SkellySim: A simulation package for cytoskeletal dynamics in the flow-dominated regime

SkellySim is a simulation framework designed to simulate flexible filaments and mobile rigid bodies, undergoing hydrodynamic interactions with or without an enclosing periphery. The previous incarnation of this code was written in C++, based on a finite difference scheme, with the governing equations linearized by hand. It ran efficiently on large clusters but was not designed to be easy to install or run on personal machines. In this talk, we discuss a rewrite of SkellySim in Julia, which leverages automatic differentiation to directly solve the non-linear governing equations. This leads to dramatically simpler code, allowing many improvements: flexible discretizations, including the use of spectral methods; direct imposition of constraints, improving numerical stability; easy extensibility, enabling new features such as steric interactions; and the ability to leverage heterogeneous compute architectures, including large cluster nodes and GPUs. The code is easy to install and provides surprisingly good performance on laptops. Current applications target streaming flows in drosophila oocytes, and aster positioning and dynamics.