Agent-Based Model Derived from module 7 elements · 6 transitions

Agent-based cargo routing model of endosomal recycling, lysosomal degradation, and cytosolic escape

Simulates 100 discrete cargo/nanoparticle agents traversing the seven stages of the module under uniform uncalibrated default transition rates (base_rate = 0.45, competing_inhibitor_factor = 0.25). In wild-type baseline trafficking, active RAB7A/ESCRT late endosomal maturation (escrt_rab7_late_endosome) attenuates the cytosolic escape transition from acidified early endosomes, resulting in ~47% recycling (ehd1_recycling_branch), ~43% lysosomal degradation (ctsd_lysosomal_degradation), and ~10% cytosolic escape (cytosolic_cargo_escape) — reproducing the qualitative hierarchy observed by LysoTag barcoding (~8% baseline cytosolic LNP escape in vivo; PMID:41814093). Perturbing individual stages reproduces the qualitative direction of genetic and pharmacological blocks across the pathway.

Module: Intracellular endosomal trafficking and cargo routing — clathrin/AP-2 uptake, V-ATPase acidification, EHD1 recycling vs. ESCRT/RAB7A late-endosomal maturation, CTSD lysosomal proteolysis, and cytosolic escape Source YAML: modules/endosomal_trafficking_routing.yaml

Compartment Trafficking & Discrete Cargo Routing

t = 24 / 24

Cargo Occupancy Trajectory (t = 0 .. 24)

Derived Transition Rules & Effective Flux Rates

From Stage To Stage Predicate Modulators / Competing Branches Effective Rate