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Continuous Levels-of-Detail and Visual Abstraction for Seamless Molecular Visualization

Julius Parulek, Daniel Jönsson, Timo Ropinski, Stefan Bruckner, Anders Ynnerman, Ivan Viola

JOURNAL ARTICLE: Computer Graphics Forum, 2014. To appear in an upcoming issue. DOI: 10.1111/cgf.12349

Abstract

Molecular visualization is often challenged with rendering of large molecular structures in real time. We introduce a novel approach that enables us to show even large protein complexes. Our method is based on the level-of-detail concept, where we exploit three different abstractions combined in one visualization. Firstly, molecular surface abstraction exploits three different surfaces, solvent-excluded surface (SES), Gaussian kernels and van der Waals spheres, combined as one surface by linear interpolation. Secondly, we introduce three shading abstraction levels and a method for creating seamless transitions between these representations. The SES representation with full shading and added contours stands in focus while on the other side a sphere representation of a cluster of atoms with constant shading and without contours provide the context. Thirdly, we propose a hierarchical abstraction based on a set of clusters formed on molecular atoms. All three abstraction models are driven by one importance function classifying the scene into the near-, mid- and far-field. Moreover, we introduce a methodology to render the entire molecule directly using the A-buffer technique, which further improves the performance. The rendering performance is evaluated on series of molecules of varying atom counts.

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Computer Graphics Forum

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BibTeX

@ARTICLE{Parulek-2014-CLV,
  author = {Julius Parulek and Daniel J{\"o}nsson and Timo Ropinski and Stefan
	Bruckner and Anders Ynnerman and Ivan Viola},
  title = {Continuous Levels-of-Detail and Visual Abstraction for Seamless Molecular
	Visualization},
  journal = {Computer Graphics Forum},
  year = {2014},
  month = may,
  note = {To appear in an upcoming issue},
  abstract = {Molecular visualization is often challenged with rendering of large
	molecular structures in real time. We introduce a novel approach
	that enables us to show even large protein complexes. Our method
	is based on the level-of-detail concept, where we exploit three different
	abstractions combined in one visualization. Firstly, molecular surface
	abstraction exploits three different surfaces, solvent-excluded surface
	(SES), Gaussian kernels and van der Waals spheres, combined as one
	surface by linear interpolation. Secondly, we introduce three shading
	abstraction levels and a method for creating seamless transitions
	between these representations. The SES representation with full shading
	and added contours stands in focus while on the other side a sphere
	representation of a cluster of atoms with constant shading and without
	contours provide the context. Thirdly, we propose a hierarchical
	abstraction based on a set of clusters formed on molecular atoms.
	All three abstraction models are driven by one importance function
	classifying the scene into the near-, mid- and far-field. Moreover,
	we introduce a methodology to render the entire molecule directly
	using the A-buffer technique, which further improves the performance.
	The rendering performance is evaluated on series of molecules of
	varying atom counts.},
  doi = {10.1111/cgf.12349},
  keywords = {level of detail algorithms, implicit surfaces, clustering, scientific
	visualization},
}






 Last Modified: Stefan Bruckner, 2014-09-22