The effect of extreme confinement on the nonlinear-optical response of quantum wires

This work focuses on understanding the nonlinear-optical response of a 1-D quantum wire embedded in 2-D space when quantum-size effects in the transverse direction are minimized using an extremely weighted delta function potential. Our aim is to establish the fundamental basis for understanding the effect of geometry on the nonlinear-optical response of quantum loops that are formed into a network of quantum wires. Using the concept of leaky quantum wires, it is shown that in the limit of full confinement, the sum rules are obeyed when the transverse infinite-energy continuum states are included. While the continuum states associated with the transverse wavefunction do not contribute to the nonlinear optical response, they are essential to preserving the validity of the sum rules. This work is a building block for future studies of nonlinear-optical enhancement of quantum graphs (which include loops and bent wires) based on their geometry. These properties are important in quantum mechanical modeling of any response function of quantum-confined systems, including the nonlinear-optical response of any system in which there is confinement in at leat one dimension, such as nanowires, which provide confinement in two dimensions

Physical Results from Unphysical Simulations

We calculate various properties of pseudoscalar mesons in partially quenched QCD using chiral perturbation theory through next-to-leading order. Our results can be used to extrapolate to QCD from partially quenched simulations, as long as the latter use three light dynamical quarks. In other words, one can use unphysical simulations to extract physical quantities - in this case the quark masses, meson decay constants, and the Gasser-Leutwyler parameters L_4-L_8. Our proposal for determining L_7 makes explicit use of an unphysical (yet measurable) effect of partially quenched theories, namely the double-pole that appears in certain two-point correlation functions. Most of our calculations are done for sea quarks having up to three different masses, except for our result for L_7, which is derived for degenerate sea quarks.Comment: 26 pages, 12 figures (discussion on discretization errors at end of sec. IV clarified; minor improvements in presentation; results unchanged

Partially quenched chiral perturbation theory without Φ0\Phi_0

This paper completes the argument that lattice simulations of partially quenched QCD can provide quantitative information about QCD itself, with the aid of partially quenched chiral perturbation theory. A barrier to doing this has been the inclusion of $\Phi_0$, the partially quenched generalization of the $\eta'$, in previous calculations in the partially quenched effective theory. This invalidates the low energy perturbative expansion, gives rise to many new unknown parameters, and makes it impossible to reliably calculate the relation between the partially quenched theory and low energy QCD. We show that it is straightforward and natural to formulate partially quenched chiral perturbation theory without $\Phi_0$, and that the resulting theory contains the effective theory for QCD without the $\eta'$. We also show that previous results, obtained including $\Phi_0$, can be reinterpreted as applying to the theory without $\Phi_0$. We contrast the situation with that in the quenched effective theory, where we explain why it is necessary to include $\Phi_0$. We also compare the derivation of chiral perturbation theory in partially quenched QCD with the standard derivation in unquenched QCD. We find that the former cannot be justified as rigorously as the latter, because of the absence of a physical Hilbert space. Finally, we present an encouraging result: unphysical double poles in certain correlation functions in partially quenched chiral perturbation theory can be shown to be a property of the underlying theory, given only the symmetries and some plausible assumptions.Comment: 45 pages, no figure

Simulations with different lattice Dirac operators for valence and sea quarks

We discuss simulations with different lattice Dirac operators for sea and valence quarks. A goal of such a "mixed" action approach is to probe deeper the chiral regime of QCD by enabling simulations with light valence quarks. This is achieved by using chiral fermions as valence quarks while computationally inexpensive fermions are used in the sea sector. Specifically, we consider Wilson sea quarks and Ginsparg-Wilson valence quarks. The local Symanzik action for this mixed theory is derived to O(a), and the appropriate low energy chiral effective Lagrangian is constructed, including the leading O(a) contributions. Using this Lagrangian one can calculate expressions for physical observables and determine the Gasser-Leutwyler coefficients by fitting them to the lattice data.Comment: 17 pages, 1 ps figure (2 clarification paragraphs added

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells. Despite its widespread use, there are considerable differences in how these experiments are conducted, how the results are scored and evaluated for quality, and how the data and metadata are archived for public use. These practices affect the quality and utility of any global ChIP experiment. Through our experience in performing ChIP-seq experiments, the ENCODE and modENCODE consortia have developed a set of working standards and guidelines for ChIP experiments that are updated routinely. The current guidelines address antibody validation, experimental replication, sequencing depth, data and metadata reporting, and data quality assessment. We discuss how ChIP quality, assessed in these ways, affects different uses of ChIP-seq data. All data sets used in the analysis have been deposited for public viewing and downloading at the ENCODE (http://encodeproject.org/ENCODE/) and modENCODE (http://www.modencode.org/) portals

