Zobrazeno 1 - 10
of 81
pro vyhledávání: '"John E Stone"'
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
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
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
Publikováno v:
PLoS Computational Biology, Vol 10, Iss 3, p e1003488 (2014)
Nuclear pore complexes (NPCs) form gateways for material transfer across the nuclear envelope of eukaryotic cells. Disordered proteins, rich in phenylalanine-glycine repeat motifs (FG-nups), form the central transport channel. Understanding how nups
Externí odkaz:
https://doaj.org/article/ca6613e931c24f9288befdaf3cf1d2b0
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:
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
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
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
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
Publikováno v:
Computing in Science & Engineering. 24:4-6
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.