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Numerical Methods in Matlab

This repository contains Matlab functions of several popular numerical methods for solving differential equations such as Gillespie's stochastic method and Runge-Kutta 4th order method.

Getting started

Prerequisites

  • Matlab 2013a or higher (tested until Matlab 2017a)

Installing

Simply copy the Matlab files in src to your working directory, make sure that the file is included in your path and call as required.

Testing

A few test cases have been set up in test that showcases the use of the models in solving differential equations. For instance, to test Runge-Kutta, simply run runTestRK.m in Matlab console.

runTestAll.py runs both the Runge-Kutta test file and the Gillespie test file and compares the results with a plot. Both solvers solve the concentrations of species A, B and C that undergo the reversible reaction

A + B <-> C

You should get something like the following image where the smooth lines are the results calculated by Runge-Kutta methods and the erratic lines are those solved by the Gillespie method.

testimage

Deploying

Gillespie stochastic method

This method requires the following:

  • Intial state array (X)
  • a timestep (dt)
  • stochiometry matrix (v)
  • propensityFunction.m as per the reaction rate of each reaction and species.

In reality the model can simply be called as

X_nx = gillespieSolver(X,v, final_time, @propensityFunction);

to get the value of the state array at the specified final_time. Since Gillespie's method gives a non-uniform time according to the values of the propensity function, it can be editted as follows to save values at every timestep dt.

X = [N_A, N_B, N_C]

for it = 2:nt
	X_nx = gillespieSolver(X,v, delta_t,@propensityFunction);
	X = X_nx;
end

Make sure to update the state array after every timestep.

Runge-Kutta method

You will need to edit

  • gradient.m as per the differential equations that you wish to solve.

For instance

eqns(1)

represents the derivative of the first component with respect to time.

In your main Matlab file, specify a timestep (delta_t) and the initial value of your variables (@ time = 0). Put the main equation in a for loop and update the time after ever timestep.

input = [x; y; z];

for it = 2:nt
    
    current_t = (it-1)*delta_t;
    
    sol = rungeKuttaFourth(input, current_t, delta_t);

    % Update the input
    input = [sol(1);sol(2);sol(3)]

 end