This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.Recent single molecule experiments on single stranded DNA have shown that the form the DNA takes is dependent on its method of formation. Our collaborator Mara Prentiss has shown that slow thermal melting creates ?short? single strands that have a base separation of 0.54 nm while unzipping creates a ?long? form with base separation of 0.7-0.8 nm. We propose to study these experiments by using molecular dynamics to calculate free energy profiles of single stranded DNA as a function of base pair separation. This may require multiple free energy profiles as we study the effects of temperature and initial conditions on the extension. In addition we would like to take this opportunity to explore the Teragrid resources for future requests for allocations.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
5P41RR006009-17
Application #
7601514
Study Section
Special Emphasis Panel (ZRG1-BCMB-Q (40))
Project Start
2007-08-01
Project End
2008-07-31
Budget Start
2007-08-01
Budget End
2008-07-31
Support Year
17
Fiscal Year
2007
Total Cost
$314
Indirect Cost
Name
Carnegie-Mellon University
Department
Biostatistics & Other Math Sci
Type
Schools of Arts and Sciences
DUNS #
052184116
City
Pittsburgh
State
PA
Country
United States
Zip Code
15213
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