相关论文: GCMe: Efficient implementation of the Gaussian cor…
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…
We present an extension of the standard polarizable quantum mechanic/molecular mechanics (QM/MM) approach for treating environmental effects on excited state properties of embedded systems. A quantum polarizable atom model is derived from a…
Brownian dynamics of colloidal particles on complex surfaces has found important applications in diverse physical, chemical and biological processes. However, current Brownian dynamics simulation algorithms mostly work for relatively simple…
Bottom-up coarse-grained (CG) modeling expands the spatial and temporal scales of molecular simulation by seeking a reduced, thermodynamically consistent representation of an atomistic model. Developments in CG theory have largely focused…
We numerically study dynamical properties of the one-component Gaussian Core Model in the supercooled states. We find that nucleation is suppressed as density increases. Concomitantly the system exhibits glassy slow dynamics characterized…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
We discuss the reliability of integral-equation methods based on several commonly used closure relations in determining the phase diagram of coarse-grained models of soft-matter systems characterized by mutually interacting soft and…
Discrete particle simulation, a combined approach of computational fluid dynamics and discrete methods such as DEM (Discrete Element Method), DSMC (Direct Simulation Monte Carlo), SPH (Smoothed Particle Hydrodynamics), PIC…
We develop a computational method for modeling electrostatic interactions of arbitrarily-shaped, polarizable objects on colloidal length scales, including colloids/nanoparticles, polymers, and surfactants, dispersed in explicit ion…
This paper focuses on molecular dynamics (MD) modeling of graphene reinforced cross-linked epoxy (Gr-Ep) nanocomposite. The goal is to study the influence of geometry, and concentration of reinforcing nanographene sheet (NGS) on interfacial…
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…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
Accelerated coarse-graining (CG) algorithms for simulating heterogeneous chemical reactions on surface systems have recently gained much attention. In the present paper, we consider such an issue by investigating the oscillation behavior of…
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
Molecular dynamics simulations of interacting soft disks confined in a heterogeneous quenched matrix of soft obstacles show dynamics which is fundamentally different from that of hard disks. The interactions between the disks can enhance…
Quantum mechanics/molecular mechanics (QM/MM) is a standard computational tool for describing chemical reactivity in systems with many degrees of freedom, including polymers, enzymes, and reacting molecules in complex solvents. However,…
In this paper, we describe a soil-fluid-structure interaction model that combines soil mechanics (saturated sediments), fluid mechanics (seawater or air), and solid mechanics (structures). The formulation combines the Material Point Method,…
We present a density-functional study of a binary phase-separating mixture of soft core particles immersed in a random matrix of quenched soft core particles of larger size. This is a model for a binary polymer mixture immersed in a…