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      Origin of 1/ f noise in hydration dynamics on lipid membrane surfaces

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          Abstract

          Water molecules on lipid membrane surfaces are known to contribute to membrane stability by connecting lipid molecules and acting as a water bridge. Although water structures and diffusivities near the membrane surfaces have been extensively studied, hydration dynamics on the surfaces has remained an open question. Here we investigate residence time statistics of water molecules on the surface of lipid membranes using all-atom molecular dynamics simulations. We show that hydration dynamics on the lipid membranes exhibits 1/ f noise. Constructing a dichotomous process for the hydration dynamics, we find that residence times in each state follow a power-law with exponential cutoff and that the process can be regarded as a correlated renewal process where interoccurrence times are correlated. The results imply that the origin of the 1/ f noise in hydration dynamics on the membrane surfaces is a combination of a power-law distribution with cutoff of interoccurrence times of switching events and a long-term correlation between the interoccurrence times. These results suggest that the 1/ f noise attributed to the correlated renewal process may contribute to the stability of the hydration layers and lipid membranes.

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          A molecular jump mechanism of water reorientation.

          Despite long study, a molecular picture of the mechanism of water reorientation is still lacking. Using numerical simulations, we find support for a pathway in which the rotating water molecule breaks a hydrogen bond (H-bond) with an overcoordinated first-shell neighbor to form an H-bond with an undercoordinated second-shell neighbor. The H-bond cleavage and the molecular reorientation occur concertedly and not successively as usually considered. This water reorientation mechanism involves large-amplitude angular jumps, rather than the commonly accepted sequence of small diffusive steps, and therefore calls for reinterpretation of many experimental data wherein water rotational relaxation is assumed to be diffusive.
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            Protein conformational dynamics probed by single-molecule electron transfer.

            Electron transfer is used as a probe for angstrom-scale structural changes in single protein molecules. In a flavin reductase, the fluorescence of flavin is quenched by a nearby tyrosine residue by means of photo-induced electron transfer. By probing the fluorescence lifetime of the single flavin on a photon-by-photon basis, we were able to observe the variation of flavin-tyrosine distance over time. We could then determine the potential of mean force between the flavin and the tyrosine, and a correlation analysis revealed conformational fluctuation at multiple time scales spanning from hundreds of microseconds to seconds. This phenomenon suggests the existence of multiple interconverting conformers related to the fluctuating catalytic reactivity.
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              Random Time-Scale Invariant Diffusion and Transport Coefficients

              Single particle tracking of mRNA molecules and lipid granules in living cells shows that the time averaged mean squared displacement \(\overline{\delta^2}\) of individual particles remains a random variable while indicating that the particle motion is subdiffusive. We investigate this type of ergodicity breaking within the continuous time random walk model and show that \(\overline{\delta^2}\) differs from the corresponding ensemble average. In particular we derive the distribution for the fluctuations of the random variable \(\overline{\delta^2}\). Similarly we quantify the response to a constant external field, revealing a generalization of the Einstein relation. Consequences for the interpretation of single molecule tracking data are discussed.
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                Author and article information

                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group
                2045-2322
                06 March 2015
                2015
                : 5
                : 8876
                Affiliations
                [1 ]Department of Mechanical Engineering, Keio University , 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
                [2 ]Department of Pharmacology, School of Medicine, Keio University , 35 Shinanomachi, Shinju-ku, Tokyo 160-8582, Japan
                Author notes
                Article
                srep08876
                10.1038/srep08876
                4351557
                25743377
                07e65719-a4d6-4580-be2b-8b20b2549d8f
                Copyright © 2015, Macmillan Publishers Limited. All rights reserved

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder in order to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 23 October 2014
                : 09 February 2015
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