Periods of second kind differentials of (n,s)-curves

For elliptic curves, expressions for the periods of elliptic integrals of the second kind in terms of theta-constants, have been known since the middle of the 19th century. In this paper we consider the problem of generalizing these results to curves of higher genera, in particular to a special class of algebraic curves, the so-called $(n,s)$-curves. It is shown that the representations required can be obtained by the comparison of two equivalent expressions for the projective connection, one due to Fay-Wirtinger and the other from Klein-Weierstrass. As a principle example, we consider the case of the genus two hyperelliptic curve, and a number of new Thomae and Rosenhain-type formulae are obtained. We anticipate that our analysis for the genus two curve can be extended to higher genera hyperelliptic curves, as well as to other classes of $(n,s)$ non-hyperelliptic curves.Comment: 21 page

Quasiperiodic localized oscillating solutions in the discrete nonlinear Schr\"odinger equation with alternating on-site potential

We present what we believe to be the first known example of an exact quasiperiodic localized stable solution with spatially symmetric large-amplitude oscillations in a non-integrable Hamiltonian lattice model. The model is a one-dimensional discrete nonlinear Schr\"odinger equation with alternating on-site energies, modelling e.g. an array of optical waveguides with alternating widths. The solution bifurcates from a stationary discrete gap soliton, and in a regime of large oscillations its intensity oscillates periodically between having one peak at the central site, and two symmetric peaks at the neighboring sites with a dip in the middle. Such solutions, termed 'pulsons', are found to exist in continuous families ranging arbitrarily close both to the anticontinuous and continuous limits. Furthermore, it is shown that they may be linearly stable also in a regime of large oscillations.Comment: 4 pages, 4 figures, to be published in Phys. Rev. E. Revised version: change of title, added Figs. 1(b),(c), 4 new references + minor clarification

SOBA: sequence ontology bioinformatics analysis

The advent of cheaper, faster sequencing technologies has pushed the task of sequence annotation from the exclusive domain of large-scale multi-national sequencing projects to that of research laboratories and small consortia. The bioinformatics burden placed on these laboratories, some with very little programming experience can be daunting. Fortunately, there exist software libraries and pipelines designed with these groups in mind, to ease the transition from an assembled genome to an annotated and accessible genome resource. We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers for rapid feedback during annotation software development and testing. SOBA also provides annotation consistency feedback to ensure correct use of terminology within annotations, and guides users to add new terms to the Sequence Ontology when required. SOBA is available at http://www.sequenceontology.org/cgi-bin/soba.cgi

Properties of the series solution for Painlevé I

We present some observations on the asymptotic behaviour of the coefficients in the Laurent series expansion of solutions of the first Painlevé equation. For the general solution, explicit recursive formulae for the Taylor expansion of the tau-function around a zero are given, which are natural extensions of analogous formulae for the elliptic sigma function, as given by Weierstrass. Numerical and exact results on the symmetric solution which is singular at the origin are also presented

Deriving bases for Abelian functions

We present a new method to explicitly define Abelian functions associated with algebraic curves, for the purpose of finding bases for the relevant vector spaces of such functions. We demonstrate the procedure with the functions associated with a trigonal curve of genus four. The main motivation for the construction of such bases is that it allows systematic methods for the derivation of the addition formulae and differential equations satisfied by the functions. We present a new 3-term 2-variable addition formulae and a complete set of differential equations to generalise the classic Weierstrass identities for the case of the trigonal curve of genus four.Comment: 35page

New Kinds of Acoustic Solitons

We find that the modified sine-Gordon equation belonging to the class of the soliton equations describes the propagation of extremely short transverse acoustic pulses through the low-temperature crystal containing paramagnetic impurities with effective spin S=1/2 in the Voigt geometry case. The features of nonlinear dynamics of strain field and effective spins, which correspond to the different kinds of acoustic solitons, are studied.Comment: 9 pages, 1 figur

Discrete soliton mobility in two-dimensional waveguide arrays with saturable nonlinearity

We address the issue of mobility of localized modes in two-dimensional nonlinear Schr\"odinger lattices with saturable nonlinearity. This describes e.g. discrete spatial solitons in a tight-binding approximation of two-dimensional optical waveguide arrays made from photorefractive crystals. We discuss numerically obtained exact stationary solutions and their stability, focussing on three different solution families with peaks at one, two, and four neighboring sites, respectively. When varying the power, there is a repeated exchange of stability between these three solutions, with symmetry-broken families of connecting intermediate stationary solutions appearing at the bifurcation points. When the nonlinearity parameter is not too large, we observe good mobility, and a well defined Peierls-Nabarro barrier measuring the minimum energy necessary for rendering a stable stationary solution mobile.Comment: 19 pages, 4 figure

Evidence for moving breathers in a layered crystal insulator at 300K

We report the ejection of atoms at a crystal surface caused by energetic breathers which have travelled more than 10^7 unit cells in atomic chain directions. The breathers were created by bombardment of a crystal face with heavy ions. This effect was observed at 300K in the layered crystal muscovite, which has linear chains of atoms for which the surrounding lattice has C_2 symmetry. The experimental techniques described could be used to study breathers in other materials and configurations.Comment: 7 pages, 3 figure

Deriving N-soliton solutions via constrained flows

The soliton equations can be factorized by two commuting x- and t-constrained flows. We propose a method to derive N-soliton solutions of soliton equations directly from the x- and t-constrained flows.Comment: 8 pages, AmsTex, no figures, to be published in Journal of Physics

Generalised Elliptic Functions

We consider multiply periodic functions, sometimes called Abelian functions, defined with respect to the period matrices associated with classes of algebraic curves. We realise them as generalisations of the Weierstras P-function using two different approaches. These functions arise naturally as solutions to some of the important equations of mathematical physics and their differential equations, addition formulae, and applications have all been recent topics of study. The first approach discussed sees the functions defined as logarithmic derivatives of the sigma-function, a modified Riemann theta-function. We can make use of known properties of the sigma function to derive power series expansions and in turn the properties mentioned above. This approach has been extended to a wide range of non hyperelliptic and higher genus curves and an overview of recent results is given. The second approach defines the functions algebraically, after first modifying the curve into its equivariant form. This approach allows the use of representation theory to derive a range of results at lower computational cost. We discuss the development of this theory for hyperelliptic curves and how it may be extended in the future.Comment: 16 page