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MARVEL Hazards Evaluation evaluated the impacts of MARVEL operations, hazards, and postulated accidents. The hazard evaluation of MARVEL events and associated operations was performed for selection and evaluation of safety classification of systems, structures, and components (SSCs) and SSC safety functions, and for selection of design basis accidents (DBAs) applicable to the MARVEL microreactor design.
Biological organisms are complex systems that are composed of functional networks of interacting molecules and macro-molecules. Complex phenotypes are the result of orchestrated, hierarchical, heterogeneous collections of expressed genomic variants. However, the effects of these variants are the result of historic selective pressure and current environmental and epigenetic signals, and, as such, their co-occurrence can be seen as genome-wide correlations in a number of different manners. Biomass recalcitrance (i.e., the resistance of plants to degradation or deconstruction, which ultimately enables access to a plant's sugars) is a complex polygenic phenotype of high importance to biofuels initiatives. This study makes use of data derived from the re-sequenced genomes from over 800 different Populus trichocarpa genotypes in combination with metabolomic and pyMBMS data across this population, as well as co-expression and co-methylation networks in order to better understand the molecular interactions involved in recalcitrance, and identify target genes involved in lignin biosynthesis/degradation. A Lines Of Evidence (LOE) scoring system is developed to integrate the information in the different layers and quantify the number of lines of evidence linking genes to target functions. This new scoring system was applied to quantify the lines of evidence linking genes to lignin-related genes and phenotypes across the network layers, and allowed for the generation of new hypotheses surrounding potential new candidate genes involved in lignin biosynthesis in P. trichocarpa, including various AGAMOUS-LIKE genes. Lastly, the resulting Genome Wide Association Study networks, integrated with Single Nucleotide Polymorphism (SNP) correlation, co-methylation, and co-expression networks through the LOE scores are proving to be a powerful approach to determine the pleiotropic and epistatic relationships underlying cellular functions and, as such, the molecular basis for complex phenotypes, such as recalcitrance.
Several mesoporous silica nanoparticle (MSN) contrast agents have been synthesized using a co-condensation method to incorporate two different Gd 3+ complexes at very high loadings (15.5–28.8 wt %). These MSN contrast agents, with an MCM-41 type pore structure, were characterized using a variety of methods including SEM and TEM, nitrogen adsorption measurements, thermogravimetric analysis (TGA), direct current plasma (DCP) spectroscopy, and powder X-ray diffraction (PXRD). The magnetic resonance (MR) relaxivities of these contrast agents were determined using a 3 T MR scanner. The $r_1$ relaxivities of these nanoparticles range from 4.1 to 8.4 mM –1 s –1 on a per Gd basis. Additionally, the MSN particles were functionalized with an organic fluorophore and cancer cell targeting peptide to allow for demonstration of both the optical and MR contrast enhancing capabilities in vitro.
A sufficiently large temperature anisotropy can sometimes drive various types of electromagnetic plasma micro-instabilities, which can play an important role in the dynamics of relativistic pair plasmas in space, astrophysics, and laboratory environments. Here, we provide a detailed description of the cyclotron instability of parallel propagating electromagnetic waves in relativistic pair plasmas on the basis of a relativistic anisotropic distribution function. Using plasma kinetic theory and particle-in-cell simulations, we study the influence of the relativistic temperature and the temperature anisotropy on the collective and noncollective modes of these plasmas. Growth rates and dispersion curves from the linear theory show a good agreement with simulations results.
