EUKARYO: An Agent-Based, Interactive, Virtual Reality Simulation of a Eukaryotic Cell

Game engines provide sophisticated tools for rendering virtual environments. Their capabilities make them suitable for constructing detailed virtual environments. In this thesis, we present Eukaryo, an interactive, 3D model of a eukaryotic cell that was implemented in Unity and Unreal Engine. Eukaryo utilises mathematical modelling towards modelling enzyme kinetics, and agent-based modelling to illustrate the interaction between the individual proteins in the cell. Using hybrid modelling, Eukaryo is able to model the interactions for a diverse range of biological processes, such as protein activation pathways and cytoskeleton self-assembly. Further to this, Eukaryo provides support for virtual reality devices, such as the CAVE and Oculus Rift headset; users can immerse themselves in a virtual biomolecular environment. By combining state-of-the-art biological simulations with the 3D visualisations and real-time interactivity, Eukaryo provides an innovative environment for exploring cellular processes to convey the complexity in systems that constitute the machinery of life.

Name thesis:degree_name

Master of Science (MSc)

Discipline thesis:degree_discipline

Computer Science

Grantor dc:publisher.institution

Graduate Studies

Year dc:date.issued

2016

Author dc:creator

• Yuen, Douglas Wing-Kwok

Advisor dc:contributor.advisor

• Jacob, Christian

Committee members dc:contributor.committeemember

• Denzinger, Jörg
• Katz, Larry

• Biology--Cell
• Computer Science

Statement dc:rights

• University 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.

Language dc:language.iso

eng

DOI

http://dx.doi.org/10.11575/PRISM/25962

OAI identifier oai:identifier

oai:ucalgary.scholaris.ca:11023/3177