https://doi.org/10.1002/pro.4380
On a Hybrid Continuum-Kinetic Model for Complex Fluids
A. Chertock, P. Degond, G. Dimarco, and M. Lukáčová-Medvid'ová
Partial Differ. Equ. Appl. 3, Paper No. 63, 28 pp. (2022)
Link: https://doi.org/10.1007/s42985-022-00198-9
Convergence and Error Analysis for Compressible Fluid Flows with Random Data: Monte Carlo Method
E. Feireisl, M. Lukáčová-Medvid'ová, B. She, B., Y. Yuan
Math. Mod. Meth. Appl. Sci. 32 (14), 2887-2925 (2022)
Link: https://doi.org/10.1142/S0218202522500671
Understanding and Modeling Polymers: The Challenge of Multiple Scales
F. Schmid
ACS Polymers Au 3, 28-58 (2022)
Link: https://doi.org/10.1021/acspolymersau.2c00049
Water Uptake by Gecko beta-Keratin and the Influence of the Relative Humidity on its Mechanical and Volumetric Properties
M. Khani, T. Materzok, H. Eslami, S. Gorb, and F. Müller-Plathe
J. R. Soc. Interface 19, 20220372 (2022)
Link: https://doi.org/10.1098/rsif.2022.0372
How Ethanolic Disinfectants Disintegrate Coronavirus Model Membranes: A Dissipative-Particle-Dynamics Simulation Study
T. Zhou, Z. Wu, S. Das, H. Eslami, and F. Müller-Plathe
Journal of Chemical Theory and Computation 18, 2597–2615 (2022)
Link: https://doi.org/10.1021/acs.jctc.1c01120
Self-Assembly of Model Triblock Janus Colloidal Particles in Two Dimensions
K. Bahri, H. Eslami, and Florian Müller-Plathe
Journal of Chemical Theory and Computation 18, 1870–1882 (2022)
Link: https://doi.org/10.1021/acs.jctc.1c01116
Mobility of polymer melts in a regular array of carbon nanotubes
S.A.N. Alberti, J. Schneider, and F. Müller-Plathe
Journal of Chemical Theory and Computation 18, 3285–3295 (2022)
Link: https://doi.org/10.1021/acs.jctc.1c01281
Boron-Modified Perhydropolysilazane Towards Facile and Economical Synthesis of Amorphous SiBN Ceramic with Excellent Thermal Stability
Y. Zhan, W. Li, T. Jiang, C. Fasel, E. Ricohermoso III, J. Bernauer, Z. Yu, Z. Wu, F. Müller-Plathe, L. Molina-Luna, R. Grottenmüller, and R. Riedel
Journal of Advanced Ceramics 11, 1104–1116 (2022)
Link: https://doi.org/10.1007/s40145-022-0597-z
Slip-Spring Hybrid Particle-Field Model for Coarse-Graining Branched Polymer Melts: Polystyrene Melts as an Example
Z. Wu and F. Müller-Plathe
Journal of Chemical Theory and Computation 18, 3814–3828 (2022)
Link: https://doi.org/10.1021/acs.jctc.2c00107
Roughness volumes: An improved RoughMob concept for predicting the increase of molecular mobility upon coarse-graining
M.K. Meinel and F. Müller-Plathe
The Journal of Physical Chemistry B 126, 3737−3747 (2022)
Link: https://doi.org/10.1021/acs.jpcb.2c00944
Passive probe particle in an active bath: can we tell it is out of equilibrium?
Jeanine Shea, Gerhard Jung, Friederike Schmid
Soft Matter, 2022,18, 6965-6973, (2022)
Link: https://doi.org/10.1039/d2sm00905f
Force Generation in Confined Active Fluids: The Role of Microstructure
Shuvojit Paul, Ashreya Jayaram, N Narinder, Thomas Speck, Clemens Bechinger
Physical Review Letters 129, 058001 (2022)
Link: https://doi.org/10.1103/PhysRevLett.129.058001
Penalization method for the Navier-Stokes-Fourier system
Danica Basarić, Eduard Feireisl, Mária Lukáčová-Medviďová, Hana Mizerová, Yuhuan Yuan
ESAIM: Mathematical Modelling and Numerical Analysis, (2022)
Link: https://doi.org/10.1051/m2an/2022063
Existence of Dissipative Solutions to the Compressible Navier-Stokes System with Potential Temperature Transport
M. Lukáčová-Medvid'ová, A. Schömer
Journal of Mathematical Fluid Mechanics 24, 82 (2022)
Link: https://doi.org/10.1007/s00021-022-00713-3
Global existence of weak solutions to viscoelastic phase separation: Part I Regular Case
Aaron Brunk, Mária Lukáčová-Medvid'ová
Nonlinearity 35, 3417-3458, (2022)
Link: https://doi.org/10.1088/1361-6544/ac5920
Global existence of weak solutions to viscoelastic phase separation: Part II Degenerate Case
A. Brunk, M. Lukáčová-Medvid'ová
Nonlinearity 35, 3459-3486, (2022)
Link: https://doi.org/10.1088/1361-6544/ac591e
A variational framework for the inverse Henderson problem of statistical mechanics
Fabio Frommer and Martin Hanke
Letters in Mathematical Physics 112, 71, (2022)
Link: https://doi.org/10.1007/s11005-022-01563-w
Employing Artificial Neural Networks to Identify Reaction Coordinates and Pathways for Self-Assembly
Jörn H. Appeldorn, Simon Lemcke, Thomas Speck, Arash Nikoubashman
The Journal of Physical Chemistry B 126 (27), 5007-5016, (2022)
Link: https://doi.org/10.1021/acs.jpcb.2c02232
Wavefunction-Based Electrostatic-Embedding QM/MM Using CFOUR through MiMiC
Till Kirsch, Jógvan Magnus Haugaard Olsen, Viacheslav Bolnykh, Simone Meloni, Emiliano Ippoliti, Ursula Rothlisberger, Michele Cascella, Jürgen Gauss
Journal of Chemical Theory and Computation 18 (1),13-24 (2022)
Link: https://doi.org/10.1021/acs.jctc.1c00878
Cross-correlation corrected friction in generalized Langevin models: Application to the continuous Asakura–Oosawa model
Viktor Klippenstein, Nico F. A. van der Vegt
The Journal of Chemical Physics 157, 044103 (2022)
Link: https://doi.org/10.1063/5.0093056
A multi-scale method for complex flows of non-Newtonian fluids
F. Tedeschi, G.G. Giusteri, L. Yelash, M. Lukáčová-Medvid’ova
Mathematics in Engineering 4, 6 (2022)
Link: https://doi.org/10.3934/mine.2022050
Existence, Regularity and Weak-Strong Uniqueness for Three-Dimensional Peterlin Viscoelastic Model
Brunk, A., Lu, Y., and Lukáčová-Medvid'ová, M.
Commun. Math. Sci. 20, 2022, 201-230 (2022)
Link: https://doi.org/10.4310/CMS.2022.v20.n1.a6
Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials
Benjamin Pampel and Omar Valsson
Journal of Chemical Theory and Computation 18, 7, 4127–4141 (2022)
Link: https://doi.org/10.1021/acs.jctc.2c00197
Where Lennard-Jones Potentials Fail: Iterative Optimization of Ion–Water Pair Potentials Based on Ab Initio Molecular Dynamics Data
Marvin P. Bernhardt, Yuki Nagata, Nico F.A. van der Vegt
Journal of Physical Chemistry Letters 13, 16, 3712–3717 (2022)
Link: https://doi.org/10.1021/acs.jpclett.2c00121
2021 - Publications
Glass transition temperature prediction of disordered molecular solids
Kun-Han Lin, Leanne Paterson, Falk May, Denis Andrienko
NPJ Comp. Materials 7, 179 (2021)
Link: https://doi.org/10.1038/s41524-021-00647-w
On the origin of controlled anisotropic growth of monodisperse gold nanobipyramids
S.K. Meena, F. Lerouge, P. Baldeck, Ch. Andraud, M. Garavelli, S. Parola, M. Sulpizi, I. Rivalta
Nanoscale 13, 15292-15300 (2021)
Link: https://doi.org/10.1039/d1nr01768c
Circuits and excitations to enable Brownian token-based computing with skyrmions
Maarten A. Brems, Mathias Kläui, Peter Virnau
Applied Physics Letters 119, 132405 (2021)
Link: https://doi.org/10.1063/5.0063584
Second-order invariants of the inviscid Lundgren-Monin-Novikov equations for 2d vorticity fields
V.N. Grebenev, A.N. Grichkov, M. Oberlack, M. Waclawczyk
Z. Angew. Mathematik und Physik 72, 129 (2021)
Link: https://doi.org/10.1007/s00033-021-01562-2
Extremes of the 2d scale-inhomogeneous discrete Gaussian free field: Extremal process in the weakly correlated regime
Maximilian Fels, Lisa Hartung
ALEA - Latin American Journal of Probability and Mathematical Statistics 18, 1689-1718 (2021)
Link: https://doi.org/10.30757/ALEA.v18-62
Extremes of the 2d scale-inhomogeneous discrete Gaussian free field: Convergence of the maximum in the regime of weak correlations
Maximilian Fels, Lisa Hartung
ALEA - Latin American Journal of Probability and Mathematical Statistics 18, 18901-1930 (2021)
Link: https://doi.org/10.30757/ALEA.v18-71
Chemical Design Rules for Non-Fullerene Acceptors in Organic Solar Cells
A. Markina, K.-H. Lin, W. Liu, C. Pölking, Y. Firdaus, D.R. Villalva, J.I. Khan, S.H.K. Paleti, G.T. Harrison, J. Gorenflot, W. Zhang, S. de Wolf, I. McCulloch, T.D. Anthopoulos, D. Baran, F. Laquai, D. Andrienko
Adv. Energy Materials 11, 2102363 (2021)
Link: https://doi.org/10.1002/aenm.202102363
A model reduction approach for inverse problems with operator valued data
Jürgen Dölz, Herbert Egger, Matthias Schlottbohm
Numerische Mathematik 148, 889-917 (2021)
Link: https://doi.org/10.1007/s00211-021-01224-5
The nanoscale structure of the Pt-water double layer under bias revealed
Remi Khatib, Ashwinee Kumar, Stefano Sanvito, Marialore Sulpizi, Clotilde S. Cucinotta
Electrochimica Acta 391, 138875 (2021)
Link: https://doi.org/10.1016/j.electacta.2021.138875
On the Stability of Harmonic Coupling Methods with Application to Electric Machines
H. Egger, M. Haruyunyan, M. Merkel, S. Schops
Scientific Computing in Electrical Engineering 36, 117-125 (2021)
Link: https://doi.org/10.1007/978-3-030-84238-3\_12
On the structure preserving high-order approximation of quasistatic poroelasticity
H. Egger, M. Sabouri
Mathematics and Computers in Simulation 189, 237-252 (2021)
Link: https://doi.org/10.1016/j.matcom.2020.12.029
Multistep and Runge-Kutta convolution quadrature methods for coupled dynamical systems
H. Egger, K. Schmidt, V. Shashkov
J. Comp. Appl. Math. 387, 112618 (2021)
Link: https://doi.org/10.1016/j.cam.2019.112618
A fast and oblivious matrix compression algorithm for Volterra integral operators
J. Dölz, H. Egger, V. Shashkov
Adv. Comp. Math. 47, 81 (2021)
Link: https://doi.org/10.1007/s10444-021-09902-6
A Convolution Quadrature Method for Maxwell's Equations in Dispersive Media
Jürgen Dolz, Herbert Egger, Vsevolod Shashkov
Sci. Computing in Electrical Engineering (SCEE 2020) 36, 107-115 (2021)
Link: https://doi.org/10.1007/978-3-030-84238-3\_11
Studying the Evolution of Neural Activation Patterns During Training of Feed-Forward ReLU Networ
David Hartmann, Daniel Franzen, Sebastian Brodehl
Frontiers in Artificial Intelligence 4 (2021)
Link: https://doi.org/10.3389/frai.2021.642374
Modeling of biomolecular machines in non-equilibrium steady states
