Saturday, January 31, 2015

NOVA video on emergence

NOVA is a Science TV show on PBS in the USA. 
This is a nice 12 minute segment on emergence, first shown in 2007. It focuses mostly on computing, origin of life, and has brief allusions to flocking.

Readers in the USA can watch a higher quality of the video on the NOVA site.

Friday, January 30, 2015

Spin fluctuation dynamics in bad metals

In a Mott insulator the electrons are localised leading to local magnetic moments that weakly interact with one another via superexchange. This means there is a new low-energy scale associated with spin dynamics. But, at the level of Dynamical Mean-Field Theory (DMFT) there is no superexchange and the local frequency-dependent spin susceptibility is a delta function, as discussed here.

In a Fermi liquid the charge and spin degrees of freedom are both delocalised and the energy scale for spin dynamics Es is defined by the Fermi energy (or coherence temperature). As the Mott insulator is approached Es becomes small, much less than the bare Fermi energy. Furthermore, Es is associated with “kinks” in the quasi-particle dispersion relations seen in Angle Resolved PhotoEmission Spectroscopy (ARPES) experiments on strongly correlated materials. This is discussed in this post which features the graph below for zero temperature.

However, in the bad metal state, it is not clear what the spin fluctuation excitation spectrum is, as it has not been calculated yet. It is not clear to me why, although I know from conversations it is partly due to technical challenges associated with calculating real frequency correlation functions over a wide temperature range. This earlier post discusses the slow spin dynamics in a bad metal when Hund's rule matter.
I am interested in a similar calculation for a single non-degenerate Hubbard model, i.e. how does chi_s(omega) evolve with temperature.

The total spectral weight should be large due to the local magnetic moments associated with the breakdown of Kondo screening associated with the Fermi liquid to bad metal crossover that occurs with increasing temperature.

Understanding and describing the spin dynamics is particularly important, since it will may help distinguish between two alternative pictures of the bad metal,
(i) highly damped quasi-particles or
(ii) almost localised charges with localised spin degrees of freedom,
i.e. is the bad metal closer to a Fermi liquid or a Mott insulator?
In other words, is a wave vector or spatial (waves or particles) picture most appropriate?

Calculations of the specific heat and the uniform static spin susceptibility (using the Finite Temperature Lattice Method) for a Hubbard model on the triangular lattice at half filling, found little change as one went from the bad metal to the Mott insulator. My intuition is that this suggests the bad metal spin dynamics are like those in the Mott insulator, but the only way to clearly show that is through an explicit calculation of chi_s(omega).

Thursday, January 29, 2015

The cheapest and cleanest energy source is efficiency

The Economist has a good editorial
Seize the day
The fall in the price of oil and gas provides a once-in-a-generation opportunity to fix bad energy policies

Governments need to do two main things.
First, cut fuel subsidies. This is particularly important in the Majority world, as this favours the wealthy, who can afford to drive cars. Indonesia has just done this and used the saves to fund education and welfare.
Second, cut subsidies that encourage oil and gas exploration and production, rather than renewables.

There is also a 10 page special report
Let there be light 
Thanks to better technology and improved efficiency, energy is becoming cleaner and more plentiful

The two most striking graphs are those below.

Tuesday, January 27, 2015

Should I apply for this grant?

In a post last year A survival and sanity guide for new faculty I suggested that they should not apply for every grant possible or take on every prospective graduate student. I was asked to write something about what criteria might be used for making these decisions. Here, I will just focus on the grant issue. Hopefully, later I will discuss students.

First, you should acknowledge that you do have a choice. Don't let pressure from others make you think you don't. Alternatives to not applying including waiting for a year, or putting in an application jointly with another colleague.

This is a tricky and subjective issue for which there is no clear answer. Here, I will suggest some questions to ask yourself.

Do I really need the grant?
Do I actually need the money to do the research? Or do I need the grant for career reasons? If you are an experimentalist and have no ongoing funding to pay for supplies such as liquid helium then there is a very good reason to apply. On the other hand if you are a theorist and already have several students, getting a postdoc might be nice, but hardly essential.
If your institution won't give you tenure without this particular grant then you obviously should apply.  On the other hand, if you want to get the grant largely because it is "prestigious", maybe you should give it a miss.

