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PhD Defense - Christopher Badi' Abdul-Wahid

Start: 3/27/2015 at 2:00PM
End: 3/27/2015 at 5:00PM
Location: 315 Stinson Remick
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Christopher Badi' Abdul-Wahid

Dissertation Defense

March 27, 2015        2:00 pm        315 Stinson Remick


Dr. Jesus Izaguirre

Committee Members:

Dr. Colin McMillan        Dr. Christopher Sweet        Dr. Douglas Thain

Faculty and students are welcome to attend the preserntation portion of the defense.

Light snacks and refreshments will be served.


A Software Pipeline for Ensemble Molecular Dynamics


Proteins are the "machines of life" and understanding their motions is crucial to understanding the nature of various diseases, for instance Alzheimer's and Huntington's.Molecular Dynamics simulations are useful since they provide a atom-level resolution of a protein's motion.

Of particular interest are measuring the rates at which different molecular conformations interchange. A significant bottleneck in the use of molecular dynamics is the difference in timescales. As a result, simulations require billions of steps to access slow motions such as protein folding. This work describes the development of a software pipeline to address this issue.

The result is a set of software packages aimed at facilitating specific points is the study of proteins: exploratory simulations, conformational sampling, and rate calculations. Due to the large number of simulations that need to be run, each step supports the use of distributed systems and supports long-running applications and fault-tolerance.