Friday, March 27, 2020

Recommendations needed on reference management software

A wonderful advance of the past decade for academic life (yes, there are some!) has been the availability of software to manage references and all those journal article PDFs that we download (to read later :)).

About ten years ago I started using Papers. It was brilliant. Papers 2 wasn't as good, but still did the job. And, well Papers 3 has become a burden. My version crashes continually and does not seem to have some of the features of Papers 1 that I found useful (e.g. ability to easily email a copy of an article). I am a bit slow and discovered today that it is not me (and my limited tech-savvy) that is the problem but the software itself. Online there are many negative reviews...

So I need to change to another platform. Any suggestions?
Essential requirements for the replacement include the following.

  • runs on a Mac
  • can import all my files from Papers 3 
  • is easy to install and use
Alternatives I am aware of include Mendeley and Bookends
I would particularly like to hear from anyone who has made the transition and any associated problems they have had (and solved easily :)).

Thursday, March 26, 2020

Introducing universality and particularity

Every person is unique. No two people on earth are identical. We differ in physical appearance, personality, fingerprints, heartbeat, gait, and DNA. Such differences are used to identify criminals and in the surveillance of citizens by nation states. Yet in other ways all humans are the same. We all have brains, hearts, and lungs. All our bodies use the same biochemistry to stay alive: whether to breathe oxygen, digest food, or fight infections. Arguably, on some level, we all have common aspirations: to survive, to be loved, to be happy, and to find meaning and purpose. Yet these aspirations find many particular expressions. All humans have certain universal qualities and properties, from the biomolecular to the social. Yet at a finer level of detail, there is a particularity of each of these properties. This paradox of ``same and not the same’’ can be viewed as a tension between universality and particularity.

All academic disciplines search for universals; they are used to categorise, to conceptualise, and to theorise. Biologists classify species of plants and animals and types of cells and viruses. All of these different biological systems make use of the same biomolecules (DNA, RNA, and proteins), and biochemical reactions. The same genetic code uses the information encoded in a piece of DNA to make proteins with a specific function. Anthropologists study the immense diversity of human cultures and societies. This diversity can be understood in terms of certain universal concepts such as kinship, sexual relations, family, ritual, community, economics, and religion. Linguists study the structure and grammar of the thousands of different human languages.  Given the diverse world that we live in many of us find the universality that different academic disciplines have discovered over the past century surprising and exciting.

Condensed matter physicists study the incredible diversity of different states of matter and the transitions between them. A surprising discovery is that there is much more universality than might be expected. In this chapter, I will discuss the nature of this universality, the different associated length scales associated with phase transitions, and how this universality emerges. The insight of Landau (chapter 4) was correct: many of the chemical and structural details of materials are irrelevant to understanding phase transitions. Furthermore, a precise classification of different types of phase transitions (universality classes) can be made. Even superconducting and superfluid and a subset of some magnetic transitions are in the same class. The determinants of the universality classes are the symmetry of the order in a state of matter and the spatial dimensionality of the system.

In society today there is significant public debate about morality; what is universal and what is particular to specific individuals, societies, or situations? Philosophers have debated universals for centuries. Many academic disciplines have discovered certain universal patterns, yet struggle to understand how universality does or does not emerge in the presence of particularity.  This struggle is due to the complexity of the systems of interest, including the many different scales present. Condensed matter physics provides a concrete and beautiful example where we do understand how to relate universality and particularity.

Would your non-scientist friends and relatives find this interesting? comprehensible?
I welcome suggestions.

Monday, March 23, 2020

Maintaining your mental health now

A significant impact of the COVID-19 pandemic will not just be on physical health but also global mental health. This problem should not be underestimated. People who might normally have good mental health may struggle because of new stresses and anxieties. Those of us who struggle need to be particularly vigilant. Fortunately, this is getting some significant attention. An example of expert advice is here.

I want to give my own non-expert personal perspective, just to keep the issue on the agenda, and to process my own thoughts and experiences.

