Multiscale Molecular Visualization

Haichao Miao, Tobias Klein, David Kouřil, Peter Mindek, Karsten Schatz, M. Eduard Gröller, Barbora Kozlíková, Tobias Isenberg, Ivan Viola*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

18 Scopus citations

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 basics and describe a number of domain-specific tasks that drive this work. These tasks, in turn, serve as the general structure of the following survey. First, we discuss methods that support the visual analysis of molecular dynamics simulations. We discuss, in particular, visual abstraction and temporal aggregation. In the second part, we survey multiscale approaches that support the design, analysis, and manipulation of DNA nanostructures and related concepts for abstraction, scale transition, scale-dependent modeling, and navigation of the resulting abstraction spaces. In the third part of the survey, we showcase approaches that support 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, visibility management, visual guidance, camera control, and support of depth perception. We close the survey with a brief listing of important tools that implement many of the discussed approaches and a conclusion that provides some research challenges in the field.

Original languageEnglish (US)
Pages (from-to)1049-1070
Number of pages22
JournalJournal of Molecular Biology
Volume431
Issue number6
DOIs
StatePublished - Mar 15 2019

Keywords

  • DNA nanotechnology
  • modelitics
  • molecular dynamics
  • molecular visualization
  • visual abstraction

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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