Zobrazeno 1 - 10
of 81
pro vyhledávání: '"John E. Stone"'
Autor:
Benjamin R. Gilbert, Zane R. Thornburg, Troy A. Brier, Jan A. Stevens, Fabian Grünewald, John E. Stone, Siewert J. Marrink, Zaida Luthey-Schulten
Publikováno v:
Frontiers in Cell and Developmental Biology, Vol 11 (2023)
Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication and inheritance of genetic material. By creating a computational framework to model systems of replicating bacterial
Externí odkaz:
https://doaj.org/article/42b2539a78d14ebabeca3d47e234ce28
Autor:
Elwasif, Wael, Godoy, William, Hagerty, Nick, Harris, J. Austin, Hernandez, Oscar, Joo, Balint, Kent, Paul, Lebrun-Grandie, Damien, Maccarthy, Elijah, Vergara, Veronica G. Melesse, Messer, Bronson, Miller, Ross, Opal, Sarp, Bastrakov, Sergei, Bussmann, Michael, Debus, Alexander, Steinger, Klaus, Stephan, Jan, Widera, Rene, Bryngelson, Spencer H., Berre, Henry Le, Radhakrishnan, Anand, Young, Jefferey, Chandrasekaran, Sunita, Ciorba, Florina, Simsek, Osman, Spiga, Kate Clark Filippo, Hammond, Jeff, Hardy, John E. Stone. David, Keller, Sebastian, Trott, Jean-Guillaume Piccinali. Christian
Publikováno v:
Proceedings of the HPC Asia 2023 Workshops, pg 35-49
This paper assesses and reports the experience of ten teams working to port,validate, and benchmark several High Performance Computing applications on a novel GPU-accelerated Arm testbed system. The testbed consists of eight NVIDIA Arm HPC Developer
Externí odkaz:
http://arxiv.org/abs/2209.09731
Autor:
Anda Trifan, Defne Gorgun, Michael Salim, Zongyi Li, Alexander Brace, Maxim Zvyagin, Heng Ma, Austin Clyde, David Clark, David J Hardy, Tom Burnley, Lei Huang, John McCalpin, Murali Emani, Hyenseung Yoo, Junqi Yin, Aristeidis Tsaris, Vishal Subbiah, Tanveer Raza, Jessica Liu, Noah Trebesch, Geoffrey Wells, Venkatesh Mysore, Thomas Gibbs, James Phillips, S Chakra Chennubhotla, Ian Foster, Rick Stevens, Anima Anandkumar, Venkatram Vishwanath, John E Stone, Emad Tajkhorshid, Sarah A Harris, Arvind Ramanathan
Publikováno v:
The International Journal of High Performance Computing Applications. 36:603-623
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceut
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::faee1bb3ad255746c2c9936d47964798
https://doi.org/10.1177/10943420221113513
https://doi.org/10.1177/10943420221113513
Autor:
Mohammad Soroush Barhaghi, Brad Crawford, Gregory Schwing, David J. Hardy, John E. Stone, Loren Schwiebert, Jeffrey Potoff, Emad Tajkhorshid
Publikováno v:
Journal of Chemical Theory and Computation. 18:4983-4994
py-MCMD, an open-source Python software, provides a robust workflow layer that manages communication of relevant system information between the simulation engines NAMD and GOMC and generates coherent thermodynamic properties and trajectories for anal
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7dfa21db5a28cc095e820da415bcaefa
https://doi.org/10.1021/acs.jctc.1c00911
https://doi.org/10.1021/acs.jctc.1c00911
Publikováno v:
Proc UrgentHPC 2021 (2021)
Over the past 18 months, the need to perform atomic detail molecular dynamics simulations of the SARS-CoV-2 virion, its spike protein, and other structures related to the viral infection cycle has led biomedical researchers worldwide to urgently seek
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c00dd098175d359b65d8c720777e0725
https://pubmed.ncbi.nlm.nih.gov/36573923
https://pubmed.ncbi.nlm.nih.gov/36573923
Autor:
John E. Stone, Kevin S. Griffin, Jefferson Amstutz, David E. DeMarle, William R. Sherman, Johannes Gunther
Publikováno v:
Computing in scienceengineering. 24(2)
ANARI is a new 3-D rendering API, an emerging Khronos standard that enables visualization applications to leverage the state-of-the-art rendering techniques across diverse hardware platforms and rendering engines. Visualization applications have hist
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5c42c60207ae601b31f41006c3e1b1fd
https://pubmed.ncbi.nlm.nih.gov/36465066
https://pubmed.ncbi.nlm.nih.gov/36465066
Publikováno v:
Computing in Science & Engineering. 24:4-6
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::e23cbdee3dd76cbde0d62b5e2dec9782
https://doi.org/10.1109/mcse.2022.3163480
https://doi.org/10.1109/mcse.2022.3163480
Publikováno v:
eLife, Vol 5 (2016)
Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods,
Externí odkaz:
https://doaj.org/article/a634c22656b84df4bcb1ce5b496cfa36
Publikováno v:
Computing in Science & Engineering
Computing in science & engineering
Computing in science & engineering
Enveloped viruses infect host cells via fusion of their viral envelope with the plasma membrane. Upon cell entry, viruses gain access to all the macromolecular machinery necessary to replicate, assemble, and bud their progeny from the infected cell.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::304b44b8d3b27e87c8252fe65663a12a
https://doi.org/10.1109/mcse.2020.3020508
https://doi.org/10.1109/mcse.2020.3020508
Autor:
Junqi Yin, Tom Burnley, Tom Gibbs, Venkatram Vishwanath, Emad Tajkhorshid, Sarah A. Harris, Murali Emani, Vishal Subbiah, Lei Huang, John McCalpin, David A Clark, Jessica Liu, Arvind Ramanathan, Austin Clyde, Zongyi Li, Anda Trifan, James Phillips, Hyunseung Yoo, Rick Stevens, Ian Foster, A. Tsaris, Maxim Zvyagin, Geoffrey Wells, Michael A. Salim, Alexander Brace, John E. Stone, Animashree Anandkumar, Chakra Chennubhotla, David J. Hardy, Heng Ma, Venkatesh Mysore, Noah Trebesch, Defne Gorgun
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) replication transcription complex (RTC) is a multi-domain protein responsible for replicating and transcribing the viral mRNA inside a human cell. Attacking RTC function with pharmaceut
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::81502ca224787b1c6a40d364732268f7
https://doi.org/10.1101/2021.10.09.463779
https://doi.org/10.1101/2021.10.09.463779