Relative Entropy in Biological Systems

In this paper we review various information-theoretic characterizations of the approach to equilibrium in biological systems. The replicator equation, evolutionary game theory, Markov processes and chemical reaction networks all describe the dynamics of a population or probability distribution. Under suitable assumptions, the distribution will approach an equilibrium with the passage of time. Relative entropy - that is, the Kullback--Leibler divergence, or various generalizations of this - provides a quantitative measure of how far from equilibrium the system is. We explain various theorems that give conditions under which relative entropy is nonincreasing. In biochemical applications these results can be seen as versions of the Second Law of Thermodynamics, stating that free energy can never increase with the passage of time. In ecological applications, they make precise the notion that a population gains information from its environment as it approaches equilibrium.Comment: 20 page

2-Vector Spaces and Groupoids

This paper describes a relationship between essentially finite groupoids and 2-vector spaces. In particular, we show to construct 2-vector spaces of Vect-valued presheaves on such groupoids. We define 2-linear maps corresponding to functors between groupoids in both a covariant and contravariant way, which are ambidextrous adjoints. This is used to construct a representation--a weak functor--from Span(Gpd) (the bicategory of groupoids and spans of groupoids) into 2Vect. In this paper we prove this and give the construction in detail.Comment: 44 pages, 5 figures - v2 adds new theorem, significant changes to proofs, new sectio

Extended matter coupled to BF theory

Recently, a topological field theory of membrane-matter coupled to BF theory in arbitrary spacetime dimensions was proposed [1]. In this paper, we discuss various aspects of the four-dimensional theory. Firstly, we study classical solutions leading to an interpretation of the theory in terms of strings propagating on a flat spacetime. We also show that the general classical solutions of the theory are in one-to-one correspondence with solutions of Einstein's equations in the presence of distributional matter (cosmic strings). Secondly, we quantize the theory and present, in particular, a prescription to regularize the physical inner product of the canonical theory. We show how the resulting transition amplitudes are dual to evaluations of Feynman diagrams coupled to three-dimensional quantum gravity. Finally, we remove the regulator by proving the topological invariance of the transition amplitudes.Comment: 27 pages, 7 figure

Exotic Statistics for Strings in 4d BF Theory

After a review of exotic statistics for point particles in 3d BF theory, and especially 3d quantum gravity, we show that string-like defects in 4d BF theory obey exotic statistics governed by the 'loop braid group'. This group has a set of generators that switch two strings just as one would normally switch point particles, but also a set of generators that switch two strings by passing one through the other. The first set generates a copy of the symmetric group, while the second generates a copy of the braid group. Thanks to recent work of Xiao-Song Lin, we can give a presentation of the whole loop braid group, which turns out to be isomorphic to the 'braid permutation group' of Fenn, Rimanyi and Rourke. In the context 4d BF theory this group naturally acts on the moduli space of flat G-bundles on the complement of a collection of unlinked unknotted circles in R^3. When G is unimodular, this gives a unitary representation of the loop braid group. We also discuss 'quandle field theory', in which the gauge group G is replaced by a quandle.Comment: 41 pages, many figures. New version has minor corrections and clarifications, and some added reference

An Invitation to Higher Gauge Theory

In this easy introduction to higher gauge theory, we describe parallel transport for particles and strings in terms of 2-connections on 2-bundles. Just as ordinary gauge theory involves a gauge group, this generalization involves a gauge '2-group'. We focus on 6 examples. First, every abelian Lie group gives a Lie 2-group; the case of U(1) yields the theory of U(1) gerbes, which play an important role in string theory and multisymplectic geometry. Second, every group representation gives a Lie 2-group; the representation of the Lorentz group on 4d Minkowski spacetime gives the Poincar\'e 2-group, which leads to a spin foam model for Minkowski spacetime. Third, taking the adjoint representation of any Lie group on its own Lie algebra gives a 'tangent 2-group', which serves as a gauge 2-group in 4d BF theory, which has topological gravity as a special case. Fourth, every Lie group has an 'inner automorphism 2-group', which serves as the gauge group in 4d BF theory with cosmological constant term. Fifth, every Lie group has an 'automorphism 2-group', which plays an important role in the theory of nonabelian gerbes. And sixth, every compact simple Lie group gives a 'string 2-group'. We also touch upon higher structures such as the 'gravity 3-group' and the Lie 3-superalgebra that governs 11-dimensional supergravity.Comment: 60 pages, based on lectures at the 2nd School and Workshop on Quantum Gravity and Quantum Geometry at the 2009 Corfu Summer Institut