Steady-state

Simulation

Temporal simulation is performed using the Systems Biology Toolbox 2 http://www.sbtoolbox.org/ environment with numerical integration using ode45. The catalytical model is specified by

********** MODEL NAME
Dimensionless form. Catalytical.

********** MODEL NOTES
Kinetic model of trap-RNA system.
Parameters are estimated from literature.

********** MODEL STATES
d/dt(m) = 1 - m - k_s*alpha_m*m*s/(beta_m*beta_s)
d/dt(s) = (beta_s/beta_m)*(alpha_s/alpha_m - s - k_r*alpha_m * s * r /(beta_s*beta_r))
d/dt(r) = (beta_r/beta_m)*(alpha_r/alpha_m - r)

m(0) = 1
s(0) = 0
r(0) = 0                                    

********** MODEL PARAMETERS
alpha_m = 10
alpha_s = 0
alpha_r = 0
beta_m = 0.0257
beta_s = 0.0257
beta_r = 0.0257
k_s = 0.00082
k_r = 0.0082

********** MODEL VARIABLES

********** MODEL REACTIONS
	
********** MODEL FUNCTIONS

********** MODEL EVENTS
event = gt(time,1), alpha_s, 40
event = gt(time,3), alpha_r, 200
event = gt(time,6), alpha_r, 0
********** MODEL MATLAB FUNCTIONS

File:DTU Model7.txt

The partly stoichiometric model is specified by

********** MODEL NAME
Dimensionless form. Stoichiometric.

********** MODEL NOTES
Kinetic model of trap-RNA system.
Parameters are estimated from literature.

********** MODEL STATES
d/dt(m) = 1 - m - k_s*alpha_m*m*s/(beta_m*beta_s)
d/dt(s) = (beta_s/beta_m)*(alpha_s/alpha_m - s - k_r*alpha_m * s * r /(beta_s*beta_r))
d/dt(r) = (beta_r/beta_m)*(alpha_r/alpha_m - r - k_r*alpha_m * s * r /(beta_s*beta_r))

m(0) = 1
s(0) = 0
r(0) = 0                                    

********** MODEL PARAMETERS
alpha_m = 1
alpha_s = 0
alpha_r = 0
beta_m = 0.0257
beta_s = 0.0257
beta_r = 0.0257
k_s = 0.00082
k_r = 0.0082

********** MODEL VARIABLES

********** MODEL REACTIONS
	
********** MODEL FUNCTIONS

********** MODEL EVENTS
event = gt(time,1), alpha_s, 40
event = gt(time,3), alpha_r, 200
event = gt(time,6), alpha_r, 0
********** MODEL MATLAB FUNCTIONS

File:DTU Model8.txt

The script running simulation and generating figures.