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Showing posts from June, 2014

The challenge of molecular crystal structure prediction

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Garnet Chan gave a nice talk at the Condensed Phase Dynamics meeting about recent work on the problem of using computational methods to predict the crystal structure of organic molecular crystals. He began with the provocative statement of John Maddox , long-time editor of Nature, that One of the continuing scandals in the physical sciences is that it remains impossible to predict the structure of even the simplest crystalline solids from a knowledge of their composition. I previously posted  about this "scandal". Molecular crystals are particularly challenging because they often form polymorphs , i.e. several distinct competing crystal structures, that have energies differing on the scale of 1 kJ/mol [0.2 kcal/mol ~ 10 meV]. Calculating the absolute and relative energies of different crystal structures to this level of accuracy is a formidable challenge, going far beyond what is realistic with most electronic structure methods, such as those based on Density Function

Talk on Diabatic state models for methine dyes

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Tomorrow I am giving a talk at the Condensed Phase Dynamics meeting in Telluride. The slides are here . It is largely based on two papers with Seth Olsen. A three-state effective Hamiltonian for symmetric cationic diarylmethanes A two-state model of twisted intramolecular charge-transfer in monomethine dyes

Significant advances in quantum chemical simulations of large systems

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Yesterday at the Condensed Phase Dynamics meeting in Telluride there we nice talks by  Eran Rabani  and  Todd Martinez highlighting recent advances they have independently made in simulating large systems. Rabani is largely concerned with solid systems such as silicon nanoparticles and Martinez with hundreds of reacting molecules. Rabani's work with Roi Baer and Daniel Neuhauser is a highly creative and original  stochastic approach to doing electronic structure calculations.  Instead of explicitly determining wave-functions [or Kohn-Sham orbitals in DFT] they use stochastic wave functions [a random phase is assigned to each point on a spatial grid] and compute one-particle expectation values as averages over the ensemble of stochastic wave-functions. For Kohn-Sham Density Functional Theory they obtain sub-linear scaling of the computational cost with system size , as reported in this PRL.  Some of the original problems with the approach [slow converge for systems involving w

Condensed phase dynamics in Telluride

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Last night I was stranded at Denver airport en route to the bi-annual Condensed phase dynamics meeting at the Telluride Science Research Center.  This is the third time I have been to this wonderful meeting. Getting there can be a real hassle. But, then you look at the scenery and enjoy the science and it seems worth it. Unfortunately, due to the travel delays I missed the first two talks, by Joe Subotnik and Nandini Ananth. Dominika Zgid gave a chemist's perspective on "How to make dynamical mean theory quantitative". Some of her work was discussed in a my last  post. Today she mostly discussed a generalisation of iterative perturbation theory as an "impurity solver" for DMFT problems with multiple orbitals. See this preprint. Peter Rossky discussed quantum chemical simulations of exciton dynamics in conjugated polymers. This was motivated by an experiment reported in Science that claimed evidence for quantum coherent transport of excitons alo

Quantum chemistry meets dynamical mean-field theory

I often discuss these two topics, but in separate posts. But, both are concerned with strong electronic correlations; one in molecules and the other in solids. Is it possible to bring them together in a mutually beneficial manner? 1. How could quantum chemistry of finite molecules benefit from DMFT? This is considered in a PRL from Columbia. An earlier post reviewed nice work that used LDA+DMFT to study myoglobin. [See also a recent PNAS ]. Broadly, I think DMFT will be most appropriate and useful in molecular problems that look something like an Anderson impurity problem: a single metal atom with a fluctuating magnetic moment and/or valence that is coupled to a large number of approximately degenerate electronic states. Indeed myoglobin falls in this class. 2. How could DMFT treatments of solids benefit from quantum chemistry methods? Three answers to are considered in a nice JCP by Dominika Zgid and Garnet Chan. A. It provides a way/framework to extend quantum chemica

