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Solvent diffusion outside macromolecular surfaces
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical & Computational Biophysics. (Theoretical & Computational Biophysics)ORCID iD: 0000-0002-2734-2794
KTH, School of Engineering Sciences (SCI), Theoretical Physics, Theoretical Biological Physics.ORCID iD: 0000-0002-7448-4664
1998 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 57, 791-796 p.Article in journal (Refereed) Published
Abstract [en]

The effect of the inhomogeneous environment upon solvent molecules close to a macromolecular surface is evaluated from a molecular-dynamics simulation of a protein, myoglobin, in water solution. The simulation is analyzed in terms of a mean-field potential from the protein upon the water molecules and spatially varying translational diffusion coefficients for solvent molecules in directions parallel and perpendicular to the protein surface. The diffusion coefficients can be obtained from the slope of the average-square displacements vs time, as well as from the integral of the velocity autocorrelation functions. It is shown that the former procedure gives a lot of ambiguities due to the variation of the slope of the curve with time. The latter, however, after analytic correction for the contribution from algebraic long-time tails, furnish a much more reliable alternative.

Place, publisher, year, edition, pages
1998. Vol. 57, 791-796 p.
National Category
Theoretical Chemistry
Identifiers
URN: urn:nbn:se:kth:diva-82564DOI: 10.1103/PhysRevE.57.791OAI: oai:DiVA.org:kth-82564DiVA: diva2:498362
Note

NR 20140805

Available from: 2012-02-12 Created: 2012-02-12 Last updated: 2017-12-07Bibliographically approved

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Lindahl, ErikEdholm, Olle

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