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
