The phase transition in random catalytic sets

The notion of (auto) catalytic networks has become a cornerstone in understanding the possibility of a sudden dramatic increase of diversity in biological evolution as well as in the evolution of social and economical systems. Here we study catalytic random networks with respect to the final outcome diversity of products. We show that an analytical treatment of this longstanding problem is possible by mapping the problem onto a set of non-linear recurrence equations. The solution of these equations show a crucial dependence of the final number of products on the initial number of products and the density of catalytic production rules. For a fixed density of rules we can demonstrate the existence of a phase transition from a practically unpopulated regime to a fully populated and diverse one. The order parameter is the number of final products. We are able to further understand the origin of this phase transition as a crossover from one set of solutions from a quadratic equation to the other.Comment: 7 pages, ugly eps files due to arxiv restriction

Diassociative algebras and Milnor's invariants for tangles

We extend Milnor's mu-invariants of link homotopy to ordered (classical or virtual) tangles. Simple combinatorial formulas for mu-invariants are given in terms of counting trees in Gauss diagrams. Invariance under Reidemeister moves corresponds to axioms of Loday's diassociative algebra. The relation of tangles to diassociative algebras is formulated in terms of a morphism of corresponding operads.Comment: 17 pages, many figures; v2: several typos correcte

The Number of Different Binary Functions Generated by NK-Kauffman Networks and the Emergence of Genetic Robustness

We determine the average number $\vartheta (N, K)$, of \textit{NK}-Kauffman networks that give rise to the same binary function. We show that, for $N \gg 1$, there exists a connectivity critical value $K_c$ such that $\vartheta(N,K) \approx e^{\phi N}$ ($\phi > 0$) for $K < K_c$ and $\vartheta(N,K) \approx 1$ for $K > K_c$. We find that $K_c$ is not a constant, but scales very slowly with $N$, as $K_c \approx \log_2 \log_2 (2N / \ln 2)$. The problem of genetic robustness emerges as a statistical property of the ensemble of \textit{NK}-Kauffman networks and impose tight constraints in the average number of epistatic interactions that the genotype-phenotype map can have.Comment: 4 figures 18 page

Robustness of Transcriptional Regulation in Yeast-like Model Boolean Networks

We investigate the dynamical properties of the transcriptional regulation of gene expression in the yeast Saccharomyces Cerevisiae within the framework of a synchronously and deterministically updated Boolean network model. By means of a dynamically determinant subnetwork, we explore the robustness of transcriptional regulation as a function of the type of Boolean functions used in the model that mimic the influence of regulating agents on the transcription level of a gene. We compare the results obtained for the actual yeast network with those from two different model networks, one with similar in-degree distribution as the yeast and random otherwise, and another due to Balcan et al., where the global topology of the yeast network is reproduced faithfully. We, surprisingly, find that the first set of model networks better reproduce the results found with the actual yeast network, even though the Balcan et al. model networks are structurally more similar to that of yeast.Comment: 7 pages, 4 figures, To appear in Int. J. Bifurcation and Chaos, typos were corrected and 2 references were adde

Teleportation, Braid Group and Temperley--Lieb Algebra

We explore algebraic and topological structures underlying the quantum teleportation phenomena by applying the braid group and Temperley--Lieb algebra. We realize the braid teleportation configuration, teleportation swapping and virtual braid representation in the standard description of the teleportation. We devise diagrammatic rules for quantum circuits involving maximally entangled states and apply them to three sorts of descriptions of the teleportation: the transfer operator, quantum measurements and characteristic equations, and further propose the Temperley--Lieb algebra under local unitary transformations to be a mathematical structure underlying the teleportation. We compare our diagrammatical approach with two known recipes to the quantum information flow: the teleportation topology and strongly compact closed category, in order to explain our diagrammatic rules to be a natural diagrammatic language for the teleportation.Comment: 33 pages, 19 figures, latex. The present article is a short version of the preprint, quant-ph/0601050, which includes details of calculation, more topics such as topological diagrammatical operations and entanglement swapping, and calls the Temperley--Lieb category for the collection of all the Temperley--Lieb algebra with physical operations like local unitary transformation

