{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "d0259ef8",
   "metadata": {
    "lines_to_next_cell": 0
   },
   "source": [
    "## `A <-> B` reaction, with 1st-order kinetics in both directions,\n",
    "### taken to equilibrium\n",
    "\n",
    "Diffusion NOT done"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "63cc2f2f-d73c-4f47-b9d8-bf6545e0d24d",
   "metadata": {},
   "source": [
    "### TAGS :  \"reactions 2D\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "514caa8d-0b1b-4526-af21-96f7cbcb0fe6",
   "metadata": {},
   "outputs": [],
   "source": [
    "LAST_REVISED = \"Dec. 16, 2024\"\n",
    "LIFE123_VERSION = \"1.0-rc.1\"        # Library version this experiment is based on"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "7da2e6ab-2b18-4952-b2eb-1e2ce61bfb36",
   "metadata": {},
   "outputs": [],
   "source": [
    "#import set_path                    # Using MyBinder?  Uncomment this before running the next cell!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "922f1ee7",
   "metadata": {},
   "outputs": [],
   "source": [
    "#import sys\n",
    "#sys.path.append(\"C:/some_path/my_env_or_install\")   # CHANGE to the folder containing your venv or libraries installation!\n",
    "# NOTE: If any of the imports below can't find a module, uncomment the lines above, or try:  import set_path   \n",
    "\n",
    "from experiments.get_notebook_info import get_notebook_basename\n",
    "\n",
    "from life123 import UniformCompartment, BioSim2D, GraphicLog"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "48630be5",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "-> Output will be LOGGED into the file 'reaction_1.log.htm'\n"
     ]
    }
   ],
   "source": [
    "# Initialize the HTML logging\n",
    "log_file = get_notebook_basename() + \".log.htm\"    # Use the notebook base filename for the log file\n",
    "# Set up the use of some specified graphic (Vue) components\n",
    "GraphicLog.config(filename=log_file,\n",
    "                  components=[\"vue_cytoscape_2\"],\n",
    "                  extra_js=\"https://cdnjs.cloudflare.com/ajax/libs/cytoscape/3.21.2/cytoscape.umd.js\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "12ad037c-fd9b-43e5-b59d-22f3010951f0",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of reactions: 1 (at temp. 25 C)\n",
      "0: A <-> B  (kF = 3 / kR = 2 / delta_G = -1,005.1 / K = 1.5) | 1st order in all reactants & products\n",
      "Set of chemicals involved in the above reactions: {'B', 'A'}\n"
     ]
    }
   ],
   "source": [
    "# Initialize the system.  NOTE: Diffusion not done\n",
    "uc = UniformCompartment(names=[\"A\", \"B\"])\n",
    "\n",
    "# Reaction A <-> B , with 1st-order kinetics in both directions\n",
    "uc.add_reaction(reactants=\"A\", products=\"B\", forward_rate=3., reverse_rate=2.)\n",
    "\n",
    "uc.describe_reactions()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "bad0134c",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[GRAPHIC ELEMENT SENT TO LOG FILE `reaction_1.log.htm`]\n"
     ]
    }
   ],
   "source": [
    "# Send the plot to the HTML log file\n",
    "uc.plot_reaction_network(\"vue_cytoscape_2\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "e927653f-e165-4203-8f0f-c8f2d8876265",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SYSTEM STATE at Time t = 0:\n",
      "Species `A`:\n",
      "      0     1    2    3\n",
      "0  10.0  20.0  0.0  0.0\n",
      "1   0.0   0.0  0.0  0.0\n",
      "2   0.0   0.0  0.0  5.0\n",
      "Species `B`:\n",
      "      0     1    2      3\n",
      "0  50.0  35.0  0.0    0.0\n",
      "1   0.0   0.0  0.0    0.0\n",
      "2   0.0   0.0  0.0  100.0\n"
     ]
    }
   ],
   "source": [
    "bio = BioSim2D(n_bins=(3,4), reaction_handler=uc)\n",
    "\n",
    "bio.set_bin_conc_all_species(bin_x=0, bin_y=0, conc_list=[10.,50.])\n",
    "bio.set_bin_conc_all_species(bin_x=0, bin_y=1, conc_list=[20.,35.])\n",
    "bio.set_bin_conc_all_species(bin_x=2, bin_y=3, conc_list=[5.,100.])\n",
    "\n",
    "bio.describe_state()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "23137f05-bdc3-46a6-9101-c0f0d98071a5",
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "id": "0b8318bf",
   "metadata": {
    "tags": []
   },
   "source": [
    "## First step"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "97f6ad20",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "bio.delta_reactions:\n",
      " [[[  7.    1.    0.    0. ]\n",
      "  [  0.    0.    0.    0. ]\n",
      "  [  0.    0.    0.   18.5]]\n",
      "\n",
      " [[ -7.   -1.    0.    0. ]\n",
      "  [  0.    0.    0.    0. ]\n",
      "  [  0.    0.    0.  -18.5]]]\n"
     ]
    }
   ],
   "source": [
    "# First step (NOTE: here we're using a lower-level function that doesn't update the system state;\n",
    "#                   it only computes the delta_reactions array)\n",
    "bio.reaction_step(delta_time=0.1)\n",
    "print(\"bio.delta_reactions:\\n\", bio.delta_reactions)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "93b53e77",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SYSTEM STATE at Time t = 0.1:\n",
      "Species `A`:\n",
      "      0     1    2     3\n",
      "0  17.0  21.0  0.0   0.0\n",
