CUDA Accelerated Blobby Molecular Surface Generation

• Published in: Parallel Processing and Applied Mathematics pp. 347 - 356
• Main Authors: D’Agostino, Daniele, Decherchi, Sergio, Galizia, Antonella, Colmenares, José, Quarati, Alfonso, Rocchia, Walter, Clematis, Andrea
• Format: Book Chapter
• Language: English
• Published: Berlin, Heidelberg Springer Berlin Heidelberg 2012
• Series: Lecture Notes in Computer Science
• Subjects: Blobby Molecular Surface; GPU Computing; Parallel Molecular Surface Generation
• ISBN: 3642314635; 9783642314636
• ISSN: 0302-9743; 1611-3349
• DOI: 10.1007/978-3-642-31464-3_35

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.