Low-lying continuum states of drip-line Oxygen isotopes

Low-lying continuum states of exotic oxygen isotopes are studied, by introducing the Continuum-Coupled Shell Model (CCSM) characterized by an infinite wall placed very far and by an interaction for continuum coupling constructed in a close relation to realistic shell-model interaction. Neutron emission spectra from exotic oxygen isotopes are calculated by the doorway-state approach in heavy-ion multi-nucleon transfer reactions. The results agree with experiment remarkably well, as an evidence that the continuum effects are stronger than $\sim$1 MeV, consistently with the shell evolution in exotic nuclei. The results by this CCSM doorway-state approach are compared with calculations on neutron-scattering resonance peaks made within the CCSM phase-shift approach and also with those obtained in the Gamow shell model, by taking the same interaction. Remarkable similarities in peak energies and certain differences in widths are then obtained.Comment: This paper has been withdrawn by the author due to the publication in PTEP journal with considerable expansion. The re-submission to arXiv has been given up due to the differences in style files, et

Gamow shell-model calculations of drip-line oxygen isotopes

We employ the Gamow shell model (GSM) to describe low-lying states of the oxygen isotopes 24O and 25O. The many-body Schrodinger equation is solved starting from a two-body Hamiltonian defined by a renormalized low-momentum nucleon-nucleon (NN) interaction, and a spherical Berggren basis. The Berggren basis treats bound, resonant, and continuum states on an equal footing, and is therefore an appropriate representation of loosely bound and unbound nuclear states near threshold. We show that such a basis is necessary in order to obtain a detailed and correct description of the low-lying 1+ and 2+ excited states in 24O. On the other hand, we find that a correct description of binding energy systematics of the ground states is driven by proper treatment and inclusion of many-body correlation effects. This is supported by the fact that we get 25O unstable with respect to 24O in both oscillator and Berggren representations starting from a 22O core. Furthermore, we show that the structure of these loosely bound or unbound isotopes are strongly influenced by the 1S0 component of the NN interaction. This has important consequences for our understanding of nuclear stability.Comment: 5 pages, 3 figure

In-Medium Similarity Renormalization Group for Nuclei

We present a new ab-initio method that uses similarity renormalization group (SRG) techniques to continuously diagonalize nuclear many-body Hamiltonians. In contrast with applications of the SRG to two- and three-nucleon interactions in free space, we perform the SRG evolution "in medium" directly in the $A$-body system of interest. The in-medium approach has the advantage that one can approximately evolve $3,...,A$-body operators using only two-body machinery based on normal-ordering techniques. The method is nonperturbative and can be tailored to problems ranging from the diagonalization of closed-shell nuclei to the construction of effective valence shell-model Hamiltonians and operators. We present first results for the ground-state energies of $^4$He, $^{16}$O and $^{40}$Ca, which have accuracies comparable to coupled-cluster calculations.Comment: 4pages, 4 figures, to be published in PR

Discovering Restricted Regular Expressions with Interleaving

Discovering a concise schema from given XML documents is an important problem in XML applications. In this paper, we focus on the problem of learning an unordered schema from a given set of XML examples, which is actually a problem of learning a restricted regular expression with interleaving using positive example strings. Schemas with interleaving could present meaningful knowledge that cannot be disclosed by previous inference techniques. Moreover, inference of the minimal schema with interleaving is challenging. The problem of finding a minimal schema with interleaving is shown to be NP-hard. Therefore, we develop an approximation algorithm and a heuristic solution to tackle the problem using techniques different from known inference algorithms. We do experiments on real-world data sets to demonstrate the effectiveness of our approaches. Our heuristic algorithm is shown to produce results that are very close to optimal.Comment: 12 page

Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes

ISWI proteins form the catalytic core of a subset of ATP-dependent chromatin remodelling activities in eukaryotes from yeast to man. Many of these complexes have been found to reposition nucleosomes, but with different directionalities. We find that the yeast Isw1a, Isw2 and Chd1 enzymes preferentially move nucleosomes towards more central locations on short DNA fragments whereas Isw1b does not. Importantly, the inherent positioning properties of the DNA play an important role in determining where nucleosomes are relocated to by all of these enzymes. However, a key difference is that the Isw1a, Isw2 and Chd1 enzymes are unable to move nucleosomes to positions closer than 15 bp from a DNA end whereas Isw1b can. We also find that there is a correlation between the inability of enzymes to move nucleosomes close to DNA ends and the preferential binding to nucleosomes bearing linker DNA. These observations suggest that the accessibility of linker DNA together with the positioning properties of the underlying DNA play important roles in determining the outcome of remodelling by these enzymes

Chromosomes and Expression Mechanisms

Introduction Whether one considers a single cell or a multicellular organism, a complex and precisely coordinated series of regulatory events and communications is required to ensure its proper configuration and function. One of the major goals in biology is to understand how cells differentiate into specific types to perform their roles in vivo. Genome sequencing projects have produced enormous amounts of data that are beginning to reveal the blue print of body plans for various organisms. Despite this wealth of new information, we are still far from understanding how cells differentiate. This is, in part, because we are not yet able to fully appreciate how this genetic information is being read by the transcription machineries. It is widely accepted that specific gene expression patterns are responsible for differentiation and maintenance of specific cell types, with mistakes in these regulatory steps often leading to developmental defects and the onset of cancers. Therefore, understanding the mechanisms of transcriptional control is a necessary prerequisite to achieve this major goal in biology. To this end, we need to know more about the substrate of transcription (chromatin), as well as the effectors of transcription (transcription factors). The theme of this issue of Current Opinion in Genetics & Development is the mechanism of transcriptional regulation, with an emphasis on latest topics in this rapidly moving area of research. Because chromatin structure deeply affects transcription at multiple stages, a significant portion of this issue is devoted to the mechanisms related to chromatin regulation