Related papers: DynamO: A free O(N) general event-driven molecular…
Our computers today, from sophisticated servers to small smartphones, operate based on the same computing model, which requires running a sequence of discrete instructions, specified as an algorithm. This sequential computing paradigm has…
DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely…
Quantum simulation represents the most promising quantum application to demonstrate quantum advantage on near-term noisy intermediate-scale quantum (NISQ) computers, yet available quantum simulation algorithms are prone to errors and thus…
The simmer package brings discrete-event simulation to R. It is designed as a generic yet powerful process-oriented framework. The architecture encloses a robust and fast simulation core written in C++ with automatic monitoring…
This master thesis introduces the idea of dynamic cutoffs in molecular dynamics simulations, based on the distance between particles and the interface, and presents a solution for detecting interfaces in real-time. Our dynamic cutoff method…
Dynamical maps describe general transformations of the state of a physical system, and their iteration can be interpreted as generating a discrete time evolution. Prime examples include classical nonlinear systems undergoing transitions to…
Conventional molecular dynamics (MD) simulations struggle when simulating particles with steeply varying interaction potentials, due to the need to use a very short time step. Here, we demonstrate that an event-driven Monte Carlo (EDMC)…
Molecular dynamics simulations use statistical mechanics at the atomistic scale to enable both the elucidation of fundamental mechanisms and the engineering of matter for desired tasks. The behavior of molecular systems at the microscale is…
We introduce MENO (''Matrix Exponential-based Neural Operator''), a hybrid surrogate modeling framework for efficiently solving stiff systems of ordinary differential equations (ODEs) that exhibit a sparse nonlinear structure. In such…
Digital quantum computers have the potential to simulate complex quantum systems. The spin-boson model is one of such systems, used in disparate physical domains. Importantly, in a number of setups, the spin-boson model is open, i.e. the…
This paper presents a 2D/3D Free Surface Lattice Boltzmann Method simulation package called LBfoam for the simulation of foaming processes. The model incorporates the essential physics of foaming phenomena: gas diffusion into nucleated…
Hybrid quantum-classical algorithms are among the most promising systems to implement quantum computing under the Noisy-Intermediate Scale Quantum (NISQ) technology. In this paper, at first, we investigate a quantum dynamics algorithm for…
We present our ongoing work aimed at accelerating a particle-resolved direct numerical simulation model designed to study aerosol-cloud-turbulence interactions. The dynamical model consists of two main components - a set of fluid dynamics…
Driven particles in presence of crowded environment, obstacles or kinetic constraints often exhibit negative differential mobility (NDM) due to their decreased dynamical activity. We propose a new mechanism for complex many-particle systems…
Discrete simulation methods are efficient tools to investigate the complex behaviors of complex fluids made of either dry granular materials or dilute suspensions. By contrast, materials made of soft and/or concentrated units (emulsions,…
This paper discusses the latest generation of the MONARC (MOdels of Networked Analysis at Regional Centers) simulation framework, as a design and modelling tool for large scale distributed systems applied to HEP experiments. A…
So far there have been several efforts for developing software process simulators. However, the approaches for developing the simulators seem to have been ad-hoc and no systematic methodology exists. Since modeling and simulation in support…
Modern analog computers are ideally suited to solving large systems of ordinary differential equations at high speed with low energy consumtion and limited accuracy. In this article, we survey N-body physics, applied to a simple water model…
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…
Droplets form a cornerstone of the spatiotemporal organization of biomolecules in cells. These droplets are controlled using physical processes like chemical reactions and imposed gradients, which are costly to simulate using traditional…