## Applied Category Theory Course: Resource Theories

12 May, 2018

My course on applied category theory is continuing! After a two-week break where the students did exercises, I’m back to lecturing about Fong and Spivak’s book Seven Sketches. Now we’re talking about “resource theories”. Resource theories help us answer questions like this:

1. Given what I have, is it possible to get what I want?
2. Given what I have, how much will it cost to get what I want?
3. Given what I have, how long will it take to get what I want?
4. Given what I have, what is the set of ways to get what I want?

Resource theories in their modern form were arguably born in these papers:

• Bob Coecke, Tobias Fritz and Robert W. Spekkens, A mathematical theory of resources.

• Tobias Fritz, Resource convertibility and ordered commutative monoids.

We are lucky to have Tobias in our course, helping the discussions along! He’s already posted some articles on resource theory here on this blog:

• Tobias Fritz, Resource convertibility (part 1), Azimuth, 7 April 2015.

• Tobias Fritz, Resource convertibility (part 2), Azimuth, 10 April 2015.

• Tobias Fritz, Resource convertibility (part 3), Azimuth, 13 April 2015.

We’re having fun bouncing between the relatively abstract world of monoidal preorders and their very concrete real-world applications to chemistry, scheduling, manufacturing and other topics. Here are the lectures so far:

## Effective Thermodynamics for a Marginal Observer

8 May, 2018

guest post by Matteo Polettini

Suppose you receive an email from someone who claims “here is the project of a machine that runs forever and ever and produces energy for free!” Obviously he must be a crackpot. But he may be well-intentioned. You opt for not being rude, roll your sleeves, and put your hands into the dirt, holding the Second Law as lodestar.

Keep in mind that there are two fundamental sources of error: either he is not considering certain input currents (“hey, what about that tiny hidden cable entering your machine from the electrical power line?!”, “uh, ah, that’s just to power the “ON” LED”, “mmmhh, you sure?”), or else he is not measuring the energy input correctly (“hey, why are you using a Geiger counter to measure input voltages?!”, “well, sir, I ran out of voltmeters…”).

In other words, the observer might only have partial information about the setup, either in quantity or quality. Because he has been marginalized by society (most crackpots believe they are misunderstood geniuses) we will call such observer “marginal,” which incidentally is also the word that mathematicians use when they focus on the probability of a subset of stochastic variables.

In fact, our modern understanding of thermodynamics as embodied in statistical mechanics and stochastic processes is founded (and funded) on ignorance: we never really have “complete” information. If we actually had, all energy would look alike, it would not come in “more refined” and “less refined” forms, there would not be a differentials of order/disorder (using Paul Valery’s beautiful words), and that would end thermodynamic reasoning, the energy problem, and generous research grants altogether.

Even worse, within this statistical approach we might be missing chunks of information because some parts of the system are invisible to us. But then, what warrants that we are doing things right, and he (our correspondent) is the crackpot? Couldn’t it be the other way around? Here I would like to present some recent ideas I’ve been working on together with some collaborators on how to deal with incomplete information about the sources of dissipation of a thermodynamic system. I will do this in a quite theoretical manner, but somehow I will mimic the guidelines suggested above for debunking crackpots. My three buzzwords will be: marginal, effective, and operational.

### “Complete” thermodynamics: an out-of-the-box view

The laws of thermodynamics that I address are:

• The good ol’ Second Law (2nd)

• The Fluctuation-Dissipation Relation (FDR), and the Reciprocal Relation (RR) close to equilibrium.

• The more recent Fluctuation Relation (FR)1 and its corollary the Integral Fluctuation Relation (IFR), which have been discussed on this blog in a remarkable post by Matteo Smerlak.

The list above is all in the “area of the second law”. How about the other laws? Well, thermodynamics has for long been a phenomenological science, a patchwork. So-called stochastic thermodynamics is trying to put some order in it by systematically grounding thermodynamic claims in (mostly Markov) stochastic processes. But it’s not an easy task, because the different laws of thermodynamics live in somewhat different conceptual planes. And it’s not even clear if they are theorems, prescriptions, or habits (a bit like in jurisprudence2).

Within stochastic thermodynamics, the Zeroth Law is so easy nobody cares to formulate it (I do, so stay tuned…). The Third Law: no idea, let me know. As regards the First Law (or, better, “laws”, as many as there are conserved quantities across the system/environment interface…), we will assume that all related symmetries have been exploited from the offset to boil down the description to a minimum.

This minimum is as follows. We identify a system that is well separated from its environment. The system evolves in time, the environment is so large that its state does not evolve within the timescales of the system3. When tracing out the environment from the description, an uncertainty falls upon the system’s evolution. We assume the system’s dynamics to be described by a stochastic Markovian process.

