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Sample records for accurate structural parameters

  1. Accurate structure and dynamics of the metal-site of paramagnetic metalloproteins from NMR parameters using natural bond orbitals.

    PubMed

    Hansen, D Flemming; Westler, William M; Kunze, Micha B A; Markley, John L; Weinhold, Frank; Led, Jens J

    2012-03-14

    A natural bond orbital (NBO) analysis of unpaired electron spin density in metalloproteins is presented, which allows a fast and robust calculation of paramagnetic NMR parameters. Approximately 90% of the unpaired electron spin density occupies metal-ligand NBOs, allowing the majority of the density to be modeled by only a few NBOs that reflect the chemical bonding environment. We show that the paramagnetic relaxation rate of protons can be calculated accurately using only the metal-ligand NBOs and that these rates are in good agreement with corresponding rates measured experimentally. This holds, in particular, for protons of ligand residues where the point-dipole approximation breaks down. To describe the paramagnetic relaxation of heavy nuclei, also the electron spin density in the local orbitals must be taken into account. Geometric distance restraints for (15)N can be derived from the paramagnetic relaxation enhancement and the Fermi contact shift when local NBOs are included in the analysis. Thus, the NBO approach allows us to include experimental paramagnetic NMR parameters of (15)N nuclei as restraints in a structure optimization protocol. We performed a molecular dynamics simulation and structure determination of oxidized rubredoxin using the experimentally obtained paramagnetic NMR parameters of (15)N. The corresponding structures obtained are in good agreement with the crystal structure of rubredoxin. Thus, the NBO approach allows an accurate description of the geometric structure and the dynamics of metalloproteins, when NMR parameters are available of nuclei in the immediate vicinity of the metal-site.

  2. Accurate Structure and Dynamics of the Metal-Site of Paramagnetic Metalloproteins from NMR Parameters Using Natural Bond Orbitals

    PubMed Central

    2012-01-01

    A natural bond orbital (NBO) analysis of unpaired electron spin density in metalloproteins is presented, which allows a fast and robust calculation of paramagnetic NMR parameters. Approximately 90% of the unpaired electron spin density occupies metal–ligand NBOs, allowing the majority of the density to be modeled by only a few NBOs that reflect the chemical bonding environment. We show that the paramagnetic relaxation rate of protons can be calculated accurately using only the metal–ligand NBOs and that these rates are in good agreement with corresponding rates measured experimentally. This holds, in particular, for protons of ligand residues where the point-dipole approximation breaks down. To describe the paramagnetic relaxation of heavy nuclei, also the electron spin density in the local orbitals must be taken into account. Geometric distance restraints for 15N can be derived from the paramagnetic relaxation enhancement and the Fermi contact shift when local NBOs are included in the analysis. Thus, the NBO approach allows us to include experimental paramagnetic NMR parameters of 15N nuclei as restraints in a structure optimization protocol. We performed a molecular dynamics simulation and structure determination of oxidized rubredoxin using the experimentally obtained paramagnetic NMR parameters of 15N. The corresponding structures obtained are in good agreement with the crystal structure of rubredoxin. Thus, the NBO approach allows an accurate description of the geometric structure and the dynamics of metalloproteins, when NMR parameters are available of nuclei in the immediate vicinity of the metal-site. PMID:22329704

  3. Accurate Stellar Parameters for Exoplanet Host Stars

    NASA Astrophysics Data System (ADS)

    Brewer, John Michael; Fischer, Debra; Basu, Sarbani; Valenti, Jeff A.

    2015-01-01

    A large impedement to our understanding of planet formation is obtaining a clear picture of planet radii and densities. Although determining precise ratios between planet and stellar host are relatively easy, determining accurate stellar parameters is still a difficult and costly undertaking. High resolution spectral analysis has traditionally yielded precise values for some stellar parameters but stars in common between catalogs from different authors or analyzed using different techniques often show offsets far in excess of their uncertainties. Most analyses now use some external constraint, when available, to break observed degeneracies between surface gravity, effective temperature, and metallicity which can otherwise lead to correlated errors in results. However, these external constraints are impossible to obtain for all stars and can require more costly observations than the initial high resolution spectra. We demonstrate that these discrepencies can be mitigated by use of a larger line list that has carefully tuned atomic line data. We use an iterative modeling technique that does not require external constraints. We compare the surface gravity obtained with our spectral synthesis modeling to asteroseismically determined values for 42 Kepler stars. Our analysis agrees well with only a 0.048 dex offset and an rms scatter of 0.05 dex. Such accurate stellar gravities can reduce the primary source of uncertainty in radii by almost an order of magnitude over unconstrained spectral analysis.

  4. Accurate SHAPE-directed RNA structure determination

    PubMed Central

    Deigan, Katherine E.; Li, Tian W.; Mathews, David H.; Weeks, Kevin M.

    2009-01-01

    Almost all RNAs can fold to form extensive base-paired secondary structures. Many of these structures then modulate numerous fundamental elements of gene expression. Deducing these structure–function relationships requires that it be possible to predict RNA secondary structures accurately. However, RNA secondary structure prediction for large RNAs, such that a single predicted structure for a single sequence reliably represents the correct structure, has remained an unsolved problem. Here, we demonstrate that quantitative, nucleotide-resolution information from a SHAPE experiment can be interpreted as a pseudo-free energy change term and used to determine RNA secondary structure with high accuracy. Free energy minimization, by using SHAPE pseudo-free energies, in conjunction with nearest neighbor parameters, predicts the secondary structure of deproteinized Escherichia coli 16S rRNA (>1,300 nt) and a set of smaller RNAs (75–155 nt) with accuracies of up to 96–100%, which are comparable to the best accuracies achievable by comparative sequence analysis. PMID:19109441

  5. Accurate Parameter Estimation for Unbalanced Three-Phase System

    PubMed Central

    Chen, Yuan

    2014-01-01

    Smart grid is an intelligent power generation and control console in modern electricity networks, where the unbalanced three-phase power system is the commonly used model. Here, parameter estimation for this system is addressed. After converting the three-phase waveforms into a pair of orthogonal signals via the α β-transformation, the nonlinear least squares (NLS) estimator is developed for accurately finding the frequency, phase, and voltage parameters. The estimator is realized by the Newton-Raphson scheme, whose global convergence is studied in this paper. Computer simulations show that the mean square error performance of NLS method can attain the Cramér-Rao lower bound. Moreover, our proposal provides more accurate frequency estimation when compared with the complex least mean square (CLMS) and augmented CLMS. PMID:25162056

  6. Accurate parameter estimation for unbalanced three-phase system.

    PubMed

    Chen, Yuan; So, Hing Cheung

    2014-01-01

    Smart grid is an intelligent power generation and control console in modern electricity networks, where the unbalanced three-phase power system is the commonly used model. Here, parameter estimation for this system is addressed. After converting the three-phase waveforms into a pair of orthogonal signals via the α β-transformation, the nonlinear least squares (NLS) estimator is developed for accurately finding the frequency, phase, and voltage parameters. The estimator is realized by the Newton-Raphson scheme, whose global convergence is studied in this paper. Computer simulations show that the mean square error performance of NLS method can attain the Cramér-Rao lower bound. Moreover, our proposal provides more accurate frequency estimation when compared with the complex least mean square (CLMS) and augmented CLMS.

  7. Machine learning of parameters for accurate semiempirical quantum chemical calculations

    SciTech Connect

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-04-14

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempirical OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.

  8. Machine learning of parameters for accurate semiempirical quantum chemical calculations

    DOE PAGES

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-04-14

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

  9. Direct computation of parameters for accurate polarizable force fields

    SciTech Connect

    Verstraelen, Toon Vandenbrande, Steven; Ayers, Paul W.

    2014-11-21

    We present an improved electronic linear response model to incorporate polarization and charge-transfer effects in polarizable force fields. This model is a generalization of the Atom-Condensed Kohn-Sham Density Functional Theory (DFT), approximated to second order (ACKS2): it can now be defined with any underlying variational theory (next to KS-DFT) and it can include atomic multipoles and off-center basis functions. Parameters in this model are computed efficiently as expectation values of an electronic wavefunction, obviating the need for their calibration, regularization, and manual tuning. In the limit of a complete density and potential basis set in the ACKS2 model, the linear response properties of the underlying theory for a given molecular geometry are reproduced exactly. A numerical validation with a test set of 110 molecules shows that very accurate models can already be obtained with fluctuating charges and dipoles. These features greatly facilitate the development of polarizable force fields.

  10. Clinically accurate fetal ECG parameters acquired from maternal abdominal sensors

    PubMed Central

    CLIFFORD, Gari; SAMENI, Reza; WARD, Mr. Jay; ROBINSON, Julian; WOLFBERG, Adam J.

    2011-01-01

    OBJECTIVE To evaluate the accuracy of a novel system for measuring fetal heart rate and ST-segment changes using non-invasive electrodes on the maternal abdomen. STUDY DESIGN Fetal ECGs were recorded using abdominal sensors from 32 term laboring women who had a fetal scalp electrode (FSE) placed for a clinical indication. RESULTS Good quality data for FHR estimation was available in 91.2% of the FSE segments, and 89.9% of the abdominal electrode segments. The root mean square (RMS) error between the FHR data calculated by both methods over all processed segments was 0.36 beats per minute. ST deviation from the isoelectric point ranged from 0 to 14.2% of R-wave amplitude. The RMS error between the ST change calculated by both methods averaged over all processed segments was 3.2%. CONCLUSION FHR and ST change acquired from the maternal abdomen is highly accurate and on average is clinically indistinguishable from FHR and ST change calculated using FSE data. PMID:21514560

  11. Isomerism of Cyanomethanimine: Accurate Structural, Energetic, and Spectroscopic Characterization.

    PubMed

    Puzzarini, Cristina

    2015-11-25

    The structures, relative stabilities, and rotational and vibrational parameters of the Z-C-, E-C-, and N-cyanomethanimine isomers have been evaluated using state-of-the-art quantum-chemical approaches. Equilibrium geometries have been calculated by means of a composite scheme based on coupled-cluster calculations that accounts for the extrapolation to the complete basis set limit and core-correlation effects. The latter approach is proved to provide molecular structures with an accuracy of 0.001-0.002 Å and 0.05-0.1° for bond lengths and angles, respectively. Systematically extrapolated ab initio energies, accounting for electron correlation through coupled-cluster theory, including up to single, double, triple, and quadruple excitations, and corrected for core-electron correlation and anharmonic zero-point vibrational energy, have been used to accurately determine relative energies and the Z-E isomerization barrier with an accuracy of about 1 kJ/mol. Vibrational and rotational spectroscopic parameters have been investigated by means of hybrid schemes that allow us to obtain rotational constants accurate to about a few megahertz and vibrational frequencies with a mean absolute error of ∼1%. Where available, for all properties considered, a very good agreement with experimental data has been observed.

  12. Distillation tray structural parameter study: Phase 1

    NASA Technical Reports Server (NTRS)

    Winter, J. Ronald

    1991-01-01

    The purpose here is to identify the structural parameters (plate thickness, liquid level, beam size, number of beams, tray diameter, etc.) that affect the structural integrity of distillation trays in distillation columns. Once the sensitivity of the trays' dynamic response to these parameters has been established, the designer will be able to use this information to prepare more accurate specifications for the construction of new trays. Information is given on both static and dynamic analysis, modal response, and tray failure details.

  13. Parameter Estimation of Ion Current Formulations Requires Hybrid Optimization Approach to Be Both Accurate and Reliable

    PubMed Central

    Loewe, Axel; Wilhelms, Mathias; Schmid, Jochen; Krause, Mathias J.; Fischer, Fathima; Thomas, Dierk; Scholz, Eberhard P.; Dössel, Olaf; Seemann, Gunnar

    2016-01-01

    Computational models of cardiac electrophysiology provided insights into arrhythmogenesis and paved the way toward tailored therapies in the last years. To fully leverage in silico models in future research, these models need to be adapted to reflect pathologies, genetic alterations, or pharmacological effects, however. A common approach is to leave the structure of established models unaltered and estimate the values of a set of parameters. Today’s high-throughput patch clamp data acquisition methods require robust, unsupervised algorithms that estimate parameters both accurately and reliably. In this work, two classes of optimization approaches are evaluated: gradient-based trust-region-reflective and derivative-free particle swarm algorithms. Using synthetic input data and different ion current formulations from the Courtemanche et al. electrophysiological model of human atrial myocytes, we show that neither of the two schemes alone succeeds to meet all requirements. Sequential combination of the two algorithms did improve the performance to some extent but not satisfactorily. Thus, we propose a novel hybrid approach coupling the two algorithms in each iteration. This hybrid approach yielded very accurate estimates with minimal dependency on the initial guess using synthetic input data for which a ground truth parameter set exists. When applied to measured data, the hybrid approach yielded the best fit, again with minimal variation. Using the proposed algorithm, a single run is sufficient to estimate the parameters. The degree of superiority over the other investigated algorithms in terms of accuracy and robustness depended on the type of current. In contrast to the non-hybrid approaches, the proposed method proved to be optimal for data of arbitrary signal to noise ratio. The hybrid algorithm proposed in this work provides an important tool to integrate experimental data into computational models both accurately and robustly allowing to assess the often non

  14. A simple and accurate resist parameter extraction method for sub-80-nm DRAM patterns

    NASA Astrophysics Data System (ADS)

    Lee, Sook; Hwang, Chan; Park, Dong-Woon; Kim, In-Sung; Kim, Ho-Chul; Woo, Sang-Gyun; Cho, Han-Ku; Moon, Joo-Tae

    2004-05-01

    Due to the polarization effect of high NA lithography, the consideration of resist effect in lithography simulation becomes increasingly important. In spite of the importance of resist simulation, many process engineers are reluctant to consider resist effect in lithography simulation due to time-consuming procedure to extract required resist parameters and the uncertainty of measurement of some parameters. Weiss suggested simplified development model, and this model does not require the complex kinetic parameters. For the device fabrication engineers, there is a simple and accurate parameter extraction and optimizing method using Weiss model. This method needs refractive index, Dill"s parameters and development rate monitoring (DRM) data in parameter extraction. The parameters extracted using referred sequence is not accurate, so that we have to optimize the parameters to fit the critical dimension scanning electron microscopy (CD SEM) data of line and space patterns. Hence, the FiRM of Sigma-C is utilized as a resist parameter-optimizing program. According to our study, the illumination shape, the aberration and the pupil mesh point have a large effect on the accuracy of resist parameter in optimization. To obtain the optimum parameters, we need to find the saturated mesh points in terms of normalized intensity log slope (NILS) prior to an optimization. The simulation results using the optimized parameters by this method shows good agreement with experiments for iso-dense bias, Focus-Exposure Matrix data and sub 80nm device pattern simulation.

  15. Bayesian parameter estimation of a k-ε model for accurate jet-in-crossflow simulations

    DOE PAGES

    Ray, Jaideep; Lefantzi, Sophia; Arunajatesan, Srinivasan; Dechant, Lawrence

    2016-05-31

    Reynolds-averaged Navier–Stokes models are not very accurate for high-Reynolds-number compressible jet-in-crossflow interactions. The inaccuracy arises from the use of inappropriate model parameters and model-form errors in the Reynolds-averaged Navier–Stokes model. In this study, the hypothesis is pursued that Reynolds-averaged Navier–Stokes predictions can be significantly improved by using parameters inferred from experimental measurements of a supersonic jet interacting with a transonic crossflow.

  16. STRUCTURAL PARAMETERS OF GALAXIES IN CANDELS

    SciTech Connect

    Van der Wel, A.; Chang, Yu-Yen; Rix, H.-W.; Bell, E. F.; Haeussler, B.; Hartley, W.; McGrath, E. J.; Cheung, E.; Faber, S. M.; Kocevski, D. D.; Mozena, M.; McIntosh, D. H.; Barden, M.; Ferguson, H. C.; Grogin, N. A.; Koekemoer, A. M.; Lotz, J.; Galametz, A.; Kartaltepe, J. S.; and others

    2012-12-15

    We present global structural parameter measurements of 109,533 unique, H{sub F160W}-selected objects from the CANDELS multi-cycle treasury program. Sersic model fits for these objects are produced with GALFIT in all available near-infrared filters (H{sub F160W}, J{sub F125W} and, for a subset, Y{sub F105W}). The parameters of the best-fitting Sersic models (total magnitude, half-light radius, Sersic index, axis ratio, and position angle) are made public, along with newly constructed point-spread functions for each field and filter. Random uncertainties in the measured parameters are estimated for each individual object based on a comparison between multiple, independent measurements of the same set of objects. To quantify systematic uncertainties, we create a mosaic with simulated galaxy images with a realistic distribution of input parameters and then process and analyze the mosaic in an identical manner as the real data. We find that accurate and precise measurements-to 10% or better-of all structural parameters can typically be obtained for galaxies with H{sub F160W} < 23, with comparable fidelity for basic size and shape measurements for galaxies to H{sub F160W} {approx} 24.5.

  17. Accurate Classification of RNA Structures Using Topological Fingerprints

    PubMed Central

    Li, Kejie; Gribskov, Michael

    2016-01-01

    While RNAs are well known to possess complex structures, functionally similar RNAs often have little sequence similarity. While the exact size and spacing of base-paired regions vary, functionally similar RNAs have pronounced similarity in the arrangement, or topology, of base-paired stems. Furthermore, predicted RNA structures often lack pseudoknots (a crucial aspect of biological activity), and are only partially correct, or incomplete. A topological approach addresses all of these difficulties. In this work we describe each RNA structure as a graph that can be converted to a topological spectrum (RNA fingerprint). The set of subgraphs in an RNA structure, its RNA fingerprint, can be compared with the fingerprints of other RNA structures to identify and correctly classify functionally related RNAs. Topologically similar RNAs can be identified even when a large fraction, up to 30%, of the stems are omitted, indicating that highly accurate structures are not necessary. We investigate the performance of the RNA fingerprint approach on a set of eight highly curated RNA families, with diverse sizes and functions, containing pseudoknots, and with little sequence similarity–an especially difficult test set. In spite of the difficult test set, the RNA fingerprint approach is very successful (ROC AUC > 0.95). Due to the inclusion of pseudoknots, the RNA fingerprint approach both covers a wider range of possible structures than methods based only on secondary structure, and its tolerance for incomplete structures suggests that it can be applied even to predicted structures. Source code is freely available at https://github.rcac.purdue.edu/mgribsko/XIOS_RNA_fingerprint. PMID:27755571

  18. An accurate Fortran code for computing hydrogenic continuum wave functions at a wide range of parameters

    NASA Astrophysics Data System (ADS)

    Peng, Liang-You; Gong, Qihuang

    2010-12-01

    The accurate computations of hydrogenic continuum wave functions are very important in many branches of physics such as electron-atom collisions, cold atom physics, and atomic ionization in strong laser fields, etc. Although there already exist various algorithms and codes, most of them are only reliable in a certain ranges of parameters. In some practical applications, accurate continuum wave functions need to be calculated at extremely low energies, large radial distances and/or large angular momentum number. Here we provide such a code, which can generate accurate hydrogenic continuum wave functions and corresponding Coulomb phase shifts at a wide range of parameters. Without any essential restrict to angular momentum number, the present code is able to give reliable results at the electron energy range [10,10] eV for radial distances of [10,10] a.u. We also find the present code is very efficient, which should find numerous applications in many fields such as strong field physics. Program summaryProgram title: HContinuumGautchi Catalogue identifier: AEHD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHD_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1233 No. of bytes in distributed program, including test data, etc.: 7405 Distribution format: tar.gz Programming language: Fortran90 in fixed format Computer: AMD Processors Operating system: Linux RAM: 20 MBytes Classification: 2.7, 4.5 Nature of problem: The accurate computation of atomic continuum wave functions is very important in many research fields such as strong field physics and cold atom physics. Although there have already existed various algorithms and codes, most of them can only be applicable and reliable in a certain range of parameters. We present here an accurate FORTRAN program for

  19. Time resolved diffuse optical spectroscopy with geometrically accurate models for bulk parameter recovery

    PubMed Central

    Guggenheim, James A.; Bargigia, Ilaria; Farina, Andrea; Pifferi, Antonio; Dehghani, Hamid

    2016-01-01

    A novel straightforward, accessible and efficient approach is presented for performing hyperspectral time-domain diffuse optical spectroscopy to determine the optical properties of samples accurately using geometry specific models. To allow bulk parameter recovery from measured spectra, a set of libraries based on a numerical model of the domain being investigated is developed as opposed to the conventional approach of using an analytical semi-infinite slab approximation, which is known and shown to introduce boundary effects. Results demonstrate that the method improves the accuracy of derived spectrally varying optical properties over the use of the semi-infinite approximation. PMID:27699137

  20. Time resolved diffuse optical spectroscopy with geometrically accurate models for bulk parameter recovery

    PubMed Central

    Guggenheim, James A.; Bargigia, Ilaria; Farina, Andrea; Pifferi, Antonio; Dehghani, Hamid

    2016-01-01

    A novel straightforward, accessible and efficient approach is presented for performing hyperspectral time-domain diffuse optical spectroscopy to determine the optical properties of samples accurately using geometry specific models. To allow bulk parameter recovery from measured spectra, a set of libraries based on a numerical model of the domain being investigated is developed as opposed to the conventional approach of using an analytical semi-infinite slab approximation, which is known and shown to introduce boundary effects. Results demonstrate that the method improves the accuracy of derived spectrally varying optical properties over the use of the semi-infinite approximation.

  1. FAST TRACK COMMUNICATION Accurate estimate of α variation and isotope shift parameters in Na and Mg+

    NASA Astrophysics Data System (ADS)

    Sahoo, B. K.

    2010-12-01

    We present accurate calculations of fine-structure constant variation coefficients and isotope shifts in Na and Mg+ using the relativistic coupled-cluster method. In our approach, we are able to discover the roles of various correlation effects explicitly to all orders in these calculations. Most of the results, especially for the excited states, are reported for the first time. It is possible to ascertain suitable anchor and probe lines for the studies of possible variation in the fine-structure constant by using the above results in the considered systems.

  2. Accurate estimation of motion blur parameters in noisy remote sensing image

    NASA Astrophysics Data System (ADS)

    Shi, Xueyan; Wang, Lin; Shao, Xiaopeng; Wang, Huilin; Tao, Zhong

    2015-05-01

    The relative motion between remote sensing satellite sensor and objects is one of the most common reasons for remote sensing image degradation. It seriously weakens image data interpretation and information extraction. In practice, point spread function (PSF) should be estimated firstly for image restoration. Identifying motion blur direction and length accurately is very crucial for PSF and restoring image with precision. In general, the regular light-and-dark stripes in the spectrum can be employed to obtain the parameters by using Radon transform. However, serious noise existing in actual remote sensing images often causes the stripes unobvious. The parameters would be difficult to calculate and the error of the result relatively big. In this paper, an improved motion blur parameter identification method to noisy remote sensing image is proposed to solve this problem. The spectrum characteristic of noisy remote sensing image is analyzed firstly. An interactive image segmentation method based on graph theory called GrabCut is adopted to effectively extract the edge of the light center in the spectrum. Motion blur direction is estimated by applying Radon transform on the segmentation result. In order to reduce random error, a method based on whole column statistics is used during calculating blur length. Finally, Lucy-Richardson algorithm is applied to restore the remote sensing images of the moon after estimating blur parameters. The experimental results verify the effectiveness and robustness of our algorithm.

  3. BIOFILM IMAGE RECONSTRUCTION FOR ASSESSING STRUCTURAL PARAMETERS

    PubMed Central

    Renslow, Ryan; Lewandowski, Zbigniew; Beyenal, Haluk

    2011-01-01

    The structure of biofilms can be numerically quantified from microscopy images using structural parameters. These parameters are used in biofilm image analysis to compare biofilms, to monitor temporal variation in biofilm structure, to quantify the effects of antibiotics on biofilm structure and to determine the effects of environmental conditions on biofilm structure. It is often hypothesized that biofilms with similar structural parameter values will have similar structures; however, this hypothesis has never been tested. The main goal was to test the hypothesis that the commonly used structural parameters can characterize the differences or similarities between biofilm structures. To achieve this goal 1) biofilm image reconstruction was developed as a new tool for assessing structural parameters, 2) independent reconstructions using the same starting structural parameters were tested to see how they differed from each other, 3) the effect of the original image parameter values on reconstruction success was evaluated and 4) the effect of the number and type of the parameters on reconstruction success was evaluated. It was found that two biofilms characterized by identical commonly used structural parameter values may look different, that the number and size of clusters in the original biofilm image affect image reconstruction success and that, in general, a small set of arbitrarily selected parameters may not reveal relevant differences between biofilm structures. PMID:21280029

  4. Polynomial fitting of DT-MRI fiber tracts allows accurate estimation of muscle architectural parameters.

    PubMed

    Damon, Bruce M; Heemskerk, Anneriet M; Ding, Zhaohua

    2012-06-01

    Fiber curvature is a functionally significant muscle structural property, but its estimation from diffusion-tensor magnetic resonance imaging fiber tracking data may be confounded by noise. The purpose of this study was to investigate the use of polynomial fitting of fiber tracts for improving the accuracy and precision of fiber curvature (κ) measurements. Simulated image data sets were created in order to provide data with known values for κ and pennation angle (θ). Simulations were designed to test the effects of increasing inherent fiber curvature (3.8, 7.9, 11.8 and 15.3 m(-1)), signal-to-noise ratio (50, 75, 100 and 150) and voxel geometry (13.8- and 27.0-mm(3) voxel volume with isotropic resolution; 13.5-mm(3) volume with an aspect ratio of 4.0) on κ and θ measurements. In the originally reconstructed tracts, θ was estimated accurately under most curvature and all imaging conditions studied; however, the estimates of κ were imprecise and inaccurate. Fitting the tracts to second-order polynomial functions provided accurate and precise estimates of κ for all conditions except very high curvature (κ=15.3 m(-1)), while preserving the accuracy of the θ estimates. Similarly, polynomial fitting of in vivo fiber tracking data reduced the κ values of fitted tracts from those of unfitted tracts and did not change the θ values. Polynomial fitting of fiber tracts allows accurate estimation of physiologically reasonable values of κ, while preserving the accuracy of θ estimation.

  5. A Weibull statistics-based lignocellulose saccharification model and a built-in parameter accurately predict lignocellulose hydrolysis performance.

    PubMed

    Wang, Mingyu; Han, Lijuan; Liu, Shasha; Zhao, Xuebing; Yang, Jinghua; Loh, Soh Kheang; Sun, Xiaomin; Zhang, Chenxi; Fang, Xu

    2015-09-01

    Renewable energy from lignocellulosic biomass has been deemed an alternative to depleting fossil fuels. In order to improve this technology, we aim to develop robust mathematical models for the enzymatic lignocellulose degradation process. By analyzing 96 groups of previously published and newly obtained lignocellulose saccharification results and fitting them to Weibull distribution, we discovered Weibull statistics can accurately predict lignocellulose saccharification data, regardless of the type of substrates, enzymes and saccharification conditions. A mathematical model for enzymatic lignocellulose degradation was subsequently constructed based on Weibull statistics. Further analysis of the mathematical structure of the model and experimental saccharification data showed the significance of the two parameters in this model. In particular, the λ value, defined the characteristic time, represents the overall performance of the saccharification system. This suggestion was further supported by statistical analysis of experimental saccharification data and analysis of the glucose production levels when λ and n values change. In conclusion, the constructed Weibull statistics-based model can accurately predict lignocellulose hydrolysis behavior and we can use the λ parameter to assess the overall performance of enzymatic lignocellulose degradation. Advantages and potential applications of the model and the λ value in saccharification performance assessment were discussed.

  6. A Weibull statistics-based lignocellulose saccharification model and a built-in parameter accurately predict lignocellulose hydrolysis performance.

    PubMed

    Wang, Mingyu; Han, Lijuan; Liu, Shasha; Zhao, Xuebing; Yang, Jinghua; Loh, Soh Kheang; Sun, Xiaomin; Zhang, Chenxi; Fang, Xu

    2015-09-01

    Renewable energy from lignocellulosic biomass has been deemed an alternative to depleting fossil fuels. In order to improve this technology, we aim to develop robust mathematical models for the enzymatic lignocellulose degradation process. By analyzing 96 groups of previously published and newly obtained lignocellulose saccharification results and fitting them to Weibull distribution, we discovered Weibull statistics can accurately predict lignocellulose saccharification data, regardless of the type of substrates, enzymes and saccharification conditions. A mathematical model for enzymatic lignocellulose degradation was subsequently constructed based on Weibull statistics. Further analysis of the mathematical structure of the model and experimental saccharification data showed the significance of the two parameters in this model. In particular, the λ value, defined the characteristic time, represents the overall performance of the saccharification system. This suggestion was further supported by statistical analysis of experimental saccharification data and analysis of the glucose production levels when λ and n values change. In conclusion, the constructed Weibull statistics-based model can accurately predict lignocellulose hydrolysis behavior and we can use the λ parameter to assess the overall performance of enzymatic lignocellulose degradation. Advantages and potential applications of the model and the λ value in saccharification performance assessment were discussed. PMID:26121186

  7. Precise and accurate assessment of uncertainties in model parameters from stellar interferometry. Application to stellar diameters

    NASA Astrophysics Data System (ADS)

    Lachaume, Regis; Rabus, Markus; Jordan, Andres

    2015-08-01

    In stellar interferometry, the assumption that the observables can be seen as Gaussian, independent variables is the norm. In particular, neither the optical interferometry FITS (OIFITS) format nor the most popular fitting software in the field, LITpro, offer means to specify a covariance matrix or non-Gaussian uncertainties. Interferometric observables are correlated by construct, though. Also, the calibration by an instrumental transfer function ensures that the resulting observables are not Gaussian, even if uncalibrated ones happened to be so.While analytic frameworks have been published in the past, they are cumbersome and there is no generic implementation available. We propose here a relatively simple way of dealing with correlated errors without the need to extend the OIFITS specification or making some Gaussian assumptions. By repeatedly picking at random which interferograms, which calibrator stars, and which are the errors on their diameters, and performing the data processing on the bootstrapped data, we derive a sampling of p(O), the multivariate probability density function (PDF) of the observables O. The results can be stored in a normal OIFITS file. Then, given a model m with parameters P predicting observables O = m(P), we can estimate the PDF of the model parameters f(P) = p(m(P)) by using a density estimation of the observables' PDF p.With observations repeated over different baselines, on nights several days apart, and with a significant set of calibrators systematic errors are de facto taken into account. We apply the technique to a precise and accurate assessment of stellar diameters obtained at the Very Large Telescope Interferometer with PIONIER.

  8. Significance of accurate diffraction corrections for the second harmonic wave in determining the acoustic nonlinearity parameter

    SciTech Connect

    Jeong, Hyunjo; Zhang, Shuzeng; Li, Xiongbing; Barnard, Dan

    2015-09-15

    The accurate measurement of acoustic nonlinearity parameter β for fluids or solids generally requires making corrections for diffraction effects due to finite size geometry of transmitter and receiver. These effects are well known in linear acoustics, while those for second harmonic waves have not been well addressed and therefore not properly considered in previous studies. In this work, we explicitly define the attenuation and diffraction corrections using the multi-Gaussian beam (MGB) equations which were developed from the quasilinear solutions of the KZK equation. The effects of making these corrections are examined through the simulation of β determination in water. Diffraction corrections are found to have more significant effects than attenuation corrections, and the β values of water can be estimated experimentally with less than 5% errors when the exact second harmonic diffraction corrections are used together with the negligible attenuation correction effects on the basis of linear frequency dependence between attenuation coefficients, α{sub 2} ≃ 2α{sub 1}.

  9. Accurate parameters for HD 209458 and its planet from HST spectrophotometry

    NASA Astrophysics Data System (ADS)

    del Burgo, C.; Allende Prieto, C.

    2016-08-01

    We present updated parameters for the star HD 209458 and its transiting giant planet. The stellar angular diameter θ=0.2254±0.0017 mas is obtained from the average ratio between the absolute flux observed with the Hubble Space Telescope and that of the best-fitting Kurucz model atmosphere. This angular diameter represents an improvement in precision of more than four times compared to available interferometric determinations. The stellar radius R⋆=1.20±0.05 R⊙ is ascertained by combining the angular diameter with the Hipparcos trigonometric parallax, which is the main contributor to its uncertainty, and therefore the radius accuracy should be significantly improved with Gaia's measurements. The radius of the exoplanet Rp=1.41±0.06 RJ is derived from the corresponding transit depth in the light curve and our stellar radius. From the model fitting, we accurately determine the effective temperature, Teff=6071±20 K, which is in perfect agreement with the value of 6070±24 K calculated from the angular diameter and the integrated spectral energy distribution. We also find precise values from recent Padova Isochrones, such as R⋆=1.20±0.06 R⊙ and Teff=6099±41 K. We arrive at a consistent picture from these methods and compare the results with those from the literature.

  10. Parameter identification of civil engineering structures

    NASA Technical Reports Server (NTRS)

    Juang, J. N.; Sun, C. T.

    1980-01-01

    This paper concerns the development of an identification method required in determining structural parameter variations for systems subjected to an extended exposure to the environment. The concept of structural identifiability of a large scale structural system in the absence of damping is presented. Three criteria are established indicating that a large number of system parameters (the coefficient parameters of the differential equations) can be identified by a few actuators and sensors. An eight-bay-fifteen-story frame structure is used as example. A simple model is employed for analyzing the dynamic response of the frame structure.

  11. Accurate fundamental parameters and detailed abundance patterns from spectroscopy of 93 solar-type Kepler targets

    NASA Astrophysics Data System (ADS)

    Bruntt, H.; Basu, S.; Smalley, B.; Chaplin, W. J.; Verner, G. A.; Bedding, T. R.; Catala, C.; Gazzano, J.-C.; Molenda-Żakowicz, J.; Thygesen, A. O.; Uytterhoeven, K.; Hekker, S.; Huber, D.; Karoff, C.; Mathur, S.; Mosser, B.; Appourchaux, T.; Campante, T. L.; Elsworth, Y.; García, R. A.; Handberg, R.; Metcalfe, T. S.; Quirion, P.-O.; Régulo, C.; Roxburgh, I. W.; Stello, D.; Christensen-Dalsgaard, J.; Kawaler, S. D.; Kjeldsen, H.; Morris, R. L.; Quintana, E. V.; Sanderfer, D. T.

    2012-06-01

    We present a detailed spectroscopic study of 93 solar-type stars that are targets of the NASA/Kepler mission and provide detailed chemical composition of each target. We find that the overall metallicity is well represented by Fe lines. Relative abundances of light elements (CNO) and α elements are generally higher for low-metallicity stars. Our spectroscopic analysis benefits from the accurately measured surface gravity from the asteroseismic analysis of the Kepler light curves. The accuracy on the log g parameter is better than 0.03 dex and is held fixed in the analysis. We compare our Teff determination with a recent colour calibration of VT-KS [TYCHO V magnitude minus Two Micron All Sky Survey (2MASS) KS magnitude] and find very good agreement and a scatter of only 80 K, showing that for other nearby Kepler targets, this index can be used. The asteroseismic log g values agree very well with the classical determination using Fe I-Fe II balance, although we find a small systematic offset of 0.08 dex (asteroseismic log g values are lower). The abundance patterns of metals, α elements and the light elements (CNO) show that a simple scaling by [Fe/H] is adequate to represent the metallicity of the stars, except for the stars with metallicity below -0.3, where α-enhancement becomes important. However, this is only important for a very small fraction of the Kepler sample. We therefore recommend that a simple scaling with [Fe/H] be employed in the asteroseismic analyses of large ensembles of solar-type stars.

  12. Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation

    PubMed Central

    Ralph, Duncan K.; Matsen, Frederick A.

    2016-01-01

    VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D, or J genes, or from an N-addition (a.k.a. non-templated insertion). Previous work has used simple parametric distributions to model transitions from state to state in a hidden Markov model (HMM) of VDJ recombination, and assumed that mutations occur via the same process across sites. However, codon frame and other effects have been observed to violate these parametric assumptions for such coding sequences, suggesting that a non-parametric approach to modeling the recombination process could be useful. In our paper, we find that indeed large modern data sets suggest a model using parameter-rich per-allele categorical distributions for HMM transition probabilities and per-allele-per-position mutation probabilities, and that using such a model for inference leads to significantly improved results. We present an accurate and efficient BCR sequence annotation software package using a novel HMM “factorization” strategy. This package, called partis (https://github.com/psathyrella/partis/), is built on a new general-purpose HMM compiler that can perform efficient inference given a simple text description of an HMM. PMID:26751373

  13. Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation.

    PubMed

    Ralph, Duncan K; Matsen, Frederick A

    2016-01-01

    VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor (BCR) sequences for a remarkable diversity of antigens. It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop, in particular for broadly-neutralizing antibodies against HIV and influenza. A fundamental step in such sequence analysis is to annotate each base as coming from a specific one of the V, D, or J genes, or from an N-addition (a.k.a. non-templated insertion). Previous work has used simple parametric distributions to model transitions from state to state in a hidden Markov model (HMM) of VDJ recombination, and assumed that mutations occur via the same process across sites. However, codon frame and other effects have been observed to violate these parametric assumptions for such coding sequences, suggesting that a non-parametric approach to modeling the recombination process could be useful. In our paper, we find that indeed large modern data sets suggest a model using parameter-rich per-allele categorical distributions for HMM transition probabilities and per-allele-per-position mutation probabilities, and that using such a model for inference leads to significantly improved results. We present an accurate and efficient BCR sequence annotation software package using a novel HMM "factorization" strategy. This package, called partis (https://github.com/psathyrella/partis/), is built on a new general-purpose HMM compiler that can perform efficient inference given a simple text description of an HMM. PMID:26751373

  14. Effective Temperatures of Selected Main-Sequence Stars with the Most Accurate Parameters

    NASA Astrophysics Data System (ADS)

    Soydugan, F.; Eker, Z.; Soydugan, E.; Bilir, S.; Gökçe, E. Y.; Steer, I.; Tüysüz, M.; Šenyüz, T.; Demircan, O.

    2015-07-01

    In this study we investigate the distributions of the properties of detached double-lined binaries (DBs) in the mass-luminosity, mass-radius, and mass-effective temperature diagrams. We have improved the classical mass-luminosity relation based on the database of DBs by Eker et al. (2014a). Based on the accurate observational data available to us we propose a method for improving the effective temperatures of eclipsing binaries with accurate mass and radius determinations.

  15. Comparing anisotropic displacement parameters in protein structures.

    PubMed

    Merritt, E A

    1999-12-01

    The increasingly widespread use of synchrotron-radiation sources and cryo-preparation of samples in macromolecular crystallography has led to a dramatic increase in the number of macromolecular structures determined at atomic or near-atomic resolution. This permits expansion of the structural model to include anisotropic displacement parameters U(ij) for individual atoms. In order to explore the physical significance of these parameters in protein structures, it is useful to be able to compare quantitatively the electron-density distribution described by the refined U(ij) values associated with corresponding crystallographically independent atoms. This paper presents the derivation of an easily calculated correlation coefficient in real space between two atoms modeled with anisotropic displacement parameters. This measure is used to investigate the degree of similarity between chemically equivalent but crystallographically independent atoms in the set of protein structural models currently available from the Protein Data Bank.

  16. Accurate Atmospheric Parameters at Moderate Resolution Using Spectral Indices: Preliminary Application to the MARVELS Survey

    NASA Astrophysics Data System (ADS)

    Ghezzi, Luan; Dutra-Ferreira, Letícia; Lorenzo-Oliveira, Diego; Porto de Mello, Gustavo F.; Santiago, Basílio X.; De Lee, Nathan; Lee, Brian L.; da Costa, Luiz N.; Maia, Marcio A. G.; Ogando, Ricardo L. C.; Wisniewski, John P.; González Hernández, Jonay I.; Stassun, Keivan G.; Fleming, Scott W.; Schneider, Donald P.; Mahadevan, Suvrath; Cargile, Phillip; Ge, Jian; Pepper, Joshua; Wang, Ji; Paegert, Martin

    2014-12-01

    Studies of Galactic chemical, and dynamical evolution in the solar neighborhood depend on the availability of precise atmospheric parameters (effective temperature T eff, metallicity [Fe/H], and surface gravity log g) for solar-type stars. Many large-scale spectroscopic surveys operate at low to moderate spectral resolution for efficiency in observing large samples, which makes the stellar characterization difficult due to the high degree of blending of spectral features. Therefore, most surveys employ spectral synthesis, which is a powerful technique, but relies heavily on the completeness and accuracy of atomic line databases and can yield possibly correlated atmospheric parameters. In this work, we use an alternative method based on spectral indices to determine the atmospheric parameters of a sample of nearby FGK dwarfs and subgiants observed by the MARVELS survey at moderate resolving power (R ~ 12,000). To avoid a time-consuming manual analysis, we have developed three codes to automatically normalize the observed spectra, measure the equivalent widths of the indices, and, through a comparison of those with values calculated with predetermined calibrations, estimate the atmospheric parameters of the stars. The calibrations were derived using a sample of 309 stars with precise stellar parameters obtained from the analysis of high-resolution FEROS spectra, permitting the low-resolution equivalent widths to be directly related to the stellar parameters. A validation test of the method was conducted with a sample of 30 MARVELS targets that also have reliable atmospheric parameters derived from the high-resolution spectra and spectroscopic analysis based on the excitation and ionization equilibria method. Our approach was able to recover the parameters within 80 K for T eff, 0.05 dex for [Fe/H], and 0.15 dex for log g, values that are lower than or equal to the typical external uncertainties found between different high-resolution analyses. An additional test was

  17. Accurate atmospheric parameters at moderate resolution using spectral indices: Preliminary application to the marvels survey

    SciTech Connect

    Ghezzi, Luan; Da Costa, Luiz N.; Maia, Marcio A. G.; Ogando, Ricardo L. C.; Dutra-Ferreira, Letícia; Lorenzo-Oliveira, Diego; Porto de Mello, Gustavo F.; Santiago, Basílio X.; De Lee, Nathan; Lee, Brian L.; Ge, Jian; Wisniewski, John P.; González Hernández, Jonay I.; Stassun, Keivan G.; Cargile, Phillip; Pepper, Joshua; Fleming, Scott W.; Schneider, Donald P.; Mahadevan, Suvrath; Wang, Ji; and others

    2014-12-01

    Studies of Galactic chemical, and dynamical evolution in the solar neighborhood depend on the availability of precise atmospheric parameters (effective temperature T {sub eff}, metallicity [Fe/H], and surface gravity log g) for solar-type stars. Many large-scale spectroscopic surveys operate at low to moderate spectral resolution for efficiency in observing large samples, which makes the stellar characterization difficult due to the high degree of blending of spectral features. Therefore, most surveys employ spectral synthesis, which is a powerful technique, but relies heavily on the completeness and accuracy of atomic line databases and can yield possibly correlated atmospheric parameters. In this work, we use an alternative method based on spectral indices to determine the atmospheric parameters of a sample of nearby FGK dwarfs and subgiants observed by the MARVELS survey at moderate resolving power (R ∼ 12,000). To avoid a time-consuming manual analysis, we have developed three codes to automatically normalize the observed spectra, measure the equivalent widths of the indices, and, through a comparison of those with values calculated with predetermined calibrations, estimate the atmospheric parameters of the stars. The calibrations were derived using a sample of 309 stars with precise stellar parameters obtained from the analysis of high-resolution FEROS spectra, permitting the low-resolution equivalent widths to be directly related to the stellar parameters. A validation test of the method was conducted with a sample of 30 MARVELS targets that also have reliable atmospheric parameters derived from the high-resolution spectra and spectroscopic analysis based on the excitation and ionization equilibria method. Our approach was able to recover the parameters within 80 K for T {sub eff}, 0.05 dex for [Fe/H], and 0.15 dex for log g, values that are lower than or equal to the typical external uncertainties found between different high-resolution analyses. An

  18. On identifiability of flexible structure parameters

    NASA Technical Reports Server (NTRS)

    Joshi, S. M.; Goglia, G. L.

    1983-01-01

    This report investigates the identifiability of modal parameters of flexible structures. Expressions are derived for Cramer-Rao lower bounds for the modal parameters, that is, frequencies, damping ratios and mode shapes or slopes. The optimal initial state, which maximizes the trace of the Fisher information matrix in the absence of persistent input, is obtained. The concepts discussed are applied to a finite-element model of the 122 meter hoop/column antenna. The numerical results show that the identifiability of the structural frequencies is excellent, followed by that of the damping ratios and the mode-slopes.

  19. Accurate nuclear masses from a three parameter Kohn-Sham DFT approach (BCPM)

    SciTech Connect

    Baldo, M.; Robledo, L. M.; Schuck, P.; Vinas, X.

    2012-10-20

    Given the promising features of the recently proposed Barcelona-Catania-Paris (BCP) functional [1], it is the purpose of this work to still improve on it. It is, for instance, shown that the number of open parameters can be reduced from 4-5 to 2-3, i.e. by practically a factor of two without deteriorating the results.

  20. Accurate parameters of the oldest known rocky-exoplanet hosting system: Kepler-10 revisited

    SciTech Connect

    Fogtmann-Schulz, Alexandra; Hinrup, Brian; Van Eylen, Vincent; Christensen-Dalsgaard, Jørgen; Kjeldsen, Hans; Silva Aguirre, Víctor; Tingley, Brandon

    2014-02-01

    Since the discovery of Kepler-10, the system has received considerable interest because it contains a small, rocky planet which orbits the star in less than a day. The system's parameters, announced by the Kepler team and subsequently used in further research, were based on only five months of data. We have reanalyzed this system using the full span of 29 months of Kepler photometric data, and obtained improved information about its star and the planets. A detailed asteroseismic analysis of the extended time series provides a significant improvement on the stellar parameters: not only can we state that Kepler-10 is the oldest known rocky-planet-harboring system at 10.41 ± 1.36 Gyr, but these parameters combined with improved planetary parameters from new transit fits gives us the radius of Kepler-10b to within just 125 km. A new analysis of the full planetary phase curve leads to new estimates on the planetary temperature and albedo, which remain degenerate in the Kepler band. Our modeling suggests that the flux level during the occultation is slightly lower than at the transit wings, which would imply that the nightside of this planet has a non-negligible temperature.

  1. Fast and accurate search for non-coding RNA pseudoknot structures in genomes

    PubMed Central

    Huang, Zhibin; Wu, Yong; Robertson, Joseph; Feng, Liang; Malmberg, Russell L.; Cai, Liming

    2008-01-01

    Motivation: Searching genomes for non-coding RNAs (ncRNAs) by their secondary structure has become an important goal for bioinformatics. For pseudoknot-free structures, ncRNA search can be effective based on the covariance model and CYK-type dynamic programming. However, the computational difficulty in aligning an RNA sequence to a pseudoknot has prohibited fast and accurate search of arbitrary RNA structures. Our previous work introduced a graph model for RNA pseudoknots and proposed to solve the structure–sequence alignment by graph optimization. Given k candidate regions in the target sequence for each of the n stems in the structure, we could compute a best alignment in time O(ktn) based upon a tree width t decomposition of the structure graph. However, to implement this method to programs that can routinely perform fast yet accurate RNA pseudoknot searches, we need novel heuristics to ensure that, without degrading the accuracy, only a small number of stem candidates need to be examined and a tree decomposition of a small tree width can always be found for the structure graph. Results: The current work builds on the previous one with newly developed preprocessing algorithms to reduce the values for parameters k and t and to implement the search method into a practical program, called RNATOPS, for RNA pseudoknot search. In particular, we introduce techniques, based on probabilistic profiling and distance penalty functions, which can identify for every stem just a small number k (e.g. k ≤ 10) of plausible regions in the target sequence to which the stem needs to align. We also devised a specialized tree decomposition algorithm that can yield tree decomposition of small tree width t (e.g. t ≤ 4) for almost all RNA structure graphs. Our experiments show that with RNATOPS it is possible to routinely search prokaryotic and eukaryotic genomes for specific RNA structures of medium to large sizes, including pseudoknots, with high sensitivity and high

  2. Proline puckering parameters for collagen structure simulations

    SciTech Connect

    Wu, Di

    2015-03-15

    Collagen is made of triple helices rich in proline residues, and hence is influenced by the conformational motions of prolines. Because the backbone motions of prolines are restricted by the helical structures, the only side chain motion—proline puckering—becomes an influential factor that may affect the stability of collagen structures. In molecular simulations, a proper proline puckering population is desired so to yield valid results of the collagen properties. Here we design the proline puckering parameters in order to yield suitable proline puckering populations as demonstrated in the experimental results. We test these parameters in collagen and the proline dipeptide simulations. Compared with the results of the PDB and the quantum calculations, we propose the proline puckering parameters for the selected collagen model simulations.

  3. Beyond Ellipse(s): Accurately Modelling the Isophotal Structure of Galaxies with ISOFIT and CMODEL

    NASA Astrophysics Data System (ADS)

    Ciambur, B. C.

    2015-09-01

    This work introduces a new fitting formalism for isophotes that enables more accurate modeling of galaxies with non-elliptical shapes, such as disk galaxies viewed edge-on or galaxies with X-shaped/peanut bulges. Within this scheme, the angular parameter that defines quasi-elliptical isophotes is transformed from the commonly used, but inappropriate, polar coordinate to the “eccentric anomaly.” This provides a superior description of deviations from ellipticity, better capturing the true isophotal shape. Furthermore, this makes it possible to accurately recover both the surface brightness profile, using the correct azimuthally averaged isophote, and the two-dimensional model of any galaxy: the hitherto ubiquitous, but artificial, cross-like features in residual images are completely removed. The formalism has been implemented into the Image Reduction and Analysis Facility tasks Ellipse and Bmodel to create the new tasks “Isofit,” and “Cmodel.” The new tools are demonstrated here with application to five galaxies, chosen to be representative case-studies for several areas where this technique makes it possible to gain new scientific insight. Specifically: properly quantifying boxy/disky isophotes via the fourth harmonic order in edge-on galaxies, quantifying X-shaped/peanut bulges, higher-order Fourier moments for modeling bars in disks, and complex isophote shapes. Higher order (n > 4) harmonics now become meaningful and may correlate with structural properties, as boxyness/diskyness is known to do. This work also illustrates how the accurate construction, and subtraction, of a model from a galaxy image facilitates the identification and recovery of over-lapping sources such as globular clusters and the optical counterparts of X-ray sources.

  4. Accurate Prediction of Severe Allergic Reactions by a Small Set of Environmental Parameters (NDVI, Temperature)

    PubMed Central

    Andrianaki, Maria; Azariadis, Kalliopi; Kampouri, Errika; Theodoropoulou, Katerina; Lavrentaki, Katerina; Kastrinakis, Stelios; Kampa, Marilena; Agouridakis, Panagiotis; Pirintsos, Stergios; Castanas, Elias

    2015-01-01

    Severe allergic reactions of unknown etiology,necessitating a hospital visit, have an important impact in the life of affected individuals and impose a major economic burden to societies. The prediction of clinically severe allergic reactions would be of great importance, but current attempts have been limited by the lack of a well-founded applicable methodology and the wide spatiotemporal distribution of allergic reactions. The valid prediction of severe allergies (and especially those needing hospital treatment) in a region, could alert health authorities and implicated individuals to take appropriate preemptive measures. In the present report we have collecterd visits for serious allergic reactions of unknown etiology from two major hospitals in the island of Crete, for two distinct time periods (validation and test sets). We have used the Normalized Difference Vegetation Index (NDVI), a satellite-based, freely available measurement, which is an indicator of live green vegetation at a given geographic area, and a set of meteorological data to develop a model capable of describing and predicting severe allergic reaction frequency. Our analysis has retained NDVI and temperature as accurate identifiers and predictors of increased hospital severe allergic reactions visits. Our approach may contribute towards the development of satellite-based modules, for the prediction of severe allergic reactions in specific, well-defined geographical areas. It could also probably be used for the prediction of other environment related diseases and conditions. PMID:25794106

  5. An Accurate and Generic Testing Approach to Vehicle Stability Parameters Based on GPS and INS

    PubMed Central

    Miao, Zhibin; Zhang, Hongtian; Zhang, Jinzhu

    2015-01-01

    With the development of the vehicle industry, controlling stability has become more and more important. Techniques of evaluating vehicle stability are in high demand. As a common method, usually GPS sensors and INS sensors are applied to measure vehicle stability parameters by fusing data from the two system sensors. Although prior model parameters should be recognized in a Kalman filter, it is usually used to fuse data from multi-sensors. In this paper, a robust, intelligent and precise method to the measurement of vehicle stability is proposed. First, a fuzzy interpolation method is proposed, along with a four-wheel vehicle dynamic model. Second, a two-stage Kalman filter, which fuses the data from GPS and INS, is established. Next, this approach is applied to a case study vehicle to measure yaw rate and sideslip angle. The results show the advantages of the approach. Finally, a simulation and real experiment is made to verify the advantages of this approach. The experimental results showed the merits of this method for measuring vehicle stability, and the approach can meet the design requirements of a vehicle stability controller. PMID:26690154

  6. Can a combination of ultrasonographic parameters accurately evaluate concussion and guide return-to-play decisions?

    PubMed

    Cartwright, Michael S; Dupuis, Janae E; Bargoil, Jessica M; Foster, Dana C

    2015-09-01

    Mild traumatic brain injury, often referred to as concussion, is a common, potentially debilitating, and costly condition. One of the main challenges in diagnosing and managing concussion is that there is not currently an objective test to determine the presence of a concussion and to guide return-to-play decisions for athletes. Traditional neuroimaging tests, such as brain magnetic resonance imaging, are normal in concussion, and therefore diagnosis and management are guided by reported symptoms. Some athletes will under-report symptoms to accelerate their return-to-play and others will over-report symptoms out of fear of further injury or misinterpretation of underlying conditions, such as migraine headache. Therefore, an objective measure is needed to assist in several facets of concussion management. Limited data in animal and human testing indicates that intracranial pressure increases slightly and cerebrovascular reactivity (the ability of the cerebral arteries to auto-regulate in response to changes in carbon dioxide) decreases slightly following mild traumatic brain injury. We hypothesize that a combination of ultrasonographic measurements (optic nerve sheath diameter and transcranial Doppler assessment of cerebrovascular reactivity) into a single index will allow for an accurate and non-invasive measurement of intracranial pressure and cerebrovascular reactivity, and this index will be clinically relevant and useful for guiding concussion diagnosis and management. Ultrasound is an ideal modality for the evaluation of concussion because it is portable (allowing for evaluation in many settings, such as on the playing field or in a combat zone), radiation-free (making repeat scans safe), and relatively inexpensive (resulting in nearly universal availability). This paper reviews the literature supporting our hypothesis that an ultrasonographic index can assist in the diagnosis and management of concussion, and it also presents limited data regarding the

  7. Can a combination of ultrasonographic parameters accurately evaluate concussion and guide return-to-play decisions?

    PubMed

    Cartwright, Michael S; Dupuis, Janae E; Bargoil, Jessica M; Foster, Dana C

    2015-09-01

    Mild traumatic brain injury, often referred to as concussion, is a common, potentially debilitating, and costly condition. One of the main challenges in diagnosing and managing concussion is that there is not currently an objective test to determine the presence of a concussion and to guide return-to-play decisions for athletes. Traditional neuroimaging tests, such as brain magnetic resonance imaging, are normal in concussion, and therefore diagnosis and management are guided by reported symptoms. Some athletes will under-report symptoms to accelerate their return-to-play and others will over-report symptoms out of fear of further injury or misinterpretation of underlying conditions, such as migraine headache. Therefore, an objective measure is needed to assist in several facets of concussion management. Limited data in animal and human testing indicates that intracranial pressure increases slightly and cerebrovascular reactivity (the ability of the cerebral arteries to auto-regulate in response to changes in carbon dioxide) decreases slightly following mild traumatic brain injury. We hypothesize that a combination of ultrasonographic measurements (optic nerve sheath diameter and transcranial Doppler assessment of cerebrovascular reactivity) into a single index will allow for an accurate and non-invasive measurement of intracranial pressure and cerebrovascular reactivity, and this index will be clinically relevant and useful for guiding concussion diagnosis and management. Ultrasound is an ideal modality for the evaluation of concussion because it is portable (allowing for evaluation in many settings, such as on the playing field or in a combat zone), radiation-free (making repeat scans safe), and relatively inexpensive (resulting in nearly universal availability). This paper reviews the literature supporting our hypothesis that an ultrasonographic index can assist in the diagnosis and management of concussion, and it also presents limited data regarding the

  8. Can a Combination of Ultrasonographic Parameters Accurately Evaluate Concussion and Guide Return-to-Play Decisions?

    PubMed Central

    Cartwright, Michael S.; Dupuis, Janae E.; Bargoil, Jessica M.; Foster, Dana C.

    2015-01-01

    Mild traumatic brain injury, often referred to as concussion, is a common, potentially debilitating, and costly condition. One of the main challenges in diagnosing and managing concussion is that there is not currently an objective test to determine the presence of a concussion and to guide return-to-play decisions for athletes. Traditional neuroimaging tests, such as brain magnetic resonance imaging, are normal in concussion, and therefore diagnosis and management are guided by reported symptoms. Some athletes will under-report symptoms to accelerate their return-to-play and others will over-report symptoms out of fear of further injury or misinterpretation of underlying conditions, such as migraine headache. Therefore, an objective measure is needed to assist in several facets of concussion management. Limited data in animal and human testing indicates that intracranial pressure increases slightly and cerebrovascular reactivity (the ability of the cerebral arteries to auto-regulate in response to changes in carbon dioxide) decreases slightly following mild traumatic brain injury. We hypothesize that a combination of ultrasonographic measurements (optic nerve sheath diameter and transcranial Doppler assessment of cerebrovascular reactivity) into a single index will allow for an accurate and non-invasive measurement of intracranial pressure and cerebrovascular reactivity, and this index will be clinically relevant and useful for guiding concussion diagnosis and management. Ultrasound is an ideal modality for the evaluation of concussion because it is portable (allowing for evaluation in many settings, such as on the playing field or in a combat zone), radiation-free (making repeat scans safe), and relatively inexpensive (resulting in nearly universal availability). This paper reviews the literature supporting our hypothesis that an ultrasonographic index can assist in the diagnosis and management of concussion, and it also presents limited data regarding the

  9. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

    PubMed Central

    Sela, Itamar; Ashkenazy, Haim; Katoh, Kazutaka; Pupko, Tal

    2015-01-01

    Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. However, from the same set of sequences different MSAs are often inferred, depending on the methodologies used and the assumed parameters. Much effort has recently been devoted to improving the ability to identify unreliable alignment regions. Detecting such unreliable regions was previously shown to be important for downstream analyses relying on MSAs, such as the detection of positive selection. Here we developed GUIDANCE2, a new integrative methodology that accounts for: (i) uncertainty in the process of indel formation, (ii) uncertainty in the assumed guide tree and (iii) co-optimal solutions in the pairwise alignments, used as building blocks in progressive alignment algorithms. We compared GUIDANCE2 with seven methodologies to detect unreliable MSA regions using extensive simulations and empirical benchmarks. We show that GUIDANCE2 outperforms all previously developed methodologies. Furthermore, GUIDANCE2 also provides a set of alternative MSAs which can be useful for downstream analyses. The novel algorithm is implemented as a web-server, available at: http://guidance.tau.ac.il. PMID:25883146

  10. Line Shape Parameters for CO_2 Transitions: Accurate Predictions from Complex Robert-Bonamy Calculations

    NASA Astrophysics Data System (ADS)

    Lamouroux, Julien; Gamache, Robert R.

    2013-06-01

    A model for the prediction of the vibrational dependence of CO_2 half-widths and line shifts for several broadeners, based on a modification of the model proposed by Gamache and Hartmann, is presented. This model allows the half-widths and line shifts for a ro-vibrational transition to be expressed in terms of the number of vibrational quanta exchanged in the transition raised to a power p and a reference ro-vibrational transition. Complex Robert-Bonamy calculations were made for 24 bands for lower rotational quantum numbers J'' from 0 to 160 for N_2-, O_2-, air-, and self-collisions with CO_2. In the model a Quantum Coordinate is defined by (c_1 Δν_1 + c_2 Δν_2 + c_3 Δν_3)^p where a linear least-squares fit to the data by the model expression is made. The model allows the determination of the slope and intercept as a function of rotational transition, broadening gas, and temperature. From these fit data, the half-width, line shift, and the temperature dependence of the half-width can be estimated for any ro-vibrational transition, allowing spectroscopic CO_2 databases to have complete information for the line shape parameters. R. R. Gamache, J.-M. Hartmann, J. Quant. Spectrosc. Radiat. Transfer. {{83}} (2004), 119. R. R. Gamache, J. Lamouroux, J. Quant. Spectrosc. Radiat. Transfer. {{117}} (2013), 93.

  11. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters.

    PubMed

    Sela, Itamar; Ashkenazy, Haim; Katoh, Kazutaka; Pupko, Tal

    2015-07-01

    Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. However, from the same set of sequences different MSAs are often inferred, depending on the methodologies used and the assumed parameters. Much effort has recently been devoted to improving the ability to identify unreliable alignment regions. Detecting such unreliable regions was previously shown to be important for downstream analyses relying on MSAs, such as the detection of positive selection. Here we developed GUIDANCE2, a new integrative methodology that accounts for: (i) uncertainty in the process of indel formation, (ii) uncertainty in the assumed guide tree and (iii) co-optimal solutions in the pairwise alignments, used as building blocks in progressive alignment algorithms. We compared GUIDANCE2 with seven methodologies to detect unreliable MSA regions using extensive simulations and empirical benchmarks. We show that GUIDANCE2 outperforms all previously developed methodologies. Furthermore, GUIDANCE2 also provides a set of alternative MSAs which can be useful for downstream analyses. The novel algorithm is implemented as a web-server, available at: http://guidance.tau.ac.il.

  12. Accurate Analytical and Statistical Approaches to Reduce O-C Discrepancies in the Precessional Parameters

    NASA Astrophysics Data System (ADS)

    Martínez, M. J.; Marco, F. J.; López, J. A.

    2009-02-01

    The Hipparcos catalog provides a reference frame at optical wavelengths for the new International Celestial Reference System (ICRS). This new reference system was adopted following the resolution agreed at the 23rd IAU General Assembly held in Kyoto in 1997. Differences in the Hipparcos system of proper motions and the previous materialization of the reference frame, the FK5, are expected to be caused only by the combined effects of the motion of the equinox of the FK5 and the precession of the equator and the ecliptic. Several authors have pointed out an inconsistency between the differences in proper motion of the Hipparcos-FK5 and the correction of the precessional values derived from VLBI and lunar laser ranging (LLR) observations. Most of them have claimed that these discrepancies are due to slightly biased proper motions in the FK5 catalog. The different mathematical models that have been employed to explain these errors have not fully accounted for the discrepancies in the correction of the precessional parameters. Our goal here is to offer an explanation for this fact. We propose the use of independent parametric and nonparametric models. The introduction of a nonparametric model, combined with the inner product in the square integrable functions over the unitary sphere, would give us values which do not depend on the possible interdependencies existing in the data set. The evidence shows that zonal studies are needed. This would lead us to introduce a local nonparametric model. All these models will provide independent corrections to the precessional values, which could then be compared in order to study the reliability in each case. Finally, we obtain values for the precession corrections that are very consistent with those that are currently adopted.

  13. Accurate response surface approximations for weight equations based on structural optimization

    NASA Astrophysics Data System (ADS)

    Papila, Melih

    Accurate weight prediction methods are vitally important for aircraft design optimization. Therefore, designers seek weight prediction techniques with low computational cost and high accuracy, and usually require a compromise between the two. The compromise can be achieved by combining stress analysis and response surface (RS) methodology. While stress analysis provides accurate weight information, RS techniques help to transmit effectively this information to the optimization procedure. The focus of this dissertation is structural weight equations in the form of RS approximations and their accuracy when fitted to results of structural optimizations that are based on finite element analyses. Use of RS methodology filters out the numerical noise in structural optimization results and provides a smooth weight function that can easily be used in gradient-based configuration optimization. In engineering applications RS approximations of low order polynomials are widely used, but the weight may not be modeled well by low-order polynomials, leading to bias errors. In addition, some structural optimization results may have high-amplitude errors (outliers) that may severely affect the accuracy of the weight equation. Statistical techniques associated with RS methodology are sought in order to deal with these two difficulties: (1) high-amplitude numerical noise (outliers) and (2) approximation model inadequacy. The investigation starts with reducing approximation error by identifying and repairing outliers. A potential reason for outliers in optimization results is premature convergence, and outliers of such nature may be corrected by employing different convergence settings. It is demonstrated that outlier repair can lead to accuracy improvements over the more standard approach of removing outliers. The adequacy of approximation is then studied by a modified lack-of-fit approach, and RS errors due to the approximation model are reduced by using higher order polynomials. In

  14. Estimating Building Simulation Parameters via Bayesian Structure Learning

    SciTech Connect

    Edwards, Richard E; New, Joshua Ryan; Parker, Lynne Edwards

    2013-01-01

    Many key building design policies are made using sophisticated computer simulations such as EnergyPlus (E+), the DOE flagship whole-building energy simulation engine. E+ and other sophisticated computer simulations have several major problems. The two main issues are 1) gaps between the simulation model and the actual structure, and 2) limitations of the modeling engine's capabilities. Currently, these problems are addressed by having an engineer manually calibrate simulation parameters to real world data or using algorithmic optimization methods to adjust the building parameters. However, some simulations engines, like E+, are computationally expensive, which makes repeatedly evaluating the simulation engine costly. This work explores addressing this issue by automatically discovering the simulation's internal input and output dependencies from 20 Gigabytes of E+ simulation data, future extensions will use 200 Terabytes of E+ simulation data. The model is validated by inferring building parameters for E+ simulations with ground truth building parameters. Our results indicate that the model accurately represents parameter means with some deviation from the means, but does not support inferring parameter values that exist on the distribution's tail.

  15. Structural Parameters of the Small Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    Knierman, K.; Zaritsky, D.

    2002-05-01

    Using UBVI photometry from the Magellanic Cloud Photometric Survey, we measure the structural parameters of the Small Magellanic Cloud. By selecting different stellar populations, we create star count maps of the young, intermediate, and old population of the Small Magellanic Cloud. Ellipse fitting to the contours of the density of the intermediate and old populations rather than to the luminosity, which is weighted toward the young stars, enables us to study the dynamically-relaxed stellar populations. We discuss related topics such as our determination of the center of the galaxy, the inclination of the system to the line-of-sight, and the line-of-sight depth of the SMC.

  16. Optimization of tissue physical parameters for accurate temperature estimation from finite-element simulation of radiofrequency ablation

    NASA Astrophysics Data System (ADS)

    Subramanian, Swetha; Mast, T. Douglas

    2015-09-01

    Computational finite element models are commonly used for the simulation of radiofrequency ablation (RFA) treatments. However, the accuracy of these simulations is limited by the lack of precise knowledge of tissue parameters. In this technical note, an inverse solver based on the unscented Kalman filter (UKF) is proposed to optimize values for specific heat, thermal conductivity, and electrical conductivity resulting in accurately simulated temperature elevations. A total of 15 RFA treatments were performed on ex vivo bovine liver tissue. For each RFA treatment, 15 finite-element simulations were performed using a set of deterministically chosen tissue parameters to estimate the mean and variance of the resulting tissue ablation. The UKF was implemented as an inverse solver to recover the specific heat, thermal conductivity, and electrical conductivity corresponding to the measured area of the ablated tissue region, as determined from gross tissue histology. These tissue parameters were then employed in the finite element model to simulate the position- and time-dependent tissue temperature. Results show good agreement between simulated and measured temperature.

  17. Optimization of tissue physical parameters for accurate temperature estimation from finite-element simulation of radiofrequency ablation.

    PubMed

    Subramanian, Swetha; Mast, T Douglas

    2015-10-01

    Computational finite element models are commonly used for the simulation of radiofrequency ablation (RFA) treatments. However, the accuracy of these simulations is limited by the lack of precise knowledge of tissue parameters. In this technical note, an inverse solver based on the unscented Kalman filter (UKF) is proposed to optimize values for specific heat, thermal conductivity, and electrical conductivity resulting in accurately simulated temperature elevations. A total of 15 RFA treatments were performed on ex vivo bovine liver tissue. For each RFA treatment, 15 finite-element simulations were performed using a set of deterministically chosen tissue parameters to estimate the mean and variance of the resulting tissue ablation. The UKF was implemented as an inverse solver to recover the specific heat, thermal conductivity, and electrical conductivity corresponding to the measured area of the ablated tissue region, as determined from gross tissue histology. These tissue parameters were then employed in the finite element model to simulate the position- and time-dependent tissue temperature. Results show good agreement between simulated and measured temperature. PMID:26352462

  18. Accurate determination of atomic structure of multiwalled carbon nanotubes by nondestructive nanobeam electron diffraction

    SciTech Connect

    Liu Zejian; Zhang Qi; Qin Luchang

    2005-05-09

    We report a method that allows direct, systematic, and accurate determination of the atomic structure of multiwalled carbon nanotubes by analyzing the scattering intensities on the nonequatorial layer lines in the electron diffraction pattern. Complete structure determination of a quadruple-walled carbon nanotube is described as an example, and it was found that the intertubular distance varied from 0.36 nm to 0.5 nm with a mean value of 0.42 nm.

  19. Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions

    PubMed Central

    Chen, Xiaolin; Luo, Zhihong; Li, Jiaming; Ning, Chuangang

    2016-01-01

    Ionization potential (IP) is defined as the amount of energy required to remove the most loosely bound electron of an atom, while electron affinity (EA) is defined as the amount of energy released when an electron is attached to a neutral atom. Both IP and EA are critical for understanding chemical properties of an element. In contrast to accurate IPs and structures of neutral atoms, EAs and structures of negative ions are relatively unexplored, especially for the transition metal anions. Here, we report the accurate EA value of Fe and fine structures of Fe− using the slow electron velocity imaging method. These measurements yield a very accurate EA value of Fe, 1235.93(28) cm−1 or 153.236(34) meV. The fine structures of Fe− were also successfully resolved. The present work provides a reliable benchmark for theoretical calculations, and also paves the way for improving the EA measurements of other transition metal atoms to the sub cm−1 accuracy. PMID:27138292

  20. Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions

    NASA Astrophysics Data System (ADS)

    Chen, Xiaolin; Luo, Zhihong; Li, Jiaming; Ning, Chuangang

    2016-05-01

    Ionization potential (IP) is defined as the amount of energy required to remove the most loosely bound electron of an atom, while electron affinity (EA) is defined as the amount of energy released when an electron is attached to a neutral atom. Both IP and EA are critical for understanding chemical properties of an element. In contrast to accurate IPs and structures of neutral atoms, EAs and structures of negative ions are relatively unexplored, especially for the transition metal anions. Here, we report the accurate EA value of Fe and fine structures of Fe‑ using the slow electron velocity imaging method. These measurements yield a very accurate EA value of Fe, 1235.93(28) cm‑1 or 153.236(34) meV. The fine structures of Fe‑ were also successfully resolved. The present work provides a reliable benchmark for theoretical calculations, and also paves the way for improving the EA measurements of other transition metal atoms to the sub cm‑1 accuracy.

  1. Accurate Electron Affinity of Iron and Fine Structures of Negative Iron ions.

    PubMed

    Chen, Xiaolin; Luo, Zhihong; Li, Jiaming; Ning, Chuangang

    2016-01-01

    Ionization potential (IP) is defined as the amount of energy required to remove the most loosely bound electron of an atom, while electron affinity (EA) is defined as the amount of energy released when an electron is attached to a neutral atom. Both IP and EA are critical for understanding chemical properties of an element. In contrast to accurate IPs and structures of neutral atoms, EAs and structures of negative ions are relatively unexplored, especially for the transition metal anions. Here, we report the accurate EA value of Fe and fine structures of Fe(-) using the slow electron velocity imaging method. These measurements yield a very accurate EA value of Fe, 1235.93(28) cm(-1) or 153.236(34) meV. The fine structures of Fe(-) were also successfully resolved. The present work provides a reliable benchmark for theoretical calculations, and also paves the way for improving the EA measurements of other transition metal atoms to the sub cm(-1) accuracy. PMID:27138292

  2. Dielectric-dependent Density Functionals for Accurate Electronic Structure Calculations of Molecules and Solids

    NASA Astrophysics Data System (ADS)

    Skone, Jonathan; Govoni, Marco; Galli, Giulia

    Dielectric-dependent hybrid [DDH] functionals have recently been shown to yield highly accurate energy gaps and dielectric constants for a wide variety of solids, at a computational cost considerably less than standard GW calculations. The fraction of exact exchange included in the definition of DDH functionals depends (self-consistently) on the dielectric constant of the material. In the present talk we introduce a range-separated (RS) version of DDH functionals where short and long-range components are matched using material dependent, non-empirical parameters. Comparing with state of the art GW calculations and experiment, we show that such RS hybrids yield accurate electronic properties of both molecules and solids, including energy gaps, photoelectron spectra and absolute ionization potentials. This work was supported by NSF-CCI Grant Number NSF-CHE-0802907 and DOE-BES.

  3. Parameter identification of material constants in a composite shell structure

    SciTech Connect

    Martinez, D.R.; Carne, T.G.

    1988-01-01

    One of the basic requirements in engineering analysis is the development of a mathematical model describing the system. Frequently, comparisons with test data are used as a measurement of the adequacy of the model. An attempt is typically made to update or improve the model to provide a test-verified analysis tool. System identification provides a systematic procedure for accomplishing this task. The terms system identification, parameter estimation, and model correlation all refer to techniques that use test information to update or verify mathematical models. The goal of system identification is to improve the correlation of model predictions with measured test data, and produce accurate, predictive models. For nonmetallic structures the modeling task is often difficult due to uncertainties in the elastic constants. In this work a parameter identification procedure was used to determine the elastic constants of a cylindrical, graphite epoxy composite shell. A finite element model of the shell was created, which included uncertain orthotropic elastic constants. A modal survey test was then performed on the shell. The resulting modal data, along with the finite element model of the shell, were used in a Bayes estimation algorithm. This permitted the use of covariance matrices to weight the confidence in the initial parameter values as well as confidence in the measured test data. The estimation procedure also employed the concept of successive linearization to obtain an approximate solution to the original nonlinear estimation problem. 17 refs., 7 figs.

  4. An accurate, efficient algorithm for calculation of quantum transport in extended structures

    SciTech Connect

    Godin, T.J.; Haydock, R.

    1994-05-01

    In device structures with dimensions comparable to carrier inelastic scattering lengths, the quantum nature of carriers will cause interference effects that cannot be modeled by conventional techniques. The basic equations that govern these ``quantum`` circuit elements present significant numerical challenges. The authors describe the block recursion method, an accurate, efficient method for solving the quantum circuit problem. They demonstrate this method by modeling dirty inversion layers.

  5. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers.

    PubMed

    Hattne, Johan; Echols, Nathaniel; Tran, Rosalie; Kern, Jan; Gildea, Richard J; Brewster, Aaron S; Alonso-Mori, Roberto; Glöckner, Carina; Hellmich, Julia; Laksmono, Hartawan; Sierra, Raymond G; Lassalle-Kaiser, Benedikt; Lampe, Alyssa; Han, Guangye; Gul, Sheraz; DiFiore, Dörte; Milathianaki, Despina; Fry, Alan R; Miahnahri, Alan; White, William E; Schafer, Donald W; Seibert, M Marvin; Koglin, Jason E; Sokaras, Dimosthenis; Weng, Tsu-Chien; Sellberg, Jonas; Latimer, Matthew J; Glatzel, Pieter; Zwart, Petrus H; Grosse-Kunstleve, Ralf W; Bogan, Michael J; Messerschmidt, Marc; Williams, Garth J; Boutet, Sébastien; Messinger, Johannes; Zouni, Athina; Yano, Junko; Bergmann, Uwe; Yachandra, Vittal K; Adams, Paul D; Sauter, Nicholas K

    2014-05-01

    X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements.

  6. Order parameter for structural heterogeneity in disordered solids.

    PubMed

    Tong, Hua; Xu, Ning

    2014-07-01

    We construct a structural order parameter from the energy equipartition of normal modes of vibration to quantify the structural heterogeneity in disordered solids. The order parameter exhibits strong spatial correlations with low-temperature dynamics and local structural entropy. To characterize the role of particles with the most defective local structures identified by the order parameter, we pin them and measure the system response. It turns out that particles with the largest value of the order parameter are responsible for the quasilocalized low-frequency vibration, instability, softening, and nonaffinity of disordered solids. The order parameter thus crucially links the heterogeneous structure to low-temperature dynamics and mechanical properties of disordered solids.

  7. CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval

    PubMed Central

    Karim, Rezaul; Aziz, Mohd. Momin Al; Shatabda, Swakkhar; Rahman, M. Sohel; Mia, Md. Abul Kashem; Zaman, Farhana; Rakin, Salman

    2015-01-01

    The number of entries in a structural database of proteins is increasing day by day. Methods for retrieving protein tertiary structures from such a large database have turn out to be the key to comparative analysis of structures that plays an important role to understand proteins and their functions. In this paper, we present fast and accurate methods for the retrieval of proteins having tertiary structures similar to a query protein from a large database. Our proposed methods borrow ideas from the field of computer vision. The speed and accuracy of our methods come from the two newly introduced features- the co-occurrence matrix of the oriented gradient and pyramid histogram of oriented gradient- and the use of Euclidean distance as the distance measure. Experimental results clearly indicate the superiority of our approach in both running time and accuracy. Our method is readily available for use from this website: http://research.buet.ac.bd:8080/Comograd/. PMID:26293226

  8. Reconstruction of biofilm images: combining local and global structural parameters

    SciTech Connect

    Resat, Haluk; Renslow, Ryan S.; Beyenal, Haluk

    2014-11-07

    Digitized images can be used for quantitative comparison of biofilms grown under different conditions. Using biofilm image reconstruction, it was previously found that biofilms with a completely different look can have nearly identical structural parameters and that the most commonly utilized global structural parameters were not sufficient to uniquely define these biofilms. Here, additional local and global parameters are introduced to show that these parameters considerably increase the reliability of the image reconstruction process. Assessment using human evaluators indicated that the correct identification rate of the reconstructed images increased from 50% to 72% with the introduction of the new parameters into the reconstruction procedure. An expanded set of parameters especially improved the identification of biofilm structures with internal orientational features and of structures in which colony sizes and spatial locations varied. Hence, the newly introduced structural parameter sets helped to better classify the biofilms by incorporating finer local structural details into the reconstruction process.

  9. Parameter identification of material constants in a composite shell structure

    NASA Technical Reports Server (NTRS)

    Martinez, David R.; Carne, Thomas G.

    1988-01-01

    One of the basic requirements in engineering analysis is the development of a mathematical model describing the system. Frequently comparisons with test data are used as a measurement of the adequacy of the model. An attempt is typically made to update or improve the model to provide a test verified analysis tool. System identification provides a systematic procedure for accomplishing this task. The terms system identification, parameter estimation, and model correlation all refer to techniques that use test information to update or verify mathematical models. The goal of system identification is to improve the correlation of model predictions with measured test data, and produce accurate, predictive models. For nonmetallic structures the modeling task is often difficult due to uncertainties in the elastic constants. A finite element model of the shell was created, which included uncertain orthotropic elastic constants. A modal survey test was then performed on the shell. The resulting modal data, along with the finite element model of the shell, were used in a Bayes estimation algorithm. This permitted the use of covariance matrices to weight the confidence in the initial parameter values as well as confidence in the measured test data. The estimation procedure also employed the concept of successive linearization to obtain an approximate solution to the original nonlinear estimation problem.

  10. Accurate calculation of control-augmented structural eigenvalue sensitivities using reduced-order models

    NASA Technical Reports Server (NTRS)

    Livne, Eli

    1989-01-01

    A method is presented for generating mode shapes for model order reduction in a way that leads to accurate calculation of eigenvalue derivatives and eigenvalues for a class of control augmented structures. The method is based on treating degrees of freedom where control forces act or masses are changed in a manner analogous to that used for boundary degrees of freedom in component mode synthesis. It is especially suited for structures controlled by a small number of actuators and/or tuned by a small number of concentrated masses whose positions are predetermined. A control augmented multispan beam with closely spaced natural frequencies is used for numerical experimentation. A comparison with reduced-order eigenvalue sensitivity calculations based on the normal modes of the structure shows that the method presented produces significant improvements in accuracy.

  11. Screened exchange hybrid density functional for accurate and efficient structures and interaction energies.

    PubMed

    Brandenburg, Jan Gerit; Caldeweyher, Eike; Grimme, Stefan

    2016-06-21

    We extend the recently introduced PBEh-3c global hybrid density functional [S. Grimme et al., J. Chem. Phys., 2015, 143, 054107] by a screened Fock exchange variant based on the Henderson-Janesko-Scuseria exchange hole model. While the excellent performance of the global hybrid is maintained for small covalently bound molecules, its performance for computed condensed phase mass densities is further improved. Most importantly, a speed up of 30 to 50% can be achieved and especially for small orbital energy gap cases, the method is numerically much more robust. The latter point is important for many applications, e.g., for metal-organic frameworks, organic semiconductors, or protein structures. This enables an accurate density functional based electronic structure calculation of a full DNA helix structure on a single core desktop computer which is presented as an example in addition to comprehensive benchmark results. PMID:27240749

  12. Accurate Damage Location in Complex Composite Structures and Industrial Environments using Acoustic Emission

    NASA Astrophysics Data System (ADS)

    Eaton, M.; Pearson, M.; Lee, W.; Pullin, R.

    2015-07-01

    The ability to accurately locate damage in any given structure is a highly desirable attribute for an effective structural health monitoring system and could help to reduce operating costs and improve safety. This becomes a far greater challenge in complex geometries and materials, such as modern composite airframes. The poor translation of promising laboratory based SHM demonstrators to industrial environments forms a barrier to commercial up take of technology. The acoustic emission (AE) technique is a passive NDT method that detects elastic stress waves released by the growth of damage. It offers very sensitive damage detection, using a sparse array of sensors to detect and globally locate damage within a structure. However its application to complex structures commonly yields poor accuracy due to anisotropic wave propagation and the interruption of wave propagation by structural features such as holes and thickness changes. This work adopts an empirical mapping technique for AE location, known as Delta T Mapping, which uses experimental training data to account for such structural complexities. The technique is applied to a complex geometry composite aerospace structure undergoing certification testing. The component consists of a carbon fibre composite tube with varying wall thickness and multiple holes, that was loaded under bending. The damage location was validated using X-ray CT scanning and the Delta T Mapping technique was shown to improve location accuracy when compared with commercial algorithms. The onset and progression of damage were monitored throughout the test and used to inform future design iterations.

  13. 5D model for accurate representation and visualization of dynamic cardiac structures

    NASA Astrophysics Data System (ADS)

    Lin, Wei-te; Robb, Richard A.

    2000-05-01

    Accurate cardiac modeling is challenging due to the intricate structure and complex contraction patterns of myocardial tissues. Fast imaging techniques can provide 4D structural information acquired as a sequence of 3D images throughout the cardiac cycle. To mode. The beating heart, we created a physics-based surface model that deforms between successive time point in the cardiac cycle. 3D images of canine hearts were acquired during one complete cardiac cycle using the DSR and the EBCT. The left ventricle of the first time point is reconstructed as a triangular mesh. A mass-spring physics-based deformable mode,, which can expand and shrink with local contraction and stretching forces distributed in an anatomically accurate simulation of cardiac motion, is applied to the initial mesh and allows the initial mesh to deform to fit the left ventricle in successive time increments of the sequence. The resulting 4D model can be interactively transformed and displayed with associated regional electrical activity mapped onto anatomic surfaces, producing a 5D model, which faithfully exhibits regional cardiac contraction and relaxation patterns over the entire heart. The model faithfully represents structural changes throughout the cardiac cycle. Such models provide the framework for minimizing the number of time points required to usefully depict regional motion of myocardium and allow quantitative assessment of regional myocardial motion. The electrical activation mapping provides spatial and temporal correlation within the cardiac cycle. In procedures which as intra-cardiac catheter ablation, visualization of the dynamic model can be used to accurately localize the foci of myocardial arrhythmias and guide positioning of catheters for optimal ablation.

  14. The crystallization of biological macromolecules under microgravity: a way to more accurate three-dimensional structures?

    PubMed

    Lorber, Bernard

    2002-09-23

    The crystallization of proteins and other biological particles (including nucleic acids, nucleo-protein complexes and large assemblies such as nucleosomes, ribosomal subunits or viruses) in a microgravity environment can produce crystals having lesser defects than crystals prepared under normal gravity on earth. Such microgravity-grown crystals can diffract X-rays to a higher resolution and have a lower mosaic spread. The inferred electron density maps can be richer in details owing to which more accurate three-dimensional structure models can be built. Major results reported in this field of research are reviewed. Novel ones obtained with the Advanced Protein Crystallization Facility are presented. For structural biology, practical applications and implications associated with crystallization and crystallography onboard the International Space Station are discussed.

  15. DR-TAMAS: Diffeomorphic Registration for Tensor Accurate Alignment of Anatomical Structures.

    PubMed

    Irfanoglu, M Okan; Nayak, Amritha; Jenkins, Jeffrey; Hutchinson, Elizabeth B; Sadeghi, Neda; Thomas, Cibu P; Pierpaoli, Carlo

    2016-05-15

    In this work, we propose DR-TAMAS (Diffeomorphic Registration for Tensor Accurate alignMent of Anatomical Structures), a novel framework for intersubject registration of Diffusion Tensor Imaging (DTI) data sets. This framework is optimized for brain data and its main goal is to achieve an accurate alignment of all brain structures, including white matter (WM), gray matter (GM), and spaces containing cerebrospinal fluid (CSF). Currently most DTI-based spatial normalization algorithms emphasize alignment of anisotropic structures. While some diffusion-derived metrics, such as diffusion anisotropy and tensor eigenvector orientation, are highly informative for proper alignment of WM, other tensor metrics such as the trace or mean diffusivity (MD) are fundamental for a proper alignment of GM and CSF boundaries. Moreover, it is desirable to include information from structural MRI data, e.g., T1-weighted or T2-weighted images, which are usually available together with the diffusion data. The fundamental property of DR-TAMAS is to achieve global anatomical accuracy by incorporating in its cost function the most informative metrics locally. Another important feature of DR-TAMAS is a symmetric time-varying velocity-based transformation model, which enables it to account for potentially large anatomical variability in healthy subjects and patients. The performance of DR-TAMAS is evaluated with several data sets and compared with other widely-used diffeomorphic image registration techniques employing both full tensor information and/or DTI-derived scalar maps. Our results show that the proposed method has excellent overall performance in the entire brain, while being equivalent to the best existing methods in WM.

  16. Multidimensional Item Response Theory Parameter Estimation with Nonsimple Structure Items

    ERIC Educational Resources Information Center

    Finch, Holmes

    2011-01-01

    Estimation of multidimensional item response theory (MIRT) model parameters can be carried out using the normal ogive with unweighted least squares estimation with the normal-ogive harmonic analysis robust method (NOHARM) software. Previous simulation research has demonstrated that this approach does yield accurate and efficient estimates of item…

  17. Fuzzy Reasoning to More Accurately Determine Void Areas on Optical Micrographs of Composite Structures

    NASA Technical Reports Server (NTRS)

    Dominquez, Jesus A.; Tate, Lanetra C.; Wright, M. Clara; Caraccio, Anne

    2013-01-01

    Accomplishing the best-performing composite matrix (resin) requires that not only the processing method but also the cure cycle generate low-void-content structures. If voids are present, the performance of the composite matrix will be significantly reduced. This is usually noticed by significant reductions in matrix-dominated properties, such as compression and shear strength. Voids in composite materials are areas that are absent of the composite components: matrix and fibers. The characteristics of the voids and their accurate estimation are critical to determine for high performance composite structures. One widely used method of performing void analysis on a composite structure sample is acquiring optical micrographs or Scanning Electron Microscope (SEM) images of lateral sides of the sample and retrieving the void areas within the micrographs/images using an image analysis technique. Segmentation for the retrieval and subsequent computation of void areas within the micrographs/images is challenging as the gray-scaled values of the void areas are close to the gray-scaled values of the matrix leading to the need of manually performing the segmentation based on the histogram of the micrographs/images to retrieve the void areas. The use of an algorithm developed by NASA and based on Fuzzy Reasoning (FR) proved to overcome the difficulty of suitably differentiate void and matrix image areas with similar gray-scaled values leading not only to a more accurate estimation of void areas on composite matrix micrographs but also to a faster void analysis process as the algorithm is fully autonomous.

  18. The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures

    PubMed Central

    Holton, James M; Classen, Scott; Frankel, Kenneth A; Tainer, John A

    2014-01-01

    In macromolecular crystallography, the agreement between observed and predicted structure factors (Rcryst and Rfree) is seldom better than 20%. This is much larger than the estimate of experimental error (Rmerge). The difference between Rcryst and Rmerge is the R-factor gap. There is no such gap in small-molecule crystallography, for which calculated structure factors are generally considered more accurate than the experimental measurements. Perhaps the true noise level of macromolecular data is higher than expected? Or is the gap caused by inaccurate phases that trap refined models in local minima? By generating simulated diffraction patterns using the program MLFSOM, and including every conceivable source of experimental error, we show that neither is the case. Processing our simulated data yielded values that were indistinguishable from those of real data for all crystallographic statistics except the final Rcryst and Rfree. These values decreased to 3.8% and 5.5% for simulated data, suggesting that the reason for high R-factors in macromolecular crystallography is neither experimental error nor phase bias, but rather an underlying inadequacy in the models used to explain our observations. The present inability to accurately represent the entire macromolecule with both its flexibility and its protein-solvent interface may be improved by synergies between small-angle X-ray scattering, computational chemistry and crystallography. The exciting implication of our finding is that macromolecular data contain substantial hidden and untapped potential to resolve ambiguities in the true nature of the nanoscale, a task that the second century of crystallography promises to fulfill. Database Coordinates and structure factors for the real data have been submitted to the Protein Data Bank under accession 4tws. PMID:25040949

  19. Fuzzy Reasoning to More Accurately Determine Void Areas on Optical Micrographs of Composite Structures

    NASA Astrophysics Data System (ADS)

    Dominguez, Jesus A.; Tate, Lanetra C.; Wright, M. Clara; Caraccio, Anne

    2013-12-01

    Accomplishing the best-performing composite matrix (resin) requires that not only the processing method but also the cure cycle generate low-void-content structures. If voids are present, the performance of the composite matrix will be significantly reduced. This is usually noticed by significant reductions in matrix-dominated properties, such as compression and shear strength. Voids in composite materials are areas that are absent of the composite components: matrix and fibers. The characteristics of the voids and their accurate estimation are critical to determine for high performance composite structures. One widely used method of performing void analysis on a composite structure sample is acquiring optical micrographs or Scanning Electron Microscope (SEM) images of lateral sides of the sample and retrieving the void areas within the micrographs/images using an image analysis technique. Segmentation for the retrieval and subsequent computation of void areas within the micrographs/images is challenging as the gray-scaled values of the void areas are close to the gray-scaled values of the matrix leading to the need of manually performing the segmentation based on the histogram of the micrographs/images to retrieve the void areas. The use of an algorithm developed by NASA and based on Fuzzy Reasoning (FR) proved to overcome the difficulty of suitably differentiate void and matrix image areas with similar gray-scaled values leading not only to a more accurate estimation of void areas on composite matrix micrographs but also to a faster void analysis process as the algorithm is fully autonomous.

  20. Accurate airway segmentation based on intensity structure analysis and graph-cut

    NASA Astrophysics Data System (ADS)

    Meng, Qier; Kitsaka, Takayuki; Nimura, Yukitaka; Oda, Masahiro; Mori, Kensaku

    2016-03-01

    This paper presents a novel airway segmentation method based on intensity structure analysis and graph-cut. Airway segmentation is an important step in analyzing chest CT volumes for computerized lung cancer detection, emphysema diagnosis, asthma diagnosis, and pre- and intra-operative bronchoscope navigation. However, obtaining a complete 3-D airway tree structure from a CT volume is quite challenging. Several researchers have proposed automated algorithms basically based on region growing and machine learning techniques. However these methods failed to detect the peripheral bronchi branches. They caused a large amount of leakage. This paper presents a novel approach that permits more accurate extraction of complex bronchial airway region. Our method are composed of three steps. First, the Hessian analysis is utilized for enhancing the line-like structure in CT volumes, then a multiscale cavity-enhancement filter is employed to detect the cavity-like structure from the previous enhanced result. In the second step, we utilize the support vector machine (SVM) to construct a classifier for removing the FP regions generated. Finally, the graph-cut algorithm is utilized to connect all of the candidate voxels to form an integrated airway tree. We applied this method to sixteen cases of 3D chest CT volumes. The results showed that the branch detection rate of this method can reach about 77.7% without leaking into the lung parenchyma areas.

  1. Advances in parameter estimation techniques applied to flexible structures

    NASA Technical Reports Server (NTRS)

    Maben, Egbert; Zimmerman, David C.

    1994-01-01

    In this work, various parameter estimation techniques are investigated in the context of structural system identification utilizing distributed parameter models and 'measured' time-domain data. Distributed parameter models are formulated using the PDEMOD software developed by Taylor. Enhancements made to PDEMOD for this work include the following: (1) a Wittrick-Williams based root solving algorithm; (2) a time simulation capability; and (3) various parameter estimation algorithms. The parameter estimations schemes will be contrasted using the NASA Mini-Mast as the focus structure.

  2. On choosing the order parameter of modulated magnetic structures

    SciTech Connect

    Murtazaev, A. K. Ibaev, Zh. G.

    2013-02-15

    Long-period modulated structures in the anisotropic Ising model with competing interactions (the ANNNI model) are studied by Monte Carlo methods. A new order parameter in the form of modulated phase amplitude is proposed for describing modulated structures. It is shown that the properties of the modulated phase-paramagnetic phase transition can be investigated by using the amplitude as the order parameter.

  3. Accurate electronic-structure description of Mn complexes: a GGA+U approach

    NASA Astrophysics Data System (ADS)

    Li, Elise Y.; Kulik, Heather; Marzari, Nicola

    2008-03-01

    Conventional density-functional approach often fail in offering an accurate description of the spin-resolved energetics in transition metals complexes. We will focus here on Mn complexes, where many aspects of the molecular structure and the reaction mechanisms are still unresolved - most notably in the oxygen-evolving complex (OEC) of photosystem II and the manganese catalase (MC). We apply a self-consistent GGA + U approach [1], originally designed within the DFT framework for the treatment of strongly correlated materials, to describe the geometry, the electronic and the magnetic properties of various manganese oxide complexes, finding very good agreement with higher-order ab-initio calculations. In particular, the different oxidation states of dinuclear systems containing the [Mn2O2]^n+ (n= 2, 3, 4) core are investigated, in order to mimic the basic face unit of the OEC complex. [1]. H. J. Kulik, M. Cococcioni, D. A. Scherlis, N. Marzari, Phys. Rev. Lett., 2006, 97, 103001

  4. A survey of factors contributing to accurate theoretical predictions of atomization energies and molecular structures

    NASA Astrophysics Data System (ADS)

    Feller, David; Peterson, Kirk A.; Dixon, David A.

    2008-11-01

    High level electronic structure predictions of thermochemical properties and molecular structure are capable of accuracy rivaling the very best experimental measurements as a result of rapid advances in hardware, software, and methodology. Despite the progress, real world limitations require practical approaches designed for handling general chemical systems that rely on composite strategies in which a single, intractable calculation is replaced by a series of smaller calculations. As typically implemented, these approaches produce a final, or "best," estimate that is constructed from one major component, fine-tuned by multiple corrections that are assumed to be additive. Though individually much smaller than the original, unmanageable computational problem, these corrections are nonetheless extremely costly. This study presents a survey of the widely varying magnitude of the most important components contributing to the atomization energies and structures of 106 small molecules. It combines large Gaussian basis sets and coupled cluster theory up to quadruple excitations for all systems. In selected cases, the effects of quintuple excitations and/or full configuration interaction were also considered. The availability of reliable experimental data for most of the molecules permits an expanded statistical analysis of the accuracy of the approach. In cases where reliable experimental information is currently unavailable, the present results are expected to provide some of the most accurate benchmark values available.

  5. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

    PubMed

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-02-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.

  6. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations

    PubMed Central

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-01-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-‘one-click’ experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/. PMID:26894674

  7. Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

    PubMed

    Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

    2016-02-01

    Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/. PMID:26894674

  8. Low-energy structures of benzene clusters with a novel accurate potential surface.

    PubMed

    Bartolomei, M; Pirani, F; Marques, J M C

    2015-12-01

    The benzene-benzene (Bz-Bz) interaction is present in several chemical systems and it is known to be crucial in understanding the specificity of important biological phenomena. In this work, we propose a novel Bz-Bz analytical potential energy surface which is fine-tuned on accurate ab initio calculations in order to improve its reliability. Once the Bz-Bz interaction is modeled, an analytical function for the energy of the Bzn clusters may be obtained by summing up over all pair potentials. We apply an evolutionary algorithm (EA) to discover the lowest-energy structures of Bzn clusters (for n=2-25), and the results are compared with previous global optimization studies where different potential functions were employed. Besides the global minimum, the EA also gives the structures of other low-lying isomers ranked by the corresponding energy. Additional ab initio calculations are carried out for the low-lying isomers of Bz3 and Bz4 clusters, and the global minimum is confirmed as the most stable structure for both sizes. Finally, a detailed analysis of the low-energy isomers of the n = 13 and 19 magic-number clusters is performed. The two lowest-energy Bz13 isomers show S6 and C3 symmetry, respectively, which is compatible with the experimental results available in the literature. The Bz19 structures reported here are all non-symmetric, showing two central Bz molecules surrounded by 12 nearest-neighbor monomers in the case of the five lowest-energy structures.

  9. Numerical parameter constraints for accurate PIC-DSMC simulation of breakdown from arc initiation to stable arcs

    NASA Astrophysics Data System (ADS)

    Moore, Christopher; Hopkins, Matthew; Moore, Stan; Boerner, Jeremiah; Cartwright, Keith

    2015-09-01

    Simulation of breakdown is important for understanding and designing a variety of applications such as mitigating undesirable discharge events. Such simulations need to be accurate through early time arc initiation to late time stable arc behavior. Here we examine constraints on the timestep and mesh size required for arc simulations using the particle-in-cell (PIC) method with direct simulation Monte Carlo (DMSC) collisions. Accurate simulation of electron avalanche across a fixed voltage drop and constant neutral density (reduced field of 1000 Td) was found to require a timestep ~ 1/100 of the mean time between collisions and a mesh size ~ 1/25 the mean free path. These constraints are much smaller than the typical PIC-DSMC requirements for timestep and mesh size. Both constraints are related to the fact that charged particles are accelerated by the external field. Thus gradients in the electron energy distribution function can exist at scales smaller than the mean free path and these must be resolved by the mesh size for accurate collision rates. Additionally, the timestep must be small enough that the particle energy change due to the fields be small in order to capture gradients in the cross sections versus energy. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE's National Nuclear Security Administration under Contract DE-AC04-94AL85000.

  10. Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials.

    PubMed

    Boereboom, Jelle M; Potestio, Raffaello; Donadio, Davide; Bulo, Rosa E

    2016-08-01

    Adaptive quantum mechanical (QM)/molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution. Reactive subregions are modeled with an accurate QM potential energy expression while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the QM expression. It would be desirable to model such a system with a single adaptive Hamiltonian, but thus far this has resulted in distorted structures at the boundary between the two regions. Solving this long outstanding problem will allow microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties. The difficulty lies in the complex QM potential energy expression, with a many-body expansion that contains higher order terms. Here, we outline a Hamiltonian adaptive multiscale scheme within the framework of many-body potentials. The adaptive expressions are entirely general, and complementary to all standard (nonadaptive) QM/MM embedding schemes available. We demonstrate the merit of our approach on a molecular system defined by two different MM potentials (MM/MM'). For the long-range interactions a numerical scheme is used (particle mesh Ewald), which yields energy expressions that are many-body in nature. Our Hamiltonian approach is the first to provide both energy conservation and the correct solvent structure everywhere in this system. PMID:27332140

  11. A non-empirical, parameter-free, hybrid functional for accurate calculations of optoelectronic properties of finite systems

    NASA Astrophysics Data System (ADS)

    Brawand, Nicholas; Vörös, Márton; Govoni, Marco; Galli, Giulia

    The accurate prediction of optoelectronic properties of molecules and solids is a persisting challenge for current density functional theory (DFT) based methods. We propose a hybrid functional where the mixing fraction of exact and local exchange is determined by a non-empirical, system dependent function. This functional yields ionization potentials, fundamental and optical gaps of many, diverse systems in excellent agreement with experiments, including organic and inorganic molecules and nanocrystals. We further demonstrate that the newly defined hybrid functional gives the correct alignment between the energy level of the exemplary TTF-TCNQ donor-acceptor system. DOE-BES: DE-FG02-06ER46262.

  12. Accurate molecular structure and spectroscopic properties for nucleobases: A combined computational - microwave investigation of 2-thiouracil as a case study

    PubMed Central

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L.

    2015-01-01

    The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier Transform Microwave spectrometers. The joint experimental – computational study allowed us to determine accurate molecular structure and spectroscopic properties for the title molecule, but more important, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules. PMID:24002739

  13. Sensitivity analysis of structural parameters to measurement noninvariance: A Bayesian approach

    NASA Astrophysics Data System (ADS)

    Kang, Yoon Jeong

    Most previous studies have argued that the validity of group comparisons of structural parameters is dependent on the extent to which measurement invariance is met. Although some researchers have supported the concept of partial invariance, there is still no clear-cut partial invariance level which is needed to make valid group comparisons. In addition, relatively little attention has been paid to the implications of failing measurement invariance (e.g., partial measurement invariance) on group comparison on the underlying latent constructs in the multiple-group confirmatory factor analysis (MGCFA) framework. Given this, the purpose of the current study was to examine the extent to which measurement noninvariance affects structural parameter comparisons across populations in the MGCFA framework. Particularly, this study takes a Bayesian approach to investigate the sensitivity of the posterior distribution of structural parameter difference to varying types and magnitudes of noninvariance across two populations. A Monte Carlo simulation was performed to empirically investigate the sensitivity of structural parameters to varying types and magnitudes of noninvariant measurement models across two populations from a Bayesian approach. In order to assess the sensitivity of noninvariance conditions, three outcome variables were evaluated: (1) accuracy of statistical conclusion on structural parameter difference, (2) precision of the estimated structural parameter difference, and (3) bias in the posterior mean of structural parameter difference. Inconsistent with findings of previous studies, the results of this study showed that the three outcome variables were not sensitive to varying types and magnitudes of noninvariance across all conditions. Instead, the three outcome variables were sensitive to sample size, factor loading size, and prior distribution. These results indicate that even under a large magnitude of measurement noninvariance, accurate conclusions and

  14. Accounting for environmental variability, modeling errors, and parameter estimation uncertainties in structural identification

    NASA Astrophysics Data System (ADS)

    Behmanesh, Iman; Moaveni, Babak

    2016-07-01

    This paper presents a Hierarchical Bayesian model updating framework to account for the effects of ambient temperature and excitation amplitude. The proposed approach is applied for model calibration, response prediction and damage identification of a footbridge under changing environmental/ambient conditions. The concrete Young's modulus of the footbridge deck is the considered updating structural parameter with its mean and variance modeled as functions of temperature and excitation amplitude. The identified modal parameters over 27 months of continuous monitoring of the footbridge are used to calibrate the updating parameters. One of the objectives of this study is to show that by increasing the levels of information in the updating process, the posterior variation of the updating structural parameter (concrete Young's modulus) is reduced. To this end, the calibration is performed at three information levels using (1) the identified modal parameters, (2) modal parameters and ambient temperatures, and (3) modal parameters, ambient temperatures, and excitation amplitudes. The calibrated model is then validated by comparing the model-predicted natural frequencies and those identified from measured data after deliberate change to the structural mass. It is shown that accounting for modeling error uncertainties is crucial for reliable response prediction, and accounting only the estimated variability of the updating structural parameter is not sufficient for accurate response predictions. Finally, the calibrated model is used for damage identification of the footbridge.

  15. Towards an accurate specific reaction parameter density functional for water dissociation on Ni(111): RPBE versus PW91.

    PubMed

    Jiang, Bin; Guo, Hua

    2016-08-01

    In search for an accurate description of the dissociative chemisorption of water on the Ni(111) surface, we report a new nine-dimensional potential energy surface (PES) based on a large number of density functional theory points using the RPBE functional. Seven-dimensional quantum dynamical calculations have been carried out on the RPBE PES, followed by site averaging and lattice effect corrections, yielding sticking probabilities that are compared with both the previous theoretical results based on a PW91 PES and experiment. It is shown that the RPBE functional increases the reaction barrier, but has otherwise a minor impact on the PES topography. Better agreement with experimental results is obtained with the new PES, but the agreement is still not quantitative. Possible sources of the remaining discrepancies are discussed.

  16. Straightforward and accurate technique for post-coupler stabilization in drift tube linac structures

    NASA Astrophysics Data System (ADS)

    Khalvati, Mohammad Reza; Ramberger, Suitbert

    2016-04-01

    The axial electric field of Alvarez drift tube linacs (DTLs) is known to be susceptible to variations due to static and dynamic effects like manufacturing tolerances and beam loading. Post-couplers are used to stabilize the accelerating fields of DTLs against tuning errors. Tilt sensitivity and its slope have been introduced as measures for the stability right from the invention of post-couplers but since then the actual stabilization has mostly been done by tedious iteration. In the present article, the local tilt-sensitivity slope TSn' is established as the principal measure for stabilization instead of tilt sensitivity or some visual slope, and its significance is developed on the basis of an equivalent-circuit diagram of the DTL. Experimental and 3D simulation results are used to analyze its behavior and to define a technique for stabilization that allows finding the best post-coupler settings with just four tilt-sensitivity measurements. CERN's Linac4 DTL Tank 2 and Tank 3 have been stabilized successfully using this technique. The final tilt-sensitivity error has been reduced from ±100 %/MHz down to ±3 %/MHz for Tank 2 and down to ±1 %/MHz for Tank 3. Finally, an accurate procedure for tuning the structure using slug tuners is discussed.

  17. Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation.

    PubMed

    Sharma, Virag; Elghafari, Anas; Hiller, Michael

    2016-06-20

    Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes. PMID:27016733

  18. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples.

    PubMed

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

    2016-05-01

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis.

  19. COSMOS: accurate detection of somatic structural variations through asymmetric comparison between tumor and normal samples

    PubMed Central

    Yamagata, Koichi; Yamanishi, Ayako; Kokubu, Chikara; Takeda, Junji; Sese, Jun

    2016-01-01

    An important challenge in cancer genomics is precise detection of structural variations (SVs) by high-throughput short-read sequencing, which is hampered by the high false discovery rates of existing analysis tools. Here, we propose an accurate SV detection method named COSMOS, which compares the statistics of the mapped read pairs in tumor samples with isogenic normal control samples in a distinct asymmetric manner. COSMOS also prioritizes the candidate SVs using strand-specific read-depth information. Performance tests on modeled tumor genomes revealed that COSMOS outperformed existing methods in terms of F-measure. We also applied COSMOS to an experimental mouse cell-based model, in which SVs were induced by genome engineering and gamma-ray irradiation, followed by polymerase chain reaction-based confirmation. The precision of COSMOS was 84.5%, while the next best existing method was 70.4%. Moreover, the sensitivity of COSMOS was the highest, indicating that COSMOS has great potential for cancer genome analysis. PMID:26833260

  20. Accurate determination of interface trap state parameters by admittance spectroscopy in the presence of a Schottky barrier contact: Application to ZnO-based solar cells

    NASA Astrophysics Data System (ADS)

    Marin, Andrew T.; Musselman, Kevin P.; MacManus-Driscoll, Judith L.

    2013-04-01

    This work shows that when a Schottky barrier is present in a photovoltaic device, such as in a device with an ITO/ZnO contact, equivalent circuit analysis must be performed with admittance spectroscopy to accurately determine the pn junction interface recombination parameters (i.e., capture cross section and density of trap states). Without equivalent circuit analysis, a Schottky barrier can produce an error of ˜4-orders of magnitude in the capture cross section and ˜50% error in the measured density of trap states. Using a solution processed ZnO/Cu2O photovoltaic test system, we apply our analysis to clearly separate the contributions of interface states at the pn junction from the Schottky barrier at the ITO/ZnO contact so that the interface state recombination parameters can be accurately characterized. This work is widely applicable to the multitude of photovoltaic devices, which use ZnO adjacent to ITO.

  1. A two-parameter kinetic model based on a time-dependent activity coefficient accurately describes enzymatic cellulose digestion

    PubMed Central

    Kostylev, Maxim; Wilson, David

    2014-01-01

    Lignocellulosic biomass is a potential source of renewable, low-carbon-footprint liquid fuels. Biomass recalcitrance and enzyme cost are key challenges associated with the large-scale production of cellulosic fuel. Kinetic modeling of enzymatic cellulose digestion has been complicated by the heterogeneous nature of the substrate and by the fact that a true steady state cannot be attained. We present a two-parameter kinetic model based on the Michaelis-Menten scheme (Michaelis L and Menten ML. (1913) Biochem Z 49:333–369), but with a time-dependent activity coefficient analogous to fractal-like kinetics formulated by Kopelman (Kopelman R. (1988) Science 241:1620–1626). We provide a mathematical derivation and experimental support to show that one of the parameters is a total activity coefficient and the other is an intrinsic constant that reflects the ability of the cellulases to overcome substrate recalcitrance. The model is applicable to individual cellulases and their mixtures at low-to-medium enzyme loads. Using biomass degrading enzymes from a cellulolytic bacterium Thermobifida fusca we show that the model can be used for mechanistic studies of enzymatic cellulose digestion. We also demonstrate that it applies to the crude supernatant of the widely studied cellulolytic fungus Trichoderma reesei and can thus be used to compare cellulases from different organisms. The two parameters may serve a similar role to Vmax, KM, and kcat in classical kinetics. A similar approach may be applicable to other enzymes with heterogeneous substrates and where a steady state is not achievable. PMID:23837567

  2. A Study of the Parameters for Solar Structure Inversion Methods

    NASA Astrophysics Data System (ADS)

    Rabello-Soares, M. C.; Basu, Sarbani; Christensen-Dalsgaard, J.

    The observed solar p-mode frequencies provide an extremely useful diagnostic of the internal structure of the Sun, and permit us to test in considerable detail the physics used in the theory of stellar structure. Two implementations of the optimally localized averages (OLA) method are amongst the most commonly used techniques for inverting helioseismic data, namely the Subtractive Optimally Localized Averages (SOLA) and Multiplicative Optimally Localized Averages (MOLA). In both of them, there are a number of parameters that must be chosen in order to find the solution. Proper choice of the parameters is very important to determine correctly the variation of the internal structure along the solar radius. In this work, we make a detailed analysis on the influence of each parameter on the solution and indicate how to arrive at an optimal set of parameters for a given data set.

  3. SEMICONDUCTOR INTEGRATED CIRCUITS: Accurate metamodels of device parameters and their applications in performance modeling and optimization of analog integrated circuits

    NASA Astrophysics Data System (ADS)

    Tao, Liang; Xinzhang, Jia; Junfeng, Chen

    2009-11-01

    Techniques for constructing metamodels of device parameters at BSIM3v3 level accuracy are presented to improve knowledge-based circuit sizing optimization. Based on the analysis of the prediction error of analytical performance expressions, operating point driven (OPD) metamodels of MOSFETs are introduced to capture the circuit's characteristics precisely. In the algorithm of metamodel construction, radial basis functions are adopted to interpolate the scattered multivariate data obtained from a well tailored data sampling scheme designed for MOSFETs. The OPD metamodels can be used to automatically bias the circuit at a specific DC operating point. Analytical-based performance expressions composed by the OPD metamodels show obvious improvement for most small-signal performances compared with simulation-based models. Both operating-point variables and transistor dimensions can be optimized in our nesting-loop optimization formulation to maximize design flexibility. The method is successfully applied to a low-voltage low-power amplifier.

  4. One-photon mass-analyzed threshold ionization (MATI) spectroscopy of pyridine: determination of accurate ionization energy and cationic structure.

    PubMed

    Lee, Yu Ran; Kang, Do Won; Kim, Hong Lae; Kwon, Chan Ho

    2014-11-01

    Ionization energies and cationic structures of pyridine were intensively investigated utilizing one-photon mass-analyzed threshold ionization (MATI) spectroscopy with vacuum ultraviolet radiation generated by four-wave difference frequency mixing in Kr. The present one-photon high-resolution MATI spectrum of pyridine demonstrated a much finer and richer vibrational structure than that of the previously reported two-photon MATI spectrum. From the MATI spectrum and photoionization efficiency curve, the accurate ionization energy of the ionic ground state of pyridine was confidently determined to be 73,570 ± 6 cm(-1) (9.1215 ± 0.0007 eV). The observed spectrum was almost completely assigned by utilizing Franck-Condon factors and vibrational frequencies calculated through adjustments of the geometrical parameters of cationic pyridine at the B3LYP/cc-pVTZ level. A unique feature unveiled through rigorous analysis was the prominent progression of the 10 vibrational mode, which corresponds to in-plane ring bending, and the combination of other totally symmetric fundamentals with the ring bending overtones, which contribute to the geometrical change upon ionization. Notably, the remaining peaks originate from the upper electronic state ((2)A2), as predicted by high-resolution photoelectron spectroscopy studies and symmetry-adapted cluster configuration interaction calculations. Based on the quantitatively good agreement between the experimental and calculated results, it was concluded that upon ionization the pyridine cation in the ground electronic state should have a planar structure of C(2v) symmetry through the C-N axis.

  5. One-photon mass-analyzed threshold ionization (MATI) spectroscopy of pyridine: Determination of accurate ionization energy and cationic structure

    SciTech Connect

    Lee, Yu Ran; Kang, Do Won; Kim, Hong Lae E-mail: hlkim@kangwon.ac.kr; Kwon, Chan Ho E-mail: hlkim@kangwon.ac.kr

    2014-11-07

    Ionization energies and cationic structures of pyridine were intensively investigated utilizing one-photon mass-analyzed threshold ionization (MATI) spectroscopy with vacuum ultraviolet radiation generated by four-wave difference frequency mixing in Kr. The present one-photon high-resolution MATI spectrum of pyridine demonstrated a much finer and richer vibrational structure than that of the previously reported two-photon MATI spectrum. From the MATI spectrum and photoionization efficiency curve, the accurate ionization energy of the ionic ground state of pyridine was confidently determined to be 73 570 ± 6 cm{sup −1} (9.1215 ± 0.0007 eV). The observed spectrum was almost completely assigned by utilizing Franck-Condon factors and vibrational frequencies calculated through adjustments of the geometrical parameters of cationic pyridine at the B3LYP/cc-pVTZ level. A unique feature unveiled through rigorous analysis was the prominent progression of the 10 vibrational mode, which corresponds to in-plane ring bending, and the combination of other totally symmetric fundamentals with the ring bending overtones, which contribute to the geometrical change upon ionization. Notably, the remaining peaks originate from the upper electronic state ({sup 2}A{sub 2}), as predicted by high-resolution photoelectron spectroscopy studies and symmetry-adapted cluster configuration interaction calculations. Based on the quantitatively good agreement between the experimental and calculated results, it was concluded that upon ionization the pyridine cation in the ground electronic state should have a planar structure of C{sub 2v} symmetry through the C-N axis.

  6. Petermann I and II spot size: Accurate semi analytical description involving Nelder-Mead method of nonlinear unconstrained optimization and three parameter fundamental modal field

    NASA Astrophysics Data System (ADS)

    Roy Choudhury, Raja; Roy Choudhury, Arundhati; Kanti Ghose, Mrinal

    2013-01-01

    A semi-analytical model with three optimizing parameters and a novel non-Gaussian function as the fundamental modal field solution has been proposed to arrive at an accurate solution to predict various propagation parameters of graded-index fibers with less computational burden than numerical methods. In our semi analytical formulation the optimization of core parameter U which is usually uncertain, noisy or even discontinuous, is being calculated by Nelder-Mead method of nonlinear unconstrained minimizations as it is an efficient and compact direct search method and does not need any derivative information. Three optimizing parameters are included in the formulation of fundamental modal field of an optical fiber to make it more flexible and accurate than other available approximations. Employing variational technique, Petermann I and II spot sizes have been evaluated for triangular and trapezoidal-index fibers with the proposed fundamental modal field. It has been demonstrated that, the results of the proposed solution identically match with the numerical results over a wide range of normalized frequencies. This approximation can also be used in the study of doped and nonlinear fiber amplifier.

  7. Effective Parameters on Seismic Design of Rectangular Underground Structures

    SciTech Connect

    Amiri, G. Ghodrati; Maddah, N.; Mohebi, B.

    2008-07-08

    Underground structures are a significant part of the transportation in the modern society and in the seismic zones should withstand against both seismic and static loadings. Embedded structures should conform to ground deformations during the earthquake but almost exact evaluation of structure to ground distortion is critical. Several two-dimensional finite difference models are used to find effective parameters on racking ratio (structure to ground distortion) including flexibility ratio, various cross sections, embedment depth, and Poisson's ratio of soil. Results show that influence of different cross sections, by themselves is negligible but embedment depth in addition to flexibility ratio and Poisson's ratio is known as a consequential parameter. A comparison with pseudo-static method (simplified frame analysis) is also performed. The results show that for a stiffer structure than soil, racking ratio decreases as the depth of burial decreases; on the other hand, shallow and flexible structures can suffer greater distortion than deeper ones up to 30 percents.

  8. Coupling 1D Navier Stokes equation with autoregulation lumped parameter networks for accurate cerebral blood flow modeling

    NASA Astrophysics Data System (ADS)

    Ryu, Jaiyoung; Hu, Xiao; Shadden, Shawn C.

    2014-11-01

    The cerebral circulation is unique in its ability to maintain blood flow to the brain under widely varying physiologic conditions. Incorporating this autoregulatory response is critical to cerebral blood flow modeling, as well as investigations into pathological conditions. We discuss a one-dimensional nonlinear model of blood flow in the cerebral arteries that includes coupling of autoregulatory lumped parameter networks. The model is tested to reproduce a common clinical test to assess autoregulatory function - the carotid artery compression test. The change in the flow velocity at the middle cerebral artery (MCA) during carotid compression and release demonstrated strong agreement with published measurements. The model is then used to investigate vasospasm of the MCA, a common clinical concern following subarachnoid hemorrhage. Vasospasm was modeled by prescribing vessel area reduction in the middle portion of the MCA. Our model showed similar increases in velocity for moderate vasospasms, however, for serious vasospasm (~ 90% area reduction), the blood flow velocity demonstrated decrease due to blood flow rerouting. This demonstrates a potentially important phenomenon, which otherwise would lead to false-negative decisions on clinical vasospasm if not properly anticipated.

  9. Uncertainty in dual permeability model parameters for structured soils.

    PubMed

    Arora, B; Mohanty, B P; McGuire, J T

    2012-01-01

    Successful application of dual permeability models (DPM) to predict contaminant transport is contingent upon measured or inversely estimated soil hydraulic and solute transport parameters. The difficulty in unique identification of parameters for the additional macropore- and matrix-macropore interface regions, and knowledge about requisite experimental data for DPM has not been resolved to date. Therefore, this study quantifies uncertainty in dual permeability model parameters of experimental soil columns with different macropore distributions (single macropore, and low- and high-density multiple macropores). Uncertainty evaluation is conducted using adaptive Markov chain Monte Carlo (AMCMC) and conventional Metropolis-Hastings (MH) algorithms while assuming 10 out of 17 parameters to be uncertain or random. Results indicate that AMCMC resolves parameter correlations and exhibits fast convergence for all DPM parameters while MH displays large posterior correlations for various parameters. This study demonstrates that the choice of parameter sampling algorithms is paramount in obtaining unique DPM parameters when information on covariance structure is lacking, or else additional information on parameter correlations must be supplied to resolve the problem of equifinality of DPM parameters. This study also highlights the placement and significance of matrix-macropore interface in flow experiments of soil columns with different macropore densities. Histograms for certain soil hydraulic parameters display tri-modal characteristics implying that macropores are drained first followed by the interface region and then by pores of the matrix domain in drainage experiments. Results indicate that hydraulic properties and behavior of the matrix-macropore interface is not only a function of saturated hydraulic conductivity of the macroporematrix interface (Ksa ) and macropore tortuosity (lf ) but also of other parameters of the matrix and macropore domains.

  10. Crystalline structure and symmetry dependence of acoustic nonlinearity parameters

    NASA Technical Reports Server (NTRS)

    Cantrell, John H.

    1994-01-01

    A quantitative measure of elastic wave nonlinearity in crystals is provided by the acoustic nonlinearity parameters. The nonlinearity parameters are defined for arbitrary propagation modes for solids of arbitrary crystalline symmetry and are determined along the pure mode propagation directions for 33 crystals of cubic symmetry from data reported in the literature. The magnitudes of the nonlinearity parameters are found to exhibit a strong dependence on the crystalline structure and symmetries associated with the modal direction in the solid. Calculations based on the Born-Mayer potential for crystals having a dominant repulsive contribution to the elastic constants from the interatomic pair potential suggest that the origin of the structure dependence is associated with the shape rather than the strength of the potential. Considerations based on variations in crystal symmetry during loading along pure mode propagation directions of face-centered-cubic solids provide a qualitative explanation for the dependence of the acoustic nonlinearity parameters on modal direction.

  11. On the choice of parameters in solar-structure inversion

    NASA Astrophysics Data System (ADS)

    Rabello-Soares, M. C.; Basu, Sarbani; Christensen-Dalsgaard, J.

    1999-10-01

    The observed solar p-mode frequencies provide a powerful diagnostic of the internal structure of the Sun and permit us to test in considerable detail the physics used in the theory of stellar structure. Among the most commonly used techniques for inverting such helioseismic data are two implementations of the optimally localized averages (OLA) method, namely the subtractive optimally localized averages (SOLA) and multiplicative optimally localized averages (MOLA). Both are controlled by a number of parameters, the proper choice of which is very important for a reliable inference of the solar internal structure. Here we make a detailed analysis of the influence of each parameter on the solution and indicate how to arrive at an optimal set of parameters for a given data set.

  12. Physical parameters of Au-n-InP structures

    NASA Astrophysics Data System (ADS)

    Touhami, R.; Ravelet, S.

    1999-05-01

    An approach suitable for determining the physical parameters of Au-oxide-n-InP structures is presented in this article. This approach consists in describing the Au-oxide-n-InP structures by a modified current-voltage model in which both least squares and Newton-Raphson methods are used in the parameter determination. The Au-oxide-n-InP samples under study are either oxidized by air or treated with oxygen plasma. The ideality factor, the series resistance, the effective Richardson constant, and the effective barrier height of these structures are computed by means of the current voltage model. A better estimation of these parameters is obtained when we consider another definition of the Richardson constant, namely, the correct value of the Richardson constant. Physical parameters such as the barrier lowering at zero bias due to the image force, the barrier height at 0 K, the correct value of the Richardson constant, and the tunnel coefficient are then simulated. The values of these parameters obtained for Au-oxide-n-InP structures are in good agreement with those published in the literature.

  13. Accurate localization of supernumerary mediastinal parathyroid adenomas by a combination of structural and functional imaging.

    PubMed

    Mackie, G C; Schlicht, S M

    2004-09-01

    Reoperation for refractory or recurrent hyperparathyroidism following parathyroidectomy carries the potential for increased morbidity and the possibility of failure to localize and remove the lesion intraoperatively. Reported herein are three cases demonstrating the combined use of sestamibi scintigraphy, CT and MR for accurate localization of mediastinal parathyroid adenomas.

  14. Influence analysis of structural parameters and operating parameters on electromagnetic properties of HTS linear induction motor

    NASA Astrophysics Data System (ADS)

    Fang, J.; Sheng, L.; Li, D.; Zhao, J.; Li, Sh.; Qin, W.; Fan, Y.; Zheng, Q. L.; Zhang, W.

    A novel High Temperature Superconductor Linear Induction Motor (HTS LIM) is researched in this paper. Since the critical current and the electromagnetic force of the motor are determined mainly by the primary slot leakage flux, the main magnetic flux and eddy current respectively, in order to research the influence of structural parameters and operating parameters on electromagnetic properties of HTS LIM, the motor was analyzed by 2D transient Finite Element Method (FEM). The properties of the motor, such as the maximum slot leakage flux density, motor thrust, motor vertical force and critical current are analyzed with different structural parameters and operating parameters. In addition, an experimental investigation was carried out on prototype HTS motor. Electrical parameters were deduced from these tests and also compared with the analysis results from FEM. AC losses of one HTS coil in the motor were measured and AC losses of all HTS coils in HTS LIM were estimated. The results in this paper could provide reference for the design and research on the HTS LIM.

  15. Extension of the AMBER force field for nitroxide radicals and combined QM/MM/PCM approach to the accurate determination of EPR parameters of DMPOH in solution

    PubMed Central

    Hermosilla, Laura; Prampolini, Giacomo; Calle, Paloma; García de la Vega, José Manuel; Brancato, Giuseppe; Barone, Vincenzo

    2015-01-01

    A computational strategy that combines both time-dependent and time-independent approaches is exploited to accurately model molecular dynamics and solvent effects on the isotropic hyperfine coupling constants of the DMPO-H nitroxide. Our recent general force field for nitroxides derived from AMBER ff99SB is further extended to systems involving hydrogen atoms in β-positions with respect to NO. The resulting force-field has been employed in a series of classical molecular dynamics simulations, comparing the computed EPR parameters from selected molecular configurations to the corresponding experimental data in different solvents. The effect of vibrational averaging on the spectroscopic parameters is also taken into account, by second order vibrational perturbation theory involving semi-diagonal third energy derivatives together first and second property derivatives. PMID:26584116

  16. Testing parameters in structural equation modeling: every "one" matters.

    PubMed

    Gonzalez, R; Griffin, D

    2001-09-01

    A problem with standard errors estimated by many structural equation modeling programs is described. In such programs, a parameter's standard error is sensitive to how the model is identified (i.e., how scale is set). Alternative but equivalent ways to identify a model may yield different standard errors, and hence different Z tests for a parameter, even though the identifications produce the same overall model fit. This lack of invariance due to model identification creates the possibility that different analysts may reach different conclusions about a parameter's significance level even though they test equivalent models on the same data. The authors suggest that parameters be tested for statistical significance through the likelihood ratio test, which is invariant to the identification choice. PMID:11570231

  17. A robust and accurate center-frequency estimation (RACE) algorithm for improving motion estimation performance of SinMod on tagged cardiac MR images without known tagging parameters.

    PubMed

    Liu, Hong; Wang, Jie; Xu, Xiangyang; Song, Enmin; Wang, Qian; Jin, Renchao; Hung, Chih-Cheng; Fei, Baowei

    2014-11-01

    A robust and accurate center-frequency (CF) estimation (RACE) algorithm for improving the performance of the local sine-wave modeling (SinMod) method, which is a good motion estimation method for tagged cardiac magnetic resonance (MR) images, is proposed in this study. The RACE algorithm can automatically, effectively and efficiently produce a very appropriate CF estimate for the SinMod method, under the circumstance that the specified tagging parameters are unknown, on account of the following two key techniques: (1) the well-known mean-shift algorithm, which can provide accurate and rapid CF estimation; and (2) an original two-direction-combination strategy, which can further enhance the accuracy and robustness of CF estimation. Some other available CF estimation algorithms are brought out for comparison. Several validation approaches that can work on the real data without ground truths are specially designed. Experimental results on human body in vivo cardiac data demonstrate the significance of accurate CF estimation for SinMod, and validate the effectiveness of RACE in facilitating the motion estimation performance of SinMod.

  18. Design parameter analysis of hybrid optimal controlled structures

    SciTech Connect

    Cheng, F.Y.; Tian, P.

    1994-12-31

    This paper presents a hybrid control system composed of an active hydraulic actuator and a passive liquid-mass damper. The system is built with structural bracing and can reduce structural dynamic response by providing passive inertia force, passive damping force and active control force. Fundamental equations governing the hybrid control system are derived and influence parameters are numerically analyzed. Numerical results show that in this hybrid control system the effective liquid-mass plays an important role in reducing structural dynamic response and requiring smaller control forces than either passive or active control system.

  19. An overview of STRUCTURE: applications, parameter settings, and supporting software

    PubMed Central

    Porras-Hurtado, Liliana; Ruiz, Yarimar; Santos, Carla; Phillips, Christopher; Carracedo, Ángel; Lareu, Maria V.

    2013-01-01

    Objectives: We present an up-to-date review of STRUCTURE software: one of the most widely used population analysis tools that allows researchers to assess patterns of genetic structure in a set of samples. STRUCTURE can identify subsets of the whole sample by detecting allele frequency differences within the data and can assign individuals to those sub-populations based on analysis of likelihoods. The review covers STRUCTURE's most commonly used ancestry and frequency models, plus an overview of the main applications of the software in human genetics including case-control association studies (CCAS), population genetics, and forensic analysis. The review is accompanied by supplementary material providing a step-by-step guide to running STRUCTURE. Methods: With reference to a worked example, we explore the effects of changing the principal analysis parameters on STRUCTURE results when analyzing a uniform set of human genetic data. Use of the supporting software: CLUMPP and distruct is detailed and we provide an overview and worked example of STRAT software, applicable to CCAS. Conclusion: The guide offers a simplified view of how STRUCTURE, CLUMPP, distruct, and STRAT can be applied to provide researchers with an informed choice of parameter settings and supporting software when analyzing their own genetic data. PMID:23755071

  20. PROMALS3D web server for accurate multiple protein sequence and structure alignments.

    PubMed

    Pei, Jimin; Tang, Ming; Grishin, Nick V

    2008-07-01

    Multiple sequence alignments are essential in computational sequence and structural analysis, with applications in homology detection, structure modeling, function prediction and phylogenetic analysis. We report PROMALS3D web server for constructing alignments for multiple protein sequences and/or structures using information from available 3D structures, database homologs and predicted secondary structures. PROMALS3D shows higher alignment accuracy than a number of other advanced methods. Input of PROMALS3D web server can be FASTA format protein sequences, PDB format protein structures and/or user-defined alignment constraints. The output page provides alignments with several formats, including a colored alignment augmented with useful information about sequence grouping, predicted secondary structures and consensus sequences. Intermediate results of sequence and structural database searches are also available. The PROMALS3D web server is available at: http://prodata.swmed.edu/promals3d/. PMID:18503087

  1. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

  2. Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

    PubMed

    Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

    2009-12-24

    In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure. PMID:19950907

  3. Expressing oceanic turbulence parameters by atmospheric turbulence structure constant.

    PubMed

    Baykal, Yahya

    2016-02-20

    The parameters composing oceanic turbulence are the wavelength, link length, rate of dissipation of kinetic energy per unit mass of fluid, rate of dissipation of mean-squared temperature, Kolmogorov microscale, and the ratio of temperature to salinity contributions to the refractive index spectrum. The required physical entities such as the average intensity and the scintillation index in the oceanic medium are formulated by using the power spectrum of oceanic turbulence, which is described by oceanic turbulence parameters. On the other hand, there exists a rich archive of formulations and results for the above-mentioned physical entities in atmospheric turbulence, where the parameters describing the turbulence are the wavelength, the link length, and the structure constant. In this paper, by equating the spherical wave scintillation index solutions in the oceanic and atmospheric turbulences, we have expressed the oceanic turbulence parameters by an equivalent structure constant used in turbulent atmosphere. Such equivalent structure constant will help ease reaching solutions of similar entities in an oceanic turbulent medium by employing the corresponding existing solutions, which are valid in an atmospheric turbulent medium.

  4. Electronic structure calculations of ESR parameters of melanin units.

    PubMed

    Batagin-Neto, Augusto; Bronze-Uhle, Erika Soares; Graeff, Carlos Frederico de Oliveira

    2015-03-21

    Melanins represent an important class of natural pigments present in plants and animals that are currently considered to be promising materials for applications in optic and electronic devices. Despite their interesting properties, some of the basic features of melanins are not satisfactorily understood, including the origin of their intrinsic paramagnetism. A number of experiments have been performed to investigate the electron spin resonance (ESR) response of melanin derivatives, but until now, there has been no consensus regarding the real structure of the paramagnetic centers involved. In this work, we have employed electronic structure calculations to evaluate the ESR parameters of distinct melanin monomers and dimers in order to identify the possible structures associated with unpaired spins in this biopolymer. The g-factors and hyperfine constants of the cationic, anionic and radicalar structures were investigated. The results confirm the existence of at least two distinct paramagnetic centers in melanin structure, identifying the chemical species associated with them and their roles in electrical conductivity.

  5. Accurate metal-site structures in proteins obtained by combining experimental data and quantum chemistry.

    PubMed

    Ryde, Ulf

    2007-02-14

    The use of molecular mechanics calculations to supplement experimental data in standard X-ray crystallography and NMR refinements is discussed and it is shown that structures can be locally improved by the use of quantum chemical calculations. Such calculations can also be used to interpret the structures, e.g. to decide the protonation state of metal-bound ligands. They have shown that metal sites in crystal structures are frequently photoreduced or disordered, which makes the interpretation of the structures hard. Similar methods can be used for EXAFS refinements to obtain a full atomic structure, rather than a set of metal-ligand distances.

  6. Wheat streak mosaic virus-Structural parameters for a Potyvirus

    SciTech Connect

    Parker, Lauren; Kendall, Amy; Berger, P.H.; Shiel, P.J.; Stubbs, Gerald . E-mail: gerald.stubbs@vanderbilt.edu

    2005-09-15

    Wheat streak mosaic virus is a Tritimovirus, a member of the Potyviridae family, which includes the very large Potyvirus genus. We have examined wheat streak mosaic virus by electron microscopy and fiber diffraction from partially oriented sols, and analyzed the results to estimate the symmetry and structural parameters of the viral helix. The virions have an apparent radius of 63 {+-} 5 A. The viral helix has a pitch of 33.4 A {+-} 0.6 A. There appear to be 6.9 subunits per turn of the helix, although we cannot completely eliminate values of 5.9 or 7.9 for this parameter.

  7. The role of structural parameters in DNA cyclization

    DOE PAGES

    Alexandrov, Ludmil B.; Bishop, Alan R.; Rasmussen, Kim O.; Alexandrov, Boian S.

    2016-02-04

    The intrinsic bendability of DNA plays an important role with relevance for myriad of essential cellular mechanisms. The flexibility of a DNA fragment can be experimentally and computationally examined by its propensity for cyclization, quantified by the Jacobson-Stockmayer J factor. In this paper, we use a well-established coarse-grained three-dimensional model of DNA and seven distinct sets of experimentally and computationally derived conformational parameters of the double helix to evaluate the role of structural parameters in calculating DNA cyclization.

  8. Microwave spectrum, structural parameters, and quadrupole coupling for 1,2-dihydro-1,2-azaborine.

    PubMed

    Daly, Adam M; Tanjaroon, Chakree; Marwitz, Adam J V; Liu, Shih-Yuan; Kukolich, Stephen G

    2010-04-21

    The first microwave spectrum for 1,2-dihydro-1,2-azaborine has been measured in the frequency range 7-18 GHz, providing accurate rotational constants and nitrogen and boron quadrupole coupling strengths for three isotopomers, H(6)C(4)(11)B(14)N, H(6)C(4)(10)B(14)N, and H(5)DC(4)(11)B(14)N. The measured rotational constants were used to accurately determine coordinates for the substituted atoms and provide sufficient data to determine most of the important structural parameters for this molecule. The spectra were obtained using a pulsed beam Fourier transform microwave spectrometer, with sufficient resolution to allow accurate measurements of (14)N, (11)B, and (10)B nuclear quadrupole hyperfine interactions. High-level ab initio calculations provided structural parameters and quadrupole coupling strengths that are in very good agreement with measured values. The rotational constants for the parent compound are A = 5657.335(1), B = 5349.2807(5), and C = 2749.1281(4) MHz, yielding the inertial defect Delta(0) = 0.02 amu x A(2) for the ground-state structure. The observed near-zero and positive inertial defect clearly indicates that the molecular structure of 1,2-dihydro-1,2-azaborine is planar. The least-squares fit analysis to determine the azaborine ring structure yielded the experimental bond lengths and 2sigma errors R(B-N) = 1.45(3) A, R(B-C) = 1.51(1) A, and R(N-C) = 1.37(3) A for the ground-state structure. Interbond angles for the ring were also determined. An extended Townes-Dailey population analysis of the boron and nitrogen quadrupole coupling constants provided the valence p-electron occupancy p(c) = 0.3e for boron and p(c) = 1.3e for nitrogen.

  9. Seeking: Accurate Measurement Techniques for Deep-Bone Density and Structure

    NASA Technical Reports Server (NTRS)

    Sibonga, Jean

    2009-01-01

    We are seeking a clinically-useful technology with enough sensitivity to assess the microstructure of "spongy" bone that is found in the marrow cavities of whole bones. However, this technology must be for skeletal sites surrounded by layers of soft tissues, such as the spine and the hip. Soft tissue interferes with conventional imaging and using a more accessible area -- for example, the wrist or the ankle of limbs-- as a proxy for the less accessible skeletal regions, will not be accurate. A non-radioactive technology is strongly preferred.

  10. Table of periodic properties of fullerenes based on structural parameters.

    PubMed

    Torrens, Francisco

    2004-01-01

    The periodic table (PT) of the elements suggests that hydrogen could be the origin of everything else. The construction principle is an evolutionary process that is formally similar to those of Darwin and Oparin. The Kekulé structure count and permanence of the adjacency matrix of fullerenes are related to structural parameters involving the presence of contiguous pentagons p, q and r. Let p be the number of edges common to two pentagons, q the number of vertices common to three pentagons, and r the number of pairs of nonadjacent pentagon edges shared between two other pentagons. Principal component analysis (PCA) of the structural parameters and cluster analysis (CA) of the fullerenes permit classifying them and agree. A PT of the fullerenes is built based on the structural parameters, PCA and CA. The periodic law does not have the rank of the laws of physics. (1) The properties of the fullerenes are not repeated; only, and perhaps, their chemical character. (2) The order relationships are repeated, although with exceptions. The proposed statement is the following: The relationships that any fullerene p has with its neighbor p + 1 are approximately repeated for each period.

  11. Parameter and Structure Inference for Nonlinear Dynamical Systems

    NASA Technical Reports Server (NTRS)

    Morris, Robin D.; Smelyanskiy, Vadim N.; Millonas, Mark

    2006-01-01

    A great many systems can be modeled in the non-linear dynamical systems framework, as x = f(x) + xi(t), where f() is the potential function for the system, and xi is the excitation noise. Modeling the potential using a set of basis functions, we derive the posterior for the basis coefficients. A more challenging problem is to determine the set of basis functions that are required to model a particular system. We show that using the Bayesian Information Criteria (BIC) to rank models, and the beam search technique, that we can accurately determine the structure of simple non-linear dynamical system models, and the structure of the coupling between non-linear dynamical systems where the individual systems are known. This last case has important ecological applications.

  12. Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional

    NASA Astrophysics Data System (ADS)

    Sun, Jianwei; Remsing, Richard C.; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L.; Perdew, John P.

    2016-09-01

    One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.

  13. Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional.

    PubMed

    Sun, Jianwei; Remsing, Richard C; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L; Perdew, John P

    2016-09-01

    One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science. PMID:27554409

  14. PDBparam: Online Resource for Computing Structural Parameters of Proteins

    PubMed Central

    Nagarajan, R.; Archana, A.; Thangakani, A. Mary; Jemimah, S.; Velmurugan, D.; Gromiha, M. Michael

    2016-01-01

    Understanding the structure–function relationship in proteins is a longstanding goal in molecular and computational biology. The development of structure-based parameters has helped to relate the structure with the function of a protein. Although several structural features have been reported in the literature, no single server can calculate a wide-ranging set of structure-based features from protein three-dimensional structures. In this work, we have developed a web-based tool, PDBparam, for computing more than 50 structure-based features for any given protein structure. These features are classified into four major categories: (i) interresidue interactions, which include short-, medium-, and long-range interactions, contact order, long-range order, total contact distance, contact number, and multiple contact index, (ii) secondary structure propensities such as α-helical propensity, β-sheet propensity, and propensity of amino acids to exist at various positions of α-helix and amino acid compositions in high B-value regions, (iii) physicochemical properties containing ionic interactions, hydrogen bond interactions, hydrophobic interactions, disulfide interactions, aromatic interactions, surrounding hydrophobicity, and buriedness, and (iv) identification of binding site residues in protein–protein, protein–nucleic acid, and protein–ligand complexes. The server can be freely accessed at http://www.iitm.ac.in/bioinfo/pdbparam/. We suggest the use of PDBparam as an effective tool for analyzing protein structures. PMID:27330281

  15. Structural modal parameter identification and damage diagnosis based on Hilbert-Huang transform

    NASA Astrophysics Data System (ADS)

    Han, Jianping; Zheng, Peijuan; Wang, Hongtao

    2014-03-01

    Traditional modal parameter identification methods have many disadvantages, especially when used for processing nonlinear and non-stationary signals. In addition, they are usually not able to accurately identify the damping ratio and damage. In this study, methods based on the Hilbert-Huang transform (HHT) are investigated for structural modal parameter identification and damage diagnosis. First, mirror extension and prediction via a radial basis function (RBF) neural network are used to restrain the troublesome end-effect issue in empirical mode decomposition (EMD), which is a crucial part of HHT. Then, the approaches based on HHT combined with other techniques, such as the random decrement technique (RDT), natural excitation technique (NExT) and stochastic subspace identification (SSI), are proposed to identify modal parameters of structures. Furthermore, a damage diagnosis method based on the HHT is also proposed. Time-varying instantaneous frequency and instantaneous energy are used to identify the damage evolution of the structure. The relative amplitude of the Hilbert marginal spectrum is used to identify the damage location of the structure. Finally, acceleration records at gauge points from shaking table testing of a 12-story reinforced concrete frame model are taken to validate the proposed approaches. The results show that the proposed approaches based on HHT for modal parameter identification and damage diagnosis are reliable and practical.

  16. Automatic classification of protein structures using physicochemical parameters.

    PubMed

    Mohan, Abhilash; Rao, M Divya; Sunderrajan, Shruthi; Pennathur, Gautam

    2014-09-01

    Protein classification is the first step to functional annotation; SCOP and Pfam databases are currently the most relevant protein classification schemes. However, the disproportion in the number of three dimensional (3D) protein structures generated versus their classification into relevant superfamilies/families emphasizes the need for automated classification schemes. Predicting function of novel proteins based on sequence information alone has proven to be a major challenge. The present study focuses on the use of physicochemical parameters in conjunction with machine learning algorithms (Naive Bayes, Decision Trees, Random Forest and Support Vector Machines) to classify proteins into their respective SCOP superfamily/Pfam family, using sequence derived information. Spectrophores™, a 1D descriptor of the 3D molecular field surrounding a structure was used as a benchmark to compare the performance of the physicochemical parameters. The machine learning algorithms were modified to select features based on information gain for each SCOP superfamily/Pfam family. The effect of combining physicochemical parameters and spectrophores on classification accuracy (CA) was studied. Machine learning algorithms trained with the physicochemical parameters consistently classified SCOP superfamilies and Pfam families with a classification accuracy above 90%, while spectrophores performed with a CA of around 85%. Feature selection improved classification accuracy for both physicochemical parameters and spectrophores based machine learning algorithms. Combining both attributes resulted in a marginal loss of performance. Physicochemical parameters were able to classify proteins from both schemes with classification accuracy ranging from 90-96%. These results suggest the usefulness of this method in classifying proteins from amino acid sequences.

  17. Controllability of brushite structural parameters using an applied magnetic field.

    PubMed

    Kuznetsov, V N; Yanovska, A A; Stanislavov, A S; Danilchenko, S N; Kalinkevich, A N; Sukhodub, L F

    2016-03-01

    The paper studies the influence of low intensity static magnetic field on brushite structural and microstructural parameters using the X-ray diffraction and the transmission electron microscopy. This effect was shown to have various influences on DCPD (Dicalcium Phosphate Dihydrate) structure depending on a magnetic field configuration or time of synthesis, which allows achieving controllability of the main properties of an obtained material. The influence of the magnetic field leads mostly to the decrease of crystallite sizes with no impact on the crystal lattice parameters. In (0 2 0) and (1 5 0) planes the growth of crystallite sizes is observed after 2 and 3 days of crystallization, respectively. The analysis of different contributions to peak broadening in [0 b 0] direction showed a similar trend for the crystallite sizes with the lower lattice microstrains after 2 days of synthesis. The effect similar to the preferred orientation was observed and classified with the Harris method.

  18. Controllability of brushite structural parameters using an applied magnetic field.

    PubMed

    Kuznetsov, V N; Yanovska, A A; Stanislavov, A S; Danilchenko, S N; Kalinkevich, A N; Sukhodub, L F

    2016-03-01

    The paper studies the influence of low intensity static magnetic field on brushite structural and microstructural parameters using the X-ray diffraction and the transmission electron microscopy. This effect was shown to have various influences on DCPD (Dicalcium Phosphate Dihydrate) structure depending on a magnetic field configuration or time of synthesis, which allows achieving controllability of the main properties of an obtained material. The influence of the magnetic field leads mostly to the decrease of crystallite sizes with no impact on the crystal lattice parameters. In (0 2 0) and (1 5 0) planes the growth of crystallite sizes is observed after 2 and 3 days of crystallization, respectively. The analysis of different contributions to peak broadening in [0 b 0] direction showed a similar trend for the crystallite sizes with the lower lattice microstrains after 2 days of synthesis. The effect similar to the preferred orientation was observed and classified with the Harris method. PMID:26706562

  19. DFTB Parameters for the Periodic Table: Part 1, Electronic Structure.

    PubMed

    Wahiduzzaman, Mohammad; Oliveira, Augusto F; Philipsen, Pier; Zhechkov, Lyuben; van Lenthe, Erik; Witek, Henryk A; Heine, Thomas

    2013-09-10

    A parametrization scheme for the electronic part of the density-functional based tight-binding (DFTB) method that covers the periodic table is presented. A semiautomatic parametrization scheme has been developed that uses Kohn-Sham energies and band structure curvatures of real and fictitious homoatomic crystal structures as reference data. A confinement potential is used to tighten the Kohn-Sham orbitals, which includes two free parameters that are used to optimize the performance of the method. The method is tested on more than 100 systems and shows excellent overall performance.

  20. SAW parameters on Y-cut langasite structured materials.

    PubMed

    Puccio, Derek; Malocha, Donald C; Saldanha, Nancy; da Cunha, Mauricio Pereira

    2007-09-01

    This paper presents results and investigations of several new, man-made piezoelectric single crystal, Czochralski-grown substrate materials for surface acoustic waves (SAW) applications. These materials, langanite (LGN), langatate (LGT), Sr3TaGa3Si2O14 (STGS), Sr3NbGa3Si2O14 (SNGS), Ca3TaGa3Si2O14 (CTGS), and Ca3NbGa3Si2O14 (CNGS), have the same structure as langasite (LGS) and are of the same crystal class as quartz. These compounds are denser than quartz, resulting in lower phase velocities. They also have higher coupling. Unlike quartz and lithium niobate, there is no degradation of material properties below the material melting points resulting in the possibility of extreme high-temperature operation (> 1000 degrees C). This paper gives a summary of extracted SAW material parameters for various propagation angles on Y-cut substrates of the six materials. Parameters included are electromechanical coupling, phase velocity, transducer capacitance, metal strip reflectivity, and temperature coefficient of frequency. Using previously published fundamental material constants, extracted parameters are compared with predictions for LGT and LGN. In addition, power flow angle and fractional frequency curvature data are reported for propagation angles on CTGS and CNGS Y-cut substrates that exhibit temperature compensation near room temperature. Detailed descriptions of the SAW parameter extraction techniques are given. A discussion of the results is provided, including a comparison of extracted parameters and an overview of possible SAW applications.

  1. Polyallelic structural variants can provide accurate, highly informative genetic markers focused on diagnosis and therapeutic targets: Accuracy vs. Precision.

    PubMed

    Roses, A D

    2016-02-01

    Structural variants (SVs) include all insertions, deletions, and rearrangements in the genome, with several common types of nucleotide repeats including single sequence repeats, short tandem repeats, and insertion-deletion length variants. Polyallelic SVs provide highly informative markers for association studies with well-phenotyped cohorts. SVs can influence gene regulation by affecting epigenetics, transcription, splicing, and/or translation. Accurate assays of polyallelic SV loci are required to define the range and allele frequency of variable length alleles. PMID:26517180

  2. HAAD: A quick algorithm for accurate prediction of hydrogen atoms in protein structures.

    PubMed

    Li, Yunqi; Roy, Ambrish; Zhang, Yang

    2009-08-20

    Hydrogen constitutes nearly half of all atoms in proteins and their positions are essential for analyzing hydrogen-bonding interactions and refining atomic-level structures. However, most protein structures determined by experiments or computer prediction lack hydrogen coordinates. We present a new algorithm, HAAD, to predict the positions of hydrogen atoms based on the positions of heavy atoms. The algorithm is built on the basic rules of orbital hybridization followed by the optimization of steric repulsion and electrostatic interactions. We tested the algorithm using three independent data sets: ultra-high-resolution X-ray structures, structures determined by neutron diffraction, and NOE proton-proton distances. Compared with the widely used programs CHARMM and REDUCE, HAAD has a significantly higher accuracy, with the average RMSD of the predicted hydrogen atoms to the X-ray and neutron diffraction structures decreased by 26% and 11%, respectively. Furthermore, hydrogen atoms placed by HAAD have more matches with the NOE restraints and fewer clashes with heavy atoms. The average CPU cost by HAAD is 18 and 8 times lower than that of CHARMM and REDUCE, respectively. The significant advantage of HAAD in both the accuracy and the speed of the hydrogen additions should make HAAD a useful tool for the detailed study of protein structure and function. Both an executable and the source code of HAAD are freely available at http://zhang.bioinformatics.ku.edu/HAAD.

  3. Fine structure in proton radioactivity: An accurate tool to ascertain the breaking of axial symmetry in {sup 145}Tm

    SciTech Connect

    Arumugam, P.; Ferreira, L. S.; Maglione, E.

    2008-10-15

    With a proper formalism for proton emission from triaxially deformed nuclei, we perform exact calculations of decay widths for the decays to ground and first excited 2{sup +} states in the daughter nucleus. Our results for rotational spectrum, decay width and fine structure in the case of the nucleus {sup 145}Tm lead for the first time to an accurate identification of triaxial deformation using proton emission. This work also puts in evidence the advantage of proton emission over the conventional probes to study nuclear structure at the proton drip-line.

  4. SCAN: An Efficient Density Functional Yielding Accurate Structures and Energies of Diversely-Bonded Materials

    NASA Astrophysics Data System (ADS)

    Sun, Jianwei

    The accuracy and computational efficiency of the widely used Kohn-Sham density functional theory (DFT) are limited by the approximation to its exchange-correlation energy Exc. The earliest local density approximation (LDA) overestimates the strengths of all bonds near equilibrium (even the vdW bonds). By adding the electron density gradient to model Exc, generalized gradient approximations (GGAs) generally soften the bonds to give robust and overall more accurate descriptions, except for the vdW interaction which is largely lost. Further improvement for covalent, ionic, and hydrogen bonds can be obtained by the computationally more expensive hybrid GGAs, which mix GGAs with the nonlocal exact exchange. Meta-GGAs are still semilocal in computation and thus efficient. Compared to GGAs, they add the kinetic energy density that enables them to recognize and accordingly treat different bonds, which no LDA or GGA can. We show here that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-GGA improves significantly over LDA and the standard Perdew-Burke-Ernzerhof GGA for geometries and energies of diversely-bonded materials (including covalent, metallic, ionic, hydrogen, and vdW bonds) at comparable efficiency. Often SCAN matches or improves upon the accuracy of a hybrid functional, at almost-GGA cost. This work has been supported by NSF under DMR-1305135 and CNS-09-58854, and by DOE BES EFRC CCDM under DE-SC0012575.

  5. Accurate Fabrication of Hydroxyapatite Bone Models with Porous Scaffold Structures by Using Stereolithography

    NASA Astrophysics Data System (ADS)

    Maeda, Chiaki; Tasaki, Satoko; Kirihara, Soshu

    2011-05-01

    Computer graphic models of bioscaffolds with four-coordinate lattice structures of solid rods in artificial bones were designed by using a computer aided design. The scaffold models composed of acryl resin with hydroxyapatite particles at 45vol. % were fabricated by using stereolithography of a computer aided manufacturing. After dewaxing and sintering heat treatment processes, the ceramics scaffold models with four-coordinate lattices and fine hydroxyapatite microstructures were obtained successfully. By using a computer aided analysis, it was found that bio-fluids could flow extensively inside the sintered scaffolds. This result shows that the lattice structures will realize appropriate bio-fluid circulations and promote regenerations of new bones.

  6. Measurements of microwave spectra and structural parameters for methylferrocene

    NASA Astrophysics Data System (ADS)

    Margolis, David S.; Tanjaroon, Chakree; Kukolich, Stephen G.

    2002-08-01

    Rotational transitions for methylferrocene were measured, in the 4-12 GHz range, using a Flygare-Balle type, pulsed-beam Fourier transform spectrometer. Mono-substituted ferrocenes are nearprolate asymmetric tops with a and b dipole moment components, providing numerous possible transitions in this frequency range. Eighteen rotational constants were calculated from the data for six isotopomers. 59 transitions were measured for the normal isotopomer, and much smaller data sets were obtained for the 54Fe, and four 13C isotopomers. Despite the small data sets for 13C and 54Fe transitions, good fits were obtained with small standard deviations ranging from 2 to 5 kHz. The eighteen A, B, and C rotational constants were used to determine the structural parameters for methylferrocene. Measured rotational constants for the normal isotopomer are: A=1592.6050(6), B=957.2565(4), and C=825.9892(4) MHz. The values for the averaged structural parameters are: r1)(Fe-C)=2.050(7 A, r2)(C-C(cyclopentadienyl ligands)=1.433(7) A and r3(C-CH3))=1.52(2 A (for the methyl cyclopentadienyl ligand). Small splittings (20-30 kHz) were observed for some transitions, and these could be due to proton hyperfine structure or small internal rotation splittings. The structural parameters for this complex were calculated using density functional theory (DFT) methods, and the results are in very good agreement with the measured values. Results are compared with earlier measurements on substituted ferrocenes. Distortions of the substituted cyclopentadienyl ligand are significantly smaller than those observed for chloroferrocene.

  7. Combining Evolutionary Information and an Iterative Sampling Strategy for Accurate Protein Structure Prediction.

    PubMed

    Braun, Tatjana; Koehler Leman, Julia; Lange, Oliver F

    2015-12-01

    Recent work has shown that the accuracy of ab initio structure prediction can be significantly improved by integrating evolutionary information in form of intra-protein residue-residue contacts. Following this seminal result, much effort is put into the improvement of contact predictions. However, there is also a substantial need to develop structure prediction protocols tailored to the type of restraints gained by contact predictions. Here, we present a structure prediction protocol that combines evolutionary information with the resolution-adapted structural recombination approach of Rosetta, called RASREC. Compared to the classic Rosetta ab initio protocol, RASREC achieves improved sampling, better convergence and higher robustness against incorrect distance restraints, making it the ideal sampling strategy for the stated problem. To demonstrate the accuracy of our protocol, we tested the approach on a diverse set of 28 globular proteins. Our method is able to converge for 26 out of the 28 targets and improves the average TM-score of the entire benchmark set from 0.55 to 0.72 when compared to the top ranked models obtained by the EVFold web server using identical contact predictions. Using a smaller benchmark, we furthermore show that the prediction accuracy of our method is only slightly reduced when the contact prediction accuracy is comparatively low. This observation is of special interest for protein sequences that only have a limited number of homologs.

  8. Expanding the model: anisotropic displacement parameters in protein structure refinement.

    PubMed

    Merritt, E A

    1999-06-01

    Recent technological improvements in crystallographic data collection have led to a surge in the number of protein structures being determined at atomic or near-atomic resolution. At this resolution, structural models can be expanded to include anisotropic displacement parameters (ADPs) for individual atoms. New protocols and new tools are needed to refine, analyze and validate such models optimally. One such tool, PARVATI, has been used to examine all protein structures (peptide chains >50 residues) for which expanded models including ADPs are available from the Protein Data Bank. The distribution of anisotropy within each of these refined models is broadly similar across the entire set of structures, with a mean anisotropy A in the range 0.4-0.5. This is a significant departure from a purely isotropic model and explains why the inclusion of ADPs yields a substantial improvement in the crystallographic residuals R and Rfree. The observed distribution of anisotropy may prove useful in the validation of very high resolution structures. A more complete understanding of this distribution may also allow the development of improved protein structural models, even at lower resolution.

  9. Nonlinear system identification of base-excited structures using an intelligent parameter varying (IPV) modeling approach

    NASA Astrophysics Data System (ADS)

    Saadat, Soheil; Buckner, Gregory D.; Furukawa, Tadatoshi; Noori, Mohammad N.

    2003-07-01

    Health monitoring and damage detection strategies for base-excited structures typically rely on accurate models of the system dynamics. Restoring forces in these structures can exhibit highly non-linear characteristics, thus accurate non-linear system identification is critical. Parametric system identification approaches are commonly used, but require a priori knowledge of restoring force characteristics. Non-parametric approaches do not require this a priori information, but they typically lack direct associations between the model and the system dynamics, providing limited utility for health monitoring and damage detection. In this paper a novel system identification approach, the Intelligent Parameter Varying (IPV) method, is used to identify constitutive non-linearities in structures subject to seismic excitations. IPV overcomes the limitations of traditional parametric and non-parametric approaches, while preserving the unique benefits of each. It uses embedded radial basis function networks to estimate the constitutive characteristics of inelastic and hysteretic restoring forces in a multi-degree-of-freedom structure. Simulation results are compared to those of a traditional parametric approach, the prediction error method. These results demonstrate the effectiveness of IPV in identifying highly nonlinear restoring forces, without a priori information, while preserving a direct association with the structural dynamics.

  10. CRYSpred: accurate sequence-based protein crystallization propensity prediction using sequence-derived structural characteristics.

    PubMed

    Mizianty, Marcin J; Kurgan, Lukasz A

    2012-01-01

    Relatively low success rates of X-ray crystallography, which is the most popular method for solving proteins structures, motivate development of novel methods that support selection of tractable protein targets. This aspect is particularly important in the context of the current structural genomics efforts that allow for a certain degree of flexibility in the target selection. We propose CRYSpred, a novel in-silico crystallization propensity predictor that uses a set of 15 novel features which utilize a broad range of inputs including charge, hydrophobicity, and amino acid composition derived from the protein chain, and the solvent accessibility and disorder predicted from the protein sequence. Our method outperforms seven modern crystallization propensity predictors on three, independent from training dataset, benchmark test datasets. The strong predictive performance offered by the CRYSpred is attributed to the careful design of the features, utilization of the comprehensive set of inputs, and the usage of the Support Vector Machine classifier. The inputs utilized by CRYSpred are well-aligned with the existing rules-of-thumb that are used in the structural genomics studies. PMID:21919861

  11. CRYSpred: accurate sequence-based protein crystallization propensity prediction using sequence-derived structural characteristics.

    PubMed

    Mizianty, Marcin J; Kurgan, Lukasz A

    2012-01-01

    Relatively low success rates of X-ray crystallography, which is the most popular method for solving proteins structures, motivate development of novel methods that support selection of tractable protein targets. This aspect is particularly important in the context of the current structural genomics efforts that allow for a certain degree of flexibility in the target selection. We propose CRYSpred, a novel in-silico crystallization propensity predictor that uses a set of 15 novel features which utilize a broad range of inputs including charge, hydrophobicity, and amino acid composition derived from the protein chain, and the solvent accessibility and disorder predicted from the protein sequence. Our method outperforms seven modern crystallization propensity predictors on three, independent from training dataset, benchmark test datasets. The strong predictive performance offered by the CRYSpred is attributed to the careful design of the features, utilization of the comprehensive set of inputs, and the usage of the Support Vector Machine classifier. The inputs utilized by CRYSpred are well-aligned with the existing rules-of-thumb that are used in the structural genomics studies.

  12. Constrained maximum likelihood modal parameter identification applied to structural dynamics

    NASA Astrophysics Data System (ADS)

    El-Kafafy, Mahmoud; Peeters, Bart; Guillaume, Patrick; De Troyer, Tim

    2016-05-01

    A new modal parameter estimation method to directly establish modal models of structural dynamic systems satisfying two physically motivated constraints will be presented. The constraints imposed in the identified modal model are the reciprocity of the frequency response functions (FRFs) and the estimation of normal (real) modes. The motivation behind the first constraint (i.e. reciprocity) comes from the fact that modal analysis theory shows that the FRF matrix and therefore the residue matrices are symmetric for non-gyroscopic, non-circulatory, and passive mechanical systems. In other words, such types of systems are expected to obey Maxwell-Betti's reciprocity principle. The second constraint (i.e. real mode shapes) is motivated by the fact that analytical models of structures are assumed to either be undamped or proportional damped. Therefore, normal (real) modes are needed for comparison with these analytical models. The work done in this paper is a further development of a recently introduced modal parameter identification method called ML-MM that enables us to establish modal model that satisfies such motivated constraints. The proposed constrained ML-MM method is applied to two real experimental datasets measured on fully trimmed cars. This type of data is still considered as a significant challenge in modal analysis. The results clearly demonstrate the applicability of the method to real structures with significant non-proportional damping and high modal densities.

  13. STRUCTURAL PARAMETERS FOR 10 HALO GLOBULAR CLUSTERS IN M33

    SciTech Connect

    Ma, Jun

    2015-05-15

    In this paper, we present the properties of 10 halo globular clusters (GCs) with luminosities L ≃ 5–7 × 10{sup 5} L{sub ⊙} in the Local Group galaxy M33 using images from the Hubble Space Telescope WFPC2 in the F555W and F814W bands. We obtained the ellipticities, position angles, and surface brightness profiles for each GC. In general, the ellipticities of the M33 sample clusters are similar to those of the M31 clusters. The structural and dynamical parameters are derived by fitting the profiles to three different models combined with mass-to-light ratios (M/L values) from population-synthesis models. The structural parameters include core radii, concentration, half-light radii, and central surface brightness. The dynamical parameters include the integrated cluster mass, integrated binding energy, central surface mass density, and predicted line of sight velocity dispersion at the cluster center. The velocity dispersions of the four clusters predicted here agree well with the observed dispersions by Larsen et al. The results here showed that the majority of the sample halo GCs are better fitted by both the King model and the Wilson model than the Sérsic model. In general, the properties of the clusters in M33, M31, and the Milky Way fall in the same regions of parameter spaces. The tight correlations of cluster properties indicate a “fundamental plane” for clusters, which reflects some universal physical conditions and processes operating at the epoch of cluster formation.

  14. A simplified method for random vibration analysis of structures with random parameters

    NASA Astrophysics Data System (ADS)

    Ghienne, Martin; Blanzé, Claude

    2016-09-01

    Piezoelectric patches with adapted electrical circuits or viscoelastic dissipative materials are two solutions particularly adapted to reduce vibration of light structures. To accurately design these solutions, it is necessary to describe precisely the dynamical behaviour of the structure. It may quickly become computationally intensive to describe robustly this behaviour for a structure with nonlinear phenomena, such as contact or friction for bolted structures, and uncertain variations of its parameters. The aim of this work is to propose a non-intrusive reduced stochastic method to characterize robustly the vibrational response of a structure with random parameters. Our goal is to characterize the eigenspace of linear systems with dynamic properties considered as random variables. This method is based on a separation of random aspects from deterministic aspects and allows us to estimate the first central moments of each random eigenfrequency with a single deterministic finite elements computation. The method is applied to a frame with several Young's moduli modeled as random variables. This example could be expanded to a bolted structure including piezoelectric devices. The method needs to be enhanced when random eigenvalues are closely spaced. An indicator with no additional computational cost is proposed to characterize the ’’proximity” of two random eigenvalues.

  15. Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens

    SciTech Connect

    Park, Min-Sun; Park, Sung Yong; Miller, Keith R.; Collins, Edward J.; Lee, Ha Youn

    2013-11-01

    Designing an optimal HIV-1 vaccine faces the challenge of identifying antigens that induce a broad immune capacity. One factor to control the breadth of T cell responses is the surface morphology of a peptide–MHC complex. Here, we present an in silico protocol for predicting peptide–MHC structure. A robust signature of a conformational transition was identified during all-atom molecular dynamics, which results in a model with high accuracy. A large test set was used in constructing our protocol and we went another step further using a blind test with a wild-type peptide and two highly immunogenic mutants, which predicted substantial conformational changes in both mutants. The center residues at position five of the analogs were configured to be accessible to solvent, forming a prominent surface, while the residue of the wild-type peptide was to point laterally toward the side of the binding cleft. We then experimentally determined the structures of the blind test set, using high resolution of X-ray crystallography, which verified predicted conformational changes. Our observation strongly supports a positive association of the surface morphology of a peptide–MHC complex to its immunogenicity. Our study offers the prospect of enhancing immunogenicity of vaccines by identifying MHC binding immunogens.

  16. The Dirac equation in electronic structure calculations: Accurate evaluation of DFT predictions for actinides

    SciTech Connect

    Wills, John M; Mattsson, Ann E

    2012-06-06

    Brooks, Johansson, and Skriver, using the LMTO-ASA method and considerable insight, were able to explain many of the ground state properties of the actinides. In the many years since this work was done, electronic structure calculations of increasing sophistication have been applied to actinide elements and compounds, attempting to quantify the applicability of DFT to actinides and actinide compounds and to try to incorporate other methodologies (i.e. DMFT) into DFT calculations. Through these calculations, the limits of both available density functionals and ad hoc methodologies are starting to become clear. However, it has also become clear that approximations used to incorporate relativity are not adequate to provide rigorous tests of the underlying equations of DFT, not to mention ad hoc additions. In this talk, we describe the result of full-potential LMTO calculations for the elemental actinides, comparing results obtained with a full Dirac basis with those obtained from scalar-relativistic bases, with and without variational spin-orbit. This comparison shows that the scalar relativistic treatment of actinides does not have sufficient accuracy to provide a rigorous test of theory and that variational spin-orbit introduces uncontrolled errors in the results of electronic structure calculations on actinide elements.

  17. A FIB-nanotomography method for accurate 3D reconstruction of open nanoporous structures.

    PubMed

    Mangipudi, K R; Radisch, V; Holzer, L; Volkert, C A

    2016-04-01

    We present an automated focused ion beam nanotomography method for nanoporous microstructures with open porosity, and apply it to reconstruct nanoporous gold (np-Au) structures with ligament sizes on the order of a few tens of nanometers. This method uses serial sectioning of a well-defined wedge-shaped geometry to determine the thickness of individual slices from the changes in the sample width in successive cross-sectional images. The pore space of a selected region of the np-Au is infiltrated with ion-beam-deposited Pt composite before serial sectioning. The cross-sectional images are binarized and stacked according to the individual slice thicknesses, and then processed using standard reconstruction methods. For the image conditions and sample geometry used here, we are able to determine the thickness of individual slices with an accuracy much smaller than a pixel. The accuracy of the new method based on actual slice thickness is assessed by comparing it with (i) a reconstruction using the same cross-sectional images but assuming a constant slice thickness, and (ii) a reconstruction using traditional FIB-tomography method employing constant slice thickness. The morphology and topology of the structures are characterized using ligament and pore size distributions, interface shape distribution functions, interface normal distributions, and genus. The results suggest that the morphology and topology of the final reconstructions are significantly influenced when a constant slice thickness is assumed. The study reveals grain-to-grain variations in the morphology and topology of np-Au. PMID:26906523

  18. SENSITIVITY OF STRUCTURAL RESPONSE TO GROUND MOTION SOURCE AND SITE PARAMETERS.

    USGS Publications Warehouse

    Safak, Erdal; Brebbia, C.A.; Cakmak, A.S.; Abdel Ghaffar, A.M.

    1985-01-01

    Designing structures to withstand earthquakes requires an accurate estimation of the expected ground motion. While engineers use the peak ground acceleration (PGA) to model the strong ground motion, seismologists use physical characteristics of the source and the rupture mechanism, such as fault length, stress drop, shear wave velocity, seismic moment, distance, and attenuation. This study presents a method for calculating response spectra from seismological models using random vibration theory. It then investigates the effect of various source and site parameters on peak response. Calculations are based on a nonstationary stochastic ground motion model, which can incorporate all the parameters both in frequency and time domains. The estimation of the peak response accounts for the effects of the non-stationarity, bandwidth and peak correlations of the response.

  19. Structural and functional screening in human induced-pluripotent stem cell-derived cardiomyocytes accurately identifies cardiotoxicity of multiple drug types

    SciTech Connect

    Doherty, Kimberly R. Talbert, Dominique R.; Trusk, Patricia B.; Moran, Diarmuid M.; Shell, Scott A.; Bacus, Sarah

    2015-05-15

    Safety pharmacology studies that evaluate new drug entities for potential cardiac liability remain a critical component of drug development. Current studies have shown that in vitro tests utilizing human induced pluripotent stem cell-derived cardiomyocytes (hiPS-CM) may be beneficial for preclinical risk evaluation. We recently demonstrated that an in vitro multi-parameter test panel assessing overall cardiac health and function could accurately reflect the associated clinical cardiotoxicity of 4 FDA-approved targeted oncology agents using hiPS-CM. The present studies expand upon this initial observation to assess whether this in vitro screen could detect cardiotoxicity across multiple drug classes with known clinical cardiac risks. Thus, 24 drugs were examined for their effect on both structural (viability, reactive oxygen species generation, lipid formation, troponin secretion) and functional (beating activity) endpoints in hiPS-CM. Using this screen, the cardiac-safe drugs showed no effects on any of the tests in our panel. However, 16 of 18 compounds with known clinical cardiac risk showed drug-induced changes in hiPS-CM by at least one method. Moreover, when taking into account the Cmax values, these 16 compounds could be further classified depending on whether the effects were structural, functional, or both. Overall, the most sensitive test assessed cardiac beating using the xCELLigence platform (88.9%) while the structural endpoints provided additional insight into the mechanism of cardiotoxicity for several drugs. These studies show that a multi-parameter approach examining both cardiac cell health and function in hiPS-CM provides a comprehensive and robust assessment that can aid in the determination of potential cardiac liability. - Highlights: • 24 drugs were tested for cardiac liability using an in vitro multi-parameter screen. • Changes in beating activity were the most sensitive in predicting cardiac risk. • Structural effects add in

  20. Topology Synthesis of Structures Using Parameter Relaxation and Geometric Refinement

    NASA Technical Reports Server (NTRS)

    Hull, P. V.; Tinker, M. L.

    2007-01-01

    Typically, structural topology optimization problems undergo relaxation of certain design parameters to allow the existence of intermediate variable optimum topologies. Relaxation permits the use of a variety of gradient-based search techniques and has been shown to guarantee the existence of optimal solutions and eliminate mesh dependencies. This Technical Publication (TP) will demonstrate the application of relaxation to a control point discretization of the design workspace for the structural topology optimization process. The control point parameterization with subdivision has been offered as an alternative to the traditional method of discretized finite element design domain. The principle of relaxation demonstrates the increased utility of the control point parameterization. One of the significant results of the relaxation process offered in this TP is that direct manufacturability of the optimized design will be maintained without the need for designer intervention or translation. In addition, it will be shown that relaxation of certain parameters may extend the range of problems that can be addressed; e.g., in permitting limited out-of-plane motion to be included in a path generation problem.

  1. THE LUMINOSITY PROFILE AND STRUCTURAL PARAMETERS OF THE ANDROMEDA GALAXY

    SciTech Connect

    Courteau, Stephane; Widrow, Lawrence M.; McDonald, Michael; Guhathakurta, Puragra; Zhu Yucong

    2011-09-20

    We have constructed an extended composite luminosity profile for the Andromeda galaxy, M31, and have decomposed it into three basic luminous structural components: a bulge, a disk, and a halo. The dust-free Spitzer/Infrared Array Camera (IRAC) imaging and extended spatial coverage of ground-based optical imaging and deep star counts allow us to map M31's structure from its center to 22 kpc along the major axis. We apply, and address the limitations of, different decomposition methods for the one-dimensional luminosity profiles and two-dimensional images. These methods include nonlinear least-squares and Bayesian Monte Carlo Markov chain analyses. The basic photometric model for M31 has a Sersic bulge with shape index n {approx_equal} 2.2 {+-} .3 and effective radius R{sub e} = 1.0 {+-} 0.2 kpc, and a dust-free exponential disk of scale length R{sub d} = 5.3 {+-} .5 kpc; the parameter errors reflect the range between different decomposition methods. Despite model covariances, the convergence of solutions based on different methods and current data suggests a stable set of structural parameters. The ellipticities ({epsilon} = 1 - b/a) of the bulge and the disk from the IRAC image are 0.37 {+-} 0.03 and 0.73 {+-} 0.03, respectively. The bulge parameter n is rather insensitive to bandpass effects and its value (2.2) suggests a first rapid formation via mergers followed by secular growth from the disk. The M31 halo has a two-dimensional power-law index {approx_equal} - 2.5 {+-} 0.2 (or -3.5 in three-dimensional), comparable to that of the Milky Way. We find that the M31 bulge light is mostly dominant over the range R{sub min} {approx}< 1.2 kpc. The disk takes over in the range 1.2 kpc {approx}< R{sub min} {approx}< 9 kpc, whereas the halo dominates at R{sub min} {approx}> 9 kpc. The stellar nucleus, bulge, disk, and halo components each contribute roughly 0.05%, 23%, 73%, and 4% of the total light of M31 out to 200 kpc along the minor axis. Nominal errors for the

  2. Variation in the modal parameters of space structures

    NASA Technical Reports Server (NTRS)

    Crawley, Edward F.; Barlow, Mark S.; Van Schoor, Marthinus C.; Bicos, Andrew S.

    1992-01-01

    An analytic and experimental study of gravity and suspension influences on space structural test articles is presented. A modular test article including deployable, erectable, and rotary modules was assembled in three one- and two-dimensional structures. The two deployable modules utilized cable diagonal bracing rather than rigid cross members; within a bay of one of the deployable modules, the cable preload was adjustable. A friction lock was used on the alpha joint to either allow or prohibit rotary motion. Suspension systems with plunge fundamentals of 1, 2, and 5 Hz were used for ground testing to evaluate the influences of suspension stiffness. Assembly and reassembly testing was performed, as was testing on two separate shipsets at two test sites. Trends and statistical variances in modal parameters are presented as a function of force amplitude, joint preload, reassembly, shipset and suspension. Linear finite element modeling of each structure provided analytical results for 0-g unsuspended and 1-g suspended models, which are correlated with the analytical model.

  3. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    SciTech Connect

    Dunn, Nicholas J. H.; Noid, W. G.

    2015-12-28

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed “pressure-matching” variational principle to determine a volume-dependent contribution to the potential, U{sub V}(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing U{sub V}, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that U{sub V} accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the “simplicity” of the model.

  4. Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids

    NASA Astrophysics Data System (ADS)

    Dunn, Nicholas J. H.; Noid, W. G.

    2015-12-01

    The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of all-atom (AA) models for molecular liquids. In particular, we consider 1, 2, and 3-site CG models for heptane, as well as 1 and 3-site CG models for toluene. For each model, we employ the multiscale coarse-graining method to determine interaction potentials that optimally approximate the configuration dependence of the many-body potential of mean force (PMF). We employ a previously developed "pressure-matching" variational principle to determine a volume-dependent contribution to the potential, UV(V), that approximates the volume-dependence of the PMF. We demonstrate that the resulting CG models describe AA density fluctuations with qualitative, but not quantitative, accuracy. Accordingly, we develop a self-consistent approach for further optimizing UV, such that the CG models accurately reproduce the equilibrium density, compressibility, and average pressure of the AA models, although the CG models still significantly underestimate the atomic pressure fluctuations. Additionally, by comparing this array of models that accurately describe the structure and thermodynamic pressure of heptane and toluene at a range of different resolutions, we investigate the impact of bottom-up coarse-graining upon thermodynamic properties. In particular, we demonstrate that UV accounts for the reduced cohesion in the CG models. Finally, we observe that bottom-up coarse-graining introduces subtle correlations between the resolution, the cohesive energy density, and the "simplicity" of the model.

  5. Voronoi-cell finite difference method for accurate electronic structure calculation of polyatomic molecules on unstructured grids

    SciTech Connect

    Son, Sang-Kil

    2011-03-01

    We introduce a new numerical grid-based method on unstructured grids in the three-dimensional real-space to investigate the electronic structure of polyatomic molecules. The Voronoi-cell finite difference (VFD) method realizes a discrete Laplacian operator based on Voronoi cells and their natural neighbors, featuring high adaptivity and simplicity. To resolve multicenter Coulomb singularity in all-electron calculations of polyatomic molecules, this method utilizes highly adaptive molecular grids which consist of spherical atomic grids. It provides accurate and efficient solutions for the Schroedinger equation and the Poisson equation with the all-electron Coulomb potentials regardless of the coordinate system and the molecular symmetry. For numerical examples, we assess accuracy of the VFD method for electronic structures of one-electron polyatomic systems, and apply the method to the density-functional theory for many-electron polyatomic molecules.

  6. A Simple and Accurate Analysis of Conductivity Loss in Millimeter-Wave Helical Slow-Wave Structures

    NASA Astrophysics Data System (ADS)

    Datta, S. K.; Kumar, Lalit; Basu, B. N.

    2009-04-01

    Electromagnetic field analysis of a helix slow-wave structure was carried out and a closed form expression was derived for the inductance per unit length of the transmission-line equivalent circuit of the structure, taking into account the actual helix tape dimensions and surface current on the helix over the actual metallic area of the tape. The expression of the inductance per unit length, thus obtained, was used for estimating the increment in the inductance per unit length caused due to penetration of the magnetic flux into the conducting surfaces following Wheeler’s incremental inductance rule, which was subsequently interpreted for the attenuation constant of the propagating structure. The analysis was computationally simple and accurate, and accrues the accuracy of 3D electromagnetic analysis by allowing the use of dispersion characteristics obtainable from any standard electromagnetic modeling. The approach was benchmarked against measurement for two practical structures, and excellent agreement was observed. The analysis was subsequently applied to demonstrate the effects of conductivity on the attenuation constant of a typical broadband millimeter-wave helical slow-wave structure with respect to helix materials and copper plating on the helix, surface finish of the helix, dielectric loading effect and effect of high temperature operation - a comparative study of various such aspects are covered.

  7. Effect of mechanical parameters on dielectric elastomer minimum energy structures

    NASA Astrophysics Data System (ADS)

    Shintake, Jun; Rosset, Samuel; Floreano, Dario; Shea, Herbert R.

    2013-04-01

    Soft robotics may provide many advantages compared to traditional robotics approaches based on rigid materials, such as intrinsically safe physical human-robot interaction, efficient/stable locomotion, adaptive morphology, etc. The objective of this study is to develop a compliant structural actuator for soft a soft robot using dielectric elastomer minimum energy structures (DEMES). DEMES consist of a pre-stretched dielectric elastomer actuator (DEA) bonded to an initially planar flexible frame, which deforms into an out-of-plane shape which allows for large actuation stroke. Our initial goal is a one-dimensional bending actuator with 90 degree stroke. Along with frame shape, the actuation performance of DEMES depends on mechanical parameters such as thickness of the materials and pre-stretch of the elastomer membrane. We report here the characterization results on the effect of mechanical parameters on the actuator performance. The tested devices use a cm-size flexible-PCB (polyimide, 50 μm thickness) as the frame-material. For the DEA, PDMS (approximately 50 μm thickness) and carbon black mixed with silicone were used as membrane and electrode, respectively. The actuators were characterized by measuring the tip angle and the blocking force as functions of applied voltage. Different pre-stretch methods (uniaxial, biaxial and their ratio), and frame geometries (rectangular with different width, triangular and circular) were used. In order to compare actuators with different geometries, the same electrode area was used in all the devices. The results showed that the initial tip angle scales inversely with the frame width, the actuation stroke and the blocking force are inversely related (leading to an interesting design trade-off), using anisotropic pre-stretch increased the actuation stroke and the initial bending angle, and the circular frame shape exhibited the highest actuation performance.

  8. Structural Design Parameters for Highly Birefringent Coordination Polymers.

    PubMed

    Thompson, John R; Katz, Michael J; Williams, Vance E; Leznoff, Daniel B

    2015-07-01

    A series of coordination polymer materials incorporating the highly anisotropic 2-(2-pyridyl)-1,10-phenanthroline (phenpy) building block have been synthesized and structurally characterized. M(phenpy)[Au(CN)2]2 (M = Cd, Mn) are isostructural and form a 1-D chain through bridging [Au(CN)2](-) units and extend into a 2-D sheet through aurophilic interactions. M(phenpy)(H2O)[Au(CN)2]2·2H2O (M = Cd, Mn, and Zn) are also isostructural but differ from the first set via the inclusion of a water molecule into the coordination sphere, resulting in a 1-D topology through aurophilic interactions. In(phenpy)(Cl)2[Au(CN)2]·0.5H2O forms a dimer through bridging chlorides and contains a free [Au(CN)2](-) unit. In the plane of the primary crystal growth direction, the birefringence values (Δn) of 0.37(2) (Cd(phenpy)[Au(CN)2]2), 0.50(3) (In(phenpy)(Cl)2[Au(CN)2]·0.5H2O), 0.56(3) and 0.59(6) (M(phenpy)(H2O)[Au(CN)2]2·2H2O M = Cd and Zn, respectively) were determined. β, a structural parameter defined by phenpy units rotated in the A-C plane relative to the light propagation (C) direction, was found to correlate to Δn magnitudes. The addition of a carbon-carbon double bond to terpy has increased the molecular polarizability anisotropy of the building block, and all structures have reduced deviation from planarity in comparison to terpy and terpy derivative structures, leading to these higher Δn values, which are among the highest reported for crystalline solids. PMID:26098267

  9. Modal parameter extraction from large operating structures using ambient excitation

    SciTech Connect

    James, G.H. III; Carne, T.G.; Mayes, R.L.

    1995-12-31

    A technique called the Natural Excitation Technique or has been developed to response extract response parameters from large operational structure when subjected to random and unmeasured forces such as wind, road noise, aerodynamics, or waves. Six applications of NExT to ambient excitation testing and NExT analysis are surveyed in this paper with a minimum of technical detail. In the first application, NExT was applied to a controlled-yaw Horizontal-Axis Wind Turbine (HAWT). By controlling the yaw degree of freedom an important class of rotating coordinate system effects are reduced. A new shape extraction procedure was applied to this data set with good results. The second application was to a free-yaw HAWT. The complexity of the response has prompted further analytical studies and the development of a specialized visualization package. The third application of NExT was to a parked three-bladed Vertical-Axis Wind Turbine (VAWT) in which traditional modal testing could not excite all modes of interest. The shape extraction process used cross-correlation functions directly in a time-domain shape-fitting routine. The fourth application was to ground transportation systems. Ongoing work to improve driver and passenger comfort in tractor-trailer vehicles and to refine automobile body and tire models will use NExT. NExT has been used to process ambient vibration data for Finite Element Model correlation and is being used to study Structural Health Monitoring with ambient excitation. Shape fitting was performed using amplitude and phase information taken directly from the cross-spectra. The final application is to an offshore structure. This work is on-going, however initial studies have found a high-modal density, high noise content, and sparse data set.

  10. Efficient and accurate linear algebraic methods for large-scale electronic structure calculations with nonorthogonal atomic orbitals

    NASA Astrophysics Data System (ADS)

    Teng, H.; Fujiwara, T.; Hoshi, T.; Sogabe, T.; Zhang, S.-L.; Yamamoto, S.

    2011-04-01

    The need for large-scale electronic structure calculations arises recently in the field of material physics, and efficient and accurate algebraic methods for large simultaneous linear equations become greatly important. We investigate the generalized shifted conjugate orthogonal conjugate gradient method, the generalized Lanczos method, and the generalized Arnoldi method. They are the solver methods of large simultaneous linear equations of the one-electron Schrödinger equation and map the whole Hilbert space to a small subspace called the Krylov subspace. These methods are applied to systems of fcc Au with the NRL tight-binding Hamiltonian [F. Kirchhoff , Phys. Rev. BJCOMEL1098-012110.1103/PhysRevB.63.195101 63, 195101 (2001)]. We compare results by these methods and the exact calculation and show them to be equally accurate. The system size dependence of the CPU time is also discussed. The generalized Lanczos method and the generalized Arnoldi method are the most suitable for the large-scale molecular dynamics simulations from the viewpoint of CPU time and memory size.

  11. Extraction of accurate structure-factor amplitudes from Laue data: wavelength normalization with wiggler and undulator X-ray sources.

    PubMed

    Srajer, V; Crosson, S; Schmidt, M; Key, J; Schotte, F; Anderson, S; Perman, B; Ren, Z; Teng, T Y; Bourgeois, D; Wulff, M; Moffat, K

    2000-07-01

    Wavelength normalization is an essential part of processing of Laue X-ray diffraction data and is critically important for deriving accurate structure-factor amplitudes. The results of wavelength normalization for Laue data obtained in nanosecond time-resolved experiments at the ID09 beamline at the European Synchrotron Radiation Facility, Grenoble, France, are presented. Several wiggler and undulator insertion devices with complex spectra were used. The results show that even in the most challenging cases, such as wiggler/undulator tandems or single-line undulators, accurate wavelength normalization does not require unusually redundant Laue data and can be accomplished using typical Laue data sets. Single-line undulator spectra derived from Laue data compare well with the measured incident X-ray spectra. Successful wavelength normalization of the undulator data was also confirmed by the observed signal in nanosecond time-resolved experiments. Single-line undulators, which are attractive for time-resolved experiments due to their high peak intensity and low polychromatic background, are compared with wigglers, based on data obtained on the same crystal. PMID:16609201

  12. Millimeter-wave interferometry: an attractive technique for fast and accurate sensing of civil and mechanical structures

    NASA Astrophysics Data System (ADS)

    Kim, Seoktae; Nguyen, Cam

    2014-04-01

    This paper discusses the RF interferometry at millimeter-wave frequencies for sensing applications and reports the development of a millimeter-wave interferometric sensor operating around 35 GHz. The sensor is completely realized using microwave integrated circuits (MICs) and microwave monolithic integrated circuits (MMICs). It has been used for various sensing including displacement and velocity measurement. The sensor achieves a resolution and maximum error of only 10 μm and 27 μm, respectively, for displacement sensing and can measure velocity as low as 27.7 mm/s with a resolution about 2.7mm/s. Quick response and accurate sensing, as demonstrated by the developed millimeter-wave interferometric sensor, make the millimeter-wave interferometry attractive for sensing of various civil and mechanical structures.

  13. THE STAR CLUSTERS OF THE LARGE MAGELLANIC CLOUD: STRUCTURAL PARAMETERS

    SciTech Connect

    Werchan, Felicia; Zaritsky, Dennis E-mail: dzaritsky@as.arizona.edu

    2011-08-15

    We present and analyze the radial luminosity profiles of a sample of 1066 stellar clusters in the Large Magellanic Cloud (LMC). By design, this study closely follows the compilation by Hill and Zaritsky of the structural parameters of stellar clusters in the Small Magellanic Cloud (SMC). Both King and Elson-Fall-Freeman model profiles are fit to V-band surface brightness profiles measured from the Magellanic Cloud Photometric Survey images. We tabulate the concentration, central surface brightness, tidal radii, 90% enclosed luminosity radii (r{sub 90}), and local background luminosity density. Over two-thirds of the clusters in the sample are adequately fit by one or both of these models. One notable and systematic exception, as in the SMC, is those clusters that lack a central brightness concentration, the 'ring' clusters. While the bulk properties of the clusters are similar between the LMC and SMC populations, we find that the LMC lacks clusters that are as large, either in terms of core radii or r{sub 90}, as the largest in the SMC, perhaps a signature of larger tidal stresses in the LMC.

  14. STRUCTURAL PARAMETERS OF THE MESSIER 87 GLOBULAR CLUSTERS

    SciTech Connect

    Madrid, Juan P.; Harris, William E.; Blakeslee, John P.; Gomez, MatIas

    2009-11-01

    We derive structural parameters for approx2000 globular clusters in the giant Virgo elliptical Messier 87 (M87) using extremely deep Hubble Space Telescope images in F606W (V) and F814W (I) taken with the ACS/WFC. The cluster scale sizes (half-light radii r{sub h} ) and ellipticities are determined from point-spread-function -convolved King-model profile fitting. We find that the r{sub h} distribution closely resembles the inner Milky Way clusters, peaking at r{sub h} approx = 2.5 pc and with virtually no clusters more compact than r{sub h} approx = 1 pc. The metal-poor clusters have on average an r{sub h} 24% larger than the metal-rich ones. The cluster scale size shows a gradual and noticeable increase with galactocentric distance. Clusters are very slightly larger in the bluer waveband V, a possible hint that we may be beginning to see the effects of mass segregation within the clusters. We also derived a color magnitude diagram for the M87 globular cluster system which shows a striking bimodal distribution.

  15. Analysing DNA structural parameters using a mesoscopic model

    NASA Astrophysics Data System (ADS)

    Amarante, Tauanne D.; Weber, Gerald

    2014-03-01

    The Peyrard-Bishop model is a mesoscopic approximation to model DNA and RNA molecules. Several variants of this model exists, from 3D Hamiltonians, including torsional angles, to simpler 2D versions. Currently, we are able to parametrize the 2D variants of the model which allows us to extract important information about the molecule. For example, with this technique we were able recently to obtain the hydrogen bonds of RNA from melting temperatures, which previously were obtainable only from NMR measurements. Here, we take the 3D torsional Hamiltonian and set the angles to zero. Curiously, in doing this we do not recover the traditional 2D Hamiltonians. Instead, we obtain a different 2D Hamiltonian which now includes a base pair step distance, commonly known as rise. A detailed knowledge of the rise distance is important as it determines the overall length of the DNA molecule. This 2D Hamiltonian provides us with the exciting prospect of obtaining DNA structural parameters from melting temperatures. Our results of the rise distance at low salt concentration are in good qualitative agreement with those from several published x-ray measurements. We also found an important dependence of the rise distance with salt concentration. In contrast to our previous calculations, the elastic constants now show little dependence with salt concentrations which appears to be closer to what is seen experimentally in DNA flexibility experiments.

  16. Materials and characterization using acoustic nonlinearity parameters and harmonic generation - Effects of crystalline and amorphous structures

    NASA Technical Reports Server (NTRS)

    Cantrell, John H.; Yost, William T.

    1990-01-01

    The effects of material structure on the nonlinearity parameters are reviewed. Problems discussed include definition of nonlinearity parameters, square-law nonlinearity and collinear beam-mixing, structure dependence of the nonlinearity parameters, negative nonlinearity parameters, and implications for materials characterization.

  17. Structural and functional screening in human induced-pluripotent stem cell-derived cardiomyocytes accurately identifies cardiotoxicity of multiple drug types.

    PubMed

    Doherty, Kimberly R; Talbert, Dominique R; Trusk, Patricia B; Moran, Diarmuid M; Shell, Scott A; Bacus, Sarah

    2015-05-15

    Safety pharmacology studies that evaluate new drug entities for potential cardiac liability remain a critical component of drug development. Current studies have shown that in vitro tests utilizing human induced pluripotent stem cell-derived cardiomyocytes (hiPS-CM) may be beneficial for preclinical risk evaluation. We recently demonstrated that an in vitro multi-parameter test panel assessing overall cardiac health and function could accurately reflect the associated clinical cardiotoxicity of 4 FDA-approved targeted oncology agents using hiPS-CM. The present studies expand upon this initial observation to assess whether this in vitro screen could detect cardiotoxicity across multiple drug classes with known clinical cardiac risks. Thus, 24 drugs were examined for their effect on both structural (viability, reactive oxygen species generation, lipid formation, troponin secretion) and functional (beating activity) endpoints in hiPS-CM. Using this screen, the cardiac-safe drugs showed no effects on any of the tests in our panel. However, 16 of 18 compounds with known clinical cardiac risk showed drug-induced changes in hiPS-CM by at least one method. Moreover, when taking into account the Cmax values, these 16 compounds could be further classified depending on whether the effects were structural, functional, or both. Overall, the most sensitive test assessed cardiac beating using the xCELLigence platform (88.9%) while the structural endpoints provided additional insight into the mechanism of cardiotoxicity for several drugs. These studies show that a multi-parameter approach examining both cardiac cell health and function in hiPS-CM provides a comprehensive and robust assessment that can aid in the determination of potential cardiac liability.

  18. Accurate molecular structure and spectroscopic properties of nucleobases: a combined computational-microwave investigation of 2-thiouracil as a case study.

    PubMed

    Puzzarini, Cristina; Biczysko, Malgorzata; Barone, Vincenzo; Peña, Isabel; Cabezas, Carlos; Alonso, José L

    2013-10-21

    The computational composite scheme purposely set up for accurately describing the electronic structure and spectroscopic properties of small biomolecules has been applied to the first study of the rotational spectrum of 2-thiouracil. The experimental investigation was made possible thanks to the combination of the laser ablation technique with Fourier transform microwave spectrometers. The joint experimental-computational study allowed us to determine the accurate molecular structure and spectroscopic properties of the title molecule, but more importantly, it demonstrates a reliable approach for the accurate investigation of isolated small biomolecules.

  19. Extending the molecular size in accurate quantum-chemical calculations: the equilibrium structure and spectroscopic properties of uracil.

    PubMed

    Puzzarini, Cristina; Barone, Vincenzo

    2011-04-21

    The equilibrium structure of uracil has been investigated using both theoretical and experimental data. With respect to the former, quantum-chemical calculations at the coupled-cluster level in conjunction with a triple-zeta basis set have been carried out. Extrapolation to the basis set limit, performed employing the second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections have also been considered. Based on the available rotational constants for various isotopic species together with corresponding computed vibrational corrections, the semi-experimental equilibrium structure of uracil has been determined for the first time. Theoretical and semi-experimental structures have been found in remarkably good agreement, thus pointing out the limitations of previous experimental determinations. Molecular and spectroscopic properties of uracil have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the revision of the dipole moment. On the whole, it has been proved that the computational procedure presented is able to provide parameters with the proper accuracy to support experimental investigations of large molecules of biological interest.

  20. Accurate collision-induced line-coupling parameters for the fundamental band of CO in He - Close coupling and coupled states scattering calculations

    NASA Technical Reports Server (NTRS)

    Green, Sheldon; Boissoles, J.; Boulet, C.

    1988-01-01

    The first accurate theoretical values for off-diagonal (i.e., line-coupling) pressure-broadening cross sections are presented. Calculations were done for CO perturbed by He at thermal collision energies using an accurate ab initio potential energy surface. Converged close coupling, i.e., numerically exact values, were obtained for coupling to the R(0) and R(2) lines. These were used to test the coupled states (CS) and infinite order sudden (IOS) approximate scattering methods. CS was found to be of quantitative accuracy (a few percent) and has been used to obtain coupling values for lines to R(10). IOS values are less accurate, but, owing to their simplicity, may nonetheless prove useful as has been recently demonstrated.

  1. Hunting for hydrogen: random structure searching and prediction of NMR parameters of hydrous wadsleyite.

    PubMed

    Moran, Robert F; McKay, David; Pickard, Chris J; Berry, Andrew J; Griffin, John M; Ashbrook, Sharon E

    2016-04-21

    The structural chemistry of materials containing low levels of nonstoichiometric hydrogen is difficult to determine, and producing structural models is challenging where hydrogen has no fixed crystallographic site. Here we demonstrate a computational approach employing ab initio random structure searching (AIRSS) to generate a series of candidate structures for hydrous wadsleyite (β-Mg2SiO4 with 1.6 wt% H2O), a high-pressure mineral proposed as a repository for water in the Earth's transition zone. Aligning with previous experimental work, we solely consider models with Mg3 (over Mg1, Mg2 or Si) vacancies. We adapt the AIRSS method by starting with anhydrous wadsleyite, removing a single Mg(2+) and randomly placing two H(+) in a unit cell model, generating 819 candidate structures. 103 geometries were then subjected to more accurate optimisation under periodic DFT. Using this approach, we find the most favourable hydration mechanism involves protonation of two O1 sites around the Mg3 vacancy. The formation of silanol groups on O3 or O4 sites (with loss of stable O1-H hydroxyls) coincides with an increase in total enthalpy. Importantly, the approach we employ allows observables such as NMR parameters to be computed for each structure. We consider hydrous wadsleyite (∼1.6 wt%) to be dominated by protonated O1 sites, with O3/O4-H silanol groups present as defects, a model that maps well onto experimental studies at higher levels of hydration (J. M. Griffin et al., Chem. Sci., 2013, 4, 1523). The AIRSS approach adopted herein provides the crucial link between atomic-scale structure and experimental studies. PMID:27020937

  2. Hunting for hydrogen: random structure searching and prediction of NMR parameters of hydrous wadsleyite.

    PubMed

    Moran, Robert F; McKay, David; Pickard, Chris J; Berry, Andrew J; Griffin, John M; Ashbrook, Sharon E

    2016-04-21

    The structural chemistry of materials containing low levels of nonstoichiometric hydrogen is difficult to determine, and producing structural models is challenging where hydrogen has no fixed crystallographic site. Here we demonstrate a computational approach employing ab initio random structure searching (AIRSS) to generate a series of candidate structures for hydrous wadsleyite (β-Mg2SiO4 with 1.6 wt% H2O), a high-pressure mineral proposed as a repository for water in the Earth's transition zone. Aligning with previous experimental work, we solely consider models with Mg3 (over Mg1, Mg2 or Si) vacancies. We adapt the AIRSS method by starting with anhydrous wadsleyite, removing a single Mg(2+) and randomly placing two H(+) in a unit cell model, generating 819 candidate structures. 103 geometries were then subjected to more accurate optimisation under periodic DFT. Using this approach, we find the most favourable hydration mechanism involves protonation of two O1 sites around the Mg3 vacancy. The formation of silanol groups on O3 or O4 sites (with loss of stable O1-H hydroxyls) coincides with an increase in total enthalpy. Importantly, the approach we employ allows observables such as NMR parameters to be computed for each structure. We consider hydrous wadsleyite (∼1.6 wt%) to be dominated by protonated O1 sites, with O3/O4-H silanol groups present as defects, a model that maps well onto experimental studies at higher levels of hydration (J. M. Griffin et al., Chem. Sci., 2013, 4, 1523). The AIRSS approach adopted herein provides the crucial link between atomic-scale structure and experimental studies.

  3. Absorption spectroscopy of the rubidium dimer in an overheated vapor: An accurate check of molecular structure and dynamics

    SciTech Connect

    Beuc, R.; Movre, M.; Horvatic, V.; Vadla, C.; Dulieu, O.; Aymar, M.

    2007-03-15

    Experimental studies of the absorption spectrum of the Rb{sub 2} dimer are performed in the 600-1100 nm wavelength range for temperatures between 615 and 745 K. The reduced absorption coefficient is measured by spatially resolved white light absorption in overheated rubidium vapor with a radial temperature gradient, which enables simultaneous measurements at different temperatures. Semiclassical and quantum spectral simulations are obtained by taking into account all possible transitions involving the potential curves stemming from the 5 {sup 2}S+5 {sup 2}S and 5 {sup 2}S+5 {sup 2}P asymptotes. The most accurate experimental potential curves are used where available, and newly calculated potential curves and transition dipole moments otherwise. The overall consistency of the theoretical model with the experimental interpretation is obtained only if the radial dependence of both the calculated transition dipole moments and the spin-orbit coupling is taken into account. This highlights the low-resolution absorption spectroscopy as a valuable tool for checking the accuracy of molecular electronic structure calculations.

  4. Parameter Optimization and Field Validation of the Functional–Structural Model GREENLAB for Maize

    PubMed Central

    GUO, YAN; MA, YUNTAO; ZHAN, ZHIGANG; LI, BAOGUO; DINGKUHN, MICHAEL; LUQUET, DELPHINE; DE REFFYE, PHILIPPE

    2006-01-01

    • Background and Aims There are three reasons for the increasing demand for crop models that build the plant on the basis of architectural principles and organogenetic processes: (1) realistic concepts for developing new crops need to be guided by such models; (2) there is an increasing interest in crop phenotypic plasticity, based on variable architecture and morphology; and (3) engineering of mechanized cropping systems requires information on crop architecture. The functional–structural model GREENLAB was recently presented that simulates resource-dependent plasticity of plant architecture. This study introduces a new methodology for crop parameter optimization against measured data called multi-fitting, validates the calibrated model for maize with independent field data, and describes a technique for 3D visualization of outputs. • Methods Maize was grown near Beijing during the 2000, 2001 and 2003 (two sowing dates) summer seasons in a block design with four to five replications. Detailed morphological and topological observations were made on the plant architecture throughout the development of the four crops. Data obtained in 2000 was used to establish target files for parameter optimization using the generalized least square method, and parameter accuracy was evaluated by coefficient of variance. In situ plant digitization was used to establish 3D symbol files for organs that were then used to translate model outputs directly into 3D representations for each time step of model execution. •Key Results and Conclusions Multi-fitting against several target files obtained at different growth stages gave better parameter accuracy than single fitting at maturity only, and permitted extracting generic organ expansion kinetics from the static observations. The 2000 model gave excellent predictions of plant architecture and vegetative growth for the other three seasons having different temperature regimes, but predictions of inter-seasonal variability of

  5. Determination of Structural and Morphological Parameters of Human Bulbar Conjunctiva from Optical Diffuse Reflectance Spectra

    NASA Astrophysics Data System (ADS)

    Lisenko, S. A.; Firago, V. A.; Kugeiko, M. M.; Kubarko, A. I.

    2016-09-01

    We have developed a method for on-the-fl y retrieval of the volume concentration of blood vessels, the average diameter of the blood vessels, the blood oxygenation level, and the molar concentrations of chromophores in the bulbar conjunctiva from its diffuse reflectance spectra, measured when the radiation delivery and detection channels are spatially separated. The relationship between the diffuse reflectance spectrum of the conjunctiva and its unknown parameters is described in terms of an analytical model, constructed on the basis of a highly accurate approximation analog of the Monte Carlo method. We have studied the effect of localization of hemoglobin in erythrocytes and localization of erythrocytes in the blood vessels on the power of the retrieval of structural and morphological parameters for the conjunctiva. We developed a device for obtaining video images of the conjunctiva and contactless measurements of its diffuse reflectance spectrum. By comparing simulated diffuse reflectance spectra of the conjunctiva with the experimental measurements, we established a set of chromophores which must be taken into account in the model for reproducing the experimental data within the measurement error. We observed absorption bands for neuroglobin in the experimental spectra, and provided a theoretical basis for the possibility of determining its absolute concentrations in the conjunctiva. We have shown that our method can detect low bilirubin concentrations in blood.

  6. Microwave spectra and gas phase structural parameters for N-hydroxypyridine-2(1H)-thione.

    PubMed

    Daly, Adam M; Mitchell, Erik G; Sanchez, Daniel A; Block, Eric; Kukolich, Stephen G

    2011-12-22

    The microwave spectrum for N-hydroxypyridine-2(1H)-thione (pyrithione) was measured in the frequency range 6-18 GHz, providing accurate rotational constants and nitrogen quadrupole coupling strengths for three isotopologues, C(5)H(4)(32)S(14)NOH, C(5)H(4)(32)S(14)NOD, and C(5)H(4)(34)S(14)NOH. Pyrithione was found to be in a higher concentration in the gas phase than the other tautomer, 2-mercaptopyridine-N-oxide (MPO). Microwave spectroscopy is best suited to determine which structure predominates in the gas phase. The measured rotational constants were used to accurately determine the coordinates of the substituted atoms and provided sufficient data to determine some of the important structural parameters for pyrithione, the only tautomer observed in the present work. The spectra were obtained using a pulsed-beam Fourier transform microwave spectrometer, with sufficient resolution to allow accurate measurements of the (14)N nuclear quadrupole hyperfine interactions. Ab initio calculations provided structural parameters and quadrupole coupling strengths that are in very good agreement with measured values. The experimental rotational constants for the parent compound are A = 3212.10(1), B = 1609.328(7), and C = 1072.208(6) MHz, yielding the inertial defect Δ(0) = -0.023 amu·Å(2) for the C(5)H(4)(32)S(14)NOH isotopologue. The observed near zero inertial defect clearly indicates a planar structure. The least-squares fit structural analysis yielded the experimental bond lengths R(O-H) = 0.93(2) Å, R(C-S) = 1.66(2) Å, and angle (N-O-H) = 105(4)° for the ground state structure.

  7. Microwave spectra and gas phase structural parameters for N-hydroxypyridine-2(1H)-thione.

    PubMed

    Daly, Adam M; Mitchell, Erik G; Sanchez, Daniel A; Block, Eric; Kukolich, Stephen G

    2011-12-22

    The microwave spectrum for N-hydroxypyridine-2(1H)-thione (pyrithione) was measured in the frequency range 6-18 GHz, providing accurate rotational constants and nitrogen quadrupole coupling strengths for three isotopologues, C(5)H(4)(32)S(14)NOH, C(5)H(4)(32)S(14)NOD, and C(5)H(4)(34)S(14)NOH. Pyrithione was found to be in a higher concentration in the gas phase than the other tautomer, 2-mercaptopyridine-N-oxide (MPO). Microwave spectroscopy is best suited to determine which structure predominates in the gas phase. The measured rotational constants were used to accurately determine the coordinates of the substituted atoms and provided sufficient data to determine some of the important structural parameters for pyrithione, the only tautomer observed in the present work. The spectra were obtained using a pulsed-beam Fourier transform microwave spectrometer, with sufficient resolution to allow accurate measurements of the (14)N nuclear quadrupole hyperfine interactions. Ab initio calculations provided structural parameters and quadrupole coupling strengths that are in very good agreement with measured values. The experimental rotational constants for the parent compound are A = 3212.10(1), B = 1609.328(7), and C = 1072.208(6) MHz, yielding the inertial defect Δ(0) = -0.023 amu·Å(2) for the C(5)H(4)(32)S(14)NOH isotopologue. The observed near zero inertial defect clearly indicates a planar structure. The least-squares fit structural analysis yielded the experimental bond lengths R(O-H) = 0.93(2) Å, R(C-S) = 1.66(2) Å, and angle (N-O-H) = 105(4)° for the ground state structure. PMID:22070758

  8. Constructing Approximate Confidence Intervals for Parameters with Structural Equation Models

    ERIC Educational Resources Information Center

    Cheung, Mike W. -L.

    2009-01-01

    Confidence intervals (CIs) for parameters are usually constructed based on the estimated standard errors. These are known as Wald CIs. This article argues that likelihood-based CIs (CIs based on likelihood ratio statistics) are often preferred to Wald CIs. It shows how the likelihood-based CIs and the Wald CIs for many statistics and psychometric…

  9. Recovering a Probabilistic Knowledge Structure by Constraining Its Parameter Space

    ERIC Educational Resources Information Center

    Stefanutti, Luca; Robusto, Egidio

    2009-01-01

    In the Basic Local Independence Model (BLIM) of Doignon and Falmagne ("Knowledge Spaces," Springer, Berlin, 1999), the probabilistic relationship between the latent knowledge states and the observable response patterns is established by the introduction of a pair of parameters for each of the problems: a lucky guess probability and a careless…

  10. Identification of random variation in structures and their parameter estimates.

    SciTech Connect

    Farrar, C. R.; Aumann, R. J.; McCarty, A. A.; Olson, C. C.

    2002-01-01

    Structures that are members of an ensemble of nominally identical systems actually differ due to variations in details among individuals. Furthermore, there are variations in the system response of an individual structure that can be attributed to unmeasured conditions (such as temperature and humidity) that are present during experiments. Finally, noise is present in all measurements of structural excitations and responses. For these reasons, there is always random variation associated with the characterizations of structural dynamic systems, and descriptions of results must be in statistical or probabilistic terms;. This study identifies and assesses the sources and the degrees of randomness in a metric of structural dynamics of a given system through experiments and analysis.

  11. Derivation of tree stem structural parameters from static terrestrial laser scanning data

    NASA Astrophysics Data System (ADS)

    Tian, Wei; Lin, Yi; Liu, Yajing; Niu, Zheng

    2014-11-01

    Accurate tree-level characteristic information is increasingly demanded for forest management and environment protection. The cutting-edge remote sensing technique of terrestrial laser scanning (TLS) shows the potential of filling this gap. This study focuses on exploring the methods for deriving various tree stem structural parameters, such as stem position, diameter at breast height (DBH), the degree of stem shrinkage, and the elevation angle and azimuth angle of stem inclination. The data for test was collected with a Leica HDS6100 TLS system in Seurasaari, Southern Finland in September 2010. In the field, the reference positions and DBHs of 100 trees were measured manually. The isolation of individual trees is based on interactive segmentation of point clouds. The estimation of stem position and DBH is based on the schematic of layering and then least-square-based circle fitting in each layer. The slope of robust fit line between the height of each layer and DBH is used to characterize the stem shrinkage. The elevation angle of stem inclination is described by the angle between the ground plane and the fitted stem axis. The angle between the north direction and the fitted stem axis gives the azimuth angle of stem inclination. The estimation of the DBHs performed with R square (R2) of 0.93 and root mean square error (RMSE) of 0.038m.The average angle corresponding to stem shrinkage is -1.86°. The elevation angles of stem inclinations are ranged from 31° to 88.3°. The results have basically validated TLS for deriving multiple structural parameters of stem, which help better grasp tree specialties.

  12. Spectral structure of Earth rotation parameter series (SHA).

    NASA Astrophysics Data System (ADS)

    Zhu, Yuanlan; Zhu, Wenyao

    Using the Marple algorithm of AR spectrum, the authors have analysed the spectral structure of ERP(SHA) series. Some main periodical terms of both polar motion and Earth rotation have been derived well from this series. This shows that the ERP(SHA) series can be reliably applied to astronomical and geophysical researches.

  13. Structure parameters in rotating Couette-Poiseuille channel flow

    NASA Technical Reports Server (NTRS)

    Knightly, George H.; Sather, D.

    1986-01-01

    It is well-known that a number of steady state problems in fluid mechanics involving systems of nonlinear partial differential equations can be reduced to the problem of solving a single operator equation of the form: v + lambda Av + lambda B(v) = 0, v is the summation of H, lambda is the summation of one-dimensional Euclid space, where H is an appropriate (real or complex) Hilbert space. Here lambda is a typical load parameter, e.g., the Reynolds number, A is a linear operator, and B is a quadratic operator generated by a bilinear form. In this setting many bifurcation and stability results for problems were obtained. A rotating Couette-Poiseuille channel flow was studied, and it showed that, in general, the superposition of a Poiseuille flow on a rotating Couette channel flow is destabilizing.

  14. Structure parameters in rotating Couette-Poiseuille channel flow

    NASA Astrophysics Data System (ADS)

    Knightly, George H.; Sather, D.

    It is well-known that a number of steady state problems in fluid mechanics involving systems of nonlinear partial differential equations can be reduced to the problem of solving a single operator equation of the form: v + lambda Av + lambda B(v) = 0, v is the summation of H, lambda is the summation of one-dimensional Euclid space, where H is an appropriate (real or complex) Hilbert space. Here lambda is a typical load parameter, e.g., the Reynolds number, A is a linear operator, and B is a quadratic operator generated by a bilinear form. In this setting many bifurcation and stability results for problems were obtained. A rotating Couette-Poiseuille channel flow was studied, and it showed that, in general, the superposition of a Poiseuille flow on a rotating Couette channel flow is destabilizing.

  15. Quantitative structure parameters from the NMR spectroscopy of quadrupolar nuclei

    SciTech Connect

    Perras, Frederic A.

    2015-12-15

    Here, nuclear magnetic resonance (NMR) spectroscopy is one of the most important characterization tools in chemistry, however, 3/4 of the NMR active nuclei are underutilized due to their quadrupolar nature. This short review centers on the development of methods that use solid-state NMR of quadrupolar nuclei for obtaining quantitative structural information. Namely, techniques using dipolar recoupling as well as the resolution afforded by double-rotation are presented for the measurement of spin–spin coupling between quadrupoles, enabling the measurement of internuclear distances and connectivities.

  16. Cosmological parameter estimation with large scale structure observations

    SciTech Connect

    Dio, Enea Di; Montanari, Francesco; Durrer, Ruth; Lesgourgues, Julien E-mail: Francesco.Montanari@unige.ch E-mail: Julien.Lesgourgues@cern.ch

    2014-01-01

    We estimate the sensitivity of future galaxy surveys to cosmological parameters, using the redshift dependent angular power spectra of galaxy number counts, C{sub ℓ}(z{sub 1},z{sub 2}), calculated with all relativistic corrections at first order in perturbation theory. We pay special attention to the redshift dependence of the non-linearity scale and present Fisher matrix forecasts for Euclid-like and DES-like galaxy surveys. We compare the standard P(k) analysis with the new C{sub ℓ}(z{sub 1},z{sub 2}) method. We show that for surveys with photometric redshifts the new analysis performs significantly better than the P(k) analysis. For spectroscopic redshifts, however, the large number of redshift bins which would be needed to fully profit from the redshift information, is severely limited by shot noise. We also identify surveys which can measure the lensing contribution and we study the monopole, C{sub 0}(z{sub 1},z{sub 2})

  17. On the atmospheric structure and fundamental parameters of red supergiants

    NASA Astrophysics Data System (ADS)

    Wittkowski, M.; Arroyo-Torres, B.; Marcaide, J. M.; Abellan, F. J.; Chiavassa, A.; Freytag, B.; Scholz, M.; Wood, P. R.; Hauschildt, P. H.

    2015-01-01

    We present near-infrared spectro-interferometric studies of red supergiant (RSG) stars using the VLTI/AMBER instrument, which are compared to previously obtained similar observations of AGB stars. Our observations indicate spatially extended atmospheric molecular layers of water vapor and CO, similar as previously observed for Mira stars. Data of VY~CMa indicate that the molecular layers are asymmetric, possibly clumpy. Thanks to the spectro-interferometric capabilities of the VLTI/AMBER instrument, we can isolate continuum bandpasses, estimate fundamental parameters of our sources, locate them in the HR diagram, and compare their positions to recent evolutionary tracks. For the example of VY CMa, this puts it close to evolutionary tracks of initial mass 25-32 M ⊙. Comparisons of our data to hydrostatic model atmospheres, 3d simulations of convection, and 1d dynamic model atmospheres based on self-excited pulsation models indicate that none of these models can presently explain the observed atmospheric extensions for RSGs. The mechanism that levitates the atmospheres of red supergiant is thus a currently unsolved problem.

  18. Parameters affecting the accuracy of oxide thickness prediction in thin metal-oxide-semiconductor structures

    NASA Astrophysics Data System (ADS)

    Mohaidat, J. M.; Ahmad-Bitar, Riyad N.

    2004-01-01

    On the basis of the solution of the time dependent Schrödinger equation within the framework of the effective mass theory, a complete quantum mechanical electron tunneling through a biased square potential model with abrupt interfaces was deduced. Barriers of 3 eV height and widths up to 140 Å were investigated. Current density-voltage ( J- V) curves were computed for Al/SiO 2/ n+Si structure. The computed J- V curves exhibited oscillations at applied voltages above (Fowler-Nordheim tunneling) and below (direct tunneling) 3 V. For oxide thickness estimation, the position of the oscillation extrema from this quantum mechanical model were fitted to a wave interference formula and showed excellent agreement for oxide layer widths less than 50 Å. However, a systematic deviation appeared for layers larger than 50 Å. We show that the electron energy distribution at the injection layer and the electron effective mass on layers other than the oxide layer are important parameters for accurate oxide thickness estimation.

  19. Further Studies of Forest Structure Parameter Retrievals Using the Echidna® Ground-Based Lidar

    NASA Astrophysics Data System (ADS)

    Strahler, A. H.; Yao, T.; Zhao, F.; Yang, X.; Schaaf, C.; Wang, Z.; Li, Z.; Woodcock, C. E.; Culvenor, D.; Jupp, D.; Newnham, G.; Lovell, J.

    2012-12-01

    Ongoing work with the Echidna® Validation Instrument (EVI), a full-waveform, ground-based scanning lidar (1064 nm) developed by Australia's CSIRO and deployed by Boston University in California conifers (2008) and New England hardwood and softwood (conifer) stands (2007, 2009, 2010), confirms the importance of slope correction in forest structural parameter retrieval; detects growth and disturbance over periods of 2-3 years; provides a new way to measure the between-crown clumping factor in leaf area index retrieval using lidar range; and retrieves foliage profiles with more lower-canopy detail than a large-footprint aircraft scanner (LVIS), while simulating LVIS foliage profiles accurately from a nadir viewpoint using a 3-D point cloud. Slope correction is important for accurate retrieval of forest canopy structural parameters, such as mean diameter at breast height (DBH), stem count density, basal area, and above-ground biomass. Topographic slope can induce errors in parameter retrievals because the horizontal plane of the instrument scan, which is used to identify, measure, and count tree trunks, will intersect trunks below breast height in the uphill direction and above breast height in the downhill direction. A test of three methods at southern Sierra Nevada conifer sites improved the range of correlations of these EVI-retrieved parameters with field measurements from 0.53-0.68 to 0.85-0.93 for the best method. EVI scans can detect change, including both growth and disturbance, in periods of two to three years. We revisited three New England forest sites scanned in 2007-2009 or 2007-2010. A shelterwood stand at the Howland Experimental Forest, Howland, Maine, showed increased mean DBH, above-ground biomass and leaf area index between 2007 and 2009. Two stands at the Harvard Forest, Petersham, Massachusetts, suffered reduced leaf area index and reduced stem count density as the result of an ice storm that damaged the stands. At one stand, broken tops were

  20. The Araucaria Project: accurate stellar parameters and distance to evolved eclipsing binary ASAS J180057-2333.8 in Sagittarius Arm

    NASA Astrophysics Data System (ADS)

    Suchomska, K.; Graczyk, D.; Smolec, R.; Pietrzyński, G.; Gieren, W.; Stȩpień, K.; Konorski, P.; Pilecki, B.; Villanova, S.; Thompson, I. B.; Górski, M.; Karczmarek, P.; Wielgórski, P.; Anderson, R. I.

    2015-07-01

    We have analyzed the double-lined eclipsing binary system ASAS J180057-2333.8 from the All Sky Automated Survey (ASAS) catalogue. We measure absolute physical and orbital parameters for this system based on archival V-band and I-band ASAS photometry, as well as on high-resolution spectroscopic data obtained with ESO 3.6 m/HARPS and CORALIE spectrographs. The physical and orbital parameters of the system were derived with an accuracy of about 0.5-3 per cent. The system is a very rare configuration of two bright well-detached giants of spectral types K1 and K4 and luminosity class II. The radii of the stars are R1 = 52.12 ± 1.38 and R2 = 67.63 ± 1.40 R⊙ and their masses are M1 = 4.914 ± 0.021 and M2 = 4.875 ± 0.021 M⊙. The exquisite accuracy of 0.5 per cent obtained for the masses of the components is one of the best mass determinations for giants. We derived a precise distance to the system of 2.14 ± 0.06 kpc (stat.) ± 0.05 (syst.) which places the star in the Sagittarius-Carina arm. The Galactic rotational velocity of the star is Θs = 258 ± 26 km s-1 assuming Θ0 = 238 km s-1. A comparison with PARSEC isochrones places the system at the early phase of core helium burning with an age of slightly larger than 100 million years. The effect of overshooting on stellar evolutionary tracks was explored using the MESA star code.

  1. Is scoring system of computed tomography based metric parameters can accurately predicts shock wave lithotripsy stone-free rates and aid in the development of treatment strategies?

    PubMed Central

    Badran, Yasser Ali; Abdelaziz, Alsayed Saad; Shehab, Mohamed Ahmed; Mohamed, Hazem Abdelsabour Dief; Emara, Absel-Aziz Ali; Elnabtity, Ali Mohamed Ali; Ghanem, Maged Mohammed; ELHelaly, Hesham Abdel Azim

    2016-01-01

    Objective: The objective was to determine the predicting success of shock wave lithotripsy (SWL) using a combination of computed tomography based metric parameters to improve the treatment plan. Patients and Methods: Consecutive 180 patients with symptomatic upper urinary tract calculi 20 mm or less were enrolled in our study underwent extracorporeal SWL were divided into two main groups, according to the stone size, Group A (92 patients with stone ≤10 mm) and Group B (88 patients with stone >10 mm). Both groups were evaluated, according to the skin to stone distance (SSD) and Hounsfield units (≤500, 500–1000 and >1000 HU). Results: Both groups were comparable in baseline data and stone characteristics. About 92.3% of Group A rendered stone-free, whereas 77.2% were stone-free in Group B (P = 0.001). Furthermore, in both group SWL success rates was a significantly higher for stones with lower attenuation <830 HU than with stones >830 HU (P < 0.034). SSD were statistically differences in SWL outcome (P < 0.02). Simultaneous consideration of three parameters stone size, stone attenuation value, and SSD; we found that stone-free rate (SFR) was 100% for stone attenuation value <830 HU for stone <10 mm or >10 mm but total number SWL sessions and shock waves required for the larger stone group were higher than in the smaller group (P < 0.01). Furthermore, SFR was 83.3% and 37.5% for stone <10 mm, mean HU >830, SSD 90 mm and SSD >120 mm, respectively. On the other hand, SFR was 52.6% and 28.57% for stone >10 mm, mean HU >830, SSD <90 mm and SSD >120 mm, respectively. Conclusion: Stone size, stone density (HU), and SSD is simple to calculate and can be reported by radiologists to applying combined score help to augment predictive power of SWL, reduce cost, and improving of treatment strategies. PMID:27141192

  2. Nuclear structure with accurate chiral perturbation theory nucleon-nucleon potential: Application to 6Li and 10B

    SciTech Connect

    Navratil, P; Caurier, E

    2003-10-14

    The authors calculate properties of A = 6 system using the accurate charge-dependent nucleon-nucleon (NN) potential at fourth order of chiral perturbation theory. By application of the ab initio no-core shell model (NCSM) and a variational calculation in the harmonic oscillator basis with basis size up to 16 {h_bar}{Omega} they obtain the {sup 6}Li binding energy of 28.5(5) MeV and a converged excitation spectrum. Also, they calculate properties of {sup 10}B using the same NN potential in a basis space of up to 8 {h_bar}{Omega}. The results are consistent with results obtained by standard accurate NN potentials and demonstrate a deficiency of Hamiltonians consisting of only two-body terms. At this order of chiral perturbation theory three-body terms appear. It is expected that inclusion of such terms in the Hamiltonian will improve agreement with experiment.

  3. Effects of structural parameters and rigidity of driving diaphragm on flow characteristics of micro valveless pump.

    PubMed

    Xie, Hai-bo; Fu, Xin; Yang, Hua-yong

    2003-01-01

    The structure and operating principle of micro valveless pump were investigated theoretically and experimentally. The mathematical model of pressure and flow rate within the micro nozzle/diffuser was established to analyze the effects of nozzle/diffuser parameters on the output flow rate of the micro valveless pump. The experiments were carried out with different structural parameters, driving frequencies, vibration amplitudes and stiffness of the driving diaphragms. Effects of the structural parameters and driving conditions on the operation performance of the pump are discussed in detail. The work provides useful reference for structure optimization selection of the driving diaphragm of micro valveless pump.

  4. Effects of fundamental structure parameters on dynamic responses of submerged floating tunnel under hydrodynamic loads

    NASA Astrophysics Data System (ADS)

    Long, Xu; Ge, Fei; Wang, Lei; Hong, Youshi

    2009-06-01

    This paper investigates the effects of structure parameters on dynamic responses of submerged floating tunnel (SFT) under hydrodynamic loads. The structure parameters includes buoyancy-weight ratio (BWR), stiffness coefficients of the cable systems, tunnel net buoyancy and tunnel length. First, the importance of structural damp in relation to the dynamic responses of SFT is demonstrated and the mechanism of structural damp effect is discussed. Thereafter, the fundamental structure parameters are investigated through the analysis of SFT dynamic responses under hydrodynamic loads. The results indicate that the BWR of SFT is a key structure parameter. When BWR is 1.2, there is a remarkable trend change in the vertical dynamic response of SFT under hydrodynamic loads. The results also indicate that the ratio of the tunnel net buoyancy to the cable stiffness coefficient is not a characteristic factor affecting the dynamic responses of SFT under hydrodynamic loads.

  5. CONDENSED MATTER: STRUCTURE, MECHANICAL AND THERMAL PROPERTIES: An Accurate Image Simulation Method for High-Order Laue Zone Effects

    NASA Astrophysics Data System (ADS)

    Cai, Can-Ying; Zeng, Song-Jun; Liu, Hong-Rong; Yang, Qi-Bin

    2008-05-01

    A completely different formulation for simulation of the high order Laue zone (HOLZ) diffractions is derived. It refers to the new method, i.e. the Taylor series (TS) method. To check the validity and accuracy of the TS method, we take polyvinglidene fluoride (PVDF) crystal as an example to calculate the exit wavefunction by the conventional multi-slice (CMS) method and the TS method. The calculated results show that the TS method is much more accurate than the CMS method and is independent of the slice thicknesses. Moreover, the pure first order Laue zone wavefunction by the TS method can reflect the major potential distribution of the first reciprocal plane.

  6. Effective parameters in beam acoustic metamaterials based on energy band structures

    NASA Astrophysics Data System (ADS)

    Jing, Li; Wu, Jiu Hui; Guan, Dong; Hou, Mingming; Kuan, Lu; Shen, Li

    2016-07-01

    We present a method to calculate the effective material parameters of beam acoustic metamaterials. The effective material parameters of a periodic beam are calculated as an example. The dispersion relations and energy band structures of this beam are calculated. Subsequently, the effective material parameters of the beam are investigated by using the energy band structures. Then, the modal analysis and transmission properties of the beams with finite cells are simulated in order to confirm the correctness of effective approximation. The results show that the periodic beam can be equivalent to the homogeneous beam with dynamic effective material parameters in passband.

  7. Effect of UV light on different structural and transport parameters of cellophane membranes

    SciTech Connect

    Benavente, J.; Vazquez, M.I.; De Abajo, J.

    1996-01-01

    A comparative study of UV light influence on structural and transport parameters of cellophane membranes was made. Changes in the chemical structure and electrical behavior of cellophane membranes were considered by determining the hydraulic permeability, salt diffusion coefficient, and resistance values, as well as some geometrical parameters, for an untreated membrane and two differently UV-treated cellophane membranes. Differences in the characteristic parameters for the three samples showed that radiation mainly affected the membrane structure, while only small changes in membrane electrical behavior were determined.

  8. The rapidly pulsating subdwarf B star PG 1325+101. II. Structural parameters from asteroseismology

    NASA Astrophysics Data System (ADS)

    Charpinet, S.; Silvotti, R.; Bonanno, A.; Fontaine, G.; Brassard, P.; Chayer, P.; Green, E. M.; Bergeron, P.; Bernabei, S.; Leccia, S.; Kjeldsen, H.; Janulis, R.; Frasca, A.; Østensen, R.; Kim, S.-L.; Park, B.-G.; Jiang, X.; Reed, M. D.; Patterson, R. S.; Gietzen, K. M.; Clark, P. J.; Wolf, G. W.; Lipkin, Y.; Formiggini, L.; Leibowitz, E.; Oswalt, T. D.; Rudkin, M.; Johnston, K.

    2006-11-01

    We present a detailed analysis of the rapidly pulsating subdwarf B star (or EC14026 star) PG 1325+101. This analysis exploits the outcome of dedicated multisite observations using time-series photometry that revealed the presence of (at least) 15 periodicities in the luminosity modulation of this star (Silvotti et al. 2006, A&A, 459, 557, Paper I). Based on high-S/N, medium-resolution spectra obtained at the Steward Observatory's 2.3 m Telescope and at the 6.5 m MMT Telescope, new NLTE spectroscopic derivations of the atmospheric parameters of PG 1325+101 are presented. The mean values of T_eff = 35 050 ± 220 K, log g=5.81 ± 0.04, and log N(He)/N(H) = -1.70± 0.02 are in agreement with previous determinations, but are significantly more accurate. These improved spectroscopic parameters are essential for isolating a unique asteroseismic model solution for the observed pulsation spectrum of PG 1325+101. Using the "forward modeling" approach, our combined spectroscopic and asteroseismic analysis leads objectively to the identification of the (k, ℓ) indices of the 12 independent modes observed in this star, and to the determination of its structural parameters. The periods correspond to low-order acoustic modes with adjacent values of k and having degrees ℓ=0-4. They define a band of unstable modes, in agreement with nonadiabatic pulsation theory. The average dispersion achieved between the observed periods and the periods of the corresponding theoretical modes of the optimal model is only 0.46% (˜ 0.54 s), comparable to the results from similar analyses of other EC14026 stars analysed to date. The inferred structural parameters of PG 1325+101 are Teff= 35 050 ± 220 K, log g=5.811±0.004, log M{env}/M*=-4.18±0.10, M*=0.50±0.01 M⊙ (i.e., close to the canonical mass of extreme horizontal branch stars), R/R⊙=0.145±0.002, and L/L⊙=28.3±1.5. In addition, by combining detailed model atmosphere calculations with V=14.019±0.012, we estimate that this star

  9. Boron carbide: Consistency of components, lattice parameters, fine structure and chemical composition makes the complex structure reasonable

    NASA Astrophysics Data System (ADS)

    Werheit, Helmut

    2016-10-01

    The complex, highly distorted structure of boron carbide is composed of B12 and B11C icosahedra and CBC, CBB and B□B linear elements, whose concentration depends on the chemical composition each. These concentrations are shown to be consistent with lattice parameters, fine structure data and chemical composition. The respective impacts on lattice parameters are estimated and discussed. Considering the contributions of the different structural components to the energy of the overall structure makes the structure and its variation within the homogeneity range reasonable; in particular that of B4.3C representing the carbon-rich limit of the homogeneity range. Replacing in B4.3C virtually the B□B components by CBC yields the hypothetical moderately distorted B4.0C (structure formula (B11C)CBC). The reduction of lattice parameters related is compatible with recently reported uncommonly prepared single crystals, whose compositions deviate from B4.3C.

  10. PSSP-RFE: Accurate Prediction of Protein Structural Class by Recursive Feature Extraction from PSI-BLAST Profile, Physical-Chemical Property and Functional Annotations

    PubMed Central

    Yu, Sanjiu; Zhang, Yuan; Luo, Zhong; Yang, Hua; Zhou, Yue; Zheng, Xiaoqi

    2014-01-01

    Protein structure prediction is critical to functional annotation of the massively accumulated biological sequences, which prompts an imperative need for the development of high-throughput technologies. As a first and key step in protein structure prediction, protein structural class prediction becomes an increasingly challenging task. Amongst most homological-based approaches, the accuracies of protein structural class prediction are sufficiently high for high similarity datasets, but still far from being satisfactory for low similarity datasets, i.e., below 40% in pairwise sequence similarity. Therefore, we present a novel method for accurate and reliable protein structural class prediction for both high and low similarity datasets. This method is based on Support Vector Machine (SVM) in conjunction with integrated features from position-specific score matrix (PSSM), PROFEAT and Gene Ontology (GO). A feature selection approach, SVM-RFE, is also used to rank the integrated feature vectors through recursively removing the feature with the lowest ranking score. The definitive top features selected by SVM-RFE are input into the SVM engines to predict the structural class of a query protein. To validate our method, jackknife tests were applied to seven widely used benchmark datasets, reaching overall accuracies between 84.61% and 99.79%, which are significantly higher than those achieved by state-of-the-art tools. These results suggest that our method could serve as an accurate and cost-effective alternative to existing methods in protein structural classification, especially for low similarity datasets. PMID:24675610

  11. Structural modelling and control design under incomplete parameter information: The maximum-entropy approach

    NASA Technical Reports Server (NTRS)

    Hyland, D. C.

    1983-01-01

    A stochastic structural control model is described. In contrast to the customary deterministic model, the stochastic minimum data/maximum entropy model directly incorporates the least possible a priori parameter information. The approach is to adopt this model as the basic design model, thus incorporating the effects of parameter uncertainty at a fundamental level, and design mean-square optimal controls (that is, choose the control law to minimize the average of a quadratic performance index over the parameter ensemble).

  12. Parameter identification methods for improving structural dynamic models. Ph.D. Thesis

    NASA Technical Reports Server (NTRS)

    Lawrence, Charles

    1988-01-01

    There is an increasing need to develop Parameter Identification methods for improving structural dynamic models, based on the inability of engineers to produce mathematical models which correlate with experimental data. This research explores the efficiency of combining Component Mode Synthesis (substructuring) methods with Parameter Identification procedures in order to improve analytical modeling of structural components and their connections. Improvements are computed in terms of physical stiffness and damping parameters in order that the physical characteristics of the model can be better understood. Connections involving both viscous and friction damping are investigated. Substructuring methods are utilized to reduce the complexity of the identification problem. Component and inter-component structural connection properties are evaluated and identified independently, thus simplifying the identification problem. It is shown that modal test data is effective for identifying modeling problems associated with structural components, and for determining the stiffness and damping properties of intercomponent connections. In general, Parameter Identification is improved when greater quantities of experimental data are available.

  13. PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

    EPA Science Inventory

    The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

  14. Standard Errors of Estimated Latent Variable Scores with Estimated Structural Parameters

    ERIC Educational Resources Information Center

    Hoshino, Takahiro; Shigemasu, Kazuo

    2008-01-01

    The authors propose a concise formula to evaluate the standard error of the estimated latent variable score when the true values of the structural parameters are not known and must be estimated. The formula can be applied to factor scores in factor analysis or ability parameters in item response theory, without bootstrap or Markov chain Monte…

  15. Bias-Corrected Estimation of Noncentrality Parameters of Covariance Structure Models

    ERIC Educational Resources Information Center

    Raykov, Tenko

    2005-01-01

    A bias-corrected estimator of noncentrality parameters of covariance structure models is discussed. The approach represents an application of the bootstrap methodology for purposes of bias correction, and utilizes the relation between average of resample conventional noncentrality parameter estimates and their sample counterpart. The…

  16. Determination of Structural Parameters of Thin-Film Photocatalytic Materials by BDS

    NASA Astrophysics Data System (ADS)

    Korte, Dorota; Franko, Mladen

    2015-09-01

    A method for determination of structural parameters of some thin-film photocatalytic materials is presented. The analysis was based on the material's thermal parameter dependences on its surface structure or porosity and was thus performed by the use of beam deflection spectroscopy (BDS) supported by theoretical analysis made in the framework of complex geometrical optics. The results obtained by BDS were than compared with those received on the basis of AFM and SEM measurements and found to be in good agreement.

  17. Accurate determination of the fine-structure intervals in the 3P ground states of C-13 and C-12 by far-infrared laser magnetic resonance

    NASA Technical Reports Server (NTRS)

    Cooksy, A. L.; Saykally, R. J.; Brown, J. M.; Evenson, K. M.

    1986-01-01

    Accurate values are presented for the fine-structure intervals in the 3P ground state of neutral atomic C-12 and C-13 as obtained from laser magnetic resonance spectroscopy. The rigorous analysis of C-13 hyperfine structure, the measurement of resonant fields for C-12 transitions at several additional far-infrared laser frequencies, and the increased precision of the C-12 measurements, permit significant improvement in the evaluation of these energies relative to earlier work. These results will expedite the direct and precise measurement of these transitions in interstellar sources and should assist in the determination of the interstellar C-12/C-13 abundance ratio.

  18. Functional connectivity and structural covariance between regions of interest can be measured more accurately using multivariate distance correlation.

    PubMed

    Geerligs, Linda; Cam-Can; Henson, Richard N

    2016-07-15

    Studies of brain-wide functional connectivity or structural covariance typically use measures like the Pearson correlation coefficient, applied to data that have been averaged across voxels within regions of interest (ROIs). However, averaging across voxels may result in biased connectivity estimates when there is inhomogeneity within those ROIs, e.g., sub-regions that exhibit different patterns of functional connectivity or structural covariance. Here, we propose a new measure based on "distance correlation"; a test of multivariate dependence of high dimensional vectors, which allows for both linear and non-linear dependencies. We used simulations to show how distance correlation out-performs Pearson correlation in the face of inhomogeneous ROIs. To evaluate this new measure on real data, we use resting-state fMRI scans and T1 structural scans from 2 sessions on each of 214 participants from the Cambridge Centre for Ageing & Neuroscience (Cam-CAN) project. Pearson correlation and distance correlation showed similar average connectivity patterns, for both functional connectivity and structural covariance. Nevertheless, distance correlation was shown to be 1) more reliable across sessions, 2) more similar across participants, and 3) more robust to different sets of ROIs. Moreover, we found that the similarity between functional connectivity and structural covariance estimates was higher for distance correlation compared to Pearson correlation. We also explored the relative effects of different preprocessing options and motion artefacts on functional connectivity. Because distance correlation is easy to implement and fast to compute, it is a promising alternative to Pearson correlations for investigating ROI-based brain-wide connectivity patterns, for functional as well as structural data.

  19. CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study.

    PubMed

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina

    2015-09-01

    The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC

  20. CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study.

    PubMed

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Cimino, Paola; Penocchio, Emanuele; Puzzarini, Cristina

    2015-09-01

    The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC

  1. Early Type Galaxies and Structural Parameters from ESO Public Survey KiDS

    NASA Astrophysics Data System (ADS)

    Roy, N.; Napolitano, N. R.; La Barbera, F.; Tortora, C.; Getman, F.; Radovich, M.; Capaccioli, M.

    The Kilo Degree survey (KiDS) is a large-scale optical imaging survey carried out with the VLT Survey Telescope (VST), which is the ideal tool for galaxy evolution studies. We expect to observe millions of galaxies for which we extract the structural parameters in four wavebands (u, g, r and i). This sample will represent the largest dataset with measured structural parameters up to a redshift z = 0. 5. In this paper we will introduce the sample, and describe the 2D fitting procedure using the 2DPHOT environment and the validation of the parameters with an external catalog.

  2. Gap between technically accurate information and socially appropriate information for structural health monitoring system installed into tall buildings

    NASA Astrophysics Data System (ADS)

    Mita, Akira

    2016-04-01

    The importance of the structural health monitoring system for tall buildings is now widely recognized by at least structural engineers and managers at large real estate companies to ensure the structural safety immediately after a large earthquake and appeal the quantitative safety of buildings to potential tenants. Some leading real estate companies decided to install the system into all tall buildings. Considering this tendency, a pilot project for the west area of Shinjuku Station supported by the Japan Science and Technology Agency was started by the author team to explore a possibility of using the system to provide safe spaces for commuters and residents. The system was installed into six tall buildings. From our experience, it turned out that viewing only from technological aspects was not sufficient for the system to be accepted and to be really useful. Safe spaces require not only the structural safety but also the soundness of key functions of the building. We need help from social scientists, medical doctors, city planners etc. to further improve the integrity of the system.

  3. Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities.

    PubMed

    Venner, Eric; Lisewski, Andreas Martin; Erdin, Serkan; Ward, R Matthew; Amin, Shivas R; Lichtarge, Olivier

    2010-01-01

    High-throughput Structural Genomics yields many new protein structures without known molecular function. This study aims to uncover these missing annotations by globally comparing select functional residues across the structural proteome. First, Evolutionary Trace Annotation, or ETA, identifies which proteins have local evolutionary and structural features in common; next, these proteins are linked together into a proteomic network of ETA similarities; then, starting from proteins with known functions, competing functional labels diffuse link-by-link over the entire network. Every node is thus assigned a likelihood z-score for every function, and the most significant one at each node wins and defines its annotation. In high-throughput controls, this competitive diffusion process recovered enzyme activity annotations with 99% and 97% accuracy at half-coverage for the third and fourth Enzyme Commission (EC) levels, respectively. This corresponds to false positive rates 4-fold lower than nearest-neighbor and 5-fold lower than sequence-based annotations. In practice, experimental validation of the predicted carboxylesterase activity in a protein from Staphylococcus aureus illustrated the effectiveness of this approach in the context of an increasingly drug-resistant microbe. This study further links molecular function to a small number of evolutionarily important residues recognizable by Evolutionary Tracing and it points to the specificity and sensitivity of functional annotation by competitive global network diffusion. A web server is at http://mammoth.bcm.tmc.edu/networks.

  4. Parameter estimation in a structural acoustic system with fully nonlinear coupling conditions

    NASA Technical Reports Server (NTRS)

    Banks, H. T.; Smith, Ralph C.

    1994-01-01

    A methodology for estimating physical parameters in a class of structural acoustic systems is presented. The general model under consideration consists of an interior cavity which is separated from an exterior noise source by an enclosing elastic structure. Piezoceramic patches are bonded to or embedded in the structure; these can be used both as actuators and sensors in applications ranging from the control of interior noise levels to the determination of structural flaws through nondestructive evaluation techniques. The presence and excitation of patches, however, changes the geometry and material properties of the structure as well as involves unknown patch parameters, thus necessitating the development of parameter estimation techniques which are applicable in this coupled setting. In developing a framework for approximation, parameter estimation and implementation, strong consideration is given to the fact that the input operator is unbonded due to the discrete nature of the patches. Moreover, the model is weakly nonlinear. As a result of the coupling mechanism between the structural vibrations and the interior acoustic dynamics. Within this context, an illustrating model is given, well-posedness and approximations results are discussed and an applicable parameter estimation methodology is presented. The scheme is then illustrated through several numerical examples with simulations modeling a variety of commonly used structural acoustic techniques for systems excitations and data collection.

  5. Parasitic analysis and π-type Butterworth-Van Dyke model for complementary-metal-oxide-semiconductor Lamb wave resonator with accurate two-port Y-parameter characterizations

    NASA Astrophysics Data System (ADS)

    Wang, Yong; Goh, Wang Ling; Chai, Kevin T.-C.; Mu, Xiaojing; Hong, Yan; Kropelnicki, Piotr; Je, Minkyu

    2016-04-01

    The parasitic effects from electromechanical resonance, coupling, and substrate losses were collected to derive a new two-port equivalent-circuit model for Lamb wave resonators, especially for those fabricated on silicon technology. The proposed model is a hybrid π-type Butterworth-Van Dyke (PiBVD) model that accounts for the above mentioned parasitic effects which are commonly observed in Lamb-wave resonators. It is a combination of interdigital capacitor of both plate capacitance and fringe capacitance, interdigital resistance, Ohmic losses in substrate, and the acoustic motional behavior of typical Modified Butterworth-Van Dyke (MBVD) model. In the case studies presented in this paper using two-port Y-parameters, the PiBVD model fitted significantly better than the typical MBVD model, strengthening the capability on characterizing both magnitude and phase of either Y11 or Y21. The accurate modelling on two-port Y-parameters makes the PiBVD model beneficial in the characterization of Lamb-wave resonators, providing accurate simulation to Lamb-wave resonators and oscillators.

  6. Parasitic analysis and π-type Butterworth-Van Dyke model for complementary-metal-oxide-semiconductor Lamb wave resonator with accurate two-port Y-parameter characterizations.

    PubMed

    Wang, Yong; Goh, Wang Ling; Chai, Kevin T-C; Mu, Xiaojing; Hong, Yan; Kropelnicki, Piotr; Je, Minkyu

    2016-04-01

    The parasitic effects from electromechanical resonance, coupling, and substrate losses were collected to derive a new two-port equivalent-circuit model for Lamb wave resonators, especially for those fabricated on silicon technology. The proposed model is a hybrid π-type Butterworth-Van Dyke (PiBVD) model that accounts for the above mentioned parasitic effects which are commonly observed in Lamb-wave resonators. It is a combination of interdigital capacitor of both plate capacitance and fringe capacitance, interdigital resistance, Ohmic losses in substrate, and the acoustic motional behavior of typical Modified Butterworth-Van Dyke (MBVD) model. In the case studies presented in this paper using two-port Y-parameters, the PiBVD model fitted significantly better than the typical MBVD model, strengthening the capability on characterizing both magnitude and phase of either Y11 or Y21. The accurate modelling on two-port Y-parameters makes the PiBVD model beneficial in the characterization of Lamb-wave resonators, providing accurate simulation to Lamb-wave resonators and oscillators. PMID:27131699

  7. Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure.

    PubMed

    Piquemal, Jean-Philip; Perera, Lalith; Cisneros, G Andrés; Ren, Pengyu; Pedersen, Lee G; Darden, Thomas A

    2006-08-01

    Molecular dynamics simulations were performed using a modified amoeba force field to determine hydration and dynamical properties of the divalent cations Ca2+ and Mg2+. The extension of amoeba to divalent cations required the introduction of a cation specific parametrization. To accomplish this, the Thole polarization damping model parametrization was modified based on the ab initio polarization energy computed by a constrained space orbital variation energy decomposition scheme. Excellent agreement has been found with condensed phase experimental results using parameters derived from gas phase ab initio calculations. Additionally, we have observed that the coordination of the calcium cation is influenced by the size of the periodic water box, a recurrent issue in first principles molecular dynamics studies.

  8. A highly accurate protein structural class prediction approach using auto cross covariance transformation and recursive feature elimination.

    PubMed

    Li, Xiaowei; Liu, Taigang; Tao, Peiying; Wang, Chunhua; Chen, Lanming

    2015-12-01

    Structural class characterizes the overall folding type of a protein or its domain. Many methods have been proposed to improve the prediction accuracy of protein structural class in recent years, but it is still a challenge for the low-similarity sequences. In this study, we introduce a feature extraction technique based on auto cross covariance (ACC) transformation of position-specific score matrix (PSSM) to represent a protein sequence. Then support vector machine-recursive feature elimination (SVM-RFE) is adopted to select top K features according to their importance and these features are input to a support vector machine (SVM) to conduct the prediction. Performance evaluation of the proposed method is performed using the jackknife test on three low-similarity datasets, i.e., D640, 1189 and 25PDB. By means of this method, the overall accuracies of 97.2%, 96.2%, and 93.3% are achieved on these three datasets, which are higher than those of most existing methods. This suggests that the proposed method could serve as a very cost-effective tool for predicting protein structural class especially for low-similarity datasets.

  9. Evaluation of Structural Equation Mixture Models: Parameter Estimates and Correct Class Assignment

    ERIC Educational Resources Information Center

    Tueller, Stephen; Lubke, Gitta

    2010-01-01

    Structural equation mixture models (SEMMs) are latent class models that permit the estimation of a structural equation model within each class. Fitting SEMMs is illustrated using data from 1 wave of the Notre Dame Longitudinal Study of Aging. Based on the model used in the illustration, SEMM parameter estimation and correct class assignment are…

  10. Effect of the parameters of a sandwich structure with a honeycomb core on its soundproofing capacity

    NASA Astrophysics Data System (ADS)

    Tkachev, A. A.

    Expressions for estimating the soundproofing capacity of sandwich structures with a honeycomb core are obtained by using equations of transverse vibrations of a plate with allowance for the flexural and shear waves. The expressions provide an adequate description of the experimentally observed effects and make it possible to predict the effect of the parameters of a structure on its soundproofing efficiency.

  11. A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation

    PubMed Central

    Lu, Zhi John; Turner, Douglas H.; Mathews, David H.

    2006-01-01

    A complete set of nearest neighbor parameters to predict the enthalpy change of RNA secondary structure formation was derived. These parameters can be used with available free energy nearest neighbor parameters to extend the secondary structure prediction of RNA sequences to temperatures other than 37°C. The parameters were tested by predicting the secondary structures of sequences with known secondary structure that are from organisms with known optimal growth temperatures. Compared with the previous set of enthalpy nearest neighbor parameters, the sensitivity of base pair prediction improved from 65.2 to 68.9% at optimal growth temperatures ranging from 10 to 60°C. Base pair probabilities were predicted with a partition function and the positive predictive value of structure prediction is 90.4% when considering the base pairs in the lowest free energy structure with pairing probability of 0.99 or above. Moreover, a strong correlation is found between the predicted melting temperatures of RNA sequences and the optimal growth temperatures of the host organism. This indicates that organisms that live at higher temperatures have evolved RNA sequences with higher melting temperatures. PMID:16982646

  12. Accurate flexible fitting of high-resolution protein structures to small-angle x-ray scattering data using a coarse-grained model with implicit hydration shell.

    PubMed

    Zheng, Wenjun; Tekpinar, Mustafa

    2011-12-21

    Small-angle x-ray scattering (SAXS) is a powerful technique widely used to explore conformational states and transitions of biomolecular assemblies in solution. For accurate model reconstruction from SAXS data, one promising approach is to flexibly fit a known high-resolution protein structure to low-resolution SAXS data by computer simulations. This is a highly challenging task due to low information content in SAXS data. To meet this challenge, we have developed what we believe to be a novel method based on a coarse-grained (one-bead-per-residue) protein representation and a modified form of the elastic network model that allows large-scale conformational changes while maintaining pseudobonds and secondary structures. Our method optimizes a pseudoenergy that combines the modified elastic-network model energy with a SAXS-fitting score and a collision energy that penalizes steric collisions. Our method uses what we consider a new implicit hydration shell model that accounts for the contribution of hydration shell to SAXS data accurately without explicitly adding waters to the system. We have rigorously validated our method using five test cases with simulated SAXS data and three test cases with experimental SAXS data. Our method has successfully generated high-quality structural models with root mean-squared deviation of 1 ∼ 3 Å from the target structures.

  13. High Resolution/High Fidelity Seismic Imaging and Parameter Estimation for Geological Structure and Material Characterization

    SciTech Connect

    Ru-Shan Wu, Xiao-Bi Xie, Thorne Lay

    2005-06-06

    In this project, we develop new theories and methods for multi-domain one-way wave-equation based propagators, and apply these techniques to seismic modeling, seismic imaging, seismic illumination and model parameter estimation in 3D complex environments. The major progress of this project includes: (1) The development of the dual-domain wave propagators. We continue to improve the one-way wave-equation based propagators. Our target is making propagators capable of handling more realistic velocity models. A wide-angle propagator for transversely isotropic media with vertically symmetric axis (VTI) has been developed for P-wave modeling and imaging. The resulting propagator is accurate for large velocity perturbations and wide propagation angles. The thin-slab propagator for one-way elastic-wave propagation is further improved. With the introduction of complex velocities, the quality factors Qp and Qs have been incorporated into the thin-slab propagator. The resulting viscoelastic thin-slab propagator can handle elastic-wave propagation in models with intrinsic attenuations. We apply this method to complex models for AVO modeling, random media characterization and frequency-dependent reflectivity simulation. (2) Exploring the Information in the Local Angle Domain. Traditionally, the local angle information can only be extracted using the ray-based method. We develop a wave-equation based technique to process the local angle domain information. The approach can avoid the singularity problem usually linked to the high-frequency asymptotic method. We successfully apply this technique to seismic illumination and the resulting method provides a practical tool for three-dimensional full-volume illumination analysis in complex structures. The directional illumination also provides information for angle-domain imaging corrections. (3) Elastic-Wave Imaging. We develop a multicomponent elastic migration method. The application of the multicomponent one-way elastic propagator

  14. A new methodology for non-contact accurate crack width measurement through photogrammetry for automated structural safety evaluation

    NASA Astrophysics Data System (ADS)

    Jahanshahi, Mohammad R.; Masri, Sami F.

    2013-03-01

    In mechanical, aerospace and civil structures, cracks are important defects that can cause catastrophes if neglected. Visual inspection is currently the predominant method for crack assessment. This approach is tedious, labor-intensive, subjective and highly qualitative. An inexpensive alternative to current monitoring methods is to use a robotic system that could perform autonomous crack detection and quantification. To reach this goal, several image-based crack detection approaches have been developed; however, the crack thickness quantification, which is an essential element for a reliable structural condition assessment, has not been sufficiently investigated. In this paper, a new contact-less crack quantification methodology, based on computer vision and image processing concepts, is introduced and evaluated against a crack quantification approach which was previously developed by the authors. The proposed approach in this study utilizes depth perception to quantify crack thickness and, as opposed to most previous studies, needs no scale attachment to the region under inspection, which makes this approach ideal for incorporation with autonomous or semi-autonomous mobile inspection systems. Validation tests are performed to evaluate the performance of the proposed approach, and the results show that the new proposed approach outperforms the previously developed one.

  15. Accurate extraction of Lagrangian coherent structures over finite domains with application to flight data analysis over Hong Kong International Airport.

    PubMed

    Tang, Wenbo; Chan, Pak Wai; Haller, George

    2010-03-01

    Locating Lagrangian coherent structures (LCS) for dynamical systems defined on a spatially limited domain present a challenge because trajectory integration must be stopped at the boundary for lack of further velocity data. This effectively turns the domain boundary into an attractor, introduces edge effects resulting in spurious ridges in the associated finite-time Lyapunov exponent (FTLE) field, and causes some of the real ridges of the FTLE field to be suppressed by strong spurious ridges. To address these issues, we develop a finite-domain FTLE method that renders LCS with an accuracy and fidelity that is suitable for automated feature detection. We show the application of this technique to the analysis of velocity data from aircraft landing at the Hong Kong International Airport.

  16. Large eddy simulations of surface roughness parameter sensitivity to canopy-structure characteristics

    DOE PAGES

    Maurer, K. D.; Bohrer, G.; Ivanov, V. Y.

    2014-11-27

    Surface roughness parameters are at the core of every model representation of the coupling and interactions between land-surface and atmosphere, and are used in every model of surface fluxes. However, most models assume these parameters to be a fixed property of plant functional type and do not vary them in response to spatial or temporal changes to canopy structure. In part, this is due to the difficulty of reducing the complexity of canopy structure and its spatiotemporal dynamic and heterogeneity to less than a handful of parameters describing its effects of atmosphere–surface interactions. In this study we use large-eddy simulationsmore » to explore, in silico, the effects of canopy structure characteristics on surface roughness parameters. We performed a virtual experiment to test the sensitivity of resolved surface roughness to four axes of canopy structure: (1) leaf area index, (2) the vertical profile of leaf density, (3) canopy height, and (4) canopy gap fraction. We found roughness parameters to be highly variable, but were able to find positive relationships between displacement height and maximum canopy height, aerodynamic canopy height and maximum canopy height and leaf area index, and eddy-penetration depth and gap fraction. We also found negative relationships between aerodynamic canopy height and gap fraction, and between eddy-penetration depth and maximum canopy height and leaf area index. Using a decade of wind and canopy structure observations in a site in Michigan, we tested the effectiveness of our model-resolved parameters in predicting the frictional velocity over heterogeneous and disturbed canopies. We compared it with three other semi-empirical models and with a decade of meteorological observations. We found that parameterizations with fixed representations of roughness performed relatively well. Nonetheless, some empirical approaches that incorporate seasonal and inter-annual changes to the canopy structure performed even better than

  17. A PDE-based methodology for modeling, parameter estimation and feedback control in structural and structural acoustic systems

    NASA Technical Reports Server (NTRS)

    Banks, H. T.; Brown, D. E.; Metcalf, Vern L.; Silcox, R. J.; Smith, Ralph C.; Wang, Yun

    1994-01-01

    A problem of continued interest concerns the control of vibrations in a flexible structure and the related problem of reducing structure-borne noise in structural acoustic systems. In both cases, piezoceramic patches bonded to the structures have been successfully used as control actuators. Through the application of a controlling voltage, the patches can be used to reduce structural vibrations which in turn lead to methods for reducing structure-borne noise. A PDE-based methodology for modeling, estimating physical parameters, and implementing a feedback control scheme for problems of this type is discussed. While the illustrating example is a circular plate, the methodology is sufficiently general so as to be applicable in a variety of structural and structural acoustic systems.

  18. Towards Efficient and Accurate Description of Many-Electron Problems: Developments of Static and Time-Dependent Electronic Structure Methods

    NASA Astrophysics Data System (ADS)

    Ding, Feizhi

    Understanding electronic behavior in molecular and nano-scale systems is fundamental to the development and design of novel technologies and materials for application in a variety of scientific contexts from fundamental research to energy conversion. This dissertation aims to provide insights into this goal by developing novel methods and applications of first-principle electronic structure theory. Specifically, we will present new methods and applications of excited state multi-electron dynamics based on the real-time (RT) time-dependent Hartree-Fock (TDHF) and time-dependent density functional theory (TDDFT) formalism, and new development of the multi-configuration self-consist field theory (MCSCF) for modeling ground-state electronic structure. The RT-TDHF/TDDFT based developments and applications can be categorized into three broad and coherently integrated research areas: (1) modeling of the interaction between moleculars and external electromagnetic perturbations. In this part we will first prove both analytically and numerically the gauge invariance of the TDHF/TDDFT formalisms, then we will present a novel, efficient method for calculating molecular nonlinear optical properties, and last we will study quantum coherent plasmon in metal namowires using RT-TDDFT; (2) modeling of excited-state charge transfer in molecules. In this part, we will investigate the mechanisms of bridge-mediated electron transfer, and then we will introduce a newly developed non-equilibrium quantum/continuum embedding method for studying charge transfer dynamics in solution; (3) developments of first-principles spin-dependent many-electron dynamics. In this part, we will present an ab initio non-relativistic spin dynamics method based on the two-component generalized Hartree-Fock approach, and then we will generalized it to the two-component TDDFT framework and combine it with the Ehrenfest molecular dynamics approach for modeling the interaction between electron spins and nuclear

  19. Integrative structural annotation of de novo RNA-Seq provides an accurate reference gene set of the enormous genome of the onion (Allium cepa L.).

    PubMed

    Kim, Seungill; Kim, Myung-Shin; Kim, Yong-Min; Yeom, Seon-In; Cheong, Kyeongchae; Kim, Ki-Tae; Jeon, Jongbum; Kim, Sunggil; Kim, Do-Sun; Sohn, Seong-Han; Lee, Yong-Hwan; Choi, Doil

    2015-02-01

    The onion (Allium cepa L.) is one of the most widely cultivated and consumed vegetable crops in the world. Although a considerable amount of onion transcriptome data has been deposited into public databases, the sequences of the protein-coding genes are not accurate enough to be used, owing to non-coding sequences intermixed with the coding sequences. We generated a high-quality, annotated onion transcriptome from de novo sequence assembly and intensive structural annotation using the integrated structural gene annotation pipeline (ISGAP), which identified 54,165 protein-coding genes among 165,179 assembled transcripts totalling 203.0 Mb by eliminating the intron sequences. ISGAP performed reliable annotation, recognizing accurate gene structures based on reference proteins, and ab initio gene models of the assembled transcripts. Integrative functional annotation and gene-based SNP analysis revealed a whole biological repertoire of genes and transcriptomic variation in the onion. The method developed in this study provides a powerful tool for the construction of reference gene sets for organisms based solely on de novo transcriptome data. Furthermore, the reference genes and their variation described here for the onion represent essential tools for molecular breeding and gene cloning in Allium spp.

  20. An accurately preorganized IRES RNA structure enables eIF4G capture for initiation of viral translation.

    PubMed

    Imai, Shunsuke; Kumar, Parimal; Hellen, Christopher U T; D'Souza, Victoria M; Wagner, Gerhard

    2016-09-01

    Many viruses bypass canonical cap-dependent translation in host cells by using internal ribosomal entry sites (IRESs) in their transcripts; IRESs hijack initiation factors for the assembly of initiation complexes. However, it is currently unknown how IRES RNAs recognize initiation factors that have no endogenous RNA binding partners; in a prominent example, the IRES of encephalomyocarditis virus (EMCV) interacts with the HEAT-1 domain of eukaryotic initiation factor 4G (eIF4G). Here we report the solution structure of the J-K region of this IRES and show that its stems are precisely organized to position protein-recognition bulges. This multisite interaction mechanism operates on an all-or-nothing principle in which all domains are required. This preorganization is accomplished by an 'adjuster module': a pentaloop motif that acts as a dual-sided docking station for base-pair receptors. Because subtle changes in the orientation abrogate protein capture, our study highlights how a viral RNA acquires affinity for a target protein. PMID:27525590

  1. Assessing General Relationships Between Above-Ground Biomass and Vegetation Structure Parameters for Improved Carbon Estimate from Lidar Remote Sensing

    NASA Astrophysics Data System (ADS)

    Ni-Meister, W.; Lee, S.; Strahler, A. H.; Woodcock, C. E.; Schaaf, C.; Yao, T.; Ranson, J.; Sun, G.; Blair, J. B.

    2009-12-01

    Lidar remote sensing uses vegetation height to estimate large-scale above-ground biomass. However, lidar height and biomass relationships are empirical and thus often lead to large uncertainties in above-ground biomass estimates. This study uses vegetation structure measurements from field: an airborne lidar (Laser Vegetation Imaging Sensor, LVIS)) and a full wave form ground-based lidar (Echidna® validation instrument, EVI) collected in the New England region in 2003 and 2007, to investigate using additional vegetation structure parameters besides height for improved above-ground biomass estimation from lidar. Our field data analysis shows that using woody volume (approximated by the product of basal area and top 10% tree height) and vegetation type (conifer/softwood or deciduous/hardwood forests, providing wood density) has the potential to improve above-ground biomass estimates at large scale. This result is comparable to previous work by Chave et al. (2005), which focused on individual trees. However this study uses a slightly different approach, and our woody volume is estimated differently from Chave et al. (2005). Previous studies found that RH50 is a good predictor of above-ground biomass (Drake et al., 2002; 2003). Our LVIS data analysis shows that structure parameters that combine height and gap fraction, such as RH100*cover and RH50*cover, perform similarly or even better than RH50. We also found that the close relationship of RH100*cover and RH50*cover with woody volume explains why they are good predictors of above-ground biomass. RH50 is highly related to RH100*cover, and this explains why RH50 is a better predictor of biomass than RH100. This study shows that using structure parameters combining height and gap fraction improve above-ground biomass estimate compared to height alone, and fusion of lidar and optical remote sensing (to provide vegetation type) will provide better above-ground biomass estimates than lidar alone. Ground lidar analysis

  2. A novel method for finding the initial structure parameters of optical systems via a genetic algorithm

    NASA Astrophysics Data System (ADS)

    Jun, LIU; Huang, Wei; Hongjie, Fan

    2016-02-01

    A novel method for finding the initial structure parameters of an optical system via the genetic algorithm (GA) is proposed in this research. Usually, optical designers start their designs from the commonly used structures from a patent database; however, it is time consuming to modify the patented structures to meet the specification. A high-performance design result largely depends on the choice of the starting point. Accordingly, it would be highly desirable to be able to calculate the initial structure parameters automatically. In this paper, a method that combines a genetic algorithm and aberration analysis is used to determine an appropriate initial structure of an optical system. We use a three-mirror system as an example to demonstrate the validity and reliability of this method. On-axis and off-axis telecentric three-mirror systems are obtained based on this method.

  3. Method of m-line spectroscopy, a good tool to determine and control the optical parameters of waveguide structures

    NASA Astrophysics Data System (ADS)

    Auguściuk, ElŻbieta

    2013-01-01

    Method of spectroscopy m-line is an accurate method for determination of the optical parameters of the planar and stripe waveguides. In this method, the laser beam is coupled to the waveguide (e.g. by the prism) in the form of discrete angles. If the layer of the solid or liquid material is deposited on the waveguide, the change in the coupling angle is observed. Modified method of the m-line spectroscopy allows for determination of the optical parameters of deposited layers with high accuracy. Moreover, modification of the waveguide structure obtained via deposition of consecutive layers and changes the ability to propagate not only in the same waveguide. Modified method of m-line spectroscopy has found many potential applications in various areas such as: technological control of the applied layers quality; modification of the light propagation in the waveguide structures; utilization in the preventive medicine for diabetic diseases; food-control of the level of nutrients in vegetables (e.g. sugar level in white beets).

  4. Cohesive energy and structural parameters of binary oxides of groups IIA and IIIB from diffusion quantum Monte Carlo

    DOE PAGES

    Santana, Juan A.; Krogel, Jaron T.; Kent, Paul R. C.; Reboredo, Fernando A.

    2016-05-03

    We have applied the diffusion quantum Monte Carlo (DMC) method to calculate the cohesive energy and the structural parameters of the binary oxides CaO, SrO, BaO, Sc2O3, Y2O3 and La2O3. The aim of our calculations is to systematically quantify the accuracy of the DMC method to study this type of metal oxides. The DMC results were compared with local and semi-local Density Functional Theory (DFT) approximations as well as with experimental measurements. The DMC method yields cohesive energies for these oxides with a mean absolute deviation from experimental measurements of 0.18(2) eV, while with local and semi-local DFT approximations themore » deviation is 3.06 and 0.94 eV, respectively. For lattice constants, the mean absolute deviation in DMC, local and semi-local DFT approximations, are 0.017(1), 0.07 and 0.05 , respectively. In conclusion, DMC is highly accurate method, outperforming the local and semi-local DFT approximations in describing the cohesive energies and structural parameters of these binary oxides.« less

  5. Analysis of Parameters Assessment on Laminated Rubber-Metal Spring for Structural Vibration

    NASA Astrophysics Data System (ADS)

    Salim, M. A.; Putra, A.; Mansor, M. R.; Musthafah, M. T.; Akop, M. Z.; Abdullah, M. A.

    2016-02-01

    This paper presents the analysis of parameter assessment on laminated rubber-metal spring (LR-MS) for vibrating structure. Three parameters were selected for the assessment which are mass, Young's modulus and radius. Natural rubber materials has been used to develop the LR-MS model. Three analyses were later conducted based on the selected parameters to the LR-MS performance which are natural frequency, location of the internal resonance frequency and transmissibility of internal resonance. Results of the analysis performed were plotted in frequency domain function graph. Transmissibility of laminated rubber-metal spring (LR-MS) is changed by changing the value of the parameter. This occurrence was referred to the theory from open literature then final conclusion has been make which are these parameters have a potential to give an effects and trends for LR-MS transmissibility.

  6. The mechanical and acoustic properties of two-dimensional pentamode metamaterials with different structural parameters

    NASA Astrophysics Data System (ADS)

    Cai, Xuan; Wang, Lei; Zhao, Zhigao; Zhao, Aiguo; Zhang, Xiangdong; Wu, Tao; Chen, Hong

    2016-09-01

    The effective mechanical and acoustic properties of two-dimensional pentamode metamaterials (PMs) with different structural parameters are investigated in this paper. It is found that with varying structural parameters, the effective bulk modulus and density remain constant as the same as those of water, while the figure of merit, i.e., the ratio of the bulk modulus to the shear modulus (B/G) gradually increases due to the decrease of the shear modulus. However, full wave simulations reveal that with the increase of B/G, the acoustic scattering becomes more and more intense, which indicates that the acoustic properties of pentamode metamaterials gradually deviate from those of water. These anomalous acoustic behaviors are proposed to arise from the existence of the bending modes in pentamode microstructures. Our results show that for pentamode metamaterials, the mechanical properties cannot be simply translated to their acoustic properties, and the structural parameters affect the mechanical and acoustic properties in much different ways.

  7. Modal parameters of space structures in 1 G and 0 G

    NASA Technical Reports Server (NTRS)

    Bicos, Andrew S.; Crawley, Edward F.; Barlow, Mark S.; Van Schoor, Marthinus C.; Masters, Brett

    1993-01-01

    Analytic and experimental results are presented from a study of the changes in the modal parameters of space structural test articles from one- to zero-gravity. Deployable, erectable, and rotary modules was assembled to form three one- and two-dimensional structures, in which variations in bracing wire and rotary joint preload could be introduced. The structures were modeled as if hanging from a suspension system in one gravity, and unconstrained, as if free floating in zero-gravity. The analysis is compared with ground experimental measurements, which were made on a spring-wire suspension system with a nominal plunge frequency of one Hertz, and with measurements made on the Shuttle middeck. The degree of change in linear modal parameters as well as the change in nonlinear nature of the response is examined. Trends in modal parameters are presented as a function of force amplitude, joint preload, reassembly, shipset, suspension, and ambient gravity level.

  8. Effect of counter- and co-ions on the structural transport parameters of sulfoacid cationite membranes

    NASA Astrophysics Data System (ADS)

    Demina, O. A.; Falina, I. V.; Kononenko, N. A.; Demin, A. V.

    2016-08-01

    The diffusion permeability and specific electroconductivity of MK-40 sulfoacid cationite and Nafion 425 membranes are studied experimentally in NaOH, NaCl, and HCl solutions with various concentrations. The resulting concentration dependences of the electrodiffusion characteristics and data on the nonexchange sorption of the electrolytes are used to calculate the structural transport parameters of the membranes in terms of a two-phase conduction model. Analysis of a set of parameters, including the electroconductivity and diffusion permeability of the membrane gel phase, the volume fractions of the conductive phases, and a parameter that reflects their relative positions, the Donnan constant, and the diffusion coefficients of counter and co-ions in the membrane gel phase reveals the effect the nature of counter- and co-ions has on the electrodiffusion, structural, and sorption characteristics of sulfoacid cationite membranes with different types of structure.

  9. Intensity Inhomogeneity Correction of Structural MR Images: A Data-Driven Approach to Define Input Algorithm Parameters

    PubMed Central

    Ganzetti, Marco; Wenderoth, Nicole; Mantini, Dante

    2016-01-01

    Intensity non-uniformity (INU) in magnetic resonance (MR) imaging is a major issue when conducting analyses of brain structural properties. An inaccurate INU correction may result in qualitative and quantitative misinterpretations. Several INU correction methods exist, whose performance largely depend on the specific parameter settings that need to be chosen by the user. Here we addressed the question of how to select the best input parameters for a specific INU correction algorithm. Our investigation was based on the INU correction algorithm implemented in SPM, but this can be in principle extended to any other algorithm requiring the selection of input parameters. We conducted a comprehensive comparison of indirect metrics for the assessment of INU correction performance, namely the coefficient of variation of white matter (CVWM), the coefficient of variation of gray matter (CVGM), and the coefficient of joint variation between white matter and gray matter (CJV). Using simulated MR data, we observed the CJV to be more accurate than CVWM and CVGM, provided that the noise level in the INU-corrected image was controlled by means of spatial smoothing. Based on the CJV, we developed a data-driven approach for selecting INU correction parameters, which could effectively work on actual MR images. To this end, we implemented an enhanced procedure for the definition of white and gray matter masks, based on which the CJV was calculated. Our approach was validated using actual T1-weighted images collected with 1.5 T, 3 T, and 7 T MR scanners. We found that our procedure can reliably assist the selection of valid INU correction algorithm parameters, thereby contributing to an enhanced inhomogeneity correction in MR images. PMID:27014050

  10. Assessing general relationships between aboveground biomass and vegetation structure parameters for improved carbon estimate from lidar remote sensing

    NASA Astrophysics Data System (ADS)

    Ni-Meister, Wenge; Lee, Shihyan; Strahler, Alan H.; Woodcock, Curtis E.; Schaaf, Crystal; Yao, Tian; Ranson, K. Jon; Sun, Guoqing; Blair, J. Bryan

    2010-06-01

    Lidar-based aboveground biomass is derived based on the empirical relationship between lidar-measured vegetation height and aboveground biomass, often leading to large uncertainties of aboveground biomass estimates at large scales. This study investigates whether the use of any additional lidar-derived vegetation structure parameters besides height improves aboveground biomass estimation. The analysis uses data collected in the field and with the Laser Vegetation Imaging Sensor (LVIS), and the Echidna® validation instrument (EVI), a ground-based hemispherical-scanning lidar data in New England in 2003 and 2007. Our field data analysis shows that using wood volume (approximated by the product of basal area and top 10% tree height) and vegetation type (conifer/softwood or deciduous/hardwood forests, providing wood density) has the potential to improve aboveground biomass estimates at large scales. This result is comparable to previous individual-tree based analyses. Our LVIS data analysis indicates that structure parameters that combine height and gap fraction, such as RH100*cover and RH50*cover, are closely related to wood volume and thus biomass particularly for conifer forests. RH100*cover and RH50*cover perform similarly or even better than RH50, a good biomass predictor found in previous study. This study shows that the use of structure parameters that combine height and gap fraction (rather than height alone) improves the aboveground biomass estimate, and that the fusion of lidar and optical remote sensing (to provide vegetation type) will provide better aboveground biomass estimates than using lidar alone. Our ground lidar analysis shows that EVI provides good estimates of wood volume, and thus accurate estimates of aboveground biomass particularly at the stand level.

  11. Proposal for electronic nematic order parameter sensitive to intra unit cell structures

    NASA Astrophysics Data System (ADS)

    Lawler, Michael; Fujita, K.; Schmidt, A.; Lee, Jhinhwan; Kim, Chung Koo; Eisaki, H.; Uchida, S.; Davis, J. C.; Sethna, J. P.; Kim, Eun-Ah

    2010-03-01

    We propose an order parameter for detecting signatures of electronic nematic ordering using local probes such as scanning tunneling microscopy(STM). The order parameter is designed to measure rotational symmetry breaking without prejudice towards translational symmetry breaking -- achieved by focusing on intra unit cell structures. This order parameter utilizes Fourier space information much the same way as in diffraction measurements, opening the possibility for a comparative study of nematicity between different probes. Our study is primarily motivated by the patterns observed in STM measurements on underdoped cuprates. We discuss theoretical implications of our results in this light.

  12. A new method of differential structural analysis of gamma-family basic parameters

    NASA Technical Reports Server (NTRS)

    Melkumian, L. G.; Ter-Antonian, S. V.; Smorodin, Y. A.

    1985-01-01

    The maximum likelihood method is used for the first time to restore parameters of electron photon cascades registered on X-ray films. The method permits one to carry out a structural analysis of the gamma quanta family darkening spots independent of the gamma quanta overlapping degree, and to obtain maximum admissible accuracies in estimating the energies of the gamma quanta composing a family. The parameter estimation accuracy weakly depends on the value of the parameters themselves and exceeds by an order of the values obtained by integral methods.

  13. Experimental investigation of the statistical interrelation between the magnetic and mechanical parameters of structural steels

    SciTech Connect

    Aronov, A.Ya.; Popov, A.N.; Morozova, V.M.; Nichipuruk, A.P.

    1988-11-01

    The article examines the possibilities of the statistical method of solving problems of electromagnetic quality control of the mechanical properties of structural steels with the use of teaching sampling of electromagnetic and mechanical parameters of specimens of steel 38KhS expressing the regularities of their changes in different regimes of martempering with subsequent tempering and austempering. To obtain a model correlating these parameters, the method of primary components jointly with multiple regression analysis was used. The results of the investigation showed that the mechanical parameters can be determined with a high degree of reliability.

  14. Critical parameters of hard-core Yukawa fluids within the structural theory

    NASA Astrophysics Data System (ADS)

    Bahaa Khedr, M.; Osman, S. M.

    2012-10-01

    A purely statistical mechanical approach is proposed to account for the liquid-vapor critical point based on the mean density approximation (MDA) of the direct correlation function. The application to hard-core Yukawa (HCY) fluids facilitates the use of the series mean spherical approximation (SMSA). The location of the critical parameters for HCY fluid with variable intermolecular range is accurately calculated. Good agreement is observed with computer simulation results and with the inverse temperature expansion (ITE) predictions. The influence of the potential range on the critical parameters is demonstrated and the universality of the critical compressibility ratio is discussed. The behavior of the isochoric and isobaric heat capacities along the equilibrium line and the near vicinity of the critical point is discussed in details.

  15. k.p Parameters with Accuracy Control from Preexistent First-Principles Band Structure Calculations

    NASA Astrophysics Data System (ADS)

    Sipahi, Guilherme; Bastos, Carlos M. O.; Sabino, Fernando P.; Faria Junior, Paulo E.; de Campos, Tiago; da Silva, Juarez L. F.

    The k.p method is a successful approach to obtain band structure, optical and transport properties of semiconductors. It overtakes the ab initio methods in confined systems due to its low computational cost since it is a continuum method that does not require all the atoms' orbital information. From an effective one-electron Hamiltonian, the k.p matrix representation can be calculated using perturbation theory and the parameters identified by symmetry arguments. The parameters determination, however, needs a complementary approach. In this paper, we developed a general method to extract the k.p parameters from preexistent band structures of bulk materials that is not limited by the crystal symmetry or by the model. To demonstrate our approach, we applied it to zinc blende GaAs band structure calculated by hybrid density functional theory within the Heyd-Scuseria-Ernzerhof functional (DFT-HSE), for the usual 8 ×8 k.p Hamiltonian. Our parameters reproduced the DFT-HSE band structure with great accuracy up to 20% of the first Brillouin zone (FBZ). Furthermore, for fitting regions ranging from 7-20% of FBZ, the parameters lie inside the range of values reported by the most reliable studies in the literature. The authors acknowledge financial support from the Brazilian agencies CNPq (Grant #246549/2012-2) and FAPESP (Grants #2011/19333-4, #2012/05618-0 and #2013/23393-8).

  16. The effect of neutron radiation on the photoelectric parameters of ITO-GaSe structures

    SciTech Connect

    Kovalyuk, Z. D. Litovchenko, P. G.; Politanska, O. A.; Sydor, O. N.; Katerynchuk, V. N.; Lastovetsky, V. F.; Litovchenko, O. P.; Dubovoy, V. K.; Polivtsev, L. A.

    2007-05-15

    The effect of 1-MeV neutrons on the photoelectric parameters of ITO-GaSe heterostructures was studied. It is shown that the observed variations in the current-voltage characteristics are caused by the effect of penetrating radiation on both components of the structure, which brings about an increase in the resistance of the heterostructures. The presence of exciton fine structure in the photosensitivity spectra after irradiation indicates that GaSe retains high structural quality notwithstanding the introduced radiation defects. The results obtained are accounted for by spatial redistribution of doping impurity in GaSe and structural changes in the ITO films.

  17. Characterization of the Local Structure in Liquid Water by Various Order Parameters

    PubMed Central

    2015-01-01

    A wide range of geometric order parameters have been suggested to characterize the local structure of liquid water and its tetrahedral arrangement, but their respective merits have remained elusive. Here, we consider a series of popular order parameters and analyze molecular dynamics simulations of water, in the bulk and in the hydration shell of a hydrophobic solute, at 298 and 260 K. We show that these parameters are weakly correlated and probe different distortions, for example the angular versus radial disorders. We first combine these complementary descriptions to analyze the structural rearrangements leading to the density maximum in liquid water. Our results reveal no sign of a heterogeneous mixture and show that the density maximum arises from the depletion in interstitial water molecules upon cooling. In the hydration shell of the hydrophobic moiety of propanol, the order parameters suggest that the water local structure is similar to that in the bulk, with only a very weak depletion in ordered configurations, thus confirming the absence of any iceberg-type structure. Finally, we show that the main structural fluctuations that affect water reorientation dynamics in the bulk are angular distortions, which we explain by the jump hydrogen-bond exchange mechanism. PMID:26054933

  18. Accurate structure, thermodynamics and spectroscopy of medium-sized radicals by hybrid Coupled Cluster/Density Functional Theory approaches: the case of phenyl radical

    PubMed Central

    Barone, Vincenzo; Biczysko, Malgorzata; Bloino, Julien; Egidi, Franco; Puzzarini, Cristina

    2015-01-01

    The CCSD(T) model coupled with extrapolation to the complete basis-set limit and additive approaches represents the “golden standard” for the structural and spectroscopic characterization of building blocks of biomolecules and nanosystems. However, when open-shell systems are considered, additional problems related to both specific computational difficulties and the need of obtaining spin-dependent properties appear. In this contribution, we present a comprehensive study of the molecular structure and spectroscopic (IR, Raman, EPR) properties of the phenyl radical with the aim of validating an accurate computational protocol able to deal with conjugated open-shell species. We succeeded in obtaining reliable and accurate results, thus confirming and, partly, extending the available experimental data. The main issue to be pointed out is the need of going beyond the CCSD(T) level by including a full treatment of triple excitations in order to fulfil the accuracy requirements. On the other hand, the reliability of density functional theory in properly treating open-shell systems has been further confirmed. PMID:23802956

  19. Parameter-Free Hydrogen-Bond Definition to Classify Protein Secondary Structure.

    PubMed

    Haghighi, Hasti; Higham, Jonathan; Henchman, Richard H

    2016-08-25

    DSSP is the most commonly used method to assign protein secondary structure. It is based on a hydrogen-bond definition with an energy cutoff. To assess whether hydrogen bonds defined in a parameter-free way may give more generality while preserving accuracy, we examine a series of hydrogen-bond definitions to assign secondary structure for a series of proteins. Assignment by the strongest-acceptor bifurcated definition with provision for unassigned donor hydrogens, termed the SABLE method, is found to match DSSP with 95% agreement. The small disagreement mainly occurs for helices, turns, and bends. While there is no absolute way to assign protein secondary structure, avoiding molecule-specific cutoff parameters should be advantageous in generalizing structure-assignment methods to any hydrogen-bonded system. PMID:27067825

  20. Influence of nitric acid treatment in different media on X-ray structural parameters of coal

    SciTech Connect

    Sudip Maity; Ashim Choudhury

    2008-11-15

    The treatment of coal with nitric acid in aqueous and non-aqueous media introduces changes in the chemical and spatial structure of the organic mass. Four coals of different rank have been treated with nitric acid in aqueous and glacial acetic acid media for assessing the changes in the structural parameters by the X-ray diffraction (XRD) technique. Slow-scan XRD has been performed for the raw and treated coals, and X-ray structural parameters (d002, Lc, and Nc) and aromaticity (fa) have been determined by profile-fitting software. Considerable variation of the structural parameters has been observed with respect to the raw coals. The d002 values have decreased in aqueous medium but increased in acetic acid medium; however, Lc, Nc, and fa values have increased in aqueous medium but decreased in acetic acid medium. It is also observed that considerable oxidation takes place during nitric acid treatment in aqueous medium, but nitration is the predominant phenomenon in acetic acid medium. Disordering of the coal structure increases in acetic acid medium, but a reverse trend is observed in the aqueous medium. As a result, structurally modified coals (SMCs) are derived as new coal-derived substances. 15 refs., 6 figs., 3 tabs.

  1. Single-Mode Projection Filters for Modal Parameter Identification for Flexible Structures

    NASA Technical Reports Server (NTRS)

    Huang, Jen-Kuang; Chen, Chung-Wen

    1988-01-01

    Single-mode projection filters are developed for eigensystem parameter identification from both analytical results and test data. Explicit formulations of these projection filters are derived using the orthogonal matrices of the controllability and observability matrices in the general sense. A global minimum optimization algorithm is applied to update the filter parameters by using the interval analysis method. The updated modal parameters represent the characteristics of the test data. For illustration of this new approach, a numerical simulation for the MAST beam structure is shown by using a one-dimensional global optimization algorithm to identify modal frequencies and damping. Another numerical simulation of a ten-mode structure is also presented by using a two-dimensional global optimization algorithm to illustrate the feasibility of the new method. The projection filters are practical for parallel processing implementation.

  2. Measurement of manufacturing resolution for two photon polymerization structures with different manufacturing parameters

    NASA Astrophysics Data System (ADS)

    Chung, Tien-Tung; Li, Wan-Jou; Chen, Sheng-Yuan; Hoi, Chi-Hou

    2015-02-01

    This paper studied manufacturing resolutions of micro structures made by two photon polymerization (TPP) technology with different manufacturing parameters. The light source used for the TPP manufacturing system was a low-cost 532 nm Nd:YAG green laser, and the material used was commercial resin Photomer 3015. Two objective lenses, one with magnification of 100 times (100x) and numerical aperture (NA) of 1.3 and the other with 50x and NA0.8 were used in TPP production. The manufacturing resolution, which is also named as voxel size, changed with different manufacturing parameters such as laser power and exposure time. The measurement results of TPP structures manufactured with different manufacturing parameters indicated that the minimum line width produced by the 100x-NA1.3 lens could be reduced down to 67 nanometer (nm), which was quite good for TPP systems with low-cost Nd:YAG laser.

  3. Effect of scintillometer height on structure parameter of the refractive index of air measurements

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Scintillometers measure amount of scintillations by emitting a beam of light over a horizontal path and expresses as the atmospheric turbulence structure parameter as the refractive index of air (Cn**2). Cn**2 represents the turbulent strength of the atmosphere and describes the ability of the atmos...

  4. Methods for the identification of material parameters in distributed models for flexible structures

    NASA Technical Reports Server (NTRS)

    Banks, H. T.; Crowley, J. M.; Rosen, I. G.

    1986-01-01

    Theoretical and numerical results are presented for inverse problems involving estimation of spatially varying parameters such as stiffness and damping in distributed models for elastic structures such as Euler-Bernoulli beams. An outline of algorithms used and a summary of computational experiences are presented.

  5. Simulating solute transport in a structured field soil: uncertainty in parameter identification and predictions.

    PubMed

    Larsbo, Mats; Jarvis, Nicholas

    2005-01-01

    Dual-permeability models have been developed to account for the significant effects of macropore flow on contaminant transport, but their use is hampered by difficulties in estimating the additional parameters required. Therefore, our objective was to evaluate data requirements for parameter identification for predictive modeling with the dual-permeability model MACRO. Two different approaches were compared: sequential uncertainty fitting (SUFI) and generalized likelihood uncertainty estimation (GLUE). We investigated six parameters controlling macropore flow and pesticide sorption and degradation, applying MACRO to a comprehensive field data set of bromide andbentazone [3-isopropyl-1H-2,1,3-benzothiadiazin-4(3H)-one-2,2dioxide] transport in a structured soil. The GLUE analyses of parameter conditioning for different combinations of observations showed that both resident and flux concentrations were needed to obtain highly conditioned and unbiased parameters and that observations of tracer transport generally improved the conditioning of macropore flow parameters. The GLUE "behavioral" parameter sets covered wider parameter ranges than the SUFI posterior uncertainty domains. Nevertheless, estimation uncertainty ranges defined by the 5th and 95th percentiles were similar and many simulations randomly sampled from the SUFI posterior uncertainty domains had negative model efficiencies (minimum of -3.2). This is because parameter correlations are neglected in SUFI and the posterior uncertainty domains were not always determined correctly. For the same reasons, uncertainty ranges for predictions of bentazone losses through drainflow for good agricultural practice in southern Sweden were 27% larger for SUFI compared with GLUE. Although SUFI proved to be an efficient parameter estimation tool, GLUE seems better suited as a method of uncertainty estimation for predictions.

  6. Parameter-dependent vibration-attenuation controller design for electro-hydraulic actuated linear structural systems

    NASA Astrophysics Data System (ADS)

    Weng, Falu; Mao, Weijie

    2012-03-01

    The problem of robust active vibration control for a class of electro-hydraulic actuated structural systems with time-delay in the control input channel and parameter uncertainties appearing in all the mass, damping and stiffness matrices is investigated in this paper. First, by introducing a linear varying parameter, the nonlinear system is described as a linear parameter varying (LPV) model. Second, based on this LPV model, an LMI-based condition for the system to be asymptotically stabilized is deduced. By solving these LMIs, a parameter-dependent controller is established for the closedloop system to be stable with a prescribed level of disturbance attenuation. The condition is also extended to the uncertain case. Finally, some numerical simulations demonstrate the satisfying performance of the proposed controller.

  7. The Structural Parameters of the Globular Clusters in M31 with PAndAS

    NASA Astrophysics Data System (ADS)

    Woodley, Kristin; Pan-Andromeda Archaeological Survey (PAndAS), The

    2012-05-01

    The Pan-Andromeda Archaeological Survey (PAndAS) has obtained images with the Canada France Hawaii Telescope using the instrument MegaCam, covering over 400 square degrees in the sky and extending beyond 150 kpc in radius from the center of M31. With this extensive data set, we have measured the structural parameters of all confirmed globular clusters in M31 as well as for a large fraction of the candidate globular clusters in the Revised Bologna Catalog V.4 (Galleti et al. 2004, A&A, 416, 917). In this paper, we present their parameters, including their core-, effective (half-light)-, and tidal radii, as well as their ellipticities measured in a homogeneous manner with ISHAPE (Larsen 1999, A&AS, 139, 393). We examine these parameters as functions of radial position, luminosity, color, metallicity, and age. We also use our measurements as an additional parameter to help constrain the candidacy of the unconfirmed globular clusters.

  8. Large-eddy simulations of surface roughness parameter sensitivity to canopy-structure characteristics

    DOE PAGES

    Maurer, K. D.; Bohrer, G.; Kenny, W. T.; Ivanov, V. Y.

    2015-04-30

    Surface roughness parameters, namely the roughness length and displacement height, are an integral input used to model surface fluxes. However, most models assume these parameters to be a fixed property of plant functional type and disregard the governing structural heterogeneity and dynamics. In this study, we use large-eddy simulations to explore, in silico, the effects of canopy-structure characteristics on surface roughness parameters. We performed a virtual experiment to test the sensitivity of resolved surface roughness to four axes of canopy structure: (1) leaf area index, (2) the vertical profile of leaf density, (3) canopy height, and (4) canopy gap fraction.more » We found roughness parameters to be highly variable, but uncovered positive relationships between displacement height and maximum canopy height, aerodynamic canopy height and maximum canopy height and leaf area index, and eddy-penetration depth and gap fraction. We also found negative relationships between aerodynamic canopy height and gap fraction, as well as between eddy-penetration depth and maximum canopy height and leaf area index. We generalized our model results into a virtual "biometric" parameterization that relates roughness length and displacement height to canopy height, leaf area index, and gap fraction. Using a decade of wind and canopy-structure observations in a site in Michigan, we tested the effectiveness of our model-driven biometric parameterization approach in predicting the friction velocity over heterogeneous and disturbed canopies. We compared the accuracy of these predictions with the friction-velocity predictions obtained from the common simple approximation related to canopy height, the values calculated with large-eddy simulations of the explicit canopy structure as measured by airborne and ground-based lidar, two other parameterization approaches that utilize varying canopy-structure inputs, and the annual and decadal means of the surface roughness parameters at

  9. A Survey of Compact Star Clusters in the South-West Field of the M 31 Disk. Structural Parameters

    NASA Astrophysics Data System (ADS)

    Šablevičiūtė, I.; Vansevičius, V.; Kodaira, K.; Narbutis, D.; Stonkutė, R.; Bridžius, A.

    We present structural parameters for 51 compact star clusters from the survey of star clusters conducted in the South-West field of the M 31 disk by Kodaira et al. (2004). Structural parameters of the clusters were derived by fitting the 2-D King and EFF (Elson, Fall and Freeman 1987) models to the V-band cluster images. Structural parameters derived for two M 31 clusters, which are in common with the study based on the HST data (Barmby et al. 2002), are consistent with earlier determination. The M 31 star cluster structural parameters in general are compatible with the corresponding Milky Way galaxy and Magellanic Clouds cluster parameters.

  10. Structural parameters determining the transition temperature of tetragonal KH2PO4-type crystals

    NASA Astrophysics Data System (ADS)

    Ichikawa, M.; Amasaki, D.; Gustafsson, T.; Olovsson, I.

    2001-09-01

    A systematic study of the structural parameters determining the ferroelectric phase transition temperature Tc in tetragonal KH2PO4 (KDP)-type crystals MH2XO4 has been performed by searching the correlation between different structural parameters and Tc. It has been revealed that the transition temperature is determined not only by the hydrogen-bond distance R, as reported earlier, but also by the distortion of XO4 (via O-X-O angle α1) and the packing of M and XO4 along the c axis (via the rotation angle θ around the c axis); α1 reflects the dipole moment of XO4 and θ may influence the amplitude of optical vibration of M and XO4. The contribution of each structural part to the transition temperature Tc in the tetragonal KDP family has been revealed in a comprehensive way for ferroelectrics.

  11. Structural parameters and dynamic loading identification from incomplete measurements: Approach and validation

    NASA Astrophysics Data System (ADS)

    Xu, Bin; He, Jia; Rovekamp, Roger; Dyke, Shirley J.

    2012-04-01

    System identification is becoming more important in structural dynamic applications including structural model update, damage detection primarily due to the rapid increase in the number of damaged or deteriorated engineering structures, and load identification for remaining service life forecasting. Time-domain identification techniques based on measured vibration data, e.g. the least-squares estimation (LSE), have been studied for a relatively long time and shown to be useful. However, the traditional least-squares techniques require that all the external excitation measurements should be available, which may not be the case for many practical applications. In this paper, by introducing a weighted positive definite matrix to the objective function and a learning coefficient using the information in the previous iterations in the identification approach to improve the convergence performance, an alternative iterative approach for both structural parameters and dynamic loading identification, referred to as weighted adaptive iterative least-squares estimation with incomplete measured excitations (WAILSE-IME), was proposed. The accuracy, convergence, and robustness of the proposed approach was demonstrated via numerical simulation on a six-story shear building model with noise-free and different levels of noise-polluted structural dynamic response measurements. The effects of the positive weight matrix, the learning coefficient, and the sampling duration on the convergence and the accuracy of the proposed approach were discussed and the results were compared with available related literature results. Results show that the proposed approach can simultaneously identify structural parameters and unknown excitations within very limited iterations with high accuracy and shows its robustness even noise-polluted dynamic response measurements are utilized. Furthermore, the approach was validated via available experimental measurements for a four-story frame structure excited

  12. Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile, and accurate RNA structure analysis

    PubMed Central

    Smola, Matthew J.; Rice, Greggory M.; Busan, Steven; Siegfried, Nathan A.; Weeks, Kevin M.

    2016-01-01

    SHAPE chemistries exploit small electrophilic reagents that react with the 2′-hydroxyl group to interrogate RNA structure at single-nucleotide resolution. Mutational profiling (MaP) identifies modified residues based on the ability of reverse transcriptase to misread a SHAPE-modified nucleotide and then counting the resulting mutations by massively parallel sequencing. The SHAPE-MaP approach measures the structure of large and transcriptome-wide systems as accurately as for simple model RNAs. This protocol describes the experimental steps, implemented over three days, required to perform SHAPE probing and construct multiplexed SHAPE-MaP libraries suitable for deep sequencing. These steps include RNA folding and SHAPE structure probing, mutational profiling by reverse transcription, library construction, and sequencing. Automated processing of MaP sequencing data is accomplished using two software packages. ShapeMapper converts raw sequencing files into mutational profiles, creates SHAPE reactivity plots, and provides useful troubleshooting information, often within an hour. SuperFold uses these data to model RNA secondary structures, identify regions with well-defined structures, and visualize probable and alternative helices, often in under a day. We illustrate these algorithms with the E. coli thiamine pyrophosphate riboswitch, E. coli 16S rRNA, and HIV-1 genomic RNAs. SHAPE-MaP can be used to make nucleotide-resolution biophysical measurements of individual RNA motifs, rare components of complex RNA ensembles, and entire transcriptomes. The straightforward MaP strategy greatly expands the number, length, and complexity of analyzable RNA structures. PMID:26426499

  13. Measuring the matter energy density and Hubble parameter from large scale structure

    SciTech Connect

    Lee, Seokcheon

    2014-02-01

    We investigate the method to measure both the present value of the matter energy density contrast and the Hubble parameter directly from the measurement of the linear growth rate which is obtained from the large scale structure of the Universe. From this method, one can obtain the value of the nuisance cosmological parameter Ω{sub m0} (the present value of the matter energy density contrast) within 3% error if the growth rate measurement can be reached z > 3.5. One can also investigate the evolution of the Hubble parameter without any prior on the value of H{sub 0} (the current value of the Hubble parameter). Especially, estimating the Hubble parameter are insensitive to the errors on the measurement of the normalized growth rate fσ{sub 8}. However, this method requires the high z (z > 3.5) measurement of the growth rate in order to get the less than 5% errors on the measurements of H(z) at z ≤ 1.2 with the redshift bin Δz = 0.2. Thus, this will be suitable for the next generation large scale structure galaxy surveys like WFMOS and LSST.

  14. Airborne-Measured Spatially-Averaged Temperature and Moisture Turbulent Structure Parameters Over a Heterogeneous Surface

    NASA Astrophysics Data System (ADS)

    Platis, Andreas; Martinez, Daniel; Bange, Jens

    2014-05-01

    Turbulent structure parameters of temperature and humidity can be derived from scintillometer measurements along horizontal paths of several 100 m to several 10 km. These parameters can be very useful to estimate the vertical turbulent heat fluxes at the surface (applying MOST). However, there are many assumptions required by this method which can be checked using in situ data, e.g. 1) Were CT2 and CQ2 correctly derived from the initial CN2 scintillometer data (structure parameter of density fluctuations or refraction index, respectively)? 2) What is the influence of the surround hetereogeneous surface regarding its footprint and the weighted averaging effect of the scintillometer method 3) Does MOST provide the correct turbulent fluxes from scintillometer data. To check these issues, in situ data from low-level flight measurements are well suited, since research aircraft cover horizontal distances in very short time (Taylor's hypothesis of a frozen turbulence structure can be applyed very likely). From airborne-measured time series the spatial series are calculated and then their structure functions that finally provide the structure parameters. The influence of the heterogeneous surface can be controlled by the definition of certain moving-average window sizes. A very useful instrument for this task are UAVs since they can fly very low and maintain altitude very precisely. However, the data base of such unmanned operations is still quite thin. So in this contribution we want to present turbulence data obtained with the Helipod, a turbulence probe hanging below a manned helicopter. The structure parameters of temperature and moisture, CT2 and CQ2, in the lower convective boundary layer were derived from data measured using the Helipod in 2003. The measurements were carried out during the LITFASS03 campaign over a heterogeneous land surface around the boundary-layer field site of the Lindenberg Meteorological Observatory-Richard-Aßmann-Observatory (MOL) of the

  15. Influence of Choice of Null Network on Small-World Parameters of Structural Correlation Networks

    PubMed Central

    Hosseini, S. M. Hadi; Kesler, Shelli R.

    2013-01-01

    In recent years, coordinated variations in brain morphology (e.g., volume, thickness) have been employed as a measure of structural association between brain regions to infer large-scale structural correlation networks. Recent evidence suggests that brain networks constructed in this manner are inherently more clustered than random networks of the same size and degree. Thus, null networks constructed by randomizing topology are not a good choice for benchmarking small-world parameters of these networks. In the present report, we investigated the influence of choice of null networks on small-world parameters of gray matter correlation networks in healthy individuals and survivors of acute lymphoblastic leukemia. Three types of null networks were studied: 1) networks constructed by topology randomization (TOP), 2) networks matched to the distributional properties of the observed covariance matrix (HQS), and 3) networks generated from correlation of randomized input data (COR). The results revealed that the choice of null network not only influences the estimated small-world parameters, it also influences the results of between-group differences in small-world parameters. In addition, at higher network densities, the choice of null network influences the direction of group differences in network measures. Our data suggest that the choice of null network is quite crucial for interpretation of group differences in small-world parameters of structural correlation networks. We argue that none of the available null models is perfect for estimation of small-world parameters for correlation networks and the relative strengths and weaknesses of the selected model should be carefully considered with respect to obtained network measures. PMID:23840672

  16. Influence of choice of null network on small-world parameters of structural correlation networks.

    PubMed

    Hosseini, S M Hadi; Kesler, Shelli R

    2013-01-01

    In recent years, coordinated variations in brain morphology (e.g., volume, thickness) have been employed as a measure of structural association between brain regions to infer large-scale structural correlation networks. Recent evidence suggests that brain networks constructed in this manner are inherently more clustered than random networks of the same size and degree. Thus, null networks constructed by randomizing topology are not a good choice for benchmarking small-world parameters of these networks. In the present report, we investigated the influence of choice of null networks on small-world parameters of gray matter correlation networks in healthy individuals and survivors of acute lymphoblastic leukemia. Three types of null networks were studied: 1) networks constructed by topology randomization (TOP), 2) networks matched to the distributional properties of the observed covariance matrix (HQS), and 3) networks generated from correlation of randomized input data (COR). The results revealed that the choice of null network not only influences the estimated small-world parameters, it also influences the results of between-group differences in small-world parameters. In addition, at higher network densities, the choice of null network influences the direction of group differences in network measures. Our data suggest that the choice of null network is quite crucial for interpretation of group differences in small-world parameters of structural correlation networks. We argue that none of the available null models is perfect for estimation of small-world parameters for correlation networks and the relative strengths and weaknesses of the selected model should be carefully considered with respect to obtained network measures.

  17. Surface structures of cerium oxide nanocrystalline particles from the size dependence of the lattice parameters

    NASA Astrophysics Data System (ADS)

    Tsunekawa, S.; Ito, S.; Kawazoe, Y.

    2004-10-01

    Cerium oxide nanocrystalline particles are synthesized and monodispersed in the size range from 2 to 8nm in diameter. The dependence of the lattice parameters on particle size is obtained by x-ray and electron diffraction analyses. The size dependence well coincides with the estimation based on the assumption that the surface is composed of one layer of Ce2O3 and the inside consists of CeO2. The effect of particle size on lattice parameters is discussed from the differences in the fabrication method and the surface structure.

  18. Least-squares sequential parameter and state estimation for large space structures

    NASA Technical Reports Server (NTRS)

    Thau, F. E.; Eliazov, T.; Montgomery, R. C.

    1982-01-01

    This paper presents the formulation of simultaneous state and parameter estimation problems for flexible structures in terms of least-squares minimization problems. The approach combines an on-line order determination algorithm, with least-squares algorithms for finding estimates of modal approximation functions, modal amplitudes, and modal parameters. The approach combines previous results on separable nonlinear least squares estimation with a regression analysis formulation of the state estimation problem. The technique makes use of sequential Householder transformations. This allows for sequential accumulation of matrices required during the identification process. The technique is used to identify the modal prameters of a flexible beam.

  19. Interlocking order parameter fluctuations in structural transitions between adsorbed polymer phases.

    PubMed

    Martins, Paulo H L; Bachmann, Michael

    2016-01-21

    By means of contact-density chain-growth simulations of a simple coarse-grained lattice model for a polymer grafted at a solid homogeneous substrate, we investigate the complementary behavior of the numbers of surface-monomer and monomer-monomer contacts under various solvent and thermal conditions. This pair of contact numbers represents an appropriate set of order parameters that enables the distinct discrimination of significantly different compact phases of polymer adsorption. Depending on the transition scenario, these order parameters can interlock in perfect cooperation. The analysis helps understand the transitions from compact filmlike adsorbed polymer conformations into layered morphologies and dissolved adsorbed structures, respectively, in more detail.

  20. Under proper control, oxidation of proteins with known chemical structure provides an accurate and absolute method for the determination of their molar concentration.

    PubMed

    Guermant, C; Azarkan, M; Smolders, N; Baeyens-Volant, D; Nijs, M; Paul, C; Brygier, J; Vincentelli, J; Looze, Y

    2000-01-01

    Oxidation at 120 degrees C of inorganic and organic (including amino acids, di- and tripeptides) model compounds by K(2)Cr(2)O(7) in the presence of H(2)SO(4) (mass fraction: 0.572), Ag(2)SO(4) (catalyst), and HgSO(4) results in the quantitative conversion of their C-atoms into CO(2) within 24 h or less. Under these stressed, well-defined conditions, the S-atoms present in cysteine and cystine residues are oxidized into SO(3) while, interestingly, the oxidation states of all the other (including the N-) atoms normally present in a protein do remain quite unchanged. When the chemical structure of a given protein is available, the total number of electrons the protein is able to transfer to K(2)Cr(2)O(7) and thereof, the total number of moles of Cr(3+) ions which the protein is able to generate upon oxidation can be accurately calculated. In such cases, unknown protein molar concentrations can thus be determined through straightforward spectrophotometric measurements of Cr(3+) concentrations. The values of molar absorption coefficients for several well-characterized proteins have been redetermined on this basis and observed to be in excellent agreement with the most precise values reported in the literature, which fully assesses the validity of the method. When applied to highly purified proteins of known chemical structure (more generally of known atomic composition), this method is absolute and accurate (+/-1%). Furthermore, it is well adapted to series measurements since available commercial kits for chemical oxygen demand (COD) measurements can readily be adapted to work under the experimental conditions recommended here for the protein assay. PMID:10610688

  1. Complete regional waveform modeling to estimate seismic velocity structure and source parameters for CTBT monitoring

    SciTech Connect

    Bredbeck, T; Rodgers, A; Walter, W

    1999-07-23

    The velocity structures and source parameters estimated by waveform modeling provide valuable information for CTBT monitoring. The inferred crustal and uppermost mantle structures advance understanding of tectonics and guides regionalization for event location and identification efforts. Estimation of source parameters such as seismic moment, depth and mechanism (whether earthquake, explosion or collapse) is crucial to event identification. In this paper we briefly outline some of the waveform modeling research for CTBT monitoring performed in the last year. In the future we will estimate structure for new regions by modeling waveforms of large well-observed events along additional paths. Of particular interest will be the estimation of velocity structure in aseismic regions such as most of Africa and the Former Soviet Union. Our previous work on aseismic regions in the Middle East, north Africa and south Asia give us confidence to proceed with our current methods. Using the inferred velocity models we plan to estimate source parameters for smaller events. It is especially important to obtain seismic moments of earthquakes for use in applying the Magnitude-Distance Amplitude Correction (MDAC; Taylor et al., 1999) to regional body-wave amplitudes for discrimination and calibrating the coda-based magnitude scales.

  2. The identification of a distributed parameter model for a flexible structure

    NASA Technical Reports Server (NTRS)

    Banks, H. T.; Gates, S. S.; Rosen, I. G.; Wang, Y.

    1986-01-01

    A computational method is developed for the estimation of parameters in a distributed model for a flexible structure. The structure we consider (part of the RPL experiment) consists of a cantilevered beam with a thruster and linear accelerometer at the free end. The thruster is fed by a pressurized hose whose horizontal motion effects the transverse vibration of the beam. The Euler-Bernoulli theory is used to model the vibration of the beam and treat the hose-thruster assembly as a lumped or point mass-dashpot-spring system at the tip. Using measurements of linear acceleration at the tip, it is estimated that the parameters (mass, stiffness, damping) and a Voight-Kelvin viscoelastic structural damping parameter for the beam using a least squares fit to the data. Spline based approximations to the hybrid (coupled ordinary and partial differential equations) system are considered; theoretical convergence results and numerical studies with both simulation and actual experimental data obtained from the structure are presented and discussed.

  3. Inrush Current Simulation of Two Windings Power Transformer using Machine Parameters Estimated by Design Procedure of Winding Structure

    NASA Astrophysics Data System (ADS)

    Tokunaga, Yoshitaka; Kubota, Kunihiro

    This paper presents estimation techniques of machine parameters for two windings power transformer using design procedure of winding structure. Especially, it is very difficult to obtain machine parameters for transformers in customers' facilities. Using estimation techniques, machine parameters could be calculated from the only nameplate data of these transformers. Subsequently, EMTP-ATP simulation of the inrush current was carried out using machine parameters estimated by design procedure of winding structure and simulation results were reproduced measured waveforms.

  4. Sub-diffusive scattering parameter maps recovered using wide-field high-frequency structured light imaging

    PubMed Central

    Kanick, Stephen Chad; McClatchy, David M.; Krishnaswamy, Venkataramanan; Elliott, Jonathan T.; Paulsen, Keith D.; Pogue, Brian W.

    2014-01-01

    This study investigates the hypothesis that structured light reflectance imaging with high spatial frequency patterns (fx) can be used to quantitatively map the anisotropic scattering phase function distribution (P(θs)) in turbid media. Monte Carlo simulations were used in part to establish a semi-empirical model of demodulated reflectance (Rd) in terms of dimensionless scattering (μs′fx−1) and γ, a metric of the first two moments of the P(θs) distribution. Experiments completed in tissue-simulating phantoms showed that simultaneous analysis of Rd spectra sampled at multiple fx in the frequency range [0.05-0.5] mm−1 allowed accurate estimation of both μs′(λ) in the relevant tissue range [0.4-1.8] mm−1, and γ(λ) in the range [1.4-1.75]. Pilot measurements of a healthy volunteer exhibited γ-based contrast between scar tissue and surrounding normal skin, which was not as apparent in wide field diffuse imaging. These results represent the first wide-field maps to quantify sub-diffuse scattering parameters, which are sensitive to sub-microscopic tissue structures and composition, and therefore, offer potential for fast diagnostic imaging of ultrastructure on a size scale that is relevant to surgical applications. PMID:25360357

  5. Flight parameters monitoring system for tracking structural integrity of rotary-wing aircraft

    NASA Technical Reports Server (NTRS)

    Mohammadi, Jamshid; Olkiewicz, Craig

    1994-01-01

    Recent developments in advanced monitoring systems used in conjunction with tracking structural integrity of rotary-wing aircraft are explained. The paper describes: (1) an overview of rotary-wing aircraft flight parameters that are critical to the aircraft loading conditions and each parameter's specific requirements in terms of data collection and processing; (2) description of the monitoring system and its functions used in a survey of rotary-wing aircraft; and (3) description of the method of analysis used for the data. The paper presents a newly-developed method in compiling flight data. The method utilizes the maneuver sequence of events in several pre-identified flight conditions to describe various flight parameters at three specific weight ranges.

  6. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  7. Magnetic fields, plasma densities, and plasma beta parameters estimated from high-frequency zebra fine structures

    NASA Astrophysics Data System (ADS)

    Karlický, M.; Jiricka, K.

    2002-10-01

    Using the recent model of the radio zebra fine structures (Ledenev et al. 2001) the magnetic fields, plasma densities, and plasma beta parameters are estimated from high-frequency zebra fine structures. It was found that in the flare radio source of high-frequency (1-2 GHz) zebras the densities and magnetic fields vary in the intervals of (1-4)×1010 cm-3 and 40-230 G, respectively. Assuming then the flare temperature as about of 107K, the plasma beta parameters in the zebra radio sources are in the 0.05-0.81 interval. Thus the plasma pressure effects in such radio sources, especially in those with many zebra lines, are not negligible.

  8. On-orbit nonlinear structural parameters realization via artificial neural network

    SciTech Connect

    Gluck, R.; Dai, H.; Karplus, W.J.

    1994-09-01

    Structural parameters realization is formulated as a pattern recognition problem. Candidate mathematical models are designated as `patterns` with which computer simulations are conducted to generate simulated system responses. Patterns are organized into pattern classes in a topdown dichotomous manner based on the variation of the simulated system responses such that the coherence property of patterns within any pattern class is embedded. An adaptive neural network serves as a pattern classifier. The actual response of the real world system is classified as the pattern class of the most similar system response to determine the most probable mathematical descriptors of structural parameters. The proposed methodology was successfully applied to the realization of the disturbance damping torques at the alpha gimbals of the Phase I Space Station Freedom model. Our experimental data were obtained analytically by simulation with additive Gaussian noise. The results are encouraging, showing a high percentage of correct classification in a noisy environment. 9 refs.

  9. Investigation of Tsunami Hydrodynamic Parameters in Inundation Zones with Different Structural Layouts

    NASA Astrophysics Data System (ADS)

    Ozer Sozdinler, Ceren; Yalciner, Ahmet Cevdet; Zaytsev, Andrey

    2015-03-01

    In this study, we analyze the tsunami parameter "hydrodynamic demand" (HD) using advanced numerical modeling. The HD can be defined as the square of the Froude number, which represents the relative value of the drag force (damage level) of tsunami waves in the inundation zone. The other key hydrodynamic parameters investigated in this study include maximum flow depth (inundation depth), maximum current velocity and its direction, and maximum water elevation and discharge flux occurring during tsunami inundation. The analyses are performed on regular-shaped basins with various orientations and distribution of coastal and land structures in order to provide comparisons of the results in a number of different case studies. We also provide information for defining damage levels in residential areas and for testing the performance of coastal protection structures.

  10. Experimental demonstration on structure-parameter dependence of photonic crystal optical spectrum.

    PubMed

    Wang, Chunxia; Kan, Qiang; Xu, Xingsheng; Du, Wei; Chen, Hongda

    2009-02-01

    We present fabrication and experimental measurement of a series of photonic crystal waveguides and coupled structure of PC waveguide and PC micro-cavity. The complete devices consist of an injector taper down from 3 microm into a triangular-lattice air-holes single-line-defect waveguide. We fabricated these devices on a silicon-on-insulator substrate and characterized them using tunable laser source. We've obtained high-efficiency light propagation and broad flat spectrum response of photonic-crystal waveguides. A sharp attenuation at photonic crystal waveguide mode edge was observed for most structures. The edge of guided band is shifted about 31 nm with the 10 nm increase of lattice constant. Mode resonance was observed in coupled structure. Our experimental results indicate that the optical spectra of photonic crystal are very sensitive to structure parameters. PMID:19441451

  11. Structural characterization of coagulant Moringa oleifera Lectin and its effect on hemostatic parameters.

    PubMed

    Luz, Luciana de Andrade; Silva, Mariana Cristina Cabral; Ferreira, Rodrigo da Silva; Santana, Lucimeire Aparecida; Silva-Lucca, Rosemeire Aparecida; Mentele, Reinhard; Oliva, Maria Luiza Vilela; Paiva, Patricia Maria Guedes; Coelho, Luana Cassandra Breitenbach Barroso

    2013-07-01

    Lectins are carbohydrate recognition proteins. cMoL, a coagulant Moringa oleifera Lectin, was isolated from seeds of the plant. Structural studies revealed a heat-stable and pH resistant protein with 101 amino acids, 11.67 theoretical pI and 81% similarity with a M. oleifera flocculent protein. Secondary structure content was estimated as 46% α-helix, 12% β-sheets, 17% β-turns and 25% unordered structures belonging to the α/β tertiary structure class. cMoL significantly prolonged the time required for blood coagulation, activated partial thromboplastin (aPTT) and prothrombin times (PT), but was not so effective in prolonging aPTT in asialofetuin presence. cMoL acted as an anticoagulant protein on in vitro blood coagulation parameters and at least on aPTT, the lectin interacted through the carbohydrate recognition domain. PMID:23537800

  12. Estimating free-body modal parameters from tests of a constrained structure

    NASA Technical Reports Server (NTRS)

    Cooley, Victor M.

    1993-01-01

    Hardware advances in suspension technology for ground tests of large space structures provide near on-orbit boundary conditions for modal testing. Further advances in determining free-body modal properties of constrained large space structures have been made, on the analysis side, by using time domain parameter estimation and perturbing the stiffness of the constraints over multiple sub-tests. In this manner, passive suspension constraint forces, which are fully correlated and therefore not usable for spectral averaging techniques, are made effectively uncorrelated. The technique is demonstrated with simulated test data.

  13. Temperature dependence diode parameters studies of Al/CuPc/n-Si/Al structure

    NASA Astrophysics Data System (ADS)

    Kumar, Ratnesh; Kaur, Ramneek; Sharma, Mamta; Kaur, Maninder; Tripathi, S. K.

    2015-08-01

    This paper presents the fabrication of Al/CuPc/n-Si/Al metal-organic-semiconductor diode. The copper phthalocyanine as organic layer is deposited on Si substrate by thermal evaporation technique. The temperature dependent current-voltage measurements are performed on Al/CuPc/n-Si structure. The important diode parameters i.e. the barrier height and ideality factor have been calculated. The temperature dependence of barrier height and ideality factor has been studied.

  14. Parameter degeneracy in neutrino oscillation — Solution network and structural overview

    NASA Astrophysics Data System (ADS)

    Minakata, Hisakazu; Uchinami, Shoichi

    2010-04-01

    It is known that there is a phenomenon called “parameter degeneracy” in neutrino oscillation measurement of lepton mixing parameters; A set of the oscillation probabilities, e.g., P( ν μ → ν e ) and its CP-conjugate Pleft( {{{bar ν }_μ } to {{bar ν }_e}} right) at a particular neutrino energy does not determine uniquely the values of θ 13 and δ. With use of the approximate form of the oscillation probability á la Cervera et al., a complete analysis of the eightfold parameter degeneracy is presented. We propose a unified view of the various types of the degeneracy as invariance of the oscillation probabilities under discrete mappings of the mixing parameters. Explicit form of the mapping is obtained either by symmetry argument, or by deriving exact analytic expressions of all the degeneracy solutions for a given true solution. Due to the one-to-one mapping structure the degeneracy solutions are shown to form a network. We extend our analysis into the parameter degeneracy in T- and CPT-conjugate measurement as well as to the setup with the golden and the silver channels, P( ν e → ν μ ) and P( ν e → ν τ ). Some characteristic features of the degeneracy solutions in CP-conjugate measurement, in particular their energy dependences, are illuminated by utilizing the explicit analytic solutions.

  15. Global Bifurcation Structure and Parameter Dependence of the Hodgkin-Huxley Equations

    NASA Astrophysics Data System (ADS)

    Pan, Zhenxing; Doi, Shinji

    The Hodgkin-Huxley (HH) equations of a squid giant axon are the most important mathematical model in electrophysiology and biology, and are also important in the development of various biologically inspired intelligent devices such as artificial neuron device and neural networks. The HH equations, however, include various constants or parameters whose values were determined based on physiological experiments, and thus the values possess inherent ambiguities. Also, the ‘constants’ are not really constant but change temporally. Thus, in this paper, we study the effects of the change of the constants or parameters on the dynamics of the HH equations and consider the parameter dependence and sensitivity of the equations; we study the bifurcation structure of the HH equations by changing their various parameters. In particular, we take the voltage-dependency of the dynamics of so-called gating variables as typical bifurcation parameters and show that the HH dynamics is very sensitive to the steady-state functions but not sensitive to the time ‘constants’ of gating variables.

  16. Explicitly integrating parameter, input, and structure uncertainties into Bayesian Neural Networks for probabilistic hydrologic forecasting

    SciTech Connect

    Zhang, Xuesong; Liang, Faming; Yu, Beibei; Zong, Ziliang

    2011-11-09

    Estimating uncertainty of hydrologic forecasting is valuable to water resources and other relevant decision making processes. Recently, Bayesian Neural Networks (BNNs) have been proved powerful tools for quantifying uncertainty of streamflow forecasting. In this study, we propose a Markov Chain Monte Carlo (MCMC) framework to incorporate the uncertainties associated with input, model structure, and parameter into BNNs. This framework allows the structure of the neural networks to change by removing or adding connections between neurons and enables scaling of input data by using rainfall multipliers. The results show that the new BNNs outperform the BNNs that only consider uncertainties associated with parameter and model structure. Critical evaluation of posterior distribution of neural network weights, number of effective connections, rainfall multipliers, and hyper-parameters show that the assumptions held in our BNNs are not well supported. Further understanding of characteristics of different uncertainty sources and including output error into the MCMC framework are expected to enhance the application of neural networks for uncertainty analysis of hydrologic forecasting.

  17. A versatile phenomenological model for the S-shaped temperature dependence of photoluminescence energy for an accurate determination of the exciton localization energy in bulk and quantum well structures

    NASA Astrophysics Data System (ADS)

    Dixit, V. K.; Porwal, S.; Singh, S. D.; Sharma, T. K.; Ghosh, Sandip; Oak, S. M.

    2014-02-01

    Temperature dependence of the photoluminescence (PL) peak energy of bulk and quantum well (QW) structures is studied by using a new phenomenological model for including the effect of localized states. In general an anomalous S-shaped temperature dependence of the PL peak energy is observed for many materials which is usually associated with the localization of excitons in band-tail states that are formed due to potential fluctuations. Under such conditions, the conventional models of Varshni, Viña and Passler fail to replicate the S-shaped temperature dependence of the PL peak energy and provide inconsistent and unrealistic values of the fitting parameters. The proposed formalism persuasively reproduces the S-shaped temperature dependence of the PL peak energy and provides an accurate determination of the exciton localization energy in bulk and QW structures along with the appropriate values of material parameters. An example of a strained InAs0.38P0.62/InP QW is presented by performing detailed temperature and excitation intensity dependent PL measurements and subsequent in-depth analysis using the proposed model. Versatility of the new formalism is tested on a few other semiconductor materials, e.g. GaN, nanotextured GaN, AlGaN and InGaN, which are known to have a significant contribution from the localized states. A quantitative evaluation of the fractional contribution of the localized states is essential for understanding the temperature dependence of the PL peak energy of bulk and QW well structures having a large contribution of the band-tail states.

  18. Towards accurate structural characterization of metal centres in protein crystals: the structures of Ni and Cu T{sub 6} bovine insulin derivatives

    SciTech Connect

    Frankaer, Christian Grundahl; Mossin, Susanne; Ståhl, Kenny; Harris, Pernille

    2014-01-01

    The level of structural detail around the metal sites in Ni{sup 2+} and Cu{sup 2+} T{sub 6} insulin derivatives was significantly improved by using a combination of single-crystal X-ray crystallography and X-ray absorption spectroscopy. Photoreduction and subsequent radiation damage of the Cu{sup 2+} sites in Cu insulin was followed by XANES spectroscopy. Using synchrotron radiation (SR), the crystal structures of T{sub 6} bovine insulin complexed with Ni{sup 2+} and Cu{sup 2+} were solved to 1.50 and 1.45 Å resolution, respectively. The level of detail around the metal centres in these structures was highly limited, and the coordination of water in Cu site II of the copper insulin derivative was deteriorated as a consequence of radiation damage. To provide more detail, X-ray absorption spectroscopy (XAS) was used to improve the information level about metal coordination in each derivative. The nickel derivative contains hexacoordinated Ni{sup 2+} with trigonal symmetry, whereas the copper derivative contains tetragonally distorted hexacoordinated Cu{sup 2+} as a result of the Jahn–Teller effect, with a significantly longer coordination distance for one of the three water molecules in the coordination sphere. That the copper centre is of type II was further confirmed by electron paramagnetic resonance (EPR). The coordination distances were refined from EXAFS with standard deviations within 0.01 Å. The insulin derivative containing Cu{sup 2+} is sensitive towards photoreduction when exposed to SR. During the reduction of Cu{sup 2+} to Cu{sup +}, the coordination geometry of copper changes towards lower coordination numbers. Primary damage, i.e. photoreduction, was followed directly by XANES as a function of radiation dose, while secondary damage in the form of structural changes around the Cu atoms after exposure to different radiation doses was studied by crystallography using a laboratory diffractometer. Protection against photoreduction and subsequent

  19. A modal test of a space-truss for structural parameter identification

    SciTech Connect

    Carne, T.G.; Mayes, R.L.; Levine-West, M.B.

    1992-12-01

    The Jet Propulsion Laboratory is developing a large space-truss to support a micro-precision interferometer. A finite element model will be used to design and place passive and active elements in the truss to suppress vibration. To improve the model`s predictive capability, it is desirable to identify uncertain structural parameters in the model by utilizing experimental modal data. Testing of both the components and the system was performed to obtain the data necessary to identify the structural parameters. Extracting a modal model, absent of bias errors, from measured data requires great care in test design and implementation. Testing procedures that are discussed include: verification of non-constraining shaker attachment, quantification of the non-linear structural response, and the design and effects of suspension systems used to simulate a free structure. In addition to these procedures, the accuracy of the measured frequency response functions are evaluated by comparing functions measured with random excitation, using various frequency resolutions, and with step sine excitation.

  20. A modal test of a space-truss for structural parameter identification

    SciTech Connect

    Carne, T.G.; Mayes, R.L. ); Levine-West, M.B. )

    1992-01-01

    The Jet Propulsion Laboratory is developing a large space-truss to support a micro-precision interferometer. A finite element model will be used to design and place passive and active elements in the truss to suppress vibration. To improve the model's predictive capability, it is desirable to identify uncertain structural parameters in the model by utilizing experimental modal data. Testing of both the components and the system was performed to obtain the data necessary to identify the structural parameters. Extracting a modal model, absent of bias errors, from measured data requires great care in test design and implementation. Testing procedures that are discussed include: verification of non-constraining shaker attachment, quantification of the non-linear structural response, and the design and effects of suspension systems used to simulate a free structure. In addition to these procedures, the accuracy of the measured frequency response functions are evaluated by comparing functions measured with random excitation, using various frequency resolutions, and with step sine excitation.

  1. Developing Dynamic Digital Image Techniques with Continuous Parameters to Detect Structural Damage

    PubMed Central

    Sung, Wen-Pei

    2013-01-01

    Several earthquakes with strong magnitude occurred globally at various locations, especially the unforgettable tsunami disaster caused by the earthquake in Indonesia and Japan. If the characteristics of structures can be well understood to implement new technology, the damages caused by most natural disasters can be significantly alleviated. In this research, dynamic digital image correlation method for using continuous parameter is applied for developing a low-cost digital image correlation coefficient method with advanced digital cameras and high-speed computers. The experimental study using cantilever test object with defect control confirms that the vibration mode calculated using this proposed method can highly express the defect locations. This proposed method combined with the sensitivity of Inter-Story Drift Mode Shape, IDMS, can also reveal the damage degree of damage structure. These test and analysis results indicate that this proposed method is high enough for applying to achieve the object of real-time online monitoring of structure. PMID:24023530

  2. Review of parameters influencing the structural response of a submerged body under cavitation conditions

    NASA Astrophysics Data System (ADS)

    Escaler, X.; De La Torre, O.; Farhat, M.

    2015-12-01

    Submerged structures that operate under extreme flows are prone to suffer large scale cavitation attached to their surfaces. Under such conditions the added mass effects differ from the expected ones in pure liquids. Moreover, the existence of small gaps between the structure and surrounding bodies filled with fluid also influence the dynamic response. A series of experiments and numerical simulations have been carried out with a truncated NACA0009 hydrofoil mounted as a cantilever beam at the LMH-EPFL cavitation tunnel. The three first modes of vibration have been determined and analysed under various hydrodynamic conditions ranging from air and still water to partial cavitation and supercavitation. A remote nonintrusive excitation system with piezoelectric patches has been used for the experiments. The effects of the cavity properties and the lateral gap size on the natural frequencies and mode shapes have been determined. As a result, the significance of several parameters in the design of such structures is discussed.