How much work is involved in the application? 
Many applications run to 50-100 plus pages and can take up most of your time for 2 to 4 weeks. Be realistic. It will take longer than you think, particularly if you are inexperienced and don't have administrative/secretarial support. It can also be very stressful trying to write an application while juggling many other responsibilities.

What is the opportunity cost of applying?
Would all this time and energy be better spent doing something else: increasing the quality of a different grant application, writing a paper, actually doing research, spending more time with your current group members, ... going on a vacation! These alternatives may increase your chances with other funding opportunities. These alternatives may also be a lot more worthwhile and enjoyable.

What are my chances of success?
Be realistic. Many grant programs, particularly in the USA, are now down to less than ten per cent. But, it is not completely random. For some applicants, the chances will be significantly higher, for others, even lower. To help evaluate your chances ask,

Do I know someone, particularly a peer, who got one of these grants?
Look at the list of successful previous applicants. Consider their research fields, track records, "visibility", and political connections (especially to the decision makers). Are they comparable to yours?

To help decide, if possible ask the advice of a senior person without a vested interest who will be objective and honest.

I welcome comments and suggestions.

Friday, January 23, 2015

Overselling cross disciplinarity

I wrote a post How (not) to break into a field. Some of those ideas where supported when I recently started reading Paul Krugman's nice little book, The Self-Organizing Economy

Early in the book he notes:
the authors of articles and books on complexity almost never talk to serious economists or read what serious economists write; as a result, claims about the applicability of the new ideas to economics are usually coupled with statements about how economies work (and what economists know) that are so ill-informed as to make any economist who happens to encounter them dismiss the whole enterprise. 
But it does not have to be that way.
Unfortunately, you could replace "complexity" with quantum information theory and "economics" with chemistry, biology, or condensed matter physics.
Or,  astrophysicists and cancer, ... physicists and the origin of life .... string theorists and condensed matter ....

On the positive side, Krugman then discusses some nice simple "economic" models that produce spatial or temporal organisation, and power laws. He also briefly relates what he is doing to ideas of emergence and Phil Anderson.

My only disappointment is that there is no real data in the book. However, if you want to see some real data for scaling laws in economics and finance see this helpful review which contains curves such as the one below.

Thursday, January 22, 2015

Quantum protons in enzymes

A number of proteins involve short strong hydrogen bonds [also known as low-barrier bonds] and there is considerable debate about how important or relevant they are for functionality. A particularly interesting enzyme is KetoSteroid Isomerase (KSI) which features such bonds. Its structure and mechanism has recently been elucidated by some beautiful experiments using mutants near the active site.

There is a nice paper
Quantum delocalization of protons in the hydrogen-bond network of an enzyme active site
Lu Wang, Stephen D. Fried, Steven G. Boxer, and Thomas E. Markland

This is a combined experimental and theoretical study of isotope substitution effects where the protons are replaced with deuterium. This allows one to probe the effects of the zero-point motion of the protons in hydrogen bonds. You can see zero-point energy with a pH meter.

The authors measure the change in the pKa [acidity] with H/D substitution of the different amino acid residues in the active site of KSI. Significantly, they find that for one of the KSI tyrosine's the pKa change is much larger than the change in water. Furthermore, they calculate this change using an ab initio path integral molecular dynamics simulation, obtaining a value in reasonable agreement with experiment.

The large isotope effect arises because of the significant quantum delocalisation of the protons in the H-bond network near the tyrosine's. This is illustrated in the figure below, showing the probability of finding a proton along the co-ordinate associated with proton transfer between the two different tyrosine's [when nu_16=0 the proton is equidistant between the Tyr16 and Tyr57 residues].

