Related papers: Simple and efficent algorithm for large scale mole…
Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…
It was recently demonstrated that a simple Monte Carlo (MC) algorithm involving the swap of particle pairs dramatically accelerates the equilibrium sampling of simulated supercooled liquids. We propose two numerical schemes integrating the…
A common feature of wall-bounded turbulent particle-laden flows is enhanced particle concentrations in a thin layer near the wall due to a phenomenon known as turbophoresis. Even at relatively low bulk volume fractions, particle-particle…
Recent results on supercomputers show that beyond 65K cores, the efficiency of molecular dynamics simulations of interfacial systems decreases significantly. In this paper, we introduce a dynamic cutoff method (DCM) for interfacial systems…
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…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…
Memcomputing is a novel paradigm of computation that utilizes dynamical elements with memory to both store and process information on the same physical location. Its building blocks can be fabricated in hardware with standard electronic…
We present an algorithm for the simulation of the exact real-time dynamics of classical many-body systems with discrete energy levels. In the same spirit of kinetic Monte Carlo methods, a stochastic solution of the master equation is found,…
We test the performances of two different approaches to the computation of forces for molecular dynamics simulations on Graphics Processing Units. A "vertex-based" approach, where a computing thread is started per particle, is compared to a…
We present a number of novel algorithms, based on mathematical optimization formulations, in order to solve a homogeneous multiprocessor scheduling problem, while minimizing the total energy consumption. In particular, for a system with a…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
Molecular dynamics (MD) simulation is one of the past decade's most important tools for enabling biology scientists and researchers to explore human health and diseases. However, due to the computation complexity of the MD algorithm, it…
The simulation of granular media is usually done either with event-driven codes that treat collisions as instantaneous but have difficulty with very dense packings, or with molecular dynamics methods that approximate rigid grains using a…
In this paper, we propose the first optimum process scheduling algorithm for an increasingly prevalent type of heterogeneous multicore (HEMC) system that combines high-performance big cores and energy-efficient small cores with the same…
We develop randomized quantum algorithms to simulate quantum collision models, also known as repeated interaction schemes, which provide a rich framework to model various open-system dynamics. The underlying technique involves composing…
Quantum computers have the potential to efficiently simulate the dynamics of many interacting quantum particles, a classically intractable task of central importance to fields ranging from chemistry to high-energy physics. However,…
We present a cluster kinetic Monte-Carlo algorithm for active matter systems of self-propelled particles with special focus on steric interactions. The kinetic event-chain algorithm is based on the event-chain Monte-Carlo method and is…
With the continuous growth of processing power for scientific computing, first principles Born-Oppenheimer molecular dynamics (MD) simulations are becoming increasingly popular for the study of a wide range of problems in materials science,…
Solvent-mediated hydrodynamic interactions between colloidal particles can significantly alter their dynamics. We discuss the implementation of Stokesian dynamics in leading approximation for streaming processors as provided by the compute…
The blossoming of interest in colloids and nano-particles has given renewed impulse to the study of hard-body systems. In particular, hard spheres have become a real test system for theories and experiments. It is therefore necessary to…