Condensed concepts

Brian Martin  has a helpful article  Countering supervisor exploitation  that considers the problem of Ph.D students and junior researchers being expected to include inappropriate co-authors in their publications. In some cases their work is completely stolen by superiors. Martin has practical and realistic advice including the options of acquiesce, leave, complain, or resist. He also gives the wise advice of clarifying the issue of co-authorship criteria and the senior persons track record on the issue before joining a research group. Based on my limited and anecdotal experience, I fear these problems are more prevalent than is acknowledged, and they are getting worse. I add a few other dimensions to this problem of inappropriate co-authorship. First, senior people are not always the problem. Sometimes it is junior people who want to include honorary senior co-authors because they think that will "curry favour" with them or increase the chance of the paper being publ

I have heard it claimed that some string theorists say that the theory does make experimentally testable predictions because it predicts gravity! I think this is silly because it is a postdiction or retrodiction , i.e., one is explaining already known phenomena not suggesting new experiments. However, we should not just make fun of string theorists, because most of us actually do it to! For example, "our LDA calculations predict a bond length of 2.145 Angstroms, compared to the experimental value of 2.15 Angstroms"  "our numerical simulations for this Hubbard model predict a superconducting transition temperature of 150 K." I do it too! In my latest paper I just counted 11 times where I wrote things like "our model predicts….". Yet in every case it concerns quantities that have already been observed. Why do we use "predict" like this? My guess is that it is because once we write down some model Hamiltonian and make some sort of approx

There is an interesting JACS article Are There Really Low-Barrier Hydrogen Bonds in Proteins? The Case of Photoactive Yellow Protein Marc Nadal-Ferret, Ricard Gelabert, Miquel Moreno, and José M. Lluch Low-barrier hydrogen bonds are characterised by an energy barrier to proton transfer that is comparable to the vibrational zero-point energy. As a consequence the proton is delocalised between the donor and the acceptor atoms. Previously I posted about the general issue of whether these bonds exist in proteins, and more importantly whether they have a functional role. Before I started working on H-bonds I wrote a post about new experimental studies claiming that the photoactive yellow protein has a low barrier H-bond (LBHB). The relevant geometry and the two relevant H-bonds [2.52 and 2.56 Angstroms] are shown below. The key issue this JACS paper addresses is in several very recent papers, Saito and Ishikita  (33-35)  have claimed that …  the chemical properties of the  p CA··

In the conservative Australian magazine Quadrant there is a provocative piece  Why Australian universities are just not good enough , by James Allan, a Professor in the law school at University of Queensland. It pains me to admit that some of his criticisms and concerns are largely accurate. Allan is to be affirmed for bringing some of these issues to public debate. Whether, some of provocative language will help is debatable. Some of the problems I have highlighted previously on this blog. But he also makes a good case that some of the problems are particularly worse in Australia than other countries. The problems [many of which are inter-related] include: lack of mobility of undergraduates [students just go to the best university in their home city] leading to a lack of real competition between universities within major cities large first year classes   an acceptance of students doing part-time paid work that distracts from studies centralised decision making leading to obscur

A previous post considered the large orbital magnetoresistance observed in PdCo2  and reported in a recent  PRL . The magnetoresistance depends significantly on the direction of the intralayer field. Below I show the results of a very simple model calculation, that explain several key features of the observations. The essential physics of the model was mentioned in the PRL, but the authors reported a full numerical calculation of the magnetoresistance. The outer hexagon below is the first Brillouin zone within the layers. The inner green hexagon is the Fermi surface.  The observations explained by the model include: the magnetoresistance for intralayer fields can be orders of magnitude larger than fields perpendicular to the layers, for fields in the [110] direction the magnetoresistance saturates at high fields [but, it looks like the experimental value is larger than the predicted value of 200%] and the resistance will decrease monotonically with decreasing temperature,

This morning I am giving a talk on mental health for scientists at CSIRO at Dutton Park , just over the river from UQ. Here are the slides. It is similar to a talk I have given before. I have added a personal disclaimer slide. Sad that I feel that I need to do that. On the subject, there was recently a pretty disturbing article on the Guardian website about mental health issues in UK universities, particularly among Ph.D students.

