Team:UT Dallas/immunobot modeling

• Overview
  • Home
  • About Us
  • Gallery
  • BioBricks
  • Acknowledgments
• Immunobots
  • Introduction
  • Animation
  • Modeling
  • Results
• Killbots
  • Introduction
  • Results
• Human Practices
  • Considerations
  • Safety
• Notebook
  • Protocols
  • Calendar
  • DNA Ladders
• Android Apps
  • Ligation Calculator
  • NEB Double Digest
• Data

Model and simulation

The signaling network from the input of external ligand signal to the output of the tumbling state of a E coli cell can be quantitatively described by a modular model. The model is formulated based on the law of mass action and Michaelis-Menten mechanism and contains four relatively independent modules that are explained in detail below.

Module 1: Activation of ToxR receptor
In this module, the ligand signal activates the ToxR receptor into a dimerized complex formed with the ligand, which is the active state of the receptor. The biochemical reaction can be illustrated as:

where L, R, C and C2 represent the concentration of external ligand, free receptor, recptor-ligand complex, and the dimerized receptor-ligand complex. The first reaction represents the binding/unbinding between the free receptor and the ligand. The second reaction represents the dimerization /undimerization conversions between C and C2. The conservation of the total concentration of the receptor can be written as: