Atomistic visualization of mesoscopic whole-cell simulations using ray-casted instancing

Computer Graphics Forum

Volumn 32, Issue 8, 2013, Pages 195-206

  Falk, Martin ^a   Krone, Michael ^a   Ertl, Thomas ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

Author keywords

atomic representation; I.3.6 Computer Graphics : Methodology and Techniques Graphics data structures and data types; I.3.7 Computer Graphics : Three Dimensional Graphics and Realism Raytracing; J.3 Computer Applications : Life and Medical Sciences Biology and genetics; protein data base; ray casting; visualization

Indexed keywords

ACCELERATION CONTROL; ATOMS; CELLS; COMPUTER GRAPHICS; COMPUTER GRAPHICS EQUIPMENT; CYTOLOGY; DATA VISUALIZATION; FLOW VISUALIZATION; GRAPHICS PROCESSING UNIT; PROTEINS; RENDERING (COMPUTER GRAPHICS); SUPERCONDUCTING MATERIALS; VISUALIZATION;

ATOMIC REPRESENTATION; I.3.6 [ COMPUTER GRAPHICS]: METHODOLOGY AND TECHNIQUES - GRAPHICS DATA STRUCTURES AND DATA TYPES; I.3.7 [COMPUTER GRAPHICS]: THREE-DIMENSIONAL GRAPHICS AND REALISM - RAYTRACING; LIFE AND MEDICAL SCIENCES-BIOLOGY AND GENETICS; PROTEIN DATA; RAY CASTING;

THREE DIMENSIONAL COMPUTER GRAPHICS;

EID: 84890949318     PISSN: 01677055     EISSN: 14678659     Source Type: Journal    
DOI: 10.1111/cgf.12197     Document Type: Article

References (33)

