Tag Archive: research

Nov 16

Modern art in research.

Which combination to take?

Although it looks a bit like a modern piece of art, it is one more attempt at trying to find an optimum combination of parameters.

I’m currently trying to find “the best choice” for U and J for a DFT+U based project… DFT??? Density Functional Theory. This is an approximate method which is used in computational materials science to calculate the quantum mechanical behavior of electrons in matter. Instead of solving the Schrödinger equation, known from any quantum mechanic course, one solves the Hohenberg-Kohn-Sham equations. In these equations it are not the electrons which play a central role (which they do in the Schrödinger equations) but the electron density. Hohenberg, Kohn and Sham were able to show that their equations give the exact same results as the Schrödinger equations. There is, however, one small caveat: you need to have an “exact” exchange-correlation functional (a functional is just a function of a function). Unfortunately there is no known analytic form for this functional, so one needs to use approximated functionals. As you probably guessed, with these approximate functionals the solution of the Hohenberg-Kohn-Sham equations is no longer an exact solution.

For some molecules or solids the error is much larger than average due to the error in the exchange-correlation functional. These systems are therefore called “strongly-correlated” systems. Over the years, several ways have been devised to solve this problem in DFT. One of them is called DFT+U. It entails adding additional coulomb interactions (Hubbard-U-potential) between the “strongly interacting electrons”. However this additional interaction depends on the system at hand, so one always needs to fit this parameter against one of more properties one is interested in. The law of conservation of misery, however, makes sure that improving one property goes hand in hand with a deterioration of another property.

Since actual DFT+U has two independent parameters (U and J, though for many systems they can be dependent reducing to a single parameter) I had quite some fun running calculations for a 21×21 grid of possible pairs. Afterward, collecting the data I wanted to use for fitting purposes took my script about 2h! 😯 Unfortunately the 10 properties of interest I wanted to fit give optimum (U,J)-pair all over the grid. In the picture above, you see my most recent attempt at trying to deal with them. It shows for the entire grid how many of the 10 properties are reasonably well fit.There are two regions which fit 6 properties; One around (U,J)=(5,10) and another around (U,J)=(8.5,17.5). There will be more work before this gives a satisfactory result, the show will go on.

Apr 12

Call for Abstracts: Condensed Matter Science in Porous Frameworks: On Zeolites, Metal- and Covalent-Organic Frameworks

Flyer for the Colloquium on Porous Frameworks at the CMD26Together with Ionut Tranca (TU Eindhoven, The Netherlands) and Bartłomiej Szyja (Wrocław University of Technology, Poland) I am organizing a colloquium “Condensed Matter Science in Porous Frameworks: On Zeolites, Metal- and Covalent-Organic Frameworks” which will take place during the 26th biannual Conference & Exhibition CMD26 – Condensed Matter in Groningen (September 4th – 9th, 2016). During our colloquium, we hope to bring together experimental and theoretical researchers working in the field of porous frameworks, providing them the opportunity to present and discuss their latest work and discoveries.

Zeolites, Metal-Organic Frameworks, and Covalent-Organic Frameworks are an interesting class of hybrid materials. They are situated at the boundary of research fields, with properties akin to both molecules and solids. In addition, their porosity puts them at the boundary between surfaces and bulk materials, while their modular nature provides a wealthy playground for materials design.

We invite you to submit your abstract for oral or poster contributions to our colloquium. Poster contributions participate in a Best Poster Prize competition.

The deadline for abstract submission is April 30th, 2016.

The extended deadline for abstract submission is May 14th, 2016.

 

CMD26 – Condensed Matter in Groningen is an international conference, organized by the Condensed Matter Division of the European Physical Society, covering all aspects of condensed matter physics, including soft condensed matter, biophysics, materials science, quantum physics and quantum simulators, low temperature physics, quantum fluids, strongly correlated materials, semiconductor physics, magnetism, surface and interface physics, electronic, optical and structural properties of materials. The scientific programme will consist of a series of plenary and semi-plenary talks and Mini-colloquia. Within each Mini-colloquium, there will be invited lectures, oral contributions and posters.

 

Feel free to distribute this call for abstracts and our flyer and we hope to see you in Groningen!

Mar 01

Helium flash: the beginning of a new chapter.

During the past two and a half years, part of being a delocalized physicist has meant for me that I had to work at one end of the country while my girlfriend and son lived at the other. Today this situation drastically changed, as I moved with my FWO-postdoctoral project from my alma mater to the University of Hasselt, where I started in the Wide Band Gap Materials group of Prof. Ken Haenen.

