The Unified Method: I Non-Linearizable Problems on the Half-Line

Boundary value problems for integrable nonlinear evolution PDEs formulated on the half-line can be analyzed by the unified method introduced by one of the authors and used extensively in the literature. The implementation of this general method to this particular class of problems yields the solution in terms of the unique solution of a matrix Riemann-Hilbert problem formulated in the complex $k$-plane (the Fourier plane), which has a jump matrix with explicit $(x,t)$-dependence involving four scalar functions of $k$, called spectral functions. Two of these functions depend on the initial data, whereas the other two depend on all boundary values. The most difficult step of the new method is the characterization of the latter two spectral functions in terms of the given initial and boundary data, i.e. the elimination of the unknown boundary values. For certain boundary conditions, called linearizable, this can be achieved simply using algebraic manipulations. Here, we present an effective characterization of the spectral functions in terms of the given initial and boundary data for the general case of non-linearizable boundary conditions. This characterization is based on the analysis of the so-called global relation, on the analysis of the equations obtained from the global relation via certain transformations leaving the dispersion relation of the associated linearized PDE invariant, and on the computation of the large $k$ asymptotics of the eigenfunctions defining the relevant spectral functions.Comment: 39 page

Non-Linear Evolution Equations with Non-Analytic Dispersion Relations in 2+1 Dimensions. Bilocal Approach

A method is proposed of obtaining (2+1)-dimensional non- linear equations with non-analytic dispersion relations. Bilocal formalism is shown to make it possible to represent these equations in a form close to that for their counterparts in 1+1 dimensions.Comment: 13 pages, to be published in J. Phys.

An Integrable Shallow Water Equation with Linear and Nonlinear Dispersion

We study a class of 1+1 quadratically nonlinear water wave equations that combines the linear dispersion of the Korteweg-deVries (KdV) equation with the nonlinear/nonlocal dispersion of the Camassa-Holm (CH) equation, yet still preserves integrability via the inverse scattering transform (IST) method. This IST-integrable class of equations contains both the KdV equation and the CH equation as limiting cases. It arises as the compatibility condition for a second order isospectral eigenvalue problem and a first order equation for the evolution of its eigenfunctions. This integrable equation is shown to be a shallow water wave equation derived by asymptotic expansion at one order higher approximation than KdV. We compare its traveling wave solutions to KdV solitons.Comment: 4 pages, no figure

Integrable nonlinear equations on a circle

The concept of integrable boundary value problems for soliton equations on $\mathbb{R}$ and $\mathbb{R}_+$ is extended to bounded regions enclosed by smooth curves. Classes of integrable boundary conditions on a circle for the Toda lattice and its reductions are found.Comment: 23 page

Linearizability of the Perturbed Burgers Equation

We show in this letter that the perturbed Burgers equation $u_t = 2uu_x + u_{xx} + \epsilon ( 3 \alpha_1 u^2 u_x + 3\alpha_2 uu_{xx} + 3\alpha_3 u_x^2 + \alpha_4 u_{xxx} )$ is equivalent, through a near-identity transformation and up to order \epsilon, to a linearizable equation if the condition $3\alpha_1 - 3\alpha_3 - 3/2 \alpha_2 + 3/2 \alpha_4 = 0$ is satisfied. In the case this condition is not fulfilled, a normal form for the equation under consideration is given. Then, to illustrate our results, we make a linearizability analysis of the equations governing the dynamics of a one-dimensional gas.Comment: 10 pages, RevTeX, no figure

Multidimensional Inverse Scattering of Integrable Lattice Equations

We present a discrete inverse scattering transform for all ABS equations excluding Q4. The nonlinear partial difference equations presented in the ABS hierarchy represent a comprehensive class of scalar affine-linear lattice equations which possess the multidimensional consistency property. Due to this property it is natural to consider these equations living in an N-dimensional lattice, where the solutions depend on N distinct independent variables and associated parameters. The direct scattering procedure, which is one-dimensional, is carried out along a staircase within this multidimensional lattice. The solutions obtained are dependent on all N lattice variables and parameters. We further show that the soliton solutions derived from the Cauchy matrix approach are exactly the solutions obtained from reflectionless potentials, and we give a short discussion on inverse scattering solutions of some previously known lattice equations, such as the lattice KdV equation.Comment: 18 page

Extension of Hereditary Symmetry Operators

Two models of candidates for hereditary symmetry operators are proposed and thus many nonlinear systems of evolution equations possessing infinitely many commutative symmetries may be generated. Some concrete structures of hereditary symmetry operators are carefully analyzed on the base of the resulting general conditions and several corresponding nonlinear systems are explicitly given out as illustrative examples.Comment: 13 pages, LaTe

Residue Geometry Networks: A Rigidity-Based Approach to the Amino Acid Network and Evolutionary Rate Analysis.

Amino acid networks (AANs) abstract the protein structure by recording the amino acid contacts and can provide insight into protein function. Herein, we describe a novel AAN construction technique that employs the rigidity analysis tool, FIRST, to build the AAN, which we refer to as the residue geometry network (RGN). We show that this new construction can be combined with network theory methods to include the effects of allowed conformal motions and local chemical environments. Importantly, this is done without costly molecular dynamics simulations required by other AAN-related methods, which allows us to analyse large proteins and/or data sets. We have calculated the centrality of the residues belonging to 795 proteins. The results display a strong, negative correlation between residue centrality and the evolutionary rate. Furthermore, among residues with high closeness, those with low degree were particularly strongly conserved. Random walk simulations using the RGN were also successful in identifying allosteric residues in proteins involved in GPCR signalling. The dynamic function of these residues largely remain hidden in the traditional distance-cutoff construction technique. Despite being constructed from only the crystal structure, the results in this paper suggests that the RGN can identify residues that fulfil a dynamical function.A.S.F. is supported by a Doctoral Research Award from Microsoft Research. S.E.A. is supported by The Royal Society (UK). D.J.C. is supported by a Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme. A.W.C. is supported by the Winton Programme for the Physics of Sustainability.This is the final version of the article. It first appeared from Nature Publishing Group at http://dx.doi.org/10.1038/srep33213

A tree of linearisable second-order evolution equations by generalised hodograph transformations

We present a list of (1+1)-dimensional second-order evolution equations all connected via a proposed generalised hodograph transformation, resulting in a tree of equations transformable to the linear second-order autonomous evolution equation. The list includes autonomous and nonautonomous equations.Comment: arXiv version is already officia

Spectral decomposition for the Dirac system associated to the DSII equation

A new (scalar) spectral decomposition is found for the Dirac system in two dimensions associated to the focusing Davey--Stewartson II (DSII) equation. Discrete spectrum in the spectral problem corresponds to eigenvalues embedded into a two-dimensional essential spectrum. We show that these embedded eigenvalues are structurally unstable under small variations of the initial data. This instability leads to the decay of localized initial data into continuous wave packets prescribed by the nonlinear dynamics of the DSII equation