How exactly the system evolves and what is the relationship between system and environment will be described in more detail below. Here let us take an “out of the box” view. We resolve the environment into several reservoirs labeled by index $\alpha$. Each of these reservoirs is “at equilibrium” on its own (whatever that means4). Now, the idea is that each reservoir tries to impose “its own equilibrium” on the system, and that their competition leads to a flow of currents across the system/environment interface. Each time an amount of the reservoir’s resource crosses the interface, a “thermodynamic cost” has to be to be paid or gained (be it a chemical potential difference for a molecule to go through a membrane, or a temperature gradient for photons to be emitted/absorbed, etc.).

The fundamental quantities of stochastic thermodynamic modeling thus are:

• On the “-dynamic” side: the time-integrated currents $\Phi^t_\alpha$, independent among themselves5. Currents are stochastic variables distributed with joint probability density

$P(\{\Phi_\alpha\}_\alpha)$

• On the “thermo-” side: The so-called thermodynamic forces or “affinities”6 $\mathcal{A}_\alpha$ (collectively denoted $\mathcal{A}$). These are tunable parameters that characterize reservoir-to-reservoir gradients, and they are not stochastic. For convenience, we conventionally take them all positive.

Dissipation is quantified by the entropy production:

$\sum \mathcal{A}_\alpha \Phi^t_\alpha$

We are finally in the position to state the main results. Be warned that in the following expressions the exact treatment of time and its scaling would require a lot of specifications, but keep in mind that all these relations hold true in the long-time limit, and that all cumulants scale linearly with time.

FR: The probability of observing positive currents is exponentially favoured with respect to negative currents according to

$P(\{\Phi_\alpha\}_\alpha) / P(\{-\Phi_\alpha\}_\alpha) = \exp \sum \mathcal{A}_\alpha \Phi^t_\alpha$

Comment: This is not trivial, it follows from the explicit expression of the path integral, see below.

IFR: The exponential of minus the entropy production is unity

$\big\langle \exp - \sum \mathcal{A}_\alpha \Phi^t_\alpha \big\rangle_{\mathcal{A}} =1$

Homework: Derive this relation from the FR in one line.

2nd Law: The average entropy production is not negative

$\sum \mathcal{A}_\alpha \left\langle \Phi^t_\alpha \right\rangle_{\mathcal{A}} \geq 0$

Homework: Derive this relation using Jensen’s inequality.

Equilibrium: Average currents vanish if and only if affinities vanish:

$\left\langle \Phi^t_\alpha \right\rangle_{\mathcal{A}} \equiv 0, \forall \alpha \iff \mathcal{A}_\alpha \equiv 0, \forall \alpha$

Homework: Derive this relation taking the first derivative w.r.t. ${\mathcal{A}_\alpha}$ of the IFR. Notice that also the average depends on the affinities.

S-FDR: At equilibrium, it is impossible to tell whether a current is due to a spontaneous fluctuation (quantified by its variance) or to an external perturbation (quantified by the response of its mean). In a symmetrized (S-) version:

$\left. \frac{\partial}{\partial \mathcal{A}_\alpha}\left\langle \Phi^t_{\alpha'} \right\rangle \right|_{0} + \left. \frac{\partial}{\partial \mathcal{A}_{\alpha'}}\left\langle \Phi^t_{\alpha} \right\rangle \right|_{0} = \left. \left\langle \Phi^t_{\alpha} \Phi^t_{\alpha'} \right\rangle \right|_{0}$

Homework: Derive this relation taking the mixed second derivatives w.r.t. ${\mathcal{A}_\alpha}$ of the IFR.

RR: The reciprocal response of two different currents to a perturbation of the reciprocal affinities close to equilibrium is symmetrical:

$\left. \frac{\partial}{\partial \mathcal{A}_\alpha}\left\langle \Phi^t_{\alpha'} \right\rangle \right|_{0} - \left. \frac{\partial}{\partial \mathcal{A}_{\alpha'}}\left\langle \Phi^t_{\alpha} \right\rangle \right|_{0} = 0$

Homework: Derive this relation taking the mixed second derivatives w.r.t. ${\mathcal{A}_\alpha}$ of the FR.

Notice the implication scheme: FR ⇒ IFR ⇒ 2nd, IFR ⇒ S-FDR, FR ⇒ RR.

### “Marginal” thermodynamics (still out-of-the-box)

Now we assume that we can only measure a marginal subset of currents $\{\Phi_\mu^t\}_\mu \subset \{\Phi_\alpha^t\}_\alpha$ (index $\mu$ always has a smaller range than $\alpha$), distributed with joint marginal probability

$P(\{\Phi_\mu\}_\mu) = \int \prod_{\alpha \neq \mu} d\Phi_\alpha \, P(\{\Phi_\alpha\}_\alpha)$

Notice that a state where these marginal currents vanish might not be an equilibrium, because other currents might still be whirling around. We call this a stalling state.

