A Framework for Universality in Physics, Computer Science, and Beyond
Turing machines and spin models share a notion of universality according to which some simulate all others. Is there a theory of universality that captures this notion? We set up a categorical framework for universality which includes as instances universal Turing machines, universal spin models, NP completeness, top of a preorder, denseness of a subset, and more. By identifying necessary conditions for universality, we show that universal spin models cannot be finite. We also characterize when universality can be distinguished from a trivial one and use it to show that universal Turing machines are non-trivial in this sense. Our framework allows not only to compare universalities within each instance, but also instances themselves. We leverage a Fixed Point Theorem inspired by a result of Lawvere to establish that universality and negation give rise to unreachability (such as uncomputability). As such, this work sets the basis for a unified approach to universality and invites the study of further examples within the framework.
Gonda, Tomáš
August 29, 2024
Read article
A compositional account of motifs, mechanisms, and dynamics in biochemical regulatory networks
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.
Aduddell, Rebekah
May 12, 2024
Read article