Tuesday, December 27, 2011

Valuable refereeing

The work of reviewers is essential for the peer-reviewing system, but is sometimes somewhat underestimated. It takes time, no matter how well written a paper is. And we receive more and more papers to review each time (e.g. this year I received ca. 40 manuscripts, not counting revisions). There are who call for payments, given that it takes up valuable time, which could have been spent on research, education, or (most likely) free time with the family.

One possible way of achieving this would be through a discount on journal rates. Being a computational chemistry software developer gives also discount on these programs, so applying the same reasoning would make sense. The question would be how to do this. Peer reviewing is anonymous (and should be so), so only the reviewer and the editor (journal) know about it. Of course, the journals themselves should be able to produce a list of numbers at the end of the year, indicating that e.g. Univ. of Girona (UdG) has provided 100 referee reports for 2011. This could then be used to generate a discount for the UdG on the price for that journal.
But I see a number of problems:
1) much depends on the journals, with few controlling mechanisms for the universities
2) should the reports be weighted according to the impact factor of the journal?
3) most importantly, in the end it won't matter.

The reason for point 3 is that the scientific journals are mainly bought by universities (I think), e.g. by the same researchers that act as reviewer. Therefore, in the end the journals may give e.g. a 50% discount. BUT, the costs of printing the journals remains the same, and which has to be paid (mainly) by the same universities, and therefore the baseline rate will simply go up. In the fictitious example of a 50% discount, the baseline rate would go up by a factor 2, over which a 50% discount would simply give the same costs as before. Therefore, this system would probably not matter very much.

An alternative would be to pay the reviewers for their time, but this would be an enormous hassle, from which probably the banks would benefit mainly (and the scientific journals themselves, who would have to hire extra administrative personnel, whose costs would have to be fitted into the journal charges). The only viable solution I see is that the journals give the reviewers credits, with which the reviewers can buy scientific journals etc. Given that several journal publishers have in house book departments, this would be simple and straightforward to implement.

Tuesday, December 20, 2011

The strangest man (P.A.M. Dirac)

I just finished reading the biography of Paul Dirac, "The strangest man: The hidden life of a quantum genius". And the title does justice to the content, he seemed indeed to be a very strange man. Emotionally crippled, socially handicapped, he was not easy to work or live with. Talking to him often involved a question followed by either "Yes", "No" or a long pause. Many times he even did not respond at all. In the book is mentioned one typical example, about a discussion/fight between his wife and him, in which she asked him: "What would you do if I left you?". After a pause of half a minute, his response was: "I'd say: 'Goodbye dear'".

After from his contributions to science, the book deals with the possible origin of his strangeness (autism), describes his background (family life), digestive problems (only solved at the end of his life), and his many friends/colleagues (e.g. Bohr, Kapitza, Einstein). Many are the "Dirac quotes", which can be found online at several places (e.g. here), including quotes about him ("There is no God, and Dirac is his prophet"). All in all, it is an interesting read, sometimes it is obvious that the writer (Graham Farmelo) is really a big fan, but overall an objective picture about the man and his work.
(it was also interesting to read about the Cavendish etc. and see returning many of the names, such as Bernal and Rutherford, that were also present in the biography of Rosalind Franklin; note this previous entry)

Tuesday, November 1, 2011

Obituary for Hans Wynberg

Today is Tots Sants here in Catalunya, in which all those who have passed away are remembered. And how fitting that today an obituary appeared for Hans Wynberg. He was a famous professor in Organic Chemistry in Groningen, but already retired when I started my chemistry studies. Therefore, I had to "make do" with Ben Feringa, another famous organic chemist (molecular motors, retrosynthesis).

Feringa and Bert Meijer have written an obituary for Wynberg, to be published in Angewandte Chemie, which highlights aspects of his personal and scientific life. An interesting read, in honor of an interesting man.

Monday, October 31, 2011

Kilogram is no longer a kg

The definition of the kilogram will be changed, as described in more detail here.
New recommendations of the Consultative Committee for Units of the International Bureau of Weights and Measures have been accepted, which define the kg in relation to the Planck constant.

