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Calculations of inflaton decays and reheating: with applications to no-scale inflation models
We discuss inflaton decays and reheating in no-scale Starobinsky-like models of inflation, calculating the effective equation-of-state parameter, w, during the epoch of inflaton decay, the reheating temperature, T{sub reh}, and the number of inflationary e-folds, N{sub ∗}, comparing analytical approximations with numerical calculations. We then illustrate these results with applications to models based on no-scale supergravity and motivated by generic string compactifications, including scenarios where the inflaton is identified as an untwisted-sector matter field with direct Yukawa couplings to MSSM fields, and where the inflaton decays via gravitational-strength interactions. Finally, we use our results to discuss the constraints on these models imposed by present measurements of the scalar spectral index n{sub s} and the tensor-to-scalar perturbation ratio r, converting them into constraints on N{sub ∗}, the inflaton decay rate and other parameters of specific no-scale inflationary models.
PIXiE: an algorithm for automated ion mobility arrival time extraction and collision cross section calculation using global data association
Abstract Motivation Drift tube ion mobility spectrometry coupled with mass spectrometry (DTIMS-MS) is increasingly implemented in high throughput omics workflows, and new informatics approaches are necessary for processing the associated data. To automatically extract arrival times for molecules measured by DTIMS at multiple electric fields and compute their associated collisional cross sections (CCS), we created the PNNL Ion Mobility Cross Section Extractor (PIXiE). The primary application presented for this algorithm is the extraction of data that can then be used to create a reference library of experimental CCS values for use in high throughput omics analyses. Results We demonstrate the utility of this approach by automatically extracting arrival times and calculating the associated CCSs for a set of endogenous metabolites and xenobiotics. The PIXiE-generated CCS values were within error of those calculated using commercially available instrument vendor software. Availability and implementation PIXiE is an open-source tool, freely available on Github. The documentation, source code of the software, and a GUI can be found at https://github.com/PNNL-Comp-Mass-Spec/PIXiE and the source code of the backend workflow library used by PIXiE can be found at https://github.com/PNNL-Comp-Mass-Spec/IMS-Informed-Library. Supplementary information Supplementary data are available at Bioinformatics online.
Electronic Structure and Optical Properties of Cu 2 ZnGeSe 4 . First-Principles Calculations and Vacuum-Ultraviolet Spectroscopic Ellipsometric Studies
Cu 2 ZnGeSe 4 is of interest for the development of next-generation thin-film photovoltaic technologies. To understand its electronic structure and related fundamental optical properties, we perform first-principles calculations for three structural variations: kesterite, stannite, and primitive-mixed CuAu phases. The calculated data are compared with the room-temperature dielectric functionϵ=ϵ1+iϵ2 spectrum of polycrystalline Cu 2 ZnGeSe 4 determined by vacuum-ultraviolet spectroscopic ellipsometry in the photon-energy range of 0.7 to 9.0 eV. Ellipsometric data are modeled with the sum of eight Tauc-Lorentz oscillators, and the best-fit model yields the band-gap and Tauc-gap energies of 1.25 and 1.19 eV, respectively. A comparison of overall peak shapes and relative intensities between experimental spectra and the calculated ϵ data for three structural variations suggests that the sample may not have a pure (ordered) kesterite phase. We found that the complex refractive index N=n+ik, normal-incidence reflectivity R, and absorption coefficients α are calculated from the modeled ϵ spectrum, which are also compared with those of Cu 2 ZnSnSe 4 . The spectral features for Cu 2 ZnGeSe 4 appear to be weaker and broader than those for Cu 2 ZnSnSe 4 , which is possibly due to more structural imperfections presented in Cu 2 ZnGeSe 4 than Cu 2 ZnSnSe 4 .
Electromagnetic response of C 12 : A first-principles calculation
Here, the longitudinal and transverse electromagnetic response functions of $^{12}$C are computed in a ``first-principles'' Green's function Monte Carlo calculation, based on realistic two- and three-nucleon interactions and associated one- and two-body currents. We find excellent agreement between theory and experiment and, in particular, no evidence for the quenching of measured versus calculated longitudinal response. This is further corroborated by a re-analysis of the Coulomb sum rule, in which the contributions from the low-lying $J^\pi\,$=$\, 2^+$, $0^+$ (Hoyle), and $4^+$ states in $^{12}$C are accounted for explicitly in evaluating the total inelastic strength.
Use of radial symmetry for the calculation of cylindrical absorption coefficients and optimal capillary loadings
The problem of numerically evaluating absorption correction factors for cylindrical samples has been revisited using a treatment that fully takes advantage of the sample symmetry. It is shown that the path lengths for all points within the sample at all possible diffraction angles can be trivially determined once the angle-dependent distance distribution for a single line of points is calculated. This provides advantages in both computational efficiency and in gaining an intuitive understanding of the effects of absorption on diffraction data. A matrix of absorption coefficients calculated for µR products between 0 and 20 for diffraction angles θ D of 0° to 90° were used to examine the influence of (1) capillary diameter and of (2) sample density on the overall scattered intensity as a function of diffraction angle, where µ is the linear absorption coefficient for the sample and R is the capillary radius. Based on this analysis, the optimal sample loading for a capillary experiment to maximize diffraction at angles of 0 – 50° is in general expected to be achieved when the maximum radius capillary compatible with the beam is used, and when the sample density is adjusted to be 3/(4µR) of its original density.
