Efficient Doubling on Genus Two Curves over Binary Fields

In most algorithms involving elliptic and hyperelliptic curves, the costliest part consists in computing multiples of ideal classes. This paper investigates how to compute faster doubling over fields of characteristic two. We derive explicit doubling formulae making strong use of the defining equation of the curve. We analyze how many field operations are needed depending on the curve making clear how much generality one loses by the respective choices. Note, that none of the proposed types is known to be weak – one only could be suspicious because of the more special types. Our results allow to choose curves from a large enough variety which have extremely fast doubling needing only half the time of an addition. Combined with a sliding window method this leads to fast computation of scalar multiples. We also speed up the general case

Using LISREL to analyze genetic and environmental covariance structure

Describes a method in which the linear structural relationships (LISREL) computer program is used for the genetic analysis of covariance structure. The method is illustrated with simulated and published twin data, including an analysis of twin data by N. G. Martin et al (1981) on psychomotor performance during alcohol intoxication

Master equation approach to DNA-breathing in heteropolymer DNA

After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies between less than one to a few kT. This causes the opening of intermittent single-stranded bubbles. Their unzipping and zipping dynamics can be monitored by single molecule fluorescence or NMR methods. We here establish a dynamic description of this DNA-breathing in a heteropolymer DNA in terms of a master equation that governs the time evolution of the joint probability distribution for the bubble size and position along the sequence. The transfer coefficients are based on the Poland-Scheraga free energy model. We derive the autocorrelation function for the bubble dynamics and the associated relaxation time spectrum. In particular, we show how one can obtain the probability densities of individual bubble lifetimes and of the waiting times between successive bubble events from the master equation. A comparison to results of a stochastic Gillespie simulation shows excellent agreement.Comment: 12 pages, 8 figure

Cantor type functions in non-integer bases

Cantor's ternary function is generalized to arbitrary base-change functions in non-integer bases. Some of them share the curious properties of Cantor's function, while others behave quite differently

Counting points on hyperelliptic curves over finite fields

International audienceWe describe some algorithms for computing the cardinality of hyperelliptic curves and their Jacobians over finite fields. They include several methods for obtaining the result modulo small primes and prime powers, in particular an algorithm à la Schoof for genus 2 using Cantor's division polynomials. These are combined with a birthday paradox algorithm to calculate the cardinality. Our methods are practical and we give actual results computed using our current implementation. The Jacobian groups we handle are larger than those previously reported in the literature

Bubble merging in breathing DNA as a vicious walker problem in opposite potentials

We investigate the coalescence of two DNA-bubbles initially located at weak domains and separated by a more stable barrier region in a designed construct of double-stranded DNA. In a continuum Fokker-Planck approach, the characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behavior, while at high temperatures, the bubble corners perform drift-diffusion towards coalescence. In the calculations, we map the bubble dynamics on the problem of two vicious walkers in opposite potentials. We also present a discrete master equation approach to the bubble coalescence problem. Numerical evaluation and stochastic simulation of the master equation show excellent agreement with the results from the continuum approach. Given that the coalesced state is thermodynamically stabilized against a state where only one or a few base pairs of the barrier region are re-established, it appears likely that this type of setup could be useful for the quantitative investigation of thermodynamic DNA stability data as well as the rate constants involved in the unzipping and zipping dynamics of DNA, in single molecule fluorescence experiments.Comment: 24 pages, 11 figures; substantially extended version of cond-mat/0610752; v2: minor text changes, virtually identical to the published versio

Why do people fail to turn good intentions into action? : The role of executive control processes in the translation of healthy eating intentions into action in young Scottish adults

Non peer reviewedPublisher PD

Nonequilibrium effects in DNA microarrays: a multiplatform study

It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15h in standard protocols (Hooyberghs et al. Phys. Rev. E 81, 012901 (2010)). In this paper we discuss how this breakdown of thermodynamic equilibrium could be detected in microarray experiments without resorting to real time hybridization data, which are difficult to implement in standard experimental conditions. The method is based on the analysis of the distribution of fluorescence intensities I from different spots for probes carrying base mismatches. In thermal equilibrium and at sufficiently low concentrations, log I is expected to be linearly related to the hybridization free energy $\Delta G$ with a slope equal to $1/RT_{exp}$, where $T_{exp}$ is the experimental temperature and R is the gas constant. The breakdown of equilibrium results in the deviation from this law. A model for hybridization kinetics explaining the observed experimental behavior is discussed, the so-called 3-state model. It predicts that deviations from equilibrium yield a proportionality of $\log I$ to $\Delta G/RT_{eff}$. Here, $T_{eff}$ is an effective temperature, higher than the experimental one. This behavior is indeed observed in some experiments on Agilent arrays. We analyze experimental data from two other microarray platforms and discuss, on the basis of the results, the attainment of equilibrium in these cases. Interestingly, the same 3-state model predicts a (dynamical) saturation of the signal at values below the expected one at equilibrium.Comment: 27 pages, 9 figures, 1 tabl