Thomas Speck
The Journal of Chemical Physics 155, 230901 (2021)
Link: https://doi.org/10.1063/5.0070922
Cross-correlation corrected friction in (generalized) Langevin models
Viktor Klippenstein, Nico F. A. van der Vegt
The Journal of Chemical Physics 154 (19), 191102 (2021)
Link: https://doi.org/10.1063/5.0049324
Hunting active Brownian particles: Learning optimal behavior
Marcel Gerhard, Ashreya Jayaram, Andreas Fischer, and Thomas Speck
Physical Review Letters 104, 054614, (2021)
Link: https://doi.org/10.1103/PhysRevE.104.054614
Direct Calculation of Entropic Components in Cohesive Interaction Free Energies
Saminath Bharadwaj, Shadrack B. Jabes, Nico F. A. van der Vegt
The Journal of Physical Chemistry B 125, 11026-11035 (2021)
Link: https://doi.org/10.1021/acs.jpcb.1c05748
Fluctuation–dissipation relations far from equilibrium: a case study
Gerhard Jung, Friederike Schmid
Soft Matter 17 (26), 6413-6425 (2021)
Link: https://doi.org/10.1039/D1SM00521A
Introducing Memory in Coarse-Grained Molecular Simulations
Viktor Klippenstein, Madhusmita Tripathy, Gerhard Jung, Friederike Schmid, Nico F. A. van der Vegt
The Journal of Physical Chemistry B125 (19), 4931-4954 (2021)
Link: https://doi.org/10.1021/acs.jpcb.1c01120
Mathematical analysis of some iterative methods for the reconstruction of memory kernels
Martin Hanke
ETNA - Electronic Transactions on Numerical Analysis 54, 483-498 (2021)
Link: https://doi.org/10.1553/etna_vol54s483
Model reduction techniques for the computation of extended Markov parameterizations for generalized Langevin equations
N Bockius, J Shea, G Jung, F Schmid, M Hanke
Journal of Physics: Condensed Matter 33 (21), 214003 (2021)
Link: https://doi.org/10.1088/1361-648X/abe6df
Effects of shear flow on the structure and dynamics of ionic liquids in a metallic nanoconfinement
Samuel Ntim, Marialore Sulpizi
Physical Chemistry Chemical Physics 23, 24357-24364 (2021)
Link: https://doi.org/10.1039/d1cp01055g
Role of pH in the synthesis and growth of gold nanoparticles using L-Asparagine: A combined experimental and simulation study
Ricardo Baez, Luis A. Baptista, Samuel Ntim, Paulraj Manidurai, Shirly Espinoza, Charusheela Ramanan, Robinson Cortes-Huerto, Marialore Sulpizi
Journal of Physics: Condensed Matter, (2021)
Link: https://doi.org/10.1088/1361-648X/abf6e3
Dynamical properties across different coarse-grained models for ionic liquids
Joseph F Rudzinski, Sebastian Kloth, Svenja Wörner, Tamisra Pal, Kurt Kremer, Tristan Bereau, Michael Vogel
Journal of Physics: Condensed Matter 33 (22), 224001 (2021)
Link: https://doi.org/10.1088/1361-648x/abe6e1
Simulation of Elastomers by Slip-Spring Dissipative Particle Dynamics
J. Schneider, F. Fleck, H. A. Karimi-Varzaneh, F. Müller-Plathe
Macromolecules 54, 5155 (2021)
Link: https://doi.org/10.1021/acs.macromol.1c00567
The Role of the Envelope Protein in the Stability of a Coronavirus Model Membrane against an Ethanolic Disinfectant
S. Das, M.K. Meinel, Z. Wu, F. Müller-Plathe
The Journal of Chemical Physics, 245101 (2021)
Link: https://doi.org/10.1063/5.0055331
Sequence-Engineering Polyethylene–Polypropylene Copolymers with High Thermal Conductivity Using a Molecular-Dynamics-Based Genetic Algorithm
Tianhang Zhou, Zhenghao Wu, Hari Krishna Chilukoti, Florian Müller-Plathe
Journal of Chemical Theory and Computation17 (6),3772-3782 (2021)
Link: https://doi.org/10.1021/acs.jctc.1c00134
Combination of Hybrid Particle-Field Molecular Dynamics and Slip-Springs for the Efficient Simulation of Coarse-Grained Polymer Models: Static and Dynamic Properties of Polystyrene Melts
Zhenghao Wu, Giuseppe Milano, and Florian Müller-Plathe
Journal of Chemical Theory and Computation 17, 474–487 (2021)
Link: https://doi.org/10.1021/acs.jctc.0c00954
Atomistic hybrid particle-field molecular dynamics combined with slip-springs: Restoring entangled dynamics to simulations of polymer melts
Z. Wu, A. Kalogirou, A. De Nicola, G. Milano, F. Müller-Plathe
Journal of Computational Chemistry 42, 6-18 (2021)
Link: https://doi.org/10.1002/jcc.26428
Knotting Behaviour of Polymer Chains in the Melt State for Soft-core Models with and without Slip-springs
Zhenghao Wu, Simon N. A. Alberti, Jurek Schneider, Florian Müller-Plathe
Journal of Physics: Condensed Matter, (2021)
Link: https://doi.org/10.1088/1361-648X/abef25
Mechanisms of Nucleation and Solid−Solid-Phase Transitions in Triblock Janus Assemblies
Hossein Eslami, Ali Gharibi and Florian Müller-Plathe
Journal of Chemical Theory and Computation 17 (3), 1742−1754 (2021)
Link: https://doi.org/10.1021/acs.jctc.0c01080
Interactions in active colloids
Benno Liebchen, Aritra K Mukhopadhyay
Journal of Physics: Condensed Matter 34 (8), 083002 (2021)
Link: https://doi.org/10.1088/1361-648X/ac3a86
Active droploids
Jens Grauer, Falko Schmidt, Jesús Pineda, Benjamin Midtvedt, Hartmut Löwen, Giovanni Volpe, Benno Liebchen
Nature Communications 12 (1), 6005 (2021)
Link: https://doi.org/10.1038/s41467-021-26319-3
Coarse-grained model of a nanoscale-segregated ionic liquid for simulations of low-temperature structure and dynamics
Sebastian Kloth, Marvin P Bernhardt, Nico F A van der Vegt, Michael Vogel
Journal of Physics: Condensed Matter 33 (20), 204002 (2021)
Link: https://doi.org/10.1088/1361-648X/abe606
An interplay of excluded-volume and polymer–(co)solvent attractive interactions regulates polymer collapse in mixed solvents
Swaminath Bharadwaj, Divya Nayar, Cahit Dalgicdir, Nico F. A. van der Vegt
The Journal of Chemical Physics154 (13), 134903 (2021)
Link: https://doi.org/10.1063/5.0046746
Iterative integral equation methods for structural coarse-graining
Marvin P. Bernhardt, Martin Hanke, Nico F. A. van der Vegt
The Journal of Chemical Physics 154 (8), 084118 (2021)
Link: https://doi.org/10.1063/5.0038633
Ultra-coarse-graining of homopolymers in inhomogeneous systems
Fabian Berressem, Christoph Scherer, Denis Andrienko, Arash Nikoubashman
Journal of Physics: Condensed Matter 33 (25), 254002 (2021)
Link: https://doi.org/10.1088/1361-648X/abf6e2
Computing inelastic neutron scattering spectra from molecular dynamics trajectories
Thomas F. Harrelson, Makena Dettmann, Christoph Scherer, Denis Andrienko, Adam J. Moulé, Roland Faller
Scientific Reports 11 (1), 7938 (2021)
Link: https://doi.org/10.1038/s41598-021-86771-5
BoltzmaNN: Predicting effective pair potentials and equations of state using neural networks
F. Berressem and A. Nikoubashman
The Journal of Chemical Physics 154, 124123 (2021)
Link: https://doi.org/10.1063/5.0045441
Force probe simulations using an adaptive resolution scheme
Marco Oestereich, J Gauss, Gregor Diezemann
Journal of Physics: Condensed Matter 33, 194005 (2021)
Link: https://doi.org/10.1088/1361-648X/abed18
Density-functional-theory approach to the Hamiltonian adaptive resolution simulation method
L A Baptista, R C Dutta, M Sevilla, M Heidari, R Potestio, K Kremer, R Cortes-Huerto
Journal of Physics: Condensed Matter 33 (18), 184003 (2021)
Link: https://doi.org/10.1088/1361-648X/abed1d
Dynamic coarse-graining of polymer systems using mobility functions
Bing Li, Kostas Daoulas, Friederike Schmid
Journal of Physics: Condensed Matter 33 (19), 194004 (2021)
Link: https://doi.org/10.1088/1361-648X/abed1b
Comparing equilibration schemes of high-molecular-weight polymer melts with topological indicators
Luca Tubiana, Hideki Kobayashi, Raffaello Potestio, Burkhard Duenweg, Kurt Kremer, Peter Virnau, Kostas Daoulas
Journal of Physics: Condensed Matter, (2021)
Link: https://doi.org/10.1088/1361-648x/abf20c
General Nonlinearities in SO(2)-Equivariant CNNs
Daniel Franzen, Michael Wand
NeurIPS 2021 Proceedings paper
Link: https://proceedings.neurips.cc/paper_files/paper/2021/file/4bfbd52f4e8466dc12aaf30b7e057b66-Paper.pdf
Adversarial reverse mapping of condensed-phase molecular structures: Chemical transferability
Marc Stieffenhofer, Tristan Bereau, Michael Wand
APL Materials 9 (3), 031107 (2021)
Link: https://doi.org/10.1063/5.0039102
Adsorption Active Diblock Copolymers as Universal Agents for Unusual Barrier-Free Transitions in Stimuli-Responsive Brushes
Shuanhu Qi, Leonid I. Klushin, Alexander M. Skvortsov, Friederike Schmid
Macromolecules 54 (6), 2592-2603 (2021)
Link: https://doi.org/10.1021/acs.macromol.0c02095
Systematic derivation of hydrodynamic equations for viscoelastic phase separation
Dominic Spiller, Aaron Brunk, Oliver Habrich, Herbert Egger, Mária Lukáčová-Medvid'ová and Burkhard Dünweg
Journal of Physics: Condensed Matter 33 (36), 364001 (2021)
Link: https://doi.org/10.1088/1361-648X/ac0d17
Analysis of a viscoelastic phase separation model
Aaron Brunk, Burkhard Dünweg, Herbert Egger, Oliver Habrich, Mária Lukáčová-Medvid'ová, Dominic Spiller
Journal of Physics: Condensed Matter 33 (23), 234002 (2021)
Link: https://doi.org/10.1088/1361-648X/abeb13
A Second-Order Finite Element Method with Mass Lumping for Maxwell's Equations on Tetrahedra
Herbert Egger, Bogdan Radu
SIAM Journal on Numerical Analysis 59 (2), 864-885 (2021)
Link: https://doi.org/10.1137/20m1318912
Shear thinning in oligomer melts - molecular origins and applications
R. Datta, L. Yelash, F. Schmid, F. Kummer, M. Oberlack, M. Lukáčová-Medvid'ová, P. Virnau
Polymers 13 (16), 2806 (2021)
Link: https://doi.org/10.3390/polym13162806
Computing oscillatory solutions of the Euler system via K-convergence
Eduard Feireisl, Mária Lukáčová–Medvid’ová, Bangwei She, Yue Wang
Mathematical Models and Methods in Applied Sciences 31 (03), 537-576 (2021)
Link: https://doi.org/10.1142/S0218202521500123
Commensurability between Element Symmetry and the Number of Skyrmions Governing Skyrmion Diffusion in Confined Geometries
