Publications

List of all publications sorted by year

2022
2021
2020
2019
2018
2017
2016
2015
before 2015

2022 - Publications

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)
see publication


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
J. Chem. Theor. Comput. 18, 2597–2615 (2022)
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Self-Assembly of Model Triblock Janus Colloidal Particles in Two Dimensions
K. Bahri, H. Eslami, and Florian Müller-Plathe
J. Chem. Theor. Comput. 18, 1870–1882 (2022)
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Mobility of polymer melts in a regular array of carbon nanotubes
S.A.N. Alberti, J. Schneider, and F. Müller-Plathe
J. Chem. Theor. Comput. 18, 3285–3295 (2022)
see publication


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
J. Adv. Ceram. 11, 1104–1116 (2022)
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Slip-Spring Hybrid Particle-Field Model for Coarse-Graining Branched Polymer Melts: Polystyrene Melts as an Example
Z. Wu and F. Müller-Plathe
J. Chem. Theor. Comput. 18, 3814–3828 (2022)
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Roughness volumes: An improved RoughMob concept for predicting the increase of molecular mobility upon coarse-graining
M.K. Meinel and F. Müller-Plathe
J. Phys. Chem. B 126, 3737−3747 (2022)
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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)
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Force Generation in Confined Active Fluids: The Role of Microstructure
Paul, Shuvojit and Jayaram, Ashreya and Narinder, N and Speck, Thomas and Bechinger, Clemens
Physical Review Letters 129, 058001, (2022)
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Improving the Efficiency of Variationally Enhanced Sampling with Wavelet-Based Bias Potentials
Benjamin Pampel and Omar Valsson
Journal of Chemical Theory and Computation 2022, 18, 7, 4127–4141
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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)
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Existence of Dissipative Solutions to the Compressible Navier-Stokes System with Potential Temperature Transport
M. Lukacova-Medvidova, A. Schömer
Journal of Mathematical Fluid Mechanics 24(82), (2022)
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Global existence of weak solutions to viscoelastic phase separation: Part I Regular Case
Aaron Brunk, Maria Lukacova-Medvidova
Nonlinearity 35, 3417-3458, (2022)
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Global existence of weak solutions to viscoelastic phase separation: Part II Degenerate Case
A. Brunk, M. Lukacova-Medvidova
Nonlinearity 35, 3459-3486, (2022)
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A variational framework for the inverse Henderson problem of statistical mechanics
Fabio Frommer and Martin Hanke
Letters in Mathematical Physics 112, 71, (2022)
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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)
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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)
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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
The Journal of Physical Chemistry Letters. 2022, 13, 16, 3712–3717
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Cross-correlation corrected friction in (generalized) Langevin models:Application to the continuous Asakura–Oosawa model
Viktor Klippenstein, Nico F. A. van der Vegt
Journal of Chemical Physics 157, 044103 (2022)
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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)
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2021 - Publications

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)
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Hunting active Brownian particles: Learning optimal behavior
Marcel Gerhard, Ashreya Jayaram, Andreas Fischer, and Thomas Speck
Physical Review Letters 104, 054614, (2021)
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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)
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Fluctuation–dissipation relations far from equilibrium: a case study
Gerhard Jung, Friederike Schmid
Soft Matter 17 (26), 6413-6425 (2021)
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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)
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Mathematical analysis of some iterative methods for the reconstruction of memory kernels
Martin Hanke
ETNA - Electronic Transactions on Numerical Analysis 54, 483-498 (2021)
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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)
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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)
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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)
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Simulation of Elastomers by Slip-Spring Dissipative Particle Dynamics
J. Schneider, F. Fleck, H. A. Karimi-Varzaneh, F. Müller-Plathe
Macromolecules 54, 5155 (2021)
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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
Journal of Chemical Physics, 245101 (2021)
see publication


