{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Multi-complex analysis example\n", "\n", "Analyze a set of multiple complexes representing different states of HCR polymerization (Dirks and Pierce, Proc Natl Acad Sci USA, 2004) \n", "\n", "Strand species: \n", "Initiator i1 \n", "Hairpin h1 \n", "Hairpin h2 \n", "\n", "Material: DNA \n", "Temperature: 23 C \n", "\n", "While we illustrate analysis of a set of complexes here, we recommend performing a test tube analysis so that one does not presuppose which complexes will form in solution (see tube analysis example notebook). " ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "data": { "text/html": [ "Complex results:
Complex | \n", "Pfunc | \n", "ΔG (kcal/mol) | \n", "MFE (kcal/mol) | \n", "
---|---|---|---|
(h1) | \n", "3.8928e+20 | \n", "-27.901 | \n", "-27.740 | \n", "
(h2) | \n", "7.5022e+20 | \n", "-28.287 | \n", "-27.979 | \n", "
(i1) | \n", "6.0965e+0 | \n", "-1.064 | \n", "0.000 | \n", "
(i1+h1) | \n", "6.1982e+31 | \n", "-43.081 | \n", "-41.379 | \n", "
(i1+h1+h2) | \n", "7.8258e+62 | \n", "-85.225 | \n", "-83.629 | \n", "
(i1+h1+h1+h2) | \n", "2.2947e+94 | \n", "-127.866 | \n", "-126.035 | \n", "
(i1+h1+h2+h1+h2) | \n", "1.5846e+117 | \n", "-158.814 | \n", "-155.648 | \n", "