Plant Tissue Growth Simulation
Computational biology research with auxin transport modeling
Extended semicircular leaf model with auxin transport and PIN polarization for computational biology research using the Jönsson lab’s Tissue Simulator.
Overview
This project involved extending a plant tissue growth simulator to model auxin transport and cell division in leaf development. The simulation helps understand how hormonal signals guide cellular organization during plant growth.
Tech Stack
- C++ - Core simulation engine
- Python - XML scripting for model configuration
- VirtualLeaf/Organism-Tissue Simulator - Jönsson lab framework
- Paraview - 3D visualization of tissue structures
- WSL/Ubuntu - Development environment
Key Components
Cell Division Modeling
- Implemented cell division logic based on growth thresholds
- Integrated with existing tissue mechanics
Auxin Diffusion
- Simulated auxin hormone transport between cells
- Debugged variable index mismatches in diffusion equations
PIN Polarization
- Modeled auxin efflux carrier protein distribution
- Analyzed effects on tissue patterning
Visualization
- Generated 3D tissue structures in Paraview
- Created time-series animations of growth dynamics
Challenges
Debugging C++ simulation c