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)
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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)
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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)
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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)
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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)
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Interactions in active colloids
Benno Liebchen, Aritra K Mukhopadhyay
Journal of Physics: Condensed Matter 34 (8), 083002 (2021)
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Active droploids
Jens Grauer, Falko Schmidt, Jesús Pineda, Benjamin Midtvedt, Hartmut Löwen, Giovanni Volpe, Benno Liebchen
Nature Communications 12 (1), (2021)
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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)
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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)
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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)
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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)
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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), (2021)
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BoltzmaNN: Predicting effective pair potentials and equations of state using neural networks
F. Berressem and A. Nikoubashman
Journal of Chemical Physics 154, 124123 (2021)
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Force probe simulations using an adaptive resolution scheme
Marco Oestereich, J Gauss, Gregor Diezemann
Journal of Physics: Condensed Matter, (2021)
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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)
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Dynamic coarse-graining of polymer systems using mobility functions
Bing Li, Kostas Daoulas, Friederike Schmid
Journal of Physics: Condensed Matter 33 (19), 194004 (2021)
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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)
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Adversarial reverse mapping of condensed-phase molecular structures: Chemical transferability
Marc Stieffenhofer, Tristan Bereau, Michael Wand
APL Materials 9 (3), 031107 (2021)
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Dynamic coarse-graining of polymer systems using mobility functions
Bing Li, Kostas Daoulas, Friederike Schmid
Journal of Physics: Condensed Matter 33 (19), 194004 (2021)
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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)
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Existence, regularity and weak-strong uniqueness for the three-dimensional Peterlin viscoelastic model
Brunk, A., Lu, Y. and Lukáčová-Medviďová, M.
Communications in Mathematical Sciences , (2021)
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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)
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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)
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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)
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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, (2021)
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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)
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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)
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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)
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Numerical methods for compressible fluid flows
E. Feireisl, M. Lukacova-Medvidova, H. Mizerova, B. She
Springer, Modeling, Simulation and Applications, Vol.20 (2021)
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Probability theory of active suspensions
B. Deußen, M. Oberlack, Y. Wang
Physics of Fluids 33 (6), 061902 (2021)
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Vorticity Determines the Force on Bodies Immersed in Active Fluids
Thomas Speck, Ashreya Jayaram
Physical Review Letters 126 (13), (2021)
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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)
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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
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2020 - Publications

Characterizing Polymer Hydration Shell Compressibilities with the Small-System Method
Madhusmita Tripathy, Swaminath Bharadwaj, Shadrack Jabes B., Nico F. A. van der Vegt
Nanomaterials 10 (8), 1460 (2020)
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Role of image charges in ionic liquid confined between metallic interfaces
Samuel Ntim, Marialore Sulpizi
Physical Chemistry Chemical Physics 22 (19), 10786-10791 (2020)
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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)
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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)
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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)
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Coarse-grained model of a nanoscale-segregated ionic liquid for simulations of low-temperature structure and dynamics
Joseph F. Rudzinski and Tristan Bereau
Journal of Chemical Physics 153, 214110 (2020)
see publication


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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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Automated determination of hybrid particle-field parameters by machine learning
Morten Ledum, Sigbjørn Løland Bore, Michele Cascella
Molecular Physics 118 (19-20), e1785571 (2020)
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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
Angewandte Chemie International Edition, (2020)
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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)
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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)
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Can Soft Models Describe Polymer Knots?
Jianrui Zhang, Hendrik Meyer, Peter Virnau, Kostas Ch. Daoulas
Macromolecules 53 (23), 10475-10486 (2020)
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Adversarial reverse mapping of equilibrated condensed-phase molecular structures
Marc Stieffenhofer, Michael Wand, Tristan Bereau
Machine Learning: Science and Technology 1, 045014 (2020)
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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)
see publication