My delocalization will now take the form of Metal-Organic Frameworks on the one side and Diamond based materials on the other. As the sole computational solid state physicist in an otherwise entirely experimental group (and even institute) I seem to have returned to a well known configuration (At Ghent university I was initially the house-theoretician of the SCRiPTS group). Also the idea of performing calculations on diamond brings back memories, since this allotrope of carbon lives two levels above the germanium on which Pt nanowires grow. All-in-all I look forward to an exciting time. But first things first: getting my HPC credentials and data safely transported from the one end of the country to the other.

Nov 28

Sidekick

This year I participated in the Robbert Dijkgraaf essay-contest 2015.
The central theme of the contest was imagination, and in my contribution
I presented the role of imagination in computational materials science,
and why it is so important for this field

The original Dutch version of the essay can be found here.

 

Imagine a world where you can actually see atoms. Even more, you can use them as LEGOs and manipulate them to do your bidding. Imagine a world in which you can switch off the laws of nature, or create new ones which are more to your liking. In such a world, you are in charge. Welcome to my world: the world of “computational materials science“.

It would be a nice start for a commercial for this research field. The accompanying clip would then show images fading into one another of supercomputers and animations of chemical and biochemical processes at the atomic scale. Moving in a fast-forward pace into our future with science-fiction-like orbital labs where calculated materials are immediately transformed into new medicine, ultra-thin screens and applications for the aerospace industry. scifilabThe ever faster flood of images culminates in the final slogan:”Simulate the future” with a subtext urging you to go study computational materials science. I assume that such a clip would tempt peoples imagination. It addresses our human urge to create, and holds the promise that you can do anything you want, as long as you can imagine it. In fact, your imagination becomes the only limiting factor.

As with most commercial, this one also presents reality slightly more beautiful than it actually is. As for any other scientist in any other field, your contribution to progress as a computational materials scientist is rather more limited than you would like it to be. This is a normal aspect of science. The presented divine omnipotence and omniscience, on the other had, are attainable. As a computational scientist you do have absolute control over the atomic positions and the forces at play. In contrast, an experimental scientist is forced to deal with the quirks of nature and his or her machinery. This omnipotence allows you to create any world you can imagine…inside a computer.

As a scientist, you wish to understand the world around you. This limits the freedom you gained through your omnipotence, unless you would choose to join a team of game-designers. It, however, does not mean that your creativity is curtailed in any way. On the contrary. Where the team of game-designers knows the entire story to be told, including rules and laws of nature relevant for the game world, this is not the case for computational materials science. For the latter it is often their quest to discover the story-line as they go, including relevant laws of nature. As a computational materials scientist, you become the narrator, whose task consist of thinking up new stories time and time again. The narrator, who needs to tweak existing plots, extending or confining story-lines, until the final story fits the shape of reality.

Luckily, you are not alone to bring this daunting task to a successful end. You always have the support of your loyal sidekick: your supercomputer. Using its brute force, your sidekick calculates the effects of any intrigue or plot twist you can imagine. Based on your introductory chapter, in which you describe the world and its natural laws, it will allow the story to unfold. By asking him the right questions, and comparing his answers to reality, you learn which parts of your story don’t really fit reality yet.

Ouroboros benzene. source: wikipediaHow you should rewrite your introductory chapter differs every time. Sometimes it is clear what is going on: an essential character is missing (e.g. an impurity atom which is distorting the crystal lattice), or the character lives at the wrong location (not site A, then let us see about site B?). It becomes more difficult when a character refuses to play the role it was dealt (e.g. Pt atoms that remain invisible for STM, so who is going to play the role of the nanowire we observe?). The most difficult situation occurs with the need for a full rewrite of the introductory chapter. This provides too much freedom, since it is our knowledge of the limitations of reality which provides the necessary support and guidance for drafting the story-line. In such a case, you need an inspiring idea which provides you with a new point of view. Inspiration can come in many forms and at any time, often when least expected. A well-known example is this of the theoretical chemist Kekulé who, in a daydream, saw a snake bite its own tail. As a result Kekulé was able to envision the ring-shape of the benzene molecule. Such wonderful problem solving twists-of-mind are rare. They are often the consequence of long and intense study of a single problem, which drive you to the limit, since they require you to imagine something you have never thought of before. In management-circles this is called “thinking-outside-the-box”, which sound a lot easier than it actually is. It does not mean that all of the sudden everything goes, you always have to bear in mind the actual box you started from.

As a computational materials scientist you have to combine your omnipotence over your virtual world with your power to imagine new worlds, hoping to see a glimmer of reality in the reflections of your silicon chips.

Nov 28

Sidekick

Met dit essay nam ik deel aan de Robbert Dijkgraaf essay-prijs 2015.
Dit jaar was het thema verbeelding, en in mijn bijdrage doe ik een
poging de rol van verbeelding naar voren te brengen binnen
computationeel materiaalonderzoek. Ik probeer eveneens uit te
leggen hoe ik computationeel onderzoek zie als onderzoeksdomein. 

Een vertaling naar het Engels kan hier gevonden worden.

