相关论文: An OrthoBoXY-Method for Various Alternative Box Ge…
Recently, an analytical expression for the system size dependence and direction-dependence of self-diffusion coefficients for neat liquids due to hydrodynamic interactions has been derived for molecular dynamics (MD) simulations using…
A practical correction formula relating the self-diffusion coefficient of dense liquids from molecular dynamics simulations with periodic boundary conditions to the self-diffusion coefficient in the thermodynamic limit is discussed. This…
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…
Translational diffusion coefficients are routinely estimated from molecular dynamics simulations. Linear fits to mean squared displacement (MSD) curves have become the de facto standard, from simple liquids to complex biomacromolecules.…
Self-diffusion coefficients, $D^*$, are routinely estimated from molecular dynamics simulations by fitting a linear model to the observed mean-squared displacements (MSDs) of mobile species. MSDs derived from simulation exhibit statistical…
We investigate finite-size effects on diffusion in confined fluids using molecular dynamics simulations and hydrodynamic calculations. Specifically, we consider a Lennard-Jones fluid in slit pores without slip at the interface and show that…
In molecular dynamics simulations under periodic boundary conditions, particle positions are typically wrapped into a reference box. For diffusion coefficient calculations using the Einstein relation, the particle positions need to be…
We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a…
A microscopic model able to describe simultaneously the dynamic viscosity and the self-diffusion coefficient of fluids is presented. This model is shown to emerge from the introduction of fractional calculus in a usual model of condensed…
Self- and binary Maxwell-Stefan diffusion coefficients were determined by equilibrium molecular dynamics simulations with the Green-Kubo method. This study covers self-diffusion coefficients at liquid states for eight pure fluids, i.e.…
We propose a general methodology for calculating the self-diffusion tensor from molecular dynamics for a liquid with a liquid-gas or liquid-solid interface. The standard method used in bulk fluids, based on computing the mean square…
We present tables for self-diffusion coefficients of the Lennard-Jones liquids and gases for various model formulas in the modified free volume theory of diffusion in the case of reduced temperatures $T^{\ast}=6.0$, 4.0, 1.3, 1.0, 0.8, 0.7…
Hypothesis: The structural details, viscosity trends and dynamic phenomena in t-butanol/water solutions are closely related on the molecular scales across the entire composition range. Utilizing the experimental small- and wide-angle x-ray…
[ This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in The Journal of Chemical Physics, 157, 024504 (2022) and may be found at:…
We study scaling laws characterizing the inter-diffusive zone between two miscible fluids flowing side by side in a Y-shape laminar micromixer using the lattice Boltzmann method. The lattice Boltzmann method solves the coupled 3D…
Statistically stationary and homogeneous shear turbulence (SS-HST) is investigated by means of a new direct numerical simulation code, spectral in the two horizontal directions and compact-finite-differences in the direction of the shear.…
Self-diffusion in a two-dimensional simple fluid is investigated by both analytical and numerical means. We investigate the anomalous aspects of self-diffusion in two-dimensional fluids with regards to the mean square displacement, the…
This study introduces a novel point-wise diffusion model that processes spatio-temporal points independently to efficiently predict complex physical systems with shape variations. This methodological contribution lies in applying forward…
Aims: We study the changes in the properties of turbulence driven by the magnetorotational instability in a shearing box, as the computational domain size in the radial direction is varied relative to the height Methods: We perform 3D…
In the present article the diffusion equation is used to model the spatio-temporal dynamics of a tumor, taking into account the heterogeneous of the medium. This approach makes it possible to take into account the complex geometric shape of…