The new definition is: 'the kilogram is such that the Planck constant is exactly 6.6260693 x 10-34 joule-seconds'. The kilogram can be defined in terms of the Planck constant given that the unit of the Planck constant is equal to the unit of action - J s = kg m2 s-1 - and the second and metre have fixed numerical values in terms of the numerical values of the caesium hyperfine splitting frequency and the speed of light in a vacuum, respectively. So fixing the magnitude of the unit kg m2 s-1 has the effect of defining the kilogram.

And just to cleanup the SI system, three other units were updated as well (mole, ampere, Kelvin).

The ancient unit of kg, a cylinder of platinum-iridium that was cast in 1879, can therefore be put to rest now.

Sopar de despedida Carles

Tuesday, September 27, 2011

Premi extraordinari de doctorat 2010 for Sílvia Osuna

The Consell de Govern of the University of Girona has decided to award the Premi Extraordinari de doctorat 2010 to Sílvia Osuna for her PhD thesis "Theoretical studies of the exohedral reactivity of fullerene compounds".

For her thesis she had already received the grade excel·lent cum laude.


Wednesday, August 17, 2011

Summer conferences

This summer I have been to a number of conferences:

- XXVII Reunió Anual de la XRQTC in Tarragona
- WATOC'11 in Santiago de Compostela
- Reunión Bienal de la RSEQ in Valencia
- ICBIC'15 in Vancouver

At all conferences there were many, many interesting talks, just to mention a few names: Ken Houk, Henry Rzepa, Adoración Quiroga, Miquel Costas, Harry Gray, Sason Shaik, Max Holthausen, Luigi Casella, Prashant Kamat, Jesús Ugalde, Peter Gill, Pau Ballester, etc. etc.
The topics ranged wide as well, from DNA to iron-complexes, to methodology, to neurological disorders, molecular cages, etc.

Some of the topics brought forward on these meetings will be discussed here in the coming weeks.

Wednesday, June 1, 2011

Marie Curie fellowships: Come to Girona

The European Union has opened the call for the next Marie Curie fellowships.

With these fellowships you could come to the beautiful city of Girona, to work in the Institut de Química Computacional. We are a strong team of computational chemists that study a variety of different chemical, biological and physical systems.

There are two different fellowships to join our team, depending on your current situation:
- International Incoming Fellowship (IIF), for when you are currently working outside the EU
- Intra-European Fellowship (IEF), for when you are currently working within the EU

Please note, only candidates with strong CV and publication record are normally awarded by the EU, so if you think about joining our group, please contact me first.

The deadline is in both cases: 11 August 2011.

Popularity poll DFT2011

Last year we held the first of an annual series of popularity polls of density functionals. We have just opened the 2011 edition, which will be open from June 1 until October 1.

Please participate!!!

Monday, April 4, 2011

The injustice of rankings

I've just seen the Top 100 Chemists list, as collected by ISI. In it, they report the impact these chemists have made by dividing the total number of citations by the number of papers in the years 2000-2010. So far, so good.

However, by doing the ranking myself, I noticed that the scientist with the most impact (Charles M. Lieber, 240 citations per paper on average) in fact does not belong to the top. He is not even in the top 100!!!
(according to Essential Science Indicators, he's actually number 123)

What is wrong? Am I looking at different things? No.
ISI has looked only at chemists with at least 50 papers.
This is reminiscent of the h-index, where not the total number of citations count, but also the number of well-cited papers; i.e. an author with one well-cited paper (J.S. Cottrell, or D.M. Creasy, or D.J.C. Pappin, all with 2715 citations for 1 paper) has a h-index of 1, while a scientist like Charles Lieber (75 papers, 18200 citations) has probably at least a h-index of 75 (according to WOS, in total his is 107).
In itself this filtering makes some sense, but can have some unwanted side-effects. For instance, what to think of K.L. Kelly with an average of 366 citations per paper? This might still be debatable, because 10 is still a small number of papers.

