Real-Time 3D Microtubule Gliding Simulation

  • Greg Gutmann
  • Daisuke Inoue
  • Akira Kakugo
  • Akihiko Konagaya
Conference paper
Part of the Communications in Computer and Information Science book series (CCIS, volume 461)


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 in silico, 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 technical challenges when creating a real-time 3D simulation is balancing the 3D rendering and the computing performance. GPU programming plays an essential role in balancing the millions of tasks, and makes this real-time 3D simulation possible. By the use of 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.


Microtubule Gliding Assay real-time 3D simulation CUDA DirectX 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Greg Gutmann
    • 1
  • Daisuke Inoue
    • 2
  • Akira Kakugo
    • 2
    • 3
  • Akihiko Konagaya
    • 1
  1. 1.Department of Computational Intelligence and Systems ScienceTokyo Institute of TechnologyYokohamaJapan
  2. 2.Faculty of ScienceHokkaido UniversitySapporoJapan
  3. 3.Graduate School of Chemical Sciences and EngineeringHokkaido UniversitySapporoJapan

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