Related papers: DynamO: A free O(N) general event-driven molecular…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Discovering the governing laws underpinning physical and chemical phenomena is a key step towards understanding and ultimately controlling systems in science and engineering. We introduce Discovery of Dynamical Systems via Moving Horizon…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
Runko is a new open-source plasma simulation framework implemented in C++ and Python. It is designed to function as an easy-to-extend general toolbox for simulating astrophysical plasmas with different theoretical and numerical models.…
Our focus is on simulating the dynamics of non-interacting particles including the effects of an external potential, which, under certain assumptions, can be formally described by the Dean-Kawasaki equation. The Dean-Kawasaki equation can…
We implement two recently developed fast Coulomb solvers, HSMA3D [J. Chem. Phys. 149 (8) (2018) 084111] and HSMA2D [J. Chem. Phys. 152 (13) (2020) 134109], into a new user package HSMA for molecular dynamics simulation engine LAMMPS. The…
SALMON (Scalable Ab-initio Light-Matter simulator for Optics and Nanoscience, http://salmon-tddft.jp) is a software package for the simulation of electron dynamics and optical properties of molecules, nanostructures, and crystalline solids…
We present an algorithm for the control of complex networks and other nonlinear, high-dimensional dynamical systems. The computational approach is based on the recently-introduced concept of compensatory perturbations -- intentional…
Simflowny is an open platform which automatically generates efficient parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support simultaneously a quite…
A commonly held view in the turbomachinery community is that finite element methods are not well-suited for very large-scale thermomechanical simulations. We seek to dispel this notion by presenting performance data for a collection of…
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…
In this work, we study dynamic programming (DP) algorithms for partially observable Markov decision processes with jointly continuous and discrete state-spaces. We consider a class of stochastic systems which have coupled discrete and…
Warm dense matter systems created in the laboratory are highly dynamical. In such cases electron dynamics is often needed to accurately simulate the evolution and properties of the system. Large systems force one to make simple…
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…
Design considerations for molecular dynamics algorithms capable of taking advantage of the computational power of a graphics processing unit (GPU) are described. Accommodating the constraints of scalable streaming-multiprocessor hardware…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Nowadays there is a large availability of discrete event simulation software that can be easily used in different domains: from industry to supply chain, from healthcare to business management, from training to complex systems design.…
Quantum simulation is a prominent application of quantum computers. While there is extensive previous work on simulating finite-dimensional systems, less is known about quantum algorithms for real-space dynamics. We conduct a systematic…
We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of physics simulation environments, as well as interaction potentials and neural networks…
A new Markov Chain Monte Carlo method for simulating the dynamics of molecular systems characterized by hard-core interactions is introduced. In contrast to traditional Kinetic Monte Carlo approaches, where the state of the system is…