David Glowacki

VIRTUAL REALITY AND REAL-TIME MOLECULAR DYNAMICS FOR (BIO)CHEMISTRY

The use of large tangible models has a long history within both chemistry and biochemistry, perhaps most famously captured by Watson and Crick’s model of DNA. Room-sized “Kendrew” models1 were popular within protein modelling and visualization in the 1950s/60s (prior to widely available commodity computational machinery), allowing researchers to understand the first protein crystal structures. Models like these have played an important role in chemical research, allowing us to visualize the design intricacies of complicated nano-architectures across both biology and materials science.

Driven by the consumer market, state-of-the-art virtual reality (VR) hardware now allows us to carry out broad new classes of video-gaming tasks which were previously impossible: wielding light-sabres, making 3d sculptures, and even simulating surgery. Applying these technologies to the molecular sciences allows us to re-engage with the sorts of large, immersive, tangible models that were once popular in molecular research.2 Along with state-of-the-art advances in high performance computing (HPC), we can even go one step further: whereas the older models were time stationary objects that could only capture a single conformation of a molecule (e.g., a protein or DNA crystal structure), it is now possible to construct room-sized tangible models of molecular structures which are “animated” by rigorous dynamics, building on the significant progress that has been made in computational molecular physics over the last 60 years.3

I will discuss (and hopefully demo) the work we have carried out to design a new environment which fuses commodity VR and GPU-accelerated HPC to allow (up to 8) researcher(s) to natively inhabit a fully interactive 3d virtual molecular simulation environment. Using wireless ‘atomic tweezers’, it is possible to fluidly chaperone a real-time research-grade biomolecular MD simulation in a fully co-located 3d space with surgical precision. This platform opens up a new domain of “interactive simulation”, allowing researchers to tackle a range of biomolecular design problems as they interactively explore dynamical pathways and conformational states in hyperdimensional biomolecular systems. I will discuss some initial applications of our multi-person VR-HPC environment, including our attempts to understand the fundamental kinetic mechanisms and dynamical pathways whereby small molecular ligands (e.g., a drug or substrate) dock with a larger molecular receptor (a protein or enzyme).4

[1]           Kendrew et al., Nature 181, 662 (1958);

[2]           Glowacki et al., Multi Person Molecular Virtual Reality: https://vimeo.com/200789130;

[3]           O’Connor et al., in Supercomputing 2016 (2016);

[4]           Glowacki, O’Connor, Deeks, Interactive drug docking using real-time MD within the Nano Simbox: https://vimeo.com/202556275;