Wednesday, November 30, 2016

Photosynthesis is incoherent

Beginning in 2007 luxury journals published some experimental papers making claims that quantum coherence was essential to photosynthesis. This was followed by a lot of theoretical papers claiming support. I was skeptical about these claims and in the first few years of this blog wrote several posts highlighting problems with the experiments, theory, interpretation, and hype.

Here is a recent paper that repeats one of the first experiments.

Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer Hong-Guang Duan, Valentyn I. Prokhorenko, Richard Cogdell, Khuram Ashraf, Amy L. Stevens, Michael Thorwart, R. J. Dwayne Miller
During the first steps of photosynthesis, the energy of impinging solar photons is transformed into electronic excitation energy of the light-harvesting biomolecular complexes. The subsequent energy transfer to the reaction center is understood in terms of exciton quasiparticles which move on a grid of biomolecular sites on typical time scales less than 100 femtoseconds (fs). Since the early days of quantum mechanics, this energy transfer is described as an incoherent Forster hopping with classical site occupation probabilities, but with quantum mechanically determined rate constants. This orthodox picture has been challenged by ultrafast optical spectroscopy experiments with the Fenna-Matthews-Olson protein in which interference oscillatory signals up to 1.5 picoseconds were reported and interpreted as direct evidence of exceptionally long-lived electronic quantum coherence. Here, we show that the optical 2D photon echo spectra of this complex at ambient temperature in aqueous solution do not provide evidence of any long-lived electronic quantum coherence, but confirm the orthodox view of rapidly decaying electronic quantum coherence on a time scale of 60 fs. Our results give no hint that electronic quantum coherence plays any biofunctional role in real photoactive biomolecular complexes. Since this natural energy transfer complex is rather small and has a structurally well defined protein with the distances between bacteriochlorophylls being comparable to other light-harvesting complexes, we anticipate that this finding is general and directly applies to even larger photoactive biomolecular complexes.
I do not find the 60 fsec timescale surprising. In 2008, Joel Gilmore and I published a review of experiment and theory on a wide range of biomolecules (in a warm wet environment) that suggested that tens of femtoseconds is the relevant time scale for decoherence.

I found the following section of the paper (page 7) interesting and troubling.
The results shown in Figs. 3 (a) and (b) prove that any electronic coherence vanishes within a dephasing time window of 60 fs. It is important to emphasize that the dephasing time determined like this is consistent with the dephasing time of τhom = 60 fs independently derived from the experiment (see above). It is important to realize that this cross-check constitutes the simplest and most direct test for the electronic dephasing time in 2D spectra. In fact, the only unique observable in 2D pho- ton echo spectroscopy is the homogeneous lineshape. The use of rephasing processes in echo spectroscopies removes the inhomogeneous broadening and this can be directly inferred by the projection of the spectrum on the antidiagonal that shows the correlation between the excitation and probe fields. This check of self-consistency has not been made earlier and is in complete contradiction to the assertion made in earlier works. Moreover, our direct observation of the homogeneous line width is in agreement with independent FMO data of Ref. 12. This study finds an ∼ 100 cm−1 homogeneous line width estimated from the low-temperature data taken at 77 K, which corresponds to an electronic coherence time of ∼ 110 fs, in line with our result given the difference in temperature. In fact, if any long lived electronic coherences were operating on the 1 ps timescale as claimed previously (1), the antidiagonal line width would have to be on the order of 10 cm−1, and would appear as an extremely sharp ridge in the 2D inhomogeneously broadened spectrum (see Supplementary Materials). The lack of this feature conspicuously points to the misassignment of the long lived features to long lived electronic coherences where as now established in the present work is due to weak vibrational coherences. The frequencies of these oscillations, their lifetimes, and amplitudes all match those expected for molecular modes (41, 42) and not long-lived electronic coherences.

Monday, November 28, 2016

Polanyi and Emergence before "More is Different"

The common narrative in physics is that the limitations of reductionism, the importance of emergence, and the stratification of scientific fields and concepts were first highlighted in 1972,  by P.W. Anderson in a classic article, "More is Different" published in Science. Anderson nicely used broken symmetry as an example of an organising principle that occurs at one strata and as a result of the thermodynamic limit.

The article was based on lectures Anderson gave in 1967.
The article actually does not seem to contain the word "emergence". He talks about new properties "arising".

I recently learned how similar ideas about emergence and the stratification of fields was enunciated earlier by Michael Polanyi, in The Tacit Dimension, published in 1966, based on his 1962 Terry Lectures at Yale.
The book contains a chapter entitled "Emergence".

Here is a quote:
you cannot derive a vocabulary from phonetics; you cannot derive the grammar of language from its vocabulary; a correct use of grammar does not account for good style; and a good style does not provide the content of a piece of prose. ... it is impossible to represent the organizing principles of a higher level by the laws governing its isolated particulars.
Much of the chapter focuses on biology and the inadequacy of genetic reductionism. These ideas were expanded in a paper, "Life's irreducible structure," published in Science in 1968.

I recently learned about Polanyi's contribution from
The concept of emergence in social sciences: its history and importance
G.M. Hodgson

Here is a bit of random background.

Before turning to philosophy, Polanyi worked very successfully in Physical Chemistry. Some readers will know him for his contributions to reaction rate theory, the transition state, a diabatic state description of proton transfer, the LEPS potential energy surface based on valence bond theory, ...

Polanyi was the Ph.D. advisor of Eugene Wigner. Melvin Calvin, a postdoc with Polanyi, and his son, John Polanyi, went on to win Nobel Prizes in Chemistry.

Google Scholar lists "The Tacit Dimension" with almost 25,000 citations.
The book was recently republished with a new foreword by Amartya Sen, Nobel Laureate in Economics.

Friday, November 25, 2016

Should you quit social media?

The New York Times has an interesting Op-ed. piece Quit Social Media. Your Career May Depend on It, by Cal Newport, a faculty member in computer science at Georgetown University.

When I saw the headline I thought the point was going to be an important one that has been made many times before; people sometimes post stupid stuff on social media and get fired as a result. Don't do it!
However, that is not his point.
Rather, he says social media is bad for two reasons:

1. It is a distraction that prevents deep thinking and sustained  "deep" work. Because you are constantly looking at your phone, tablet, or laptop or posting on it, you don't have the long periods of "quiet" time that are needed for substantial achievement.

2. Real substantial contributions will get noticed and recognised without you constantly "tweeting" or posting about what you are doing or have done. Cut back on the self-promotion.

Overall, I agree.

When I discussed this and my post about 13 hour days with two young scientists at an elite institution they said: "you really have no idea how much time some people are wasting on social media while in the lab." Ph.D students and postdocs may be physically present but not necessarily mentally or meaningfully engaged.

A similar argument for restraint, but with different motivations, is being advocated by Sherry Turkle, a psychologist at MIT. Here is a recent interview.

I welcome discussion.

Thursday, November 24, 2016

The many scales of emergence in the Haldane spin chain

The spin-1 antiferromagnetic Heisenberg chain provides a nice example of emergence in a quantum many-body system. Specifically, there are three distinct phenomena that emerge that were difficult to anticipate: the energy gap conjectured by Haldane, topological order, and the edge excitations with spin-1/2.

An interesting question is whether anyone could have ever predicted these from just knowing the atomic and crystal structure of a specific material. I suspect Laughlin and Pines would say no.

To understand the emergent properties one needs to derive effective Hamiltonians at several different length and energy scales. I have tried to capture this in the diagram below. In the vertical direction, the length scales get longer and the energy scales get smaller.

It is interesting that one can get the Haldane gap from the non-linear sigma model. However, it coarse grains too much and won't give the topological order or the edge excitations.

It seems to me that the profundity of the emergence that occurs at the different strata (length scales) is different. At the lower levels, the emergence is perhaps more "straightforward" and less surprising or less singular (in the sense of Berry).

Aside. I spend too much time making this figure in PowerPoint. Any suggestions on a quick and easy way to make such figures?

Any comments on the diagram would be appreciated.

Wednesday, November 23, 2016

It has dubious origins.

I find this a bit embarrassing because there are many scientists, more distinguished than I, who do not have pages.
When people tell me how impressed they are I tell them the story.

Almost ten years ago some enthusiasts of "quantum biology" invited me to contribute a chapter to a book on the subject. The chapter I wrote, together with two students, was different from most of the other chapters because we focussed on realistic models and estimates for quantum decoherence in biomolecules. (Some of the material is here.) This leads one to be very skeptical about the whole notion that quantum coherence can play a significant role in biomolecular function, let alone biological processes. Most other authors are true believers.

I believe that to promote the book one of the editors had one of his Ph.D. students [who appeared to also do a some of the grunt work of the book editing] create a Wikipedia page for the book and for all of the senior authors. These pages emphasised the contribution to the book and the connection to quantum biology.

The "history" of my page states it was created by an account that
An editor has expressed a concern that this account may be a sock puppet of Bunzil (talk · contribs · logs).
I have since edited my page to remove links and references to the book since it is not something I want to be defined by.

An aside. Today I updated the page because when giving talks I got tired of sometimes being introduced based on outdated information on the page.

Hardly, a distinguished history....

The xkcd cartoon is from here.

Monday, November 21, 2016

The "twin" excited electronic state in strong hydrogen bonds

One of the key predictions of the diabatic state picture of hydrogen bonding is that there should be an excited electronic state (a twin state) which is the "anti-bonding" combination of the two diabatic states associated with the ground state H-bond.
Recently, I posted about a possible identification of this state in malonaldehyde.

The following recent paper is relevant.

Symmetry breaking in the axial symmetrical configurations of enolic propanedial, propanedithial, and propanediselenal: pseudo Jahn–Teller effect versus the resonance-assisted hydrogen bond theory
Elahe Jalali, Davood Nori-Shargh

The key figure is below. The lowest B2 state is the twin state.
In the diabatic state picture, Delta is half of the off-diagonal matrix element that couples the two diabatic states.
Similar diagrams occur when O is replaced with S or Se.

The paper does not discuss twin states, but interprets everything in terms of the framework of the
(A1 + B2) ⊗ bpseudo-Jahn-Teller effect.

It uses TD-DFT (Time-dependent Density Functional Theory). It is contentious how reliable that is for excited states in organic molecules.
The diabatic states are not explicitly constructed.
These issues could be addressed by using higher level quantum chemistry and constructing the diabatic states by a systematic procedure, as was done by Seth Olsen for a family of methine dye molecules.

A video illustrating the length scales of the universe

Sometimes when I speak about science to church groups I show the old (1977) video Powers of Ten which nicely illustrates the immense scale of the universe and orders of magnitude.
I often wished there was a more polished modern version.
Yesterday it was pointed out to me there is, Cosmic Eye.

