# Source Backbone

This is the current citation spine for the model. The app should eventually expose these as structured references in the reviewer panel.

## Electron Transport and PMF

1. Alberts et al., Molecular Biology of the Cell, "Electron-Transport Chains and Their Proton Pumps." NCBI Bookshelf. https://www.ncbi.nlm.nih.gov/books/NBK26904/
2. Nolfi-Donegan et al., "Mitochondrial electron transport chain: Oxidative phosphorylation, oxidant production, and methods of measurement." Redox Biology, 2020. https://pmc.ncbi.nlm.nih.gov/articles/PMC7767752/
3. Dzbek and Korzeniewski, "Control Over the Contribution of the Mitochondrial Membrane Potential and Proton Gradient to the Protonmotive Force." Journal of Biological Chemistry, 2008. https://pmc.ncbi.nlm.nih.gov/articles/PMC2662253/

## Quantum Electron Transfer

4. Martin and Matyushov, "Electron-transfer chain in respiratory complex I." Scientific Reports, 2017. https://pmc.ncbi.nlm.nih.gov/articles/PMC5511282/
5. Page et al., "Distance metrics for heme protein electron tunneling." 2008 PMC record. https://pmc.ncbi.nlm.nih.gov/articles/PMC2536628/
6. Moser et al., "Guidelines for tunneling in enzymes." Biochimica et Biophysica Acta, 2010. https://pmc.ncbi.nlm.nih.gov/articles/PMC3509937/
7. Stuchebrukhov, "Long-Distance Electron Tunneling in Proteins." Laser Physics, 2010. https://pmc.ncbi.nlm.nih.gov/articles/PMC4213181/

## Structural Anchors

8. RCSB PDB 5XTD, "Cryo-EM structure of human respiratory complex I." https://www.rcsb.org/structure/5XTD
9. RCSB PDB 8Q1U, "Inward-facing, open1 proteoliposome complex I at 3.3 A, after deactivation treatment." https://www.rcsb.org/structure/8Q1U
10. RCSB PDB 5XTH, "Cryo-EM structure of human respiratory supercomplex I1III2IV1." https://www.rcsb.org/structure/5XTH
11. RCSB PDB 5XTI, "Cryo-EM architecture of human respiratory chain megacomplex-I2III2IV2." https://www.rcsb.org/structure/5XTI
12. RCSB PDB 5XTE, "Cryo-EM structure of human respiratory complex III (cytochrome bc1 complex)." https://www.rcsb.org/structure/5XTE
13. RCSB PDB 6TT7, "Ovine ATP synthase 1a state." https://www.rcsb.org/structure/6TT7

## ROS and Reverse Electron Transport

14. Robb et al., "Control of mitochondrial superoxide production by reverse electron transport at complex I." Journal of Biological Chemistry, 2018. https://pmc.ncbi.nlm.nih.gov/articles/PMC6016480/
15. Brand, "The sites and topology of mitochondrial superoxide production." Experimental Gerontology, 2010. https://pmc.ncbi.nlm.nih.gov/articles/PMC2879443/

## Aging

16. Gomez and Hagen, "Age-related decline in mitochondrial bioenergetics: Does supercomplex destabilization determine lower oxidative capacity and higher superoxide production?" Seminars in Cell & Developmental Biology, 2012. https://pmc.ncbi.nlm.nih.gov/articles/PMC4096948/
17. Rosca et al., "Supercomplexes of the Mitochondrial Electron Transport Chain Decline in the Aging Rat Heart." Archives of Biochemistry and Biophysics, 2009. https://pmc.ncbi.nlm.nih.gov/articles/PMC2762268/

## Cancer Metabolism

18. Wallace, "Mitochondria and cancer." Nature Reviews Cancer, 2012. https://www.nature.com/articles/nrc3365
19. Sabharwal and Schumacker, "Mitochondrial ROS in cancer: initiators, amplifiers or an Achilles' heel?" Nature Reviews Cancer, 2014. https://www.nature.com/articles/nrc3803
20. Cassim et al., "Warburg and Beyond: The Power of Mitochondrial Metabolism to Collaborate or Replace Fermentative Glycolysis in Cancer." Cancers, 2020. https://www.mdpi.com/2072-6694/12/5/1119

## Model Honesty Notes

- Several citations support broad mechanisms rather than the exact reduced-order equations used in this app.
- Parameter values in presets are effective scenario values. They are not a substitute for tissue-specific calibration.
- The next scientific upgrade should fit the model against selected experimental datasets for respiration, P/O, proton leak, and RET ROS.