We provide a holistic view of galaxy evolution at high redshifts z ≳ 4, which incorporates the constraints from various astrophysical/cosmological probes, including the estimate of the cosmic star formation rate (SFR) density from UV/IR surveys and long gamma-ray burst (GRBs) rates, the cosmic reionization history following the latest Planck measurements, and the missing satellites issue. We achieve this goal in a model-independent way by exploiting the SFR functions derived by Mancuso et al. on the basis of an educated extrapolation of the latest UV/far-IR data from HST / Herschel , and already tested against a number of independent observables. Our SFR functions integrated down to a UV magnitude limit M {sub UV} ≲ −13 (or SFR limit around 10{sup −2} M {sub ⊙} yr{sup −1}) produce a cosmic SFR density in excellent agreement with recent determinations from IR surveys and, taking into account a metallicity ceiling Z ≲ Z {sub ⊙}/2, with the estimates from long GRB rates. They also yield a cosmic reionization history consistent with that implied by the recent measurements of the Planck mission of the electron scattering optical depth τ {sub es} ≈ 0.058; remarkably, this result is obtained under a conceivable assumption regarding the average value f {sub esc} ≈ 0.1 of the escape fraction for ionizing photons. We demonstrate via the abundance-matching technique that the above constraints concurrently imply galaxy formation becoming inefficient within dark matter halos of mass below a few 10{sup 8} M {sub ⊙}; pleasingly, such a limit is also required so as not to run into the missing satellites issue. Finally, we predict a downturn of the Galaxy luminosity function faintward of M {sub UV} ≲ −12, and stress that its detailed shape, to be plausibly probed in the near future by the JWST , will be extremely informative on the astrophysics of galaxy formation in small halos, or even on the microscopic nature of the dark matter.
We introduce a framework, based on the expansion of the distribution function on a Hermite- Laguerre polynomial basis, to study the effects of collisions on magnetized plasma instabilities at arbitrary mean-free path. Focusing on the drift-wave instability, we show that our framework allows retrieving established collisional and collisionless limits. At the intermediate collisionalities relevant for present and future magnetic nuclear fusion devices, deviations with respect to collision operators used in state-of-the-art turbulence simulation codes show the need for retaining the full Coulomb operator in order to obtain both the correct instability growth rate and eigenmode spectrum, with potentially important implications to the understanding of plasma turbulence. The exponential convergence of the spectral representation that we propose makes the representation of the velocity space dependence, including the full collision operator, optimally efficient.
We present a novel approach for solving steady-state stochastic partial differential equations in high-dimensional random parameter space. The proposed approach combines spatial domain decomposition with basis adaptation for each subdomain. The basis adaptation is used to address the curse of dimensionality by constructing an accurate low-dimensional representation of the stochastic PDE solution (probability density function and/or its leading statistical moments) in each subdomain. Restricting the basis adaptation to a specific subdomain affords finding a locally accurate solution. Then, the solutions from all of the subdomains are stitched together to provide a global solution. We support our construction with numerical experiments for a steady-state diffusion equation with a random spatially dependent coefficient. Our results show that accurate global solutions can be obtained with significantly reduced computational costs.
Energies from the GW approximation and the Bethe–Salpeter equation (BSE) are benchmarked against the excitation energies of transition-metal (Cu, Zn, Ag, and Cd) single atoms and monoxide anions. We demonstrate that best estimates of GW quasiparticle energies at the complete basis set limit should be obtained via extrapolation or closure relations, while numerically converged GW -BSE eigenvalues can be obtained on a finite basis set. Calculations using real-space wave functions and pseudopotentials are shown to give best-estimate GW energies that agree (up to the extrapolation error) with calculations using all-electron Gaussian basis sets. We benchmark the effects of a vertex approximation (ΓLDA) and the mean-field starting point in GW and the BSE, performing computations using a real-space, transition-space basis and scalar-relativistic pseudopotentials. Here, while no variant of GW improves on perturbative G 0 W 0 at predicting ionization energies, G 0 W 0 Γ LDA -BSE computations give excellent agreement with experimental absorption spectra as long as off-diagonal self-energy terms are included. We also present G 0 W 0 quasiparticle energies for the CuO – , ZnO – , AgO – , and CdO – anions, in comparison to available anion photoelectron spectra.
On the basis of the self-consistent theory of finite Fermi systems, the energies of alphadecay chains were calculated for several new superheavy nuclei discovered recently in experiments of the Dubna-Livermore Collaboration headed by Yu.Ts. Oganessian. The approach in question is implemented on the basis of the generalized method of the density functional proposed by Fayans and his coauthors. The version used here relies on the functional DF3-a proposed recently for describing a wide array of nuclear data, including data on superheavy nuclei. A detailed comparison of the results obtained on this basis with the predictions of different approaches, including the self-consistent Skyrme-Hartree-Fock method, the micro-macro method in the version developed by Sobiczewski and his coauthors, and the phenomenological method of Liran and his coauthors, is performed. The resulting alpha-decay energies are used to calculate respective lifetimes with the aid of the phenomenological Parkhomenko-Sobiczewski formula.
