Mechanical phase transitions in biopolymer networks
| dc.contributor.advisor | MacKintosh, Fred C. | |
| dc.creator | Arzash, Sadjad | |
| dc.date.accessioned | 2021-12-06T19:38:12Z | |
| dc.date.available | 2021-12-06T19:38:12Z | |
| dc.date.created | 2021-12 | |
| dc.date.issued | 2021-12-03 | |
| dc.date.submitted | December 2021 | |
| dc.date.updated | 2021-12-06T19:38:13Z | |
| dc.description.abstract | Biopolymer networks are vital components of all living organisms. Cytoskeleton, as a complex intercellular network composed of fibrous proteins such as filamentous actin (F-actin), microtubules and intermediate filaments, provides mechanical stability for the cell. Extracellular matrix (ECM), on the other hand, is an interwoven structure of proteins and polysaccharides that are secreted by cells into their extracellular space. This network not only provides a way to hold cells together and facilitate tissue formation, but is also a means of communication between the exterior and interior of the cells. These fiber networks are constantly under both external and internal stresses. It has been observed that the mechanical behavior of biopolymer networks is significantly different from classic elastic materials such as rubber and synthetic polymers, e.g., they exhibit a highly nonlinear strain-stiffening under shear. In this thesis, we focus on the mechanics of biopolymers using coarse-grained simulations of spring networks with stretching and bending interactions. Prior work has shown that these computational models can explain the rheological experiments of reconstituted biopolymer gels. Intrigued by the stability of frames, Maxwell showed that structures with central-force interactions are unstable under small deformations if their average connectivity or coordination number falls below the critical isostatic point $z_c = 2d$, where $d$ is dimensionality. Experiments confirm that the average connectivity of biopolymer networks is far below $z_c$. Under a finite applied strain, a subisostatic network undergoes a transition from a floppy to a rigid state at a critical strain that depends on the connectivity and geometry of the network. It has been shown that this strain-induced transition is critical in nature. Using finite-size scaling methods, we obtain various non-mean-field critical exponents for this mechanical phase transition. By applying the classic real-space renormalization idea, we identify scaling relations between these exponents. To test these relations, we use various computational models in 2D and 3D. Furthermore, we explore the effects of thermal fluctuations as a stabilization field in central-force subisostatic networks under nonlinear strains. Finally, to understand the stress relaxation behavior in F-actin solutions, we develop a model based on the master equations by including polymerization, depolymerization, and severing reactions that captures the general behavior observed in experimental studies. | |
| dc.format.mimetype | application/pdf | |
| dc.identifier.citation | Arzash, Sadjad. "Mechanical phase transitions in biopolymer networks." (2021) Diss., Rice University. <a href="https://hdl.handle.net/1911/111740">https://hdl.handle.net/1911/111740</a>. | |
| dc.identifier.uri | https://hdl.handle.net/1911/111740 | |
| dc.language.iso | eng | |
| dc.rights | Copyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder. | |
| dc.subject | phase transitions | |
| dc.subject | critical phenomena | |
| dc.subject | fiber networks | |
| dc.subject | mechanics of biopolymers | |
| dc.subject | scaling exponents | |
| dc.subject | finite-size scaling | |
| dc.subject | rheology of fibrous networks | |
| dc.title | Mechanical phase transitions in biopolymer networks | |
| dc.type | Thesis | |
| dc.type.material | Text | |
| thesis.degree.department | Chemical and Biomolecular Engineering | |
| thesis.degree.discipline | Engineering | |
| thesis.degree.grantor | Rice University | |
| thesis.degree.level | Doctoral | |
| thesis.degree.name | Doctor of Philosophy |
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