Methods and Issues for the Combined Use of Integral Experiments and Covariance Data: Results of a NEA International Collaborative Study
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Background: Next-generation sequencing (NGS) technologies have provided researchers with vast possibilities in various biological and biomedical research areas. Efficient data mining strategies are in high demand for large scale comparative and evolutional studies to be performed on the large amounts of data derived from NGS projects. Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining. Methods: We report a novel procedure to analyse NGS data using topic modeling. It consists of four major procedures: NGS data retrieval, preprocessing, topic modeling, and data mining using Latent Dirichlet Allocation (LDA) topic outputs. The NGS data set of the Salmonella enterica strains were used as a case study to show the workflow of this procedure. The perplexity measurement of the topic numbers and the convergence efficiencies of Gibbs sampling were calculated and discussed for achieving the best result from the proposed procedure. Results: The output topics by LDA algorithms could be treated as features of Salmonella strains to accurately describe the genetic diversity of fliC gene in various serotypes. The results of a two-way hierarchical clustering and data matrix analysis on LDA-derived matrices successfully classified Salmonella serotypes based on the NGS data. The implementation of topic modeling in NGS data analysis procedure provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data. Conclusion: The implementation of topic modeling in NGS data analysis provides a new way to elucidate genetic information from NGS data, and identify the gene-phenotype relationships and biomarkers, especially in the era of biological and medical big data.
In this work, we propose the use of Isogeometric Analysis (IGA) within the context of the Material Point Method (MPM), and refer to the approach as IGA-MPM. We use the idea of IGA, and its instantiation based on Non-Uniform Rational B-Splines (NURBS), to build higher-order accurate and smooth approximation for MPM. Higher-order smoothness yields a continuous representation of the strain rate, and, as a result, prevents jumps in the stress and other history variables as the material points cross the element boundaries. Furthermore, NURBS can exactly represent all conic sections and the corresponding symmetries in the solution, which may be important in some applications. Several numerical examples of increasing complexity are presented, and show the ability of IGA-MPM to eliminate the well known cell-crossing instability of the conventional MPM. In addition, the examples presented demonstrate improved accuracy, convergence, and symmetry preservation of IGA-MPM compared to the conventional MPM, both for rectilinear and curved geometries.
The possibility of reconstructing the neutron flux density of a W-Be photoneutron source using neutron activation analysis of Ag, Mn, Fe, Mn, and Ti samples is considered. The use of simple functions as AE{sup –B}, describing particular regions of the spectrum, as a reconstruction option is discussed. The dependence of the deviation of the measured reaction rates on those calculated in this study on the parameters of approximating functions is investigated. The convergence of the reconstruction results is obtained by increasing the amount of experimental data. This reconstruction method can be used for the operational measurement of the thermal neutron flux density of the photoneutron source and for the optimization of the source parameters.
Concentrating solar power researchers are evaluating the potential of the supercritical carbon dioxide recompression cycle to improve the thermal efficiency and decrease the capital costs of next-generation systems. This analysis investigates the steady-state off-design performance of a recompression cycle integrated with two-tank sensible-heat thermal energy storage as the ambient temperature and heat-transfer fluid (HTF) inlet conditions to the cycle change. This paper presents off-design component models and then cycle convergence and control models to maximize net cycle power output while constraining the high-side pressure and air-cooler fan power to their respective design values and fixing the cycle HTF outlet temperature to its design value. Results show that inventory control and air-cooler fan power are important control parameters that can be optimized to maximize off-design power output as the ambient temperature and HTF mass flow rate diverge from design. The high-side pressure and fan power constraints cause the cycle net power to degrade when the ambient temperature is warmer than the design value, and this study calculates a maximum mass flow rate for hot days above which the cycle cannot achieve the design HTF outlet temperature. Finally, the analysis shows that optimizing compressor shaft speeds can improve cold-day performance by around 1.5 percentage points and part-load performance by up to 2.5 percentage points versus a baseline case with no active compressor control.