Chengkun Song, Nico Kerber, Jan Rothörl, Yuqing Ge, Klaus Raab, Boris Seng, Maarten A. Brems, Florian Dittrich, Robert M. Reeve, Jianbo Wang, Qingfang Liu, Peter Virnau, Mathias Kläui
Advanced Functional Materials 31 (19), 2010739 (2021)
Link: https://doi.org/10.1002/adfm.202010739
Book: Numerical methods for compressible fluid flows
E. Feireisl, M. Lukáčová-Medvid'ová, H. Mizerova, B. She
Springer, Modeling, Simulation and Applications, Vol. 20 (2021)
Link: https://doi.org/10.1007/978-3-030-73788-7
Probability theory of active suspensions
B. Deußen, M. Oberlack, Y. Wang
Physics of Fluids 33 (6), 061902 (2021)
Link: https://doi.org/10.1063/5.0047227
Vorticity Determines the Force on Bodies Immersed in Active Fluids
Thomas Speck, Ashreya Jayaram
Physical Review Letters 126 (13), (2021)
Link: https://doi.org/10.1103/PhysRevLett.126.138002
High-order simulation scheme for active particles driven by stress boundary conditions
B Deußen, A Jayaram, F Kummer, Y Wang, T Speck, M Oberlack
Journal of Physics: Condensed Matter33 (24),244004 (2021)
Link: https://doi.org/10.1088/1361-648X/abf8cf
Wall slip and bulk yielding in soft particle suspensions
Gerhard Jung, Suzanne M. Fielding
Journal of Rheology 65 (2), 199-212 (2021) Publication resulting from a PhD secondment of Gerhard Jung (TRR student) in Durham in 2018
Link: https://doi.org/10.1122/8.0000171
General Nonlinearities in SO(2)-Equivariant CNNs
Daniel Franzen, Michael Wand
NeurIPS 2021 Proceedings paper
Link: https://proceedings.neurips.cc/paper_files/paper/2021/file/4bfbd52f4e8466dc12aaf30b7e057b66-Paper.pdf
2020 - Publications
Skyrmion Lattice Phases in Thin Film Multilayer
Jakub Zázvorka, Florian Dittrich, Yuqing Ge, Nico Kerber, Klaus Raab, Thomas Winkler, Kai Litzius, Martin Veis, Peter Virnau, Mathias Kläui
Advanced Functional Materials 30 (46), 2004037 (2020)
Link: https://doi.org/10.1002/adfm.202004037
Convergence of finite volume schemes for the Euler equations via dissipative measure--valued solutions
E. Feireisl, M. Lukáčová-Medvid’ová, H. Mizerová
Foundations of Computational Mathematics 20, 923-966 (2020)
Link: https://doi.org/10.1007/s10208-019-09433-z
A finite volume scheme for the Euler system inspired by the two velocities approach
E. Feireisl, M. Lukáčová-Medvid'ová, H. Mizerova
Numerical Mathematics 144 (89-132), (2020)
Link: https://doi.org/10.1007/s00211-019-01078-y
K-convergence of finite volume solutions of the Euler equations
Mária Lukáčová-Medvid'ová
Finite volues for complex applications IX, 323, 25-37 (2020)
Link: https://doi.org/10.1007/978-3-030-43651-3\_2
K-convergence as a new tool in numerical analysis
E.Feireisl, M. Lukáčová-Medvid'ová, H. Mizerova
IMA Journal of Numerical Analysis 40, 2227–2255 (2020)
Link: https://doi.org/10.1093/imanum/drz045
On the convergence of a finite volume method for the Navier–Stokes–Fourier system
E.Feireisl, M. Lukáčová-Medvid'ová, H. Mizerova, B. She
IMA Journal of Numerical Analysis, (2020)
Link: https://doi.org/10.1093/imanum/draa060
Compression-induced anti-nematic order in glassy and semicrystalline polymers
Sara Jabbari-Farouji, Damien Vandembroucq
Soft Matter 16 (1), 102-106 (2020)
Link: https://doi.org/10.1039/c9sm01848d
Emergent pattern formation of active magnetic suspensions in an external field
Fabian R Koessel, Sara Jabbari-Farouji
New Journal of Physics 22 (10), 103007 (2020)
Link: https://doi.org/10.1088/1367-2630/abb64d
Quorum-sensing active particles with discontinuous motility
Andreas Fischer, Friederike Schmid, Thomas Speck
Physical Review E101 (1), 012601 (2020)
Link: https://doi.org/10.1103/PhysRevE.101.012601
From scalar to polar active matter: Connecting simulations with mean-field theory
Ashreya Jayaram, Andreas Fischer, Thomas Speck
Physical Review E 101 (2), (2020)
Link: https://doi.org/10.1103/PhysRevE.101.022602
Statistical theory of helical turbulence
B. Deußen, D. Dierkes, and M. Oberlack
Physics of Fluids 32 (6), 065109 (2020)
Link: https://doi.org/10.1063/5.0010874
How Alcoholic Disinfectants Affect Coronavirus Model Membranes: Membrane Fluidity, Permeability, and Disintegration
Hossein Eslami, Shubhadip Das, Tianhang Zhou, Florian Müller-Plathe
The Journal of Physical Chemistry B 124, 10374-10385 (2020)
Link: https://doi.org/10.1021/acs.jpcb.0c08296
Hamiltonian and alias-free hybrid particle-field molecular dynamic
Sigbjørb Løland Bore, Michele Cascella
The Journal of Chemical Physics 152, 094106 (2020)
Link: https://doi.org/10.1063/5.0020733
Characterizing Polymer Hydration Shell Compressibilities with the Small-System Method
Madhusmita Tripathy, Swaminath Bharadwaj, Shadrack B. Jabes, Nico F. A. van der Vegt
Nanomaterials 10 (8), 1460 (2020)
Link: https://doi.org/10.3390/nano10081460
Role of image charges in ionic liquid confined between metallic interfaces
Samuel Ntim, Marialore Sulpizi
Physical Chemistry Chemical Physics 22 (19), 10786-10791 (2020)
Link: https://doi.org/10.1039/d0cp00409j
Structure and Dynamics of Solid/Liquid Interfaces
Marie‐Pierre Gaigeot Marialore Sulpizi
Surface and Interface Science: Volume 7: Liquid and Biological Interfaces Volume 7 (Chapter 50), 143-193 (2020)
Link: https://doi.org/10.1002/9783527680597.ch50
Surface Charges at the CaF 2 /Water Interface Allow Very Fast Intermolecular Vibrational‐Energy Transfer
Dominika Lesnicki, Zhen Zhang, Mischa Bonn, Marialore Sulpizi, Ellen H. G. Backus
Angewandte Chemie International Edition 59 (31), 13116-13121 (2020)
Link: https://doi.org/10.1002/anie.202004686
Oberflächenladungen an der CaF 2 ‐Wasser‐Grenzfläche erlauben eine sehr schnelle intermolekulare Übertragung von Schwingungsenergie
Dominika Lesnicki, Zhen Zhang, Mischa Bonn, Marialore Sulpizi, Ellen H. G. Backus
Angewandte Chemie 132 (31), 13217-13222 (2020)
Link: https://doi.org/10.1002/ange.202004686
Coarse-grained model of a nanoscale-segregated ionic liquid for simulations of low-temperature structure and dynamics
Joseph F. Rudzinski and Tristan Bereau
The Journal of Chemical Physics 153, 214110 (2020)
Link: https://doi.org/10.1063/5.0031249
Loss of Molecular Roughness upon Coarse-Graining Predicts the Artificially Accelerated Mobility of Coarse-Grained Molecular Simulation Models
M. K. Meinel, F. Müller-Plathe
Journal of Chemical Theory and Computation 16, 1411 (2020)
Link: https://doi.org/10.1021/acs.jctc.9b00943
Application of the 2PT model to understanding entropy change in molecular coarse-graining
Marvin P. Bernhardt, Marco Dallavalle, Nico F. A. Van der Vegt
Soft Materials 18 (2-3), 274-289 (2020)
Link: https://doi.org/10.1080/1539445X.2020.1737118
Free Energies of the Disassembly of Viral Capsids from a Multiscale Molecular Simulation Approach
Matias Martinez, Christopher D. Cooper, Adolfo B. Poma, Horacio V. Guzman
J. Chem. Inf. Modeling 60, 974-981 (2020)
Link: https://doi.org/10.1021/acs.jcim.9b00883
A generalized Newton iteration for computing the solution of the inverse Henderson problem
Fabrice Delbary, Martin Hanke, Dmitry Ivanizki
Inverse Problems in Science and Engineering, 1-25 (2020)
Link: https://doi.org/10.1080/17415977.2019.1710504
Supramolecular Packing Drives Morphological Transitions of Charged Surfactant Micelles
Ken Schäfer, Hima Bindu Kolli, Mikkel Killingmoe Christensen, Sigbjørn Løland Bore, Gregor Diezemann, Jürgen Gauss, Giuseppe Milano, Reidar Lund, Michele Cascella
Angewandte Chemie International Edition 59 (42), 18591-18598 (2020)
Link: https://doi.org/10.1002/anie.202004522
Force-dependent folding pathways in mechanically interlocked calixarene dimers via atomistic force quench simulations
Ken Schäfer, Gregor Diezemann
Molecular Physics 118 (19-20), e1743886 (2020)
Link: https://doi.org/10.1080/00268976.2020.1743886
Adaptive Resolution Molecular Dynamics Technique
M. Praprotnik, R. Cortes-Huerto, R. Potestio, L. Delle Site
Handbook of Materials Modeling, Pages 1443-1457, Springer International Publishing (2020)
Link: https://doi.org/10.1007/978-3-319-44677-6_89
Why Do Elastin-Like Polypeptides Possibly Have Different Solvation Behaviors in Water–Ethanol and Water–Urea Mixtures?
Yani Zhao, Manjesh K. Singh, Kurt Kremer, Robinson Cortes-Huerto, Debashish Mukherji
Macromolecules 53 (6), 2101-2110 (2020)
Link: https://doi.org/10.1021/acs.macromol.9b02123
Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model
Yani Zhao, Robinson Cortes-Huerto, Kurt Kremer, Joseph F. Rudzinski
The Journal of Physical Chemistry B124 (20),4097-4113 (2020)
Link: https://doi.org/10.1021/acs.jpcb.0c01949
Open-boundary Hamiltonian adaptive resolution. From grand canonical to non-equilibrium molecular dynamics simulations
Maziar Heidari, Kurt Kremer, Ramin Golestanian, Raffaello Potestio, Robinson Cortes-Huerto
The Journal of Chemical Physics 152 (19), 194104 (2020)
Link: https://doi.org/10.1063/1.5143268
Automated determination of hybrid particle-field parameters by machine learning
Morten Ledum, Sigbjørn Løland Bore, Michele Cascella
Molecular Physics 118 (19-20), e1785571 (2020)
Link: https://doi.org/10.1080/00268976.2020.1785571
Hybrid particle-field molecular dynamics under constant pressure
Sigbjørn Løland Bore, Hima Bindu Kolli, Antonio De Nicola, Maksym Byshkin, Toshihiro Kawakatsu, Giuseppe Milano, Michele Cascella
The Journal of Chemical Physics 152, 184908 (2020)
Link: https://doi.org/10.1063/5.0007445
The Grignard Reaction – Unraveling a Chemical Puzzle
Raphael Mathias Peltzer, Jürgen Gauss, Odile Eisenstein, Michele Cascella
Journal of the American Chemical Society 142 (6), 2984-2994 (2020)
Link: https://doi.org/10.1021/jacs.9b11829
A minimal Gō-model for rebuilding whole genome structures from haploid single-cell Hi-C data
S. Wettermann, M. Brems, J.T. Siebert, G.T. Vu, T.J. Stevens, P. Virnau
Computational Materials Science 173, 109178 (2020)
Link: https://doi.org/10.1016/j.commatsci.2019.109178
Can Soft Models Describe Polymer Knots?