The phone app can be purchased here for $1. Friday, November 18, 2016 Desperately seeking Weyl semi-metals In 2011 it was proposed that pyrochlore iridates (such as Y2Ir2O7) could exhibit the properties of a Weyl semi-metal, the three-dimensional analog of the Dirac cone found in graphene. Since the sociology of condensed matter research is driven by exotica this paper stimulated numerous theoretical and experimental studies. However, as often is the case, things turn out to be more complicated and it seems unlikely that these materials exhibit a Weyl semi-metal. This past week I have read several nice papers that address the issue. Variation of optical conductivity spectra in the course of bandwidth-controlled metal-insulator transitions in pyrochlore iridates K. Ueda, J. Fujioka, and Y. Tokura There is a very nice phase diagram which shows systematic trends as a function of the ionic radius of the rare earth element R=Y, Dy, Gd, ... Most of the materials are antiferromagnetic insulators. The colour shading describes the low energy spectral weight in the optical conductivity up to 0.3 eV. Blue is an insulator and red actually means a very small low energy spectral weight. N can be thought of as the number of charge carriers per unit cell. Specifically, if this was a simple weakly interacting Fermi liquid N=1. Thus, the value of 0.05 for Pr signifies strong electron correlations. [Unfortunately, the paper talks about this as "weak correlations"]. In fact, as shown below even in the metallic phase at T=50 K one cannot see the Drude peak down to 10 meV. This presents a theoretical challenge to explain this massive redistribution of spectral weight. Slater to Mott Crossover in the Metal to Insulator Transition of Nd2Ir2O7 M. Nakayama, Takeshi Kondo, Z. Tian, J. J. Ishikawa, M. Halim, C. Bareille, W. Malaeb, K. Kuroda, T. Tomita, S. Ideta, K. Tanaka, M. Matsunami, S. Kimura, N. Inami, K. Ono, H. Kumigashira, L. Balents, S. Nakatsuji, and S. Shin This ARPES study does find band touching at the magnetic metal-insulator transition temperature but as the temperature is lowered the spectral weight is suppressed and there is no sign of Weyl points. Phase Diagram of Pyrochlore Iridates: All-in–All-out Magnetic Ordering and Non-Fermi-Liquid Properties H Shinaoka, S Hoshino, M Troyer, P Werner This LDA+DMFT study shows that a three-band description is important for the R=Y compound. This sets the stage for describing the phase diagram above. I thank Prachi Telang for discussions at IISER Pune about these materials and bad semi-metals that stimulated this post. Wednesday, November 16, 2016 Many reasons why you should NOT work 13 hours per day I am very disturbed at how I encounter people, particularly young people, who work ridiculously long hours. Furthermore, it worries me that some are deluded about what they might achieve by doing this. Due to a variety of cultural pressures I think Ph.D. students from the Majority World are particularly prone to this. First let's not debate exactly how many hours is too many or exceptions to the generalisations below. At the end I will give some caveats. Here are some reasons why very long hours are not a good idea. Something may snap. And, when it does it will be very costly. It may be your mental or physical health, or your spouse, or your children, ... Don't think it won't happen. It does. Long hours may be making you quite inefficient and unproductive. You become tired and can't think as clearly and so make more mistakes, have less ideas, and find it harder to prioritise. It is a myth that long hours is mostly what you need to do to survive or prosper in science. I claim dumb luck is the biggest determining factor in getting a faculty position. Furthermore, when I look at people [students, postdocs, facutly] I don't observe a lot of correlation between real productivity and the hours they work. There are other things that are much more important than long hours. Some of these I have covered in posts about basic but important skills. Others include knowing the big picture, giving good talks, ... These are necessary but not sufficient conditions for survival. Yet many who are "lab slaves" seem oblivious to do this. They may have unrealistic expectations about what the long hours will lead to. Some even think long hours are a sufficient condition for survival. You may be wasting a lot of time. Because you can't think clearly and/or just do whatever your boss or manager tells you to, you may spend a lot of time on tasks that have almost no chance of succeeding: poorly formulated experiments or calculations, applying for grants or jobs out of your league, submitting papers to luxury journals, ... There are also all those papers that you or your boss did not finish. You worked long hours in the lab to get the data and then the paper was never brought to completion because you and/or your boss had moved on to the next crisis/opportunity/hot topic. It may rob you of your joy of doing science. It may be an addiction. Workaholism is as dangerous and as costly as alcoholism, drug and sexual addictions. The only difference is that workaholism is often seen as a virtue. You DO have a choice. One of the great lies of life in the affluent modern West is that people do not have many choices. This is exactly what employers and governments want us to believe. A problem is that people make choices [e.g. I have to get a permanent job in a research university, I have to have a big house, I have to send my kids to a private school, ...] that then severely constrain other choices. You may be being exploited. Universities and many PI's love cheap and compliant labour, whether it is grad students, "adjunct faculty" [teaching staff on short term contracts], or "visiting scholars" from the Majority World. A few years from now you may regret it. You may have left academia and realise you could have got your current job without working 3 extra hours a day. Why did you do it? Your spouse [if they are still around] sure wishes you hadn't. How many hours is too many? I don't know. There is significant variability in people's stamina and makeup. There are also differences in personal circumstances [e.g. a single person versus someone with two young children at home]. Different tasks in science [analytical calculations, writing, discussing, device fabrication, computer coding, babysitting experiments, ...] differ significantly in how taxing they are intellectually, physically, or emotionally. Also, there may be certain deadlines or tasks that require long hours for a short period of time [a visit to a synchrotron, monitoring a chemical reaction that takes 18 hours, the last week of finishing a thesis, ...] . This is not what I am talking about. I am talking about an unhealthy lifestyle that does not deliver what it claims to. How do you get