An Improved Q-value Measurement Technique
Frequency measurements with Q-value technique accounting for surface resistance of resonator
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Unique genetic signatures in HIV-1 subtype A1 and A1D recombinant envelope glycoprotein distinguish contemporary transmitted/founder viruses from historical strains in East Africa
Introduction: The envelope glycoprotein (Env) of HIV-1 Transmitted/Founder (T/F) viruses in subtypes B and C carries distinct genetic signatures that enhance transmission fitness, augment infectivity and immune evasion. However, there is limited data on such signatures in T/F subtypes A1, D and A1D recombinants that predominate East Africa’s HIV epidemic.Methods: We used phylogenetically corrected approaches to detect distinct genetic signatures by comparing 44 contemporary HIV-1 T/F Envs with 229 historical Envs of the same subtype in East Africa.Results and Discussion: Subtype analysis based on the full-length Env gene of contemporary T/F viruses revealed a high proportion of subtype A1, followed by A1D recombinants, and fewer subtype D. Signature analysis revealed that the contemporary subtype A1 T/Fs were more likely to select distinct amino acids, including M22 in the signal peptide, R82 in gp120, A172 in the V2 loop, E230 in the glycosite 230, K275 in the D loop, Y317 in the V3 loop, K476 and N477 in the CD4 contact site, when compared with the historical Envs (q-value < 0.2). Conversely, the contemporary subtype A1 T/F Envs were less likely to carry the amino acids Q432 in the CD4 contact site, and the L784 signature within the LLP-2 (q-value < 0.2). The A1D recombinant T/Fs were more likely to select the D620 in the C-helix, but under selected the L34 in gp120, P299 in the V3 loop and Y643 in the Heptad repeat-2, compared to the historical Envs (q-value < 0.2). The distinct signature sites reported in this study may contribute to the successful establishment of acute infection as well as the persistence of long-term infection. Therefore, effective therapeutics and vaccines may target these distinct amino acid signatures especially for the East African region as it may be necessary to employ subtype-specific vaccines according to the subtype distribution.
59 BASIC BIOLOGICAL SCIENCES↗
Insights from multinucleon transfer reactions in 206 Pb+ 118 Sn
Multinucleon transfer reactions for the 206 Pb + 118 Sn system were measured at E lab = 1200 MeV using the PRISMA large solid-angle magnetic spectrometer. The experiment was conducted at laboratory angles around the grazing angle, covering an angular range of approximately 20°. The resulting differential and total cross sections, along with Q-value distributions for various neutron and proton pick-up and stripping channels, are presented. The Q-value distributions suggest a transition from quasi-elastic to deep inelastic collision processes, particularly in channels involving nucleon transfers. The experimental results have been compared with GRAZING code calculations, showing good agreement for few-nucleon transfer channels, while channels with large nucleon transfers are underestimated, indicating the involvement of more complex processes.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
CHARMM-GUI Bicelle Builder : An Extension of Membrane Builder for Modeling and Simulation of Bicelle Systems
Membrane mimetics, such as detergent micelles, nanodiscs, and amphipol complexes, which can provide membrane-like environments while retaining small and soluble features, have been utilized to study membrane proteins. A bicelle, composed of varying lipids and detergents, is a useful membrane mimetic because the lipid-to-detergent ratio, the q-value, can be adjusted to alter the properties of the aggregate, including the thickness and size of the bicelle. However, building a bicelle model for modeling and simulation studies requires nontrivial efforts, even for experts. We introduce CHARMM-GUI Bicelle Builder, a web-based platform that can generate various all-atom bicelle systems via a graphical user interface with all available lipids and detergents in Membrane Builder. To illustrate and validate Bicelle Builder with practical systems, we have modeled and simulated