{ "cells": [ { "cell_type": "markdown", "id": "c3b90917-d8b3-4644-a485-b22d440272b9", "metadata": {}, "source": [ "## One-bin Association/Dissociation reaction `A + B <-> C`\n", "### with 1st-order kinetics for each species, taken to equilibrium\n", "\n", "Diffusion not applicable (just 1 bin)\n", "\n", "See also the experiment _\"reactions_single_compartment/react_3\"_ " ] }, { "cell_type": "markdown", "id": "1e74fd56-a767-41de-b06a-ee171d7812c7", "metadata": {}, "source": [ "### TAGS : \"reactions 1D\"" ] }, { "cell_type": "code", "execution_count": 1, "id": "1634a05f-032d-483e-a760-76229ce79567", "metadata": {}, "outputs": [], "source": [ "LAST_REVISED = \"May 4, 2025\"\n", "LIFE123_VERSION = \"1.0.0rc3\" # Library version this experiment is based on" ] }, { "cell_type": "code", "execution_count": 2, "id": "a8f89c58-e3b5-4a07-96ec-6f7455db1bf5", "metadata": {}, "outputs": [], "source": [ "#import set_path # Using MyBinder? Uncomment this before running the next cell!" ] }, { "cell_type": "code", "execution_count": 3, "id": "f5117d69", "metadata": {}, "outputs": [], "source": [ "#import sys, os\n", "#os.getcwd()\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 ChemData, BioSim1D, check_version\n", "\n", "from life123 import GraphicLog" ] }, { "cell_type": "code", "execution_count": 4, "id": "5209dfc4-825a-4d41-95f6-aefb7fca75f1", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "OK\n" ] } ], "source": [ "check_version(LIFE123_VERSION)" ] }, { "cell_type": "code", "execution_count": null, "id": "95122f3c-b9c7-4ed4-9190-51350c295f07", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": 5, "id": "ada82175-1d15-4213-b834-5a5d8e2dd31e", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "-> Output will be LOGGED into the file 'reaction_4.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", "\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": 6, "id": "d8f2d83d-97bc-4f57-8f71-c0923f0334ed", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "SYSTEM STATE at Time t = 0:\n", "1 bins and 3 chemical species:\n" ] }, { "data": { "text/html": [ "
\n", "\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
SpeciesDiff rateBin 0
0ANone10.0
1BNone50.0
2CNone20.0
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" ], "text/plain": [ " Species Diff rate Bin 0\n", "0 A None 10.0\n", "1 B None 50.0\n", "2 C None 20.0" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Initialize the system. NOTE: Diffusion not applicable (using just 1 bin)\n", "chem_data = ChemData(names=[\"A\", \"B\", \"C\"], plot_colors=['red', 'darkorange', 'green'])\n", "\n", "bio = BioSim1D(n_bins=1, chem_data=chem_data)\n", "\n", "bio.set_uniform_concentration(chem_index=0, conc=10.)\n", "bio.set_uniform_concentration(chem_index=1, conc=50.)\n", "bio.set_uniform_concentration(chem_index=2, conc=20.)\n", "\n", "bio.describe_state()\n" ] }, { "cell_type": "code", "execution_count": 7, "id": "42760c32-a4f2-4f8b-96c0-8f98b484189d", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Number of reactions: 1 (at temp. 25 C)\n", "0: A + B <-> C (kF = 5 / kR = 2 / delta_G = -2,271.4 / K = 2.5) | 1st order in all reactants & products\n", "Set of chemicals involved in the above reactions: {\"B\" (darkorange), \"C\" (green), \"A\" (red)}\n" ] } ], "source": [ "# Specify the reaction\n", "reactions = bio.get_reactions()\n", "\n", "# Reaction A + B <-> C , with 1st-order kinetics for each species\n", "reactions.add_reaction(reactants=[\"A\" , \"B\"], products=\"C\",\n", " forward_rate=5., reverse_rate=2.)\n", "\n", "reactions.describe_reactions()" ] }, { "cell_type": "code", "execution_count": 8, "id": "25f70c0f-621e-413f-bc93-336d38d462d7", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "[GRAPHIC ELEMENT SENT TO LOG FILE `reaction_4.log.htm`]\n" ] } ], "source": [ "# Send the plot of the reaction network to the HTML log file\n", "reactions.plot_reaction_network(\"vue_cytoscape_2\")" ] }, { "cell_type": "code", "execution_count": null, "id": "b351573c-275c-434f-8301-4ed54197e0cc", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": 9, "id": "39ec6840-ad21-4afb-9213-f27669817605", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "History enabled for bins None and chemicals None (None means 'all')\n" ] } ], "source": [ "# Let's enable history - by default for all chemicals and all bins\n", "bio.enable_history(take_snapshot=True, caption=\"Initial state\")" ] }, { "cell_type": "code", "execution_count": 10, "id": "d89603fb-b14c-40ce-bdea-ebe36c2f726b", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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SYSTEM TIMEABCcaption
