This is your life: birth, sex, and death!

Symmetry breaking is integral to biology. Spatial symmetry is broken as cells differentiate and also as organs form. Time reversal symmetry is broken in the life history of the development of individuals: from birth to death, it is heading just one way.

The fourth article in The Economist, Biology briefs, is Making your way in the world: An individual’s life story is a dance to the music of time. Here is the opening paragraph.

The organs of a body are a spatial division of labour, one created by different genes being turned on in different cells. The same process serves to give individual lives a division of labour over time. Complex algae, animals, fungi and plants all have predictable life histories which separate out three basic aspects of development—the creation of an autonomous individual, growth and reproduction—and run them sequentially.

There is also a fourth stage: death!

Individual identity is tied up with sex.

A lot of the complexity here is to do with sex... Sex is clearly the start of something new: a novel individual with a novel genetic blueprint...

When a human embryo is born as a baby, it already contains almost all of the organs which that individual will ever possess. This comes about first by the repeated division of the initial, fertilised egg into many cells that have the potential to become any part of the body.

Then symmetry breaking occurs: left and right, head and tail are delineated. 

Then, around the 16th day of development, the [human] embryo folds in on itself... [and the] body plan begin to take on a physical form, defining the head and the tail (for human embryos do, indeed, have tails), the left and the right, the inner and the outer.

...a butterfly embryo develops not only the organs needed in order to be a caterpillar, but also starter packs, called imaginal discs, for the organs that will be needed in adulthood.

Plants have two separate life histories, which alternate from generation to generation—though this is rarely obvious to human observers.

These two life histories (mating and dispersal) are associated with  "two, radically different, types of body": gametophytes, the mating body type, and sporophyte the dispersal body type. The life cycle of ferns is pictured below.

Here is a beautiful video of the life cycle of a butterfly.

Aside: There is a nice discussion of symmetry breaking and pattern formation in biology in chapter 7 of Fearful Symmetry: Is God a Geometer? by Ian Stewart and Marty Golubitsky.

The tension between efficiency, innovation, and adaptability

 If organisations are emergent can they be managed? This is the question I discussed in a previous post, stimulated by an article, The Dialogic Mindset: Leading Emergent Change in a Complex World by Gervase Bushe and Robert Marshak. They make the following claims.

To be sustainably successful, organizations have to manage learning as well as performing. This is one of the core paradoxes of management and organization theory: how to create organizations that can be simultaneously innovative and efficient; that is, how to best organize in order to learn and perform at the same time? 

The most efficient forms of organizing, like assemblyline manufacturing, are also the least able to adapt and change. Our business models for succeeding in complex, uncertain environments, like popular music or pharmaceuticals, are highly inefficient and spend lots of money on innovation hoping for one monster hit to pay it all back. Learning and performing are paradoxically related because when someone is focused on performing well, they usually are not learning anything, and vice versa.

This tension is represented in the diagram below. 

I think a good metaphor for the desired combination of efficiency, innovation, and adaptability is a jet ski. This is nicely shown in this cool video (taken about 100 km south of Brisbane). 

My choice of metaphor was inspired by discussions with a colleague who has taken a  Prince2 Agile Project Management course. To illustrate the need for a combination of efficiency and agility they use the metaphor of a jet fighter. I do not like military metaphors, because of their association with violence and the corrupt military-industrial complex. I work with people in the Majority World and such a metaphor may have a negative association. For example, a recent article in The Economist expressed concern that Nigeria is falling apart, partly due to internal insurgencies. It contains the observation

Money could come from cutting wasteful spending by the armed forces on jet fighters, which are not much use for guarding schools. 

So the challenge for real leaders (not managers) is to foster an organisational culture that balances efficiency, adaptability, and innovation. 

Role of quantum nuclear motion in biomolecular systems

 Total I am giving a talk, "Effect of quantum nuclear motion on hydrogen bonds in complex molecular materials" at Light-matter Interactions from scratch: Theory and Experiments at the Border with Biology 

Here are the slides

The talk provides a concrete example of the tutorial on constructing simple model Hamiltonians for complex materials that I give before the talk. It relates to the bio theme of the meeting through work on isotopic fractionation in proteins and the recent paper below. It makes use of the simple model that I talk about.

Unusual Spectroscopic and Electric Field Sensitivity of Chromophores with Short Hydrogen Bonds: GFP and PYP as Model Systems

Chi-Yun Lin and Steven G. Boxer

Tutorial on modelling quantum dynamics in biomolecules

This week I am giving two (virtual) talks at a meeting

Light-matter Interactions from scratch: Theory and Experiments at the Border with Biology 

supported by the ICTP (International Center for Theoretical Physics) in Trieste.

