Date of Award
Doctor of Philosophy (PhD)
Living matter is a class of soft matter systems that maintains itself away from thermodynamic equilibrium by the continual consumption of chemical energy. Indi- vidual proteins consume energy and break detailed balance to drive active force generation by molecular motors, force-dependent binding kinetics, and chemically driven (dis)assembly. These non-equilibrium dynamics propagate across heterogeneous structures to drive essential life processes such as replication, migration, and shape change at the scale of both single cells and multicellular tissues. While much work has been done to understand the molecular processes underlying each individual non-equilibrium behaviors, we lack a general understanding of how the microscopic breaking of detailed balance translates to large-scale cellular behaviors and materials properties.Using the tools of non-equilibrium thermodynamics, this thesis examines this question by measuring energy dissipation during dynamical and mechanical phase transitions seen in experiments, simulations, and theoretical models of biological materials. We choose the actomyosin cytoskeleton, a network composed of polymeric proteins (actin) that are driven away from thermodynamic equilibrium by the activity of molecular motors (myosin), as our model system. Actomyosin contains the three types of non-equilibrium driving we will focus on: force generation, non-equilibrium binding kinetics, and active (dis)assembly. At the subcellular level, analysis of actin filament motions in experiments shows that energy dissipated through bending controls the transition between stable and contractile steady states. Using simulations, we show that non-equilibrium binding kinetics of molecular motors controls a fluid-solid phase transition characterized by thermodynamic quantities with opposite symmetries under time-reversal. At the cellular level, we develop new tools for measuring irreversibility in spatiotemporal dynamics to analyze the energetic costs of oscillations and synchronization of a model biochemical oscillator inspired by (dis)assembly driven actomyosin dynamics. Throughout this thesis, we show that a cell’s distance from equilibrium, quantified by energy dissipation, tunes its mechanical properties and dynamics. This provides a framework to unify disparate biological function through the lens of non-equilibrium thermodynamics.
Seara, Daniel, "Energetics of Biological Mechanics and Dynamics" (2021). Yale Graduate School of Arts and Sciences Dissertations. 112.