Condensed concepts

In Telluride last week Peter Rossky gave a nice talk about work in his group on electronic properties and excited state dynamics of conjugated molecules such as PPV used in LEDs and Organic Photovoltaics. One thing he emphasized was that cartoon pictures of these molecules as rigid and planar are not accurate. At room temperature molecules such a PPV can flop around substantially, as described in this paper.

Next tuesday I am visiting the Chemistry Department at University of Washington. I am giving a seminar on "Charge distribution near oxygen vacancies in cerium oxides". It is based on Elvis Shoko's Ph.D thesis work, also done with Michael Smith. A nice summary is in a review article we just published. I will post a copy of the talk when it is ready, but it will be similar to a seminar that Elvis gave at the oral defense of his thesis. At UW I am looking forward to meeting Charlie Campbell and Xiaosong Li. Unfortunately, Oleg Prezhdo will not be there because he is moving to Rochester.

Many interesting chemical processes involve non-adiabatic processes, i.e., they involve transitions between different potential energy surfaces and thus a break-down of the Born-Oppenheimer approximation. Calculating the rate of such processes (even in "toy" models, let alone full electronic structure theory calculations) is a great challenge. One of the most stimulating talks I heard last week in Telluride was by Joe Subotnik. He gave a nice review of this problem and the "Tully problems" used as a benchmark. Strategies for treating the problem with increasing sophistication (and computational cost) are something like: Ehrenfest mean-field dynamics Surface hopping Ehrenfest + decoherence (Prezhdo, Rossky, Schwartz...) Semi-classical dynamics (Miller–Meyer–Stock–Thoss formalism) Partial Wigner transforms (Kapral) Multiple spawning Full nuclear quantum dynamics A recent J. Chem. Phys. paper by Joe also gives a good overview. This is all stuff I need to get a bet

This week I am on holidays (vacation) with my nieces in Portland, Oregon. Yesterday, we went to the Oregon Museum of Science and Industry ( OMSI ). By chance, they had a special visiting exhibit, Einstein: the world through his eyes. It included the medal and certificates for his Nobel Prize (shown above with my nieces) and the original hand-written manuscript for his 1917 paper on general relativity. One thing I always find interesting is how little play his 1905 paper on B rownian motion gets. I agree that for theoretical physics this paper was not as important as the special relativity paper and photoelectric papers of 1905. However, it can be argued that for science I actually think this was the most important paper of the 4 from 1905. After all, this led to Perrin's Brownian motion experiments in 1909 which finally convinced people that atoms really did exist (and recognised in the 1926 Nobel Prize in Physics). Furthermore, the Einstein relation between the diffusion const

The director of the UQ Physics Museum , Norm Heckenberg asked me to give a public lecture marking the centennial of the 1910 Nobel Prize in Physics . Johannes van der Waals received the Prize in 1910 "for his work on the equation of state for gases and liquids". Reading his biography and prize speech (in preparation for the talk on August 17) increased my appreciation for just how significant van der Waals work was, both in itself and in terms of what it led to. His significant achievements include: 1. realising that the gas and liquid are actually the same phase of matter and could be described by the same equation of state 2. the law of corresponding states 3. the Gibbs free energy is the fundamental quantity needed to understand transitions between different phases of matter van der Waals contributions were not just significant in that they provided an explanation for existing experimental data on a diversity of gases but they also led to completely new and unexpected

Today in Telluride I had some free time and so I hiked up the valley towards Bridal Veil falls. It turns out this is a very historic location because it is the location of the worlds first commercial AC power plant . It was built by Westinghouse and Nikola Tesla. This led to " the war of currents " with General Electric Current (headed by Thomas Edison and J.P. Morgan) who were advocating DC power.

At the 2009 Telluride School on Theoretical Chemistry John Tully (Yale) gave a series of lectures on Chemical Dynamics (both quantum and classical). The slides look very clear and helpful.

