Dynamic maintenance and visualization of molecular surfaces

Discrete Applied Mathematics

Volumn 127, Issue 1 SPEC., 2003, Pages 23-51

  Bajaj, Chandrajit L ^a   Pascucci, Valerio ^a   Shamir, Ariel ^a   Holt, Robert J ^b   Netravali, Arun N ^b  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b LUCENT TECHNOLOGIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION PROGRAMMING INTERFACES (API); COMPUTER GRAPHICS; EFFICIENCY; MOLECULAR MODELING; VISUALIZATION;

BOUNDARY REPRESENTATIONS; DYNAMIC MAINTENANCES; GEOMETRIC DATA STRUCTURES; MODELING ENVIRONMENTS; MOLECULAR CONFIGURATIONS; NON-UNIFORM RATIONAL B-SPLINES; STANDARD SOLID MODEL; VISUALIZATION OF MOLECULAR SURFACES;

TOPOLOGY;

EID: 0037375002     PISSN: 0166218X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0166-218X(02)00283-4     Document Type: Article

References (54)

1. N. Akkiraju, and H. Edelsbrunner Triangulating the surface of a molecule Discrete Appl. Math. 71 1996 5 22
2. G. Albers, T. Roos, Voronoi diagrams of moving points in higher dimensional spaces, in: Proceedings of the Third Scand. Workshop Algorithm Theory, Lecture Notes in Computer Science, Vol. 621, Springer, Berlin, 1992, pp. 399-409.
3. F. Aurenhammer Power diagrams: Properties, algorithms, and applications SIAM J. Comput. 16 1 1987 78 96
4. C.L. Bajaj, W.J. Bouma, Dynamic Voronoi diagrams and Delaunay triangulations, in: Proceedings of the Second Canadian Conference on Computational Geometry, 1990, pp. 273-277.
5. C.L. Bajaj, H.Y. Lee, R. Merkert, V. Pascucci, NURBS based B-rep models for macromolecules and their properties, in: Proceedings of the Fourth Symposium on Solid Modeling and Applications, New York, May 1997, ACM Press, New York, 1997, pp. 217-228.
6. C.L. Bajaj, V. Pascucci, Splitting a complex of convex polytopes in any dimension, in: Proceedings of the 12th Annual Symposium On Computational Geometry (ISG '96), New York, May 1996, ACM Press, New York, 1996, pp. 88-97.
7. C.L. Bajaj, V. Pascucci, Wrapping the Voronoi diagram: a constructive approach to duality, Technical Report, University of Texas at Austin, 1997.
8. C.L. Bajaj, V. Pascucci, A. Shamir, R.J. Holt, A.N. Netravali, Multiresolution molecular shapes, Technical Report 99-42, TICAM, University of Texas at Austin, 1999.
9. J.F. Blinn A generalization of algebraic surface drawing ACM Trans. Graphics 1 3 1982 235 256
10. J. Bloomenthal, with C. Bajaj, J. Blinn, M.-P. Cani-Gascuel, A. Rockwood, B. Wyvill, G. Wyvill (Eds.), Introduction to Implicit Surfaces, Morgan Kaufmann Publishers, San Francisco, 1997.
11. T.M.Y. Chan, J. Snoeyink, C.-K. Yap, Output-sensitive construction of polytopes in four dimensions and clipped Voronoi diagrams in three, in: Proceedings of the Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, San Francisco, CA, January 1995, pp. 282-291.
12. B. Chazelle An optimal convex hull algorithm in any fixed dimension Discrete Comput. Geom. 10 1993 377 409
13. 1 Voronoi diagram of moving points Comput. Geom. Theory Appl. 7 1997 73 80
14. M.L. Connolly Analytical molecular surface calculation J. Appl. Crystallogr. 16 1983 548 558
15. M.L. Connolly Solvent-accessible surfaces of proteins and nucleic acids Science 221 1983 709 713
16. M.L. Connolly, T.J. O'Donnell, and S. Warde Special issue on molecular surfaces Network Sci. 2 4 1996
17. M.L. Connolly, Molecular surfaces: a review, Network Sci. (1996).
18. T.J. O'Donnell, The scientific and artistic uses of molecular surfaces, Network Sci. (1996).
19. S. Warde, Molecular modeling and simulation of surfaces, Network Sci. (1996); http://www.netsci.org/Science/Compchem/feature{14,15,16}.html.
20. C.J.A. Delfinado, and H. Edelsbrunner An incremental algorithm for Betti numbers of simplicial complexes on the 3-sphere Comput. Aided Geom. Design 12 7 1995 771 784
21. M. Desbrun, M.-P. Gascuel, Animating soft substances with implicit surfaces, in: R. Cook (Ed.), SIGGRAPH 95 Conference Proceedings, Annual Conference Series, Los Angeles, August 1995, Addison-Wesley, Reading, MA, 1995, pp. 287-290.
22. H. Edelsbrunner Algorithms in Combinatorial Geometry EATCS Monographs on Theoretical Computer Science Vol. 10 1987 Springer Heidelberg, West Germany
23. H. Edelsbrunner, Smooth surfaces for multi-scale shape representation, in: Proceedings of the 15th Conference on Found. Softw. Tech. Theoret. Comput. Sci., Lecture Notes in Computer Science, Vol. 1026, Springer, Berlin, 1995, pp. 391-412.
