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Category: math

GoV 1 : Geometry of viruses

As you may have guessed from the symmetries of Covid-19 post, I did spend some time lately catching up with the literature on the geometric structure and symmetries of viruses. It may be fun to run a little series on this.

A virus is a parasite, so it cannot reproduce on its own and needs to invade a host cell to replicate. All information needed for this replication process is stored in a fragile DNA or RNA string, the viral genome.

This genome needs to be protected by a coating made of proteins, the viral capsid. Most viruses have an additional fatty protection layer, the envelope, decorated by virus (glyco)proteins (such as the ‘spikes’ needed to infiltrate the host cell).



Most viruses are extremely small (between 20 and 200nm), our friend the corona-virus measures between 80 and 120nm. So, its genome is also pretty small (the corona genome has around 30.000 base pairs). To maximise its information, the volume of the protective capsid must be as large as possible, and must be formed by just a few different proteins (to free as much space in the code of the genome for other operations) and clusters of them are distributed over the polyhedral capsid, as symmetric as possible.

This insight led Watson and Crick, the discoverers of the structure of DNA, to the ‘genetic economy’-proposal that most sphere-like viruses will have an icosahedral capsid because the icosahedron is the Platonic solid with the largest volume and rotational symmetry group. They argued that the capsid is most likely constructed from a single subunit (capsomere), which is repeated many times to form the protein shell.



Little is known about capsid formation, that is the process in which the capsid proteins self-assemble into an icosahedral shape, nor about the precise interplay between the genome and the capsid proteins. If we would understand these two things better it might open new possibilities for anti-viral drugs, by either blocking the self-assembly process or by breaking the genome-capsid interaction.

A first proposal for the capsid structure was put forward by Caspar and Klug. Their quasi-equivalence principle asserts that each of the 20 triangular faces of the icosahedron is subdivided in 3 subunits, each consisting of at least one protein.

Most viruses have much more than 60 proteins in their capsid, so Caspar and Klug introduced their $T$-number giving the number of proteins per subunit. One superimposes the triangulation of the icosahedron with the hexagonal plane lattice, then $T$ is the number of sub-triangles of these hexagons contained in each subunit. For $T = 7$ we have the following situation



Folding back the triangulation to form the icosahedron one then obtains a tiling consisting of hexagons (the green regions) and pentagons (the blue regions)



It turned out that many viruses with icosahedral symmetry consist of subunits having a different number of proteins, such as dimers (2 proteins), trimers (3 proteins), or pentamers (5 proteins) and these self-organise around a 2, 3, or 5-fold rotational axis of the icosahedron.

This led Reidun Twarock around 2000 to propose her virus tiling theory. This is a generalisation of the Caspar-Klug theory in which one superimposese the triangulation of the icosahedron with other tilings of the plane, consisting of two or more non-congruent tiles. Here an example which looks a bit like the aperiodic Penrose tilings of the plane.



Here’s a recent Quanta-Magazine article on Twarock’s work and potential consequences: The illuminating geometry of viruses.

And here’s an LMS Popular Lecture, from 2008, by Raidun Twarock herself: “Know your enemy – viruses under the mathematical microscope”.

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Scholze’s condensed sets and Mazzola’s path to creativity

Some months ago, Peter Scholze wrote a guest post on the Xena-blog: Liquid tensor experiment, proposing a challenge to formalise the proof of one of his results with Dustin Clausen on condensed mathematics.

Scholze and Clausen ran a masterclass in Copenhagen on condensed mathematics, which you can binge watch on YouTube starting here

Scholze also gave two courses on the material in Bonn of which the notes are available here and here.

Condensed mathematics claims that topological spaces are the wrong definition, and that one should replace them with the slightly different notion of condensed sets.

So, let’s find out what a condensed set is.

Definition: Condensed sets are sheaves (of sets) on the pro-étale site of a point.

(there’s no danger we’ll have to rewrite our undergraduate topology courses just yet…)

In his blogpost, Scholze motivates this paradigm shift by observing that the category of topological Abelian groups is not Abelian (if you put a finer topology on the same group then the identity map is not an isomorphism but doesn’t have a kernel nor cokernel) whereas the category of condensed Abelian groups is.

It was another Clausen-Scholze result in the blogpost that caught my eye.

But first, for something completely different.

In “Musical creativity”, Guerino Mazzola and co-authors introduce a seven steps path to creativity.



Here they are:

  1. Exhibiting the open question
  2. Identifying the semiotic context
  3. Finding the question’s critical sign
  4. Identifying the concept’s walls
  5. Opening the walls
  6. Displaying extended wall perspectives
  7. Evaluating the extended walls

Looks like a recipe from distant flower-power pot-infused times, no?

In Towards a Categorical Theory of Creativity for Music, Discourse, and Cognition, Mazzola, Andrée Ehresmann and co-authors relate these seven steps to the Yoneda lemma.

