Each capsule carries an engineered probiotic strain wrapped in a pH-responsive enteric shell. Shell integrity S ∈ [0,1] dissolves only once the local gut pH exceeds the coating's trigger pH:
dS/dt = −(k₀ / thickness) · max(0, pH(t) − pH_trigger)
S(0) = 1 (intact at swallow)
Bacterial viability V ∈ [0,1] decays exponentially, but at very different rates depending on whether the shell still shields the cells from stomach acid:
dV/dt = −k_v(t) · V
k_v = k_protected if S > 0.05 (shielded)
k_v = k_exposed · acidSensitivity · (1 + 4·max(0, 3 − pH(t))) if S ≤ 0.05 (exposed)
pH(t) follows position along the schematic gut path below: esophagus ≈7.0 → stomach ≈2.0 → duodenum ramping to ≈6.0 → jejunum/ileum ramping to ≈7.4 → colon ≈6.8. A thicker shell slows dissolution (protective, but may still be intact — and useless — by the time the capsule reaches the colon). A trigger pH set too low lets the coating fail while still acidic upstream, exposing the strain early; set too high, and the dose may pass through never releasing. The live "colon delivery success" readout is the fraction of capsules currently in the colon with viability above 50% — the actual therapeutic target of an oral engineered-microbiome product. This is the same model as the 3D version of this simulator, viewed here as a flattened 2D path instead of a rotating tract — drag to pan, scroll (or the +/− buttons) to zoom.
- Shell thickness — thicker coatings dissolve slower (k ∝ 1/thickness), trading protection for delayed release.
- Coating trigger pH — the pH above which the enteric polymer starts dissolving (real coatings like Eudragit® L100 trigger near pH 6).
- Total GI transit time — how many physical hours a capsule spends traversing mouth → colon; slower transit means more cumulative acid/base exposure.
- Strain acid sensitivity — a multiplier on the exposed-state death rate, standing in for how acid-tolerant the engineered chassis itself is.