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Real-time 3D Microtubule Gliding Simulation Accelerated by GPU Computing

International Journal of Automation and computing 2016年第2期13卷 108-116页

作者： Gregory Gutmann Daisuke Inoue akira kakugo Akihiko Konagaya Department of Computational Intelligence and Systems Science Tokyo Institute of Technology Faculty of Science Hokkaido University Graduate School of Chemical Sciences and Engineering Hokkaido University

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 paranleters 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 n, odel 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.

关键词： Microtubule gliding assay 3D computer graphics and simulation parallel computing performance analysis general- purpose computing on graphics processing units (GPGPU) compute unified device arshitecture (CUDA) DirectX.

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GROWTH AND MORPHOLOGY OF POLYMER-ACTIN COMPLEXES

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Chinese Journal of Polymer Science 2007年第1期25卷 47-55页

作者： Hyuck Joon Kwon Kazuhiro Shikinaka akira kakugo Hidemitsu Furukawa Yoshihito Osada 龚剑萍 Graduate School of Science Hokkaido UniversitySapporo 060-0810Japan Graduate School of Science Hokkaido UniversitySapporo 060-0810Japan SORSTJSTSapporo 060-0810Japan

F-actins are semi-flexible polyelectrolytes and can be assembled into large polymer-actin complex with polymorphism through electrostatic interaction with polycations. This study investigates the structural phase behavior and the growth of polymer-actin complexes in terms of its longitudinal and lateral sizes. Our results show that formation of polymer-actin complexes is cooperative, and morphology and growth of polymer-actin complexes depend on polycation species and concentrations of polycation and salt in a constant actin concentration. We found that the longitudinal growth and lateral growth of polymer-actin complexes are dominated by different factors. This induces the structural polymorphism of polymer-actin complexes. Major factors to influence the polymorphism of polymer-actin complexes in polyelectrolytc system have been discussed. Our results indicate that the semi-flexible polyelectrolyte nature of F-actins is important for controlling the morphology and growth ofactin architectures in cell.

关键词： F-actin Polymer-actin complex Polycation concentration (Cp) KCl concentration (Cs) Fluorescence microscopy Transmission electron microscopy (TEM) Rod-like polyelectrolyte.

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