Don't underestimate the problem, either for yourself or for others.

Practice the basics: diet, exercise, sleep and connecting to others.
Depending on your situation this may require some flexibility, creativity, and self-discipline, particularly if you are in self-isolation.

Limit screen time.
Limit news and social media updates.
Turn off most of the notifications on your phone.
I am trying to limit myself to two sessions on news sites each day. I also try and read some articles that are not about the pandemic. The ``news'' has become very predictable in Australia because we are roughly one week behind the USA and two weeks behind Italy.
The medical news goes: X positive tests, Y illnesses, Z deaths, with X, Y, and Z increasing exponentially.
The political news follows the pattern: government proposes modest measures (shut-downs and economic stimulus packages) that steadily increase to something like we have never seen since WWII.
The economic news follows a pattern too.

Limit discussion of the pandemic. 
There is a natural tendency to spend all our time talking about it.  There is some scary stuff happening, everyone we know is being affected (but in many different ways), there is lots of misinformation and incompetence, and some fascinating biology and social science. Don't avoid the subject. But, talk about other things too. My wife have to keep working on this.

Accept the situation, adapt, and move on.
Grieve your losses. Some of what you hoped to do in the next six months is not going to happen. Give yourself (and those who work for you) time to adapt, whether it is setting up a home office or putting a course online.

Be sensitive to the way the pandemic is affecting different people in very different ways, both in the short- and long-term. For some, it will probably be a minor hiccup in their life trajectory. Some are sitting at home bored and asked for recommendations as to what Netflix shows to binge on and how to have a good virtual cocktail party. Others are trying to prevent the collapse of their organisation while working at their dining table with three kids running around like crazy, and their spouse working overtime in a medical clinic. Many faculty have been asked at short notice to put their whole courses online. The level of disruption for experimentalists and theorists is significantly different.
For some, the pandemic may lead to loss of loved ones, unemployment, or bankruptcy. For others, well ``the stock market always bounces back.''

Given my mental health history, some may be concerned about me, so let me say a little about how I am doing. This year my mental health has been the best it has been for several years. Two years ago I transitioned to a half-time research-only position at the university (more on that another time). I am very thankful don't have to rapidly put a course online. I am working from home and teleconferencing with students, postdocs, and colleagues. That is going well. I am an introvert and find overseas travel stressful so being forced to abandon some meetings, both local and international, is actually a blessing. My main stress has been trying to get some others to be pro-active rather than reactive. I get frustrated at community, university, and political leaders not fully appreciating the gravity of the situation and acting slowly. I have to limit my level engagement, focusing on my sphere of influence, not my circle of concern.

Any thoughts and suggestions?
Feel free to share your own experiences.

Monday, March 16, 2020

Exponential growth: living and dying by it

"The greatest shortcoming of the human race is our inability to understand the exponential function." 
I became aware this past week that I too have this shortcoming, along with too many others, especially some political leaders and Australian university management.

The graph below is the number of cases of COVID-19 outside China versus time, as of yesterday.
It is taken from the latest WHO report.

According to Neil Howe
N = R0 ^ (T/S)
where N is the infected number, R0 is the average number of persons infected by each infected person, S is the average number of days from infection to transmission, and T (the variable) is days. Most studies of COVID-19 suggest that its R0 is about 2.3 and that its S is about 6 days. As expected, that generates an N that doubles about every 5 days.
The practical problem is if you say ``Let's wait and see. We only have a couple of confirmed cases in our community now. We don't want to over-react.'' By the time protective measures are decided upon, put in place, and actually implemented, it is too late.

Does closing schools slow the spread of coronavirus? Past outbreaks provide clues 

The Exponential Power of Now

Later I want to deconstruct the graph below, about ``flattening the curve''.
I also want to come back to an earlier post about epidemics on networks.

