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Douglas J. Ierardi
Researcher at D. E. Shaw Research
Publications - 22
Citations - 2586
Douglas J. Ierardi is an academic researcher from D. E. Shaw Research. The author has contributed to research in topics: Massively parallel & Software. The author has an hindex of 13, co-authored 22 publications receiving 2235 citations. Previous affiliations of Douglas J. Ierardi include University of Southern California.
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Journal ArticleDOI
Anton, a special-purpose machine for molecular dynamics simulation
David E. Shaw,Martin M. Deneroff,Ron O. Dror,Jeffrey S. Kuskin,Richard H. Larson,John K. Salmon,Cliff Young,Brannon Batson,Kevin J. Bowers,Jack C. Chao,Michael P. Eastwood,Joseph Gagliardo,J. P. Grossman,C. Richard Ho,Douglas J. Ierardi,István Kolossváry,John L. Klepeis,Timothy Layman,Christine McLeavey,Mark A. Moraes,Rolf Mueller,Edward C. Priest,Yibing Shan,Jochen Spengler,Michael Theobald,Brian Towles,Stanley C. Wang +26 more
TL;DR: A massively parallel machine called Anton is described, which should be capable of executing millisecond-scale classical MD simulations of such biomolecular systems and has been designed to use both novel parallel algorithms and special-purpose logic to dramatically accelerate those calculations that dominate the time required for a typical MD simulation.
Proceedings ArticleDOI
Anton 2: raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer
David E. Shaw,J. P. Grossman,Joseph A. Bank,Brannon Batson,J. Adam Butts,Jack C. Chao,Martin M. Deneroff,Ron O. Dror,Amos Even,Christopher H. Fenton,Anthony Forte,Joseph Gagliardo,Gennette Gill,Brian Greskamp,C. Richard Ho,Douglas J. Ierardi,Lev Iserovich,Jeffrey S. Kuskin,Richard H. Larson,Timothy Layman,Li-Siang Lee,Adam Lerer,Chester Li,Daniel Killebrew,Kenneth M. Mackenzie,Shark Yeuk-Hai Mok,Mark A. Moraes,Rolf Mueller,Lawrence J. Nociolo,Jon L. Peticolas,Terry Quan,Daniel Ramot,John K. Salmon,Daniele Paolo Scarpazza,U. Ben Schafer,Naseer Siddique,Christopher W. Snyder,Jochen Spengler,Ping Tak Peter Tang,Michael Theobald,Horia Toma,Brian Towles,Benjamin Vitale,Stanley C. Wang,Cliff Young +44 more
TL;DR: The architecture of Anton 2 is tailored for fine-grained event-driven operation, which improves performance by increasing the overlap of computation with communication, and also allows a wider range of algorithms to run efficiently, enabling many new software-based optimizations.
Proceedings ArticleDOI
Millisecond-scale molecular dynamics simulations on Anton
David E. Shaw,Ron O. Dror,John K. Salmon,J. P. Grossman,Kenneth M. Mackenzie,Joseph A. Bank,Cliff Young,Martin M. Deneroff,Brannon Batson,Kevin J. Bowers,Edmond Chow,Michael P. Eastwood,Douglas J. Ierardi,John L. Klepeis,Jeffrey S. Kuskin,Richard H. Larson,Kresten Lindorff-Larsen,Paul Maragakis,Mark A. Moraes,Stefano Piana,Yibing Shan,Brian Towles +21 more
TL;DR: Anton's performance when executing actual MD simulations whose accuracy has been validated against both existing MD software and experimental observations is reported, allowing the observation of aspects of protein dynamics that were previously inaccessible to both computational and experimental study.
Proceedings ArticleDOI
Anton, a special-purpose machine for molecular dynamics simulation
David E. Shaw,Martin M. Deneroff,Ron O. Dror,Jeffrey S. Kuskin,Richard H. Larson,John K. Salmon,Cliff Young,Brannon Batson,Kevin J. Bowers,Jack C. Chao,Michael P. Eastwood,Joseph Gagliardo,J. P. Grossman,C. Richard Ho,Douglas J. Ierardi,István Kolossváry,John L. Klepeis,Timothy Layman,Christine McLeavey,Mark A. Moraes,Rolf Mueller,Edward C. Priest,Yibing Shan,Jochen Spengler,Michael Theobald,Brian Towles,Stanley C. Wang +26 more
TL;DR: A massively parallel machine called Anton is described, which should be capable of executing millisecond-scale classical MD simulations of such biomolecular systems and is designed to use both novel parallel algorithms and special-purpose logic to dramatically accelerate those calculations that dominate the time required for a typical MD simulation.
Journal ArticleDOI
Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure
Ross A. Lippert,Cristian Predescu,Douglas J. Ierardi,Kenneth M. Mackenzie,Michael P. Eastwood,Ron O. Dror,David E. Shaw +6 more
TL;DR: This work presents a framework that replaces the traditional integration procedure with separate barostat, thermostat, and Newtonian particle motion updates, allowing thermostats and barostats to be applied infrequently and reduces software complexity and improves software modularity.