Deconstructing protein phase diagrams

In the process of coming up with new exam questions for my undergraduate thermodynamics and condensed matter course I came across the following pressure-temperature phase diagram for the protein ribonuclease A at pH 2.0.

It is taken from a 1995 Biochemistry paper and I came across it in the wonderful text by Dill and Bromberg.
[Aside: I wondered if the water freezing was an issue but all along the curve the solvent water is liquid because dP/dT is negative for the liquid-solid line of pure water].

Natural scientific questions are:

• What are the mechanisms of "cold" and pressure-induced denaturation? 
• What are the associated changes in protein structure?
• Is this a generic type of phase diagram for proteins?
• What role does water and hydrophobic interactions play?

A nice review article from 2002 by Smeller discusses how these diagrams are indeed generic and their shape can be understood in terms of a simple thermodynamic theory due to Hawley in 1971.
One simply expands the Gibbs free energy change to second order in T and P relative to some reference pressure P0 and temperature T0,

The pressure induced denaturation can then lead to a volume contraction. This is explained in microscopic terms in a 1998 PNAS paper by Hummer et al.,

The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins

which shows
Pressure-denatured proteins, unlike heat-denatured proteins, retain a compact structure with water molecules penetrating their core. 

When science "managers" put the cart before the horse

This week I read a nice Opinion piece in Physics World, Making an Impact in Biology by Robert Endres. It is worth reading for an update on the contributions that physicists are starting to make to biology. However, one paragraph stood out to me. I found it a bit sad, but not totally surprising:

.... bigger is not always better. When I did research at the Oak Ridge National Laboratory in the US a few years ago, managers used to say that supercomputers should be used in the upcoming field of biology-inspired research, as this would, in retrospect, justify the lab’s investment in a huge computing infrastructure. But they also worried that someone would get “lucky” and find a smaller, more tractable, model or a more efficient algorithm to solve the same problem on a laptop – making the lab’s investment into such projects superfluous. 

Moving to Princeton University shortly afterwards, I realized that these worries were well founded.Top researchers, by asking the right questions and using clever models, could produce high-impact research results without ever needing supercomputers. 

Endres stresses (as I would) that supercomputers have a role in research but should be just  viewed as a possible tool towards for scientific understanding, hopefully the weapon of last resort... They are just a means to an end. Furthermore, funding and politics must never determine scientific strategy.

The cartoon is courtesy of Bob Laughlin.

Long live Fermi liquid theory!

Two important signatures of a Fermi liquid metal are that at low temperatures (i.e. much less than the Fermi temperature) the specific heat is proportional to temperature and the magnetic susceptibility is independent of temperature. Both are proportional to the density of states at the Fermi energy and one can form a dimensionless ratio, the Sommerfeld-Wilson ratio:

R is unity for a non-interacting gas of fermions and is 2 for the impurity contribution in the single impurity Kondo model [Yamada proposed this highly non-trivial result and Wilson confirmed it with the numerical renormalization group].

An important property of heavy fermion metals both the specific heat and susceptibility are enhanced by approximately the same amount. This can be seen in the plot below, where the solid line corresponds to a Wilson ratio of unity.

The plot was first made in Barbara Jones 1985 Cornell Ph.D thesis. 

This version is from Piers Coleman's review article Heavy Fermions: Electrons at the edge of Magnetism.

More than 10 years ago I wrote a paper Wilson's ratio and the spin splitting of magnetic oscillations in quasi-two dimensional metals.
I failed to get it published because of subtle issues about vertex corrections. Nevertheless, the preprint still seems to be of some use to people. See for example, the recent preprint Direct observation of multiple spin zeroes in the underdoped high temperature superconductor YBa2Cu3O6+x

The first 100 days of your postdoc

A standard by which US presidents are judged is by what they achieve in their first 100 days. The benchmark is the first hundred days of FDRs presidency where he began the New Deal.
I believe I once overheard Piers Coleman say that he thought new postdocs should produce a paper in their first 100 days in order to gain momentum and to position themselves for their next job.
This seemed a little extreme to me and almost impossible for many projects. But perhaps that is the point! You should not embark on ambitious projects (especially developing complex new software and building new equipment).

I aim for my postdocs to have submitted a first author paper within 6 months of starting. Most have and I think this has helped build confidence and momentum.

Graphics in LaTeX

In case it is of use to anyone I post this.
I have been occasionally struggling with the inclusion of graphics when running pdfLaTeX on my Mac. Partly this arises from having collaborators who are using PCs and different interfaces for LaTeX.
I found this page following solved my problems.

Emergence of mistakes

The review article that Ben Powell and I just finished,
Quantum frustration in organic Mott insulators: from spin liquids to unconventional superconductors, has just appeared online in Reports on Progress in Physics.

Unfortunately, Figure 1 was incorrectly produced. [We corrected it in the proofs stage and it appears the copy editor did not follow our instructions]. The correct version is below

The Superconducting dance

This cool video was produced by I2CAM as part of the Emergent Universe online science museum.