A new arbitrary Polynomial Chaos (aPC) method is presented for moderately high-dimensional problems characterised by limited input data availability. The proposed methodology improves the algorithm of aPC and extends the method, that was previously only introduced as tensor product expansion, to moderately high-dimensional stochastic problems. The fundamental idea of aPC is to use the statistical moments of the input random variables to develop the polynomial chaos expansion. This approach provides the possibility to propagate continuous or discrete probability density functions and also histograms (data sets) as long as their moments exist, are finite and the determinant of the moment matrix is strictly positive. For cases with limited data availability, this approach avoids bias and fitting errors caused by wrong assumptions. In this work, an alternative way to calculate the aPC is suggested, which provides the optimal polynomials, Gaussian quadrature collocation points and weights from the moments using only a handful of matrix operations on the Hankel matrix of moments. It can therefore be implemented without requiring prior knowledge about statistical data analysis or a detailed understanding of the mathematics of polynomial chaos expansions. The extension to more input variables suggested in this work, is an anisotropic and adaptive version of Smolyak's algorithm that is solely based on the moments of the input probability distributions. It is referred to as SAMBA (PC), which is short for Sparse Approximation of Moment-Based Arbitrary Polynomial Chaos. It is illustrated that for moderately high-dimensional problems (up to 20 different input variables or histograms) SAMBA can significantly simplify the calculation of sparse Gaussian quadrature rules. SAMBA's efficiency for multivariate functions with regard to data availability is further demonstrated by analysing higher order convergence and accuracy for a set of nonlinear test functions with 2, 5 and 10 different input distributions or histograms.
The reaction of MnTe with AgSbTe 2 in an equimolar ratio (ATMS) provides a new semiconductor, AgMnSbTe 3 . AgMnSbTe 3 crystallizes in an average rock-salt NaCl structure with Ag, Mn, and Sb cations statistically occupying the Na sites. AgMnSbTe 3 is a p-type semiconductor with a narrow band gap of ~0.33 eV. A pair distribution function analysis indicates that local distortions are associated with the location of the Ag atoms in the lattice. Density functional theory calculations suggest a specific electronic band structure with multi-peak valence band maxima prone to energy convergence. In addition, Ag 2 Te nanograins precipitate at grain boundaries of AgMnSbTe 3 . Here, the energy offset of the valance band edge between AgMnSbTe 3 and Ag 2 Te is ~0.05 eV, which implies that Ag 2 Te precipitates exhibit a negligible effect on the hole transmission. As a result, ATMS exhibits a high power factor of ~12.2 μWcm -1 K -2 at 823 K, ultralow lattice thermal conductivity of ~0.34 Wm -1 K -1 (823 K), high peak ZT of ~1.46 at 823 K, and high average ZT of ~0.87 in the temperature range of 400–823 K.
Abstract Evapotranspiration (ET) plays an important role in land‐atmosphere coupling of energy, water, and carbon cycles. Following deforestation, ET is typically observed to decrease substantially as a consequence of decreases in leaf area and roots and increases in runoff. Changes in ET (latent heat flux) revise the surface energy and water budgets, which further affects large‐scale atmospheric dynamics and feeds back positively or negatively to long‐term forest sustainability. In this study, we used observations from a recent synthesis of 29 pairs of adjacent intact and deforested FLUXNET sites to improve model parameterization of stomatal characteristics, photosynthesis, and soil water dynamics in version 1 of the Energy Exascale Earth System Model (E3SM) Land Model (ELMv1). We found that default ELMv1 predicts an increase in ET after deforestation, likely leading to incorrect estimates of the effects of deforestation on land‐atmosphere coupling. The calibrated model accurately represented the FLUXNET observed deforestation effects on ET. Importantly, the search for global optimal parameters converged at values consistent with recent observational syntheses, confirming the reliability of the calibrated physical parameters. Applying this improved model parameterization to the globe scale reduced the bias of annual ET simulation by up to ~600 mm/year. Analysis on the roles of parameters suggested that future model development to improve ET simulation should focus on stomatal resistance and soil water‐related parameterizations. Finally, our predicted differences in seasonal ET changes from deforestation are large enough to substantially affect land‐atmosphere coupling and should be considered in such studies.
