\contentsline {section}{\numberline {}Single Cell Dynamics}{1}{section.1}
\contentsline {subsection}{\numberline {}Growth}{1}{subsection.1.1}
\contentsline {subsection}{\numberline {}Cellular Composition}{2}{subsection.1.2}
\contentsline {subsection}{\numberline {}Cellular Composition}{3}{subsection.1.3}
\contentsline {subsection}{\numberline {}Nucleotides}{4}{subsection.1.4}
\contentsline {subsection}{\numberline {}Nucleotides}{5}{subsection.1.5}
\contentsline {subsection}{\numberline {}Translation}{6}{subsection.1.6}
\contentsline {subsection}{\numberline {}Translation}{7}{subsection.1.7}
\contentsline {subsection}{\numberline {}Translation}{8}{subsection.1.8}
\contentsline {subsection}{\numberline {}Stalled Ribosomes}{9}{subsection.1.9}
\contentsline {subsection}{\numberline {}Stalled Ribosomes}{10}{subsection.1.10}
\contentsline {subsection}{\numberline {}Chromosome Organization}{11}{subsection.1.11}
\contentsline {subsection}{\numberline {}Chromosome Organization}{12}{subsection.1.12}
\contentsline {subsection}{\numberline {}Chromosome Organization}{13}{subsection.1.13}
\contentsline {subsection}{\numberline {}Chromosome Organization}{14}{subsection.1.14}
\contentsline {subsection}{\numberline {}Chromosome Organization}{15}{subsection.1.15}
\contentsline {subsection}{\numberline {}Chromosome Organization}{16}{subsection.1.16}
\contentsline {section}{\numberline {}Population Dynamics}{17}{section.2}
\contentsline {subsection}{\numberline {}Growth}{17}{subsection.2.1}
\contentsline {subsection}{\numberline {}Cellular Composition}{18}{subsection.2.2}
\contentsline {subsection}{\numberline {}Metabolism}{19}{subsection.2.3}
\contentsline {subsection}{\numberline {}Energy Production}{20}{subsection.2.4}
\contentsline {subsection}{\numberline {}Nucleotide Concentrations}{21}{subsection.2.5}
\contentsline {subsection}{\numberline {}Amino Acid Counts}{22}{subsection.2.6}
\contentsline {subsection}{\numberline {}Process ATP Requirements}{23}{subsection.2.7}
\contentsline {subsection}{\numberline {}Process ATP Allocations}{24}{subsection.2.8}
\contentsline {subsection}{\numberline {}Process ATP Usages}{25}{subsection.2.9}
\contentsline {subsection}{\numberline {}Process GTP Requirements}{26}{subsection.2.10}
\contentsline {subsection}{\numberline {}Process GTP Allocations}{27}{subsection.2.11}
\contentsline {subsection}{\numberline {}Process GTP Usages}{28}{subsection.2.12}
\contentsline {subsection}{\numberline {}Replication Initiation}{29}{subsection.2.13}
\contentsline {subsection}{\numberline {}Replication}{30}{subsection.2.14}
\contentsline {subsection}{\numberline {}Replication}{31}{subsection.2.15}
\contentsline {subsection}{\numberline {}Replication}{32}{subsection.2.16}
\contentsline {subsection}{\numberline {}Transcription}{33}{subsection.2.17}
\contentsline {subsection}{\numberline {}RNA Maturation}{34}{subsection.2.18}
\contentsline {subsection}{\numberline {}RNA Maturation}{35}{subsection.2.19}
\contentsline {subsection}{\numberline {}Translation}{36}{subsection.2.20}
\contentsline {subsection}{\numberline {}Protein Maturation}{37}{subsection.2.21}
\contentsline {subsection}{\numberline {}Protein Maturation}{38}{subsection.2.22}
\contentsline {subsection}{\numberline {}Supercoiling}{39}{subsection.2.23}
\contentsline {subsection}{\numberline {}DNA Repair}{40}{subsection.2.24}
\contentsline {subsection}{\numberline {}Cell Division}{41}{subsection.2.25}
\contentsline {subsection}{\numberline {}Cell Division}{42}{subsection.2.26}
\contentsline {subsection}{\numberline {}Immune Activation}{43}{subsection.2.27}
\contentsline {subsection}{\numberline {}Unsynchronized Population}{44}{subsection.2.28}
\contentsline {subsection}{\numberline {}Simulation Runtime}{45}{subsection.2.29}