Jianrui Zhang, Hendrik Meyer, Peter Virnau, Kostas Ch. Daoulas
Macromolecules 53 (23), 10475-10486 (2020)
Link: https://doi.org/10.1021/acs.macromol.0c02079
Adversarial reverse mapping of equilibrated condensed-phase molecular structures
Marc Stieffenhofer, Michael Wand, Tristan Bereau
Machine Learning: Science and Technology 1, 045014 (2020)
Link: https://doi.org/10.1088/2632-2153/abb6d4
Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids
Christoph Scherer, René Scheid, Denis Andrienko, Tristan Bereau
Journal of Chemical Theory and Computation 16 (5), 3194-3204 (2020)
Link: https://doi.org/10.1021/acs.jctc.9b01256
Defects and defect engineering in Soft Matter
Amir Jangizehi, Friederike Schmid, Pol Besenius, Kurt Kremer, Sebastian Seiffert
Soft Matter 16 (48), 10809-10859 (2020)
Link: https://doi.org/10.1039/d0sm01371d
Dynamic Self-Consistent Field Approach for Studying Kinetic Processes in Multiblock Copolymer Melts
Friederike Schmid, Bing Li
Polymers 12 (10), 2205 (2020)
Link: https://doi.org/10.3390/polym12102205
Bottom-up Construction of Dynamic Density Functional Theories for Inhomogeneous Polymer Systems from Microscopic Simulations
Sriteja Mantha, Shuanhu Qi, Friederike Schmid
Macromolecules 53 (9), 3409-3423 (2020)
Link: https://doi.org/10.1021/acs.macromol.0c00130
Using Copolymers to Design Tunable Stimuli-Reponsive Brushes
Shuanhu Qi, Leonid I. Klushin, Alexander M. Skvortsov, Friederike Schmid
Macromolecules 53 (13), 5326-5336 (2020)
Link: https://doi.org/10.1021/acs.macromol.0c00674
On the Energy Stable Approximation of Hamiltonian and Gradient Systems
Herbert Egger, Oliver Habrich, Vsevolod Shashkov
Computational Methods in Applied Mathematics 21 (2), 335-349 (2020)
Link: https://doi.org/10.1515/cmam-2020-0025/html
On a Second-Order Multipoint Flux Mixed Finite Element Methods on Hybrid Meshes
Herbert Egger, Bogdan Radu
SIAM Journal on Numerical Analysis 58 (3), 1822-1844 (2020)
Link: https://doi.org/10.1137/19M1236862
Chemotaxis on networks: Analysis and numerical approximation
Herbert Egger, Lukas Schöbel-Kröhn
ESAIM: Mathematical Modelling and Numerical Analysis 54 (4), 1339-1372 (2020)
Link: https://doi.org/10.1051/m2an/2019069
Structure Preserving Discretization of Allen–Cahn Type Problems Modeling the Motion of Phase Boundaries
Anke Böttcher, Herbert Egger
Vietnam Journal of Mathematics 48 (4), 847-863 (2020)
Link: https://doi.org/10.1007/s10013-020-00428-w
A mass-lumped mixed finite element method for acoustic wave propagation
Herbert Egger, Bogdan Radu
Numerische Mathematik 145 (2), 239-269 (2020)
Link: https://doi.org/10.1007/978-3-030-44101-2\_2
On the transport limit of singularly perturbed convection–diffusion problems on networks
Herbert Egger, Nora Philippi
Mathematical Methods in the Applied Sciences 44 (6), 5005-5020 (2020)
Link: https://doi.org/10.1002/mma.7084
Semiautomatic construction of lattice Boltzmann models
Dominic Spiller, Burkhard Dünweg
Physical Review E101 (4), (2020)
Link: https://doi.org/10.1103/PhysRevE.101.043310
2019 - Publications
Thermal skyrmion diffusion used in a reshuffler device
Jakub Zázvorka, Florian Jakobs, Daniel Heinze, Niklas Keil, Sascha Kromin, Samridh Jaiswal, Kai Litzius, Gerhard Jakob, Peter Virnau, Daniele Pinna, Karin Everschor-Sitte, Levente Rózsa, Andreas Donges, Ulrich Nowak, Mathias Kläui
Nature Nanotechnology 14 (7), 658-661 (2019)
https://doi.org/10.1038/s41565-019-0436-8
Convergence of a finite volume scheme for the compressible Navier-Stokes system
E.Feireisl, M. Lukáčová-Medvid'ová, H. Mizerova
ESAIM: Mathematical Modelling and Numerical Analysis. 53, 1957–1979 (2019)
https://doi.org/10.1051/m2an/2019043
An asymptotic preserving scheme for kinetic chemotaxis models in two space dimensions
A. Chertock, A. Kurganov, M. Lukáčová-Medvid'ová, S. Nur Oezcan
Kinetic and Related Models 12 (1), 195–216 (2019)
https://doi.org/10.3934/krm.2019009
Supramolecular copolymers predominated by alternating order: Theory and application
Reinier van Buel, Daniel Spitzer, Christian Marijan Berac, Paul van der Schoot, Pol Besenius, Sara Jabbari-Farouji
The Journal of Chemical Physics 151 (1), 014902 (2019)
https://doi.org/10.1063/1.5097577
Controlling stability and transport of magnetic microswimmers by an external field
Fabian R. Koessel, Sara Jabbari-Farouji
EPL (Europhysics Letters)125 (2), 28001 (2019)
https://doi.org/10.1209/0295-5075/125/28001
ESPResSo++ 2.0: Advanced methods for multiscale molecular simulation
Horacio V. Guzman, Nikita Tretyakov, Hideki Kobayashi, Aoife C. Fogarty, Karsten Kreis, Jakub Krajniak, Christoph Junghans, Kurt Kremer, Torsten Stuehn
Computer Physics Communications 238, 66-76 (2019)
https://doi.org/10.1016/j.cpc.2018.12.017
Spontaneous spatiotemporal ordering of shape oscillations enhances cell migration
Matteo Campo, Simon K. Schnyder, John J. Molina, Thomas Speck, Ryoichi Yamamoto
Soft Matter 15 (24), 4939-4946 (2019)
https://doi.org/10.1039/c9sm00526a
Order–Order Phase Transitions Induced by Supercritical Carbon Dioxide in Triblock Copolymer Thin Films
Anabella A. Abate, Giang Thi Vu, Cristian M. Piqueras, María Cecilia del Barrio, Leopoldo R. Gómez, Gabriel Catalini, Friederike Schmid, Daniel A. Vega
Macromolecules 52 (20), 7786-7797 (2019)
https://doi.org/10.1021/acs.macromol.9b01278
Tackling the Limitations of Copolymeric Small Interfering RNA Delivery Agents by a Combined Experimental-Computational Approach
I. Tabujew, M. Heidari, C. Freidel, M. Helm, L. Tebbe, U. Woflrum, K. Nagel-Wolfrum, K. Koynov, P. Biehl, F.H. Schacher, R. Potestio, K. Peneva
Biomacromolecules 20, 4389-4406 (2019)
https://doi.org/10.1021/acs.biomac.9b01061
Anomalous Slowdown of Polymer Detachment Dynamics on Carbon Nanotubes
Daniel A. Vega, Andrey Milchev, Friederike Schmid, Mariano Febbo
Physical Review Letters 122, 218003 (2019)
https://doi.org/10.1103/PhysRevLett.122.218003
Classical nucleation theory for the crystallization kinetics in sheared liquids
David Richard, Thomas Speck
Physical Review E 99, 062801 (2019)
https://doi.org/10.1103/PhysRevE.99.062801
Conditional reversible work coarse-grained models with explicit electrostatics - An application to butylmethylimidazolium ionic liquids
Gregor Deichmann and Nico F. A. van der Vegt
Journal of Chemical Theory and Computation 15, 1187-1198 (2019)
https://doi.org/10.1021/acs.jctc.8b00881
Phase equilibria modeling with systematically coarse-grained models - A comparative study on state point transferability
Gregor Deichmann, Marco Dallavalle, David Rosenberger and Nico F. A. van der Vegt
The Journal of Physical Chemistry B123, 504-515 (2019)
https://doi.org/10.1021/acs.jpcb.8b07320
Frequency-Dependent Dielectric Polarizability of Flexible Polyelectrolytes in Electrolyte Solution: A Dissipative Particle Dynamics Simulation
Gerhard Jung, Sebastian Kasper, Friederike Schmid
Journal of The Electrochemical Society 166 (9), B3194-B3202 (2019)
https://doi.org/10.1149/2.0231909jes
Heterogeneous Interactions between Gas-Phase Pyruvic Acid and Hydroxylated Silica Surfaces: A Combined Experimental and Theoretical Study
Yuan Fang, Dominika Lesnicki, Kristin J. Wall, Marie-Pierre Gaigeot, Marialore Sulpizi, Veronica Vaida, Vicki H. Grassian
The Journal of Physical Chemistry A123 (5), 983-991 (2019)
https://doi.org/10.1021/acs.jpca.8b10224
Understanding the Acidic Properties of the Amorphous Hydroxylated Silica Surface
Maciej Gierada, Frank De Proft, Marialore Sulpizi, Frederik Tielens
The Journal of Physical Chemistry C123 (28), 17343-17352 (2019)
https://doi.org/10.1021/acs.jpcc.9b04137
Direct route to reproducing pair distribution functions with coarse-grained models via transformed atomistic cross correlations
Svenja J. Wörner, Tristan Bereau, Kurt Kremer, Joseph F. Rudzinski
The Journal of Chemical Physics 151 (24), 244110 (2019)
https://doi.org/10.1063/1.5131105
Automated detection of many-particle solvation states for accurate characterizations of diffusion kinetics
Joseph F. Rudzinski, Marc Radu, Tristan Bereau
The Journal of Chemical Physics 150 (2), 024102 (2019)
https://doi.org/10.1063/1.5064808
On the relevance of electrostatic interactions for the structural relaxation of ionic liquids: A molecular dynamics simulation study
Tamisra Pal, Michael Vogel
The Journal of Chemical Physics 150 (12), 124501 (2019)
https://doi.org/10.1063/1.5085508
Non-equilibrium Markov state modeling of periodically driven biomolecules
Fabian Knoch, Thomas Speck
The Journal of Chemical Physics 150 (5), 054103 (2019)
https://doi.org/10.1063/1.5055818
Self-assembly mechanisms of triblock Janus particles
H. Eslami, N. Khanjari, F. Müller-Plathe
Journal of Chemical Theory and Computation 15, 1345–1354 (2019)
https://doi.org/10.1021/acs.jctc.8b00713
Gaussian charge distributions for incorporation of electrostatic interactions in dissipative particle dynamics: Application to self-assembly of surfactants
H. Eslami, M. Khani, F. Müller-Plathe
Journal of Chemical Theory and Computation 15, 4197−4207 (2019)
https://doi.org/10.1021/acs.jctc.9b0017
Influence of Polymer Bidispersity on the Effective Particle–Particle Interactions in Polymer Nanocomposites
Gianmarco Munaò, Antonio De Nicola, Florian Müller-Plathe, Toshihiro Kawakatsu, Andreas Kalogirou, Giuseppe Milano
Macromolecules 52, 8826-8839 (2019)
https://doi.org/10.1021/acs.macromol.9b01367
Does Preferential Adsorption Drive Cononsolvency?
