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      Structural variation of alpha-synuclein with temperature by a coarse-grained approach with knowledge-based interactions

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      AIP Advances

      AIP Publishing

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          Most cited references 44

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          The bond fluctuation method: a new effective algorithm for the dynamics of polymers in all spatial dimensions

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            Deriving effective mesoscale potentials from atomistic simulations.

            We demonstrate how an iterative method for potential inversion from distribution functions developed for simple liquid systems can be generalized to polymer systems. It uses the differences in the potentials of mean force between the distribution functions generated from a guessed potential and the true distribution functions to improve the effective potential successively. The optimization algorithm is very powerful: convergence is reached for every trial function in few iterations. As an extensive test case we coarse-grained an atomistic all-atom model of polyisoprene (PI) using a 13:1 reduction of the degrees of freedom. This procedure was performed for PI solutions as well as for a PI melt. Comparisons of the obtained force fields are drawn. They prove that it is not possible to use a single force field for different concentration regimes. Copyright 2003 Wiley Periodicals, Inc.
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              Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation

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                Author and article information

                Journal
                AIP Advances
                AIP Advances
                AIP Publishing
                2158-3226
                September 2015
                September 2015
                : 5
                : 9
                : 092504
                Affiliations
                [1 ]Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, OH 45433, USA
                [2 ]Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, MS 39406, USA
                Article
                10.1063/1.4927544
                © 2015

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