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

Suppression of Conductance in a Topological Insulator Nanostep Junction

We investigate quantum transport via surface states in a nanostep junction on the surface of a 3D topological insulator that involves two different side surfaces. We calculate the conductance across the junction within the scattering matrix formalism and find that as the bias voltage is increased, the conductance of the nanostep junction is suppressed by a universal factor of 1/3 compared to the conductance of a similar planar junction based on a single surface of a topological insulator. We also calculate and analyze the Fano factor of the nanostep junction and predict that the Fano factor saturates at 1/5, five times smaller than for a Poisson process

Full Current Statistics in Diffusive Normal-Superconductor Structures

We study the current statistics in normal diffusive conductors in contact with a superconductor. Using an extension of the Keldysh Green's function method we are able to find the full distribution of charge transfers for all temperatures and voltages. For the non-Gaussian regime, we show that the equilibrium current fluctuations are enhanced by the presence of the superconductor. We predict an enhancement of the nonequilibrium current noise for temperatures below and voltages of the order of the Thouless energy E_Th=D/L^2. Our calculation fully accounts for the proximity effect in the normal metal and agrees with experimental data. We demonstrate that the calculation of the full current statistics is in fact simpler than a concrete calculation of the noise.Comment: 4 pages, 2 figures (included

Brownian refrigeration by hybrid tunnel junctions

Voltage fluctuations generated in a hot resistor can cause extraction of heat from a colder normal metal electrode of a hybrid tunnel junction between a normal metal and a superconductor. We extend the analysis presented in [Phys. Rev. Lett. 98, 210604 (2007)] of this heat rectifying system, bearing resemblance to a Maxwell's demon. Explicit analytic calculations show that the entropy of the total system is always increasing. We then consider a single electron transistor configuration with two hybrid junctions in series, and show how the cooling is influenced by charging effects. We analyze also the cooling effect from nonequilibrium fluctuations instead of thermal noise, focusing on the shot noise generated in another tunnel junction. We conclude by discussing limitations for an experimental observation of the effect.Comment: 16 pages, 16 figure

Infrared catastrophe and tunneling into strongly correlated electron systems: Exact solution of the x-ray edge limit for the 1D electron gas and 2D Hall fluid

In previous work we have proposed that the non-Fermi-liquid spectral properties in a variety of low-dimensional and strongly correlated electron systems are caused by the infrared catastrophe, and we used an exact functional integral representation for the interacting Green's function to map the tunneling problem onto the x-ray edge problem, plus corrections. The corrections are caused by the recoil of the tunneling particle, and, in systems where the method is applicable, are not expected to change the qualitative form of the tunneling density of states (DOS). Qualitatively correct results were obtained for the DOS of the 1D electron gas and 2D Hall fluid when the corrections to the x-ray edge limit were neglected and when the corresponding Nozieres-De Dominicis integral equations were solved by resummation of a divergent perturbation series. Here we reexamine the x-ray edge limit for these two models by solving these integral equations exactly, finding the expected modifications of the DOS exponent in the 1D case but finding no changes in the DOS of the 2D Hall fluid with short-range interaction. We also provide, for the first time, an exact solution of the Nozieres-De Dominicis equation for the 2D electron gas in the lowest Landau level.Comment: 6 pages, Revte

Andreev reflection eigenvalue density in mesoscopic conductors

The energy-dependent Andreev reflection eigenvalues determine the transport properties of normal-superconducting systems. We evaluate the eigenvalue density to get an insight into formation of resonant electron-hole transport channels. The circuit-theory-like method developed can be applied to any generic mesoscopic conductor or combinations thereof. We present the results for experimentally relevant cases of a diffusive wire and a double tunnel junction.Comment: 5 pages, 3 figure