What metabolic pathways does Lumen simulate?

Lumen models glycolysis and gluconeogenesis, the pentose phosphate pathway, the Calvin and Krebs cycles, pyruvate dehydrogenase, lactate and ethanol fermentation, beta-oxidation and fatty-acid synthesis, glycogen and starch, respiratory and photosynthetic electron transport, ATP synthase, bacteriorhodopsin, NNT and reactive-oxygen scavenging. Each organism is one kinetic model whose reactions are balanced in elements and charge and named by their BiGG identifiers.

How does the electron transport chain work in Lumen?

Each membrane reaction's free energy comes from its carriers' midpoint potentials (and, for the photosystems, the energy of the photons absorbed), plus the cost of moving charge against the proton-motive force. The gradient therefore slows the pumps that build it, and ATP synthase runs forward or backward as its ΔG says. The figure draws one representative copy of each complex turning over at the model's rate, slowed so it can be followed.

What is allosteric regulation in cellular metabolism?

Enzymes are sped up or slowed by molecules other than their substrates. In Lumen, regulation is one factor in each rate, beside saturation and thermodynamics: ATP inhibits phosphofructokinase and AMP relieves it, NADH/NAD⁺ slows the Krebs cycle's dehydrogenases, and light switches the Calvin cycle's enzymes on. The inspector shows each factor for any enzyme.

What organism presets are available?

Five: a cyanobacterium (a thylakoid), an animal cell (a mitochondrial crista, with a matrix), an obligate anaerobe (a plasma membrane under a cell wall), a plant chloroplast (a thylakoid with a granum) and a halophilic archaeon (its purple membrane). Each has its own reactions, compartments, pools and environment, and a custom composite has everything.

Does Lumen collect any personal data?

Lumen's simulation state stays in the browser and the app has no account or simulation-state upload. The portfolio site may record aggregate page-view metadata separately from the metabolic state.

Is Lumen free and open source?

Yes. Lumen's source is available on GitHub under the GNU Affero General Public License v3.0.

What is oxidative phosphorylation?

Electron transport from NADH or succinate to oxygen pumps protons across the membrane, and ATP synthase lets them back: its rotor's ring of c subunits turns once for three ATP, so a mammalian mitochondrion's eight-subunit ring takes 8/3 protons per ATP, and exporting the ATP costs about one more. In Lumen this coupling is thermodynamic: with little ADP the gradient rises until the chain nearly stalls (respiratory control), and an uncoupler collapses it.

Lumen — Interactive Cellular Metabolism Simulator

What is Lumen?

Lumen is an interactive model of how cells make and spend energy. Each organism is a kinetic model: its metabolites are concentrations, and its reactions run at rates set by thermodynamics, saturation and regulation. The figure is a window onto that model, slowed so it can be followed: the membrane in cross-section above, the carbon network as a transit map below. Click an enzyme to pulse it and watch the push spread or die.

Metabolic pathways

The network covers glycolysis and gluconeogenesis, the pentose phosphate pathway, the Calvin and Krebs cycles, pyruvate dehydrogenase, lactate and ethanol fermentation, beta-oxidation and fatty-acid synthesis, glycogen and starch, electron transport, ATP synthesis and the scavenging of reactive oxygen. Every reaction is balanced in elements and charge.

Thermodynamics and regulation

Each rate is a capacity times three factors: thermodynamics (1 − e^ΔG/RT, so no reaction runs against its ΔG), saturation with substrates, and regulation by effectors such as ATP, citrate, NADH/NAD⁺ and light. The proton gradient enters every membrane reaction's ΔG, so a full gradient slows the chain that builds it: respiratory control.

Control of flux

Holding an enzyme raises its activity by 10% against an unchanged copy of the cell. At the steady state, each flux's fractional response is the enzyme's flux control coefficient over it. Control is shared among enzymes and shifts with conditions.

Reactive oxygen species

Complex I and the Q-cycle leak superoxide, faster as the proton-motive force rises. Superoxide dismutase, catalase and glutathione peroxidase (which spends NADPH) remove it; what remains damages the membrane, which then leaks protons, and repair spends ATP.

Fatty acid metabolism

Beta-oxidation breaks fatty acids into acetyl-CoA two carbons at a round, reducing FAD and NAD⁺. Fatty-acid synthesis runs on its own enzymes, spending ATP and NADPH. Both share the acetyl-CoA pool with the Krebs cycle, where a cell decides whether it burns fat or stores it.

Organism presets

Five organisms each have their own reactions, compartments, pools and membrane: a cyanobacterium, an animal cell with its mitochondrial matrix, an obligate anaerobe, a plant chloroplast and a halophilic archaeon.

Accessibility

Lumen provides keyboard shortcuts, labeled controls, light, dark and sunlight-following themes, and numerical readouts; the enzyme card reaches every enzyme from the keyboard, and the conditions' values are sliders. With reduced motion requested, Lumen opens on a still frame, and the model clock can be paused.

See also: Worldline for particle physics, Shoals for options trading, Miasma for epidemics.

Learning outcomes

After using Lumen, students should be able to: trace simulated carbon flow through glycolysis, pyruvate processing, the Krebs cycle, and linked biosynthetic routes; explain how the proton-motive force couples electron transfer to ATP synthesis and limits it (respiratory control); read an enzyme's rate as thermodynamics, saturation and regulation; interpret a flux control coefficient; compare respiratory, photosynthetic, and fermentative network states; and describe how electron leaks, scavenging, and NADPH availability affect ROS and cell health.

Prerequisites

Basic chemistry (atoms, molecules, chemical bonds, redox reactions). Familiarity with cell structure (mitochondria, chloroplasts) is helpful but not required — the simulator introduces each organelle through its organism presets.

References

P. Mitchell, "Coupling of phosphorylation to electron and hydrogen transfer by a chemi-osmotic type of mechanism" (1961). J. M. Berg, J. L. Tymoczko, and L. Stryer, Biochemistry, 9th ed. (W.H. Freeman, 2019).