pure bicelles consisting of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids with 1,2-dihexanoyl-sn-glycero-3-phosphocholine (C6DHPC) detergents and protein–bicelle complexes, composed of DMPC with C6DHPC, foscholine-10 (FOS10), and lysophosphatidylcholine-12 (LPC12) detergents. Our simulation results indicate that Bicelle Builder can generate reliable and robust bicelle models with and without proteins that retain DMPC bilayer characteristics. Bicelle Builder is expected to help researchers better understand not only bicelles themselves but also atomistic-level structures of protein–bicelle complexes that are often difficult to access through experimental approaches.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Sensitivity of the CUPID experiment to $0\nu \beta \beta$ decay of 100 Mo
CUPID is a next-generation bolometric experiment to search for neutrinoless double-beta decay ($0\nu \beta \beta$ ) of 100 Mo using Li 2 MoO 4 scintillating crystals. It will operate 1596 crystals at ~10 mK in the CUORE cryostat at the Laboratori Nazionali del Gran Sasso in Italy. Each crystal will be facing two Ge-based bolometric light detectors for α rejection. We compute the discovery and the exclusion sensitivity of CUPID to $0\nu \beta \beta$ in a Frequentist and a Bayesian framework. This computation is done numerically based on pseudo-experiments. For the CUPID baseline scenario, with a background and an energy resolution of 1.0 x 10 –4 counts/keV/kg/yr and 5 keV FWHM at the Q-value, respectively, this results in a Bayesian exclusion sensitivity (90% c.i.) of $\hat{T}_{1/2} > 1.6 \times 10^{27} \ \textrm{yr}$, corresponding to the effective Majorana neutrino mass of $\hat{m}_{\beta \beta } < \ 9.6$ – 28 meV. The Frequentist discovery sensitivity (3σ ) is $\hat{T}_{1/2}= 1.0 \times 10^{27} \ \textrm{yr}$, corresponding to $\hat{m}_{\beta \beta }= \ 12$ – 36 meV.
Alfonso, K. [Virginia Polytechnic Institute and St↗
Evolutionary problems of Cepheids and other giants investigated with new radiative opacities
Comparison of evolutionary tracks, pulsation constants, and linearized pulsational-stability coefficients for stellar models applicable to the problems of classical Cepheids, whose structures were calculated using the Cox-Stewart (1965) opacities and a recently computed set of opacities. The latter are based on the hot 'Thomas-Fermi' statistical model of the atom for all elements heavier than hydrogen and helium; they contain larger helium and metals contributions, but a smaller hydrogen contribution than the former ones for the same chemical composition. The difference in metals contribution affects mainly the location and shape of the evolutionary tracks on the H-R diagram, while the difference in hydrogen and helium contributions has its greatest effect on the pulsational properties of the Cepheid models. From the comparison of evolutionary tracks it is concluded that: (1) the theoretical M/L relation for evolved giants is changed very little by using the second set of opacities; (2) Q-values for the fundamental mode of radial pulsation in Cepheid envelope models increase if the second set is used, but the classical mass discrepancy remains; and (3) the second set leads to pulsational-instability.
Carson, T. R.↗
Internal friction and velocity measurements
The Q of a lunar basalt sample was measured under varying vacuum conditions, and it was found that even at pressures as low as 10 to the -7th to 10 to the -10th torr, substantial increases in Q with decreasing pressure are observed, while the resonant frequency increases only slightly. This suggests that only small amounts of volatiles are sufficient to increase the internal friction (lower the Q) dramatically. The technique of vibrating encapsulated samples in the torsional mode was used to measure Q of terrestrial rocks as a function of hydrostatic pressure under lunar vacuum conditions. Young's modulus measurements in the temperature range 25-600 C under a variety of conditions including high vacuum show no evidence of any irreversibility upon temperature cycling and no indication that the high Q-values obtained are associated with any permanent structure changes such as the formation of lossless 'welded' contacts.
