The phase diagram of random threshold networks

Threshold networks are used as models for neural or gene regulatory networks. They show a rich dynamical behaviour with a transition between a frozen and a chaotic phase. We investigate the phase diagram of randomly connected threshold networks with real-valued thresholds h and a fixed number of inputs per node. The nodes are updated according to the same rules as in a model of the cell-cycle network of Saccharomyces cereviseae [PNAS 101, 4781 (2004)]. Using the annealed approximation, we derive expressions for the time evolution of the proportion of nodes in the "on" and "off" state, and for the sensitivity $\lambda$. The results are compared with simulations of quenched networks. We find that for integer values of h the simulations show marked deviations from the annealed approximation even for large networks. This can be attributed to the particular choice of the updating rule.Comment: 8 pages, 6 figure

Effects of Preference for Attachment to Low-degree Nodes on the Degree Distributions of a Growing Directed Network and a Simple Food-Web Model

We study the growth of a directed network, in which the growth is constrained by the cost of adding links to the existing nodes. We propose a new preferential-attachment scheme, in which a new node attaches to an existing node i with probability proportional to 1/k_i, where k_i is the number of outgoing links at i. We calculate the degree distribution for the outgoing links in the asymptotic regime (t->infinity), both analytically and by Monte Carlo simulations. The distribution decays like k c^k/Gamma(k) for large k, where c is a constant. We investigate the effect of this preferential-attachment scheme, by comparing the results to an equivalent growth model with a degree-independent probability of attachment, which gives an exponential outdegree distribution. Also, we relate this mechanism to simple food-web models by implementing it in the cascade model. We show that the low-degree preferential-attachment mechanism breaks the symmetry between in- and outdegree distributions in the cascade model. It also causes a faster decay in the tails of the outdegree distributions for both our network growth model and the cascade model.Comment: 10 pages, 7 figures. A new figure added. Minor modifications made in the tex

Nonlinear earthquake behaviour of highway tunnels

This paper describes the Arhavi Highway Tunnel which has two tubes, its geometrical properties, finite element model, and the nonlinear earthquake behaviour under a huge ground motion considering soil-structure interaction. The Arhavi Highway Tunnel is one of the tallest tunnels constructed in the Black Sea region of Turkey as part of the Coast Road Project. The tunnel has two tubes and each of them is about 1000 m tall. In the study, the modal analyses of the tunnel considering soil-structure interaction are performed and natural frequencies and mode shapes are obtained. Then, nonlinear transient analysis of the tunnel using Drucker-Prager criteria is performed applying acceleration components of 1992 Erzincan, Turkey earthquake's ground motion. In the time history analyses, Rayleigh damping coefficients are calculated using main natural frequency obtained from modal analysis. Element matrices are computed using the Gauss numerical integration technique. The Newmark method is used in the solution of the equation of motion. Because too much memory for the analyses is required, the first 7.5 s of the ground motions, which is the most effective duration, is taken into account in calculations. The displacement and stress results are observed to be the allowable level of the concrete material

Investigating of Mechanical Properties of Mortars Based on Fly Ash and Blast Furnace Slag Activated with Alkali

Alkali activated mortars obtained from granulated blast furnace slag and fly ash were used instead of Portland cement by activating with alkali. Sodium silicate and sodium hydroxide were activated blast furnace slag and fly ash. Mortar samples were prepared 40x40x160 mm as prismatic samples according to TS EN 196-1 and they were cured at room temperature. Compressive and flexural strength of the mortar samples including blast furnace slag and fly ash were investigated by experimenting

Structural, Vibrational and Electronic Properties of Single Layer Hexagonal Crystals of Groups IV and V

Using first-principles density functional theory calculations, we investigate a family of stable two-dimensional crystals with chemical formula $A_2B_2$, where $A$ and $B$ belong to groups IV and V, respectively ($A$ = C, Si, Ge, Sn, Pb; $B$ = N, P, As, Sb, Bi). Two structural symmetries of hexagonal lattices $P\bar{6}m2$ and $P\bar{3}m1$ are shown to be dynamically stable, named as $\alpha$- and $\beta$-phases correspondingly. Both phases have similar cohesive energies, and the $\alpha$-phase is found to be energetically favorable for structures except CP, CAs, CSb and CBi, for which the $\beta$-phase is favored. The effects of spin-orbit coupling and Hartree-Fock corrections to exchange-correlation are included to elucidate the electronic structures. All structures are semiconductors except CBi and PbN, which have metallic character. SiBi, GeBi and SnBi have direct band gaps, whereas the remaining semiconductor structures have indirect band gaps. All structures have quartic dispersion in their valence bands, some of which make the valence band maximum and resemble a Mexican hat shape. SnAs and PbAs have purely quartic valence band edges, i.e. $E{\sim}{-}\alpha k^4$, a property reported for the first time. The predicted materials are candidates for a variety of applications. Owing to their wide band gaps, CP, SiN, SiP, SiAs, GeN, GeP can find their applications in optoelectronics. The relative band positions qualify a number of the structures as suitable for water splitting, where CN and SiAs are favorable at all pH values. Structures with quartic band edges are expected to be efficient for thermoelectric applications