$\mathrm{stalling:} \qquad \langle \Phi_\mu \rangle \equiv 0, \quad \forall \mu$

My central question is: can we associate to these currents some effective affinity $\mathcal{Q}_\mu$ in such a way that at least some of the results above still hold true? And, are all definitions involved just a fancy mathematical construct, or are they operational?

First the bad news: In general the FR is violated for all choices of effective affinities:

$P(\{\Phi_\mu\}_\mu) / P(\{-\Phi_\mu\}_\mu) \neq \exp \sum \mathcal{Q}_\mu \Phi^t_\mu$

This is not surprising and nobody would expect that. How about the IFR?

Marginal IFR: There are effective affinities such that

$\left\langle \exp - \sum \mathcal{Q}_\mu \Phi^t_\mu \right\rangle_{\mathcal{A}} =1$

Mmmhh. Yeah. Take a closer look this expression: can you see why there actually exists an infinite choice of “effective affinities” that would make that average cross 1? Which on the other hand is just a number, so who even cares? So this can’t be the point.

The fact is, the IFR per se is hardly of any practical interest, as are all “absolutes” in physics. What matters is “relatives”: in our case, response. But then we need to specify how the effective affinities depend on the “real” affinities. And here steps in a crucial technicality, whose precise argumentation is a pain. Basing on reasonable assumptions7, we demonstrate that the IFR holds for the following choice of effective affinities:

$\mathcal{Q}_\mu = \mathcal{A}_\mu - \mathcal{A}^{\mathrm{stalling}}_\mu$,

where $\mathcal{A}^{\mathrm{stalling}}$ is the set of values of the affinities that make marginal currents stall. Notice that this latter formula gives an operational definition of the effective affinities that could in principle be reproduced in laboratory (just go out there and tune the tunable until everything stalls, and measure the difference). Obviously:

Stalling: Marginal currents vanish if and only if effective affinities vanish:

$\left\langle \Phi^t_\mu \right\rangle_{\mathcal{A}} \equiv 0, \forall \mu \iff \mathcal{A}_\mu \equiv 0, \forall \mu$

Now, according to the inference scheme illustrated above, we can also prove that:

Effective 2nd Law: The average marginal entropy production is not negative

$\sum \mathcal{Q}_\mu \left\langle \Phi^t_\mu \right\rangle_{\mathcal{A}} \geq 0$

S-FDR at stalling:

$\left. \frac{\partial}{\partial \mathcal{A}_\mu}\left\langle \Phi^t_{\mu'} \right\rangle \right|_{\mathcal{A}^{\mathrm{stalling}}} + \left. \frac{\partial}{\partial \mathcal{A}_{\mu'}}\left\langle \Phi^t_{\mu} \right\rangle \right|_{\mathcal{A}^{\mathrm{stalling}}} = \left. \left\langle \Phi^t_{\mu} \Phi^t_{\mu'} \right\rangle \right|_{\mathcal{A}^{\mathrm{stalling}}}$

Notice instead that the RR is gone at stalling. This is a clear-cut prediction of the theory that can be experimented with basically the same apparatus with which response theory has been experimentally studied so far (not that I actually know what these apparatus are…): at stalling states, differing from equilibrium states, the S-FDR still holds, but the RR does not.

### Into the box

You’ve definitely gotten enough at this point, and you can give up here. Please exit through the gift shop.

If you’re stubborn, let me tell you what’s inside the box. The system’s dynamics is modeled as a continuous-time, discrete configuration-space Markov “jump” process. The state space can be described by a graph $G=(I, E)$ where $I$ is the set of configurations, $E$ is the set of possible transitions or “edges”, and there exists some incidence relation between edges and couples of configurations. The process is determined by the rates $w_{i \gets j}$ of jumping from one configuration to another.

We choose these processes because they allow some nice network analysis and because the path integral is well defined! A single realization of such a process is a trajectory

$\omega^t = (i_0,\tau_0) \to (i_1,\tau_1) \to \ldots \to (i_N,\tau_N)$

A “Markovian jumper” waits at some configuration $i_n$ for some time $\tau_n$ with an exponentially decaying probability $w_{i_n} \exp - w_{i_n} \tau_n$ with exit rate $w_i = \sum_k w_{k \gets i}$, then instantaneously jumps to a new configuration $i_{n+1}$ with transition probability $w_{i_{n+1} \gets {i_n}}/w_{i_n}$. The overall probability density of a single trajectory is given by

$P(\omega^t) = \delta \left(t - \sum_n \tau_n \right) e^{- w_{i_N}\tau_{i_N}} \prod_{n=0}^{N-1} w_{j_n \gets i_n} e^{- w_{i_n} \tau_{i_n}}$

One can in principle obtain the probability distribution function of any observable defined along the trajectory by taking the marginal of this measure (though in most cases this is technically impossible). Where does this expression come from? For a formal derivation, see the very beautiful review paper by Weber and Frey, but be aware that this is what one would intuitively come up with if one had to simulate with the Gillespie algorithm.

