Accelerated visualization of transparent molecular surfaces in molecular dynamics

The reactivity of the biomolecular structures is highly influenced by their structural features. Thus, studying these features along with the exploration of their dynamic behavior helps to understand the processes ongoing in living cells. This can be reached by the visual representation of these pro...

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Vydáno v:IEEE Pacific Visualization Symposium s. 112 - 119
Hlavní autoři: Jurcik, Adam, Parulek, Julius, Sochor, Jiri, Kozlikova, Barbora
Médium: Konferenční příspěvek Journal Article
Jazyk:angličtina
Vydáno: IEEE 01.04.2016
Témata:
Algorithms
Cavity resonators
Dynamics
Exploration
Feature extraction
I.3.5 [Computational Geometry and Object Modeling] — Boundary representations
I.3.7 [Three-Dimensional Graphics and Realism] — Visible line/surface algorithms
Molecular dynamics
Proteins
Real time
Real-time systems
Rendering (computer graphics)
Representations
Surface treatment
Visualization
Voids
ISSN:2165-8773
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Abstract The reactivity of the biomolecular structures is highly influenced by their structural features. Thus, studying these features along with the exploration of their dynamic behavior helps to understand the processes ongoing in living cells. This can be reached by the visual representation of these processes as visualization is one of the most natural ways to convey such information. However, none of the currently available techniques provides the biochemists with an intuitive real-time representation of the dynamic movements of molecules and precise geometrical based extraction of their structural features performed instantly. In this paper we introduce such a technique enabling the user to compute and also to visualize the molecular surface along with inner voids. To obtain a better insight into the molecule, our technique enables to visualize the molecular surface transparently. The opacity can be adjusted by changing user-defined parameters in order to enhance the perception of the surfaces of inner voids. All integrated algorithms run in real-time which gives the user a big variety of exploration possibilities. The importance of our approach is even amplified with respect to the fact that currently the size of molecular dynamics simulations is increasing dramatically and offline rendering thus becomes impracticable. The usability of our technique was evaluated by the domain experts.
AbstractList The reactivity of the biomolecular structures is highly influenced by their structural features. Thus, studying these features along with the exploration of their dynamic behavior helps to understand the processes ongoing in living cells. This can be reached by the visual representation of these processes as visualization is one of the most natural ways to convey such information. However, none of the currently available techniques provides the biochemists with an intuitive real-time representation of the dynamic movements of molecules and precise geometrical based extraction of their structural features performed instantly. In this paper we introduce such a technique enabling the user to compute and also to visualize the molecular surface along with inner voids. To obtain a better insight into the molecule, our technique enables to visualize the molecular surface transparently. The opacity can be adjusted by changing user-defined parameters in order to enhance the perception of the surfaces of inner voids. All integrated algorithms run in real-time which gives the user a big variety of exploration possibilities. The importance of our approach is even amplified with respect to the fact that currently the size of molecular dynamics simulations is increasing dramatically and offline rendering thus becomes impracticable. The usability of our technique was evaluated by the domain experts.
Author Parulek, Julius
Kozlikova, Barbora
Jurcik, Adam
Sochor, Jiri
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  givenname: Julius
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  givenname: Jiri
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  fullname: Sochor, Jiri
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  givenname: Barbora
  surname: Kozlikova
  fullname: Kozlikova, Barbora
  email: kozlikova@fi.muni.cz
  organization: Masaryk Univ., Brno, Czech Republic
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SubjectTerms Algorithms
Cavity resonators
Dynamics
Exploration
Feature extraction
I.3.5 [Computational Geometry and Object Modeling] — Boundary representations
I.3.7 [Three-Dimensional Graphics and Realism] — Visible line/surface algorithms
Molecular dynamics
Proteins
Real time
Real-time systems
Rendering (computer graphics)
Representations
Surface treatment
Visualization
Voids
Title Accelerated visualization of transparent molecular surfaces in molecular dynamics
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