UNESCO has declared 2014 the  International Year of Crystallography . This is to mark 100 years since Max von Laue got the Nobel Prize for discovering diffraction of x-rays by crystals. The International Union of Crystallography has produced some nice educational resources for the occasion. But, I actually prefer this video from the Royal Institution for the Bragg centenary last year. Due to the involvement of UNESCO there are initiatives to promote crystallography in the developing world. The map below highlights the problem, and shows how science is so under-resourced in Africa. They are also highlighting how crystallography can aid the development of new materials relevant to pressing issues of clean water, food security, renewable energy, health, and green industry. Although this is true I have mixed feelings about this. Scientific and technological breakthroughs could potentially help the Majority World in this way. However, the main obstacles to addressing many of thes

I think double proton transfer can be pretty amazing. The picture below shows two possible quantum states of a porphycene molecule. Note two things. First, the two states differ by the location of the two hydrogen atoms [protons]. Second, the location of eight of the double bonds is different. At low temperatures the ground state of the molecule is a linear superposition of the two states. The definitive signature of this is the tunnel splitting of the vibrational states, as shown above. This is seen experimentally, as reported here. At higher temperatures does not see a splitting and there is a temperature activated conversion between the two tautomers. The ground state can be written as a superposition of two Born-Oppenheimer states [products of nuclear and electronic wave functions]  Psi = |L>|A> + |R>|B> where |L> and |R> are the two nuclear states and |A> and |B> the two electronic states.  These are approximately orthogona

Dumb luck. Over the years I have seen some very impressive people not get permanent jobs and some less able scientists who did. What is the difference? I feel that sometimes it is just a matter of being at the right place at the right time. There are many "random" factors that affect both the global and local availability of positions: the economy, changes in government policies, new funding initiatives, new discoveries, new fashions, expanding or shrinking budgets, geopolitical events, changes in Deans and Department Chairs, the whims of influential individuals, retirement or resignation of individuals, .... All of these factors are beyond your control. If you accept this strong random element to the process there are some important corollaries I discuss below. But, first a qualification. I am not claiming it is totally random and that everyone has an equal chance. For the top few per cent of postdocs [world wide] it is almost a certainty they will get a job. For t

Hydrogen bonding represents a particular challenge to computational quantum chemistry. The figures below show the energy of two different "proton sponge" molecules as a function of the position of a proton as it moves between the donor and acceptor. They are taken from a nice paper I blogged about before. The different curves correspond to different "levels" of theory and methods. MP2 stands for second-order perturbation theory (Moller-Plesset) beyond Hartree-Fock. The other four methods involve density functional theory [DFT] with different functionals. The different methods give significantly different values for the energy barrier [or whether it exists all] and the positions of the minima. Which method is "correct", i.e. the most reliable? How does one decide? What can one benchmark against? Higher level quantum chemistry [e.g. multi-reference methods] are not possible on large molecules. Do these differences matter? After al

About twenty years ago I applied for my first grant. The science section was about 10 pages and that took me a couple of months to write since I was a novice. The admin. stuff and CV was probably an extra 10 pages. Before I submitted it the Director of the university "Research office", a career administrator, looked it over and suggested a couple of cosmetic changes. In todays dollars, the grant was about $120K per year for 5 years. That did not include overhead, which seemed to be a secret between the university and the government. A couple of years later I applied for another grant to hire a postdoc for 3 years. A month after I submitted the application I realised that in the rush I had forgotten to include my publication list in the application. I wandered over to the Research Office, which was located in a house just off campus. I apologised for my mistake and asked them if they could do anything. They contacted the funding agency who said "no problem. just send th

Last week lithium batteries kept coming up. Chandra Varma wrote a cursory piece Mott Physics, Mixed Valence, Oxygen Valence, in Lithium ion batteries  at the Journal Club for the Condensed Matter Physics. He pointed out that these batteries use some materials involving cobaltate [CoO2] layers similar to those in superconducting sodium cobaltate. Furthermore, insights are being gained from ARPES. But, I struggled to see the way forward for any significant involvement of quantum many-body theorists. The most useful connection was the figure below in the article that Chandra reviews. I would think that LDA+DMFT calculations would be ideal for addressing whether these cartoon pictures are correct. One question will be the role of Hund's rule coupling. The Economist had an article about Tesla motors which makes electric cars and is really trying to develop the lithium battery technology further. The company stock capitalisation is now half that of General Motors! But GM se

I love the Solid State Simulations software for teaching. Unfortunately, it is getting increasingly difficult to install on the latest operating systems. I have it running o.k. on my Mac. But the students in my class can't get it to install on Windows 8. If anyone has overcome this obstacle, please let us know how.

