The Theory of Devices

20 June, 2017

I’m visiting the University of Genoa and talking to two category theorists: Marco Grandis and Giuseppe Rosolini. Grandis works on algebraic topology and higher categories, while Rosolini works on the categorical semantics of programming languages.

Yesterday, Marco Grandis showed me a fascinating paper by his thesis advisor:

• Gabriele Darbo, Aspetti algebrico-categoriali della teoria dei dispotivi, Symposia Mathematica IV (1970), Istituto Nazionale di Alta Matematica, 303–336.

It’s closely connected to Brendan Fong’s thesis, but also different—and, of course, much older. According to Grandis, Darbo was the first person to work on category theory in Italy. He’s better known for other things, like ‘Darbo’s fixed point theorem’, but this piece of work is elegant, and, it seems to me, strangely ahead of its time.

The paper’s title translates as ‘Algebraic-categorical aspects of the theory of devices’, and its main concept is that of a ‘universe of devices’: a collection of devices of some kind that can be hooked up using wires to form more devices of this kind. Nowadays we might study this concept using operads—but operads didn’t exist in 1970, and Darbo did quite fine without them.

The key is the category \mathrm{FinCorel}, which has finite sets as objects and ‘corelations’ as morphisms. I explained corelations here:

Corelations in network theory, 2 February 2016.

Briefly, a corelation from a finite set X to a finite set Y is a partition of the disjoint union of X and Y. We can get such a partition from a bunch of wires connecting points of X and Y. The idea is that two points lie in the same part of the partition iff they’re connected, directly or indirectly, by a path of wires. So, if we have some wires like this:

they determine a corelation like this:

There’s an obvious way to compose corelations, giving a category \mathrm{FinCorel}.

Gabriele Darbo doesn’t call them ‘corelations’: he calls them ‘trasduttori’. A literal translation might be ‘transducers’. But he’s definitely talking about corelations, and like Fong he thinks they are basic for studying ways to connect systems.

Darbo wants a ‘universe of devices’ to assign to each finite set X a set D(X) of devices having X as their set of ‘terminals’. Given a device in D(X) and a corelation f \colon X \to Y, thought of as a bunch of wires, he wants to be able to attach these wires to the terminals in X and get a new device with Y as its set of terminals. Thus he wants a map D(f): D(X) \to D(Y). If you draw some pictures, you’ll see this should give a functor

D : \mathrm{FinCorel} \to \mathrm{Set}

Moreover, if we have device with a set X of terminals and a device with a set Y of terminals, we should be able to set them side by side and get a device whose set of terminals form the set X + Y, meaning the disjoint union of X and Y. So, Darbo wants to have maps

\delta_{X,Y} : D(X) \times D(Y) \to D(X + Y)

If you draw some more pictures you can convince yourself that \delta should be a lax symmetric monoidal functor… if you’re one of the lucky few who knows what that means. If you’re not, you can look it up in many places, such as Section 1.2 here:

• Brendan Fong, The Algebra of Open and Interconnected Systems, Ph.D. thesis, University of Oxford, 2016. (Blog article here.)

Darbo does not mention lax symmetric monoidal functors, perhaps because such concepts were first introduced by Mac Lane only in 1968. But as far as I can tell, Darbo’s definition is almost equivalent to this:

Definition. A universe of devices is a lax symmetric monoidal functor D \colon \mathrm{FinCorel} \to \mathrm{Set}.

One difference is that Darbo wants there to be exactly one device with no terminals. Thus, he assumes D(\emptyset) is a one-element set, say 1, while the definition above would only demand the existence of a map \delta \colon 1 \to D(\emptyset) obeying a couple of axioms. That gives a particular ‘favorite’ device with no terminals. I believe we get Darbo’s definition from the above one if we further assume \delta is the identity map. This makes sense if we take the attitude that ‘a device is determined by its observable behavior’, but not otherwise. This attitude is called ‘black-boxing’.

Darbo does various things in his paper, but the most exciting to me is his example connected to linear electrical circuits. He defines, for any pair of objects V and I in an abelian category C, a particular universe of devices. He calls this the universe of linear devices having V as the object of potentials and I as the object of currents.

