Graphics processing unit-based triangulations of Blinn molecular surfaces

Concurrency and Computation: Practice and Experience

Volumn 23, Issue 17, 2011, Pages 2280-2291

  Dias, Sérgio E D ^a   Gomes, Abel J P ^a  

^a UNIVERSITY OF BEIRA INTERIOR   (Portugal)

Author keywords

Blinn surfaces; CUDA; molecular surfaces; OpenCL; triangulations

Indexed keywords

COMPUTER GRAPHICS; COMPUTER GRAPHICS EQUIPMENT; PROGRAM PROCESSORS; PROTEINS; TRIANGULATION;

CUDA; GEOMETRIC STRUCTURE; GRAPHICS PROCESSING; MARCHING CUBES ALGORITHM; MOLECULAR SURFACES; OPENCL; PERFORMANCE ANALYSIS; TRIANGULATION ALGORITHMS;

GRAPHICS PROCESSING UNIT;

EID: 80054939748     PISSN: 15320626     EISSN: 15320634     Source Type: Journal    
DOI: 10.1002/cpe.1783     Document Type: Article

References (19)

1. Lee B, Richards F,. The interpretation of protein structures: estimation of static accessibility. Journal of Molecular Biology 1971; 55: 379-380.
2. Connolly M,. Solvent-accessible surfaces of proteins and nucleic acids. Science 1983; 221: 709-713.
3. Richards F,. Areas, volumes, packing, and protein structure. Annual Review of Biophysics and Bioengineering 1977; 6: 151-176.
4. Connolly M,. Analytical molecular surface calculation. Journal of Applied Crystallography 1983; 16: 548-558.
5. Vorobjev Y, Hermans J,. SIMS: Computation of a smooth invariant molecular surface. Biophysical Journal 1997; 73: 722-732. (Pubitemid 27337607)
6. Blinn J,. A generalization of algebraic surface drawing. ACM Transactions on Graphics 1982; 1: 235-256.
7. Raposo A, Queiroz J, et al,. Triangulation of molecular surfaces using an isosurface continuation algorithm. In Proceedings of the 2009 International Conference on Computational Science and Its Applications (ICCSA'2009). IEEE Press, 2009; 145-153.
8. Dias S, Bora K, et al,. CUDA-based triangulations of convolution molecular surfaces. In Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing, Workshop on Emerging Computational Methods for Life Sciences (ECMLS'2010). ACM Press, 2010; 531-540.
9. Akkiraju N, Edelsbrunner H,. Triangulating the surface of a molecule. Discrete Applied Mathematics 1996; 71: 5-22. (Pubitemid 126391769)
10. Newman T, Byrd J, et al,. High performance SIMD marching cubes isosurface extraction on commodity computers. Computers & Graphics 2004; 28: 213-233.
11. Lorensen W, Cline H,. Marching cubes: a high resolution 3D surface construction algorithm. ACM SIGGRAPH Computer Graphics 1987; 21: 163-169. (Pubitemid 18521954)
12. Lewiner T, Lopes H, et al,. Efficient implementation of marching cubes' cases with topological guarantees. Journal of Graphics, GPU, and Game Tools 2003; 8: 1-15.
13. D'Agostino D, Merelli I, et al,. A parallel workflow for the reconstruction of molecular surfaces. In Advances in Parallel Computing, Vol. 15. IOS Press, 2008; 147-154.
14. Geiss R,. Generating complex procedural terrains using the GPU. In GPU Gems 3, Nguyen H, (ed.). Addison-Wesley Professional: Upper Saddle River, NJ, 2007.
15. Uralsky Y,. DX 10: Pratical metaballs and implicit surfaces. In Game Developers Conference, 2006.
16. Dyken C, Ziegler G, et al,. High-speed marching cubes using histopyramids. Computer Graphics Forum 2008; 27: 2028-2039.
17. Bloomenthal J, Shoemake K,. Convolution surfaces. Computer Graphics 1991; 25: 251-256.
18. Gomes A, Voiculescu I, et al,. Implicit Curves and Surfaces: Mathematics, Data Structures and Algorithms. Springer-Verlag London, Inc.; 2009.
19. Harris M, Sengupta S, et al,. Parallel prefix sum scan with CUDA. In GPU Gems 3, Nguyen H, (ed.). Addison-Wesley Professional: Upper Saddle River, NJ, 2007.