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Interactive Visualization of Molecular Dynamics Simulation Data / NAIF ALHARBI

Swansea University Author: NAIF ALHARBI

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DOI (Published version): 10.23889/SUthesis.56609

Abstract

Molecular Dynamics Simulations (MD) plays an essential role in the field of computational biology. The simulations produce extensive high-dimensional, spatio-temporal data describ-ing the motion of atoms and molecules. A central challenge in the field is the extraction and visualization of useful be...

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Published: Swansea 2020
Institution: Swansea University
Degree level: Doctoral
Degree name: Ph.D
Supervisor: Laramee, Robert S.
URI: https://cronfa.swan.ac.uk/Record/cronfa56609
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first_indexed 2021-03-31T15:04:42Z
last_indexed 2021-04-21T03:24:14Z
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For the sake of exploration, I was provided with a large and complex membrane simulation. I contributed solutions to his data challenges by developing a set of novel visual-ization tools to help him get a better understanding of his simulation data. I employed both scientific and information visualization, and applied concepts of abstraction and dimensions projection in the proposed solutions. The first solution enables the user to interactively fil-ter and highlight dynamic and complex trajectory constituted by motions of molecules. The molecular dynamic trajectories are identified based on path length, edge length, curvature, and normalized curvature, and their combinations. The tool exploits new interactive visual-ization techniques and provides a combination of 2D-3D path rendering in a dual dimension representation to highlight differences arising from the 2D projection on a plane. The sec-ond solution introduces a novel abstract interaction space for Protein-Lipid interaction. The proposed solution addresses the challenge of visualizing complex, time-dependent interactions between protein and lipid molecules. It also proposes a fast GPU-based implementation that maps lipid-constituents involved in the interaction onto the abstract protein interaction space. I also introduced two abstract level-of-detail (LoD) representations with six levels of detail for lipid molecules and protein interaction. Finally, I proposed a novel framework consisting of four linked views: A time-dependent 3D view, a novel hybrid view, a clustering timeline, and a details-on-demand window. The framework exploits abstraction and projection to enable the user to study the molecular interaction and the behavior of the protein-protein interaction and clusters. I introduced a selection of visual designs to convey the behavior of protein-lipid interaction and protein-protein interaction through a unified coordinate system. Abstraction is used to present proteins in hybrid 2D space, and a projected tiled space is used to present both Protein-Lipid Interaction (PLI) and Protein-Protein Interaction (PPI) at the particle level in a heat-map style visual design. Glyphs are used to represent PPI at the molecular level. I coupled visually separable visual designs in a unified coordinate space. The result lets the user study both PLI and PPI separately, or together in a unified visual analysis framework.</abstract><type>E-Thesis</type><journal/><volume/><journalNumber/><paginationStart/><paginationEnd/><publisher/><placeOfPublication>Swansea</placeOfPublication><isbnPrint/><isbnElectronic/><issnPrint/><issnElectronic/><keywords>Visualization, Interactive Visualization, Molecular Dynamic</keywords><publishedDay>26</publishedDay><publishedMonth>4</publishedMonth><publishedYear>2020</publishedYear><publishedDate>2020-04-26</publishedDate><doi>10.23889/SUthesis.56609</doi><url/><notes>A selection of third party content is redacted or is partially redacted from this thesis.</notes><college>COLLEGE NANME</college><CollegeCode>COLLEGE CODE</CollegeCode><institution>Swansea University</institution><supervisor>Laramee, Robert S.