Monday, March 30, 2009

Can strong electronic correlations save the planet?

Leone Spiccia (Monash University) gave a really interesting Chemistry seminar today concerning bioinspired manganese clusters for the photocatalytic oxidation of water. This chemical reaction is a key component of producing hydrogen from water for a hydrogen economy. The associated paper is here. The bioinspired material is centred around a cubic [Mn4O4] cluster. A similar (but not structurally identical) cluster is present in Photosystem II (PSII) and is the only known natural system that is able to oxidize water using visible light. These metal-oxide clusters are particularly interesting from the point of view of a strongly correlated electron system. In both the natural and artificial systems there appears to be still uncertainty about basic questions such as:

What is the oxidation and spin state of each of the four manganese ions at each of the stages of the photocatalytic cycle?

Are the electrons localised or delocalised over the manganese cluster?

Modelling of electron spin resonance experiments on the S2 oxidation state (this is just one of the five charge states the cluster takes during the cycle) in terms of Heisenberg model Hamiltonians has provided some constraints on the geometry, valence states, and magnetic interactions. Two papers I found informative are here and here. The second paper found a d electron configuration quite different to that found in similar synthetic systems.

A beautiful review has considered the interplay of electron magnetic exchange and electron transfer in protein metal complexes in terms of the same type of double exchange Hamiltonians that are relevant to colossal magnetoresistance materials.

Overview of some of my research interests

Here are the slides for a talk I gave in Cambridge ealier this year, for the Joint Annual meeting of I2CAM and INTELBIOMAT.

Sunday, March 29, 2009

One of the reasons I started this blog

I could not have said it better than this, taken from the Siris blog.

I consider blogging to be a very informal type of publishing - like putting up thoughts on your door, with a note asking for comments, or like brainstorming sessions. Nothing in this weblog is done rigorously: it's a place for jottings and first impressions. Because I consider posts here to be 'literary seedings' rather than finished products, nothing here should be taken as if it were anything more than an attempt to rough out some basic thoughts on various issues. Learning to look at any topic philosophically requires, I think, jumping right in, even knowing that you might be making a fool of yourelf; so that's what I do. My primary interest in most topics is the flow and structure of reasoning they involve rather than their actual conclusions, so most of my posts are about that. If, however, you find me making a clear factual error, let me know; blogging is a great way to get rid of misconceptions.

Make your Ph.D easier , more productive, and more enjoyable

Some practical suggestions to save (significant amounts of) time

Manage your supervisor, Know the literature, Dont get isolated, Get help, Protect your mental health.

Manage your supervisor

Make sure you have weekly meetings. Set the agenda. Send a report before the meeting. Have questions prepared. Send a summary of the meeting, including action points for each of you.
Don’t wait for him/her to write the paper or to solve a problem. Take control of your project. Respect your supervisors wisdom and experience BUT don’t assume they are infallible.

Don’t get isolated.

Isolation leads to discouragement and often a lot of time going down dead ends. Discussion with and feedback from other postgrads (even when they don’t know what you are talking about) often breaks logjams.

Get help.

From other students, postdocs, lecturers.
Ask them for feedback.
Know the literature. It can save you a LOT of time, trying to reinvent the wheel.

Protect your mental health

Depression, stress, and anxiety is a common problem among your demographic group: highly gifted and busy people.

Read “A Ph.D is Not Enough!” by Peter Feibelman.

Friday, March 27, 2009

Emergence, chaos, and complexity in chemistry

The first issue of the new journal Nature Chemistry has a nice "thesis" article by Bruce C. Gibb suggesting that chemists may benefit from a greater engagement with chaos theory. The article mentions the most famous example of nonlinear dynamics in chemistry: the Belousov-Zhabotinsky reaction and I followed the link to the beautiful videos on YouTube.

Perhaps due to space limitations, the article did mention that Prigogine received the Nobel Prize in Chemistry in 1977 for developing the theory of such non-equilibrium states or "dissipative structures". A nice accessible introduction is in the undergraduate text, Modern Thermodynamics, chapter 19, by Dilip Konderpudi and Ilya Prigogine (Wiley, 1998).

These non-equilibrium states illustrate several important points

* complex spatial and temporal patterns can emerge from simply local dynamics

* the nature of the emergent structure is independent of most of the specific details of the chemical and physical composition of the components

* open systems do not always tend towards homogeneous and static equilibrium states
(i.e., the second law of thermodynamics does not preclude the emergence of order)

Take a notebook to seminars! You are not James Watson!

Quite a few graduate students don't bring a notebook to seminars or group meeting and just listen. Are they just putting in time?
I always take some notes, partly to help me concentrate and stay engaged. As I struggle to follow along or see the point, I try to write down a key idea, claim, or question that the speaker or topic is raising. This helps me get something out of the talk. I hope to do some of this in future blogs. Students not taking notes, reminded me of a story from the Double Helix, by James Watson. Crick got quite upset at Watson because he went to a seminar by Rosalind Franklin, but could not remember a crucial detail because he did not take notes. Nevertheless, they still worked out the structure of DNA!

Thursday, March 26, 2009

Walter Kauzmann (1916 -2009): the master of thermodynamics

Walter Kauzmann was a pioneer in understanding condensed phases of matter. Two of his most important contributions to science (the hydrophobic interaction and a paradox concerning glasses) were made using his profound understanding of thermodynamics. He first introduced the notion of a hydrophobic interaction. Before any structures of proteins were known he deduced solely from thermodynamic data on the solvation of small organic molecules that a protein must fold so that the non-polar amino acids are predominantly in the centre of the protein. I discuss this in a lecture I often give to undergraduates at the University of Queensland in the course PHYS2020: Thermodynamics and Condensed Matter Physics.

Kauzmann wrote a beautiful article, Reminiscences of a life in protein physical chemistry, that I warmly recommend. One point he makes repeatedly in the article is that in science (and life) people will often believe what they want to believe rather than what the evidence before them suggests they should believe. The article recounts some of the "silly" things (from the perspective of our knowledge today) people believed about proteins in the 1950's, and how reluctant the advocates of these theories were to give up on them. Those of us trying to understand complex materials today, and especially biomolecular function, should be sobered and chastened by this lesson from history.

Kauzmann co-authored with David Eisenberg the definitive monograph on water and a beautiful "ancient" text, Quantum Chemistry (1957) which I found extremely helpful as an undergraduate and today.

Bruce Alberts testifies to Kauzmann's personal legacy in this fascinating article where he describes how Kauzmann mentored him. Alberts is currently the Editor in chief of the journal Science, a former past president of the National Academy of Sciences in the USA, and a co-author of the definitive text, The Molecular Biology of the Cell.

More about Kauzmann's life is available here. I was privileged to have some personal interaction with him, while a graduate student (in physics not chemistry) at Princeton, because he was a long-time friend of my late father. However, I did not realize what a great scientist he was and how much I could have learnt from him. Back then I was a some-what narrow-minded physicist who had not developed a fascination with problems at the interface of chemistry and physics. Youth is wasted on the young!