 

Stel je een wereld voor waarin je atomen kunt zien. Meer nog, je kunt ze stapelen als legoblokken en manipuleren naar eigen goeddunken. Stel je een wereld voor waarin je de natuurwetten kunt aan- of afzetten, een wereld waar je zelf nieuwe natuurwetten kunt schrijven. In zo een wereld heb jij het voor het zeggen. Welkom in mijn wereld, de wereld van het “computationele materiaalonderzoek“.

Het zou een mooi begin zijn van een reclamespot voor dit onderzoeksgebied. In de bijhorende clip krijg je in elkaar overgaande beelden te zien van supercomputers enerzijds en animaties van chemische en biochemische processen op de atomaire schaal anderzijds. Het geheel wordt dan doorgelinkt aan onze eigen toekomst met sciencefictionachtige laboratoria waar de berekende materialen direct worden omgezet tot nieuwe medicijnen, flinterdunne beeldschermen en toepassing voor de ruimtevaart. De steeds sneller elkaar opvolgende beelden scifilabculmineren dan in de slotslogan: “Simuleer de toekomst!” met als onderschrift de aansporing om computationeel materiaalonderzoek te gaan studeren. Ik stel me voor dat zo’n reclameclip wel tot de verbeelding zou spreken. Het spreekt onze menselijke drang om te creëren aan met de belofte dat je alles kunt, als je het je maar kunt voorstellen. Je verbeelding is de enige beperkende factor.

Zoals bij de meeste reclamespots wordt ook in deze de werkelijkheid iets mooier voorgesteld dan ze is. Zoals voor elke andere wetenschapper geldt immers dat je bijdrage aan de vooruitgang beperkter is dan je zou willen. De gepresenteerde goddelijke almacht en alwetendheid liggen wel binnen handbereik. Als computationeel onderzoeker heb je immers absolute controle over de plaatsing van atomen en de inwerkende krachten, iets waar een experimenteel onderzoeker deels is overgelaten aan de grillen van de natuur en zijn of haar apparatuur. Deze controlevrijheid laat je toe, binnen een computer, elke wereld te creëren die je maar kunt bedenken.

Als wetenschapper wil je de wereld om je heen begrijpen, wat bovenstaande vrijheden inperkt, tenzij je ervoor kiest om in een team van computergame-designers aan de slag gaan. Dit betekent niet dat je creativiteit wordt beknot, integendeel. Waar bij het ontwerpteam het volledige verhaal bekend is, inclusief de regels en natuurwetten van de wereld waarin je speelt, is dat niet het geval bij computationeel materiaalonderzoek. Meer nog, vaak is het net je opdracht het verhaal gaandeweg te ontdekken, inclusief de natuurwetten die relevant zijn. Je wordt als het ware een verteller die telkens nieuwe verhalen moet bedenken, of bestaande plots moet aanpassen, uitbreiden of beperken, tot de verhaallijn past in de vorm van de werkelijkheid.

Je staat er gelukkig niet alleen voor om een goede afloop te regelen. Je wordt bijgestaan door je trouwe sidekick: je supercomputer. Deze is in staat met brute kracht de gekste plotwendingen door te rekenen. Op basis van jouw inleidende hoofdstuk, waarin je de wereld en haar natuurwetten schetst, zal hij het verhaal verder laten ontplooien. Door dan de juiste vragen te stellen en de antwoorden met de werkelijkheid te vergelijken kom je erachter waar je verhaal nog niet helemaal in de werkelijkheid past.

Hoe je je inleidende hoofdstuk daarop moet aanpassen verschilt per geval. Soms is het duidelijk wat er aan de hand is: er ontbreekt een cruciaal personage (bijvoorbeeld een onzuiverheidsatoom dat het kristaalrooster verstoord) of het personage woont op de foute plaats (toch niet op de plaats van atoom A, atoom B dan maar?). Moeilijker wordt het als sommige personages weigeren de hun toebedeelde rol te spelen (Die platina-atomen zijn onzichtbaar voor de rastertunnelmicroscoop, wie speelt nu de rol van de zichtbare nanodraad?).Ouroboros benzene. source: wikipedia De lastigste situatie is wanneer een volledige herschrijving van het inleidende hoofdstuk nodig is. Hierdoor krijg je te veel vrijheid in handen, terwijl het net de gekende beperkingen zijn die je houvast geven bij het opstellen van het verhaal. Je hebt dan een idee nodig dat je een link geeft met de werkelijkheid. Inspiratie kan hier velerlei vormen aannemen en op willekeurig moment komen. Een bekende anekdote is deze van de theoretische chemicus Kekulé, die in een dagdroom een slang zichzelf in de staart zag bijten en daardoor de ringvormige structuur van de benzeenmolecule uitdokterde. Zulke wonderlijk probleemoplossende gedachtenkronkels komen zelden spontaan, maar zijn veeleer het gevolg van lang en intens werk op eenzelfde vraagstuk. Dergelijke situaties drijven je tot het uiterste, je moet je immers iets voorstellen waar je nooit eerder aan gedacht hebt. In managementkringen wordt zoiets “buiten het kader denken” genoemd, wat bedrieglijk eenvoudig klinkt. Je mag immers niet vergeten dat voor onderzoek dit niet betekent dat alles plots toegelaten is (met andere woorden, je mag het kader zeker niet uit het oog verliezen bij het dagdromen).

