arXiv subjects

John C. Baez

Publications and source records attributed to John C. Baez.

At least 55 records · Page 3Linked to original sources

arXiv2021

The Fundamental Theorem of Natural Selection

Suppose we have $n$ different types of self-replicating entity, with the population $P_i$ of the $i$th type changing at a rate equal to $P_i$ times the fitness $f_i$ of that type. Suppose the fitness $f_i$ is any continuous function of all the populations $P_1, \dots, P_n$. Let $p_i$ be the fraction of replicators that are of the $i$th type. Then $p = (p_1, \dots, p_n)$ is a time-dependent probability distribution, and we prove that its speed as measured by the Fisher information metric equals the variance in fitness. In rough terms, this says that the speed at which information is updated through natural selection equals the variance in fitness. This result can be seen as a modified version of Fisher's fundamental theorem of natural selection. We compare it to Fisher's original result as interpreted by Price, Ewens and Edwards.

q-bio.PE↗

arXiv2021

The Brownian Map

The "Brownian map" is a fundamental object in mathematics, in some sense a 2-dimensional analogue of Brownian motion. Here we briefly explain this object and a bit of its history.

math.PR↗

arXiv2021

Categories of Nets

We present a unified framework for Petri nets and various variants, such as pre-nets and Kock's whole-grain Petri nets. Our framework is based on a less well-studied notion that we call $Σ$-nets, which allow finer control over whether tokens are treated using the collective or individual token philosophy. We describe three forms of execution semantics in which pre-nets generate strict monoidal categories, $Σ$-nets (including whole-grain Petri nets) generate symmetric strict monoidal categories, and Petri nets generate commutative monoidal categories, all by left adjoint functors. We also construct adjunctions relating these categories of nets to each other, in particular showing that all kinds of net can be embedded in the unifying category of $Σ$-nets, in a way that commutes coherently with their execution semantics.

math.CT↗

arXiv2021

Open Systems in Classical Mechanics

Generalized span categories provide a framework for formalizing mathematical models of open systems in classical mechanics. We introduce categories $\mathsf{LagSy}$ and $\mathsf{HamSy}$ that respectively provide a categorical framework for the Lagrangian and Hamiltonian descriptions of open classical mechanical systems. The morphisms of $\mathsf{LagSy}$ and $\mathsf{HamSy}$ correspond to such open systems, and composition of morphisms models the construction of systems from subsystems. The Legendre transformation gives rise to a functor from $\mathsf{LagSy}$ to $\mathsf{HamSy}$ that translates from the Lagrangian to the Hamiltonian perspective.

math-ph↗

arXiv2020

The Tenfold Way

The tenfold way became important in physics around 2010: it implies that there are ten fundamentally different kinds of matter. But it goes back to 1964, when C. T. C. Wall classified real super division algebras. These are finite-dimensional real $\mathbb{Z}/2$-graded algebras where every nonzero homogeneous element is invertible. He found that besides $\mathbb{R}$, $\mathbb{C}$ and $\mathbb{H}$, which give purely even super division algebras, there are seven more. He also showed that these ten algebras are all real or complex Clifford algebras. The eight real ones represent all eight Morita equivalence classes of real Clifford algebras, and the two complex ones do the same for the complex Clifford algebras. The tenfold way thus unites real and complex Bott periodicity. In this expository article we give a quick proof that there are ten real super division algebras, and say a bit about applications of the tenfold way.

math.RA↗

arXiv2020

Higher-Dimensional Algebra I: Braided Monoidal 2-Categories

We begin with a brief sketch of what is known and conjectured concerning braided monoidal 2-categories and their applications to 4d topological quantum field theories and 2-tangles (surfaces embedded in 4-dimensional space). Then we give concise definitions of semistrict monoidal 2-categories and braided monoidal 2-categories, and show how these may be unpacked to give long explicit definitions similar to, but not quite the same as, those given by Kapranov and Voevodsky. Finally, we describe how to construct a semistrict braided monoidal 2-category Z(C) as the `center' of a semistrict monoidal category C. This is analogous to the construction of a braided monoidal category as the center, or `quantum double', of a monoidal category. As a corollary, our construction yields a strictification theorem for braided monoidal 2-categories.

