Monday, November 30, 2009
Sunday, November 29, 2009
What does the scientific community know now that we did not know when you began the research?There is a similar probing question to ask yourself before you start a project (or a new sub-project). Suppose everything goes as well as can be hoped (i.e., you are able to complete the calculation, do the measurement, get the new technique to work, or make the compound). Then will you be able to say something new? If not, is it worth even trying?
The before question is a good one for both students and supervisors to contemplate. It is too easy for supervisors (including me) to say do this extra calculation (or make this extra compound and measure all its properties) without considering enough the time cost to the student or postdoc.
Thursday, November 26, 2009
The cover letter is key.
I believe most postdoc (and many faculty) applications live or die [i.e., get to the long short list] based on the quality of the cover letter.
You need to specifically answer the following specific questions:
- Why are you interested in this specific job?
- Why are you interested in this specific research?
- Why should they hire specifically you for this specific job?
So to be specific!
Write something like:
"One of the scientific questions I am most interested in is "What is the physical mechanism for XXXX in material YYY? I recently read your nice paper "blah blah" in journal YY and I have been wondering if a similar approach might be relevant to answering my question. I welcome any suggestions from you in this regard....."Dont write:
"Dear Professor,The letter is so important you should spend at least a day writing it, even though is should fit on a single page. Should should get a range of faculty to read it and provide feeback.
I did my Ph.D on topic X and want to continue working on it [even though I have no idea as to whether you have ever worked in this area or have any interest in it]. I published lots of papers [even though most listed on the CV are "in preparation"] and will publish lots more if I come and work with you....]"
Wednesday, November 25, 2009
The chemical capacitance has certain similarities to conventional dielectric capacitance. While the latter is a measure of the ability of the system to store electrical energy in the form of polarized electric dipoles, the former is a measure of the ability of the system to store chemical energy in the form of changes in stoichiometry
Tuesday, November 24, 2009
Sunday, November 22, 2009
Saturday, November 21, 2009
Richard is also co-author of a high school physics textbook,
that Joel Gilmore (Science communicator extraordinaire and my former Ph.D student) was so impressed with he bought it off a student he was tutoring when she finished high school!
Friday, November 20, 2009
“The great power of science is its ability, through brutal objectivity, to reveal to us truth we did not anticipate.”
``mythologies are immensely powerful things, and sometimes we humans go to enormous lengths to see the world as we think it should be, even when the evidence says we are mistaken.’’
“ideologies preclude discovery. All of us see the world as we wish it were rather than as it actually is.”
There are similarities to the cautions of Walter Kauzmann, in his Reminiscences of a Life in Protein Chemistry.
Thursday, November 19, 2009
Here is a copy of the talk I gave tonight on academic careers.
Some of the feedback included:
* the importance of mental health issues (I will try and do a few future posts on this).
* dogged perseverance is often a key component to success
It would be good to get some discussion going on some of the issues I raise in the talk.
Kreger DW. Wright Institute, Berkeley, CA 94704, USA.
Psychological Reports 1995 Feb;76(1):345-6.
In a study of 29 graduate students, self-ratings of stress correlated with low scores on self-esteem but were not related to an objective indicator of actual stress. Both self-rated stress and low self-esteem scores were related to scores on depression, with a weak interaction effect.
Wednesday, November 18, 2009
There is more to life than a research career.
Be realistic and consider alternative careers.
Learn to write, to get along with other people, ....
plus previous career advice I have posted, especially this advice to Ph.D students.
But it should be noted that the case of a BEC in superfluid He is not as clear cut as in dilute atomic gases. Nevertheless, I dont think these subtleties validate ignoring 80 years of research on superfluid helium. A very useful summary of the history and the associated physical issues is contained in this nice article by Sebastian Balibar.
I think that people who are supervising Ph.D students on BEC's should be familiar with these issues, make sure their students are aware of this history, and present their work in the appropriate context. But then I am just a grumpy old condensed matter physicist....
Tuesday, November 17, 2009
Besides measuring the quantum efficiency Ando et al. find that there are three components to the light emission and all are pH dependent. One component is of unknown origin. Clearly there is a correlation between the colour of the emission and the protonation state of the chromophore.
Only in a 2006 Nature paper was a structural basis for two different emission states proposed. I am curious as to how much quantum chemistry has been done on these issues. This may help address questions such as:
What determines the quantum efficiency of emission?
How are non-radiative decay channels suppressed?
What role does the protein environment play?
