Scientific computing on Apple M1, part I: ASE and GPAW

Scientific computing on Apple M1, part I: ASE and GPAW

Getting ASE and GPAW running natively on the Apple Silicon M1 MacBook Pro, and benchmarking them against an iMac Pro.

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Atom Tractor Beam simulation game

Atom Tractor Beam simulation game

With the support of the Vienna Business Agency, we commissioned a simulation game for the Vienna Technical Museum special exhibition called “The Future of Work and Production”. This game is now released online, try it out for yourself!

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To boldly go… publishing my grant proposal in RIO

I must be honest: it was an instinctively scary prospect to publish my grant proposal, even after being funded. It condenses years of toil and accumulated knowledge – as an early-career scientist, most of my career – into a mere twenty pages of text.

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My first review article (CC-BY)

The first review article that I have written has just come out in the Beilstein Journal of Nanotechnology (CC-BY open access).

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Moving silicon atoms in graphene with atomic precision

This post is a greatly expanded adaptation of a press release I wrote to publicize our recent work appearing in Physical Review Letters.

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Comics update

I have been very negligent with updating the blog, apologies for that... Here, have some comics to make up for it!

And, finally, a genius one from Cyanide and Happiness. (c) Explosm.net.

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Stuart Firestein: The Pursuit of Ignorance (TED talk)

[youtube=http://www.youtube.com/watch?v=nq0_zGzSc8g&w=600&h=450] In one of my new favorite TED talks, neuroscientist Stuart Firestein gives a supremely entertaining yet deep account on his view of what doing science actually is all about. He really captures some essential things that I think are difficult to convey to laypeople – or indeed for scientists themselves to explicitly recognize. He gives a number of great quotations I wasn't familiar with before:

Thoroughly conscious ignorance is a prelude to every real advance in science. -James Clerk Maxwell

Science is always wrong. It never solves a problem without creating 10 more. -George Bernard Shaw

Every answer given on principle of experience begets a fresh question. -Immanuel Kant

Firestein finishes with a poignant critique of the education system. Really, really recommend watching this.

Via Open Culture.

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Physics Nobel to Englert and Higgs

As widely expected, the 2013 Nobel Prize in Physics was awarded for the Higgs boson. The committee chose to award only the theoretical prediction, omitting the experimental teams at CERN to the annoyance of some. Nobel tradition notwithstanding, apparently there were no strict rules preventing the inclusion of CERN as an organization for the physics prize, which would indeed better reflect how fundamental science is done these days. Admittedly, the Nobel committee gave a very visible nod to the experimentalist in awarding the prize

for the theoretical discovery of a mechanism that contributes to our understanding of the origin of mass of subatomic particles, and which recently was confirmed through the discovery of the predicted fundamental particle, by the ATLAS and CMS experiments at CERN’s Large Hadron Collider.

As always, Nature News and Ars Technica have good stories covering the prize, and there's also extensive reporting by the BBC. However, even awarding theoreticians for this discovery was tricky; as the Nobel committee puts it, the award was for the "Brout-Englert-Higgs (BEH)-mechanism", with only François Englert and Peter Higgs (both in their 80s) sharing the prize since Robert Brout deceased in 2011. Some have argued that very important earlier contributions from Anderson should had been recognized, as well as independent but slightly later work by Kibble, Guralnik and Hagen. As Nature News puts it:

In 1964, six physicists independently worked out how a field would resolve the problem. Robert Brout (who died in 2011) and Englert were the first to publish, in August 1964, followed three weeks later by Higgs — the only author, at the time, to allude to the heavy boson that the theory implied. Tom Kibble, Gerald Guralnik and Carl Hagen followed. “Almost nobody paid any attention,” says Ellis — mostly because physicists were unsure how to make calculations using such theories. It was only after 1971, when Gerard ’t Hooft sorted out the mathematics, that citations started shooting up and the quest for the Higgs began in earnest.

So numerous were the theorists involved, that Higgs reputedly referred to the ABEGHHK’tH (Anderson–Brout–Englert–Guralnik–Hagen–Higgs–Kibble–’t Hooft) mechanism.