Footnote: The beginning quotation
"The greatest shortcoming of the human race is our inability to understand the exponential function." 
is taken from a famous talk Arithmetic, population, and energy, by Al Bartlett, who was a Professor at University of Colorado.

The talk is based on 
Forgotten Fundamentals of the Energy Crisis, originally published in 1978 in the American Journal of Physics.

I first learned of Bartlett and his talk in the great movie, Two Raging Grannies.

Update. Henry Nourse brought to my attention an excellent article that gives a detailed analysis.

Coronavirus: Why You Must Act NowPoliticians, Community Leaders and Business Leaders: What Should You Do and When? 
Tomas Pueyo

The most important graph is the one below. It makes the point that there is a fourteen-day lag between people having the virus and being diagnosed with it.

the orange bars show you what authorities knew, and the grey ones what was really happening.
On January 21st, the number of new diagnosed cases (orange) is exploding: there are around 100 new cases. In reality, there were 1,500 new cases that day, growing exponentially. But the authorities didn’t know that. 

Friday, March 13, 2020

The significance of the discovery of cuprate superconductivity

This is some draft text for Condensed Matter Physics: A Very Short Introduction. 
Feedback appreciated.

A big change in condensed matter physics occurred in the late 1980s due to an unexpected discovery that led to whole new areas of research. Why was this discovery so significant?

Superconductivity is amazing. At extremely low temperatures, many metals can conduct electricity without generating any heat. A ``holy grail’’ of physics is to discover a material that is a superconductor at room temperature. This could revolutionise the transmission of electricity. Until 1986, the highest temperature at which superconductivity was possible was about 23 K (-250 °C), in Nb3Ge, a combination of the elements Niobium and Germanium. This requires cooling the material with liquid helium, which is expensive, and consequently limits commercial applications, such as MRI machines in hospitals.

In 1986, Alex Bednorz and Karl Muller, working at an IBM laboratory in Switzerland, investigated whether a chemical compound composed of the elements lanthanum, barium, copper, and oxygen (La, Ba, Cu, O) would be superconductor at a higher temperature. They were motivated by theoretical arguments that strong interactions between the electrons and the vibrations of the atoms could enhance the superconducting transition temperature, Tc. They found superconductivity below a Tc of 36 K, a new record. The material consisted of layers of copper and oxygen atoms and this lead to many other groups investigating similar classes of material. Within a year, materials were discovered with a Tc of 120 K (-150 °C). This was significant because superconductivity could be achieved by cooling with liquid nitrogen, which is about the same price as beer. Unfortunately, over the past thirty years, there has been little progress at increasing Tc to higher temperatures. Room temperature superconductivity remains a holy grail.

The discovery of Bednorz and Muller generated considerable excitement in the physics community, attracting many new researchers to superconductivity research. In March 1987 a special session was held during a regular meeting of the American Physical Society in New York City. A large ballroom was overflowing with more than one thousand physicists. I was one of thousands more outside watching on a TV monitor. Each speaker was only allowed three minutes to present their work and the session went long past midnight. This event was described on the front page of The New York Times as the ``Woodstock of Physics’’, in honour of the famous rock music festival held in New York state, and considered as emblematic of the 1960s.

Scientific history is full of serendipity. Some discoveries are accidental. It is now known that the reason that Bednorz and Muller chose to focus on this class of materials (strong interaction of electrons with atomic vibrations) was actually wrong. The high Tc does not arise from this interaction, but rather from a strong magnetic interaction between the electrons and from the two-dimensionality of the materials. The latter is a result of the layered crystal structure shown in Figure 5.2. Although the discovery was arguably somewhat serendipitous, its profound significance was shown in 1987, when Bednorz and Muller were awarded the Nobel Prize. In contrast, most scientists receive the prize decades after their ground-breaking discovery.

Figure 1. The repeat unit for the crystal structure of a superconducting copper oxide, BiSrCaCuO. A key ingredient is the layers of copper and oxygen atoms, which are isolated from each other by a large number of other atoms. The chemical complexity is reflected in the unit cell containing more than 50 atoms, including 5 different chemical elements.

