Related papers: A Vectorized Algorithm for Molecular Dynamics of S…
We report on a lattice based algorithm, completely vectorized for molecular dynamics simulations. Its algorithmic complexity is of the order O(N), where $N$ is the number of particles. The algorithm works very effectively when the particles…
We consider Monte Carlo algorithms for the simulation of charged lattice gases with purely local dynamics. We study the mobility of particles as a function of temperature and show that the poor mobility of particles at low temperatures is…
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…
We propose a fast method for the calculation of short-range interactions in molecular dynamics simulations. The so-called random-batch list method is a stochastic version of the classical neighbor-list method to avoid the construction of a…
We introduce a Monte-Carlo algorithm for the simulation of charged particles moving in the continuum. Electrostatic interactions are not instantaneous as in conventional approaches, but are mediated by a constrained, diffusing electric…
Correlation of interacting particles is studied in their dynamics and localization in ideal and disordered lattice systems with the help of numerical tools. Both 1D and 2D systems are considered. In 1D lattices with long-range hopping,…
We introduce a lattice gas implementation that is based on coarse-graining a Molecular Dynamics (MD) simulation. Such a lattice gas is similar to standard lattice gases, but its collision operator is informed by an underlying MD simulation.…
We propose a new model suitable for a nonequilibrium molecular dynamics (MD) simulation of electrical conductors. The model consists of classical electrons and atoms. The atoms compose a lattice vibration system. The electrons are scattered…
In the first part of a series of two papers, we present in considerable detail a collision-driven molecular dynamics algorithm for a system of nonspherical particles, within a parallelepiped simulation domain, under both periodic or…
Long ranged electrostatic interactions are time consuming to calculate in molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic framework for simulating charged particles which modifies the dynamics so as to allow…
We propose an easy to use model to solve for interacting atoms in an optical lattice. This model allows for the whole range of weakly to strongly interacting atoms, and it includes the coupling between relative and center-of-mass motion via…
Intracellular transport processes driven by molecular motors can be described by stochastic lattice models of self-driven particles. Here we focus on bidirectional transport models excluding the exchange of particles on the same track. We…
Discrete particle simulations are widely used to study large-scale particulate flows in complex geometries where particle-particle and particle-fluid interactions require an adequate representation but the computational cost has to be kept…
We propose a hierarchy of multi-level kinetic Monte Carlo methods for sampling high-dimensional, stochastic lattice particle dynamics with complex interactions. The method is based on the efficient coupling of different spatial resolution…
Learning system dynamics directly from observations is a promising direction in machine learning due to its potential to significantly enhance our ability to understand physical systems. However, the dynamics of many real-world systems are…
Here, we propose a platform based on ultra-cold fermionic molecules trapped in optical lattices to simulate nonadiabatic effects, as they appear in certain molecular dynamical problems. The idea consists of a judicious choice of two…
Quantum heuristics have shown promise in solving various optimization problems, including lattice protein folding. Equally relevant is the inverse problem, protein design, where one seeks sequences that fold to a given target structure. The…
Molecular Dynamics simulations can help scientists to gather valuable insights for physical processes on an atomic scale. This work explores various techniques for SIMD vectorization to improve the pairwise force calculation between…
In simulations of crystals, unlike liquids or gases, it may happen that the properties of the studied system depend not only on the volume of the simulation cell but also on its shape. For such cases it is desirable to change the shape of…
When particles suspended in a fluid are driven through a regular lattice of cylindrical obstacles, the particle motion is usually not simply in the direction of the force, and in the high Peclet number limit particle trajectories tend to…