00.010.050.020.0Initial state
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" ], "text/plain": [ " SYSTEM TIME A B C caption\n", "0 0.0 10.0 50.0 20.0 Initial state" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "bio.get_bin_history(bin_address=0)" ] }, { "cell_type": "code", "execution_count": null, "id": "3c71a1a3-f6b8-4f05-bf5a-267e10fe7d7e", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "id": "79e68c64-fe18-4b9b-ba17-cdef6dcf4b35", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "markdown", "id": "356e4db3-02a6-40bd-a951-841bfc6c5522", "metadata": { "tags": [] }, "source": [ "### First step" ] }, { "cell_type": "code", "execution_count": 11, "id": "b8c0d439-13f7-459c-88e2-0ae357b46c18", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "System Time is now: 0.002\n", "SYSTEM STATE at Time t = 0.002:\n", "1 bins and 3 chemical species:\n" ] }, { "data": { "text/html": [ "
\n", "\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
SpeciesDiff rateBin 0
0ANone5.08
1BNone45.08
2CNone24.92
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" ], "text/plain": [ " Species Diff rate Bin 0\n", "0 A None 5.08\n", "1 B None 45.08\n", "2 C None 24.92" ] }, "execution_count": 11, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# First step\n", "bio.react(time_step=0.002, n_steps=1)\n", "bio.describe_state()" ] }, { "cell_type": "code", "execution_count": 12, "id": "386d8052-2d92-43b0-b817-ab4a1cce3ba0", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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SYSTEM TIMEABCcaption
00.00010.0050.0020.00Initial state
10.0025.0845.0824.92
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" ], "text/plain": [ " SYSTEM TIME A B C caption\n", "0 0.000 10.00 50.00 20.00 Initial state\n", "1 0.002 5.08 45.08 24.92 " ] }, "execution_count": 12, "metadata": {}, "output_type": "execute_result" } ], "source": [ "bio.get_bin_history(bin_address=0)" ] }, { "cell_type": "code", "execution_count": null, "id": "1bf6c537-ae57-46fe-992e-f7d0fc3bb29e", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "markdown", "id": "88ec4bcc-48dc-45eb-84fc-8e6e0b259612", "metadata": {}, "source": [ "### Numerous more steps" ] }, { "cell_type": "code", "execution_count": 13, "id": "8efdf9ef-bdca-48ff-b139-6e2d9952c1d8", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "System Time is now: 0.06\n", "SYSTEM STATE at Time t = 0.06:\n", "1 bins and 3 chemical species:\n" ] }, { "data": { "text/html": [ "
\n", "\n", "\n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", " \n", "
SpeciesDiff rateBin 0
0ANone0.294878
1BNone40.294878
2CNone29.705122
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" ], "text/plain": [ " Species Diff rate Bin 0\n", "0 A None 0.294878\n", "1 B None 40.294878\n", "2 C None 29.705122" ] }, "execution_count": 13, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Numerous more steps\n", "bio.react(time_step=0.002, n_steps=29)\n", "\n", "bio.describe_state()" ] }, { "cell_type": "markdown", "id": "6b0be45c-ff0e-43d8-847a-b6e8d0e6e0ec", "metadata": { "tags": [] }, "source": [ "### Equilibrium" ] }, { "cell_type": "markdown", "id": "7f687d0d-75ab-4e29-8070-5b6f1fc80b4b", "metadata": {}, "source": [ "Consistent with the 5/2 ratio of forward/reverse rates (and the 1st order reactions),\n", "the systems settles in the following equilibrium: \n", "[A] = 0.29487831 , [B] = 40.29487831 , [C] = 29.70512169" ] }, { "cell_type": "code", "execution_count": 14, "id": "46a3ea5d-6516-4582-9958-6a80403e8f19", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "A + B <-> C\n", "Current concentrations: [A] = 0.2949 ; [B] = 40.29 ; [C] = 