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Results for “spectrum analysis”
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Genetic and Structural Analysis of SARS-CoV-2 Spike Protein for Universal Epitope Selection
Evaluation of immunogenic epitopes for universal vaccine development in the face of ongoing SARS-CoV-2 evolution remains a challenge. Herein, we investigate the genetic and structural conservation of an immunogenically relevant epitope (C662–C671) of spike (S) protein across SARS-CoV-2 variants to determine its potential utility as a broad-spectrum vaccine candidate against coronavirus diseases. Comparative sequence analysis, structural assessment, and molecular dynamics simulations of C662–C671 epitope were performed. Mathematical tools were employed to determine its mutational cost. We found that the amino acid sequence of C662–C671 epitope is entirely conserved across the observed major variants of SARS-CoV-2 in addition to SARS-CoV. Its conformation and accessibility are predicted to be conserved, even in the highly mutated Omicron variant. Costly mutational rate in the context of energy expenditure in genome replication and translation can explain this strict conservation. These observations may herald an approach to developing vaccine candidates for universal protection against emergent variants of coronavirus.
Cosmology From CMB Lensing and Delensed EE Power Spectra Using 2019-2020 SPT-3G Polarization Data
From CMB polarization data alone we reconstruct the CMB lensing power spectrum, comparable in overall constraining power to previous temperature-based reconstructions, and an unlensed E -mode power spectrum, with clear detections of the third through tenth acoustic peaks. The observations, taken in 2019 and 2020 with the South Pole Telescope (SPT) and the SPT-3G camera, cover 1500 deg 2 at 95, 150, and 220 GHz with arcminute resolution and roughly 4.9 µ K-arcmin coadded noise in polarization. The power spectrum estimates, together with systematic parameter estimates and a joint covariance matrix, follow from a Bayesian analysis using the Marginal Unbiased Score Expansion (MUSE) method. The E -mode spectrum at ℓ > 2000 and lensing spectrum at L > 350 are the most precise to date. Assuming the ΛCDM model, and using only these SPT data and priors on τ and absolute calibration from Planck, we find H 0 = 66.81 ± 0.81 km/s/Mpc, comparable in precision to the Planck determination and in 5.4 σ tension with the most precise H 0 inference derived via the distance ladder. We also find S 8 ≡ σ 8 (Ω m /0.3) 0.5 = 0.850 ± 0.017, providing further independent evidence of a slight tension with low-redshift structure probes. The ΛCDM model provides a good simultaneous fit to the combined Planck, ACT, and SPT data, and thus passes a powerful test. Combining these CMB datasets with BAO observations, we explore extensions to the ΛCDM model. We find that the effective number of neutrino species, spatial curvature, and primordial helium fraction are consistent with standard model values, and that the 95% confidence upper limit on the neutrino mass sum is 0.075 eV, close to the minimum sum expected from observations of solar and atmospheric neutrino oscillations. The SPT data are consistent with the somewhat weak (< 3 σ ) preference for excess lensing power seen in Planck and ACT data relative to predictions of the ΛCDM model given the combined Planck, ACT, and BAO data sets. Finally, we also detect at greater than 3 σ the influence of non-linear evolution in the CMB lensing power spectrum and discuss it in the context of the S 8 tension. Forthcoming SPT-3G analyses will feature deeper and wider observations in temperature and polarization, providing even tighter constraints and more powerful tests of the ΛCDM model.
Analysis of coherent Thomson scattering from a low temperature plasma
In this work, the spectrum of coherent Thomson scattering (CTS) induced by a periodic ponderomotive perturbation in a low-density low temperature plasma is considered. The analysis is performed for the case when the period of the resulting optical lattice is less than the Debye screening length in the plasma by solving an electron Boltzmann equation, where the total force is the sum of the periodic force due to the optical lattice and the electrostatic force due to self-consistent electric field in the plasma. An analogy between the CTS spectra calculated here and coherent Rayleigh scattering spectra in a neutral gas is established. For relatively low intensity for the optical lattice, the calculated CTS spectra are nearly Gaussian with widths slightly wider than the incoherent Thomson widths. We demonstrate that at higher intensities the line shape narrows and saturates to a width approximately half of that found at low lattice intensities. The proportionality of the spectral width to the square root of the electron temperature allows one to extract the electron temperature from the saturated spectra. Possible application of CTS for remote measuring the electron temperature in plasma is discussed.
