> cells are extremely crowded and busy places Cells are extremely crowded and busy... and random and violent places. Molecular biology dances in a nano moshpit from hell. The Inner Life of a Cell is badly misleading. It reinforces many educationally toxic misconceptions. Yes, the graphics technology was limiting. But the video doesn't attempt to mitigate the negative impact. For instance, adding a couple of frames of…
When we look, our visual system comprehends in terms of boundaries and empty space. Thus we know the location and motion of the different things we see. But "surfaces" and corresponding "empty spaces" don't occur at the molecular scale in living things. (What makes something a discrete "thing"? What makes something "empty"?) In cellular environments, nothing is empty, everything is touching, nothing is static, everyt…
Conformation spaces help. A thing changes shape, but the shapes are drawn from a family of likely possibilities. Your arm is likely to remain attached to your shoulder, and is less often raised up than not. Even in a tangled rugby ruck.
Some things are ambiguous, but others not. Youtube had a nice ab initio molecular dynamics simulation of water (which I've been unable to find again). As a H+ proton wanders, sometimes it seems bound to a particular water, and other times, there's more of an area effect involving several. But a water molecule's nuclei generally stick with each other.
The usual electron-density isosurface depictions have disadvantages. Picture traffic cones, say arranged in a tight grid. They have a peak, and their rims touch. Like the electron densities of atoms. But visually it isn't a problem. So replace the isosurface with a cloud, or just turn down the surface threshold, and the view is as empty as you want it to be. An electrostatic suspension of tiny flecks of neutron-star-like material floating in fluff.
With eye tracking and XR, one might play games of visual selection. Show a 3D mess of proteins, clearly rendering one protein deep inside, but leaving enough visual clues of the others, to serve a focus targets. When your eyes shift target, change which protein is rendered clearly. Or do more with that selection, like showing trajectory, or showing other proteins too, related by type or process or history. You might "see" a 3D gestalt.
The HCI of XR will be great fun.
Aside: Thanks for the youtube cytoplasm link.