However, injustice is being done to (at least) two chemists: Mohamed Eddaoudi and George M. Sheldrick. The former obtained 13196 citations for 39 papers (338 on average!), while the latter obtained 10084 citations for 47 papers, with an average of 215 per paper. This would have made him fourth (counting Eddaoudi) or third (not counting Eddaoudi), were it not for the fact that 47 is just below the magic threshold of 50...

George and Mohamed, if you want to complain to ISI, you've got my support!

Thursday, March 31, 2011

Another view of my blog

Google has added some new ways of viewing my blog:

- my favorite, the flipcard

- the stylish sidebar

- the chaotic mosaic

and some more...


Wednesday, February 16, 2011

Results for popularity poll DFT2010

We have recently held the first of an annual online poll for favorite density functionals in order to obtain a popularity adapted consensus object (PACO), as announced in a previous entry.

This “consensus” PACO functional may serve as a measure of how well the computational chemistry community is doing if compared to state-of-the-art reference data.

It will change over time and hopefully will result in gradual improvements. To track the performance of the PACO functionals, it is checked for a variety of diverse interactions: atomization energies of six representative molecules (AE6), barrier heights of hydrogen-transfer reactions (BH6), π-π stacking of anti-parallel cytosine dimer, spin-state splittings of FeFHOH and Ni(EDT)22–, excitation energies (singlet, triplet) of CO, and hydrogen-bonding in four dimers (ammonia, water, formic acid, formamide). These small systems are studied using basis sets close to the basis set limit, and compared to either coupled cluster results or experimental data.

A surprising result from the poll was that the widely-used B3LYP is in fact not the most popular density functional, but came only second after PBE0 (also known as PBE1PBE).

More information can be found in the news-item and the popularity poll webpage.

Tuesday, January 11, 2011

Parkinson's disease or not: a question of riding a bike

As is well known, Parkinson's disease is characterized by trembling hands, etc. Related to this is Parkisonism (a.k.a. Parkinson's Syndrome), a different kind of disease that should be treated differently.

Because the symptoms are quite similar, so far the correct diagnosis was difficult. But recent work by neurologists in Radboud hospital Nijmegen, has found a remarkable simple remedy, which works well maybe only for The Netherlands (or other countries where people are accustomed to use the bicycle for going around). Simply by asking the question if the patient has recently stopped riding a bike made a big difference; only some 5% of people with Parkinson's Disease did so, while of the patients with Parkinsonism some 50% did.

This simple not only saves thousands of euros of additional tests, but also in many cases can lead to a much faster diagnosis.

Monday, January 10, 2011

Spurious frequencies with ZORA/ADF solved

Just a quick note for those using ADF and ZORA, especially for optimizations
and transition state searches. There is small mismatch between the potential
and energy expressions, and always has been with ZORA.

In previous versions, this could lead to differences of 0.01 Å for bonds;
this is now improved in the 2010.01 version, where it is stated that it is
reduced to 0.0001 Å. In itself for chemical purposes this is irrelevant,
BUT it can become highly relevant when trying to calculate frequencies,
where because of this mismatch spurious imaginary frequencies may
occur, which were sometimes impossible to get rid of.

In the 2010.01 version, this seems to be solved; the problem is in the optimization,
not in the frequencies. So, simply redoing the frequency calculation does not help,
you should redo the optimization. I have noticed from a project where we had
one such annoying system with spurious imaginary frequency (of around -30 cm-1).
Using the 2010.01 version, and reoptimizing did the trick.

Saturday, January 1, 2011

Job opportunities in Girona

The next round of 3-year and 5-year fellowships from the Spanish Ministerio de Ciencias y Innovación (MICINN) will open on January 20, 2011. Deadlines are given below.

See this page for more information.

Juan de la Cierva, 3 year post-doc fellowship, deadline: 17 February.
Ramón y Cajal, 5 year post-doc fellowship, deadline: 10 February.
Note: these are the general deadlines!
The UdG deadlines are usually a few days before

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