In the ICTP tradition, one talk is a tutorial and the second talk is about my research.

Here are the slides for the tutorial on Effective Model Hamiltonians for Quantum Dynamics in Complex Molecular Materials. Feedback is welcome.

The research talk is about hydrogen bonding. I will post slides for that later.

Organ music: cells self-organise into organs

Biology involves many different scales. At each scale, one considers what are the essential components and how they interact with one another. 

All living beings are composed of organs which in turn are composed of biological cells. The functionality of an organ emerges from the interaction between cells. 

Part 3 of The Economist's excellent series on biology is How organisms are organised. Here are a few highlights.

The twin processes of differentiation (many different types of cell) and integration (a highly functional structure) [are] at the heart of what makes organs tick.

How are the structures of plants and animals different? Why?

... animals and plants have different relationships with time and space. These different ways of life require different sorts of flexibility. Animals move through space but, once adult, change shape comparatively little over time. Plants stay still in space but change shape a lot as they grow. 

Most animals seek the energy they need by hunting or foraging. Plants’ energy-seeking behaviour is a matter of growing roots to take in water and minerals, and flat, green surfaces to absorb the sunshine and carbon dioxide that make up the preponderance of their food.

Muscles, nerves, and bones need to grow to a pre-arranged design much more than branches, twigs, and leaves do.

A human has about 80 distinct organs. The brain is the most complicated organ. It has about 86 billion nerve cells (neurons). There are 133 types of these in the cortex of the brain. 

Neurons are the essential components. Then one needs to consider how these components interact with one another.

A single neuron may be connected to as many as 10,000 other neurons. There are more than one hundred different types of chemical neurotransmitters with which to send and/or receive messages at the points of connection between.

The figure below shows how neurons are connected to one another via axons. Electric signals travel along the axon by action potentials.

The brain is a highly complex system. There are a large number of components, of many different types, and the large connectivity between them, and a large number of ways they can interact with one another. Given this complexity is it really that surprising that brains can "think" and process complex information. Parenthetically, I think this is another simple reason why I think proposals of quantum consciousness are so fanciful. Before, invoking such speculative ideas I think proponents should first rule out a simpler hypothesis: 

Consciousness (defined in some simple computational sense, putting aside profound philosophical nuance) can emerge from purely classical processes in such a complex system.

Hopfield showed how associative memory could emerge from a model that is much simpler than an actual brain. To me, this gives confidence that it is reasonable to work with the classical hypothesis.

If organisations are emergent can they be managed?

 Any organisation is composed of many interacting parts. For example, a university is not just composed of staff and students, but also includes collaborators, donors, employers, suppliers, parents, graduates, and trustees. Their interactions with one another are influenced by structures, such as buildings, committees, and government policy. Furthermore, a university exists in a context: political, economic, historical, and cultural. What emerges from the interactions of all these components may be new states, for good or for ill. Like all emergent phenomena these states are hard to predict. For example, what will lead to high-quality education or a diverse student body? Can desirable outcomes be managed? What is the role of leadership in large organisations? Are there some universal principles of management that are useful for a wide range of organisations, whether corporations, NGOs, universities, or government departments?

Researching, teaching, and writing about "Organisational Development" and "management" is a massive industry; from Business schools in universities to a multitude of popular books for sale in airports. A fascinating paper is

The Dialogic Mindset: Leading Emergent Change in a Complex World by Gervase Bushe and Robert Marshak.

It questions the paradigm of the "visionary leader", "command and control", and the "performance mindset" that focuses on instrumental and measurable goal setting and achievement.

To understand the limitations of this management paradigm I find it helpful to reflect on the history and context of how it emerged (!) in the USA after World War II. After the war, veterans who returned to civilian life had experienced a particular leadership and organisational culture of the military: hierarchy, authority, process, discipline, solidarity, male, mono-cultural, ...  And, it worked in the context of war!

Many war veterans, both junior and senior, took this approach and mentality into industry, and it worked well in the American post-war economic boom of assembly-line-based large-scale manufacturing. The automotive industry, centred around Detroit, was representative. Arguably, the success was based on efficiency not innovation, limited competition in a simple market, and a homogeneous workforce. Two important figures who emerged from this Detroit era were Peter Drucker and Robert McNamara. Drucker did a seminal two-year study of General Motors, during WWII, that started his trajectory towards becoming the doyen of management studies. McNamara took his strategic planning experience in the war, and applied it successfully at Ford for 15 years, rising to become President of Ford in 1960. He then became Secretary of Defense for JFK and used the same management approach for the USA's involvement in the Vietnam war. This was an unmitigated disaster, but that did not stop him from using a similar approach when President of the World Bank.