Monday, November 16, 2009
What is the scientific question you want to answer in the next few years?
Why is this important? Why are you excited about it?
They really put the size of Australia in perspective.
Saturday, November 14, 2009
The simplest of these problems involve only the spin operators Si of electrons residing on the sites, i, of a regular lattice. Each electron can have its spin oriented either up or down, leading to a Hilbert space of 2N states, on a lattice of N sites. On this space acts the Heisenberg HamiltonianH=∑i<j JijSi⋅Sj, (1)
where the Jij are a set of short-range exchange interactions, the strongest of which have Jij>0, i.e., are antiferromagnetic. We would like to map the ground-state phase diagram of H as a function of the Jij for a variety of lattices in the limit of N→∞. Note that we are not interested in obtaining the exact wave function of the ground state: this is a hopeless task in dimensions greater than one. Rather, we would be satisfied in a qualitative characterization of each phase in the space of the Jij. Among the possible phases are
(i) a Néel phase, in which the spins have a definite orientation just as in the classical antiferromagnet, with the spin expectation values
all parallel or antiparallel to each other;
(ii) a spiral antiferromagnet, which is magnetically ordered like the Néel phase, but the
spins are not collinear;
(iii) a valence bond solid (VBS), with the spins paired into S=0 valence bonds, which then crystallize into a preferred arrangement that breaks the lattice symmetry; and
(iv) a spin liquid, with no broken symmetries, neutral S=1/2 elementary excitations, and varieties of a subtle “topological” order.
Specific examples occur for Heisenberg models on the (i) square lattice, (ii), triangular lattice, (iii) kagome lattice (probably).
An example of a model which contains all three is here.
We are still searching for an example of (iv).
Friday, November 13, 2009
An important issue is after a organic molecule absorbs a photon what conformational change will occur. Below are several options involving bond twists.
A second issue is how the charge distribution in the molecule changes upon twisting.
This kind of physics is at the heart of how your eye works. When retinal absorbs a photon it undergoes a conformational change which produces a charge separation which eventually leads to an electrical signal in your brain. It is also at the heart of designing better organic solar cells.
We considered a model Hamiltonian for a large class of dyes. The figure below shows contour plots for the first excited state potential energy surface for several parameter values. The lower part of the figure shows how the charge distribution in the molecule changes for different conformations. It is amazing how such a simple model Hamiltonian can capture such rich physics.
Thursday, November 12, 2009
Wednesday, November 11, 2009
This is a question that Donald Truhlar asks in a JACS Editorial for a Select issue of 23 papers on Molecular Modeling of Complex Chemical Systems.
How would you answer the question?
You can look in the article to see how most computational chemists would answer the question.
The article is a very nice read to a physicist because it provides a very helpful and concise summary of historical landmarks in the computational modeling of large chemical systems.
However, I disagree and am concerned with one of the opening statements in the article:
Almost all modern theoretical chemistry is computational chemistry, because most of the progress that can be made with pencil and paper without a computer has been already made. Computations on complex systems are, in my opinion, the current frontier of theoretical chemistry.I fear this does reflect the view of most in the theoretical chemistry community. However, (as a physicist) I think a much greater emphasis needs to be placed on gaining insights, finding organisation principles, and developing analytical models that complement simulations. But, that is what I am trying to do (and excited about!).
Tuesday, November 10, 2009
“purely a matter of taste, roughly equivalent to whether or not one believes mathematical language or human language to be more fundamental.”But it is interesting that he is now writing articles about multiverses...
Monday, November 9, 2009
It is interesting they also introduced a 50 Schilling note with Sigmund Freud and a 5000 Schilling note for Mozart. Is this a relative measure of their contributions to culture and society?
A key question concerning optically active molecules is what is dynamics of the excited states?
Specifically, what are the predominant non-radiative decay mechanisms. The schematic below shows several options for the energy of the potential energy surfaces versus some configurational co-ordinate. On the left both S1 and S2 excited states decay to a conical intersection with the ground state. In contrast, on the right they have distinctly different decay paths.
But how does one go beyond such schematics. It turns out that for a broad class of dyes one can justify from high level quantum chemistry calculations a description in terms of just three valence bond states (see below).
The description in terms of the three diabatic states allow us to consider a somewhat "generic" or minimal model which exhibits a number of significant features, including:
- Conical intersections between the S1 and S0 surfaces only occur for large twist angles.
- In contrast, S2/S1 intersections can occur near the Franck-Condon region.
