Good news! danceroom Spectroscopy (dS), the interactive molecular dynamics project I started three years ago, has earned its sixth award in the last 18 mos!
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open Access interactive MD research paper!
It’s been awhile… but the first danceroom Spectroscopy scientific research paper has been published as part of the Faraday Discussion Volume 169. The paper is available for open-access download at this weblink. One of the paper’s highlights – and something which I’m really excited about – is the extension of dS to allow users to interactively chaperone the dynamics of small proteins, achieved through a software interface with the OpenMM hardware-accelerated force field library maintained at Stanford University. In some preliminary user studies, we observed that users were able to accelerate some simple protein conformational changes by nearly a factor of 10,000 compared to standard blind search molecular dynamics! We already knew that people love dS, but now we’re opening up the possibility of transforming it into a simulation methodology that lets people help us tackle research problems related to biochemistry and health. Here’s a video showing the interactive protein dynamics in action:
Royal Society of Chemistry Research Award
Some good news! I was awarded the 2014 Harrison-Meldola Memorial Prize from the Royal Society of Chemistry (RSC) for “theoretical work on energy transfer processes in chemical reaction dynamics”. These prizes are awarded annually to scientists less than 7 years removed from their PhD, with the stated aim to recognize “the most meritorious and promising original investigations in chemistry and published results of those investigations“. Part of the prize involves a sponsored lecture tour, to take place sometime during 2013-2014. The other two 2014 awardees included Dr Matthew Fuchter (Imperial), and Erwin Reisner (Cambridge), both of whom are engaged in some fascinating work!
Maple Hartree Fock Quantum Chemistry Program
Basis functions corresponding to the lowest energy converged eigenvalue of the HeH+ Fock matrix
Here’s a little project that I’ve been meaning to finish for awhile now, to aid my own learning and anybody else who is interested: it’s a Maple script for a restricted closed-shell Hartree Fock program, which you can download here as a *.zip file. I wrote it using Maple 16, so it should work in v16 or later.
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dS installations: Bristol, Germany, and London
Hidden Fields dance performance, the ‘whirlpool’ scene
The past few months have seen a range of exciting danceroom Spectroscopy & Hidden Fields activities. For example, during 24 – 26th October 2013, we partnered with the Watershed Media Centre in Bristol to carry out the first ever dSFest, installed in a 21 meter diameter, 360 degree projection dome. During 4-6 January 2014, we had an installation and set of performances at the ZKM | Centre for Art and Media Technology in Germany. And over 1-2 March, we’re participating in a digital arts festival at London’s Barbican Arts Centre. There’s been a whole host of interesting media content associated with these events, including articles in The Guardian, Imperica, and the Huffington Post. And our dS photographer Paul Blakemore has recently put together a stunning photo essay describing some of the amazing shots he’s been able to capture…
dS Fest, Bristol, in the 21m diameter 360 projection dome
Royal Society Research Fellowship
Extremely exciting news! I’ve been awarded a Royal Society University Research Fellowship!! The Royal Society is the British national academy of science, and allegedly the oldest scientific academy in the world. It was established in 1660 with a charter from Charles II (hence Royal). Originally called the “the Royal Society of London for the Improvement of Natural Knowledge“, it was devoted to the “Promoting of Physico-Mathematical Experimental Learning”. Its earliest meetings were organized by Robert Hooke (of “Hooke’s Law” fame), and one of its earliest presidents was none other than Sir Isaac Newton himself.
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Kloster Seeon: Transatlantic Frontiers in Chemistry 2013
Theoreticians in the Bavarian alps (courtesy of A. Alexandrova). From left to right: D. Glowacki (Bristol), T. Jacob (Ulm), T. Miller (CalTech), A. Alexandrova (UCLA), A. Tkatchenko (Berlin), B. Strodel (Julich), and L. Jensen (Penn State)
It’s all been hectic (more on why later!) so my posts have been delayed. But I wanted to mention a fantastic conference that I attended in August, held at the Kloster Seeon monastery in the foothills of the Bavarian Alps. Jointly sponsored by the Royal Sociey of Chemistry (RSC), the American Chemical Society (ACS), and the Gesellschaft Deutscher Chemiker (GDCh).
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Telluride Meeting
rainbows over Telluride, singles (left panel) and doubles (right panel)
Between 29 Jul and 1 August 2013, I attended a meeting in the beautiful town of Telluride, Colorado, which is nestled in the Rocky Mountains at an elevation of 8,750 ft (2667 m). The meeting was held at the “Telluride Science Research Centre“, and was focussed on “The Role of Dynamics in Enzyme Catalyzed Reactions”.
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Lindau Nobel Laureate Meeting
On the train to Lindau… through the Swiss Alps from Geneva
During the first week of July, I had the privilege to attend the 63rd Lindau Nobel Laureates Meeting in the historic town of Lindau, Germany.
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2d and 3d Fourier transforms
Recently, I’ve been playing with multidimensional Fourier transforms, which is something that I’ve meant to do for awhile but finally got around to during a mini-hackathon I participated in with Fred Manby and his group members. The left hand panel above shows the function z(x,y) = cos(0.5πx + 1.5πy) + cos(1.5πx + 0.5πy); the right hand panel shows the 2d discrete FFT of z(x,y). The two peaks visible in the Fourier plot correspond to the wave vectors of each of the cosine functions ([0.5, 1.5] and [1.5, 0.5]). Using the 1d FFT routine in alglib, I wrote some C++ source code and tests to generate the plots shown above; the files testFunctions.h and testFunctions.cpp include routines for both two and three-dimensional Fourier transforms. I haven’t yet worked on optimizing this code, but it’s simple, reasonably fast, and all my tests show that it gives the correct answers!
and here’s another one, just for fun…
David Glowacki 