We present a formally exact van der Waals inclusive electronic structure theory, called FDE-vdW, based on the Frozen Density Embedding formulation of subsystem Density-Functional Theory. In subsystem DFT, the energy functional is composed of subsystem additive and non-additive terms. We show that an appropriate definition of the long-range correlation energy is given by the value of the non-additive correlation functional. This functional is evaluated using the fluctuation–dissipation theorem aided by a formally exact decomposition of the response functions into subsystem contributions. FDE-vdW is derived in detail and several approximate schemes are proposed, which lead to practical implementations of the method. We show that FDE-vdW is Casimir-Polder consistent, i.e., it reduces to the generalized Casimir-Polder formula for asymptotic inter-subsystems separations. Pilot calculations of binding energies of 13 weakly bound complexes singled out from the S22 set show a dramatic improvement upon semilocal subsystem DFT, provided that an appropriate exchange functional is employed. The convergence of FDE-vdW with basis set size is discussed, as well as its dependence on the choice of associated density functional approximant.
The Drosophila larval neuromuscular junction (NMJ), at which glutamate acts as the excitatory neurotransmitter, is a widely used model for genetic analysis of synapse function and development. Despite decades of study, the inability to reconstitute NMJ glutamate receptor function using heterologous expression systems has complicated the analysis of receptor function, such that it is difficult to resolve the molecular basis for compound phenotypes observed in mutant flies. In this paper, we find that Drosophila Neto functions as an essential component required for the function of NMJ glutamate receptors, permitting analysis of glutamate receptor responses in Xenopus oocytes. Finally, in combination with a crystallographic analysis of the GluRIIB ligand binding domain, we use this system to characterize the subunit dependence of assembly, channel block, and ligand selectivity for Drosophila NMJ glutamate receptors.
The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.
Self-consistent solutions of the Dyson equation are obtained using a plane-wave basis set for seven small molecules. Such self-consistent solutions can help to unify the different GW self-consistent schemes, reduce the scatter of results in current GW calculations, and shed light on the true effects of GW self-consistency. Unlike other works of self-consistent GW calculations, in the present work the Green's function is expressed as a matrix under the plane-wave basis set. The algorithmic details which enable such calculations are presented. Finally, the ability to solve the full Green's function using a plane-wave basis set may open the door for future beyond- GW many-body perturbation theory calculations.
The geometry optimization of 2-amino-5-nitroprydinium trifluoroacetate molecule was carried out by using Becke’s three-parameter exchange functional in conjunction with the Lee-Yang-Parr correlation functional (B3LYP) level of density functional theory (DFT) and 6-311++G(d,p) basis set at GAUSSIAN 09 program. The vibration spectrum of the title compound was simulated to predict the presence of functional groups and their vibrational modes. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies were calculated at the same level, and the obtained small energy gap shows that charge transfer occurs in the title compound. The molecular dipole moment, polarizability and hyperpolarizability parameters were determined to evaluate nonlinear optical efficiency of the title compound. Finally, the {sup 13}C and {sup 1}H Nuclear Magnetic Resonance (NMR) chemical shift values were calculated by the application of the gauge independent atomic orbital (GIAO) method. All of the calculations were carried out by using GAUSSIAN 09 program.
