Modeling Graph-Based Morphology of the Synaptic Spine Head
summary
Implements Dynamical Graph Grammars in a Mathematica package called Plenum to stochastically evolve actin filament graphs with rule-based propensities and conditional sampling; adds anisotropic filament forces, filament–membrane mechanical interaction, Lennard‑Jones buckling and Hessian‑Boltzmann sampling for thermal noise, using literature rate constants. Two validated outcomes appear: a network‑only simulation (coarse grain four actin monomers per object) produces a bimodal filament‑link distribution, and a membrane‑enclosed run (coarse grain eight) yields membrane volume growth that doubles relative to the actin skeleton and ends near half the small biological spine head (~0.05 µm³). Future porting to Kete is planned.
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chapters (14)
- 0:00Introduction
- 0:27Graph-based modeling theory
- 1:11Biological simulation modules
- 3:22Dynamical graph grammars
- 4:33Network remodeling rules
- 6:41Actin mechanics and membrane
- 9:12Actin skeleton role
- 10:37Graph grammar rules and code
- 13:53Stochastic simulation algorithm
- 16:47Simulation results no membrane
- 17:51Simulation results with membrane
- 19:38Future work
- 21:03Q&A branching mechanisms
- 22:09Q&A hybrid simulation
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