Swaminath Bharadwaj, Nico F. A. van der Vegt
Macromolecules 52 (11), 4131-4138 (2019)
https://doi.org/10.1021/acs.macromol.9b00575
A note on the uniqueness result for the inverse Henderson problem
F. Frommer, M. Hanke, S. Jansen
Journal of Mathematical Physics 60 (9), 093303 (2019)
https://doi.org/10.1063/1.5112137
Relative entropy indicates an ideal concentration for structure-based coarse graining of binary mixtures
David Rosenberger and Nico F. A. van der Vegt
Physical Review E99, 053308 (2019)
https://doi.org/10.1103/PhysRevE.99.053308
Transferability of Local Density-Assisted Implicit Solvation Models for Homogeneous Fluid Mixtures
David Rosenberger, Tanmoy Sanyal, M. Scott Shell, and Nico F. A. van der Vegt
Journal of Chemical Theory and Computation 15, 2881-2895 (2019)
https://doi.org/10.1021/acs.jctc.8b01170
Mechanical and Structural Tuning of Reversible Hydrogen Bonding in Interlocked Calixarene Nanocapsules
Stefan Jaschonek, Ken Schäfer, Gregor Diezemann
The Journal of Physical Chemistry B 123 (22), 4688-4694 (2019)
https://doi.org/10.1021/acs.jpcb.9b02676
Temperature dependent mechanical unfolding of calixarene nanocapsules studied by molecular dynamics simulations
Takashi Kato, Ken Schäfer, Stefan Jaschonek, Jürgen Gauss, Gregor Diezemann
The Journal of Chemical Physics 151 (4), 045102 (2019)
https://doi.org/10.1063/1.5111717
Surface of Half-Neutralized Diamine Triflate Ionic Liquids. A Molecular Dynamics Study of Structure, Thermodynamics, and Kinetics of Water Absorption and Evaporation
N. C. Forero-Martinez, R. Cortes-Huerto, J. F. Mora Cardozo, P. Ballone
The Journal of Physical Chemistry B123 (40), 8457-8471 (2019)
https://doi.org/10.1021/acs.jpcb.9b06619
Steering a solute between coexisting solvation states: Revisiting nonequilibrium work relations and the calculation of free energy differences
Maziar Heidari, Robinson Cortes-Huerto, Raffaello Potestio, Kurt Kremer
The Journal of Chemical Physics 151 (14), 144105 (2019)
https://doi.org/10.1063/1.5117780
Generic Model for Lamellar Self-Assembly in Conjugated Polymers: Linking Mesoscopic Morphology and Charge Transport in P3HT
Cristina Greco, Anton Melnyk, Kurt Kremer, Denis Andrienko, Kostas Ch. Daoulas
Macromolecules 52 (3), 968-981 (2019)
https://doi.org/10.1021/acs.macromol.8b01863
Shear Modulus of an Irreversible Diblock Copolymer Network from Self-Consistent Field Theory
Shuanhu Qi, Jiajia Zhou, Friederike Schmid
Macromolecules 52 (24), 9569-9577 (2019)
https://doi.org/10.1021/acs.macromol.9b01985
Polydispersity Effects on Interpenetration in Compressed Brushes
Leonid I. Klushin, Alexander M. Skvortsov, Shuanhu Qi, Torsten Kreer, Friederike Schmid
Macromolecules 52 (4), 1810-1820 (2019)
https://doi.org/10.1021/acs.macromol.8b02361
How ill-defined constituents produce well-defined nanoparticles: Effect of polymer dispersity on the uniformity of copolymeric micelles
Sriteja Mantha, Shuanhu Qi, Matthias Barz, Friederike Schmid
Physical Review Materials 3 (2), (2019)
https://doi.org/10.1103/PhysRevMaterials.3.026002
Structure preserving approximation of dissipative evolution problems
H. Egger
Numerische Mathematik 143 (1), 85-106 (2019)
https://doi.org/10.1007/s00211-019-01050-w
A hybrid mass transport finite element method for Keller–Segel type systems
J.A. Carrillo, N. Kolbe, M. Lukáčová-Medvid'ová
Journal of Scientific Computing 80, 1777-1804 (2019)
https://doi.org/10.1007/s10915-019-00997-0
Energy-stable linear schemes for polymer-solvent phase field models
P. Strasser, G. Tierra, B. Dünweg, M. Lukáčová-Medvid'ová
Computers and Mathematics with Applications 77 (1), 125-143 (2019)
https://doi.org/10.1016/j.camwa.2018.09.018
2018 - Publications
Convergence of a mixed finite element finite volume scheme for the isentropic Navier-Stokes system via dissipative measure-valued solutions
E. Feireisl, M. Lukáčová-Medvid'ová
Foundations of Computational Mathematics 18 , 703–730 (2018)
Link: https://doi.org/10.1007/s10208-017-9351-2
Asymptotic preserving error estimates for numerical solutions of compressible Navier-Stokes equations in the low Mach number regime
E. Feireisl, M. Lukáčová-Medvid'ová, S. Necasova, A. Novotny, B. She
SIAM Multiscale Modeling and Simulation 16 (1), 150–183 (2018)
Link: https://doi.org/10.1137/16M1094233
Ewald sum for hydrodynamic interactions of rigid spherical microswimmers
Tapan Chandra Adhyapak, Sara Jabbari-Farouji
The Journal of Chemical Physics 149 (14), 144110 (2018)
Link: https://doi.org/10.1063/1.5045274
Static and dynamic scaling behavior of a polymer melt model with triple-well bending potentia
Sara Jabbari-Farouji
Journal of Polymer Science B 56, 1376-1392 (2018)
Link: https://doi.org/10.1002/polb.24721
Existence and uniqueness of global classical solutions to a two dimensional two species cancer invasion haptotaxis model
Jan Giesselmann, Niklas Kolbe, Mária Lukáčová-Medvid'ová, Nikalaos Sfakianakis
Discrete and continuous dynamics systems 23, 4397-4431 (2018)
Link: https://doi.org/10.3934/dcdsb.2018169
Coil-Globule Collapse of Polystyrene Chains in Tetrahydrofuran-Water Mixtures
Tatiana I. Morozova, Arash Nikoubashman
The Journal of Physical Chemistry B 122, 2130-2137 (2018)
Link: https://doi.org/10.1021/acs.jpcb.7b10603
Atomistic and Coarse-Grained Modeling of the Adsorption of Graphene Nanoflakes at the Oil-Water Interface
Vikram Reddy Ardham, Fréderic Leroy
The Journal of Physical Chemistry B 122, 2396-2407 (2018)
Link: https://doi.org/10.1021/acs.jpcb.7b11173
Flow Behavior of Chain and Star Polymers and Their Mixture
Deepika Srivastva, Arash Nikoubashman
Polymers 10, 599 (2018)
Link: https://doi.org/10.3390/polym10060599
Communication: Is directed percolation in colloid-polymer mixtures linked to dynamic arrest?
David Richard, Patrick C. Royall, Thomas Speck
The Journal of Chemical Physics 148, 241101 (2018)
Link: https://doi.org/10.1063/1.5037680
Adsorption and structure formation of semiflexible polymers on spherical surfaces
Andrey Milchev, Sergei A. Egorov, Arash Nikoubashman, Kurt Binder
Polymer 145, 463-472 (2018)
Link: https://doi.org/10.1016/j.polymer.2018.04.054
Heterogeneous nucleation of a droplet pinned at a chemically inhomogeneous substrate: A simulation study of the two-dimensional Ising case
Marta L. Trobo, Ezequiel V. Albano, K. Binder
The Journal of Chemical Physics 148, 114701 (2018)
Link: https://doi.org/10.1063/1.5016612
Nematic order in solutions of semiflexible polymers: Hairpins, elastic constants, and the nematic-smectic transition
Andrey Milchev, Sergei A. Egorov, Kurt Binder, Arash Nikoubashman
The Journal of Chemical Physics 149, 175909 (2018)
Link: https://doi.org/10.1063/1.5049630
A generalization of the Carnahan-Starling approach with applications to four- and five-dimensional hard sphere
Dmitry Ivanizki
Phys. Lett. A 382, 1745-1751 (2018)
Link: https://doi.org/10.1016/j.physleta.2018.04.036
Crystallization of hard spheres revisited. I. Extracting kinetics and free energy landscape from forward flux sampling
David Richard, Thomas Speck
The Journal of Chemical Physics 148, 124110 (2018)
Link: https://doi.org/10.1063/1.5016277
Crystallization of hard spheres revisited. II. Thermodynamic modeling, nucleation work, and the surface of tension
David Richard, Thomas Speck
The Journal of Chemical Physics 148, 224102 (2018)
Link: https://doi.org/10.1063/1.5025394
NESSie.jl - Efficient and intuitive finite element and boundary element methods for nonlocal protein electrostatics in the Julia language
Thomas Kemmer, Sergej Rjasanow, Andreas Hildebrandt
J. Comp. Sci. 28, 193-203 (2018)
Link: https://doi.org/10.1016/j.jocs.2018.08.008
Bottom-up approach to represent dynamic properties in coarse-grained molecular simulations
Gregor Deichmann and Nico F. A. van der Vegt
The Journal of Chemical Physics 149, 244114 (2018)
Link: https://doi.org/10.1063/1.5064369
Intrinsic conformational preferences and interactions in alpha-synuclein fibrils: Insights from molecular dynamics simulations
Ioana M. Ilie, Divya Nayar, Wouter K. den Otter, Nico F. A. van der Vegt, Wim J. Briels
Journal of Chemical Theory and Computation 14, 3298-3310 (2018)
Link: https://doi.org/10.1021/acs.jctc.8b00183
Generalized Brownian dynamics: Construction and numerical integration of non-Markovian particle-based models
Gerhard Jung, Martin Hanke, Friederike Schmid
Soft Matter 14 (46), 9368-9382 (2018)
Link: https://doi.org/10.1039/C8SM01817K
Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard–Jones potential
Isidro Lorenzo Geada, Hadi Ramezani-Dakhel, Tariq Jamil, Marialore Sulpizi, Hendrik Heinz
Nature Communications 9 (1), (2018)
Link: https://doi.org/10.1038/s41467-018-03137-8
Increased Acid Dissociation at the Quartz/Water Interface
Shivam Parashar, Dominika Lesnicki, Marialore Sulpizi
Journal of Physical Chemistry Letters 9 (9),2186-2189 (2018)
Link: https://doi.org/10.1021/acs.jpclett.8b00686
Dynamical heterogeneities of rotational motion in room temperature ionic liquids evidenced by molecular dynamics simulations
Kota Usui, Johannes Hunger, Mischa Bonn, Marialore Sulpizi
The Journal of Chemical Physics 148 (19), 193811 (2018)
Link: https://doi.org/10.1063/1.5005143
A Microscopic Interpretation of Pump–Probe Vibrational Spectroscopy Using Ab Initio Molecular Dynamics
Dominika Lesnicki, Marialore Sulpizi
The Journal of Physical Chemistry B122 (25), 6604-6609 (2018)
Link: https://doi.org/10.1021/acs.jpcb.8b04159
Atypical titration curves for GaAl12 Keggin-ions explained by a joint experimental and simulation approach
Marialore Sulpizi, Johannes Lützenkirchen
The Journal of Chemical Physics 148 (22), 222836 (2018)
Link: https://doi.org/10.1063/1.5024201
A set-up for simultaneous measurement of second harmonic generation and streaming potential and some test applications
Johannes Lützenkirchen, Tim Scharnweber, Tuan Ho, Alberto Striolo, Marialore Sulpizi, Ahmed Abdelmonem
Journal of Colloid and Interface Science 529, 294-305 (2018)
Link: https://doi.org/10.1016/j.jcis.2018.06.017
Unravelling the GLY-PRO-GLU tripeptide induced reconstruction of the Au(110) surface at the molecular scale
Isidro Lorenzo Geada, Ivan Petit, Marialore Sulpizi, Frederik Tielens
Surface Science 677,271-277 (2018)
Link: https://doi.org/10.1016/j.susc.2018.07.006
Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics
Tristan Bereau, Joseph F. Rudzinski
Physical Review Letters 121 (25), (2018)
Link: https://doi.org/10.1103/physrevlett.121.256002
Highly controlled optical transport of cold atoms into a hollow-core fiber
Maria Langbecker, Ronja Wirtz, Fabian Knoch, Mohammad Noaman, Thomas Speck, Patrick Windpassinger
New Journal of Physics 20 (8), 083038 (2018)
Link: https://doi.org/10.1088/1367-2630/aad9bb
Unfolding dynamics of small peptides biased by constant mechanical forces
Fabian Knoch, Thomas Speck
Molecular Systems Design and Engineering, (2018)
Link: https://doi.org/10.1039/c7me00080d
Solid-Liquid and Solid-Solid Phase Diagrams of Self-Assembled Triblock Janus Nanoparticles from Solution
H. Eslami, K. Bahri, F. Müller-Plathe
The Journal of Physical Chemistry C122, 9235–9244 (2018)
Link: https://doi.org/10.1021/acs.jpcc.8b02043