The case for universal undergraduate exams

My wife's brother-in-law recently introduced me to the idea of the Iron triangle of higher education: at the vertices are the competing demands of access, cost, and quality . Pulling on one corner produces tensions in the other. Furthermore, different stake holders [students, parents, faculty, administrators, politicians] will prioritise one vertex over the others. Aside: the triangle is also discussed in other contexts such as health care. There is a nice essay Breaking Higher Education's Iron Triangle: Access, Cost, and Quality  by John Daniel, Asha Kanwar, and Stamenka Uvalic-Trumbic It partly focusses on the important and complex issue of the massive expansion and aspirations of university education in the majority world. But many of the issues apply to all countries. One of the concrete proposals for evaluating/ensuring quality is separating examinations from teaching institutions. Common exams would be administered by independent authorities/companies [think GR

Are USA universities in crisis?

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I have only slowly come to realise the crisis facing US universities. A tipping point was the release this week in movie theatres of the documentary The Ivory Tower . Seeing that people are willing to pay money to watch a negative documentary suggests there is a ground swell of public concern. A few other things that showed me the extent of the problem are the following. The article,  Universities on the Defensive , by  Hunter Rawlings   a former President of Cornell, and currently the President of the  Association of American Universities , a consortium of 60 of the leading North American universities. The Seattle Times recently ran a front page story about the problems of mushrooming student debt and eight myths about why college costs so much. My UQ economics colleague John Quiggin has a piece in The Chronicle of Higher Education  discussing how inequalities in the US system reflect the broader inequality in society. The table below, taken from another interesting ar

My main criteria for research quality

How does one evaluate the quality of ones own research and that of others? First, acknowledge that this is subjective. Different people have different values, personalities, and background. Here are my values. Most are somewhat interconnected. Not only is the selection of criteria below subjective but how one evaluates each one is subjective and personal. Validity. Ultimately science is about truth and reality. How confident can I be that the results (but also conclusions) actually are correct? Are the results likely to be reproduced? Are they consistent will earlier work and general principles? Of course, one can never be completely confident, but particularly with experience, once is able to weigh up the probability that results will stand the test of time. The more extra-ordinary the claims the greater the evidence must be. Reality. Ultimately, theories must have something to do with real materials and be experimentally testable in some broad sense. Research that claims to h

Deconstructing enzyme mechanism

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Enzymes are amazing molecules. They increase rates of specific chemical reactions by factors as large as a trillion. Without them there would be no biochemistry and no life. Exactly, how they work remains controversial. Broadly they significantly lower the energy of the transition state for a chemical reaction and thus lower the activation energy, Ea. Since the reaction rate scales with exp(-Ea/k_B T), lowering the barrier by one electron volt (23 kcal/mol) has a dramatic effect. But, how is this lowering of the transition state achieved? There is no doubt that simple electrostatic effects can make a major contribution, as emphasised by Ariel Warshel.  From the point of view of quantum physics, this is rather "boring". But, thats good science: going with the best and simplest explanation. However, that is not the whole story, and particularly not for all enzymes. One enzyme that is attracting significant interest is (KSI) keto-steroid isomerase, highlighted by nice work

The funny side of tenure

It is hard to get a permanent job, even for Sheldon Cooper! In some departments when a tenured or tenure-track job opens up there are many internal candidates who have been waiting for this day. Then the machinations and angst begins.... On the plane to the USA I discovered there is a funny episode of The Big Bang Theory, Tenure Turbulence , which details with a scenario like that above of competing internal candidates.

Talk on quantum hydrogen bonds for chemists

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Tomorrow I am giving a talk "Effect of quantum nuclear motion on hydrogen bonding" in the Chemistry Department at Stanford. My host is Tom Markland . Here are the slides . Much of the talk is based on this recent paper. Note that some of the talk is different to one I gave last week in the physics department at UQ. It is important to gear any talk to the backgrounds and interests of the audience.