Utilization of Colemanite waste in Concrete Design

Waste material is formed in enormous quantities during the beneficiation of raw ore. These wastes can cause both economic loss and environmental pollution. Thus, in this study, the effect of CW obtained from Eti Mine Establishments Kütahya-Emet Boron Plants on the compressive strength and cylinder splitting tensile strength of concrete and its USAbility as a concrete admixture is investigated. The results found show that utilization of Colemanite Waste is possible when it is used as additive in concrete

Strategies for the evolution of sex

We find that the hypothesis made by Jan, Stauffer and Moseley [Theory in Biosc., 119, 166 (2000)] for the evolution of sex, namely a strategy devised to escape extinction due to too many deleterious mutations, is sufficient but not necessary for the successful evolution of a steady state population of sexual individuals within a finite population. Simply allowing for a finite probability for conversion to sex in each generation also gives rise to a stable sexual population, in the presence of an upper limit on the number of deleterious mutations per individual. For large values of this probability, we find a phase transition to an intermittent, multi-stable regime. On the other hand, in the limit of extremely slow drive, another transition takes place to a different steady state distribution, with fewer deleterious mutations within the asexual population.Comment: RevTeX, 11 pages, multicolumn, including 12 figure

Tangled Nature: A model of emergent structure and temporal mode among co-evolving agents

Understanding systems level behaviour of many interacting agents is challenging in various ways, here we'll focus on the how the interaction between components can lead to hierarchical structures with different types of dynamics, or causations, at different levels. We use the Tangled Nature model to discuss the co-evolutionary aspects connecting the microscopic level of the individual to the macroscopic systems level. At the microscopic level the individual agent may undergo evolutionary changes due to mutations of strategies. The micro-dynamics always run at a constant rate. Nevertheless, the system's level dynamics exhibit a completely different type of intermittent abrupt dynamics where major upheavals keep throwing the system between meta-stable configurations. These dramatic transitions are described by a log-Poisson time statistics. The long time effect is a collectively adapted of the ecological network. We discuss the ecological and macroevolutionary consequences of the adaptive dynamics and briefly describe work using the Tangled Nature framework to analyse problems in economics, sociology, innovation and sustainabilityComment: Invited contribution to Focus on Complexity in European Journal of Physics. 25 page, 1 figur

Polaronic effects in a Gaussian quantum dot

The problem of an electron interacting with longitudinal-optical (LO) phonons is investigated in an N-dimensional quantum dot with symmetric Gaussian confinement in all directions using the Rayleigh-Schrödinger perturbation theory, a variant of the canonical transformation method of Lee-Low-Pines, and the sophisticated apparatus of the Feynman-Haken path-integral technique for the entire range of the coupling parameters and the results for N = 2 and N = 3 are obtained as special cases. It is shown that the polaronic effects are quite significant for small dots with deep confining potential well and the parabolic potential is only a poor approximation of the Gaussian confinement. The Feynman-Haken path-integral technique in general gives a good upper bound to the ground state energy for all values of the system parameters and therefore is used as a benchmark for comparison between different methods. It is shown that the perturbation theory yields for the ground state polaron self-energy a simple closed-form analytic expression containing only Gamma functions and in the weak-coupling regime it provides the lowest energy because of an efficient partitioning of the Gaussian potential and the subsequent use of a mean-field kind of treatment. The polarization potential, the polaron radius and the number of virtual phonons in the polaron cloud are obtained using the Lee-Low-Pines-Huybrechts method and their variations with respect to different parameters of the system are discussed. © 2007 Elsevier Ltd. All rights reserved

Genome-wide association study of problematic opioid prescription use in 132,113 23andMe research participants of European ancestry

The growing prevalence of opioid use disorder (OUD) constitutes an urgent health crisis. Ample evidence indicates that risk for OUD is heritable. As a surrogate (or proxy) for OUD, we explored the genetic basis of using prescription opioids \u27not as prescribed\u27. We hypothesized that misuse of opiates might be a heritable risk factor for OUD. To test this hypothesis, we performed a genome-wide association study (GWAS) of problematic opioid use (POU) in 23andMe research participants of European ancestry (N = 132,113; 21% cases). We identified two genome-wide significant loci (rs3791033, an intronic variant of KDM4A; rs640561, an intergenic variant near LRRIQ3). POU showed positive genetic correlations with the two largest available GWAS of OUD and opioid dependence (