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

 View ORCID ProfileSteffen Klein,  View ORCID ProfileMirko Cortese,  View ORCID ProfileSophie L. Winter,  View ORCID ProfileMoritz Wachsmuth-Melm,  View ORCID ProfileChristopher J. Neufeldt, Berati Cerikan,  View ORCID ProfileMegan L. Stanifer,  View ORCID ProfileSteeve Boulant,  View ORCID ProfileRalf Bartenschlager,  Petr Chlanda

View ORCID Profile

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 Iserman, Christine Roden, Mark Boerneke, Rachel Sealfon, Grace McLaughlin, Irwin Jungreis,  View ORCID ProfileChris Park, Avinash Boppana, Ethan Fritch, Yixuan J. Hou, Chandra Theesfeld, Olga G Troyanskaya, Ralph S. Baric,  View ORCID ProfileTimothy P. Sheahan, Kevin Weeks, Amy 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.

In situ structural analysis of SARS-CoV-2 spike reveals flexibility mediated by three hinges

1. View ORCID ProfileBeata Turoňová1,2,*, 
2. View ORCID ProfileMateusz Sikora3,*, 
3. View ORCID ProfileChristoph Schürmann4,*, 
4. View ORCID ProfileWim J. H. Hagen1, 
5. View ORCID ProfileSonja Welsch5, 
6. View ORCID ProfileFlorian E. C. Blanc3, 
7. View ORCID ProfileSören von Bülow3, 
8. View ORCID ProfileMichael Gecht3, 
9. View ORCID ProfileKatrin Bagola6, 
10. View ORCID ProfileCindy Hörner4,7, 
11. View ORCID ProfileGer van Zandbergen6,8,9, 
12. View ORCID ProfileJonathan Landry10, 
13. View ORCID ProfileNayara Trevisan Doimo de Azevedo10, 
14. View ORCID ProfileShyamal Mosalaganti1,2, 
15. View ORCID ProfileAndre Schwarz1, 
16. View ORCID ProfileRoberto Covino3,11, 
17. View ORCID ProfileMichael D. Mühlebach4,7, 
18. View ORCID ProfileGerhard Hummer3,12,†, 
19. View ORCID ProfileJacomine Krijnse Locker13,†, 
20. View ORCID ProfileMartin Beck1,2,†
21. 
    

Questions to ask about possible writing projects

When considering a writing project it is good to think about the nature and feasibility of the project. Here my focus is not on projects a typical scientist has to do such as writing a thesis or writing research papers. Rather I'm concerned with optional projects such as writing a review article, a popular book, a popular article, or a book chapter. I find the following questions helpful. The answers may be inter-related. Hence, answers to the earlier ones may need to be revised after answering the later ones.

What is my main message?

The goal is not to write a book or an article. The goal is to communicate something, something that is important and interesting.

Who is my audience?

This will really shape how you write the piece and where you try to publish it.

Am I the best person to write this piece?
In different words, who is my competition?

What is my real goal? 

To have fun? To enjoy the process? To learn something new? To become rich and famous?
To fulfill the tenure requirement of my university for "public engagement"? To get lots of citations? [Review articles are a good way to do this.] To show the general public why condensed matter physics is such a rich, exciting, and important field? To showcase my latest research results?

Clarifying your goal is necessary to answer the next question.

What is the likelihood I will achieve my goal?

Some of the goals above are much easier to achieve than others.

Besides me, who thinks that this project is a worthwhile endeavour?

Sometimes we are not very objective or realistic in our plans and aspirations. We may even delude ourselves about the importance of the proposed message, our ability to communicate it, and the likelihood of achieving our goal. Hence, an objective evaluation by more experienced colleagues and editors can save us time, pain, and disappointment.

What is the genre? What is the medium?

Is it a blog post, a piece in The Conversation, an article in Scientific American, a review article in a particular journal, or a textbook?
By the medium, I mean who will be my publisher (broadly defined)? Anyone can write a blog post. But if you want to publish a textbook you need a good publisher and contract.  For example, I am writing Condensed Matter Physics: A Very Short Introduction;  it is part of a series with a well-defined genre. The medium comes with some editorial support, marketing, and distribution.

What are model examples that I can use for inspiration and for comparison?

For example, with A Very Short Introduction, I have read and looked over many other in titles in the series, on a wide range of topics: Marx, Literary Theory, Complexity, Physical Chemistry, Depression, Corruption, Elementary Particles. That's helped me find ones I like and ones I don't like. Thinking through why helps me see how I want to write mine. By the way, the best one that I have read so far is Social and Cultural Anthropology.

Do I have the time, energy, and resources to see this project to completion?

It will take longer than you think. It will be harder than you think. The larger and the more ambitious the project, the greater this will be. Co-authors may lighten the workload and also enhance the project. But, they may also complicate things. Are their potential commenters on drafts or editors?

Can I do this project in stages? Can I start small and then build up to a larger project?

For example, can I go from a series of blog posts to an article and then to a popular book? This gradual approach can make things a lot more feasible. Also, one can get useful feedback along the way, both about content and level of interest. 

All these questions reflect what is happening this week for me. I am on a writer's retreat with my friends in the "holy" scribblers eclectic writing group. Each evening we discuss projects that we're working on and give another feedback. I am mostly working on my Very Short Introduction, and other members of the group represent some of my target audience. The picture above is the view from my writing desk.=

Do you have any other suggested questions? 

Feel free to share your own experiences.

Nobel Prize predictions for 2020

It is that time of year again. My physics predictions are the same as last year.

For physics this year I predict
Experiments for testing Bell inequalities and elucidating the role of entanglement in quantum physics
Alain Aspect, John Clauser, and Anton Zeilinger
They received the Wolf Prize in 2010, a common precursor to the Nobel. 

My personal preference for the next Nobel for CMP would be centred around Kondo physics since that is such a paradigm for many-body physics, maybe even comparable to BCS.

Kondo effect and heavy fermions
Jun Kondo, Frank Steglich, David Goldhaber-Gordon

Arguably the latter two might be replaced with others who worked on heavy fermions and/or Kondo in quantum dots.
Steglich discovered heavy fermion superconductivity.
Goldhaber-Gordon realised tuneable Kondo and Anderson models in quantum dots (single-electron transistors).

Unlike many, I still remain to be convinced that topological insulators are worthy of a Nobel.

How about other prizes?

The nomination deadline was January 31, before most people appreciated the significance of covid-19. I predict next year that their will be at least one prize (Chemistry, Medicine, Economics, or Peace) relating to public health and/or viruses. One possibility would be Bill and Melinda Gates for Peace.

Here are a few unusual suggestions.

Literature: Lin-Manuel Miranda for Hamilton

Peace (more likely next year): Colin Kaepernick and/or Black Lives Matter, Joshua Wong and/or other Hong Kong protestors, Jacinda Ardern.

On peace, here are some other ideas.

What do you think?