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.