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A grand canonical Monte Carlo (MC) algorithm is presented for studying the lattice gas model (LGM) of multiple protein sequence alignment, which coherently combines long-range interactions and variable-length insertions. MC simulations are…

Biomolecules · Quantitative Biology 2017-07-13 Akira R. Kinjo

Traditionally, the field of computational Bayesian statistics has been divided into two main subfields: variational methods and Markov chain Monte Carlo (MCMC). In recent years, however, several methods have been proposed based on combining…

Computation · Statistics 2017-04-19 Cheng Zhang , Babak Shahbaba , Hongkai Zhao

New hybrid Molecular Dynamics-Monte Carlo methods are proposed to increase the efficiency of constant-pressure simulations. Two variations of the isobaric Molecular Dynamics component of the algorithms are considered. In the first, we use…

Soft Condensed Matter · Physics 2009-11-07 Roland Faller , Juan J. de Pablo

We present a new Monte Carlo method for obtaining solutions of the Boltzmann equation for describing phonon transport in micro and nanoscale devices. The proposed method can resolve arbitrarily small signals (e.g. temperature differences)…

Computational Physics · Physics 2015-05-30 Jean-Philippe Peraud , Nicolas Hadjiconstantinou

A general synthetic iterative scheme is proposed to solve the Enskog equation within a Monte Carlo framework. The method demonstrates rapid convergence by reducing intermediate Monte Carlo evolution and preserves the asymptotic-preserving…

Fluid Dynamics · Physics 2025-09-26 Bin Hu , Liyan Luo , Lei Wu

One of the open challenges in quantum computing is to find meaningful and practical methods to leverage quantum computation to accelerate classical machine learning workflows. A ubiquitous problem in machine learning workflows is sampling…

Quantum Physics · Physics 2024-08-08 Owen Lockwood , Peter Weiss , Filip Aronshtein , Guillaume Verdon

We present Generative Monte Carlo (GMC), a novel paradigm for particle transport simulation that integrates generative artificial intelligence directly into the stochastic solution of the linear Boltzmann equation. By reformulating the…

Computational Physics · Physics 2025-12-17 Joseph A. Farmer , Aidan Murray , Johannes Krotz , Ryan G. McClarren

The Stochastic Weighted Particle Method (SWPM) is a Monte Carlo technique developed by Rjasanow and Wagner that generalizes Bird's Direct Simulation Monte Carlo (DSMC) method for solving the Boltzmann equation. To reduce computational cost…

Numerical Analysis · Mathematics 2021-01-06 Sonam Lama , John Zweck , Matthew Goeckner

A new approach to simulating rotational cooling using a direct simulation Monte Carlo (DSMC) method is described and applied to the rotational cooling of ammonia seeded into a helium supersonic jet. The method makes use of ab initio…

Chemical Physics · Physics 2015-11-25 O. Schullian , J. Loreau , N. Vaeck , A. van der Avoird , B. R. Heazlewood , C. J. Rennick , T. P. Softley

In plasma edge simulations, kinetic Monte Carlo (MC) is often used to simulate neutral particles and estimate source terms. For large-sized reactors, like ITER and DEMO, high particle collision rates lead to a substantial computational cost…

Computational Engineering, Finance, and Science · Computer Science 2025-09-16 Zhirui Tang , Emil Løvbak , Julian Koellermeier , Giovanni Samaey

A quantum interatomic scattering is implemented in the direct simulation Monte Carlo (DSMC) method applied to transport phenomena in rarefied gases. In contrast to the traditional DSMC method based on the classical scattering, the proposed…

Computational Physics · Physics 2025-07-16 Felix Sharipov

In this article, we propose a novel and general dimension-hopping MCMC methodology that can update all the parameters as well as the number of parameters simultaneously using simple deterministic transformations of some low-dimensional…

Computation · Statistics 2017-03-16 Moumita Das , Sourabh Bhattacharya

The goal of this paper is to study convergence and error estimates of the Monte Carlo method for the Navier-Stokes equations with random data. To discretize in space and time, the Monte Carlo method is combined with a suitable deterministic…

Numerical Analysis · Mathematics 2022-05-10 Eduard Feireisl , Mária Lukáčová - Medviďová , Bangwei She , Yuhuan Yuan

Recent work has suggested using Monte Carlo methods based on piecewise deterministic Markov processes (PDMPs) to sample from target distributions of interest. PDMPs are non-reversible continuous-time processes endowed with momentum, and…

Machine Learning · Statistics 2024-06-28 Paul Fearnhead , Sebastiano Grazzi , Chris Nemeth , Gareth O. Roberts

We develop a novel Monte Carlo strategy for the simulation of the Boltzmann-BGK model with both low-collisional and high-collisional regimes present. The presented solution to maintain accuracy in low-collisional regimes and remove…

Numerical Analysis · Mathematics 2020-12-23 Bert Mortier , Martine Baelmans , Giovanni Samaey

We propose a method for simulating the stochastic dynamics of classical spin systems with long-range interactions. The method incorporates the stochastic cutoff (SCO) method, which is originally specialized for simulating equilibrium state,…

Statistical Mechanics · Physics 2019-12-09 Taichi Hinokihara , Yuta Okuyama , Munetaka Sasaki , Seiji Miyashita

We consider the development of Monte Carlo schemes for molecules with Coulomb interactions. We generalize the classic algorithms of Bird and Nanbu-Babovsky for rarefied gas dynamics to the Coulomb case thanks to the approximation introduced…

Computational Physics · Physics 2015-03-17 Giacomo Dimarco , Russell Caflisch , Lorenzo Pareschi

This paper describes a new Monte Carlo method based on a novel stochastic potential switching algorithm. This algorithm enables the equilibrium properties of a system with potential $V$ to be computed using a Monte Carlo simulation for a…

Statistical Mechanics · Physics 2007-05-23 C. H. Mak

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…

Probability · Mathematics 2019-02-28 Djalil Chafaï , Grégoire Ferré

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,…

Statistical Mechanics · Physics 2016-07-20 Alejandro Mendoza-Coto , Rogelio Díaz-Méndez , Guido Pupillo