This week in Telluride I had some really helpful discussions with Dmitry Matyushov . I finally understood a few papers that he wrote a decade ago with Greg Voth and Marshall Newton. I had looked at least one of these paper before when Joel Gilmore and I were modelling decoherence of excited states of biological chromophores. But I did not understand them or fully appreciate their relevance or significance. I can also see the relevance to current work on methine dyes (with Seth Olsen) and on photoactive organometallic complexes (with Anthony Jacko and Ben Powell). In my papers with Joel we made the simplifying assumption (which is a standard one following Hush's treatment of intervalence charge transfer transitions): Assumption*: for the ground to excited state transition in the chromophore the transition dipole moment is much smaller than the difference of the dipole moments between the ground and excited states. This allows a direct mapping of the problem to the independent

On Unjustifiably Misrepresenting the EVB Approach While Simultaneously Adopting It In recent years, the EVB has become a widely used tool in the QM/MM modeling of reactions in condensed phases and in biological systems, with ever increasing popularity. However, despite the fact that its power and validity have been repeatedly established since 1980, a recent work (Valero, R.; et al. J. Chem. Theory Comput. 2009 , 5 , 1) has strongly criticized this approach, while not discussing the fact that one of the authors is effectively using it himself for both gas-phase and solution studies. Here, we have responded to the most serious unjustified assertions of that paper, covering both the more problematic aspects of that work and the more complex scientific aspects. Additionally, we have demonstrated that the poor EVB results shown in Valero et al. which where presented as verification of the unreliability of the EVB model were in fact obtained by the use of incorrect parameters, without comp

To mark its 125th anniversary in 2005, the journal Science highlighted 125 big questions. The ones in the top 25 that relate most to this blog are: How far can we push chemical self assembly? Do Deeper Principles Underlie Quantum Uncertainty and Nonlocality? In the following 100 there is: I s there a unified theory explaining all correlated electron systems? Is it possible to create magnetic semiconductors that work at room temperature? What is the pairing mechanism behind high-temperature superconductivity? Can we develop a general theory of the dynamics of turbulent flows and the motion of granular materials? Is superfluidity possible in a solid? If so, how? What is the structure of water? What is the nature of the glassy state? Are there limits to rational chemical synthesis? What is the ultimate efficiency of photovoltaic cells? Can we predict how proteins will fold? Please scan the lists and let me know what should and should not be there.

Here are the slides for the talk I am giving this afternoon at Condensed Phase Dynamics workshop in Telluride. It is largely based on work done with my former students Joel Gilmore and Jacques Bothma which was published in two papers: Quantum Dynamics of Electronic Excitations in Biomolecular Chromophores: Role of the Protein Environment and Solvent The role of quantum effects in proton transfer reactions in enzymes: quantum tunneling in a noisy environment?

Over the past few years I have heard claims being made that semiconductor quantum dots could be used to make efficient solar cells because they allow multiple carrier generation. The basic idea is that a high energy photon produces multiple excitons (as many as 7 had been claimed) and each exciton then decays into an electron and hole. Thus the quantum yield of charge carriers could be more than hundred per cent and significantly enhance the photocurrent in a solar cell. A review is here. Sounds exciting. Well ..... I learnt from Eran Rabani yesterday that it turns out that these claims of large quantum yields are based on a mis-interpretation of experimental data. Skimming the literature I found this recent paper which notes: uncontrolled photocharging of the nanocrystal core can lead to exaggeration of the Auger decay component and, as a result, significant deviations of the apparent [carrier multiplication] CM efficiencies from their true values. Specifically, we observe that for

There is no substitute for the important information that you gather at a small workshop from personal interaction with people with similar interests. Today, I learnt from P eter Rossky that on The Big Bang Theory Sheldon wears a different T-shirt on each show and that you can see them and buy them here .

As I have discussed in some previous posts, water is amazing stuff. It is also amazing how it continues to be a struggle to understand and to model its basic properties. Today Francesco Paesani (UC San Diego) gave a stimulating talk about his recent work on this problem. Ultimately, he wants to modeling the chemistry of aqueous aerosol surfaces (this is relevant to climate change). Here are a few things I learnt that I found particularly interesting: 67 anomalous properties of water are documented here. What is the structure of liquid water? Two extreme pictures are 1. local orientational order due to strong near-tetrahedral hydrogen-bonds which minimise enthalpy. 2. local orientational disorder characterised by nondirectional H-bonds. A recent PNAS paper that real water actual fluctuates significantly between the two. This is controversial. Is the surface of neat water neutral, acidic, or basic? There is significant controversy about this although some consider a recent C&E New