Each time I teach a course I realise there is some particular intellectual challenge for students that I take for granted because the issue has become so second nature to me. As an undergraduate I don't think I really learnt, or was taught, to make orders of magnitude estimates and then consider their consequences. I never took a course in solid state physics. I learnt every subject in a precise manner, more like applied mathematics. Perhaps, physics was not taught that way. But that is certainly how I learnt it. It was only when I went to graduate school in the US , that I had to learn to deal with orders of magnitude estimates. Indeed in the General Exam [qualifying Ph.D exam after 2 years] at Princeton there was a whole section called General Physics that did this kind of stuff. You can see some of the questions in this book.  I actually think that learning to solve these type of problems was one of the most useful things I learnt during my whole Ph.D. This is the first step i

I few times I have posted scenes from the TV show, The Big Bang Theory, that involved actual science such as topological insulators , spin ice , graphene , debunking quantum biology , or the Born-Oppenheimer approximation. Unfortunately, I think the past few years the show has degenerated into the typical Hollywood sitcom, focusing on "who is dating who now", titillation, and inane crude humour. However, I saw a great recent episode where Sheldon proposes the existence of a new superheavy element which is subsequently "discovered" by a Chinese research group. It turns out he made simple error in the units he used in his calculations and the Chinese group fabricated their results... This is actually reminiscent of a real fraud committed by at Berkeley and Darmstadt by Viktor Ninov who fabricated data and claimed the discovery of new elements. A recent case of scientific fraud at UQ made it onto the local TV news . Unfortunately, the video date has expired

There is a very interesting PRL Extremely Large Magnetoresistance in the Nonmagnetic Metal PdCoO2 Hiroshi Takatsu, Jun J. Ishikawa, Shingo Yonezawa, Harukazu Yoshino, Tatsuya Shishidou, Tamio Oguchi, Keizo Murata, and Yoshiteru Maeno This is a highly anisotropic metal with a layered crystal structure. The authors measure the interlayer resistance as a function of the magnitude and direction of a magnetic field parallel to the layers. In the abstract of the paper I have highlighted statements for which I give a different perspective, below. Extremely large magnetoresistance is realized in the nonmagnetic layered metal PdCoO2. In spite of a highly conducting metallic behavior with a simple quasi-two-dimensional hexagonal Fermi surface, the interlayer resistance reaches up to 35 000% for the field along the [1-10] direction. Furthermore, the temperature dependence of the resistance becomes nonmetallic for this field direction, while it remains metallic for fields along the [11

In last months Physics Today Steve Hagen has a very interesting and informative review of the book, Biophysics: Searching for Principles  by William Bialek. He begins, that the title of the book, makes an important point: Even the top practitioners in the field do not completely agree on its main principles or where to find them. He then describes some different perspectives, including those enunciated in leading texts, such as Phil Nelson's wonderful book [I have used it in a course and blogged about it before]. He then goes on to describe two of Bialek's principles. sensory and regulatory systems have mechanisms for managing thermal noise, particle number fluctuation, and other types of background, and that t hose mechanisms in many cases reduce noise almost to its fundamental physical limits. Examples include reaction dynamics in photosynthetic enzymes, bacterial chemotaxis, embryonic development, and bat echolocation. the principle of efficient representation, t

Unfortunately, I would say yes. I find it discouraging that some papers contain rambling speculative sections, particularly about connecting theory and experiment, However, what I did not know until today is that it is even possible to publish literal computer generated gibberish. This was described in Nature last week Publishers withdraw more than 120 gibberish papers "Conference proceedings removed from subscription databases after scientist reveals that they were computer-generated." The relevant papers were not just in some unheard of "spam" "journal" or "conference", but ones that were published by Springer and IEEE. The fraud was exposed by a computer scientist, Cyril Labbe. Labbé is no stranger to fake studies. In April 2010, he used SCIgen to generate 102 fake papers by a fictional author called Ike Antkare. Labbé showed how easy it was to add these fake papers to the Google Scholar database, boosting Ike Antkare’s h-index , a