Friday, December 19, 2014

Slides like this should be banned from talks

Increasingly I see people show slides like this in talks.


I don't see the point.
It is just a screen dump of a publication list from a CV.
There is no pedagogical value.
It is just saying, "Look, I have published lots of papers!"
Don't do it.

Wednesday, December 17, 2014

Successful researchers should move on to new hard problems

Based on anecdotal evidence I fear/suspect that metrics, luxury journals, and funding pressures have led to a shift in how some/many of the best researchers operate.

Thirty of more years ago the best researchers would operate as follows.
They would pick a difficult problem/area, work on it for a few years and when they had (hopefully) solved it they would write a few (1-3) papers about it. They would then find some challenging new problem to work on. Meanwhile lesser researchers would then write papers that would work out more of the details of the first problem.

Now, people want to work on lower risk problems with guaranteed steady "outputs". Thus, they are reluctant to "move on", particularly when they have a competitive edge in a new area. It is easy for them to churn out 10-20 more papers on natural "follow up" studies working out all the details. They are "safe" projects for graduate students. These papers may be valuable but they could probably have been done by lesser talents. From the point of view of advancing science it would have been better if the successful leader had moved onto a newer and more challenging problem.  So, why don't they? Because their publication rate might drop significantly and it would be risky/difficult to supervise so many students on new projects.

An earlier post, raised the question, Why do you keep publishing the same paper?

Is this a fair assessment? Is my concern legitimate? Or I am just naively nostalgic?

Aside: I am on vacation. You should not work on vacations. This post (and the next one) was written last week and posted by delay (cool, huh!).

Monday, December 15, 2014

Finding the twin state for hydrogen bonding in malonaldehyde


I was quite excited when I saw the picture above when I recently visited Susanta Mahapatra.

One of the key predictions of the diabatic state picture of hydrogen bonding is that there should be an excited electronic state (a twin state) which is the "anti-bonding" combination of the two diabatic states associated with the ground state H-bond.
Recently, I posted about how this state is seen in quantum chemistry calculations for the Zundel cation.

The figure above is taken from
Optimal initiation of electronic excited state mediated intramolecular H-transfer in malonaldehyde by UV-laser pulses 
K. R. Nandipati, H. Singh, S. Nagaprasad Reddy, K. A. Kumar, S. Mahapatra

The figure hinted to me that for malonaldehyde the twin state is the S2 excited state, because of the valence bond pictures shown at the bottom of the figure and because the shape of the two potential energy curves is similar to that given by the diabatic state model.
Below I have plotted the curves for a donor-acceptor distance of R=2.5 Angstroms, comparable to that in malonaldehyde.

The vertical scale is such that D=120 kcal/mol, leading to an energy gap between the ground and excited state of about 4 eV, comparable to that in the top figure [which is in atomic units, where Energy = 1 Hartree = 27.2 eV].
Note that in the first figure, there is a gap on the vertical scale and the top and bottom part of the figures involve a different linear scale.
Hence, to make a more meaningful comparison I took the potential energy curves and replotted them on a linear scale using the polynomial fits given in the paper. The results are below.


There is reasonable agreement, but only at the semi-quantitative level.
[With regard to units the distances are in atomic units (Bohr radius = 0.5 Angstroms] and comparable].

The figure below shows how the calculated transition dipole moment between the ground state and the first excited state. I was surprised that it only varied by about five per cent with change in nuclear geometry.
However, Seth Olsen pointed out to me that this small variation reflects the Franck- Condon approximation [which is very important and robust in molecular spectroscopy].
I also calculated this with the diabatic state model, assuming that the dipole moment of diabatic states did not vary with geometry and the Mulliken-Hush diabaticity condition [that the dipole operator is diagonal in the diabatic state basis] held (see Nitzan for an extensive discussion).
[The units here are 1 atomic unit = 2.6 Debye].