out of this? First take a break so you can see more clearly the problem. Set some boundaries. Just say NO! Talk to others about the issue. Aim to work smarter not longer. I welcome comments. Monday, November 14, 2016 Why are the macroscopic and microscopic related? Through a nice blog post by Anshul Kogar, I became aware of a beautiful Physics Today Reference Frame (just 2 pages!) from 1998 by Frank Wilczek Why are there Analogies between Condensed Matter and Particle Theory? It is worth reading in full and slowly. But here a few of the profound ideas that I found new and stimulating. A central result of Newton's Principia was "to prove the theorem that the gravitational force exerted by a spherically symmetric body is the same as that due to an ideal point of equal total mass at the body's center. This theorem provides quite a rigorous and precise example of how macroscopic bodies can be replaced by microscopic ones, without altering the consequent behavior. " More generally, we find that nowhere in the equations of classical mechanics [or electromagnetism] is there any quantity that fixes a definite scale of distance. Only with quantum mechanics do fundamental length scales appear: the Planck length, Compton wavelength, and Bohr radius. Planck's treatment of blackbody radiation [macroscopic phenomena] linked it to microscopic energy levels. Einstein then performed a similar link between the specific heat of a crystal and the existence of phonons: the first example of a quasi-particle. Aside: I need to think of how these two examples do or do not fit into the arguments and examples I give in my emergent quantum matter talk. Wilczek says it is certainly not logically necessary for there to be any deep resemblance between the laws of a macroworld and those of the microworld that produces it an important clue is that the laws must be" upwardly heritable" [This is Wilczek's own phrase which does not seem to have been picked up by anyone later, including himself.] the most basic conceptual principles governing physics as we know it - the principle of locality and the principle of symmetry .... - are upwardly inheritable. He then adds the "quasi material nature of apparently empty space." Overall, I think my take might be a little different. I think the reason for the analogies in the title are that there are certain organising principles for emergence [renormalisation, quasi-particles, effective Hamiltonians, spontaneous symmetry breaking] that transcend energy and length scales. The latter are just parameters in the theory. Depending on the system they can vary over twenty orders of orders of magnitude (e.g., from cold atoms to quark-gluon plasmas). But, perhaps Wilczek would say that once you have symmetry and locality you get quantum field theory and the rest follows.... What do you think? Friday, November 11, 2016 Telling students my personal teaching goals and philosophy It is strange that I have never done this. Furthermore, I don't know anyone who does. Why do this? First, it is helpful for me to think about and decide what my goals actually are, particular relating to the big picture. Second, it will be helpful for students to know. Too often they are guessing. Even worst, I fear that most just assume that my goals are theirs. Then they get frustrated if/when they discover their goals and/or values are different. So here are some goals I could think of. They are listed in order of decreasing importance to me. To help you learn to THINK. To inspire you to learn. To help you see this is a beautiful subject. To help you learn skills that are useful in other endeavors (including outside physics). The help you put this subject in the context of others. To help you learn the technical details of the subject. To be your ally not your adversary . My goals are NOT the following. (Listed in no particular order). To make you happy. To spoon feed you. To make life difficult for you. To get high scores on your evaluations of my teaching. To recruit you as a Ph.D. student to work with me. Have you ever done anything like this? Have you ever been in a class where it was done? Do you know anyone who does it? Are there benefits? Thursday, November 10, 2016 Irreversibility is an emergent property Time has a direction. Macroscopic processes are irreversible. Mixing is a simple example. The second law of thermodynamics encodes universal property of nature. Yet the microscopic laws of nature [Newton's equations or Schrodinger's equation] are time reversal invariant. There is no arrow of time in these equations. So, where does macroscopic irreversibility come from? It is helpful to think of irreversibility [broken time-reversal symmetry] as an emergent property. It only exists in the thermodynamic limit. Strictly speaking for a finite number of particles there is a "recurrence time" [whereby the system can return to close to its initial state]. However, for even as few as a thousand particles this becomes much longer than any experimental time scale. There is a nice analogy to spontaneously broken symmetry in phase transitions. Strictly speaking for a finite number of particles there is no broken symmetry as the system can tunnel backwards and forwards between different states. However, in reality for even a small macroscopic system the time scale for this is ridiculously long. Deriving irreversibility from microscopic equations is a major theoretical challenge. The first substantial contribution was that of Boltzmann's H-theorem. There are many subtleties associated with why it is not the final answer, but my understanding is superficial... This post was stimulated by some questions from students when I recently visited Vidyasagar University. Monday, November 7, 2016 A concrete example of a quantum critical metal I welcome comments on this preprint. Quantum critical local spin dynamics near the Mott metal-insulator transition in infinite dimensions Nagamalleswararao Dasari, N. S. Vidhyadhiraja, Mark Jarrell, and Ross H. McKenzie Finding microscopic models for metallic states that exhibit quantum critical properties such as$\omega/T$scaling is a major theoretical challenge. We calculate the local dynamical spin susceptibility$\chi(T,\omega)$for a Hubbard model at half filling using Dynamical Mean-Field Theory, which is exact in infinite dimensions. Qualitatively distinct behavior is found in the different regions of the phase diagram: Mott insulator, Fermi liquid metal, bad metal, and a quantum critical region above the finite temperature critical point. The signature of the latter is$\omega/T$scaling where$T\$ is the temperature. Our results are consistent with previous results showing scaling of the dc electrical conductivity and are relevant to experiments on organic charge transfer salts.
Here is the omega/T scaling, which I think is quite impressive.

