Related papers: Strategies for particle resampling in PIC simulati…
With the development of low order scaling methods for performing Kohn-Sham Density Functional Theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an…
Cosmic-ray acceleration processes in astrophysical plasmas are often investigated with fully-kinetic or hybrid kinetic numerical simulations, which enable us to describe a detailed microphysics of particle energization mechanisms. Tracing…
This study addresses the challenge of simulating realistic particle systems by proposing a novel particle decomposition scheme that improves the parallel performance of surface resolved particle simulations. Realistic particle systems often…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Many appplications in computational science are sufficiently compute-intensive that they depend on the power of parallel computing for viability. For all but the "embarrassingly parallel" problems, the performance depends upon the level of…
Biomolecular condensates are essential for cellular organization and result from phase separation in systems far from thermodynamic equilibrium. Among various models, chemically active droplets play a significant role, consisting of…
Next generation of ultra-intense laser facilities will lead to novel physical conditions ruled by collective and quantum electrodynamics effects, such as synchrotron-like emission of high-energy photons and electron-positron pair…
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…
Extracting the Hamiltonian of interacting quantum-information processing systems is a keystone problem in the realization of complex phenomena and large-scale quantum computers. The remarkable growth of the field increasingly requires…
The advent of hybrid computing platforms consisting of quantum processing units integrated with conventional high-performance computing brings new opportunities for algorithm design. By strategically offloading select portions of the…
Particle-in-cell (PIC) plasma simulations are a productive and valued tool for the study of nonlinear plasma phenomena, yet there are basic questions about the simulation methods themselves that remain unanswered. Here we study one such…
The charge and potential distributions for insulating particles approaching a substrate with regular insulating structures are studied by particle-in-cell numerical simulations. An elongated particle and substrate with elongated structures…
This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and…
The paper illustrates an application of the Resampling approach [2] for the estimation of the aircraft circulation plan reliability. Resampling is an intensive computer statistical method, which can be used effectively in the case of small…
Liquid-fabric interaction simulations using particle-in-cell (PIC) based models have been used to simulate a wide variety of phenomena and yield impressive visual results. However, these models suffer from numerical damping due to the data…
We present an efficient method to perform overdamped Brownian dynamics simulations in external force fields and for particle interactions that include a hardcore part. The method applies to particle motion in one dimension, where it is…
A coarse-grained computational model is used to investigate the effect of a fluctuating fluid membrane on the dynamics of patchy-particle assembly into virus capsid-like cores. Results from simulations for a broad range of parameters are…
This chapter is devoted to the computation of equilibrium (thermodynamic) properties of quantum systems. In particular, we will be interested in the situation where the interaction between particles is so strong that it cannot be treated as…
The widespread popularity of replica exchange and expanded ensemble algorithms for simulating complex molecular systems in chemistry and biophysics has generated much interest in enhancing phase space mixing of these protocols, thus…
We derive an equation for energy transfer from relativistic charged particles to a cold background plasma appropriate for finite-size particles that are used in particle-in-cell simulation codes. Expressions for one-, two-, and…