\BOOKMARK [1][-]{section.1}{Single Cell Dynamics}{}
\BOOKMARK [2][-]{subsection.1.1}{Growth}{section.1}
\BOOKMARK [2][-]{subsection.1.2}{Cellular Composition}{section.1}
\BOOKMARK [2][-]{subsection.1.3}{Cellular Composition}{section.1}
\BOOKMARK [2][-]{subsection.1.4}{Nucleotides}{section.1}
\BOOKMARK [2][-]{subsection.1.5}{Nucleotides}{section.1}
\BOOKMARK [2][-]{subsection.1.6}{Translation}{section.1}
\BOOKMARK [2][-]{subsection.1.7}{Translation}{section.1}
\BOOKMARK [2][-]{subsection.1.8}{Translation}{section.1}
\BOOKMARK [2][-]{subsection.1.9}{Stalled Ribosomes}{section.1}
\BOOKMARK [2][-]{subsection.1.10}{Stalled Ribosomes}{section.1}
\BOOKMARK [2][-]{subsection.1.11}{Chromosome Organization}{section.1}
\BOOKMARK [2][-]{subsection.1.12}{Chromosome Organization}{section.1}
\BOOKMARK [2][-]{subsection.1.13}{Chromosome Organization}{section.1}
\BOOKMARK [2][-]{subsection.1.14}{Chromosome Organization}{section.1}
\BOOKMARK [2][-]{subsection.1.15}{Chromosome Organization}{section.1}
\BOOKMARK [2][-]{subsection.1.16}{Chromosome Organization}{section.1}
\BOOKMARK [1][-]{section.2}{Population Dynamics}{}
\BOOKMARK [2][-]{subsection.2.1}{Growth}{section.2}
\BOOKMARK [2][-]{subsection.2.2}{Growth}{section.2}
\BOOKMARK [2][-]{subsection.2.3}{Cellular Composition}{section.2}
\BOOKMARK [2][-]{subsection.2.4}{Metabolism}{section.2}
\BOOKMARK [2][-]{subsection.2.5}{Energy Production}{section.2}
\BOOKMARK [2][-]{subsection.2.6}{Energy Production}{section.2}
\BOOKMARK [2][-]{subsection.2.7}{Nucleotide Concentrations}{section.2}
\BOOKMARK [2][-]{subsection.2.8}{Amino Acid Counts}{section.2}
\BOOKMARK [2][-]{subsection.2.9}{Process ATP Requirements}{section.2}
\BOOKMARK [2][-]{subsection.2.10}{Process ATP Allocations}{section.2}
\BOOKMARK [2][-]{subsection.2.11}{Process ATP Usages}{section.2}
\BOOKMARK [2][-]{subsection.2.12}{Process GTP Requirements}{section.2}
\BOOKMARK [2][-]{subsection.2.13}{Process GTP Allocations}{section.2}
\BOOKMARK [2][-]{subsection.2.14}{Process GTP Usages}{section.2}
\BOOKMARK [2][-]{subsection.2.15}{Replication Initiation}{section.2}
\BOOKMARK [2][-]{subsection.2.16}{Replication}{section.2}
\BOOKMARK [2][-]{subsection.2.17}{Replication}{section.2}
\BOOKMARK [2][-]{subsection.2.18}{Replication}{section.2}
\BOOKMARK [2][-]{subsection.2.19}{Transcription}{section.2}
\BOOKMARK [2][-]{subsection.2.20}{RNA Maturation}{section.2}
\BOOKMARK [2][-]{subsection.2.21}{RNA Maturation}{section.2}
\BOOKMARK [2][-]{subsection.2.22}{Translation}{section.2}
\BOOKMARK [2][-]{subsection.2.23}{Translation}{section.2}
\BOOKMARK [2][-]{subsection.2.24}{Protein Maturation}{section.2}
\BOOKMARK [2][-]{subsection.2.25}{Protein Maturation}{section.2}
\BOOKMARK [2][-]{subsection.2.26}{Supercoiling}{section.2}
\BOOKMARK [2][-]{subsection.2.27}{DNA Repair}{section.2}
\BOOKMARK [2][-]{subsection.2.28}{Cell Division}{section.2}
\BOOKMARK [2][-]{subsection.2.29}{Cell Division}{section.2}
\BOOKMARK [2][-]{subsection.2.30}{Immune Activation}{section.2}
\BOOKMARK [2][-]{subsection.2.31}{Unsynchronized Population}{section.2}
\BOOKMARK [2][-]{subsection.2.32}{Simulation Runtime}{section.2}
\BOOKMARK [1][-]{section.3}{Population Statistics}{}
