Browsing by Author "MacKintosh, Fred C."
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Item Mechanical phase transitions in biopolymer networks(2021-12-03) Arzash, Sadjad; MacKintosh, Fred C.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.Item Mechanics of Biopolymer Networks(2023-08-08) Chen, Sihan; MacKintosh, Fred C.Biopolymer networks pervade living systems, appearing in diverse structures from the cellular cytoskeleton to the extracellular matrix at the tissue level. Besides their biological significance, these networks exhibit a variety of physical phenomena arising from the collective interactions of biopolymers. One example is the cytoskeletal networks, which are continually driven out of equilibrium by the hydrolysis of adenosine triphosphate (ATP), engendering unique non-equilibrium dynamics such as force generation. Furthermore, bending fluctuations within these networks generate intriguing dynamical viscoelastic properties. Most notably, recent research has unveiled a mechanical critical phase transition in the nonlinear elasticity of athermal fiber networks. This dissertation proposes several theoretical frameworks tailored to shed light on the physics of the mechanical properties intrinsic to biopolymer networks. The first part of the thesis introduces a theoretical mechanism for the non-equilibrium force generation within cytoskeletal networks, particularly in scenarios where molecular motors are absent. Following this, we establish a theoretical model to quantify the nonlinear viscoelasticity exhibited by networks composed of transient crosslinkers. Progressing further, we construct a non-affine effective medium theory (EMT) to delineate the linear elasticity of biopolymer networks. Finally, we extend the EMT to capture the nonlinear elasticity and apply it to study the mechanical phse transition of fiber networks.Item Self-organized stress patterns drive state transitions in actin cortices(AAAS, 2018) Tan, Tzer Han; Malik-Garbi, Maya; Abu-Shah, Enas; Li, Junang; Sharma, Abhinav; MacKintosh, Fred C.; Keren, Kinneret; Schmidt, Christoph F.; Fakhri, Nikta; Center for Theoretical BiophysicsBiological functions rely on ordered structures and intricately controlled collective dynamics. This order in living systems is typically established and sustained by continuous dissipation of energy. The emergence of collective patterns of motion is unique to nonequilibrium systems and is a manifestation of dynamic steady states. Mechanical resilience of animal cells is largely controlled by the actomyosin cortex. The cortex provides stability but is, at the same time, highly adaptable due to rapid turnover of its components. Dynamic functions involve regulated transitions between different steady states of the cortex. We find that model actomyosin cortices, constructed to maintain turnover, self-organize into distinct nonequilibrium steady states when we vary cross-link density. The feedback between actin network structure and organization of stress-generating myosin motors defines the symmetries of the dynamic steady states. A marginally cross-linked state displays divergence-free long-range flow patterns. Higher cross-link density causes structural symmetry breaking, resulting in a stationary converging flow pattern. We track the flow patterns in the model actomyosin cortices using fluorescent single-walled carbon nanotubes as novel probes. The self-organization of stress patterns we have observed in a model system can have direct implications for biological functions.Item Settling dynamics of Brownian chains in viscous fluids(American Physical Society, 2022) Cunha, Lucas H.P.; Zhao, Jingjing; MacKintosh, Fred C.; Biswal, Sibani Lisa; Center for Theoretical Biological PhysicsWe investigate the dynamics of sedimenting Brownian filaments using experimental, computational, and theoretical approaches. The filaments under consideration are composed of linked colloidal particles that form bead-spring-like chains. Under the action of gravitational forces, the nonlocal hydrodynamic interactions cause the filaments to bend and rotate to get their end-to-end direction perpendicular to gravity. Different reorientation mechanisms are verified for different regimes of flexibility, characterized by the elastogravitational number. The thermal forces promote shape and orientation fluctuations around the steady configurations of the reciprocal non-Brownian chains. The competition between the reorientation mechanisms and the Brownian effects results in normal distributions of the orientation of the chains. In the stiff regime, these fluctuations cause the chains to fall faster than their reciprocal non-Brownian cases. With increasing flexibility, thermal fluctuations lead to more compact configurations of the chains and higher average settling velocity. Nonetheless, chain flexibility plays an important role on lateral migration. The interplay between elastic, gravitational, and thermal forces leads to important secondary influences on the filament settling dynamics.