Localization of Denaturation Bubbles in Random DNA Sequences

We study the thermodynamic and dynamic behaviors of twist-induced denaturation bubbles in a long, stretched random sequence of DNA. The small bubbles associated with weak twist are delocalized. Above a threshold torque, the bubbles of several tens of bases or larger become preferentially localized to \AT-rich segments. In the localized regime, the bubbles exhibit ``aging'' and move around sub-diffusively with continuously varying dynamic exponents. These properties are derived using results of large-deviation theory together with scaling arguments, and are verified by Monte-Carlo simulations.Comment: TeX file with postscript figure

Enhanced electron correlations at the SrxCa1-xVO3 surface

We report hard x-ray photoemission spectroscopy measurements of the electronic structure of the prototypical correlated oxide SrxCa1-xVO3. By comparing spectra recorded at different excitation energies, we show that 2.2 keV photoelectrons contain a substantial surface component, whereas 4.2 keV photoelectrons originate essentially from the bulk of the sample. Bulk-sensitive measurements of the O 2p valence band are found to be in good agreement with ab initio calculations of the electronic structure, with some modest adjustments to the orbital-dependent photoionization cross sections. The evolution of the O 2p electronic structure as a function of the Sr content is dominated by A-site hybridization. Near the Fermi level, the correlated V 3d Hubbard bands are found to evolve in both binding energy and spectral weight as a function of distance from the vacuum interface, revealing higher correlation at the surface than in the bulk

A web server for interactive and zoomable Chaos Game Representation images

Chaos Game Representation (CGR) is a generalized scale-independent Markov transition table, which is useful for the visualization and comparative study of genomic signature, or for the study of characteristic sequence motifs. However, in order to fully utilize the scale-independent properties of CGR, it should be accessible through scale-independent user interface instead of static images. Here we describe a web server and Perl library for generating zoomable CGR images utilizing Google Maps API, which is also easily searchable for specific motifs. The web server is freely accessible at , and the Perl library as well as the source code is distributed with the G-language Genome Analysis Environment under GNU General Public License

Analytical Solution of a Stochastic Content Based Network Model

We define and completely solve a content-based directed network whose nodes consist of random words and an adjacency rule involving perfect or approximate matches, for an alphabet with an arbitrary number of letters. The analytic expression for the out-degree distribution shows a crossover from a leading power law behavior to a log-periodic regime bounded by a different power law decay. The leading exponents in the two regions have a weak dependence on the mean word length, and an even weaker dependence on the alphabet size. The in-degree distribution, on the other hand, is much narrower and does not show scaling behavior. The results might be of interest for understanding the emergence of genomic interaction networks, which rely, to a large extent, on mechanisms based on sequence matching, and exhibit similar global features to those found here.Comment: 13 pages, 5 figures. Rewrote conclusions regarding the relevance to gene regulation networks, fixed minor errors and replaced fig. 4. Main body of paper (model and calculations) remains unchanged. Submitted for publicatio

Excess of loss reinsurance under joint survival optimality

Explicit expressions for the probability of joint survival up to time x of the cedent and the reinsurer, under an excess of loss reinsurance contract with a limiting and a retention level are obtained, under the reasonably general assumptions of any non-decreasing premium income function, Poisson claim arrivals and continuous claim amounts, modelled by any joint distribution. By stating appropriate optimality problems, we show that these results can be used to set the limiting and the retention levels in an optimal way with respect to the probability of joint survival. Alternatively, for fixed retention and limiting levels, the results yield an optimal split of the total premium income between the two parties in the excess of loss contract. This methodology is illustrated numerically on several examples of independent and dependent claim severities. The latter are modelled by a copula function. The effect of varying its dependence parameter and the marginals, on the solutions of the optimality problems and the joint survival probability, has also been explored

An Evolutionary Reduction Principle for Mutation Rates at Multiple Loci

A model of mutation rate evolution for multiple loci under arbitrary selection is analyzed. Results are obtained using techniques from Karlin (1982) that overcome the weak selection constraints needed for tractability in prior studies of multilocus event models. A multivariate form of the reduction principle is found: reduction results at individual loci combine topologically to produce a surface of mutation rate alterations that are neutral for a new modifier allele. New mutation rates survive if and only if they fall below this surface - a generalization of the hyperplane found by Zhivotovsky et al. (1994) for a multilocus recombination modifier. Increases in mutation rates at some loci may evolve if compensated for by decreases at other loci. The strength of selection on the modifier scales in proportion to the number of germline cell divisions, and increases with the number of loci affected. Loci that do not make a difference to marginal fitnesses at equilibrium are not subject to the reduction principle, and under fine tuning of mutation rates would be expected to have higher mutation rates than loci in mutation-selection balance. Other results include the nonexistence of 'viability analogous, Hardy-Weinberg' modifier polymorphisms under multiplicative mutation, and the sufficiency of average transmission rates to encapsulate the effect of modifier polymorphisms on the transmission of loci under selection. A conjecture is offered regarding situations, like recombination in the presence of mutation, that exhibit departures from the reduction principle. Constraints for tractability are: tight linkage of all loci, initial fixation at the modifier locus, and mutation distributions comprising transition probabilities of reversible Markov chains.Comment: v3: Final corrections. v2: Revised title, reworked and expanded introductory and discussion sections, added corollaries, new results on modifier polymorphisms, minor corrections. 49 pages, 64 reference