The dynamics of the Markov process can also be described by the probability of being at some configuration $i$ at time $t$, which evolves via the master equation

$\dot{p}_i(t) = \sum_j \left[ w_{ij} p_j(t) - w_{ji} p_i(t) \right]$.

We call such probability the system’s state, and we assume that the system relaxes to a uniquely defined steady state $p = \mathrm{lim}_{t \to \infty} p(t)$.

A time-integrated current along a single trajectory is a linear combination of the net number of jumps $\#^t$ between configurations in the network:

$\Phi^t_\alpha = \sum_{ij} C^{ij}_\alpha \left[ \#^t(i \gets j) - \#^t(j\gets i) \right]$

The idea here is that one or several transitions within the system occur because of the “absorption” or the “emission” of some environmental degrees of freedom, each with different intensity. However, for the moment let us simplify the picture and require that only one transition contributes to a current, that is that there exist $i_\alpha,j_\alpha$ such that

$C^{ij}_\alpha = \delta^i_{i_\alpha} \delta^j_{j_\alpha}$.

Now, what does it mean for such a set of currents to be “complete”? Here we get inspiration from Kirchhoff’s Current Law in electrical circuits: the continuity of the trajectory at each configuration of the network implies that after a sufficiently long time, cycle or loop or mesh currents completely describe the steady state. There is a standard procedure to identify a set of cycle currents: take a spanning tree $T$ of the network; then the currents flowing along the edges $E\setminus T$ left out from the spanning tree form a complete set.

The last ingredient you need to know are the affinities. They can be constructed as follows. Consider the Markov process on the network where the observable edges are removed $G' = (I,T)$. Calculate the steady state of its associated master equation $(p^{\mathrm{eq}}_i)_i$, which is necessarily an equilibrium (since there cannot be cycle currents in a tree…). Then the affinities are given by

$\mathcal{A}_\alpha = \log w_{i_\alpha j_\alpha} p^{\mathrm{eq}}_{j_\alpha} / w_{j_\alpha i_\alpha} p^{\mathrm{eq}}_{i_\alpha}$.

Now you have all that is needed to formulate the complete theory and prove the FR.

Homework: (Difficult!) With the above definitions, prove the FR.

How about the marginal theory? To define the effective affinities, take the set $E_{\mathrm{mar}} = \{i_\mu j_\mu, \forall \mu\}$ of edges where there run observable currents. Notice that now its complement obtained by removing the observable edges, the hidden edge set $E_{\mathrm{hid}} = E \setminus E_{\mathrm{mar}}$, is not in general a spanning tree: there might be cycles that are not accounted for by our observations. However, we can still consider the Markov process on the hidden space, and calculate its stalling steady state $p^{\mathrm{st}}_i$, and ta-taaa: The effective affinities are given by

$\mathcal{Q}_\mu = \log w_{i_\mu j_\mu} p^{\mathrm{st}}_{j_\mu} / w_{j_\mu i_\mu} p^{\mathrm{st}}_{i_\mu}$.

Proving the marginal IFR is far more complicated than the complete FR. In fact, very often in my field we will not work with the current’ probability density itself, but we prefer to take its bidirectional Laplace transform and work with the currents’ cumulant generating function. There things take a quite different and more elegant look.

Many other questions and possibilities open up now. The most important one left open is: Can we generalize the theory the (physically relevant) case where the current is supported on several edges? For example, for a current defined like $\Phi^t = 5 \Phi^t_{12} + 7 \Phi^t_{34}$? Well, it depends: the theory holds provided that the stalling state is not “internally alive”, meaning that if the observable current vanishes on average, then also should $\Phi^t_{12}$ and $\Phi^t_{34}$ separately. This turns out to be a physically meaningful but quite strict condition.

### Is all of thermodynamics “effective”?

Let me conclude with some more of those philosophical considerations that sadly I have to leave out of papers…

Stochastic thermodynamics strongly depends on the identification of physical and information-theoretic entropies â€” something that I did not openly talk about, but that lurks behind the whole construction. Throughout my short experience as researcher I have been pursuing a program of “relativization” of thermodynamics, by making the role of the observer more and more evident and movable. Inspired by Einstein’s Gedankenexperimenten, I also tried to make the theory operational. This program may raise eyebrows here and there: Many thermodynamicians embrace a naive materialistic world-view whereby what only matters are “real” physical quantities like temperature, pressure, and all the rest of the information-theoretic discourse is at best mathematical speculation or a fascinating analog with no fundamental bearings. According to some, information as a physical concept lingers alarmingly close to certain extreme postmodern claims in the social sciences that “reality” does not exist unless observed, a position deemed dangerous at times when the authoritativeness of science is threatened by all sorts of anti-scientific waves.

