CUDA accelerated blobby molecular surface generation

Authors:
Daniele D'Agostino;Sergio Decherchi;Antonella Galizia;José Colmenares;Alfonso Quarati;Walter Rocchia;Andrea Clematis
Affiliations:
Institute for Applied Mathematics and Information Technologies, National Research Council of Italy, Genoa, Italy;Department of Drug Discovery and Development, Italian Institute of Technology, Genoa, Italy;Institute for Applied Mathematics and Information Technologies, National Research Council of Italy, Genoa, Italy;Department of Drug Discovery and Development, Italian Institute of Technology, Genoa, Italy;Institute for Applied Mathematics and Information Technologies, National Research Council of Italy, Genoa, Italy;Department of Drug Discovery and Development, Italian Institute of Technology, Genoa, Italy;Institute for Applied Mathematics and Information Technologies, National Research Council of Italy, Genoa, Italy
Venue:
PPAM'11 Proceedings of the 9th international conference on Parallel Processing and Applied Mathematics - Volume Part I
Year:
2011

Citing 6
Cited 0

Marching cubes: A high resolution 3D surface construction algorithm

SIGGRAPH '87 Proceedings of the 14th annual conference on Computer graphics and interactive techniques
Advanced animation and rendering techniques

Advanced animation and rendering techniques
A Generalization of Algebraic Surface Drawing

ACM Transactions on Graphics (TOG)
Quality meshing of implicit solvation models of biomolecular structures

Computer Aided Geometric Design - Special issue: Applications of geometric modeling in the life sciences
CUDA-based triangulations of convolution molecular surfaces

Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing
Accelerated visualization of dynamic molecular surfaces

EuroVis'10 Proceedings of the 12th Eurographics / IEEE - VGTC conference on Visualization

Quantified Score

Hi-index	0.00

Visualization

Abstract

A proper and efficient representation of molecular surfaces is an important issue in biophysics from several view points. Molecular surfaces indeed are used for different aims, in particular for visualization, as support tools for biologists, computation, in electrostatics problems involving implicit solvents (e.g. while solving the Poisson-Boltzmann equation) or for molecular dynamics simulations. This problem has been recognized in the literature, resulting in a multitude of algorithms that differ on the basis of the adopted representation and the approach/ technology used. Among several molecular surface definitions, the Blobby surface is particularly appealing from the computational and the graphics point of view. In the paper we describe an efficient software component able to produce high-resolution Blobby surfaces for very large molecules using the CUDA architecture. Experimental results show a speedup of 35.4 considering a molecule of 90,898 atoms and a resulting mesh of 168 million triangles.