Friday, June 24, 2016

Taylor expansions are a really basic skill and concept that undergraduate physics majors need to master

This past semester I taught part of two undergraduate courses: thermodynamics for second year, and solid state physics for fourth years. I was particularly struck by two related things.

1. Taylor expansions kept coming up in many contexts: approximate forms for the Gibbs free energy (e.g. G vs. pressure is approximately a straight line with slope equal to the volume), Ginzburg-Landau theory, Sommerfeld expansion, linear response theory, perturbation theory, and solving many specific problems (e.g. where one dimensionless parameter is very small).

2. Many students really struggled with the idea and/or its application. They have all done mathematics courses where they have covered the topic but understanding and using it in a physics course eludes them.

Physics is all about approximations, both in model building and in applying specific theories to specific problems. Taylor expansions is one of the most useful and powerful methods for doing this. But, it is not just about a mathematical technique but also concepts: continuity, smoothness, perturbations, and error estimation.

Does anyone have similar experience?
Can anyone recommend helpful resources for students?

Wednesday, June 22, 2016

Academic jobs not academic careers

Words, labels, and definitions mean something. They can colour a debate or idea from the start.
A while back I changed one post label for this blog from "Developing world" to "Majority world" because I think the latter is more accurate and makes a statement.

I also recently considered changing "career advice" to "job advice".
Why might it matter?
What is the difference?
Why care?

I am increasingly concerned by the notion of an "academic career".

First, most people who aspire to an "academic career" actually don't get to have one.
University marketing departments, funding agencies, and politicians don't want to face this painful reality.
Furthermore, the young, idealistic and uncritical either don't realise this or don't want to believe it.
Increasingly, positions in academia, whether Ph.D, postdoc, mid-career fellowships, or temporary faculty, are terminal. They don't lead to another position in academia.
Only a few lucky ones will have an academic career.

Here, I should be clear that I am NOT saying people should not take these terminal positions. There are many good personal reasons to take one. You just need to be realistic about what it may or may not lead to.
Most academic positions are jobs not one stage of a career.

Second, cars career out of control. Similarly careers can career out of control as ambition, fear, greed, or the lust for power may lead people to compromise on their own health, ethics, conscience, or family commitments. Unlike a car accident this does not happen suddenly and unexpectedly but usually as a gradual process over years or even decades.

For most people academia offers jobs not careers.

Monday, June 20, 2016

A nice text on spectroscopy of biomolecules

Bill Parson kindly gave me a copy of the new edition of his book, Modern Optical SpectroscopyWith Exercises and Examples from Biophysics and Biochemistry
It is a excellent book that covers a range of topics that are of increasing importance and interest to a range of people.
I am not sure I am aware of any other books with similar scope.

Two particular audiences will benefit from engaging with the material.

1. Biochemists and biophysics who have a weak background in quantum theory and need to understand how it underpins many spectroscopic tools that are now widely used to describe and understand biomolecules.

2. Quantum physicists who are interested in the relevance (and irrelevance!) of quantum theory to biomolecular systems. For some it could be a reality check of the complexities and subtleties involved and the long and rich history associated with the subject.

I highly recommend it. I have learnt a lot from it, some it quite basic stuff I should have known.

Thursday, June 16, 2016

Hydrogen bonds and infrared absorption intensity

I just posted a preprint
Bijyalaxmi Athokpam, Sai G. Ramesh, Ross H. McKenzie

We consider how the infrared intensity of an O-H stretch in a hydrogen bonded complex varies as the strength of the H-bond varies from weak to strong. We obtain trends for the fundamental and overtone transitions as a function of donor-acceptor distance R, which is a common measure of H-bond strength. Our calculations use a simple two-diabatic state model that permits symmetric and asymmetric bonds, i.e. where the proton affinity of the donor and acceptor are equal and unequal, respectively. The dipole moment function uses a Mecke form for the free OH dipole moment, associated with the diabatic states. The transition dipole moment is calculated using one-dimensional vibrational eigenstates associated with the H-atom transfer coordinate on the ground state adiabatic surface of our model.

Over 20-fold intensity enhancements for the fundamental are found for strong H-bonds, where there are significant non-Condon effects

The isotope effect on the intensity yields a non-monotonic H/D intensity ratio as a function of R, and is enhanced by the secondary geometric isotope effect.

The first overtone intensity is found to vary non-monotonically with H-bond strength; strong enhancements are possible for strong H-bonds.
(see the figure below)
This is contrary to common assertions that H-bonding decreases overtone intensity.

