Mathematical analysis and calculation of molecular surfaces

In this article we derive a complete characterization of the Solvent Excluded Surface (SES) for molecular systems including a complete characterization of singularities of the surface. The theory is based on an implicit representation of the SES, which, in turn, is based on the signed distance funct...

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Bibliographic Details
Published in:Journal of computational physics Vol. 322; pp. 760 - 782
Main Authors: Quan, Chaoyu, Stamm, Benjamin
Format: Journal Article
Language:English
Published: Elsevier Inc 01.10.2016
Elsevier
Subjects:
Chemical Sciences
Constructive algorithm
Mathematical description
Mathematical Physics
Mathematics
Molecular surface
or physical chemistry
Solvation models
Solvent excluded surface
Theoretical and
Mathematical description
Molecular surface
Constructive algorithm
Solvent excluded surface
Solvation models
solvent excluded surface
mathematical description
constructive algorithm
solvation models
ISSN:0021-9991, 1090-2716
Online Access:Get full text
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Summary:In this article we derive a complete characterization of the Solvent Excluded Surface (SES) for molecular systems including a complete characterization of singularities of the surface. The theory is based on an implicit representation of the SES, which, in turn, is based on the signed distance function to the Solvent Accessible Surface (SAS). All proofs are constructive so that the theory allows for efficient algorithms in order to compute the area of the SES and the volume of the SES-cavity, or to visualize the surface. Further, we propose to refine the notion of SAS and SES in order to take inner holes in a solute molecule into account or not.
ISSN:0021-9991
1090-2716
DOI:10.1016/j.jcp.2016.07.007