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Atomistic Visualization of Mesoscopic Whole-Cell Simulations
Visualization Research Center (VISUS), University of Stuttgart, Germany..ORCID iD: 0000-0003-1511-5006
Visualization Research Center (VISUS), University of Stuttgart, Germany..
Visualization Research Center (VISUS), University of Stuttgart, Germany..
2012 (English)In: VCBM 12: Eurographics Workshop on Visual Computing for Biology and Medicine / [ed] Timo Ropinski and Anders Ynnerman and Charl Botha and Jos Roerdink}, The Eurographics Association , 2012, Vol. 2, p. 123-130Conference paper, Published paper (Refereed)
Abstract [en]

Molecular visualizations are a principal tool for analyzing the results of biochemical simulations. With modern GPU ray casting approaches it is only possible to render several millions of atoms at interactive frame rates unless advanced acceleration methods are employed. But even simplified cell models of whole-cell simulations consist of at least several billion atoms. However, many instances of only a few different proteins occur in the intracellular environment, which is beneficial in order to fit the data into the graphics memory. One model is stored for each protein species and rendered once per instance. The proposed method exploits recent algorithmic advances for particle rendering and the repetitive nature of intracellular proteins to visualize dynamic results from mesoscopic simulations of cellular transport processes. We present two out-of-core optimizations for the interactive visualization of data sets composed of billions of atoms as well as details on the data preparation and the employed rendering techniques. Furthermore, we apply advanced shading methods to improve the image quality including methods to enhance depth and shape perception besides non-photorealistic rendering methods.

Place, publisher, year, edition, pages
The Eurographics Association , 2012. Vol. 2, p. 123-130
Series
VCBM: Eurographics Workshop on Visual Computing for Biomedicine, ISSN 2070-5778
Keyword [en]
Glyphs, molecular rendering, visualization
National Category
Media and Communication Technology
Identifiers
URN: urn:nbn:se:liu:diva-143705DOI: 10.2312/VCBM/VCBM12/123-130ISBN: 978-3-905674-38-5 (electronic)OAI: oai:DiVA.org:liu-143705DiVA: diva2:1166253
Conference
VCBM 12: Eurographics Workshop on Visual Computing for Biology and Medicine, Norrköping, Sweden, on September 27-28, 2012
Available from: 2017-12-14 Created: 2017-12-14 Last updated: 2018-01-13

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CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf