The Discrete Frenet Frame, Inflection Point Solitons And Curve Visualization with Applications to Folded Proteins

We develop a transfer matrix formalism to visualize the framing of discrete piecewise linear curves in three dimensional space. Our approach is based on the concept of an intrinsically discrete curve, which enables us to more effectively describe curves that in the limit where the length of line segments vanishes approach fractal structures in lieu of continuous curves. We verify that in the case of differentiable curves the continuum limit of our discrete equation does reproduce the generalized Frenet equation. As an application we consider folded proteins, their Hausdorff dimension is known to be fractal. We explain how to employ the orientation of $C_\beta$ carbons of amino acids along a protein backbone to introduce a preferred framing along the backbone. By analyzing the experimentally resolved fold geometries in the Protein Data Bank we observe that this $C_\beta$ framing relates intimately to the discrete Frenet framing. We also explain how inflection points can be located in the loops, and clarify their distinctive r\^ole in determining the loop structure of foldel proteins.Comment: 14 pages 12 figure

On the curvature of vortex moduli spaces

We use algebraic topology to investigate local curvature properties of the moduli spaces of gauged vortices on a closed Riemann surface. After computing the homotopy type of the universal cover of the moduli spaces (which are symmetric powers of the surface), we prove that, for genus g>1, the holomorphic bisectional curvature of the vortex metrics cannot always be nonnegative in the multivortex case, and this property extends to all Kaehler metrics on certain symmetric powers. Our result rules out an established and natural conjecture on the geometry of the moduli spaces.Comment: 25 pages; final version, to appear in Math.

On asymptotic stability of the Skyrmion

We study the asymptotic behavior of spherically symmetric solutions in the Skyrme model. We show that the relaxation to the degree-one soliton (called the Skyrmion) has a universal form of a superposition of two effects: exponentially damped oscillations (the quasinormal ringing) and a power law decay (the tail). The quasinormal ringing, which dominates the dynamics for intermediate times, is a linear resonance effect. In contrast, the polynomial tail, which becomes uncovered at late times, is shown to be a \emph{nonlinear} phenomenon.Comment: 4 pages, 4 figures, minor changes to match the PRD versio

Dynamical algebra and Dirac quantum modes in Taub-NUT background

The SO(4,1) gauge-invariant theory of the Dirac fermions in the external field of the Kaluza-Klein monopole is investigated. It is shown that the discrete quantum modes are governed by reducible representations of the o(4) dynamical algebra generated by the components of the angular momentum operator and those of the Runge-Lenz operator of the Dirac theory in Taub-NUT background. The consequence is that there exist central and axial discrete modes whose spinors have no separated variables.Comment: 17 pages, latex, no figures. Version to appear in Class.Quantum Gra

Algorithms and literate programs for weighted low-rank approximation with missing data

Linear models identification from data with missing values is posed as a weighted low-rank approximation problem with weights related to the missing values equal to zero. Alternating projections and variable projections methods for solving the resulting problem are outlined and implemented in a literate programming style, using Matlab/Octave's scripting language. The methods are evaluated on synthetic data and real data from the MovieLens data sets

Forced Topological Nontrivial Field Configurations

The motion of a one-dimensional kink and its energy losses are considered as a model of interaction of nontrivial topological field configurations with external fields. The approach is based on the calculation of the zero modes excitation probability in the external field. We study in the same way the interaction of the t'Hooft-Polyakov monopole with weak external fields. The basic idea is to treat the excitation of a monopole zero mode as the monopole displacement. The excitation is found perturbatively. As an example we consider the interaction of the t'Hooft-Polyakov monopole with an external uniform magnetic field.Comment: 18 pages, 3 Postscript figures, RevTe

New Integrable Sectors in Skyrme and 4-dimensional CP^n Model

The application of a weak integrability concept to the Skyrme and $CP^n$ models in 4 dimensions is investigated. A new integrable subsystem of the Skyrme model, allowing also for non-holomorphic solutions, is derived. This procedure can be applied to the massive Skyrme model, as well. Moreover, an example of a family of chiral Lagrangians providing exact, finite energy Skyrme-like solitons with arbitrary value of the topological charge, is given. In the case of $CP^n$ models a tower of integrable subsystems is obtained. In particular, in (2+1) dimensions a one-to-one correspondence between the standard integrable submodel and the BPS sector is proved. Additionally, it is shown that weak integrable submodels allow also for non-BPS solutions. Geometric as well as algebraic interpretations of the integrability conditions are also given.Comment: 23 page

Topological solitons in highly anisotropic two dimensional ferromagnets

e study the solitons, stabilized by spin precession in a classical two--dimensional lattice model of Heisenberg ferromagnets with non-small easy--axis anisotropy. The properties of such solitons are treated both analytically using the continuous model including higher then second powers of magnetization gradients, and numerically for a discrete set of the spins on a square lattice. The dependence of the soliton energy $E$ on the number of spin deviations (bound magnons) $N$ is calculated. We have shown that the topological solitons are stable if the number $N$ exceeds some critical value $N_{\rm{cr}}$. For $N < N_{\rm{cr}}$ and the intermediate values of anisotropy constant $K_{\mathrm{eff}} <0.35J$ ($J$ is an exchange constant), the soliton properties are similar to those for continuous model; for example, soliton energy is increasing and the precession frequency $\omega (N)$ is decreasing monotonously with $N$ growth. For high enough anisotropy $K_{\mathrm{eff}} > 0.6 J$ we found some fundamentally new soliton features absent for continuous models incorporating even the higher powers of magnetization gradients. For high anisotropy, the dependence of soliton energy E(N) on the number of bound magnons become non-monotonic, with the minima at some "magic" numbers of bound magnons. Soliton frequency $\omega (N)$ have quite irregular behavior with step-like jumps and negative values of $\omega$ for some regions of $N$. Near these regions, stable static soliton states, stabilized by the lattice effects, exist.Comment: 17 page

Orbit-based deformation procedure for two-field models

We present a method for generating new deformed solutions starting from systems of two real scalar fields for which defect solutions and orbits are known. The procedure generalizes the approach introduced in a previous work [Phys. Rev. D 66, 101701(R) (2002)], in which it is shown how to construct new models altogether with its defect solutions, in terms of the original model and solutions. As an illustration, we work out an explicit example in detail.Comment: 15 pages, 14 figures; version to appear in PR

2+1 Dimensional Georgi-Glashow Instantons in Weyl Gauge

Semiclassical instanton solutions in the 3D SU(2) Georgi-Glashow model are transformed into the Weyl gauge. This illustrates the tunneling interpretation of these instantons and provides a smooth regularization of the singular unitary gauge. The 3D Georgi-Glashow model has both instanton and sphaleron solutions, in contrast to 3D Yang-Mills theory which has neither, and 4D Yang-Mills theory which has instantons but no sphaleron, and 4D electroweak theory which has a sphaleron but no instantons. We also discuss the spectral flow picture of fundamental fermions in a Georgi-Glashow instanton background.Comment: 22 pages, 8 figures, revtex4; v2 - references and comments adde