LifeBrush: An Illustrative Simulation Canvas for the Biological Mesoscale

Simple item page
dc.contributor.advisorJacob, Christian
dc.contributor.advisorSamavati, Faramarz Famil
dc.contributor.authorDavison, Timothy
dc.contributor.committeememberCosta Sousa, Mario
dc.contributor.committeememberOlson, Arthur
dc.contributor.committeememberWillett, Wesley J.
dc.contributor.committeememberHerzog, W.
dc.date2020-02
dc.date.accessioned2020-01-13T23:37:24Z
dc.date.available2020-01-13T23:37:24Z
dc.date.issued2020-01
dc.description.abstractAt the mesoscale, molecular machines assemble structure and orchestrate the processes of life. It is a chaotic and alien world whose scale makes communicating scientific findings a daunting challenge. Scientific illustrators confront the challenges with static illustration and video animations. With \lifeBrush{}, a virtual reality tool, we bring those static illustrations to life as interactive illustrative simulations. \lifeBrush{} is an illustrative simulation canvas, for sketching, simulating and visualizing the biological mesoscale. Like an artists paint palette, we design molecular arrangements, self-assembly rules, and generative procedures in an interactive palette. Then, we use our palette and generative algorithms to sketch illustrative simulations. We developed a novel realtime algorithm for painting and synthesizing element arrangements from a palette into virtual worlds. Our synthesis algorithm has applications for virtual world construction, and for interactively constructing illustrative mesoscale simulations. We synthesize networks of interconnected proteins filaments with sketch-based swarm grammars. To model macromolecular self-assembly, and to interactively construct macromolecular structures with our sketch-based system, we propose a realtime physics approximation based on spatial rules designed in the palette. We use our system to sketch and simulate cytoskeletal filaments in our illustrative simulation canvas. With our system, we structurally recreate, simulate and step inside some famous illustrations by the structural biologist David Goodsell.en_US
dc.identifier.citationDavison, T. (2020). LifeBrush: An Illustrative Simulation Canvas for the Biological Mesoscale (Doctoral thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.en_US
dc.identifier.doihttp://dx.doi.org/10.11575/PRISM/37450
dc.identifier.urihttp://hdl.handle.net/1880/111493
dc.language.isoengen_US
dc.publisher.facultyScienceen_US
dc.publisher.institutionUniversity of Calgaryen
dc.rightsUniversity of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.en_US
dc.subjectmesoscaleen_US
dc.subjectillustrative simulationen_US
dc.subjectagent-based modellingen_US
dc.subjectdiscrete element texture synthesisen_US
dc.subjectmacromolecular self-assemblyen_US
dc.subjectscientific illustrationen_US
dc.subjectvirtual realityen_US
dc.subjectsketch-baseden_US
dc.subjecttexture synthesisen_US
dc.subjectcomputer graphicsen_US
dc.subject.classificationBioinformaticsen_US
dc.subject.classificationBiology--Molecularen_US
dc.subject.classificationComputer Scienceen_US
dc.titleLifeBrush: An Illustrative Simulation Canvas for the Biological Mesoscaleen_US
dc.typedoctoral thesisen_US
thesis.degree.disciplineComputer Scienceen_US
thesis.degree.grantorUniversity of Calgaryen_US
thesis.degree.nameDoctor of Philosophy (PhD)en_US
ucalgary.item.requestcopytrueen_US
Files
Original bundle
Now showing 1 - 5 of 7
Thumbnail Image
Name:
ucalgary_2020_davison_timothy.pdf
Size:
145.99 MB
Format:
Adobe Portable Document Format
Description:
Main article.
Download
No Thumbnail Available
Name:
Chapter1_overview.mp4
Size:
457.27 MB
Format:
MP4
Description:
Chapter 1: overview of the lifeBrush system.
Download
No Thumbnail Available
Name:
Chapter4_bunnyPlanetSession.mp4
Size:
244.33 MB
Format:
MP4
Description:
Chapter 4: A bunny-planet design session.
Download
No Thumbnail Available
Name:
Chapter4_textureSynthesisSystemOverview.mp4
Size:
58.52 MB
Format:
MP4
Description:
Chapter 4: Texture synthesis system overview.
Download
No Thumbnail Available
Name:
Chapter9_Cytoskeleton.mp4
Size:
202.48 MB
Format:
MP4
Description:
Chapter 9: Cytoskeleton case study.
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
2.62 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Open Theses and Dissertations