Local bond order parameters for accurate determination of crystal structures in two and three dimensions
H. Eslami, P. Sedaghat, and F. Müller-Plathe
Physical Chemistry Chemical Physics 20, 27059-27068 (2018)
Link: https://doi.org/10.1039/C8CP05248D
Molecular Structure and Multi-Body Interactions in Silica-Polystyrene Nanocomposites
G. Munaò, A. Pizzirusso, A. Kalogirou, A. De Nicola, T. Kawakatsu, F. Müller-Plathe, G. Milano
Nanoscale 10, 21656–21670 (2018)
Link: https://doi.org/10.1039/C8NR05135F
Cosolvent effects on polymer hydration drive hydrophobic collapse
Divya Nayar and Nico F. A. van der Vegt
The Journal of Physical Chemistry B 122, 3587-3595 (2018)
Link: https://doi.org/10.1021/acs.jpcb.7b10780
Addressing the temperature transferability of structure based coarse graining models
David Rosenberger and Nico F. A. van der Vegt
The Journal of Physical Chemistry 20, 6617-6628 (2018)
Link: https://doi.org/10.1039/c7cp08246k
Fréchet differentiability of molecular distribution functions II. The Ursell function
Martin Hanke
Letters in Mathematical Physics 108 (2), 307-329 (2018)
Link: https://doi.org/10.1007/s11005-017-1010-7
Understanding three-body contributions to coarse-grained force fields
Christoph Scherer, Denis Andrienko
Physical Chemistry Chemical Physics 20 (34), 22387-22394 (2018)
Link: https://doi.org/10.1039/c8cp00746b
Coupling between criticality and gelation in ``sticky{''} spheres: a structural analysis
David Richard, James Hallett, Thomas Speck
Soft Matter 14, 5554-5564 (2018)
Link: https://doi.org/10.1039/c8sm00389k
Hybrid Particle-Field Molecular Dynamics Simulations of Charged Amphiphiles in an Aqueous Environment
Hima Bindu Kolli, Antonio de Nicola, Sigbjørn Løland Bore, Ken Schäfer, Gregor Diezemann, Jürgen Gauss, Toshihiro Kawakatsu, Zhong-Yuan Lu, You-Liang Zhu, Giuseppe Milano, Michele Cascella
Journal of Chemical Theory and Computation 14 (9), 4928-4937 (2018)
Link: https://doi.org/10.1021/acs.jctc.8b00466
Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding
Fabian Knoch, Ken Schäfer, Gregor Diezemann, Thomas Speck
The Journal of Chemical Physics 148 (4), 044109 (2018)
Link: https://doi.org/10.1063/1.5010435
Structural Origin of Metal Specificity in Isatin Hydrolase from Labrenzia aggregata Investigated by Computer Simulations
Lalita Uribe, Gregor Diezemann, Jürgen Gauss, Jens Preben Morth, Michele Cascella
Chemistry - A European Journal l24 (20), 5074-5077 (2018)
Link: https://doi.org/10.1002/chem.201705159
Intramolecular structural parameters are key modulators of the gel-liquid transition in coarse grained simulations of DPPC and DOPC lipid bilayers
Stefan Jaschonek, Michele Cascella, Jürgen Gauss, Gregor Diezemann, Giuseppe Milano
Biochemical and Biophysical Research Communications 498 (2), 327-333 (2018)
Link: https://doi.org/10.1016/j.bbrc.2018.10.132
Fluctuations, Finite-Size Effects and the Thermodynamic Limit in Computer Simulations: Revisiting the Spatial Block Analysis Method
Maziar Heidari, Kurt Kremer, Raffaello Potestio, Robinson Cortes-Huerto
Entropy 20 (4), 222 (2018)
Link: https://doi.org/10.3390/e20040222
Curvature as a Guiding Field for Patterns in Thin Block Copolymer Films
G.T. Vu, A.A. Abate, L.R. Gomez, A.D. Pezzutti, R.A. Register, D.A. Vega, F. Schmid
Physical Review Letters 121, 087801 (2018)
Link: https://doi.org/10.1103/PhysRevLett.121.087801
Well-Posedness of the Iterative Boltzmann Inversion
Martin Hanke
Journal of Statistical Physics 170 (3), 536-553 (2018)
Link: https://doi.org/10.1007/s10955-017-1944-2
Concurrent coupling of realistic and ideal models of liquids and solids in Hamiltonian adaptive resolution simulations
Maziar Heidari, Robinson Cortes-Huerto, Kurt Kremer, Raffaello Potestio
The European Physical Journal E41 (5), (2018)
Link: https://doi.org/10.1140/epje/i2018-11675-x
Spatially Resolved Thermodynamic Integration: An Efficient Method To Compute Chemical Potentials of Dense Fluids
Maziar Heidari, Kurt Kremer, Robinson Cortes-Huerto, Raffaello Potestio
Journal of Chemical Theory and Computation 14 (7), 3409-3417 (2018)
Link: https://doi.org/10.1021/acs.jctc.8b00002
Finite-size integral equations in the theory of liquids and the thermodynamic limit in computer simulations
M. Heidari, K. Kremer, R. Potestio, R. Cortes-Huerto
Molecular Physics 116 (21-22), 3301-3310 (2018)
Link: https://doi.org/10.1080/00268976.2018.1482429
A fundamental catalytic difference between zinc and manganese dependent enzymes revealed in a bacterial isatin hydrolase
Theis Sommer, Kaare Bjerregaard-Andersen, Lalita Uribe, Michael Etzerodt, Gregor Diezemann, Jürgen Gauss, Michele Cascella, J. Preben Morth
Scientific Reports 8 (1), 13104 (2018)
Link: https://doi.org/10.1038/s41598-018-31259-y
Mapping onto Ideal Chains Overestimates Self-Entanglements in Polymer Melts
Hendrik Meyer, Eric Horwath, Peter Virnau
ACS Macro Letters 7 (6), 757-761 (2018)
Link: https://doi.org/10.1021/acsmacrolett.8b00210
Phase transitions in single macromolecules: Loop-stretch transition versus loop adsorption transition in end-grafted polymer chains
Shuangshuang Zhang, Shuanhu Qi, Leonid I. Klushin, Alexander M. Skvortsov, Dadong Yan, Friederike Schmid
The Journal of Chemical Physics 148 (4), 044903 (2018)
Link: https://doi.org/10.1063/1.5013346
Tuning Transition Properties of Stimuli-Responsive Brushes by Polydispersity
Shuanhu Qi, Leonid I. Klushin, Alexander M. Skvortsov, Mingjie Liu, Jiajia Zhou, Friederike Schmid
Advanced Functional Materials 28 (49), 1800745 (2018)
Link: https://doi.org/10.1002/adfm.201800745
Existence of global weak solutions to the kinetic Peterlin model
P. Gwiazda, M. Lukáčová-Medvid'ová, H. Mizerova, A. Szwierczewska-Gwiazda
Nonlinear Analysis: Real World Applications 44, 465-478 (2018)
Link: https://doi.org/10.1016/j.nonrwa.2018.05.016
2017 - Publications
Free-energy barriers for crystal nucleation from fluid phases
Peter Koss, Antonia Statt, Peter Virnau, Kurt Binder
Physical Review E 96, 042609 (2017)
Link: https://doi.org/10.1103/PhysRevE.96.042609
Estimation of the critical behavior in an active colloidal system with Vicsek-like interactions
Benjamin Trefz, Jonathan T. Siebert, Thomas Speck, Kurt Binder, Peter Virnau
The Journal of Chemical Physics 146, 074901 (2017)
Link: https://doi.org/10.1063/1.4975812
Anomalous critical slowdown at a first order phase transition in single polymer chains
Shuangshuang Zhang, Shuanhu Qi, Leonid I. Klushin, Alexander M. Skvortsov, Dadong Yan, Friederike Schmid
The Journal of Chemical Physics 147, 064902 (2017)
Link: https://doi.org/10.1063/1.4997435
Conformations and orientational ordering of semiflexible polymers in spherical confinement
Andrey Milchev, Sergei A. Egorov, Arash Nikoubashman, Kurt Binder
The Journal of Chemical Physics 146, 194907 (2017)
Link: https://doi.org/10.1063/1.4983131
Molecular dynamics simulations in hybrid particle-continuum schemes: Pitfalls and caveats
S. Stalter, L. Yelash, N. Emamy, A. Statt, M. Hanke, M. Lukáčová-Medvid’ová, P. Virnau
Computer Physics Communications 224, 198-208 (2017)
Link: https://doi.org/10.1016/j.cpc.2017.10.016
Asymptotic preserving IMEX finite volume schemes for low Mach number Euler equations with gravitation
G. Bispen, M. Lukáčová-Medvid'ová, L. Yelash
Journal of Computational Physics 335, 222-248 (2017)
Link: https://doi.org/10.1016/j.jcp.2017.01.020
Reduced-order hybrid multiscale method combining the molecular dynamics and the discontinuous Galerkin method
N. Emamy, M. Lukácová-Medvid’ová, S. Stalter, P. Virnau, L. Yelash
VII International Conference on Computational Methods for Coupled Problems in Science and Engineering, Coupled Problems 2017, 15 pp. (2017)
Link: https://upcommons.upc.edu/server/api/core/bitstreams/d23e104d-eb34-4172-a25f-a88c2e732085/content
Flow properties and hydrodynamic interactions of rigid spherical microswimmers
Tapan Chandra Adhyapak, Sara Jabbari-Farouji
Physical Review E96 (5), (2017)
Link: https://doi.org/10.1103/PhysRevE.96.052608
Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes
Horacio V. Guzman, Christoph Junghans, Kurt Kremer, Torsten Stuehn
Physical Review E96 (5), (2017)
Link: https://doi.org/10.1103/PhysRevE.96.053311
Implicit-explicit and explicit projection schemes for the unsteady incompressible Navier-Stokes equations using a high-order dG method
Nehzat Emamy, Florian Kummer, Markus Mrosek, Martin Karcher, Martin Oberlack
Computers and Fluids 154, 285-295 (2017)
Link: https://doi.org/10.1016/j.compfluid.2017.06.003
MERCURY: a Transparent Guided I/O Framework for High Performance I/O Stacks
Giuseppe Congiu, Matthias Grawinkel, Federico Padua, James Morse, Tim Süß and André Brinkmann
25th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (PDP 2017), IEEE Press (2017)
Link: https://ieeexplore.ieee.org/abstract/document/7912624
Frequency-dependent hydrodynamic interaction between two solid spheres
Gerhard Jung, Friederike Schmid
Physics of Fluids 29 (12), 126101 (2017)
Link: https://doi.org/10.1063/1.5001565
Iterative Reconstruction of Memory Kernels
Gerhard Jung, Martin Hanke, Friederike Schmid
Journal of Chemical Theory and Computation 13 (6), 2481-2488 (2017)
Link: https://doi.org/10.1021/acs.jctc.7b00274
Role of the Intercrystalline Tie Chains Network in the Mechanical Response of Semicrystalline Polymers
Sara Jabbari-Farouji, Olivier Lamé, Michel Perez, Jörg Rottler, Jean-Louis Barrat
Physical Review Letters 118, 217802 (2017)
Link: https://doi.org/10.1103/PhysRevLett.118.217802
A Configurable Rule based Classful Token Bucket Filter Network Request Scheduler for the Lustre File System
Yingjin Qian, Xi LI, Shuichi Ihara, lingfang Zeng, Jürgen Kaiser, Tim Süß, Andre Brinkmann
SC'17: Proceedings of the international conference for high performance computing, networking, storage and analysis
Link: https://doi.org/10.1145/3126908.3126932
Conditional Reversible Work Coarse-Grained Models of Molecular Liquids with Coulomb Electrostatics – A Proof of Concept Study on Weakly Polar Organic Molecules
Gregor Deichmann, Nico F. A. van der Vegt
Journal of Chemical Theory and Computation 13 (12), 6158-6166 (2017)
Link: https://doi.org/10.1021/acs.jctc.7b00611
Evaluation of mapping schemes for systematic coarse graining of higher alkanes
Marco Dallavalle, Nico F. A. van der Vegt
Physical Chemistry Chemical Physics 19 (34), 23034-23042 (2017)
Link: https://doi.org/10.1039/c7cp03926c
Nanophase Segregation of Self-Assembled Monolayers on Gold Nanoparticles
Santosh Kumar Meena, Claire Goldmann, Douga Nassoko, Mahamadou Seydou, Thomas Marchandier, Simona Moldovan, Ovidiu Ersen, François Ribot, Corinne Chanéac, Clément Sanchez, David Portehault, Frederik Tielens, Marialore Sulpizi
ACS Nano11 (7), 7371-7381 (2017)
Link: https://doi.org/10.1021/acsnano.7b03616
π+–π+ stacking of imidazolium cations enhances molecular layering of room temperature ionic liquids at their interfaces
Fujie Tang, Tatsuhiko Ohto, Taisuke Hasegawa, Mischa Bonn, and Yuki Nagata
Physical Chemistry Chemical Physics 19, 2850 (2017)
Link: https://doi.org/10.1039/c6cp07034e
Communication: Is a coarse-grained model for water sufficient to compute Kapitza conductance on non-polar surfaces?