If you don’t like abelian categories, think of C as the category of finite-dimensional real vector spaces, and let V = I = \mathbb{R}. Electric potential and electric current are described by real numbers so this makes sense.

The basic idea will be familiar to Fong fans. In an electrical circuit made of purely conductive wires, when two wires merge into one we add the currents to get the current on the wire going out. When one wire splits into two we duplicate the potential to get the potentials on the wires going out. Working this out further, any corelation f : X \to Y between finite set determines two linear relations, one

f_* : I^X \rightharpoonup I^Y

relating the currents on the wires coming in to the currents on the wires going out, and one

f^* : V^Y \rightharpoonup V^X

relating the potentials on the wires going out to the potentials on the wires coming in. Here I^X is the direct sum of X copies of I, and so on; the funky arrow indicates that we have a linear relation rather than a linear map. Note that f_* goes forward while f^* goes backward; this is mainly just conventional, since you can turn linear relations around, but we’ll see it’s sort of nice.

If we let \mathrm{Rel}(A,B) be the set of linear relations between two objects A, B \in C, we can use the above technology to get a universe of devices where

D(X) = \mathrm{Rel}(V^X, I^X)

In other words, a device of this kind is simply a linear relation between the potentials and currents at its terminals!

How does D get to be a functor D : \mathrm{FinCorel} \to \mathrm{FinSet}? That’s pretty easy. We’ve defined it on objects (that is, finite sets) by the above formula. So, suppose we have a morphism (that is, a corelation) f \colon X \to Y. How do we define D(f) : D(X) \to D(Y)?

To answer this question, we need a function

D(f) : \mathrm{Rel}(V^X, I^X) \to \mathrm{Rel}(V^Y, I^Y)

Luckily, we’ve got linear relations

f_* : I^X \rightharpoonup I^Y

and

f^* : V^Y \rightharpoonup V^X

So, given any linear relation R \in \mathrm{Rel}(V^X, I^X), we just define

D(f)(R) = f_* \circ R \circ f^*

Voilà!

People who have read Fong’s thesis, or my paper with Blake Pollard on reaction networks:

• John Baez and Blake Pollard, A compositional framework for reaction networks.

will find many of Darbo’s ideas eerily similar. In particular, the formula

D(f)(R) = f_* \circ R \circ f^*

appears in Lemma 16 of my paper with Blake, where we are defining a category of open dynamical systems. We prove that D is a lax symmetric monoidal functor, which is just what Darbo proved—though in a different context, since our R is not linear like his, and for a different purpose, since he’s trying to show D is a ‘universe of devices’, while we’re trying to construct the category of open dynamical systems as a ‘decorated cospan category’.

In short: if this work of Darbo had become more widely known, the development of network theory could have been sped up by three decades! But there was less interest in a general theory of networks at the time, lax monoidal functors were brand new, operads unknown… and, sadly, few mathematicians read Italian.

Darbo has other papers, and so do his students. We should read them and learn from them! Here are a few open-access ones:

• Franco Parodi, Costruzione di un universo di dispositivi non lineari su una coppia di gruppi abeliani , Rendiconti del Seminario Matematico della Università di Padova 58 (1977), 45–54.

• Franco Parodi, Categoria degli universi di dispositivi e categoria delle T-algebre, Rendiconti del Seminario Matematico della Università di Padova 62 (1980), 1–15.

• Stefano Testa, Su un universo di dispositivi monotoni, Rendiconti del Seminario Matematico della Università di Padova 65 (1981), 53–57.

At some point I will scan in G. Darbo’s paper and make it available here.


The Geometric McKay Correspondence (Part 1)

19 June, 2017

The ‘geometric McKay correspondence’, actually discovered by Patrick du Val in 1934, is a wonderful relation between the Platonic solids and the ADE Dynkin diagrams. In particular, it sets up a connection between two of my favorite things, the icosahedron:

and the \mathrm{E}_8 Dynkin diagram:

When I recently gave a talk on this topic, I realized I didn’t understand it as well as I’d like. Since then I’ve been making progress with the help of this book:

• Alexander Kirillov Jr., Quiver Representations and Quiver Varieties, AMS, Providence, Rhode Island, 2016.

I now think I glimpse a way forward to a very concrete and vivid understanding of the relation between the icosahedron and E8. It’s really just a matter of taking the ideas in this book and working them out concretely in this case. But it takes some thought, at least for me. I’d like to enlist your help.

