# Scale Ladder

The zoom control is a scientific scale ladder. Each band has a different valid model. The visual should never imply atomistic certainty at a scale where we only have reduced-order parameters.

## 1. Cell Context

Approximate field: 10-500 micrometers.

Shows:

- mitochondrial exchange between cells
- tunneling nanotube-like bridges
- extracellular vesicle/free mitochondria concepts
- tumor/stromal/immune energetic ecology

Model status:

- qualitative system context
- no individual ETC events resolved

Information needed next:

- transfer rates by cell type
- tunneling nanotube dimensions and cargo velocities
- cancer/stromal/immune transfer case studies

## 2. Whole Mitochondrion

Approximate field: 0.5-10 micrometers.

Shows:

- outer boundary
- inner membrane/cristae
- matrix/IMS separation
- local stress and PMF zones

Model status:

- schematic morphology
- quantitative ETC values remain aggregated

Information needed next:

- crista geometry distributions
- OPA1/MICOS/crista junction constraints
- tissue-specific mitochondrial morphology

## 3. Respiratory Membrane Patch

Approximate field: 50-500 nanometers.

Shows:

- Complexes I-V
- Q diffusion in the membrane
- cytochrome c on the IMS side
- proton pumping and ATP synthase return
- ROS leak from plausible sites

Model status:

- current strongest quantitative layer
- PMF, flux, leak, ROS hazard, and P/O are computed here

Information needed next:

- supercomplex density and arrangement
- cardiolipin composition/oxidation effects
- calibrated proton leak and respiration datasets

## 4. Protein/Cofactor Chain

Approximate field: 5-50 nanometers.

Shows:

- Complex I-like cofactor chain
- FMN, Fe-S clusters, N2, Q-site handoff
- effective beta/lambda/rate terms

Model status:

- reduced network
- not a full atomistic structure

Information needed next:

- PDB/mmCIF structure loading
- cofactor coordinate extraction
- donor-acceptor edge distances
- redox potential tables by cofactor

Structural anchors:

- RCSB PDB 5XTD: human respiratory complex I
- RCSB PDB 8Q1U: bovine Q-bound Complex I comparative anchor
- RCSB PDB 5XTE: human respiratory complex III
- RCSB PDB 5XTH: human respiratory supercomplex I1III2IV1
- RCSB PDB 5XTI: human respiratory megacomplex I2III2IV2
- RCSB PDB 6TT7: ovine mammalian ATP synthase

## 5. Tunneling Window

Approximate field: 4-14 angstrom productive hop distances.

Shows:

- donor/acceptor rate model
- exponential coupling decay
- beta, lambda, effective log10(k_ET)
- relative tunneling probability

Model status:

- rate-model view
- not molecular dynamics
- not a literal electron trajectory

Information needed next:

- cofactor-specific DeltaG and lambda values
- protein-specific beta estimates
- calibration to measured ET rates where available

## Long-Term Target

The mature instrument should smoothly move through:

```text
cellular exchange -> mitochondrial network -> crista architecture -> membrane patch
-> protein structures -> cofactors -> tunneling-rate model
```

Each level should expose its own assumptions, sources, and uncertainty.