tying molecular knots in virtual reality

Over the past few months, I’ve been playing with a new integrated hardware-software framework that fuses the latest in interactive high-performance computing, the latest in virtual reality, and the latest in research-grade GPU-accelerated molecular physics. It’s really fun, and I’m basically addicted. Since we got it working, I’ve had a steady stream of colleagues knocking on my office door asking me if they can try it out. It’s slightly annoying, because I had intended to be ultra-productive during the summer lull in the academic calendar, but that has hasn’t really worked out… When my colleagues aren’t playing with it, then I’ve struggled to get much work done because I’ve mostly spent time hanging out in VR playing with my favourite molecular simulations…

The video demos a virtual reality port of the Nano Simbox, (aka “Simbox”), a tool which I’ve been developing over the years in collaboration with Bristol-based software firm iSci (aka Interactive Scientific). It lets us manipulate entirely rigorous molecular dynamics simulations (run on a massively parallel high-performance computing back-end) in real-time. We’re just now starting to explore application domains for this technology. The video in this post shows one of our first experiments: in a collaborative project carried out with artist & lecturer Becca Rose, we used the VR-Simbox to tie knots in large molecules: proteins, polyenes, and DNA. The extent to which biomolecular structures form knots is in fact an active research domain (nicely outlined in this Nature perspective by Eugene Shahknovich); many scientists have spent time trying to understand the extent to which nature utilizes knotted topologies.

Knotting is an interesting application for the VR Simbox, because the manipulations required to tie a knot in a large molecular structure like a protein are actually pretty complex. For example, if I was going to write some code to tie a molecular knot, it would end up being a rather complicated little piece of software. However, tying knots is the sort of thing that’s actually rather straightforward and intuitive for a human, because we all tie knots all the time (and the sailors and knitters amongst us are even more expert). It’s a good example of how a human working with a computer can actually accomplish things faster than a computer on its own. Over the next few months, we’ll be building a molecular virtual reality lab right here in Bristol, so stay tuned…

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