Related papers: curvedSpaceSim: A framework for simulating particl…

Spherical symmetry is ubiquitous in nature. It's therefore unfortunate that spherical system simulations are so hard, and require complete spheres with millions of interacting particles. Here we introduce an approach to model spherical…

This article describes a new, fully adaptive Particle-Multiple-Mesh numerical simulation code developed primarily for simulations of small regions (such as a group of galaxies) in a cosmological context. It integrates the equations of…

Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…

Robustly handling collisions between individual particles in a large particle-based simulation has been a challenging problem. We introduce particle merging-and-splitting, a simple scheme for robustly handling collisions between particles…

The properties of polymer liquids on hard and soft substrates are investigated by molecular dynamics simulation of a coarse-grained bead-spring model and dynamic single-chain-in-mean-field (SCMF) simulations of a soft, coarse-grained…

The simulation of large ensembles of particles is usually parallelized by partitioning the domain spatially and using message passing to communicate between the processes handling neighboring subdomains. The particles are represented as…

We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…

Many recently introduced enhanced sampling techniques are based on biasing coarse descriptors (collective variables) of a molecular system on the fly. Sometimes the calculation of such collective variables is expensive and becomes a…

Differentiable simulation is a promising toolkit for fast gradient-based policy optimization and system identification. However, existing approaches to differentiable simulation have largely tackled scenarios where obtaining smooth…

Event-driven molecular dynamics is a valuable tool in condensed and soft matter physics when particles can be modeled as hard objects or more generally if their interaction potential can be modeled in a stepwise fashion. Hard spheres model…

Owing to the computational complexity of electronic structure algorithms running on classical digital computers, the range of molecular systems amenable to simulation remains tightly circumscribed even after many decades of work. Quantum…

Physical systems behave according to their underlying dynamical equations which, in turn, can be identified from experimental data. Explaining data requires selecting mathematical models that best capture the data regularities. Identifying…

Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…

In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…

Particle-based shape modeling (PSM) is a family of approaches that automatically quantifies shape variability across anatomical cohorts by positioning particles (pseudo landmarks) on shape surfaces in a consistent configuration. Recent…

Many interesting phenomena are characterized by the complex interaction of different physical processes, each often best modeled numerically via a specific approach. In this paper, we present the design and implementation of an…

We introduce a general-purpose framework for interconnecting scientific simulation programs using a homogeneous, unified interface. Our framework is intrinsically parallel, and conveniently separates all component numerical modules in…

Impacts play a fundamental role in shaping the physical and chemical properties of the objects in our Solar System. Given the challenges in replicating such collisions through laboratory experiments, computer simulations are an important…

In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…

We describe a framework for interactive molecular dynamics in a multiuser virtual reality environment, combining rigorous cloud-mounted physical atomistic simulation with commodity virtual reality hardware, which we have made accessible to…