Back to Bushe and Marshak and today's world. They claim that

The “visionary leader” narrative and performance mindset that predominate in theories and practices of “Change Leadership” are no longer effective in an environment of multi-dimensional diversity marked by volatility, uncertainty, complexity, and ambiguity.

The prevailing narrative of leadership is based on the assumption that great leaders must [be strategic thinkers], have a vision, and the ability to lead followers to that vision. Leaders, followers, and commentators alike assume that being a visionary is indispensable to organizational leadership.

... a leading voice supporting an alternative paradigm is Heifetz’s (1998) leadership model that indirectly challenges the heroic, visionary orthodoxy. He divides the decision situations leaders face into technical problems, which can be defined and solved through a top-down imposition of technical rationality; and adaptive challenges, which can only be “solved” through the voluntary engagement of the people who will have to change what they do and how they think. 

In Heifetz’s alternative narrative of leadership, adaptive leaders identify challenges but instead of providing solutions, they encourage employees and other stakeholders to propose and act on their own solutions.

 A nice example is how employees shaped strategy at the New York Public Library. 

The problem with the standard narrative is that it overlooks that organisations are emergent entities where cause-effect relations are not understood and outcomes are hard to predict. This challenge is exacerbated today by the fact that any organisation is not an isolated entity but is immersed in a complex and rapidly changing environment. This puts a premium on innovation and adaptability. 

Future posts will explore what this might mean in practice. Can self-organising processes and emergence achieve desired outcomes by "changing the conversation"?

Colloquium on 2021 Nobel Prize in Physics II

 Here are the slides from today's talk.

How to move towards doing Deep Work

"Shallow work is non-cognitive, logistical or minor duties, often performed while distracted. These efforts require little cognitive effort, tend to create little value, and are usually easy to replicate." Examples include replying to emails, browsing websites, looking at social media, filling in forms, and attending meetings.

"Deep work is the ability to focus without distraction on a cognitively demanding task. These efforts create new value, improve your skill, and are hard to replicate.”

A colleague told me that Cal Newport's book, Deep Work, revolutionised his professional life.  These two short videos give a nice summary, focusing on quite practical ways to implement the ideas. They are both based on this article by Dan Silvestre.

Colloquium on 2021 Nobel Prize in Physics

 Every year the UQ Physics Department has a colloquium where someone describes the science behind the latest Nobel Prize. This year I am going to talk about Parisi and the spin glass problem. My colleague Henry Nourse will talk about the climate modelling part.

In preparation, I have found the book, Spin Glasses and Complexity by Daniel L. Stein and Charles M. Newman, very helpful. It is at the level of a colloquium and has a nice chapter on applications to other areas of science (e.g. proteins, simulated annealing, optimisation, computer science, ...) It enabled me to finally "understand" the background and significance of Hopfield's famous paper from 1982, "Neural networks and physical systems with emergent collective computational abilities".

Thinking about replica symmetry breaking has brought back memories of when I was a graduate student at Princeton. When I started Anderson was thinking about spin glasses a lot and had people working on it. I heard lots of talks about spin glasses, replica symmetry breaking, travelling salesmen, ultrametricity, ... Even David Gross gave a colloquium about work he did on spin glasses, with a very warm introduction by Phil. ["I introduce David Gross the condensed matter theorist"] However, once the cuprates happened at the end of 1986, Anderson seemed to largely drop the spin-glass work. Except for Dan Stein, everyone started working on cuprates. In hindsight, I wonder if that was a mistake. In particular, it might have been better for many of his students if they had worked on complexity rather than cuprates.

Next week I will post a draft of my slides. In the meantime, two questions for readers:

1. What are some specific questions you might like answered in such a colloquium?

2. What are some specific resources you may have come across about this year's prize that you found helpful or interesting?

Here are the slides.

Management is not leadership. II

 Previously, I have argued that being in management is neither a necessary nor a sufficient condition for showing leadership. I have also discussed how some articles about management, such as in the Harvard Business Review, can be helpful in academic contexts. This is in spite of the fact that I detest the idea that the university is a "business".

Here I bring the two points together. There is a nice short article in the HBR,Three Differences Between Managers and Leaders by Vineet Nayar

Counting value vs Creating value. Only managers count value; some even reduce value by disabling those who add value.

Circles of influence vs Circles of power. Managers have subordinates and leaders have followers. 

Leading people vs Managing work. Management consists of controlling a group or a set of entities to accomplish a goal. [Leaders]... influence, motivate, and enable others to contribute toward organizational success. 

Why are superfluids creepy?

 A signature effect associated with superfluidity in liquid helium is that it can climb up the walls of a container and empty the container. This is seen in the video below (beginning at 1:10).

But what is the physics behind this? 

Why is this a signature of superfluidity?

