Danceroom Spectroscopy is gonna be doing stuff in the next few months. We’re gonna be featured in Barcelona as part of the SONAR fringe. Then, we’ll be conducting some workshops with professional dancers and other experts in highly evolved forms of human movement at Bristol’s best-known contemporary art museum, the Arnolfini. Finally, it will culminate in a large (free!) public exhibition at the Arnolfini on 7 August, where they’re gonna let us rig their auditorium so that you can literally step into and interact with a visuals and sounds generated by quantum particle dynamics. Spread the word…

structure of light harvesting complex II membrane protein

On May 27-28 at the Kavli Royal Society Centre, I attended a stimulating conference on the microphysics and evolutionary adaptations that have resulted in the ability of plants and photobacteria to harvest energy from the sun. A corresponding focus of this area of research is on what aeons of natural evolution might teach humans as we attempt to engineer nano-materials to address our own planetary energy needs in an increasingly post-carbon economy. Chemical physicists who gave talks and with whom I had previous familiarity included Graham Fleming (UC Berkeley) and Greg Scholes (Toronto). And there were a number of other talks from biologists and materials physicists, including Seth Lloyd (MIT) and Richard Cogdell (Glasgow)… a recent review in Science touches on many of the issues in this fascinating and important research arena.

Here’s a video containing a description/footage of DanceRoom Spectroscopy.

And here’s a link to some tracks mixed at Changing Perspectives by Lee J. Malcolm using the DanceRoom Spectroscopy code (ToddlerSteps-MovingOn & ToddlerSteps). Click to play, or right click to download… More to come!

Check out this video of some of the sights and sounds generated by DanceRoom Spectroscopy. The people that you see in the video are interactively warping the virtual force field felt by an ensemble of 70 particles in a mixed classical-quantum Feynmann-Hibbs simulation. The sounds that you hear in the video are generated on-the-fly via analysis of particle-particle collision events which were recorded at Changing Perspectives over 18th-19th March…

On 18th-19th March, we rolled out v0.1 of DanceRoom Spectroscopy at the University of Bristol Changing Perspectives event. And it was a big hit! On the order of 800 – 1000 people experienced it, and everyone – kids, grannies, moms, dads, hippies, artists, scientists, and anarchists – were into it! We’re in the process of confirming exhibitions that will be held at the Arnolfini, a well-known Bristol contemporary art museum, in July and August. Stay tuned. For more info, check out the Arts tab of my site. We’ve also set up a Danceroom Spectroscopy Facebook page which will keep you abreast of what we’re doing with it and where you might see it…

I’ve recently been involved in a collaboration with members of the Bristol laser group. They used ultrafast infrared lasers to watch real-time product formation for a chemical reaction occurring in a liquid. Their time resolution was on the order of picosecsonds (10^-12 seconds), which allowed them to watch reaction products being produced in an excited vibrational quantum state. I was able to rationalize their experiments by showing that the gas and liquid phase reaction free energy profiles are more similar than had previously been supposed. Thus, at very short times – on the order of ~10 picoseconds – the reaction in a liquid proceeds more or less identically to what happens in a low pressure gas. This work has been funded by the EPSRC, and is featured on the cover of the 18th March issue of Science, with follow-up publications to appear shortly. Click here to view some movies of how the reaction proceeds in both a gas and a liquid.

The left and right hand graphics show overlays of the CN + cyclohexane geometries at the point where they pass over their respective transition states in a gas and in a liquid (dichloromethane). Their similarity explains in part, why at short times, the gas phase quantum state specificity carries over to liquids.

I have taken up a New Talent residency at the Pervasive Media Studio to work on the recently funded Danceroom Spectroscopy Project, which was mentioned in the Watershed news – in the context of a remarks about the 3d film industry, and alongside a picture of Avatar!

During the first couple of weeks of October, I visited Longyearbyen in Svalbard, which is located at 78 degrees north latitude, well within the Arctic Circle.  I gave a series of guest lectures at the University Centre in Svalbard (UNIS), which is the northernmost higher education/research institute in the world. The lectures covered: (1) atmospheric transport dynamics; (2) elementary chemical kinetics and photochemistry; (3) tropospheric oxidation chemistry; and (4) stratospheric ozone chemistry.  On the final day, we tied it all together to discuss two important polar atmospheric chemistry phenomena – stratospheric ozone holes, and Arctic haze.

Don’t be freaked out by the rifle; it’s a Svalbard law that people walking outside the settlements – even the surrounding hills – bear arms to warn off polar bears.

From June 30 – July 3, I attended a conference on multiscale molecular modelling (M3) in Edinburgh, and had the opportunity to talk about a rare event acceleration algorithm we’ve recently developed (more below). The conference was extremely interesting, and I had the opportunity to listen to and meet a number of experts in the field of molecular dynamics, from those who focus on very small molecular systems, like Bill Miller, to those who focus on much larger ones, like David Chandler, David E. Shaw, and Vijay Pande. Links to some photos can be found here.

The method I presented is called Boxed MD (or BXD), and it’s arisen from recent work I’ve done with Dmitry Shalashilin and Emanuele Paci. It’s sort of like a formally exact, perfect form of umbrella sampling with no messy numerical renormalization procedures involved. The biggest advantage of BXD over umbrella sampling is that it simultaneously preserves both kinetic and thermodynamic information – allowing you to obtain both rate coefficients and free energies directly from the dynamics.  Also unlike umbrella sampling, it involves no modifications to the potential energy, and it works equally for both canonical and microcanonical ensembles.  I’ve implemented it in CHARMM, and it will be available in the next release version. The method is described in detail on Dmitry’s website.

From July 20-21, I had the privelege of travelling to the beautiful historic town of Santiago de Compostela, which is the capital of the Galician province located in northwest Spain. Here’s a picture of the cathedral in Santiago. Legend has it that the bones of Jesus’ brother, St. James (San Tiago), are buried within.

I was invited to give a talk on non-adiabatic transition state theory (NA-TST). In addition to meeting up again with my collaborators in Santiago, I was also able to hear talks from some other experts in the field of theoretical chemistry that I’ve never met before – John Tully, Bill Hase, Theresa Windus, and Bruce Garret.

What is NA-TST? Whereas conventional transition state theory is only appropriate for describing ensemble averaged molecular motion on a single electronic surface, NA-TST  allows us to model the rates at which molecules hop from surface to surface. Whereas conventional TST relies on some definition of a transition state – i.e., a dynamical bottleneck in phase space – NA-TST relies on a definition of a minimum energy crossing point (MECP) between two surfaces.

I’ll be posting some code that Jeremy Harvey and myself have written for locating non-adiabatic ‘transition states’, and performing the subsequent vibrational analysis required to calculate rate coefficients. So stay tuned. I’ve recently added a microcanonical version of NA-TST to MESMER.

Here’s the conference picture.