Defects and defect engineering in Soft Matter
Amir Jangizehi, Friederike Schmid, Pol Besenius, Kurt Kremer, Sebastian Seiffert
Soft Matter 16 (48), 10809-10859 (2020)
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Dynamic Self-Consistent Field Approach for Studying Kinetic Processes in Multiblock Copolymer Melts
Friederike Schmid, Bing Li
Polymers 12 (10), 2205 (2020)
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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)
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Using Copolymers to Design Tunable Stimuli-Reponsive Brushes
Shuanhu Qi, Leonid I. Klushin, Alexander M. Skvortsov, Friederike Schmid
Macromolecules 53 (13), 5326-5336 (2020)
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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)
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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)
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Chemotaxis on networks: Analysis and numerical approximation
Herbert Egger, Lukas Schöbel-Kröhn
ESAIM: Mathematical Modelling and Numerical Analysis 54 (4), 1339-1372 (2020)
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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)
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A mass-lumped mixed finite element method for acoustic wave propagation
H. Egger, B. Radu
Numerische Mathematik 145 (2), 239-269 (2020)
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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)
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Semiautomatic construction of lattice Boltzmann models
Dominic Spiller, Burkhard Dünweg
Physical Review E101 (4), (2020)
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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)
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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)
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A finite volume scheme for the Euler system inspired by the two velocities approach
E. Feireisl, M. Lukacova-Medvidova, H. Mizerova
Numerical Mathematics 144 (89-132), (2020)
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K-convergence as a new tool in numerical analysis
E.Feireisl, M. Lukacova-Medvidova, H. Mizerova
IMA Journal of Numerical Analysis 40, 2227–2255 (2020)
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On the convergence of a finite volume method for the Navier–Stokes–Fourier system
E.Feireisl, M. Lukacova-Medvidova, H. Mizerova, B. She
IMA Journal of Numerical Analysis, (2020)
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Compression-induced anti-nematic order in glassy and semicrystalline polymers
Sara Jabbari-Farouji, Damien Vandembroucq
Soft Matter 16 (1), 102-106 (2020)
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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)
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Quorum-sensing active particles with discontinuous motility
Andreas Fischer, Friederike Schmid, Thomas Speck
Physical Review E101 (1), 012601 (2020)
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From scalar to polar active matter: Connecting simulations with mean-field theory
Ashreya Jayaram, Andreas Fischer, Thomas Speck
Physical Review E101 (2), (2020)
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Statistical theory of helical turbulence
B. Deußen, D. Dierkes, and M. Oberlack
Physics of Fluids 32 (6), 065109 (2020)
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2019 - Publications

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)
see publication


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)
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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)
see publication


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)
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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)
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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)
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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)
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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)
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Non-equilibrium Markov state modeling of periodically driven biomolecules
Fabian Knoch, Thomas Speck
The Journal of Chemical Physics 150 (5), 054103 (2019)
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Self-assembly mechanisms of triblock Janus particles
H. Eslami, N. Khanjari, F. Müller-Plathe
Journal of Chemical Theory and Computation 15, 1345–1354 (2019)
see publication


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)
see publication


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)
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Does Preferential Adsorption Drive Cononsolvency?
Swaminath Bharadwaj, Nico F. A. van der Vegt
Macromolecules 52 (11), 4131-4138 (2019)
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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)
see publication


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)
see publication


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)
see publication


Mechanical and Structural Tuning of Reversible Hydrogen Bonding in Interlocked Calixarene Nanocapsules
Stefan Jaschonek, Ken Schäfer, Gregor Diezemann
The Journal of Physical Chemistry B123 (22), 4688-4694 (2019)
see publication


Temperature dependent mechanical unfolding of calixarene nanocapsules studied by molecular dynamics simulations
Stefan Jaschonek, Ken Schäfer, Gregor Diezemann
The Journal of Physical Chemistry B123 (22), 4688-4694 (2019)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


Structure preserving approximation of dissipative evolution problems
H. Egger
Numerische Mathematik 143 (1), 85-106 (2019)
see publication


A hybrid mass transport finite element method for Keller–Segel type systems
J.A. Carrillo, N. Kolbe, M. Lukacova-Medvidova
Journal of Scientific Computing 80, 1777-1804 (2019)
see publication


Energy-stable linear schemes for polymer-solvent phase field models
P. Strasser, G. Tierra, B. Dünweg, M. Lukacova-Medvidova
Computers and Mathematics with Applications 77 (1), 125-143 (2019)
see publication


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)
see publication


Convergence of a finite volume scheme for the compressible Navier-Stokes system
E.Feireisl, M. Lukacova-Medvidova, H. Mizerova
ESAIM: Mathematical Modelling and Numerical Analysis. 53, 1957–1979 (2019)
see publication


An asymptotic preserving scheme for kinetic chemotaxis models in two space dimensions
A. Chertock, A. Kurganov, M. Lukacova-Medvidova, S. Nur Oezcan
Kinetic and Related Models 12 (1), 195–216 (2019)
see publication