The schematic below is helpful. [It is figure 1.8 in Superfluidity and Superconductivity by Tilley and Tilley.]

We need to distinguish between which parts of the underlying physics occur for all fluids and which only occur for a superfluid.

1. For any liquid in thermodynamic equilibrium inside a container there is some vapour present. Some of this vapour condenses onto the surface of the container, forming a thin film of liquid on the surface. The surface of the liquid is actually not completely flat but curves upwards at the edge of the container surface. An example of this is a concave meniscus that one sees inside a small tube.

2. For a normal fluid the surface film is relatively thin and is pinned to the container surface by the viscosity of the fluid.

3. In superfluid helium the film is thick enough that the superfluid component of the fluid can flow freely. The film also extends to the top of the container walls.

Thus, the superfluid forms a continuous film that extends up and over the container walls. 

4. Superfluid in the film can flow freely if there is a driving force. The difference in gravitational potential energy between the surfaces of the liquid inside and outside the container provides such a driving force. The physics of this is identical to that of a regular siphon. It is just that in the case of superfluid helium the "tube" is the surface film and that due to superfluidity this film can flow.

And so, that is why superfluids are creepy.

The biochemical basis of mental health basics

 Yesterday the UQ Brain Institute had an excellent webinar Brain Health for Mental Health. Four researchers discussed the scientific basis for some simple strategies to reduce the likelihood of mental illness and/or to aid its treatment. These include

eat well

exercise regularly

sleep well

reduce screen time

drink less caffeine

minimise international travel (because of the associated jet lag).

I was fascinated to see the biological and biochemical basis for these strategies. I try to implement them myself and often emphasise the importance of these basic disciplines to others.

Some of the science is fascinating in itself. Did you know you can study sleep in fruit flies?

The webinar also provides a nice example of a public engagement activity. Rather than having one person give a long talk, four different researchers speak, and each for only five minutes with about five slides each. Each talk is followed by a question from the chair. Then at the end there are questions from the live online audience.

2021 Nobel Prize in Physics: from spin glasses to complexity theory

I was delighted to hear of the award of the Nobel Prize in Physics for 2021. The committee continues to surprise us. I did not make any predictions this year, because I had nothing new to predict. I am still surprised that experimental tests of Bell inequalities (Aspect, Clauser, Zeilinger) have still not got a prize. Maybe next year.

Here I will just write about the award to Giorgio Parisi “for the discovery of the interplay of disorder and fluctuations in physical systems from atomic to planetary scales” as it involves condensed matter theory, beginning with spin glasses, and like many things with Phil Anderson!

The popular science background and the scientific background to the prize are worth reading, as always. It notes that in a Physics Today column Anderson wrote in 1988,

“The history of spin glass may be the best example I know of the dictum that a real scientific mystery is worth pursuing to the ends of the Earth for its own sake, independently of any obvious practical importance or intellectual glamour.” 

This was in the first of a series of seven Reference Frame columns he wrote on spin glasses. The fifth column described the work of Parisi.

Here I will describe the basic ideas, particularly as they show that sometimes obscure basic science questions, very abstract ideas and mathematical formulations can be useful for very practical scientific questions, across a wide range of disciplines.

A spin glass is a distinct state of matter. This means, that in terms of the Landau paradigm, there must be an order parameter and an associated broken symmetry. What are they? Parisi found the answers.

First, as one usually does in theoretical condensed matter, one needs to write down a minimal model Hamiltonian that is complex enough to capture the essential physics but is simple enough to be amenable to analytical and/or computational analysis. 

Sam Edwards and Anderson proposed the following model for a spin glass, and Ising model where the spins are on a regular lattice but the interaction between any pair of spins, J_ik, is a random Gaussian variable with zero mean and non-zero variance.

This means that the interspin interactions are equally likely to be ferromagnetic or antiferromagnetic, leading to significant frustration.

To solve such a model one needs to calculate the partition function Z for each realisation of the J's (disorder), calculate F=- T ln Z, and average over all the configurations of disorder. 

Averaging Z over disorder is just a Gaussian integral, but averaging ln Z is analytically intractable.

Anderson's physical intuition was combined with the mathematical trickery of Edwards, that he had cultivated with his earlier work on quantum field theory and soft matter.

The replica trick is based on an identity that one learns in introductory calculus.

One considers not one system but rather n identical copies (replicas) of the physical system, calculates the average of the partition function for this fictional n-system, and then treats n as a continuous analytical variable and takes the limit that n goes to zero in the formula above. Wow, that is abstract! But, it is tractable.

Personal aside: more than twenty years ago I learned and used the replica trick because (like supersymmetry) as it provides a powerful mathematical tool to treat disorder exactly in one-dimensional models. But, the spin-glass case is much richer and more subtle.

