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To achieve scalable parallel performance in Molecular Dynamics Simulations, we have modeled and implemented several dynamic spatial domain decomposition algorithms. The modeling is based upon the Bulk Synchronous Parallel architecture model (BSP), which describes supersteps of computation, communication, and synchronization. Using this model, we have(More)
Free-energy simulations have been used to estimate the change in the conformational stability of short polyalanine alpha-helices when one of the alanines is replaced by a proline residue. For substituting proline in the middle of the helix the change in free energy of folding (delta delta G degrees) was calculated as 14 kJ/mol (3.4 kcal/mol), in excellent(More)
A series of oligoalanine molecules with single amino acid replacements in the middle of the chain has been studied by molecular dynamics simulations. Differences in stability of the alpha-helix (as free energies delta delta G degrees) were estimated for the following series of residues: alpha-aminoisobutyric acid, alanine, alpha-amino-n-butyric acid,(More)
To achieve scalable parallel performance in Molecular Dynamics Simulation, we have modeled and implemented several dynamic spatial domain decomposition algorithms. The modeling is based upon Valiant’s Bulk Synchronous Parallel architecture model (BSP), which describes supersteps of computation, communication, and synchronization. We have developed(More)
The conformational probability distribution of a valine residue in the valine dipeptide and of the valine side chain in an alpha-helix, as well as the change in helix stability for replacing alanine with valine, has been calculated by molecular dynamics simulations of explicitly hydrated systems: dipeptide, tetrapeptide and 10-, 14- and 18-residue(More)
Despentapeptide insulin (DPI), an analogue of insulin, is the only analogue of insulin existing as a monomer in crystalline form so far discovered. A 31 picosecond molecular dynamics simulation of DPI was carried out in the unit cell that includes four DPI molecules, 398 water molecules, four Cd2+, eight Na+ and four Cl-. The molecular dynamics results were(More)
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