{ "cells": [ { "cell_type": "markdown", "id": "f43cd6af-d772-43f7-a4da-30bcc41c7e50", "metadata": {}, "source": [ "## Diffusion of a single chemical gradient, in the presence of membranes in its path (passive transport) \n", "Three scenarios: \n", "1) no membranes \n", "2) membranes with permeability to that chemical equal its diffusion rate\n", "3) membranes with much smaller permeability value" ] }, { "cell_type": "markdown", "id": "6398f935-72f9-458e-90ab-f02a05132302", "metadata": {}, "source": [ "### TAGS : \"membranes 1D\", \"diffusion 1D\", \"basic\"" ] }, { "cell_type": "code", "execution_count": 1, "id": "2b6f0de7-d66f-4f4e-8850-8a092fca20b8", "metadata": {}, "outputs": [], "source": [ "LAST_REVISED = \"Aug. 18, 2025\"\n", "LIFE123_VERSION = \"1.0.0rc6\" # Library version this experiment is based on" ] }, { "cell_type": "code", "execution_count": 2, "id": "806647d0-4c0b-4abf-8d86-53460378d93e", "metadata": {}, "outputs": [], "source": [ "#import set_path # Using MyBinder? Uncomment this before running the next cell!" ] }, { "cell_type": "code", "execution_count": 3, "id": "f6e0f263", "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 life123 import BioSim1D, ChemData, check_version" ] }, { "cell_type": "code", "execution_count": 4, "id": "fe26e828-4428-4754-af9b-b54739b3a109", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "OK\n" ] } ], "source": [ "check_version(LIFE123_VERSION)" ] }, { "cell_type": "code", "execution_count": null, "id": "79045ff7-ed3f-4c3a-be79-9f8a4476f3de", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "id": "5b65e11a-4f5d-4b49-aee1-dcc8159fc180", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "markdown", "id": "a61306df-44f5-4693-a304-86e9db93dd0b", "metadata": { "tags": [] }, "source": [ "# Part 1\n", "## No membranes; a simple diffusion" ] }, { "cell_type": "code", "execution_count": 5, "id": "7e81fa36-0441-4898-b504-665147c2d6ac", "metadata": {}, "outputs": [], "source": [ "# Initialize the system\n", "chem_data = ChemData(names=\"A\", \n", " diffusion_rates=600.)\n", "\n", "bio = BioSim1D(n_bins=100, chem_data=chem_data)" ] }, { "cell_type": "code", "execution_count": 6, "id": "691ce10c-71c1-4f64-ad4f-af16d2f466f2", "metadata": { "tags": [] }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "SYSTEM STATE at Time t = 0:\n", "100 bins and 1 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 90 | \n", "Bin 91 | \n", "Bin 92 | \n", "Bin 93 | \n", "Bin 94 | \n", "Bin 95 | \n", "Bin 96 | \n", "Bin 97 | \n", "Bin 98 | \n", "Bin 99 | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "A | \n", "600.0 | \n", "10.0 | \n", "10.505051 | \n", "11.010101 | \n", "11.515152 | \n", "12.020202 | \n", "12.525253 | \n", "13.030303 | \n", "13.535354 | \n", "... | \n", "55.454545 | \n", "55.959596 | \n", "56.464646 | \n", "56.969697 | \n", "57.474747 | \n", "57.979798 | \n", "58.484848 | \n", "58.989899 | \n", "59.494949 | \n", "60.0 | \n", "
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "A | \n", "600.0 | \n", "10.0 | \n", "10.505051 | \n", "11.010101 | \n", "11.515152 | \n", "12.020202 | \n", "12.525253 | \n", "13.030303 | \n", "13.535354 | \n", "... | \n", "55.454545 | \n", "55.959596 | \n", "56.464646 | \n", "56.969697 | \n", "57.474747 | \n", "57.979798 | \n", "58.484848 | \n", "58.989899 | \n", "59.494949 | \n", "60.0 | \n", "
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