Saturday, July 31, 2010

Floppy organic LEDs

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.

A sleepless seminar in Seattle

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.

Thursday, July 29, 2010

Jumping from one surface to another

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 better handle on ....

Wednesday, July 28, 2010

The next Einsteins?

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 Brownian 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 constant and viscosity was the first example of a fluctuation-dissipation relation.

Monday, July 26, 2010

A century after van der Waals Nobel Prize

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 scientific insights and discoveries, including:

a. the law of corresponding states led to some of the most important concepts in theoretical physics today: universality, scaling, and the renormalisation group.

b. the law of corresponding states guided Kamerlingh Onnes to the liquification of hydrogen and helium. this led to the discovery of superconductivity and superfluidity.

c. van der Waals theory of binary mixtures highlighted that the Gibbs free energy is the key quantity for understanding phase transitions.

d. the hypothesis of the van der Waals force for non-polar molecules (a residual attractive interaction between neutral spherical and uncharged atoms such as helium and argon) was explained by Fritz London and Eisenschitz in 1930, following the development of quantum theory. Their use of the notion of interactions mediated by virtual transitions turned out to be a foundational idea in quantum field theory where low-energy interactions are determined by high-energy states and processes.

Sunday, July 25, 2010

AC or DC?

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.

Saturday, July 24, 2010

Lectures on chemical dynamics

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.

Solvent-chromophore interactions

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):
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 boson model and exact evaluation of the full time dependence of the reduced density matrix (and thus the optical absorption lineshape) for any coupling to the environment.

Some consequences of the analysis are that:
  • the absorption and emission lines obey the mirror image rule
  • in the "high" temperature limit (which is reasonable for most solvents at room temperature) the line width is proportional to the Stokes shift and to the temperature
However, the chromophores of interest (those that occur naturally or are used to tag biomolecules) are of interest because they are bright (i.e. they have a large transition dipole moment) and so Assumption * is actually not true.

This large transition dipole moment is a natural consequence of the fact that the transitions with large oscillator strengths are coherent charge transfer transitions.

This turns out the reason why often the mirror image rule is not satisfied. In particular, the emission line can be substantially narrower than the absorption line, and they have different shapes. It also explains why one often sees vibronic structure in emission spectra but not absorption spectra. This paper discusses the basic effects of the electronic delocalisation associated with the transition dipole moment.

I think one must then modify the independent boson model to include off-diagonal terms coupling the boson bath to the two-level system. That Hamiltonian can then be transformed to a spin-boson model (at a non-zero bias) with diagonal coupling to the bath. That is then a highly non-trivial problem to solve.

Dmitry did not consider that problem but the physically relevant and analytically tractable one with the limit that:
  • the reorganisation energy is much less than the transition energy[this just means one can clearly resolve the absorption and emission bands]
  • the solvent degrees of freedom are treated classically.
There turns out that there is another effect which needs to be taken into account to get a quantitative description of line shapes: that the polarisability of the ground and excited states is not the same. This effect actually acts in the opposite direction to that of the transition dipole moment.

With this analysis Dmitry and Marshall Newton were able to obtain a quantitative description of the lineshapes of both emission and absorption for the dye Coumarin-153 in a wide range of solvents.

Friday, July 23, 2010

Best paper title and abstract ever?

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 comparing to the correct surface obtained by our program.

Big questions in science

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:

In the following 100 there is:

Is 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.

Thursday, July 22, 2010

Limited role of quantum dynamics in biomolecular function

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:

Wednesday, July 21, 2010

Deconstructing claims about multiple carrier generation in quantum dots

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 the same sample, apparent multiexciton yields can differ by a factor of 3 depending on whether the nanocrystal solution is static or stirred.
I guess it goes back to "extra-ordinary claims require extra-ordinary evidence". It cannot be emphasized enough the importance of checking results and on considering alternative explanations for data, rather than uncritically embracing the interpretation we (or others) hope to be true.

Tuesday, July 20, 2010

Important things you learn at workshops

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 Peter 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.

