Towards a robust algorithm to determine topological domains from colocalization data

One of the most important tasks in understanding the complex spatial organization of the genome consists in extracting information about this spatial organization, the function and structure of chromatin topological domains from existing experimental data, in particular, from genome colocalization (Hi-C) matrices. Here we present an algorithm allowing to reveal the underlying hierarchical domain structure of a polymer conformation from analyzing the modularity of colocalization matrices. We also test this algorithm on several model polymer structures: equilibrium globules, random fractal globules and regular fractal (Peano) conformations. We define what we call a spectrum of cluster borders, and show that these spectra behave strikingly differently for equilibrium and fractal conformations, allowing us to suggest an additional criterion to identify fractal polymer conformations

Role of Group and Phase Velocity in High-Energy Neutrino Observatories

Kuzmichev recently showed that use of phase velocity rather than group velocity for Cherenkov light signals and pulses from calibration lasers in high-energy neutrino telescopes leads to errors in track reconstruction and distance measurement. We amplify on his remarks and show that errors for four cases of interest to AMANDA, IceCube, and RICE (radio Cherenkov detector) are negligibly small.Comment: To be published in Astroparticle Physics, 6 pages, uses elsart.st

Structure and mass distribution of spiral galaxies at intermediate redshifts

Using the HST archive WFPC2 observations and rotation curves measeured by Vogt et al. (1996), we constructed self-consistent light and mass distribution models for three disk galaxies at redshifts z = 0.15, 0.90 and 0.99. The models consist of three components: the bulge, the disk and the dark matter. Spatial density distribution parameters for the components were calculated. After applying k-corrections, mass-to-light ratios for galactic disks within the maximum disk assumption are M/L_B = 4.4, 1.2 and 1.2, respectively. Corresponding central densities of dark matter halos within a truncated isothermal model are 0.0092, 0.028 and 0.015 in units M_sol/pc^3. The light distribution of galaxies in outer parts is steeper than a simple exponential disk

Backward Tamm states in left-handed metamaterials

We study the electromagnetic surface waves localized at an interface separating a one-dimensional photonic crystal and left-handed metamaterial, the so-called surface Tamm states. We demonstrate that the metamaterial allows for a flexible control of the dispersion properties of surface states, and can support the Tamm states with a backward energy flow and a vortex-like structure.Comment: 3 pages, 5 figure

When renormalizability is not sufficient: Coulomb problem for vector bosons

The Coulomb problem for vector bosons W incorporates a known difficulty; the boson falls on the center. In QED the fermion vacuum polarization produces a barrier at small distances which solves the problem. In a renormalizable SU(2) theory containing vector triplet (W^+,W^-,gamma) and a heavy fermion doublet F with mass M the W^- falls on F^+, to distances r ~ 1/M, where M can be made arbitrary large. To prevent the collapse the theory needs additional light fermions, which switch the ultraviolet behavior of the theory from the asymptotic freedom to the Landau pole. Similar situation can take place in the Standard Model. Thus, the renormalizability of a theory is not sufficient to guarantee a reasonable behavior at small distances for non-perturbative problems, such as a bound state problem.Comment: Four page

Influence of Different Alfalfa-Grass Mixtures and the Use of Additives on Nutritive Value and Fermentation of Silage

Legumes have a high nutritive value but they are known to be difficult to ensile and often result in poorly fermented silage. This is usually due to high buffering capacity and low available sugar concentration. However, the results have shown that silage quality can considerably be improved by using additives or when legume-grass mixtures are ensiled (Lättemäe & Tamm, 2002). Different legume-grass mixtures differ in their ensiling properties and also may affect the fermentation. The objective of this experiment was to study the effect of alfalfa-grass mixtures and the use of additives on nutritive value and fermentation of silage

Quantum Hall fractions for spinless Bosons

We study the Quantum Hall phases that appear in the fast rotation limit for Bose-Einstein condensates of spinless bosonic atoms. We use exact diagonalization in a spherical geometry to obtain low-lying states of a small number of bosons as a function of the angular momentum. This allows to understand or guess the physics at a given filling fraction nu, ratio of the number of bosons to the number of vortices. This is also the filling factor of the lowest Landau level. In addition to the well-known Bose Laughlin state at nu =1/2 we give evidence for the Jain principal sequence of incompressible states at nu =p/(p+- 1) for a few values of p. There is a collective mode in these states whose phenomenology is in agreement with standard arguments coming e.g. from the composite fermion picture. At filling factor one, the potential Fermi sea of composite fermions is replaced by a paired state, the Moore-Read state. This is most clearly seen from the half-flux nature of elementary excitations. We find that the hierarchy picture does not extend up to the point of transition towards a vortex lattice. While we cannot conclude, we investigate the clustered Read-Rezayi states and show evidence for incompressible states at the expected ratio of flux vs number of Bose particles.Comment: RevTeX 4, 11 pages, 13 figure

Statistics of layered zigzags: a two-dimensional generalization of TASEP

A novel discrete growth model in 2+1 dimensions is presented in three equivalent formulations: i) directed motion of zigzags on a cylinder, ii) interacting interlaced TASEP layers, and iii) growing heap over 2D substrate with a restricted minimal local height gradient. We demonstrate that the coarse-grained behavior of this model is described by the two-dimensional Kardar-Parisi-Zhang equation. The coefficients of different terms in this hydrodynamic equation can be derived from the steady state flow-density curve, the so called `fundamental' diagram. A conjecture concerning the analytical form of this flow-density curve is presented and is verified numerically.Comment: 5 pages, 4 figure

Vacuum Cherenkov radiation

Within the classical Maxwell-Chern-Simons limit of the Standard-Model Extension (SME), the emission of light by uniformly moving charges is studied confirming the possibility of a Cherenkov-type effect. In this context, the exact radiation rate for charged magnetic point dipoles is determined and found in agreement with a phase-space estimate under certain assumptions.Comment: 4 pages, REVTeX