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MATI (Microstructural Analysis Toolbox for Imaging) is a versatile MATLAB-based toolbox that combines both simulation and data fitting capabilities for microstructural dMRI research. It provides a user-friendly, GUI-driven interface that…
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.…
Lattice spin models are useful for studying critical phenomena and allow the extraction of equilibrium and dynamical properties. Simulations of such systems are usually based on Monte Carlo (MC) techniques, and the main difficulty is often…
The escalating adoption of diffusion models for applications such as image generation demands efficient parallel inference techniques to manage their substantial computational cost. However, existing diffusion parallelism inference schemes…
Many-body dissipative particle dynamics (MDPD) offers a significant speed-up in the simulation of various systems, including soft matter, in comparison with molecular dynamics (MD) simulations based on Lennard-Jones nteractions, which is…
Diffusion models have achieved remarkable progress in high-fidelity image, video, and audio generation, yet inference remains computationally expensive. Nevertheless, current diffusion acceleration methods based on distributed parallelism…
Due to the very long timescales involved (us-s), theoretical modeling of fundamental biological processes including folding, misfolding, and mechanical unraveling of biomolecules, under physiologically relevant conditions, is challenging…
Molecular dynamics (MD) simulation is a powerful computational tool to study the behavior of macromolecular systems. But many simulations of this field are limited in spatial or temporal scale by the available computational resource. In…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
We present a MATLAB-based framework for two- and three-dimensional fast Fourier transforms on multiple GPUs for large-scale numerical simulations using the pseudo-spectral Fourier method. The software implements two complementary multi-GPU…
The nonuniform fast Fourier transform (NUFFT) enables spectral methods for problems with irregularly spaced samples, with applications in medical imaging, molecular dynamics, and kinetic plasma simulations. Existing implementations are…
Geospatial Processing, such as queries based on point-to-polyline shortest distance and point-in-polygon test, are fundamental to many scientific and engineering applications, including post-processing large-scale environmental and climate…
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…
Algorithmic formulations of GPU programs provide a high-level alternative to device-specific code by expressing computations as compositions of well-defined parallel primitives (e.g., map, sort, reduce), rather than through handcrafted GPU…
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…
This paper presents FT-GAIA, a software-based fault-tolerant parallel and distributed simulation middleware. FT-GAIA has being designed to reliably handle Parallel And Distributed Simulation (PADS) models, which are needed to properly…
We describe a methodology for designing efficient parallel and distributed scientific software. This methodology utilizes sequences of mechanizable algebra--based optimizing transformations. In this study, we apply our methodology to the…
We present a MATLAB script which can use GPU acceleration to simulate a trapped ion interacting with a low-density cloud of atoms. This script, called atomiongpu.m, can massively parallelize MD simulations of trajectories of a trapped ion…
While 3D Gaussian Splatting (3DGS) has revolutionized photorealistic rendering, its vast ecosystem of assets remains incompatible with high-performance LiDAR simulation, a critical tool for robotics and autonomous driving. We present…
We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an…