Atomistic Visualization of Mesoscopic Whole-Cell Simulations (English)

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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.

  • Title:
    Atomistic Visualization of Mesoscopic Whole-Cell Simulations
  • Author / Creator:
  • Published in:
  • Publisher:
    The Eurographics Association
  • Place of publication:
    Postfach 2926, 38629 Goslar, Germany
  • Year of publication:
    2012
  • Size:
    8 pages
  • ISBN:
  • ISSN:
  • DOI:
  • Type of media:
    Conference paper
  • Type of material:
    Electronic Resource
  • Language:
    English
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Table of contents conference proceedings

The tables of contents are generated automatically and are based on the data records of the individual contributions available in the index of the TIB portal. The display of the Tables of Contents may therefore be incomplete.

1
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25
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Law, Yuen C. / Knott, Thomas / Hentschel, Bernd / Kuhlen, Torsten | 2012
33
Impact of Physical Noise Modeling on Image Segmentation in Echocardiography
Tenbrinck, Daniel / Sawatzky, Alex / Jiang, Xiaoyi / Burger, Martin / Haffner, Wladimir / Willems, Patrick / Paul, Matthias / Stypmann, Jörg | 2012
41
Lowest-Variance Streamlines for Filtering of 3D Ultrasound
Soltészová, Veronika / Helljesen, Linn Emilie Sævil / Wein, Wolfgang / Gilja, Odd Helge / Viola, Ivan | 2012
49
On the Value of Multi-Volume Visualization for Preoperative Planning of Cerebral AVM Surgery
Weiler, Florian / Rieder, Christian / David, Carlos A. / Wald, Christoph / Hahn, Horst K. | 2012
57
Combining B-Mode and Color Flow Vessel Segmentation for Registration of Hepatic CT and Ultrasound Volumes
Keil, Matthias / Laura, Cristina Oyarzun / Drechsler, Klaus / Wesarg, Stefan | 2012
65
From Imprecise User Input to Precise Vessel Segmentations
Diepenbrock, Stefan / Ropinski, Timo | 2012
73
Sketch-based Image-independent Editing of 3D Tumor Segmentations using Variational Interpolation
Heckel, Frank / Braunewell, Stefan / Soza, Grzegorz / Tietjen, Christian / Hahn, Horst K. | 2012
81
Interactive Residual Stress Modeling for Soft Tissue Simulation
Wu, Jun / Bürger, Kai / Westermann, Rüdiger / Dick, Christian | 2012
91
Visually Guided Mesh Smoothing for Medical Applications
Moench, Tobias / Kubisch, Christoph / Lawonn, Kai / Westermann, Ruediger / Preim, Bernhard | 2012
99
BrainCove: A Tool for Voxel-wise fMRI Brain Connectivity Visualization
Dixhoorn, André F. van / Milles, Julien R. / Lew, Baldur van / Botha, Charl P. | 2012
107
Deriving and Visualizing Uncertainty in Kinetic PET Modeling
Nguyen, Khoa Tan / Bock, Alexander / Ynnerman, Anders / Ropinski, Timo | 2012
115
Visualization and Exploration of 3D Toponome Data
Oeltze, Steffen / Klemm, Paul / Hillert, Reyk / Preim, Bernhard / Schubert, Walter | 2012
123
Atomistic Visualization of Mesoscopic Whole-Cell Simulations
Falk, Martin / Krone, Michael / Ertl, Thomas | 2012
131
Constrained Labeling of 2D Slice Data for Reading Images in Radiology
Mogalle, Katja / Tietjen, Christian / Soza, Grzegorz / Preim, Bernhard | 2012
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