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The study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological…
Current trends in parallel processors call for the design of efficient massively parallel algorithms for scientific computing. Parallel algorithms for Monte Carlo simulations of thermodynamic ensembles of particles have received little…
The compositional model is often used to describe multicomponent multiphase porous media flows in the petroleum industry. The fully implicit method with strong stability and weak constraints on time-step sizes is commonly used in the…
Simulating particle dynamics with high fidelity is crucial for solving real-world interaction and control tasks involving liquids in design, graphics, and robotics. Recently, data-driven approaches, particularly those based on graph neural…
In Stokesian Dynamics, particles are assumed to interact in two ways: through long-range mobility interactions and through short-range lubrication interactions. To speed up computations, in shear-driven concentrated suspensions, often found…
The resolution of dynamics in out of equilibrium quantum spin systems lies at the heart of fundamental questions among Quantum Information Processing, Statistical Mechanics and Nano-Technologies. Efficient computational simulations of…
We develop a GPU-accelerated dynamic programming (DP) method for valuing, operating, and bidding energy storage under multistage stochastic electricity prices. Motivated by computational limitations in existing models, we formulate DP…
An adpative integration technique for time advancement of particle motion in the context of coupled computational fluid dynamics (CFD) - discrete element method (DEM) simulations is presented in this work. CFD-DEM models provide an accurate…
This paper presents novel approaches to parallelizing particle interactions on a GPU when there are few particles per cell and the interactions are limited by a cutoff distance. The paper surveys classical algorithms and then introduces two…
The molecular dynamics simulation package GROMACS runs efficiently on a wide variety of hardware from commodity workstations to high performance computing clusters. Hardware features are well exploited with a combination of SIMD,…
Colloidal spheres driven through water along a circular path by an optical ring trap display unexpected dynamical correlations. We use Stokesian Dynamics simulations and a simple analytical model to demonstrate that the path's curvature…
Systems of spherical particles moving in Stokes flow are studied for a different particle internal structure and boundaries, including the Navier-slip model. It is shown that their hydrodynamic interactions are well described by treating…
We introduce a GPU-accelerated simulation tool, named Modeling on Shallow Flows with Efficient Simulation for Two-Phase Debris Flows (MoSES_2PDF), of which the input and output data can be linked to the GIS system for engineering…
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…
The never-ending computational demand from simulations of turbulence makes computational fluid dynamics (CFD) a prime application use case for current and future exascale systems. High-order finite element methods, such as the spectral…
The long time dynamics of large particles trapped in two inhomogeneous turbulent shear flows is studied experimentally. Both flows present a common feature, a shear region that separates two colliding circulations, but with different…
Recent advancements of intermediate-scale quantum processors have triggered tremendous interest in the exploration of practical quantum advantage. The simulation of fluid dynamics, a highly challenging problem in classical physics but vital…
Self-propelled particles can navigate complex environments, including viscous fluid interfaces with curved geometries. In this work, we study the emergent dynamics of a suspension of self-propelled particles confined to a stationary curved…
Colloidal particles with active boundary layers - regions surrounding the particles where nonequilibrium processes produce large velocity gradients - are common in many physical, chemical and biological contexts. The velocity or stress at…
We present an approach to molecular-dynamics simulations of ferrofluids on graphics processing units (GPUs). Our numerical scheme is based on a GPU-oriented modification of the Barnes-Hut (BH) algorithm designed to increase the parallelism…