BEGIN:VCALENDAR VERSION:2.0 PRODID:Linklings LLC BEGIN:VTIMEZONE TZID:America/Denver X-LIC-LOCATION:America/Denver BEGIN:DAYLIGHT TZOFFSETFROM:-0700 TZOFFSETTO:-0600 TZNAME:MDT DTSTART:19700308T020000 RRULE:FREQ=YEARLY;BYMONTH=3;BYDAY=2SU END:DAYLIGHT BEGIN:STANDARD TZOFFSETFROM:-0600 TZOFFSETTO:-0700 TZNAME:MST DTSTART:19701101T020000 RRULE:FREQ=YEARLY;BYMONTH=11;BYDAY=1SU END:STANDARD END:VTIMEZONE BEGIN:VEVENT DTSTAMP:20260422T000713Z LOCATION:Mile High Ballroom DTSTART;TZID=America/Denver:20231114T153000 DTEND;TZID=America/Denver:20231114T161500 UID:submissions.supercomputing.org_SC23_sess316_misc155@linklings.com SUMMARY:Progress Since the Presentation of “Millisecond-Scale Molecular Dy namics Simulations on Anton” at SC09 DESCRIPTION:David E. Shaw, Ron O. Dror, John K. Salmon, J. P. Grossman, Ke nneth M. Mackenzie, Joseph A. Bank, Cliff Young, Martin M. Deneroff, Brann on Batson, Kevin J. Bowers, Edmond Chow, Michael P. Eastwood, Douglas J. I erardi, John L. Klepeis, Jeffrey S. Kuskin, Richard H. Larson, Kreston Lin dorff-Larsen, Paul Maragakis, Mark A. Moraes, Stefano Piana, Yibing Shan, and Brian Towles\n\nIn 2009, we presented a paper at SC09 reporting on the design, construction, and use of Anton 1, a special-purpose supercomputer designed for molecular dynamics (MD) simulations of biomolecular systems. The machine’s specialized hardware dramatically increased the speed of M D calculations, making possible for the first time the simulation of biolo gical molecules at an atomic level of detail for periods on the order of a millisecond -- about two orders of magnitude beyond the previous state of the art. This enabled biomolecular simulations on a timescale at which m any critically important, but poorly understood phenomena were known to oc cur, allowing the observation of biological phenomena that were previously inaccessible to both computational and experimental study.\n\nThe followi ng year, we published a paper in the journal Science that reported on our use of Anton 1 to answer longstanding fundamental questions regardi ng the nature of protein folding and other large-scale structural changes in proteins. Some of our results were derived from an Anton 1 simulation roughly 100 times longer than the longest simulation that had previously b een reported.\n\nOver the past 10 years, we have developed and deployed tw o further generations of the Anton supercomputer. Anton 3 is dramatically faster than Anton 1, and capable of efficiently handling far larger molec ular systems. Although general-purpose supercomputers have also become mu ch faster over that period, the performance gap between Anton and general- purpose supercomputers has grown over time -- to a factor of more than 400 for biomolecular systems in a size range of considerable interest within the research and drug discovery communities.\n\nIn 2010, we made an Anton 1 machine (later upgraded to an Anton 2) available without cost for noncom mercial research use by universities and other nonprofit institutions. An ton time is allocated annually by the National Academies, and a total of 2 39 outside research groups have thus far conducted independent research pr ojects on these machines.\n\nAt D. E. Shaw Research, we have continued usi ng Anton machines both for fundamental research and for internal and colla borative drug discovery, yielding six drugs that are currently in human cl inical trials. \n\nThis talk will review the contents of our original pap er and related progress since its publication.\n\nTag: Applications, Archi tecture and Networks, Codesign\n\nRegistration Category: Tech Program Reg Pass, Workshop Reg Pass\n\nSession Chair: Daniel A. Reed (University of Ut ah)\n\n END:VEVENT END:VCALENDAR