Strange things happen for the spin glass. Soon after Edwards and Anderson's work, Thouless, Anderson, Palmer, and others made the rather puzzling discovery that not all the replicas were the same below the temperature associated with transition to the spin-glass state. The replica symmetry was broken in the spin-glass state.

Parisi proposed the order parameter below for this broken symmetry state. i denotes a lattice site, and the indices alpha and beta denote replicas. When alpha and beta have different values, the order parameter only becomes non-zero when the replicas are different.

Parisi, Toulouse, Mezard, and others then showed that there is a hierarchical structure associated with the order parameter leading to the concept of ultrametricity which can be associated with the rugged energy landscape of not just the spin-glass problem, but also optimisation problems, simulated annealing, protein folding, neural networks, ...

A nice overview that puts the theory of spin glasses in a much broader scientific context is Physics and Complexity by David Sherrington.

On Doug Natelson's blog, nanoscale views, there is a nice discussion in the comments about Parisi's Nobel and the subtle issue of the connections between separation of time scales and ultrametricity, and the connections (or not) between Parisi and climate science.

What do we really understand about cuprate superconductors?

 At a recent meeting of the condensed matter theory group at UQ we watched the first half of a Harvard (online) seminar that Steve Kivelson gave (at the end of 2020), What do we know about the essential physics of high temperature superconductivity after one third of a century?

As a springboard he takes Phil Anderson's final posting of the arXiv, Last Word's on the Cuprates, from the end of 2016. He was 93 years old then!

Kivelson considers that there are two things we really understand about the cuprates. The first, is that the d-wave superconductivity is intimately connected with the antiferromagnetism of the undoped materials.

The second, is that Tc, the superconducting transition temperature, is determined by thermal disordering of the phase of the order parameter for the superconducting state. This is in contrast to conventional superconductors, where Tc is determined by the amplitude of the order parameter vanishing. 

Kivelson's argument for the first point is based on nice work done a decade ago with Sri Raghu and Doug Scalapino, and that led to other work I have blogged about. It should be stressed that this work is a weak-coupling renormalisation group treatment and so the question remains as to whether the phase diagram for weak-coupling is adiabatically connected to that for strong coupling, which is the regime of the actual cuprate materials. In different works, as U/t increases from very small values to large values there are no phase transitions. Cluster Dynamical Mean-Field Theory (DMFT) studies give some confidence that this is the case. However, not everyone will be convinced by that.

The talk is worth watching, even if at times it gets a bit too technical. It is very important that we have such honest and open reflections about how much progress is (not) being made in a field. I largely agree with Kivelson, but do find the lack of progress rather discouraging and cannot see that this will be inspiring bright young graduate students to enter the field or for funding agencies to put more money into it.

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?

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. 

    

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

Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase

Shayantani Mukherjee and Arieh Warshel

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.

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.

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.

The emergence of condensed matter as a fundamental force in physics

What shapes the emergence and influence of a specific new academic discipline or research field? How much does context matter?

How is the discipline defined? By the objects studied, methods used, central concepts, questions asked, goals, or key discoveries? And, who gets to define the discipline: text-book authors, current researchers, distinguished academics, or university managers?

It may depend on who you ask. A discipline can be viewed from intellectual, historical, institutional, political, economic, and sociological perspectives. It all depends on what questions you ask.

Arguably, for most of the twentieth-century physics was considered the dominant field of science. We also observe today that condensed matter physics is a dominant force in physics. This is reflected in many different measures, such as numbers of practitioners, journal articles, PhDs, citations, and Nobel Prizes.

How did this happen? 

Joseph Martin is a historian who explores this question in his 2018 book, Solid State Insurrection: How the Science of Substance Made American Physics Matter. He looks particularly at physics in the USA in the political and economic context of the Cold War, focusing on the rise of solid-state physics, and its metamorphosis into condensed matter physics. The role of institutions such as government, industry, and the American Physical Society (journals, conferences, divisions) is carefully examined. Public testimony of Phil Anderson against the SSC (Superconducting SuperCollider) in 1989 is considered to be a watershed moment and highly symbolic. 

The book is carefully researched, beautifully written, and contains important new insights. I highly recommend it.

In exploring these issues I think it important to find a balance between two extremes. On the one side, there are purists and idealists who claim that physicists are the best (or even only) people to provide a useful and reliable perspective. Science is all about reality, facts, and truth, and contexts (social, political, economic) are completely irrelevant. At the other extreme are the social constructivists who think science is just about politics and power, both inside and outside the university community. Martin is to be commended that he does not tend towards either of these extremes.

A Physics Today article is adapted from the book When condensed-matter physics became king and gives a useful summary.