24. H. Edelsbrunner The union of balls and its dual shape Discrete Comput. Geom. 13 3-4 1995 415 440
25. H. Edelsbrunner Deformable smooth surface design Discrete Comput. Geom. 21 1999 87 115
26. H. Edelsbrunner, M. Facello, J. Liang, On the definition and the construction of pockets in macromolecules, Report UIUCDCS-R-95-1935, University of Illinois Urbana-Champaign, 1995.
27. H. Edelsbrunner, D.G. Kirkpatrick, and R. Seidel On the shape of a set of points in the plane IEEE Trans. Inform. Theory IT-29 1983 551 559
28. H. Edelsbrunner, and E.P. Mücke Three-dimensional alpha shapes ACM Trans. Graphics 13 1 1994 43 72
29. H. Edelsbrunner, and N.R. Shah Incremental topological flipping works for regular triangulations Algorithmica 15 1996 223 241
30. M.A. Facello, Geometric techniques for molecular shape analysis, Ph.D. Thesis, University of Illinois, 1996; Department of Computer Science, Technical Report # 1967.
31. J.J. Fu, and R.C.T. Lee Voronoi diagrams of moving points in the plane Internat. J. Comput. Geom. Appl. 1 1 1991 23 32
32. T. Fujita, K. Hirota, and K. Murakami Representation of splashing water using metaball model Fujitsu 41 2 1990 159 165 (in Japanese)
33. G. Graves The magic of metaballs Comput. Graphics World 16 5 1993 27 32
34. L. Guibas, J.S.B. Mitchell, T. Roos, Voronoi diagrams of moving points in the plane, in: Proceedings of the 17th International Workshop on Graph-Theoret. Concepts Comput. Sci., Lecture Notes in Computer Science, Vol. 570, Springer, Berlin, 1991, pp. 113-125.
35. P.M. Hubbard Approximating polyhedra with spheres for time-critical collision detection ACM Trans. Graphics 15 3 1996 179 210
36. H. Imai, M. Iri, and K. Murota Voronoi diagram in the Laguerre geometry and its applications SIAM J. Comput. 14 1985 93 100
37. S. Krishnan, D. Manocha, A. Narkhede, Representation and evaluation of boolean combinations of NURBS solids, in: Proceedings of the Fifth MSI-Stony Brook Workshop on Computational Geometry, Stony Brook, October 1995.
38. S. Kumar, D. Manocha, and A. Lastra Interactive display of large-scale NURBS models IEEE Trans. Visualization Comput. Graphics 2 4 1996 323 336
39. B. Lee, and F.M. Richards The interpretation of protein structures: estimation of static accessibility J. Appl. Crystallogr. 55 1971 379 400
40. N.L. Max Computer representation of molecular surfaces IEEE Comput. Graphics Appl. 3 5 1983 21 29
41. H. Nishimura, M. Hirai, T. Kawai, T. Kawata, I. Shirakawa, and K. Omura Object modeling by distribution function and a method of image generation Trans. IECE Jpn, Part D J68-D 4 1985 718 725
42. T. Nishita, E. Nakamae, A method for displaying metaballs by using Bézier clipping, in: Computer Graphics Forum, Vol. 13, Eurographics, Eurographics '94 Conference issue, ed. P. Wisskirchen, Basil Blackwell Ltd, Oxford, 1994, pp. 271-280.
43. T. Roos Voronoi diagrams over dynamic scenes Discrete Applied Mathematics 43 3 1993 243 259
44. T. Roos New upper bounds on Voronoi diagrams of moving points Nordic J. Comput. 4 2 1997 167 171
45. M.F. Sanner, and A.J. Olson Reduced surface: an efficient way to compute molecule surfaces Biopolymers 38 1996 305 320
46. M.F. Sanner, A.J. Olson, Real time surface reconstruction for moving molecular fragments, in: Proceedings of the Pacific Symposium on Biocomputing '97, Maui, Hawaii, January 1997.
47. M.F. Sanner, A.J. Olson, J.C. Spehner, Fast and robust computation of molecular surfaces, in: Proceedings of the 11th Annual ACM Symposium on Computational Geometry, 1995, pp. C6-C7.
48. D. Terzopoulos, and H. Qin Dynamic NURBS with geometric constraints for interactive sculpting ACM Trans. Graphics 13 2 1994 103 136
49. A. Varshney, and F.P. Brooks Jr. Fast analytical computation of Richard's smooth molecular surface G.M. Nielson, D. Bergeron, Proceedings of the Visualization '93 Conference, San Jose, CA, October 1993 1993 IEEE Computer Society Press Silver Spring, MD 300 307
50. R. Voorintholt, M.T. Kosters, and G. Vegter A very fast program for visualizing protein surfaces, channels and cavities J. Mol. Graphics 7 1989 243 245
51. J. Wernecke The Inventor Mentor 1994 Addison-Wesley Reading, MA
52. B. Wyvill, C. McPheeters, and G. Wyvill Animating soft objects Visual Comput. 2 4 1986 235 242
53. B. Wyvill, C. McPheeters, and G. Wyvill Data structure for soft objects Visual Comput. 2 4 1986 227 234
54. S. Yoshimoto Ballerinas generated by a personal computer J. Visualization Comput. Animation 3 2 1992 55 90