The challenge of water

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 News story: Storm in a teacup amplifies the controversy [in the time honoured tradition of journalism].

One really needs to include quantum nuclear dynamics to realistically model water.
Classical molecular dynamics with the standard force field gives a melting temperature of 215 K.
To do quantum dynamics one needs a high quality potential energy surface extracted from high level quantum chemistry on the water dimer. This pairwise interaction is about 85 per cent of the total interaction. One can then try to get the rest of the interactions from explicit polarisation.

Francesco then calculated a wide range of properties including the lineshapes of infra-red spectra and three-photon echo vibrational spectra.

He then considered the controversial question of how do hydrogen bonds form and break in liquid water.
This aims to test a proposal of Laage and Hynes for a:
water reorientation mechanism involves large-amplitude angular jumps, rather than the commonly accepted sequence of small diffusive steps, and therefore calls for reinterpretation of many experimental data wherein water rotational relaxation is assumed to be diffusive.

Monday, July 19, 2010

Condensed phase quantum dynamics

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 different time scales). Are there any cases of a two-state system in a condensed phase where it fails qualitatively? (e.g., because it treats the environment in the harmonic approximation)

When does the quantum nature of the environment lead to qualitative differences in the chemical dynamics?

How does the environment modify dynamics (e.g. internal conversion) associated with a conical intersection between two potential energy surfaces?

Is any progress being made in defining systematically quantum-classical boundary in QM-MM mechanics? Could entanglement measurements provide objective criteria?

Saturday, July 17, 2010

No-collapse quantum theory

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 minimal theory?

First, a completely known (pure) state of an isolated quantum system is described by a normalized state vector in a Hilbert space.

Second, the time evolution of a state vector is given by the time-dependent Schrodinger equation.

No mention is made of measurements in this formulation. Instead, measurements are described without special axioms in terms of physical interactions between systems described by state vectors (wave functions) and governed by suitable interaction Hamiltonians. Observables then emerge as a derived concept.

Basically, I agree with these and it is nice to see the arguments set out so clearly. On the other hand, I don't follow some of Max's arguments about the amount of entanglement in the macroscopic states that he discusses.

Friday, July 16, 2010

A poor metric of research quality

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 good researchers will be somewhere in the range of 30 to 70 per cent. But, neither a high nor low number necessarily seems good to me.
For example, this number could be high because the researcher is just a bit player in a much larger team effort led but other institutions. Or one still only publishes papers with ones Ph.D advisor (and on the same topic!).
On the other hand, a high number may result because the researcher always recruits world leaders with complimentary expertise for projects. I think this is increasingly important for basic materials science.

But a low number could be either good or bad, too. For example, low number may be because a researcher is the world leader in a particular area and they have built up a self-contained team at their own institution.
On the other hand, a low number may be a result of mediocrity: e.g. no one wants to collaborate with them, or they settle for doing everything themselves rather than collaborate with world leaders with complementary expertise.

I also think whether this number is a good metric for quality will vary significantly with the research project, field and the level of specialisation and the extent it is multi-disciplinary.

Hawking's cat had a Nazi genealogy

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

Thursday, July 15, 2010

Justifying a common mantra

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.

A useful file sharing resource for collaborations

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.

Wednesday, July 14, 2010

The limited relevance of quantum coherence in photosynthesis

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.

Experimental signatures of entanglement (such as violation of Bell inequalities) have not yet been observed in photosynthetic systems.
I fear a reason why people talk about entanglement in photosynthesis is because of its compelling "sex appeal", particularly to people in the quantum information community.
Were such speculations necessary to get the first paper on this subject into Nature?

It is debatable whether quantum coherence in the one exciton sector itself is a signature of entanglement.

The fact that quantum coherence of excitons between a pair of chromophores imbedded inside the relevant membrane proteins can exist for hundreds of femtoseconds (even at room temperature) is actually not that surprising, being consistent with simple model calculations with physically realistic parameters.

Tuesday, July 13, 2010

Perfectionism and procrastination

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."

