{ "cells": [ { "cell_type": "markdown", "id": "4e50d971", "metadata": {}, "source": [ "### One-bin A <-> 3B reaction, with 1st-order kinetics in both directions, taken to equilibrium\n", "### Examine State Space trajectory, using [A] and [B] as state variables\n", "\n", "Based on experiment `1D/reaction/reaction_2`\n", "\n", "Diffusion not applicable (just 1 bin).\n", "\n", "This is the 1D version of the single-compartment reaction by the same name\n", "\n", "LAST REVISED: May 6, 2024" ] }, { "cell_type": "code", "execution_count": 1, "id": "09b4fb67-3976-40c0-9e56-7060d243db7d", "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": "e49a243f", "metadata": {}, "outputs": [], "source": [ "from experiments.get_notebook_info import get_notebook_basename\n", "\n", "from src.modules.chemicals.chem_data import ChemData\n", "from src.life_1D.bio_sim_1d import BioSim1D\n", "\n", "import plotly.express as px\n", "import plotly.graph_objects as go\n", "from src.modules.visualization.graphic_log import GraphicLog" ] }, { "cell_type": "code", "execution_count": 3, "id": "180bfbdd", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "-> Output will be LOGGED into the file 'state_space_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", "\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": 4, "id": "2bbdb53f", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "SYSTEM STATE at Time t = 0:\n", "1 bins and 2 species:\n", " Species 0 (A). Diff rate: None. Conc: [10.]\n", " Species 1 (B). Diff rate: None. Conc: [50.]\n" ] } ], "source": [ "# Initialize the system\n", "chem_data = ChemData(names=[\"A\", \"B\"]) # NOTE: Diffusion not applicable (just 1 bin)\n", "\n", "\n", "\n", "# Reaction A <-> 3B , with 1st-order kinetics in both directions\n", "chem_data.add_reaction(reactants=[\"A\"], products=[(3,\"B\",1)], forward_rate=5., reverse_rate=2.)\n", "\n", "bio = BioSim1D(n_bins=1, chem_data=chem_data)\n", "\n", "bio.set_uniform_concentration(species_index=0, conc=10.)\n", "bio.set_uniform_concentration(species_index=1, conc=50.)\n", "\n", "bio.describe_state()" ] }, { "cell_type": "code", "execution_count": 5, "id": "06fe0be5", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Number of reactions: 1 (at temp. 25 C)\n", "0: A <-> 3 B (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', 'A'}\n" ] } ], "source": [ "chem_data.describe_reactions()" ] }, { "cell_type": "code", "execution_count": 6, "id": "3f53fbc7", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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SYSTEM TIMEABcaption
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" ], "text/plain": [ " SYSTEM TIME A B caption\n", "0 0 10.0 50.0 " ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Save the state of the concentrations of all species at bin 0\n", "bio.add_snapshot(bio.bin_snapshot(bin_address = 0))\n", "bio.get_history()" ] }, { "cell_type": "code", "execution_count": 7, "id": "4b5e75e5", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "[GRAPHIC ELEMENT SENT TO LOG FILE `state_space_1.log.htm`]\n" ] } ], "source": [ "# Send the plot to the HTML log file\n", "chem_data.plot_reaction_network(\"vue_cytoscape_2\")" ] }, { "cell_type": "markdown", "id": "dfb4e9e3", "metadata": { "tags": [] }, "source": [ "### To equilibrium" ] }, { "cell_type": "code", "execution_count": 8, "id": "b2500732", "metadata": {}, "outputs": [], "source": [ "# Using smaller steps that in experiment reaction_2, to avoid the initial overshooting\n", "bio.react(time_step=0.05, n_steps=10, snapshots={\"frequency\": 1, \"sample_bin\": 0})" ] }, { "cell_type": "code", "execution_count": 9, "id": "c995c50f-4b3e-41b8-bf06-e6d64f028dfe", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "SYSTEM STATE at Time t = 0.5:\n", "1 bins and 2 species:\n", " Species 0 (A). Diff rate: None. Conc: [14.54390679]\n", " Species 1 (B). Diff rate: None. Conc: [36.36827963]\n" ] } ], "source": [ "bio.describe_state()" ] }, { "cell_type": "code", "execution_count": 10, "id": "494466ba-f534-44c0-a65b-b4976340017a", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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" ], "text/plain": [ " SYSTEM TIME A B caption\n", "0 0.00 10.000000 50.000000 \n", "1 0.05 12.500000 42.500000 \n", "2 0.10 13.625000 39.125000 \n", "3 0.15 14.131250 37.606250 \n", "4 0.20 14.359063 36.922812 \n", "5 0.25 14.461578 36.615266 \n", "6 0.30 14.507710 36.476870 \n", "7 0.35 14.528470 36.414591 \n", "8 0.40 14.537811 36.386566 \n", "9 0.45 14.542015 36.373955 \n", "10 0.50 14.543907 36.368280 " ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "bio.get_history()" ] }, { "cell_type": "code", "execution_count": 11, "id": "d168a44c", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "A <-> 3 B\n", "Final concentrations: [A] = 14.54 ; [B] = 36.37\n", "1. Ratio of reactant/product concentrations, adjusted for reaction orders: 2.50059\n", " Formula used: [B] / [A]\n", "2. Ratio of forward/reverse reaction rates: 2.5\n", "Discrepancy between the two values: 0.02341 %\n", "Reaction IS in equilibrium (within 1% tolerance)\n", "\n" ] }, { "data": { "text/plain": [ "True" ] }, "execution_count": 11, "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": "markdown", "id": "3f5fd10b", "metadata": { "tags": [] }, "source": [ "# Plots of changes of concentration with time" ] }, { "cell_type": "code", "execution_count": 12, "id": "0832782c", "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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{ "color": "#2a3f5f" } }, "ternary": { "aaxis": { "gridcolor": "white", "linecolor": "white", "ticks": "" }, "baxis": { "gridcolor": "white", "linecolor": "white", "ticks": "" }, "bgcolor": "#E5ECF6", "caxis": { "gridcolor": "white", "linecolor": "white", "ticks": "" } }, "title": { "x": 0.05 }, "xaxis": { "automargin": true, "gridcolor": "white", "linecolor": "white", "ticks": "", "title": { "standoff": 15 }, "zerolinecolor": "white", "zerolinewidth": 2 }, "yaxis": { "automargin": true, "gridcolor": "white", "linecolor": "white", "ticks": "", "title": { "standoff": 15 }, "zerolinecolor": "white", "zerolinewidth": 2 } } }, "title": { "text": "Reaction A <-> 3B . Changes in [A] and [B] over time" }, "xaxis": { "anchor": "y", "autorange": true, "domain": [ 0, 1 ], "range": [ 0, 0.49999999999999994 ], "title": { "text": "SYSTEM TIME" }, "type": "linear" }, "yaxis": { "anchor": "x", "autorange": true, "domain": [ 0, 1 ], "range": [ 7.777777777777778, 52.22222222222222 ], "title": { "text": "concentration" }, "type": "linear" } } }, "text/html": [ "
" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "df = bio.get_history()\n", "\n", "px.line(data_frame=df, x=\"SYSTEM TIME\", y=[\"A\", \"B\"], \n", " title=\"Reaction A <-> 3B . Changes in [A] and [B] over time\",\n", " color_discrete_sequence = ['navy', 'darkorange'],\n", " labels={\"value\":\"concentration\", \"variable\":\"Chemical\"})" ] }, { "cell_type": "code", "execution_count": null, "id": "c4e0120d-1541-4552-a2d0-8100a3fea8d9", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "markdown", "id": "e647f76c-4503-48be-b96a-22e81c9fadc5", "metadata": {}, "source": [ "## Same data, but shown differently" ] }, { "cell_type": "code", "execution_count": 13, "id": "85b3c06f", "metadata": {}, "outputs": [ { "data": { "application/vnd.plotly.v1+json": { "config": { "plotlyServerURL": "https://plot.ly" }, "data": [ { "hovertemplate": "A=%{x}
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[ [ 0, "#0d0887" ], [ 0.1111111111111111, "#46039f" ], [ 0.2222222222222222, "#7201a8" ], [ 0.3333333333333333, "#9c179e" ], [ 0.4444444444444444, "#bd3786" ], [ 0.5555555555555556, "#d8576b" ], [ 0.6666666666666666, "#ed7953" ], [ 0.7777777777777778, "#fb9f3a" ], [ 0.8888888888888888, "#fdca26" ], [ 1, "#f0f921" ] ], "type": "histogram2d" } ], "histogram2dcontour": [ { "colorbar": { "outlinewidth": 0, "ticks": "" }, "colorscale": [ [ 0, "#0d0887" ], [ 0.1111111111111111, "#46039f" ], [ 0.2222222222222222, "#7201a8" ], [ 0.3333333333333333, "#9c179e" ], [ 0.4444444444444444, "#bd3786" ], [ 0.5555555555555556, "#d8576b" ], [ 0.6666666666666666, "#ed7953" ], [ 0.7777777777777778, "#fb9f3a" ], [ 0.8888888888888888, "#fdca26" ], [ 1, "#f0f921" ] ], "type": "histogram2dcontour" } ], "mesh3d": [ { "colorbar": { "outlinewidth": 0, "ticks": "" }, "type": "mesh3d" } ], "parcoords": [ { "line": { "colorbar": { "outlinewidth": 0, "ticks": "" } }, "type": "parcoords" } ], "pie": [ { "automargin": 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" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Combine the two above plots, while using the layout of fig1 (which includes the title and annotations)\n", "all_fig = go.Figure(data=fig0.data + fig1.data, layout = fig1.layout)\n", "all_fig.show()" ] }, { "cell_type": "markdown", "id": "4fe369cf-d2c0-454c-a3f9-9794008be8d8", "metadata": {}, "source": [ "#### Note how the trajectory is progressively slowing down towards the dynamical system's \"attractor\" (equilibrium state of the reaction)" ] }, { "cell_type": "code", "execution_count": null, "id": "7f982020", "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": "3.8.10" } }, "nbformat": 4, "nbformat_minor": 5 }