Bridging the chemistry-physics divide

My UQ colleague Ben Powell has written a nice set of notes An introduction to effective low-energy Hamiltonians in condensed matter physics and chemistry. They will be particularly useful for beginning graduate students. They have already been helpful to theoretical chemists and physicists who struggle to understand each other, when actually talking about the same thing. The notes will be published in a forthcoming book edited by Jeff Reimers.

Are flourescent proteins exotic?

"Biochemistry is the search for the chemistry that works."

Just how special, unique, and fine-tuned are biomolecules?

There are a wide range of proteins which have functionalities based on their optical properties. One outstanding example are flourescent proteins. Seth Olsen and I just completed a paper which uses high-level quantum chemistry calculations to show that the low-lying excited states of the chromophore

molecule in the green flourescent protein has a natural description in terms of the resonant colour theory of organic dyes developed in the middle of the twentieth century by Brooker, Platt, and Moffitt.

[Aside: this is the same Platt of multiple alternative hypothesis fame!].

Brooker showed how one could relate the absorption wavelength of an asymmetric methine dye molecule to the absorption wavelengths of two symmetric parent dyes.

The figure above shows that the anion of the

chromophore for GFP (which is what is responsible for the light emission) is a Brooker dye which is "on resonance", i.e. its ground state and first excited state contain equal superpositions of two valence bond states with electrons displaced to the left and the right of the methine bridge (central carbon atom).

How I use the h-index

I am a big fan of the h-index, when used appropriately.

I review numerous research grant applications and job applications and I find the h-index is a good filter to consider how seriously to take an application.

In comparing theory to experiment any discrepancy by an order of magnitude is usually a pretty good indicator that a theory is in trouble. Factors of 2 to 5 can also be useful.

What I find interesting and useful about the h-index is that there are often differences by factors of as much as 2 to 3 between individuals at the same career stage and applying for the same job or grant. I find it surprising that there are such large variations. Furthermore, there appears to be no correlation between the h-index and how much noise an individual makes about the significance of their work.

Some things I do keep in mind are:

-the younger the person the less reliable and useful the h-index

-differences of less than fifty per cent (e.g., 9 vs. 12 or 20 vs. 24) are of no significance

-different sub-fields have different traditions of citing each others works

One thing I never do is to look up an individual's h-index just out of curiousity. I only look it up if I have to actually evaluate the person.

Searching for a unified description of charge transport in molecular materials

Chemical Reviews just released a special issue on Materials for Electronics. There is a helpful article by David Weiss and Martin Abkowitz, Advances in Organic Photoconductor Technology. They note:

The story of the development of electrophotography is an object lesson in the connections between technology development, product development, and scientific understanding.

I found Section 6.1: Charge transport models particularly useful. It contains a critical and succinct discussion of the challenge of coming up with a model which can describe the dependence of the charge mobility on intermolecular separation, temperature, and electric field of a wide class of materials.

The conclusion is "questions remain and a complete description of charge transport in (molecularly doped polymers) MDPs remains elusive"

Rules for writing any paper

My postdoctoral advisor, John Wilkins, hammered into me Rules for Writing a PRL.

I recommend not just reading these rules, but reading them again and again, and moreover, putting it them into practice.

I think these rules are actually relevant to writing any paper.

The key point is to finish and polish the figures and the captions first. They should be self-explanatory and usually illustrate most of the key results of the paper.

Mixed valence: physicists vs. chemists II

In compounds which Varma characterized by homogeneous mixed-valence, each ion is assigned (at least by physicists) the same, non-integer, valence which is a result of a quantum mechanical superposition of two integral valences occuring on each ion.

Compounds exhibiting this type of mixed-valence include, CePd3, TmSe, SmB6 where the valences of the ions are 3.45, 2.72 and 3.7 for Ce, Tm, and Sm, respectively. In TmSe, the valence of 2.72 for the Tm ion is a result of valence fluctuations of this ion between the Tm2+ and Tm3+ states.

A distinctive experimental signature of homogeneous mixed valence is that the ground state is a spin singlet (and so has not net magnetic moment) even if one or both of the two oxidation states of the metal ion have a non-zero spin and magnetic moment. This is seen in the temperature dependence of the magnetic susceptibility. At high temperatures it has a Curie form characteristic of a magnetic moment. At low temperatures it saturates to a finite value. It also means there can be an absence of an Electron Spin Resonance (ESR) signal normally associated with metal ions with integer valence.

Other signatures were reviewed by Varma, including inter-ionic distances in the crystal structure that are intermediate between those normally associated with metal ions with integer valence. There can also be large Debye-Waller factors associated with large fluctuations in these distances.

Electronic correlations in cerium oxides

Today, Elvis Shoko had his Ph.D oral exam. He passed! Congratulations, Elvis!

I thought his talk before the interview with the assessors was a nice summary of his thesis.