Friday, August 1, 2014

My paper submission strategy

Getting papers published can be a slow, inefficient, and frustrating process. For what it worth here is the strategy and associated rationale that I have generally evolved over the years. My primary goals are:
  • engage relevant people with what I am doing
  • get constructive feedback on the paper and the science
  • get the paper published as smoothly and quickly as possible.
Here are my usual steps:

1. get a local colleague to read the paper for feedback
2. put the paper on the arXiv [and write a post about it on this blog].
3. send the preprint to a few people who might be referees or be able to provide useful feedback
4. revise the paper in response to feedback, including another proof read
5. submit the paper to a journal, sometimes suggesting people who have provided positive feedback already as possible referees.

A few comments and rationale.

My target journals are mostly Physical Review B and Journal of Chemical Physics. About once a year I send something to PRL. For idealistic reasons, I abstain from the luxury journals and want to minimise publishing in journals from commercial publishers such as Elsevier. Going down the journal "food chain" involves continually reformatting a paper, wasting a lot of time.

If you publish in American Chemical Society journals it is not clear you can post on the arXiv.

Why not exchange steps 2 and 3? i.e. send it out for private comment before putting on the arXiv. I used to sometimes do that. However, I had a few instances where people would say things like, "we have some similar results, can we submit at the same time" or "we have some related experimental results can we publish together" or "lets combine your paper with ours" or "you really should also calculate XYZ ....". This can lead to significant time delays and (particularly in hindsight) debatable benefits. Ignoring their advice or requests can be awkward. If the paper is already on the arXiv it pre-empts some of this.

I welcome comments. What is your preferred strategy?

Thursday, July 31, 2014

Chemistry is local. In praise of Wannier.

In several posts I have emphasised that Chemistry is local.
This is illustrated by the fact that specific bonds within a molecule have approximately the same length, energy, and vibrational frequency regardless of the details of the molecule, particularly the distant parts.
This locality leads to useful concepts and theoretical approaches such as Atoms in Molecules, Natural Bond Orbitals, Valence Bond theory.
However, this locality is at variance with Molecular Orbital theory and the Kohn-Sham orbitals in Density Functional Theory (DFT); the orbitals can be completely delocalised over the whole molecule.

What are the implications for solid state physics?
Band theory is the analogue of molecular orbital theory. Bloch electronic wave functions are completely delocalised throughout the crystal.
Wannier orbitals are the physics analogue of Boys orbitals in chemistry.

In 1984 Phil Anderson wrote:
The Wannier functions are still one of the most useful but underutilized methodologies of solid state physics, and in particular it is in the language of Wannier functions that I feel the chemical implications of band theory are most effectively expressed. 
Of course the reason is that most of the concepts of chemistry are local concepts, such as bonds, ions, complexes, etc., while band theory is a global structure, in which the wave functions permeate the entire system and the eigenenergies depend on the position of every atom everywhere. There is no a priori reason why band theory should lead to such a chemically intuitive result as that the carbon—carbon single bond should have roughly the same energy and bond length whenever it appears, the Oxygen anion should have a constant radius and negative electron affinity, etc. 
This same weakness is shared by band theory’s chemical equivalent, the molecular orbital theory of Hund and Mulliken. From the very first, there was a vain attempt to restore locality by the use of atomic states and the valence-bond idea, very much advocated by Pauling, but only Pauling’s great ingenuity in applying the vague concept of “resonance” and his enormous prestige kept this scheme afloat as long as it has been: it is just not a valid way of doing quantum mechanics, and fails completely in the case of metals and of the organic chemical equivalent of metals, namely aromatic compounds and graphite, and is not very useful elsewhere except in the hands of a master empiricist such as Pauling. 
Nonetheless many local basis: how is this compatible with quantum mechanics? This is the enigma to which Wannier functions give us a very precise and clear answer. Not only that, but with a bit of ingenuity it is possible to modify the local functions in such a way as to give one a simple, accurate and serviceable method for quantum chemical calculations.
P.W. Anderson, Chemical Pseudopotentials, Physics Reports 1984

The discussion of resonating valence bond (RVB) theory is a bit harsh ("it is not just a valid way of doing quantum mechanics") and ironic given that only three years later Anderson introduced his RVB theory of superconductivity!

Indeed, the past two decades has seen a resurgence of interest in and use of Wannier functions.
Here is a recent Reviews of Modern Physics on the subject.

Wednesday, July 30, 2014

Seeing the effects of relativity with the naked eye

Our natural tendency is to think that to see the effects of Einstein's special theory of relativity you have to be travelling at some significant fraction of the speed of light. However, this is not the case. In solid state physics I am aware of three concrete phenomena that are purely due to relativistic effects.

1. Gold metal is the colour "gold".
According to Wikipedia, "non-relativistic gold would be white. The relativistic effects are raising the 5d orbital and lowering the 6s orbital.[11]"

2. Mercury is a liquid at room temperature.
This is nicely discussed in a recent blog post by Henry Rzepa concerning a recent paper that shows that relativistic effects shift the melting temperature by about 100 K.