I think, on the contrary, that making concepts relative and effective and by summoning the observer explicitly is a laic and prudent position that serves as an antidote to radical subjectivity. The other way around—clinging to the objectivity of a preferred observer, which is implied in any materialistic interpretation of thermodynamics, e.g. by assuming that the most fundamental degrees of freedom are the positions and velocities of gas’s molecules—is the dangerous position, expecially when the role of such preferred observer is passed around from the scientist to the technician and eventually to the technocrat, who would be induced to believe there are simple technological fixes to complex social problems

How do we reconcile observer-dependency and the laws of physics? The object and the subject? On the one hand, much like the position of an object depends on the reference frame, so much so entropy and entropy production do depend on the observer and the particular apparatus that he controls or experiment he is involved with. On the other hand, much like motion is ultimately independent of position and it is agreed upon by all observers that share compatible measurement protocols, so much so the laws of thermodynamics are independent of that particular observer’s quantification of entropy and entropy production (e.g., the effective Second Law holds independently of how much the marginal observer knows of the system, if he operates according to our phenomenological protocol…). This is the case even in the every-day thermodynamics as practiced by energetic engineers et al., where there are lots of choices to gauge upon, and there is no other external warrant that the amount of dissipation being quantified is the “true” one (whatever that means…)—there can only be trust in one’s own good practices and methodology.

So in this sense, I like to think that all observers are marginal, that this effective theory serves as a dictionary by which different observers practice and communicate thermodynamics, and that we should not revere the laws of thermodynamics as “true” idols, but rather as tools of good scientific practice.

### References

• M. Polettini and M. Esposito, Effective fluctuation and response theory, arXiv:1803.03552.

In this work we give the complete theory and numerous references to work of other people that was along the same lines. We employ a “spiral” approach to the presentation of the results, inspired by the pedagogical principle of Albert Baez.

• M. Polettini and M. Esposito, Effective thermodynamics for a marginal observer, Phys. Rev. Lett. 119 (2017), 240601, arXiv:1703.05715.

This is a shorter version of the story.

• B. Altaner, M. Polettini and M. Esposito, Fluctuation-dissipation relations far from equilibrium, Phys. Rev. Lett. 117 (2016), 180601, arXiv:1604.0883.

An early version of the story, containing the FDR results but not the full-fledged FR.

• G. Bisker, M. Polettini, T. R. Gingrich and J. M. Horowitz, Hierarchical bounds on entropy production inferred from partial information, J. Stat. Mech. (2017), 093210, arXiv:1708.06769.

Some extras.

• M. F. Weber and E. Frey, Master equations and the theory of stochastic path integrals, Rep. Progr. Phys. 80 (2017), 046601, arXiv:1609.02849.

Great reference if one wishes to learn about path integrals for master equation systems.

### Footnotes

1 There are as many so-called “Fluctuation Theorems” as there are authors working on them, so I decided not to call them by any name. Furthermore, notice I prefer to distinguish between a relation (a formula) and a theorem (a line of reasoning). I lingered more on this here.

2 “Just so you know, nobody knows what energy is.”—Richard Feynman.

I cannot help but mention here the beautiful book by Shapin and Schaffer, Leviathan and the Air-Pump, about the Boyle vs. Hobbes diatribe about what constitutes a “matter of fact,” and Bruno Latour’s interpretation of it in We Have Never Been Modern. Latour argues that “modernity” is a process of separation of the human and natural spheres, and within each of these spheres a process of purification of the unit facts of knowledge and the unit facts of politics, of the object and the subject. At the same time we live in a world where these two spheres are never truly separated, a world of “hybrids” that are at the same time necessary “for all practical purposes” and unconceivable according to the myths that sustain the narration of science, of the State, and even of religion. In fact, despite these myths, we cannot conceive a scientific fact out of the contextual “network” where this fact is produced and replicated, and neither we can conceive society out of the material needs that shape it: so in this sense “we have never been modern”, we are not quite different from all those societies that we take pleasure of studying with the tools of anthropology. Within the scientific community Latour is widely despised; probably he is also misread. While it is really difficult to see how his analysis applies to, say, high-energy physics, I find that thermodynamics and its ties to the industrial revolution perfectly embodies this tension between the natural and the artificial, the matter of fact and the matter of concern. Such great thinkers as Einstein and Ehrenfest thought of the Second Law as the only physical law that would never be replaced, and I believe this is revelatory. A second thought on the Second Law, a systematic and precise definition of all its terms and circumstances, reveals that the only formulations that make sense are those phenomenological statements such as Kelvin-Planck’s or similar, which require a lot of contingent definitions regarding the operation of the engine, while fetishized and universal statements are nonsensical (such as that masterwork of confusion that is “the entropy of the Universe cannot decrease”). In this respect, it is neither a purely natural law—as the moderns argue, nor a purely social construct—as the postmodern argue. One simply has to renounce to operate this separation. While I do not have a definite answer on this problem, I like to think of the Second Law as a practice, a consistency check of the thermodynamic discourse.

