title: Modeling kinetics and equilibrium of membranes with fields: milestoning analysis and implication to permeation.
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.
authors.affiliation: Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA.
authors.forename: Alfredo E
authors.initials: AE
authors.lastname: Cardenas
authors.affiliation: Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA.
authors.forename: Ron
authors.initials: R
authors.lastname: Elber
mesh_terms: D003198:Computer Simulation; D004058:Diffusion / Q000528:radiation effects; D004574:Electromagnetic Fields; D004735:Energy Transfer; D007700:Kinetics; D008051:Lipid Bilayers / Q000737:chemistry* / Q000528:radiation effects; D008956:Models, Chemical; D008958:Models, Molecular; D010539:Permeability; D010713:Phosphatidylcholines / Q000737:chemistry* / Q000528:radiation effects; D013314:Stress, Mechanical; D014867:Water / Q000737:chemistry*
chemical_list: D008051:Lipid Bilayers; D010713:Phosphatidylcholines; D014867:Water; C017251:1,2-oleoylphosphatidylcholine
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