Real-time 3D microtubule gliding simulation accelerated by GPU computing

Springer Science and Business Media LLC - Tập 13 - Trang 108-116 - 2016
Gregory Gutmann1, Daisuke Inoue2, Akira Kakugo2,3, Akihiko Konagaya1
1Department of Computational Intelligence and Systems Science, Tokyo Institute of Technology, Yokohama, Japan
2Faculty of Science, Hokkaido University, Sapporo, Japan
3Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan

Tóm tắt

A microtubule gliding assay is a biological experiment observing the dynamics of microtubules driven by motor proteins fixed on a glass surface. When appropriate microtubule interactions are set up on gliding assay experiments, microtubules often organize and create higher-level dynamics such as ring and bundle structures. In order to reproduce such higher-level dynamics on computers, we have been focusing on making a real-time 3D microtubule simulation. This real-time 3D microtubule simulation enables us to gain more knowledge on microtubule dynamics and their swarm movements by means of adjusting simulation parameters in a real-time fashion. One of the technical challenges when creating a real-time 3D simulation is balancing the 3D rendering and the computing performance. Graphics processor unit (GPU) programming plays an essential role in balancing the millions of tasks, and makes this real-time 3D simulation possible. By the use of general-purpose computing on graphics processing units (GPGPU) programming we are able to run the simulation in a massively parallel fashion, even when dealing with more complex interactions between microtubules such as overriding and snuggling. Due to performance being an important factor, a performance model has also been constructed from the analysis of the microtubule simulation and it is consistent with the performance measurements on different GPGPU architectures with regards to the number of cores and clock cycles.

Tài liệu tham khảo

S. Murata, A. Konagaya, S. Kobayashi, H. Saito, M. Hagiya. Molecular robotics: A new paradigm for artifacts. New Generation Computing, vol. 31, no. 1, pp. 27–45, 2013. J. Howard, A. J. Hudspeth, R. D. Vale. Movement of microtubules by single kinesin molecules. Nature, vol. 342, no. 6246, pp. 154–158, 1989. K. J. Böhm, R. Stracke, P. Mühlig, E. Unger. Motor protein-driven unidirectional transport of micrometer-sized cargoes across isopolar microtubule arrays. Nanotechnology, vol. 12, no. 3, pp. 238–244, 2001. T. Fischer, A. Agarwal, H. Hess. A smart dust biosensor powered by kinesin motors. Nature Nanotechnology, vol.4, no. 3, pp. 162–166, 2009. A. M. R. Kabir, S. Wada, D. Inoue, Y. Tamura, T. Kajihara, H. Mayama, K. Sada, A. Kakugo, J. P. Gong. Formation of ring-shaped assembly of microtubules with a narrow size distribution at an air–buffer interface. Soft Matter, vol. 8, no. 42, pp. 10863–10867, 2012. D. Inoue, A. M.R. Kabir, H. Mayama, J. P.Gong, K. Sada, A. Kakugo. Growth of ring-shaped microtubule assemblies through stepwise active self-organisation. Soft Matter, vol. 9, no. 29, pp. 7061–7068, 2013. A. M. R. Kabir, D. Inoue, A. Kakugo, A. Kamei, J. P. Gong. Prolongation of the active lifetime of a biomolecular motor for in vitro motility assay by using an inert atmosphere. Langmuir, vol. 27, no. 22, pp. 13659–13668, 2011. A. M. R. Kabir, D. Inoue, A. Kakugo, K. Sada, J. P. Gong. Active self-organization of microtubules in an inert chamber system. Polymer Journal, vol. 44, no. 6, pp. 607–611, 2012. P. Kraikivski, R. Lipowsky, J. Kierfeld. Enhanced ordering of interacting filaments by molecular motors. Physical Review Letters, vol. 96, no. 25, pp. 258103, 2006. K. Y. Kong, A. I. Marcus, P. Giannakakou, C. Alberti, M. D. Wang. A two dimensional simulation of microtubule dynamics. In Proceedings of International Conference on Information Technology and Applications in Biomedicine, IEEE, Shenzhen, China, pp. 461–462, 2008. A. Sherrod, W. Jones. Beginning DirectX 11 Game Programming, Boston, USA: Course Technology PTR, 2011. F. D. Luna. Introduction to 3D Game Programming: With DirectX 11, Dulles, USA: Mercury Learning & Information, 2012.