Search · four archives
Search · four archives
12 papers · ranked by Valyu relevance
Pauli Virtanen, Ralf Gommers, Travis E. Oliphant, Matt Haberland + 30 more
SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories…
Charles R. Harris, K. Jarrod Millman, Stéfan J. van der Walt, Ralf Gommers + 22 more
'Ralf Gommers' 'Pauli Virtanen' 'David Cournapeau' 'Eric Wieser' 'Julian Taylor' 'Sebastian Berg' 'Nathaniel J. Smith' 'Robert Kern' 'Matti Picus' 'Stephan Hoyer' 'Marten H. van Kerkwijk' 'Matthew Brett' 'Allan Haldane' 'Jaime Fernández del Río' 'Mark Wiebe' 'Pearu Peterson' 'Pierre Gérard-Marchant' 'Kevin Sheppard'…
Berk Ekmekci, Charles E. McAnany, Cameron Mura, Francis Ouellette
Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in molecular biology, biochemistry, and other biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware…
Eilif Muller, James A. Bednar, Markus Diesmann, Marc-Oliver Gewaltig + 2 more
'Michael Hines' 'Andrew P. Davison'] This Research Topic of Frontiers in Neuroinformatics is dedicated to the memory of Rolf Kötter (1961-2010), who was the Frontiers Associate Editor responsible for this Research Topic, and who gave us considerable support and encouragement during the process of conceiving and…
Authors not listed
With the rapid growth of chemical data and information, there is an increasing need for chemistry undergraduates to master Python tools for analyzing large chemical datasets and extracting key or feature information. Currently, more than 100,000 types of metal-organic frameworks (MOFs), as the material recently awarded…
Authors not listed
The field of chemical reaction dynamics has evolved considerably since its inception, driven by advances in computational power and theoretical methodologies. While ab initio molecular dynamics (AIMD) simulations offer high accuracy by computing forces directly from electronic structure theory, its high computational…
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Molecular Dynamics (MD) simulations are essential for studying the time evolution of molecular systems. Still, their efficiency is often bottlenecked by file-based Inter-Process Communication (IPC) between MD and Electronic Structure (ES) programs. We present a socket-based IPC implementation that dramatically…
Madushanka Manathunga, Hasan Metin Aktulga, Andreas W. Goetz, Kenneth M. Merz + 1 more
We have ported and optimized the GPU accelerated QUICK and AMBER based ab initio QM/MM implementation on AMD GPUs. This encompasses the entire Fock matrix build and force calculation in QUICK including one-electron integrals, two-electron repulsion integrals, exchange-correlation quadrature, and linear algebra…
Raphaël Robidas, Claude Legault
Computational chemistry is an increasingly active field due to the improvement of computing resources and theoretical tools. However, its use remains usually limited to technically-inclined users due to the technical challenges of preparing, launching and analyzing calculations. In this context, we have developed…
Oliver Lee, Malte Gather, Eli Zysman-Colman
We describe a new tool for the efficient management of computational chemistry. Digichem is a program that automates and simplifies nearly the entire computational pipeline, including large-scale batch submission of calculations, analysis and results parsing, the generation of 3D density plots and 2D graphs of…
Authors not listed
Computing electrostatic interactions remains the bottleneck of molecular dynamics (MD) simulations despite more than a century of effort in developing methods to accelerate the calculation. Previously we have developed the Spherical Grid and Treecode (SGT) and Gauss-Legendre-Spherical-t (GLST) algorithms for…
James S. Sims, William L. George, Steven G. Satterfield, Howard K. Hung + 21 more
'Howard K. Hung' 'John G. Hagedorn' 'Peter M. Ketcham' 'Terence J. Griffin' 'Stanley A. Hagstrom' 'Julien C. Franiatte' 'Garnett W. Bryant' 'W. Jaskólski' 'Nicos S. Martys' 'Charles E. Bouldin' 'Vernon Simmons' 'Oliver P. Nicolas' 'James A. Warren' 'Barbara A. am Ende' 'John E. Koontz' 'B. James Filla' 'Vital G.…