The rotational symmetry group of the icosahedron is a subgroup of \mathrm{SO}(3) with 60 elements, so its double cover up in \mathrm{SU}(2) has 120. This double cover is called the binary icosahedral group, but I’ll call it \Gamma for short.

This group \Gamma is the star of the show, the link between the icosahedron and E8. To visualize this group, it’s good to think of \mathrm{SU}(2) as the unit quaternions. This lets us think of the elements of \Gamma as 120 points in the unit sphere in 4 dimensions. They are in fact the vertices of a 4-dimensional regular polytope, which looks like this:



It’s called the 600-cell.

Since \Gamma is a subgroup of \mathrm{SU}(2) it acts on \mathbb{C}^2, and we can form the quotient space

S = \mathbb{C}^2/\Gamma

This is a smooth manifold except at the origin—that is, the point coming from 0 \in \mathbb{C}^2. There’s a singularity at the origin, and this where \mathrm{E}_8 is hiding! The reason is that there’s a smooth manifold \widetilde{S} and a map

\pi : \widetilde{S} \to S

that’s one-to-one and onto except at the origin. It maps 8 spheres to the origin! There’s one of these spheres for each dot here:

Two of these spheres intersect in a point if their dots are connected by an edge; otherwise they’re disjoint.

The challenge is to find a nice concrete description of \widetilde{S}, the map \pi : \widetilde{S} \to S, and these 8 spheres.

But first it’s good to get a mental image of S. Each point in this space is a \Gamma orbit in \mathbb{C}^2, meaning a set like this:

\{g x : \; g \in \Gamma \}

for some x \in \mathbb{C}^2. For x = 0 this set is a single point, and that’s what I’ve been calling the ‘origin’. In all other cases it’s 120 points, the vertices of a 600-cell in \mathbb{C}^2. This 600-cell is centered at the point 0 \in \mathbb{C}^2, but it can be big or small, depending on the magnitude of x.

So, as we take a journey starting at the origin in S, we see a point explode into a 600-cell, which grows and perhaps also rotates as we go. The origin, the singularity in S, is a bit like the Big Bang.

Unfortunately not every 600-cell centered at the origin is of the form I’ve shown:

\{g x : \; g \in \Gamma \}

It’s easiest to see this by thinking of points in 4d space as quaternions rather than elements of \mathbb{C}^2. Then the points g \in \Gamma are unit quaternions forming the vertices of a 600-cell, and multiplying g on the right by x dilates this 600-cell and also rotates it… but we don’t get arbitrary rotations this way. To get an arbitrarily rotated 600-cell we’d have to use both a left and right multiplication, and consider

\{x g y : \; g \in \Gamma \}

for a pair of quaternions x, y.

Luckily, there’s a simpler picture of the space S. It’s the space of all regular icosahedra centered at the origin in 3d space!

To see this, we start by switching to the quaternion description, which says

S = \mathbb{H}/\Gamma

Specifying a point x \in \mathbb{H} amounts to specifying the magnitude \|x\| together with x/\|x\|, which is a unit quaternion, or equivalently an element of \mathrm{SU}(2). So, specifying a point in

\{g x : \; g \in \Gamma \} \in \mathbb{H}/\Gamma

amounts to specifying the magnitude \|x\| together with a point in \mathrm{SU}(2)/\Gamma. But \mathrm{SU}(2) modulo the binary icosahedral group \Gamma is the same as \mathrm{SO(3)} modulo the icosahedral group (the rotational symmetry group of an icosahedron). Furthermore, \mathrm{SO(3)} modulo the icosahedral group is just the space of unit-sized icosahedra centered at the origin of \mathbb{R}^3.

So, specifying a point

\{g x : \; g \in \Gamma \} \in \mathbb{H}/\Gamma

amounts to specifying a nonnegative number \|x\| together with a unit-sized icosahedron centered at the origin of \mathbb{R}^3. But this is the same as specifying an icosahedron of arbitrary size centered at the origin of \mathbb{R}^3. There’s just one subtlety: we allow the size of this icosahedron to be zero, but then the way it’s rotated no longer matters.

