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Funding Update: Jan 14, 2011

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Algorithms for Next-Generation Genomics
Start Date: Jan. 1, 2011
Expires: Dec. 31, 2011
Awarded Amount to Date: $83,988
Principal Investigator: Benjamin Raphael
Sponsor: Brown University

The project aims to develop algorithms for new and emerging high-throughput DNA sequencing technologies. According to the abstract, the PI plans to develop algorithms for genome assembly and discovery of DNA sequence variants, some of which will rely on the availability of a reference genome sequence, while others will operate de novo. For the latter algorithms, the PI plans to design algorithms that use longer-range DNA sequence information generated by newer single-molecule and nanopore sequencing technologies.


Computational Studies of Folding and Dynamics of Proteins
Start Date: Jan. 1, 2011
Expires: Dec. 31, 2011
Awarded Amount to Date: $201,749
Principal Investigator: Angel Garcia
Sponsor: Rensselaer Polytechnic Institute

The grant abstract states that the project's objective is to study the folding and unfolding equilibrium and kinetics of model proteins "with increased degree of complexity" and the functional dynamics of proteins. According to the abstract, the simulations will "explore the effects of co-solvents and hydrostatic pressure on the transition states and will help understand the effect of solvent in determining the transition state of proteins and will provide a measure of the folding/unfolding activation volumes." On the functional dynamics side, the PI plans to "correlate the existence of sub-states in the energy landscape with functional states of the proteins." Both aspects of the project will be studied using Markov state models built from a large number of independent simulations.


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