Publications

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

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

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

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

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

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

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

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