Wednesday, September 29, 2021

The very human side to universities

My wife and I started watching the series The Chair, a comedy about an English department in an affluent liberal arts university in the Northeastern USA. We thought the first episode was a bit too soapy and stopped watching. But then, I read an article claiming that The Chair Is Netflix’s Best Drama in Years: "The near-perfect show elegantly skewers the subject of free speech on campus." So, we kept watching and were glad we did. But, I think it is really about much more than "free speech".

What I appreciate the most is that it brings out just how human (fallible, creative, caring, contradictory, selfish, egotistical, ridiculous, ...) all the players in the university are: students, faculty, administrators, families, ... There is much to laugh at, to groan about, and to celebrate. And, this is why we need the humanities.

For me, the best scene is the disciplinary hearing in the final episode. The embattled English department Chair says:

“Why should [students] trust us? The world is burning and we’re sitting up here worried about our endowment? Our latest ranking on U.S. News & World Report?”

She then asks the Dean, "when did you last teach a class?" [I think all senior managers should be required to do some teaching.]

Nancy Wang Yuen has a nice article in the LA Times, I’m an Asian American woman in academia. Here’s what ‘The Chair’ gets right

One thing I think the series got badly wrong was how engaged the students were. They came to class, had done the required reading, asked questions, and were not on their phones! Oh, to teach a class in Hollywood!

If you have watched the series, what did you think?

Friday, September 24, 2021

Time management and mental health

Mental health and time management continue to be a big issue for many, including me. Both challenges are compounded by the upheaval associated with the pandemic.

I have only recently come to see that time management is not just an issue of efficiency and productivity. It is but also about stress reduction and good mental health. I like order and so I am less anxious and less prone to overstimulation if my environment is free of clutter and I have well-defined tasks. Clutter (books, papers, folders,...) in plain view reminds me of unfinished tasks and can distract me. Clutter can also be electronic (e.g., on my computer "desktop" or email inbox).


Things I need to be more disciplined about include the following.

I love learning new things. Hence, I am easily distracted, particularly when online.

I need a clear goal for each task.

I am finding regularly reviewing these questions and suggestions helpful. In particular, I try to have built into my schedule the following before dinner.

a. Take Priya (our cute dog) to the park for ball time. This helps clear my head and        keeps her happy. 

b. Get ready for the next day.

    Put away all files, papers, and books, both physical and electronic.

    Plan the following day, especially making time blocks for specific tasks, both large and small.

    Collect all the materials I need for tomorrow.

On a related matter, a colleague has been singing the praises of Cal Newport's new book, A World Without Email: Reimaging Work in the Age of Overload. Just reading the first chapter reminds me how deep the problem is. Fortunately, he has some concrete suggestions of possible solutions.

If you have read it, I welcome comments on it.

Another colleague told me that Newport's book, Deep Work, revolutionised his professional life. Previously, I have posted about Deep Work, including his argument that we should quit social media. 


Tuesday, September 21, 2021

Nanoscale machines in nature

Part two of the Biology brief in The Economist is Cells and how to run them: All life is made of cells, and cells depend on membranes

A few of the main ideas are the following. Cells are either prokaryotic (bacterium) or eukaryotic (animals). Cell membranes are made of lipids that spontaneously form structures due to an interplay between hydrophobic and hydrophilic interactions. The boundary of prokaryotic cells is the membrane. Eukaryotic cells are more complex, containing many organelles (mitochondria), whose boundary are membranes.

Cells are little factories that can multiply themselves and perform distinct biological functions. It requires energy to maintain the cell shape and for it to manufacture new things. Inside and out is maintained by a difference in the concentration of protons (hydrogen ions) across the membrane. There are two aspects to this. First, the electron transport chain produces the protons. Second, a specific protein in the membrane, ATP synthase, pumps protons across the membrane.

The electron transfer chains are driven either by respiration or photosynthesis. 

Energy for processes in the cell is provided by breaking ATP down to ADP. The reverse process is driven by the kinetic energy of rotation (at about 6000 rpm) of the part of the ATP synthase protein.  ATP is Adenosine triphosphate.

To me the amazing/awesome/cool/miraculous thing is what the hardware can do. These are nanoscale chemical machines and factories. The video below shows a simulation of the ATP synthase protein that is located within cell membranes. It acts as a proton pump to maintain the concentration imbalance between the outside and inside of the cell and to convert ADP to ATP.

I learnt from this how the ATP synthase spins in only one direction and the rotation corresponds to sequential conformational changes in the protein subunits.

There is a beautiful discussion of the underlying physics in a chapter in Biological Physics by Phil Nelson. I have written a brief summary here.