Is There Evidence for X-Ray Emitting Plasma Very Close to the Photospheres of O Stars?
Aims. We reexamine the implications of the recent HESS observations of the blazar 1ES0229+200 for constraining the extragalactic mid-infrared background radiation. Methods. We examine the effect of gamma-ray absorption by the extragalactic infrared radiation on predicted intrinsic spectra for this blazar and compare our results with the observational data. Results. We find agreement with our previous results on the shape of the infrared spectral energy distribution, contrary to the recent assertion of the HESS group. Our analysis indicates that 1ES0229+200 has a very hard intrinsic spectrum with a spectral index between 1.1 +/- 0.3 and 1.5 +/- 0.3 in the energy range between approx.0.5 TeV and approx.15 TeV. Conclusions. Under the assumptions that (1) the models of Stecker et al. (2006, ApJ, 648, 774) as derived from numerous detailed infrared observations are reasonable, and (2) spectral indexes in the range 1 < gamma < 1.5 are obtainable from relativistic shock acceleration under the astrophysical conditions extant in blazar flares (Stecker et al. 2007, ApJ, 667, L29), the fits to the observations of 1ES0229+200 using our previous infrared spectral energy distributions are consistent with both the infrared and gamma-ray observations. Our analysis presents evidence indicating that the energy spectrum of relativistic particles in 1ES0229+200 is produced by relativistic shock acceleration, producing an intrinsic -ray spectrum with index 1 < gamma < 1.5 and with no evidence of a peak in the spectral energy distribution up to energies approx.15 TeV.
Planck 2018 results. V. CMB power spectra and likelihoods
We describe the legacy Planck cosmic microwave background (CMB) likelihoods derived from the 2018 data release. The overall approach is similar in spirit to the one retained for the 2013 and 2015 data release, with a hybrid method using different approximations at low ( ℓ < 30) and high ( ℓ ≥ 30) multipoles, implementing several methodological and data-analysis refinements compared to previous releases. With more realistic simulations, and better correction and modelling of systematic effects, we can now make full use of the CMB polarization observed in the High Frequency Instrument (HFI) channels. The low-multipole EE cross-spectra from the 100 GHz and 143 GHz data give a constraint on the ΛCDM reionization optical-depth parameter τ to better than 15% (in combination with the TT low- ℓ data and the high- ℓ temperature and polarization data), tightening constraints on all parameters with posterior distributions correlated with τ . We also update the weaker constraint on τ from the joint TEB likelihood using the Low Frequency Instrument (LFI) channels, which was used in 2015 as part of our baseline analysis. At higher multipoles, the CMB temperature spectrum and likelihood are very similar to previous releases. A better model of the temperature-to-polarization leakage and corrections for the effective calibrations of the polarization channels (i.e., the polarization efficiencies) allow us to make full use of polarization spectra, improving the ΛCDM constraints on the parameters θ MC , ω c , ω b , and H 0 by more than 30%, and n s by more than 20% compared to TT-only constraints. Extensive tests on the robustness of the modelling of the polarization data demonstrate good consistency, with some residual modelling uncertainties. At high multipoles, we are now limited mainly by the accuracy of the polarization efficiency modelling. Using our various tests, simulations, and comparison between different high-multipole likelihood implementations, we estimate the consistency of the results to be better than the 0.5 σ level on the ΛCDM parameters, as well as classical single-parameter extensions for the joint likelihood (to be compared to the 0.3 σ levels we achieved in 2015 for the temperature data alone on ΛCDM only). Minor curiosities already present in the previous releases remain, such as the differences between the best-fit ΛCDM parameters for the ℓ < 800 and ℓ > 800 ranges of the power spectrum, or the preference for more smoothing of the power-spectrum peaks than predicted in ΛCDM fits. These are shown to be driven by the temperature power spectrum and are not significantly modified by the inclusion of the polarization data. Overall, the legacy Planck CMB likelihoods provide a robust tool for constraining the cosmological model and represent a reference for future CMB observations.