The Asymptotic Number of Attractors in the Random Map Model

The random map model is a deterministic dynamical system in a finite phase space with n points. The map that establishes the dynamics of the system is constructed by randomly choosing, for every point, another one as being its image. We derive here explicit formulas for the statistical distribution of the number of attractors in the system. As in related results, the number of operations involved by our formulas increases exponentially with n; therefore, they are not directly applicable to study the behavior of systems where n is large. However, our formulas lend themselves to derive useful asymptotic expressions, as we show.Comment: 16 pages, 1 figure. Minor changes. To be published in Journal of Physics A: Mathematical and Genera

On the Robustness of NK-Kauffman Networks Against Changes in their Connections and Boolean Functions

NK-Kauffman networks {\cal L}^N_K are a subset of the Boolean functions on N Boolean variables to themselves, \Lambda_N = {\xi: \IZ_2^N \to \IZ_2^N}. To each NK-Kauffman network it is possible to assign a unique Boolean function on N variables through the function \Psi: {\cal L}^N_K \to \Lambda_N. The probability {\cal P}_K that \Psi (f) = \Psi (f'), when f' is obtained through f by a change of one of its K-Boolean functions (b_K: \IZ_2^K \to \IZ_2), and/or connections; is calculated. The leading term of the asymptotic expansion of {\cal P}_K, for N \gg 1, turns out to depend on: the probability to extract the tautology and contradiction Boolean functions, and in the average value of the distribution of probability of the Boolean functions; the other terms decay as {\cal O} (1 / N). In order to accomplish this, a classification of the Boolean functions in terms of what I have called their irreducible degree of connectivity is established. The mathematical findings are discussed in the biological context where, \Psi is used to model the genotype-phenotype map.Comment: 17 pages, 1 figure, Accepted in Journal of Mathematical Physic

The dynamics of critical Kauffman networks under asynchronous stochastic update

We show that the mean number of attractors in a critical Boolean network under asynchronous stochastic update grows like a power law and that the mean size of the attractors increases as a stretched exponential with the system size. This is in strong contrast to the synchronous case, where the number of attractors grows faster than any power law.Comment: submitted to PR

Survey for Galaxies Associated with z~3 Damped Lyman alpha Systems I: Spectroscopic Calibration of u'BVRI Photometric Selection

We present a survey for z~3 Lyman break galaxies (LBGs) associated with damped Lyman alpha systems (DLAs) with the primary purpose of determining the DLA-LBG cross-correlation. This paper describes the acquisition and analysis of imaging and spectroscopic data of 9 quasar fields having 11 known z~3 DLAs covering an area of 465 arcmin^2. Using deep u'BVRI images, 796 LBG candidates to an apparent R_AB magnitude of 25.5 were photometrically selected from 17,343 sources detected in the field. Spectroscopic observations of 529 LBG candidates using Keck LRIS yielded 339 redshifts. We have conservatively identified 211 z>2 objects with =3.02+/-0.32. We discuss our method of z~3 LBG identification and present a model of the u'BVRI photometric selection function. We use the 339 spectra to evaluate our u'BVRI z~3 Lyman break photometric selection technique.Comment: 26 pages, 6 tables, 11 figures, accepted for publication in Ap

Annealing schedule from population dynamics

We introduce a dynamical annealing schedule for population-based optimization algorithms with mutation. On the basis of a statistical mechanics formulation of the population dynamics, the mutation rate adapts to a value maximizing expected rewards at each time step. Thereby, the mutation rate is eliminated as a free parameter from the algorithm.Comment: 6 pages RevTeX, 4 figures PostScript; to be published in Phys. Rev.