What is Cyano?
Cyano is an interactive cellular metabolism simulator that traces how cells produce and consume energy through interconnected biochemical pathways. Click enzyme labels on the canvas to advance reactions step by step, or enable autoplay to watch the full metabolic network operate continuously.
Metabolic Pathways
One shared metabolite store connects glycolysis and gluconeogenesis, the pentose phosphate pathway, the Calvin and Krebs cycles, pyruvate processing, ethanol fermentation and salvage, beta-oxidation, simplified fatty-acid synthesis, electron transport, ATP synthesis, and ROS scavenging.
Regulation
The reaction dispatcher applies explicit feedback gates before substrate mutation. High ATP inhibits phosphofructokinase and slows citrate synthase; high NADH inhibits isocitrate dehydrogenase and, together with accumulated acetyl-CoA, blocks pyruvate dehydrogenase. NADPH, FADH&sub2;, and low ATP gate other paths.
Reactive Oxygen Species
Electron-transfer steps at NDH-1 and the Q-cycle have a small random leak chance. Active ROS lowers cell health; SOD and catalase remove a free tier, while glutathione peroxidase can consume NADPH to remove more. Health recovers when no active ROS remains.
Fatty Acid Metabolism
Beta-oxidation breaks fatty acids into acetyl-CoA units, generating FADH₂ and NADH per cycle. The reverse pathway, fatty acid synthesis, consumes NADPH and ATP. Both pathways share the acetyl-CoA pool with the Krebs cycle, creating the metabolic intersection that determines whether a cell burns or stores fat.
Organism Presets
Five stylized presets configure the network: cyanobacterium, animal cell, obligate anaerobe, plant chloroplast, and archaeon. Each selects pathway locks, light and oxygen state, and initial ATP/NADH/NADPH/FADH&sub2; ratios.
Accessibility
Cyano provides keyboard shortcuts, labeled controls, light/dark/simulation-following themes, and numerical sidebar readouts. Electron, proton, and photon particles create continuous motion during active reactions; step-by-step mode is available instead of autoplay.
See also: Geon for particle physics, Shoals for options trading, Gerry for electoral fairness.
Learning Outcomes
After using Cyano, students should be able to: trace simulated carbon flow through glycolysis, pyruvate processing, the Krebs cycle, and linked biosynthetic routes; explain how the model's proton gradient couples electron transfer to ATP synthesis; identify the cofactor ratios that gate key enzymes; 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).