A 3D Multiscale Model of Chemotaxis in Bacteria
Date
2015-07-09
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Abstract
We present a multiscale 3D model of a colony of \ecoli\ bacteria. We simulate four distinct yet computationally interconnected levels. Each level represents a layer of detail with each level getting progressively more complex.
We present a multiscale 3D model of a colony of \ecoli\ bacteria. We simulate four distinct yet computationally interconnected levels.
In the first and second level, we simulate chemical diffusion in the environment to capture the colony population’s chemotactic behaviour. The bacterium interact with a discrete grid which models diffusion of chemicals. The first level presents this population behaviour in the form of a colour gradient, and proceeding to the second level we present the behaviour as particles.
The third level, the chemotactic motions of the individual bacterium is presented. And in the fourth level, the cellular processes that drive the chemotactic behaviour is presented.
We show four interconnected model layers that capture the biological processes from the colony layer down to the level of interacting molecules. The aim of this work is to construct a platform that enhances understanding of natural life by serving as a valuable educational tool.
Moving into the third level a single bacterium cell is presented in the simulation. In this third level, the chemotactic motions of the individual cell is presented. In the fourth level, we present the cellular processes that drive the chemotactic behaviour. Implementation of the cellular process is comprised of the two key chemotactic pathway responses: excitation and adaptation. Together the two responses regulate the motor and influence the movement of the bacterium through the agar medium.
We show four interconnected model layers that capture the biological processes from the colony layer down to the level of interacting molecules.
The simulation's visual effects, interactivity and biological relevance are the foundations of this thesis. The aim of this work is to construct a platform that enhances understanding of natural life by serving as a valuable educational tool.
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Keywords
Bioinformatics, Biology--Cell, Computer Science
Citation
Wu, A. (2015). A 3D Multiscale Model of Chemotaxis in Bacteria (Master's thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca. doi:10.11575/PRISM/24626