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Modeling kinetics and equilibrium of membranes with fields: milestoning analysis and implication to permeation.

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The Journal of chemical physics

AIP Publishing

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      Abstract

      Coarse graining of membrane simulations by translating atomistic dynamics to densities and fields with Milestoning is discussed. The space of the membrane system is divided into cells and the different cells are characterized by order parameters presenting the number densities. The dynamics of the order parameters are probed with Milestoning. The methodology is illustrated here for a phospholipid membrane system (a hydrated bilayer of DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) lipid molecules). Significant inhomogeneity in membrane internal number density leads to complex free energy landscape and local maps of transition times. Dynamics and distributions of cavities within the membrane assist the permeation of nonpolar solutes such as xenon atoms. It is illustrated that quantitative and detailed dynamics of water transport through DOPC membrane can be analyzed using Milestoning with fields. The reaction space for water transport includes at least two slow variables: the normal to the membrane plane, and the water density.

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        Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

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          A smooth particle mesh Ewald method

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            Author and article information

            Affiliations
            [1 ] Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA.
            Journal
            J Chem Phys
            The Journal of chemical physics
            AIP Publishing
            1089-7690
            0021-9606
            Aug 07 2014
            : 141
            : 5
            25106564
            10.1063/1.4891305
            4119198

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