Cruciform structures are a common DNA feature important for regulating biological processes

DNA cruciforms play an important role in the regulation of natural processes involving DNA. These structures are formed by inverted repeats, and their stability is enhanced by DNA supercoiling. Cruciform structures are fundamentally important for a wide range of biological processes, including replication, regulation of gene expression, nucleosome structure and recombination. They also have been implicated in the evolution and development of diseases including cancer, Werner's syndrome and others

Evolution of the Bianchi I, the Bianchi III and the Kantowski-Sachs Universe: Isotropization and Inflation

We study the Einstein-Klein-Gordon equations for a convex positive potential in a Bianchi I, a Bianchi III and a Kantowski-Sachs universe. After analysing the inherent properties of the system of differential equations, the study of the asymptotic behaviors of the solutions and their stability is done for an exponential potential. The results are compared with those of Burd and Barrow. In contrast with their results, we show that for the BI case isotropy can be reached without inflation and we find new critical points which lead to new exact solutions. On the other hand we recover the result of Burd and Barrow that if inflation occurs then isotropy is always reached. The numerical integration is also done and all the asymptotical behaviors are confirmed.Comment: 22 pages, 12 figures, Self-consistent Latex2e File. To be published in Phys. Rev.

Low-density series expansions for directed percolation IV. Temporal disorder

We introduce a model for temporally disordered directed percolation in which the probability of spreading from a vertex $(t,x)$, where $t$ is the time and $x$ is the spatial coordinate, is independent of $x$ but depends on $t$. Using a very efficient algorithm we calculate low-density series for bond percolation on the directed square lattice. Analysis of the series yields estimates for the critical point $p_c$ and various critical exponents which are consistent with a continuous change of the critical parameters as the strength of the disorder is increased.Comment: 11 pages, 3 figure

Meningococcal genetic variation mechanisms viewed through comparative analysis of Serogroup C strain FAM18

Copyright @ 2007 Public Library of ScienceThe bacterium Neisseria meningitidis is commonly found harmlessly colonising the mucosal surfaces of the human nasopharynx. Occasionally strains can invade host tissues causing septicaemia and meningitis, making the bacterium a major cause of morbidity and mortality in both the developed and developing world. The species is known to be diverse in many ways, as a product of its natural transformability and of a range of recombination and mutation-based systems. Previous work on pathogenic Neisseria has identified several mechanisms for the generation of diversity of surface structures, including phase variation based on slippage-like mechanisms and sequence conversion of expressed genes using information from silent loci. Comparison of the genome sequences of two N. meningitidis strains, serogroup B MC58 and serogroup A Z2491, suggested further mechanisms of variation, including C-terminal exchange in specific genes and enhanced localised recombination and variation related to repeat arrays. We have sequenced the genome of N. meningitidis strain FAM18, a representative of the ST-11/ET-37 complex, providing the first genome sequence for the disease-causing serogroup C meningococci; it has 1,976 predicted genes, of which 60 do not have orthologues in the previously sequenced serogroup A or B strains. Through genome comparison with Z2491 and MC58 we have further characterised specific mechanisms of genetic variation in N. meningitidis, describing specialised loci for generation of cell surface protein variants and measuring the association between noncoding repeat arrays and sequence variation in flanking genes. Here we provide a detailed view of novel genetic diversification mechanisms in N. meningitidis. Our analysis provides evidence for the hypothesis that the noncoding repeat arrays in neisserial genomes (neisserial intergenic mosaic elements) provide a crucial mechanism for the generation of surface antigen variants. Such variation will have an impact on the interaction with the host tissues, and understanding these mechanisms is important to aid our understanding of the intimate and complex relationship between the human nasopharynx and the meningococcus.This work was supported by the Wellcome Trust through the Beowulf Genomics Initiative

Switching dynamics of surface stabilized ferroelectric liquid crystal cells: effects of anchoring energy asymmetry

We study both theoretically and experimentally switching dynamics in surface stabilized ferroelectric liquid crystal cells with asymmetric boundary conditions. In these cells the bounding surfaces are treated differently to produce asymmetry in their anchoring properties. Our electro-optic measurements of the switching voltage thresholds that are determined by the peaks of the reversal polarization current reveal the frequency dependent shift of the hysteresis loop. We examine the predictions of the uniform dynamical model with the anchoring energy taken into account. It is found that the asymmetry effects are dominated by the polar contribution to the anchoring energy. Frequency dependence of the voltage thresholds is studied by analyzing the properties of time-periodic solutions to the dynamical equation (cycles). For this purpose, we apply the method that uses the parameterized half-period mappings for the approximate model and relate the cycles to the fixed points of the composition of two half-period mappings. The cycles are found to be unstable and can only be formed when the driving frequency is lower than its critical value. The polar anchoring parameter is estimated by making a comparison between the results of modelling and the experimental data for the shift vs frequency curve. For a double-well potential considered as a deformation of the Rapini-Papoular potential, the branch of stable cycles emerges in the low frequency region separated by the gap from the high frequency interval for unstable cycles.Comment: 35 pages, 15 figure

Symplectically Covariant Schr\"{o}dinger Equation in Phase Space

A classical theorem of Stone and von Neumann says that the Schr\"{o}dinger representation is, up to unitary equivalences, the only irreducible representation of the Heisenberg group on the Hilbert space of square-integrable functions on configuration space. Using the Wigner-Moyal transform we construct an irreducible representation of the Heisenberg group on a certain Hilbert space of square-integrable functions defined on phase space. This allows us to extend the usual Weyl calculus into a phase-space calculus and leads us to a quantum mechanics in phase space, equivalent to standard quantum mechanics. We also briefly discuss the extension of metaplectic operators to phase space and the probabilistic interpretation of the solutions of the phase space Schr\"{o}dinger equationComment: To appear in J Phys

Chaos in neural networks with a nonmonotonic transfer function

Time evolution of diluted neural networks with a nonmonotonic transfer function is analitically described by flow equations for macroscopic variables. The macroscopic dynamics shows a rich variety of behaviours: fixed-point, periodicity and chaos. We examine in detail the structure of the strange attractor and in particular we study the main features of the stable and unstable manifolds, the hyperbolicity of the attractor and the existence of homoclinic intersections. We also discuss the problem of the robustness of the chaos and we prove that in the present model chaotic behaviour is fragile (chaotic regions are densely intercalated with periodicity windows), according to a recently discussed conjecture. Finally we perform an analysis of the microscopic behaviour and in particular we examine the occurrence of damage spreading by studying the time evolution of two almost identical initial configurations. We show that for any choice of the parameters the two initial states remain microscopically distinct.Comment: 12 pages, 11 figures. Accepted for publication in Physical Review E. Originally submitted to the neuro-sys archive which was never publicly announced (was 9905001