\BOOKMARK [2][-]{subsection.3.1}{Biomass Composition}{section.3}
\BOOKMARK [2][-]{subsection.3.2}{Biomass Composition}{section.3}
\BOOKMARK [2][-]{subsection.3.3}{Metabolite Concentrations}{section.3}
\BOOKMARK [2][-]{subsection.3.4}{dNMP Composition}{section.3}
\BOOKMARK [2][-]{subsection.3.5}{Nucleotide Composition}{section.3}
\BOOKMARK [2][-]{subsection.3.6}{Nucleotide Composition}{section.3}
\BOOKMARK [2][-]{subsection.3.7}{Nucleotide Composition}{section.3}
\BOOKMARK [2][-]{subsection.3.8}{Amino Acid Composition}{section.3}
\BOOKMARK [2][-]{subsection.3.9}{Amino Acid Composition}{section.3}
\BOOKMARK [2][-]{subsection.3.10}{Amino Acid Composition}{section.3}
\BOOKMARK [2][-]{subsection.3.11}{RNA Composition}{section.3}
\BOOKMARK [2][-]{subsection.3.12}{RNA Composition}{section.3}
\BOOKMARK [2][-]{subsection.3.13}{Gene Expression}{section.3}
\BOOKMARK [2][-]{subsection.3.14}{Gene Expression}{section.3}
\BOOKMARK [2][-]{subsection.3.15}{tRNA Expression}{section.3}
\BOOKMARK [2][-]{subsection.3.16}{tRNA Expression}{section.3}
\BOOKMARK [2][-]{subsection.3.17}{Protein Expression}{section.3}
\BOOKMARK [2][-]{subsection.3.18}{Protein Expression}{section.3}
\BOOKMARK [2][-]{subsection.3.19}{Macromolecule Expression}{section.3}
\BOOKMARK [2][-]{subsection.3.20}{Macromolecular Complexes}{section.3}
\BOOKMARK [2][-]{subsection.3.21}{RNA Half Lives}{section.3}
\BOOKMARK [2][-]{subsection.3.22}{RNA Half Lives}{section.3}
\BOOKMARK [2][-]{subsection.3.23}{Replication}{section.3}
\BOOKMARK [2][-]{subsection.3.24}{Secondary Replication Initiation}{section.3}
\BOOKMARK [2][-]{subsection.3.25}{RNA Synthesis}{section.3}
\BOOKMARK [2][-]{subsection.3.26}{Protein Synthesis}{section.3}
\BOOKMARK [2][-]{subsection.3.27}{Cell Cycle Phase Durations}{section.3}
\BOOKMARK [2][-]{subsection.3.28}{Cell Cycle Phase Distribution}{section.3}
\BOOKMARK [2][-]{subsection.3.29}{Cell Cycle Phase Lengths}{section.3}
\BOOKMARK [2][-]{subsection.3.30}{Cumulative Growth Vs. Cell Cycle Phase Durations}{section.3}
\BOOKMARK [2][-]{subsection.3.31}{Cumulative Growth Vs. Cell Cycle Phase Times}{section.3}
\BOOKMARK [2][-]{subsection.3.32}{Initial Growth Vs. Cell Cycle Phase Durations}{section.3}
\BOOKMARK [2][-]{subsection.3.33}{Initial Growth Vs. Cell Cycle Phase Times}{section.3}
\BOOKMARK [2][-]{subsection.3.34}{Initial Vs. Cumulative Growth}{section.3}
\BOOKMARK [2][-]{subsection.3.35}{Initial Growth Rate Vs. End Time}{section.3}
\BOOKMARK [2][-]{subsection.3.36}{Final Growth Rate Vs. End Time}{section.3}
\BOOKMARK [2][-]{subsection.3.37}{Cell Mass Distribution}{section.3}
\BOOKMARK [2][-]{subsection.3.38}{Blocked Decay Events}{section.3}
\BOOKMARK [2][-]{subsection.3.39}{Process ATP Usage}{section.3}
\BOOKMARK [2][-]{subsection.3.40}{Process GTP Usage}{section.3}
\BOOKMARK [2][-]{subsection.3.41}{Warnings}{section.3}
\BOOKMARK [1][-]{section.4}{Simulation Structure}{}
\BOOKMARK [2][-]{subsection.4.1}{Metabolic Model}{section.4}
\BOOKMARK [2][-]{subsection.4.2}{Shared Gene Products}{section.4}
\BOOKMARK [2][-]{subsection.4.3}{Shared Metabolites}{section.4}
\BOOKMARK [2][-]{subsection.4.4}{Shared Metabolites}{section.4}
\BOOKMARK [2][-]{subsection.4.5}{Shared Metabolites}{section.4}