Date

2019

Document Type

Dissertation

Degree

Doctor of Philosophy

Department

Physics

First Adviser

Vavylonis, Dimitrios

Abstract

Actin filaments are vital for different network structures in living cells. Dur- ing cytokinesis, they form a contractile ring containing myosin motor proteins and actin filament cross-linkers to separate one cell into two cells. Recent experimental studies have quantified the bundle, ring, and network structures that form when actin filaments polymerize in confined environments in vitro, in the presence of varying concentrations of cross-linkers and motor proteins. In this study, we per- formed numerical simulations to investigate the effect of actin spherical confinement and cross-linking in ring formation. We used a spring-bead model and Brownian dy- namics to simulate semiflexible actin filaments that polymerize in a confining sphere with a rate proportional to the monomer concentration. We simulate cross-linking implicitly as an attractive short-range potential between filament beads. Applying the model for different size of the confining spheres shows that the probability of ring formation decreases by increasing the radius (at fixed initial monomer concen- tration), in agreement with prior experimental data. We observed and quantified other forms of networks for larger radii. We describe the effect of filament length, attractive interaction, and actin monomer concentration.To capture the accurate mechanical and chemical properties of each crosslink- ing proteins, we introduce a new coarse-grained model that accounts explicitly for individual crosslinkers. Using this approach, we were able to reproduce the correct fascin-actin bundle persistence length and study these networks as a function of crosslinking protein concentration and confinement.Finally, we created synthetic movies of sheared and rotated polymer networks starting from our Brownian dynamics simulation of attractive semiflexible polymers. These images were used in the testing and development of biopolymer network image analysis software TSAOX (Trackable Stretching Open Active Contours). Using TSOAX, we were able to successfully track the imposed deformations.

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