Jacob, ChristianSamavati, Faramarz FamilDavison, Timothy2020-01-132020-01-132020-01Davison, T. (2020). LifeBrush: An Illustrative Simulation Canvas for the Biological Mesoscale (Doctoral thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.http://hdl.handle.net/1880/111493At 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.engUniversity 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.mesoscaleillustrative simulationagent-based modellingdiscrete element texture synthesismacromolecular self-assemblyscientific illustrationvirtual realitysketch-basedtexture synthesiscomputer graphicsBioinformaticsBiology--MolecularComputer Sciencedoctoral thesis10.11575/PRISM/37450