Vikram Reddy Ardham, Frédéric Leroy
The Journal of Chemical Physics 147 (15), 151102 (2017)
Link: http://doi.org/10.1063/1.5003199
Thermodynamics of atomistic and coarse-grained models of water on nonpolar surfaces
Vikram Reddy Ardham, Frédéric Leroy
The Journal of Chemical Physics 147 (7), 074702 (2017)
Link: http://doi.org/10.1063/1.4999337
Effects of Silica Surfaces on the Structure and Dynamics of Room-Temperature Ionic Liquids: A Molecular Dynamics Simulation Study
Tamisra Pal, Constantin Beck, Dominik Lessnich, Michael Vogel
The Journal of Physical Chemistry C 122 (1), 624-634 (2017)
Link: https://doi.org/10.1021/acs.jpcc.7b10567
Single molecule translocation in smectics illustrates the challenge for time-mapping in simulations on multiple scales
Biswaroop Mukherjee, Christine Peter, Kurt Kremer
The Journal of Chemical Physics 147 (11), 114501 (2017)
Link: https://doi.org/10.1063/1.5001482
Role of Dynamic Heterogeneities in Ionic Liquids: Insights from All-Atom and Coarse-Grained Molecular Dynamics Simulation Studies
Tamisra Pal, Michael Vogel
ChemPhysChem 18 (16), 2233-2242 (2017)
Link: https://doi.org/10.1002/cphc.201700504
Nonequilibrium Markov state modeling of the globule-stretch transition
Fabian Knoch, Thomas Speck
Physical Review E95 (1), (2017)
Link: https://doi.org/10.1103/PhysRevE.95.012503
Thermodynamic formalism for transport coefficients with an application to the shear modulus and shear viscosity
Thomas Palmer, Thomas Speck
The Journal of Chemical Physics 146 (12), 124130 (2017)
Link: https://doi.org/10.1063/1.4979124
The Hydrophobic Effect and the Role of Cosolvents
Nico F. A. van der Vegt, Divya Nayar
The Journal of Physical Chemistry B121 (43), 9986-9998 (2017)
Link: https://doi.org/10.1021/acs.jpcb.7b06453
Molecular origin of urea driven hydrophobic polymer collapse and unfolding depending on side chain chemistry
Divya Nayar, Angelina Folberth, Nico F. A. van der Vegt
Physical Chemistry Chemical Physics 19 (28), 18156-18161 (2017)
Link: https://doi.org/10.1039/c7cp01743j
Fréchet differentiability of molecular distribution functions I. L^∞ analysis
Martin Hanke
Letters in Mathematical Physics 108 (2), 285-306 (2017)
Link: https://doi.org/10.1007/s11005-017-1009-0
An inverse problem in statistical mechanics
Martin Hanke
in Oberwolfach Reports, Editor: Gerhard Huisken, ChapterReport No. 08/2017, EMS, Zürich, Series:Oberwolfach Reports, Vol.14, 424-426 (2017)
Link: https://doi.org/10.4171/OWR/2017/8
The PCPDTBT Family: Correlations between Chemical Structure, Polymorphism, and Device Performance
G. L. Schulz, F. S. U. Fischer, D. Trefz, A. Melnyk, A. Hamidi-Sakr, M. Brinkmann, D. Andrienko, S. Ludwigs
Macromolecules 50 (4), 1402-1414 (2017)
Link: https://doi.org/10.1021/acs.macromol.6b01698
Force probe simulations using a hybrid scheme with virtual sites
Ken Schäfer, Marco Oestereich, Jürgen Gauss, Gregor Diezemann
The Journal of Chemical Physics 147 (13), 134909 (2017)
Link: https://doi.org/10.1063/1.4986194
Force probe simulations of a reversibly rebinding system: Impact of pulling device stiffness
Stefan Jaschonek, Gregor Diezemann
The Journal of Chemical Physics 146 (12), 124901 (2017)
Link: https://doi.org/10.1063/1.4978678
Combined Experimental and Theoretical Investigation of Heating Rate on Growth of Iron Oxide Nanoparticles
Hamed Sharifi Dehsari, Maziar Heidari, Anielen Halda Ribeiro, Wolfgang Tremel, Gerhard Jakob, Davide Donadio, Raffaello Potestio, Kamal Asadi
Chemistry of Materials 29 (22), 9648-9656 (2017)
Link: https://doi.org/10.1021/acs.chemmater.7b02872
Particle Penetration into Polydisperse Polymer Brushes: A Theoretical Analysis
Shuanhu Qi
Macromolecular Theory and Simulations 26, 1700029 (2017)
Link: https://doi.org/10.1002/mats.201700029
Dynamic Density Functional Theories for Inhomogeneous Polymer Systems Compared to Brownian Dynamics Simulations
Shuanhu Qi, Friederike Schmid
Macromolecules 50 (24), 9831-9845 (2017)
Link: https://doi.org/10.1021/acs.macromol.7b02017
Hybrid particle-continuum simulations coupling Brownian dynamics and local dynamic density functional theory
Shuanhu Qi, Friederike Schmid
Soft Matter 13 (43), 7938-7947 (2017)
Link: https://doi.org/10.1039/c7sm01749a
Simulating copolymeric nanoparticle assembly in the co-solvent method: How mixing rates control final particle sizes and morphologies
Simon Keßler, Klaus Drese, Friederike Schmid
Polymer 126, 9-18 (2017)
Link: https://doi.org/10.1016/j.polymer.2017.07.057
Self-Assembly of Polymeric Particles in Poiseuille Flow: A Hybrid Lattice Boltzmann/External Potential Dynamics Simulation Study
Johannes Heuser, G. J. Agur Sevink, Friederike Schmid
Macromolecules 50 (11), 4474-4490 (2017)
Link: https://doi.org/10.1021/acs.macromol.6b02684
Combining cell-based hydrodynamics with hybrid particle-field simulations: efficient and realistic simulation of structuring dynamics
G. J. A. Sevink, F. Schmid, T. Kawakatsu, G. Milano
Soft Matter 13 (8), 1594-1623 (2017)
Link: https://doi.org/10.1039/c6sm02252a
Numerical analysis of the Oseen-type Peterlin viscoelastic model by the stabilized Lagrange-Galerkin method. Part I: a nonlinear scheme
Lukáčová-Medviďová, M.; Mizerová, H.; Notsu, H.; Tabata, M.
ESAIM Mathematical Modelling and Numerical Analysis 51 (5), 1637–1661. (2017)
Link: https://doi.org/10.1051/m2an/2016078
Numerical analysis of the Oseen-type Peterlin viscoelastic model by the stabilized Lagrange-Galerkin method, Part II: A linear scheme
M. Lukáčová-Medvid'ová, H. Mizerova, H. Notsu, M. Tabata
Mathematical Modelling and Numerical Analysis, (2017)
Link: https://doi.org/10.1051/m2an/2017032
An improved dissipative coupling scheme for a system of Molecular Dynamics particles interacting with a Lattice Boltzmann fluid
Nikita Tretyakov, Burkhard Dünweg
Computer Physics Communications 216, 102-108 (2017)
Link: https://doi.org/10.1016/j.cpc.2017.03.009
Global existence result for the generalized Peterlin viscoelastic model
Mária Lukáčová-Medvid'ová, Hana Mizerova, Sarka Necasova, Michael Renardy
SIAM Journal on Mathematical Analysis, 2950-2964 (2017)
Link: https://doi.org/10.1137/16M1068505
Energy-stable numerical schemes for multiscale simulations of polymer-solvent mixtures
M. Lukáčová-Medvid'ová, B. Duenweg, P. Strasser, N. Tretyakov
Mathematical Analysis of Contimuum Mechanics and Industrial Applications II ,Editor:Patrick van Meurs, Masato Kimura, Hirofumi Notsu,ChapterChap5: Interface Dynamics ,Pages1-12,Springer International Publishing AG/ Eds. Patrick van Meurs, Masato Kimura, Hirofumi Notsu (2017)
Link: https://doi.org/10.1007/978-981-10-6283-4_13
The electromagnetic nature of protein-protein interactions
Hildebrandt, A.K., Kemmer, T.. and Hildebrandt, A.
Conductive polymers: Electrical interactions in cell biology and medicine, Ze Zhang, Mahmoud Rouabhia, Simon E. Moulton, CRC Press (2017)
Link: https://www.taylorfrancis.com/chapters/edit/10.1201/9781315119007-7
2016 - Publications
Deduplication Potential of HPC Applications' Checkpoints
Jürgen Kaiser, Ramy Gad, Tim Süß, Federico Padua, Lars Nagel and André Brinkmann
IEEE International Conference on Cluster Computing (Cluster'16), Pages413--422,IEEE Press (2016)
Link: https://doi.org/10.1109/CLUSTER.2016.32
Oscillatory Interaction Between Two Like-Charged Nanoparticles Induced by Polyelectrolyte Brush-Solvent Interface
Zengju Lian, Shuanhu Qi
J. Pol. Sci. B 54, 1458-1468 (2016)
Link: https://doi.org/10.1002/polb.24036
Adsorption of polyiodobenzene molecules on the Pt(111) surface using van der Waals density functional theory
Karen Johnston, Rengin Pekoz, Davide Donadio
Surface Science 644, 113-121 (2016)
Link: https://doi.org/10.1016/j.susc.2015.09.017
Gold nanorods as plasmonic sensors for particle diffusion
Verena Wulf, Fabian Knoch, Thomas Speck, Carsten Sönnichsen
The Journal of Physical Chemistry Lett. 7, 4951-4955 (2016)
Link: https://doi.org/10.1021/acs.jpclett.6b02165
Special Issue on Structure in Glassy and Jammed Systems
Patrick C. Royall and Thomas Speck
J. Stat. Mech. 054045 (2016)
Link: https://doi.org/10.1088/1742-5468/2016/05/054045
Study of Hydrophobic Clustering in Partially Sulfonated Polystyrene Solutions with a Systematic Coarse-Grained Model
Ran Zhang, Nico F. A. van der Vegt
Macromolecules 49 (19), 7571-7580 (2016)
Link: https://doi.org/10.1021/acs.macromol.6b01132
Computing bulk and shear viscosities from simulations of fluids with dissipative and stochastic interactions
Gerhard Jung, Friederike Schmid
The Journal of Chemical Physics 144 (20), 204104 (2016)
Link: https://doi.org/10.1063/1.4950760
Droplets pinned at chemically inhomogenous substrates: A simulation study of the two-dimensional Ising cas
M.L. Trobi, E.Z. Albano, K. Binder
Physical Review E 93, 052805 (2016)
Link: https://doi.org/10.1103/PhysRevE.93.052805
A new force field including charge directionality for TMAO in aqueous solution
Kota Usui, Yuki Nagata, Johannes Hunger, Mischa Bonn and Marialore Sulpizi
The Journal of Chemical Physics 145, 064103 (2016)
Link: https://doi.org/10.1063/1.4960207
Molecular Dynamics Simulations of SFG Librational Modes Spectra of Water at the Water–Air Interface
Rémi Khatib, Taisuke Hasegawa, Marialore Sulpizi, Ellen H. G. Backus, Mischa Bonn, and Yuki Nagata
The Journal of Physical Chemistry C120 (33), 18665–18673 (2016)
Link: https://doi.org/10.1021/acs.jpcc.6b06371
Revisiting the droplet simulation approach to derive force-field parameters for water on molybdenum disulfide from wetting angle measurements
Frédéric Leroy
The Journal of Chemical Physics 145 (16), 164705 (2016)
Link: http://doi.org/10.1063/1.4966215
Research update: Computational materials discovery in soft matter
T. Bereau, D. Andrienko, K. Kremer
APL Materials 4, 053101 (2016)
Link: https://doi.org/10.1063/1.4943287
Concurrent parametrization against static and kinetic information leads to more robust coarse-grained force fields
J.F. Rudzinski, T. Bereau
The European Physical Journal Special Topics 225 (8-9), 1373-1389 (2016)
Link: https://doi.org/10.1140/epjst/e2016-60114-5
Communication: Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information
Joseph F. Rudzinski, Kurt Kremer, Tristan Bereau
The Journal of Chemical Physics 144 (5), 051102 (2016)
Link: https://doi.org/10.1063/1.4941455
Polydisperse hard spheres: crystallization kinetics in small systems and role of local structure
Matteo Campo, Thomas Speck
Journal of Statistical Mechanics: Theory and Experiment 2016 (8), 084007 (2016)
Link: https://doi.org/10.1088/1742-5468/2016/8/084007