Tittmann, B. R.↗
Realizable feed-element patterns and optimum aperture efficiency in multibeam antenna systems
The results of an earlier paper by Rahmat-Samii et al. (1981), regarding realizable patterns from feed elements that are part of an array that feeds a reflector antenna, are extended. The earlier paper used a cos exp q theta model for the element radiation pattern, whereas here a parametric study is performed, using a model that assumes a central beam of cos exp q theta shape, with a constant sidelobe level outside the central beam. Realizable q-values are constrained by the maximum directivity based on feed element area. The optimum aperture efficiency (excluding array feed network losses) in an array-reflector system is evaluated as a function of element spacing using this model as well as the model of the earlier paper. Experimental data for tapered slot antenna (TSA) arrays are in agreement with the conclusions based on the model.
Yngvesson, K. S.↗
Sequentially evaporated thin film YBa2Cu3O(7-x) superconducting microwave ring resonator
There is great interest in the application of thin film high temperature superconductors in high frequency electronic circuits. A ring resonator provides a good test vehicle for assessing the microwave losses in the superconductor and for comparing films made by different techniques. Ring resonators made of YBa2Cu3O(7-x) have been investigated on LaAlO3 substrates. The superconducting thin films were deposited by sequential electron beam evaporation of Cu, Y, and BaF2 with a post anneal. Patterning of the superconducting film was done using negative photolithography. A ring resonator was also fabricated from a thin gold film as a control. Both resonators had a gold ground plane on the backside of the substrate. The ring resonators' reflection coefficients were measured as a function of frequency from 33 to 37 GHz at temperatures ranging from 20 K to 68 K. The resonator exhibited two resonances which were at 34.5 and 35.7 GHz at 68 K. The resonant frequencies increased with decreasing temperature. The magnitude of the reflection coefficients was in the calculation of the unloaded Q-values. The performance of the evaporated and gold resonator are compared with the performance of a laser ablated YBa2Cu3O(7-x) resonator. The causes of the double resonance are discussed.
Rohrer, Norman J.↗
Microwave characterization of high-temperature superconducting thin films using stripline resonators
A method was derived for the extraction of the surface resistivity (Rs) of high-Tc superconducting (HTS) thin films at microwave frequencies, using a stripline resonator circuit. Surface resistivity values were calculated by measuring the difference in Q-values of a stripline resonator configuration when an HTS thin film was substituted for one of the metallic ground planes. Cryogenic tests were completed for several stripline resonator structures, yielding accurate predictions of the HTS thin-film performance at frequencies between 3 and 26 GHz (in harmonics of approximately 3 GHz). These results were then used to illustrate the dependence of HTS surface resistivity on frequency and temperature in the microwave frequency band.
Macdonald, Alan D.↗
Measurement and analysis of a microwave oscillator stabilized by a sapphire dielectric ring resonator for ultra-low noise
Phase-noise measurements are presented for a microwave oscillator whose frequency is stabilized by a whispering-gallery sapphire ring resonator with Q of 200,000. This mode involves little metallic conduction and allows nearly full use of the very low dielectric loss in sapphire. Several mode families have been identified, in good agreement with frequency calculations. For a 5-cm wheel resonator in a 7.6-cm container, Q values above 100,000 were found at room temperature for all of the modes in this sequence. Coupling Q-values for these same modes ranged from 10,000 (n = 5) to 100,000 (n = 10) for a WR112 waveguide port at the center of the cylinder wall of the containing can. Phase noise measurements for a transistor oscillator locked to the n = 10 (7.84-GHz) mode showed a 1/f cubed dependence for low offset frequencies, and a value of L(f) = -55 dB/Hz at an offset of 10 Hz from the carrier.
