bondlab.
MOLECULAR SANDBOXEXPERIMENT 001
SMALL MOLECULES. BIG CONNECTIONS.

mRNA meets ribosome.

Explore the physics of a molecular handshake.

Real-time physicsTHREE.JS + AMMO.JS
INITIALIZING PHYSICS
RIBOSOMELarge subunitPeptide synthesis
Small subunitmRNA binding channel
mRNA strand 5′ → 3′39 linked nucleotides
Binding contacts
Preparing your experimentLoading the Ammo.js physics engine…
Drag to orbit·Scroll to zoom
SCHEMATIC · NOT TO SCALE

The messenger

mRNA sequence · 5′ → 3′
Binding regionAUG start codon39 nucleotides
AdenineUracilGuanineCytosine
BEHIND THE EXPERIMENT

A molecular handshake.

The mRNA strand consists of 39 dynamic Ammo.js rigid bodies. Point-to-point constraints keep neighboring nucleotides connected while allowing the strand to flex.

Docking applies a guided attraction toward six sites along the small subunit’s channel. When a nucleotide is close enough, a reversible constraint connects it to the ribosome. Bond strength sets the constraint’s correction rate and the tension needed to release it. Agitation applies fluctuating forces; a nudge applies an impulse.

This is an educational schematic, not a molecular dynamics simulation. The contacts represent noncovalent interactions, not chemical bonds. Geometry, time, forces, and sequence are illustrative; initiation factors, tRNA, solvent, and translation are omitted. The large subunit is shown for orientation.

Read about mRNA–ribosome contacts