Als computationeel materiaalonderzoeker moet je dus je almacht over je virtuele wereld combineren met je eigen vermogen nieuwe werelden in gedachten te scheppen, in de hoop zo onderweg een glimp van de buitenwereld in je siliciumchip op te vangen.

Mar 19

De-activating an active atom.

It could be that I’ve perhaps found out a little bit about the structure
of atoms. You must not tell anyone anything about it. . .
–Niels Bohr (1885 – 1965),
in a letter to his brother (1912)

Getting the news that a paper got accepted for publication is exciting news, but it can also be a little bit sad since it indicates the end of a project. Little over a month ago we got this great news regarding our paper for the journal of chemical information and modeling. It was the culmination of a side project Goedele Roos and I had been working on, in an on-and-off fashion, over the last two years.

When we started the project each of us had his/her own goal in mind. In my case, it was my interest in showing that my Hirshfeld-I code could handle systems which are huge from the quantum mechanical calculation point of view. Goedele, on the other hand, was interested to see how good Hirshfeld-I charges behaved with increasing size of a molecular fraction. This is of interest for multiscale modeling approaches, for which Martin Karplus, Michael Levitt, and Arieh Warshel got the Nobel prize in chemistry in 2013. In such an approach, a large system, for example a solvated biomolecule containing tens of thousands of atoms, is split into several regions. The smallest central region, containing the part of the molecule one is interested in is studied quantum mechanically, and generally contains a few dozen up to a few hundred atoms. The second shell is much larger, and is described by force-field approaches (i.e. Newtonian mechanics) and can contain ten of thousands of atoms. Even further  from the quantum mechanically treated core a third region is described by continuum models.

What about the behavior of the charges? In a quantum mechanical approach, even though we still speak of electrons as-if referring to classical objects, we cannot point to a specific point in space to indicate: “There it is”. We only have a probability distribution in space indicating where the electron may be. As such, it also becomes hard to pinpoint an atom, and in an absolute sense measure/calculate it’s charge. However, because such concepts are so much more intuitive, many chemists and physicists have developed methods, with varying success, to split the electron probability distribution into atoms again. When applying such a scheme on the probability distributions of fractions of a large biomolecule, we would like the atoms at the center not to change to much when the fraction is made larger (i.e. contain more atoms). This would indicate that from some point onward you have included all atoms that interact with the central atoms. I think, you can already see the parallel with the multiscale modeling approach mentioned above; where that point would indicate the boundary between the quantum mechanical and the Newtonian shell.

Convergence of Hirshfeld-i charges for clusters of varying size of a biomolecule.

Convergence of Hirshfeld-I charges for clusters of varying size of a biomolecule. The black curves show the charge convergence of an active S atom, while the red curves indicate a deactivated S atom.

Although, we expected to merely be studying this convergence behavior, for the particular partitioning scheme I had implemented, we dug up an unexpected treasure. Of the set of central atoms we were interested all except one showed the nice (and boring) convergence behavior. The exception (a sulfur atom) showed a clear lack of convergence, it didn’t even show any intend toward convergence behavior even for our system containing almost 1000 atoms. However, unlike the other atoms we were checking, this S atom had a special role in the biomolecule: it was an active site, i.e. the atom where chemical reactions of the biomolecule with whatever else of molecule/atom are expected to occur.

Because this S atom had a formal charge of -1, we bound a H atom to it, and investigated this set of new fractions. In this case, the S atom, with the H atom bound to it, was no longer an active site. Lo and behold, the S atom shows perfect convergence like all other atoms of the central cluster. This shows us that an active site is more than an atom sitting at the right place at the right time. It is an atom which is reaching out to the world, interacting with other atoms over a very long range, drawing them in (>10 ångström=1 nm is very far on the atomic scale, imagine it like being able to touch someone who is standing >20 m away from you). Unfortunately, this is rather bad news for multiscale modeling, since this means that if you want to describe such an active site accurately you will need an extremely large central quantum mechanical region. When the active site is deactivated, on the other hand, a radius of ~0.5 nm around the deactivated site is already sufficient.

Similar  to Bohr, I have the feeling that “It could be that I’ve perhaps found out a little bit about the structure
of atoms.”, and it makes me happy.