Two_bacterial_groups.py

# -*- coding: utf-8 -*-
"""
Created on Thu Feb 11 13:42:37 2021

@author: savan
"""
#simulation R N S

from plate import Plate
from species import Species
import numpy as np
import helper_functions as hf

def main():
    
## experimental parameters
    D = 0.03
    rho_n = 0.5     
    rc = 3.33e-2 #6e-4
    Dc = 1e-5       
    w = 0.75 
    Da = 2.94e-6
    rho_A = 0.01    
    Dt = 0    

    environment_size = (59, 59)
    plate = Plate(environment_size)

    ##add nutrient to the plate
    U_N = np.zeros(environment_size)
    
    for i in np.linspace(0, 58, 59):
        for j in np.linspace(0,58,59):
            U_N[int(i),int(j)]=100
    N = Species("N", U_N)
    def N_behaviour(species, params):
        ## unpack params
        D, rho_n, Dc, rc, w, rho_A, Da, Dt = params
        n = D*hf.ficks(species['N'], w) - (species['R']+species['S'])*rho_n*hf.leaky_hill(s=species['N'], K=80, lam=1, max=rc, min=0) #rho_n * species['N'] * (species['R'])
        return n
    N.set_behaviour(N_behaviour)
    plate.add_species(N)

    ##add sender strain to the plate
    U_S = np.zeros(environment_size)
    for i in np.linspace(29, 29, 1):
        U_S[int(i), int(i)] = 0.001
    S = Species("S", U_S)
    def S_behaviour(species, params):
        ## unpack params
        D, rho_n, Dc, rc, w, rho_A, Da, Dt = params
        s = Dc*hf.ficks(species['S'], w) + species['S']*hf.leaky_hill(s=species['N'], K=80, lam = 1, max=rc, min=0)
        return s
    S.set_behaviour(S_behaviour)
    plate.add_species(S)
    
    ##add uninformed strain to the plate
    U_R = np.zeros(environment_size)
    for i in np.linspace(29, 29, 1):
        for j in np.linspace(29,29, 1):
            U_R[int(i), int(j)] = 0.001
    R = Species("R", U_R)
    def R_behaviour(species, params):
        ## unpack params
        D, rho_n, Dc, rc, w, rho_A, Da, Dt = params
        r = Dc*hf.ficks(species['R'], w) + species['R']*hf.leaky_hill(s=species['N'], K=80, lam = 1, max=rc, min=0)
        return r
    R.set_behaviour(R_behaviour)
    plate.add_species(R)

    params = (D, rho_n, Dc, rc, w, rho_A, Da, Dt)
    sim = plate.run(t_final = 200*60,
                    dt = 1.,
                    params = params)

    #plate.plot_simulation(sim, 3)
    idx = 0
    #colour = 'b' 
    #S = plate.get_all_species()
    plate.compare_species(sim, S, 10, idx)
    #plate.plot_conc_target(sim, S, 10)

main()