Condensed concepts

In several posts I have emphasised that Chemistry is local. This is illustrated by the fact that specific bonds within a molecule have approximately the same length, energy, and vibrational frequency regardless of the details of the molecule, particularly the distant parts. This locality leads to useful concepts and theoretical approaches such as Atoms in Molecules , Natural Bond Orbitals , Valence Bond theory . However, this locality is at variance with Molecular Orbital theory and the Kohn-Sham orbitals in Density Functional Theory (DFT); the orbitals can be completely delocalised over the whole molecule. What are the implications for solid state physics? Band theory is the analogue of molecular orbital theory. Bloch electronic wave functions are completely delocalised throughout the crystal. Wannier orbitals are the physics analogue of Boys orbitals in chemistry. In 1984 Phil Anderson wrote: The Wannier functions are still one of the most useful but underutilized methodol

Our natural tendency is to think that to see the effects of Einstein's special theory of relativity you have to be travelling at some significant fraction of the speed of light. However, this is not the case. In solid state physics I am aware of three concrete phenomena that are purely due to relativistic effects. 1. Gold metal is the colour "gold". According to Wikipedia, " non-relativistic gold would be white. The relativistic effects are raising the 5d orbital and lowering the 6s orbital. [11] " 2. Mercury is a liquid at room temperature. This is nicely discussed in a recent  blog post by Henry Rzepa concerning a recent paper  that shows that relativistic effects shift the melting temperature by about 100 K. 3. Magnetic anisotropy and hysteresis in ferromagnets. This results from spin-orbit coupling which is a consequence of relativity.

Here are several interesting and related things about retracted journal articles. 1. Some retracted articles continue to get cited! For example, today I found an interesting reference to this Science paper from 2001, only to learn it had been retracted. Furthermore, Google Scholar shows the paper has been cited several times in the past 4 years.  Indeed, some of the Schon-Batlogg papers are still cited, for scientific reasons, not just as examples of scientific fraud. (For example, this recent JACS ). 2. The Careers section of Nature has an interesting article Retractions: A Clean Slate , which makes the case that if you make an "innocent" mistake the best thing you can do is promptly make a retraction. But, there are some pitfalls. One thing that is still not clear to me is how in some cases one decides between complete retraction, partial retraction, and an erratum. 3. There is a correlation between journal impact factor and the frequency of retractions. Somehow I

One of the many problems of the news media is that they love conflict and controversy. So much so, that they will not just amplify it and feed it, but even create it. This certainly happens with the issue of climate change. This video nicely illustrates the point with humour.  

I have written many posts about what a fascinating, difficult, and important subject water is. I think it is one of the classic hard problems that does not get the attention it deserves. Science increasingly follows the latest fashionable topic that has "low-lying fruit" to pick. Hence, I was delighted to learn last year that NORDITA [Nordic Institute for Theoretical and Atomic Physics] is planning a month long program this year on Water - the Most Anomalous Liquid. I was even happier when I was invited to be part of a "Working Group" in week one to focus on "Quantum effects", led by Tom Markland.  Hopefully this will generate some interesting discussions, science, and blog posts! To increase the visual appeal of this post I searched on Google Images for "water quantum" and got some scary results, including this video marketing the "Quantum BioEnergy water clamp".  I am not sure whether we should laugh or cry!

The figure below introduces the idea of an "entropy crisis" and the Kauzmann temperature in glasses. It also leads to profound and controversial questions about the intimate connection between thermodynamics and kinetics in glasses. Each solid curve shows the temperature dependence of the entropy of a supercooled liquid, relative to that of the crystal, above T_g, the glass transition temperature. T_m is the melting temperature of the crystal. The dashed curves are entropy in the glassy state. The figure is taken from a very helpful review and adapted from Walter Kauzmann's classic 1948 paper. What is going on? The entropy of a liquid is greater than a solid [think latent heat of melting] so Delta S is positive. But, the specific heat capacity of a liquid is also greater than that of a solid [the vibrational, translational, and rotational degrees of freedom are all "softer" and less constrained]. Hence, the slope of Delta S vs. T must be positive. Now,

I sometimes here the following: "I will be on vacation [holidays/leave] next week but I am planning to do some work on the paper". "It turns out things were busier than I thought and I did not get to do much [or anything] on the paper." Vacations are meant to be vacations. Work is for work time. You need the break. Furthermore, trying to simultaneously work and spend time with family or friends is usually stressful and frustrating for everyone involved. Switch off. Take a break and enjoy it. Your productivity when you return will be greater.