To whet your appetite for the whole book, a good place to start is the concluding chapter. Martin offers two fascinating counterfactual histories: one where the Manhattan Project failed, one where APS did not keep industrial physicists in the fold.

the most active frontier of the twentieth century was not the high-energy frontier, but the complexity frontier. It was the demystification of the properties of complex matter and the applications of those properties, which remade our technological world, from home computing, stereo equipment, and cookware to communication, transportation, medicine, and warfare.

This is a tendentious framing, but it serves a purpose: it exposes the historiographical contingency of the disproportionate focus on nuclear physics, high energy physics, and cosmology, alongside the historical contingency of the dominance those fields assumed over public discourse about physics in the second half of the twentieth century. Two counterfactual scenarios help to probe that contingency further, each of which offers heuristic utility by throwing into relief the role solid state physics played, despite lacking the public acclaim of its sibling subfields, in securing the prominence of American physics.

First, given the high degree of institutional volatility in the early post–Second World War era, it is easy to imagine a counterfactual scenario in which solid state physicists migrate away from physics and into chemistry, metallurgy, and engineering, much as electrical engineering had some decades earlier. It was a contingency about which the field’s founders actively worried, and the American Physical Society council was demonstrably squeamish about clearing the type of institutional space that would give the society a more industrial flavor. Without solid state, which accounted for a large proportion of the postwar population boom, physics would have stayed smaller and grown more slowly.

We can imagine a second counterfactual scenario in which the Manhattan Project never acquired the scale or resources it needed to construct a working bomb before the end of the war in the Pacific... Suppose, for whatever reason, the Second World War ends without a dramatic, public demonstration of the power of the nucleus...  In this second scenario, solid state physicists would have been well positioned to become much more politically influential in the early Cold War, in particular on the strength of radar research,..

Aside. Earlier I posted about a nice article Martin wrote about public perceptions about condensed matter physics.

Einstein on big questions

The mere formulation of a problem is far more essential than its solution, which may be merely a matter of mathematical or experimental skills.

To raise new questions, new possibilities, to regard old problems from a new angle, requires creative imagination and marks real advance in science.

I am enough of an artist to draw freely upon my imagination. Imagination is more important than knowledge. Knowledge is limited. Imagination encircles the world.

Albert Einstein and Leopold Infeld (1938), The Evolution of Physics

I recently encountered this quotation in The Poetry and Music of Science: Comparing Creativity in Science and Art by Tom McLeish. I have heard many times the "Imagination is more important than knowledge" quote, sometimes as a dubious justification for dubious ideas. However, I did not know the context. 

My postdoctoral advisor, John Wilkins tried to drill into me, the idea in the first paragraph, that just coming up with a well-defined formulation of a problem could be a significant advance. This idea certainly had some impact on me, since I sometimes hear my non-scientist wife quote it!

On reflection, I am afraid that I too easily lose sight of this priority of defining problems, just like the method of multiple alternative hypotheses. Good science is hard.

Why am I reading this article? What question am I trying to answer?

Why am I writing this paper? What question am I trying to answer?

What is the problem I assigning a student to work on? Is it well-formulated?

Defining good research questions is hard work and requires discipline.

Springy stringy molecular crystals

Perfect crystals are elastic. When a stress is applied and then removed the crystal will bounce back to its original shape. However, in reality no crystal is perfect. If the applied stress is too large the crystal will fracture. Understanding fracture is a big deal in materials science and involves some fascinating physics, including the role of topological defects. 

There are two distinct properties: elasticity and plasticity. They are associated with temporary and permanent changes in shape in response to an applied stress.

They are quantified by the elastic stiffness and the tensile strength, respectively. They reflect material properties at quite different length scales. 

A beautiful and accessible short introduction is 

Stressed out crystals

Bart Kahr & Michael D. Ward 

This is a commentary of some work by a few of my UQ chemistry colleagues, who have made and studied a molecular crystal that is incredibly flexible, as seen in this movie.

Atomic resolution of structural changes in elastic crystals of copper(II) acetylacetonate

Anna Worthy, Arnaud Grosjean, Michael C. Pfrunder, Yanan Xu, Cheng Yan, Grant Edwards, Jack K. Clegg & John C. McMurtrie 

A particular advance is that they use a synchrotron to perform spatially resolved X-ray crystallography to determine how the crystal structure varies spatially within a bent crystal. 

The material of interest has quasi-one-dimensional antiferromagnetic interactions and has been studied theoretically by my condensed matter theory colleagues.

Mechanomagnetics in Elastic Crystals: Insights from [Cu(acac)2]

Elise P. Kenny, Anthony C. Jacko, Ben J. Powell

But there is more...

