Foldamer simulations: novel computational methods and applications to poly-phenylacetylene oligomers |
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Authors: | Elmer Sidney P Pande Vijay S |
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Institution: | Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA. |
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Abstract: | We apply several methods to probe the ensemble kinetic and structural properties of a model system of poly-phenylacetylene (pPA) oligomer folding trajectories. The kinetic methods employed included a brute force accounting of conformations, a Markovian state matrix method, and a nonlinear least squares fit to a minimalist kinetic model used to extract the folding time. Each method gave similar measures for the folding time of the 12-mer chain, calculated to be on the order of 7 ns for the complete folding of the chain from an extended conformation. Utilizing both a linear and a nonlinear scaling relationship between the viscosity and the folding time to correct for a low simulation viscosity, we obtain an upper and a lower bound for the approximate folding time within the range 70 ns
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