biological networks

2024-01-05 11:55:33 +01:00
parent 32084fe387
commit f93a89ebf3
16 changed files with 2187 additions and 0 deletions
@@ -0,0 +1,119 @@
+{
+ "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
+}