PhotochemCAD 3: Diverse Modules for Photophysical Calculations with Multiple Spectral Databases
Not provided.
An MS-CASPT2 Calculation of the Excited Electronic States of an Axial Difluoroborondipyrromethene (BODIPY) Dimer
The previously reported (Duman et al., J. Org. Chem. 2012, 77, 4516) calculated state energies of monomeric difluoroborondipyrromethene (BODIPY) and its axial dimer would suggest that these dyes are promising candidates for singlet fission, and the dimer was computed to have an unusual low-lying doubly excited state. We find that these results were affected by the use of an imbalanced active space in multireference calculations and are not correct. Multistate complete-active-space second-order perturbation theory (MS-CASPT2/cc-pVDZ) calculations using an [8,8] (8 electrons in 8 orbitals) active space for the monomer and a [16,16] active space for the dimer reproduce quite well the observed excitation energies of the S 1 states of both, and yield T 1 excitation energies well in excess of half of the S 1 excitation energies. We conclude that neither BODIPY monomer nor its axial dimer would permit exothermic singlet fission and are not worthy of investigation as potentially useful candidates, and that the unusual low-energy doubly excited states of the dimer were artifacts.
Anisotropic lattice thermal expansion of PbFeBO{sub 4}: A study by X-ray and neutron diffraction, Raman spectroscopy and DFT calculations
Highlights: • Mullite-type PbFeBO{sub 4} shows uni-axial negative coefficient of thermal expansion. • Anisotropic thermal expansion of the metric parameters was modeled using modified Grüneisen approximation. • The model includes harmonic, quasi-harmonic and intrinsic anharmonic contributions to the internal energy. • DFT calculation, temperature- and pressure-dependent Raman spectra help understand the phonon decay and associated anharmonicity. - Abstract: The lattice thermal expansion of mullite-type PbFeBO{sub 4} is presented in this study. The thermal expansion coefficients of the metric parameters were obtained from composite data collected from temperature-dependent neutron and X-ray powder diffraction between 10 K and 700 K. The volume thermal expansion was modeled using extended Grüneisen first-order approximation to the zero-pressure equation of state. The additive frame of the model includes harmonic, quasi-harmonic and intrinsic anharmonic potentials to describe the change of the internal energy as a function of temperature. The unit-cell volume at zero-pressure and 0 K was optimized during the DFT simulations. Harmonic frequencies of the optical Raman modes at the Γ-point of the Brillouin zone at 0 K were also calculated by DFT, which help to assign and crosscheck the experimental frequencies. The low-temperature Raman spectra showed significant anomaly in the antiferromagnetic regions, leading to softening or hardening of some phonons. Selected modes were analyzed using a modified Klemens model. The shift of the frequencies and the broadening of the line-widths helped to understand the anharmonic vibrational behaviors of the PbO{sub 4}, FeO{sub 6} and BO{sub 3} polyhedra as a function of temperature.
Investigation of Structural Evolution of Li 1.1 V 3 O 8 by In Situ X-ray Diffraction and Density Functional Theory Calculations
Li 1.1 V 3 O 8 is a promising cathode material for Li-ion batteries, because of its high theoretical capacity (362 mAh g-1) and good rate performance. In this study, the structural evolution of Li 1.1 V 3 O 8 material during electrochemical dis(charge) processes was investigated using a combination of theoretical calculations and experimental data. Density functional theory (DFT) was used to predict the intermediate structures at various lithiation states, as well as the stability of major phases. In order to validate these predictions, in situ X-ray diffraction (XRD) data was collected operando, allowing for the phase transformations to be monitored under current load and eliminating the possibilities of structural relaxation processes and environmental oxidation. Rietveld refinement was performed to fit the diffraction data with the DFT-derived structures and to analyze the fractions of major phases as a function of dis(charge). The DFT calculations identified three stable states that were validated by the in situ XRD result: a Li-poor α-phase (Li1), a Li-rich α-phase (Li2.5), and a β-phase (Li4). The DFT-predicted particle shape based on the surface energy of the (100), (001), and (010) planes rationalized the preferential orientation of Li 1.1 V 3 O 8 particles along the [010] direction in the electrode. Furthermore, the onset and offset of the α → β transition, as well as the phase fractions of α and β determined via in situ XRD, related well with the DFT-derived relative stability of each phase. Thus, by integrating DFT calculations with experimental work, this work provides a thorough understanding of the structural transformations in Li 1.1 V 3 O 8 during electrochemical dis(charge).
