Quality mesh generation for molecular skin surfaces using restricted union of balls

Cheng, Harry H.; Shi, Xinwei

doi:10.1016/j.comgeo.2008.10.001

Cited by 47 publications

(32 citation statements)

References 10 publications

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“…Another widely used surface is known as solvent excluded surface (SES), which is defined as the "inward-facing" part of the probing sphere as it rolls over the molecules [18,23,36]. The molecular surface can be represented analytically by a list of seamless surface patches [4,16,43] and triangular meshes can be generated using such tools as MSMS [37].…”

Section: Introductionmentioning

confidence: 99%

“…The mesh quality should be guaranteed in molecular modeling and simulation due to the fact that "skinny" triangles often cause poor approximation quality in finite/boundary element methods [27]. The molecular mesh generation approaches mentioned above can usually capture the features of a molecule (although the definition of a feature may vary), but they have either no mesh adaptation (e.g., [16]) or very low mesh quality (e.g., [9,37]). …”

Section: Introductionmentioning

confidence: 99%

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Feature-preserving adaptive mesh generation for molecular shape modeling and simulation

Holst

McCammon

2008

Journal of Molecular Graphics and Modelling

106

122

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We describe a chain of algorithms for molecular surface and volumetric mesh generation. We take as inputs the centers and radii of all atoms of a molecule and the toolchain outputs both triangular and tetrahedral meshes that can be used for molecular shape modeling and simulation. Experiments on a number of molecules are demonstrated, showing that our methods possess several desirable properties: feature-preservation, local adaptivity, high quality, and smoothness (for surface meshes). We also demonstrate an example of molecular simulation using the finite element method and the meshes generated by our method. The approaches presented and their implementations are also applicable to other types of inputs such as 3D scalar volumes and triangular surface meshes with low quality, and hence can be used for generation/improvment of meshes in a broad range of applications.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Feature-preserving adaptive mesh generation for molecular shape modeling and simulation

Holst

McCammon

2008

Journal of Molecular Graphics and Modelling

106

122

View full text Add to dashboard Cite

show abstract

“…For example, it is smooth everywhere and, although defined using an infinite number of spheres, it can be described by a finite number of quadric surface regions. Efficient algorithms have been developed recently to triangulate the skin surface [38,39]. Besides being efficient in terms of computation time, these algorithms also generate watertight skin surface meshes (i.e., without cracks) containing good quality triangles (i.e., without small angles).…”

Section: Visualizing Biomolecular Surfacesmentioning

confidence: 99%

Visual Analysis of Biomolecular Surfaces

Natarajan

Koehl

Wang

et al. 2008

Mathematics and Visualization

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Summary. Surface models of biomolecules have become crucially important for the study and understanding of interaction between biomolecules and their environment. We argue for the need for a detailed understanding of biomolecular surfaces by describing several applications in computational and structural biology. We review methods used to model, represent, characterize, and visualize biomolecular surfaces focusing on the role that geometry and topology play in identifying features on the surface. These methods enable the development of efficient computational and visualization tools for studying the function of biomolecules.

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“…Several algorithms exist to skin a molecular model to produce a C 1 continuous surface that is tangent smooth and has high mesh quality. These methods are typically either based on Delaunay triangulation [3] or by finding the isosurface of an implicit function [5]. The work of [5] derives a special subset of skins that is piece-wise quadratic.…”

Section: Related Workmentioning

confidence: 99%

“…The skinning problem is a special case of the problem of computing the envelopes of families of quadrics, which have been investigated by Paternell [2] via the use of cyclographic maps. The problem of ball skinning appears frequently in the context of computational chemistry and molecular biology, when generating surface meshes for molecular models [3] [4] [5]. Several algorithms exist to skin a molecular model to produce a C 1 continuous surface that is tangent smooth and has high mesh quality.…”

Section: Related Workmentioning

confidence: 99%

Variational Skinning of an Ordered Set of Discrete 2D Balls

Slabaugh

Ünal

Fang

et al.

Advances in Geometric Modeling and Processing

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This is the accepted version of the paper.This version of the publication may differ from the final published version. Abstract. This paper considers the problem of computing an interpolating skin of a ordered set of discrete 2D balls. By construction, the skin is constrained to be C 1 continuous, and for each ball, it touches the ball at a point and is tangent to the ball at the point of contact. Using an energy formulation, we derive differential equations that are designed to minimize the skin's arc length, curvature, or convex combination of both. Given an initial skin, we update the skin's parametric representation using the differential equations until convergence occurs. We demonstrate the method's usefulness in generating interpolating skins of balls of different sizes and in various configurations. Permanent

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Quality mesh generation for molecular skin surfaces using restricted union of balls

Cited by 47 publications

References 10 publications

Feature-preserving adaptive mesh generation for molecular shape modeling and simulation

Feature-preserving adaptive mesh generation for molecular shape modeling and simulation

Visual Analysis of Biomolecular Surfaces

Variational Skinning of an Ordered Set of Discrete 2D Balls

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