So, S is the space of icosahedra centered at the origin, with the ‘icosahedron of zero size’ being a singularity in this space. When we pass to the smooth manifold \widetilde{S}, we replace this singularity with 8 spheres, intersecting in a pattern described by the \mathrm{E}_8 Dynkin diagram.

Points on these spheres are limiting cases of icosahedra centered at the origin. We can approach these points by letting an icosahedron centered at the origin shrink to zero size in a clever way, perhaps spinning about wildly as it does.

I don’t understand this last paragraph nearly as well as I’d like! I’m quite sure it’s true, and I know a lot of relevant information, but I don’t see it. There should be a vivid picture of how this works, not just an abstract argument. Next time I’ll start trying to assemble the material that I think needs to go into building this vivid picture.


Information Processing in Chemical Networks (Part 2)

13 June, 2017

I’m in Luxembourg, and I’ll be blogging a bit about this workshop:

Dynamics, Thermodynamics and Information Processing in Chemical Networks, 13-16 June 2017, Complex Systems and Statistical Mechanics Group, University of Luxembourg. Organized by Massimiliano Esposito and Matteo Polettini.

I’ll do it in the comments!

I explained the idea of this workshop here:

Information processing in chemical networks.

and now you can see the program here.


The Mathematics of Open Reaction Networks

8 June, 2017

Next week, Blake Pollard and I will talk about our work on reaction networks. We’ll do this at Dynamics, Thermodynamics and Information Processing in Chemical Networks, a workshop at the University of Luxembourg organized by Massimiliano Esposito and Matteo Polettini. We’ll do it on Tuesday, 13 June 2017, from 11:00 to 13:00, in room BSC 3.03 of the Bâtiment des Sciences. If you’re around, please stop by and say hi!

Here are the slides for my talk:

The mathematics of open reaction networks.

Abstract. To describe systems composed of interacting parts, scientists and engineers draw diagrams of networks: flow charts, electrical circuit diagrams, signal-flow graphs, Feynman diagrams and the like. In principle all these different diagrams fit into a common framework: the mathematics of monoidal categories. This has been known for some time. However, the details are more challenging, and ultimately more rewarding, than this basic insight. Here we explain how various applications of reaction networks and Petri nets fit into this framework.

If you see typos or other problems please let me know now!

I hope to blog a bit about the workshop… it promises to be very interesting.


The Dodecahedron, the Icosahedron and E8

16 May, 2017


Here you can see the slides of a talk I’m giving:

The dodecahedron, the icosahedron and E8, Annual General Meeting of the Hong Kong Mathematical Society, Hong Kong University of Science and Technology.

It’ll take place on 10:50 am Saturday May 20th in Lecture Theatre G. You can see the program for the whole meeting here.

The slides are in the form of webpages, and you can see references and some other information tucked away at the bottom of each page.

In preparing this talk I learned more about the geometric McKay correspondence, which is a correspondence between the simply-laced Dynkin diagrams (also known as ADE Dynkin diagrams) and the finite subgroups of \mathrm{SU}(2).

There are different ways to get your hands on this correspondence, but the geometric way is to resolve the singularity in \mathbb{C}^2/\Gamma where \Gamma \subset \mathrm{SU}(2) is such a finite subgroup. The variety \mathbb{C}^2/\Gamma has a singularity at the origin–or more precisely, the point coming from the origin in \mathbb{C}^2. To make singularities go away, we ‘resolve’ them. And when you take the ‘minimal resolution’ of this variety (a concept I explain here), you get a smooth variety S with a map

\pi \colon S \to \mathbb{C}^2/\Gamma

which is one-to-one except at the origin. The points that map to the origin lie on a bunch of Riemann spheres. There’s one of these spheres for each dot in some Dynkin diagram—and two of these spheres intersect iff their two dots are connected by an edge!

In particular, if \Gamma is the double cover of the rotational symmetry group of the dodecahedron, the Dynkin diagram we get this way is E_8:

The basic reason \mathrm{E}_8 is connected to the icosahedron is that the icosahedral group is generated by rotations of orders 2, 3 and 5 while the \mathrm{E}_8 Dynkin diagram has ‘legs’ of length 2, 3, and 5 if you count right:

In general, whenever you have a triple of natural numbers a,b,c obeying

\displaystyle{ \frac{1}{a} + \frac{1}{b} + \frac{1}{c} > 1}

you get a finite subgroup of \mathrm{SU}(2) that contains rotations of orders a,b,c, and a simply-laced Dynkin diagram with legs of length a,b,c. The three most exciting cases are:

(a,b,c) = (2,3,3): the tetrahedron, and E_6,

(a,b,c) = (2,3,4): the octahedron, and E_7,

(a,b,c) = (2,3,5): the icosahedron, and E_8.

