Abstract
The solvent-excluded surface (SES) is a popular molecular representation that gives the boundary of the molecular volume with respect to a specific solvent. SESs depict which areas of a molecule are accessible by a specific solvent, which is represented as a spherical probe. Despite the popularity of SESs, their generation is still a compute-intensive process, which is often performed in a preprocessing stage prior to the actual rendering (except for small models). For dynamic data or varying probe radii, however, such a preprocessing is not feasible as it prevents interactive visual analysis. Thus, we present a novel approach for the on-the-fly generation of SESs, a highly parallelizable, grid-based algorithm where the SES is rendered using ray-marching. By exploiting modern GPUs, we are able to rapidly generate SESs directly within the mapping stage of the visualization pipeline. Our algorithm can be applied to large time-varying molecules and is scalable, as it can progressively refine the SES if GPU capabilities are insufficient. In this paper, we show how our algorithm is realized and how smooth transitions are achieved during progressive refinement. We further show visual results obtained from real-world data and discuss the performance obtained, which improves upon previous techniques in both the size of the molecules that can be handled and the resulting frame rate.
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Behley, J., Steinhage, V., Cremers, A.B.: Efficient radius neighbor search in three-dimensional point clouds. In: 2015 IEEE International Conference on Robotics and Automation (ICRA), pp. 3625–3630 (2015)
Blinn, J.F.: A generalization of algebraic surface drawing. ACM Trans. Graph. 1(3), 235–256 (1982)
Can, T., Chen, C.I., Wang, Y.F.: Efficient molecular surface generation using level-set methods. J. Mol. Graph. Model. 25(4), 442–454 (2006)
Connolly, M.L.: Analytical molecular surface calculation. J. Appl. Crystallogr. 16(5), 548–558 (1983)
Edelsbrunner, H., Mücke, E.P.: Three-dimensional alpha shapes. ACM Trans. Graph. 13(1), 43–72 (1994)
Green, S.: White paper: CUDA particles. Technical reports (2007)
Greer, J., Bush, B.L.: Macromolecular shape and surface maps by solvent exclusion. Proc. Natl. Acad. Sci. 75, 303–307 (1978)
Grottel, S., Krone, M., Müller, C., Reina, G., Ertl, T.: MegaMol—a prototyping framework for particle-based visualization. IEEE Trans. Vis. Comput. Graph. 21(2), 201–214 (2015)
Hadwiger, M., Sigg, C., Scharsach, H., Bhler, K., Gross, M.: Real-time ray-casting and advanced shading of discrete isosurfaces. Comput. Graph. Forum 24(3), 303–312 (2005)
Hermosilla, P., Guallar, V., Vinacua, A., Vázquez, P.: High quality illustrative effects for molecular rendering. Comput. Graph. 24, 113–120 (2015)
Hoetzlein, R.C.: Fast fixed-radius nearest neighbors: interactive million-particle fluids. In: GPU Technology Conference (2014)
Jurcik, A., Parulek, J., Sochor, J., Kozlikova, B.: Accelerated visualization of transparent molecular surfaces in molecular dynamics. In: IEEE Pacific Visualization Symposium, pp. 112–119 (2016)
Kozlíková, B., Krone, M., Lindow, N., Falk, M., Baaden, M., Baum, D., Viola, I., Parulek, J., Hege, H.C.: Visualization of molecular structure: state of the art revisited. Comput. Graph. Forum (2016)
Krone, M., Bidmon, K., Ertl, T.: Interactive visualization of molecular surface dynamics. IEEE Trans. Vis. Comput. Graph. 15(6), 1391–1398 (2009)
Krone, M., Grottel, S., Ertl, T.: Parallel contour-buildup algorithm for the molecular surface. In: IEEE Symposium on Biological Data Visualization, pp. 17–22 (2011)
Krone, M., Stone, J.E., Ertl, T., Schulten, K.: Fast visualization of gaussian density surfaces for molecular dynamics and particle system trajectories. EuroVis-Short Pap. 1, 67–71 (2012)
Lindow, N., Baum, D., Hege, H.C.: Ligand excluded surface: a new type of molecular surface. IEEE Trans. Vis. Comput. Graph. 20(12), 2486–2495 (2014)
Lindow, N., Baum, D., Prohaska, S., Hege, H.C.: Accelerated visualization of dynamic molecular surfaces. Comput. Graph. Forum 29(3), 943–952 (2010)
Lorensen, W.E., Cline, H.E.: Marching cubes: a high resolution 3D surface construction algorithm. ACM SIGGRAPH Comput. Graph. Interact. Tech. 21, 163–169 (1987)
Parulek, J., Viola, I.: Implicit representation of molecular surfaces. In: 2012 IEEE Pacific Visualization Symposium, pp. 217–224 (2012). doi:10.1109/PacificVis.2012.6183594
Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., Ferrin, T.E.: UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25(13), 1605–1612 (2004)
Richards, F.M.: Areas, volumes, packing, and protein structure. Ann. Rev. Biophys. Bioeng. 6(1), 151–176 (1977)
Sanner, M.F., Olson, A.J., Spehner, J.C.: Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38(3), 305–320 (1996)
Skånberg, R., Vázquez, P.P., Guallar, V., Ropinski, T.: Real-time molecular visualization supporting diffuse interreflections and ambient occlusion. IEEE Trans. Vis. Comput. Graph. 22(1), 718–727 (2016)
Tarini, M., Cignoni, P., Montani, C.: Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Trans. Vis. Comput. Graph. 12(5), 1237–1244 (2006)
Totrov, M., Abagyan, R.: The contour-buildup algorithm to calculate the analytical molecular surface. J. Struct. Biol. 116, 138–143 (1995)
Varshney, A., Brooks, F.P., Wright, W.V.: Linearly scalable computation of smooth molecular surfaces. IEEE Comput. Graph. Appl. 14(5), 19–25 (1994)
Xu, D., Zhang, Y.: Generating triangulated macromolecular surfaces by Euclidean distance transform. PLoS ONE 4(12), e8140 (2009)
Yu, Z.: A List-based method for fast generation of molecular surfaces. In: International Conference of the IEEE Engineering in Medicine and Biology Society, vol. 31, pp. 5909–5912 (2009)
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This work has been partially supported by Grant TIN2014-52211-C2-1-R and Grant CTQ2016-79138-R from the Spanish Ministerio de Economía y Competitividad with FEDER funds, and by the German Research Foundation (DFG) as part of Collaborative Research Center SFB 716.
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Hermosilla, P., Krone, M., Guallar, V. et al. Interactive GPU-based generation of solvent-excluded surfaces. Vis Comput 33, 869–881 (2017). https://doi.org/10.1007/s00371-017-1397-2
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DOI: https://doi.org/10.1007/s00371-017-1397-2