Students need to walk before they can run

There is an interesting Editorial in the Journal of Chemical Education
Science Education for Global Sustainability: What Is Necessary for Teaching, Learning, and Assessment Strategies?
by Uri Zoller.

I agree with many of his concerns and sentiments. Clearly he has thought about the relevant issues and worked hard at trying to implement them. I particularly like the sample exam questions he uses to illustrate his goals.

However, I feel that some of his proposed solutions are unrealistic (e.g., no text books) and unhelpful to students, particularly for beginning undergraduates. I think (and my anecdotal observations are) that multi-disciplinary courses are either too hard (or too superficial) for such students. Students need to learn basic chemistry, physics, and biology before they can  cope with integrating these ideas in biophysics, materials science, or environmental policy.

I thank Ross Jansen-van Vuuren for bringing the article to my attention.

Books on quantum many-body theory

Previously at UQ we have run a few successful book reading groups for postdocs and graduate students. We have worked through parts of
Electronic Correlations in Molecules, and Solids by Peter Fulde
Advanced Solid State Physics by Phillip Philips
A Chemists Guide to Valence Bond Theory by Shaik and Hiberty

A postdoc, Tony Wright, and I are considering starting a new group based on a book on quantum many-body theory. We want a book that makes a strong connection to experiment. I welcome suggestions.

Here is my current suggestions in order of roughly decreasing preference

The Kondo Problem to Heavy Fermions by Alex Hewson.
Although focussed on the Kondo problem, it covers techniques and concepts that are more broadly applicable including Fermi liquid theory, scaling, and slave bosons.
It does connect strongly to experiment.
The e-book is available through the library.

An introduction to Many-Body Theory by Piers Coleman.
This is particularly clear, emphasizes key concepts, and has beautiful illuminating illustrations. But, perhaps we want more connection to experiment.
Available free on-line.

Many-Body Quantum Theory in Condensed Matter Physics by Henrik Bruus and Karsten Flensberg.
No path integrals. Too many Feynman diagrams? Again, perhaps we want more connection to experiment.
Multiple copies are available in the library.

Reservations about the five year h-index

Recently I encountered a new metric, the "5 year h-index" which was being used to evaluate someone's research performance. Explicity, one counts the number h of papers published in the last 5 years that have been cited more than h times. Perhaps one might argue that this is a good metric for deciding whether to give someone a grant now. Afterall, just because 10 or 20 years ago they published highly cited papers does not mean that right now they are at the cutting edge. However, I do not agree.

I think this is a highly unreliable metric because there is significant noise. Except for a few rare exceptional papers, citations within a few years of publication will be low (1-10?). Hence, comparing two people with 5 year h-indexes, say one with a 6 and another with a 10, I would contend is meaningless.

Two of the most cited papers in Physical Review journals are the EPR (Einstein Podolsky Rosen) paper and Steven Weinberg's electro-weak interaction paper. The latter attracted about one citation per year for the first 5 years after publication! The former attracted about 10 citations in the first 2 years and then none for more than ten years!

When Jorge Hirsch introduced the h-index the whole point what to find some measure for a lifetime of scientific achievement. I still think it does provide a useful coarse-grained measure for that.

Overselling ab initio computational chemistry

The great appeal of computational quantum chemistry is that it aims to be ab initio. One simply calculates the properties of molecules from Schrodinger's equation and Coulomb's law. However, the painful reality is that many methods have to include parameters (or make choices about approximations) that are determined by comparison with experiment. Indeed there is now a whole industry of people who tweak parameters in density functionals in order to get better agreement with experiment. Although I am not enthusiastic about this I can live with it as long as people are transparent about what they are doing.

A recent JACS paper Mechanism for Singlet Fission in Pentacene and Tetracene: From Single Exciton to Two Triplets from Martin Head-Gordon's group is not as transparent as it could be about whether it is ab initio. It states

The originally proposed mechanism for SF [Singlet Fission] is based on model Hamiltonians that couple of monomer states between adjacent molecules. The low coupling in the model between the single-exciton and ME states requires that a CT state be invoked as an intermediate (i.e., an indirect mechanism). This requires the assumption that the CT state is relatively low in energy and thus energetically accessible. Herein, systematic ab initio study of the low-lying excited states in tetracene and pentacene provides an alternative mechanism for the photophysics of these materials. This study provides evidence that CT states need not be directly relevant to SF in acenes.  

Because these ab initio simulations capture the correlation of many electrons, they are distinct from model Hamiltonian studies (for instance ref 22). The current understanding of SF comes from model Hamiltonians, where certain electronic states of two monomers are employed as basis sets. While model Hamiltonian studies can yield deep insights into complex physical processes such as SF [Singlet Fission], these invariably require assumptions about the physics which are embedded as model parameters. By contrast, ab initio calculations in principle allow the essential features to emerge directly from simulations.... 