From a fundamental physics point of view the superconductivity of these materials is not the only interesting and theoretically challenging property. The materials exhibit two new states of matter, known as the pseudogap state and the strange metal (see the phase diagram in Figure 5.3.). These conducting states have properties distinctly different from those found in common metals such as copper and gold.

Figure 2. Phase diagram of copper oxide superconductors. Temperature (T) versus doping. Doping describes the chemical composition of the material, particularly the density of charge carriers. The different states are antiferromagnet (AF), superconductor (SC), regular metal (FL), strange metal, and pseudogap.

Since 1986 more than ten thousand scientific papers have been published concerning possible theories to describe the different states in the phase diagram (Figure 5.3). Although some progress has been made, there is still no single accepted theory, and particularly no theory that has the simplicity and predictive power of the BCS theory of superconductivity in simple metals such as lead and tin. Developing a comprehensive theory remains one of the outstanding problems in Condensed Matter Physics.

Both experimental and theoretical studies suggest that all this rich new physics requires the low-dimensionality of these materials, i.e., they are almost living in Flatland.

But, why is low-dimensionality crucial? There is no simple explanation for this, but generally as the dimension of a system gets lower, the constituents fluctuate more (e.g. the atoms move around more), conventional orders become less stable, and new states of matter become possible.

Any comments?
Particularly how to make this more accessible and interesting to a general audience.

Wednesday, March 11, 2020

Single orbital + multiple sites = Rich physics

Since the discovery of the iron-based superconductors, it has become clear that the combination of multiple orbitals and strong correlations can lead to rich physics, beyond what one sees in single orbital routes.
An alternative route to rich physics is a single orbital model on a lattice with multiple sites in a unit cell.

Henry Nourse, Ben Powell, and I just posted a preprint
Multiple insulating phases due to the interplay of strong correlations and lattice geometry in a single-orbital Hubbard model
We find ten distinct ground states for the single-orbital Hubbard model on the decorated honeycomb lattice, which interpolates between the honeycomb and kagome lattices and is the simplest two-dimensional net. The rich phase diagram includes a real-space Mott insulator, dimer, and trimer Mott insulators, a spin-triplet Mott insulator, flat band ferromagnets, and Dirac metals. It is determined as a function of interaction strength, band filling, and hopping anisotropy, using rotationally invariant slave boson mean-field theory.

We welcome comments.

Thursday, March 5, 2020

The quantum physics of life in red and green

Life is truly amazing!
Life is beautiful!
...and it involves quantum many-body physics...

There is a beautiful (short) review
Heme: From quantum spin crossover to oxygen manager of life 
Kasper Kepp

The article involves a plethora of topics that I have discussed before on this blog. I have included relevant links.

Kepp starts with the unique (chemically fine-tuned) properties of both iron and porphyrin that enable them to play a central role in two of the most important processes in life: respiration and photosynthesis. He has a beautiful paragraph (perhaps in the style of Roald Hoffmann):
Such ligand-field transitions of iron in porphyrin were familiar to our ancestors as the characteristic red color of blood that largely defines the human psychological and cultural connotations of the color representing courage, war, danger, and suffering. 
Incidentally, pi-pi* transitions within the porphyrin-derived chlorophylls are also responsible for the green color of plants, associated with nature, life and hope, so the reader may perhaps agree that porphyrin has had vast (but alas! rarely appreciated) cultural consequences.
The oxygen molecule is a spin triplet.
Iron(II) porphyrin is in a triplet spin state (S=1). The Fe(II) is a d6 configuration in a D_4h crystal field.
When they bind together the ground state is a spin-singlet.

There are two fundamental quantum chemistry questions that are discussed.

