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Category: representations

GoV 2 : Viruses and quasi-crystals

If you look around for mathematical theories of the structure of viruses, you quickly end up with the work of Raidun Twarock and her group at the University of York.



We’ve seen her proposal to extend the Caspar-Klug classification of viruses. Her novel idea to distribute proteins on the viral capsid along Penrose-like tilings shouldn’t be taken too literally. The inherent aperiodic nature of Penrose tiles doesn’t go together well with perfect tilings of the sphere.

Instead, the observation that these capsid tilings resemble somewhat Penrose tilings is a side-effect of another great idea of the York group. Recently, they borrowed techniques from the theory of quasicrystals to gain insight in the inner structure of viruses, in particular on the interaction of the capsid with the genome.

By the crystallographic restriction theorem no $3$-dimensional lattice can have icosahedral symmetry. But, we can construct aperiodic structures (quasicrystals) which have local icosahedral structure, much like Penrose tilings have local $D_5$-symmetry

This is best explained by de Bruijn‘s theory of pentagrids (more on that another time). Here I’ll just mention the representation-theoretic idea.

The isometry group of the standard $5$-dimensional lattice $\mathbb{Z}^5$ is the group of all signed permutation $5 \times 5$ matrices $B_5$ (Young’s hyperoctahedral group). There are two distinct conjugacy classes of subgroups in $B_5$ isomorphic to $D_5$, one such subgroup generated by the permutation matrices
\[
x= \begin{bmatrix}
0 & 1 & 0 & 0 & 0 \\
0 & 0 & 1 & 0 & 0 \\
0 & 0 & 0 & 1 & 0 \\
0 & 0 & 0 & 0 & 1 \\
1 & 0 & 0 & 0 & 0 \end{bmatrix} \qquad \text{and} \qquad
y = \begin{bmatrix} 1 & 0 & 0 & 0 & 0 \\
0 & 0 & 0 & 0 & 1 \\
0 & 0 & 0 & 1 & 0 \\
0 & 0 & 1 & 0 & 0 \\
0 & 1 & 0 & 0 & 0 \end{bmatrix} \]
The traces of $x,x^2$ and $y$, together with the character table of $D_5$ tell us that this $5$-dimensional $D_5$-representation splits as the direct sum of the trivial representation and of the two irreducible $2$-dimensional representations.
\[
\mathbb{R}^5 = A \simeq T \oplus W_1 \oplus W_2 \]
with $T = \mathbb{R} d$, $W_1 = \mathbb{R} u_1 + \mathbb{R} u_2$ and $W_2 = \mathbb{R} w_1 + \mathbb{R} w_2$ where
\[
\begin{cases}
(1,1,1,1,1)=d \\
(1,c_1,c_2,c_3,c_4)= u_1 \\
(0,s_1,s_2,s_3,s_4) = u_2 \\
(1,c_2,c_4,c1,c3)= w_1 \\
(0,s_2,s_4,s_1,s_3)= w_2
\end{cases}
\]
and $c_j=cos(2\pi j/5)$ and $s_j=sin(2 \pi/5)$. We have a $D_5$-projection
\[
\pi : A \rightarrow W_1 \quad (y_0,\dots,y_4) \mapsto \sum_{i=0}^4 y_i(c_i u_1+s_i u_2) \]
The projection maps the vertices of the $5$-dimensional hypercube to a planar configuration with $D_5$-symmetry.



de Bruijn’s results say that if we take suitable ‘windows’ of lattice-points in $\mathbb{Z}^5$ and project them via the $D_5$-equivariant map $\pi$ onto the plane, then the images of these lattice points become the vertices of a rhombic Penrose tiling (and we get all such tilings by choosing our window carefully).



This explains why Penrose tilings have a local $D_5$-symmetry. I’ll try to come back to de Bruijn’s papers in future posts.

But, let’s go back to viruses and the work of Twarock’s group using methods from quasicrystals. Such aperiodic structures with a local icosahedral symmetry can be constructed along similar lines. This time one starts with the standard $6$-dimensional lattice $\mathbb{Z^6}$ with isometry group $B_6$ (signed $6 \times 6$ permutation matrices).

