Related papers: Algorithm for Mesoscopic Advection-Diffusion
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.…
A fractional diffusion equation with advection term is rigorously derived from a kinetic transport model with a linear turning operator, featuring a fat-tailed equilibrium distribution and a small directional bias due to a given vector…
Modelling random dynamical systems in continuous time, diffusion processes are a powerful tool in many areas of science. Model parameters can be estimated from time-discretely observed processes using Markov chain Monte Carlo (MCMC) methods…
Complex multidimensional stochastic dynamics can be approximately described as diffusion along reaction coordinates (RCs). If the RCs are optimally selected, the diffusive model allows one to compute important properties of the dynamics…
Explicit analytical expressions for the drag and diffusion coefficients of a spherical particle attached to the interface between two immiscible fluids are constructed for the case of a small viscosity ratio between the fluid phases. The…
We present a class of diffusion-based algorithms to draw samples from high-dimensional probability distributions given their unnormalized densities. Ideally, our methods can transport samples from a Gaussian distribution to a specified…
Stochastically evolving geometric systems are studied in shape analysis and computational anatomy for modelling random evolutions of human organ shapes. The notion of geodesic paths between shapes is central to shape analysis and has a…
Space fractional convection diffusion equation describes physical phenomena where particles or energy (or other physical quantities) are transferred inside a physical system due to two processes: convection and superdiffusion. In this…
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…
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 present here a new stochastic modelling in the constitution of fluid flow reduced-order models. This framework introduces a spatially inhomogeneous random field to represent the unresolved small-scale velocity component. Such a…
In this paper, we are concerned with the simulation of blood flow in microvascular networks and the surrounding tissue. To reduce the computational complexity of this issue, the network structures are modeled by a one-dimensional graph,…
The Navier-Stokes equations describe the motion of viscous fluids. In order to predict turbulent flows with reasonable computational time and accuracy, these equations are spatially filtered according to the large-eddy simulation (LES)…
We assess the capabilities of hydrodynamic density functional theory (DFT) to predict mass transfer across vapor-liquid interfaces by studying the response of an initially equilibrated pure component vapor-liquid system to the localized…
Several algorithms have been used for mass transfer between particles undergoing advective and macro-dispersive random walks. The mass transfer between particles is required for general reactions on, and among, particles. The mass transfer…
Turbulent, relativistic nonthermal plasmas are ubiquitous in high-energy astrophysical systems, as inferred from broadband nonthermal emission spectra. The underlying turbulent nonthermal particle acceleration (NTPA) processes have…
We present an explicit method for simulating stochastic differential equations (SDEs) that have variable diffusion coefficients and satisfy the detailed balance condition with respect to a known equilibrium density. In Tupper and Yang…
We introduce and test methods for the calibration of the diffusion term in Stochastic Partial Differential Equations (SPDEs) describing fluids. We take two approaches, one uses ideas from the singular value decomposition and the Biot-Savart…
In a previous paper, we described new analytic formulae for optically-thick supercritical accretion flows (Watarai 2006, hereafter paper 1). Here we present analytic formulae for optically-thin one-temperature accretion flows including the…
We develop an analytical diffusion-equation-type approximation scheme for the one-dimensional coagulation reaction A+A->A with partial reaction probability on particle encounters which are otherwise hard-core. The new approximation…