Search · four archives
Search · four archives
14 papers · ranked by Valyu relevance
Knut Rand, Ivar Grytten, Milena Pavlovic, Chakravarthi Kanduri + 1 more
Python is a popular and widespread programming language for scientific computing, in large part due to the powerful array programming library NumPy, which makes it easy to write clean, vectorized and efficient code for handling large datasets. A challenge with using array programming for biological data is that the…
Dilawar Singh, Steven S. Andrews
Smoldyn is a particle-based biochemical simulator that is frequently used for systems biology and biophysics research. Previously, users could only define models using text-based input or a C/C++ applicaton programming interface (API), which were convenient, but limited extensibility. We added a Python API to Smoldyn…
Chaoming Wang, Sichao He, Shouwei Luo, Yuxiang Huan + 1 more
Artificial intelligence (AI) is revolutionizing scientific research across various disciplines. The foundation of scientific research lies in rigorous scientific computing based on standardized physical units. However, current mainstream high-performance numerical computing libraries for AI generally lack native…
Pau Andrio, Adam Hospital, Cristian Ramon-Cortes, Javier Conejero + 4 more
The usage of workflows has led to progress in many fields of science, where the need to process large amounts of data is coupled with difficulty in accessing and efficiently using High Performance Computing platforms. On the one hand, scientists are focused on their problem and concerned with how to process their data.…
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…
Dileep Kishore, Srikiran Chandrasekaran
Biological systems are intrinsically noisy and this noise may determine the qualitative outcome of the system. In the absence of analytical solutions to mathematical models incorporating noise, stochastic simulation algorithms are useful to explore the possible trajectories of these systems. Algorithms used for such…
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…
Jeremy Li, Alex Rubinsteyn, Sergey Feldman, Timothy O’Donnell + 18 more
Scientific computing has become a central component of modern scientific discovery. Yet many computational tools are developed by small, specialized teams under incentives that encourage the release of rapidly prototyped tooling without commensurate attention to engineering concerns, including performance and…
Authors not listed
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…
Stephen R. Piccolo, Michael B. Frampton
When reporting research findings, scientists document the steps they followed so that others can verify and build upon the research. When those steps have been described in sufficient detail that others can retrace the steps and obtain similar results, the research is said to be reproducible. Computers play a vital…
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…