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A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…
This paper presents an accurate density computation approach for large dark matter simulations, based on a recently introduced phase-space tessellation technique and designed for massively parallel, heterogeneous cluster architectures. We…
We investigate a hybrid numerical algorithm aimed at the large-scale cosmological N-body simulation for the on-going and the future high precious sky surveys. It makes use of a truncated Fast Multiple Method (FMM) for short-range gravity,…
We report on improvements made over the past two decades to our adaptive treecode N-body method (HOT). A mathematical and computational approach to the cosmological N-body problem is described, with performance and scalability measured up…
The time step criterion plays a crucial role in direct N-body codes. If not chosen carefully, it will cause a secular drift in the energy error. Shared, adaptive time step criteria commonly adopt the minimum pairwise time step, which…
The paper presents a numerical implementation of the gravitational N-body problem with contact interactions between non-spherically shaped bodies. The work builds up on a previous implementation of the code and extends its capabilities. The…
We review the recent optimizations of gravitational $N$-body kernels for running them on graphics processing units (GPUs), on single hosts and massive parallel platforms. For each of the two main $N$-body techniques, direct summation and…
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any…
Current AMR simulations require algorithms that are highly parallelized and manage memory efficiently. As compute engines grow larger, AMR simulations will require algorithms that achieve new levels of efficient parallelization and memory…
Block compression is a widely used technique to compress textures in real-time graphics applications, offering a reduction in storage size. However, their storage efficiency is constrained by the fixed compression ratio, which substantially…
The purpose of this paper is to propose a time-step-robust cell-to-cell integration of particle trajectories in 3-D unstructured meshes in particle/mesh Lagrangian stochastic methods. The main idea is to dynamically update the mean fields…
For problems in astrophysics, planetary science and beyond, numerical simulations are often limited to simulating fewer particles than in the real system. To model collisions, the simulated particles (aka superparticles) need to be inflated…
Methods to extract information from the tracking of mobile objects/particles have broad interest in biological and physical sciences. Techniques based on simple criteria of proximity in time-consecutive snapshots are useful to identify the…
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…
Simulating physical problems involving multi-time scale coupling is challenging due to the need of solving these multi-time scale processes simultaneously. In response to this challenge, this paper proposed an explicit multi-time step…
We present a novel $N$-body simulation method that compactifies the infinite spatial extent of the Universe into a finite sphere with isotropic boundary conditions to follow the evolution of the large-scale structure. Our approach…
This paper applies the N-block PCPM algorithm to solve multi-scale multi-stage stochastic programs, with the application to electricity capacity expansion models. Numerical results show that the proposed simplified N-block PCPM algorithm,…
Modelling the cosmic large-scale structure can be done through numerical N-body simulations or by using perturbation theory. Here, we present an N-body approach that effectively implements a multi-step forward model based on Lagrangian…
Recent advances in random-walk particle-tracking have enabled direct simulation of mixing and reactions on particles by allowing the particles to interact with each other using a multi-point mass transfer scheme. The mass transfer scheme…
Structured Cartesian grids are a fundamental component in numerical simulations. Although these grids facilitate straightforward discretization schemes, their na\"{i}ve use in sparse domains leads to excessive memory overhead and…