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Machine learning algorithms are becoming increasingly prevalent and performant in the reconstruction of events in accelerator-based neutrino experiments. These sophisticated algorithms can be computationally expensive. At the same time, the…
This paper presents a heuristic for finding the optimum number of CUDA streams by using tools common to the modern AI-oriented approaches and applied to the parallel partition algorithm. A time complexity model for the GPU realization of…
The friction and diffusion coefficients of rigid spherical colloidal particles dissolved in a fluid are determined from velocity and force autocorrelation functions by mesoscale hydrodynamic simulations. Colloids with both slip and no-slip…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
We focus on implementing and optimizing a sixth-order finite-difference solver for simulating compressible fluids on a GPU using third-order Runge-Kutta integration. Since graphics processing units perform well in data-parallel tasks, this…
This paper presents a Graphics Processing Units (GPUs) acceleration method of an iterative scheme for gas-kinetic model equations. Unlike the previous GPU parallelization of explicit kinetic schemes, this work features a fast converging…
Polymerization of C60 molecular crystal under high pressure and high temperature is simulated by using linear scaling tight binding molecular dynamics (TBMD) with Graphic Processing Unit (GPU) as a computational accelerator for…
We consider numerical algorithms for the simulation of the rheology of two-dimensional vesicles suspended in a viscous Stokesian fluid. The vesicle evolution dynamics is governed by hydrodynamic and elastic forces. The elastic forces are…
Brownian dynamics of colloidal particles on complex surfaces has found important applications in diverse physical, chemical and biological processes. However, current Brownian dynamics simulation algorithms mostly work for relatively simple…
A simple model for simulating flows of active suspensions is investigated. The approach is based on dissipative particle dynamics. While the model is potentially applicable to a wide range of self-propelled particle systems, the specific…
The special computational challenges of simulating 3-D hydrodynamics in deep stellar interiors are discussed, and numerical algorithmic responses described. Results of recent simulations carried out at scale on the NSF's Blue Waters machine…
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…
Particle-particle interactions in sedimenting systems have been investigated in the present study considering the many-body hydrodynamic and electrodynamic interactions. These interactions primarily occur in two modes: near-field and…
We describe in detail how to implement a coarse-grained hybrid Molecular Dynamics and Stochastic Rotation Dynamics simulation technique that captures the combined effects of Brownian and hydrodynamic forces in colloidal suspensions. The…
Current trends in the computer graphics community propose leveraging the massive parallel computational power of GPUs to accelerate physically based simulations. Collision detection and solving is a fundamental part of this process. It is…
The Poisson-Fermi model is an extension of the classical Poisson-Boltzmann model to include the steric and correlation effects of ions and water treated as nonuniform spheres in aqueous solutions. Poisson-Boltzmann electrostatic…
We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for…
In the paper we discuss the main features of the software package for numerical simulations of the surface water dynamics. We consider an approximation of the shallow water equations together with the parallel technologies for NVIDIA CUDA…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
Mesoscopic simulations of hydrocarbon flow in source shales are challenging, in part due to the heterogeneous shale pores with sizes ranging from a few nanometers to a few micrometers. Additionally, the sub-continuum fluid-fluid and…