Ab initio many-body calculations of nucleon scattering on 4He, 7Li, 7Be, 12C and 16O

We combine a recently developed ab initio many-body approach capable of describing simultaneously both bound and scattering states, the ab initio NCSM/RGM, with an importance truncation scheme for the cluster eigenstate basis and demostrate its applicability to nuclei with mass numbers as high as 17. Using soft similarity renormalization group evolved chiral nucleon-nucleon interactions, we first calculate nucleon-4He phase shifts, cross sections and analyzing power. Next, we investigate nucleon scattering on 7Li, 7Be, 12C and 16O in coupled-channel NCSM/RGM calculations that include low-lying excited states of these nuclei. We check the convergence of phase shifts with the basis size and study A=8, 13, and 17 bound and unbound states. Our calculations predict low-lying resonances in 8Li and 8B that have not been experimentally clearly identified yet. We are able to reproduce reasonably well the structure of the A=13 low lying states. However, we find that A=17 states cannot be described without an improved treatment of 16O one-particle-one-hole excitations and alpha clustering.Comment: 18 pages, 20 figure

Transcription factor binding site prediction with multivariate gene expression data

Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between genes. During the last few years, regression models have been proposed for the de novo discovery of cis-acting regulatory sequences using gene expression data. However, when applied to multi-sample experiments, existing regression based methods model each individual sample separately. To better capture the dynamic relationships in multi-sample microarray experiments, we propose a flexible method for the joint modeling of promoter sequence and multivariate expression data. In higher order eukaryotic genomes expression regulation usually involves combinatorial interaction between several transcription factors. Experiments have shown that spacing between transcription factor binding sites can significantly affect their strength in activating gene expression. We propose an adaptive model building procedure to capture such spacing dependent cis-acting regulatory modules. We apply our methods to the analysis of microarray time-course experiments in yeast and in Arabidopsis. These experiments exhibit very different dynamic temporal relationships. For both data sets, we have found all of the well-known cis-acting regulatory elements in the related context, as well as being able to predict novel elements.Comment: Published in at http://dx.doi.org/10.1214/10.1214/07-AOAS142 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

4He experiments can serve as a database for determining the three-nucleon force

We report on microscopic calculations for the 4He compound system in the framework of the resonating group model employing realistic nucleon-nucleon and three nucleon forces. The resulting scattering phase shifts are compared to those of a comprehensive R-matrix analysis of all data in this system, which are available in numerical form. The agreement between calculation and analysis is in most cases very good. Adding three-nucleon forces yields in many cases large effects. For a few cases the new agreement is striking. We relate some differencies between calculation and analysis to specific data and discuss neccessary experiments to clarify the situation. From the results we conclude that the data of the 4He system might be well suited to determine the structure of the three-nucleon force.Comment: title changed,note added, format of figures changed, appearance of figures in black-and-white changed, Phys. Rev. C accepte

Trapping and manipulating neutral atoms with electrostatic fields

We report on experiments with cold thermal $^7$Li atoms confined in combined magnetic and electric potentials. A novel type of three-dimensional trap was formed by modulating a magnetic guide using electrostatic fields. We observed atoms trapped in a string of up to six individual such traps, a controlled transport of an atomic cloud over a distance of 400$\mu$m, and a dynamic splitting of a single trap into a double well potential. Applications for quantum information processing are discussed.Comment: 4 pages, 4 figure

Magnetic interactions of cold atoms with anisotropic conductors

We analyze atom-surface magnetic interactions on atom chips where the magnetic trapping potentials are produced by current carrying wires made of electrically anisotropic materials. We discuss a theory for time dependent fluctuations of the magnetic potential, arising from thermal noise originating from the surface. It is shown that using materials with a large electrical anisotropy results in a considerable reduction of heating and decoherence rates of ultra-cold atoms trapped near the surface, of up to several orders of magnitude. The trap loss rate due to spin flips is expected to be significantly reduced upon cooling the surface to low temperatures. In addition, the electrical anisotropy significantly suppresses the amplitude of static spatial potential corrugations due to current scattering within imperfect wires. Also the shape of the corrugation pattern depends on the electrical anisotropy: the preferred angle of the scattered current wave fronts can be varied over a wide range. Materials, fabrication, and experimental issues are discussed, and specific candidate materials are suggested.Comment: Selected as a Highlight paper in the European Physical Journal