This group has three conjugacy classes of subgroups isomorphic to $A_5$, but for only one of them this $6$-dimensional representation decomposes as the direct sum of the two irreducible $3$-dimensional representations of $A_5$ (the decompositions in the two other cases contain an irreducible of dimension $4$ or $5$ together with trivial factor(s)). A representant of the crystallographic relevant case is given by the signed permutation matrices
\[
x= \begin{bmatrix}
0 & 1 & 0 & 0 & 0 & 0 \\
1 & 0 & 0 & 0 & 0 & 0 \\
0 & 0 & 0 & -1 & 0 & 0 \\
0 & 0 & -1 & 0 & 0 & 0 \\
0 & 0 & 0 & 0 & -1 & 0 \\
0 & 0 & 0 & 0 & 0 & -1
\end{bmatrix} \qquad \text{and} \qquad y=
\begin{bmatrix}
0 & 0 & 1 & 0 & 0 & 0 \\
1 & 0 & 0 & 0 & 0 & 0 \\
0 & 1 & 0 & 0 & 0 & 0 \\
0 & 0 & 0 & 0 & -1 & 0 \\
0 & 0 & 0 & 0 & 0 & 1 \\
0 & 0 & 0 & -1 & 0 & 0
\end{bmatrix} \]

Again, using suitable windows of $\mathbb{Z}^6$-lattice points and using the $A_5$-equivariant projection to one of the two $3$-dimensional components, one obtains quasicrystals with local $A_5$-symmetry.

In this $3$-dimensional case the replacements of the thick and thin rhombi are these four parallellepipeda, known as the Amman blocks



which must be stacked together obeying the gluing condition that dots of the same colour must be adjacent.

Has anyone looked at a possible connection between the four Amman blocks (which come in pairs) and the four (paired) nucleotides in DNA? Just an idle thought…

These blocks grow into quasicrystals with local icosahedral symmetry.



The faces on the boundary of such a sphere-like quasicrystal then look a lot like a Penrose tiling.

How can we connect these group and representation-theoretic ideas to the structure of viruses? Here’s another thought-provoking proposal coming from the York group.

Take the $A_5$ subgroup of the hyperoctahedral group in six dimensiona $B_6$ generated by the above two matrices (giving a good $A_5$-equivariant projection $\pi$ to three dimensional space) and consider an intermediate group
\[
A_5 \subsetneq G \subseteq B_6 \]
Take a point in $\mathbb{R}^6$ and look at its orbit under the isometries of $G$, then all these points have the same distance from the origin in $\mathbb{R}^6$. Now, project this orbit under $\pi$ to get a collection of points in $\mathbb{R}^3$.

As $\pi$ is only $A_5$-equivariant (and not $G$-equivariant) the image points may lie in different shells from the origin. We can try to relate these shells of points to observational data on the inner structures of viruses.

Here’s a pretty convincing instance of such a correlation, taken from the thesis by Emilio Zappa “New group theoretical methods for applications in virology and quasicrystals”.



This is the inner structure of the Hepatitis B virus, showing the envelope (purple), capsid protein (cream) and genome (light blue). The coloured dots are the image points in the different shells around the origin.

Do viruses invade us from the sixth dimension??

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The symmetries of Covid-19

A natural question these days might be: “what are the rotational symmetries of the Covid-19 virus?”



Most illustrations show a highly symmetric object, suggesting it might have icosahedral symmetry. In fact, many viruses do have icosahedral symmetry as a result of the ‘genetic economy principle’ proposed by Watson and Crick in 1956, resulting in the Caspar-Klug classification of viral capsids.

But then, perhaps this icosahedral illusion is a result of design decisions illustrators made turning scientific data into pictures. Veronica Falconieri Hays wrote a beautiful article describing the effort going into this: How I built a 3d-model of the coronavirus for Scientific American. Here’s her final picture



And yes, icosahedral symmetry was one of her design decisions:

The M proteins form pairs, and it is estimated that there are 16–25 M proteins per spike on the surface of the virus. I ended up modeling 10 M protein pairs (so 20 M proteins) per spike in my model. Some researchers hypothesize that the M proteins form a lattice within the envelope (interacting with an underlying lattice of N proteins; see below). I decided to use an icosahedral sphere to create a regular distribution of the M protein dimers to hint at this hypothesis.

The spikes (or S-proteins) are the tentacles in these pictures, and one of the few hard figures on Corona is that ‘on average’ there are 74 of them.

This fact is enough to rule out icosahedral symmetry.