There is a very nice paper in Chemistry Education Research and Practice  What is a hydrogen bond? Resonance covalency in the supramolecular domain  Frank Weinhold and Roger A. Klein It relates to issues I have posted about before. In an earlier article Weinhold and Klein reviewed how most introductory chemistry textbooks claim that hydrogen bonding is essentially a classical electrostatic phenomena [some sort of dipole-dipole interaction], in spite of the fact that it is largely due to coherent quantum effects. Similar electrostatics-type assumptions are deeply embedded in the empirical point-charge potentials of widely used molecular dynamics (MD) and Monte Carlo (MC) simulation methods (Leach, 2001). These methods make no pretense to describe chemical bonding and reactivity phenomena, but are widely presumed to adequately describe H-bonding phenomena. The ubiquity of such simulation potentials in many areas of materials and biochemical research tends to reinforce and perpet

Previously I posted about some interesting theory and cold atom experiments that suggest that the spin diffusion constant D has a lower bound of about hbar/m, where m is the particle mass. Coincidentally, on the same day Sean Hartnoll posted a preprint, Theory of universal incoherent metallic transport . Based on results involving holographic duality [AdS/CFT] he conjectures that the diffusion constant satisfies the bound, D ≳ ℏ v 2 F / ( k B T ) where v_F is the Fermi velocity. I have pointed out to Sean that the ratio of this lower bound for D to the cold atom one (hbar/m) is 2 T_F/T where T_F is the Fermi temperature and T the temperature. Thus, the experiments [when normalised for trap effects] and the theory give a value of D about an order of magnitude smaller than Sean's lower bound. [My earlier post also references 2D cold atom experiments that give values for D several orders of magnitude smaller]. Sean raises the issue about how much m and T_F are renormalised b

I just finished a paper A diabatic state model for double proton transfer in hydrogen bonded  complexes Here is the abstract. Four diabatic states are used to construct a simple model for double proton  transfer in hydrogen bonded complexes. Key parameters in the model are the  proton donor-acceptor separation R and the ratio, D1/D2, between the proton  affinity of a donor with one and two protons. Depending on the values of these  two parameters the model describes four qualitatively different ground state potential energy surfaces, having zero, one, two, or four saddle points. In the  limit D2=D1 the model reduces to two decoupled hydrogen bonds. As R decreases  a transition can occur from a concerted to a sequential mechanism for double  proton transfer. I welcome comments and  suggestions.

The New York Times has a nice op-ed piece The Trouble with Brain Science  by Gary Marcus, a psychologist. It is worth reading for several reasons. First, it is a nice accessible discussion of the status and challenges of neuroscience. Second, it illustrates the scientific challenges of understanding emergent phenomena. Third, it highlights some funding/political/stategic issues that are relevant to other fields. The piece is stimulated by controversy concerning the Human Brain Project, "an approximately $1.6 billion effort that aims to build a complete computer simulation of the human brain", funded by the European Commission. The US has also funded a massive project, The Brain Initiative, focussed on developing new measurement techniques. The controversy serves as a reminder that we scientists are not only far from a comprehensive explanation of how the brain works; we’re also not even in agreement about the best way to study it, or what questions we should be asking. .

There is an interesting PLOS ONE editorial about impact factors that ends: With the usual flurry of Impact Factor announcements due to start any day now, it’s a good time to remember that it is the papers, not the journals they´re published in, that make the impact.  It also shows the graph below of the citation distribution for the journal. Note how incredibly broad and asymmetrical the distribution is. I found this interesting because several years ago I wondered what the error bar was on Impact factors , which are often reported to several decimal places. The editorial points out that the distribution is probably broader for PLOS ONE because it publishes articles from a diversity of fields. Hence, I would still like to see distributions from other journals.