  1. Exhibiting the open question = to understand the object $A$
  2. Identifying the semiotic context = to describe the category $\mathbf{C}$ of which $A$ is an object
  3. Finding the question’s critical sign = $A$ (?!)
  4. Identifying the concept’s walls = the uncontrolled behaviour of the Yoneda functor
    \[
    @A~:~\mathbf{C} \rightarrow \mathbf{Sets} \qquad C \mapsto Hom_{\mathbf{C}}(C,A) \]
  5. Opening the walls = finding an objectively creative subcategory $\mathbf{A}$ of $\mathbf{C}$
  6. Displaying extended wall perspectives = calculate the colimit $C$ of a creative diagram
  7. Evaluating the extended walls = try to understand $A$ via the isomorphism $C \simeq A$.

(Actually, I first read about these seven categorical steps in another paper which might put a smile on your face: The Yoneda path to the Buddhist monk blend.)

Remains to know what a ‘creative’ subcategory is.

The creative moment comes in here: could we not find a subcategory
$\mathbf{A}$ of $\mathbf{C}$ such that the functor
\[
Yon|_{\mathbf{A}}~:~\mathbf{C} \rightarrow \mathbf{PSh}(\mathbf{A}) \qquad A \mapsto @A|_{\mathbf{A}} \]
is still fully faithful? We call such a subcategory creative, and it is a major task in category theory to find creative categories which are as small as possible.

All the ingredients are here, but I had to read Peter Scholze’s blogpost before the penny dropped.

Let’s try to view condensed sets as the result of a creative process.

  1. Exhibiting the open question: you are a topologist and want to understand a particular compact Hausdorff space $X$.
  2. Identifying the semiotic context: you are familiar with working in the category $\mathbf{Tops}$ of all topological spaces with continuous maps as morphisms.
  3. Finding the question’s critical sign: you want to know what differentiates your space $X$ from all other topological spaces.
  4. Identifying the concept’s walls: you can probe your space $X$ with continuous maps from other topological spaces. That is, you can consider the contravariant functor (or presheaf on $\mathbf{Tops}$)
    \[
    @X~:~\mathbf{Tops} \rightarrow \mathbf{Sets} \qquad Y \mapsto Cont(Y,X) \]
    and Yoneda tells you that this functor, up to equivalence, determines the space $X$ upto homeomorphism.
  5. Opening the walls: Tychonoff tells you that among all compact Hausdorff spaces there’s a class of pretty weird examples: inverse limits of finite sets (or a bit pompous: the pro-etale site of a point). These limits form a subcategory $\mathbf{ProF}$ of $\mathbf{Tops}$.
  6. Displaying extended wall perspectives: for every inverse limit $F \in \mathbf{ProF}$ (for ‘pro-finite sets’) you can look at the set $\mathbf{X}(F)=Cont(F,X)$ of all continuous maps from $F$ to $X$ (that is, all probes of $X$ by $F$) and this functor
    \[
    \mathbf{X}=@X|_{\mathbf{ProF}}~:~\mathbf{ProF} \rightarrow \mathbf{Sets} \qquad F \mapsto \mathbf{X}(F) \]
    is a sheaf on the pre-etale site of a point, that is, $\mathbf{X}$ is the condensed set associated to $X$.
  7. Evaluating the extended walls: Clausen and Scholze observe that the assignment $X \mapsto \mathbf{X}$ embeds compact Hausdorff spaces fully faithful into condensed sets, so we can recover $X$ up to homeomorphism as a colimit from the condenset set $\mathbf{X}$. Or, in Mazzola’s terminology: $\mathbf{ProF}$ is a creative subcategory of $\mathbf{(cH)Tops}$ (all compact Hausdorff spaces).

It would be nice if someone would come up with a new notion for me to understand Mazzola’s other opus “The topos of music” (now reprinted as a four volume series).



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Richard Borcherds on Witt and the Leech lattice

A rare benefit of the Covid-situation is that Richard Borcherds decided to set up a YouTube channel with recordings of his online lectures.

Plenty of gems to be discovered there, including a talk on Monstrous Moonshine, and a talk he gave for the Archimedeans about the Sporadic Groups.

As part of his History of Science-course he addressed the question whether Witt discovered the Leech lattice.

A while ago I’ve blogged about that very same question here:

The summary of these posts being that I thought it was rather unlikely for Witt to have discovered the Leech lattice.

However, using the same sources, Borcherds rates a more than 90% probability for Witt to have indeed discovered the Leech lattice in 1940.

His evidence for this is:

  • Witt said he discovered it.
  • His construction (in his 1972 colloquium talk) is unlike any other construction of the Leech lattice.
  • Witt was the expert on Steiner systems, and the system S(5,8,24) is crucial in Leech’s construction of his lattice.

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