Monday, July 12, 2010

A truly quantum phase transition

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.

Saturday, July 10, 2010

Frauenfelder rules for an effective workshop

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.

Friday, July 9, 2010

Computational photochemistry tutorial

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.

Make your own Vuvuzela sound

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!

Thursday, July 8, 2010

Disentangling extraordinary claims about photosynthesis

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.

Opportunities for theorists

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 mobility, and
(v) charge collection at the electrodes.

Are you a wimp?

"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.

Wednesday, July 7, 2010

Deconstructing thermal transport in the pseudogap state

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 Michael Smith and I to examine how different models for the pseudogap state (particularly arcs vs. pockets) lead to qualitatively different predictions for the thermal conductivity. Our results appeared in Phys. Rev. B this week.

Boulder school lectures online

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.

Tuesday, July 6, 2010

Who should I get to write a letter of reference?

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 these ideas are gleaned from John Wilkins one page guides on Vita for the first job after the Ph.D and Writing Letters of Reference.
I did a postdoc with Wilkins and since then he has written some very nice letters on my behalf! Thanks.

Monday, July 5, 2010

Virtual drug design?

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 macromolecular complex formation.

The figure above is taken from a this paper about the action of aspirin.

Sunday, July 4, 2010

OPV cell efficiency is an emergent property

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 almost all of these calculations will be on small single and isolated molecules in the gas phase.

It was claimed that one could screen for high charge mobility materials by looking at delocalisation of frontier orbitals and the reorganisation energy associated with ionisation. However, the particularly relevant quantity is the reorganisation energy of the environment of the molecule.

The speaker claimed something like "we are our own harshest critics" and listed possible weaknesses of the project. These were most concerned with whether approaches based on density functional theory (DFT) are adequate for calculating the relevant properties of these molecules. (Many people would say they are not). However, I contend that even if one could calculate exactly the properties of single molecules in the gas phase one would be a long way from being about to determine which molecules will be the best candidates for OPVs.

I asked for a specific example of where such a computational approach has been successful for any area of science and technology. It was stated that drug companies do this all the time when screening. However, I contend the physics and chemistry of that problem is much simpler and more well defined. One knows a specific active site of a protein that ones want to find a small molecule to bind to the hinder the activity at that site. This is a ground state and very local property. In contrast, for photovoltaics excited states, dynamics, and collective effects are involved, and the relevant large scale structures are not well defined. Exactly how the properties of OPVs are related to the properties of the constituent molecules is so poorly understood I am skeptical that a brute force computational approach is going to lead to much progress.

Saturday, July 3, 2010

Splitting singlets to save the planet

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?

Friday, July 2, 2010

Understanding properties of dye-sensitizers

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.

Deconstructing excited state dynamics in conjugated polymers

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 gets a signal at all and the physical mechanism took almost 20 years.

There are many possible competing processes following photoexcitation of a singlet (exciton) state.

S1 --> P+ + P-
or T1 + T1
where P+ is a positive polaron (this is just a cation with a significant bond relaxation
in the neighbourhood of the charge)
and T1 denotes a triplet state.
The polarons have unpaired spins and will produce an ESR signal. But how does flipping these spins enhance the photoluminescence?

Some of the key results to understanding what goes on are in this PRL.
Shinar considered 2 scenarios [note the method of multiple hypotheses].
The one that is consistent with experiment is

Enhanced spin-dependent annihilation of Triplet excitons by polarons
T1 + P+ --> P+ (note this conserves charge and spin)
TPQ [triplet polaron quenching] model
(This is discussed in the classic book by Pope and Swenberg)

Shinar claims TPQ is one of the most important interactions in organic photonic materials and devices.

The picture that emerges of the photoexcitation dynamics is that in the "steady state" the number of triplet excitons and the number of polarons is about 10,000 times larger than the number of singlet excitons.
Eventually the polaron pairs recombine into a singlet exciton which decays radiatively.

Thursday, July 1, 2010

Charge transport in organic photovoltaic materials

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?