If the icosahedral rotation group (of order $60$, isomorphic to $A_5$) acts on the $74$ spikes, then each orbit consists of $60$ spikes unless that spike lies on a twofold, threefold or fivefold rotation axis, in which cases the number of spikes in its orbit are respectively $30$, $20$ or $12$. So, we can’t get a total number of $74$ spikes!

However, just looking at the number of spikes we cannot rule out octahedral symmetry!

The octahedral rotation group (of order $24$, isomorphic to $S_4$) will have orbits of size $24$ unless the spike lies on a twofold, threefold or fourfold rotation axis, giving orbits of size $12$, $8$ and $6$ respectively (the midpoints of edges, the vertices and the midpoints of faces of the octahedron), and

\[
74 = 24+24+12+8+6 \]

The most symmetric arrangement of spikes would be to subdivide each of the $8$ triangular faces of the octahedron into $6$ triangles with vertices the midpoint of the face, a vertex and a midpoint of an edge, and then to position the spikes on the axis through the vertices and midpoints of these smaller triangles.

Googling around I found very few references to symmetries of Covid-19, probably because it has an helical RNA-coil, which seems not to go well with Caspar-Klug type polyhedral viral capsids.

Here’s an exception: A structural model for the Coronavirus nucleocapsid by Federico Coscio, Alejandro D. Nadra, and Diego U. Ferreiro.



They propose a truncated octahedron as capsid (in transparent brown) with interior a continuous coil packing of blue and cyan helices. The virus membrane with the spikes and M proteins is drawn in blue.

If you have better info or references on the (conjectural) symmetries of Covid-19, please leave a comment.

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Extending McKay’s E8 graph?

If you take two Fischer involutions in the monster (elements of conjugacy class 2A) and multiply them, the resulting element surprisingly belongs to one of just 9 conjugacy classes:

1A,2A,2B,3A,3C,4A,4B,5A or 6A

The orders of these elements are exactly the dimensions of the fundamental root for the extended $E_8$ Dynkin diagram.

This is the content of John McKay’s E(8)-observation : there should be a precise relation between the nodes of the extended Dynkin diagram and these 9 conjugacy classes in such a way that the order of the class corresponds to the component of the fundamental root. More precisely, one conjectures the following correspondence:

John Duncan found such a connection by considering carefully the corresponding moonshine groups and their inter-relation. For more on this, look at the old post E8 from moonshine groups. The extended Dynkin diagram with these moonshine groups as vertices is:

Duncan does this by assigning numbers to moonshine groups: the dimension is the order of the corresponding monster element and the valency is one more than the copies of $C_2$ generated by the Atkin-Lehner involutions in the moonshine group.

One might ask whether there is a graph on all 171 moonshine groups, compatible with the valencies of every vertex.

Now, even for the 9 groups in McKay’s question, the valencies do not determine the graph uniquely and Duncan proceeds with an ad hoc condition on the edges.

There is a partition on the 9 groups by the property whether or not the index of the intersection with $\Gamma_0(2)$ is at most two. Then Duncan declares that there cannot be an edge between two groups belonging to the same class.

His motivation for this property comes from classical McKay-correspondence for the binary icosahedral group (where the vertices correspond to simple representations $S$, and the edges from $S$ to factors of $S \otimes V_2$, where $V_2$ is the restriction of the standard $2$-dimensional simple for $SU(2)$).

Of the $9$ simples there are only $4$ faithful ones, $5$ come from simples of $A_5$. Because $\Gamma_0(2)$ is a subgroup of the modular group of index 2, he then views $\Gamma_0(2)$ as similar to the subgroup $A_5$ in the binary icosahedral group, and declares a moonshine group to be faithful if its index in the intersection with $\Gamma_0(2)$ is at most two.

One might ask whether there is another, more natural, definition for having an edge (or multiple ones) between arbitrary moonshine groups.

And, what is the full graph on the 171 groups?

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Moonshine for everyone

Today, Samuel Dehority, Xavier Gonzalez, Neekon Vafa and Roger Van Peski arXived their paper Moonshine for all finite groups.

