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Haptic model of biomolecules

Simulations of chemical processes represent an important area of research. The topic of our work was an interactive model of conformational behavior of certain classes of biomolecules. We focused  on real-time simulation, which allowed the user to interact with virtual objects representing biomolecular structures. Our work was based on research done by Aleš Křenek who also supervised my master's thesis.

Our work focused on improvements of the model and its implementation.
  • Since in the first phase we deal with expensive computations performed in parallel environment, some optimizations were made and the behavior of the algorithm was experimentally evaluated [1].
  • The interaction was improved by some other means of the virtual reality environment (position tracking, stereo-vision).
  • The simulation model itself was modified in order to design more realistic setup allowing interconversions between distinct conformations [2].

Video in AVI format is available show the haptic interaction with the biomolecule.


  1. A. Křenek, I. Peterlík and L. Matyska. Building 3d state spaces of virtual environments with a tds-based algorithm,” in Recent Advances in Parallel Virtual Machine and Message Passing Interface, Berlin: Springer-Verlag LNCS, 2003. [PDF]
  2. I. Peterlík and A. Křenek. Haptically driven travelling through conformational space. in WHC ’05: Proceedings of the First Joint Eurohaptics Conference and Symposium on Haptic Interfaces for Virtual Environment and Teleoperator Systems, (Washington, DC, USA), pp. 342–347, IEEE Computer Society, 2005. [PDF]