Team:Calgary/Modelling/Method

Overview

• Updates
  
• Notebook & Parts

Membrane Computing Modelling

• Introduction
  
• Tutorials
• Results
• Paper

Differential Equation Modelling

• Method
  
• Results
  
• Basic Definitions

We've reached modelling, the fifth stop on our tour! We've looked in to two different methods of modelling our system: Differential Equation Based Modelling and Membrane Computing. Here, you can explore the similarities and differences, as well as the functions of each method. As well, you can find the results of our characterization of the signalling pathway. Once you're done, we'll move on to the Second Life component of the project HERE.

The simbiology interface from Matlab was used to simulate the differential equations model. Chemical Kinetic equations were used to build the model for simulation.
Fig : The Reaction of Species A with B to produce C and D

Fig : The Chemical Kinetic Rate Equation k is the kinetic rate constant. The size of k will determine the speed of the reaction. A smaller value of k will produce a slow reaction rate while a larger value of k will produce a fast reaction rate.
[A] is the amount of reactant A present.
The simulations were run for 50000 seconds . It was considered to be enough time for the system to reach equilibrium after disturbance. The Sundials Solver (how do they work ?)was used to run these simulations because for this model it was considered to produce optimal results. (how do simulations work?)

The system was represented by the following reactions. The reactions with double headed arrows have two rate constants(forward/ reverse rate constant). All reactions were assumed to be elementary reactions.