1. Akenine-Möller T.,: Fast 3D triangle-box overlap testing. Journal of Graphics Tools 6, 1 (2001), 29-33.
2. Amanatides J., Woo A.,: A fast voxel traversal algorithm for ray tracing. In Eurographics (Amsterdam, The Netherlands, 1987), pp. 3-10.
3. Berman H., Westbrook J., Feng Z., Gilliland G., Bhat T., Weissig H., Shindyalov I., Bourne P.,: The protein data bank. Nucleic Acids Research 28 (2000), 235-242. http://www.rcsb.org/.
4. Falk M., Krone M., Ertl T.,: Atomistic visualization of mesoscopic whole-cell simulations. In Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) (Norrköping, Sweden, 2012), vol. 2, pp. 123-130.
5. Falk M., Klann M., Reuss M., Ertl T.,: Visualization of signal transduction processes in the crowded environment of the cell. In IEEE Pacific Visualization Symposium (PacificVis) (Beijing, China, 2009), pp. 169-176.
6. Falk M., Ott M., Ertl T., Klann M., Koeppl H.,: Parallelized agent-based simulation on CPU and graphics hardware for spatial and stochastic models in biology. In International Conference on Computational Methods in Systems Biology (CMSB 2011) (Paris, France, 2011), pp. 73-82.
7. Goodsell D.,: Molecule of the month. http://www.rcsb.org/pdb/motm.do (Online, February 2013).
8. Grottel S., Reina G., Dachsbacher C., Ertl T.,: Coherent culling and shading for large molecular dynamics visualization. Computer Graphics Forum 29 (2010), 953-962.
9. Grottel S., Reina G., Ertl T.,: Optimized data transfer for time-dependent, GPU-based glyphs. In IEEE Pacific Visualization Symposium (PacificVis) (Beijing, China, 2009), pp. 65-72.
10. Grottel S., Reina G., Zauner T., Hilfer R., Ertl T.,: Particle-based rendering for porous media. In Annual SIGRAD Conference (Västerås, Sweden, 2010), pp. 45-51.
11. Gumhold S.,: Splatting illuminated ellipsoids with depth correction. In International Workshop on Vision, Modeling, and Visualization (Munich, Germany, 2003), pp. 245-252.
12. Humphrey W., Dalke A., Schulten K.,: VMD-visual molecular dynamics. Journal of Molecular Graphics 14 (1996), 33-38.
13. Holmes K. C., Popp D., Gebhard W., Kabsch W.,: Atomic model of the actin filament. Nature 347, 6288 (1990), 44-49.
14. Hadwiger M., Sigg C., Scharsach H., Bühler K., Gross M. H.,: Real-time ray-casting and advanced shading of discrete isosurfaces. Computer Graphics Forum (2005), vol. 24, pp. 303-312.
15. 7. Charles River Media (Boston, MA, United States, 2009), pp. 413-424.
16. Krone M., Stone J. E., Ertl T., Schulten K.,: Fast visualization of Gaussian density surfaces for molecular dynamics and particle system trajectories. In EuroVis Short Papers (EuroVis, 2012), vol. 1, pp. 67-71.
17. Krüger J., Westermann R.,: Acceleration techniques for GPU-based volume rendering. In IEEE Visualization (Seattle, WA, United States, 2003), pp. 287-292.
18. Lindow N., Baum D., Hege H.-C.,: Interactive rendering of materials and biological structures on atomic and nanoscopic scale. Computer Graphics Forum 31, 3 (2012), 1325-1334.
19. Lodish H., Berk A., Kaiser C. A., Krieger M., Scott M. P., Bretscher A., Ploegh H., Matsudaira P.,: Molecular Cell Biology (sixth edition)., W. H. Freeman, New York, United States, 2007.
20. Lagae A., Dutré P.,: Compact, fast and robust grids for ray tracing. Computer Graphics Forum 27, 4 (2008), 1235-1244.
21. Law C. C., Henderson A., Ahrens J.,: An application architecture for large data visualization: A case study. In IEEE Symposium on Parallel and Large-Data Visualization and Graphics (San Diego, CA, United States, 2001), pp. 125-128.
22. Laine S., Karras T.,: Efficient sparse voxel octrees. In ACM SIGGRAPH 2010 Symposium on Interactive 3D Graphics and Games (Los Angeles, CA, United States, 2010), pp. 55-63.
23. Lampe O. D., Viola I., Reuter N., Hauser H.,: Two-level approach to efficient visualization of protein dynamics. IEEE Transactions on Visualization and Computer Graphics 13, 6 (2007), 1616-1623.
24. Möller T., Trumbore B.,: Fast, minimum storage ray-triangle intersection. Journal of Graphics Tools 2, 1 (1997), 21-28.
25. Palsson B.,: The challenges of in silico biology. Nature Biotechnolgy 18, 11 (2000), 1147-1150.
26. Potmesil M., Chakravarty I.,: A lens and aperture camera model for synthetic image generation. In Proceedings of SIGGRAPH 1981, Computer Graphics 15, 3 (1981), 297-305.
27. Pogson M., Smallwood R., Qwarnstrom E., Holcombe M.,: Formal agent-based modelling of intracellular chemical interactions. Biosystems 85, 1 (2006), 37-45.
28. Shaw D. E., Maragakis P., Lindorff-Larsen K., Piana S., Dror R. O., Eastwood M. P., Bank J. A., Jumper J. M., Salmon J. K., Shan Y., Wriggers W.,: Atomic-level characterization of the structural dynamics of proteins. Science 330, 6002 (2010), 341-346.
29. Shumskiy V., Parshin A.,: GPU ray tracing-comparative study of ray-triangle intersection algorithms. In International Conference on Computer Graphics and Vision (Warsaw, Poland, 2012).
30. Saito T., Takahashi T.,: Comprehensible rendering of 3-D shapes. In Proceedings of SIGGRAPH, Computer Graphics 24, 4 (1990), 197-206.
31. Tarini M., Cignoni P., Montani C.,: Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Transactions on Visualization and Computer Graphics 12, 5 (2006), 1237-1244.
32. Wald I.,: Realtime Ray Tracing and Interactive Global Illumination. PhD thesis, Computer Graphics Group, Saarland University, 2004.
33. Wand M., Fischer M., Peter I., Meyer auf der Heide F., Straßer W.,: The randomized z-buffer algorithm: Interactive rendering of highly complex scenes. In ACM SIGGRAPH Computer Graphics and Interactive Techniques (Los Angeles, CA, United States, 2001), pp. 361-370.