Dick, G. John↗
Nonaxisymmetric evolution in protostellar disks
We present a two-dimensional, multigridded hydrodynamical simulation of the collapse of an axisymmetric, rotating, 1 solar mass protostellar cloud, which forms a resolved, hydrotastic disk. The code includes the effects of physical viscosity, radiative transfer and radiative acceleration but not magnetic fields. We examine how the disk is affected by the inclusion of turbulent viscosity by comparing a viscous simulation with an inviscid model evolved from the same initial conditions, and we derive a disk evolutionary timescale on the order of 300,000 years if alpha = 0.01. Effects arising from non-axisymmetric gravitational instabilities in the protostellar disk are followed with a three-dimensional SPH code, starting from the two-dimensional structure. We find that the disk is prone to a series of spiral instabilities with primary azimulthal mode number m = 1 and m = 2. The torques induced by these nonaxisymmetric structures elicit material transport of angular momentum and mass through the disk, readjusting the surface density profile toward more stable configurations. We present a series of analyses which characterize both the development and the likely source of the instabilities. We speculate that an evolving disk which maintains a minimum Toomre Q-value approximately 1.4 will have a total evolutionary span of several times 10(exp 5) years, comparable to, but somewhat shorter than the evolutionary timescale resulting from viscous turbulence alone. We compare the evolution resulting from nonaxisymmetric instabilities with solutions of a one-dimensional viscous diffusion equation applied to the initial surface density and temperature profile. We find that an effective alpha-value of 0.03 is a good fit to the results of the simulation. However, the effective alpha will depend on the minimum Q in the disk at the time the instability is activated. We argue that the major fraction of the transport characterized by the value of alpha is due to the action of gravitational torques, and does not arise from inherent viscosity within the smoothed particle hydrodynamics method.
Laughlin, Gregory↗
High Power Intermodulation Measurements up to 30 W of High Temperature Superconducting Filters
We have demonstrated a high power intermodulation measurement set-up capable of delivering 30 W in each of two fundamental tones. For closely spaced frequencies (less than 35 MHz), the dynamic range of the measurement is limited by the nonlinear performance of the mixer in the front end of the HP71210C spectrum analyzer. A tunable TE(sub 011) mode copper cavity was fabricated in which one of the endwalls could be adjusted shifting its resonant frequency between 5.7 and 6.6 GHz. Since the Q-value of this cavity is high, greater than 10(exp 4), and its bandwidth is small, less than 1 MHz, it can be used to attenuate the two fundamental tones relative to one of the harmonic tones, which greatly enhances the dynamic range of the measurement. This set-up can be used to measure the two-tone intermodulation distortion of any passive microwave device, e.g. a HTS filter, a connector, a cable, etc., over a frequency range of 5.9 to 6.4 GHz and a power range of 0.1 to 30 W. The third order intercept (TOI) of a prototype HTS filter measured at powers up to 30 W was +81.3 dBm.
Wilker, Charles↗
Application of Powder Diffraction Methods to the Analysis of the Atomic Structure of Nanocrystals: The Concept of the Apparent Lattice Parameter (ALP)
The applicability of standard methods of elaboration of powder diffraction data for determination of the structure of nano-size crystallites is analysed. Based on our theoretical calculations of powder diffraction data we show, that the assumption of the infinite crystal lattice for nanocrystals smaller than 20 nm in size is not justified. Application of conventional tools developed for elaboration of powder diffraction data, like the Rietveld method, may lead to erroneous interpretation of the experimental results. An alternate evaluation of diffraction data of nanoparticles, based on the so-called 'apparent lattice parameter' (alp) is introduced. We assume a model of nanocrystal having a grain core with well-defined crystal structure, surrounded by a surface shell with the atomic structure similar to that of the core but being under a strain (compressive or tensile). The two structural components, the core and the shell, form essentially a composite crystal with interfering, inseparable diffraction properties. Because the structure of such a nanocrystal is not uniform, it defies the basic definitions of an unambiguous crystallographic phase. Consequently, a set of lattice parameters used for characterization of simple crystal phases is insufficient for a proper description of the complex structure of nanocrystals. We developed a method of evaluation of powder diffraction data of nanocrystals, which refers to a core-shell model and is based on the 'apparent lattice parameter' methodology. For a given diffraction pattem, the alp values are calculated for every individual Bragg reflection. For nanocrystals the alp values depend on the diffraction vector Q. By modeling different a0tomic structures of nanocrystals and calculating theoretically corresponding diffraction patterns using the Debye functions we showed, that alp-Q plots show characteristic shapes which can be used for evaluation of the atomic structure of the core-shell system. We show, that using a simple model of a nanocrystal with spherical shape and centro-symmetric strain at the surface shell we obtain theoretical alp-Q values which match very well the alp-Q plots determined experimentally for Sic, GaN, and diamond nanopowders. The theoretical models are defined by the lattice parameter of the grain core, thickness of the surface shell, and the magnitude and distribution of the strain field in the surface shell. According to our calculations, the part of the diffraction pattern measured at relatively low diffraction vectors Q (below 10/angstrom) provides information on the surface strain, whle determination of the lattice parameters in the grain core requires measurements at large Q-values (above 15 - 20/angstrom).