However, if one looks at the Computational Details section of the paper (which comes after the Conclusion) one finds the statement.

One deficiency of CASSCF and RAS-2SF theories is the overestimation of excitation energies due to the limited degree of dynamic correlation. To overcome this difficulty, we shift the excitation energies of T1 and S1 at the equilibrium geometry to the experimental values for the acene crystals.

Surely, this fitting to experiment [of two key observables] undermines the authors claim to be doing ab initio calculations or to be superior to model calculations. Furthermore, most of the calculations in the paper involve a small number of molecules, which is surely a model for the infinite solid, in which significant screening effects may be present. Arguably, ignoring this is comparable to the significant physical assumptions present in model calculations.

Developing science demonstrations that actually teach science

Demonstrations to school students can easily degenerate into the following format. First, one does something spectacular such as the Coke-Mentos fountain or the barrel crush. Second, one tells the student how it works. I confess I have often done this. However, this is actually terrible because it reinforces the misconception that science is a noun not a verb. It teaches nothing about the scientific method.

This week my wife and I demonstrated the Coke-Mentos fountain to a group of kids at a holiday club that my church was running. In order to promote critical thinking we did some comparative measurements. The fountain was done for diet Coke, Solo (a lemon drink), and generic brand (Coles) Cola. We also compared Mentos bought in the USA (on my recent trip) and in Australia. It turned out that the former is much more effective. I later learnt that we had been scooped in this important scientific discovery. It had already been published on YouTube!



I also discovered there is some nice literature on the subject.

Mentos and the Scientific Method: A Sweet Combination in the Journal of Chemical Education.

Diet Coke and Mentos: What is really behind this physical reaction? in the American Journal of Physics. They have some impressive apparatus for making quantitative measurements. They also found that playground sand was almost as good as Mentos.
They report surface analysis studies of the Mentos, highlighting the importance of the surface roughness for nucleation sites for CO2 bubbles.

The Ultrasonic Soda Fountain: A Dramatic Demonstration of Gas Solubility in Aqueous Solutions in the Journal of Chemical Education

“Can we do That Again?” Engaging Learners and Developing Beyond the “Wow” Factor in the Science Education Review.

Finally, having good apparatus helps. From Steve Spangler science we purchased a Geyser Tube which feeds the Mentos into the Coke. With the recommended 7 US Mentos we observed fountains of 2-3 metres!

Kagome lattice antiferromagnet IS a Z_2 spin liquid

At the Journal Club for Condensed Matter there is a very nice and clear commentary Identifying a spin liquid on Kagome lattice by quantum entanglement by Ashvin Vishwanath. I learnt a lot from reading it.

It reviews two recent preprints which use numerical methods (density matrix renormalisation group = DMRG) to establish topological order in the ground state of the Heisenberg spin-1/2 model on the Kagome lattice.

An earlier post considered earlier DMRG evidence that was suggestive of a spin liquid, with an energy gap, but did not establish topological order.

Seeking simplicity in complex systems

One thing I really enjoyed and appreciated about the workshop this week has been the emphasis on developing "simple" models to describe systems that are structurally and chemically complex.
Here "simple" means that there are a just a few degrees of freedom and a few parameters in the model. "Complex" means there are many degrees of freedom.
Even when people are doing very large and demanding molecular dynamics simulations of solvated proteins the goal has been to understand the essential physics and chemistry of what is going on.

Here are a few examples.

Phil Geissler considered a  simple model for force generation in cellular processes, showing how Actin filament curvature biases branching direction.

Frank Brown considered an analytical model that could be used for Interpreting neutron spin echo experiments on lipid bilayer membranes without introducing a "fudge factor" for the value of the solvent viscosity that experimentalists had been using.

Abe Nitzan considered the simplest possible effective Hamiltonians that could be used to describe Electromagnetic and magnetic effects in molecular conduction.

Greg Voth discussed the importance of coarse graining and described an unbiased numerical method for reducing the dynamics of a protein to just a few sites. He then described recent work applying this to electron transfer in an iron hydrogenase.

Rob Coalson considered the problem of how a particular pore membrane protein worked. He considered how a polymer brush collapses when exposed to a critical concentration of binding nanoparticles. He found how the mean-field theory for a simple lattice gas type model could capture the phase transition associated with the collapse of the brush.

Dmitry Matyushov spoke about extending elastic network models for proteins to describe their response to external forces including local and global electric fields.