Showing posts with label soft matter. Show all posts
Showing posts with label soft matter. Show all posts

Wednesday, June 14, 2023

Demonstrating polymer entanglement

From Steve Spangler I learnt this "party trick" demonstration of how the polymer molecules (polyethylene) in a plastic bag are entangled with one another. 

I was not sure that it would work as easily as it did for him. But it did!




Thursday, July 8, 2021

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.

Friday, December 18, 2020

Lessons from the discovery of liquid crystals

I recently learned a little about the history of the discovery of liquid crystals, stimulated by Soft Matter: A Very Short Introduction by Tom McLeish. Besides being a fascinating story there are lessons about the importance of curiosity-driven research, interdisciplinarity, serendipity, and the long road to technology.

Friedrich Reinitzer (1857 - 1927) was a botanist and chemist who worked at the Institute of Plant Physiology in Prague. He was studying cholesterol with the aim of determining its molecular weight. He produced crystals of cholesteryl benzoate and measured their heat capacity as a function of temperature. Aside: For chemists today this measurement is known as differential scanning calorimetry (a constant source of heat is added and the temperature measured as a function of time). 

In 1888, Reinitzer observed that the crystal melted at 145.5 degrees Celsius (signified by absorption of heat), forming a milky liquid. However, at 178.5 degrees Celsius, there was a second absorption of heat, and the liquid became transparent. This suggested that there were two melting transitions. Puzzled by this Reinitzer consulted the physicist and crystallographer, Otto Lehmann, who promoted the idea that this was a new state of matter, which he dubbed a "liquid crystal" (or flowing crystal).

Today, cholesteryl benzoate is classified as a chiral nematic liquid crystal, which is also sometimes known as a cholesteric liquid crystal, in honour of the first one. A schematic of the ordering is shown below.


The milkiness was not explained until the 1960s by Pierre-Gilles de Gennes, who exploited an analogue with a superconductor in a magnetic field.

More detail is in the paper
Michel Mitov 

This discovery of liquid crystals was the first of many cases where a new state of matter was discovered by a thermodynamic measurement. Others include superfluid 4He (the lambda transition) and superfluid 3He, as I have recently highlighted.

Thursday, November 26, 2020

Signatures of soft matter

What is soft matter? 

Soft Matter: A Very Short Introduction by Tom McLeish has just been published.

McLeish identifies six characteristics of soft matter.

1. Thermal motion 

They exhibit large local spatial rearrangements of their microscopic constituents under thermal agitation. In contrast,  "hard" materials experience only small distortions due to thermal motion.

2. Structure on intermediate length scales

There are basic units ("fundamental" structures), typically involving a very large number (hundreds to thousands) of atoms, that are key to understand soft matter behaviour. These basic units are neither macroscopic nor microscopic (in the atomic sense), but rather mesoscopic (meso from the Greek word for middle). The relevant scales range from several nanometres up to a micrometer. An example of these length scales is those associated with (topological) defects in liquid crystals, such as those shown below.

Image is from here.

3. Slow dynamics

The mesoscopic length scales and complex structures lead to phenomena occurring on time scales of the order of seconds or minutes.

4. Universality

The same physical properties can arise from materials with quite different underlying chemistries.
This characteristic is of significant practical relevance. Solving a problem for one specific material can also solve it for whole families of materials. This universality is also of deep conceptual significance as understanding a general phenomenon is usually more powerful than just a specific example. 

5. Common experimental techniques

The dominant tools are microscopy, scattering (light, x-rays, neutrons), and rheometers which measure mechanical properties such as viscosity (rheology).

6. Multi-disciplinarity

Soft matter is studied by physicists, chemists, engineers, and biologists. 

The chapter titles in the book are 

Milkiness, muddiness, and inkiness [Colloids]

Sliminess and stickiness [Polymers]

Gelification and soapiness [Foams and Self-assembly]

Pearliness [Liquid crystals]

Liveliness [Active matter]

I highly recommend the book. Hopefully, later I will write a review.

Tuesday, October 20, 2020

The physics of the SARS-CoV-2 virion

 Some progress is being made in understanding the structure and dynamics of the SARS-CoV-2 virions (virus particles) that are responsible for the pandemic. A nice starting point for the non-expert is a recent article in The New York Times.


A fundamental question is what is the structure and symmetry of the virion? In particular, does it have the icosahedral symmetry possessed by many virions, as discussed in a talk I gave earlier this year and in a recent review (with lots of nice pictures). As far as I am aware, there are still no definitive results on the overall structure and symmetry. 

This preprint has some really nice images and videos such as the video below. 

SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography

Steffen KleinMirko CorteseSophie L. WinterMoritz Wachsmuth-MelmChristopher J. NeufeldtBerati CerikanMegan L. StaniferSteeve BoulantRalf Bartenschlager


Mathematical aside: the authors note that the geometric problem of how to place the spike protein (S) trimers on the surface of the virion is related to the "Tammes Problem" or the seventh unsolved mathematical problem listed by Steve Smale: how do you arrange a specific number of points on a sphere with the largest possible minimum distance between the points.

The paper below shows that the nucleocapsid protein (N) is similar to that for SARS-CoV and MERS. The protein can form dimers and tetramers, steps in the self-assembly of the whole virion.

Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate

Christiane IsermanChristine RodenMark BoernekeRachel SealfonGrace McLaughlinIrwin JungreisChris ParkAvinash BoppanaEthan FritchYixuan J. HouChandra TheesfeldOlga G TroyanskayaRalph S. BaricTimothy P. SheahanKevin WeeksAmy S. Gladfelter

Some nice soft matter physics is in the preprint below. It argues that the N protein can undergo liquid-liquid phase separation with the viral genome. Aside: even before covid, liquid-liquid phase separation was quite a hot topic in cell biology, as recently discussed by Tom McLeish. 

Architecture and self‐assembly of the SARS‐CoV‐2 nucleocapsid protein 

Qiaozhen Ye, Alan M. V. West, Steve Silletti, Kevin D. Corbett

Finally, the paper below combines molecular dynamics simulations with experiments to argue that the stalk of the spike protein has three hinges giving the head of the spike unexpected orientational freedom so it can scan the host cell surface.

The two-state model for spin crossover in organometallics

Previously, I discussed how spin-crossover is a misnomer for organometallic compounds and proposed that an effective Hamiltonian to describe...