High-throughput assessment of context-dependent effects of chromatin proteins

Background: Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest. The assay combines a previously reported multiplexing strategy based on barcoded randomly integrated reporters with Gal4-mediated tethering. We applied the assay to Drosophila heterochromatin protein 1a (HP1a), which is mo

Equivalence of Nonstatic Two-Pion-Exchange Nucleon-Nucleon Potentials

Off-shell aspects of the one-pion-exchange potential and their relationship to different forms of the nonstatic (subleading-order) chiral two-pion-exchange nucleon-nucleon potential are discussed. Various types of off-shell behavior are categorized and numerous examples are given. Recently derived potentials based on chiral approaches are supplemented by a rather general form of the two-pion-exchange potential derived using old-fashioned methods. The latter is closely related to a general form of one-pion-exchange relativistic corrections and nonstatic two-pion-exchange three-nucleon forces developed long ago.Comment: 16 pages, latex -- Phys. Rev. C (to appear) -- Published versio

Width of Radio-Loud and Radio-Quiet CMEs

In the present paper we report on the difference in angular sizes between radio-loud and radio-quiet CMEs. For this purpose we compiled these two samples of events using Wind/WAVES and SOHO/LASCO observations obtained during 1996-2005. It is shown that the radio-loud CMEs are almost two times wider than the radio-quiet CMEs (considering expanding parts of CMEs). Furthermore we show that the radio-quiet CMEs have a narrow expanding bright part with a large extended diffusive structure. These results were obtained by measuring the CME widths in three different ways.Comment: Solar Physic, in pres

Using the local density approximation and the LYP, BLYP, and B3LYP functionals within Reference--State One--Particle Density--Matrix Theory

For closed-shell systems, the local density approximation (LDA) and the LYP, BLYP, and B3LYP functionals are shown to be compatible with reference-state one-particle density-matrix theory, where this recently introduced formalism is based on Brueckner-orbital theory and an energy functional that includes exact exchange and a non-universal correlation-energy functional. The method is demonstrated to reduce to a density functional theory when the exchange-correlation energy-functional has a simplified form, i.e., its integrand contains only the coordinates of two electron, say r1 and r2, and it has a Dirac delta function -- delta(r1 - r2) -- as a factor. Since Brueckner and Hartree--Fock orbitals are often very similar, any local exchange functional that works well with Hartree--Fock theory is a reasonable approximation with reference-state one-particle density-matrix theory. The LDA approximation is also a reasonable approximation. However, the Colle--Salvetti correlation-energy functional, and the LYP variant, are not ideal for the method, since these are universal functionals. Nevertheless, they appear to provide reasonable approximations. The B3LYP functional is derived using a linear combination of two functionals: One is the BLYP functional; the other uses exact exchange and a correlation-energy functional from the LDA.Comment: 26 Pages, 0 figures, RevTeX 4, Submitted to Mol. Phy

Non-LTE Model Atmospheres for Late-Type Stars II. Restricted NLTE Calculations for a Solar-Like Atmosphere

We test our knowledge of the atomic opacity in the solar UV spectrum. Using the atomic data compiled in Paper I from modern, publicly available, databases, we perform calculations that are confronted with space-based observations of the Sun. At wavelengths longer than about 260 nm, LTE modeling can reproduce quite closely the observed fluxes; uncertainties in the atomic line data account fully for the differences between calculated and observed fluxes. At shorter wavelengths, departures from LTE appear to be important, as our LTE and restricted NLTE calculations differ. Analysis of visible-near infrared Na I and O I lines, two species that produce a negligible absorption in the UV, shows that observed departures from LTE for theses species can be reproduced very accurately with restricted (fixed atmospheric structure) NLTE calculations.Comment: 13 pages, 11 figures, to appear in Ap

Radio-loud CMEs from the disk center lacking shocks at 1 AU

A coronal mass ejection (CME) associated with a type II burst and originating close to the center of the solar disk typically results in a shock at Earth in 2-3 days and hence can be used to predict shock arrival at Earth. However, a significant fraction (about 28%) of such CMEs producing type II bursts were not associated with shocks at Earth. We examined a set of 21 type II bursts observed by the Wind/WAVES experiment at decameter-hectometric (DH) wavelengths that had CME sources very close to the disk center (within a central meridian distance of 30 degrees), but did not have a shock at Earth. We find that the near-Sun speeds of these CMEs average to ~644 km/s, only slightly higher than the average speed of CMEs associated with radio-quiet shocks. However, the fraction of halo CMEs is only ~30%, compared to 54% for the radio-quiet shocks and 91% for all radio-loud shocks. We conclude that the disk-center radio-loud CMEs with no shocks at 1 AU are generally of lower energy and they drive shocks only close to the Sun and dissipate before arriving at Earth. There is also evidence for other possible processes that lead to the lack of shock at 1 AU: (i) overtaking CME shocks merge and one observes a single shock at Earth, and (ii) deflection by nearby coronal holes can push the shocks away from the Sun-Earth line, such that Earth misses these shocks. The probability of observing a shock at 1 AU increases rapidly above 60% when the CME speed exceeds 1000 km/s and when the type II bursts propagate to frequencies below 1 MHz.Comment: 33 pages, 11 figures, 2 table