相关论文: Estimating position-dependent and anisotropic diff…
A possible way to calculate particle spectra as a function of position in pulsar wind nebulae is to solve a Fokker-Planck transport equation. This paper presents numerical solutions to the transport equation with the processes of…
In this paper we study macroscopic density equations in which the diffusion coefficient depends on a weighted spatial average of the density itself. We show that large differences (not present in the local density-dependence case) appear…
Discrete-space kinetic models, i.e., Markov state models, have emerged as powerful tools for reducing the complexity of trajectories generated from molecular dynamics simulations. These models require configuration-space representations…
Machine Learning (ML) techniques are revolutionizing the way to perform efficient materials modeling. Nevertheless, not all the ML approaches allow for the understanding of microscopic mechanisms at play in different phenomena. To address…
We study how confining the equilibrium hard-sphere fluid to restrictive one- and two-dimensional channels with smooth interacting walls modifies its structure, dynamics, and entropy using molecular dynamics and transition-matrix Monte Carlo…
Restrictions to molecular motion by barriers (membranes) are ubiquitous in biological tissues, porous media and composite materials. A major challenge is to characterize the microstructure of a material or an organism nondestructively using…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
Density-dependent diffusion is a widespread phenomenon in nature. We have examined the density-dependent diffusion behavior of some biological processes such as tumor growth and invasion [23]. Here, we extend our previous work by developing…
We investigate the diffusion of an intruder in a granular gas, with both components modeled as smooth hard spheres, both immersed in a low viscosity carrier fluid to form a particle-laden suspension. In this system, dissipative particle…
Pattern formation often occurs in confined systems, yet how boundaries shape patterning dynamics is unclear. We develop techniques to analyze confinement effects in nonlocal advection-diffusion equations, which generically capture the…
Advancements in modern semiconductor devices increasingly depend on the utilization of amorphous materials and the reduction of material thickness, pushing the boundaries of their physical capabilities. The mechanical properties of these…
Mathematical models of motility are often based on random-walk descriptions of discrete individuals that can move according to certain rules. It is usually the case that large masses concentrated in small regions of space have a great…
Molecular dynamics computer simulations are used to investigate thedynamics of a binary mixture of charged (Yukawa) particles with a size-ratio of 1:5. We find that the system undergoes a phase transition where the large particles…
Predicting the binding structure of a small molecule ligand to a protein -- a task known as molecular docking -- is critical to drug design. Recent deep learning methods that treat docking as a regression problem have decreased runtime…
Large scale molecular dynamics and grand canonical Monte Carlo simulation techniques are used to study the behavior of the interdiffusion of a solvent into an entangled polymer matrix as the state of the polymer changes from a melt to a…
Physical experiments can characterize the elastic response of granular materials in terms of macroscopic state-variables, namely volume (packing) fraction and stress, while the microstructure is not accessible and thus neglected. Here, by…
We consider the behaviour of precessional angle (phase) carried by molecules of a diffusing specimen under magnetic fields typical of magnetic resonance experiments. An evolution equation for the ensemble of particles is constructed, which…
Tracking of particles, be it a passive tracer or an actively moving bacterium in the growing bacterial colony, is a powerful technique to probe the physical properties of the environment of the particles. One of the most common measures of…
The diffusion equation is the primary tool to study the movement dynamics of a free Brownian particle, but when spatial heterogeneities in the form of permeable interfaces are present, no fundamental equation has been derived. Here we…
We introduce methods for large scale Brownian Dynamics (BD) simulation of many rigid particles of arbitrary shape suspended in a fluctuating fluid. Our method adds Brownian motion to the rigid multiblob method at a cost comparable to the…