Team:LCG-UNAM-Mexico/Simulation

 
 

 
With the aim of predicting the behavior of the system, the biochemical reactions were implemented in the SimBiology package of MATLAB, using the previously defined parameters (link a parameters and kinetics). Simulations were run for different values of the initial concentration of AHL and Ni_total (Ni_int + Ni_ext) which are the metabolites that we can directly manipulate in our experiments. A parameter scan was also run for some parameters to understand their influence on the system.
In order to gain insights into the system dynamics to elucidate the conditions needed to get the desired behavior, we performed a series of analysis on it: sensitivity analysis allowed us to identify critical parameters that needed to be defined on the most stringent way. Basis for the (right) null and left null space were calculated to obtain information about the general network behavior. Steady-states were calculated by numerical integration of the non-linear ODEs system. Finally the Jacobian of the system was calculated around the steady-states. All simulations and analysis were implemented and performed on MATLAB.

Simulation and parameter scan

Describir el comportamiento que queremos ver y por qué.
Incluir las gráficas de parameter scan, la gráfica de la vida, y el escaneo con el que definimos algunas constantes

Sensitivity analysis

Definir brevemente de que se trata, mostrar análisis a diferentes tiempos. Señalar los resultados que esperábamos y los que no

Stoichiometric matrix

Definir la información que contiene la matriz estequimétrica.
Definir los espacios nulos (link a wikipedia o matworld?)
Presentar las bases calculadas y una interpretación concisa

Steady-states

Definir estado estacionario, decir algo de la complejidad del problema y justificar la estrategia elegida (aproximación numérica)

Presentar la solución ontenida.

Jacobian

Definición general del jacobiano (link a wikipedia o mathworld?). Definición en redes bioquímicas.
Presentar el método para calcularlo y las matrices modales, junto con su interpretación y las escalas de tiempo.
Si da tiempo poner algo de análiss de estabilidad del estado estacionario (lo más probable s que no sea estable).