Computer simulations of vesicle transport in plant cells

Zarate, Jyan

Student Work

Computer simulations of vesicle transport in plant cells

Public Deposited

Computational methods are becoming increasingly important in cell biological research. Modern computer simulations allow us to simulate biological processes at the cellular and molecular level by programming theoretical equations describing the diffusion and motion of cellular components such as vesicles and actin. Here, I examine the viability of using Cytosim as a cytoskeleton simulation software and develop a framework to manage parameter scans, run concurrent simulations, and extract and analyze data from the simulation software. This framework was then used to run simulations and analyses to prove that Cytosim is a reliable simulation engine for future work by comparing existing theory versus results from the simulations. We fit the Mean Squared Displacement of vesicles to find that Cytosim accurately simulated Brownian motion for them. We estimated the persistence length of filaments by calculating the mean squared end-to-end distance and solving for it with a worm-like chain model, and found that Cytosim simulates filaments with negligible differences from their theoretical and real-world counterparts. We then did extensive simulations to evaluate the effect on a vesicle's diffusion of attaching filament of various lengths. This work establishes Cytosim as a promising base for future research at cell biological laboratories investigating vesicle-filament interactions.

This report represents the work of one or more WPI undergraduate students submitted to the faculty as evidence of completion of a degree requirement. WPI routinely publishes these reports on its website without editorial or peer review.

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