Recent progress towards chemically-specific coarse-grained simulation models with consistent dynamical properties

JF Rudzinski - Computation, 2019 - mdpi.com
Coarse-grained (CG) models can provide computationally efficient and conceptually simple
characterizations of soft matter systems. While generic models probe the underlying physics …

From adaptive resolution to molecular dynamics of open systems

R Cortes-Huerto, M Praprotnik, K Kremer… - The European Physical …, 2021 - Springer
We provide an overview of the Adaptive Resolution Simulation method (AdResS) based on
discussing its basic principles and presenting its current numerical and theoretical …

M2 macrophage-derived extracellular vesicles promote gastric cancer progression via a microRNA-130b-3p/MLL3/GRHL2 signaling cascade

Y Zhang, W Meng, P Yue, X Li - Journal of Experimental & Clinical Cancer …, 2020 - Springer
Background Transfer of noncoding microRNAs (miRNAs) by extracellular vesicles (EVs)
promotes the development of chemoresistance in many tumor types. Additionally, restoration …

Molecular simulation of liquid crystals

MP Allen - Molecular Physics, 2019 - Taylor & Francis
This article reviews recent progress in the computer simulation of liquid crystals at the
molecular level. It covers the use of simple rigid-body models of the constituent molecules …

Functional macromolecular systems: Kinetic pathways to obtain tailored structures

V Abetz, K Kremer, M Müller… - … Chemistry and Physics, 2019 - Wiley Online Library
This article aims to stimulate research on non‐equilibrium macromolecular systems, as
nowadays a large toolbox to synthesize tailored macromolecules is available. A large variety …

Dynamical properties across different coarse-grained models for ionic liquids

JF Rudzinski, S Kloth, S Wörner, T Pal… - Journal of Physics …, 2021 - iopscience.iop.org
Room-temperature ionic liquids (RTILs) stand out among molecular liquids for their rich
physicochemical characteristics, including structural and dynamic heterogeneity. The …

Coarse-grained model incorporating short-and long-range effective potentials for the fast simulation of micelle formation in solutions of ionic surfactants

SD Peroukidis, IP Stott… - The Journal of Physical …, 2022 - ACS Publications
A coarse-grained model comprising short-and long-range effective potentials, parametrized
with the iterative Boltzmann inversion (IBI) method, is presented for capturing micelle …

Application of the 2PT model to understanding entropy change in molecular coarse-graining

MP Bernhardt, M Dallavalle, NFA Van der Vegt - Soft Materials, 2020 - Taylor & Francis
The effects of coarse-graining on the thermodynamic properties of molecular liquids are
studied by computing the standard molar entropies of chloroform, 1, 4-dioxane and …

[HTML][HTML] Development of Iterative Methods for Coarse-Graining Molecular Liquids

MP Bernhardt - tuprints.ulb.tu-darmstadt.de
The enormous number of atoms in biological and macromolecular systems can prohibit the
direct application of atomistic molecular dynamics (MD) simulations. This limitation motivates …