But the puzzle is this: why does resolving the singular variety \mathbb{C}^2/\Gamma gives a smooth variety with a bunch of copies of the Riemann sphere \mathbb{C}\mathrm{P}^1 sitting over the singular point at the origin, with these copies intersecting in a pattern given by a Dynkin diagram?

It turns out the best explanation is in here:

• Klaus Lamotke, Regular Solids and Isolated Singularities, Vieweg & Sohn, Braunschweig, 1986.

In a nutshell, you need to start by blowing up \mathbb{C}^2 at the origin, getting a space X containing a copy of \mathbb{C}\mathrm{P}^1 on which \Gamma acts. The space X/\Gamma has further singularities coming from the rotations of orders a, b and c in \Gamma. When you resolve these, you get more copies of \mathbb{C}\mathrm{P}^1, which intersect in the pattern given by a Dynkin diagram with legs of length a,b and c.

I would like to understand this better, and more vividly. I want a really clear understanding of the minimal resolution S. For this I should keep rereading Lamotke’s book, and doing more calculations.

I do, however, have a nice vivid picture of the singular space \mathbb{C}^2/\Gamma. For that, read my talk! I’m hoping this will lead, someday, to an equally appealing picture of its minimal resolution.


Phosphorus Sulfides

5 May, 2017

I think of sulfur and phosphorus as clever chameleons of the periodic table: both come in many different forms, called allotropes. There’s white phosphorus, red phosphorus, violet phosphorus and black phosphorus:



and there are about two dozen allotropes of sulfur, with a phase diagram like this:



So I should have guessed that sulfur and phosphorus combine to make many different compounds. But I never thought about this until yesterday!

I’m a great fan of diamonds, not for their monetary value but for the math of their crystal structure:



In a diamond the carbon atoms do not form a lattice in the strict mathematical sense (which is more restrictive than the sense of this word in crystallography). The reason is that there aren’t translational symmetries carrying any atom to any other. Instead, there are two lattices of atoms, shown as red and blue in this picture by Greg Egan. Each atom has 4 nearest neighbors arranged at the vertices of a regular tetrahedron; the tetrahedra centered at the blue atoms are ‘right-side up’, while those centered at the red atoms are ‘upside down’.

Having thought about this a lot, I was happy to read about adamantane. It’s a compound with 10 carbons and 16 hydrogens. There are 4 carbons at the vertices of a regular tetrahedron, and 6 along the edges—but the edges bend out in such a way that the carbons form a tiny piece of a diamond crystal:

or more abstractly, focusing on the carbons and their bonds:


Yesterday I learned that phosphorus decasulfide, P4S10, follows the same pattern:



The angles deviate slightly from the value of

\arccos (-1/3) \approx 109.4712^\circ

that we’d have in a fragment of a mathematically ideal diamond crystal, but that’s to be expected.

It turns out there are lots of other phosphorus sulfides! Here are some of them:



Puzzle 1. Why do each of these compounds have exactly 4 phosphorus atoms?

I don’t know the answer! I can’t believe it’s impossible to form phosphorus–sulfur compounds with some other number of phosphorus atoms, but the Wikipedia article containing this chart says

All known molecular phosphorus sulfides contain a tetrahedral array of four phosphorus atoms. P4S2 is also known but is unstable above −30 °C.

All these phosphorus sulfides contain at most 10 sulfur atoms. If we remove one sulfur from phosphorus decasulfide we can get this:


This is the ‘alpha form’ of P4S9. There’s also a beta form, shown in the chart above.

Some of the phosphorus sulfides have pleasing symmetries, like the
alpha form of P4S4:


or the epsilon form of P4S6:


Others look awkward. The alpha form of P4S5 is an ungainly beast:

They all seem to have a few things in common:

• There are 4 phosphorus atoms.

