Brownian dynamics simulations of biological molecules

GA Huber, JA McCammon - Trends in chemistry, 2019 - cell.com
Brownian dynamics (BD) is a technique for carrying out computer simulations of physical
systems that are driven by thermal fluctuations. Biological systems at the macromolecular …

GPU tensor cores for fast arithmetic reductions

CA Navarro, R Carrasco, RJ Barrientos… - … on Parallel and …, 2020 - ieeexplore.ieee.org
This article proposes a parallel algorithm for computing the arithmetic reduction of numbers
as a set of matrix-multiply accumulate (MMA) operations that are executed simultaneously …

Analyzing GPU tensor core potential for fast reductions

R Carrasco, R Vega, CA Navarro - 2018 37th International …, 2018 - ieeexplore.ieee.org
The Nvidia GPU architecture has introduced new computing elements such as the tensor
cores, which are special processing units dedicated to perform fast matrix …

A sorting algorithm based on ordered block insertions

H Ferrada - Journal of Computational Science, 2022 - Elsevier
Among the comparison-based algorithms, insertionsort is recognized as one of the fastest
methods to sort relatively small data sets, or when the elements are relatively ordered …

DiTe2: Calculating the diffusion tensor for flexible molecules

J Campeggio, A Polimeno… - Journal of Computational …, 2019 - Wiley Online Library
We report on an extended hydrodynamic modeling of the friction tensorial properties of
flexible molecules including all types of natural, Z‐Matrix like, internal coordinates. We …

Gpu voronoi diagrams for random moving seeds

R Stevenson-Regla, CA Navarro - 2022 41st International …, 2022 - ieeexplore.ieee.org
The Voronoi Diagram is a geometrical structure that is widely used in scientific or
technological applications where proximity is a relevant aspect to consider, and it also …

Maintaining 2D Delaunay triangulations on the GPU for proximity queries of moving points

H Porro, B Crespin, N Hitschfeld, C Navarro… - … Workshop 2023 (SIAM …, 2023 - hal.science
In this paper we explore the problem of maintaining the Delaunay triangulation of moving 2D
points on the GPU with discrete time steps, using only local transformations. We show that …

A novel parallel accelerated CRPF algorithm

J Wang, J Cao, W Li, P Yu, K Huang - Applied Intelligence, 2020 - Springer
Particle filtering is one of the most important algorithms for solving state estimation of
nonlinear systems and has been widely studied in many fields. However, due to the …

GPU Voronoi Diagrams for Random Moving Seeds

R Stevenson, CA Navarro - arxiv preprint arxiv:2209.00117, 2022 - arxiv.org
The Voronoi Diagram is a geometrical structure that is widely used in scientific or
technological applications where proximity is a relevant aspect to consider, and it also …

CUDA-accelerated simulation of Brownian dynamics

K Dice, C Gray, G Walker, C Baldwin… - Proceedings of the …, 2018 - dl.acm.org
Molecular simulations are increasingly used to study nanoscale biological and synthetic
systems. To model interactions between molecules, we look to Brownian Dynamics. An n …