A general illumination model for molecular visualization

Several visual representations have been developed over the years to visualize molecular structures, and to enable a better understanding of their underlying chemical processes. Today, the most frequently used atom-based representations are the Space-filling, the Solvent Excluded Surface, the Balls-...

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Autores: Hermosilla Casajús, Pedro, Vázquez Alcocer, Pere Pau|||0000-0003-4638-4065, Vinacua Pla, Álvaro|||0000-0001-8984-4311, Ropinski, Timo
Tipo de recurso: artículo
Fecha de publicación:2018
País:España
Institución:Universitat Politècnica de Catalunya (UPC)
Repositorio:UPCommons. Portal del coneixement obert de la UPC
Idioma:inglés
OAI Identifier:oai:upcommons.upc.edu:2117/121536
Acceso en línea:https://hdl.handle.net/2117/121536
https://dx.doi.org/10.1111/cgf.13426
Access Level:acceso abierto
Palabra clave:Molecular structure -- Data processing
Information visualization -- Data processing
Visualization
Computer graphics
Regression analysis
Estructura molecular -- Informàtica
Visualització de la informació -- Informàtica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica
Àrees temàtiques de la UPC::Informàtica::Infografia
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spelling A general illumination model for molecular visualizationHermosilla Casajús, PedroVázquez Alcocer, Pere Pau|||0000-0003-4638-4065Vinacua Pla, Álvaro|||0000-0001-8984-4311Ropinski, TimoMolecular structure -- Data processingInformation visualization -- Data processingVisualizationComputer graphicsRegression analysisEstructura molecular -- InformàticaVisualització de la informació -- InformàticaÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàticaÀrees temàtiques de la UPC::Informàtica::InfografiaSeveral visual representations have been developed over the years to visualize molecular structures, and to enable a better understanding of their underlying chemical processes. Today, the most frequently used atom-based representations are the Space-filling, the Solvent Excluded Surface, the Balls-and-Sticks, and the Licorice models. While each of these representations has its individual benefits, when applied to large-scale models spatial arrangements can be difficult to interpret when employing current visualization techniques. In the past it has been shown that global illumination techniques improve the perception of molecular visualizations; unfortunately existing approaches are tailored towards a single visual representation. We propose a general illumination model for molecular visualization that is valid for different representations. With our illumination model, it becomes possible, for the first time, to achieve consistent illumination among all atom-based molecular representations. The proposed model can be further evaluated in real-time, as it employs an analytical solution to simulate diffuse light interactions between objects. To be able to derive such a solution for the rather complicated and diverse visual representations, we propose the use of regression analysis together with adapted parameter sampling strategies as well as shape parametrization guided sampling, which are applied to the geometric building blocks of the targeted visual representations. We will discuss the proposed sampling strategies, the derived illumination model, and demonstrate its capabilities when visualizing several dynamic molecules.Peer Reviewed20182018-06-0120182018-09-27journal articlehttp://purl.org/coar/resource_type/c_6501AMhttp://purl.org/coar/version/c_ab4af688f83e57aainfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/2117/121536https://dx.doi.org/10.1111/cgf.13426reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)InglésengAgencia Estatal de Investigación http://doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016 TIN2017-88515-C2-1-R VISUALIZACION, MODELADO, SIMULACION E INTERACCION CON MODELOS 3D. APLICACIONES EN CIENCIAS DE LA VIDA Y ENTORNOS RURALES Y URBANOSopen accesshttp://purl.org/coar/access_right/c_abf2info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/1215362026-05-27T15:37:01Z
dc.title.none.fl_str_mv A general illumination model for molecular visualization
title A general illumination model for molecular visualization
spellingShingle A general illumination model for molecular visualization
Hermosilla Casajús, Pedro
Molecular structure -- Data processing
Information visualization -- Data processing
Visualization
Computer graphics
Regression analysis
Estructura molecular -- Informàtica
Visualització de la informació -- Informàtica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica
Àrees temàtiques de la UPC::Informàtica::Infografia
title_short A general illumination model for molecular visualization
title_full A general illumination model for molecular visualization
title_fullStr A general illumination model for molecular visualization
title_full_unstemmed A general illumination model for molecular visualization
title_sort A general illumination model for molecular visualization
dc.creator.none.fl_str_mv Hermosilla Casajús, Pedro
Vázquez Alcocer, Pere Pau|||0000-0003-4638-4065
Vinacua Pla, Álvaro|||0000-0001-8984-4311
Ropinski, Timo
author Hermosilla Casajús, Pedro
author_facet Hermosilla Casajús, Pedro
Vázquez Alcocer, Pere Pau|||0000-0003-4638-4065
Vinacua Pla, Álvaro|||0000-0001-8984-4311
Ropinski, Timo
author_role author
author2 Vázquez Alcocer, Pere Pau|||0000-0003-4638-4065
Vinacua Pla, Álvaro|||0000-0001-8984-4311
Ropinski, Timo
author2_role author
author
author
dc.subject.none.fl_str_mv Molecular structure -- Data processing
Information visualization -- Data processing
Visualization
Computer graphics
Regression analysis
Estructura molecular -- Informàtica
Visualització de la informació -- Informàtica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica
Àrees temàtiques de la UPC::Informàtica::Infografia
topic Molecular structure -- Data processing
Information visualization -- Data processing
Visualization
Computer graphics
Regression analysis
Estructura molecular -- Informàtica
Visualització de la informació -- Informàtica
Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica
Àrees temàtiques de la UPC::Informàtica::Infografia
description Several visual representations have been developed over the years to visualize molecular structures, and to enable a better understanding of their underlying chemical processes. Today, the most frequently used atom-based representations are the Space-filling, the Solvent Excluded Surface, the Balls-and-Sticks, and the Licorice models. While each of these representations has its individual benefits, when applied to large-scale models spatial arrangements can be difficult to interpret when employing current visualization techniques. In the past it has been shown that global illumination techniques improve the perception of molecular visualizations; unfortunately existing approaches are tailored towards a single visual representation. We propose a general illumination model for molecular visualization that is valid for different representations. With our illumination model, it becomes possible, for the first time, to achieve consistent illumination among all atom-based molecular representations. The proposed model can be further evaluated in real-time, as it employs an analytical solution to simulate diffuse light interactions between objects. To be able to derive such a solution for the rather complicated and diverse visual representations, we propose the use of regression analysis together with adapted parameter sampling strategies as well as shape parametrization guided sampling, which are applied to the geometric building blocks of the targeted visual representations. We will discuss the proposed sampling strategies, the derived illumination model, and demonstrate its capabilities when visualizing several dynamic molecules.
publishDate 2018
dc.date.none.fl_str_mv 2018
2018-06-01
2018
2018-09-27
dc.type.none.fl_str_mv journal article
http://purl.org/coar/resource_type/c_6501
AM
http://purl.org/coar/version/c_ab4af688f83e57aa
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/121536
https://dx.doi.org/10.1111/cgf.13426
url https://hdl.handle.net/2117/121536
https://dx.doi.org/10.1111/cgf.13426
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Agencia Estatal de Investigación http://doi.org/10.13039/501100011033 Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016 TIN2017-88515-C2-1-R VISUALIZACION, MODELADO, SIMULACION E INTERACCION CON MODELOS 3D. APLICACIONES EN CIENCIAS DE LA VIDA Y ENTORNOS RURALES Y URBANOS
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
_version_ 1869417766488899584
score 15.301603

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