Government reforms of Australian universities

The Australian government recently announced some major reforms of the funding of universities. Students will have to pay more themselves and universities will be allowed to set tuition at the level they want. As before, tuition is paid for by a loan scheme ( HECS ) that students only pay back in taxation after they start earning above a threshold amount. Interest on the loans will higher than before. Here are a couple of responses from Australian academics. Nobel laureate  Brian Schmidt has an article in today's Australian Students should not shoulder the burden He highlights one of the "dirty secrets" of the Australian system. Student fees are a one-size-fits-all system, where every university gets the same amount of income, This system, after the uncapping of the number of student places allocated to each university in 2012, has led to the perverse incentive that rewards the teaching of large numbers of students at the lowest possible cost. Revenue raised fro

Classification of topological orders

Quantum many-body states such as quantum Hall states, spin liquids, and topological insulators differ from superconductors, superfluids, and anti-ferromagnets in that they do not exhibit spontaneously broken symmetries. The latter is a major organising principle of quantum condensed matter: the broken symmetry can be used to distinguish different states and leads to new low-energy collective excitations (Goldstone bosons). So, how does one characterise and categorise different states without broken symmetries? Topological order has been proposed by Xiao-Gang Wen to be the relevant organising principle. An earlier post considered the role of edge states in such a classification. How does topology enter? 1. Consider a fractional quantum Hall system on different surfaces with different genus (sphere, torus, connected donuts, ...). Then the ground state is degenerate (in the thermodynamic limit) and the degeneracy depends on the genus of the surface. In contrast, if one conside

Teaching undergraduates about quasi-particles

When I first learnt and later taught solid state physics the concept of a quasi-particle only came up in the context of Fermi liquid theory. Yet, quasi-particles are a profound and central concept of quantum many-body theory. Hence, it is important that students be exposed to this idea as soon and as much as possible. I probably slowly started to appreciate this by looking at Phil Anderson's classic Concepts in Solids. It is based on lectures given at Cambridge in 1961-2, and inspired Josephson to invent his effect. The second half of the book is all about quasi-particles. So when teaching "Ashcroft and Mermin" there are several distinct opportunities to introduce quasi-particles, besides in the context of Fermi liquid theory. These are holes, phonons, and magnons in a ferromagnet. The case of holes I discussed earlier. I was both embarrassed and pleased that when I taught magnons this year, one of the students asked, "Aren't these quasi-particles?"

Translating bureaucratic jargon

To support the move to online mode, an extensive communication and change management process is being developed in consultation with stakeholders and UQ-wide communities I had to read this several times. Does this mean "we are going to tell everyone concerned what is happening" ? On a related note, in the Times Higher Education Supplement there is a provocative article A very Stalinist management model that compares current practices in UK universities to those in Stalin's Russia. The author,  Craig Brandist is Professor of cultural theory and intellectual history in the Department of Russian and Slavonic studies within the University of Sheffield. In the print edition the article title was  "My Rallies of Endeavour Will Ensure the Impact Our Dear Leaders Desire."  

Quantum science seminar on hydrogen bonds

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Each week at UQ there is a Quantum Science seminar. This is attended by people working in cold atoms, quantum information, condensed matter, quantum optics, and quantum engineered systems, mostly theorists. I am giving the seminar this week. I endeavoured to write an abstract that might be attractive and comprehensible to a broad audience. Here it is The effect of quantum nuclear motion on hydrogen bonding Most of chemistry can be understood by treating the atoms in molecules as classical particles. Quantum zero-point motion and tunnelling do not play a key role. Important exceptions are molecules involving hydrogen bonding, including water, proton sponges, organic acids, and some enzymes. Quantum nuclear effects are revealed by isotope substitution experiments where hydrogen is replaced by deuterium. I will introduce a simple model for hydrogen bonding [1] based on a two-dimensional electronic Hilbert space that gives potential energy surfaces that can be used to calculate the qu