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The mechanism of diffusion in supercooled liquids is investigated from the potential energy landscape point of view, with emphasis on the crossover from high- to low-T dynamics. Molecular dynamics simulations with a time dependent mapping…
A hybrid mesoscopic multi-particle collision model is used to study diffusion-influenced reaction kinetics. The mesoscopic particle dynamics conserves mass, momentum and energy so that hydrodynamic effects are fully taken into account.…
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine…
This paper introduces a comprehensive unified framework for constructing multi-view diffusion geometries through intertwined multi-view diffusion trajectories (MDTs), a class of inhomogeneous diffusion processes that iteratively combine the…
Recently, the Diffusion Probabilistic Model (DPM)-based methods have achieved substantial success in the field of medical image segmentation. However, most of these methods fail to enable the diffusion model to learn edge features and…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
Metadynamics is an enhanced sampling method of great popularity, based on the on-the-fly construction of a bias potential that is function of a selected number of collective variables. We propose here a change in perspective that shifts the…
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics…
Simulations of SiC crystal growth using molecular dynamics (MD) have become popular in recent years. They, however, simulate very fast deposition rates, to reduce computational costs. Therefore, they are more akin to surface sputtering,…
Metal clusters are partway between molecular and bulk systems and thus exhibit special physical and chemical properties. Atoms can rearrange within a cluster to form different structural isomers. Internal degrees of freedom and the…
Precession of a converged beam during acquisition of a 4D-STEM dataset improves strain, orientation, and phase mapping accuracy by averaging over continuous angles of illumination. Precession experiments usually rely on integrated systems,…
We derive a phase field crystal model that couples the diffusive evolution of a microscopic structure with the fast dynamics of a macroscopic velocity field, explicitly accounting for the relaxation of elastic excitations. This model…
The planar front of a growing a crystal is often destroyed by instabilities. In the case of growth from a condensed phase, the most frequent ones are diffusion instabilities, which will be but briefly discussed in simple terms in chapter…
The large amount of powder diffraction data for which the corresponding crystal structures have not yet been identified suggests the existence of numerous undiscovered, physically relevant crystal structure prototypes. In this paper, we…
We report on a novel extension of the recent phase-field crystal (PFC) method introduced in [Elder et al., Phys. Rev. Lett., Vol. 88, 245701:1-4 (2002)], which incorporates elastic interactions as well as crystal plasticity and diffusive…
Inspired by recent advances in the manipulation of atoms trapped near 1D waveguides and pro- posals to use surface acoustic waves on piezoelectric substrates for the same purpose, we show the potential of two-dimensional platforms. We…
Development generating diffraction-related valuable expressions and formulas capable of initiating new era for diffraction and for scientific domains that use it provided. The main expression, among these, gives diffracted intensity as…
Molecular dynamics simulations are a powerful tool to study diffusion processes in battery electrolyte and electrode materials. From a single molecular dynamics simulation many properties relevant to diffusion can be obtained, including the…
We introduce a construction to embed a quasiperiodic lattice of obstacles into a single unit cell of a higher-dimensional space, with periodic boundary conditions. This construction transparently shows the existence of channels in these…
Recently, hybrid models have emerged that combine microscopic and mesoscopic regimes in a single stochastic reaction-diffusion simulation. Microscopic simulations track every individual molecule and are generally more accurate. Mesoscopic…