Using X-ray spectrum imaging to quantify fission gas in high-burnup UO2 fuel
Analysis of fission gas bubbles (FGBs) in light-water reactor (LWR) fuel is needed to improve the understanding and predictive capability of fuel evolution under normal- and transient conditions. One of the most important parameters of a FGB is the pressure of the gas, primarily Xe, inside it. Bubble volume and location (inter- vs. intragranular) are important considerations as well. However, experimental analysis of such bubbles is challenging due to their small size and embedded nature, and usefulness of the data requires large numbers be analyzed. This paper proposes a method to measure the pressure of Xe bubbles using X-ray spectrum imaging (XSI) in scanning transmission electron microscopy (STEM). From X-ray generation and instrumental parameters, the number of Xe atoms yielding a given number of Xe L-series X-ray counts is estimated, and then from the estimated volume of the bubble the Xe density is estimated, which can then be converted to pressure via an equation-of-state. We apply the method to XSI datasets from high burnup (HBu) fuel from North Anna 1 reactor in as-irradiated and post-LOCA-test conditions and find Xe pressures in the FGBs clustered around 1 GPa.
Improved Upper Limit on Degree-scale CMB B -mode Polarization Power from the 670 Square-degree POLARBEAR Survey
We report an improved measurement of the degree-scale cosmic microwave background B-mode angular-power spectrum over 670 deg 2 sky area at 150 GHz with Polarbear. In the original analysis of the data, errors in the angle measurement of the continuously rotating half-wave plate, a polarization modulator, caused significant data loss. By introducing an angle-correction algorithm, the data volume is increased by a factor of 1.8. We report a new analysis using the larger data set. We find the measured B-mode spectrum is consistent with the ΛCDM model with Galactic dust foregrounds. We estimate the contamination of the foreground by cross-correlating our data and Planck 143, 217, and 353 GHz measurements, where its spectrum is modeled as a power law in angular scale and a modified blackbody in frequency. We place an upper limit on the tensor-to-scalar ratio r < 0.33 at 95% confidence level after marginalizing over the foreground parameters.
A measurement by BOOMERANG of multiple peaks in the angular power spectrum of the cosmic microwave background
This paper presents a measurement of the angular power spectrum of the Cosmic Microwave Background from l = 75 to l = 1025 (~10' to 5 degrees) from a combined analysis of four 150 GHz channels in the BOOMERANG experiment. The spectrum contains multiple peaks and minima, as predicted by standard adiabatic-inflationary models in which the primordial plasma undergoes acoustic oscillations.
Anharmonic exciton dynamics and energy dissipation in liquid water from two-dimensional infrared spectroscopy
Water’s extended hydrogen-bond network results in rich and complex dynamics on the sub-picosecond time scale. In this paper, we present a comprehensive analysis of the two-dimensional infrared (2D IR) spectrum of O–H stretching vibrations in liquid H{sub 2}O and their interactions with bending and intermolecular vibrations. By exploring the dependence of the spectrum on waiting time, temperature, and laser polarization, we refine our molecular picture of water’s complex ultrafast dynamics. The spectral evolution following excitation of the O–H stretching resonance reveals vibrational dynamics on the 50–300 fs time scale that are dominated by intermolecular delocalization. These O–H stretch excitons are a result of the anharmonicity of the nuclear potential energy surface that arises from the hydrogen-bonding interaction. The extent of O–H stretching excitons is characterized through 2D depolarization measurements that show spectrally dependent delocalization in agreement with theoretical predictions. Furthermore, we show that these dynamics are insensitive to temperature, indicating that the exciton dynamics alone set the important time scales in the system. Finally, we study the evolution of the O–H stretching mode, which shows highly non-adiabatic dynamics suggestive of vibrational conical intersections. We argue that the so-called heating, commonly observed within ∼1 ps in nonlinear IR spectroscopy of water, is a nonequilibrium state better described by a kinetic temperature rather than a Boltzmann distribution. Our conclusions imply that the collective nature of water vibrations should be considered in describing aqueous solvation.
