Release Notes

Fluxion

What's New

Fluxion now models a second organ — the liver — alongside the muscle cell, and couples the two through the shared bloodstream. You can watch the classic division of labor between them: a working muscle spills lactate into the blood, and the liver takes it up and rebuilds it into glucose — the Cori cycle — all under hormonal control.

• The liver, as a full organ. In the Body view, a liver now sits alongside the muscle. Click it to scope every analysis tab — the live plot, the metabolite explorer, reaction capacity, diagnostics, and the flow map — to the liver, just as you can for the muscle and the bloodstream. It runs its own complete biochemistry, not a copy of the muscle's.
• Blood-glucose control by insulin and glucagon. A lumped pancreas reads the shared blood glucose and sets the two counter-regulatory hormones. When blood glucose is high the liver stores it as glycogen; when it falls, glucagon switches the liver over to making glucose — mobilizing its glycogen and running gluconeogenesis, rebuilding glucose from lactate and other precursors. Muscle, in turn, takes glucose up more eagerly when insulin is high.
• The Cori cycle. Lactate from anaerobic muscle now travels through the blood to the liver, which turns it back into glucose and returns it to circulation. During hard exercise the muscle outpaces the liver and blood lactate rises, as it does in life; in recovery the liver clears it and blood glucose is defended throughout.
• Fat and ketone metabolism. The resting and fasting liver burns fatty acids delivered by the blood and converts the surplus into ketone bodies, which it exports for other tissues to use — the fat-fuel counterpart of the Cori cycle.
• A whole-body bloodstream. The shared blood now carries glucose, lactate, oxygen, carbon dioxide, insulin, glucagon, fatty acids, and ketone bodies between organs. Oxygen and carbon dioxide are now exchanged for the whole body at once — one set of lungs — so switching oxygen off makes every organ go anaerobic together, and each analysis tab is labeled with the organ or the blood it is showing.
• A reworked acid-base model. Intracellular pH is now tracked by accounting for every proton each reaction releases or takes up, and the body regulates its acid-base balance the way a real one does — across the cell membrane and through the kidneys and lungs. As a result the whole two-organ body now holds a steady, physiological pH at rest.
• A faster simulation engine. The solver core has been reworked so each step of the simulation is computed more efficiently — the reaction rates are now evaluated in batches, and the model's Jacobian is calculated exactly instead of being estimated numerically. Simulations finish sooner and the live view stays smooth, and the improvement grows as the body gains more organs. The results are unchanged: every concentration, flux, membrane voltage, and pH comes out exactly as before, checked against a locked reference of the whole model.

Bug Fixes

• Uninstalling Fluxion now removes the empty bundled-dependency folders that could previously leave the installation directory behind.

Known Issues

• The liver's mitochondria run at a lower energy state than a real liver's — the inner-membrane voltage sits low and the matrix is more oxidized than it should be. The model still keeps the liver energized and defends blood glucose, but one visible consequence is that the blood beta-hydroxybutyrate-to-acetoacetate (ketone) ratio reads lower than in life. Correcting this needs a deeper recalibration of the liver's respiratory chain, planned for a future update.
• Resting blood levels of lactate, carbon dioxide, and ketone bodies read low in absolute terms, because the modeled liver is small relative to the shared blood pool and delivers little into it. How they rise and fall between fed and fasting states — the behavior the model is teaching — is correct; only the absolute resting numbers are understated.
• During prolonged oxygen-free work the cell drifts slightly alkaline instead of acidifying. With the new acid-base model the body now holds a steady, correct pH at rest and acidifies properly under a hard exercise load, but a very long run with oxygen switched off still lets the cell and the blood drift a few tenths of a pH unit too high. Correcting it needs further work on the cell's proton budget.