3 This assumption really belongs to a time, the XIXth century, when resources were virtually infinite on planet Earth…

4 As we will see shortly, we define equilibrium as that state where there are no currents at the interface between the system and the environment, so what is the environment’s own definition of equilibrium?!

5 This because we have already exploited the First Law.

6 This nomenclature comes from alchemy, via chemistry (think of Goethe’s The elective affinities…), it propagated in the XXth century via De Donder and Prigogine, and eventually it is still present in language in Luxembourg because in some way we come from the “late Brussels school”.

7 Basically, we ask that the tunable parameters are environmental properties, such as temperatures, chemical potentials, etc. and not internal properties, such as the energy landscape or the activation barriers between configurations.

## A Compositional Framework for Reaction Networks

30 July, 2017

For a long time Blake Pollard and I have been working on ‘open’ chemical reaction networks: that is, networks of chemical reactions where some chemicals can flow in from an outside source, or flow out. The picture to keep in mind is something like this:

where the yellow circles are different kinds of chemicals and the aqua boxes are different reactions. The purple dots in the sets X and Y are ‘inputs’ and ‘outputs’, where certain kinds of chemicals can flow in or out.

Here’s our paper on this stuff:

• John Baez and Blake Pollard, A compositional framework for reaction networks, Reviews in Mathematical Physics 29, 1750028.

Blake and I gave talks about this stuff in Luxembourg this June, at a nice conference called Dynamics, thermodynamics and information processing in chemical networks. So, if you’re the sort who prefers talk slides to big scary papers, you can look at those:

• John Baez, The mathematics of open reaction networks.

• Blake Pollard, Black-boxing open reaction networks.

But I want to say here what we do in our paper, because it’s pretty cool, and it took a few years to figure it out. To get things to work, we needed my student Brendan Fong to invent the right category-theoretic formalism: ‘decorated cospans’. But we also had to figure out the right way to think about open dynamical systems!

In the end, we figured out how to first ‘gray-box’ an open reaction network, converting it into an open dynamical system, and then ‘black-box’ it, obtaining the relation between input and output flows and concentrations that holds in steady state. The first step extracts the dynamical behavior of an open reaction network; the second extracts its static behavior. And both these steps are functors!

Lawvere had the idea that the process of assigning ‘meaning’ to expressions could be seen as a functor. This idea has caught on in theoretical computer science: it’s called ‘functorial semantics’. So, what we’re doing here is applying functorial semantics to chemistry.

Now Blake has passed his thesis defense based on this work, and he just needs to polish up his thesis a little before submitting it. This summer he’s doing an internship at the Princeton branch of the engineering firm Siemens. He’s working with Arquimedes Canedo on ‘knowledge representation’.

But I’m still eager to dig deeper into open reaction networks. They’re a small but nontrivial step toward my dream of a mathematics of living systems. My working hypothesis is that living systems seem ‘messy’ to physicists because they operate at a higher level of abstraction. That’s what I’m trying to explore.

Here’s the idea of our paper.

### The idea

Reaction networks are a very general framework for describing processes where entities interact and transform int other entities. While they first showed up in chemistry, and are often called ‘chemical reaction networks’, they have lots of other applications. For example, a basic model of infectious disease, the ‘SIRS model’, is described by this reaction network:

$S + I \stackrel{\iota}{\longrightarrow} 2 I \qquad I \stackrel{\rho}{\longrightarrow} R \stackrel{\lambda}{\longrightarrow} S$

We see here three types of entity, called species:

$S$: susceptible,
$I$: infected,
$R$: resistant.

We also have three `reactions’:

$\iota : S + I \to 2 I$: infection, in which a susceptible individual meets an infected one and becomes infected;
$\rho : I \to R$: recovery, in which an infected individual gains resistance to the disease;
$\lambda : R \to S$: loss of resistance, in which a resistant individual becomes susceptible.

In general, a reaction network involves a finite set of species, but reactions go between complexes, which are finite linear combinations of these species with natural number coefficients. The reaction network is a directed graph whose vertices are certain complexes and whose edges are called reactions.

