Related papers: DynamO: A free O(N) general event-driven molecular…
The incoherent dynamical properties of open quantum systems are generically attributed to an ongoing correlation between the system and its environment. Here, we propose a novel way to assess the nature of these system-environment…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
Parameter estimation for ordinary differential equations (ODEs) plays a fundamental role in the analysis of dynamical systems. Generally lacking closed-form solutions, ODEs are traditionally approximated using deterministic solvers.…
Continuous scaling of the VLSI system leaves a great challenge on manufacturing and optical proximity correction (OPC) is widely applied in conventional design flow for manufacturability optimization. Traditional techniques conducted OPC by…
We have developed and implemented a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation…
When granular systems are modeled by frictionless hard spheres, particle-particle collisions are considered as instantaneous events. This implies that while the velocities change according to the collision rule, the positions of the…
ESPResSo 4.0 is an extensible simulation package for research on soft matter. This versatile molecular dynamics program was originally developed for coarse-grained simulations of charged systems Limbach et al., Comput. Phys. Commun. 174,…
Long-term fluid dynamics forecasting is a critically important problem in science and engineering. While neural operators have emerged as a promising paradigm for modeling systems governed by partial differential equations (PDEs), they…
Digital quantum simulation on quantum systems require algorithms that can be implemented using finite quantum resources. Recent studies have demonstrated digital quantum simulation of open quantum systems on Noisy Intermediate-Scale Quantum…
In molecular simulations, efficient methods for investigating equilibration and slow relaxation in dense systems are crucial yet challenging. This study focuses on the diffusional characteristics of monodisperse hard disk systems at…
To simulate the dynamics of fluid with polydisperse particles on macroscale level, one has to solve hydrodynamic equations with several relaxation terms, representing momentum transfer from fluid to particles and vice versa. For small…
This work introduces ParAMS -- a versatile Python package that aims to make parameterization workflows in computational chemistry and physics more accessible, transparent and reproducible. We demonstrate how ParAMS facilitates the parameter…
In this work animations of the random walk movement using a freeware Algodoo were done in order to support teaching the concepts of Brownian Motion. The random walk movement were simulate considering elastic collision between the particles…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
Simulations of chemical dynamics are a powerful means for understanding chemistry. However, classical computers struggle to simulate many chemical processes, especially non-adiabatic ones, where the Born-Oppenheimer approximation breaks…
We analyze the complexity of classically simulating continuous-time dynamics of locally interacting quantum spin systems with a constant rate of entanglement breaking noise. We prove that a polynomial time classical algorithm can be used to…
Linear dissipative differential equation is a fundamental model for a large number of physical systems, such as quantum dynamics with non-Hermitian Hamiltonian, open quantum system dynamics, diffusion process and damped system. In this…
Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…