Friday, July 31, 2015

An important but basic research skill: not getting too distracted

Making progress in science requires significant focus and discipline. In some sense you need to put in your 10,000 hours. People can distracted by all sorts of non-scientific pursuits: Facebook, romance, family dramas, hobbies, partying, .... But this post is about scientific distractions. I illustrate this will two extreme caricatures.

John really wants to understand his Ph.D project in experimental solid state physics at a deep level. He thinks the quantum measurement problem is really interesting and so he is reading a lot of papers about that. The software he needs for his experiment is functional but he does not like some of the way it interfaces with other software and so he is rewriting it all. In one month he is giving a talk at a conference and so he is not going in the lab for the next month because he wants to give a really nice talk. Whenever his advisor gives him a paper to look at he not only reads it but some of the background references. He spends a lot of time talking to people in a theoretical biophysics group because he thinks what they are doing is pretty interesting....
He is going to struggle to finish his Ph.D in the normal time frame.

Joan is very focussed on her Ph.D project in computational chemistry. She spends most of her time writing and debugging code. She only goes to seminars that she thinks are directly related to her project. The only papers that she has read are those written by her advisor. She rarely talks to students outside her research group. She will finish her Ph.D in a timely manner but may struggle to get a postdoc because she does not have the big picture or an ability to communicate with others outside her narrow area.

So there is balance between the extremes of John and Joan. Too many distractions is bad. But occasionally a "distraction" can be very helpful. I am not sure how to find the balance.

Harden McConnell was a very successful physical chemist. In the last few years of his life he wrote a fascinating scientific autobiography on a web site. In The Young Scientist - My experiences he writes
 My main blunder throughout my career was a kind of scientific introversion – not paying attention to the scientific work of others. As a stellar example, Clyde Hutchison was starting up research on paramagnetic resonance not many steps away from where I sat in the Eckhardt Physics building of the University of Chicago. It’s never too late to look over your shoulder and see what others are doing, and talk to them.
I thank Steve Boxer for bringing Harden McConnell's site to my attention.

Wednesday, July 29, 2015

Coupled electron-proton transfer: adiabatic or non-adiabatic?

Sharon Hammes-Schiffer gave an interesting talk in Telluride last week about coupled electron-proton transfer.
[A couple of my earlier posts on this fascinating subject are here and here].

Here are a few things that stood out.

There are a lot more people working on this problem now than twenty years ago. This is because of possible solar energy applications.

Diabatic states are the key to understanding. There are four relevant states. Simply the proton can be on the donor or acceptor. The electron can be on the donor or the acceptor. Whether the process is concerted or sequential depends on the relative energy of these four states.

A key question is whether the process is adiabatic or non-adiabatic.
What are the key experimental signatures of each?
One contrast is coupled electron-proton transfer (EPT) and hydrogen atom transfer (HAT).

The two cases are nicely embodied respectively in the model systems
HAT - benzyl/toluene
EPT - phenoxly/phenol
The theoretical details are worked out here.

In some enzymes such as soybean lipoxygenase (SLO) there are very large kinetic isotope effects (~80) for proton transfer, orders of magnitude larger than expected. Many people, including me, have struggled to understand this in terms of proton tunnelling in an adiabatic picture with coupling to an environment. 
However, the relevant reactions are actually coupled electron-proton transfer, in the non-adiabatic regime. The key equation to understand both the magnitude and temperature dependence of the isotope effect is

taken from this paper.

A recent paper compares the theory to a mutant of SLO in which the isotope effect becomes ~500 as a result of the increase in the proton donor-acceptor distance R.

One minor point on how this relates to my talk. I said that quantum nuclear effects [and H/D isotope] effects were largest [and very subtle] in hydrogen bonding for donor-acceptor distances of R= 2.4-2.5 Angstroms. In contrast, here the isotope effects actually get larger with increasing R, with R=2.7 A for the wild-type SLO and increasing to 2.8-2.9 A with the selected mutations. I thank Sharon for pointing out this difference to me.

Monday, July 27, 2015

Quantum biology smells bad

I am skeptical of the grand and speculative claims of "quantum biology". 
There is a nice paper in PNAS which systematically considers the specific claim that smell is based on sensing the vibrational frequencies of particular molecules, and rebuts it from both theoretical and experimental points of view.

Implausibility of the vibrational theory of olfaction
Eric Block, Seogjoo Jang, Hiroaki Matsunami, Sivakumar Sekharan, Bérénice Dethier, Mehmed Z. Ertem, Sivaji Gundala, Yi Pan, Shengju Li, Zhen Li, Stephene N. Lodge, Mehmet Ozbil, Huihong Jiang, Sonia F. Penalba, Victor S. Batista, and Hanyi Zhuang.

I thank Suggy Jang for bringing the paper to my attention.

Thursday, July 23, 2015

Triplet superconductivity in a quasi-one-dimensional metal

Last week I was at Stanford and my collaborators and I finished a paper
Spin triplet superconductivity in a weak-coupling Hubbard model for the quasi-one-dimensional compound Li0.9Mo6O17
Weejee Cho, Christian Platt, Ross H. McKenzie, and Srinivas Raghu
The purple bronze Li_0.9Mo_6O_17 is of interest due to its quasi-one-dimensional electronic structure and the possible Luttinger liquid behavior resulting from it. For sufficiently low temperatures, it is a superconductor with a pairing symmetry that is still to be determined.  To shed light on this issue, we analyze a minimal Hubbard model for this material involving four Molybdenum orbitals per unit cell near quarter filling, using asymptotically exact perturbative renormalization group methods. We find that spin triplet odd-parity superconductivity is the dominant instability. Approximate nesting properties of the two quasi-one-dimensional Fermi surfaces enhance certain second-order processes, which play crucial roles in determining the structure of the pairing gap.  Notably, we find that the gap has “accidental nodes”, i.e. it has more sign changes than required by the point-group symmetry.
Earlier relevant posts are:
Weak coupling can give important insights which describes the renormalisation group method used in the paper and results obtained using it.
Desperately seeking triplet superconductors

We welcome comments.
Hopefully the paper will stimulate experiments to definitively determine the nature of the superconducting pairing.