The simulation is a real tour de force. It uses a "force field" calculated "on the fly" from density functional theory with the B3LYP-D3 functional.
These simulations treat both the nuclear and electronic degrees of freedom quantum mechanically in the active-site QM region and also incorporate the fluctuations of the protein and solvent environment in the MM region. The simulations consisted of between 47 and 68 QM atoms and more than 52,000 MM atoms describing the rest of the protein and solvent. 
These simulations, which until recently would have been computationally prohibitive, were made possible by 
accelerating the path integral molecular dynamics convergence using a generalized Langevin equation, 
using new methods to accelerate the extraction of isotope effects, and 
exploiting graphical processing units (GPUs) to perform efficient electronic structure theory evaluations through an interface to the TeraChem code. 
Such a combination yielded almost three orders of magnitude speedup compared with existing AI-PIMD approaches.
Being able to perform such detailed stimulations will allow critical examination of controversial claims that short hydrogen bonds and proton tunnelling is a key ingredient in the functionality of specific enzymes.

Wednesday, January 21, 2015

Where is all this blog traffic coming from?

Normally this blog attracts about 700 page views per day, according to blogspot. However, yesterday it got 5000! I have no idea why. Presumably someone with a significant following Tweeted it.
If you know the answer, please let me know, even if you are a robot!

I have not seen a traffic increase like that this since I pointed out that Greg Scholes' "quantum biology" paper in Nature involved fitting 20 data points to a curve with 17 parameters.

Tuesday, January 20, 2015

The baby Natures: exclusivity for the masses

The Economist recently ran a report, entitled Exclusivity for everybody with the subtitle "The modern luxury industry rests on a paradox, but is booming nonetheless."
The paradox is that luxury/status brands such as Gucci, Cartier, Louis Vutton got their name because they were so exclusive [expensive]. But now they are mass produced and mass marketed to middle classes, even in the Majority World.

I realised that this is just what the mother of luxury journals, Nature Publishing Group, has done too. Now everyone can have a Nature paper too!

Monday, January 19, 2015

How does your audience feel?

Last year Physics Today had an interesting article
Psychological insights for improved physics teaching
Lauren Aguilar, Greg Walton and Carl Wieman

It generated a lot of letters in last months issue.
I think it raises some issues that are not thought or talked about enough. Here, I just want to suggest that psychology does play a role in research seminars and conference seminars too. Speakers and their messages are not just judged on their scientific merits. In particular, our views are sometimes influenced by our emotions, positive or negative.

Over the past year I think I have heard talks that have evoked in me responses such as

negative- boredom, confusion, frustration, anger, feeling inadequate, ....

positive- excitement, intellectual stimulation, curiousity, feeling clever, ....

The former can come from talks that are obscure, too technical, poorly prepared, patronising, or full of hype...

I have to confess, that as much a I try to be objective, I think my negative evaluations are amplified by the emotions.

Positive emotions can come from actually learning or understanding something new. Here I have an anecdotal observation. I think I have noticed that some of my colleagues evaluations of speakers, job candidates, and Ph.D candidates is greatly embellished when they learn just one thing from a talk, even if it is something really basic, that they did not know or understand before.

Friday, January 16, 2015

Should funding agencies spread the money around?


The whole process of applying for [and mostly not getting] funding can be very frustrating. Generally, I am empathetic to colleagues who share their disappointments with me. However, there are two situations I am not particularly sympathetic too.

Professor A is well funded and applies for an extra grant and does not get it.

Professor B's grant application is successful but does not receive the full requested amount.

I am even less sympathetic when A or B's spouse complains to me about this.

These decisions need to be considered in a broader context. Funding agencies do have limited budgets and they need to consider what is going to be for institutions and a country in the long term.

Consider the following vignettes of different faculty.

John Smith is 45 and holds multiple grants. He has 3 postdocs and 11 Ph.D students. He publishes in luxury journals.

Sue Jones has been an assistant professor for 3 years and has one Ph.D student, funded with start up funds. She is yet to get an external grant.

Jane Doe is 60 and a member of the National Academy of Sciences. She does not have enough money to hire a postdoc. She often publishes PRLs based on international collaborations.

Joe Blogs is 50, but has not had an external grant for one year. Next year he won't be able to even pay for liquid helium for his lab or travel to conferences.

Steve Sun has tenure, one grant, and two Ph.D students. Occasionally he gets postdocs on external fellowships.