We consider the two-photon exchange contribution to the 2P-2S Lamb shift in muonic deuterium in the framework of forward dispersion relations. The dispersion integrals are evaluated with minimal model dependence using experimental data on elastic deuteron form factors and inelastic electron-deuteron scattering, both in the quasielastic and hadronic range. The subtraction constant that is required to ensure convergence of the dispersion relation for the forward Compton amplitude T{sub 1} (ν,Q{sup 2}) is related to the deuteron magnetic polarizability β(Q{sup 2}) and represents the main source of uncertainty in our analysis. We obtain for the Lamb shift ΔE{sub 2P-2S} = 1.620±0.190 meV and discuss ways to further reduce this uncertainty.
We report on the analyses of x-ray-imaging spectroscopy data from experiments to study interspecies ion separation in direct-drive inertial-confinement-fusion experiments on the Omega laser facility. This is a continuation of recent, related research [S. C. Hsu et al., Euro Phys. Lett. 115, 65001 (2016); T. R. Joshi et al., Phys. Plasmas 24, 056305 (2017)]. The targets were argon (Ar)-doped, deuterium (D2)-filled spherical plastic shells of varying D2-Ar relative and total gas pressures. We used a time- and space-integrated spectrometer, streaked crystal spectrometer, and up to three time-gated multi-monochromatic x-ray imagers (MMIs) fielded along different lines of sight to record x-ray spectral features obtained from the implosions. The MMI data were recorded between first-shock convergence and slightly before the neutron bang time. We confirm the presence of interspecies ion separation as reported in our recent work. Extensions to the previous work include (a) the inclusion of shell mix in the data analysis, which slightly changes the amount of inferred species separation, (b) observation of species separation closer to the neutron bang time, and (c) fielding of the particle x-ray temporal diagnostic (PXTD) [H. Sio et al., Rev. Sci. Instrum. 87, 11D701 (2016)] to infer the relative timing between the neutron bang time and peak x-ray emission. Experimentally inferred species separation is compared with radiation-hydrodynamic simulations that include a multi-ion-species transport model.
We introduce a simplified method to model the interatomic interactions of high entropy alloys based on a lookup table of cluster energies. Furthermore, these interactions are employed in replica exchange Monte Carlo simulations with histogram analysis to obtain thermodynamic properties across a broad temperature range. Kikuchi's cluster variation method entropy formalism is applied to directly calculate entropy from statistics on short- and long-range chemical order, and we discuss the convergence of the entropy as clusters of differing size are included. A high temperature series expansion aids in our understanding of the convergence. Computer codes implementing these methods, and supporting data, are freely available on the internet.
The increasing penetration of distributed energy resources (DERs) leads to voltage issues across distribution networks, necessitating voltage calculations by utilities. Electric model-free voltage calculation offers an enticing solution. However, most researches mainly focus on primary distribution networks ignoring secondary distribution networks and commonly overlook extreme voltage case calculations, which require the model’s extrapolation abilities. Here, in addressing the gaps, this paper presents a customized physics-inspired neural network (PINN) model, the structure of which is inspired by the derived coupled power flow model of primary-secondary distribution networks. To ensure precision and rapid convergence, a crafted training framework for the PINN model is proposed. The PINN’s “structure-mimetic” design enables superior extrapolation for unseen scenarios and enhances physical information awareness. We demonstrate this through two applications: hosting capacity analysis and customer-transformer connectivity. The effectiveness and advantages of the proposed PINN model are validated on two public testing systems and one utility distribution feeder model.
