The role of hydrodynamic interactions in the dynamics and viscoelasticity of actin networks
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2012.
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| Format: | Thesis |
| Language: | eng |
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Massachusetts Institute of Technology
2012
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| Online Access: | http://hdl.handle.net/1721.1/70419 |
| _version_ | 1826215095745642496 |
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| author | Karimi, Reza, Ph. D. Massachusetts Institute of Technology |
| author2 | Mohammad R. K. Mofrad. |
| author_facet | Mohammad R. K. Mofrad. Karimi, Reza, Ph. D. Massachusetts Institute of Technology |
| author_sort | Karimi, Reza, Ph. D. Massachusetts Institute of Technology |
| collection | MIT |
| description | Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2012. |
| first_indexed | 2024-09-23T16:16:48Z |
| format | Thesis |
| id | mit-1721.1/70419 |
| institution | Massachusetts Institute of Technology |
| language | eng |
| last_indexed | 2024-09-23T16:16:48Z |
| publishDate | 2012 |
| publisher | Massachusetts Institute of Technology |
| record_format | dspace |
| spelling | mit-1721.1/704192019-04-11T10:35:47Z The role of hydrodynamic interactions in the dynamics and viscoelasticity of actin networks Karimi, Reza, Ph. D. Massachusetts Institute of Technology Mohammad R. K. Mofrad. Massachusetts Institute of Technology. Dept. of Mechanical Engineering. Massachusetts Institute of Technology. Dept. of Mechanical Engineering. Mechanical Engineering. Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2012. Cataloged from PDF version of thesis. Includes bibliographical references (p. 143-146). Actin, the primary component of the cytoskeleton, is the most studied semi-flexible filament, yet its dynamics remains elusive. We show that hydrodynamic interactions (HIs) significantly alter the time scale of actin deformation by 2-20 fold at different levels of network structure. For a single fiber, HIs between the mesh-sized segments can change the net force by up to 7 fold. Relaxation times are underestimated, if HIs are ignored, but mode shapes are not affected. HIs can explain deviation of the relaxation times from standard worm like chain models, speculated to be due to internal viscosity of the filament. HIs affect filament alignment, a necessary step for bundle formation. Ignoring HIs can result in up to 20-fold overestimation of shear loss modulus in the 2 ym range investigated. Even for a 1 mg/ml F-actin (0.1% volume fraction), HIs cannot be neglected whether the network is discretized into beads or rods. A shear loss modulus, slightly dependent on system-size, can be defined consistent with (intrinsic) viscoelasticity. However, axial loss modulus follows a quadratic system-size dependency consistent with poroelasticity. Our results suggest that including HIs is critical for consistency in theoretical models or analyzing experimental observation in cytoskeleton mechanics and dynamics. We also propose a new rod method to incorporate the HIs accurately and effectively. This method includes HIs in the larger systems, the same way as typical bead models, but it can decrease the computational cost by up to 100,000 fold. The primary part of this thesis deals with the viscous properties of the cytoskeletal actin networks investigated via theoretical bottom-up approaches in the nm to pm ranges. However, initially we focus on elastic properties of arterial tissue in the pm to mm ranges via an experimental top-down approach. We develop a combined robust registration and inverse elasticity method to investigate the mechanical properties of arterial tissue. We quantify the accuracy of this method with simulated problems and in vitro gels. This method can identify lipid pools via OCT (optical coherence tomography) and assess plaque rupture risk for cardiovascular diagnosis. The method can also be used as a model-based registration technique.Key words: Actin, Hydrodynamic Interactions, Relaxation Time, Cytoskeleton, Rod Model, Brownian Dynamics, Viscoelasticity, Poroelasticity, Length-Scale Dependent, Inverse Elasticity Problem, Registration, Optical Coherence Tomography (OCT), Atherosclerotic Plaque, Cardiovascular Mechanics. by Reza Karimi. Ph.D. 2012-04-26T18:51:44Z 2012-04-26T18:51:44Z 2012 2012 Thesis http://hdl.handle.net/1721.1/70419 785168732 eng From p. 131 of text: Attached CD contains all related codes for: 1. Inverse and Registration Elasticity Problem, including the custom-built FEM core and related scripts in both Matlab and C++. I have also included FFT library and related Matlab libraries for completeness. Every time Matlab is updated, the libraries should also be checked for compatibility and correct dynamic links (dl). 2. Matlab code for Hydrodynamic Interaction of bead/rod models and specific scripts for analyzing the role of Hydrodynamic Interactions in Actin's Dynamic. M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission. http://dspace.mit.edu/handle/1721.1/7582 146 p. application/pdf Massachusetts Institute of Technology |
| spellingShingle | Mechanical Engineering. Karimi, Reza, Ph. D. Massachusetts Institute of Technology The role of hydrodynamic interactions in the dynamics and viscoelasticity of actin networks |
| title | The role of hydrodynamic interactions in the dynamics and viscoelasticity of actin networks |
| title_full | The role of hydrodynamic interactions in the dynamics and viscoelasticity of actin networks |
| title_fullStr | The role of hydrodynamic interactions in the dynamics and viscoelasticity of actin networks |
| title_full_unstemmed | The role of hydrodynamic interactions in the dynamics and viscoelasticity of actin networks |
| title_short | The role of hydrodynamic interactions in the dynamics and viscoelasticity of actin networks |
| title_sort | role of hydrodynamic interactions in the dynamics and viscoelasticity of actin networks |
| topic | Mechanical Engineering. |
| url | http://hdl.handle.net/1721.1/70419 |
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