Wednesday, March 21, 2018

Why am I interested in platypus milk?

A fundamental principle of molecular biology is that structure determines properties which determine biological function. This is what drives massive scientific industry of protein structure determination. An interesting press report led me to read the following paper.

Structural characterization of a novel monotreme-specific protein with antimicrobial activity from the milk of the platypus J. Newman, J. A. Sharp, A. K. Enjapoori, J. Bentley, K. R. Nicholas, T. E. Adams and T. S. Peat

The reason this got my attention was that my late father would have been very interested in the paper. A major research interest of his was milk proteins and he did write several papers on the milk proteins of the echnida and platypus. These fascinating animals are unique to Australia and Papua New Guinea and are the only monotremes (mammals that lay eggs) on the planet. My father collaborated with a biologist, Mervyn Griffiths, who was a colourful character, and was adept at finding and catching the platypus and echidnas in the wild and then milking them.

The paper is of scientific interest for two reasons. First, this particular platypus milk protein has anti-bacterial properties. Second, it has a fairly unusual structure, and having a fold that is not found in any other protein. The key question then remains as to whether this unique structural feature is responsible for the biological function.

The presence of the many alpha helices has led the authors to refer to this protein to the Shirley Temple protein in memory of the child movie star's many hair ringlets.

I was happy that an earlier paper about the anti-microbial action by some of the same authors cited many of my fathers papers on monotreme milk proteins, including one paper co-authored with Sir David Phillips. In that paper they tried to deduce the structure of echidna lysozyme and alpha-lactalbumin from similarities to other proteins. Almost 25 years later the platypus paper gives a much more robust determination. This illustrates the expanding success of protein crystallography. In that period the Protein Data Bank has increased from about 1,000 to more than 100,000 protein structures.

Friday, March 16, 2018

Not all email is created equal

Every few years I write a post about problems that email creates. Such a post is here.
Over the past few years, I have become aware that smartphones have reduced the effectiveness and efficiency of email. Many people now read email on a smartphone and this increases the likelihood that
- they read it even faster and so are less likely to digest anything of substance
- they won't open or can't read attachments properly
- they are less likely to reply
- if they do reply, they are more likely to have a knee-jerk response
- it is a less important communication channel that SMS, Messenger, WhatsApp, ...
- they are more likely to forward a message that they should think twice about forwarding
- they will not take the action that the email requests.

If the email message is "Shall we meet at 1pm for lunch?" then none of this matters.
However, there are some email messages that consider weightier matters such a detailed discussion of a scientific question, a proposed new policy of substance,  a personal relationship issue, ...

I welcome suggestions on how to tackle this problem.

Wednesday, March 14, 2018

"Bad fluids" near the superfluid transition

There is an interesting preprint
Viscosity Bound Violation in Viscoelastic Fermi Liquids 
 Matthew P. Gochan, Hua Li, Kevin S. Bedell

They consider the unitary Fermi gas within the framework of Fermi liquid theory. This system undergoes a superfluid transition at a temperature of about 0.17 times T_F (the Fermi temperature). They calculate the shear viscosity as a function of temperature. (I think) the complete temperature dependence is obtained by interpolating between the low-temperature and high-temperature limits.

The motivation for the study is the conjectured universal bound for the ratio of the shear viscosity to the entropy density, based on the AdS-CFT conjecture, beloved by string theorists.

The authors find that the conjectured bound is violated because the viscosity can become arbitrarily small near the superfluid transition due to large scattering from superfluid fluctuations. This is because the mean free path becomes arbitrarily small, i.e. the system is similar to a bad metal.
Unfortunately, the preprint does not reference some earlier relevant work on the shear viscosity of the unitary Fermi gas or on the bad metal near a Mott transition.

I thank Alejandro Mezio for bringing the preprint to my attention.

Monday, March 12, 2018

A new class of "spin ice" materials

Two of my UQ colleagues have just finished a nice paper:
Spin-state ice in geometrically frustrated spin-crossover materials 
Jace Cruddas, B. J. Powell

The paper brings together two fascinating topics I have written about before, spin crossover materials and spin ice. One thing that it is a little worrying and disappointing about spin ice materials is that there seem to be only two (?) of them!
This paper argues that some spin crossover materials may be a new class of materials that realise ice physics (residual entropy, emergent gauge fields, monopoles, ...) Here, the Ising spin variable is the two possible spin states (High Spin and Low Spin). These materials have the potential advantage that they may be tuneable due to the creativity of synthetic chemists.
The mechanism of the interaction between spins is rather unique and interesting. It is not an exchange interaction but rather and effective interaction mediated by the spin-lattice interaction, which in these compounds is arguably large.
It is also interesting that the sign of the frustrating interactions (which are key to the stability of the ice) is determined by the anharmonic potential associated with intermolecular interactions in the spin crossover compound.

Wednesday, March 7, 2018

Universities are not holiday resorts for undergraduates!

In different words, No College Kid Needs a Water Park to Study
This is a disturbing New York Times opinion piece by James V Koch, who has been president of two universities in the USA.