q-alg↗

arXiv2020

Structured Cospans

One goal of applied category theory is to better understand networks appearing throughout science and engineering. Here we introduce "structured cospans" as a way to study networks with inputs and outputs. Given a functor $L \colon \mathsf{A} \to \mathsf{X}$, a structured cospan is a diagram in $\mathsf{X}$ of the form $L(a) \rightarrow x \leftarrow L(b)$. If $\mathsf{A}$ and $\mathsf{X}$ have finite colimits and $L$ is a left adjoint, we obtain a symmetric monoidal category whose objects are those of $\mathsf{A}$ and whose morphisms are isomorphism classes of structured cospans. This is a hypergraph category. However, it arises from a more fundamental structure: a symmetric monoidal double category where the horizontal 1-cells are structured cospans. We show how structured cospans solve certain problems in the closely related formalism of "decorated cospans", and explain how they work in some examples: electrical circuits, Petri nets, and chemical reaction networks.

math.CT↗

arXiv2020

Operads for Designing Systems of Systems

System of systems engineering seeks to analyze, design and deploy collections of systems that together can flexibly address an array of complex tasks. In the Complex Adaptive System Composition and Design Environment program, we developed "network operads" as a tool for designing and tasking systems of systems, and applied them to domains including maritime search and rescue. The network operad formalism offers new ways to handle changing levels of abstraction in system-of-system design and tasking.

cs.SE↗

arXiv2020

Enriched Lawvere Theories for Operational Semantics

Enriched Lawvere theories are a generalization of Lawvere theories that allow us to describe the operational semantics of formal systems. For example, a graph enriched Lawvere theory describes structures that have a graph of operations of each arity, where the vertices are operations and the edges are rewrites between operations. Enriched theories can be used to equip systems with operational semantics, and maps between enriching categories can serve to translate between different forms of operational and denotational semantics. The Grothendieck construction lets us study all models of all enriched theories in all contexts in a single category. We illustrate these ideas with the SKI-combinator calculus, a variable-free version of the lambda calculus.

math.CT↗

arXiv2020

A Compositional Framework for Reaction Networks

Reaction networks, or equivalently Petri nets, are a general framework for describing processes in which entities of various kinds interact and turn into other entities. In chemistry, where the reactions are assigned "rate constants", any reaction network gives rise to a nonlinear dynamical system called its "rate equation". Here we generalize these ideas to "open" reaction networks, which allow entities to flow in and out at certain designated inputs and outputs. We treat open reaction networks as morphisms in a category. Composing two such morphisms connects the outputs of the first to the inputs of the second. We construct a functor sending any open reaction network to its corresponding "open dynamical system". This provides a compositional framework for studying the dynamics of reaction networks. We then turn to statics: that is, steady state solutions of open dynamical systems. We construct a "black-boxing" functor that sends any open dynamical system to the relation that it imposes between input and output variables in steady states. This extends our earlier work on black-boxing for Markov processes.

math-ph↗

arXiv2020

Network Models

Networks can be combined in various ways, such as overlaying one on top of another or setting two side by side. We introduce "network models" to encode these ways of combining networks. Different network models describe different kinds of networks. We show that each network model gives rise to an operad, whose operations are ways of assembling a network of the given kind from smaller parts. Such operads, and their algebras, can serve as tools for designing networks. Technically, a network model is a lax symmetric monoidal functor from the free symmetric monoidal category on some set to $\mathbf{Cat}$, and the construction of the corresponding operad proceeds via a symmetric monoidal version of the Grothendieck construction.

math.CT↗

arXiv2020

Struggles with the Continuum

Our assumption that spacetime is a continuum leads to many challenges in mathematical physics. Singularities, divergent integrals and the like threaten many of our favorite theories, from Newtonian gravity to classical electrodynamics, quantum electrodynamics and the Standard Model. In general relativity, singularities are intimately connected to some of the theory's most dramatic successful predictions. We survey these problems and the large amount of work that has gone into dealing with them.

math-ph↗

arXiv2019

Network Models from Petri Nets with Catalysts

Petri networks and network models are two frameworks for the compositional design of systems of interacting entities. Here we show how to combine them using the concept of a "catalyst": an entity that is neither destroyed nor created by any process it engages in. In a Petri net, a place is a catalyst if its in-degree equals its out-degree for every transition. We show how a Petri net with a chosen set of catalysts gives a network model. This network model maps any list of catalysts from the chosen set to the category whose morphisms are all the processes enabled by this list of catalysts. Applying the Grothendieck construction, we obtain a category fibered over the category whose objects are lists of catalysts. This category has as morphisms all processes enabled by some list of catalysts. While this category has a symmetric monoidal structure that describes doing processes in parallel, its fibers also have premonoidal structures that describe doing one process and then another while reusing the catalysts.

