Interview with Don Hurst

An interview with Don Hurst regarding his experiences in a one-room school house.https://scholars.fhsu.edu/ors/1064/thumbnail.jp

Characterisation of a phoP P1vir transduction defect and the implication for the regulation of the extracytoplasmic stress response in Escherichia coli

The sensor kinase PhoQ and its cognate response regulator PhoP constitute a two-component system, which is primarily responsible for sensing and responding to Mg2+ starvation in Escherichia coli. Additionally, there is growing evidence of regulatory links between PhoPQ and constituents of the outer membrane. Furthermore, it has been shown that PhoPQ is regulated negatively by MicA, an sRNA controlled by sigmaE. Encoded by rpoE, sigmaE is an alternative sigma factor that is activated in response to extracytoplasmic stress, specifically misfolded outer membrane proteins. Surprisingly, it was not possible to generate ?phoP mutants, using P1vir transduction under standard conditions and kanamycin as the selective agent. Furthermore, a statistical analysis of these results indicates they cannot be explained by chance alone. The results show that PhoP is required for sigmaE activity in an RseA-independent manner, thereby suggesting that PhoP is a chief regulator of sigmaE activity. It is likely that diminished sigmaE activity in a phoP mutant, extracytoplasmic stress and OM deformation, caused by the reagents used in P1vir transduction, are responsible for the inability to transduce the phoP allele. Finally, evidence has been found relating to a second mechanism through which PhoP directly represses rpoE expression, thereby introducing further complexity into the regulator relationship that exists between sigmaE and PhoP

The role of evolutionary time, diversification rates and dispersal in determining the global diversity of a large radiation of passerine birds

Aim: Variation in species diversity among different geographic areas may result from differences in speciation and extinction rates, immigration and time for diversification. An area with high species diversity may be the result of a high net diversification rate, multiple immigration events from adjacent regions,anda long time available for the accumulation of species (know as the "time-for-speciation effect"). Here, we examine the relative importance of the three aforementionedprocesses in shaping the geographic diversity patterns of a large radiation of passerine birds. Location: Global Time period: Early Miocene to present Major taxa studied: Babblers (Aves: Passeriformes) Methods: Using a comprehensive phylogeny of extant species (~90% sampled) and distributions of the world's babblers, we reconstructed their biogeographic history and analysed the diversification dynamics. We examined how species richness correlates with the timing of regional colonization, the number of immigration events and the rate of speciation within all 13 geographic distribution regions. Results: We found thatbabblers likely originated in the Sino-Himalayan Mountains (SHM) in the early Miocene, suggesting a long time for diversification and species accumulation within the SHM. Regression analyses showed the regional diversity of babblers can be well explained by the timing of the first colonization within of these areas, while differences in rates of speciation or immigration have far weaker effects. Nonetheless, the rapid speciation of Zosteropsduring the Pleistocene has accounted for the increased diversification and accumulation of species in the oceanic islands. Main conclusions: Our results suggest that the global diversity patterns of babblers have predominantly been shaped by the time-for-speciation effect. Our findings also support an origin centred in tropical and subtropical parts of the SHM, with a cradle of recent diversification in the oceanic islands of the Indo-Pacific region, which provides new insights into the generation of global biodiversity hotspots.A near-complete phylogeny of babblers has been reconstructed in BEAST 1.8.4 based on 12 gene loci

Critical and Near-Critical Branching Processes

Scale-free dynamics in physical and biological systems can arise from a variety of causes. Here, we explore a branching process which leads to such dynamics. We find conditions for the appearance of power laws and study quantitatively what happens to these power laws when such conditions are violated. From a branching process model, we predict the behavior of two systems which seem to exhibit near scale-free behavior--rank-frequency distributions of number of subtaxa in biology, and abundance distributions of genotypes in an artificial life system. In the light of these, we discuss distributions of avalanche sizes in the Bak-Tang-Wiesenfeld sandpile model.Comment: 9 pages LaTex with 10 PS figures. v.1 of this paper contains results from non-critical sandpile simulations that were excised from the published versio

A self-adjusted Monte Carlo simulation as model of financial markets with central regulation

Properties of the self-adjusted Monte Carlo algorithm applied to 2d Ising ferromagnet are studied numerically. The endogenous feedback form expressed in terms of the instant running averages is suggested in order to generate a biased random walk of the temperature that converges to criticality without an external tuning. The robustness of a stationary regime with respect to partial accessibility of the information is demonstrated. Several statistical and scaling aspects have been identified which allow to establish an alternative spin lattice model of the financial market. It turns out that our model alike model suggested by S. Bornholdt, Int. J. Mod. Phys. C {\bf 12} (2001) 667, may be described by L\'evy-type stationary distribution of feedback variations with unique exponent $\alpha_1 \sim 3.3$. However, the differences reflected by Hurst exponents suggest that resemblances between the studied models seem to be nontrivial.Comment: 19 pages, 9 figures, 30 reference

Piecewise Linear Models for the Quasiperiodic Transition to Chaos

We formulate and study analytically and computationally two families of piecewise linear degree one circle maps. These families offer the rare advantage of being non-trivial but essentially solvable models for the phenomenon of mode-locking and the quasi-periodic transition to chaos. For instance, for these families, we obtain complete solutions to several questions still largely unanswered for families of smooth circle maps. Our main results describe (1) the sets of maps in these families having some prescribed rotation interval; (2) the boundaries between zero and positive topological entropy and between zero length and non-zero length rotation interval; and (3) the structure and bifurcations of the attractors in one of these families. We discuss the interpretation of these maps as low-order spline approximations to the classic ``sine-circle'' map and examine more generally the implications of our results for the case of smooth circle maps. We also mention a possible connection to recent experiments on models of a driven Josephson junction.Comment: 75 pages, plain TeX, 47 figures (available on request

Multifractal Behaviour of n-Simplex Lattice

We study the asymptotic behaviour of resistance scaling and fluctuation of resistance that give rise to flicker noise in an {\em n}-simplex lattice. We propose a simple method to calculate the resistance scaling and give a closed-form formula to calculate the exponent, $\beta_L$, associated with resistance scaling, for any n. Using current cumulant method we calculate the exact noise exponent for n-simplex lattices.Comment: Latex, 9 pages including one figur