      "1   0.0   0.0  0.0   0.0\n",
      "2   0.0   0.0  0.0  23.5\n",
      "Species `B`:\n",
      "      0     1    2     3\n",
      "0  43.0  34.0  0.0   0.0\n",
      "1   0.0   0.0  0.0   0.0\n",
      "2   0.0   0.0  0.0  81.5\n"
     ]
    }
   ],
   "source": [
    "bio.system += bio.delta_reactions       # Matrix operation to update all the concentrations\n",
    "bio.system_time += 0.1\n",
    "\n",
    "bio.describe_state()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "1dfcfa0b-ae89-4fdc-af96-54ada6f7f555",
   "metadata": {
    "tags": []
   },
   "source": [
    "## Second step"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "4a32fd45-f20d-4bed-99cb-3b611656e1be",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SYSTEM STATE at Time t = 0.2:\n",
      "Species `A`:\n",
      "      0     1    2      3\n",
      "0  20.5  21.5  0.0   0.00\n",
      "1   0.0   0.0  0.0   0.00\n",
      "2   0.0   0.0  0.0  32.75\n",
      "Species `B`:\n",
      "      0     1    2      3\n",
      "0  39.5  33.5  0.0   0.00\n",
      "1   0.0   0.0  0.0   0.00\n",
      "2   0.0   0.0  0.0  72.25\n"
     ]
    }
   ],
   "source": [
    "# NOTE: now, we're using a highel-level function that also updates the system state\n",
    "bio.react(time_step=0.1, n_steps=1)\n",
    "bio.describe_state()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "c8f2dcc9-7343-47b0-9e2c-4157add49e32",
   "metadata": {},
   "source": [
    "## Many more steps, to equilibrium"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "42be106a-095e-4d0e-8c24-a8d03370eff7",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SYSTEM STATE at Time t = 0.9999999999999999:\n",
      "Species `A`:\n",
      "           0          1    2          3\n",
      "0  23.986328  21.998047  0.0   0.000000\n",
      "1   0.000000   0.000000  0.0   0.000000\n",
      "2   0.000000   0.000000  0.0  41.963867\n",
      "Species `B`:\n",
      "           0          1    2          3\n",
      "0  36.013672  33.001953  0.0   0.000000\n",
      "1   0.000000   0.000000  0.0   0.000000\n",
      "2   0.000000   0.000000  0.0  63.036133\n"
     ]
    }
   ],
   "source": [
    "bio.react(time_step=0.1, n_steps=8)\n",
    "bio.describe_state()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "51fefb11-5382-4e2e-87e4-f175884e9fcf",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SYSTEM STATE at Time t = 2.0000000000000004:\n",
      "Species `A`:\n",
      "           0          1    2          3\n",
      "0  23.999987  21.999998  0.0   0.000000\n",
      "1   0.000000   0.000000  0.0   0.000000\n",
      "2   0.000000   0.000000  0.0  41.999965\n",
      "Species `B`:\n",
      "           0          1    2          3\n",
      "0  36.000013  33.000002  0.0   0.000000\n",
      "1   0.000000   0.000000  0.0   0.000000\n",
      "2   0.000000   0.000000  0.0  63.000035\n"
     ]
    }
   ],
   "source": [
    "bio.react(time_step=0.1, n_steps=10)\n",
    "bio.describe_state()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9b66fc29-20a2-4be9-9248-5fff187aa773",
   "metadata": {},
   "source": [
    "### The system has now reached equilibrium\n",
    "### in individual bins, which remain separate because we're NOT doing diffusion in this experiment"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4458f3e5-3cd5-4f88-a79f-0dc134bcf309",
   "metadata": {},
   "source": [
    "Verify the equilibrium in each of the active bins"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "a0d8cc78-870c-45af-90dc-10f50bf3bc40",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "A <-> B\n",
      "Final concentrations: [A] = 24 ; [B] = 36\n",
      "1. Ratio of reactant/product concentrations, adjusted for reaction orders: 1.5\n",
      "    Formula used:  [B] / [A]\n",
      "2. Ratio of forward/reverse reaction rates: 1.5\n",
      "Discrepancy between the two values: 9.271e-05 %\n",
      "Reaction IS in equilibrium (within 1% tolerance)\n",
      "\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bio.reaction_dynamics.is_in_equilibrium(rxn_index=0, conc={\"A\": 23.99998665, \"B\": 36.00001335})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "46a41b53-b4c5-4de3-84d5-3fd1024c2652",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "A <-> B\n",
      "Final concentrations: [A] = 22 ; [B] = 33\n",
      "1. Ratio of reactant/product concentrations, adjusted for reaction orders: 1.5\n",
      "    Formula used:  [B] / [A]\n",
      "2. Ratio of forward/reverse reaction rates: 1.5\n",
      "Discrepancy between the two values: 1.447e-05 %\n",
      "Reaction IS in equilibrium (within 1% tolerance)\n",
      "\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bio.reaction_dynamics.is_in_equilibrium(rxn_index=0, conc={\"A\": 21.99999809, \"B\": 33.00000191})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "91e85f0a-a186-408f-864e-08bc6acb9591",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bio.reaction_dynamics.is_in_equilibrium(rxn_index=0, conc={\"A\": 41.99996471, \"B\": 63.00003529}, explain=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6c75c6ba",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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