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We apply the event-chain Monte Carlo algorithm to the three-dimensional ferromagnetic Heisenberg model. The algorithm is rejection-free and also realizes an irreversible Markov chain that satisfies global balance. The autocorrelation…

Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a…

MomentClosure.jl is a Julia package providing automated derivation of the time-evolution equations of the moments of molecule numbers for virtually any chemical reaction network using a wide range of moment closure approximations. It…

We introduce version 2.0 of the SmoQyDQMC.jl package, a Julia implementation of the determinant quantum Monte Carlo algorithm. SmoQyDQMC.jl supports generalized tight-binding Hamiltonians with local and extended Hubbard and generalized…

Artifacts arise in the simulations of electrolytes using periodic boundary conditions (PBC). We show the origin of these artifacts are the periodic image charges and the constraint of charge neutrality inside the simulation box, both of…

We have developed the Monte Carlo simulation program JEWEL 1.0 (Jet Evolution With Energy Loss), which interfaces a perturbative final state parton shower with medium effects occurring in ultra-relativistic heavy ion collisions. This is…

We apply the event-chain Monte Carlo algorithm to classical continuum spin models on a lattice and clarify the condition for its validity. In the two-dimensional XY model, it outperforms the local Monte Carlo algorithm by two orders of…

We present a simple, general purpose, quantum Monte-Carlo algorithm for out-of-equilibrium interacting nanoelectronics systems. It allows one to systematically compute the expansion of any physical observable (such as current or density) in…

We introduce a powerful Monte Carlo (MC) algorithm for the atomistic simulation of bulk models of oligo- and poly-thiophenes by redesigning MC moves originally developed for considerably simpler polymer structures and architectures, such as…

A Monte Carlo method to sample the classical configurational canonical ensemble is introduced. In contrast to the Metropolis algorithm, where trial moves can be rejected, in this approach collisions take place. The implementation is…

Monte Carlo event generators are central to high-energy physics analysis. However, workflows based on handwritten scripts can be difficult to reuse, modify, and reproduce when multiple Monte Carlo models, tune variations, run variations,…

We describe OHBA Software Library for the analysis of electrophysiological data (osl-ephys). This toolbox builds on top of the widely used MNE-Python package and provides unique analysis tools for magneto-/electro-encephalography (M/EEG)…

A novel Stochastic Event-Driven Molecular Dynamics (SEDMD) algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with…

We describe a new open-source Python-based package for high accuracy correlated electron calculations using quantum Monte Carlo (QMC) in real space: PyQMC. PyQMC implements modern versions of QMC algorithms in an accessible format, enabling…

The ionic environment of biomolecules strongly influences their structure, conformational stability, and inter-molecular interactions.This paper introduces GIBS, a grand-canonical Monte Carlo (GCMC) simulation program for computing the…

The Monte Carlo model JEWEL 1.0 (Jet Evolution With Energy Loss) simulates parton shower evolution in the presence of a dense QCD medium. In its current form medium interactions are modelled as elastic scattering based on perturbative…

We propose an efficient Monte Carlo algorithm for the off-lattice simulation of dense hard sphere polymer melts using cluster moves, called event chains, which allow for a rejection-free treatment of the excluded volume. Event chains also…

We develop a multilevel Monte Carlo (MLMC)-FEM algorithm for linear, elliptic diffusion problems in polytopal domain $\mathcal D\subset \mathbb R^d$, with Besov-tree random coefficients. This is to say that the logarithms of the diffusion…

KMCLib is a general framework for lattice kinetic Monte Carlo (KMC) simulations. The program can handle simulations of the diffusion and reaction of millions of particles in one, two, or three dimensions, and is designed to be easily…

We present a rigorous efficient event-chain Monte Carlo algorithm for long-range interacting particle systems. Using a cell-veto scheme within the factorized Metropolis algorithm, we compute each single-particle move with a fixed number of…