Related papers: GIBS: A grand-canonical Monte Carlo simulation pro…
In conventional molecular simulation, metastable structures often survive over considerable computational time, resulting in difficulties in simulating equilibrium states. In order to overcome this difficulty, here we propose a newly…
Biips is a software platform for automatic Bayesian inference with interacting particle systems. Biips allows users to define their statistical model in the probabilistic programming BUGS language, as well as to add custom functions or…
Investigating critical phenomena or phase transitions is of high interest in physics and chemistry, for which Monte Carlo (MC) simulations, a crucial tool for numerically analyzing macroscopic properties of given systems, are often hindered…
Purpose: This work advances a Monte Carlo (MC) method to combine ionizing radiation physics with optical physics, in a manner which was implicitly designed for deployment with the most widely accessible parallelization and portability…
Glauber models are used to calculate geometric quantities in the initial state of heavy ion collisions, such as impact parameter, number of participating nucleons and initial eccentricity. Experimental heavy-ion collaboration, in particular…
Coulomb and log-gases are exchangeable singular Boltzmann-Gibbs measures appearing in mathematical physics at many places, in particular in random matrix theory. We explore experimentally an efficient numerical method for simulating such…
Monte Carlo methods are essential tools for Bayesian inference. Gibbs sampling is a well-known Markov chain Monte Carlo (MCMC) algorithm, extensively used in signal processing, machine learning, and statistics, employed to draw samples from…
Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees of freedom and multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular…
The particle Gibbs sampler is a Markov chain Monte Carlo (MCMC) algorithm to sample from the full posterior distribution of a state-space model. It does so by executing Gibbs sampling steps on an extended target distribution defined on the…
A recent reformulation [1] of the problem of Coulomb gases in the presence of a dynamical dielectric medium showed that finite temperature simulations of such systems can be accomplished on the basis of completely local Hamiltonians on a…
I present a brief review of the existing models for particle multiplicity evaluation in heavy ion collisions which are at our disposal in the form of Monte Carlo simulators. Models are classified according to the physical mechanisms with…
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…
The electrostatic, entropic and surface interactions between a macroion (nanoparticle or biomolecule), surrounding ions and water molecules play a fundamental role in the behavior and function of colloidal systems. However, the molecular…
We describe a Monte Carlo scheme for the grand canonical simulation study of fluid phase equilibria in highly size-asymmetrical binary mixtures. The method utilizes an expanded ensemble in which the insertion and deletion of large particles…
Carbon-hydrogen plasmas and hydrocarbon materials are of broad interest to laser shock experimentalists, high energy density physicists, and astrophysicists. Accurate equations of state (EOS) of hydrocarbons are valuable for various studies…
For the first time, we report a unified microscopic-macroscopic Monte Carlo simulation of gas-grain chemistry in cold interstellar clouds in which both the gas-phase and the grain surface chemistry are simulated by a stochastic technique.…
Understanding the sodium-storage mechanism in hard carbon (HC) anodes is crucial for advancing sodium-ion battery (SIB) technology. However, the intrinsic complexity of HC microstructures and their interactions with sodium remain not fully…
Heavy-ion collisions can be simulated by means of comprehensive approaches, to include the many different reaction mechanisms which may contribute. QMD models and their relativistic extensions are examples of these approaches based on Monte…
Long ranged electrostatic interactions are time consuming to calculate in molecular dynamics and Monte-Carlo simulations. We introduce an algorithmic framework for simulating charged particles which modifies the dynamics so as to allow…
Context. While synthesis of organic molecules in molecular clouds or protoplanetary disks is complex, observations of interstellar grains, analyses of carbonaceous chondrites, and UV photochemistry experiments are rapidly developing and…