1,812 research outputs found

    Mining residue contacts in proteins using local structure predictions

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    Josephson effect test for triplet pairing symmetry

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    The critical current modulation and the spontaneous flux of the vortex states in corner Josephson junctions between Sr2_2RuO4_4 and a conventional s-wave superconductor are calculated as a function of the crystal orientation, and the magnetic field. For Sr2_2RuO4_4 we assume two nodeless p-wave pairing states. Also we use the nodal ff-wave states B1g×EuB_{1g}\times E_u and B2g×EuB_{2g} \times E_u, and one special p-wave state having line nodes. It is seen that the critical current depends solely on the topology of the gap.Comment: 22 pages, 12 figure

    Okazaki fragment maturation in yeast: II. Cooperation between the polymerase and 3′-5′-exonuclease activities of Pol δ in the creation of a ligatable nick

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    To address the different functions of Pol δ and FEN1 (Rad27) in Okazaki fragment maturation, exonuclease-deficient polymerase Pol δ-01 and Pol δ-5DV (corresponding to alleles pol3–01-(D321A, E323A) and pol3–5DV-(D520V), respectively) were purified and characterized in this process. In the presence of the replication clamp PCNA, both wild-type and exo− Pol δ carried out strand displacement synthesis with similar rates; however, initiation of strand displacement synthesis was much more efficient with Pol δ-exo−. When Pol δ-exo− encountered a downstream primer, it paused with 3–5 nucleotides of the primer displaced, whereas the wild type carried out precise gap filling. Consequently, in the absence of FEN1, Pol δ exonuclease activity was essential for closure of simple gaps by DNA ligase. Compared with wild type, Okazaki fragment maturation with Pol δ-exo−proceeded with an increased duration of nick translation prior to ligation. Maturation was efficient in the absence of Dna2 and required Dna2 only when FEN1 activity was compromised. In agreement with these results, the proposed generation of double strand breaks inpol3-exo − rad27 mutants was suppressed by the overexpression of DNA2. Further genetic studies showed that pol3-exo − rad27 double mutants were sensitive to alkylation damage consistent with an in vivo defect in gap filling by exonuclease-deficient Pol δ

    Ideal Gases in Time-Dependent Traps

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    We investigate theoretically the properties of an ideal trapped gas in a time-dependent harmonic potential. Using a scaling formalism, we are able to present simple analytical results for two important classes of experiments: free expansion of the gas upon release of the trap; and the response of the gas to a harmonic modulation of the trapping potential is investigated. We present specific results relevant to current experiments on trapped Fermions.Comment: 5 pages, 3 eps figure

    Antiferromagnetic Domains and Superconductivity in UPt3

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    We explore the response of an unconventional superconductor to spatially inhomogeneous antiferromagnetism (SIAFM). Symmetry allows the superconducting order parameter in the E-representation models for UPt3 to couple directly to the AFM order parameter. The Ginzburg-Landau equations for coupled superconductivity and SIAFM are solved numerically for two possible SIAFM configurations: (I) abutting antiferromagnetic domains of uniform size, and (II) quenched random disorder of `nanodomains' in a uniform AFM background. We discuss the contributions to the free energy, specific heat, and order parameter for these models. Neither model provides a satisfactory account of experiment, but results from the two models differ significantly. Our results demonstrate that the response of an E_{2u} superconductor to SIAFM is strongly dependent on the spatial dependence of AFM order; no conclusion can be drawn regarding the compatibility of E_{2u} superconductivity with UPt3 that is independent of assumptions on the spatial dependence of AFMComment: 12 pages, 13 figures, to appear in Phys. Rev.

