Recently, there has been growing interest in industry, academia, and government in the field of bioinformatics, due to the large amounts of data being generated by the many genome sequencing and protein sequencing projects taking place worldwide. So far, few computational techniques have been able to provide insights about the relationship between sequence and physical properties for these biopolymers. The sequence analysis techniques used in this massive computational project may be relevant to analysis methods for those datasets as well.
This project is an enumeration of the conformations of several different sizes of polymers on a lattice. When each conformation is found, an energy value is calculated for it-based on the spatial separations of monomers in the conformation. The energy spectrum is now being found for several different interaction models (Potts interactions, hydrophobic type interactions, and Miyazawa-Jernigan interactions) and for 500 different sequences of monomer species along the chain.
Jeff Chuang, Graduate Student Researcher
Physically, these researchers wish to determine the scaling of several quantities with polymer length (free energy, density of states, standard deviation of the free energy, freezing temperature). These are key issues in protein folding. All of these quantities can be calculated from knowledge of the energy of the conformations of the polymer. Enumerations are then performed for both compact and unconstrained polymers. For the compact polymers (polymers packed into a dense conformation), the above quantities for chains of length 18, 27, 36, and 48 are calculated. For the unconstrained polymers, enumerations of polymers of lengths 10 to 18 are performed.
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URL: http://www.msi.umn.edu/about/publications/annualreport/ar2000/depts/IT/PhysAstron/Physics/grosberg.html |
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