Related papers: Optimisation of a Brownian dynamics algorithm for …
A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with…
The immersed boundary lattice Boltzmann method (IB-LBM) has been widely used in the simulation of fluid-solid interaction and particulate flow problems, since proposed in 2004. However, it is usually a non-trivial task to retain the…
High-dimensional simulation optimization is notoriously challenging. We propose a new sampling algorithm that converges to a global optimal solution and suffers minimally from the curse of dimensionality. The algorithm consists of two…
We present a finite-horizon optimization algorithm that extends the established concept of Dual Dynamic Programming (DDP) in two ways. First, in contrast to the linear costs, dynamics, and constraints of standard DDP, we consider problems…
We investigate the dynamics and the pathways of the collapse of a single, semiflexible polymer in a poor solvent via 3-D Brownian Dynamics simulations. Earlier work indicates that the condensation of semiflexible polymers generically…
Computing equilibrium concentrations of molecular complexes is generally analytically intractable and requires numerical approaches. In this work we focus on the polymer-monomer level, where indivisible molecules (monomers) combine to form…
To enhance the scalability and performance of the traditional finite-difference time-domain (FDTD) methods, a three-dimensional summation-by-parts simultaneous approximation term (SBP-SAT) FDTD method is developed to solve complex…
We present a clear and rigorous derivation of the Ewald-like method for calculation of the electrostatic energy of the systems infinitely periodic in two-dimensions and of finite size in the third dimension (slabs) which is significantly…
A mixed basis approach based on density functional theory is extended to one-dimensional(1D) systems. The basis functions here are taken to be the localized B-splines for the two finite non-periodic dimensions and the plane waves for the…
An efficient technique to simulate turbulent particle-laden flow at high mass loadings within the four-way coupled simulation regime is presented. The technique implements large eddy simulation, discrete phase simulation, a deterministic…
Traditional models of wormlike chains in shear flows at finite temperature approximate the equation of motion via finite difference discretization (bead and rod models). We introduce here a new method based on a spectral representation in…
To minimise systematic errors in Monte Carlo simulations of charged particles, long range electrostatic interactions have to be calculated accurately and efficiently. Standard approaches, such as Ewald summation or the naive application of…
Exact and asymptotic formulas relating to dynamical correlations for overdamped Brownian motion are obtained. These formulas include a generalization of the $f$-sum rule from the theory of quantum fluids, a formula relating the static…
The effect of excluded volume interactions on the structure of a polymer in shear flow is investigated by Brownian Dynamics simulations for chains with size $30\leq N\leq 300$. The main results concern the structure factor $S({\bf q})$ of…
Integration against a probability distribution given its unnormalized density is a central task in Bayesian inference and other fields. We introduce new methods for approximating such expectations with a small set of weighted samples --…
We develop a computational method for modeling electrostatic interactions of arbitrarily-shaped, polarizable objects on colloidal length scales, including colloids/nanoparticles, polymers, and surfactants, dispersed in explicit ion…
Broyden's method is a general method commonly used for nonlinear systems of equations, when very little information is available about the problem. We develop an approach based on Broyden's method for nonlinear eigenvalue problems. Our…
Computationally modeling the behavior of wavelength-sized non-spherical particles in optical tweezers can give insight into the existence and stability of trapping equilibria as well as the optical manipulation of such particles more…
Two-level logic minimization is a central problem in logic synthesis, and has applications in reliability analysis and automated reasoning. This paper represents a method of minimizing Boolean sum of products function with binary decision…
This paper presents a general and robust method for the fluid-structure interaction of membranes and shells undergoing large displacement and large added-mass effects by coupling an immersed-boundary method with a shell finite-element…