Radio-frequency dressed state potentials for neutral atoms

Potentials for atoms can be created by external fields acting on properties like magnetic moment, charge, polarizability, or by oscillating fields which couple internal states. The most prominent realization of the latter is the optical dipole potential formed by coupling ground and electronically excited states of an atom with light. Here we present an experimental investigation of the remarkable properties of potentials derived from radio-frequency (RF) coupling between electronic ground states. The coupling is magnetic and the vector character allows to design state dependent potential landscapes. On atom chips this enables robust coherent atom manipulation on much smaller spatial scales than possible with static fields alone. We find no additional heating or collisional loss up to densities approaching $10^{15}$ atoms / cm$^3$ compared to static magnetic traps. We demonstrate the creation of Bose-Einstein condensates in RF potentials and investigate the difference in the interference between two independently created and two coherently split condensates in identical traps. All together this makes RF dressing a powerful new tool for micro manipulation of atomic and molecular systems

Properties of 8^{8}Be and 12^{12}C deduced from the folding--potential model

The $\alpha$--$\alpha$ differential cross sections are analyzed in the optical model using a double--folded potential. With the knowledge of this potential bound and resonance--state properties of $\alpha$--cluster states in $^{8}$Be and $^{12}$C as well as astrophysical S--factors of $^{4}$He($\alpha$,$\gamma$)$^{8}$Be and $^{8}$Be($\alpha$,$\gamma$)$^{12}$C are calculated. $\Gamma_{\gamma}$--widths and B(E2)--values are deduced.Comment: 2 pages LaTeX, 2 figures can be obtained from the author

A novel compartment, the 'subqpical stem' of the aerial hyphae, is the location of a sigN-dependent, developmentally distinct transcription in Streptomyces coelicolor.

Streptomyces coelicolor has nine SigB-like RNA polymerase sigma factors, several of them implicated in morphological differentiation and/or responses to different stresses. One of the nine, SigN, is the focus of this article. A constructed sigN null mutant was delayed in development and exhibited a bald phenotype when grown on minimal medium containing glucose as carbon source. One of two distinct sigN promoters, sigNP1, was active only during growth on solid medium, when its activation coincided with aerial hyphae formation. Transcription from sigNP1 was readily detected in several whi mutants (interrupted in morphogenesis of aerial mycelium into spores), but was absent from all bld mutants tested, suggesting that sigNP1 activity was restricted to the aerial hyphae. It also depended on sigN, thus sigN was autoregulated. Mutational and transcription studies revealed no functional significance to the location of sigN next to sigF, encoding another SigB-like sigma factor. We identified another potential SigN target, nepA, encoding a putative small secreted protein. Transcription of nepA originated from a single, aerial hyphae-specific and sigN-dependent promoter. While in vitro run-off transcription using purified SigN on the Bacillus subtilis ctc promoter confirmed that SigN is an RNA polymerase sigma factor, SigN failed to initiate transcription from sigNP1 and from the nepA promoter in vitro. Additional in vivo data indicated that further nepA upstream sequences, which are likely to bind a potential activator, are required for successful transcription. Using a nepA–egfp transcriptional fusion we located nepA transcription to a novel compartment, the ‘subapical stem’ of the aerial hyphae. We suggest that this newly recognized compartment defines an interface between the aerial and vegetative parts of the Streptomyces colony and might also be involved in communication between these two compartments

Network approaches for formalizing conceptual models in ecosystem-based management

Funding Intermodel comparisons were supported through funding from the NOAA Integrated Ecosystem Assessment Program. P.S. McDonald’s involvement was funded in part by a grant from Washington Sea Grant, University of Washington, pursuant to National Oceanic and Atmospheric Administration Award number NA14OAR4170078. Funding for RPW was supported by the National Marine Fisheries Service (NMFS)/Sea Grant Population and Ecosystem Dynamics Graduate Fellowship via federal award NA14OAR4170077. Acknowledgements We would like to acknowledge and thank the participants of the NOAA Integrated Ecosystem Assessment Program conceptual network modelling workshop at Baton Rouge, LA in July 2018. The discussions at this meeting formed some of the basis for the ideas presented in this manuscript. We also thank J. Moss and two anonymous reviewers for valuable comments on earlier manuscript drafts. The findings and conclusions in this article are those of the authors and do not necessarily represent the views of the National Marine Fisheries Service, NOAA. Reference to trade names does not imply endorsement by the National Marine Fisheries Service, NOAA. This is NOAA Integrated Ecosystem Assessment Program contribution number 2021_3.Peer reviewedPostprin