> Curious, it appears that you guys use a highly focused beam on small particles, like 1 W focused into a diffraction limited spot, right?
That's correct.
> How come the bio-molecules that you're manipulating with this light don't just "burn up"? Is it because they're mostly transparent at that wavelength? Or you're only exciting a marker molecule that is stuck to them?
We trap and manipulate a micron-sized polystyrene sphere that the proteins are attached to, not the proteins themselves. The microspheres don't burn up because they don't strongly absorb (i.e., they're mostly transparent) at the laser's frequency. Paper, on the other hand, absorbs strongly and ignites.
Optical traps rely on the momentum of light and the fact that a microsphere displaced from the diffraction-limited spot refracts light in direction of the displacement. Since momentum is conserved, the light directed away from the center of the trap creates a force that pushes the sphere toward the trap. If the light were mostly absorbed or scattered, this force would be along the axis of the beam.