\contentsline {section}{\numberline {}Population Statistics}{46}{section.3}
\contentsline {subsection}{\numberline {}Biomass Composition}{46}{subsection.3.1}
\contentsline {subsection}{\numberline {}Biomass Composition}{47}{subsection.3.2}
\contentsline {subsection}{\numberline {}dNMP Composition}{48}{subsection.3.3}
\contentsline {subsection}{\numberline {}Nucleotide Composition}{49}{subsection.3.4}
\contentsline {subsection}{\numberline {}Nucleotide Composition}{50}{subsection.3.5}
\contentsline {subsection}{\numberline {}Nucleotide Composition}{51}{subsection.3.6}
\contentsline {subsection}{\numberline {}Amino Acid Composition}{52}{subsection.3.7}
\contentsline {subsection}{\numberline {}Amino Acid Composition}{53}{subsection.3.8}
\contentsline {subsection}{\numberline {}Amino Acid Composition}{54}{subsection.3.9}
\contentsline {subsection}{\numberline {}RNA Composition}{55}{subsection.3.10}
\contentsline {subsection}{\numberline {}RNA Composition}{56}{subsection.3.11}
\contentsline {subsection}{\numberline {}Gene Expression}{57}{subsection.3.12}
\contentsline {subsection}{\numberline {}Gene Expression}{58}{subsection.3.13}
\contentsline {subsection}{\numberline {}tRNA Expression}{59}{subsection.3.14}
\contentsline {subsection}{\numberline {}tRNA Expression}{60}{subsection.3.15}
\contentsline {subsection}{\numberline {}Protein Expression}{61}{subsection.3.16}
\contentsline {subsection}{\numberline {}Protein Expression}{62}{subsection.3.17}
\contentsline {subsection}{\numberline {}Macromolecular Complexes}{63}{subsection.3.18}
\contentsline {subsection}{\numberline {}RNA Half Lives}{64}{subsection.3.19}
\contentsline {subsection}{\numberline {}RNA Half Lives}{65}{subsection.3.20}
\contentsline {subsection}{\numberline {}Replication}{66}{subsection.3.21}
\contentsline {subsection}{\numberline {}RNA Synthesis}{67}{subsection.3.22}
\contentsline {subsection}{\numberline {}Protein Synthesis}{68}{subsection.3.23}
\contentsline {subsection}{\numberline {}Cell Cycle Phase Durations}{69}{subsection.3.24}
\contentsline {subsection}{\numberline {}Cell Cycle Phase Distribution}{70}{subsection.3.25}
\contentsline {subsection}{\numberline {}Cell Cycle Phase Lengths}{71}{subsection.3.26}
\contentsline {subsection}{\numberline {}Cumulative Growth Vs. Cell Cycle Phase Durations}{72}{subsection.3.27}
\contentsline {subsection}{\numberline {}Cumulative Growth Vs. Cell Cycle Phase Times}{73}{subsection.3.28}
\contentsline {subsection}{\numberline {}Initial Growth Vs. Cell Cycle Phase Durations}{74}{subsection.3.29}
\contentsline {subsection}{\numberline {}Initial Growth Vs. Cell Cycle Phase Times}{75}{subsection.3.30}
\contentsline {subsection}{\numberline {}Initial Vs. Cumulative Growth}{76}{subsection.3.31}
\contentsline {subsection}{\numberline {}Initial Growth Rate Vs. End Time}{77}{subsection.3.32}
\contentsline {subsection}{\numberline {}Final Growth Rate Vs. End Time}{78}{subsection.3.33}
\contentsline {subsection}{\numberline {}Cell Mass Distribution}{79}{subsection.3.34}
\contentsline {subsection}{\numberline {}Blocked Decay Events}{80}{subsection.3.35}
\contentsline {subsection}{\numberline {}Process ATP Usage}{81}{subsection.3.36}
\contentsline {subsection}{\numberline {}Process GTP Usage}{82}{subsection.3.37}
\contentsline {subsection}{\numberline {}Warnings}{83}{subsection.3.38}
\contentsline {section}{\numberline {}Simulation Structure}{84}{section.4}
\contentsline {subsection}{\numberline {}Metabolic Model}{84}{subsection.4.1}
\contentsline {subsection}{\numberline {}Shared Gene Products}{85}{subsection.4.2}
\contentsline {subsection}{\numberline {}Shared Metabolites}{86}{subsection.4.3}
\contentsline {subsection}{\numberline {}Shared Metabolites}{87}{subsection.4.4}
\contentsline {subsection}{\numberline {}Shared Metabolites}{88}{subsection.4.5}