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The systematic errors due to the practical implementation of the Contact Dynamics method for simulation of dense granular media are examined. It is shown that, using the usual iterative solver to simulate a chain of rigid particles,…
We theoretically study the propagation of light through a cold atomic medium, where the effects of motion, laser intensity, atomic density, and polarization can all modify the properties of the scattered light. We present two different…
Classical molecular dynamics simulations are performed on LiF in the framework of the polarizable ion model. The overlap-repulsion and polarization terms of the interaction potential are derived on a purely non empirical, first-principles…
A combination of molecular-dynamics (MD) computer simulation and mode-coupling theory (MCT) is used to elucidate the structure-dynamics relation in sodium-silicate melts (NSx) of varying sodium concentration. Using only the partial static…
The propagation of incoherent elastic energy in a three-dimensional solid due to the scattering by many, randomly placed and oriented, pinned dislocation segments, is considered in a continuum mechanics framework. The scattering mechanism…
A vibrational model of transport properties of dense fluids assumes that solid-like oscillations of atoms around their temporary equilibrium positions dominate the dynamical picture. The temporary equilibrium positions of atoms do not form…
We use a long, all-atom molecular dynamics (MD) simulation combined with theoretical modeling to investigate the dynamics of selected lipid atoms and lipid molecules in a hydrated diyristoyl-phosphatidylcholine (DMPC) lipid bilayer. From…
Dislocation climb mobilities, assuming vacancy bulk diffusion, are derived and implemented in dislocation dynamics simulations to study the coarsening of vacancy prismatic loops in fcc metals. When loops cannot glide, the comparison of the…
By performing molecular dynamics simulations with up to 132 million coarse-grained particles in half-micron sized boxes, we show that hydrodynamics quantitatively explains the finite-size effects on diffusion of lipids, proteins, and carbon…
Molecular dynamics (MD) has long been the de facto choice for simulating complex atomistic systems from first principles. Recently deep learning models become a popular way to accelerate MD. Notwithstanding, existing models depend on…
We examine the behavior of the diffusion coefficient of the ST2 model of water over a broad region of the phase diagram via molecular dynamics simulations. The ST2 model has an accessible liquid-liquid transition between low-density and…
In this work, we aimed to replicate and extend the results presented in the DiffFluid paper[1]. The DiffFluid model showed that diffusion models combined with Transformers are capable of predicting fluid dynamics. It uses a denoising…
Particle-particle interactions in sedimenting systems have been investigated in the present study considering the many-body hydrodynamic and electrodynamic interactions. These interactions primarily occur in two modes: near-field and…
Understanding and accurately predicting hydrogen diffusion in materials is challenging due to the complex interactions between hydrogen defects and the crystal lattice. These interactions span large length and time scales, making them…
The diffusivity of tagged particles is demonstrated to be heterogeneous on time scales comparable to or less than the structural relaxation time %taking place at the interparticle distance in a highly supercooled liquid via 3D molecular…
The thermal characteristics of silicon between 15 and 300 deg K are investigated by applying a computer program on the solution of the differential heat diffusion equation. The computer model is linked to high-purity silicon through a set…
A practical introduction to stochastic modelling of reaction-diffusion processes is presented. No prior knowledge of stochastic simulations is assumed. The methods are explained using illustrative examples. The article starts with the…
A model for diffusion in liquids that couples the dynamics of tracer particles to a fluctuating Stokes equation for the fluid is investigated in the limit of large Schmidt number. In this limit, the concentration of tracers is shown to…
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…
Quantum diffusion is studied via dissipative Madelung hydrodynamics. Initially the wave packet spreads ballistically, than passes for an instant through normal diffusion and later tends asymptotically to a sub-diffusive law. It is shown…