</supervisor><degreelevel>Doctoral</degreelevel><degreename>Ph.D</degreename><degreesponsorsfunders>Saudi Embassy, London</degreesponsorsfunders><apcterm/><lastEdited>2021-04-20T16:40:33.6028626</lastEdited><Created>2021-03-31T16:01:56.5641504</Created><path><level id="1">Faculty of Science and Engineering</level><level id="2">School of Mathematics and Computer Science - Computer Science</level></path><authors><author><firstname>NAIF</firstname><surname>ALHARBI</surname><order>1</order></author></authors><documents><document><filename>56609__19717__d6f60c2933e14f1f813af7ad14206285.pdf</filename><originalFilename>Alharbi_Naif_PhD_Thesis_Final_Redacted.pdf</originalFilename><uploaded>2021-04-20T16:38:56.5781372</uploaded><type>Output</type><contentLength>6356349</contentLength><contentType>application/pdf</contentType><version>Redacted version - open access</version><cronfaStatus>true</cronfaStatus><documentNotes>Copyright: The author, Naif Ghazi Alharbi, 2020.</documentNotes><copyrightCorrect>true</copyrightCorrect><language>eng</language></document></documents><OutputDurs/></rfc1807>
spelling 2021-04-20T16:40:33.6028626 v2 56609 2021-03-31 Interactive Visualization of Molecular Dynamics Simulation Data f51736da794e4aeb5608a5b5a28d646e NAIF ALHARBI NAIF ALHARBI true false 2021-03-31 Molecular Dynamics Simulations (MD) plays an essential role in the field of computational biology. The simulations produce extensive high-dimensional, spatio-temporal data describ-ing the motion of atoms and molecules. A central challenge in the field is the extraction and visualization of useful behavioral patterns from these simulations. Throughout this thesis, I collaborated with a computational biologist who works on Molecular Dynamics (MD) Simu-lation data. For the sake of exploration, I was provided with a large and complex membrane simulation. I contributed solutions to his data challenges by developing a set of novel visual-ization tools to help him get a better understanding of his simulation data. I employed both scientific and information visualization, and applied concepts of abstraction and dimensions projection in the proposed solutions. The first solution enables the user to interactively fil-ter and highlight dynamic and complex trajectory constituted by motions of molecules. The molecular dynamic trajectories are identified based on path length, edge length, curvature, and normalized curvature, and their combinations. The tool exploits new interactive visual-ization techniques and provides a combination of 2D-3D path rendering in a dual dimension representation to highlight differences arising from the 2D projection on a plane. The sec-ond solution introduces a novel abstract interaction space for Protein-Lipid interaction. The proposed solution addresses the challenge of visualizing complex, time-dependent interactions between protein and lipid molecules. It also proposes a fast GPU-based implementation that maps lipid-constituents involved in the interaction onto the abstract protein interaction space. I also introduced two abstract level-of-detail (LoD) representations with six levels of detail for lipid molecules and protein interaction. Finally, I proposed a novel framework consisting of four linked views: A time-dependent 3D view, a novel hybrid view, a clustering timeline, and a details-on-demand window. The framework exploits abstraction and projection to enable the user to study the molecular interaction and the behavior of the protein-protein interaction and clusters. I introduced a selection of visual designs to convey the behavior of protein-lipid interaction and protein-protein interaction through a unified coordinate system. Abstraction is used to present proteins in hybrid 2D space, and a projected tiled space is used to present both Protein-Lipid Interaction (PLI) and Protein-Protein Interaction (PPI) at the particle level in a heat-map style visual design. Glyphs are used to represent PPI at the molecular level. I coupled visually separable visual designs in a unified coordinate space. The result lets the user study both PLI and PPI separately, or together in a unified visual analysis framework. E-Thesis Swansea Visualization, Interactive Visualization, Molecular Dynamic 26 4 2020 2020-04-26 10.23889/SUthesis.56609 A selection of third party content is redacted or is partially redacted from this thesis. COLLEGE NANME COLLEGE CODE Swansea University Laramee, Robert S. Doctoral Ph.D Saudi Embassy, London 2021-04-20T16:40:33.6028626 2021-03-31T16:01:56.5641504 Faculty of Science and Engineering School of Mathematics and Computer Science - Computer Science NAIF ALHARBI 1 56609__19717__d6f60c2933e14f1f813af7ad14206285.pdf Alharbi_Naif_PhD_Thesis_Final_Redacted.pdf 2021-04-20T16:38:56.5781372 Output 6356349 application/pdf Redacted version - open access true Copyright: The author, Naif Ghazi Alharbi, 2020. true eng
