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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>REMINDER!!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></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><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:place w:st="on"><st1:City w:st="on">Chicago</st1:City></st1:place><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'><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, please contact
Ponda Barnes at <a href="mailto:pondabarnes@tti-c.org">pondabarnes@tti-c.org</a>.<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'>For future TTI-C 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>(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>).</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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