    A Dual Geometry of the Hadron in Dense Matter

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    We identify the dual geometry of the hadron phase of dense nuclear matter and investigate the confinement/deconfinement phase transition. We suggest that the low temperature phase of the RN black hole with the full backreaction of the bulk gauge field is described by the zero mass limit of the RN black hole with hard wall. We calculated the density dependence of critical temperature and found that the phase diagram closes. We also study the density dependence of the rho meson mass.Comment: 16 pages, 4 figures, typos corrected, references adde

    Extracellular Vesicles as Drug Carriers for Enzyme Replacement Therapy to Treat CLN2 Batten Disease: Optimization of Drug Administration Routes

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    CLN2 Batten disease (BD) is one of a broad class of lysosomal storage disorders that is characterized by the deficiency of lysosomal enzyme, TPP1, resulting in a build-up of toxic intracellular storage material in all organs and subsequent damage. A major challenge for BD therapeutics is delivery of enzymatically active TPP1 to the brain to attenuate progressive loss of neurological functions. To accomplish this daunting task, we propose the harnessing of naturally occurring nanoparticles, extracellular vesicles (EVs). Herein, we incorporated TPP1 into EVs released by immune cells, macrophages, and examined biodistribution and therapeutic efficacy of EV-TPP1 in BD mouse model, using various routes of administration. Administration through intrathecal and intranasal routes resulted in high TPP1 accumulation in the brain, decreased neurodegeneration and neuroinflammation, and reduced aggregation of lysosomal storage material in BD mouse model, CLN2 knock-out mice. Parenteral intravenous and intraperitoneal administrations led to TPP1 delivery to peripheral organs: liver, kidney, spleen, and lungs. A combination of intrathecal and intraperitoneal EV-TPP1 injections significantly prolonged lifespan in BD mice. Overall, the optimization of treatment strategies is crucial for successful applications of EVs-based therapeutics for BD

    On the sample size dependence of the critical current density in MgB2_2 superconductors

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    Sample size dependent critical current density has been observed in magnesium diboride superconductors. At high fields, larger samples provide higher critical current densities, while at low fields, larger samples give rise to lower critical current densities. The explanation for this surprising result is proposed in this study based on the electric field generated in the superconductors. The dependence of the current density on the sample size has been derived as a power law jR1/nj\propto R^{1/n} (nn is the nn factor characterizing EjE-j curve E=Ec(j/jc)nE=E_c(j/j_c)^n). This dependence provides one with a new method to derive the nn factor and can also be used to determine the dependence of the activation energy on the current density.Comment: Revtex, 4 pages, 5 figure

    X-ray standing wave and reflectometric characterization of multilayer structures

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    Microstructural characterization of synthetic periodic multilayers by x-ray standing waves have been presented. It has been shown that the analysis of multilayers by combined x-ray reflectometry (XRR) and x-ray standing wave (XSW) techniques can overcome the deficiencies of the individual techniques in microstructural analysis. While interface roughnesses are more accurately determined by the XRR technique, layer composition is more accurately determined by the XSW technique where an element is directly identified by its characteristic emission. These aspects have been explained with an example of a 20 period Pt/C multilayer. The composition of the C-layers due to Pt dissolution in the C-layers, Ptx_{x}C1x_{1-x}, has been determined by the XSW technique. In the XSW analysis when the whole amount of Pt present in the C-layers is assumed to be within the broadened interface, it l eads to larger interface roughness values, inconsistent with those determined by the XRR technique. Constraining the interface roughness values to those determined by the XRR technique, requires an additional amount of dissolved Pt in the C-layers to expl ain the Pt fluorescence yield excited by the standing wave field. This analysis provides the average composition Ptx_{x}C1x_{1-x} of the C-layers .Comment: 12 pages RevTex, 10 eps figures embedde

    Loop effects and non-decoupling property of SUSY QCD in gbtHg b\to tH^{-}

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    One-loop SUSY QCD radiative correction to gbtHgb \to tH^{-} cross section is calculated in the Minimal Supersymmetric Standard Model. We found that SUSY QCD is non-decoupling if the gluino mass and the parameter μ\mu, AtA_t or AbA_b are at the same order and get large. The non-decoupling contribution can be enhanced by large tanβ\tan\beta and therefore large corrections to the hadronic production rates at the Tevatron and LHC are expected in the large tanβ\tan\beta limit. The fundamental reason for such non-decoupling behavior is found to be some couplings in the loops being proportional to SUSY mass parameters.Comment: 15 pages, 5 PS figures. A proof of non-decouplings of SUSY-QCD, Comments on corresponding QCD correction and references adde
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