I am really looking forward to this week at the Telluride Science Research Center for the workshop on Condensed Phase Dynamics. (The scenery should be good too!). In part preparation I re-read a nice review (the 1997 Spiers Memorial Lecture) by Joshua Jortner. This week I hope I can learn more from others on the big questions in the field, from the perspective of theoretical chemistry. Here is a random selection of some of my questions, as a physicist. [Cows are spherical but do have udders....]. Note, the focus is on qualitative differences and on "chemical" dynamics of a system in a condensed phase environment, i.e. a quantum system interacting with a large environment. Can we succinctly state some of the main concepts, organising principles, physical quantities? The spin boson model describes the coupling of two quantum states in the presence of an environment seems to capture a wide range of phenomena. (electron transfer, dynamic stokes shifts, competition between dif

What happens when you make a measurement on a quantum system? Does one have to introduce additional axioms into quantum theory (as Born and Bohr) did to understand measurements? On my last plane trip I read some of a really nice paper, Experimental motivation and emprical consistency in minimal no-collapse quantum mechanics , by Max Schlosshauer . Based on a review of experiments involving SQUIDs and molecular interferometry he argues that: (i) the universal validity of unitary dynamics and the superposition principle has been confirmed far into the mesoscopic and macroscopic realm in all experiments conducted thus far; (ii) all observed ‘‘restrictions’’ can be correctly and comple tely accounted for by taking into account environmental decoherence effects; (iii) no positive experimental evidence exists for physical state-vector collapse "Ohhhhhhh. ... Look at that, Schuster. ... Dogs are so cute when they try to comprehend quantum mechanics." What are the assumptions in this

Australia has just begun their own version of the UK Research Assessment Exercise (RAE). Ours is called the ERA ( Excellence in Research for Australia ). [Although I show my age and the fact that I grew up reading Time magazine because I always think of the ERA as the Equal Rights Amendment ]. Like the RAE the reporting requirements and the associated bureaucracy are onerous. Whether the ERA will end up having the same profound implications as the RAE in the UK remains to be seen. As part of the data gathering I was required to provide the following statistic: the fraction of my publications during 2003-2008 that involved co-authors who were not from my institution. (It turned out to be 40 per cent). I did not get the opportunity to ask whether we wanted this number to be high or low. I realise this is just one of many metrics that will be used to judge research quality. Nevertheless, it seems to me that this metric is a rather problematic measure of research quality. I suspect most g

Stephen Hawking is famously quoted as saying: "When I hear about Schroedinger's cat, I reach for my gun." Today I learnt that this is his version of the famous line, often associated with Nazi leaders: "when I hear the word culture, I reach for my gun" There is a fascinating history on Wikipedia about the actual origin and context of the latter saying in the Nazi play, Schalgeter

When one reads papers about quantum lattice models a key "dogma" that is often implicitly assumed is that a gap in the excitation spectrum (with particular quantum numbers, e.g. triplets) is equivalent to short-range spatial correlations in some corresponding variable (e.g. spin-spin correlations). Finding a rigorous justification for these kind a assertions is hard. However, a paper by Matthew Hastings does it under reasonably general conditions.

I have just started using Dropbox to share files with other people. Ben Powell and I are currently writing a review article together and it is proving extremely useful and pretty much bug free (provided more than one person is not editing a file at the same time!). It saves the need to keep emailing each other the latest version of all the files. It is also a much easier way to share large files and folders than emailing them. Highly recommended.

Things that I think need to be born in mind. In just a few very specific photosynthetic systems quantum coherence has been observed to last less than a psec at liquid nitrogen temperatures. It is far from a universal phenomenon. People have to go to exotic locales (such as the bottom of hot springs in Yellowstone) to find the relevant proteins. Claims that coherence exists at room temperature are based on curve fitting with an excessive number of free parameters. Biomolecules can only perform highly specific functions because they have specific properties. However, the converse does not necessarily apply. i.e., The existence of a specific property in a biomolecule does not imply that the property is then necessary for the function of the molecule. Many photosynthetic systems harvest light without quantum coherence. Evolution optimises function. However, this does not imply that every property of a biomolecule must be optimised for function. Experimental signatures of entanglement

The Dimensions of perfectionism Frost et al., Cognitive Theory and Research 14, 449 (1990) [cited 500+ times] • Excessive concern about making mistakes • High personal standards • Perception of high parental expectations • Perception of high parental criticism • Doubting of the quality of ones actions • Preference for order and organisation An interesting study [which may have never been cited!] I found in ISI but not online claims "Surprisingly, graduate students may procrastinate on academic tasks even more than do undergraduate students. Perfectionism also has been found to be high among graduate students."

