Cytonaut

A first-person journey inside a living human cell.

You are a speck adrift in the cytoplasm of a pancreatic beta cell, the cell that makes insulin. Fly anywhere, look anywhere, point at any structure to learn what it is and what it does, and watch its real molecular machinery run. Everything is procedural: no downloaded models, textures or audio files.

Run it

npm install

npm run dev

Then open http://localhost:5183. Needs a desktop browser with WebGL 2, a keyboard and a mouse.

npm run build

npm test

Controls

Key	Action
Mouse	Look around
W A S D	Swim
Space / C	Rise / sink
Shift	Boost
Scroll	Change cruise speed
E or click	Inspect whatever is under the circle
Tab	Codex of every structure
T	Guided tour (21 stops)
G	Story: follow one insulin molecule from gene to bloodstream (16 steps)
X	Cutaway view (membranes fade so you can see inside)
[ and ]	Slow down / speed up the cell's processes
P	Pause processes
M	Sound on / off
Esc	Menu and settings

What is in the cell

18 organelle-level structures and 80 inspectable parts (98 codex entries), each with a description, its function, its parts, real numbers, and notes on what the model simplifies.

Structure	What you can watch
Plasma membrane	Individual lipids and cholesterol up close; Na+/K+ pump (3 Na+ out, 2 K+ in per ATP); GLUT1 glucose entry; K_ATP and voltage-gated Ca2+ channels opening and closing; GLP-1 receptor signalling; clathrin-coated pits
Extracellular matrix	Banded collagen fibrils outside the cell; integrins linking them to the actin cortex
Cytosol	Glucokinase clamping onto glucose; glycolysis flux from membrane to mitochondria
Cytoskeleton	Microtubules with their tubulin lattice and growing/shrinking plus ends; kinesin and dynein walking hand over hand with cargo; cortical actin; intermediate filament cage
Centrosome	Two orthogonal centrioles (nine triplets each), pericentriolar material, gamma-tubulin ring complexes nucleating microtubules
Nucleus	Double envelope, nuclear pore complexes at true scale, lamina, chromatin territories, nucleosomes, nucleoli; RNA polymerase II transcribing the insulin gene; mRNA export; ribosome subunit export
Rough ER	Cisternae studded with ribosomes; SRP delivering a ribosome; Sec61 translocation, signal peptidase, BiP, PDI
Ribosomes	Elongation cycle: tRNAs through the A, P and E sites, mRNA ratcheting, the chain growing
Smooth ER	Tubule network; SERCA pumping Ca2+ in, IP3 receptors releasing it; lipid droplets
Golgi apparatus	Polarized stack, cargo maturing cis to trans, trans-Golgi network, M6P receptors
Transport vesicles	COPII, COPI and clathrin-coated vesicles budding, shedding coats and fusing
Mitochondria	Cristae; TCA cycle; electrons through Complex I, ubiquinone, III, cytochrome c, IV to oxygen; protons pumped (4, 4, 2); ATP synthase rotors spinning; ADP/ATP exchange
Insulin granules	Immature granules maturing as proinsulin is cut to insulin; SNARE complexes; Ca2+-triggered exocytosis
Lysosomes	V-ATPase acidification, hydrolases, LAMP lining, digestion
Peroxisomes	Fatty acid beta-oxidation; catalase turning 2 H2O2 into 2 H2O + O2
Endosomes	Recycling tubules; intraluminal vesicles forming in multivesicular bodies
Autophagosome	A phagophore engulfing a worn-out mitochondrion, sealing, fusing with a lysosome

One loop drives the whole cell

A beta cell's job is glucose-stimulated insulin secretion, and the cell cycles through it continuously: glucose rises and enters through GLUT1, mitochondria raise the ATP/ADP ratio, K_ATP channels close, the membrane depolarizes from about -70 mV, voltage-gated Ca2+ channels open, and Ca2+ triggers insulin granules to fuse with the membrane. The HUD shows glucose, ATP and membrane potential as it happens, and the membrane itself glows as it depolarizes.

Accuracy

The aim is that a biology teacher finds nothing wrong, and that everything simplified is stated.

• Scale. 1 world unit is 100 nm. Organelles are at their true relative sizes. Molecular machines are drawn larger than life (usually 2 to 8 times) and in far smaller numbers, so they can be seen working. Each entry states its true size and how much it was enlarged.
• Speed. Every process is slowed. Each entry gives the real rate. Inspecting something slows the cell further so each step can be read as it happens.
• Liberties. You can pass through membranes, which a real particle could not. Interiors are thinned out so you can see. Each entry has a "How accurate is this model?" note.
• Human-specific details. Human beta cells use mainly GLUT1; human peroxisomes have no urate oxidase crystal; mammalian ATP synthase has an 8-subunit c-ring (about 2.7 H+ per ATP).
• Sources. Organelle-level entries cite Alberts, Molecular Biology of the Cell (7th ed.), Lodish, Molecular Cell Biology (9th ed.), Lehninger (8th ed.), and two reviews (Rorsman and Ashcroft 2018; Boyer 1997).

The codex text has not been reviewed by a practising cell biologist. Treat it as a careful study aid, not a primary source.

How it is built

Vite, TypeScript and three.js. No UI framework and no external assets.

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