If I honestly look at the quality of the science these faculty are doing it is comparable, particularly if I factor out the hype, luxury journals, and factor in output relative to resources and opportunity. Saying one is better, or more strategic, or promising, is really subjective.

So, who should I fund if I have enough money for only 2 or 3 grants?
It is a hard call.
Consider what would be best for the country and field as a whole.
John will probably just do more of the same, and will power on regardless of whether he gets another grant. It may actually better for everyone if he got more focussed, both on topics and people.
Sue not getting a grant may mean she does not get tenure, which could mean a big waste of her and her universities time and resources. If she limps through, her career may never really take off and she will be a burden.
Given Jane's career experience and wisdom, an investment in a postdoc for her could be a strategic one.
If Joe does not get a grant, his research program may shut down and he will spend the last 15-20 years of his career, not doing any research, but still costing the university a lot of money.
Although an extra grant for Steve would be nice it is not essential to his survival.
If I was making the final call I would probably not give two grants but three smaller grants to Sue, Jane, and Joe.
What would you do?

I hope this illustrates the complexity of distributing funding. On the one hand you want to reward excellence and dot want to promote equity. You want to allow people to expand in to new areas. But you also need to consider things from a broad perspective.

Different countries handle this quite differently. 
In the USA there is a significantly different success rate for "renewals" and new applications. In Australia, there is no such distinction. Traditionally, Canada has given out a lot of small grants, so the success rate is high and most faculty have one grant so they can survive. Most faculty cannot afford to hire postdocs. Yet Canada is moving towards a more "elite" system. In contrast, in Australia, just a few faculty have grants and they are substantial compared to North America. But, funding is becoming even more concentrated among those associated with "Centres of Excellence". In Europe many faculty have a guaranteed level of funding that is associated with their position, until they retire.

My main point is that I think the money should be spread around more than it is most countries. However, to what extent and how I am not sure.

I welcome discussion.

Thursday, January 15, 2015

Satire of reductionism run amok

The "cartoon" below appeared at CERN.
I learnt about it from a commenter on Peter Woit's excellent blog, Not even wrong.

Note, "The problem of condensed matter: they still don't get it".

Friday, January 9, 2015

Born for success in quantum many-body theory?

To succeed you need to be at the right place at the right time.

In my last post I discussed how in his book Outliers, Malcolm Gladwell presented some fascinating cases of how in certain fields those who were successful were all born within a few years of each other. For example, consider the list of 75 most wealthy people in history. 14 of them are Americans born between 1831-1840. The most successful computer entrepreneurs were born between 1953 and 1956.

So I thought I would do a little "experiment" to see if anything like this happened in theoretical physics. In the twenty years after World War Two, a revolution in quantum many-body theory occurred. People applied new methods of quantum field theory to problems in solid state physics and nuclear physics. In principle any scientist between the ages of 25 and 65 could have been involved in that revolution. But, were they?

Without thinking too much I wrote down the first twelve names that came to mind.  The list is below. Then I looked up their dates of birth. Here are the results.

P.W. Anderson; December 13, 1923
Walter Kohn, March 9, 1923
Jun Kondo; February 6, 1930
A. Abrikosov; June 25, 1928
Lev Gorkov; June 14, 1929
J. Luttinger; December 2, 1923
David Pines; June 8, 1924
Keith Brueckner; March 19, 1924
Gerald Brown; July 22, 1926
Freeman Dyson; December 15, 1923
J.R. Schrieffer; May 31, 1931
John Hubbard; October 27, 1931

Pretty amazing to me!

Does this show anything? It is hard to know.
The 1923 crowd were old enough that they had just finished their Ph.D by 1950 when the quantum field theory methods were developed by Feynman and Schwinger, and Dyson did his synthesis. Most were just old enough to have missed combat action (and the associated trauma or death!) in WWII. But, they were young enough to be ambitious and open to new ideas. They were young enough to be not too tied down by teaching or administration so they could finish their 10,000 hours.

Given the surprising results I thought of another revolution: dynamical mean-field theory. Here are some key players and their birth dates.