Rajiv Singh has a nice clear Viewpoint in Physics, Does quantum mechanics play a role in critical phenomena? It discusses a recent PRL by Anders Sandvik that found some unexpected behaviour (logarithmic corrections to scaling) near the quantum critical point of a Heisenberg model which is the best candidate for deconfined quantum criticality. Many quantum critical points in d spatial dimensions are expected to have properties similar to corresponding classical critical points in d+1 dimensions. So when does quantum physics really matter? Rajiv gives a nice discussion of how quantum interference effects associated with Berry's phases may lead to qualitatively different behaviour. For example, the existence of a critical point where the order parameters O1 and O2 of two physically distinct phases both vanish (as in the figure above) are not expected in classical Landau theory unless parameters are finely tuned.

Hans Frauenfelder (1922-) is arguably the doyen of biological physics. I am told that he considered that for a workshop or conference to be effective one third to one half of the time should be devoted to questions and open discussion. These "Frauenfelder rules" have been rightly adopted by I2CAM as a requirement for any workshops that they fund .

A very effective way to start learning what computational chemistry can and cannot do is to start doing hands on tutorials of concrete examples. Last week, at the I2CAM workshop on photovoltaics, Jeff Reimers ran a hands on workshop where participants calculated photochemical properties associated with charge separation and recombination in a specific donor-acceptor molecule. Here is the tutorial sheet and you can run Jeff's CNDO (Complete Neglect of Differential Overlap) [something like a Hubbard model..] code on the nanohub . Besides being hands on, and very chemically focused, I also like the tutorial because it discusses solvent effects, kinetics, and Marcus-Hush theory.

Something on a lighter note.... This week I helped my dear wife do some science demos for a kids holiday club that our church ran. She found this really cool demo on Steve Spangler science labs: Make your own Vuvuzela sound . You place a nut inside a balloon and can make a sound just like a vuvuzela. Its great!

Shaul Mukamel has a helpful paper, Signatures of quasiparticle entanglement in multidimensional nonlinear optical spectroscopy of aggregates It addresses some important issues that have been discussed (ranted about?) on this blog before. Here is a good paragraph: The fact that exciton states may be delocalized among chromophores is obviously interesting and implies quantum communication between them, provided it survives decoherence effects due to the surrounding medium. One could then justifiably argue that the chromophores are entangled and that the dynamics is profoundly quantum in nature. However, as shown here, these quantum effects can be easily eliminated by basing the description on the delocalized exciton modes. This paper is a concrete realisation of a point Shaul made at a Workshop on Quantum Efficiency in the Black Forest last year. I thank Seth Olsen for bringing the paper to my attention.

A nice gentle review is Molecular Understanding of Organic Solar Cells: The Challenges by Bredas, Norton, Cornil, and Coropceanu. It reviews our limited understanding of five key processes in an organic solar cell (i) optical absorption and exciton formation, (ii) exciton migration to the donor−acceptor interface, (iii) exciton dissociation into charge carriers, resulting in the appearance of holes in the donor and electrons in the acceptor, (iv) charge-carrier mobil ity, and (v) charge collection at the electrodes.

"Only wimps study the general case. Real scientists work through examples." Beresford Parlett This is often quoted by Sir Michael Berry FRS . Although it does not rate a mention on his interesting quotations page. I thank Ben Powell for bringing the quote to my attention.

A key question concerning the cuprate superconductors is what is the relationship between the pseudogap state and superconductivity? I previously posted about some beautiful STM data that shows no change in the excitation spectrum of underdoped cuprates when the temperature increases above the transition temperature. Similar physics is seen in ARPES data and in the thermal conductivity data shown below, taken from this PRL by Doiron-Leyraud et al. The bottom panel shows that the zero temperature value of kappa(T)/T changes little as a function of doping. In a d-wave superconductor this quantity has a universal non-zero value that is determined by the size of the gap. The upper panel shows how the transition temperature varies with doping, vanishing below p=0.05. It is striking that the thermal conductivity suggests that the excitation spectrum is unchanged in the non-superconducting samples. This fact that the thermal conductivity is a powerful probe of the pseudogap state led Micha

The 2010 Boulder School for Condensed and Materials Physics (July 6-30, at the University of Colorado, Boulder) is entitled "Computational and Conceptual Approaches to Quantum Many-Body Systems". This year the School will again employ a webcast system that allows for real-time streaming of video/audio of its proceedings, including all the lectures, questions, answers, and discussions. This is a great resource for people who cannot attend this great event.