Originally, Moonshine was thought to be connected to the Monster group. McKay and Thompson observed that the first coefficients of the normalized elliptic modular invariant

\[
J(\tau) = q^{-1} + 196884 q + 21493760 q^2 + 864229970 q^3 + \ldots
\]

could be written as sums of dimensions of the first few irreducible representations of the monster group:

\[
1=1,~\quad 196884=196883+1,~\quad 21493760=1+196883+21296876,~\quad … \]

Soon it transpired that there ought to be an infinite dimensional graded vectorspace, the moonshine module

\[
V^{\sharp} = \bigoplus_{n=-1}^{\infty}~V^{\sharp}_n \]

with every component $V^{\sharp}_n$ being a representation of the monster group $\mathbb{M}$ of which the dimension coincides with the coefficient of $q^n$ in $J(\tau)$.

It only got better, for any conjugacy class $[ g ]$ of the monster, if you took the character series

\[
T_g(\tau) = \sum_{n=-1}^{\infty} Tr(g | V^{\sharp}_n) q^n \]

you get a function invariant under the action of the subgroup

\[
\Gamma_0(n) = \{ \begin{bmatrix} a & b \\ c & d \end{bmatrix}~:~c = 0~mod~n \} \]

acting via transformations $\tau \mapsto \frac{a \tau + b}{c \tau + d}$ on the upper half plane where $n$ is the order of $g$ (or, for the experts, almost).

Soon, further instances of ‘moonshine’ were discovered for other simple groups, the unifying feature being that one associates to a group $G$ a graded representation $V$ such that the character series of this representation for an element $g \in G$ is an invariant modular function with respect to the subgroup $\Gamma_0(n)$ of the modular group, with $n$ being the order of $g$.

Today, this group of people proved that there is ‘moonshine’ for any finite group whatsoever.

They changed the definition of moonshine slightly to introduce the notion of moonshine of depth $d$ which meant that they want the dimension sequence of their graded module to be equal to $J(\tau)$ under the action of the normalized $d$-th Hecke operator, which means equal to

\[
\sum_{ac=d,0 \leq b < c} J(\frac{a \tau + b}{c}) \]
as they are interested in the asymptotic behaviour of the components $V_n$ with respect to the regular representation of $G$.

What baffled me was their much weaker observation (remark 2) saying that you get ‘moonshine’ in the form described above, that is, a graded representation $V$ such that for every $g \in G$ you get a character series which is invariant under $\Gamma_0(n)$ with $n=ord(g)$ (and no smaller divisor of $n$), for every finite group $G$.

And, more importantly, you can explain this to any student taking a first course in group theory as all you need is Cayley’s theorem stating that any finite group is a subgroup of some symmetric group $S_n$.

Here’s the idea: take the original monster-moonshine module $V^{\sharp}$ but forget all about the action of $\mathbb{M}$ (that is, consider it as a plain vectorspace) and consider the graded representation

\[
V = (V^{\sharp})^{\otimes n} \]

with the natural action of $S_n$ on the tensor product.

Now, embed a la Cayley $G$ into $S_n$ then you know that the order of $g \in G$ is the least common multiple of the cycle lengths of the permutation it it send to. Now, it is fairly trivial to see that the character series of $V$ with respect to $g$ (having cycle lengths $(k_1,k_2,\dots,k_l)$, including cycles of length one) is equal to the product

\[
J(k_1 \tau) J(k_2 \tau) \dots J(k_l \tau) \]

which is invariant under $\Gamma_0(n)$ with $n = lcm(k_i)$ (but no $\Gamma_0(m)$ with $m$ a proper divisor of $n$).

For example, for $G=S_4$ we have as character series of $(V^{\sharp})^{\otimes 4}$

\[
(1)(2)(3)(4) \mapsto J(\tau)^4 \]

\[
(12)(3)(4) \mapsto J(2 \tau) J(\tau)^2 \]

\[
(12)(34) \mapsto J(2 \tau)^2 \]

\[
(123)(4) \mapsto J(3 \tau) J(\tau) \]

\[
(1234) \mapsto J(4 \tau) \]

Clearly, the main results of the paper are much more subtle, but I’m already happy with this version of ‘moonshine for everyone’!

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Stirring a cup of coffee

Please allow for a couple of end-of-semester bluesy ramblings. I just finished grading the final test of the last of five courses I lectured this semester.

Most of them went, I believe, rather well.

As always, it was fun to teach an introductory group theory course to second year physics students.