The vertical scale here is the magnitude of the dipole moment in one of the diabatic states. This is also the approximate value of the dipole moment of the molecule at "high" temperatures above which there is no coherent tunnelling between the two isomers, i.e. the proton is localised on the left or right side of the value. The experimental value reported here is about 2.6 Debye.
This is consistent with the claim that the diabatic state model gets the essential physics of the electronic transition.

But, of course the real molecule is more complex. For example, between the S0 and S1 states there is a "dark" S1 state, characterised as a n to pi* transition where n is the lone pair orbital on the oxygen. The three states and their associated conical intersections are discussed in a nice paper by Joshua Coe and Todd Martinez.

I think a good way to more rigorously test/establish/disprove the diabatic state picture is to use one of the "unbiased" recipes to construct diabatic states, such as that discussed here, from high-level computational chemistry.

Friday, December 12, 2014

Battling the outbreak of High Impact Factor Syndrome

Hooray for Carl Caves!
He has an excellent piece The High-impact-factor syndrome on The Back Page of the American Physical Society News.

Before giving a response I highlight some noteworthy sentences. I encourage reading the article in full, particularly the concrete recommendations at the end.
.... if you think it’s only a nightmare,.... , you need to wake up. Increasingly, scientists, especially junior scientists, are being evaluated in terms of the number of publications they have in HIF journals, a practice I call high-impact-factor syndrome (HIFS).

I’ve talked to enough people to learn that HIFS is less prevalent in physics and the other hard sciences than in biology and the biomedical sciences and also is less prevalent in North America than in Europe, East Asia, and Australia. For many readers, therefore, this article might be a wake-up call; if so, keep in mind that your colleagues elsewhere and in other disciplines might already have severe cases. Moreover, most physicists I talk to have at least a mild form of the disease.
Do you have HIFS? Here is a simple test. You are given a list of publications, rank-ordered by number of citations, for two physicists working in the same sub-discipline. All of the first physicist’s publications are in PRL and PRA, and all of the second’s are in Nature and Nature Physics. In terms of the citation numbers and publication dates, the two publication records are identical. You are asked which physicist has had more impact.

If you have even the slightest inclination to give the nod to the second physicist, you are suffering from HIFS.

In the case of junior scientists, the situation is more complicated [than senior scientists]. Their publication records are thinner and more recent. The focus shifts from evaluating accomplishment to trying to extract from the record some measure of potential. ...... even if you think publication in HIF journals is informative, it is not remotely as instructive as evaluation of the full record, which includes the actual research papers and the research they report, plus letters of recommendation, research presentations, and interviews. When HIFS intrudes into this evaluation, it amounts to devaluing a difficult, time-consuming, admittedly imperfect process in favor of an easy, marginally informative proxy whose only claim on our attention is that it is objective.

Relying on HIF leads to poor decisions, and the worse and more frequent such decisions are, the more they reinforce the HIFS-induced incentive structure. As physicists, we should know better. We know data must be treated with respect and not be pushed to disclose information it doesn’t have, and we know that just because a number is objective doesn’t mean it is meaningful or informative.
 
Even more pernicious than applying HIFS to individuals is the influence it exerts on the way we practice physics. Social scientists call this Campbell’s law: “The more any quantitative social indicator is used for social decision-making, the more subject it will be to corruption pressures and the more apt it will be to distort and corrupt the social processes it is intended to monitor.”  This social-science law is nearly as ironclad as a physical law. In the case of HIFS, there will be gaming of the system. Moreover, our research agenda will change: If rewards flow to those who publish in HIF journals, we will move toward doing the research favored by those journals. 
No matter how highly you think of the editors of the HIF journals, they are independent of and unaccountable to the research community, they do not represent the entire range of research in the sciences or in physics, and their decisions are inevitably colored by what sells their magazines.

What to do?
I just list a few of the concrete and excellent recommendations Carl makes. We are not helpless.
Educate administrators that the HIF shortcut, though not devoid of information, is only marginally useful. For any scientist, junior or senior, an evaluation of research potential and accomplishment requires a careful consideration of the scientist’s entire record. A good administrator doesn’t need to be taught this, so this might be a mechanism for identifying and weeding out defective administrators.