A recent Science paper describes ice fibers that were particularly flexible.

Elastic ice microfibers

Peizhen Xu, Bowen Cui, Yeqiang Bu, Hongtao Wang, Xin Guo, Pan Wang, Y. Ron Shen, Limin Tong

Emergence of complex patterns

I think it is amazing how in the universe we see diverse and beautiful patterns and structures. Even relatively simple systems can self-organise to produce things one would not expect or predict. Consider clouds, turbulent flows, leopard spots, a tree leaf, spiral galaxies, biological cells...

It is also amazing and beautiful that we can develop relatively simple mathematical models that can produce similar patterns.

This is emergence!

Here is a beautiful example that recently came to my attention.

The associated PRL is

Faraday-Wave Contact-Line Shear Gradient Induces Streaming and Tracer Self-Organization: From Vortical to Hedgehoglike Patterns

Héctor Alarcón, Matías Herrera-Muñoz, Nicolas Périnet, Nicolás Mujica, Pablo Gutiérrez, and Leonardo Gordillo

There is also a Physics story too.

Chemical fingerprints on blood diamonds

“Fortunately, the majority of gentlemen who are persuaded to steal things don’t really know a huge amount about science”

This is a choice quote in a fascinating article, New Australian technology tracks down gold thieves and blood diamonds ["New tech to trace dodgy diamonds" in the print edition] in the Australian Financial Review (AFR) Weekend.

It describes the work of John Watling, Chief Scientist at the company Source Certain. Basically by measuring the relative amounts of different trace elements [chemical impurities] in a sample of gold or diamond one can determine what mine that it has come from.

Sage wisdom on computational materials science

Roald Hoffmann and Jean-Paul Malrieu are two of my favourite living theoretical chemists. Both greatly value the role of concepts and intellectual clarity in theory. Hoffmann has featured in 22 posts on this blog.

They recently published a wonderful trilogy in  Angewandte Chemie.

Simulation vs. Understanding: A Tension, in Quantum Chemistry and Beyond. 

Part A. Stage Setting

Part B. The March of Simulation, for Better or Worse

Part C. Toward Consilience

I add this trilogy to my list of 5 papers every computational chemistry student should read, suggested by me a decade ago. [Malrieu is author of one of those and Hoffmann co-author of another.]

Although the trilogy addresses and uses specific examples from computational quantum chemistry it is just as relevant to anyone interested in computational materials science. Actually, I hope that anyone interested in materials science would read and digest it as it gives a sober and balanced perspective about the relationship between theory, simulation, and understanding.

Articles are timely as they address hype about how AI techniques will "revolutionise" materials theory. 

The articles are beautifully written and engage with broader themes such as philosophy of science, culture, art, and politics.

Finally, I just love this photo of the two authors, both in their eighties. the photo reflects some of the joy they find in science, so beautifully expressed in these articles.

I thank Ben Powell for bringing the papers to my attention.

Covid-19 in a different world

 

Covid-19 has turned the world upside down. Different people and communities have had very different experiences. In my state of Queensland, it is almost a different world. To illustrate I share the data above, which prompted a three-day lockdown in Brisbane. For reference, Queensland has a population of 5.2 million.

A number of factors have contributed to the relatively positive situation. Australia is an island. Our borders were closed early. There was unity between state and federal governments. Generally, lockdowns have been pronounced promptly. Although Australians do not like authority and are a rebellious bunch, lockdowns and mask mandates have generally been observed. We are not immune from conspiracy theories and vaccine hesitancy. But, overall we have not been plagued by the same level of "politicisation" that has hobbled other countries. 

In some ways, I feel I am living in a different world.

Yet, some of this good fortune should not lead to pride and complacency. Things may still come unstuck. The Delta variant is spreading in Sydney and half the country is in lockdown. The government vaccine rollout has been dubbed a "stroll out".  Only 12 percent of the population has been fully vaccinated. Australia is currently ranked last among the OECD countries. 

The associated "blame game" has even been featured in The New York Times.

Is condensed matter physics too abstract?

Condensed matter physics is about the properties of real materials. Real stuff that you can see and touch and that you can use to make very practical things like TV screens and mobile phones. Yet, I find it fascinating and somewhat ironic that in condensed matter theory very abstract ideas and mathematical techniques keep cropping up (and being extremely useful): variable spatial dimensions, imaginary frequencies, topology, Chern numbers, conformal invariance, ...

Yet, there is a danger with abstraction. Theoretical condensed matter is not pure mathematics. Perhaps, too often fancy and beautiful mathematics is prized over physical intuition and insight. Theory may take precedence over experiment. How does one find the appropriate balance?

This is part of broader issues about the role of abstraction and formality in education.

