Life, Death and Preferential Attachment

Scientific communities are characterized by strong stratification. The highly skewed frequency distribution of citations of published scientific papers suggests a relatively small number of active, cited papers embedded in a sea of inactive and uncited papers. We propose an analytically soluble model which allows for the death of nodes. This model provides an excellent description of the citation distributions for live and dead papers in the SPIRES database. Further, this model suggests a novel and general mechanism for the generation of power law distributions in networks whenever the fraction of active nodes is small.Comment: 5 pages, 2 figure

Circlator: automated circularization of genome assemblies using long sequencing reads

The assembly of DNA sequence data is undergoing a renaissance thanks to emerging technologies capable of producing reads tens of kilobases long. Assembling complete bacterial and small eukaryotic genomes is now possible, but the final step of circularizing sequences remains unsolved. Here we present Circlator, the first tool to automate assembly circularization and produce accurate linear representations of circular sequences. Using Pacific Biosciences and Oxford Nanopore data, Circlator correctly circularized 26 of 27 circularizable sequences, comprising 11 chromosomes and 12 plasmids from bacteria, the apicoplast and mitochondrion of Plasmodium falciparum and a human mitochondrion. Circlator is available at http://sanger-pathogens.github.io/circlator/

Spectral Analysis and the Dynamic Response of Complex Networks

The eigenvalues and eigenvectors of the connectivity matrix of complex networks contain information about its topology and its collective behavior. In particular, the spectral density $\rho(\lambda)$ of this matrix reveals important network characteristics: random networks follow Wigner's semicircular law whereas scale-free networks exhibit a triangular distribution. In this paper we show that the spectral density of hierarchical networks follow a very different pattern, which can be used as a fingerprint of modularity. Of particular importance is the value $\rho(0)$, related to the homeostatic response of the network: it is maximum for random and scale free networks but very small for hierarchical modular networks. It is also large for an actual biological protein-protein interaction network, demonstrating that the current leading model for such networks is not adequate.Comment: 4 pages 14 figure

Mitochondrial and chloroplast stress responses are modulated in distinct touch and chemical inhibition phases

Previous studies have identified a range of transcription factors that modulate retrograde regulation of mitochondrial and chloroplast functions in Arabidopsis (Arabidopsis thaliana). However, the relative importance of these regulators and whether they act downstream of separate or overlapping signaling cascades is still unclear. Here, we demonstrate that multiple stress-related signaling pathways, with distinct kinetic signatures, converge on overlapping gene sets involved in energy organelle function. The transcription factor ANAC017 is almost solely responsible for transcript induction of marker genes around 3 to 6 h after chemical inhibition of organelle function and is a key regulator of mitochondrial and specific types of chloroplast retrograde signaling. However, an independent and highly transient gene expression phase, initiated within 10 to 30 min after treatment, also targets energy organelle functions, and is related to touch and wounding responses. Metabolite analysis demonstrates that this early response is concurrent with rapid changes in tricarboxylic acid cycle intermediates and large changes in transcript abundance of genes encoding mitochondrial dicarboxylate carrier proteins. It was further demonstrated that transcription factors AtWRKY15 and AtWRKY40 have repressive regulatory roles in this touch-responsive gene expression. Together, our results show that several regulatory systems can independently affect energy organelle function in response to stress, providing different means to exert operational control

Singularities of Nonlinear Elliptic Systems

Through Morrey's spaces (plus Zorko's spaces) and their potentials/capacities as well as Hausdorff contents/dimensions, this paper estimates the singular sets of nonlinear elliptic systems of the even-ordered Meyers-Elcrat type and a class of quadratic functionals inducing harmonic maps.Comment: 18 pages Communications in Partial Differential Equation

Strings in extremal BTZ black holes

We study the spectrum of the worldsheet theory of the bosonic closed string in the massless and extremal rotating BTZ black holes. We use a hyperbolic Wakimoto representation of the SL(2,R) currents to construct vertex operators for the string modes on these backgrounds. We argue that there are tachyons in the twisted sector, but these are not localised near the horizon. We study the relation to the null orbifold in the limit of vanishing cosmological constant. We also discuss the problem of extending this analysis to the supersymmetric case.Comment: 20 pages, no figure

