Accelerated Visualization of Dynamic Molecular Surfaces

Molecular surfaces play an important role in studying the interactions between molecules. Visualizing the dynamic behavior of molecules is particularly interesting to gain insights into a molecular system. Only recently it has become possible to interactively visualize dynamic molecular surfaces usi...

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Veröffentlicht in:Computer graphics forum Jg. 29; H. 3; S. 943 - 952
Hauptverfasser: Lindow, Norbert, Baum, Daniel, Prohaska, Steffen, Hege, Hans-Christian
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Oxford, UK Blackwell Publishing Ltd 01.06.2010
Schlagworte:
algebraic surfaces
Algorithms
C (programming language)
Casting
Computer graphics
Dynamical systems
Dynamics
Gain
I.3.7 [Computer Graphics]: Three-Dimensional Graphics and Realism-ray tracing
I.3.7 [Computer Graphics]: Three‐Dimensional Graphics and Realism—ray tracing, visible line/surface algorithms, algebraic surfaces
J.3 [Life and Medical Sciences]: Biology and Genetics-molecular dynamics
J.3 [Life and Medical Sciences]: Biology and Genetics—molecular dynamics, molecular surfaces
molecular surfaces
Molecules
Studies
visible line/surface algorithms
Visualization
ISSN:0167-7055, 1467-8659
Online-Zugang:Volltext
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Zusammenfassung:Molecular surfaces play an important role in studying the interactions between molecules. Visualizing the dynamic behavior of molecules is particularly interesting to gain insights into a molecular system. Only recently it has become possible to interactively visualize dynamic molecular surfaces using ray casting techniques. In this paper, we show how to further accelerate the construction and the rendering of the solvent excluded surface (SES) and the molecular skin surface (MSS). We propose several improvements to reduce the update times for displaying these molecular surfaces. First, we adopt a parallel approximate Voronoi diagram algorithm to compute the MSS. This accelerates the MSS computation by more than one order of magnitude on a single core. Second, we demonstrate that the contour‐buildup algorithm is ideally suited for computing the SES due to its inherently parallel structure. For both parallel algorithms, we observe good scalability up to 8 cores and, thus, obtain interactive frame rates for molecular dynamics trajectories of up to twenty thousand atoms for the SES and up to a few thousand atoms for the MSS. Third, we reduce the rendering time for the SES using tight‐fitting bounding quadrangles as rasterization primitives. These primitives also accelerate the rendering of the MSS. With these improvements, the interactive visualization of the MSS of dynamic trajectories of a few thousand atoms becomes for the first time possible. Nevertheless, the SES remains a few times faster than the MSS.
Bibliographie:istex:81D8FA669634D23B0BB3C3ECB1FE49306584841B
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ArticleID:CGF1693
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ISSN:0167-7055
1467-8659
DOI:10.1111/j.1467-8659.2009.01693.x