Increasingly I hear talk about how different academic disciplines have lost confidence in their identity, autonomy, and legitimacy. They are "in crisis", "have an uncertain future", or "need to re-invent themselves". These concerns range from physical chemistry to political science. For example, yesterday I heard a talk along these lines from David Armitage , Chair of the History Department at Harvard. Generally, I think this anxiety is bad for the discipline and is often for the wrong reasons. Furthermore, those who stay the course will ultimately be successful. Those who get caught up in the latest soul searching re-invention will dissipate their energies on some passing fad. Why do people loose confidence in their discipline and the value of what they are doing? A. Unhealthy comparisons with other disciplines and jealousy. The rates of advance of knowledge vary across disciplines and at different periods of time. There may be a decade where one d

One ingredient to surviving [and "succeeding"] in science is having a few individuals write supportive letters of reference when you apply for jobs, tenure, and/or promotion. Previously, I posted some thoughts about Who should I get to write a letter of reference? Avoid making last minute requests to people. This may lead to hastily written letters, no letter, or just "recycling" of old letters. It is worth thinking about who you may need or want to write a letter for you in the next year or so. Then maintain and/or cultivate that relationship. In particular, that means making sure they know what you have been up to scientifically for the last few years. It is idealistic to think that your former advisor/supervisor has been reading all your latest papers, particularly if (hopefully) you have moved into different areas . Hence, occasional update emails, visits, and chats at conferences are a good investment. I suspect, that one unfortunate consequence of the ris

Physics Today has an interesting review by Noah Graham of the recent book Exploring Quantum Mechanics: A Collection of 700+ Solved Problems for Students, Lecturers, and Researchers , by Victor Galitski, Boris Karnakov, Vladimir Kogan, and Victor Galitski Jr   Galitski Jr points out in the preface, this sort of thorough, detailed collection is a product of “people living and working in completely different times, and they were quite different from us, today’s scientists: with their attention spans undiminished by constant exposure to email, internet, and television, and with their minds free of petty worries about citation counts, indices, and rankings, they were able to devote 100% of their attention to science and take the time to focus on difficult problems that really mattered. ” It looks like a great book.

Acids become weaker in heavy water (Di-Deuterium oxide) than in regular water. The pKa of an acid is a quantitative measure of the strength of an acid, i.e. how readily it gives up protons. pKa is related to the equilibrium constant Ka and Gibbs free energy change associated with the chemical reaction. This is all nicely described on Wikipedia. The figure below [taken from this article ] shows the isotope effect on pKa, i.e. the difference between the value of the pKa in heavy and regular water. There appears to be a rough correlation with the magnitude of pKa, but for most Delta pKa ~ 0.5. The largest value is for neat water (pKa=14). So how is Delta pKa related to zero-point energy? This way of looking at the problem is stated in a 50 year old J. Chem. Ed. paper by Kreevoy who says it allows students to see concrete effects of Heisenberg’s uncertainty principle. It has the nice picture below, for acetic acid, which explains the basic physics. Dissociation of the acid l

Why don't we ever bump students down? When considering final grades for students near a particular cutoff you will hear statements such as: "He got 48 % but he handed in all the assignments and worked really hard. We should bump him up to 50% so he can pass".  "She got 78% but she asked lots of good questions in class so we should bump her up to 80% and give her an A."  This seems reasonable and compassionate. However, if you said something like the following, people might say you were being harsh and unfair. "She got 80% but talking to her showed she really had a superficial understanding and just crammed for the exam. We should bump her down to 79% and give her a B."  "He got 51% but skipped most of the lectures and appeared not to do much work. We should bump him down to 49% and fail him." If we were consistent we would be willing to consider such arguments. Bumping should go both ways. I can think of one related exception to

In 1995 a group of distinguished scientists were asked by Science magazine about outstanding problems that should receive attention in the following decade. The answers are compiled here , and ironically entitled, "Through a glass lightly". Phil Anderson said: The deepest and most interesting unsolved problem in solid state theory is probably the theory of the nature of glass and the glass transition. This could be the next breakthrough in the next decade. Although I know this remains an important problem it has been a bit of a mystery to me. However, my understanding has increased by hearing a couple of nice talks in Telluride by David Reichman.  This has been solidified [pun intended!] by reading a very accessible (and short) review Supercooled liquids and the glass transition by Pablo Debenedetti and Frank Stillinger. I think I now have a crude/basic understanding of a few of the key ideas including defining the glass transition temperature strong versus fragile gl