Take a look at the San Francisco Declaration on Research Assessment (DORA) which is aimed directly at combating HIFS. Consider adopting its principles and signing the declaration yourself. DORA comes out of the biosciences; signing might help bioscientists put out the fire that is raging through their disciplines and could help to prevent the smoldering in physics from bursting into flame.

Include in ads for positions at your institution a standard statement along the following lines: “Number of publications in high-impact-factor journals will not be a factor in assessing research accomplishments or potential.”

Adopting this final recommendation would send an unambiguous message to everybody concerned: applicants, letter writers, evaluators, and administrators. Making it a commonplace could, I believe, actually change things.
I agree with all of the above. However, I do differ with Carl on a few points. These disagreements are a matter of degree.

1. I groaned where I saw that he lists the impact factors of journals with four and five significant figures. Surely two or three is appropriate.

2. I am more skeptical about using citations to aid decisions. I think they are almost meaningless for young people. They can be of some use in filtering for senior people. But I also think they largely tell us things we already know.

3. Carl suggests we need to recommit to finding the best vehicle to communicate our science and select journals accordingly. I think this is irrelevant. We know the answer: post the paper on the arXiv and possibly email a copy to 5-10 people who may be particularly interested. I argued previously that journals have become irrelevant to science communication. Journals only continue to exist for reasons of institutional inertia and career evaluation purposes.

4. My biggest concern with HIFS is not the pernicious and disturbing impact on careers but the real negative impact on the quality of science. 
This is the same concern as that of Randy Schekman.
Simply put, luxury journals encourage and reward crappy science. Specifically they promote speculative and unjustified claims and hype. "Quantum biology" is a specific example. Just a few examples are here, here, and here.

Why does this matter?
Science is about truth. It is about careful and systematic work that considers differ possible explanations and not claiming more than the data actually does or does not show.

Once a bad paper gets published in a luxury journal it attracts attention.
Some people just ignore it, with a smirk or grimace.
Others waste precious time, grant money, and student and postdoc lives showing the paper is wrong.
Others actually believe it uncritically. They jump on the fashionable band wagon. They continue to promote the ideas until they move onto the next dubious fashion. They also waste precious resources.

The media believes the hype. You then get bizarre things like The Economist listing among their top 5 Science and Technology books of the year a book on quantum biology (groan...).

Wednesday, December 10, 2014

Strong non-adiabatic effects in a prototype chemical system

This post concerns what may be the fast known internal conversion process in a chemical system, non-radiative decay times in the range of 3-8 femtoseconds. Internal conversion is the process whereby in a molecule there is a non-radiative transition between electronic excited states (without change in spin quantum number). This is by definition a break-down of the Born-Oppenheimer approximation.

Much is rightly made of the fascinating and important fact that excited states of DNA and RNA undergo "ultra-fast" non-radiative decay to their electronic ground state. This photo-stability is important to avoid mutations and protect genetic information. Conical intersections are key. The time scale for comparison is the order of a picosecond.

The figure below is taken from

It shows the wavelength dependence of the intensity of emission from a 3d (Rydberg) excited state.

There are several things that are noteworthy about the experimental data, given that this is a gas phase spectra.

1. The large width of the spectra. In energy units this is of the order of an eV. Gas phase spectra for electronic transitions in typical molecules are usually extremely sharp (See here for a typical example). 

2. The two peaks, suggesting the presence of two electronic transitions.

3. The strong isotope effects. For strictly electronic transitions between adiabatic states, there should be no dependence on the nuclear masses. This suggests strong vibronic and quantum nuclear effects.

So what is going on?
The key physics is that of the Jahn-Teller effect, conical intersections, and non-adiabatic effects.
For H3 there is geometry of an equilateral triangle which has C3 symmetry. There are then two degenerate electronic ground states with E symmetry, and experience E x epsilon Jahn-Teller effect leading to the two adiabatic potential energy surfaces shown below. They touch at a conical intersection. The two peaks in the spectra above correspond to transitions to these two different surfaces.

