Modelling and simulating twitching bacteria and phytoglycogen nanoparticles

Abstract

This thesis covers work conducted on two projects. Each of these projects involve application in the field of biology, and both have been completed through the use of computer simulation techniques. The first project is modelling and simulating the collective motion of twitching bacteria. This problem consists of hundreds of moving twitchers that can be modelled, tracked, and analysed easily through the use of computer simulation and visualization. Each twitcher was modelled as four spheres held into a rod-like configuration, and make use of two dummy spheres to guide twitching motility. Here, three different models of twitching motility were produced, and simulations confirmed the emergence of collective motion in each model. The second project involves the use of atomistic simulations with the purpose of investigating the structure of phytoglycogen nanoparticles. Here, simulations allow us to analyse a reduced structure in atomistic detail. Simulations were conducted of a group of amylopectin branches solvated in water in order to study their interactions with each other, with water, and with beta-carotene. The interactions observed were a combination of hydrophobic and hydrophilic interactions, suggesting that phytoglycogen might be amphiphilic in nature.