{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Problem 3.4: Modeling inducers in a toggle switch\n", "\n", "
" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "*This problem is still a draft.*\n", "\n", "In our analysis of the Gardner and Collins synthetic toggle switch, we did not include a way to represent the addition of the inducer signals. Such signals typically function by decreasing a receptor's affinity for its target binding site, in other words by increasing the value of the Hill repression constant $k$. In the nondimensionalized system, we see that $k_x$ (and correspondingly, $k_y$) appear both in the dimensionless concentration $\\tilde{x}$ and in the dimensionless production term $\\tilde{\\beta}_x$.\n", " \n", "Create an interactive plot representing the following scenario:\n", "\n", "* The circuit is built with parameters $\\beta, \\gamma, n$ fixed to be $\\beta = 10$, $\\gamma = 1$, $n=10$.\n", "* The plot has sliders for $k_x$ and $k_y$, which represent the presence of inducer signal to inactivate the repressors $X$ and $Y$, respectively. (Note that this representation assumes that the inducer's action is linearly proportional to its concentration, which is typically not true but gives the right qualitative result).\n", "* The plot shows how the nullclines, in dimensionless concentration space, change as you add and remove the inducer signals.\n", "\n", "What insights did you gain from the visualization?" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "
" ] } ], "metadata": { "anaconda-cloud": {}, "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": "3.9.7" } }, "nbformat": 4, "nbformat_minor": 4 }