If we attach a positive real number called a rate constant to each reaction, a reaction network determines a system of differential equations saying how the concentrations of the species change over time. This system of equations is usually called the rate equation. In the example I just gave, the rate equation is

$\begin{array}{ccl} \displaystyle{\frac{d S}{d t}} &=& r_\lambda R - r_\iota S I \\ \\ \displaystyle{\frac{d I}{d t}} &=& r_\iota S I - r_\rho I \\ \\ \displaystyle{\frac{d R}{d t}} &=& r_\rho I - r_\lambda R \end{array}$

Here $r_\iota, r_\rho$ and $r_\lambda$ are the rate constants for the three reactions, and $S, I, R$ now stand for the concentrations of the three species, which are treated in a continuum approximation as smooth functions of time:

$S, I, R: \mathbb{R} \to [0,\infty)$

The rate equation can be derived from the law of mass action, which says that any reaction occurs at a rate equal to its rate constant times the product of the concentrations of the species entering it as inputs.

But a reaction network is more than just a stepping-stone to its rate equation! Interesting qualitative properties of the rate equation, like the existence and uniqueness of steady state solutions, can often be determined just by looking at the reaction network, regardless of the rate constants. Results in this direction began with Feinberg and Horn’s work in the 1960’s, leading to the Deficiency Zero and Deficiency One Theorems, and more recently to Craciun’s proof of the Global Attractor Conjecture.

In our paper, Blake and I present a ‘compositional framework’ for reaction networks. In other words, we describe rules for building up reaction networks from smaller pieces, in such a way that its rate equation can be figured out knowing those those of the pieces. But this framework requires that we view reaction networks in a somewhat different way, as ‘Petri nets’.

Petri nets were invented by Carl Petri in 1939, when he was just a teenager, for the purposes of chemistry. Much later, they became popular in theoretical computer science, biology and other fields. A Petri net is a bipartite directed graph: vertices of one kind represent species, vertices of the other kind represent reactions. The edges into a reaction specify which species are inputs to that reaction, while the edges out specify its outputs.

You can easily turn a reaction network into a Petri net and vice versa. For example, the reaction network above translates into this Petri net:

Beware: there are a lot of different names for the same thing, since the terminology comes from several communities. In the Petri net literature, species are called places and reactions are called transitions. In fact, Petri nets are sometimes called ‘place-transition nets’ or ‘P/T nets’. On the other hand, chemists call them ‘species-reaction graphs’ or ‘SR-graphs’. And when each reaction of a Petri net has a rate constant attached to it, it is often called a ‘stochastic Petri net’.

While some qualitative properties of a rate equation can be read off from a reaction network, others are more easily read from the corresponding Petri net. For example, properties of a Petri net can be used to determine whether its rate equation can have multiple steady states.

Petri nets are also better suited to a compositional framework. The key new concept is an ‘open’ Petri net. Here’s an example:

The box at left is a set X of ‘inputs’ (which happens to be empty), while the box at right is a set Y of ‘outputs’. Both inputs and outputs are points at which entities of various species can flow in or out of the Petri net. We say the open Petri net goes from X to Y. In our paper, we show how to treat it as a morphism $f : X \to Y$ in a category we call $\textrm{RxNet}$.

Given an open Petri net with rate constants assigned to each reaction, our paper explains how to get its ‘open rate equation’. It’s just the usual rate equation with extra terms describing inflows and outflows. The above example has this open rate equation:

$\begin{array}{ccr} \displaystyle{\frac{d S}{d t}} &=& - r_\iota S I - o_1 \\ \\ \displaystyle{\frac{d I}{d t}} &=& r_\iota S I - o_2 \end{array}$

Here $o_1, o_2 : \mathbb{R} \to \mathbb{R}$ are arbitrary smooth functions describing outflows as a function of time.

Given another open Petri net $g: Y \to Z,$ for example this:

it will have its own open rate equation, in this case

$\begin{array}{ccc} \displaystyle{\frac{d S}{d t}} &=& r_\lambda R + i_2 \\ \\ \displaystyle{\frac{d I}{d t}} &=& - r_\rho I + i_1 \\ \\ \displaystyle{\frac{d R}{d t}} &=& r_\rho I - r_\lambda R \end{array}$

Here $i_1, i_2: \mathbb{R} \to \mathbb{R}$ are arbitrary smooth functions describing inflows as a function of time. Now for a tiny bit of category theory: we can compose $f$ and $g$ by gluing the outputs of $f$ to the inputs of $g.$ This gives a new open Petri net $gf: X \to Z,$ as follows:

But this open Petri net $gf$ has an empty set of inputs, and an empty set of outputs! So it amounts to an ordinary Petri net, and its open rate equation is a rate equation of the usual kind. Indeed, this is the Petri net we have already seen.

As it turns out, there’s a systematic procedure for combining the open rate equations for two open Petri nets to obtain that of their composite. In the example we’re looking at, we just identify the outflows of $f$ with the inflows of $g$ (setting $i_1 = o_1$ and $i_2 = o_2$) and then add the right hand sides of their open rate equations.

