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Energy system optimization models are increasing in scope and resolution, yielding large and challenging linear programs. For a long time, the standard way to address such problems has relied on shared-memory interior-point methods (IPM),…
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…
We present teraflop-scale calculations of biomolecular electrostatics enabled by the combination of algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a…
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…
One of the current challenges in physically-based simulations, and, more specifically, fluid simulations, is to produce visually appealing results at interactive rates, capable of being used in multiple forms of media. In recent times, a…
We present a computational algorithm for computing short range forces between particles. The algorithm has two distinguishing features. First, it is optimized for multi-processor computers, and will use as many processors as are available.…
Solvent-mediated hydrodynamic interactions between colloidal particles can significantly alter their dynamics. We discuss the implementation of Stokesian dynamics in leading approximation for streaming processors as provided by the compute…
The field of plasma physics heavily relies on simulations to model various phenomena, such as instabilities, turbulence, and nonlinear behaviors that would otherwise be difficult to study from a purely theoretical approach. Simulations are…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
We present the standard electromagnetic Particle-in-Cell method, starting from the discrete approximation of derivatives on a uniform grid. The application to second-order, centered, finite-difference discretization of the equations of…
The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide…
We review common extensions of particle-in-cell (PIC) schemes which account for strong field phenomena in laser-plasma interactions. After describing the physical processes of interest and their numerical implementation, we provide…
Particle-in-Cell (PIC) simulation codes have wide applicability to first-principles modeling of multidimensional nonlinear plasma phenomena, including wake-field accelerators. This review addresses both finite difference and pseudo-spectral…
We describe an implementation of compressible inviscid fluid solvers with block-structured adaptive mesh refinement on Graphics Processing Units using NVIDIA's CUDA. We show that a class of high resolution shock capturing schemes can be…
There are many interesting physical processes which involve the generation of high density plasmas in large volumes. However, when modeling these systems numerically, the large densities and volumes present a significant computational…
This paper presents two conceptually simple methods for parallelizing a Parallel Tempering Monte Carlo simulation in a distributed volunteer computing context, where computers belonging to the general public are used. The first method uses…
Next generation High-Energy Physics (HEP) experiments are presented with significant computational challenges, both in terms of data volume and processing power. Using compute accelerators, such as GPUs, is one of the promising ways to…
Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also…
We introduce an extension of the particle-in-cell (PIC) method that captures the Landau collisional effects in the Vlasov-Maxwell-Landau equations. The method arises from a regularisation of the variational formulation of the Landau…
To effectively control large-scale distributed systems online, model predictive control (MPC) has to swiftly solve the underlying high-dimensional optimization. There are multiple techniques applied to accelerate the solving process in the…