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)
see publication


Controlling stability and transport of magnetic microswimmers by an external field
Fabian R. Koessel, Sara Jabbari-Farouji
EPL (Europhysics Letters)125 (2), 28001 (2019)
see publication


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)
see publication


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)
see publication


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)
see publication


2018 - Publications

Bottom-up approach to represent dynamic properties in coarse-grained molecular simulations
Gregor Deichmann and Nico F. A. van der Vegt
Journal of Chemical Physics 149, 244114 (2018)
see publication


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)
see publication


Generalized Langevin dynamics: construction and numerical integration of non-Markovian particle-based models
Gerhard Jung, Martin Hanke, Friederike Schmid
Soft Matter 14 (46), 9368-9382 (2018)
see publication


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)
see publication


Increased Acid Dissociation at the Quartz/Water Interface
Shivam Parashar, Dominika Lesnicki, Marialore Sulpizi
The Journal of Physical Chemistry Letters 9 (9),2186-2189 (2018)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics
Tristan Bereau, Joseph F. Rudzinski
Physical Review Letters 121 (25), (2018)
see publication


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)
see publication


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)
see publication


Unfolding dynamics of small peptides biased by constant mechanical forces
Fabian Knoch, Thomas Speck
Molecular Systems Design and Engineering, (2018)
see publication


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)
see publication


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)
see publication


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)
see publication


Cosolute effects on polymer hydration drive hydrophobic collapse
Divya Nayar and Nico F. A. van der Vegt
The Journal of Physical Chemistry B122, 3587-3595 (2018)
see publication


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)
see publication


Understanding three-body contributions to coarse-grained force fields
Christoph Scherer, Denis Andrienko
Physical Chemistry Chemical Physics 20 (34), 22387-22394 (2018)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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), (2018)
see publication


Mapping onto Ideal Chains Overestimates Self-Entanglements in Polymer Melts
Hendrik Meyer, Eric Horwath, Peter Virnau
ACS Macro Letters 7 (6), 757-761 (2018)
see publication


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)
see publication


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)
see publication


Existence of global weak solutions to the kinetic Peterlin model
P. Gwiazda, M. Lukacova-Medvid'ova, H. Mizerova, A. Szwierczewska-Gwiazda
Nonlinear Analysis: Real World Applications 44, 465-478 (2018)
see publication


Convergence of a mixed finite element finite volume scheme for the isentropic Navier-Stokes system via dissipative measure-valued solutions
E. Feireisl, M. Lukacova-Medvidova
Foundations of Computational Mathematics 18 , 703–730 (2018)
see publication


Asymptotic preserving error estimates for numerical solutions of compressible Navier-Stokes equations in the low Mach number regime
E. Feireisl, M. Lukacova-Medvidova, S. Necasova, A. Novotny, B. She
SIAM Multiscale Modeling and Simulation 16 (1), 150–183 (2018)
see publication


Ewald sum for hydrodynamic interactions of rigid spherical microswimmers
Tapan Chandra Adhyapak, Sara Jabbari-Farouji
The Journal of Chemical Physics 149 (14), 144110 (2018)
see publication


2017 - Publications

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)
see publication


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)
see publication


Frequency-dependent hydrodynamic interaction between two solid spheres
Gerhard Jung, Friederike Schmid
Physics of Fluids 29 (12), 126101 (2017)
see publication


Iterative Reconstruction of Memory Kernels
Gerhard Jung, Martin Hanke, Friederike Schmid
Journal of Chemical Theory and Computation 13 (6), 2481-2488 (2017)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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 C122 (1), 624-634 (2017)
see publication


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)
see publication


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)
see publication


Nonequilibrium Markov state modeling of the globule-stretch transition
Fabian Knoch, Thomas Speck
Physical Review E95 (1), (2017)
see publication


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)
see publication


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)
see publication


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)
see publication


Fréchet differentiability of molecular distribution functions I. L^∞ analysis
Martin Hanke
Letters in Mathematical Physics 108 (2), 285-306 (2017)
see publication


Well-Posedness of the Iterative Boltzmann Inversion
Martin Hanke
Journal of Statistical Physics 170 (3), 536-553 (2017)
see publication


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 (2017)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


