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bio-plots/bionet/6-promoter-interference.ipynb
2024-01-05 11:55:33 +01:00

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{
"cells": [
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"import numpy as np\n",
"from random import random\n",
"import matplotlib.pyplot as plt\n",
"from matplotlib.animation import FuncAnimation\n",
"\n",
"def decide (prob):\n",
" return 1 if random() <= prob else 0\n"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"pS activity: 0.016666666666666666\n",
"pA activity: 0.06666666666666667\n"
]
}
],
"source": [
"# Question 5.3.5\n",
"\n",
"L = 100\n",
"dt = .01\n",
"T = 60\n",
"\n",
"pA_rate = .1\n",
"pS_rate = .05\n",
"\n",
"pA = np.zeros(L)\n",
"pS = np.zeros(L)\n",
"\n",
"pS_counts = 0\n",
"pA_counts = 0\n",
"\n",
"\n",
"def check_collisions ():\n",
" collisions = np.where((pA == 1) & (pS == 1))\n",
" pA[collisions] = 0\n",
" pS[collisions] = 0\n",
"\n",
"\n",
" \n",
"for n in range(0,int(T / dt)):\n",
" if pA[0] == 0:\n",
" pA[0] = decide(dt * pA_rate)\n",
"\n",
" if pS[L-1] == 0:\n",
" pS[L-1] = decide(dt * pS_rate)\n",
"\n",
"\n",
" if pA[L-1] == 1 and decide(.4):\n",
" pA[L-1] = 0\n",
" pA_counts += 1\n",
" \n",
" if pS[0] == 1 and decide(.4):\n",
" pS[0] = 0\n",
" pS_counts += 1\n",
"\n",
" for i in range(1,L):\n",
" if pA[L-1-i] == 1 and decide(.4) and pA[L-i] == 0:\n",
" pA[L-1-i] = 0\n",
" pA[L-i] = 1\n",
" check_collisions()\n",
" \n",
" if pS[i] == 1 and decide(.4) and pS[i-1] == 0:\n",
" pS[i-1] = 1\n",
" pS[i] = 0\n",
" check_collisions()\n",
"\n",
"\n",
"print(f\"pS activity: {pS_counts / T}\")\n",
"print(f\"pA activity: {pA_counts / T}\")\n",
" \n",
" "
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "venv",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.10"
}
},
"nbformat": 4,
"nbformat_minor": 2
}