Related papers: Optimisation of a Brownian dynamics algorithm for …
Nonlinear behavior of electro-osmosis in dilute non-adsorbing polymer solutions with low salinity is investigated with Brownian dynamics simulations and a kinetic theory. In the Brownian simulations, the hydrodynamic interaction between the…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
Hybrid quantum mechanics / molecular mechanics (QM/MM) models successfully describe the properties of biological macromolecules. However, most QM/MM methodologies are constrained to unrealistic gas phase models, thus limiting their…
We propose a simulation method for Brownian dynamics of hard rods in one dimension for arbitrary continuous external force fields. It is an event-driven procedure based on the fragmentation and mergers of clusters formed by particles in…
A new method based on quasi-independent parallel simulations approach, replica-averaging, has been developed to study the influence of flow on mechanical force-mediated polymer processes such as denaturation and breaking of bonds. This…
The random batch Ewald (RBE) is an efficient and accurate method for molecular dynamics (MD) simulations of physical systems at the nano-/micro- scale. The method shows great potential to solve the computational bottleneck of long-range…
We develop a general optimization-theoretic framework for Bregman-Variational Learning Dynamics (BVLD), a new class of operator-based updates that unify Bayesian inference, mirror descent, and proximal learning under time-varying…
In this paper, we propose an approach for simulating wall-bounded incompressible turbulent flows by integrating the technology of random vortex method with the core principles of large-eddy simulations (LES). In particular, we employ the…
This work develops an efficient and accurate optimization algorithm to study the optimal mixing problem driven by boundary control of unsteady Stokes flows, based on the theoretical foundation laid by Hu and Wu in a series of work. The…
This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…
In this article we present first an algorithm for calculating the determining equations associated with so-called ``nonclassical method'' of symmetry reductions (a la Bluman and Cole) for systems of partial differentail equations. This…
We present a simple modification of the direct-forcing immersed boundary method (IBM) proposed by Uhlmann [J. Comput. Phys, 2005] in order to enable it to be applied to particulate flows with solid-to-fluid density ratios around unity. The…
Simulating the dynamics of charged particles in quasi-two-dimensional (quasi-2D) nanoconfined systems presents a significant computational challenge due to the long-range nature of electrostatic interactions and the geometric anisotropy. To…
The computational bottleneck of molecular dynamics is the pairwise additive long-range interactions between particles. The random batch Ewald (RBE) method provides a highly efficient and superscalable solver for long-range interactions, but…
The last few years have witnessed an explosion of new numerical methods for filament hydrodynamics. Aside from their ubiquity in biology, physics, and engineering, filaments present unique challenges from an applied-mathematical point of…
To simulate plasma phenomena, large-scale computational resources have been employed in developing high-precision and high-resolution plasma simulations. One of the main obstacles in plasma simulations is the requirement of computational…
In this paper, we obtain the existence and finite-time blow-up for the solution to a system of semilinear stochastic partial differential equations driven by a combination of Brownian and fractional Brownian motions. Under suitable…
The conformational and dynamical properties of active Brownian polymers embedded in a fluid depend on the nature of the driving mechanism, e.g., self-propulsion or external actuation of the monomers. Implementations of self-propelled and…
We derive analytic solutions for the potential and field in a one-dimensional system of masses or charges with periodic boundary conditions, in other words Ewald sums for one dimension. We also provide a set of tools for exploring the…
This work focuses on developing high-order energy-stable schemes for wave-dominated problems in closed domains using staggered finite-difference summation-by-parts (SBP FD) operators. We extend the previously presented uniform staggered…