Coarse-grained, semiflexible copolymer behavior with applications to heterochromatin
Abstract/Contents
- Abstract
- The properties of polymer materials can vary widely and depend on their organization and the identity and interactions of their monomers. By requiring many monomers to occupy adjacent spatial locations, the connectivity of a polymer amplifies relatively weak monomer interactions. In this thesis I use theoretical and computational techniques to predict the resulting phase behavior and structure. These techniques use the wormlike chain model to incorporate the structural rigidity of the polymer backbone and use coarse-graining to capture the interactions. A semiflexible polymer backbone coupled with a repulsive Flory-Huggins interaction between blocks of a random copolymer causes frustration in the microphase segregation of the monomer types. The resulting phase diagram and structures can be adjusted by varying the statistics of the random sequence and the polymer rigidity. When the interactions depend on the orientation rather than identity of the monomers, a liquid crystal phase forms. I calculate the Frank elastic constants for liquid crystal solutions of wormlike chains that interact via a Maier-Saupe type interaction. A particular focus is devoted to the application of polymer physics techniques to the biological system of chromatin. An HP1-H3K9me3 interaction model of heterochromatin is found to be capable of explaining features of Hi-C data and aid in the interpretation of ChIP-seq data. This interaction is used to provide a density-based physical explanation for the prevalence of peripheral heterochromatin
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2020; ©2020 |
| Publication date | 2020; 2020 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | MacPherson, Quinn Jerome |
|---|---|
| Degree supervisor | Doniach, S |
| Degree supervisor | Spakowitz, Andrew James |
| Thesis advisor | Doniach, S |
| Thesis advisor | Spakowitz, Andrew James |
| Thesis advisor | Qin, Jian, (Professor of Chemical Engineering) |
| Degree committee member | Qin, Jian, (Professor of Chemical Engineering) |
| Associated with | Stanford University, Department of Physics. |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Quinn MacPherson |
|---|---|
| Note | Submitted to the Department of Physics |
| Thesis | Thesis Ph.D. Stanford University 2020 |
| Location | electronic resource |
Access conditions
- Copyright
- © 2020 by Quinn Jerome MacPherson
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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