Dynamic Density Functional Theories for Inhomogeneous Polymer Systems Compared to Brownian Dynamics Simulations
Shuanhu Qi, Friederike Schmid
Macromolecules 50 (24), 9831-9845 (2017)
see publication


Hybrid particle-continuum simulations coupling Brownian dynamics and local dynamic density functional theory
Shuanhu Qi, Friederike Schmid
Soft Matter 13 (43), 7938-7947 (2017)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


Numerical analysis of the Oseen-type Peterlin viscoelastic model by the stabilized Lagrange-Galerkin method, Part II: A linear scheme
M. Lukacova-Medvidova, H. Mizerova, H. Notsu, M. Tabata
Mathematical Modelling and Numerical Analysis, (2017)
see publication


Global existence result for the generalized Peterlin viscoelastic model
Maria Lukacova - Medvidova, Hana Mizerova, Sarka Necasova, Michael Renardy
SIAM Journal on Mathematical Analysis, 1-14 (2017)
see publication


Energy-stable numerical schemes for multiscale simulations of polymer-solvent mixtures
M. Lukacova-Medvidova, 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)
see publication


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)
see publication


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, (2017)
see publication


Asymptotic preserving IMEX finite volume schemes for low Mach number Euler equations with gravitation
G. Bispen, M. Lukacova-Medvidova, L. Yelash
Journal of Computational Physics 335, 222-248 (2017)
see publication


Flow properties and hydrodynamic interactions of rigid spherical microswimmers
Tapan Chandra Adhyapak, Sara Jabbari-Farouji
Physical Review E96 (5), (2017)
see publication


Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes
Horacio V. Guzman, Christoph Junghans, Kurt Kremer, Torsten Stuehn
Physical Review E96 (5), (2017)
see publication


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)
see publication


2016 - Publications

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)
see publication


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)
see publication


A new force field including charge directionality for TMAO in aqueous solution
Kota Usui, Yuki Nagata, Johannes Hunger, Mischa Bonn and Marialore Sulpizi
Journal of Chemical Physics 145, 064103 (2016)
see publication


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)
see publication


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)
see publication


Computational materials discovery in soft matter
T. Bereau, D. Andrienko, K. Kremer
APL Materials 4, 053101 (2016)
see publication


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)
see publication


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)
see publication


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)
see publication


Nucleation pathway and kinetics of phase-separating active Brownian particles
David Richard, Hartmut Löwen, Thomas Speck
Soft Matter 12 (24), 5257-5264 (2016)
see publication


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)
see publication


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)
see publication


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)
see publication


Computational materials discovery in soft matter
T. Bereau, D. Andrienko, K. Kremer
APL Materials 4, 053101 (2016)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


Energy dissipative characteristic schemes for the diffusive Oldroyd-B viscoelastic fluid
Maria Lukacova-Medvidova, Hirofumi Notsu, Bangwei She
International Journal for Numerical Methods in Fluids, 523-557 (2016)
see publication


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)
see publication


2015 - Publications

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)
see publication


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)
see publication


Molecular Mechanism of Water Evaporation
Yuki Nagata, Kota Usui, Mischa Bonn
Physical Review Letters. 115 (23), 236102 (2015)
see publication


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)
see publication


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)
see publication


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)
see publication


Ab Initio Liquid Water Dynamics in Aqueous TMAO Solution
Kota Usui, Johannes Hunger, Marialore Sulpizi, Tatsuhiko Ohto, Mischa Bonn, and Yuki Nagata
The Journal of Physical Chemistry B119 (33), 10597–10606 (2015)
see publication


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
The Journal of Physical Chemistry Letters. 6 (22), 4499–4503 (2015)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


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)
see publication


Comparative Study of the Mechanical Unfolding Pathways of α- and β-Peptides
Lalita Uribe, Jürgen Gauss, Gregor Diezemann
The Journal of Physical Chemistry B119 (26), 8313-8320 (2015)
see publication


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)
see publication


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)
see publication


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)
see publication


Analysis and numerical solution of the Peterlin viscoelastic model (PhD Thesis)
Mizerova Hana
Johannes Gutenberg-Universität (2015)
see publication


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)
see publication


pre 2015 - Publications

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)
see publication


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)
see publication


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)
see publication


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)
see publication