3. Magnetic anisotropy and hysteresis in ferromagnets.
This results from spin-orbit coupling which is a consequence of relativity.

Tuesday, July 29, 2014

Journals should publicise their retraction index

Here are several interesting and related things about retracted journal articles.

1. Some retracted articles continue to get cited!
For example, today I found an interesting reference to this Science paper from 2001, only to learn it had been retracted. Furthermore, Google Scholar shows the paper has been cited several times in the past 4 years. Indeed, some of the Schon-Batlogg papers are still cited, for scientific reasons, not just as examples of scientific fraud. (For example, this recent JACS).

2. The Careers section of Nature has an interesting article Retractions: A Clean Slate, which makes the case that if you make an "innocent" mistake the best thing you can do is promptly make a retraction. But, there are some pitfalls. One thing that is still not clear to me is how in some cases one decides between complete retraction, partial retraction, and an erratum.

3. There is a correlation between journal impact factor and the frequency of retractions.
Somehow I did not find the graph below surprising.
This is described in an interesting editorial Retracted Science and the Retraction Index in the journal Infection and Immunity.
We defined a “retraction index” for each journal as the number of retractions in the time interval from 2001 to 2010, multiplied by 1,000, and divided by the number of published articles with abstracts. 
 ... the disproportionally high payoff associated with publishing in higher-impact journals could encourage risk-taking behavior by authors in study design, data presentation, data analysis, and interpretation that subsequently leads to the retraction of the work. 
Another possibility is that the desire of high-impact journals for clear and definitive reports may encourage authors to manipulate their data to meet this expectation. In contradistinction to the crisp, orderly results of a typical manuscript in a high-impact journal, the reality of everyday science is often a messy affair littered with nonreproducible experiments, outlier data points, unexplained results, and observations that fail to fit into a neat story. In such situations, desperate authors may be enticed to take short cuts, withhold data from the review process, overinterpret results, manipulate images, and engage in behavior ranging from questionable practices to outright fraud (26). 
Alternatively, publications in high-impact journals have increased visibility and may accordingly attract greater scrutiny that results in the discovery of problems eventually leading to retraction. It is possible that each of these explanations contributes to the correlation between retraction index and impact factor.
I look forward to the day when journals publicise their retraction index and university managers discourage their staff from publishing in certain journals because their retraction index is too high.

Monday, July 28, 2014

A realistic debate about climate change in the media

One of the many problems of the news media is that they love conflict and controversy. So much so, that they will not just amplify it and feed it, but even create it. This certainly happens with the issue of climate change. This video nicely illustrates the point with humour.


Thursday, July 24, 2014

NORDITA workshop on water

I have written many posts about what a fascinating, difficult, and important subject water is. I think it is one of the classic hard problems that does not get the attention it deserves. Science increasingly follows the latest fashionable topic that has "low-lying fruit" to pick.
Hence, I was delighted to learn last year that NORDITA [Nordic Institute for Theoretical and Atomic Physics] is planning a month long program this year on Water - the Most Anomalous Liquid.

I was even happier when I was invited to be part of a "Working Group" in week one to focus on "Quantum effects", led by Tom Markland. Hopefully this will generate some interesting discussions, science, and blog posts!

To increase the visual appeal of this post I searched on Google Images for "water quantum" and got some scary results, including this video marketing the "Quantum BioEnergy water clamp". I am not sure whether we should laugh or cry!

Tuesday, July 22, 2014

A key concept in glasses: the entropy crisis

The figure below introduces the idea of an "entropy crisis" and the Kauzmann temperature in glasses. It also leads to profound and controversial questions about the intimate connection between thermodynamics and kinetics in glasses.

Each solid curve shows the temperature dependence of the entropy of a supercooled liquid, relative to that of the crystal, above T_g, the glass transition temperature. T_m is the melting temperature of the crystal. The dashed curves are entropy in the glassy state.
The figure is taken from a very helpful review and adapted from Walter Kauzmann's classic 1948 paper.

What is going on?
The entropy of a liquid is greater than a solid [think latent heat of melting] so Delta S is positive. But, the specific heat capacity of a liquid is also greater than that of a solid [the vibrational, translational, and rotational degrees of freedom are all "softer" and less constrained]. Hence, the slope of Delta S vs. T must be positive.
Now, suppose that the liquid is supercooled so incredibly slowly that the glass does not form and you keep lowering the temperature, then at some temperature Delta S becomes negative. This extrapolated temperature [see the light blue straight line] is known as the Kauzmann temperature.

Why does this matter?
By the third law of thermodynamics, the entropy of the crystal goes to zero as the temperature goes to zero. Thus the supercooled liquid, could have negative entropy, which is physically nonsense.
Formation of the glass prevents this possibility. But, formation of the glass involves kinetics. So is there some deep connection between thermodynamics and kinetics? The review  discusses some possible connections. The extent of that connection is one of the controversial questions in glasses.