M
Matthew B. Baker
Researcher at Oak Ridge National Laboratory
Publications - 20
Citations - 384
Matthew B. Baker is an academic researcher from Oak Ridge National Laboratory. The author has contributed to research in topics: Programming paradigm & Partitioned global address space. The author has an hindex of 6, co-authored 18 publications receiving 202 citations. Previous affiliations of Matthew B. Baker include National Center for Computational Sciences & Naval Medical Center Portsmouth.
Papers
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Proceedings ArticleDOI
UCX: An Open Source Framework for HPC Network APIs and Beyond
Pavel Shamis,Manjunath Gorentla Venkata,M. Graham Lopez,Matthew B. Baker,Oscar Hernandez,Yossi Itigin,Mike Dubman,Gilad Shainer,Richard L. Graham,Liran Liss,Yiftah Shahar,Sreeram Potluri,Davide Rossetti,Donald Becker,Duncan Poole,Christopher Lamb,Sameer Kumar,Craig B. Stunkel,George Bosilca,Aurelien Bouteiller +19 more
TL;DR: This paper presents Unified Communication X, a set of network APIs and their implementations for high throughput computing, and implements the APIs and protocols, and measures the performance of overhead-critical network primitives fundamental for implementing many parallel programming models and system libraries.
Journal ArticleDOI
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.
Atanu Acharya,Rupesh Agarwal,Rupesh Agarwal,Matthew B. Baker,Jerome Baudry,Debsindhu Bhowmik,Swen Boehm,Kendall G. Byler,Samuel Yen-Chi Chen,Leighton Coates,Connor J. Cooper,Connor J. Cooper,Omar Demerdash,Isabella Daidone,John D. Eblen,John D. Eblen,Sally R. Ellingson,Stefano Forli,Jens Glaser,James C. Gumbart,John A. Gunnels,Oscar Hernandez,Stephan Irle,Stephan Irle,Daniel W. Kneller,Andrey Kovalevsky,Jeffrey M. Larkin,Travis J Lawrence,Scott LeGrand,Shih-Hsien Liu,Shih-Hsien Liu,Julie C. Mitchell,Gilchan Park,Jerry M. Parks,Jerry M. Parks,Anna Pavlova,Loukas Petridis,Loukas Petridis,Duncan Poole,Line Pouchard,Arvind Ramanathan,David M. Rogers,Diogo Santos-Martins,Aaron Scheinberg,Ada Sedova,Y. Shen,Y. Shen,Jeremy C. Smith,Jeremy C. Smith,Micholas Dean Smith,Micholas Dean Smith,Carlos Soto,A. Tsaris,Mathialakan Thavappiragasam,Andreas F. Tillack,Josh V. Vermaas,V. Q. Vuong,V. Q. Vuong,Junqi Yin,Shinjae Yoo,Mai Zahran,Laura Zanetti-Polzi +61 more
TL;DR: A supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking is presented, including the use of quantum mechanical, machine learning, and artificial intelligence methods to cluster MD trajectories and rescore docking poses.
Journal ArticleDOI
High-throughput virtual laboratory for drug discovery using massive datasets
Jens Glaser,Josh V. Vermaas,David M. Rogers,Jeff Larkin,Scott LeGrand,Swen Boehm,Matthew B. Baker,Aaron Scheinberg,Andreas F. Tillack,Mathialakan Thavappiragasam,Ada Sedova,Oscar Hernandez +11 more
TL;DR: Time-to-solution for structure-based screening of massive chemical databases for COVID-19 drug discovery has been decreased by an order of magnitude, and a virtual laboratory has been deployed at scale on up to 27,612 GPUs on the Summit supercomputer.
Posted ContentDOI
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
Atanu Acharya,Rupesh Agarwal,Matthew B. Baker,Jerome Baudry,Debsindhu Bhowmik,Swen Boehm,Kendall G. Byler,Leighton Coates,Samuel Yen-Chi Chen,Connor J. Cooper,Omar Demerdash,Isabella Daidone,John D. Eblen,Sally R. Ellingson,Stefano Forli,Jens Glaser,James C. Gumbart,John A. Gunnels,Oscar Hernandez,Stephan Irle,Jeffery Larkin,Travis J Lawrence,Scott LeGrand,Shih-Hsien Liu,Julie C. Mitchell,Gilchan Park,Jerry M. Parks,Anna Pavlova,Loukas Petridis,Duncan Poole,Line Pouchard,Arvind Ramanathan,David M. Rogers,Diogo Santos-Martins,Aaron Scheinberg,Ada Sedova,Shawn Shen,Jeremy C. Smith,Micholas Dean Smith,Carlos Soto,Aristides Tsaris,Mathialakan Thavappiragasam,Andreas F. Tillack,Josh V. Vermaas,Van Quan Vuong,Junqi Yin,Shinjae Yoo,Mai Zahran,Laura Zanetti-Polzi +48 more
TL;DR: A supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking and the use of quantum mechanical, machine learning, and AI methods to cluster MD trajectories and rescore docking poses is presented.
Journal ArticleDOI
Supercomputing Pipelines Search for Therapeutics Against COVID-19
Josh V. Vermaas,Ada Sedova,Matthew B. Baker,Swen Boehm,David M. Rogers,Jeff Larkin,Jens Glaser,Micholas Dean Smith,Oscar Hernandez,Jeremy C. Smith +9 more
TL;DR: A new drug discovery pipeline is developed using the Summit supercomputer at Oak Ridge National Laboratory to help pioneer this effort, with new platforms that incorporate GPU-accelerated simulation and allow for the virtual screening of billions of potential drug compounds in days compared to weeks or months for their ability to inhibit SARS-COV-2 proteins.