...but I guess the ABEGHHK'tH-mechanism just doesn't roll off the tongue as "Higgs" or "BEH" :)

For additional context on the theoretical developments, see this post on the LHC's Quantum Diaries blog. However, if you have any knowledge in quantum theory, I would most warmly recommend putting in the effort to read the Scientific Background from the Nobel committee, which describes the preceding and parallel developments, and later significance and discovery, in great detail and as clearly as can reasonably be expected, giving full credit where it is due. The committee even visibly acknowledge the role of the US in the discovery, which some felt needed to be explicitly defended. Of course, the Popular information document is more accessible, and very well written.

In the end, despite the potential for controversy, the decision seems to be reasonably well received, with Hagen showing the most emotion:

"Regarding the committee’s choice, “I think in all honesty, this is what I would have done,” says John Ellis, a theoretical physicist at CERN, Europe’s particle-physics lab near Geneva, Switzerland." (Nature News)

"The whole of CERN was elated today to learn that the Nobel Prize for Physics had been awarded this year to Professors François Englert and Peter Higgs for their theoretical work on what is now known as the Brout-Englert-Higgs mechanism." (Pauline Gagnon via Quantum Diaries)

"The discovery of the Higgs boson at Cern... marks the culmination of decades of intellectual effort by many people around the world." (Rolf Hauer via the BBC)

"My two collaborators, Gerald Guralnik and Carl Richard Hagen, and I contributed to that discovery, but our paper was unquestionably the last of the three to be published in Physical Review Letters in 1964 (though we naturally regard our treatment as the most thorough and complete) and it is therefore no surprise that the Swedish Academy felt unable to include us, constrained as they are by a self-imposed rule that the prize cannot be shared by more than three people. My sincere congratulations go to the two prize winners, Francois Englert and Peter Higgs." (Tom Kibble via BBC News)

“Faced with a choice between their rulebook and an evenhanded judgment, the Swedes chose the rulebook,” Hagen said in a blunt e-mail shortly thereafter. “Not a graceful concession by any means, but that department has never been my strong suit.” (Robert Hagen via the Washington Post)

“It stings a little,” Guralnik said. But he added: “All in all, it’s a great day for science. I’m really proud to have been associated with this work that has turned out to be so important.” (Gerard Guralnik via the Washington Post)

To wrap up, Ken Bloom via LHC's Quantum Diaries blog offers a very practical perspective of science in the trenches:

I suppose that my grandchildren might ask me, “Where were you when the Nobel Prize for the Higgs boson was announced?” I was at CERN, where the boson was discovered, thus giving the observational support required for the prize. And was I in the atrium of Building 40, where CERN Director General Rolf Heuer and hundreds of physicists had gathered to watch the broadcast of the announcement? Well no; I was in a small, stuffy conference room with about twenty other people.

[...]

So in the end, today was just another day at the office — where we did the same things we’ve been doing for years to make this Nobel Prize possible, and are laying the groundwork for the next one.

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Practicalities of moving abroad (VP3)

Image from Baltech If you didn’t catch them already, read the first and second parts of this post series.

An integral part of moving abroad for a postdoc is, well, the actual moving bit. Depending on the length of the stay, possible ownership of an apartment or house in the country of origin, and family considerations, the move can have many forms. In my case, since I am staying for (at least) 2 years, don't own an apartment in Finland, and have no binding reasons not to, I am moving everything to Vienna. This is thus what I will discuss in this post. Also, I am moving from one EU country to another, which makes things significantly simpler, so bear that in mind as well.


A key consideration in such a move is how to get one's stuff safely to their destination. Depending on how far you are moving and how much stuff you have, renting a van and driving it yourself could be an option. It's about 1400 km from Helsinki to Vienna, but taking a ferry to Poland or Germany would cut the distance to less than 1000 km – definitely drivable. Since I don't have that much stuff,  in principle this would had been an option for me. However, it's quite difficult to rent a van from Finland that you can return to another country, while I hear it's much easier elsewhere in Europe. Obviously, if you are moving to another continent, a professional moving company is the only option.

In any case, as I mentioned in the previous post, I have a grant specifically meant for covering moving costs (thank you, SKR!), so I didn't think twice about hiring a professional moving company to handle the move. Based on recommendations from friends and the offers I got via a handy competitive bidding service, I chose the company Pegasus Moving. They were kind enough to match the one slightly better offer I got, and some of their people are friends with colleagues of mine. I also paid for an insurance for all my stuff, whose total value I estimated at 10000 €. The cost of the move is 3750 €, and the insurance is only 220 € on top of that, so it was a non-brainer. I also got some sturdy foldable cardboard boxes for packing my stuff, which I'm in the process of doing right now.

