Pablo S. Ocal

Regulatory networks depict promoting or inhibiting interactions between molecules in a biochemical system. We introduce a category-theoretic formalism for regulatory networks, using signed graphs to model the networks and signed functors to describe occurrences of one network in another, especially occurrences of network motifs. With this foundation, we establish functorial mappings between regulatory networks and other mathematical models in biochemistry. We construct a functor from reaction networks, modeled as Petri nets with signed links, to regulatory networks, enabling us to precisely define when a reaction network could be a physical mechanism underlying a regulatory network. Turning to quantitative models, we associate a regulatory network with a Lotka-Volterra system of differential equations, defining a functor from the category of signed graphs to a category of parameterized dynamical systems. We extend this result from closed to open systems, demonstrating that Lotka-Volterra dynamics respects not only inclusions and collapsings of regulatory networks, but also the process of building up complex regulatory networks by gluing together simpler pieces. Formally, we use the theory of structured cospans to produce a lax double functor from the double category of open signed graphs to that of open parameterized dynamical systems. Throughout the paper, we ground the categorical formalism in examples inspired by systems biology.

We show that the canonical equivalences of categories between 2-dimensional (unoriented) topological quantum field theories valued in a symmetric monoidal category and (extended) commutative Frobenius algebras in that symmetric monoidal category are symmetric monoidal equivalences. As an application, we recover that the invariant of 2-dimensional manifolds given by the product of (extended) commutative Frobenius algebras in a symmetric tensor category is the multiplication of the invariants given by each of the algebras.

We endow twisted tensor products with a natural notion of counit and comultiplication, and we provide sufficient and necessary conditions making the twisted tensor product a counital coassociative coalgebra. We then characterize when the twisted tensor product of bialgebras is a bialgebra, and when the twisted tensor product of Frobenius algebras is a Frobenius algebra. Our methods are purely diagrammatic, so these results hold for (braided) monoidal categories. As an application, we recover that some quantum complete intersections are Frobenius algebras, and we construct families of noncommutative symmetric Frobenius algebras. Along the way, we also characterize when twisted tensor products of separable algebras are separable, and we prove that twisted tensor products of special Frobenius algebras are special Frobenius.

We show that the canonical equivalences of categories between 2-dimensional (unoriented) topological quantum field theories valued in a symmetric monoidal category and (extended) commutative Frobenius algebras in that symmetric monoidal category are symmetric monoidal equivalences. As an application, we recover that the invariant of 2-dimensional manifolds given by the product of (extended) commutative Frobenius algebras in a symmetric tensor category is the multiplication of the invariants given by each of the algebras.

We revisit a result of Gratz and Stevenson on the universal space that carries supports for objects of a triangulated category, in the absence of a tensor product.

We review several techniques that twist an algebra's multiplicative structure. We first consider twists by an automorphism, also known as Zhang twists, and we relate them to 2-cocycle twists of certain bialgebras. We then outline the classification and properties of twisted tensor products, and we examine twisted Segre products. Our exposition emphasizes clarity over generality, providing a wealth of interconnecting examples.

The Hochschild cohomology of a tensor product of algebras is isomorphic to a graded tensor product of Hochschild cohomology algebras, as a Gerstenhaber algebra. A similar result holds when the tensor product is twisted by a bicharacter. We present new proofs of these isomorphisms, using Volkov's homotopy liftings that were introduced for handling Gerstenhaber brackets expressed on arbitrary bimodule resolutions. Our results illustrate the utility of homotopy liftings for theoretical purposes.