Saturday, November 5, 2016

The role of simple models and concepts in computational materials science

Today I am giving the first talk in a session on Computational materials science at the 4th International Conference on Advances in Materials and Materials Processing.

Here are the slides for my talk "The role of simple models and concepts in computational materials science".

I will be referring the audience to the article such as those mentioned here, here and here that give a critical assessment of computer simulations and stress the importance of concepts.

I welcome comments, particularly as I think the talk could be stronger and clearer.

Thursday, November 3, 2016

Visit to a state university in India

Like everything in India, higher education is incredibly diverse, both in quality, resources, and culture. These statistics give some of the flavour. There are about 800 universities. A significant distinction is between state and central universities. The former are funded and controlled by state governments. The latter (and IITs, IISERs, IISc, TIFR...)  are funded and controlled by the central (i.e. national/federal) government. Broadly, the quality, resources, and autonomy (i.e. freedom from political interference) of the latter is much greater. On my many trips to India I have only visited these centrally funded institutes and universities.

This afternoon I looking forward to visiting the Physics Department of Vidyasagar University. It is funded by the West Bengal state government, and was started in 1981. It is named in honour of Ishwar Chandra Vidyasagar, a significant social reformer from the 19th century.

I am giving my talk on "Emergent Quantum Matter".
Here are the slides.

Update. I enjoyed my visit and interacting with the faculty and students. On the positive side, people were enthusiastic and there were some excellent questions from the students. I want to write a blog post about one question. On the negative side, it is sad to see how poorly places like this are resourced: whether infrastructure, lab equipment, lab supplies, library, faculty, or salaries. For example, there are 5 physics faculty members and they teach a full M.Sc. [2 years course work] to about 100 students. This is 2 courses per faculty per semester and obviously, their expertise is stretched to cover all courses. The Ph.D. students mostly have full-time jobs elsewhere and come in the afternoons and evenings to work on their projects. One travels 2 hours each way on public transport.

Wednesday, November 2, 2016

Hydrogen bonding talk at IIT-Kgp

Today I am giving a seminar, "Effect of quantum nuclear motion on hydrogen bonding" in the Chemistry Department at IIT Kharagpur. My host is Srabani Taraphder.

Here are the slides. The talk is mostly based on this paper.

Tuesday, November 1, 2016

Organic spin liquid talk at IIT-Kgp

Today I am giving a seminar in the Physics Department at Indian Institute of Technology (IIT) Kharagpur,
"Frustrated organic Mott insulators: from quantum spin liquids to superconductors."
Slides are here.

Due to the recent Nobel Prize to Haldane, I included one slide about quantum spin liquids in one dimension.

The talk material is covered in great detail in a review article, written together with Ben Powell.