The first goal of our paper is to precisely describe this procedure, and to prove that it defines a functor

$\diamond: \textrm{RxNet} \to \textrm{Dynam}$

from $\textrm{RxNet}$ to a category $\textrm{Dynam}$ where the morphisms are ‘open dynamical systems’. By a dynamical system, we essentially mean a vector field on $\mathbb{R}^n,$ which can be used to define a system of first-order ordinary differential equations in $n$ variables. An example is the rate equation of a Petri net. An open dynamical system allows for the possibility of extra terms that are arbitrary functions of time, such as the inflows and outflows in an open rate equation.

In fact, we prove that $\textrm{RxNet}$ and $\textrm{Dynam}$ are symmetric monoidal categories and that $d$ is a symmetric monoidal functor. To do this, we use Brendan Fong’s theory of ‘decorated cospans’.

Decorated cospans are a powerful general tool for describing open systems. A cospan in any category is just a diagram like this:

We are mostly interested in cospans in $\mathrm{FinSet},$ the category of finite sets and functions between these. The set $S$, the so-called apex of the cospan, is the set of states of an open system. The sets $X$ and $Y$ are the inputs and outputs of this system. The legs of the cospan, meaning the morphisms $i: X \to S$ and $o: Y \to S,$ describe how these inputs and outputs are included in the system. In our application, $S$ is the set of species of a Petri net.

For example, we may take this reaction network:

$A+B \stackrel{\alpha}{\longrightarrow} 2C \quad \quad C \stackrel{\beta}{\longrightarrow} D$

treat it as a Petri net with $S = \{A,B,C,D\}$:

and then turn that into an open Petri net by choosing any finite sets $X,Y$ and maps $i: X \to S$, $o: Y \to S$, for example like this:

(Notice that the maps including the inputs and outputs into the states of the system need not be one-to-one. This is technically useful, but it introduces some subtleties that I don’t feel like explaining right now.)

An open Petri net can thus be seen as a cospan of finite sets whose apex $S$ is ‘decorated’ with some extra information, namely a Petri net with $S$ as its set of species. Fong’s theory of decorated cospans lets us define a category with open Petri nets as morphisms, with composition given by gluing the outputs of one open Petri net to the inputs of another.

We call the functor

$\diamond: \textrm{RxNet} \to \textrm{Dynam}$

gray-boxing because it hides some but not all the internal details of an open Petri net. (In the paper we draw it as a gray box, but that’s too hard here!)

We can go further and black-box an open dynamical system. This amounts to recording only the relation between input and output variables that must hold in steady state. We prove that black-boxing gives a functor

$\square: \textrm{Dynam} \to \mathrm{SemiAlgRel}$

(yeah, the box here should be black, and in our paper it is). Here $\mathrm{SemiAlgRel}$ is a category where the morphisms are semi-algebraic relations between real vector spaces, meaning relations defined by polynomials and inequalities. This relies on the fact that our dynamical systems involve algebraic vector fields, meaning those whose components are polynomials; more general dynamical systems would give more general relations.

That semi-algebraic relations are closed under composition is a nontrivial fact, a spinoff of the Tarski–Seidenberg theorem. This says that a subset of $\mathbb{R}^{n+1}$ defined by polynomial equations and inequalities can be projected down onto $\mathbb{R}^n$, and the resulting set is still definable in terms of polynomial identities and inequalities. This wouldn’t be true if we didn’t allow inequalities. It’s neat to see this theorem, important in mathematical logic, showing up in chemistry!

### Structure of the paper

Okay, now you’re ready to read our paper! Here’s how it goes:

In Section 2 we review and compare reaction networks and Petri nets. In Section 3 we construct a symmetric monoidal category $\textrm{RNet}$ where an object is a finite set and a morphism is an open reaction network (or more precisely, an isomorphism class of open reaction networks). In Section 4 we enhance this construction to define a symmetric monoidal category $\textrm{RxNet}$ where the transitions of the open reaction networks are equipped with rate constants. In Section 5 we explain the open dynamical system associated to an open reaction network, and in Section 6 we construct a symmetric monoidal category $\textrm{Dynam}$ of open dynamical systems. In Section 7 we construct the gray-boxing functor

$\diamond: \textrm{RxNet} \to \textrm{Dynam}$

In Section 8 we construct the black-boxing functor

$\square: \textrm{Dynam} \to \mathrm{SemiAlgRel}$

We show both of these are symmetric monoidal functors.

Finally, in Section 9 we fit our results into a larger ‘network of network theories’. This is where various results in various papers I’ve been writing in the last few years start assembling to form a big picture! But this picture needs to grow….

## Information Processing in Chemical Networks (Part 2)

13 June, 2017

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:

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:

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.

## 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!

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:

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.