Related papers: Coarse-Graining and Scaling in Dissipative Particl…
The aim of this article is to provide a scheme for simulating diffusion processes evolving in one-dimensional discontinuous media. This scheme does not rely on smoothing the coefficients that appear in the infinitesimal generator of the…
This work presents new parallelizable numerical schemes for the integration of Dissipative Particle Dynamics with Energy conservation (DPDE). So far, no numerical scheme introduced in the literature is able to correctly preserve the energy…
Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at atomic resolution. However, a coarse graining model must be formulated such that the conclusions we draw from it…
Linear systems with large differences between coefficients ("discontinuous coefficients") arise in many cases in which partial differential equations(PDEs) model physical phenomena involving heterogeneous media. The standard approach to…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
Multiscale molecular modeling is widely applied in scientific research of molecular properties over large time and length scales. Two specific challenges are commonly present in multiscale modeling, provided that information between the…
Thermophoresis is an effective method to drive the motion of nanoparticles in fluids. The transport of nanoparticles in polymer networks has significant fundamental and applied importance in biology and medicine, and can be described as…
Coarse-grained molecular dynamics often sacrifices accuracy and transferability for computational efficiency, but the use of machine learned potentials is helping coarse-grained models attain performance on par with atomistic molecular…
We propose and investigate a method for identifying timescales of dissipation in nonequilibrium steady states modeled as discrete-state Markov jump processes. The method is based on how the irreversibility-measured by the statistical…
We implemented a coarse-graining procedure to construct mesoscopic models of complex molecules. The final aim is to obtain better results on properties depending on slow modes of the molecules. Therefore the number of particles considered…
Hybrid particle-field methods are computationally efficient approaches for modelling soft matter systems. So far applications of these methodologies have been limited to constant volume conditions. Here, we reformulate particle-field…
Diffusion Probabilistic Field (DPF) models the distribution of continuous functions defined over metric spaces. While DPF shows great potential for unifying data generation of various modalities including images, videos, and 3D geometry, it…
A proper treatment of electrostatic interactions is crucial for the accurate calculation of forces in computer simulations. Electrostatic interactions are typically modeled using Ewald based methods, which have become one of the…
A method of adapting smoothed particle hydrodynamics (SPH) with periodic boundary conditions for use with the special purpose device GRAPE is presented. GRAPE (GRAvity PipE) solves the Poisson and force equations for an N-body system by…
The applicability to dense hard sphere colloidal suspensions of a general coarse-graining approach called Record Dynamics (RD) is tested by extensive molecular dynamics simulations. We reproduce known results as logarithmic diffusion and…
Complex fluids exhibit structure on a wide range of length and time scales, and hierarchical approaches are necessary to investigate all facets of their often unusual properties. The study of idealized coarse-grained models at different…
Many-body dissipative particle dynamics (MDPD) is a mesoscale method capable of reproducing liquid-vapour coexistence in a single simulation. Despite having been introduced more than a decade ago, this method remains broadly unexplored and,…
The viscosity and self-diffusion constant of particle-based mesoscale hydrodynamic methods, multi-particle collision dynamics (MPC) and dissipative particle dynamics (DPD), are investigated, both with and without angular-momentum…
Coarse-grained (CG) models facilitate an efficient exploration of complex systems by reducing the unnecessary degrees of freedom of the fine-grained (FG) system while recapitulating major structural correlations. Unlike structural…
Three dimensional molecular dynamics simulations of cohesive dissipative powders under a plane shear are performed. We find the various phases depending on the dimensionless shear rate and the dissipation rate as well as the density. We…