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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Vydané v:Journal of computational physics Ročník 322; s. 760 - 782
Hlavní autori: Quan, Chaoyu, Stamm, Benjamin
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: Elsevier Inc 01.10.2016
Elsevier
Predmet:
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
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Popis
Shrnutí: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