971 resultados para Arc adjacency operator


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"27 November 1963."

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"30 November 1960."

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Arc repressor mutants containing from three to 15 multiple-alanine substitutions have spectral properties expected for native Arc proteins, form heterodimers with wild-type Arc, denature cooperatively with Tms equal to or greater than wild type, and, in some cases, fold as much as 30-fold faster and unfold as much as 50-fold slower than wild type. Two of the mutants, containing a total of 14 different substitutions, also footprint operator DNA in vitro. The stability of some of the proteins with multiple-alanine mutations is significantly greater than that predicted from the sum of the single substitutions, suggesting that a subset of the wild-type residues in Arc may interact in an unfavorable fashion. Overall, these results show that almost half of the residues in Arc can be replaced by alanine en masse without compromising the ability of this small, homodimeric protein to fold into a stable, native-like structure.

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Mnt, a tetrameric repressor encoded by bacteriophage P22, uses N-domain dimers to contact each half of its operator site. Experiments with a double mutant and structural homology with the P22 Arc repressor suggest that contacts made by Arg-28 and stabilized by Glu-33 are largely responsible for dimer–dimer cooperativity in Mnt. These dimer–dimer contacts are energetically more important for operator binding than solution tetramerization, which is mediated by an independent C-terminal coiled-coil domain. Indeed, once one dimer of the Mnt tetramer contacts an operator half site, binding of the second dimer occurs with an effective concentration much lower than that expected if both dimers were flexibly tethered. These results suggest that binding of the second dimer introduces some strain into the protein–DNA complex, a mechanism that could serve to limit the affinity of operator binding and to prevent strong binding of the Mnt tetramer to nonoperator sites.

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In studies of variants of the P(ant) promoter of bacteriophage P22, the Arc protein was found not only to slow the rate at which RNA polymerase forms open complexes but also to accelerate the rate at which the enzyme clears the promoter. These dual activities permit Arc, bound at a single operator subsite, to act as an activator or as a repressor of different promoter variants. For example, Arc activates a P(ant) variant for which promoter clearance is rate limiting in the presence and absence of Arc but represses a closely related variant for which open-complex formation becomes rate limiting in the presence of Arc. The acceleration of promoter clearance by Arc requires occupancy of the operator subsite proximal to the -35 region and is diminished when Arc bears a mutation in Arg-23, a residue that makes a DNA-backbone contact in the operator complex.

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We apply techniques of zeta functions and regularized products theory to study the zeta determinant of a class of abstract operators with compact resolvent, and in particular the relation with other spectral functions.

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Shallow subsurface layers of gold nanoclusters were formed in polymethylmethacrylate (PMMA) polymer by very low energy (49 eV) gold ion implantation. The ion implantation process was modeled by computer simulation and accurately predicted the layer depth and width. Transmission electron microscopy (TEM) was used to image the buried layer and individual nanoclusters; the layer width was similar to 6-8 nm and the cluster diameter was similar to 5-6 nm. Surface plasmon resonance (SPR) absorption effects were observed by UV-visible spectroscopy. The TEM and SPR results were related to prior measurements of electrical conductivity of Au-doped PMMA, and excellent consistency was found with a model of electrical conductivity in which either at low implantation dose the individual nanoclusters are separated and do not physically touch each other, or at higher implantation dose the nanoclusters touch each other to form a random resistor network (percolation model). (C) 2009 American Vacuum Society. [DOI: 10.1116/1.3231449]

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In the case of quantum wells, the indium segregation leads to complex potential profiles that are hardly considered in the majority of the theoretical models. The authors demonstrated that the split-operator method is useful tool for obtaining the electronic properties in these cases. Particularly, they studied the influence of the indium surface segregation in optical properties of InGaAs/GaAs quantum wells. Photoluminescence measurements were carried out for a set of InGaAs/GaAs quantum wells and compared to the results obtained theoretically via split-operator method, showing a good agreement.

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In this paper, we estimate the losses during teleportation processes requiring either two high-Q cavities or a single bimodal cavity. The estimates were carried out using the phenomenological operator approach introduced by de Almeida et al. [Phys. Rev. A 62, 033815 (2000)].

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Estimates of greenhouse-gas emissions from deforestation are highly uncertain because of high variability in key parameters and because of the limited number of studies providing field measurements of these parameters. One such parameter is burning efficiency, which determines how much of the original forest`s aboveground carbon stock will be released in the burn, as well as how much will later be released by decay and how much will remain as charcoal. In this paper we examined the fate of biomass from a semideciduous tropical forest in the ""arc of deforestation,"" where clearing activity is concentrated along the southern edge of the Amazon forest. We estimated carbon content, charcoal formation and burning efficiency by direct measurements (cutting and weighing) and by line-intersect sampling (LIS) done along the axis of each plot before and after burning of felled vegetation. The total aboveground dry biomass found here (219.3 Mg ha(-1)) is lower than the values found in studies that have been done in other parts of the Amazon region. Values for burning efficiency (65%) and charcoal formation (6.0%, or 5.98 Mg C ha(-1)) were much higher than those found in past studies in tropical areas. The percentage of trunk biomass lost in burning (49%) was substantially higher than has been found in previous studies. This difference may be explained by the concentration of more stems in the smaller diameter classes and the low humidity of the fuel (the dry season was unusually long in 2007, the year of the burn). This study provides the first measurements of forest burning parameters for a group of forest types that is now undergoing rapid deforestation. The burning parameters estimated here indicate substantially higher burning efficiency than has been found in other Amazonian forest types. Quantification of burning efficiency is critical to estimates of trace-gas emissions from deforestation. (C) 2009 Elsevier B.V. All rights reserved.

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This work presents a non-linear boundary element formulation applied to analysis of contact problems. The boundary element method (BEM) is known as a robust and accurate numerical technique to handle this type of problem, because the contact among the solids occurs along their boundaries. The proposed non-linear formulation is based on the use of singular or hyper-singular integral equations by BEM, for multi-region contact. When the contact occurs between crack surfaces, the formulation adopted is the dual version of BEM, in which singular and hyper-singular integral equations are defined along the opposite sides of the contact boundaries. The structural non-linear behaviour on the contact is considered using Coulomb`s friction law. The non-linear formulation is based on the tangent operator in which one uses the derivate of the set of algebraic equations to construct the corrections for the non-linear process. This implicit formulation has shown accurate as the classical approach, however, it is faster to compute the solution. Examples of simple and multi-region contact problems are shown to illustrate the applicability of the proposed scheme. (C) 2011 Elsevier Ltd. All rights reserved.