{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "19564ec4-168a-481e-ba02-6d3fe0ce5fef",
   "metadata": {},
   "source": [
    "### Exploring the data structures of MEMBRANES, and reactions in them \n",
    "#### - with NO DIFFUSION\n",
    "\n",
    "LAST REVISED: July 14, 2023"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "51fce5bd-df35-4b06-8a3b-50901e1e3a0d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Added 'D:\\Docs\\- MY CODE\\BioSimulations\\life123-Win7' to sys.path\n"
     ]
    }
   ],
   "source": [
    "import set_path      # Importing this module will add the project's home directory to sys.path"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "14506983",
   "metadata": {},
   "outputs": [],
   "source": [
    "from src.modules.chemicals.chem_data import ChemData as chem\n",
    "\n",
    "from src.life_1D.bio_sim_1d import BioSim1D"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "81b9c228-ab44-48ce-b0a1-99b52bcbaf98",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SYSTEM STATE at Time t = 0:\n",
      "5 bins and 3 species:\n",
      "  Species 0 (A). Diff rate: None. Conc: |4.0|4.0()4.0|4.0|4.0|4.0|\n",
      "  Species 1 (B). Diff rate: None. Conc: |8.0|8.0()8.0|8.0|8.0|8.0|\n",
      "  Species 2 (C). Diff rate: None. Conc: |12.0|12.0()12.0|12.0|12.0|12.0|\n"
     ]
    }
   ],
   "source": [
    "chem_data = chem(names=[\"A\", \"B\", \"C\"])     # NOTE: Diffusion not done\n",
    "bio = BioSim1D(n_bins=5, chem_data=chem_data)\n",
    "\n",
    "bio.set_membranes(membrane_pos=[1])   # A single membrane, passing thru bin 1\n",
    "\n",
    "bio.set_all_uniform_concentrations(conc_list=[4., 8., 12.])\n",
    "\n",
    "bio.describe_state()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "5816fe14-c3d4-48ee-8e2e-fac3af6ea662",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SYSTEM STATE at Time t = 0:\n",
      "5 bins and 3 species:\n",
      "  Species 0 (A). Diff rate: None. Conc: |4.0|10.0()55.0|4.0|4.0|4.0|\n",
      "  Species 1 (B). Diff rate: None. Conc: |8.0|20.0()8.0|8.0|8.0|8.0|\n",
      "  Species 2 (C). Diff rate: None. Conc: |12.0|30.0()30.0|12.0|12.0|12.0|\n"
     ]
    }
   ],
   "source": [
    "bio.set_bin_conc(bin_address=1, species_name=\"A\", conc=10.)\n",
    "bio.set_bin_conc(bin_address=1, species_name=\"A\", conc=55., across_membrane=True)\n",
    "bio.set_bin_conc(bin_address=1, species_name=\"B\", conc=20.)\n",
    "bio.set_bin_conc(bin_address=1, species_name=\"C\", conc=30., both_sides=True)\n",
    "\n",
    "bio.describe_state()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "45084a50-2421-4f5d-995b-227f5e4d623e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SYSTEM STATE at Time t = 0:\n",
      "5 bins and 3 species:\n",
      "  Species 0 (A). Diff rate: None. Conc: |4.0|10.0()55.0|4.0|4.0|55.0|\n",
      "  Species 1 (B). Diff rate: None. Conc: |8.0|20.0()8.0|8.0|8.0|8.0|\n",
      "  Species 2 (C). Diff rate: None. Conc: |12.0|30.0()30.0|12.0|12.0|30.0|\n"
     ]
    }
   ],
   "source": [
    "# Make the last bin match all the concentrations of the \"post-membrane\" section of bin 1\n",
    "bio.set_bin_conc(bin_address=4, species_name=\"A\", conc=55.)\n",
    "bio.set_bin_conc(bin_address=4, species_name=\"C\", conc=30.)\n",
    "\n",
    "bio.describe_state()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "fc5b6db9-5b30-4319-85ce-6730c0ec5fb9",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Number of reactions: 1 (at temp. 25 C)\n",
      "0: A + B <-> C  (kF = 8 / kR = 2 / Delta_G = -3,436.56 / K = 4) | 1st order in all reactants & products\n"
     ]
    }
   ],
   "source": [
    "# Reaction A + B <-> C , with 1st-order kinetics in both directions, mostly forward\n",
    "bio.chem_data.add_reaction(reactants=[\"A\", \"B\"], products=[\"C\"], forward_rate=8., reverse_rate=2.)\n",
    "\n",
    "bio.chem_data.describe_reactions()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "6abf3304-caff-4d4b-9c93-a71c949f2726",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SYSTEM STATE at Time t = 0.002:\n",
      "5 bins and 3 species:\n",
      "  Species 0 (A). Diff rate: None. Conc: |3.536|6.92()48.08|3.536|3.536|48.08|\n",
      "  Species 1 (B). Diff rate: None. Conc: |7.536|16.92()1.08|7.536|7.536|1.08|\n",
