Quantifying metabolite transition events and permeation pathways across synthetic carboxysome shells. To quantify the permeability of small molecular compounds -CO2, O2, HCO3 -, 3phosphoglycerate (3-PGA), RuBP, we track permeation events for these metabolites across a synthetic carboxysome shell using classical MD simulations. Individual all-atom MD simulations are performed for each metabolite at high concentration (500 mM) to increase sampling of observed transition events for an aggregate of 1.5 µs per metabolite. To monitor for permeation events, we track the radial position for each metabolite molecule relative to the carboxysome center, and monitor trajectory traces for the radial position as a function of time (Fig. ). If the trace for a specific small molecule can be found on both sides of the carboxysome shell, it must have crossed the shell, and is a permeation event.