title Interactive Visualization of Molecular Dynamics Simulation Data
spellingShingle Interactive Visualization of Molecular Dynamics Simulation Data
NAIF ALHARBI
title_short Interactive Visualization of Molecular Dynamics Simulation Data
title_full Interactive Visualization of Molecular Dynamics Simulation Data
title_fullStr Interactive Visualization of Molecular Dynamics Simulation Data
title_full_unstemmed Interactive Visualization of Molecular Dynamics Simulation Data
title_sort Interactive Visualization of Molecular Dynamics Simulation Data
author_id_str_mv f51736da794e4aeb5608a5b5a28d646e
author_id_fullname_str_mv f51736da794e4aeb5608a5b5a28d646e_***_NAIF ALHARBI
author NAIF ALHARBI
author2 NAIF ALHARBI
format E-Thesis
publishDate 2020
institution Swansea University
doi_str_mv 10.23889/SUthesis.56609
college_str Faculty of Science and Engineering
hierarchytype
hierarchy_top_id facultyofscienceandengineering
hierarchy_top_title Faculty of Science and Engineering
hierarchy_parent_id facultyofscienceandengineering
hierarchy_parent_title Faculty of Science and Engineering
department_str School of Mathematics and Computer Science - Computer Science{{{_:::_}}}Faculty of Science and Engineering{{{_:::_}}}School of Mathematics and Computer Science - Computer Science
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description Molecular Dynamics Simulations (MD) plays an essential role in the field of computational biology. The simulations produce extensive high-dimensional, spatio-temporal data describ-ing the motion of atoms and molecules. A central challenge in the field is the extraction and visualization of useful behavioral patterns from these simulations. Throughout this thesis, I collaborated with a computational biologist who works on Molecular Dynamics (MD) Simu-lation data. For the sake of exploration, I was provided with a large and complex membrane simulation. I contributed solutions to his data challenges by developing a set of novel visual-ization tools to help him get a better understanding of his simulation data. I employed both scientific and information visualization, and applied concepts of abstraction and dimensions projection in the proposed solutions. The first solution enables the user to interactively fil-ter and highlight dynamic and complex trajectory constituted by motions of molecules. The molecular dynamic trajectories are identified based on path length, edge length, curvature, and normalized curvature, and their combinations. The tool exploits new interactive visual-ization techniques and provides a combination of 2D-3D path rendering in a dual dimension representation to highlight differences arising from the 2D projection on a plane. The sec-ond solution introduces a novel abstract interaction space for Protein-Lipid interaction. The proposed solution addresses the challenge of visualizing complex, time-dependent interactions between protein and lipid molecules. It also proposes a fast GPU-based implementation that maps lipid-constituents involved in the interaction onto the abstract protein interaction space. I also introduced two abstract level-of-detail (LoD) representations with six levels of detail for lipid molecules and protein interaction. Finally, I proposed a novel framework consisting of four linked views: A time-dependent 3D view, a novel hybrid view, a clustering timeline, and a details-on-demand window. The framework exploits abstraction and projection to enable the user to study the molecular interaction and the behavior of the protein-protein interaction and clusters. I introduced a selection of visual designs to convey the behavior of protein-lipid interaction and protein-protein interaction through a unified coordinate system. Abstraction is used to present proteins in hybrid 2D space, and a projected tiled space is used to present both Protein-Lipid Interaction (PLI) and Protein-Protein Interaction (PPI) at the particle level in a heat-map style visual design. Glyphs are used to represent PPI at the molecular level. I coupled visually separable visual designs in a unified coordinate space. The result lets the user study both PLI and PPI separately, or together in a unified visual analysis framework.
published_date 2020-04-26T04:11:41Z
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score 11.035874

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