Cell

Research-first interactive simulation of biological life from physical foundations: atom -> molecule -> membrane -> organelle -> cell -> tissue -> organ.

The project is intentionally multiscale. A single first-principles simulation from quantum electrons to a full organ is not computationally realistic on consumer hardware, so the system should use layered models that exchange state through well-defined inputs and outputs.

First Target

Build an interactive 3D environment that shows the real-time formation and interaction of two oppositely charged ions, with electron probability present in the model even when hidden visually.

Run The Prototype

npm install
npm run dev

Then open the local URL printed by Vite. The prototype now spans milestones 001 and 002: an N-ion electrostatic engine with selectable scenes (Na+/Cl- gas-phase bond, Na+/K+ repulsion, and a 6-ion NaCl cluster), per-ion force vectors, electron-probability visibility, total-energy and energy-drift readouts, and temperature/damping/solvent controls with scroll-to-zoom.

The Na–Cl model is source-backed, not tuned: ion masses, ionic radii, the Coulomb constant, and the short-range Pauli repulsion all come from published measurements, so the simulated bond relaxes to the experimental 0.236 nm bond length (verified by test). See docs/sources.md.

Verify

npm test
npm run build

First Cell Type

Start with epithelial cells because they naturally expose the questions this project cares about:

• inside vs outside
• apical vs basolateral surfaces
• transcellular and paracellular transport
• tight junctions, adherens junctions, desmosomes, and basal lamina
• nutrients, ions, water, signals, waste, force, and energy exchange

Documentation Map

• Project charter
• Research index
• Multiscale architecture
• Platform recommendation
• Atomic foundations
• Epithelial cell starting scope
• Input/output registry
• Milestone 001: two-ion formation
• Milestone 002: many-ion system
• Source ledger

Project Rule

Every simulated object should eventually have:

• a source-backed description
• a scale and unit system
• inputs and outputs
• relations to existing objects
• equations or rules of motion when known
• visual representation and hidden state representation
• confidence level and assumptions