Developing accurate quantum chemical approaches for calculating p K a s is of broad interest. Useful accuracy can be obtained by using density functional theory (DFT) in combination with a polarizable continuum solvent model. However, some classes of molecules present problems for this approach, yielding errors greater than 5 p K units. Various methods have been developed to improve the accuracy of the combined strategy. These methods perform well but either do not generalize or introduce additional degrees of freedom, increasing the computational cost. The Solvation Model based on Density (SMD) has emerged as one of the most commonly used continuum solvent models. Nevertheless, for some classes of organic compounds, e.g., thiols, the p K a s calculated with the original SMD model show errors of 6–10 p K units, and we traced these errors to inaccuracies in the solvation free energies of the anions. To improve the accuracy of p K a s calculated with DFT and the SMD model, we developed a scaled solvent-accessible surface approach for constructing the solute–solvent boundary. By using a “direct” approach, in which all quantities are computed in the presence of the continuum solvent, the use of thermodynamic cycles is avoided. Furthermore, no explicit water molecules are required. Three benchmark data sets of experimentally measured p K a values, including 28 carboxylic acids, 10 aliphatic amines, and 45 thiols, were used to assess the optimized SMD model, which we call SMD with a scaled solvent-accessible surface (SMD sSAS ). Of the methods tested, the M06-2X density functional approximation, 6-31+G(d,p) basis set, and SMD sSAS solvent model provided the most accurate p K a s for each set, yielding mean unsigned errors of 0.9, 0.4, and 0.5 p K units, respectively, for carboxylic acids, aliphatic amines, and thiols. As a result, this approach is therefore useful for efficiently calculating the p K a s of environmentally relevant functional groups.
A combinatorially optimized, range-separated hybrid, meta-GGA density functional with VV10 nonlocal correlation is presented in this paper. The final 12-parameter functional form is selected from approximately 10 × 10 9 candidate fits that are trained on a training set of 870 data points and tested on a primary test set of 2964 data points. The resulting density functional, ωB97M-V, is further tested for transferability on a secondary test set of 1152 data points. For comparison, ωB97M-V is benchmarked against 11 leading density functionals including M06-2X, ωB97X-D, M08-HX, M11, ωM05-D, ωB97X-V, and MN15. Encouragingly, the overall performance of ωB97M-V on nearly 5000 data points clearly surpasses that of all of the tested density functionals. Finally, in order to facilitate the use of ωB97M-V, its basis set dependence and integration grid sensitivity are thoroughly assessed, and recommendations that take into account both efficiency and accuracy are provided.
Infrared spectra of spiropentane (C{sub 5}H{sub 8}) have been recorded at a resolution (0.002 cm{sup -1}) sufficient to resolve for the first time individual rovibrational lines. This initial report presents the ground state constants for this molecule determined from the detailed analysis of the {nu}16 (b2) parallel band at 993 cm{sup -1}. In addition, the determination included more than 2000 ground state combination-differences deduced from partial analyses of four other infrared-allowed bands, the {nu}24(e) perpendicular band at 780 cm{sup -1} and three (b2) parallel bands at 1540 cm{sup -1} ({nu}14), 1568 cm{sup -1} ({nu}5+{nu}16), and 2098 cm{sup -1} ({nu}5+{nu}14). In each of the latter four cases, the spectra show complications; in the case of {nu}24, these complications are due to rotational l-type doublings, and in the case of the parallel bands, the spectral complexities are due to Fermi resonance and Coriolis interactions of the upper states with nearby levels. The unraveling of these is underway but the assignment of many of these transitions permit the confident use of the ground state differences in determining the following constants for the ground state (in units of cm{sup -1}): B0 = 0.1394736(2), DJ = 2.458(1) x 10{sup -8}, DJK = 8.28(3) x 10{sup -8}. For the unperturbed {nu}16 fundamental, more than 3000 transitions were fit and the band origin was found to be at 992.53793(2) cm{sup -1}. The numbers in parentheses are the uncertainties (two standard deviations) in the value of the last digit of the constants. Surprisingly, the very accurate B0 value measured here is lower than the value (0.1418 cm{sup -1}) calculated from an electron diffraction structure, instead of being higher, as expected. Where possible, the rovibrational results are compared with those computed at the anharmonic level using the B3LYP density functional method with a cc-pVTZ basis set. These too suggest that the electron diffraction results are in question.
Density functional theory (DFT) Born-Oppenheimer molecular dynamics (BOMD) simulations of metal clusters are presented. The calculations have been performed with the deMon2k [1] code employing all-electron basis sets and local and non-local functionals. The capability to perform reasonable long (∼ 100 ps) first-principle BOMD simulations in order to explore potential energy landscape of metallic clusters will be presented [2,3]. The evolution of the cluster structures and properties, such as polarizability and heat capacity, with temperature is discussed.