The application of the boundary integral equation method (BIE) to the elastoplastic torsion problem is considered. It is found that the BIE is very suitable for the elastoplastic analysis of the torsion of prismatic bars. A comparison of the BIE with the finite difference method shows savings for the BIE concerning the number of unknowns which have to be determined and also a much faster convergence rate. Attention is given to the problem of an edge-notched beam in pure bending, taking into account a biharmonic formulation and a displacement formulation.
A numerical technique is presented for the design of two-dimensional supercritical wing sections with low wave drag. The method is a design mode of the analysis code H which gives excellent agreement with experimental results and is widely used in the aircraft industry. Topics covered include the partial differential equations of transonic flow, the computational procedure and results; the design procedure; a convergence theorem; and description of the code.
Mathematical analysis of the optimal search of a nonlinear spacecraft trajectory to arrive at a set of desired targets is presented. A high precision integrated trajectory program and several optimization software libraries are used to search for a converged nonlinear spacecraft trajectory. Several examples for the Galileo Jupiter Orbiter and the Ocean Topography Experiment (TOPEX) are presented that illustrate a variety of the optimization methods used in nonlinear spacecraft trajectory searches.
Results are presented from temporally dense measurements of crustal deformation associated with the convergence of the Eurasian (EUR), Pacific, North American, and Philippine Sea (PHS) plates, carried out in April 1988 by a 10-station GPS fixed-point network established in central Japan. Using regional orbit relaxation methods, the analysis of the first 17-month data revealed significant horizontal deformation across the Suruga trough. Namely, it was found that a site in the northern tip of PHS plate moved nearly westward with a velocity of 28 +/-5 mm per year, and a site at the southeastern tip of EUR plate moved south-southwestward with a velocity of 18 +/-5 mm per year. A significant vertical uplift with a velocity of 20 mm/yr was detected at a site inland of the Tokai district located in the Akaishi uplift zone and at a site on the Hatsushima Island in Sagami Bay.
The mutual forcing of a midlatitude upper-tropospheric jet streak by organized mesoscale adiabatic and diabatic processes within a simulated convective system (SCS) is investigated. Using isentropic diagnostics, results from a three-dimensional numerical simulation of an SCS are examined to study the isallobaric flow field, modes of dominant ageostrophic motion, and stability changes in relation to the mutual interdependence of adiabatic processes and latent heat release. Isentropic analysis affords an explicit isolation of a component of isallobaric flow associated with diabatic processes within the SCS. Prior to convective development within the simulations, atmospheric destabilization occurs through adiabatic ageostrophic mass adjustment and low-level convergence in association with the preexisting synoptic-scale upper-tropospheric jet streak. The SCS develops in a baroclinic zone and quickly initiates a vigorous mass circulation. By the mature stage, a pronounced vertical couplet of low-level convergence and upper-level mass divergence is established, linked by intense midtropospoheric diabatic heating. Significant divergence persists aloft for several hours subsequent to SCS decay. The dominant role of ageostrophic motion within which the low-level mass convergence develops is the adiabatic isallobaric component, while the mass divergence aloft develops principally through the diabatic isallobaric component. Both compnents are intrinsically linked to the convectively forced vertical mass transport. The inertial diabatic ageostrophic component is largest near the level of maximum heating and is responsible for the development of inertial instability to the north of SCS, resulting in this quadrant being preferred for outflow. The inertial advective component, the dominant term that produces the new downstream wind maximum, rapidly develops north of the SCS and through mutual adjustment creates the baroclinic support for the new jet streak.
The project is based upon research of Tessler et al. (1994) on an improved variational formulation for post-processing stress predictions in Finite Element Analysis. The methodology, called Smoothing Element Analysis (SEA), employs a three-node smoothing finite element. The present effort focused on verifying the basic constant strain criterion for the three-node smoothing element subject to a set of internal penalty constraints. The convergence characteristics of the element are assessed by first deriving the constrained form of the assumed element stress and stress gradient fields, and then by verifying the validity of the constant strain criterion once the element penalty constraints are explicitly imposed. The analytical investigation is carried out with the use of the symbolic manipulation code 'Mathematica'.