Related papers: Optimisation of a Brownian dynamics algorithm for …
Brownian Dynamics algorithms are widely used for simulating soft-matter and biochemical systems. In recent times, their application has been extended to the simulation of coarse-grained models of cellular networks in simple organisms. In…
We discuss the design of state-of-the-art numerical methods for molecular dynamics, focusing on the demands of soft matter simulation, where the purposes include sampling and dynamics calculations both in and out of equilibrium. We discuss…
The theory of the dynamics of polymers in solution is developed coming from the hydrodynamic theory of the Brownian motion (BM) and the Rouse-Zimm (RZ) model. It is shown that the time correlation functions describing the polymer motion…
We use the general framework of summation-by-parts operators to construct conservative, energy-stable, and well-balanced semidiscretizations of two different nonlinear systems of dispersive shallow water equations with varying bathymetry:…
Position based dynamics is a powerful technique for simulating a variety of materials. Its primary strength is its robustness when run with limited computational budget. We develop a novel approach to address problems with PBD for…
We consider the natural generalization of the Schr\"{o}dinger equation to Markovian open system dynamics: the so-called the Lindblad equation. We give a quantum algorithm for simulating the evolution of an $n$-qubit system for time $t$…
Fluctuating hydrodynamics based techniques have been developed in recent years for the simulation of Brownian motion of particles. These mesoscale simulation tools are viable approaches for problems where molecular dynamics simulations may…
To the present day, the Beenakker-Mazur (BM) method is the most comprehensive statistical physics approach to the calculation of short-time transport properties of colloidal suspensions. A revised version of the BM method with an improved…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
We present a new method, in the following called MMM2D, to accurately calculate the electrostatic energy and forces on charges being distributed in a two dimensional periodic array of finite thickness. It is not based on an Ewald summation…
We present a computer simulation of entangled polymer solutions at equilibrium. The chains repel each other via a soft Gaussian potential, appropriate for semi-dilute solutions at the scale of a correlation blob. The key innovation to…
We present a technique to efficiently compute long-range interactions in systems with periodic boundary conditions. We extend the well-known Ewald method by using a linear combination of screening Gaussian charge distributions instead of…
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's…
A mesoscopic, mixed particle- and field-based Brownian dynamics methodology for the simulation of entangled polymer melts has been developed. Polymeric beads consist of several Kuhn segments, and their motion is dictated by the Helmholtz…
We have extended the multilevel summation (MLS) method, originally developed to evaluate long-range Coulombic interactions in molecular dynamics (MD) simulations [Skeel et al., J. Comput. Chem., 23, 673 (2002)], to handle dispersion…
Strongly coupled immersed boundary (IB) methods solve the nonlinear fluid and structural equations of motion simultaneously for strongly enforcing the no-slip constraint on the body. Handling this constraint requires solving several large…
In this work we develop the Spectral Ewald Accelerated Stokesian Dynamics (SEASD), a novel computational method for dynamic simulations of polydisperse colloidal suspensions with full hydrodynamic interactions. SEASD is based on the…
The tumbling dynamics of individual polymers in semidilute solution is studied by large-scale non-equilibrium mesoscale hydrodynamic simulations. We find that the tumbling time is equal to the non-equilibrium relaxation time of the polymer…
Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the…
We developed a parallel Bayesian optimization algorithm for large eddy simulations. These simulations challenge optimization methods because they take hours or days to compute, and their objective function contains noise as turbulent…