<reponame>PollyJeffrey/Competition-modelling-paper<gh_stars>1-10
import numpy as np
from scipy import stats

#Define number of molecules and parameter values for the model
nl = 500
nr1 = 30
nr2 = 50
kr1 = pow(10,-3)
kr2 = pow(10,-3)
kd1 = 100
kd2 = 100
kf1 = kr1/kd1
kf2 = kr1/kd2   

N1 = min(nr1,nl)
N2 = min(nr2,nl)

#Set the epsilon threshold and the value of alpha for the steady state MCA
epsilon = pow(10,-5)
alpha = 1

#Set number of monomers of type 2 to reach
N = 10

#Function to compute the MCA steady state distribution in order to compute E[M1]
def MCA_steady_state_dist():
   #Initiate the list of nl values for each iteration
   nl_values = [nl]
   
   #Compute the first expected values using nli = nl
   expected_m1 = (kf1*nr1*nl_values[0])/(kr1+kf1*nl_values[0])
   expected_m2 = (kf2*nr2*nl_values[0])/(kr2+kf2*nl_values[0])
   
   expected_m1_values = [expected_m1]
   expected_m2_values = [expected_m2]
   
   nl_values = [nl]
   
   #Run Algorithm 1
   diff_m1 = 1
   diff_m2 = 1
   while abs(diff_m1) > epsilon or abs(diff_m2) > epsilon:
      nl_values.append((nl - expected_m1_values[-1] - expected_m2_values[-1])*alpha + nl_values[-1]*(1-alpha))
   
      expected_m1_i = (kf1*nr1*nl_values[-1])/(kr1+kf1*nl_values[-1])
      expected_m2_i = (kf2*nr2*nl_values[-1])/(kr2+kf2*nl_values[-1])
   
      diff_m1 = expected_m1_i-expected_m1_values[-1]
      diff_m2 = expected_m2_i-expected_m2_values[-1]
   
      expected_m1_values.append(expected_m1_i)
      expected_m2_values.append(expected_m2_i)
   
   #Compute the steady state probabilities for the two MCs using the effective value of nl
   SS_m1_MCA = []
   for m1 in range(N1+1):
      p = (kf1*nl_values[-1])/(kr1+(kf1*nl_values[-1]))
      pi_m1 = stats.binom(nr1,p).pmf(m1)
      SS_m1_MCA.append(pi_m1)
   
   SS_m2_MCA = []
   for m2 in range(N2+1):
      p = (kf2*nl_values[-1])/(kr2+(kf2*nl_values[-1]))
      pi_m2 = stats.binom(nr2,p).pmf(m2)
      SS_m2_MCA.append(pi_m2)
   
   pi_mca_1 = np.empty((len(SS_m2_MCA),len(SS_m1_MCA)))
   for i in range(len(SS_m2_MCA)):
      for j in range(len(SS_m1_MCA)):
         pi_mca_1[i,j] = SS_m2_MCA[i]*SS_m1_MCA[j]
   
   #Set to zero the probabilities for any states not in the state space
   for i in range(N2+1):
      for j in range(N1+1):
         if i + j  > nl:
            pi_mca_1[i,j] = 0
   
   #Normalise to compute the final steady state distribution computed via the MCA
   pi_MCA = pi_mca_1/np.sum(pi_mca_1)
   return pi_MCA

#Compute the expected number of monomers of type 1 in steady state
def MCA_expected_m1():
   parts1 = []
   for m1 in range(N1+1):
      cols1 = []
      for m2 in range(min(N2,nl-m1)+1):
         cols1.append(pi_MCA[m2,m1])
      parts1.append(m1*np.sum(cols1))
   exp_m1 = np.sum(parts1)
   return exp_m1

#Function to compute the mean time to reach N monomers of type 2 from initial state 0
def MCA_mean_time(exp_m1):
   nl_star = nl-exp_m1
   
   #Define all of the rates of the 1D Markov process
   lambda_i = []
   mu_i = []
   for i in range(N+1):
      lambda_f = kf2*(nr2-i)*(nl_star-i)
      lambda_i.append(lambda_f)
      mu_b = kr2*i
      mu_i.append(mu_b)

   #Compute the mean time to reach N monomers from initial state 0
   times = []
   T0 = 1/lambda_i[0]
   times.append(T0)
   for i in range(1,N):
      Ti = 1/lambda_i[i] + (mu_i[i+1]/lambda_i[i])*times[i-1]
      times.append(Ti)

   mean_time = np.sum(times)         
   return mean_time

#Run the code to compute the mean time to reach N monomers of type 2 from initial state (m1,m2)=(0,0)
pi_MCA = MCA_steady_state_dist()
exp_m1_MCA = MCA_expected_m1()
Time_MCA = MCA_mean_time(exp_m1_MCA)

import numpy as np
from scipy import stats

#Define number of molecules and parameter values for the model
nl = 500
nr1 = 30
nr2 = 50
kr1 = pow(10,-3)
kr2 = pow(10,-3)
kd1 = 100
kd2 = 100
kf1 = kr1/kd1
kf2 = kr1/kd2   

N1 = min(nr1,nl)
N2 = min(nr2,nl)

