MEDYAN.jl: Agent-based modeling of active matter and whole cells

Agent-based modeling of the whole cell has emerged as a frontier of modern research. To address this challenge, we developed MEDYAN, a mechano-chemical forcefield and simulation software, in C++. Our new Julia package is 10x faster. To achieve this result, the overall architecture was redesigned and various Julia packages were leveraged. I will describe our strategy for combining stochastic reaction diffusion dynamics with movable membrane and filament mechanics. See medyan.org for more details.

MEDYAN.jl is the next-generation implementation of our lab’s agent-based model of the cell cytoskeleton. Our goal is to describe the emergent behavior of a cell in terms of basic chemical and mechanical interactions between individual proteins. By rewriting our object-oriented C++ implementation in Julia we were able to speed up simulations by over 10x. We changed the overall framework architecture and used various high-performance Julia packages, including Optim.jl, CellListMap.jl, and JumpProcesses.jl to achieve this speed up. I will describe our strategy for combining stochastic reaction diffusion with deformable membrane and filament mechanics. Lastly, I will show some of the current applications of our model to study neuron growth and the T-cell immune synapse in collaboration with various experimental groups. For more details of the C++ based framework, please go to medyan.org.