Modifying the dipole moment through the Mecke parameters is found to have a stronger effect on the overtone than the fundamental. We compare our findings with those for specific molecular systems analysed through experiments and theory in earlier works. Our model results compare favourably for strong and medium strength symmetric H-bonds. However, for weak asymmetric bonds we find much smaller effects than in earlier work, raising questions about whether the simple model used is missing some key physical ingredient in this regime.

Comments are welcome.

Wednesday, June 15, 2016

The formidable challenge of science in the Majority World, 2.

There is an interesting article in the latest issue of Nature Chemistry, Challenges and opportunities for chemistry in Africa, by Berhanu Abegaz, the Executive Director of the African Academy of Sciences.

He begins by discussing how metrics don't really give an accurate picture of what is going on, before discussing how natural products chemistry is a significant area of interest. But then he moves to the formidable challenges of science and education in such an under-resourced continent....

It was encouraging to me personally that Abegaz spends several paragraphs summarising a paper I co-authored three years ago with Ross van Vuuren and Malcolm Buchanan. He has far greater expertise and experience than us and so it was nice to see that our modest contribution was valuable.

As an aside, this brought home to me again the issue of the important distinction between token and substantial citations. Most citations I receive are token and so it is really encouraging to have a substantial one occasionally.

Previously I posted about some worthwhile initiatives on physics in Africa. It is encouraging that the International Centre for Theoretical Physics is starting a new initiative in Rwanda.

Monday, June 13, 2016

Quantum viscosity talk

Tomorrow I am giving the weekly Quantum sciences seminar at UQ.
Here are my slides.

The title and abstract below are written to try an attract a general audience.

I welcome any comments.

TITLE: Absence of a quantum limit to the shear viscosity of strongly interacting fermion systems

ABSTRACT: Are there fundamental limits to how small the shear viscosity of a macroscopic fluid can be? Could Planck’s constant and the Heisenberg uncertainty principle determine that lower bound? In 2005 mathematical techniques from string theory and black hole physics (!) were used to conjecture a lower bound for the ratio of the shear viscosity to the entropy of all fluids. From both theory and experiment, this bound appears to be respected in ultracold atoms and the quark-gluon plasma. However, we have shown that this bound is strongly violated in the "bad metal" regime that occurs near a Mott insulator, and described by a Hubbard model [1]. I will give a basic introduction to shear viscosity, the conjectured bounds, bad metals, and our results.

[1] N. Pakhira and R.H. McKenzie, Phys. Rev. B 92, 125103 (2015).

Thursday, June 9, 2016

A basic but important skill: critical reading of theoretical papers

Previously I posted about learning how to critically read experimental papers. 

A theory paper may claim
"We can understand property X of material Y by studying effective Hamiltonian A with approximation B and calculating property C."

Again it is as simple as ABC.

1. Effective Hamiltonian A may not be appropriate for material Y.
The effective Hamiltonian could be a Hubbard model or something more "ab initio" or a classical force field in molecular dynamics. It could be the model itself of the parameters in the model that are not appropriate. An important question is if you change the parameters or the model slightly how much do the results change. Another question, is what justification is there for using A? Sometimes there are very solid and careful justifications. Other times there is just folklore.

2. Approximation B may be unreliable, at least in the relevant parameter regime.

Once one has defined an interesting Hamiltonian calculating a measurable observable is usually highly non-trivial. Numerous consistency checks and benchmarking against more reliable (but more complicated and expensive) methods is necessary to have some degree of confidence in results. This is time consuming and not glamorous. The careful and the experienced do this. Others don't.

3. The calculated property C may not be the same as the measured property X.

What is "easy" (o.k. possible or somewhat straightforward) to measure is not necessarily "easy" to calculate and visa versa. For example, measuring the temperature dependence of the electrical resistance is "easier" than calculating it. Calculating the temperature dependence of the chemical potential in a Hubbard model is "easier" than measuring it.
Hence, connecting C and X can be non-trivial.

4. There may be alternative (more mundane) explanations.
The experiment was wrong. Or, a more careful calculation of a simpler model Hamiltonian can describe the experiment.

Theory papers are simpler to understand and critique when they are not as ambitious and more focused than the claim above. For example, if they just claim
"effective Hamiltonian A for material Y can be justified"
"approximation B is reliable for Hamiltonian A in a specific parameter regime"
"property C and X are intricately connected".

Finally, one should consider whether the results are consistent with earlier work. If not, why not?

Can you think of other considerations for critical reading of theoretical papers?
I have tried to keep it simple here.