      "  Species 2 (C). Diff rate: None. Conc: |12.464|33.08()36.92|12.464|12.464|36.92|\n"
     ]
    }
   ],
   "source": [
    "bio.react(time_step=0.002, n_steps=1)\n",
    "bio.describe_state()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2468c2e9-18be-4b46-b51a-ace15531fc3d",
   "metadata": {},
   "source": [
    "### Note how (in the absence of diffusion, which we're neglecting) the concentrations on the \"post-membrane side\" of bin 1 continue to match those of bin 5"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d19d67cd-a3d7-4fb5-ba16-c820c55344a8",
   "metadata": {},
   "source": [
    "## Now continue to reaction equilibrium"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "68cbe07b-0920-4c09-8b7a-800999c1175a",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SYSTEM STATE at Time t = 0.202:\n",
      "5 bins and 3 species:\n",
      "  Species 0 (A). Diff rate: None. Conc: |0.7932534523016194|0.8970947370566021()47.20020986266437|0.7932534523016194|0.7932534523016194|47.20020986266437|\n",
      "  Species 1 (B). Diff rate: None. Conc: |4.793253452301623|10.897094737056594()0.20020986266437912|4.793253452301623|4.793253452301623|0.20020986266437912|\n",
      "  Species 2 (C). Diff rate: None. Conc: |15.206746547698396|39.10290526294337()37.79979013733563|15.206746547698396|15.206746547698396|37.79979013733563|\n"
     ]
    }
   ],
   "source": [
    "bio.react(time_step=0.002, n_steps=100)\n",
    "bio.describe_state()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4efbc61b-efa9-49eb-b1f3-0c901fffdd8a",
   "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": "07ac2214-aec4-4b1f-8ad7-328c729cc35c",
   "metadata": {},
   "source": [
    "Verify the equilibrium in each of the active bins"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "c92cf0dc-9055-4b4a-8692-7f32b1ac435e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "A + B <-> C\n",
      "Final concentrations:  [C] = 15.21 ; [A] = 0.7933 ; [B] = 4.793\n",
      "1. Ratio of reactant/product concentrations, adjusted for reaction orders: 3.99939\n",
      "    Formula used:  [C] / ([A][B])\n",
      "2. Ratio of forward/reverse reaction rates: 4.0\n",
      "Discrepancy between the two values: 0.01521 %\n",
      "Reaction IS in equilibrium (within 1% tolerance)\n",
      "\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bio.reaction_dynamics.is_in_equilibrium(rxn_index=0, conc={\"A\": 0.7932534523016195, \"B\": 4.793253452301622, \"C\": 15.206746547698396})\n",
    "# A was largely the limiting reagent"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "b9b74e29-de37-4257-9693-ab226eda6449",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "A + B <-> C\n",
      "Final concentrations:  [C] = 39.1 ; [A] = 0.8971 ; [B] = 10.9\n",
      "1. Ratio of reactant/product concentrations, adjusted for reaction orders: 4\n",
      "    Formula used:  [C] / ([A][B])\n",
      "2. Ratio of forward/reverse reaction rates: 4.0\n",
      "Discrepancy between the two values: 2.259e-07 %\n",
      "Reaction IS in equilibrium (within 1% tolerance)\n",
      "\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bio.reaction_dynamics.is_in_equilibrium(rxn_index=0, conc={\"A\": 0.897094737056602, \"B\": 10.897094737056594, \"C\": 39.10290526294337})\n",
    "# A was largely the limiting reagent"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "7cc098bc-3d68-4f4d-a754-e5c8cedd7e9c",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "A + B <-> C\n",
      "Final concentrations:  [C] = 37.8 ; [A] = 47.2 ; [B] = 0.2002\n",
      "1. Ratio of reactant/product concentrations, adjusted for reaction orders: 4\n",
      "    Formula used:  [C] / ([A][B])\n",
      "2. Ratio of forward/reverse reaction rates: 4.0\n",
      "Discrepancy between the two values: 0 %\n",
      "Reaction IS in equilibrium (within 1% tolerance)\n",
      "\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "bio.reaction_dynamics.is_in_equilibrium(rxn_index=0, conc={\"A\": 47.20020986266437, \"B\": 0.20020986266437912, \"C\": 37.79979013733563})\n",
    "# This time, with ample [A], the limiting reagent was B"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f7b5f5b7",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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