A joint analysis of Planck and BICEP2 B modes including dust polarization uncertainty
We analyze BICEP2 and Planck data using a model that includes CMB lensing, gravity waves, and polarized dust. Recently published Planck dust polarization maps have highlighted the difficulty of estimating the amount of dust polarization in low intensity regions, suggesting that the polarization fractions have considerable uncertainties and may be significantly higher than previous predictions. In this paper, we start by assuming nothing about the dust polarization except for the power spectrum shape, which we take to be C{sub l}{sup BB,dust} ∝ l{sup -2.42}. The resulting joint BICEP2+Planck analysis favors solutions without gravity waves, and the upper limit on the tensor-to-scalar ratio is r<0.11, a slight improvement relative to the Planck analysis alone which gives r<0.13 (95% c.l.). The estimated amplitude of the dust polarization power spectrum agrees with expectations for this field based on both HI column density and Planck polarization measurements at 353 GHz in the BICEP2 field. Including the latter constraint on the dust spectrum amplitude in our analysis improves the limit further to r < 0.09, placing strong constraints on theories of inflation (e.g., models with r>0.14 are excluded with 99.5% confidence). We address the cross-correlation analysis of BICEP2 at 150 GHz with BICEP1 at 100 GHz as a test of foreground contamination. We find that the null hypothesis of dust and lensing with 0r= gives Δ χ{sup 2} < 2 relative to the hypothesis of no dust, so the frequency analysis does not strongly favor either model over the other. We also discuss how more accurate dust polarization maps may improve our constraints. If the dust polarization is measured perfectly, the limit can reach r < 0.05 (or the corresponding detection significance if the observed dust signal plus the expected lensing signal is below the BICEP2 observations), but this degrades quickly to almost no improvement if the dust calibration error is 20% or larger or if the dust maps are not processed through the BICEP2 pipeline, inducing sampling variance noise.
Molecular Structure and Crystallization Dynamics of Poly(3-hydroxyl alkanoate) with Medium-Chain Length Biosynthesized from Pseudomonas putida
The molecular structure of poly(3-hydroxyalkanoate) (P3HA) with medium-chain length, biosynthesized from Psuedomonas putida (P. putida), was investigated by thermal analysis, X-ray diffraction, and infrared spectrum. Cultivation in a medium of nonanoic acid and a mixed substrate of nonanoic acid and glycerin as carbon sources provided P3HA with monomer units of 7 and 9 carbons (P3HA{sub n}) and 5, 6, 7, 8, 9, and 10 carbons (P3HA{sub mix}). Since these P3HA has comparatively long side chains, the crystallinity was as low as about 10%. It was suggested that the hydrogen bonding plays an important role in constructing the crystal. The lamellar thickness was 1.20 nm, estimated from the melting temperature depression. This lamellar thickness corresponds to two repeating units. Crystallinity depending on time was observed by the CO stretching mode in the infrared spectrum, and then Avrami’s theory was applied to analyze the crystallization mechanism. The crystallization rate of P3HA{sub n} was very low, on the order of a few hours. An Avrami exponent of 1.45 was estimated from the slope of the Avrami plot. This shows that the conformational arrangement is presumably promoted along the chain axis. The slow crystallization is attributed to the long side chain, which prevents aggregation of the polymer chains.
Au 38 (SPh) 24 : Au 38 Protected with Aromatic Thiolate Ligands
Au38(SR)24 is one of the most extensively investigated gold nanomolecules along with Au25(SR)18 and Au144(SR)60. However, so far it has only been prepared using aliphatic-like ligands, where R = –SC6H13, -SC12H25 and –SCH2CH2Ph. Au38(SCH2CH2Ph)24 when reacted with HSPh undergoes core-size conversion to Au36(SPh)24, and existing literature suggest that Au38(SPh)24 cannot be synthesized. Here, contrary to prevailing knowledge, we demonstrate that Au38(SPh)24 can be prepared if the ligand exchanged conditions are optimized, without any formation of Au36(SPh)24. Conclusive evidence is presented in the form of MALDI-MS, ESI-MS characterization, and optical spectra of Au38(SPh)24 in a solid glass form showing distinct differences from that of Au38(S-aliphatic)24. Theoretical analysis confirms experimental assignment of the optical spectrum and shows that the stability of Au38(SPh)24 is comparable to that of its aliphatic analogues, but results from different physical origins, with a significant component of ligand-ligand attractive interactions.