Unfortunately, this rush to spend public money (and/or student tuition) by university managers appears to be global. In the UK, there is an article in the Financial Times Magazine
University challenge: the race for money, students and status.
From Swansea to Sheffield and Southampton to Strathclyde, universities are now engaged in a spending spree: renovating campuses and building lecture theatres, laboratories, libraries and halls of residence. “What we know is that students and their parents, when they go on open days, they are impressed by shiny buildings,” says Nick Hillman, an adviser to the universities minister David Willetts from 2010 to 2013 who now runs the Higher Education Policy Institute, a think-tank.  
But as cranes dominate campus skylines, debts are mounting on vice-chancellors’ ledgers.....
It is happening in Australia too. The picture below is the new building for the Faculty of Business and Law at the University of Newcastle, which was relocated from the suburbs to prime real estate in the city to increase "profile". A faculty member told me that the office space and opportunities to interact with students are much worse than in their old building.

At UQ all the occupants of one floor of the physics building have been forced to vacate their offices so a Dean can build a new office suite on top of the building. The university is planning to spend $150 million on a new student union and fitness centre. This is to "enhance the undergraduate student experience." They seem to be trying to keep up with the Australian National University, whose ambitious plans have already lead to legal action and recently almost got "washed away".

We should not lose sight of a basic truth. The quality of an education is not determined by the "quality" of the buildings on campus but rather by the quality of the people inside the buildings. It is just like how the quality of a scientific paper is not determined by the journal in which it is published in but rather by the contents of the paper. I like the following thought experiment. Suppose you took all of the Harvard faculty and relocated them to the Mediocre Australian University campus, and relocated all the MAU faculty to the Harvard campus. After 3 years where will MAU and Harvard have moved to in the "rankings"?

Again, a lot of this relates to what your vision is for university education and what you believe the mission of the university should be.

Monday, March 5, 2018

How are DMFT, DMET, and slave bosons related?

Several years ago I posted about Density Matrix Embedding Theory (DMET), proposed as a (computationally cheaper) alternative to Dynamical Mean-Field Theory (DMFT).

An important question is what is the relationship (if any) between the two methods?
Given that the two methods are formulated in quite different ways it was not clear to me at all whether these question could be answer in any sort of definitive way.

There is a very nice paper which does answers this question in a precise way, with the bonus of also giving the relationship of both methods with rotationally invariant slave bosons (RISB).

Dynamical mean-field theory, density-matrix embedding theory, and rotationallyinvariant slave bosons: A unified perspective 
Thomas Ayral, Tsung-Han Lee, and Gabriel Kotliar

The main results are summarised in the Figure below. A result that is useful and insightful is that DMET corresponds to RISB with the quasi-particle weight set to unity (Z=1). There is then no band narrowing associated with the correlations. Given this is a key aspect of strongly correlated electron systems, I think this is a significant shortcoming of DMET. I am also a bit confused about how DMET can then capture a Mott transition.

Friday, March 2, 2018

Origin of the strong spin-phonon coupling in transition metal complexes

Spin crossover (SCO) materials are fascinating and raise many interesting questions.
Here I want to address the underlying physics of why there is a large change in bond length (typically 10-20 per cent) when the spin state of the complex changes. Basically, it is because the ligand field splitting Delta changes significantly with bond length. The change in spin state is associated with electrons moving between from the upper d -levels on the metal ion  (e_g in an octahedral complex) to the upper levels (t_g2).

What is the physical origin of this splitting?
How does Delta vary with the distance between the metal (M) and the ligand L?

One can answer the second question theoretically with quantum chemistry computations and experimentally by changing the ligand L, which leads to changes in bond length. The figure below is taken from the book, Ligand Field Theory and its Applications.

The variation of Delta and the bond length with ligand reflects the spectrochemical series.
Quantum chemistry computations show a similar variation for a given complex by varying the M-L distance. For example, see Figure S5 in the Supplementary Material for this paper.

What is the physical origin of this splitting?
A first guess is from "crystal field theory" that associates the energy level splitting with classic electrostatic effects. This gives a value that falls of as the sixth power of the M-L distance, and makes the concrete (and roughly correct ) prediction that for an octahedral complex the e_g levels move up by 3/2 times the amount that the t_2g levels move down. For a tetrahedral complex the opposite happens. However, there are two significant problems with this prediction. First, the predicted splitting is an order of magnitude too small. Second, this model predicts the opposite trend to the spectrochemical series.
A better description is obtained from "ligand field theory" where the splitting arises from covalent bonding between the d-orbitals on the metal and the p-orbitals on the ligand. For an octahedral complex, the t_2g (e_g) orbitals have positive (zero or negative) overlap with the ligand orbitals.

It is interesting (and disturbing?) that the authors of the figure above compare the data for Delta vs. R to power laws, 1/R^6 and 1/R^5.  For the data R varies by about 10 per cent. To distinguish between power laws one should be comparing data over several orders of magnitude!
In reality, the data is just as consistent with a linear decay.

What is of interest to me is the magnitude of the decay, G= 1 eV/Angstrom. The next step is to argue why this is "large". The change in bond length with spin crossover will be approximately G/B where B is the elastic constant for the bond.