• Each phosphorus atom is connected to 3 or 4 atoms, at most one of which is phosphorus.

• Each sulfur atom is connected to 1 or 2 atoms, which must all be phosphorus.

The pictures seem pretty consistent about showing a ‘double bond’ when a sulfur atom is connected to just 1 phosphorus. However, they don’t show a double bond when a phosphorus atom is connected to just 3 sulfurs.

Puzzle 2. Can you draw molecules obeying the 3 rules listed above that aren’t on the chart?

Of all the phosphorus sulfides, P4S10 is not only the biggest and most symmetrical, it’s also the most widely used. Humans make thousands of tons of the stuff! It’s used for producing organic sulfur compounds.

People also make P4S3: it’s used in strike-anywhere matches. This molecule is not on the chart I showed you, and it also violates one of the rules I made up:



Somewhat confusingly, P4S10 is not only called phosphorus decasulfide: it’s also called phosphorus pentasulfide. Similarly, P4S3 is called phosphorus sesquisulfide. Since the prefix ‘sesqui-’ means ‘one and a half’, there seems to be some kind of division by 2 going on here.


Diamondoids

2 May, 2017

I have a new favorite molecule: adamantane. As you probably know, someone is said to be ‘adamant’ if they are unshakeable, immovable, inflexible, unwavering, uncompromising, resolute, resolved, determined, firm, rigid, or steadfast. But ‘adamant’ is also a legendary mineral, and the etymology is the same as that for ‘diamond’.

The molecule adamantane, shown above, features 10 carbon atoms arranged just like a small portion of a diamond crystal! It’s a bit easier to see this if you ignore the 16 hydrogen atoms and focus on the carbon atoms and bonds between those:


It’s a somewhat strange shape.

Puzzle 1. Give a clear, elegant description of this shape.

Puzzle 2. What is its symmetry group? This is really two questions: I’m asking about the symmetry group of this shape as an abstract graph, but also the symmetry group of this graph as embedded in 3d Euclidean space, counting both rotations and reflections.

Puzzle 3. How many ‘kinds’ of carbon atoms does adamantane have? In other words, when we let the symmetry group of this graph act on the set of vertices, how many orbits are there? (Again this is really two questions, depending on which symmetry group we use.)

Puzzle 4. How many kinds of bonds between carbon atoms does adamantane have? In other words, when we let the symmetry group of this graph act on the set of edges, how many orbits are there? (Again, this is really two questions.)

You can see the relation between adamantane and a diamond if you look carefully at a diamond crystal, as shown in this image by H. K. D. H. Bhadeshia:


or this one by Greg Egan:



Even with these pictures at hand, I find it a bit tough to see the adamantane pattern lurking in the diamond! Look again:


Adamantane has an interesting history. The possibility of its existence was first suggested by a chemist named Decker at a conference in 1924. Decker called this molecule ‘decaterpene’, and registered surprise that nobody had made it yet. After some failed attempts, it was first synthesized by the Croatian-Swiss chemist Vladimir Prelog in 1941. He later won the Nobel prize for his work on stereochemistry.

However, long before it was synthesized, adamantane was isolated from petroleum by the Czech chemists Landa, Machacek and Mzourek! They did it in 1932. They only managed to make a few milligrams of the stuff, but we now know that petroleum naturally contains between .0001% and 0.03% adamantane!

Adamantane can be crystallized:

but ironically, the crystals are rather soft. It’s all that hydrogen. It’s also amusing that adamantane has an odor: supposedly it smells like camphor!

Adamantane is just the simplest of the molecules called diamondoids.
These are a few:


1 is adamantane.

2 is called diamantane.

3 is called triamantane.

4 is called isotetramantane, and it comes in two mirror-image forms.

Here are some better pictures of diamantane:


People have done lots of chemical reactions with diamondoids. Here are some things they’ve done with the next one, pentamantane:



Many different diamondoids occur naturally in petroleum. Though the carbon in diamonds is not biological in origin, the carbon in diamondoids found in petroleum is. This was shown by studying ratios of carbon isotopes.

Eric Drexler has proposed using diamondoids for nanotechnology, but he’s talking about larger molecules than those shown here.

For more fun along these lines, try:

Diamonds and triamonds, Azimuth, 11 April 2016.