[HTML][HTML] Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code

L López-Villellas, CCK Mikkelsen… - Computer Physics …, 2023 - Elsevier
In molecular dynamics simulations we can often increase the time step by imposing
constraints on bond lengths and bond angles. This allows us to extend the length of the time …

A mathematical modelling for solar irradiance reduction of sunshades and some near-future albedo modification approaches for mitigation of global warming

BB Alagoz, C Keles, A Ates, B Baran - Journal of Atmospheric and Solar …, 2024 - Elsevier
To address the global warming problem, one of the space-based geoengineering solutions
suggests the construction of an occluding disc that can work as a solar curtain to mitigate …

A survey of the parallel performance and accuracy of Poisson solvers for electronic structure calculations

P García‐Risueño, J Alberdi‐Rodriguez… - Journal of …, 2014 - Wiley Online Library
We present an analysis of different methods to calculate the classical electrostatic Hartree
potential created by charge distributions. Our goal is to provide the reader with an estimation …

Harvesting the aggregate computing power of commodity computers for supercomputing applications

D Regassa, H Yeom, Y Son - Applied Sciences, 2022 - mdpi.com
Distributed supercomputing is becoming common in different companies and academia.
Most of the parallel computing researchers focused on harnessing the power of commodity …

Ab initio study of the thermodynamic, electronic and optical properties of WC (Bh) phase ZnO under pressure

MA Kamboh, H Wang, L Wang, L Hao, Y Su… - Materials Science and …, 2021 - Elsevier
The present investigation highlights the structural, thermodynamic, electronic, and optical
properties of WC (B h) phase ZnO calculated by means of first principles and Debye model …

A performance comparison of data and memory allocation strategies for sequence aligners on NUMA architectures

J Lenis, MA Senar - Cluster Computing, 2017 - Springer
Over the last several years, many sequence alignment tools have appeared and become
popular for the fast evolution of next generation sequencing technologies. Obviously …

Nanoscale size effect and phonon properties of silicon material through simple spectral energy density analysis based on molecular dynamics

J Chen, X Zhang - Journal of Physics: Condensed Matter, 2019 - iopscience.iop.org
Due to the importance of spectral analysis for the development of highly efficient
semiconductor silicon devices and the complexity of current research techniques, the …

[图书][B] High Performance Programming for Soft Computing

OHM Ross, R Sepulveda - 2014 - books.google.com
This book examines the present and future of soft computer techniques. It explains how to
use the latest technological tools, such as multicore processors and graphics processing …

Accurate and efficient constrained molecular dynamics of polymers through Newton's method and special purpose code

L López-Villellas, CCK Mikkelsen, JJ Galano-Frutos… - bioRxiv, 2022 - biorxiv.org
In molecular dynamics simulations we can often increase the time step by imposing
constraints on internal degrees of freedom, such as bond lengths and bond angles. This …

On the Performance of BWA on NUMA Architectures

J Lenis, MA Senar - 2015 IEEE Trustcom/BigDataSE/ISPA, 2015 - ieeexplore.ieee.org
Rapid progress in genome sequencing techniques is creating the necessity of advanced
algorithms to process such information in reasonable time. Alignment applications such as …