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Discrete particle simulations have become the standard in science and industrial applications exploring the properties of particulate systems. Most of such simulations rely on the concept of interacting spherical particles to describe the…
Atomistic modeling of thin-film processes provides an avenue not only for discovering key chemical mechanisms of the processes but also to extract quantitative metrics on the events and reactions taking place at the gas-surface interface.…
We summarize a series of numerical experiments of collisional dynamics in dense stellar systems such as globular clusters (GCs) and in weakly collisional plasmas using a novel simulation technique, the so-called Multi-particle collision…
In this paper, we demonstrate the efficiency of simulations via direct computation of the partition function under various macroscopic conditions, such as different temperatures or volumes. The method can compute partition functions by…
We have developed a new, very efficient numerical scheme to solve the CR diffusion convection equation that can be applied to the study of the nonlinear time evolution of CR modified shocks for arbitrary spatial diffusion properties. The…
Coarse-graining or model reduction is a term describing a range of approaches used to extend the time-scale of molecular simulations by reducing the number of degrees of freedom. In the context of molecular simulation, standard…
Machine learning force fields possess unprecedented potential in achieving both accuracy and efficiency in molecular simulations. Nevertheless, their application in organic systems is often hindered by structural collapse during simulation…
The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…
A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with…
Molecular dynamics (MD) simulations are used to investigate $^1$H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk $n$-C$_5$H$_{12}$ to $n$-C$_{17}$H$_{36}$ hydrocarbons and bulk water. The MD simulations of the $^1$H NMR…
We propose a versatile feedback scheme for both single- and multi-user multiple-input multiple-output (MIMO) frequency division duplex (FDD) systems. Particularly, we propose utilizing a Gaussian mixture model (GMM) with a reduced number of…
Discrete gradients (DG) or more exactly discrete gradient methods are time integration schemes that are custom-built to preserve first integrals or Lyapunov functions of a given ordinary differential equation (ODE). In conservative…
The recent progress of linear-scaling or O(N) methods in the density functional theory (DFT) is remarkable. We expect that first-principles molecular dynamics (FPMD) simulations based on DFT can now treat more realistic and complex systems…
Smoothed dissipative particle dynamics (SDPD) is a widely used particle-based method for modelling soft matter systems at mesoscopic and macroscopic scales, offering thermodynamic consistency and direct control over the fluid's transport…
Molecular dynamics is the primary computational method by which modern structural biology explores macromolecule structure and function. Boltzmann generators have been proposed as an alternative to molecular dynamics, by replacing the…
Discrete-state, continuous-time Markov models are becoming commonplace in the modelling of biochemical processes. The mathematical formulations that such models lead to are opaque, and, due to their complexity, are often considered…
Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible…
Modified Newtonian dynamics (MOND) is a promising alternative to dark matter. To further test the theory, there is a need for fluid- and particle-dynamics simulations. The force in MOND is not a direct particle-particle interaction, but…
In this paper, we perform molecular dynamics (MD) simulations to study the two-dimensional packing process of both monosized and random size particles with radii ranging from $1.0 \, \mu m$ to $7.0 \, \mu m$. The system was allowed to…
Molecular Dynamics (MD) simulations are essential for accurately predicting the physical and chemical properties of large molecular systems across various pressure and temperature ensembles. However, the high computational costs associated…