Related papers: Explicit-Solute Implicit-Solvent Molecular Simulat…
Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional…
Electrostatic interactions play crucial roles in biophysical processes such as protein folding and molecular recognition. Poisson-Boltzmann equation (PBE)-based models have emerged as widely used in modeling these important processes.…
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…
We present a GPU-friendly framework for real-time implicit simulation of elastic material in the presence of frictional contacts. The integration of hyperelasticity, non-interpenetration contact, and friction in real-time simulations…
This work presents a robust and efficient sharp interface immersed boundary (IBM) framework, which is applicable for all-speed flow regimes and is capable of handling arbitrarily complex bodies (stationary or moving). The work deploys an…
This paper explores the impact of simulator accuracy on architecture design decisions in the general-purpose graphics processing unit (GPGPU) space. We perform a detailed, quantitative analysis of the most popular publicly available GPU…
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…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
Graphics Processing Units (GPUs) are high performance co-processors originally intended to improve the use and quality of computer graphics applications. Once, researchers and practitioners noticed the potential of using GPU for general…
Viscoelastic surface rheology plays an important role in multiphase systems. A typical example is the actin cortex which surrounds most animal cells. It shows elastic properties for short time scales and behaves viscous for longer time…
With the advent of high-performance computing techniques, the data for analysis has grown significantly. Here, graphic processing unit (GPU) based program kernels are discussed to exploit parallelism in the analysis codes specific to…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Fluid-structure interaction (FSI) simulation of biological systems presents significant computational challenges, particularly for applications involving large structural deformations and contact mechanics, such as heart valve dynamics.…
Particle-In-Cell (PIC) methods are frequently used for kinetic, high-fidelity simulations of plasmas. Implicit formulations of PIC algorithms feature strong conservation properties, up to numerical round-off errors, and are not subject to…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
We introduce CaLES, a GPU-accelerated finite-difference solver designed for large-eddy simulations (LES) of incompressible wall-bounded flows in massively parallel environments. Built upon the existing direct numerical simulation (DNS)…
We develop a matrix-free Full Approximation Storage (FAS) multigrid solver based on staggered finite differences and implemented on GPU in MATLAB. To enhance performance, intermediate variables are reused, and an X-shape Multi-Color…
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 show feasibility and benefits of porting an adaptive multi-scale kinetic-fluid code to CPU-GPU systems. Challenges are due to the irregular data access for adaptive Cartesian mesh, vast difference of computational cost between kinetic…
In this paper, a new progressive mesh algorithm is introduced in order to perform fast physical simulations by the use of a lattice Boltzmann method (LBM) on a single-node multi-GPU architecture. This algorithm is able to mesh automatically…