Palosz, B.↗
Effect of the Chemical State of the Surface on the Relaxation of the Surface Shell Atoms in SiC and GaN Nanocrystals
The effect of the chemical state of the surface of nanoparticles on the relaxation in the near-surface layer was examined using the concept of the apparent lattice parameter (alp) determined for different diffraction vectors Q. The apparent lattice parameter is a lattice parameter determined either from an individual Bragg reflection, or from a selected region of the diffraction pattern. At low diffraction vectors the Bragg peak positions are affected mainly by the structure of the near-surface layer, while at high Q-values only the interior of the nano-grain contributes to the diffraction pattern. Following the measurements on raw (as prepared) powders we investigated powders cleaned by annealing at 400C under vacuum, and the same powders wetted with water. Theoretical alp-Q plots showed that the structure of the surface layer depends on the sample treatment. Semi-quantitative analysis based on the comparison of the experimental and theoretical alp-Q plots was performed. Theoretical alp-Q relations were obtained from the diffraction patterns calculated for models of nanocrystals with a strained surface layer using the Debye functions.
Palosz, B.↗
Carbon Nanofiber-Based, High-Frequency, High-Q, Miniaturized Mechanical Resonators
High Q resonators are a critical component of stable, low-noise communication systems, radar, and precise timing applications such as atomic clocks. In electronic resonators based on Si integrated circuits, resistive losses increase as a result of the continued reduction in device dimensions, which decreases their Q values. On the other hand, due to the mechanical construct of bulk acoustic wave (BAW) and surface acoustic wave (SAW) resonators, such loss mechanisms are absent, enabling higher Q-values for both BAW and SAW resonators compared to their electronic counterparts. The other advantages of mechanical resonators are their inherently higher radiation tolerance, a factor that makes them attractive for NASA s extreme environment planetary missions, for example to the Jovian environments where the radiation doses are at hostile levels. Despite these advantages, both BAW and SAW resonators suffer from low resonant frequencies and they are also physically large, which precludes their integration into miniaturized electronic systems. Because there is a need to move the resonant frequency of oscillators to the order of gigahertz, new technologies and materials are being investigated that will make performance at those frequencies attainable. By moving to nanoscale structures, in this case vertically oriented, cantilevered carbon nanotubes (CNTs), that have larger aspect ratios (length/thickness) and extremely high elastic moduli, it is possible to overcome the two disadvantages of both bulk acoustic wave (BAW) and surface acoustic wave (SAW) resonators. Nano-electro-mechanical systems (NEMS) that utilize high aspect ratio nanomaterials exhibiting high elastic moduli (e.g., carbon-based nanomaterials) benefit from high Qs, operate at high frequency, and have small force constants that translate to high responsivity that results in improved sensitivity, lower power consumption, and im - proved tunablity. NEMS resonators have recently been demonstrated using topdown, lithographically fabricated ap - proaches to form cantilever or bridgetype structures. Top-down approaches, however, rely on complicated and expensive e-beam lithography, and often require a release mechanism. Reso - nance effects in structures synthesized using bottom-up approaches have also recently been reported based on carbon nanotubes, but such approaches have relied on a planar two-dimensional (2D) geometry. In this innovation, vertically aligned tubes synthesized using a bottom- up approach have been considered, where the vertical orientation of the tubes has the potential to increase integration density even further. The simulation of a vertically oriented, cantilevered carbon nanotube was performed using COMSOL Multi - physics, a finite element simulation package. All simulations were performed in a 2D geometry that provided consistent results and minimized computational complexity. The simulations assumed a vertically oriented, cantilevered nanotube of uniform density (1.5 g/cu cm). An elastic modulus was assumed to be 600 GPa, relative permittivity of the nanotube was assumed to be 5.0, and Poisson s ratio was assumed to be 0.2. It should be noted that the relative permittivity and Poisson s ratio for the nanotubes of interest are not known accurately. However, as in previous simulations, the relative permittivity and Poisson s ratios were treated as weak variables in the simulation, and no significant changes were recognized when these variables were varied.