- When the molecule has left-right symmetry, all intersections are associated with con- or dis-rotations and never with single bond twists.
- For asymmetric molecules (i.e. where the bridge couples more strongly to one end) then the S2 and S1 surfaces bias torsion about different bonds.
- Charge localization and torsion pathway biasing are correlated.
BTW, if you look at the paper look at the great job Seth did at writing Informative section headings!
Sunday, November 8, 2009
Thinking in the alternative resonating valence bond picture there will be three alternative Lewis structures
The extent to which the lower two structures contribute will increase the C-O bond length and reduce the C-O stretch frequency.
It should be possible to describe the low lying excited states in terms of a complete active space with 4 electrons in 3 orbitals (a pi* orbital on the C=O bridge, and a pi orbital on the left and right fragments).
Saturday, November 7, 2009
Anderson suggests that emergence is the mechanism for consilience (the unifying of disparate pieces of knowledge) and reduction is the evidence for it. Theories may be under-determined, i.e., there may be many possible theories that can explain what is actually known. Hence, a successful theory may not actually correspond to what is happening. If there are only a few constraints (hypotheses, observations) that a theory must satisfy it has sometimes been the case that more than one theory can satisfy the constraints. However, as the number of constraints increases, acceptance of a theory is more likely and it becomes hard to conceive of alternative theories that could satisfy these constraints. Reduction can greatly increase the number of conditions that a theory must satisfy. For example, any alternative to quantum theory must be able to explain all known principles of atomic physics and of chemistry. Anderson concludes ``it is as impossible to `socially construct’ science as it is to invent A. Abrikosov or your mother-in-law.’’
Anderson mentions work of Kirkpatrick concerning the problem of satisfying many constraints. An example is this Science paper.
Friday, November 6, 2009
It is wonderful that last year the US Postal Service issued new stamps featuring four prominent scientists. Pauling and Bardeen were indeed masters in unravelling emergent phenomenon using quantum many-body theory.
Update (2016). I just discovered that in 2005 there was one for Josiah Willard Gibbs and Feynman.
Thursday, November 5, 2009
Ketocyanine dyes are of considerable interest. An example is shown above. What are the essential ingredients that determine their photophysical properties? The figure below is from a nice paper which compares essential differences between cyanines (CY), ketocyanines (KCY), and squarenes (SQ).
The difference between the upper and lower panels (A and B) relates [I think] to whether one has an even (A) or odd (B) number of p-electron centres on each of the molecular units on the left and right side of the central C=O bridge. Apparently, this is following a "composite molecule" approach in a book by Fabian and Hartmann.
A complementary approach to describing optical properties of these materials is within a resonating valence bond approach. There will be three dominant resonant structures, similar to those advocated by Pauling for urea. [I will try and get a picture]. Such an approach will naturally lead to two low-lying singlet excited states.
This type of resonance is of great biochemical significance since it leads to the planarity of amide groups in polypeptides, something figured out by Pauling and Corey in 1952, an emphasized because it is required for the alpha helix of proteins.
Wednesday, November 4, 2009
Also measure the temperature dependence of the thermopower. The associated energy scale will be much less than the activation energy of the mobility. This is seen nicely in the figure below taken from a review by Salamon and Jaime about colossal mangetoresistance materials.
[You can left click on the figure to make it larger.]
Yes. There is essentially no difference. This is not boring. It is fascinating.
The figure is taken from a beautiful Science paper by Seamus Davis group. It represents images from the fourier transform of STM images of the surface of an underdoped cuprate superconductor. From bottom to top the temperature increases from 0.1Tc to 1.5Tc where Tc is the superconducting transition temperature.
Basically this shows that at low energies the pseudogap phase has the identical excitation spectrum as a phase-disordered version of the d-wave superconducting state.
Tuesday, November 3, 2009
The figures below show how the potential energy surface varies with twisting about the central carbon atom of the molecule.
Similar experiments on methine dyes such as the green flourescent protein chromophore would be wonderful!
Monday, November 2, 2009
[Left click to enlarge and make legible.]
A Ph.D is not enough! A guide to survival in science by Peter Feibelman.
15 years ago I discovered this book, read it, and wrote the enthusiastic review above. I still think it has much wise, practical and helpful advice. I try to get everyone I work with to read it.
Sunday, November 1, 2009
- What are similarities and differences between the cuprates and pnictides?
- Is the key difference, the pnictides are less strongly correlated?
- If so, how does one describe/explain the magnetic order in the pnictides?