MODEL EVIDENCE · REVISION 2026.07
The science behind
each simulated rule.
This is not a bibliography used as decoration. Every entry below says what the source constrains, what BiologicalSetup actually implements, which constants were adapted, and where the claim stops.
- Primary sources
- —
- Implemented mechanisms
- 10
- Illustrative parameter sets
- 7
- Clinical claims
- 0
A paper can support an equation or constrain a mechanism without validating the whole simulator. Parameters marked illustrative were chosen for a stable, observable browser experiment and must not be treated as organism-, culture-, or patient-specific predictions.
EXECUTABLE MODEL CATALOG
Equation → engine → evidence
All time stepping is independent of rendering frame rate.
| Mechanism | Implemented form | Units / step | Evidence status | Validity boundary |
|---|---|---|---|---|
| Field transport | ∂c/∂t = D∇²c + q − kc |
µm² s⁻¹ · 50 ms | canonical law | 2D effective-depth, no-flux plane |
| Growth + uptake | µ = µmax S/(Ks + S) |
mM, pg · 50 ms | adapted | Illustrative E. coli-like agent |
| Run–tumble sensing | λ = λ₀ exp[−χ(mfast − mslow)] |
seconds · 50 ms | coarse-grained | Two-filter temporal comparison |
| Immune pursuit | dθ = bias(∇c)dt + σdW |
µm s⁻¹ · 50 ms | reduced-order | Generic cue, no receptor model |
| Engulfment | search → contact → cup e∈[0,1] → cargo |
15 s illustrative dwell | adapted | No phagosome or killing chemistry |
| Host stress | dz/dt = burden − recovery |
dimensionless proxy | illustrative | Not viability, toxicity, or inflammation |
| Neural voltage | C dV/dt = −gL(V−EL) + I + g(Erev−V) |
pA, pF, nS, mV · 1 ms | canonical reduction | Synthetic LIF network |
| Calcium label | spike → indicator increment → exponential decay |
qualitative proxy | conceptual constraint | No named GCaMP calibration |
| Phase-like view | geometry → qualitative optical contrast |
normalized display | illustrative | Not a wave-optical reconstruction |
| Determinism | seed + actions + fixed steps → state hash |
64-bit seed | engineering method | Guaranteed only within engine version |
PRIMARY LITERATURE
Claim-to-source map
No references match this filter.
CLAIM GATE
What these sources do not make this.
- Not a calibrated infection or immune-response predictor.
- Not a toxicity, viability, drug-response, or treatment model.
- Not a reconstructed cortical circuit or electrophysiology tool.
- Not a quantitative microscope, photon detector, or spectral model.
- Not portable across model versions without an explicit migration.