Maple Hartree Fock Program

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. (To open, right-click the link, save it locally, and then open with Maple – else you just get a bunch of XML) I wrote it using Maple 16, so it should work in v16 or later. Maple is inexpensive for those working in education, and it includes loads of convenient mathematics functions that are transparent and easily call-able, which saves lots of work!

At the moment, it uses an SCF procedure to solve a simple HeH+ wave function in a basis set of contracted Gaussian functions. It includes detailed comments, and follows closely the text on p 106 – 176 of the book ‘Modern Quantum Chemistry’ (MQC) by Szabo & Ostlund. This Maple script could easily be extended to larger molecular systems, but the time required to calculate the two-electron integrals will mean that you’ll spend a lot of time staring at your computer screen! Incidentally, it turns out that Maple 16′s standard integrate command is pretty speedy for evaluating the overlap & kinetic energy integrals. For two-electron and nuclear repulsion integrals, it’s not so good! So I’ve used the analytical formulas in Appendix A of MQC.

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Basis functions corresponding to the lowest energy converged eigenvalue of the HeH+ Fock matrix

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dS installations: Bristol, Germany, and London

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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…

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dS Fest, Bristol, in the 21m diameter 360 projection dome

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Royal Society Research Fellowship

ExtremRS-logoely 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.

My research fellowship is to carry out a programme entitled “Beyond equilibrium: Ultrafast solution-phase dynamics and enzyme catalysis”, building on several of the scientific problems I’ve been thinking about and working on of late. After two rounds of cuts, I had an interview in April. The setting, Royal Society HQ in London, is a nice piece of real estate, that’s for sure. In mid-May, I was offered the fellowship, with a start date of 1 October 2013, hosted by Bristol University! These fellowships are an amazing opportunity: they provide 5-10 years of funding, and a tremendous amount of intellectual freedom, so just my cup of tea!

Click here for a link to the University of Bristol press release.

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Kloster Seeon: Transatlantic Frontiers in Chemistry 2013

the theoreticians, in the Bavarian alps (photo 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)

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), the aim of the meeting was to bring together some exciting early-career chemists across the UK, USA, and Germany in order to facilitate international networking across diverse chemistry disciplines. The venue was amazing: Kloster Seeon is the site of a 10th century Benedictine monastery, located on an island in the middle of a pristine lake in the Alpine foothills, where I took early morning swims.

I presented in a session entitled ‘Applied Theory’, and had the opportunity to hear loads of amazingly talented scientists discuss their research across biochemistry, materials science, soft matter, theory & computation, organic chemistry, etc. One particular morning, I took a lovely early-morning bicycle ride through the Bavarian countryside along with some fellow theoretical chemists - Alexandre Tkatchenko (Berlin), Anastassia Alexandrova (UCLA), and Thomas Miller (CalTech). The latter two I will be visiting shortly in Los Angeles!

I took the scenic route back to Bristol, through the Austrian alps (passing through Salzburg and Villach) en route to Venice, where I wandered the city exploring the 2013 Biennale. I eventually made my way to Milan to fly back to Bristol.

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Telluride Meeting

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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”. My presentation built off a paper I wrote with some Bristol colleagues. The meeting was extremely interactive: each speaker was scheduled for 60 mins – but for most talks, there was at least as much discussion and interruption as there was presentation! For several of the attendees, I had some level of familiarity with their published work – e.g., Sunny Xie (Harvard), Amnon Kohen (Iowa), Jiali Gao (Minnesota), Judith Klinman (Berkeley), Sharon Hammes-Schiffer (Illinois), and Peter Wright (Scripps) – a pretty qualified set of folks… and they certainly grilled me! It was good fun. I also met some scientists I hadn’t know before – e.g., Pratul Agarwal, Chris Cheatum, Feng Gai, Brian Dyer, and Bob Callender – all of whom were great. The full meeting participant list is available here.

The night before my talk, I was sitting in a cafe putting the final touches on my presentation… and a massive bear nearly walked into the cafe! I reckon he smelled food left over on some plates that hadn’t yet been cleared away! Luckily, the cafe patrons slammed the door shut in time so he couldn’t get it. Good thing too: I was zoned out wearing my noise-canceling headphones, and I was sitting right next to the door he tried to walk through!

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Lindau Nobel Laureate Meeting

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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. This annual event is attended by 30-40 Nobel Laureates who deliver seminars over four days to a selective group of ~600 young scientists from over 50 different countries! It was brilliant. Lindau is a beautiful little island on an Alpine lake. I had the chance to chat with an inspiring range of scientific peers. Unlike most countries, the UK had no formal delegation, but I was well looked after by Andrew Holmes and the Australians. I even got to have dinner with a few different Nobel Laureates, including Rudolf Marcus (a scientific hero of mine, whose contributions to RRKM theory I utilize extensively), Harry Kroto, and John Walker. It was interesting to listen to these icons of science reflecting on scientific past, present, and future. Richard Ernst, one of the inventors of MRI, delivered a lecture which particularly sticks in my mind: he showed us his own MRI scans, and described how he now spends his free time using optical Raman spectroscopy to analyze Tibetan mandala paintings, uncovering details about their historical origins… I love it. My colleague Stephanie Harris interviewed Ernst. She’s graciously provided a draft, which is available here.

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2d and 3d Fourier transforms

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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…

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