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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics
Tristan Bereau, Joseph F. Rudzinski
Physical Review Letters 121 (25), (2018)
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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)
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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)
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Unfolding dynamics of small peptides biased by constant mechanical forces
Fabian Knoch, Thomas Speck
Molecular Systems Design and Engineering, (2018)
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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)
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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)
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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)
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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)
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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)
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Understanding three-body contributions to coarse-grained force fields
Christoph Scherer, Denis Andrienko
Physical Chemistry Chemical Physics 20 (34), 22387-22394 (2018)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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Mapping onto Ideal Chains Overestimates Self-Entanglements in Polymer Melts
Hendrik Meyer, Eric Horwath, Peter Virnau
ACS Macro Letters 7 (6), 757-761 (2018)
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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)
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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)
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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)
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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)
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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)
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Ewald sum for hydrodynamic interactions of rigid spherical microswimmers
Tapan Chandra Adhyapak, Sara Jabbari-Farouji
The Journal of Chemical Physics 149 (14), 144110 (2018)
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