2026-08-14 –, Room 4
MEDYAN.jl is a framework for modeling the cytoskeletal filaments and associated proteins that shape and move cells. New declarative rules for dynamic mechanical and chemical bonds, accelerated by new spatial data structures, enable simulations as large as a whole T-cell or as detailed as the individual reactions in a motor protein step. These improvements help bridge the gap between single molecules and cell behavior on timescales of minutes and length scales of micrometers.
I will describe the new collision detection system for accelerating force and distance calculations between point, line segment, and triangle objects, including data structures and algorithms in the reusable SimplexCellLists.jl package.
I will also describe the new system for handling the dynamic mechanical and chemical links that can form and break between entities during a simulation. Users can write declarative rules for any custom force law, reaction rate, and reaction effect. These rules leverage Julia to generate efficient multi-threaded force kernels. The chemical reaction rules are accelerated with spatial data structures from SimplexCellLists.jl. Link topology is tracked using generational-index graphs via UniqueIDs.jl, enabling efficient creation and deletion of transient connections. This modular and extensible system is important for describing the variety of protein interactions and chemistry in the cell.
PhD student in biophysics, University of Maryland College Park