Long-Range Excitation of Collective Modes in Mesoscopic Metal Clusters

We develop a semiclassical theory for the long range excitation of plasmon resonances in atomic clusters, based on the doorway hypothesis. The effect of the width of the plasmon resonance is fully taken into account. As an application we study plasmon excitation in small Sodium clusters, in collisions with electrons and protons.Comment: 18 pages, 4 figure

Sum Rules and Spin-Dependent Polarizabilities of the Deuteron in Effective Field Theory

We construct sum rules for the forward vector and tensor polarizabilities for any spin-$S$ target and apply them to the spin-1 deuteron. We calculate these polarizabilities of the deuteron to the next-to-leading order in the pionless effective field theory.Comment: 10 pages, figures include

The Polarizability of the Deuteron

The scalar and tensor polarizabilities of the deuteron are calculated using the recently developed effective field theory that describes nucleon-nucleon interactions. Leading and next-to-leading order contributions in the perturbative expansion predict a scalar electric polarizability of 0.595 fm^3. The tensor electric polarizability receives contributions starting at next-to-leading order from the exchange of a single potential pion and is found to be -0.062 fm^3. We compute the leading contributions to the scalar and tensor magnetic polarizabilities, finding 0.067 fm^3 and 0.195 fm^3, respectively.Comment: 13 pages, 4 figures as 6 eps files, latex. References adde

Nucleon-Nucleon Effective Field Theory Without Pions

Nuclear processes involving momenta much below the mass of the pion may be described by an effective field theory in which the pions do not appear as explicit degrees of freedom. The effects of the pion and all other virtual hadrons are reproduced by the coefficients of gauge-invariant local operators involving the nucleon field. Nucleon-nucleon scattering phase shift data constrains many of the coefficients that appear in the effective Lagrangean but at some order in the expansion coefficients enter that must be constrained by other observables. We compute several observables in the two-nucleon sector up to next-to-next-to leading order in the effective field theory without pions, or to the order at which a counterterm involving four-nucleon field operators is encountered. Effective range theory is recovered from the effective field theory up to the order where relativistic corrections enter or where four-nucleon-external current local operators arise. For the deuteron magnetic moment, quadrupole moment and the $np\to d\gamma$ radiative capture cross section a four-nucleon-one-photon counterterm exists at next-to-leading order. The electric polarizability and electric charge form factor of the deuteron are determined up to next-to-next-to-leading order, which includes the first appearance of relativistic corrections.Comment: 27 pages, 8 figures, latex. SD-mixing, quadrupole moment modifie

ChIP-chip versus ChIP-seq: Lessons for experimental design and data analysis

<p>Abstract</p> <p>Background</p> <p>Chromatin immunoprecipitation (ChIP) followed by microarray hybridization (ChIP-chip) or high-throughput sequencing (ChIP-seq) allows genome-wide discovery of protein-DNA interactions such as transcription factor bindings and histone modifications. Previous reports only compared a small number of profiles, and little has been done to compare histone modification profiles generated by the two technologies or to assess the impact of input DNA libraries in ChIP-seq analysis. Here, we performed a systematic analysis of a modENCODE dataset consisting of 31 pairs of ChIP-chip/ChIP-seq profiles of the coactivator CBP, RNA polymerase II (RNA PolII), and six histone modifications across four developmental stages of <it>Drosophila melanogaster</it>.</p> <p>Results</p> <p>Both technologies produce highly reproducible profiles within each platform, ChIP-seq generally produces profiles with a better signal-to-noise ratio, and allows detection of more peaks and narrower peaks. The set of peaks identified by the two technologies can be significantly different, but the extent to which they differ varies depending on the factor and the analysis algorithm. Importantly, we found that there is a significant variation among multiple sequencing profiles of input DNA libraries and that this variation most likely arises from both differences in experimental condition and sequencing depth. We further show that using an inappropriate input DNA profile can impact the average signal profiles around genomic features and peak calling results, highlighting the importance of having high quality input DNA data for normalization in ChIP-seq analysis.</p> <p>Conclusions</p> <p>Our findings highlight the biases present in each of the platforms, show the variability that can arise from both technology and analysis methods, and emphasize the importance of obtaining high quality and deeply sequenced input DNA libraries for ChIP-seq analysis.</p