This is concerned mostly with applying for postdoc and junior faculty positions. People who must -your current supervisor -your previous supervisor People who may help your cause -someone who does not have a vested interest in your success and so is more objective than your Ph.D supervisor -has a reputation for writing reliable assessments -someone who is personally known and respected by those reading the letter People who should not is someone - who won't get around to sending in the letter -who has a reputation for writing ridiculous inflated letters ("This is the best student I ever had" for every student!) -writes generic letters ("Dr. X is a nice person who does good work.") -who does not really know you -who is at the same level as the position you are applying for As you get more senior you need to be getting letters from people less connected to you (e.g., from institutions you have not worked at) and with increasing seniority and reputation. Some of th

To what extent does computational chemistry actually guide drug design? This came up in the previous post concerning "virtual screening" of candidate molecules for organic photovoltaics. Seth Olsen brought to my attention a nice article, Virtual Screening: an endless staircase, by Gisbert Schneider that appeared earlier this year in Nature Reviews Drug Discovery. Here is part of the abstract: Computational chemistry — in particular, virtual screening — can provide valuable contributions in hit- and lead-compound discovery. Numerous software tools have been developed for this purpose. However, despite the applicability of virtual screening technology being well established, it seems that there are relatively few examples of drug discovery projects in which virtual screening has been the key contributor. Furthermore, the article says: Substantial progress in virtual screening requires a profound understanding of the forces that govern protein folding and the dynamics of macrom

As discussed in a previous post , the efficiency of organic photovoltaic ( OPV ) cells appears to be largely determined by solid state (and thus collective) effects such as aggregation , sample morphology, and disorder. A striking example of this is that the efficiency of a cell can be improved significantly by annealing the thin film (i.e., just taking the film and slowly heating and then cooling it). Hence, efficiency is an emergent property and reductionist theoretical approaches that focus on the properties of isolated constituent molecules have debatable value. At the I2CAM workshop this past week the most disappointing presentation was that from the Harvard clean energy project , led by Alan Aspuru-Gizek . This very ambitious project aims to using the world wide grid of computers (including your own PC) to run quantum chemistry codes to calculate properties of hundreds of thousands of molecules to screen them as candidates for use in OPVs . However, it must be stressed that alm

A really nice talk at the I2CAM workshop on organic photovoltaics this week was the one given by Christopher Bardeen, Exciton Fission and Electronic Delocalisation in Organic Semiconductors. Here, I will just explain some of the beautiful physics of how you can split a singlet exciton into two triplet excitons. First, the group theory. The product of two triplet states can be written Presumably, a similar identity holds for l=1 spherical harmonics. How might this happen in a conjugated organic molecule? The Figure below is taken from a seminal paper by Tavan and Schulten. The singlet Ag- state shown above is "dark" and also plays a key role in photosynthetic systems, as discussed here.

At the conference today, my colleague Seth Olsen gave a talk Stucture-Property Relationships for Conjugated Organic Dyes. The goal is to provide a rigorous quantum chemical justification for empirical relationships such as that shown in the curve above, which shows how the absorption wavelength of a conjugated dyes varies with different substitutions at the point R in the molecule. Much of the talk is based on his recent paper in Journal Chemical Theory and Computation.

Joseph Shinar (Ames Lab, Iowa State) gave a nice talk today about using optically detected magnetic resonance (ODMR) to elucidate the dynamics of optically excited states in conjugated polymers. First, two "human interest" asides. 1. The results of this research led to share prices of some companies going up and down. 2. Shinar said he build his first ODMR spectrometer using an ESR spectrometer he got from a dumpster outside the chemistry building at the Technion in Israel. Basically what one does in this experiment is to monitor an optical property (such as photoluminescence) at the same time that one applies a microwave field and magnetic field. When the microwave field frequency is on resonance with that required to induce transitions between different Zeeman levels on sees changes in the optical property. Seeing any detectable change may be surprising because one does not necessarily expect optical properties to be so spin dependent. It turns out understanding why one g

Today I am chairing a session on charge transport at an I2CAM Exploratory Workshop, Complex Interactions and Mechanisms in Organic Photovoltaics being held here at UQ. I have written quite a few posts on this topic before. I believe some of the key questions concerning charge transport in molecular materials are: What is the mechanism of charge transport? What is the origin of the observed electric field dependent mobility? What determines the relative magnitude of electron and hole mobilities? How does mobility depend on the intermolecular separation and relative orientation? Would thermopower measurements be helpful in determining the charge transport mechanism?