Evidence of magnetic field decay in massive main-sequence stars

A significant fraction of massive main-sequence stars show strong, large-scale magnetic fields. The origin of these fields, their lifetimes, and their role in shaping the characteristics and evolution of massive stars are currently not well understood. We compile a catalogue of 389 massive main-sequence stars, 61 of which are magnetic, and derive their fundamental parameters and ages. The two samples contain stars brighter than magnitude 9 in the V band and range in mass between 5 and 100 Msun. We find that the fractional main-sequence age distribution of all considered stars follows what is expected for a magnitude limited sample, while that of magnetic stars shows a clear decrease towards the end of the main sequence. This dearth of old magnetic stars is independent of the choice of adopted stellar evolution tracks, and appears to become more prominent when considering only the most massive stars. We show that the decreasing trend in the distribution is significantly stronger than expected from magnetic flux conservation. We also find that binary rejuvenation and magnetic suppression of core convection are unlikely to be responsible for the observed lack of older magnetic massive stars, and conclude that its most probable cause is the decay of the magnetic field, over a time span longer than the stellar lifetime for the lowest considered masses, and shorter for the highest masses. We then investigate the spin-down ages of the slowly rotating magnetic massive stars and find them to exceed the stellar ages by far in many cases. The high fraction of very slowly rotating magnetic stars thus provides an independent argument for a decay of the magnetic fields.Comment: Accepted for publication on A&A; 9 pages, 8 figure

Herbert Simon's decision-making approach: Investigation of cognitive processes in experts

This is a post print version of the article. The official published can be obtained from the links below - PsycINFO Database Record (c) 2010 APA, all rights reserved.Herbert Simon's research endeavor aimed to understand the processes that participate in human decision making. However, despite his effort to investigate this question, his work did not have the impact in the “decision making” community that it had in other fields. His rejection of the assumption of perfect rationality, made in mainstream economics, led him to develop the concept of bounded rationality. Simon's approach also emphasized the limitations of the cognitive system, the change of processes due to expertise, and the direct empirical study of cognitive processes involved in decision making. In this article, we argue that his subsequent research program in problem solving and expertise offered critical tools for studying decision-making processes that took into account his original notion of bounded rationality. Unfortunately, these tools were ignored by the main research paradigms in decision making, such as Tversky and Kahneman's biased rationality approach (also known as the heuristics and biases approach) and the ecological approach advanced by Gigerenzer and others. We make a proposal of how to integrate Simon's approach with the main current approaches to decision making. We argue that this would lead to better models of decision making that are more generalizable, have higher ecological validity, include specification of cognitive processes, and provide a better understanding of the interaction between the characteristics of the cognitive system and the contingencies of the environment

Dynamical Transition in the Open-boundary Totally Asymmetric Exclusion Process

We revisit the totally asymmetric simple exclusion process with open boundaries (TASEP), focussing on the recent discovery by de Gier and Essler that the model has a dynamical transition along a nontrivial line in the phase diagram. This line coincides neither with any change in the steady-state properties of the TASEP, nor the corresponding line predicted by domain wall theory. We provide numerical evidence that the TASEP indeed has a dynamical transition along the de Gier-Essler line, finding that the most convincing evidence was obtained from Density Matrix Renormalisation Group (DMRG) calculations. By contrast, we find that the dynamical transition is rather hard to see in direct Monte Carlo simulations of the TASEP. We furthermore discuss in general terms scenarios that admit a distinction between static and dynamic phase behaviour.Comment: 27 pages, 18 figures. v2 to appear in J Phys A features minor corrections and better-quality figure

Dynamics of the Wang-Landau algorithm and complexity of rare events for the three-dimensional bimodal Ising spin glass

We investigate the performance of flat-histogram methods based on a multicanonical ensemble and the Wang-Landau algorithm for the three-dimensional +/- J spin glass by measuring round-trip times in the energy range between the zero-temperature ground state and the state of highest energy. Strong sample-to-sample variations are found for fixed system size and the distribution of round-trip times follows a fat-tailed Frechet extremal value distribution. Rare events in the fat tails of these distributions corresponding to extremely slowly equilibrating spin glass realizations dominate the calculations of statistical averages. While the typical round-trip time scales exponential as expected for this NP-hard problem, we find that the average round-trip time is no longer well-defined for systems with N >= 8^3 spins. We relate the round-trip times for multicanonical sampling to intrinsic properties of the energy landscape and compare with the numerical effort needed by the genetic Cluster-Exact Approximation to calculate the exact ground state energies. For systems with N >= 8^3 spins the simulation of these rare events becomes increasingly hard. For N >= 14^3 there are samples where the Wang-Landau algorithm fails to find the true ground state within reasonable simulation times. We expect similar behavior for other algorithms based on multicanonical sampling.Comment: 9 pages, 12 figure