相关论文: Algorithm for molecular dynamics simulations of sp…
Interacting spin systems are of fundamental relevance in different areas of physics, as well as in quantum information science, and biology. These spin models represent the simplest, yet not fully understood, manifestation of quantum…
Numerical simulation of fluids plays an essential role in modeling many physical phenomena, such as weather, climate, aerodynamics and plasma physics. Fluids are well described by the Navier-Stokes equations, but solving these equations at…
We present a method to sample reactive pathways via biased molecular dynamics simulations in trajectory space. We show that the use of enhanced sampling techniques enables unconstrained exploration of multiple reaction routes. Time…
Symplectic integrators offer vastly superior performance over traditional numerical techniques for conservative dynamical systems, but their application to \emph{dissipative} systems is inherently difficult due to dissipative systems' lack…
Molecular dynamics algorithms are subject to some amount of error dependent on the size of the time step that is used. This error can be corrected by periodically updating the system with a Metropolis criteria, where the integration step is…
We show that all existing methods quantifying rotational motion in molecular fluids eventually fail in systems undergoing complex rotational motion characterised by slow, heterogeneous, or intermittent dynamics. This impacts in particular…
Advanced algorithms are necessary to obtain faster-than-real-time dynamic simulations in a number of different physical problems that are characterized by widely disparate time scales. Recent advanced dynamic Monte Carlo algorithms that…
We present, in a unifying way, the main components of three asynchronous event-driven algorithms for simulating physical systems of interacting particles. The first example, hard-particle molecular dynamics, is well-known. We also present a…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
In this article we introduce a novel coupled algorithm for massively parallel direct numerical simulations of electrophoresis in microfluidic flows. This multiphysics algorithm employs an Eulerian description of fluid and ions, combined…
An explicit second-order numerical method to integrate the isokinetic equations of motion is derived by fitting circular arcs through every three consecutive points of the discretized trajectory, so that the tangent and the curvature…
Symplectic numerical schemes for reversible dynamical systems predict the solution reliably over large times as well, and are a good starting point for extension to schemes for simulating irreversible situations like viscoelastic wave…
Magnetohydrodynamics (MHD) describes the interaction between electrically conducting fluids and electromagnetic fields. We propose and analyze a symplectic, second-order algorithm for the evolutionary MHD system in Els\"asser variables. We…
In dynamic Monte Carlo simulations, using for example the Metropolis dynamic, it is often required to simulate for long times and to simulate large systems. We present an overview of advanced algorithms to simulate for larger times and to…
Computer simulation of the time evolution in a classical system is a standard numerical method, used in numerous scientific articles in Natural Science. Almost all the simulations are performed by discrete Molecular Dynamics (MD). The…
We present an improved method for computing incompressible viscous flow around suspended rigid particles using a fixed and uniform computational grid. The main idea is to incorporate Peskin's regularized delta function approach [Acta…
A general framework for performing event-driven simulations of systems with semi-flexible or rigid bodies interacting under impulsive torques and forces is outlined. Two different approaches are presented. In the first, the dynamics and…
The \textit{Spirit} framework is designed for atomic scale spin simulations of magnetic systems of arbitrary geometry and magnetic structure, providing a graphical user interface with powerful visualizations and an easy to use scripting…
In this paper we provide two representations for stochastic ion channel kinetics, and compare the performance of exact simulation with a commonly used numerical approximation strategy. The first representation we present is a random time…
Magnetic helicity is robustly conserved in systems with very large magnetic Reynolds numbers, including most systems of astrophysical interest, and unlike kinetic and magnetic energy is not dissipated at small scales. This plays a major…