Nucleation pathway and kinetics of phase-separating active Brownian particles
David Richard, Hartmut Löwen, Thomas Speck
Soft Matter 12 (24), 5257-5264 (2016)
Link: https://doi.org/10.1039/c6sm00485g
Comparison of Different TMAO Force Fields and Their Impact on the Folding Equilibrium of a Hydrophobic Polymer
Francisco Rodríguez-Ropero, Philipp Rötzscher, Nico F. A. van der Vegt
The Journal of Physical Chemistry B120 (34), 8757-8767 (2016)
Link: https://doi.org/10.1021/acs.jpcb.6b04100
Comparison of iterative inverse coarse-graining methods
David Rosenberger, Martin Hanke, Nico F.A. van der Vegt
The European Physical Journal Special Topics 225 (8-9), 1323-1345 (2016)
Link: https://doi.org/10.1140/epjst/e2016-60120-1
Comparison of systematic coarse-graining strategies for soluble conjugated polymers
Christoph Scherer and Denis Andrienko
The European Physical Journal Special Topics 225, 1441-1461, (2016)
Link: https://doi.org/10.1140/epjst/e2016-60154-9
Determining Factors for the Unfolding Pathway of Peptides, Peptoids, and Peptidic Foldamers
Lalita Uribe, Jürgen Gauss, Gregor Diezemann
The Journal of Physical Chemistry B120 (40),10433-10441 (2016);
Link: https://doi.org/10.1021/acs.jpcb.6b06784
From Classical to Quantum and Back: A Hamiltonian Scheme for Adaptive Multiresolution Classical/Path-Integral Simulations
Karsten Kreis, Mark E. Tuckerman, Davide Donadio, Kurt Kremer, Raffaello Potestio
Journal of Chemical Theory and Computationut. 12 (7), 3030-3039 (2016)
Link: https://doi.org/10.1021/acs.jctc.6b00242
Accurate and general treatment of electrostatic interaction in Hamiltonian adaptive resolution simulations
M. Heidari, R. Cortes-Huerto, D. Donadio, R. Potestio
The European Physical Journal Special Topics 225 (8-9), 1505-1526 (2016)
Link: https://doi.org/10.1140/epjst/e2016-60151-6
Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials
Jelle M. Boereboom, Raffaello Potestio, Davide Donadio, Rosa E. Bulo
Journal of Chemical Theory and Computationut. 12 (8), 3441-3448 (2016)
Link: https://doi.org/10.1021/acs.jctc.6b00205
Polydisperse Polymer Brushes: Internal structure, critical behavior, and interaction with flow
Shuanhu Qi, Leonid I. Klushin, Alexander M. Skvortsov, Friederike Schmid
Macromolecules 49, 9665-9683 (2016)
Link: https://doi.org/10.1021/acs.macromol.6b02026
Numerical reduction of self-consistent field models of macromolecular systems
A. Disterhoft, T. Raasch, F. Schmid
Proceedings in Applied Mathematics and Mechanics 16, 915-916 (2016)
Link: https://doi.org/10.1002/pamm.201610446
A hybrid particle-continuum resolution method and its application to a homopolymer solution
S. Qi, H. Behringer, T. Raasch, F. Schmid
The European Physical Journal Special Topics 225 (8-9), 1527-1549 (2016)
Link: https://doi.org/10.1140/epjst/e2016-60096-8
The Cassie-Wenzel transition of fluids on nanostructured substrates: Macroscopic force balance versus microscopic density-functional theory
Nikita Tretyakov, Periklis Papadopoulos, Doris Vollmer, Hans-Jürgen Butt, Burkhard Dünweg, Kostas Ch. Daoulas
The Journal of Chemical Physics 145 (13), 134703 (2016)
Link: https://doi.org/10.1063/1.4963792
Energy dissipative characteristic schemes for the diffusive Oldroyd-B viscoelastic fluid
Mária Lukáčová-Medvid'ová, Hirofumi Notsu, Bangwei She
International Journal for Numerical Methods in Fluids, 523-557 (2016)
Link: https://doi.org/10.1002/fld.4195
2015 - Publications
Analysis and numerical solution of the Peterlin viscoelastic model (PhD Thesis)
Mizerova Hana
Johannes Gutenberg-Universität (2015)
Link: https://doi.org/10.25358/openscience-3633
Analysis of the ECMWF Storage Landscape
Matthias Grawinkel, Lars Nagel, Markus Mäsker, Federico Padua, André Brinkmann, Lennart Sorth
Proceedings of the 13th USENIX Conference on File and Storage Technologies {FAST} 2015, Santa Clara, CA, USA,Pages15 - 27, Usenix (2015)
Link: https://www.usenix.org/conference/fast15/technical-sessions/presentation/grawinkel
The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption
Stephan Köhler, Friederike Schmid, Giovanni Settanni
PLOS Comput. Biology 11, e1004346 (2015)
Link: https://doi.org/10.1371/journal.pcbi.1004346
The role of shear in crystallization kinetics: From suppression to enhancement
David Richard, Thomas Speck
Sci. Rep. 5, 14610 (2015)
Link: https://doi.org/10.1038/srep14610
Solvent Determines Nature of Effective Interactions between Nanoparticles in Polymer Brushes},
Zengju Lian, Shuanhu Qi, Jiajia Zhou, Friederike Schmid
The Journal of Physical Chemistry B 119, 4099-4108 (2015)
Link: https://doi.org/10.1021/jp511911g
Flows and mixing in channels with misaligned superhydrophobic walls
Tatiana V. Nizkaya, Evgeny S. Asmolov, Jiajia Zhou, Friederike Schmid, Olga I. Vinogradova
Physical Review E91 (3), (2015)
Link: https://doi.org/10.1103/PhysRevE.91.033020
Computer simulations of single particles in external electric field
Jiajia Zhou, Friederike Schmid
Soft matter 11, 6728-6739 (2015)
Link: https://doi.org/10.1039/c5sm01485a
Molecular Mechanism of Water Evaporation
Yuki Nagata, Kota Usui, Mischa Bonn
Physical Review Letters. 115 (23), 236102 (2015)
Link: https://doi.org/10.1103/PhysRevLett.115.236102
The surface roughness, but not the water molecular orientation varies with temperature at the water–air interface
Yuki Nagata, Taisuke Hasegawa, Ellen H. G. Backus, Kota Usui, Seiji Yoshimune, Tatsuhiko Ohto, Mischa Bonn
Physical Chemistry Chemical Physics 17 (36), 23559-23564 (2015)
Link: https://doi.org/10.1039/c5cp04022a
Ultrafast Vibrational Dynamics of Water Disentangled by Reverse Nonequilibrium Ab Initio Molecular Dynamics Simulations
Yuki Nagata, Seiji Yoshimune, Cho-Shuen Hsieh, Johannes Hunger, Mischa Bonn
Physical Review X5 (2), 021002 (2015)
Link: https://doi.org/10.1103/PhysRevX.5.021002
Toward ab initio molecular dynamics modeling for sum-frequency generation spectra; an efficient algorithm based on surface-specific velocity-velocity correlation function
Tatsuhiko Ohto, Kota Usui, Taisuke Hasegawa, Mischa Bonn, Yuki Nagata
The Journal of Chemical Physics 143 (12),124702 (2015)
Link: https://doi.org/10.1063/1.4931106
Ab Initio Liquid Water Dynamics in Aqueous 10.1063/5.0264104TMAO Solution
Kota Usui, Johannes Hunger, Marialore Sulpizi, Tatsuhiko Ohto, Mischa Bonn, and Yuki Nagata
The Journal of Physical Chemistry B 119 (33), 10597–10606 (2015)
Link: https://doi.org/10.1021/acs.jpcb.5b02579
Lipid Carbonyl Groups Terminate the Hydrogen Bond Network of Membrane-Bound Water
Tatsuhiko Ohto, Ellen H. G. Backus, Cho-Shuen Hsieh, Marialore Sulpizi, Mischa Bonn, and Yuki Nagata
Journal of Physical Chemistry Letters. 6 (22), 4499–4503 (2015)
Link: https://doi.org/10.1021/acs.jpclett.5b02141
Solid-liquid work of adhesion of coarse-grained models of n-hexane on graphene layers derived from the conditional reversible work method
Vikram Reddy Ardham, Gregor Deichmann, Nico F. A. van der Vegt, Frédéric Leroy
The Journal of Chemical Physics 143 (24), 243135 (2015)
Link: https://doi.org/10.1063/1.4936253
Parametrizing Nonbonded Interactions from Wetting Experiments via the Work of Adhesion: Example of Water on Graphene Surfaces
Frédéric Leroy, Shengyuan Liu, Jianguo Zhang
The Journal of Physical Chemistry C119 (51), 28470-28481 (2015)
Link: https://doi.org/10.1021/acs.jpcc.5b10267
A molecular dynamics simulations study on the relations between dynamical heterogeneity, structural relaxation, and self-diffusion in viscous liquids
Patrick Henritzi, André Bormuth, Felix Klameth, Michael Vogel
The Journal of Chemical Physics 143 (16), 164502 (2015)
Link: https://doi.org/10.1063/1.4933208
Cycle representatives for the coarse-graining of systems driven into a non-equilibrium steady state
Fabian Knoch, Thomas Speck
New Journal of Physics 17 (11), 115004 (2015)
Link: https://doi.org/10.1088/1367-2630/17/11/115004
Mechanism of Polymer Collapse in Miscible Good Solvents
Francisco Rodríguez-Ropero, Timir Hajari, Nico F. A. van der Vegt
The Journal of Physical Chemistry B119 (51), 15780-15788 (2015)
Link: https://doi.org/10.1021/acs.jpcb.5b10684
Mechanical unfolding pathway of a model β-peptide foldamer
Lalita Uribe, Stefan Jaschonek, Jürgen Gauss, Gregor Diezemann
The Journal of Chemical Physics 142 (20), 204901 (2015)
Link: https://doi.org/10.1063/1.4921371
Comparative Study of the Mechanical Unfolding Pathways of α- and β-Peptides
Lalita Uribe, Jürgen Gauss, Gregor Diezemann
The Journal of Physical Chemistry B 119 (26), 8313-8320 (2015)
Link: https://doi.org/10.1021/acs.jpcb.5b04044
Reply to comments by R. Klein on Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations
K. Kreis, A. C. Fogarty, K. Kremer, R. Potestio
The European Physical Journal Special Topics 224 (12), 2505-2506 (2015)
Link: https://doi.org/10.1140/epjst/e2015-02533-5
Advantages and challenges in coupling an ideal gas to atomistic models in adaptive resolution simulations
K. Kreis, A. C. Fogarty, K. Kremer, R. Potestio
The European Physical Journal Special Topics 224 (12), 2289-2304 (2015)
Link: https://doi.org/10.1140/epjst/e2015-02412-1
Stimuli-Responsive Brushes with Active Minority Components: Monte Carlo Study and Analytical Theory
Shuanhu Qi, Leonid I. Klushin, Alexander M. Skvortsov, Alexey A. Polotsky, Friederike Schmid
Macromolecules 48 (11), 3775-3787 (2015)
Link: https://doi.org/10.1021/acs.macromol.5b00563
pre 2015 - Publications
Optimizing scientific file I/O patterns using advice based knowledge
Giuseppe Congiu, Matthias Grawinkel, Federico Padua, James Morse, Tim Süß, André Brinkmann
Proceedings of the International Conference on Cluster Computing (CLUSTER), Madrid, Spain,IEEE (2014)
Link: https://ieeexplore.ieee.org/abstract/document/6968763
Bottom-up derivation of conservative and dissipative interactions for coarse-grained molecular liquids with the conditional reversible work method
Gregor Deichmann, Valentina Marcon, Nico F. A. van der Vegt
The Journal of Chemical Physics 141 (22), 224109 (2014)
Link: https://doi.org/10.1063/1.4903454
Using field theory to construct hybrid particle–continuum simulation schemes with adaptive resolution for soft matter systems
Shuanhu Qi, Hans Behringer, Friederike Schmid
New Journal of Physics 15 (12), 125009 (2013)
Link: https://doi.org/10.1088/1367-2630/15/12/125009
Accelerated GPU simulation of compressible flow by the discontinuous evolution Galerkin method
B. J. Block, M. Lukáčová-Medvid’ová, P. Virnau, L. Yelash
The European Physical Journal Special Topics 210 (1), 119-132 (2012)
Link: https://doi.org/10.1140/epjst/e2012-01641-0