A Practical Approach to Wave Function Propagation, Hopping Probabilities, and Time Steps in Surface Hopping Calculations
We compare several established approaches for propagating wave functions and calculating hopping probabilities within the fewest switches surface hopping (FSSH) algorithm for difficult cases with many electronic states and many trivial crossings. If only a single time step (Δt c ) is employed, we find that no published approach can accurately capture the dynamics correctly unless Δt c → 0 (which is not computationally feasible). If multiple time steps are employed, for a fixed classical time step (Δt c ), a robust scheme can be found for dynamically choosing quantum time steps (δt q1 and δt q2 ) and calculating hopping probabilities so that one can systematically reduce all errors and achieve maximally efficient accuracy; scattering calculations confirm that one can choose a fairly large classical time step. Furthermore, the robust scheme presented here uses both the “local diabatic” and adiabatic interpolation and thus borrows elements from both the Granucci/Persico and Meek/Levine algorithms. Our findings should be broadly applicable in the future.
Large Scale GW Calculations
We present GW calculations of molecules, ordered and disordered solids and interfaces, which employ an efficient contour deformation technique for frequency integration and do not require the explicit evaluation of virtual electronic states nor the inversion of dielectric matrices. We also present a parallel implementation of the algorithm which takes advantage of separable expressions of both the single particle Green's function and the screened Coulomb interaction. The method can be used starting from density functional theory calculations performed with semilocal or hybrid functionals. We applied the newly developed technique to GW calculations of systems of unprecedented size, including water/semiconductor interfaces with thousands of electrons.
Alkaline earth ion exchange study in pure silica LTA zeolites using periodic first-principles calculations
Experiments show that Zeolites, such as Linde Type A (LTA), are promising materials for radioactive decontamination processes. In this work, the thermodynamic properties associated with alkaline earth ion (Ca2+, Sr2+ and Ba2+) exchange in pure silica LTA was studied using periodic first-principles calculations. The adsorption energies of alkaline earth ions compared with that of Na+ were investigated. The driving force for the alkaline earth exchange and related isotherms were calculated, and analyzed as a function of the electron chemical potential. The results demonstrate that Na+ in a pure silica LTA can completely be removed by Ba2+ and almost completely be removed by Sr2+ from a stream, but cannot be effectively exchanged by Ca2+. We also showed that electron-donating dopants should suppress the Sr2+ and Ba2+ ion exchange, and that there is a substantial preference for incorporating Ba2+ over Sr2+. Lastly, the substantial difference between the adsorption energies of the ions in an assumed vacuum and those computed in water suggests that a solvation model is needed for accurate representation of ion adsorption in an LTA zeolite.
Accurate quantum dynamics calculations of vibrational spectrum of dideuteromethane CH{sub 2}D{sub 2}
We report a rigorous variational study of the infrared (IR) vibrational spectra of both CH{sub 2}D{sub 2} and {sup 13}CH{sub 2}D{sub 2} isotopomers using an exact molecular Hamiltonian. Calculations are carried out using a recently developed multi-layer Lanczos algorithm based on the accurate refined Wang and Carrington potential energy surface of methane and the low-order truncated ab initio dipole moment surface of Yurchenko et al. [J. Mol. Spectrosc. 291, 69 (2013)]. All well converged 357 vibrational energy levels up to 6100 cm{sup −1} of CH{sub 2}D{sub 2} are obtained, together with a comparison to previous calculations and 91 experimental bands available. The calculated frequencies are in excellent agreement with the experimental results and give a root-mean-square error of 0.67 cm{sup −1}. In particular, we also compute the transition intensities from the vibrational ground state for both isotopomers. Based on the theoretical results, 20 experimental bands are suggested to be re-assigned. Surprisingly, an anomalous C isotopic effect is discovered in the nν{sub 5} modes of CH{sub 2}D{sub 2}. The predicted IR spectra provide useful information for understanding those unknown bands.
Enhancing the accuracy of XPS calculations: Exploring hybrid basis set schemes for CVS-EOMIP-CCSD calculations
Reliable computational methodologies and basis sets for modeling x-ray spectra are essential for extracting and interpreting electronic and structural information from experimental x-ray spectra. In particular, the trade-off between numerical accuracy and computational cost due to the size of the basis set is a major challenge, since molecular orbitals undergo extreme relaxation in the core-hole state. To gain clarity on the changes in electronic structure induced by the formation of a core-hole, the use of sufficiently flexible basis for expanding the orbitals, particularly for the core region, has been shown to be essential. This work focuses on the refinement of core-hole ionized state calculations using the equation-of-motion coupled cluster family of methods through an extensive analysis on the effectiveness of “hybrid” and mixed basis sets. In this investigation, we utilize the CVS-EOMIP-CCSD method in combination and construct hybrid basis sets piecewise from readily available Dunning’s correlation consistent basis sets in order to calculate x-ray ionization energies (IEs) for a set of small gas phase molecules. Our results provide insights into the impact of basis sets on the CVS-EOMIP-CCSD calculations of K-edge IEs of first-row p-block elements. Furthermore, these insights enable us to understand more about the basis set dependence of the core IEs computed and allow us to establish a protocol for deriving reliable and cost-effective theoretical estimates for computing IEs of small molecules containing such elements.