Robert Pezer

ColorHOR---novel graphical algorithm for fast scan of alpha satellite higher-order repeats and HOR annotation for GenBank sequence of human genome

MOTIVATION GenBank data are at present lacking alpha satellite higher-order repeat (HOR) annotation. Furthermore, exact HOR consensus lengths have not been reported so far. Given the fast growth of sequence databases in the centromeric region, it is of increasing interest to have efficient tools for computational identification and analysis of HORs from known sequences. RESULTS We develop a graphical user interface method, ColorHOR, for fast computational identification of HORs in a given genomic sequence, without requiring a priori information on the composition of the genomic sequence. ColorHOR is based on an extension of the key-string algorithm and provides a color representation of the order and orientation of HORs. For the key string, we use a robust 6 bp string from a consensus alpha satellite and its representative nature is tested. ColorHOR algorithm provides a direct visual identification of HORs (direct and/or reverse complement). In more detail, we first illustrate the ColorHOR results for human chromosome 1. Using ColorHOR we determine for the first time the HOR annotation of the GenBank sequence of the whole human genome. In addition to some HORs, corresponding to those determined previously biochemically, we find new HORs in chromosomes 4, 8, 9, 10, 11 and 19. For the first time, we determine exact consensus lengths of HORs in 10 chromosomes. We propose that the HOR assignment obtained by using ColorHOR be included into the GenBank database.

Gap random-phase lattice solitons.

We theoretically study gap random-phase lattice solitons (gap-RPLSs) in nonlinear waveguide arrays with self-defocusing nonlinearity. We find that the intensity structure and statistical (coherence) properties of gap-RPLSs conform to the lattice periodicity, while their Floquet-Bloch power spectrum is multi-humped with peaks in the anomalous diffractions regions. It is shown that a gap-RPLS can be generated when a simple incoherent beam with bell-shaped power spectrum and single-hump intensity is launched at a proper angle into the waveguide array. The input incoherent beam evolves in the lattice while shedding off some radiation, and eventually attains the features of gap-RPLS.

Momentum distribution dynamics of a tonks-girardeau gas: Bragg reflections of a quantum many-body wavepacket

The dynamics of the momentum distribution and the reduced single-particle density matrix (RSPDM) of a Tonks-Girardeau gas is studied in the context of Bragg-reflections of a manybody wavepacket.

Low-lying states in the doubly odd nucleus 132Pr from beta decay of 132Nd

Abstract The low-lying level scheme of the odd-odd nucleus 132Pr has been investigated for the first time. The radioactive nuclei were produced by bombarding 96Mo targets with a 225 MeV 40Ca beam. Levels in 132Pr have been populated from the 132Nd β-decay. A new value of its half-life has been measured: T 1 2 = 88 ± 7 s . The activities produced in the reaction have been transported with a He-jet device and γγt, Xγt, e−γt coincidence measurements performed. Internal conversion coefficients have been measured with a magnetic lens spectrometer. The experimental level scheme of 132Pr is compared to theoretical calculations performed with the interacting boson-fermion-fermion model (IBFFM).

Observation of random-phase gap solitons in photonic lattices

We report the first experimental observation of gap random-phase lattice solitons. We observe their self-trapping conformed to the lattice periodicity in real space, as well as their multi-humped power spectrum in k-space.

Free expansion of a Lieb-Liniger gas: Asymptotic form of the wave functions

The asymptotic form of the wave functions describing a freely expanding Lieb-Liniger gas is derived by using a Fermi-Bose transformation for time-dependent states, and the stationary phase approximation. We find that asymptotically the wave functions approach the Tonks-Girardeau (TG) structure as they vanish when any two of the particle coordinates coincide. We point out that the properties of these asymptotic states can significantly differ from the properties of a TG gas in a ground state of an external potential. The dependence of the asymptotic wave function on the initial state is discussed. The analysis encompasses a large class of initial conditions, including the ground states of a Lieb-Liniger gas in physically realistic external potentials. It is also demonstrated that the interaction energy asymptotically decays as a universal power law with time, Eint ∝ t 3 .

Dark stationary matter waves via parity-selective filtering in a Tonks-Girardeau gas

We propose a scheme for observing dark stationary waves in a Tonks-Girardeau (TG) gas. The scheme is based on parity-selective dynamical filtering of the gas via a time-dependent potential, which excites the gas from its ground state towards a desired specially-tailored many-body state. These excitations of the TG gas are analogous to linear partially coherent nondiffracting beams in optics, as evident from the mapping between the quantum dynamics of the TG gas and the propagation of incoherent light in one-dimensional linear photonic structures.

Combinatorial level densities from a relativistic structure model

A new model for calculating nuclear level densities is investigated. The singlenucleon spectra are calculated in a relativistic mean-field model with energy-dependent effective mass, which yields a realistic density of single-particle states at the Fermi energy. These microscopic single-nucleon states are used in a fast combinatorial algorithm for calculating the non-collective excitations of nuclei. The method, when applied to magic and semi-magic nuclei, such as 60 Ni, 114 Sn and 208 Pb, reproduces the cumulative number of experimental states at low excitation energy, as well as the s-wave neutron resonance spacing at the neutron binding energy. Experimental level densities above 10 MeV are reproduced by multiplying the non-collective level densities by a simple vibrational enhancement factor. Problems to be solved in the extension to open-shell nuclei are discussed.

Lieb-Liniger gas in a constant-force potential

We use Gaudin’s Fermi-Bose mapping operator to calculate exact solutions for the Lieb-Liniger model in a linear (constant-force) potential (the constructed exact stationary solutions are referred to as the Lieb-Liniger-Airy wave functions). The ground-state properties of the gas in the wedgelike trapping potential are calculated in the strongly interacting regime by using Girardeau’s FermiBose mapping and the pseudopotential approach in the 1/c approximation (c denotes the strength of the interaction). We point out that quantum dynamics of Lieb-Liniger wave packets in the linear potential can be calculated by employing an N-dimensional Fourier transform as in the case of free expansion.

Generalized Bethe formula (GBF) and combinatorial calculations for the systematics of Pb nuclei

Abstract Total level densities and state densities up to 40 MeV of excitation energy are calculated combinatorially for the systematics of Pb nuclei using independent nucleons in the realistic single particle spectra. These combinatorial level densities are well fitted by GBF, both for doubly closed shell nucleus 208 Pb and away from the shell closure. The corresponding GBF parameters exhibit smooth behavior with the change of the neutron number N , having pronounced extrema at the double shell closure. The GBF fit to the combinatorial results is compared with the fit of standard Bethe formula (BF) and of the Ignatyuk formula.