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A GPU-accelerated version of the lattice Boltzmann method for efficient simulation of soft materials is introduced. Unlike standard approaches, this method reconstructs the distribution functions from available hydrodynamic variables…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
Neural network-based molecular dynamics (NNMD) simulations incorporating long-range electrostatic interactions have significantly extended the applicability to heterogeneous and ionic systems, enabling effective modeling critical physical…
Understanding nucleation from aqueous solutions is of fundamental importance in a multitude of fields, ranging from materials science to biophysics. The complex solvent-mediated interactions in aqueous solutions hamper the development of a…
We propose a simplified version of local molecular field (LMF) theory to treat Coulomb interactions in simulations of ionic fluids. LMF theory relies on splitting the Coulomb potential into a short-ranged part that combines with other…
There exist several methods for simulating biological and physical systems as represented by chemical reaction networks. Systems with low numbers of particles are frequently modelled as discrete-state Markov jump processes and are typically…
First-principles simulations of many-fermion systems are commonly limited by the computational requirements of processing large data objects. As a remedy, we propose the use of low-rank approximations of three-body interactions, which are…
In this work we introduce three ideas that can further improve particle FRNN physics simulations running on RT Cores; i) a real-time update/rebuild ratio optimizer for the bounding volume hierarchy (BVH) structure, ii) a new RT core use,…
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…
In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…
A crucial aspect in the simulation of electrochemical interfaces consists in treating the distribution of electronic charge of electrode materials that are put in contact with an electrolyte solution. Recently, it has been shown how a…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
We propose a collision-oriented particle system to approximate a class of Landau-type equations. This particle system is formally derived from a particle system with random collisions in the grazing regime, and happens to be a special…
We develop an accurate, highly efficient and scalable random batch sum-of-Gaussians (RBSOG) method for molecular dynamics simulations of systems with long-range interactions. The idea of the RBSOG method is based on a sum-of-Gaussians…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…
Biological cells can exchange messages through soluble molecules or membrane-bound receptors. In particular in the latter case, the interaction is usually located in specific regions of the interacting cells and may depend on or induce…
Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…
Molecular simulations in an open environment, involving ion exchange, are necessary to study various systems, from biosystems to confined electrolytes. However, grand-canonical simulations are often computationally demanding in condensed…
Direct numerical simulation of liquid-gas-solid flows is uncommon due to the considerable computational cost. As the grid spacing is determined by the smallest involved length scale, large grid sizes become necessary -- in particular if the…