Robustness and Stability of the Gene Regulatory Network Involved in DV Boundary Formation in the Drosophila Wing

Gene regulatory networks have been conserved during evolution. The Drosophila wing and the vertebrate hindbrain share the gene network involved in the establishment of the boundary between dorsal and ventral compartments in the wing and adjacent rhombomeres in the hindbrain. A positive feedback-loop between boundary and non-boundary cells and mediated by the activities of Notch and Wingless/Wnt-1 leads to the establishment of a Notch dependent organizer at the boundary. By means of a Systems Biology approach that combines mathematical modeling and both in silico and in vivo experiments in the Drosophila wing primordium, we modeled and tested this regulatory network and present evidence that a novel property, namely refractoriness to the Wingless signaling molecule, is required in boundary cells for the formation of a stable dorsal-ventral boundary. This new property has been validated in vivo, promotes mutually exclusive domains of Notch and Wingless activities and confers stability to the dorsal-ventral boundary. A robustness analysis of the regulatory network complements our results and ensures its biological plausibility

NNLO Calculation of Two-Nucleon Scattering in EFT for a Two Yukawa Toy Model

The effective field theory (EFT) for a toy model of nucleons interacting via a short range and a long range Yukawa potential is presented. The scattering amplitude in the 1S0 channel is calculated up to NNLO using KSW power counting scheme. A particular expansion of the amplitude about the pole at low (imaginary) momentum is used to derive matching conditions for the EFT couplings. In addition, after imposing constraints from a Renormalization Group analysis, there are no new free parameters in the amplitude at NNLO. Comparing the NNLO phase shifts to the full model we show that the EFT expansion is converging.Comment: 24 pages, 11 EPS figures, revtex; typos in formulae corrected; More typos corrected, expressions in appendix added, minor changes in style, graph Fig3(b) replace

Transcriptional Regulation by CHIP/LDB Complexes

It is increasingly clear that transcription factors play versatile roles in turning genes “on” or “off” depending on cellular context via the various transcription complexes they form. This poses a major challenge in unraveling combinatorial transcription complex codes. Here we use the powerful genetics of Drosophila combined with microarray and bioinformatics analyses to tackle this challenge. The nuclear adaptor CHIP/LDB is a major developmental regulator capable of forming tissue-specific transcription complexes with various types of transcription factors and cofactors, making it a valuable model to study the intricacies of gene regulation. To date only few CHIP/LDB complexes target genes have been identified, and possible tissue-dependent crosstalk between these complexes has not been rigorously explored. SSDP proteins protect CHIP/LDB complexes from proteasome dependent degradation and are rate-limiting cofactors for these complexes. By using mutations in SSDP, we identified 189 down-stream targets of CHIP/LDB and show that these genes are enriched for the binding sites of APTEROUS (AP) and PANNIER (PNR), two well studied transcription factors associated with CHIP/LDB complexes. We performed extensive genetic screens and identified target genes that genetically interact with components of CHIP/LDB complexes in directing the development of the wings (28 genes) and thoracic bristles (23 genes). Moreover, by in vivo RNAi silencing we uncovered novel roles for two of the target genes, xbp1 and Gs-alpha, in early development of these structures. Taken together, our results suggest that loss of SSDP disrupts the normal balance between the CHIP-AP and the CHIP-PNR transcription complexes, resulting in down-regulation of CHIP-AP target genes and the concomitant up-regulation of CHIP-PNR target genes. Understanding the combinatorial nature of transcription complexes as presented here is crucial to the study of transcription regulation of gene batteries required for development

Fungal volatile organic compounds: emphasis on their plant growth-promoting

Fungal volatile organic compounds (VOCs) commonly formed bioactive interface between plants and countless of microorganisms on the above- and below-ground plant-fungus interactions. Fungal-plant interactions symbolize intriguingly biochemical complex and challenging scenarios that are discovered by metabolomic approaches. Remarkably secondary metabolites (SMs) played a significant role in the virulence and existence with plant-fungal pathogen interaction; only 25% of the fungal gene clusters have been functionally identified, even though these numbers are too low as compared with plant secondary metabolites. The current insights on fungal VOCs are conducted under lab environments and to apply small numbers of microbes; its molecules have significant effects on growth, development, and defense system of plants. Many fungal VOCs supported dynamic processes, leading to countless interactions between plants, antagonists, and mutualistic symbionts. The fundamental role of fungal VOCs at field level is required for better understanding, so more studies will offer further constructive scientific evidences that can show the cost-effectiveness of ecofriendly and ecologically produced fungal VOCs for crop welfare