Related papers: Biomolecular electrostatics using a fast multipole…
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…
In this work, we have developed a multiscale computational algorithm to couple finite element method with an open source molecular dynamics code --- the Large scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) --- to perform…
The goal of this work is to parallelize the multistep scheme for the numerical approximation of the backward stochastic differential equations (BSDEs) in order to achieve both, a high accuracy and a reduction of the computation time as…
The continuum theory applied to bimolecular electrostatics leads to an implicit-solvent model governed by the Poisson-Boltzmann equation. Solvers relying on a boundary integral representation typically do not consider features like…
The capacity to predict and control bioprocesses is perhaps one of the most important objectives of biotechnology. Computational simulation is an established methodology for the design and optimization of bioprocesses, where the finite…
Direct numerical simulation (DNS) for gas-solid flow is implemented on a multi-scale supercomputing system, Mole-8.5, featuring massive parallel GPU-CPU hybrid computing, for which the lattice Boltzmann method (LBM) is deployed together…
The Boltzmann transport equation (BTE) with electron-phonon (e-ph) interactions computed from first principles is widely used to study electronic transport and nonequilibrium dynamics in materials. Calculating the e-ph collision integral is…
RPYFMM is a software package for the efficient evaluation of the potential field governed by the Rotne-Prager-Yamakawa (RPY) tensor interactions in biomolecular hydrodynamics simulations. In our algorithm, the RPY tensor is decomposed as a…
A novel and scalable geometric multi-level algorithm is presented for the numerical solution of elliptic partial differential equations, specially designed to run with high occupancy of streaming processors inside Graphics Processing…
We present an implementation of the quantum mechanics/molecular mechanics (QM/MM) method for periodic systems using GPU accelerated QM methods, a distributed multipole formulation of the electrostatics, and a pseudo-bond treatment of the…
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…
This work focuses on model preparation for electrostatic simulations of CAD designs to realize a rapid virtual prototyping concept. We present a boundary element method (BEM) allowing discontinuous fields between surfaces. The corresponding…
Fast Multipole Methods (FMM) are a fundamental operation for the simulation of many physical problems. The high performance design of such methods usually requires to carefully tune the algorithm for both the targeted physics and the…
We present GridFF, an efficient method for simulating molecules on rigid substrates, derived from techniques used in protein-ligand docking in biochemistry. By projecting molecule-substrate interactions onto precomputed spatial grids with…
We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based…
Traditional logic programming relies on symbolic computation on the CPU, which can limit performance for large-scale inference tasks. Recent advances in GPU hardware enable high-throughput matrix operations, motivating a shift toward…
We present the numerical methods and GPU-accelerated implementation underlying a Total Lagrangian finite element framework for finite-deformation flexible multibody dynamics, introduced in the companion paper [1]. The framework supports…
The Poisson-Boltzmann (PB) model governs the electrostatics of solvated biomolecules, i.e., potential, field, energy, and force. These quantities can provide useful information about protein properties, functions, and dynamics. By…
Boundary element methods (BEM) reduce a partial differential equation in a domain to an integral equation on the domain's boundary. They are particularly attractive for solving problems on unbounded domains, but handling the dense matrices…
Maximal Biclique Enumeration (MBE) holds critical importance in graph theory with applications extending across fields such as bioinformatics, social networks, and recommendation systems. However, its computational complexity presents…