Non-adiabatic coupling leads to rapid transitions between the surfaces leading to the ultra-ultra-fast internal conversion and the very broad spectra. This is calculated in the paper, leading to the theoretical curves shown in the top figure.


More recently, Susanta and some of his students, have considered the relative importance of (off-diagonal) non-adiabatic effects, the geometric phase [associated with the conical intersection], and Born-Huang (diagonal) corrections to explaining the spectra.
They find that the first has by far the most dominant effect. The latter two have very small effects that look like they will be difficult to disentangle from experiment. I discussed the elusiveness of experimental signatures of the geometric phase in an earlier post.
  
I thank Susanta Mahapatra for explaining this nice work to me, on my recent visit to his group.

Tuesday, December 9, 2014

Topping the bad university employer rankings

Stefan Grimm was a Professor of Medicine at Imperial College London. It was deemed by his supervisors that he was not bringing enough grant income into his department. Tragically, he was later found dead at his home. Email correspondence from Grimm and from his supervisors has been made public on a blog.

It is very sad and disturbing.

This was my first encounter with this excellent blog DCs Improbable Science written by David Colquohoun FRS, Emeritus Professor of Pharmacology at University College London.
He also has an interesting post that is rightly critical of an Australian universities for taking millions in "research funding" from dubious vitamin, herb, and supplement companies.
He also has important posts exposing metrics and hype in luxury journals.

Friday, December 5, 2014

Quantum capacitance is the charge compressibility

In a quantum many-body system a key thermodynamic quantity is the charge compressibility, the derivative of the charge density with respect to the chemical potential d n/d mu.

In a degenerate Fermi gas kappa is simply proportional to the density of states at the Fermi energy.
kappa is zero in a Mott insulator. As the Mott transition is approached, the behaviour of kappa is non-trivial. For a band width (or frustration) controlled Mott transition that occurs at half filling, Jure Kokalj and I showed how kappa smoothly approached zero as the Mott transition was approached. However, there is some debate as to what happens for doping controlled transitions, e.g. does kappa diverge as one approaches the Mott insulator.

One thing I had wondered about was how one actually measures kappa accurately in an experiment. Varying the chemical potential and/or charge density is not always possible or straightforward.
See for example, Figure 10 in this review by Jaklic and Prelovsek, which compares experimental results on the cuprates with calculations for the t-J model.
The experimental error bars are large.

At the recent Australasian Workshop on Emergent Quantum MatterChris Lobb gave a nice talk about "Atomtronics" where he talked about how you define R, L, and C [resistance, inductance, and capacitance] in cold atom transport experiments. He argued that the capacitance was related to
d mu/dn. This got my attention.
Michael Fuhrer pointed out how there were measurements of the "quantum capacitance" for graphene.

Recent measurements for graphene are in this nice paper. They give a helpful review of the technique and the relevant equations.



Personally, I don't find this "derivation" completely obvious, but can follow the algebraic steps.

Why is C_Q called the "quantum capacitance"? This wasn't at all clear to me.
But, there is a helpful discussion in a paper,
Quantum capacitance devices by Serge Luryi

For a non-interacting two dimensional fermion gas the density of states scales inversely with the square of hbar. Hence, it diverges as hbar goes to zero. This means the quantum capacitance diverges and the "quantum" term C_Q in the equation [1] disappears.

In the graphene paper, the authors extract the renormalised Fermi velocity as a function of the density [band filling] and compare to renormalisation group calculations, that take into account electron-electron interactions, and predict a logarithmic dependence, as shown below. Red and blue are the theory, and experimental curves, respectively.


As exciting as the above is, it is still not clear to me how to measure the "quantum capacitance" for a multi-layer system.

Update. (December 10, 2014)
Lu Li brought to my attention his measurements of the capacitance of the 2DEG at the LaAlO3/SrTiO3 interfaceand earlier measurements of negative compressibility of correlated two dimensional electron gases (2DEGs) by Eisenstein and by Kravchenko.
Background theory has been discussed extensively by Kopp and Mannhart.