Pierre de Gennes (1932-2007) was arguably the founder of soft matter as a research field, as recognized by the Nobel Prize in Physics in 1991. He began his career working on superconductivity and went on to develop a unified framework to understand soft matter (liquid crystals, polymers, foams, colloids...), introducing ideas such as order parameters, scaling, renormalisation, and universality.

After his Nobel, de Gennes gave many lectures in French high schools, which were then published as a book, Fragile Objects: Soft Matter, Hard Science, and the Thrill of Discovery. I highly recommend it, both as a popular introduction to soft matter, but also to hear the perspective of a great scientist on education and research.

de Gennes spent almost his whole life living and working in France. In the book he rants about the French system, particularly its obsession with entrance exams, mathematics, formality, and the abstract.

“Manual skills, visual acumen, the sense of observation, an interest for the physical world which surrounds us, are all qualities that are neglected or downgraded.”

“To work in a garage seems to me the best initiation to a professional life.”

“Ignorance of the real world causes grave distortions.”

“the positivist prejudice”

I found this fascinating because one thing de Gennes is famous for is showing how some properties of a polymer can be understood by considering a theory involving a vector of dimension n, where n was a continuous variable, in the limit where n approaches zero! That is pretty abstract! But, I guess the point is that he is not against abstraction, exams, and mathematics, per se. Rather, he is against them taking on a life of their own.

de Gennes concerns are also shared by Henri Alloul (well known for beautiful NMR experiments on strongly correlated electron materials) author of Introduction to the Physics of Electrons in Solids. In the Preface, he writes, 

In many countries, teaching traditions have always given pride of place to a formal, and essentially deductive, presentation of the physics, i.e., starting from formal hypotheses and leading up to observable consequences. This deductive approach leaves a purely a posteriori verificational role to observation, and hides the thinking that has gone into building up the models in the first place. Here we shall adopt the opposite approach, which begins with the fact that in science in general, and in solid state physics in particular, the qualitative understanding of a phenomenon is an important step which precedes the formulation of any theoretical development. We thus urge the reader to carry out a careful examination of the deeper significance of experimental observations, in order to understand the need for specific models and carry out realistic approximations.

The debate about abstract mathematics is also central to contrasting views about the Institute for Advanced Study at Princeton.

de Gennes's views would have also resonated with Harry Kroto who shared The Nobel Prize in Chemistry for the discovery of buckyballs. He credited playing with Meccano as a child as very important in his scientific development.

Sweet demonstrations of phase transitions

This week my wife and I did some science experiments with kids, aged about 8-12, at a holiday kids club organised by our church. The first day we did rockets, using the old standbys of baking soda rockets and mentos and coke.

On the second day, we did the science of chocolate. Ten years ago (!) we had done this based on some demonstrations developed at Harvard, described in this paper The Science of Chocolate: Interactive Activities on Phase Transitions, Emulsification, and Nucleation. 

Teaching kids about phase transitions with ice and steam is not quite as exciting or memorable as them melting chocolate in their mouths. An important scientific idea is:

Physical properties of matter (such as melting temperature) change with differences in chemical composition.

This is illustrated by the different melting temperatures of white, milk, and dark chocolate.

We also tried to mix water and oil, with and without the presence of detergent. This illustrates ideas about emulsification, including hydrophobic interactions. This is relevant to the production of nice smooth and uniform chocolate because the cocoa powder can only dissolve in the cocoa butter when an emulsifier is present.

Discussing chocolate is also an opportunity to discuss Milton Hershey (USA) and the Cadbury family (UK). They were not only philanthropists but were proactive in taking care of employees and their families, e.g. constructing schools, parks, and affordable housing. Richard and George Cadbury developed the garden village of Bournville; now a major suburb of Birmingham. I particularly like this sentence in the Wikipedia entry on George Cadbury, showing how he was far ahead of his time.

In 1901, disgusted by the imperialistic policy of the Balfour government and opposed to the Boer War, Cadbury bought the Daily News and used the paper to campaign for old age pensions and against the war and sweatshop labour.^[4]

Other scientific articles of interest include the following. The first two discuss how there are six different polymorphs (crystal structures) of chocolate. The competition between these states comes into play with tempering, snapping, shine, and smoothness. [Aside: In general, calculating the relative energies of different polymorphs of molecular materials is a major scientific challenge.]

Chocolate: A Marvelous Natural Product of Chemistry, Ginger Tannenbaum

Using Differential Scanning Calorimetry To Explore the Phase Behavior of Chocolate Michael J. Smith

The kitchen as a physics classroom Amy C Rowat, Naveen N Sinha, Pia M Sörensen, Otger Campàs, Pere Castells, Daniel Rosenberg, Michael P Brenner and David A Weitz