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A coarse-grained simulation model eliminates microscopic degrees of freedom and represents a polymer by a simplified structure. A priori, two classes of coarse-grained models may be distinguished: those which are designed for a specific…
The Kremer-Grest (KG) polymer model is a standard model for studying generic polymer properties in Molecular Dynamics simulations. It owes its popularity to its simplicity and computational efficiency, rather than its ability to represent…
Coarse-grained (CG) force field methods for molecular systems are a crucial tool to simulate large biological macromolecules and are therefore essential for characterisations of biomolecular systems. While state-of-the-art deep learning…
Achieving optimal solubility of active substances in polymeric carriers is of fundamental importance for a number of industrial applications, including targeted drug delivery within the growing field of nanomedicine. However, its…
We present a novel thermodynamically guided, low-noise, time-scale bridging, and pertinently efficient strategy for the dynamic simulation of microscopic models for complex fluids. The systematic coarse-graining method is exemplified for…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
Molecular dynamics (MD) simulations enable the description of ma- terial properties and processes with atomistic detail by numerically solv- ing the time evolution of every atom in the system. We introduce Poly- merModeler, a…
In recent years, molecular dynamics (MD) simulations have emerged as a pivotal tool for understanding the structure, dynamics, and phase behavior in charged soft matter systems. To explore phenomena across greater length and time scales in…
Coarse-grained (CG) models parameterized using atomistic reference data, i.e., 'bottom up' CG models, have proven useful in the study of biomolecules and other soft matter. However, the construction of highly accurate, low resolution CG…
The most popular and universally predictive protein simulation models employ all-atom molecular dynamics (MD), but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model…
The development of coarse-grained (CG) molecular models typically requires a time-consuming iterative tuning of parameters in order to have the approximated CG models behaving correctly and consistently with, e.g., available…
Coarse-grained (CG) models can provide computationally efficient and conceptually simple characterizations of soft matter systems. While generic models probe the underlying physics governing an entire family of free-energy landscapes,…
Pyrene-functional PMMAs were prepared via ATRP-controlled polymerization and click reaction, as efficient dispersing agents for the exfoliation of few-layered graphene sheets (GS) in easily processable low boiling point chloroform. In…
To evaluate shear viscosity of ethylene glycol oligomers (EGO)/water binary mixture by means of coarse-grained molecular dynamics (CG-MD) simulations, we proposed the self-diffusion-coefficient-based parameterization of non-bonded…
The long time dynamics of polymeric materials has been extensively studied in the past through various experimental techniques and computer simulations. While computer simulations typically treat generic, simplified models, experiments deal…
The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However,…
The properties of soft electronic materials depend on the coupling of electronic and conformational degrees of freedom over a wide range of spatiotemporal scales. Description of such properties requires multiscale approaches capable of, at…
Coarse-grained molecular dynamics (CGMD) is a technique developed as a concurrent multiscale model that couples conventional molecular dynamics (MD) to a more coarse-grained description of the periphery. The coarse-grained regions are…
We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and…
Molecular dynamics simulations of biomolecules have been widely adopted in biomedical studies. As classical point-charge models continue to be used in routine biomolecular applications, there have been growing demands on developing…