1. What is the electronic structure (many-body wave function) of the ground state for oxygen bound to heme?

2. What is the mechanism for the ``spin-forbidden'' transition of the oxygen binding?

The first question has a long history. Like almost anything important and profound in quantum chemistry it goes back to Linus Pauling! In 1936 Pauling and Coryell argued that the ground state is
essentially a neutral O=O binding with two of its electrons to iron to produce a formally iron(II) if both the bonding electrons were confined to O2, corre- sponding to the non-bonding limit of neutral parts, but a formally iron(I) if the Fe–O bond were to be considered covalent. 
In 1960, McClure suggested a valence-bond formulation based on triplet–triplet coupling, which is appealing by the low promotion energies required to access these states, rather than the singlet states. In 1964, Weiss suggested, based on analogy to chemical reactions in aqueous solution, that the true ferrous hemeO2 adduct was mainly of the superoxo-iron(III) type caused by ‘‘electron transfer” from iron to O2. 
Goddard and Olafson suggested an ozone model of the adduct in 1975 which emphasized the four-electron three-center bond with maintained triplet state of dioxygen as in the McClure model with less electronic reorganization to explain the reversible binding. 
In 1977, Pauling maintained his original view again, the same year that Huynh, Case, and Karplus did a first attempt to bridge these views by performing early quantum chemical calculations that diplomatically emphasized the importance of both Weiss and Pauling resonance forms. 
However, interpretation depends on model language, orbital localization, and transformation between valence bond and orbital formalisms:  
In terms of molecular orbital theory, the wave function was a multi-configurational state dominated by the Pauling configuration; however, if one uses valence bond theory considerations, it can be interpreted as having large Weiss character. Thus, the multi-configurational state produced from CASPT2 is interpreted differently by different models. This partly explains why the trenches were so deeply dug during the exchange between Pauling, Goddard, McClure, and Weiss; all were right, and all were wrong. 
This is just another example of unnecessary conflicts about valence bond vs. molecular orbital (VB vs. MO). 
In terms of valence structures, the ground state was summarized by Shaik and Chen as having contributions from both Weiss, Pauling, and McClure forms, the first .. dominating. 
Ironically DFT ends up providing a useful language after all! 
The charge assignments to O2 are very dependent on calculation scheme, and both the orbitals, valence structures, and atomic charges that defined the Weiss-Pauling debate are non-observable. In contrast, the electron density is observable as are the geometries and spectroscopic data...
Molecular orbitals are not physical observables but calculational constructs. MO's don't exist.

In different words, one can take a many-body wave-function and make a linear unitary transformation of the molecular orbitals. The Slater determinants do not change. [The value of a determinant is invariant to a change of basis.]

Now. Question 2.
What is the mechanism for the ``spin-forbidden'' transition of the oxygen binding?

Kepp talks about spin-orbit coupling and the fact that it is small for oxygen, motivating a discussion of a "broad crossing mechanism".  However, I am not sure this is relevant. I don't see the binding as necessarily spin forbidden. As the oxygen approaches the heme the two triplet states can mix to form a total spin singlet.
This is analogous to bringing two hydrogen atoms (each of which is spin 1/2) together to form a hydrogen molecule (which is spin zero). A multi-configurational wavefunction has no problem with this. But DFT-based approximations, which use a single determinant cannot describe this smooth crossover.

Other things of particular interest to me that are discussed in the review include the central role of back bonding and the success of the TPSSh functional in DFT calculations for organometallics.

Unfortunately, the review does not mention recent work by Weber et al, applying DMFT to the problem of oxygen binding to haemoglobin.

Monday, March 2, 2020

What science tattoo would you get?

At the UQ condensed matter theory group meeting, we had an interesting discussion about this question?

A Google image search produces some interesting options.
I don't know if these are real or some are photoshopped.

Would you get an equation, a molecule, a phase diagram, or  .... ?

From condensed matter, nothing particularly stands out to me. But I do think that Einstein's gravity equations (above) are pretty amazing.

                                              The Theory of Everything

BTW. I am no fan of tattoos and can never imagine getting one of any kind.

So, what science tattoo might you get?