Computational models of assembly, structure and damage to collagen IV networks
<p>Collagen IV networks play a key structural role in the human ocular lens capsule. However, their structure is not well understood, and is hypothesised to undergo significant changes over a lifetime, resulting in a loss of ability to accommodate different focal depths. In this thesis, a rang...
| Main Author: | |
|---|---|
| Other Authors: | |
| Format: | Thesis |
| Language: | English |
| Published: |
2022
|
| Subjects: |
| _version_ | 1797108575688982528 |
|---|---|
| author | Bailey, MHJ |
| author2 | Wilson, M |
| author_facet | Wilson, M Bailey, MHJ |
| author_sort | Bailey, MHJ |
| collection | OXFORD |
| description | <p>Collagen IV networks play a key structural role in the human ocular lens capsule. However, their structure is not well understood, and is hypothesised to undergo significant changes over a lifetime, resulting in a loss of ability to accommodate different focal depths. In this thesis, a range of computational models and methods are developed, which aim to help better understand the properties of 2D networks of biopolymers, especially inspired by collagen IV.</p>
<p>The available experimental images of collagen-containing networks are assessed and an image analysis protocol is developed. A Monte Carlo method is designed, which introduces disorder into simplified graph-based networks by switching edges. In addition, Molecular Dynamics is used to simulate coarse-grained polymers which attract one another at their headgroups. These coarse-grained polymers are shown to self-assemble into a variety of interesting network structures. The coarse-grained polymer approach is combined with a Molecular Statics scheme to calculate mechanical properties of the network, and understand how the networks behave when stretched. A model that can mimic the ageing of the network over a lifetime is developed. To better understand how lens capsule motion may damage collagen IV networks, the rupturing behaviour of the polymer networks is examined by stretching ordered hexagonal networks linearly and sinusoidally until they break. This is compared to the rupturing behaviour of networks containing defects.</p>
<p>The MD method is used to assess the surface roughness and dimensionality of polymer networks, which is quantified by a fractal dimension. Finally, a new type of persistence diagram is used to quantify and visualise damage to ring structures in a network over time.</p> |
| first_indexed | 2024-03-07T07:29:19Z |
| format | Thesis |
| id | oxford-uuid:b890424f-7b58-40c0-b171-ce7009edd962 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T07:29:19Z |
| publishDate | 2022 |
| record_format | dspace |
| spelling | oxford-uuid:b890424f-7b58-40c0-b171-ce7009edd9622022-12-23T11:16:32ZComputational models of assembly, structure and damage to collagen IV networksThesishttp://purl.org/coar/resource_type/c_db06uuid:b890424f-7b58-40c0-b171-ce7009edd962CollagenComputational chemistryEnglishHyrax Deposit2022Bailey, MHJWilson, M<p>Collagen IV networks play a key structural role in the human ocular lens capsule. However, their structure is not well understood, and is hypothesised to undergo significant changes over a lifetime, resulting in a loss of ability to accommodate different focal depths. In this thesis, a range of computational models and methods are developed, which aim to help better understand the properties of 2D networks of biopolymers, especially inspired by collagen IV.</p> <p>The available experimental images of collagen-containing networks are assessed and an image analysis protocol is developed. A Monte Carlo method is designed, which introduces disorder into simplified graph-based networks by switching edges. In addition, Molecular Dynamics is used to simulate coarse-grained polymers which attract one another at their headgroups. These coarse-grained polymers are shown to self-assemble into a variety of interesting network structures. The coarse-grained polymer approach is combined with a Molecular Statics scheme to calculate mechanical properties of the network, and understand how the networks behave when stretched. A model that can mimic the ageing of the network over a lifetime is developed. To better understand how lens capsule motion may damage collagen IV networks, the rupturing behaviour of the polymer networks is examined by stretching ordered hexagonal networks linearly and sinusoidally until they break. This is compared to the rupturing behaviour of networks containing defects.</p> <p>The MD method is used to assess the surface roughness and dimensionality of polymer networks, which is quantified by a fractal dimension. Finally, a new type of persistence diagram is used to quantify and visualise damage to ring structures in a network over time.</p> |
| spellingShingle | Collagen Computational chemistry Bailey, MHJ Computational models of assembly, structure and damage to collagen IV networks |
| title | Computational models of assembly, structure and damage to collagen IV networks |
| title_full | Computational models of assembly, structure and damage to collagen IV networks |
| title_fullStr | Computational models of assembly, structure and damage to collagen IV networks |
| title_full_unstemmed | Computational models of assembly, structure and damage to collagen IV networks |
| title_short | Computational models of assembly, structure and damage to collagen IV networks |
| title_sort | computational models of assembly structure and damage to collagen iv networks |
| topic | Collagen Computational chemistry |
| work_keys_str_mv | AT baileymhj computationalmodelsofassemblystructureanddamagetocollagenivnetworks |