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Abstract

The molecular world is an exciting field of science. Since technology has advanced it is finally possible to discover the arrangements of the single atoms in molecules. With this data, complex systems like viruses, bacteria and cells, made out of millions of atoms can be modeled. Such systems are often called biological mesoscale structures and many visualization techniques have been developed to model them. This is not an easy task as such systems are very complex and need a lot of processing time to render. An essential part of the visualization is the collision detection and resolving as in the real world molecules do not overlap. We reimplemented the Fast Fixed-Radius Nearest Neighbors algorithm that was designed by Hoetzlein to find all colliding pairs of atoms, calculated forces which are then applied on the molecules in order to resolve the overlaps. To test this method we constructed a model of a lipid bilayer and found that it was able to resolve collisions with up to four million atoms in real time. We reviewed further improvements of our algorithm and are positive that it can be used as a efficient collision detection for mesoscale environments.

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BibTeX

@bachelorsthesis{Pauschenwein_2022,
  title =      "Real-Time Collision Detection and Handling of Molecules for
               Animation and Modelling",
  author =     "Johannes Pauschenwein",
  year =       "2022",
  abstract =   "The molecular world is an exciting field of science. Since
               technology has advanced it is finally possible to discover
               the arrangements of the single atoms in molecules. With this
               data, complex systems like viruses, bacteria and cells, made
               out of millions of atoms can be modeled. Such systems are
               often called biological mesoscale structures and many
               visualization techniques have been developed to model them.
               This is not an easy task as such systems are very complex
               and need a lot of processing time to render. An essential
               part of the visualization is the collision detection and
               resolving as in the real world molecules do not overlap. We
               reimplemented the Fast Fixed-Radius Nearest Neighbors
               algorithm that was designed by Hoetzlein to find all
               colliding pairs of atoms, calculated forces which are then
               applied on the molecules in order to resolve the overlaps.
               To test this method we constructed a model of a lipid
               bilayer and found that it was able to resolve collisions
               with up to four million atoms in real time. We reviewed
               further improvements of our algorithm and are positive that
               it can be used as a efficient collision detection for
               mesoscale environments. ",
  month =      jan,
  address =    "Favoritenstrasse 9-11/E193-02, A-1040 Vienna, Austria",
  school =     "Research Unit of Computer Graphics, Institute of Visual
               Computing and Human-Centered Technology, Faculty of
               Informatics, TU Wien ",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2022/Pauschenwein_2022/",
}