Kaul, Anupama B.↗
Development of Metallic Magnetic Calorimeters for High Precision Measurements of Calorimetric Re-187 and Ho-163 Spectra
The measurement of calorimetric spectra following atomic weak decays, beta (b) and electron capture (EC), of nuclides having a very low Q-value, can provide an impressively high sensitivity to a non-vanishing neutrino mass. The achievable sensitivity in this kind of experiments is directly connected to the performance of the used detectors. In particular an energy resolution of a few eV and a pulse formation time well below 1 microsecond are required. Low temperature Metallic Magnetic Calorimeters (MMCs) for soft X-rays have already shown an energy resolution of 2.0 eV FWHM and a pulse rise-time of about 90 ns for fully micro-fabricated detectors. We present the use of MMCs for high precision measurements of calorimetric spectra following the beta-decay of Re-187 and the EC of Ho-163. We show results obtained with detectors optimized for Re-187 and for Ho-163 experiments respectively. While the detectors equipped with superconducting Re absorbers have not yet reached the aimed performance, a first detector prototype with a Au absorber having implanted Ho-163 ions already shows excellent results. An energy resolution of 12 eV FWHM and a rise time of 90 ns were measured.
Ranitzsch, P. C.-O.↗
Radiation Quality Effects on Transcriptome Profiles in 3-d Cultures After Particle Irradiation
In this work, we evaluate the differential effects of low- and high-LET radiation on 3-D organotypic cultures in order to investigate radiation quality impacts on gene expression and cellular responses. Reducing uncertainties in current risk models requires new knowledge on the fundamental differences in biological responses (the so-called radiation quality effects) triggered by heavy ion particle radiation versus low-LET radiation associated with Earth-based exposures. We are utilizing novel 3-D organotypic human tissue models that provide a format for study of human cells within a realistic tissue framework, thereby bridging the gap between 2-D monolayer culture and animal models for risk extrapolation to humans. To identify biological pathway signatures unique to heavy ion particle exposure, functional gene set enrichment analysis (GSEA) was used with whole transcriptome profiling. GSEA has been used extensively as a method to garner biological information in a variety of model systems but has not been commonly used to analyze radiation effects. It is a powerful approach for assessing the functional significance of radiation quality-dependent changes from datasets where the changes are subtle but broad, and where single gene based analysis using rankings of fold-change may not reveal important biological information. We identified 45 statistically significant gene sets at 0.05 q-value cutoff, including 14 gene sets common to gamma and titanium irradiation, 19 gene sets specific to gamma irradiation, and 12 titanium-specific gene sets. Common gene sets largely align with DNA damage, cell cycle, early immune response, and inflammatory cytokine pathway activation. The top gene set enriched for the gamma- and titanium-irradiated samples involved KRAS pathway activation and genes activated in TNF-treated cells, respectively. Another difference noted for the high-LET samples was an apparent enrichment in gene sets involved in cycle cycle/mitotic control. It is plausible that the enrichment in these particular pathways results from the complex DNA damage resulting from high-LET exposure where repair processes are not completed during the same time scale as the less complex damage resulting from low-LET radiation.
Patel, Z. S.↗