Self-assembly of biological heteropolymers
Name
1201521709-MIT.pdf
Size
10.97 MB
Format
Adobe PDF
Checksum (MD5)
fd4aff971914eb708c4651ff685bd5f9
Author(s)
Falk, Martin Jin-teng.
Advisor(s)
Michael P. Brenner and Leonid A. Mirny.
Date Issued
2020
Publisher
Massachusetts Institute of Technology
Abstract
In this thesis, we are primarily concerned with understanding the complicated geometrical and topological structures that polymers can adopt. We first consider this in the context of chromatin, the polymer of DNA and associated proteins. Our experiments and coarse-grained modeling suggest that attractions between heterochromatic regions are central to the separation of the active and inactive genome in nuclei. We adopt a similar strategy of coarse-grained polymer modeling in order to devise a collagen-like scheme for twisting polymers together. We found that such scheme generically includes the presence of defects, which we speculate could be useful in designing hierarchical assemblies of twisted filaments. In order to extend strategies for twisting of filaments to arbitrary braid topologies, we constructed a simple numerical model for a device that manipulates float-attached wires with capillary interactions between the walls of the device and the float. We use this model to rationalize design rules for the device, and to predict the motion of the float in non-trivial geometries. Finally, we study the dynamics of a two-dimensional seven-particle cluster as it relaxes from an extended, polymer-like state. We find that this system rarely reaches its (non-degenerate) global free energy minimum.
Description
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, February, 2020
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 115-122).
Subjects
Physics.
MIT Department
Massachusetts Institute of Technology. Department of Physics
Terms of Use
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