Walter Metzner; July 21, 1961
Dieter Vollhardt; September 8, 1951
Antoine Georges; ?, 1961
Gabi Kotliar: February 26, 1957
Mark Jarrell; September 19, 1960

I could not find birth dates for Andy Millis or Vlad Dobrosavljević, but based on undergraduate degree I estimated they were both around 1960.

Is it all random?
Is there anything to learn from this?

Thursday, January 8, 2015

What are the ingredients for success in science?

Everyone in my family just finished reading Outliers: the Story of Success by Malcolm Gladwell. I highly recommend it. Gladwell is a gifted writer and tells a great story. The book has led to some lively family discussions.

Gladwell takes a diverse set of social science research and weaves it together into a coherent, compelling, and fascinating tale. In the process he debunks several popular myths about what makes some individuals extremely successful and others not. It certainly contradicts the mantra, particularly in the USA, that "you can be anything you want to be.... just dream it.... work hard ... pull yourself up by your bootstraps...  and it will happen..."

Aside: In the book "success" is implicitly defined narrowly as professional success and public acclaim.  I would prefer a much broader definition. Personally, I think you can be "successful" in that sense and be a "failure" as a human being.

Some of the ideas that Gladwell promotes include:

The Matthew effect.
Opportunities lead to more opportunities that lead to more opportunities.
Why is it that most players in the Canadian National Hockey League were born in January, February, or March?

The 10,000 hour rule.
A necessary (but not sufficient) condition for success in a specialised field/task, whether classical music or computer programming, is to have practised the craft for at least 10,000 hours.

IQ tests are poor predictors of professional success.

Being born at the right time matters.
Being at the right place at the right time matters.
Is it just pure coincidence that the nine most successful computer entrepreneurs [Gates, Jobs, Allen, Ballmer, Joy, Schmidt, Khosla, ..] were all born in the period 1953-1955?

Family background matters.
Why did J. Robert Oppenheimer succeed and Christopher Langan fail?

Cultural background matters.
Why did Korea Airlines have a terrible safety record and Qantas an excellent one?
[Australians are egalitarian and have little respect for authority.]
Why do people descended from rice farming communities perform so well on standardised mathematics tests?

What does all this have to do with science?

1. It you "succeed" don't let it go to your head. If you "fail" don't despair. Don't compare yourself to others.
It has little to do with who you are as a person or how gifted you are.
It has more to do with what opportunities you have been given and being at the right place at the right time. The biggest determinant in landing a permanent academic job is ... dumb luck.

2. I really worry that scientific careers no longer allow people to put in their 10,000 hours. Instead they are chasing quick flashy results, continually reformatting papers to resubmit to luxury journals, chasing grants, or helping their bosses/advisors do these things.

3. We should not promote the myth that students who struggle initially with mathematics and science just "don't get it" and should not keep studying it.

4. Good robust social science research should inform public policy.

My next post will "test" the idea that being born at the "right" time mattered in the history of quantum many-body theory.

Wednesday, January 7, 2015

Why do young people leave academic science?

In most cases it is because they simply don't have the option of continuing. However, now it seems some are leaving because of disillusionment.

Doug Natelson has a thoughtful (and depressing) post Long odds: and how we spend our time. He discusses how he is currently writing three grant proposals that have an approximately 5 per cent chance of success, and raises the question of whether this is really a good use of his time? I would clearly say no. But he and many people in the US system are trapped. Personally I don't apply for anything with a success rate of less than 10 per cent. But in Australia we have the "luxury" that there are programs with a success rate of slightly less than 20 per cent.