They will come pick up my stuff next Monday, so hopefully everything is packed by then! Moving the stuff to Vienna will take 8-10 days, so I'll have to live out of a suitcase for a few days at both ends.


The other very important ingredient of a successful move is naturally the apartment one is moving into! Again, within the EU, there are very few barriers to renting an apartment in another country – likely they will want to see your employment contract and salary, as was the case for me – but apart from that, funded postdocs seem to be welcome tenants. Your mileage may, however, vary.

Again my situation was made much simpler by the aforementioned moving grant. In Vienna, most apartments are rented by housing agencies, and unlike in Finland, their fees are paid by the tenant. One friendly broker told me that this is the way it should be to ensure that the tenant, and not the renter, is the principal customer of the agency. Not sure about that, but I did receive very good service from a couple of agencies despite my lack of German. In Vienna, the agency fees seem to typically be 2 months rent, plus some mandatory registration costs etc. With a 3 month rent guarantee the fees stack up to almost 4000 euros, tidily eating up the second half of my grant. Sure am glad I got it.

I started browsing apartments on the internet 3-4 months before the move, but this turned out to be a bit too early. Most apartments get rented in less than two months, so even if you find a nice one, they won't keep it empty for that long. But it was useful to find good sites and get a feeling for the market beforehand – incidentally, rental prices in Vienna seem to be about 2/3 of the Helsinki level, which is nice. Having found a few nice possibilities, I set up several showings with the brokers for two days in the of July, and booked a flight to check them out in person. Although one could make a choice just based on the pictures and a floor plan (and perhaps having a local friend or colleague visit a showing), going there in person definitely made things smoother.

In the end I only ended up going to the showings for both of my top 2 apartments. They were extremely different in nature for about the same price, and I before I knew it, I had offers from both just waiting for my signature to confirm. A couple of rounds of Facebook consultation amongst my circle of friends,  and an evaluation of the yearly temperatures and rainfall trends in Vienna, cinched the case for a bit smaller apartment with a large roof terrace. As is typical for me, it was the first apartment I looked at. The agency offered a package service for handling the electricity contract, registering with the authorities and various bits and pieces for 200 €, which I also took.

Now I'll just have to find a nice  fridge (want: ice cube machine!) for the new apartment, as they apparently almost never come equipped with one down there. At least it's not missing the entire kitchen as I hear is not uncommon in Berlin :)


Apart from those two major issues, there's a bunch of practicalities to take care of. I've had to let go of my current apartment, end the internet, electricity and insurance contracts, register the move with the authorities, and so on. Nothing particularly different from just moving within the country.

On the Austrian side I still haven't got much else apart from the apartment set up. To get internet you need a bank account, and to get a bank account you need to be registered with the city officials, and to do that you need to have the official signed contract for the apartment. I'm just getting the last bit in the chain sorted out now. So I've figured that I'll take care of all that when I'm there. Of course, I'll get a phone number and email from the university, and will have to buy a laptop from my grant there (holding out for the new Haswell Macbook Pro's, though). I can graciously keep my present Aalto laptop until then.

Speaking of email, leaving my present affiliation at Aalto is a big deal. I've had the same email – first as a student at the Helsinki University of Technology and later as a graduate student and postdoc at Aalto – for 11 years. All of my online life is linked to that email. So I am now future-proofing my online presence by getting an iki.fi forwarding address, which I can then point to where I happen to be affiliated at. I only wish I had done this 6 years ago :) I'm also sure there are similar services in other countries as well.


Those were pretty much the main points I had in mind. I'll be sure to update / follow-up if any surprising issues crop up. You're also very welcome to ask in the comments if there's anything particular you would like the hear more about!

I've been seeing and saying goodbyes to a lot of friends over the summer, and am holding a farewell party of sorts next weekend. Thus I feel socially well prepared for the move, which is something I feel is a very good idea to pay some attention to. You don't want to feel like there's loads of unfinished business before starting a new life in a new country.

So, I have a one-way flight to Vienna on Saturday August 31st morning – wish me luck!

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Peter Suber's Open Access

Peter Suber's 2012 book "Open Access" is now – appropriately enough – openly available from the publisher, as announced by Peter on Google+:

I'm happy to announce that my book on OA (Open Access, MIT Press, 2012) is now OA. The book came out in mid-June last year, and the OA editions came out one year later, right on schedule. My thanks to MIT Press.

As it says on the tin: essential reading.

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