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

07/28/2023, 2:00 PM2:30 PM UTC
32-G449 (Kiva)

Abstract:

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.

Description:

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.

Platinum sponsors

JuliaHub

Gold sponsors

ASML

Silver sponsors

Pumas AIQuEra Computing Inc.Relational AIJeffrey Sarnoff

Bronze sponsors

Jolin.ioBeacon BiosignalsMIT CSAILBoeing

Academic partners

NAWA

Local partners

Postmates

Fiscal Sponsor

NumFOCUS