29.71\n", "1. Ratio of reactant/product concentrations, adjusted for reaction orders: 2.49999\n", " Formula used: [C] / ([A][B])\n", "2. Ratio of forward/reverse reaction rates: 2.5\n", "Discrepancy between the two values: 0.0003107 %\n", "Reaction IS in equilibrium (within 1% tolerance)\n", "\n" ] }, { "data": { "text/plain": [ "True" ] }, "execution_count": 14, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Verify that the reaction has reached equilibrium\n", "bio.reaction_dynamics.is_in_equilibrium(rxn_index=0, conc=bio.bin_snapshot(bin_address = 0))" ] }, { "cell_type": "code", "execution_count": 15, "id": "6975a1e8-d708-401f-ab7f-78c183f765bf", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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SYSTEM TIMEABCcaption
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" ], "text/plain": [ " SYSTEM TIME A B C caption\n", "0 0.000 10.000000 50.000000 20.000000 Initial state\n", "1 0.002 5.080000 45.080000 24.920000 \n", "2 0.004 2.889616 42.889616 27.110384 \n", "3 0.006 1.758712 41.758712 28.241288 \n", "4 0.008 1.137262 41.137262 28.862738 \n", "5 0.010 0.784874 40.784874 29.215126 \n", "6 0.012 0.581625 40.581625 29.418375 \n", "7 0.014 0.463266 40.463266 29.536734 \n", "8 0.016 0.393960 40.393960 29.606040 \n", "9 0.018 0.353248 40.353248 29.646752 \n", "10 0.020 0.329288 40.329288 29.670712 \n", "11 0.022 0.315171 40.315171 29.684829 \n", "12 0.024 0.306849 40.306849 29.693151 \n", "13 0.026 0.301940 40.301940 29.698060 \n", "14 0.028 0.299045 40.299045 29.700955 \n", "15 0.030 0.297336 40.297336 29.702664 \n", "16 0.032 0.296328 40.296328 29.703672 \n", "17 0.034 0.295734 40.295734 29.704266 \n", "18 0.036 0.295383 40.295383 29.704617 \n", "19 0.038 0.295176 40.295176 29.704824 \n", "20 0.040 0.295053 40.295053 29.704947 \n", "21 0.042 0.294981 40.294981 29.705019 \n", "22 0.044 0.294939 40.294939 29.705061 \n", "23 0.046 0.294914 40.294914 29.705086 \n", "24 0.048 0.294899 40.294899 29.705101 \n", "25 0.050 0.294890 40.294890 29.705110 \n", "26 0.052 0.294885 40.294885 29.705115 \n", "27 0.054 0.294882 40.294882 29.705118 \n", "28 0.056 0.294880 40.294880 29.705120 \n", "29 0.058 0.294879 40.294879 29.705121 \n", "30 0.060 0.294878 40.294878 29.705122 " ] }, "execution_count": 15, "metadata": {}, "output_type": "execute_result" } ], "source": [ "bio.get_bin_history(bin_address=0)" ] }, { "cell_type": "markdown", "id": "8a4576cc-d927-4776-a691-2001bba5d1b7", "metadata": {}, "source": [ "## Note: `A` (now largely depleted) is largely the limiting reagent" ] }, { "cell_type": "markdown", "id": "d82cb7fe-0bd2-4b3e-bbec-6f5b70d0e5ae", "metadata": { "tags": [] }, "source": [ "## Plots of changes of concentration with time" ] }, { "cell_type": "code", "execution_count": 16, "id": "9bbcb023-ab41-495d-8d8c-f02a568d48bf", "metadata": {}, "outputs": [ { "data": { "text/html": [ " \n", " " ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.plotly.v1+json": { "config": { "plotlyServerURL": "https://plot.ly" }, "data": [ { "hovertemplate": "Chemical=A
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Concentrations at bin 0" }, "xaxis": { "anchor": "y", "autorange": true, "domain": [ 0, 1 ], "range": [ 0, 0.06000000000000004 ], "title": { "text": "SYSTEM TIME" }, "type": "linear" }, "yaxis": { "anchor": "x", "autorange": true, "domain": [ 0, 1 ], "range": [ -2.466517339921377, 52.76139564946955 ], "title": { "text": "Concentration" }, "type": "linear" } } }, "text/html": [ "
" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "bio.plot_history_single_bin(bin_address=0, \n", " title=\"Reaction A + B <-> C . Concentrations at bin 0\")" ] }, { "cell_type": "markdown", "id": "ea1bbd14-90d4-480d-946c-f0ce30d61df1", "metadata": {}, "source": [ "## For more in-depth analysis of this reaction, including variable time steps, see the experiment _\"reactions_single_compartment/react_3\"_ " ] }, { "cell_type": "code", "execution_count": null, "id": "57b81064", "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "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": "3.9.13" } }, "nbformat": 4, "nbformat_minor": 5 }