Fluxion

What's New

• The Reaction Flow Map has been rebuilt from the ground up. Every pathway diagram now arranges itself automatically instead of relying on fixed positions: each box grows to fit its label, the connecting arrows route cleanly through the gaps between boxes, and every section resizes to hold whatever it contains. The maps are far easier to read and hold up at any window or monitor size.
• The citric acid cycle is now drawn as a true loop, with each enzyme sitting between the two metabolites it connects. Glycolysis snakes across two rows so the whole pathway stays legible, and the Complete Overview lays out every metabolite and reaction in the model at once without a single box or label colliding.

Improvements

• The flow map fits and scales to any monitor or window size. "Fit View" always frames the entire diagram with its title in view, the mouse wheel zooms in and out around the pointer, and dragging pans across the larger maps.
• Long enzyme names are wrapped onto short lines, and every reaction rate and concentration stays fully readable inside its box.

Bug Fixes

• Flow-map arrows no longer cut through boxes; they begin and end cleanly at the box edges.
• Box labels and reaction values no longer overflow or get clipped by their boxes.
• Pathway sections no longer overlap one another or spill their contents past their borders.
• The Reaction Flow Map now opens at a sensible zoom instead of fully zoomed out.

Known Issues

• The respiratory slip that oxidises the resting matrix is modelled as a single lumped pathway, which leaves a few small artefacts: the membrane potential dips slightly at the very lowest workloads before falling as work increases, the resting cell takes a little longer to settle to a perfectly steady state, and oxidative metabolism runs a touch less efficient than the textbook oxygen-to-ATP ratio. Smoothing these needs a deeper rework that lets the chain's coupling vary continuously with the driving force, which is planned.
• During prolonged oxygen-free work the modelled cell drifts slightly alkaline instead of acidifying, because exported lactate carries its acid out to the blood pool, which is not modelled as buffered.