Visual verification and analysis of cluster detection for molecular dynamics

IEEE Transactions on Visualization and Computer Graphics

Volumn 13, Issue 6, 2007, Pages 1624-1631

  Grottel, S ^a   Reina, G ^a   Vrabec, J ^a   Ertl, T ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

Author keywords

Cluster detection analysis; Evolution graph view; Glyph visualization; Molecular dynamics visualization; Out of core techniques; Time dependent scattered data

Indexed keywords

CLUSTER DETECTION ANALYSIS; EVOLUTION GRAPH VIEW; GLYPH VISUALIZATION; MOLECULAR DYNAMICS VISUALIZATION; OUT-OF-CORE TECHNIQUES; TIME DEPENDENT SCATTERED DATA;

ALGORITHMS; CLOUDS; CLUSTER ANALYSIS; CONDENSATION; DATA VISUALIZATION; DROPS; STEAM TURBINES; THERMODYNAMICS;

MOLECULAR DYNAMICS;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CLUSTER ANALYSIS; COMPUTER ASSISTED DIAGNOSIS; COMPUTER GRAPHICS; COMPUTER SIMULATION; CONFORMATION; EVALUATION; IMAGE ENHANCEMENT; METHODOLOGY; SURFACE PROPERTY; THREE DIMENSIONAL IMAGING; VALIDATION STUDY;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTER GRAPHICS; COMPUTER SIMULATION; IMAGE ENHANCEMENT; IMAGE INTERPRETATION, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; SURFACE PROPERTIES;

EID: 35948996956     PISSN: 10772626     EISSN: None     Source Type: Journal    
DOI: 10.1109/TVCG.2007.70614     Document Type: Article

References (39)

