The weighted-volume derivative of a space-filling diagram

被引：47

作者：

Edelsbrunner, H

Koehl, P ^{[1
]}

机构：

[1] Stanford Univ, Dept Biol Struct, Stanford, CA 94305 USA

[2] Duke Univ, Dept Comp Sci, Durham, NC 27708 USA

[3] Raindrop Geomag, Res Triangle Pk, NC 27709 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2003年 / 100卷 / 05期

关键词：

molecular dynamics; implicit solvent models; spheres; Delaumay triangulation;

D O I：

10.1073/pnas.0537830100

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Computing the volume occupied by individual atoms in macromolecular structures has been the subject of research for several decades. This interest has grown in the recent years, because weighted volumes are widely used in implicit solvent models. Applications of the latter in molecular mechanics simulations require that the derivatives of these weighted volumes be known. In this article, we give a formula for the volume derivative of a molecule modeled as a space-filling diagram made up of balls in motion. The formula is given in terms of the weights, radii, and distances between the centers as well as the sizes of the facets of the power diagram restricted to the space-filling diagram. Special attention is given to the detection and treatment of singularities as well as discontinuities of the derivative.

引用

页码：2203 / 2208

页数：6

共 45 条

[1] Generalized born models of macromolecular solvation effects [J].