README.md

C-Code developed for modeling stochastically the CheY-P molarity in the neighbourhood of flagella motors

Scientific background availabe in Preprint at bioRxiv [Stochastic model for the CheY-P molarity in the neighbourhood of E. coli flagella motors] (https://www.biorxiv.org/content/10.1101/831990v1.full).

Code1 instructions

Code files:

• definciones.c: File for initial setup of parameters for numerical simulations.
• definciones.h: File for setting number of bacteria (nbac) and number of flagella (nfla)
• main.c : File with code flow.
• export.c: File where .dat files are created for saving data.
• RATtransition: File where numerical simulations, flagella states and flagellar transitions are calculated.

This branch can be used for two purposees:

• The code is set to obtain RTD and TTD for non unstimulated scenarios (Tumble bias=0.15). Data is saved in the savefilesTimesDist.dat file where the first column saves the Runs time and the second column saves the Tumbles time.

• Obtain steady state probability density function for molar Chey-P concentration, where the following changes must be done:
  In definciones.h change:

   nfla=1; 
   nbac=1; 
  

  In definciones.c change:

   double dtickshut = 15000.0; 
  

  In main.c:

   uncomment ->     if(tiempo > 100.0 && fmod(dticks,100.0)==0.0){ 
         		  savefilesCheypDist(tmpcheyp[0][0],meancheyp/(nfla*nbac*(dticks))); 
       		}; 
  
   File savefilesCheypDist.dat will have two columns separated by comma (CSV) where the first column is Chey-P values obtained from 
   numerical integration and the second one is the mean value obtained over time.
  

For more information see Usage_notes.pdf .