#Set the epsilon threshold and the value of alpha for the steady state MCA
epsilon = pow(10,-5)
alpha = 1

#Set number of monomers of type 2 to reach
N = 10

#Function to compute the MCA steady state distribution in order to compute E[M1]
def MCA_steady_state_dist():
   #Initiate the list of nl values for each iteration
   nl_values = [nl]
   
   #Compute the first expected values using nli = nl
   expected_m1 = (kf1*nr1*nl_values[0])/(kr1+kf1*nl_values[0])
   expected_m2 = (kf2*nr2*nl_values[0])/(kr2+kf2*nl_values[0])
   
   expected_m1_values = [expected_m1]
   expected_m2_values = [expected_m2]
   
   nl_values = [nl]
   
   #Run Algorithm 1
   diff_m1 = 1
   diff_m2 = 1
   while abs(diff_m1) > epsilon or abs(diff_m2) > epsilon:
      nl_values.append((nl - expected_m1_values[-1] - expected_m2_values[-1])*alpha + nl_values[-1]*(1-alpha))
   
      expected_m1_i = (kf1*nr1*nl_values[-1])/(kr1+kf1*nl_values[-1])
      expected_m2_i = (kf2*nr2*nl_values[-1])/(kr2+kf2*nl_values[-1])
   
      diff_m1 = expected_m1_i-expected_m1_values[-1]
      diff_m2 = expected_m2_i-expected_m2_values[-1]
   
      expected_m1_values.append(expected_m1_i)
      expected_m2_values.append(expected_m2_i)
   
   #Compute the steady state probabilities for the two MCs using the effective value of nl
   SS_m1_MCA = []
   for m1 in range(N1+1):
      p = (kf1*nl_values[-1])/(kr1+(kf1*nl_values[-1]))
      pi_m1 = stats.binom(nr1,p).pmf(m1)
      SS_m1_MCA.append(pi_m1)
   
   SS_m2_MCA = []
   for m2 in range(N2+1):
      p = (kf2*nl_values[-1])/(kr2+(kf2*nl_values[-1]))
      pi_m2 = stats.binom(nr2,p).pmf(m2)
      SS_m2_MCA.append(pi_m2)
   
   pi_mca_1 = np.empty((len(SS_m2_MCA),len(SS_m1_MCA)))
   for i in range(len(SS_m2_MCA)):
      for j in range(len(SS_m1_MCA)):
         pi_mca_1[i,j] = SS_m2_MCA[i]*SS_m1_MCA[j]
   
   #Set to zero the probabilities for any states not in the state space
   for i in range(N2+1):
      for j in range(N1+1):
         if i + j  > nl:
            pi_mca_1[i,j] = 0
   
   #Normalise to compute the final steady state distribution computed via the MCA
   pi_MCA = pi_mca_1/np.sum(pi_mca_1)
   return pi_MCA

#Compute the expected number of monomers of type 1 in steady state
def MCA_expected_m1():
   parts1 = []
   for m1 in range(N1+1):
      cols1 = []
      for m2 in range(min(N2,nl-m1)+1):
         cols1.append(pi_MCA[m2,m1])
      parts1.append(m1*np.sum(cols1))
   exp_m1 = np.sum(parts1)
   return exp_m1

#Function to compute the mean time to reach N monomers of type 2 from initial state 0
def MCA_mean_time(exp_m1):
   nl_star = nl-exp_m1
   
   #Define all of the rates of the 1D Markov process
   lambda_i = []
   mu_i = []
   for i in range(N+1):
      lambda_f = kf2*(nr2-i)*(nl_star-i)
      lambda_i.append(lambda_f)
      mu_b = kr2*i
      mu_i.append(mu_b)

   #Compute the mean time to reach N monomers from initial state 0
   times = []
   T0 = 1/lambda_i[0]
   times.append(T0)
   for i in range(1,N):
      Ti = 1/lambda_i[i] + (mu_i[i+1]/lambda_i[i])*times[i-1]
      times.append(Ti)

   mean_time = np.sum(times)         
   return mean_time

#Run the code to compute the mean time to reach N monomers of type 2 from initial state (m1,m2)=(0,0)
pi_MCA = MCA_steady_state_dist()
exp_m1_MCA = MCA_expected_m1()
Time_MCA = MCA_mean_time(exp_m1_MCA)
#Define number of molecules and parameter values for the model #Set the epsilon threshold and the value of alpha for the steady state MCA #Set number of monomers of type 2 to reach #Function to compute the MCA steady state distribution in order to compute E[M1] #Initiate the list of nl values for each iteration #Compute the first expected values using nli = nl #Run Algorithm 1 #Compute the steady state probabilities for the two MCs using the effective value of nl #Set to zero the probabilities for any states not in the state space #Normalise to compute the final steady state distribution computed via the MCA #Compute the expected number of monomers of type 1 in steady state #Function to compute the mean time to reach N monomers of type 2 from initial state 0 #Define all of the rates of the 1D Markov process #Compute the mean time to reach N monomers from initial state 0 #Run the code to compute the mean time to reach N monomers of type 2 from initial state (m1,m2)=(0,0)