Related papers: Enabling Simulation of High-Dimensional Micro-Macr…
In this article we introduce a novel coupled algorithm for massively parallel direct numerical simulations of electrophoresis in microfluidic flows. This multiphysics algorithm employs an Eulerian description of fluid and ions, combined…
This paper is devoted to computational algorithms designed to describe the classical Ising magnet in some specific cases when an additional macroscopic restriction in form of constant charge density exists in the system. We developed and…
The transport and manipulation of particles and cells in microfluidic devices has become a core methodology in domains ranging from molecular biology to manufacturing and drug design. The rational design and operation of such devices can…
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…
We present a GPU implementation of LAMMPS, a widely-used parallel molecular dynamics (MD) software package, and show 5x to 13x single node speedups versus the CPU-only version of LAMMPS. This new CUDA package for LAMMPS also enables…
The Massive Parallel Computing (MPC) model gained popularity during the last decade and it is now seen as the standard model for processing large scale data. One significant shortcoming of the model is that it assumes to work on static…
Cardiovascular disease affects millions of people worldwide and its social and economic cost clearly motivates scientific research. Computer simulation can lead to a better understanding of cardiac physiology, and for pathology presents…
Large-scale molecular dynamics simulations with high accuracy have been increasingly popular for their capability to bridge the gap between atomistic modeling and mesoscale phenomena. Both machine learning potentials and enhanced sampling…
The ability to timely process significant amounts of continuously updated spatial data is mandatory for an increasing number of applications. Parallelism enables such applications to face this data-intensive challenge and allows the devised…
We propose a new hybrid topology optimization algorithm based on multigrid approach that combines the parallelization strategy of CPU using OpenMP and heavily multithreading capabilities of modern Graphics Processing Units (GPU). In…
The Cox proportional hazards model stands as a widely-used semi-parametric approach for survival analysis in medical research and many other fields. Numerous extensions of the Cox model have further expanded its versatility. Statistical…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
The Morse-Smale complex is a well studied topological structure that represents the gradient flow behavior between critical points of a scalar function. It supports multi-scale topological analysis and visualization of feature-rich…
Pedestrian movement, although ubiquitous and well-studied, is still not that well understood due to the complicating nature of the embedded social dynamics. Interest among researchers in simulating pedestrian movement and interactions has…
In this work we present an efficient implementation of Canonical Monte Carlo simulation for Coulomb many body systems on graphics processing units (GPU). Our method takes advantage of the GPU Single Instruction, Multiple Data (SIMD)…
Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC…
A finite-difference Micromagnetic solver is presented utilizing the C++ Accelerated Massive Parallelism (C++ AMP). The high speed performance of a single Graphics Processing Unit (GPU) is demonstrated compared to a typical CPU-based solver.…
Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD)…
With large-scale Integral Field Spectroscopy (IFS) surveys of thousands of galaxies currently under-way or planned, the astronomical community is in need of methods, techniques and tools that will allow the analysis of huge amounts of data.…
We address in this thesis the current need to design new parallel algorithms and tools that ease the development of geodynamic modelling applications that are suited for today's and tomorrow's hardware. We present (1) the MATLAB HPC…