[Sem-coll] Applied Math Seminars & Colloquium Next Week

Joe Millham jmillham at iit.edu
Fri Mar 19 17:00:42 CDT 2010


Please join the Applied Math department for the following Seminars and
Colloquia.  All are welcome to attend, and refreshments will be served
at some events.  For a complete and updated listing of the
department's seminars, please visit the seminar webpage:
http://www.iit.edu/csl/am/colloquia/

Department Colloquium
Monday, March 22   4:40 pm  E1 106
Jinbo Xu, Toyota Technological Institute, University of Chicago
"Optimization Techniques for Protein Structure Prediction"
See abstract below
Refreshments served at 4:15 in E1 112
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Meshfree Methods Seminar
Monday, March 22   1:50 pm  AM 222
Greg Fasshauer, IIT Applied Math
"Meshfree Methods for High Fidelity Numerical Simulations of Viscous
Incompressible Flow"
See abstract below
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Department Colloquium
Monday, March 22   4:40 pm  E1 106
Jinbo Xu, Toyota Technological Institute, University of Chicago
"Optimization Techniques for Protein Structure Prediction"
Abstract:
Given the primary sequence of a protein, can we predict its
three-dimensional structure by computational methods? This is one of
the most important and difficult problems in computational molecular
biology and has tremendous implications for many applications such as
drug design.

This talk will present efficient algorithms to solve two key problems
of protein structure prediction: protein threading by linear
programming and protein side-chain packing via tree-decomposition. The
linear programming approach can empirically solve the protein
threading  problem within polynomial-time, although this problem is
NP-hard in theory. The tree-decomposition algorithm not only runs very
efficiently in practice, but also yields a polynomial-time
approximation scheme for some typical cases.

Two protein structure prediction programs, RAPTOR for threading and
TreePack for side-chain packing, have been developed based on the
abovementioned algorithms. RAPTOR ranks first among all the programs
of its category in CASP5, 3rd in CASP6 and 2nd in CASP8, the most
recognized competition in the community of protein structure
prediction. Without losing any prediction accuracy, TreePack runs up
to 90 times faster than SCWRL, a widely-used side-chain packing
program. TreePack can also solve some instances that SCWRL fails. Both
programs have demonstrated success in real-world structure prediction
and functional annotations.
Refreshments served at 4:15 in E1 112
++++++++++++++++++++++++++

Meshfree Methods Seminar
Monday, March 22   1:50 pm  AM 222
Greg Fasshauer, IIT Applied Math
"Meshfree Methods for High Fidelity Numerical Simulations of Viscous
Incompressible Flow"
Abstract:
We discuss ideas for a new adaptive algorithm that will enable us to
tackle the problems of moving boundaries and fluid-surface
interactions. This algorithm combines the flexibility and accuracy of
RBFs with a Lagrangian framework for the Navier-Stokes equations that
simplifies adaptation to a constantly changing domain. Our method
should be able to perform numerical simulations for arbitrary moving
domains, including problems associated with free-surface flows,
fluid-surface interaction or moving boundaries. Preliminary analysis
of our method shows that our approach can successfully compete with
current state-of-the-art methods. This is joint work with Paritosh
Mokhasi and Dietmar Rempfer.



see you there,



--------
Joe Millham

Administrative Assistant
Department of Applied Mathematics
Illinois Institute of Technology
Engineering-1 Room 208
10 W. 32rd St.
Chicago IL 60616
312.567.8984 (Phone)
312.567.3135 (Fax)



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