Thank you David that is helpful to think about.
I will try to find references and guess what might work in terms of visually representing it. Much of what I've seen of the motions of molecules or cellular structures are either too insanely fast for humans to process or it's clearly just invented to better tell the particular story. I will be heavily leaning toward the latter unless told otherwise by a client - right now I'm just making this for my own purposes so I have a lot more leeway and I will be modeling all the imagery myself or importing it from the pdb database - so they will all be consistently at the same scale. I'm tempted to just make the scene scale at 1µm (micrometer) but if that would make everything too weird for Houdini dynamics then maybe I'd just fake it with using a larger scale like 1 mm or 1 cm.

I know Houdini's scene scale default is 1 unit = 1 meter and that it can be changed to be whatever you want but you can run into problems with DOPS and maybe POPS. I am starting a project with cellular and molecular forms and wondering if I need to change the scale to be that small. I'm not concerned too much about scientific accuracy with regard to forces such as gravity, etc at that scale as it would likely be different and I wouldn't know what the accurate equivalent would be in any event. Maybe just change it to millimeters?

Looks utterly amazing! Can't wait to hear more about it.

I haven't been able to find any information if a study group or similar might be available for learning Vex. I'm thinking that working with a small group of beginners might be helpful in learning Vex - as well as other topics in Houdini. Despite its potential for helping the code-challenged to get peer support and encouragement - it doesn't seem to be a thing with learning Houdini or CGI in general that I've ever seen. I get that with many areas in Houdini you can probably teach yourself on your own - but something like Vex - being able to ask questions and solve problems with others who are on similar levels of skill could be quite valuable and help people with sticking with it. Anyone interested?

Does this website (https://cmivfx.com/home) actually still work? I get all kinds of warnings of it being suspicious in my browser as well as many broken image links, etc. Also, this tutorial could be useful but it looks to be from an ancient version of Houdini and not sure if many things would still work or be relevant. The price seems pricey but fair for such an old version and for just one tutorial (if you subscribe for a month) but I'm not sure I'd trust giving them credit card info, etc. Any thoughts?