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<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>TTI-C Guest Speaker<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Presented by: <st1:City w:st="on">Toyota</st1:City>
Technological Institute at <st1:City w:st="on"><st1:place w:st="on">Chicago</st1:place></st1:City><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Speaker: Ron Dror<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Speaker’s home page: <a
href="http://people.csail.mit.edu/rondror">http://people.csail.mit.edu/rondror</a><o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Date: Tuesday, October 9, 2007<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Time: 12:00<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Location:<span style='mso-spacerun:yes'> </span>TTI-C
Conference room, 2<sup>nd</sup> floor<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><b
style='mso-bidi-font-weight:normal'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial;font-weight:bold;mso-bidi-font-weight:
normal'>Title</span></font></b><font size=2 face=Arial><span style='font-size:
10.0pt;font-family:Arial'>: </span></font><span style='mso-fareast-language:
JA'>Elucidating Protein Function via Fast, Scalable Molecular Dynamics
Simulations Ron Dror, D. E. Shaw Research<o:p></o:p></span></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><font size=3
face="Times New Roman"><span style='font-size:12.0pt;font-weight:bold;
mso-bidi-font-weight:normal'>Abstract: <o:p></o:p></span></font></b></p>
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><font size=3
face="Times New Roman"><span style='font-size:12.0pt;font-weight:bold;
mso-bidi-font-weight:normal'><o:p> </o:p></span></font></b></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt;mso-fareast-language:
JA'>Although molecular dynamics (MD) simulations of biomolecular systems often
run for days to months, many events of great scientific interest and
pharmaceutical relevance occur on long time scales that remain beyond reach.<span
style='mso-spacerun:yes'> </span>Such events include functionally
important changes in protein structures, folding of proteins to their native
three-dimensional structures, and interactions between proteins or between
proteins and candidate drug molecules.<span style='mso-spacerun:yes'>
</span>We present several new algorithms that significantly accelerate parallel
MD simulations compared with current state-of-the-art codes.<span
style='mso-spacerun:yes'> </span>These methods are embodied in a newly
developed MD code called Desmond that achieves unprecedented simulation
throughput and parallel scalability on commodity clusters.<span
style='mso-spacerun:yes'> </span>For example, on a standard benchmark,
Desmond's performance on a conventional Opteron cluster with 2K processors
slightly exceeded the reported performance of IBM's Blue Gene/L machine with
32K processors running its Blue Matter MD code.<span
style='mso-spacerun:yes'> </span>The ability to perform long MD simulations
quickly has allowed us to provide an atomically detailed explanation for the
mechanisms of several proteins, including the sodium-proton antiporter NhaA.<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt;mso-fareast-language:
JA'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt;mso-fareast-language:
JA'>This is joint work with Kevin Bowers, Edmond Chow, Huafeng Xu, Shy Arkin,
Michael Eastwood, Brent Gregersen, Morten Jensen, John Klepeis, Istvan
Kolossvary, Mark Moraes, Federico Sacerdoti, John Salmon, Yibing Shan, and
David Shaw<o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt;mso-fareast-language:
JA'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><span
class=GramE><font size=3 face="Times New Roman"><span style='font-size:12.0pt;
mso-fareast-language:JA'>If you have any questions or would like to meet the
speaker,</span></font></span><span style='mso-fareast-language:JA'> please
contact Ponda Barnes at <a href="mailto:pondabarnes@tti-c.org">pondabarnes@tti-c.org</a>.<o:p></o:p></span></p>
<p class=MsoNormal style='mso-layout-grid-align:none;text-autospace:none'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt;mso-fareast-language:
JA'>For future <span class=GramE>TTI-C</span> events please visit </span><a
href="http://ttic.uchicago.edu/cal/month.php"
title="http://ttic.uchicago.edu/cal/month.php">http://ttic.uchicago.edu/cal/month.php</a>.
<span style='mso-spacerun:yes'> </span><span class=GramE>(TTI-C <st1:address
w:st="on"><st1:Street w:st="on">1427 E. 60<sup>th</sup> Street</st1:Street>, <st1:City
w:st="on">Chicago</st1:City>, <st1:State w:st="on">IL</st1:State></st1:address>).</span></font><span
style='mso-fareast-language:JA'><o:p></o:p></span></p>
<p class=MsoNormal><b style='mso-bidi-font-weight:normal'><font size=3
face="Times New Roman"><span style='font-size:12.0pt;font-weight:bold;
mso-bidi-font-weight:normal'><o:p> </o:p></span></font></b></p>
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