{'fraction_non_alphanumeric': 0.015055467511885896, 'fraction_numerical': 0.001584786053882726, 'mean_word_length': 6.055865921787709, 'pattern_counts': {'":': 0, '<': 0, '<?xml version=': 0, '>': 0, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
Molecular transport and packing underlie increasing ribosome productivity in faster growing cells

Faster growing cells must make proteins more quickly. Increasing ribosome abundance only partly accounts for increased protein production; the productivity of individual ribosomes must also increase, almost doubling via an unknown mechanism. To investigate, we model translation elongation in Escherichia coli by explicitly representing spatially-resolved transport and reactions among individual molecules each occupying finite volume. We predict that physical transport of individual ternary complexes accounts for ~80% of elongation latency. We find crowding increases at faster growth, which predictably decreases diffusion of ternary complexes, but that crowding also improves proximity between ternary complexes and ribosomes. Despite slowed diffusion, we predict that improved proximity wins out, offering a simple mechanism for how individual elongating ribosomes become more productive. We speculate how crowding imposes a physical limit on growth rate and likely undergirds cellular behavior more broadly. Our work reveals a fundamental mechanism arising from physical transport at the colloidal scale that cannot be obtained via kinetics-only modeling.