But, the main point of this post is to highlight two comments on Doug's post from postdocs who just left academic science because of disillusionment. I think their concerns are justified (and alarming) and I have no answer for them.
This is why (or rather one of the reasons) why I recently left my postdoc in physics and went to industry. I saw how my friends who were PIs would talk about how they never had time to think about new ideas because they were so busy chasing grants (when they weren't advising students, teaching, do administrative work, etc.), and I didn't want that sort of life. You recently talked about sensationalizing in the scientific popular media, but these long odds for grants also of course cause grant-writers to sensationalize the impact and benefits of their own research. This is generally considered "normal" and "necessary", but I believe it's as scientifically dishonest as fabricating data. Scientists are not only the judges of what's scientifically correct or not, but they should also be the judges of what's scientifically important (because who else can judge this besides them?). This latter function of scientists has almost completely been destroyed in my opinion over the course of my time in science with the adoption of business-like ethics that academia has increasingly taken on. I don't know if this new "ethics" is caused by the funding shortfall or whether it is related to a general trend in society of caring less about one's responsibility to society and more about how to advance one's own interests at society's expense, but it's problematic nonetheless. Science needs to be drastically reformed. 
The second commenter writes.
 I agree completely with the anonymous postdoc from above. I also was a postdoc who left academia very recently. On paper, I think I have good enough credentials to get a decent tenure track position (prestigious groups, high h-index, etc.), but instead, I am also leaving academia for the same reasons as Anon1 mentioned. It has become increasingly obvious to me over the last several years that if I stay in academia, I probably will never do any actual good research. I think I have some good ideas, but I just do not think I could ever work well or have the ability to pursue non-safe ideas within the current funding system/climate. And if I do not think that I will be able to do good novel research, what is the point of going into academia? I see both the pursuit of ideas that could have a high chance of failure and teaching students as the goals and benefits of an academic career. But increasingly it seems that playing it safe and spending every waking hour pursuing grant money is what is expected instead, especially when applying to grants with such long odds. I certainly don't think of myself as some sad story of a great researcher who would have changed the world. Quite the contrary - I am just a normal person, and I am also happy with my choice to leave. But I do think that if Anon1 above and I both came to the same conclusion, then there probably is some other person out there who really did have the next great idea, but will leave because our academic research system is changing for the worse. And that is sad.
There is also another sad consequence. Those who remain in academia will tend be those who are content not doing much real science, but are more interested in self-promotion, quite comfortable hyping their research and using students as cheap labour for paper factories. It is just like how some claim university administration tends to attract people who are more interested in power and high salaries rather than in actual teaching, research, and community service.

I welcome comments, particularly from those who have, or are considering, leaving academic science for similar reasons.

Friday, January 2, 2015

Significant blog posts from 2014

Best Wishes for the New Year!

In the past, at the end of each year I have listed my most popular [i.e. most viewed] posts of the year. Unfortunately, on blogspot it is now difficult to figure that out. So, here I list ten of the more popular posts I thought were significant/satisfying.

Is the mobility of protons in water high?

Are there quantum limits to transport coefficients?

Slow spin dynamics in the bad Hund's metal

Seeking definitive signatures of quantum criticality

How 5 years of blogging has changed me

My paper submission strategy

A survival and sanity guide for new faculty

Latest talk on mental health for scientists

Is publishing debatable conclusions now encouraged?

An empirical potential to benchmark computational chemistry for hydrogen bonding?

It is particularly satisfying to me that half of these posts are about deep scientific issues, not just my rants about luxury journals, metrics, neoliberalism, quantum biology, ....

Thanks again to my readers. I really appreciate all the positive feedback and encouragement I receive. But, I still dream of more comments and discussion.

Effective cover letters for faculty job applications

Put yourself in the shoes of a search committee member. They will receive 100 plus applications. Most committee members are not in the same field as you. They are going to quickly skim your cover letter. You need to be clear. You need to get their attention. You need to give them some reason to believe that might want to have you as their colleague.
Here are a few general suggestions. Below I list sites with more specific recommendations.

1. You are applying for a faculty position, not another postdoc.
It should be clear that you have a plan to establish an independent research program, an interest in teaching, an interest in advising graduate students, and a plan to get funding. The more specific the better.

2. A good way to indicate an interest in teaching and in the specific department is to suggest specific courses, both graduate and undergraduate, that you should teach.

3. List a few people in the department who you might collaborate with [especially theorists with experimentalists and visa versa].

4. Don't be too technical about your research. This is difficult because you have two distinct audiences. The first is non experts. You need to show that you are working in an exciting and growing field and are poised to make significant contributions. To the experts you need to show you know your stuff and are proposing realistic and important projects.

This site also has a lot of other useful advice.