{ "cells": [ { "cell_type": "markdown", "id": "8382e30e-2fac-41f1-ae50-baf0fc9f4f22", "metadata": {}, "source": [ "# Membranes in 1D : Data Structure\n", "\n", "## Data Structure and Visualization of Membranes in 1D\n", "\n", "No simulations done here; for diffusion and transport across membranes, please see `membranes_2` and other experiments" ] }, { "cell_type": "markdown", "id": "d5cc70a6-8aea-4b15-9351-af69a3664dab", "metadata": {}, "source": [ "### TAGS : \"membranes 1D\", \"basic\", \"quick-start\"" ] }, { "cell_type": "code", "execution_count": 1, "id": "2b08132b-3002-444a-aaa4-68eb37342237", "metadata": {}, "outputs": [], "source": [ "LAST_REVISED = \"June 4, 2025\"\n", "LIFE123_VERSION = \"1.0.0rc6\" # Library version this experiment is based on" ] }, { "cell_type": "code", "execution_count": 2, "id": "1302ee3c-4c75-4e67-9b77-d75d27d6d29a", "metadata": {}, "outputs": [], "source": [ "#import set_path # Using MyBinder? Uncomment this before running the next cell!" ] }, { "cell_type": "code", "execution_count": 3, "id": "911ca4cb", "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 life123 import BioSim1D, ChemData, check_version" ] }, { "cell_type": "code", "execution_count": 4, "id": "ff5b7f09-0b8b-4b10-bf4f-cb5b7b9f269a", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "OK\n" ] } ], "source": [ "check_version(LIFE123_VERSION)" ] }, { "cell_type": "code", "execution_count": null, "id": "0b243ad6-10d9-420e-b786-1be74bfe36de", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "markdown", "id": "6faab103-5731-4c26-ad2a-a36a117167a1", "metadata": {}, "source": [ "## Prepare the initial system\n", "with a single non-zero bin concentration of the single chemical `A`, near the left edge of the system" ] }, { "cell_type": "code", "execution_count": 5, "id": "35b682f7-dfbd-44ec-8e72-6165b66a1007", "metadata": {}, "outputs": [], "source": [ "chem_data = ChemData(names=[\"A\", \"B\"], plot_colors=[\"turquoise\", \"green\"])\n", "\n", "bio = BioSim1D(n_bins=21, chem_data=chem_data)" ] }, { "cell_type": "code", "execution_count": 6, "id": "733f6bbe-956e-46f1-87ae-50e91e44f6e1", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "SYSTEM STATE at Time t = 0:\n", "21 bins and 2 chemical species\n" ] }, { "data": { "text/html": [ "
| \n", " | Species | \n", "Diff rate | \n", "Bin 0 | \n", "Bin 1 | \n", "Bin 2 | \n", "Bin 3 | \n", "Bin 4 | \n", "Bin 5 | \n", "Bin 6 | \n", "Bin 7 | \n", "... | \n", "Bin 11 | \n", "Bin 12 | \n", "Bin 13 | \n", "Bin 14 | \n", "Bin 15 | \n", "Bin 16 | \n", "Bin 17 | \n", "Bin 18 | \n", "Bin 19 | \n", "Bin 20 | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "A | \n", "None | \n", "0.0 | \n", "5.0000 | \n", "10.000000 | \n", "15.00000 | \n", "20.000000 | \n", "25.000000 | \n", "30.000000 | \n", "35.000000 | \n", "... | \n", "55.000000 | \n", "60.000000 | \n", "65.000000 | \n", "70.000000 | \n", "75.000000 | \n", "80.000000 | \n", "85.000000 | \n", "90.00000 | \n", "95.000000 | \n", "100.0000 | \n", "
| 1 | \n", "B | \n", "None | \n", "10.0 | \n", "12.8166 | \n", "14.654369 | \n", "14.87464 | \n", "13.400864 | \n", "10.745211 | \n", "7.830581 | \n", "5.669873 | \n", "... | \n", "11.473776 | \n", "13.909157 | \n", "14.986019 | \n", "14.330127 | \n", "12.169419 | \n", "9.254789 | \n", "6.599136 | \n", "5.12536 | \n", "5.345631 | \n", "7.1834 | \n", "
2 rows × 23 columns
\n", "| \n", " | A | \n", "B | \n", "
|---|---|---|
| 0 | \n", "0.0 | \n", "10.000000 | \n", "
| 1 | \n", "5.0 | \n", "12.816600 | \n", "
| 2 | \n", "10.0 | \n", "14.654369 | \n", "
| 3 | \n", "15.0 | \n", "14.874640 | \n", "
| 4 | \n", "20.0 | \n", "13.400864 | \n", "
| 5 | \n", "25.0 | \n", "10.745211 | \n", "
| 6 | \n", "30.0 | \n", "7.830581 | \n", "
| 7 | \n", "35.0 | \n", "5.669873 | \n", "
| 8 | \n", "40.0 | \n", "5.013981 | \n", "
| 9 | \n", "45.0 | \n", "6.090843 | \n", "
| 10 | \n", "50.0 | \n", "8.526224 | \n", "
| 11 | \n", "55.0 | \n", "11.473776 | \n", "
| 12 | \n", "60.0 | \n", "13.909157 | \n", "
| 13 | \n", "65.0 | \n", "14.986019 | \n", "
| 14 | \n", "70.0 | \n", "14.330127 | \n", "
| 15 | \n", "75.0 | \n", "12.169419 | \n", "
| 16 | \n", "80.0 | \n", "9.254789 | \n", "
| 17 | \n", "85.0 | \n", "6.599136 | \n", "
| 18 | \n", "90.0 | \n", "5.125360 | \n", "
| 19 | \n", "95.0 | \n", "5.345631 | \n", "
| 20 | \n", "100.0 | \n", "7.183400 | \n", "