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The Massive Parallel Computation (MPC) model is a theoretical framework for popular parallel and distributed platforms such as MapReduce, Hadoop, or Spark. We consider the task of computing a large matching or small vertex cover in this…
Markov Chain Monte Carlo (MCMC) algorithms are essential tools in computational statistics for sampling from unnormalised probability distributions, but can be fragile when targeting high-dimensional, multimodal, or complex target…
Atomistic simulations of heat transport in complex materials are costly and hard to converge. This has led to the development of several noise-reduction techniques applicable to equilibrium molecular-dynamics (MD) simulations. We analyze…
This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their…
Using a so-called hemispherical model we derive a general transport equation for cosmic ray and thermal particles scattered in pitch angle by magnetic inhomogeneities in a moving collisionless plasma. The weak scattering through 90 degrees…
The use of computer simulations techniques is an advantageous tool in order to evaluate and select the most appropriated site for radionuclides confinement. Modelling different scenarios allow to take decisions about which is the most…
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…
We present and discuss a variance-reduced stochastic particle method for simulating the relaxation-time model of the Boltzmann transport equation. The present paper focuses on the dilute gas case, although the method is expected to directly…
Reconstructing 4D or 6D phase space distributions from 1D or 2D measurements is a challenging inverse problem encountered in particle accelerators. Entropy maximization is an established method to incorporate prior information in the…
Molecular dynamics (MD)-based path sampling algorithms are a very important class of methods used to study the energetics and kinetics of rare (bio)molecular events. They sample the highly informative but highly unlikely reactive…
An efficient numerical scheme for solving transport equations for tokamak plasmas within an integrated modelling framework is presented. The plasma transport equations are formulated as diffusion-advection equations in two coordinates (a…
Thermal radiative transfer models physical phenomena ranging from supernovas in astrophysics to radiation from a hohlraum striking a fusion target in plasma physics. Transport and absorption of particles in radiative transfer at different…
Monte Carlo (MC) simulation is considered as the most accurate method for radiation dose calculations. Accuracy of a source model for a linear accelerator is critical for the overall dose calculation accuracy. In this paper, we presented an…
This paper explores a variant of bipartite matching problem, referred to as the Spatiotemporal Random Bipartite Matching Problem (ST-RBMP), that accommodates randomness and heterogeneity in the spatial distributions and temporal arrivals of…
A full-F, isothermal, electromagnetic, gyro-fluid model is used to simulate plasma turbulence in a COMPASS-sized, diverted tokamak. A parameter scan covering three orders of magnitude of plasma resistivity and two values for the ion to…
In recent years, machine learning interatomic potentials (MLIPs) have attracted significant attention as a method that enables large-scale, long-time atomistic simulations while maintaining accuracy comparable to electronic structure…
Computational systems and methods are often being used in biological research, including the understanding of cancer and the development of treatments. Simulations of tumor growth and its response to different drugs are of particular…
We summarize a series of numerical experiments of collisional dynamics in dense stellar systems such as globular clusters (GCs) and in weakly collisional plasmas using a novel simulation technique, the so-called Multi-particle collision…
A novel hybrid Monte Carlo transport scheme is demonstrated in a scene with solar illumination, scattering and absorbing 2D atmosphere, a textured reflecting mountain, and a small detector located in the sky (mounted on a satellite or a…
Stable, accurate, divergence-free simulation of magnetized supersonic turbulence is a severe test of numerical MHD schemes and has been surprisingly difficult to achieve due to the range of flow conditions present. Here we present a new,…