Multiscale Molecular Visualization

Haichao Miao, Tobias Klein, David Kouřil, Peter Mindek, Karsten Schatz, Meister Eduard Gröller, Barbora Kozlikova, Tobias Isenberg, Ivan Viola
Multiscale Molecular Visualization
Journal of Molecular Biology, 6(31):1049-1070, January 2019. [Paper]

Information

Abstract

We provide a high-level survey of multiscale molecular visualization techniques, with a focus on application-domain questions, challenges, and tasks. We provide a general introduction to molecular visualization basicsand describe a number of domain-specific tasks that drive this work. These tasks, in turn, serve as the generalstructure of the following survey. First, we discuss methods that support the visual analysis of moleculardynamics simulations. We discuss, in particular, visual abstraction and temporal aggregation. In the secondpart, we survey multiscale approaches that support the design, analysis, and manipulation of DNAnanostructures and related concepts for abstraction, scale transition, scale-dependent modeling, andnavigation of the resulting abstraction spaces. In the third part of the survey, we showcase approaches thatsupport interactive exploration within large structural biology assemblies up to the size of bacterial cells.We describe fundamental rendering techniques as well as approaches for element instantiation, visibilitymanagement, visual guidance, camera control, and support of depth perception. We close the survey with abrief listing of important tools that implement many of the discussed approaches and a conclusion thatprovides some research challenges in the field.

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BibTeX

@article{Miao_2019,
  title =      "Multiscale Molecular Visualization",
  author =     "Haichao Miao and Tobias Klein and David Kou\v{r}il and Peter
               Mindek and Karsten Schatz and Meister Eduard Gr\"{o}ller and
               Barbora Kozlikova and Tobias Isenberg and Ivan Viola",
  year =       "2019",
  abstract =   "We provide a high-level survey of multiscale molecular
               visualization techniques, with a focus on application-domain
               questions, challenges, and tasks. We provide a general
               introduction to molecular visualization basicsand describe a
               number of domain-specific tasks that drive this work. These
               tasks, in turn, serve as the generalstructure of the
               following survey. First, we discuss methods that support the
               visual analysis of moleculardynamics simulations. We
               discuss, in particular, visual abstraction and temporal
               aggregation. In the secondpart, we survey multiscale
               approaches that support the design, analysis, and
               manipulation of DNAnanostructures and related concepts for
               abstraction, scale transition, scale-dependent modeling,
               andnavigation of the resulting abstraction spaces. In the
               third part of the survey, we showcase approaches thatsupport
               interactive exploration within large structural biology
               assemblies up to the size of bacterial cells.We describe
               fundamental rendering techniques as well as approaches for
               element instantiation, visibilitymanagement, visual
               guidance, camera control, and support of depth perception.
               We close the survey with abrief listing of important tools
               that implement many of the discussed approaches and a
               conclusion thatprovides some research challenges in the
               field.",
  month =      jan,
  doi =        "10.1016/j.jmb.2018.09.004.",
  journal =    "Journal of Molecular Biology",
  number =     "31",
  volume =     "6",
  pages =      "1049--1070",
  keywords =   "molecular visualization, molecular dynamics, modelitics, DNA
               nanotechnology, visual abstraction",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2019/Miao_2019/",
}