PCA and K-Means decipher genome

In this paper, we aim to give a tutorial for undergraduate students studying statistical methods and/or bioinformatics. The students will learn how data visualization can help in genomic sequence analysis. Students start with a fragment of genetic text of a bacterial genome and analyze its structure. By means of principal component analysis they ``discover'' that the information in the genome is encoded by non-overlapping triplets. Next, they learn how to find gene positions. This exercise on PCA and K-Means clustering enables active study of the basic bioinformatics notions. Appendix 1 contains program listings that go along with this exercise. Appendix 2 includes 2D PCA plots of triplet usage in moving frame for a series of bacterial genomes from GC-poor to GC-rich ones. Animated 3D PCA plots are attached as separate gif files. Topology (cluster structure) and geometry (mutual positions of clusters) of these plots depends clearly on GC-content.Comment: 18 pages, with program listings for MatLab, PCA analysis of genomes and additional animated 3D PCA plot

Persistent Orbital Degeneracy in Carbon Nanotubes

The quantum-mechanical orbitals in carbon nanotubes are doubly degenerate over a large number of states in the Coulomb blockade regime. We argue that this experimental observation indicates that electrons are reflected without mode mixing at the nanotube-metal contacts. Two electrons occupying a pair of degenerate orbitals (a ``shell'') are found to form a triplet state starting from zero magnetic field. Finally, we observe unexpected low-energy excitations at complete filling of a four-electron shell.Comment: 6 pages, 4 figure

Differential expansion for link polynomials

The differential expansion is one of the key structures reflecting group theory properties of colored knot polynomials, which also becomes an important tool for evaluation of non-trivial Racah matrices. This makes highly desirable its extension from knots to links, which, however, requires knowledge of the $6j$-symbols, at least, for the simplest triples of non-coincident representations. Based on the recent achievements in this direction, we conjecture a shape of the differential expansion for symmetrically-colored links and provide a set of examples. Within this study, we use a special framing that is an unusual extension of the topological framing from knots to links. In the particular cases of Whitehead and Borromean rings links, the differential expansions are different from the previously discovered.Comment: 11 page

Enhanced relativistic harmonics by electron nanobunching

It is shown that when an few-cycle, relativistically intense, p-polarized laser pulse is obliquely incident on overdense plasma, the surface electrons may form ultra-thin, highly compressed layers, with a width of a few nanometers. These electron "nanobunches" emit synchrotron radiation coherently. We calculate the one-dimensional synchrotron spectrum analytically and obtain a slowly decaying power-law with an exponent of 4/3 or 6/5. This is much flatter than the 8/3 power of the BGP (Baeva-Gordienko-Pukhov) spectrum, produced by a relativistically oscillating bulk skin layer. The synchrotron spectrum cut-off frequency is defined either by the electron relativistic $\gamma$-factor, or by the thickness of the emitting layer. In the numerically demonstrated, locally optimal case, the radiation is emitted in the form of a single attosecond pulse, which contains almost the entire energy of the full optical cycle.Comment: to appear in Physics of Plasma

Why is the nuclear symmetry energy so uncertain at supra-saturation densities?

Within the interacting Fermi gas model for isospin asymmetric nuclear matter, effects of the in-medium three-body interaction and the two-body short-range tensor force due to the $\rho$ meson exchange as well as the short-range nucleon correlation on the high-density behavior of the nuclear symmetry energy are demonstrated respectively in a transparent way. Possible physics origins of the extremely uncertain nuclear symmetry energy at supra-saturation densities are discussed.Comment: Added discussions and revised format. Version to appear in Phys. Rev. C (2010

Chiral expansion of the π0→γγ\pi^0\rightarrow\gamma\gamma decay width

A chiral field theory of mesons has been applied to study the contribution of the current quark masses to the $\pi^0\rightarrow\gamma\gamma$ decay width at the next leading order. $2\%$ enhancement has been predicted and there is no new parameter.Comment: 9 page