The underlying quantum chemistry is explored in

Monday, September 13, 2021

Vertex corrections do matter

For an experimentalist one of the "easiest" quantities to measure for a metal is the electrical resistivity. Yet, for a many-body theorist working on models for strongly correlated electron systems this is one of the most difficult quantities to calculate, without making strong and debatable assumptions. One of the key questions is whether vertex corrections do matter. Ten years ago I summarised some of the issues.

This issue is nicely addressed in this nice paper from 2019.

Conductivity in the Square Lattice Hubbard Model at High Temperatures: Importance of Vertex Corrections

J. Vučičević, J. Kokalj, R. Žitko, N. Wentzell, D. Tanasković, and J. Mravlje

Besides the general issue of understanding the importance of vertex corrections, the paper is partly motivated by recent experiments on ultracold atoms that were compared to the results of calculations for a Hubbard model, using the finite-temperature Lanczos method (which essentially gives exact results on small finite lattices (e.g. 4 x 4)) and cluster Dynamical Mean-Field Theory (DMFT) (which does not include vertex corrections and has some momentum dependence in the self energy).

Before looking at the results I should point out the parameter values for the calculations. They are done for a Hubbard model on a square lattice. The half-bandwidth D=4t where t is the hopping parameter and U=10t. For the graphs below the doping p=0.1 (comparable to optimal doping in the cuprates).

Most importantly, the lowest temperature for which reliable calculations can be performed is T=0.2D=0.8t. In the cuprates, t is about 0.3 eV and so this lowest temperature corresponds to about 3000 K!, i.e. well above the superconducting Tc and the range of resistivity measurements on real materials. Most solids melt at these high temperatures.

Nevertheless, the results are important for two reasons. 

First, the experiments on ultracold atoms are in this temperature regime. [Aside: again this shows how fermion cold atom experiments are a long long way from simulating cuprates, contrary to some hype a decade ago]. 

Second, we are desperate for reliable results, and so it is worth knowing something about the possible importance of vertex corrections, even at very high temperatures. [Aside: my first guess would have been that they are not very important since I would have thought that correlations would be short-range and hand waving from Ward's identity would suggest that it follows the vertex corrections are small. This is wrong.]

In the figure above the top panel is the charge compressibility versus temperature. This is a thermodynamic quantity and the results show that most of the methods give similar results suggesting that the corresponding vertex corrections are small, at least above 0.1D.

The lower panel shows the temperature dependence of the resistivity and suggests that vertex corrections do lead to quantitative, but not qualitative differences. I guess the resistivity is in units of the quantum of resistance. Each rectangle has a vertical dimension of 5 units and so the resistivity is in excess of the Mott-Ioffe-Regel limit, i.e. the system is a bad metal. 

The figure above shows the frequency dependence of the optical conductivity for T=0.5D. There is a Drude peak at zero frequency and the broad peak near omega=2.5D=U corresponds to transitions between the lower and upper Hubbard band. DMFT is qualitatively correct but does differ from FTLM, showing the importance of vertex corrections.

Tuesday, September 7, 2021

Biology in a nutshell: emergence at many levels

 One of the many great things about The Economist magazine is that they run "Briefing" articles that give brief readable introductions and analyses to important topics, ranging from racism to taxation to climate change. Last year they ran a series about new ideas in economics.

They are currently running a series, Biology Briefs. Each week, for six weeks, there is a two-page article on one key topic in modern biology. They are naturally divided by different scales: molecules, cells, organs, individual lives, species, and living planets. 

The most important idea in molecular biology: DNA encodes information that is used to make specific proteins.

Replication: the protein DNA polymerase makes new DNA molecules with the same sequence of base pairs

Transcription: the protein RNA polymerase makes single strands of RNA that have the same genetic information.

Translation: the protein ribosome reads the information in the mRNA and uses it to make chains of amino acids (with specific sequences determined by the RNA sequence). These polymers then fold spontaneously into proteins with specific functions.

There is much that is amazing and awesome about this, including that people have been able to figure all this out. What I find most amazing/miraculous/awesome/cool is not the software but rather the hardware, i.e. the proteins that act as nanoscale biochemical factories, particularly the ribosome.

Wednesday, September 1, 2021

Towards real materials applications

There is a chasm between finding a material that has a desirable property that is key to a technological application and producing a commercial product. In the hype about materials research, the width of this chasm is too often glossed over.

The Structure of Materials by Samuel M. Allen and Edwin L. Thomas (based on a course in Materials Science and Engineering at MIT) introduces the tetrahedron of
structure, properties, processing, and performance. In condensed matter physics the focus is largely on the relationship between structure and properties. But, for engineering, these are both also related to performance and processing (i.e. ability to make materials and devices).

 The book also emphasises the multiple length scales associated with the structure of "real" materials. The scales range from the atomic scale of Angstroms to the scale of micrometers associated with objects such as grain boundaries, topological defects, and domain walls. These longer length scales are also relevant in liquid crystals, glasses, and polymers.