Related papers: Stochastic Simulation of Reaction-Diffusion System…
We develop a statistical toolbox for a quantitative model evaluation of stochastic reaction-diffusion systems modeling space-time evolution of biophysical quantities on the intracellular level. Starting from space-time data $X_N(t,x)$, as,…
The effects of thermal fluctuations on nanoscale flows are captured by a numerical scheme that is underpinned by fluctuating hydrodynamics. A stochastic lubrication equation (SLE) is solved on non-uniform adaptive grids to study a series of…
In this paper we discuss the formulation of the fuctuating Navier-Stokes (FNS) equations for multi-species, non-reactive fluids. In particular, we establish a form suitable for numerical solution of the resulting stochastic partial…
We describe the implementation and testing of a smoothed particle hydrodynamics (SPH) code that solves the equations of radiation hydrodynamics in the flux-limited diffusion (FLD) approximation. The SPH equations of radiation hydrodynamics…
A space discrete approximation to a highly nonlinear reaction-diffusion system endowed with a stochastic dynamical boundary condition is analyzed and the convergence of the discrete scheme to the solution to the corresponding continuum…
Numerical radiation-hydrodynamics (RHD) for non-relativistic flows is a challenging problem because it encompasses processes acting over a very broad range of timescales, and where the relative importance of these processes often varies by…
To achieve efficient and accurate long-time integration, we propose a fast, accurate, and stable high-order numerical method for solving fractional-in-space reaction-diffusion equations. The proposed method is explicit in nature and…
We study numerical methods for dissipative particle dynamics (DPD), which is a system of stochastic differential equations and a popular stochastic momentum-conserving thermostat for simulating complex hydrodynamic behavior at mesoscales.…
We model chaotic diffusion, in a symplectic 4D map by using the result of a theorem that was developed for stochastically perturbed integrable Hamiltonian systems. We explicitly consider a map defined by a free rotator (FR) coupled to a…
Recent works have derived and proven the large-population mean-field limit for several classes of particle-based stochastic reaction-diffusion (PBSRD) models. These limits correspond to systems of partial integral-differential equations…
In this paper we introduce a novel method to simulate lateral diffusion of inclusions in a fluctuating membrane. The regarded systems are governed by two dynamic processes: the height fluctuations of the membrane and the diffusion of the…
We develop computational methods that incorporate shear into fluctuating hydrodynamics methods. We are motivated by the rheological responses of complex fluids and soft materials. Our approach is based on continuum stochastic hydrodynamic…
The modeling and simulation of stochastic reaction-diffusion processes is a topic of steady interest that is approached with a wide range of methods. \rev{At the level of particle-resolved descriptions, where chemical reactions are coupled…
We propose a novel family of asymptotically stable, implicit-explicit, adaptive, time integration method (denoted with the $\theta$-method) for the solution of the fractional advection-diffusion-reaction (FADR) equations. This family of…
It is essential that mesoscopic simulations of reactive systems reproduce the correct statistical distributions at thermodynamic equilibrium. By considering a compressible fluctuating hydrodynamics (FHD) simulation method of ideal gas…
We study the dynamics of elastic interfaces-membranes-immersed in thermally excited fluids. The work contains three components: the development of a numerical method, a purely theoretical approach, and numerical simulation. In developing a…
This work proposes stochastic partial differential equations (SPDEs) as a practical tool to replicate clustering effects of more detailed particle-based dynamics. Inspired by membrane-mediated receptor dynamics on cell surfaces, we…
We simulate the mesoscopic dynamics of droplets formed by phase separated fluids at nanometer scales where thermal fluctuations are significant. Both spherical droplets fully immersed in a second fluid and sessile droplets which are also in…
Simulating spatiotemporal turbulence with high fidelity remains a cornerstone challenge in computational fluid dynamics (CFD) due to its intricate multiscale nature and prohibitive computational demands. Traditional approaches typically…
In this paper we study the problem of computing the effective diffusivity for a particle moving in chaotic and stochastic flows. In addition we numerically investigate the residual diffusion phenomenon in chaotic advection. The residual…