math.CT↗

arXiv2019

Quantropy

There is a well-known analogy between statistical and quantum mechanics. In statistical mechanics, Boltzmann realized that the probability for a system in thermal equilibrium to occupy a given state is proportional to exp(-E/kT) where E is the energy of that state. In quantum mechanics, Feynman realized that the amplitude for a system to undergo a given history is proportional to exp(-S/i hbar) where S is the action of that history. In statistical mechanics we can recover Boltzmann's formula by maximizing entropy subject to a constraint on the expected energy. This raises the question: what is the quantum mechanical analogue of entropy? We give a formula for this quantity, which we call "quantropy". We recover Feynman's formula from assuming that histories have complex amplitudes, that these amplitudes sum to one, and that the amplitudes give a stationary point of quantropy subject to a constraint on the expected action. Alternatively, we can assume the amplitudes sum to one and that they give a stationary point of a quantity we call "free action", which is analogous to free energy in statistical mechanics. We compute the quantropy, expected action and free action for a free particle, and draw some conclusions from the results.

quant-ph↗

arXiv2019

Quantum Techniques for Stochastic Mechanics

Some ideas from quantum theory are just beginning to percolate back to classical probability theory. For example, there is a widely used and successful theory of "chemical reaction networks", which describes the interactions of molecules in a stochastic rather than quantum way. Computer science and population biology use the same ideas under a different name: "stochastic Petri nets". But if we look at these theories from the perspective of quantum theory, they turn out to involve creation and annihilation operators, coherent states and other well-known ideas - but in a context where probabilities replace amplitudes. We explain this connection as part of a detailed analogy between quantum mechanics and stochastic mechanics. We use this analogy to present new proofs of two major results in the theory of chemical reaction networks: the deficiency zero theorem and the Anderson-Craciun-Kurtz theorem. We also study the overlap of quantum mechanics and stochastic mechanics, which involves Hamiltonians that can generate either unitary or stochastic time evolution. These Hamiltonians are called "Dirichlet forms", and they arise naturally from electrical circuits made only of resistors.

quant-ph↗

arXiv2018

Coarse-Graining Open Markov Processes

Coarse-graining is a standard method of extracting a simple Markov process from a more complicated one by identifying states. Here we extend coarse-graining to open Markov processes. An "open" Markov process is one where probability can flow in or out of certain states called "inputs" and "outputs". One can build up an ordinary Markov process from smaller open pieces in two basic ways: composition, where we identify the outputs of one open Markov process with the inputs of another, and tensoring, where we set two open Markov processes side by side. In previous work, Fong, Pollard and the first author showed that these constructions make open Markov processes into the morphisms of a symmetric monoidal category. Here we go further by constructing a symmetric monoidal double category where the 2-morphisms are ways of coarse-graining open Markov processes. We also extend the already known "black-boxing" functor from the category of open Markov processes to our double category. Black-boxing sends any open Markov process to the linear relation between input and output data that holds in steady states, including nonequilibrium steady states where there is a nonzero flow of probability through the process. To extend black-boxing to a functor between double categories, we need to prove that black-boxing is compatible with coarse-graining.

math-ph↗

arXiv2018

A Compositional Framework for Passive Linear Networks

Passive linear networks are used in a wide variety of engineering applications, but the best studied are electrical circuits made of resistors, inductors and capacitors. We describe a category where a morphism is a circuit of this sort with marked input and output terminals. In this category, composition describes the process of attaching the outputs of one circuit to the inputs of another. We construct a functor, dubbed the "black box functor", that takes a circuit, forgets its internal structure, and remembers only its external behavior. Two circuits have the same external behavior if and only if they impose same relation between currents and potentials at their terminals. The space of these currents and potentials naturally has the structure of a symplectic vector space, and the relation imposed by a circuit is a Lagrangian linear relation. Thus, the black box functor goes from our category of circuits to the category of symplectic vector spaces and Lagrangian linear relations. We prove that this functor is We prove that this functor is symmetric monoidal and indeed a hypergraph functor. We assume the reader is familiar with category theory, but not with circuit theory or symplectic linear algebra.

math.CT↗

arXiv2018

Biochemical Coupling Through Emergent Conservation Laws

Bazhin has analyzed ATP coupling in terms of quasiequilibrium states where fast reactions have reached an approximate steady state while slow reactions have not yet reached equilibrium. After an expository introduction to the relevant aspects of reaction network theory, we review his work and explain the role of emergent conserved quantities in coupling. These are quantities, left unchanged by fast reactions, whose conservation forces exergonic processes such as ATP hydrolysis to drive desired endergonic processes.

q-bio.MN↗