Personally, I did enjoy our Lie theory course the most, given for a mixed public of both mathematics and physics students. We did the spin-group $SU(2)$ and its connection with $SO_3(\mathbb{R})$ in gruesome detail, introduced the other classical groups, and proved complete reducibility of representations. The funnier part was applying this to the $U(1) \times SU(2) \times SU(3)$-representation of the standard model and its extension to the $SU(5)$ GUT.

Ok, but with a sad undertone, was the second year course on representations of finite groups. Sad, because it was the last time I’m allowed to teach it. My younger colleagues decided there’s no place for RT on the new curriculum.

Soit.

The final lecture is often an eye-opener, or at least, I hope it is/was.

Here’s the idea: someone whispers in your ear that there might be a simple group of order $60$. Armed with only the Sylow-theorems and what we did in this course we will determine all its conjugacy classes, its full character table, and finish proving that this mysterious group is none other than $A_5$.

Right now I’m just a tad disappointed only a handful of students came close to solving the same problem for order $168$ this afternoon.

Clearly, I gave them ample extra information: the group only has elements of order $1,2,3,4$ and $7$ and the centralizer of one order $2$ element is the dihedral group of order $8$. They had to determine the number of distinct irreducible representations, that is, the number of conjugacy classes. Try it yourself (Solution at the end of this post).

For months I felt completely deflated on Tuesday nights, for I had to teach the remaining two courses on that day.

There’s this first year Linear Algebra course. After teaching for over 30 years it was a first timer for me, and probably for the better. I guess 15 years ago I would have been arrogant enough to insist that the only way to teach linear algebra properly was to do representations of quivers…

Now, I realise that linear algebra is perhaps the only algebra course the majority of math-students will need in their further career, so it is best to tune its contents to the desires of the other colleagues: inproducts, determinants as volumes, Markov-processes and the like.

There are thousands of linear algebra textbooks, the one feature they all seem to lack is conciseness. What kept me going throughout this course was trying to come up with the shortest proofs ever for standard results. No doubt, next year the course will grow on me.

Then, there was a master course on algebraic geometry (which was supposed to be on scheme theory, moduli problems such as the classification of fat points (as in the car crash post, etale topology and the like) which had a bumpy start because class was less prepared on varieties and morphisms than I had hoped for.

Still, judging on the quality of the papers students are beginning to hand in (today I received one doing serious stuff with stacks) we managed to cover a lot of material in the end.

I’m determined to teach that first course on algebraic geometry myself next year.

Which brought me wondering about the ideal content of such a course.

Half a decade ago I wrote a couple of posts such as Mumford’s treasure map, Grothendieck’s functor of points, Manin’s geometric axis and the like, which are still quite readable.

In the functor of points-post I referred to a comment thread Algebraic geometry without prime ideals at the Secret Blogging Seminar.

As I had to oversee a test this afternoon, I printed out all comments (a full 29 pages!) and had a good time reading them. At the time I favoured the POV advocated by David Ben-Zvi and Jim Borger (functor of points instead of locally ringed schemes).

Clearly they are right, but then so was I when I thought the ‘right’ way to teach linear algebra was via quiver-representations…

We’ll see what I’ll try out next year.

You may have wondered about the title of this post. It’s derived from a paper Raf Bocklandt (of the Korteweg-de Vries Institute in Amsterdam) arXived some days ago: Reflections in a cup of coffee, which is an extended version of a Brouwer-lecture he gave. Raf has this to say about the Brouwer fixed-point theorem.

“The theorem is usually explained in worldly terms by looking at a cup of coffee. In this setting it states that no matter how you stir your cup, there will always be a point in the liquid that did not change position and if you try to move that part by further stirring you will inevitably move some other part back into its original position. Legend even has it that Brouwer came up with the idea while stirring in a real cup, but whether this is true we’ll never know. What is true however is that Brouwers refections on the topic had a profound impact on mathematics and would lead to lots of new developments in geometry.”

I wish you all a pleasant end of 2016 and a much better 2017.

As to the 168-solution: Sylow says there are 8 7-Sylows giving 48 elements of order 7. The centralizer of each of them must be $C_7$ (given the restriction on the order of elements) so two conjugacy classes of them. Similarly each conjugacy class of an order 3 element must contain 56 elements. There is one conjugacy class of an order 2 element having 21 elements (because the centralizer is $D_4$) giving also a conjugacy class of an order 4 element consisting of 42 elements. Together with the identity these add up to 168 so there are 6 irreducible representations.

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