1. M. P. Allen and D. J. Tildesley. Computer Simulation of Liquids. Oxford University Press, 1987.
2. amira. http://www.amiravis.com/.
3. C. Bajaj, P. Djeu, V. Siddavanahalli, and A. Thane. Texmol: Interactive visual exploration of large flexible multi-component molecular complexes. In VIS '04: Proceedings of the conference on Visualization '04, pages 243-250. IEEE Computer Society, 2004.
4. M. Botsch, A. Wiratanaya, and L. Kobbelt. Efficient high quality rendering of point sampled geometry. In EGRW "02: Proceedings of the 13th Eurographics workshop on Rendering, pages 53-64, 2002.
5. B. Cabral and L. Leedom. Imaging vector fields using line integral convolution. In Proceedings of SIGGRAPH, pages 263-270. ACM. Press, 1993.
6. E. B. Dam, M. Koch, and M. Lillholm. Quaternions, interpolation and animation. Technical report, Department of Computer Science, University of Copenhagen, 1998.
7. W. DeLano. Pymol: An open-source molecular graphics tool. CCP4 Newsletter On Protein Crystallography, 40, 2002.
8. J. A. Fisk, M. M. Rudek, J. L. Katz, D. Beiersdorf, and H. Uchtmann. The homogeneous nucleation of cesium vapor. Atmospheric Research, 46:211-222, 1998.
9. I. Ford. Statistical mechanics of nucleation: a review. In Proceedings of the Institution of Mechanical Engineers, Part C, Journal of Mechanical Engineering Science, volume 218, pages 883-899, August 2004.
10. S. Gumhold. Splatting illuminated ellipsoids with depth correction. In Proceedings of 8th International Fall Workshop on Vision, Modelling and Visualization, pages 245-252, 2003.
11. A. Halm, L. Offen, and D. Fellner. BioBrowser: A Framework for Fast Protein Visualization. In Proceedings of EUROGRAPHICS ?IEEE VGTC Symposium on Visualization Eurovis '05, pages 287-294, 2005.
12. T. L. Hill. Molecular clusters in imperfect gases. The Journal of Chemical Physics, 23:617-622, April 1955.
13. D. Honeycutt and H. C. Andersen. Molecular dynamics study of melting and freezing of small Lennard-Jones clisters. Journal of Physics and Chemistry, 91:4950-4963, 1987.
14. M. Hopf and T. Ertl. Hierarchical Splatting of Scattered Data. In Proceedings of IEEE Visualization '03. IEEE, 2003.
15. M. Hopf, M. Luttenberger, and T. Ertl. Hierarchical Splatting of Scattered 4D Data. IEEE Computer Graphics and Applications, 24(4):64-72, 2004.
16. W. Humphrey, A. Dalke, and K. Schulten. Vmd - visual molecular dynamics. Journal of Molecular Graphics, 14:33-38, 1996.
17. V. Interrante and C. Grosch. Visualizing 3D flow. IEEE Computer Graphics and Applications, 18(4):49-53, 1998.
18. B. Jobard, G. Erlebacher, and M. Y Hussaini. Lagrangian-Eulerian Advection of Noise and Dye Textures for Unsteady Flow Visualization. IEEE Transactions on Visualization and Computer Graphics, 8(3):211-222, 2002.
19. T. Klein and T. Ertl. Illustrating Magnetic Field Lines using a Discrete Particle Model. In Workshop on Vision, Modelling, and Visualization VMV '04, 2004.
20. P. J. Kraulis. Molscript - a program, to produce both detailed and schematic picts of protein structures. Journal of Applied Crystallography, 24:946-950, 1991.
21. D. Laney, P.-T. Bremer, A. Mascarenhas, P. Miller, and V. Pascucci. Understanding the structure of the turbulent mixing layer in hydrodynamic instabilities. IEEE Trans. Vis. Comput. Graph., 12(5): 1053-1060, 2006.
22. E. Martz. Protein explorer: Easy yet powerful macromolecular visualization. Trends in Biochemical Sciences, 27:107-109, 2002. http://proteinexplorer.org.
23. N. Max. Hierarchical molecular modelling with ellipsoids. Journal of Molecular Graphics and Modelling, 23(3):233-238, 2004.
24. R. Pajarola, M. Sainz, and P. Guidotti. Confetti: Object-space point blending and splatting. IEEE Transactions on Visualization and Computer Graphics, 10(5):598-608, 2004.
25. E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt, E. C. Meng, and T. E. Ferrin. Ucsf chimera - a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13):1605-1612, 2004.
26. G. Reina and T. Ertl. Hardware-Accelerated Glyphs for Mono- and Dipoles in Molecular Dynamics Visualization. In Proceedings of EUROGRAPHICS ?IEEE VGTC Symposium on Visualization Eurovis '05, 2005.
27. L. Ren, H. Pfister, and M. Zwicker. Object Space EWA Surface Splatting: A Hardware Accelerated Approach to High Quality Point Rendering. Computer Graphics Forum, 21(3), 2002.
28. J. W. P. Schmelzer, G. S. Boltachev, and V. G. Baidakov. Is Gibbs' thermodynamic theory of heterogeneous systems really perfect? In J. W. P. Schmelzer, editor, Nucleation Theory and Applications, pages 418-446. Wiley-VCH, 2005.
29. T. Schnabel, J. Vrabec, and H. Hasse. Molecular modeling of hydrogen bonding fluids: Monomethyamine, dimethylamine, and water revised. In W. E. Nagel, W. Jäger, and M. Resch, editors, High Performance Computing in Science and Engineering '06, pages 515-525. Springer, 2006.
30. A. Sharma, A. Nakano, R. K. Kalia, P. Vashishta, S. Kodiyalam, P. Miller, W. Zhao, X. Liu, T. J. Campbell, and A. Haas. Immersive and interactive exploration of billion-atom systems. Presence, 12(1):85-95, 2003.
31. T. C. Sprenger, M. H. Gross, A. Eggenberger, and M. Kaufmann. A Framework for Physically-Based Information Visualization. In Proceedings of Eurographics Workshop on Visualization '97, pages 77-86, 1997.
32. Y Suzuki, I. Fujishiro, L. Chen, and H. Nakamura. Case Study: Hardware-Accelerated Selective LIC Volume Rendering. In Proceedings of IEEE Visualization, pages 485-488, 2002.
33. M. Tarini, P. Cignoni, and C. Montani. Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Trans. Vis. Comput. Graph., 12(5):1237-1244, 2006.
34. E. Tejada, J. Gois, L. G. Nonato, A. Castelo, and T. Ertl. Hardware-accelerated Extraction and Rendering of Point Set Surfaces. In Proceedings of EUROGRAPHICS ?IEEE VGTC Symposium on Visualization Eurovis '06, pages 21-28, 2006.
35. M. Volmer and A. Weber. Keimbildung in gesättigten Gebilden. Zeltschrift für Physikalische Chemie A, 119:277-301, 1926. (in German).
36. J. Vrabec, J. Stoll, and H. Hasse. A set of molecular models for symmetric quadrupolar fluids. Journal of Physical Chemistry B, 105:12126-12133, 2001.
37. D. Weiskopf and T. Ertl. A Hybrid Physical/Device-Space Approach for Spatio-Temporally Coherent Interactive Texture Advection on Curved Surfaces. In Proceedings of Graphics Interface 2004, pages 263-270, 2004.
38. D. Weiskopf, T. Schafhitzel, and T. Ertl. Real-Time Advection and Volumetric Illumination for the Visualization of 3D Unsteady Flow. In Proceedings of EG/IEEE TCVG Symposium on Visualization Eurovis '05, pages 13-20, 2005.
39. M. Zwicker, H. Pfister, J. van Baar, and M. Gross. Surface splatting. In SIGGRAPH '01: Proceedings of the 28th annual conference on Computer graphics and interactive techniques, pages 371-378. ACM Press, 2001.