Tuesday, July 21, 2015

Telluride talk on competing quantum effects

Tomorrow I am giving a talk, "Competing quantum effects in hydrogen bonding: geometric isotope effects and isotope fractionation" at the meeting on Quantum effects in condensed phase systems

Here is the current version of the slides.

The talk is largely based on these two papers

Effect of quantum nuclear motion on hydrogen bonding

Isotopic fractionation in proteins as a measure of hydrogen bond length

Monday, July 20, 2015

Quantum nuclear effects in condensed phase chemistry

I am currently in Telluride for a meeting on Quantum effects in condensed phase systems. Two years ago I attended a similar meeting and in preparing it has been helpful to re-read several posts I wrote stimulated by that meeting.

In my first post, I listed possible quantum effects [zero-point motion, tunnelling, geometric phases, entanglement, ...] and pointed how generally one expects a condensed phase environment [protein, glass, solvent] for a molecular system will tend to reduce these quantum effects by decoherence.

I then asked two big questions.
Are there any instances where the environment can
A. enhance quantum effects?
B. lead to qualitatively new effects (e.g. associated with collective degrees of freedom) that are absent in the gas phase?

I clarified what I meant by a trivial vs. non-trivial enhancement of a quantum effect, from a physics point of view. An example of a "trivial" enhancement is where the environment changes the molecular geometry to enhance the effect. But I stressed that such an enhancement may be highly valuable from a chemistry or biochemistry point of view.

In a comment, Gautam Menon suggested that the Surface Enhanced Raman scattering was a nice example of a non-trivial enhancement. It is certainly spectacular, with enhancements as large as 10^11. However, I am not sure this is the type of quantum effect I am thinking of. The actual mechanism of the effect is still debated [see this paper] and I am not qualified to consider the relative merits of the alternative explanations, but it does look to me like it could be viewed as a semi-classical effect.

Tom Miller suggested to me that the solvation of single electrons and the associated polarons may be a suitable example of B.

I suggested that there were two important organising principles for describing and understanding quantum nuclear effects
1. Competing quantum effects
2. Rate processes can be dominated by rare quantum events.

I am looking forward to the meeting.

Sunday, July 19, 2015

Yoichuro Nambu (1921-2015): spontaneously broken symmetry in particle physics

Yoichuro Nambu died earlier this month, and there was an obituary in the New York Times yesterday. He shared the Nobel Prize in Physics in 2008, and is best known for this paper

Dynamical Model of Elementary Particles Based on an Analogy with Superconductivity. I 
 Y. Nambu and G. Jona-Lasinio

I reproduce the abstract below because it really does summarise the work and is a nice example of a beautifully written abstract.
It is suggested that the nucleon mass arises largely as a self-energy of some primary fermion field through the same mechanism as the appearance of energy gap in the theory of superconductivity. The idea can be put into a mathematical formulation utilizing a generalized Hartree-Fock approximation which regards real nucleons as quasi-particle excitations. We consider a simplified model of nonlinear four-fermion interaction which allows a γ5-gauge group. An interesting consequence of the symmetry is that there arise automatically pseudoscalar zero-mass bound states of nucleon-antinucleon pair which may be regarded as an idealized pion. In addition, massive bound states of nucleon number zero and two are predicted in a simple approximation.
 The theory contains two parameters which can be explicitly related to observed nucleon mass and the pion-nucleon coupling constant. Some paradoxical aspects of the theory in connection with the γ5 transformation are discussed in detail.
I offer a few minor contextual comments, in order of decreasing significance.

1. Nambu's work is a very nice example of the cross-fertilisation between solid state physics and elementary particle physics. Before Nambu's paper it went mostly one way: solid state theorists used field theoretical techniques. However, Nambu showed how significant new insights in particle physics could be obtained from solid state analogues.

2. Before Nambu there was a lot of concern about the fact that BCS theory was not gauge invariant. He clarified this to the point that these objections were considered dealt with. However, I still get confused about this because of subtle issues about the Goldstone boson [associated with the broken U(1) gauge symmetry of electromagnetism] being "renormalised" by the Coulomb interaction leading to gapped plasmons. Even today there is still debate about whether there is a spontaneously broken symmetry or whether superconductors are topologically ordered, as advocated here.

3. One elegant and technical aspect of this paper was that he introduced the Nambu matrices for describing superconductivity. These and the associated Lie algebras naturally generalise to more complicated situations such field theories and superfluid 3He where the order parameter has 3 spin and 3 orbital degrees of freedom. I found this approach incredibly useful when I did my Ph.D thesis on order parameter collective modes in superfluid 3He-B. Some of this is described here.

4. Was Nambu at the right place at the right time?
 In a previous post, Born for success in quantum many-body theory, I noted how more than half of the founders of the application of field theory techniques to solid state physics were born between 1923 and 1926. Nambu was born in 1921.