A very basic simulation of liquid argon was created in fortran and then rendered using threejs. It utilized the example code on the threejs website here. I just mapped the particle positions to ones I got from my simulation. Literally nothing special was done, but its another example of how anyone can use this framework to create 3d visualizations.
This is another example of utilizing a threejs provided example and inputting your own files into it. The original example can be found here.. The mesh was created and animated in the free 3d modeling program Blender then exported as a glb file. The glb file was then rendered using webGL and Threejs. This was the blender addon used to export the mesh.