相关论文: Small ionic radii limit time step in Martini 3 mol…
Colloids have a striking relevance in a wide spectrum of industrial formulations, spanning from personal care products to protective paints. Their behaviour can be easily influenced by extremely weak forces, which disturb their…
We develop a method for simulating colloidal suspensions using multiparticle collision dynamics (MPCD) with a discrete particle model represented as a rigid body. The key steps for incorporating the rigid-body constraints are to thermalize…
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…
The purpose of this paper is to propose a time-step-robust cell-to-cell integration of particle trajectories in 3-D unstructured meshes in particle/mesh Lagrangian stochastic methods. The main idea is to dynamically update the mean fields…
In colloidal systems, Brownian motion emerges from the massive separation of time and length scales associated to characteristic dynamics of the solute and solvent constituents. This separation of scales produces several temporal regimes in…
Elastic filaments are vital to biological, physical and engineering systems, from cilia driving fluid in the lungs to artificial swimmers and micro-robotics. Simulating slender structures requires intricate balance of elastic, body, active,…
Phase mixing is a fundamental kinetic process that governs dissipation and stability in collisionless plasmas, but its inherent filamentation in velocity space creates major challenges for both high-fidelity simulations and reduced-order…
Molecular dynamics (MD) simulations remain the gold standard for studying protein dynamics, but their computational cost limits access to biologically relevant timescales. Recent generative models have shown promise in accelerating…
An effective paradigm for simulating the dynamics of robots that locomote and manipulate is multi-rigid body simulation with rigid contact. This paradigm provides reasonable tradeoffs between accuracy, running time, and simplicity of…
Machine learning interatomic potentials (MLIPs) have proven to be wildly useful for molecular dynamics simulations, powering countless drug and materials discovery applications. However, MLIPs face two primary bottlenecks preventing them…
We report a molecular dynamics (MD) study of the collective dynamics of a simple monatomic liquid -interacting through a two body potential that mimics that of lithium- across the liquid-glass transition. In the glassy phase we find…
Transport of ions in molecular-scale confined spaces is central to all aspects of life and technology: into a crack, it may break steel within days; through a membrane separator, it determines the efficiency of electrochemical energy…
Planet-disk interactions can produce kinematic signatures in protoplanetary disks. While recent observations have detected non-Keplerian gas motions in disks, their origins are still being debated. To explore this, we conduct 3D…
Recent applications (e.g. active gels and self-assembly of elastic sheets) motivate the need to efficiently simulate the dynamics of thin elastic sheets. We present semi-implicit time stepping algorithms to improve the time step constraints…
In this paper we present the results of a large-scale numerical investigation of structural properties of a model of cell membrane, simulated as a bilayer of flexible molecules in vacuum. The study was performed by carrying out extensive…
Kinetic instabilities are one of the most challenging aspects in computational plasma physics. Accurately capturing their onset and evolution requires fine resolution of the high-dimensional distribution functions of each relevant species,…
Analysis of ion-kinetic instabilities in solar wind plasmas is crucial for understanding energetics and dynamics throughout the heliosphere, as evident from spacecraft observations of complex ion velocity distribution functions (VDFs) and…
Water plays a key role in biological membrane transport. In ion channels and water-conducting pores (aquaporins), one dimensional confinement in conjunction with strong surface effects changes the physical behavior of water. In molecular…
We propose a method for multi-scale hybrid simulations of molecular dynamics (MD) and computational fluid dynamics (CFD). In the method, usual lattice-mesh based simulations are applied for CFD level, but each lattice is associated with a…
Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…