Heterostructured Au–Ir Catalysts for Enhanced Oxygen Evolution Reaction
Electrochemical water splitting operated under acidic conditions provides a clean approach to generate hydrogen fuels. Currently, the sluggish kinetics of oxygen evolution reaction (OER) at the anode is a bottleneck limiting the acidic water splitting. Here, we report that the OER activity of Ir, one of the most commonly used OER catalysts, can be boosted by forming phase boundaries with Au. Mixed Au and Ir catalysts were synthesized on carbon paper electrodes, which underwent structural evolution under the OER environment to form an Au-Ir interface-rich structure. Compared with Ir catalyst, which requires an overpotential of ~393 mV to achieve a current density of 10 mA/cm 2 in 0.1 M HClO 4 electrolyte, the evolved Au-Ir catalyst shows a lower overpotential at ~351 mV. X-ray photoelectronic spectrum (XPS) study, in conjunction with electrochemical analysis on the surface-site-normalized activity, reveals that the improved OER performance is due to the presence of Au/Ir interfaces in the catalysts. In addition to Ir, the strategy of accelerating OER via Au/Ir interfaces has been further applied to IrCo, IrNi, and IrCu alloy catalysts. Here, with the broad applicability of the strategy demonstrated, this study opens a new route to design OER catalysts for efficient acidic water splitting.
Interpretable machine learning models classify minerals via spectroscopy
Developing methods to identify mineral species confidently and rapidly from Raman spectral analysis is critical to numerous fields. Traditionally, analysis relies on pattern matching the Raman spectrum of an unknown dataset with a supporting library of well-characterized spectral data, which may prove difficult for environmental samples that are poorly crystalline or phase mixtures. Here, we developed interpretable machine learning models that can classify uranium minerals by secondary oxyanion chemistry and other physicochemical properties based solely on Raman spectra. This new ML method produces a mineral profile of physical and chemical properties for an unknown sample and can rapidly classify or identify unknown minerals from Raman data, without the need for an exact pattern match in a spectral library. Training models are validated by 1. Strong correlation of high confidence model regions with published spectroscopic assignments and 2. Correct classification of a mineral not present in training data. Training data are from the Compendium of Uranium Raman and Infrared Experimental Spectra and available crystallographic information files within the open-source Smart Spectral Matching scientific framework. Physically meaningful classifier models can rapidly identify key structural and chemical information about unknown uranium minerals and the overall methodology is broadly applicable for mineral phases.
A reinterpretation of the electronic spectrum of pyrrole: A quantum dynamics study
The first band in the electronic spectrum of pyrrole is calculated from wavepacket propagations performed using the MCTDH method. To do so, two model Hamiltonians are constructed to describe seven low-lying excited electronic states of pyrrole. These Hamiltonians are based on the vibronic coupling model, and are parameterised via fitting to extensive CASPT2 and EOM-CCSD calculations. A detailed analysis of the structure of pyrrole's electronic spectrum in the range 5.5 to 6.5 eV is made. The role of intensity borrowing from transitions to ππ{sup *} states by lower-lying 3s and 3p Rydberg states is assessed, and reassignments of much of the spectrum are subsequently made which indicate that most of the states in the spectrum are predominantly Rydberg in character. The resulting conclusions drawn serve to highlight the limitations of assignments based on the matching of calculated vertical excitation energies and the positions of peak maxima observed in electronic spectra.
Collision induced ultraviolet structure in nitrogen radar REMPI spectra
We present 2 + 2 radar REMPI measurements in molecular nitrogen under atmospheric conditions and observe a strong interference in the (1,0) vibrational band of the a{sup 1}Π{sub g} ← X{sup 1}Σ{sub g}{sup +} electronic manifold. The interference is suppressed by using circularly polarized light, permitting rotational analysis of the 2 + 2 radar REMPI spectrum. It is observed in pure nitrogen, though the structure varies with gas composition. The structure also varies with temperature and pressure. These results indicate that it is collision induced. We hypothesize that the source of the interference is a 3 + 1 REMPI process through the a{sup ″1}Σ{sub g}{sup +} electronic state.