Living on the edge of chaos: minimally nonlinear models of genetic regulatory dynamics

Linearized catalytic reaction equations modeling e.g. the dynamics of genetic regulatory networks under the constraint that expression levels, i.e. molecular concentrations of nucleic material are positive, exhibit nontrivial dynamical properties, which depend on the average connectivity of the reaction network. In these systems the inflation of the edge of chaos and multi-stability have been demonstrated to exist. The positivity constraint introduces a nonlinearity which makes chaotic dynamics possible. Despite the simplicity of such minimally nonlinear systems, their basic properties allow to understand fundamental dynamical properties of complex biological reaction networks. We analyze the Lyapunov spectrum, determine the probability to find stationary oscillating solutions, demonstrate the effect of the nonlinearity on the effective in- and out-degree of the active interaction network and study how the frequency distributions of oscillatory modes of such system depend on the average connectivity.Comment: 11 pages, 5 figure

Parametric ordering of complex systems

Cellular automata (CA) dynamics are ordered in terms of two global parameters, computable {\sl a priori} from the description of rules. While one of them (activity) has been used before, the second one is new; it estimates the average sensitivity of rules to small configurational changes. For two well-known families of rules, the Wolfram complexity Classes cluster satisfactorily. The observed simultaneous occurrence of sharp and smooth transitions from ordered to disordered dynamics in CA can be explained with the two-parameter diagram

Density classification on infinite lattices and trees

Consider an infinite graph with nodes initially labeled by independent Bernoulli random variables of parameter p. We address the density classification problem, that is, we want to design a (probabilistic or deterministic) cellular automaton or a finite-range interacting particle system that evolves on this graph and decides whether p is smaller or larger than 1/2. Precisely, the trajectories should converge to the uniform configuration with only 0's if p1/2. We present solutions to that problem on the d-dimensional lattice, for any d>1, and on the regular infinite trees. For Z, we propose some candidates that we back up with numerical simulations

Thalidomide-induced Teratogenesis : History and Mechanisms

Peer reviewedPublisher PD

On the stability of standing matter waves in a trap

We discuss excited Bose-condensed states and find the criterion of dynamical stability of a kink-wise state, i.e., a standing matter wave with one nodal plane perpendicular to the axis of a cylindrical trap. The dynamical stability requires a strong radial confinement corresponding to the radial frequency larger than the mean-field interparticle interaction. We address the question of thermodynamic instability related to the presence of excitations with negative energy.Comment: 4 pages, 3 figure

Topology and Evolution of Technology Innovation Networks

The web of relations linking technological innovation can be fairly described in terms of patent citations. The resulting patent citation network provides a picture of the large-scale organization of innovations and its time evolution. Here we study the patterns of change of patents registered by the US Patent and Trademark Office (USPTO). We show that the scaling behavior exhibited by this network is consistent with a preferential attachment mechanism together with a Weibull-shaped aging term. Such attachment kernel is shared by scientific citation networks, thus indicating an universal type of mechanism linking ideas and designs and their evolution. The implications for evolutionary theory of innovation are discussed.Comment: 6 pages, 5 figures, submitted to Physical Review

Normal Modes of a Vortex in a Trapped Bose-Einstein Condensate

A hydrodynamic description is used to study the normal modes of a vortex in a zero-temperature Bose-Einstein condensate. In the Thomas-Fermi (TF) limit, the circulating superfluid velocity far from the vortex core provides a small perturbation that splits the originally degenerate normal modes of a vortex-free condensate. The relative frequency shifts are small in all cases considered (they vanish for the lowest dipole mode with |m|=1), suggesting that the vortex is stable. The Bogoliubov equations serve to verify the existence of helical waves, similar to those of a vortex line in an unbounded weakly interacting Bose gas. In the large-condensate (small-core) limit, the condensate wave function reduces to that of a straight vortex in an unbounded condensate; the corresponding Bogoliubov equations have no bound-state solutions that are uniform along the symmetry axis and decay exponentially far from the vortex core.Comment: 15 pages, REVTEX, 2 Postscript figures, to appear in Phys. Rev. A. We have altered the material in Secs. 3B and 4 in connection with the normal modes that have |m|=1. Our present treatment satisfies the condition that the fundamental dipole mode of a condensate with (or without) a vortex should have the bare frequency $\omega_\perp

Factors associated with the decision to investigate child protective services referrals: a systematic review

Background: Limited resources for child protection create challenging decision situations for child protective services (CPS) workers at the point of intake. A body of research has examined the factors associated with worker decisions and processes using a variety of methodological approaches to gain knowledge on decision-making. However, few attempts have been made to systematically review this literature. Objective: As part of a larger project on decision-making at intake, this systematic review addressed the question of the factors associated with worker decisions to investigate alleged maltreatment referrals. Methods: Quantitative studies that examined factors associated with screening decisions in CPS practice settings were included in the review. Database and other search methods were used to identify research published in English over a 35-year period (1980-2015). Findings: Of 1,147 identified sources, 18 studies were selected for full data extraction. The studies were conducted in the U.S., Canada, and Sweden and varied in methodological quality. Most studies examined case factors with few studies examining other domains. Conclusions: To inform CPS policy and practice, additional research is needed to examine the relationships between decision-making factors and case outcomes. Greater attention needs to be given to the organizational and external factors that influence decision-making

Using Topological Statistics to Detect Determinism in Time Series

Statistical differentiability of the measure along the reconstructed trajectory is a good candidate to quantify determinism in time series. The procedure is based upon a formula that explicitly shows the sensitivity of the measure to stochasticity. Numerical results for partially surrogated time series and series derived from several stochastic models, illustrate the usefulness of the method proposed here. The method is shown to work also for high--dimensional systems and experimental time seriesComment: 23 RevTeX pages, 14 eps figures. To appear in Physical Review

Asymptotically stable phase synchronization revealed by autoregressive circle maps

A new type of nonlinear time series analysis is introduced, based on phases, which are defined as polar angles in spaces spanned by a finite number of delayed coordinates. A canonical choice of the polar axis and a related implicit estimation scheme for the potentially underlying auto-regressive circle map (next phase map) guarantee the invertibility of reconstructed phase space trajectories to the original coordinates. The resulting Fourier approximated, Invertibility enforcing Phase Space map (FIPS map) is well suited to detect conditional asymptotic stability of coupled phases. This rather general synchronization criterion unites two existing generalisations of the old concept and can successfully be applied e.g. to phases obtained from ECG and airflow recordings characterizing cardio-respiratory interaction.Comment: PDF file, 232 KB, 24 pages, 3 figures; cheduled for Phys. Rev. E (Nov) 200