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Computational fluid dynamics (CFD) studies have been increasingly used for blood flow simulations in intracranial aneurysms (ICAs). However, despite the continuous progress of body-fitted CFD solvers, generating a high quality mesh is still…
High-order Discontinuous Galerkin (DG) methods offer excellent accuracy for turbulent flow simulations, especially when implemented on GPU-oriented architectures that favor very high polynomial orders. On modern GPUs, high-order polynomial…
Brownian dynamics simulations of a coarse-grained bead-spring chain model, with Debye-H\"uckel electrostatic interactions between the beads, are used to determine the root-mean-square end-to-end vector, the radius of gyration, and various…
The immersed boundary (IB) method has become a leading approach in cardiac fluid-structure interaction (FSI) modeling due to its ability to handle large deformations and complex geometries without requiring mesh regeneration. However, the…
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)…
The progress made in accelerating simulations of fluid flow using GPUs, and the challenges that remain, are surveyed. The review first provides an introduction to GPU computing and programming, and discusses various considerations for…
Linear viscoelastic properties for a dilute polymer solution are predicted by modeling the solution as a suspension of non-interacting bead-spring chains. The present model, unlike the Rouse model, can describe the solution's rheological…
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…
We present a computer simulation of entangled polymer solutions at equilibrium. The chains repel each other via a soft Gaussian potential, appropriate for semi-dilute solutions at the scale of a correlation blob. The key innovation to…
We present an efficient implementation for running three-dimensional numerical simulations of fluid-structure interaction problems on single GPUs, based on Nvidia CUDA through Numba and Python. The incompressible flow around moving bodies…
Brownian simulations can be used to generate statistics relevant for studying molecular interactions or trafficking. However, the concurrent simulation of many Brownian trajectories at can become computationally intractable. Replacing…
This work explores the capability of simulating complex fluid flows by directly solving the Boltzmann equation. Due to the high-dimensionality of the governing equation, the substantial computational cost of solving the Boltzmann equation…
The connection between fundamental interactions acting in molecules in a fluid and macroscopically measured properties, such as the viscosity between colloidal particles coated with polymers, is studied here. The role that hydrodynamic and…
The role of solvent quality in determining the universal material properties of dilute polymer solutions undergoing steady simple shear flow is examined. A bead-spring chain representation of the polymer molecule is used, and the influence…
A high-performance implementation of a multiphase lattice Boltzmann method based on the conservative Allen-Cahn model supporting high-density ratios and high Reynolds numbers is presented. Metaprogramming techniques are used to generate…
The Gaussian Approximation, proposed originally by Ottinger [J. Chem. Phys., 90 (1) : 463-473, 1989] to account for the influence of fluctuations in hydrodynamic interactions in Rouse chains, is adapted here to derive a new mean-field…
The numerical simulation of multiphase flows involving dispersed components with large scale disparities, such as the collisions between millimeter-sized bubbles and micron-sized mineral particles in flotation, poses a significant…
Using a recently developed bead-spring model for semiflexible polymers that takes into account their natural extensibility, we report an efficient algorithm to simulate the dynamics for polymers like double-stranded DNA (dsDNA) in the…
State of art DL models are growing in size and complexity, with many modern models also increasing in heterogeneity of behavior. GPUs are still the dominant platform for DL applications, relying on a bulk-synchronous execution model which…
Accurate and efficient simulation of fluid-structure interaction (FSI) problems remains a central challenge in computational physics. High-order discontinuous Galerkin (DG) methods offer low numerical errors and excellent scalability on…