Using Simulations to Guide the Design of Biotic-Abiotic Machines

Wide availability of purified cytoskeletal proteins and advances in click chemistry have motivated interest in coupling structural and force bearing components of the cell cytoskeleton to inert structural elements to construct actuators powered by chemical potential gradients. The potential design space for such devices is vast, and computational models are called for to steer experiments. Here, we present a simulation framework that couples semiflexible polymer mechanics, molecular motor kinetics, and nonlinear gel elasticity to simulate biotic-abiotic machines. An agent-based description of cytoskeletal protein mechanics is coupled to a finite element mesh, used to simulate the elastodynamics of a passive hydrogel. In pursuit of high throughput simulations, we expedite calculations with thread parallelism and efficient modern algorithms for rapid spatial queries and finite element mesh topology optimization. We will discuss the potential of this model to anticipate emergent properties of a cytoskeletal protein actuator, such as traction forces exerted by the actomyosin gel on a boundary, and process dependence of material properties resulting from repeated cycles of activity.