An interactive cellular metabolism simulator. You step through biochemical reactions one at a time. Cofactor pools shift in real time, and you can see how glycolysis, the Krebs cycle, photosynthesis, and the electron transport chain all connect through shared metabolites.
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Interconnected pathways mapped onto a shared metabolite grid: glycolysis and gluconeogenesis, the pentose phosphate pathway, the Calvin cycle, the Krebs cycle, beta-oxidation and fatty acid synthesis, PDH, pyruvate decarboxylase, ADH (ethanol fermentation and salvage), ALDH, ACS, plus three ETC chains (linear light reactions, cyclic light reactions, oxidative phosphorylation). Bidirectional pathways (glycolysis, beta-oxidation) reverse direction with distinct cofactor requirements.
A 14-component membrane chain (PSII, NDH-1, SDH, PQ, Cyt b6f, PC, PSI, Fd, FNR, ATP synthase, Cyt c oxidase, bacteriorhodopsin, NNT, UCP) renders its proteins and electron carriers with distinct visual silhouettes.
Allosteric control points (PFK, PK-reverse, citrate synthase, isocitrate DH, PDH, G6PDH, RuBisCO activase, ACAD, FA synthesis) gate reactions based on ATP/ADP ratio, NADH/NAD+ balance, and cofactor availability. Reactive oxygen species accumulate from electron leak at Complex I and the Q-cycle; SOD, catalase, and GPx scavenge them.
Click highlighted enzyme labels on the canvas to advance reactions. Available reactions depend on substrate levels and regulation state. Right-click bidirectional enzymes to run the reverse direction.
Toggle sunlight and oxygen to shift the network between photosynthesis, aerobic respiration, and fermentation. Choose from five stylized presets (cyanobacterium, animal cell, obligate anaerobe, plant chloroplast, archaeon); each locks a different pathway/environment subset and resets the initial cofactor ratios.
Auto-play mode runs the full metabolic program with allosteric regulation gating reaction rates. Real-time sparklines track ATP, NADH, NADPH, and FADH2 ratios plus the proton gradient over a 60-second window.
Keyboard shortcuts: Space (auto-play), G (glucose), F (fatty acid), L (light), O (oxygen), U (uncoupling), 1-5 (pathway toggles), X (forward/reverse mode), R (reset), T (theme), S (sidebar).
cd path/to/a9lim.github.io && npm run build && python -m http.server --directory distThe project itself has no compile or package-install step; the parent staging build assembles shared assets. Shared design modules load from the root site via absolute paths, and reference math loads KaTeX from the configured CDN, so build from the parent repository root and serve dist/.
Vanilla JavaScript with ES6 modules loaded via <script type="module">. Canvas 2D rendering uses requestAnimationFrame. Cofactor pools (ATP+ADP, NAD+NADH, NADP+NADPH, FAD+FADH2) are strictly conserved closed systems.
main.js Entry point, render loop, sparkline sampling
colors.js Pathway color palette extending shared tokens
src/
state.js Simulation state, conserved cofactor pools
renderer.js Canvas 2D engine: layout, zoom, hit detection
enzymes.js ETC complex shapes, metabolite nodes, enzyme tags
layout.js Membrane and metabolite position computation
dashboard.js Stat bars, sparklines, active step display
particles.js Electron, proton, and photon animations
autoplay.js Automated pathway cycling, proton leak, ROS damage
regulation.js Allosteric regulation factors
organisms.js Five organism preset configurations
anim.js Fade and rotation accumulator helpers
theme.js Three-state theme toggle
ui.js DOM cache, event binding, keyboard shortcuts
info.js Metabolite info-tip data
reference.js Reference-overlay content (net equations, notes)
reactions/
dispatch.js Unified reaction dispatcher
glycolysis.js Glycolysis and gluconeogenesis
krebs.js Krebs cycle
calvin.js Calvin cycle
ppp.js Pentose phosphate pathway
etc.js ETC complexes, ATP synthase, bacteriorhodopsin, NNT
fermentation.js PDH, PDC, ADH, ALDH, ACS, ethanol fermentation
betaoxidation.js Beta-oxidation and fatty acid synthesis
ros.js ROS production and scavenging