Related papers: Equivalence analysis between Quasi-coarse-grained …
Generic coarse-grained models are designed such that they are (i) simple and (ii) computationally efficient. They do not aim at representing particular materials, but classes of materials, hence they can offer insight into universal…
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…
We report a novel hybrid method of simultaneous atomistic simulation of solids in critical regions (contacts surfaces, cracks areas, etc.), along with continuum modeling of other parts. The continuum is treated in terms of quasi-atoms of…
Active matter, responsive ("smart") materials and materials under time-dependent load are systems out of thermal equilibrium. To construct coarse-grained models for such systems, one needs to integrate out a distribution of microstates that…
Self-organized pattern formation is vital for many biological processes. Reaction-diffusion models have advanced our understanding of how biological systems develop spatial structures, starting from homogeneity. However, biological…
We propose a universal approach for analysis and fast simulations of stiff stochastic biochemical kinetics networks, which rests on elimination of fast chemical species without a loss of information about mesoscopic, non-Poissonian…
In this article we give our perspective on the successes and promise of various molecular and coarse-grained simulation approaches to probing the effect of mechanical forces in the actin cytoskeleton.
We introduce a coarse-grained model for atomic glass formers. Its elements are physically motivated local microscopic dynamical rules parameterized by observables. Results of the model are established and used to interpret the measured…
The physical processes at the interface of a low-temperature plasma and a solid are extremely complex. They involve a huge number of elementary processes in the plasma, in the solid as well as charge, momentum and energy transfer across the…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
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…
Stochastic modelling of complex systems plays an essential, yet often computationally intensive role across the quantitative sciences. Recent advances in quantum information processing have elucidated the potential for quantum simulators to…
We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and…
As a complementary tool to laboratory experiments, discrete numerical simulation, applied to granular materials, provides valuable information on the grain and contact scale microstructure, thereby enabling one to better understand the…
We present a real-space formulation for coarse-graining Kohn-Sham Density Functional Theory that significantly speeds up the analysis of material defects without appreciable loss of accuracy. The approximation scheme consists of two steps.…
Significant efforts have been devoted in the last decade towards improving the predictivity of coarse-grained models in molecular dynamics simulations and providing a rigorous justification of their use, through a combination of theoretical…
This work presents a systematic methodology for describing the transient dynamics of coarse-grained molecular systems inferred from all-atom simulated data. We suggest Langevin-type dynamics where the coarse-grained interaction potential…
We develop coarse-graining schemes for stochastic many-particle microscopic models with competing short- and long-range interactions on a d-dimensional lattice. We focus on the coarse-graining of equilibrium Gibbs states and using cluster…
The separation between molecular and mesoscopic length and time scales poses a severe limit to molecular simulations of mesoscale phenomena. We describe a hybrid multiscale computational technique which address this problem by keeping the…
A new procedure for coarse-graining dynamical triangulations is presented. The procedure provides a meaning for the relevant value of observables when "probing at large scales", e.g. the average scalar curvature. The scheme may also be…