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      Pressure Profile Calculation with Mesh Ewald Methods

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          Abstract

          The importance of calculating pressure profiles across liquid interfaces is increasingly gaining recognition, and efficient methods for the calculation of long-range contributions are fundamental in addressing systems with a large number of charges. Here, we show how to compute the local pressure contribution for mesh-based Ewald methods, retaining the typical N log N scaling as a function of the lattice nodes N. This is a considerable improvement on existing methods, which include approximating the electrostatic contribution using a large cut-off and the, much slower, Ewald calculation. As an application, we calculate the contribution to the pressure profile across the water/vapour interface, coming from different molecular layers, both including and removing the effect of thermal capillary waves. We compare the total pressure profile with the one obtained using the cutoff approximation for the calculation of the stresses, showing that the stress distribution obtained by the Harasima and Irving-Kirkwood are quite similar and shifted with respect to each other at most 0.05~nm.

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          The lateral pressure profile in membranes: a physical mechanism of general anesthesia.

          A mechanism of general anesthesia is suggested and investigated using lattice statistical thermodynamics. Bilayer membranes are characterized by large lateral stresses that vary with depth within the membrane. Incorporation of amphiphilic and other interfacially active solutes into the bilayer is predicted to increase the lateral pressure selectively near the aqueous interfaces, compensated by decreased lateral pressure toward the center of the bilayer. General anesthesia likely involves inhibition of the opening of the ion channel in a postsynaptic ligand-gated membrane protein. If channel opening increases the cross-sectional area of the protein more near the aqueous interface than in the middle of the bilayer, then the anesthetic-induced increase in lateral pressure near the interface will shift the protein conformational equilibrium to favor the closed state, since channel opening will require greater work against this higher pressure. This hypothesis provides a truly mechanistic and thermodynamic understanding of anesthesia, not just correlations of potency with structural or thermodynamic properties. Calculations yield qualitative agreement with anesthetic potency at clinical anesthetic membrane concentrations and predict the alkanol cutoff and anomalously low potencies of strongly hydrophobic molecules with little or no attraction for the aqueous interface, such as perfluorocarbons.
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            A new method for determining the interfacial molecules and characterizing the surface roughness in computer simulations. Application to the liquid-vapor interface of water.

            A new method is presented to identify the truly interfacial molecules at fluid/fluid interfaces seen at molecular resolution, a situation that regularly occurs in computer simulations. In the new method, the surface is scanned by moving a probe sphere of a given radius along a large set of test lines that are perpendicular to the plane of the interface. The molecules that are hit by the probe spheres are regarded as interfacial ones, and the position of the test spheres when they are in contact with the interfacial molecules give an estimate of the surface. The dependence of the method on various parameters, in particular, on the size of the probe sphere is discussed in detail. Based on the list of molecules identified as truly interfacial ones, two measures of the molecular scale roughness of the surface are proposed. The bivariate distribution of the lateral and normal distances of two points of the interface provides a full description of the molecular scale morphology of the surface in a statistical sense. For practical purposes two parameters related to the dependence of the average normal distance of two surface points on their lateral distance can be used. These two parameters correspond to the frequency and amplitude of the surface roughness, respectively. The new method is applied for the analysis of the molecular level structure of the liquid-vapor interface of water. As an immediate result of the application of the new method it is shown that the orientational preferences of the interfacial water molecules depend only on the local curvature of the interface, and hence the molecules located at wells of concave curvature of the rippled surface prefer the same orientations as waters located at the surface of small apolar solutes. The vast majority of the truly interfacial molecules are found to form a strongly percolating two-dimensional hydrogen bonded network at the surface, whereas no percolation is observed within the second molecular layer beyond the surface. (c) 2007 Wiley Periodicals, Inc.
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              Author and article information

              Journal
              2017-06-01
              Article
              10.1021/acs.jctc.6b00576
              1706.00305
              fcdd2b16-8a90-494f-8a04-06ea7163413d

              http://arxiv.org/licenses/nonexclusive-distrib/1.0/

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              J. Chem. Theory Comput. 2016, 12, 4509-4515
              cond-mat.soft

              Condensed matter
              Condensed matter

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