  3. Benchmarking Density Functionals on Structural Parameters of Small-/Medium-Sized Organic Molecules.

    PubMed

    Brémond, Éric; Savarese, Marika; Su, Neil Qiang; Pérez-Jiménez, Ángel José; Xu, Xin; Sancho-García, Juan Carlos; Adamo, Carlo

    2016-02-01

    In this Letter we report the error analysis of 59 exchange-correlation functionals in evaluating the structural parameters of small- and medium-sized organic molecules. From this analysis, recently developed double hybrids, such as xDH-PBE0, emerge as the most reliable methods, while global hybrids confirm their robustness in reproducing molecular structures. Notably the M06-L density functional is the only semilocal method reaching an accuracy comparable to hybrids'. A comparison with errors obtained on energetic databases (including thermochemistry, reaction barriers, and interaction energies) indicate that most of the functionals have a coherent behavior, showing low (or high) deviations on both energy and structure data sets. Only a few of them are more prone toward one of these two properties. PMID:26730741

  4. Parameter Stability of the Functional–Structural Plant Model GREENLAB as Affected by Variation within Populations, among Seasons and among Growth Stages

    PubMed Central

    Ma, Yuntao; Li, Baoguo; Zhan, Zhigang; Guo, Yan; Luquet, Delphine; de Reffye, Philippe; Dingkuhn, Michael

    2007-01-01

    Background and Aims It is increasingly accepted that crop models, if they are to simulate genotype-specific behaviour accurately, should simulate the morphogenetic process generating plant architecture. A functional–structural plant model, GREENLAB, was previously presented and validated for maize. The model is based on a recursive mathematical process, with parameters whose values cannot be measured directly and need to be optimized statistically. This study aims at evaluating the stability of GREENLAB parameters in response to three types of phenotype variability: (1) among individuals from a common population; (2) among populations subjected to different environments (seasons); and (3) among different development stages of the same plants. Methods Five field experiments were conducted in the course of 4 years on irrigated fields near Beijing, China. Detailed observations were conducted throughout the seasons on the dimensions and fresh biomass of all above-ground plant organs for each metamer. Growth stage-specific target files were assembled from the data for GREENLAB parameter optimization. Optimization was conducted for specific developmental stages or the entire growth cycle, for individual plants (replicates), and for different seasons. Parameter stability was evaluated by comparing their CV with that of phenotype observation for the different sources of variability. A reduced data set was developed for easier model parameterization using one season, and validated for the four other seasons. Key Results and Conclusions The analysis of parameter stability among plants sharing the same environment and among populations grown in different environments indicated that the model explains some of the inter-seasonal variability of phenotype (parameters varied less than the phenotype itself), but not inter-plant variability (parameter and phenotype variability were similar). Parameter variability among developmental stages was small, indicating that parameter

  5. Effect of lateral structure parameters of SiGe HBTs on synthesized active inductors

    NASA Astrophysics Data System (ADS)

    Yan-Xiao, Zhao; Wan-Rong, Zhang; Huang, Xin; Hong-Yun, Xie; Dong-Yue, Jin; Qiang, Fu

    2016-03-01

    The effect of lateral structure parameters of transistors including emitter width, emitter length, and emitter stripe number on the performance parameters of the active inductor (AI), such as the effective inductance Ls, quality factor Q, and self-resonant frequency ω0 is analyzed based on 0.35-μm SiGe BiCMOS process. The simulation results show that for AI operated under fixed current density JC, the HBT lateral structure parameters have significant effect on Ls but little influence on Q and ω0, and the larger Ls can be realized by the narrow, short emitter stripe and few emitter stripes of SiGe HBTs. On the other hand, for AI with fixed HBT size, smaller JC is beneficial for AI to obtain larger Ls, but with a cost of smaller Q and ω0. In addition, under the fixed collector current IC, the larger the size of HBT is, the larger Ls becomes, but the smaller Q and ω0 become. The obtained results provide a reference for selecting geometry of transistors and operational condition in the design of active inductors. Project supported by the Natural Science Foundation of Beijing, China (Grant Nos. 4142007 and 4122014), the National Natural Science Foundation of China (Grant No. 61574010), and the Higher Educational Science and Technology Program of Shandong Province, China (Grant No. J13LN09).

  6. Predicting hydration Gibbs energies of alkyl-aromatics using molecular simulation: a comparison of current force fields and the development of a new parameter set for accurate solvation data.

    PubMed

    Garrido, Nuno M; Jorge, Miguel; Queimada, António J; Gomes, José R B; Economou, Ioannis G; Macedo, Eugénia A

    2011-10-14

    The Gibbs energy of hydration is an important quantity to understand the molecular behavior in aqueous systems at constant temperature and pressure. In this work we review the performance of some popular force fields, namely TraPPE, OPLS-AA and Gromos, in reproducing the experimental Gibbs energies of hydration of several alkyl-aromatic compounds--benzene, mono-, di- and tri-substituted alkylbenzenes--using molecular simulation techniques. In the second part of the paper, we report a new model that is able to improve such hydration energy predictions, based on Lennard Jones parameters from the recent TraPPE-EH force field and atomic partial charges obtained from natural population analysis of density functional theory calculations. We apply a scaling factor determined by fitting the experimental hydration energy of only two solutes, and then present a simple rule to generate atomic partial charges for different substituted alkyl-aromatics. This rule has the added advantages of eliminating the unnecessary assumption of fixed charge on every substituted carbon atom and providing a simple guideline for extrapolating the charge assignment to any multi-substituted alkyl-aromatic molecule. The point charges derived here yield excellent predictions of experimental Gibbs energies of hydration, with an overall absolute average deviation of less than 0.6 kJ mol(-1). This new parameter set can also give good predictive performance for other thermodynamic properties and liquid structural information.

  7. Nodal gap structure and order parameter symmetry of the unconventional superconductor UPt₃

    DOE PAGES

    Gannon, W. J.; Halperin, W. P.; Rastovski, C.; Schlesinger, K. J.; Hlevyack, J.; Eskildsen, M. R.; Vorontsov, A. B.; Gavilano, J.; Gasser, U.; Nagy, G.

    2015-02-01

    Spanning a broad range of physical systems, complex symmetry breaking is widely recognized as a hallmark of competing interactions. This is exemplified in superfluid ³He which has multiple thermodynamic phases with spin and orbital quantum numbers S = 1 and L = 1, that emerge on cooling from a nearly ferromagnetic Fermi liquid. The heavy fermion compound UPt₃ exhibits similar behavior clearly manifest in its multiple superconducting phases. However, consensus as to its order parameter symmetry has remained elusive. Our small angle neutron scattering measurements indicate a linear temperature dependence of the London penetration depth characteristic of nodal structure ofmore » the order parameter. Our theoretical analysis is consistent with assignment of its symmetry to an L = 3 odd parity state for which one of the three thermodynamic phases in non-zero magnetic field is chiral.« less

  8. Evaluation and optimization of the structural parameter of diesel nozzle basing on synchrotron radiation imaging techniques

    NASA Astrophysics Data System (ADS)

    Wu, Z.; Gao, Y.; Gong, H.; Li, L.

    2016-04-01

    Lacking of efficient methods, industry currently uses one only parameter—fuel flow rate—to evaluate the nozzle quality, which is far from satisfying the current emission regulations worldwide. By utilizing synchrotron radiation high energy X-ray in Shanghai Synchrotron Radiation Facility (SSRF), together with the imaging techniques, the 3D models of two nozzles with the same design dimensions were established, and the influence of parameters fluctuation in the azimuthal direction were analyzed in detail. Results indicate that, due to the orifice misalignment, even with the same design dimension, the inlet rounding radius of orifices differs greatly, and its fluctuation in azimuthal direction is also large. This difference will cause variation in the flow characteristics at orifice outlet and then further affect the spray characteristics. The study also indicates that, more precise investigation and insight into the evaluation and optimization of diesel nozzle structural parameter are needed.

  9. Nodal gap structure and order parameter symmetry of the unconventional superconductor UPt₃

    SciTech Connect

    Gannon, W. J.; Halperin, W. P.; Rastovski, C.; Schlesinger, K. J.; Hlevyack, J.; Eskildsen, M. R.; Vorontsov, A. B.; Gavilano, J.; Gasser, U.; Nagy, G.

    2015-02-01

    Spanning a broad range of physical systems, complex symmetry breaking is widely recognized as a hallmark of competing interactions. This is exemplified in superfluid ³He which has multiple thermodynamic phases with spin and orbital quantum numbers S = 1 and L = 1, that emerge on cooling from a nearly ferromagnetic Fermi liquid. The heavy fermion compound UPt₃ exhibits similar behavior clearly manifest in its multiple superconducting phases. However, consensus as to its order parameter symmetry has remained elusive. Our small angle neutron scattering measurements indicate a linear temperature dependence of the London penetration depth characteristic of nodal structure of the order parameter. Our theoretical analysis is consistent with assignment of its symmetry to an L = 3 odd parity state for which one of the three thermodynamic phases in non-zero magnetic field is chiral.

  10. Cold dark matter haloes in the Planck era: evolution of structural parameters for Einasto and NFW profiles

    NASA Astrophysics Data System (ADS)

    Dutton, Aaron A.; Macciò, Andrea V.

    2014-07-01

    We present the evolution of the structure of relaxed cold dark matter (CDM) haloes in the cosmology from the Planck satellite. Our simulations cover five decades in halo mass, from dwarf galaxies to galaxy clusters. Because of the increased matter density and power spectrum normalization the concentration-mass relation in the Planck cosmology has a ˜20 per cent higher normalization at redshift z = 0 compared to Wilkinson Microwave Anisotropy Probe cosmology. We confirm that CDM haloes are better described by the Einasto profile; for example, at scales near galaxy half-light radii CDM haloes have significantly steeper density profiles than implied by Navarro-Frenk-White (NFW) fits. There is a scatter of ˜0.2 dex in the Einasto shape parameter at fixed halo mass, adding further to the diversity of CDM halo profiles. The evolution of the concentration-mass relation in our simulations is not reproduced by any of the analytic models in the literature. We thus provide a simple fitting formula that accurately describes the evolution between redshifts z = 5 and 0 for both NFW and Einasto fits. Finally, the observed concentrations and halo masses of spiral galaxies, groups and clusters of galaxies at low redshifts are in good agreement with our simulations, suggesting only mild halo response to galaxy formation on these scales.

  11. Accurate crystal-structure refinement of Ca3Ga2Ge4O14 at 295 and 100 K and analysis of the disorder in the atomic positions

    NASA Astrophysics Data System (ADS)

    Dudka, A. P.; Mill', B. V.

    2013-07-01

    The accurate X-ray diffraction study of a Ca3Ga2Ge4O14 crystal (sp. gr. P321, Z = 1) has been performed using repeated X-ray diffraction data sets collected on a diffractometer equipped with a CCD area detector at 295 and 100 K. The asymmetric disorder in the atomic positions in Ca3Ga2Ge4O14 is described in two alternative ways: with the use of anharmonic atomic displacements (at 295 K R/wR = 0.68/0.60%, 3754 reflections; at 100 K R/wR = 0.90/0.70%, 3632 reflections) and using a split model (SM) (at 295 K R/wR = 0.74/0.67%; at 100 K R/wR = 0.95/0.74%). An analysis of the probability density function that defines the probability of finding an atom at a particular point in space shows that, at 295 K, five of the seven independent atoms in the unit cell are asymmetrically disordered in the vicinity of their sites, whereas only three atoms are disordered at 100 K. At both temperatures the largest disorder is observed at the 3 f site on a twofold axis, which is a prerequisite for the formation of helicoidal chains of atoms along the c axis of the crystal and can serve as a structural basis for multiferroic properties of this family of crystals with magnetic ions.

  12. The influence of porosity and structural parameters on different kinds of gas hydrate dissociation

    PubMed Central

    Misyura, S. Y.

    2016-01-01

    Methane hydrate dissociation at negative temperatures was studied experimentally for different artificial and natural samples, differing by macro- and micro-structural parameters. Four characteristic dissociation types are discussed in the paper. The internal kinetics of artificial granule gas hydrates and clathrate hydrates in coal is dependent on the porosity, defectiveness and gas filtration rate. The density of pores distribution in the crust of formed ice decreases by the several orders of magnitude and this change significantly the rate of decay. Existing models for describing dissociation at negative temperatures do not take into account the structural parameters of samples. The dissociation is regulated by internal physical processes that must be considered in the simulation. Non-isothermal dissociation with constant external heat flux was simulated numerically. The dissociation is simulated with consideration of heat and mass transfer, kinetics of phase transformation and gas filtering through a porous medium of granules for the negative temperatures. It is shown that the gas hydrate dissociation in the presence of mainly microporous structures is fundamentally different from the disintegration of gas hydrates containing meso and macropores. PMID:27445113

  13. Earthquake focal parameters and lithospheric structure of the anatolian plateau from complete regional waveform modeling

    SciTech Connect

    Rodgers, A

    2000-12-28

    This is an informal report on preliminary efforts to investigate earthquake focal mechanisms and earth structure in the Anatolian (Turkish) Plateau. Seismic velocity structure of the crust and upper mantle and earthquake focal parameters for event in the Anatolian Plateau are estimated from complete regional waveforms. Focal mechanisms, depths and seismic moments of moderately large crustal events are inferred from long-period (40-100 seconds) waveforms and compared with focal parameters derived from global teleseismic data. Using shorter periods (10-100 seconds) we estimate the shear and compressional velocity structure of the crust and uppermost mantle. Results are broadly consistent with previous studies and imply relatively little crustal thickening beneath the central Anatolian Plateau. Crustal thickness is about 35 km in western Anatolia and greater than 40 km in eastern Anatolia, however the long regional paths require considerable averaging and limit resolution. Crustal velocities are lower than typical continental averages, and even lower than typical active orogens. The mantle P-wave velocity was fixed to 7.9 km/s, in accord with tomographic models. A high sub-Moho Poisson's Ratio of 0.29 was required to fit the Sn-Pn differential times. This is suggestive of high sub-Moho temperatures, high shear wave attenuation and possibly partial melt. The combination of relatively thin crust in a region of high topography and high mantle temperatures suggests that the mantle plays a substantial role in maintaining the elevation.

  14. THE ADVANCED CAMERA FOR SURVEYS GENERAL CATALOG: STRUCTURAL PARAMETERS FOR APPROXIMATELY HALF A MILLION GALAXIES

    SciTech Connect

    Griffith, Roger L.; Kirkpatrick, J. Davy; Cooper, Michael C.; Newman, Jeffrey A.; Moustakas, Leonidas A.; Stern, Daniel; Comerford, Julia M.; Davis, Marc; Lotz, Jennifer M.; Koekemoer, Anton M.; Barden, Marco; Conselice, Christopher J.; Capak, Peter L.; Scoville, Nick; Sheth, Kartik; Shopbell, Patrick; Faber, S. M.; Koo, David C.; Willmer, Christopher N. A.; and others

    2012-05-01

    We present the Advanced Camera for Surveys General Catalog (ACS-GC), a photometric and morphological database using publicly available data obtained with the Advanced Camera for Surveys (ACS) instrument on the Hubble Space Telescope. The goal of the ACS-GC database is to provide a large statistical sample of galaxies with reliable structural and distance measurements to probe the evolution of galaxies over a wide range of look-back times. The ACS-GC includes approximately 470,000 astronomical sources (stars + galaxies) derived from the AEGIS, COSMOS, GEMS, and GOODS surveys. GALAPAGOS was used to construct photometric (SEXTRACTOR) and morphological (GALFIT) catalogs. The analysis assumes a single Sersic model for each object to derive quantitative structural parameters. We include publicly available redshifts from the DEEP2, COMBO-17, TKRS, PEARS, ACES, CFHTLS, and zCOSMOS surveys to supply redshifts (spectroscopic and photometric) for a considerable fraction ({approx}74%) of the imaging sample. The ACS-GC includes color postage stamps, GALFIT residual images, and photometry, structural parameters, and redshifts combined into a single catalog.

  15. The influence of porosity and structural parameters on different kinds of gas hydrate dissociation.

    PubMed

    Misyura, S Y

    2016-01-01

    Methane hydrate dissociation at negative temperatures was studied experimentally for different artificial and natural samples, differing by macro- and micro-structural parameters. Four characteristic dissociation types are discussed in the paper. The internal kinetics of artificial granule gas hydrates and clathrate hydrates in coal is dependent on the porosity, defectiveness and gas filtration rate. The density of pores distribution in the crust of formed ice decreases by the several orders of magnitude and this change significantly the rate of decay. Existing models for describing dissociation at negative temperatures do not take into account the structural parameters of samples. The dissociation is regulated by internal physical processes that must be considered in the simulation. Non-isothermal dissociation with constant external heat flux was simulated numerically. The dissociation is simulated with consideration of heat and mass transfer, kinetics of phase transformation and gas filtering through a porous medium of granules for the negative temperatures. It is shown that the gas hydrate dissociation in the presence of mainly microporous structures is fundamentally different from the disintegration of gas hydrates containing meso and macropores. PMID:27445113

  16. The influence of porosity and structural parameters on different kinds of gas hydrate dissociation

    NASA Astrophysics Data System (ADS)

    Misyura, S. Y.

    2016-07-01

    Methane hydrate dissociation at negative temperatures was studied experimentally for different artificial and natural samples, differing by macro- and micro-structural parameters. Four characteristic dissociation types are discussed in the paper. The internal kinetics of artificial granule gas hydrates and clathrate hydrates in coal is dependent on the porosity, defectiveness and gas filtration rate. The density of pores distribution in the crust of formed ice decreases by the several orders of magnitude and this change significantly the rate of decay. Existing models for describing dissociation at negative temperatures do not take into account the structural parameters of samples. The dissociation is regulated by internal physical processes that must be considered in the simulation. Non-isothermal dissociation with constant external heat flux was simulated numerically. The dissociation is simulated with consideration of heat and mass transfer, kinetics of phase transformation and gas filtering through a porous medium of granules for the negative temperatures. It is shown that the gas hydrate dissociation in the presence of mainly microporous structures is fundamentally different from the disintegration of gas hydrates containing meso and macropores.

  17. The influence of porosity and structural parameters on different kinds of gas hydrate dissociation.

    PubMed

    Misyura, S Y

    2016-07-22

    Methane hydrate dissociation at negative temperatures was studied experimentally for different artificial and natural samples, differing by macro- and micro-structural parameters. Four characteristic dissociation types are discussed in the paper. The internal kinetics of artificial granule gas hydrates and clathrate hydrates in coal is dependent on the porosity, defectiveness and gas filtration rate. The density of pores distribution in the crust of formed ice decreases by the several orders of magnitude and this change significantly the rate of decay. Existing models for describing dissociation at negative temperatures do not take into account the structural parameters of samples. The dissociation is regulated by internal physical processes that must be considered in the simulation. Non-isothermal dissociation with constant external heat flux was simulated numerically. The dissociation is simulated with consideration of heat and mass transfer, kinetics of phase transformation and gas filtering through a porous medium of granules for the negative temperatures. It is shown that the gas hydrate dissociation in the presence of mainly microporous structures is fundamentally different from the disintegration of gas hydrates containing meso and macropores.

  18. Essential Parameters for Structural Analysis and Dereplication by 1H NMR Spectroscopy

    PubMed Central

    2015-01-01

    The present study demonstrates the importance of adequate precision when reporting the δ and J parameters of frequency domain 1H NMR (HNMR) data. Using a variety of structural classes (terpenoids, phenolics, alkaloids) from different taxa (plants, cyanobacteria), this study develops rationales that explain the importance of enhanced precision in NMR spectroscopic analysis and rationalizes the need for reporting Δδ and ΔJ values at the 0.1–1 ppb and 10 mHz level, respectively. Spectral simulations paired with iteration are shown to be essential tools for complete spectral interpretation, adequate precision, and unambiguous HNMR-driven dereplication and metabolomic analysis. The broader applicability of the recommendation relates to the physicochemical properties of hydrogen (1H) and its ubiquity in organic molecules, making HNMR spectra an integral component of structure elucidation and verification. Regardless of origin or molecular weight, the HNMR spectrum of a compound can be very complex and encode a wealth of structural information that is often obscured by limited spectral dispersion and the occurrence of higher order effects. This altogether limits spectral interpretation, confines decoding of the underlying spin parameters, and explains the major challenge associated with the translation of HNMR spectra into tabulated information. On the other hand, the reproducibility of the spectral data set of any (new) chemical entity is essential for its structure elucidation and subsequent dereplication. Handling and documenting HNMR data with adequate precision is critical for establishing unequivocal links between chemical structure, analytical data, metabolomes, and biological activity. Using the full potential of HNMR spectra will facilitate the general reproducibility for future studies of bioactive chemicals, especially of compounds obtained from the diversity of terrestrial and marine organisms. PMID:24895010

  19. Using Crystal Structure Groups to Understand Mössbauer parameters of Ferric Sulfates

    NASA Astrophysics Data System (ADS)

    Knutson, J.; Dyar, M. D.; Sklute, E. C.; Lane, M. D.; Bishop, J. L.

    2008-12-01

    A Mössbauer doublet assigned to ferric sulfate (Fe3D2) was identified in Paso Robles, Mars, spectra by Morris et al. (2006), who noted that its parameters are not diagnostic of any specific mineral because a number of different sulfates with varying parageneses might be responsible for this doublet. Work by Lane et al. (2008) used a multi-instrument approach based on Fe3+ sulfate spectra acquired with VNIR and midinfrared reflectance, mid-infrared emission and Mössbauer spectrometers to narrow down the possible ferric sulfate phases present at Paso Robles to ferricopiapite possibly mixed with other ferric sulfates such as butlerite, parabutlerite, fibroferrite, or metahomanite. Thus, we explore here the crystal-chemical rationale behind these interpretations of the Mössbauer results, using similarities and difference among mineral structures to explore which phases might have similar coordination polyhedra around the Fe atoms in sulfates. Work by Hawthorne et al. (2000) organizes the sulfate minerals into groups with analogous crystal structures. Mössbauer doublets assigned to ferric sulfates ubiquitously have isomer shifts (IS) of 0.40-53 mm/s so that IS is non-diagnostic. However, quadrupole splitting of doublets in these mineral groups has a wide range (0-1.4 mm/s) and the variation can be systematically correlated with different structure types. Members of the hydration series Fe2(SO4)3 · n H2O, which includes quenstedtite, coquimbite, paracoquimbite, kornelite, and lausenite have Mössbauer spectra that closely resemble singlets because of their near-zero QS. These minerals share structures involving finite clusters of sulfate tetrahedral and Fe octahedral or chains of depolymerized clusters, and all mineral species with these structures share similar Mössbauer parameters. At the other extreme, ferric sulfates with structures based on infinite sheets (hydrotalcite, alunite, jarosite), tend to have large electric field gradients at the nucleus of the Fe3

  20. Estimating Rheological Parameters of Anhydrite from Folded Evaporite sequences: Implications for Internal Dynamics of Salt Structure

    NASA Astrophysics Data System (ADS)

    Adamuszek, Marta; Dabrowski, Marcin; Schmalholz, Stefan M.; Urai, Janos L.; Raith, Alexander

    2015-04-01

    Salt structures have been identified as a potential target for hydrocarbon, CO2, or radioactive waste storage. The most suitable locations for magazines are considered in the thick and relatively homogeneous rock salt layers. However, salt structures often consist of the evaporite sequence including rock salt intercalated with other rock types e.g.: anhydrite, gypsum, potassium and magnesium salt, calcite, dolomite, or shale. The presence of such heterogeneities causes a serious disturbance in the structure management. Detailed analysis of the internal architecture and internal dynamics of the salt structure are crucial for evaluating them as suitable repositories and also their long-term stability. The goal of this study is to analyse the influence of the presence of anhydrite layers on the internal dynamics of salt structures. Anhydrite is a common rock in evaporite sequences. Its physical and mechanical properties strongly differ from the properties of rock salt. The density of anhydrite is much higher than the density of salt, thus anhydrite is likely to sink in salt causing the disturbance of the surrounding structures. This suggestion was the starting point to the discussion about the long-term stability of the magazines in salt structures [1]. However, the other important parameter that has to be taken into account is the viscosity of anhydrite. The high viscosity ratio between salt and anhydrite can restrain the layer from sinking. The rheological behaviour of anhydrite has been studied in laboratory experiments [2], but the results only provide information about the short-term behaviour. The long-term behaviour can be best predicted using indirect methods e.g. based on the analysis of natural structures that developed over geological time scale. One of the most promising are fold structures, the shape of which is very sensitive to the rheological parameters of the deforming materials. Folds can develop in mechanically stratified materials during layer

  1. Recent Developments in Parameter Estimation and Structure Identification of Biochemical and Genomic Systems

    PubMed Central

    Chou, I-Chun; Voit, Eberhard O.

    2009-01-01

    The organization, regulation and dynamical responses of biological systems are in many cases too complex to allow intuitive predictions and require the support of mathematical modeling for quantitative assessments and a reliable understanding of system functioning. All steps of constructing mathematical models for biological systems are challenging, but arguably the most difficult task among them is the estimation of model parameters and the identification of the structure and regulation of the underlying biological networks. Recent advancements in modern high-throughput techniques have been allowing the generation of time series data that characterize the dynamics of genomic, proteomic, metabolic, and physiological responses and enable us, at least in principle, to tackle estimation and identification tasks using “top-down” or “inverse” approaches. While the rewards of a successful inverse estimation or identification are great, the process of extracting structural and regulatory information is technically difficult. The challenges can generally be categorized into four areas, namely, issues related to the data, the model, the mathematical structure of the system, and the optimization and support algorithms. Many recent articles have addressed inverse problems within the modeling framework of Biochemical Systems Theory (BST). BST was chosen for these tasks because of its unique structural flexibility and the fact that the structure and regulation of a biological system are mapped essentially one-to-one onto the parameters of the describing model. The proposed methods mainly focused on various optimization algorithms, but also on support techniques, including methods for circumventing the time consuming numerical integration of systems of differential equations, smoothing overly noisy data, estimating slopes of time series, reducing the complexity of the inference task, and constraining the parameter search space. Other methods targeted issues of data

  2. Microwave spectrum and structural parameters for the formamide-formic acid dimer.

    PubMed

    Daly, Adam M; Sargus, Bryan A; Kukolich, Stephen G

    2010-11-01

    The rotational spectra for six isotopologues of the complex formed between formamide and formic acid have been measured using a pulsed-beam Fourier transform microwave spectrometer and analyzed to obtain rotational constants and quadrupole coupling parameters. The rotational constants and quadrupole coupling strengths obtained for H  (12)COOH-H(2)  (14)NCOH are A = 5889.465(2), B = 2148.7409(7), 1575.1234(6), eQq(aa) = 1.014(5), eQq(bb) = 1.99(1), and eQq(cc) = -3.00(1) MHz. Using the 15 rotational constants obtained for the H  (13)COOH, HCOOD, DCOOH, and H(2)  (15)NCHO isotopologues, key structural parameters were obtained from a least-squares structure fit. Hydrogen bond distances of 1.78 Å for R(O3⋯H1) and 1.79 Å for R(H4⋯O1) were obtained. The "best fit" value for the angle(C-O-H) of formic acid is significantly larger than the monomer value of 106.9° with an optimum value of 121.7(3)°. The complex is nearly planar with inertial defect Δ = -0.158 amu  Å(2). The formamide proton is moved out of the molecular plane by 15(3)° for the best fit structure. Density functional theory using B3PW91, HCTH407, and TPSS as well as MP2 and CCSD calculations were performed using 6-311++G(d,p) and the results were compared to experimentally determined parameters.

  3. Importance of including small body spin effects in the modelling of intermediate mass-ratio inspirals. II. Accurate parameter extraction of strong sources using higher-order spin effects

    NASA Astrophysics Data System (ADS)

    Huerta, E. A.; Gair, Jonathan R.; Brown, Duncan A.

    2012-03-01

    -4, and 10-1, respectively. LISA should also be able to determine the location of the source in the sky and the SMBH spin orientation to within ˜10-4 steradians. Furthermore, we show that by including conservative corrections up to 2.5PN order, systematic errors no longer dominate over statistical errors. This shows that search templates that include small body spin effects in the equations of motion up to 2.5PN order should allow us to perform accurate parameter extraction for IMRIs with typical signal-to-noise ratio ˜1000.

  4. Vibration suppression of distributed parameter flexible structures by Integral Consensus Control

    NASA Astrophysics Data System (ADS)

    Omidi, Ehsan; Mahmoodi, S. Nima

    2016-03-01

    Integral Consensus Control (ICC) is proposed and implemented in this paper for the first time, as a novel approach for vibration control in distributed parameter flexible structures. The ICC consists of multiple parallel first-order lossy integrators, with the goal of targeting all major participating resonant modes in the oscillation of the structure. The vibration control design is taken to a different level, by integrating the concept of consensus control design into the new dynamics. Each control patch on the flexible structure is considered as a node of a network, and a communication topology with consensus control terms are augmented in the controller design dynamics. The result is an effective vibration controller, which is also robust to failures and inconsistencies in the control system. A cantilever is used as a sample flexible structure to investigate the control method. Multi-agent representation of the system, state estimator dynamics and the ICC model are designed for the structure. Extensive numerical simulations have been conducted to show the suppression performance of the ICC under different input disturbances. A comparative study is presented to show the advantage of the decentralized design over the conventional centralized approach. The new consensus control design provides new possibilities to vibration control problems, where an effective, robust and synchronized suppression is needed.

  5. Determination of Structural and Electronic Parameters of Antimony Complex, from Theoretical Calculations

    NASA Astrophysics Data System (ADS)

    Catikkas, Berna; Kosar, Ismail

    2016-06-01

    In this study, ground states of antimony (Sbv) with organic ligands complexes were studied by using density functional theory hybrid methods in order to obtain structural, electronic and vibrational spectral parameters. The mapping molecular electrostatic potential surface of the molecules computed to information about the charge density distribution of the molecules and its chemical reactivity. Frontier molecule orbital properties, HOMO and LUMO energies, global descriptors, and the total density of state diagram analysis were performed by using the time-dependent density functional theory. For the learning nonlinear optical properties, polarizability and hyperpolarizability tensors of the molecule were calculated.

  6. Estimation of the refractive-index temperature structure parameter over the ocean.

    PubMed

    Friehe, C A

    1977-02-01

    The semiempirical equation of Wyngaard, Izumi, and Collins is combined with the bulk aerodynamic formulas to provide equations for the estimation of C(T)(2) (the refractive-index temperature structure parameter) in the atmospheric boundary layer above the sea. The equations relate C(T)(2) to easily measured quantities of average wind speed and air-sea temperature and moisture differences. Comparison with limited C(T)(2) data obtained in the marine boundary layer suggests that the estimation equations are satisfactory.

  7. Parameter identification and synchronization for uncertain network group with different structures

    NASA Astrophysics Data System (ADS)

    Li, Chengren; Lü, Ling; Sun, Ying; Wang, Ying; Wang, Wenjun; Sun, Ao

    2016-09-01

    We design a novel synchronization technique to research the synchronization of network group constituted of uncertain networks with different structures. Based on Lyapunov theorem, the selection principles of the control inputs and the parameter identification laws of the networks are determined, and synchronization conditions of the network group are obtained. Some numerical simulations are provided to verify the correctness and effectiveness of the synchronization technique. We find that the network number, the number of network nodes and network connections indeed will not affect the stability of synchronization of network group.

  8. Morphological parameters of a Spitzer survey of stellar structure in galaxies

    SciTech Connect

    Holwerda, B. W.; Muñoz-Mateos, J.-C.; Sheth, K.; Kim, T.; Meidt, S.; Mizusawa, T.; Hinz, J. L.; Zaritsky, D.; Regan, M. W.; Gil de Paz, A.; Menéndez-Delmestre, K.; Seibert, M.; Ho, L. C.; Gadotti, D. A.; Erroz-Ferrer, S. E-mail: benne.holwerda@gmail.com [Instituto de Astrofísica de Canarias, Vía Láctea s and others

    2014-01-20

    The morphology of galaxies can be quantified to some degree using a set of scale-invariant parameters. Concentration (C), asymmetry (A), smoothness (S), the Gini index (G), the relative contribution of the brightest pixels to the second-order moment of the flux (M {sub 20}), ellipticity (E), and the Gini index of the second-order moment (G{sub M} ) have all been applied to morphologically classify galaxies at various wavelengths. Here, we present a catalog of these parameters for the Spitzer Survey of stellar structure in Galaxies, a volume-limited, near-infrared (NIR) imaging survey of nearby galaxies using the 3.6 and 4.5 μm channels of the Infrared Array Camera on board the Spitzer Space Telescope. Our goal is to provide a reference catalog of NIR quantified morphology for high-redshift studies and galaxy evolution models with enough detail to resolve stellar mass morphology. We explore where normal, non-interacting galaxies—those typically found on the Hubble tuning fork—lie in this parameter space and show that there is a tight relation between concentration (C {sub 82}) and M {sub 20} for normal galaxies. M {sub 20} can be used to classify galaxies into earlier and later types (i.e., to separate spirals from irregulars). Several criteria using these parameters exist to select systems with a disturbed morphology, i.e., those that appear to be undergoing a tidal interaction. We examine the applicability of these criteria to Spitzer NIR imaging. We find that four relations, based on the parameters A and S, G and M {sub 20}, G{sub M} , C, and M {sub 20}, respectively, select outliers in morphological parameter space, but each selects different subsets of galaxies. Two criteria (G{sub M} > 0.6, G > –0.115 × M {sub 20} + 0.384) seem most appropriate to identify possible mergers and the merger fraction in NIR surveys. We find no strong relation between lopsidedness and most of these morphological parameters, except for a weak dependence of lopsidedness on

  9. An all fiber-optic multi-parameter structure health monitoring system.

    PubMed

    Hu, Chennan; Yu, Zhihao; Wang, Anbo

    2016-09-01

    In this work, we present an all fiber-optics based multi-parameter structure health monitoring system, which is able to monitor strain, temperature, crack and thickness of metal structures. This system is composed of two optical fibers, one for laser-acoustic excitation and the other for acoustic detection. A nano-second 1064 nm pulse laser was used for acoustic excitation and a 2 mm fiber Bragg grating was used to detect the acoustic vibration. The feasibility of this system was demonstrated on an aluminum test piece by the monitoring of the temperature, strain and thickness changes, as well as the appearance of an artificial crack. The multiplexing capability of this system was also preliminarily demonstrated.

  10. Structural and functional parameters of the flaviviral protease: a promising antiviral drug target

    PubMed Central

    Shiryaev, Sergey A; Strongin, Alex Y

    2010-01-01

    Flaviviruses have a single-strand, positive-polarity RNA genome that encodes a single polyprotein. The polyprotein is comprised of seven nonstructural (NS) and three structural proteins. The N- and C-terminal parts of NS3 represent the serine protease and the RNA helicase, respectively. The cleavage of the polyprotein by the protease is required to produce the individual viral proteins, which assemble a new viral progeny. Conversely, inactivation of the protease blocks viral infection. Both the protease and the helicase are conserved among flaviviruses. As a result, NS3 is a promising drug target in flaviviral infections. This article examines the West Nile virus NS3 with an emphasis on the structural and functional parameters of the protease, the helicase and their cofactors. PMID:21076642

  11. An all fiber-optic multi-parameter structure health monitoring system.

    PubMed

    Hu, Chennan; Yu, Zhihao; Wang, Anbo

    2016-09-01

    In this work, we present an all fiber-optics based multi-parameter structure health monitoring system, which is able to monitor strain, temperature, crack and thickness of metal structures. This system is composed of two optical fibers, one for laser-acoustic excitation and the other for acoustic detection. A nano-second 1064 nm pulse laser was used for acoustic excitation and a 2 mm fiber Bragg grating was used to detect the acoustic vibration. The feasibility of this system was demonstrated on an aluminum test piece by the monitoring of the temperature, strain and thickness changes, as well as the appearance of an artificial crack. The multiplexing capability of this system was also preliminarily demonstrated. PMID:27607635

  12. Influence of structural parameters on tunable photonic band gaps modulated by liquid crystals

    NASA Astrophysics Data System (ADS)

    Huang, Aiqin; Zheng, Jihong; Jiang, Yanmeng; Zhou, Zengjun; Tang, Pingyu; Zhuang, Songlin

    2011-10-01

    Tunable photonic crystals (PCs), which are infiltrated with nematic liquid crystals (LCs), tune photonic band gap (PBG) by rotating directors of LCs when applied with the external electrical field. Using the plane wave expansion method, we simulated the PBG structure of two-dimensional tunable PCs with a triangular lattice of circular column, square column and hexagon column, respectively. When PCs are composed of LCs and different substrate materials such as germanium (Ge) and silicon (Si), the influence of structural parameters including column shape and packing ration on PBG is discussed separately. Numerical simulations show that absolute PBG can't be found at any conditions, however large tuning range of polarized wave can be achieved by rotating directors of LCs. The simulation results provide theoretical guidance for the fabrication of field-sensitive polarizer with big tunable band range.

  13. Statistical Evaluation of the Identified Structural Parameters of an idling Offshore Wind Turbine

    NASA Astrophysics Data System (ADS)

    Kramers, Hendrik C.; van der Valk, Paul L. C.; van Wingerden, Jan-Willem

    2016-09-01

    With the increased need for renewable energy, new offshore wind farms are being developed at an unprecedented scale. However, as the costs of offshore wind energy are still too high, design optimization and new innovations are required for lowering its cost. The design of modern day offshore wind turbines relies on numerical models for estimating ultimate and fatigue loads of the turbines. The dynamic behavior and the resulting structural loading of the turbines is determined for a large part by its structural properties, such as the natural frequencies and damping ratios. Hence, it is important to obtain accurate estimates of these modal properties. For this purpose stochastic subspace identification (SSI), in combination with clustering and statistical evaluation methods, is used to obtain the variance of the identified modal properties of an installed 3.6MW offshore wind turbine in idling conditions. It is found that one is able to obtain confidence intervals for the means of eigenfrequencies and damping ratios of the fore-aft and side-side modes of the wind turbine.

  14. Design optimization of structural parameters for highly sensitive photonic crystal label-free biosensors.

    PubMed

    Ju, Jonghyun; Han, Yun-ah; Kim, Seok-min

    2013-01-01

    The effects of structural design parameters on the performance of nano-replicated photonic crystal (PC) label-free biosensors were examined by the analysis of simulated reflection spectra of PC structures. The grating pitch, duty, scaled grating height and scaled TiO2 layer thickness were selected as the design factors to optimize the PC structure. The peak wavelength value (PWV), full width at half maximum of the peak, figure of merit for the bulk and surface sensitivities, and surface/bulk sensitivity ratio were also selected as the responses to optimize the PC label-free biosensor performance. A parametric study showed that the grating pitch was the dominant factor for PWV, and that it had low interaction effects with other scaled design factors. Therefore, we can isolate the effect of grating pitch using scaled design factors. For the design of PC-label free biosensor, one should consider that: (1) the PWV can be measured by the reflection peak measurement instruments, (2) the grating pitch and duty can be manufactured using conventional lithography systems, and (3) the optimum design is less sensitive to the grating height and TiO2 layer thickness variations in the fabrication process. In this paper, we suggested a design guide for highly sensitive PC biosensor in which one select the grating pitch and duty based on the limitations of the lithography and measurement system, and conduct a multi objective optimization of the grating height and TiO2 layer thickness for maximizing performance and minimizing the influence of parameter variation. Through multi-objective optimization of a PC structure with a fixed grating height of 550 nm and a duty of 50%, we obtained a surface FOM of 66.18 RIU-1 and an S/B ratio of 34.8%, with a grating height of 117 nm and TiO2 height of 210 nm.

  15. Design optimization of structural parameters for highly sensitive photonic crystal label-free biosensors.

    PubMed

    Ju, Jonghyun; Han, Yun-ah; Kim, Seok-min

    2013-01-01

    The effects of structural design parameters on the performance of nano-replicated photonic crystal (PC) label-free biosensors were examined by the analysis of simulated reflection spectra of PC structures. The grating pitch, duty, scaled grating height and scaled TiO2 layer thickness were selected as the design factors to optimize the PC structure. The peak wavelength value (PWV), full width at half maximum of the peak, figure of merit for the bulk and surface sensitivities, and surface/bulk sensitivity ratio were also selected as the responses to optimize the PC label-free biosensor performance. A parametric study showed that the grating pitch was the dominant factor for PWV, and that it had low interaction effects with other scaled design factors. Therefore, we can isolate the effect of grating pitch using scaled design factors. For the design of PC-label free biosensor, one should consider that: (1) the PWV can be measured by the reflection peak measurement instruments, (2) the grating pitch and duty can be manufactured using conventional lithography systems, and (3) the optimum design is less sensitive to the grating height and TiO2 layer thickness variations in the fabrication process. In this paper, we suggested a design guide for highly sensitive PC biosensor in which one select the grating pitch and duty based on the limitations of the lithography and measurement system, and conduct a multi objective optimization of the grating height and TiO2 layer thickness for maximizing performance and minimizing the influence of parameter variation. Through multi-objective optimization of a PC structure with a fixed grating height of 550 nm and a duty of 50%, we obtained a surface FOM of 66.18 RIU-1 and an S/B ratio of 34.8%, with a grating height of 117 nm and TiO2 height of 210 nm. PMID:23470487

  16. Uncertainty quantification of relative acoustic nonlinearity parameter of guided waves for damage detection in composite structures

    NASA Astrophysics Data System (ADS)

    Hong, Ming; Mao, Zhu; Todd, Michael D.; Su, Zhongqing; Qing, Xinlin

    2015-03-01

    Nonlinear guided waves have been studied extensively for the characterization of micro-damage in plate-like structures, such as early-stage fatigue and thermal degradation in metals. Meanwhile, an increasing number of studies have reported the use of nonlinear acoustic techniques for detection of impact damage, fatigue, and thermal fatigue in composite structures. Among these techniques, the (relative) acoustic nonlinearity parameter, extracted from acousto-ultrasonic waves based on second-harmonic generation, has been considered one of the most popular tools for quantifying the detection of nonlinearity in inspected structures. Considering the complex nature of nonlinearities involved in composite materials (even under healthy conditions), and operational/environmental variability and measurement noise, the calculation of the relative acoustic nonlinearity parameter (RANP) from experimental data may suffer from considerable uncertainties, which may impair the quality of damage detection. In this study, we aim to quantify the uncertainty of the magnitude of the RANP estimator in the context of impact damage identification in unidirectional carbon fiber laminates. First, the principles of nonlinear ultrasonics are revisited briefly. A general probability density function of the RANP is then obtained through numerical evaluation in a theoretical setting. Using piezoelectric wavers, continuous sine waves are generated in the sample. Steady-state responses are acquired and processed to produce histograms of the RANP estimates before and after the impact damage. These observed histograms are consistent with the predicted distributions, and examination of the distributions demonstrates the significance of uncertainty quantification when using the RANP for damage detection in composite structures.

  17. Kinetic study of the anaerobic biodegradation of alkyl polyglucosides and the influence of their structural parameters.

    PubMed

    Ríos, Francisco; Fernández-Arteaga, Alejandro; Lechuga, Manuela; Jurado, Encarnación; Fernández-Serrano, Mercedes

    2016-05-01

    This paper reports a study of the anaerobic biodegradation of non-ionic surfactants alkyl polyglucosides applying the method by measurement of the biogas production in digested sludge. Three alkyl polyglucosides with different length alkyl chain and degree of polymerization of the glucose units were tested. The influence of their structural parameters was evaluated, and the characteristics parameters of the anaerobic biodegradation were determined. Results show that alkyl polyglucosides, at the standard initial concentration of 100 mgC L(-1), are not completely biodegradable in anaerobic conditions because they inhibit the biogas production. The alkyl polyglucoside having the shortest alkyl chain showed the fastest biodegradability and reached the higher percentage of final mineralization. The anaerobic process was well adjusted to a pseudo first-order equation using the carbon produced as gas during the test; also, kinetics parameters and a global rate constant for all the involved metabolic process were determined. This modeling is helpful to evaluate the biodegradation or the persistence of alkyl polyglucosides under anaerobic conditions in the environment and in the wastewater treatment.

  18. Simultaneous calibration of the intrinsic and extrinsic parameters of structured-light sensors

    NASA Astrophysics Data System (ADS)

    Xie, Zexiao; Wang, Xiaomin; Chi, Shukai

    2014-07-01

    A novel approach for simultaneously calibrating the intrinsic and extrinsic parameters of structured-light sensors is presented in this paper. A planar target etched with grid lines is adopted to generate calibration points. By intersecting the laser plane with the grid lines on the target some co-linear points are formed, and their 3-D coordinates are computed according to the rule of cross-ratio invariance. For obtaining non-colinear points in the laser plane, the sensor is located at several different positions by the moving of coordinate measuring machine (CMM). However, the co-linear points corresponding to different CMM positions locate at different coordinate frame. In order to establish conjugate pairs to calibrate the sensor, all of the generated points in the laser plane are transformed into the CMM machine coordinate frame. Then using the 3D points in this coordinate frame a 2D coordinate frame is established with determined direction vectors, i.e., the extrinsic parameters are calibrated. By transforming the 3D points in the CMM machine coordinate frame into the 2D coordinate frame, conjugate pairs for calibrating the intrinsic parameters are established. Experimental studies show that the planar target is simple, and it can be manufactured with high accuracy. The calibrating process is facilitating, and the calibration result possesses high accuracy.

  19. Structural Parameters Calibration for Binocular Stereo Vision Sensors Using a Double-Sphere Target.

    PubMed

    Wei, Zhenzhong; Zhao, Kai

    2016-01-01

    Structural parameter calibration for the binocular stereo vision sensor (BSVS) is an important guarantee for high-precision measurements. We propose a method to calibrate the structural parameters of BSVS based on a double-sphere target. The target, consisting of two identical spheres with a known fixed distance, is freely placed in different positions and orientations. Any three non-collinear sphere centres determine a spatial plane whose normal vector under the two camera-coordinate-frames is obtained by means of an intermediate parallel plane calculated by the image points of sphere centres and the depth-scale factors. Hence, the rotation matrix R is solved. The translation vector T is determined using a linear method derived from the epipolar geometry. Furthermore, R and T are refined by nonlinear optimization. We also provide theoretical analysis on the error propagation related to the positional deviation of the sphere image and an approach to mitigate its effect. Computer simulations are conducted to test the performance of the proposed method with respect to the image noise level, target placement times and the depth-scale factor. Experimental results on real data show that the accuracy of measurement is higher than 0.9‰, with a distance of 800 mm and a view field of 250 × 200 mm². PMID:27420063

  20. Structural Parameters Calibration for Binocular Stereo Vision Sensors Using a Double-Sphere Target

    PubMed Central

    Wei, Zhenzhong; Zhao, Kai

    2016-01-01

    Structural parameter calibration for the binocular stereo vision sensor (BSVS) is an important guarantee for high-precision measurements. We propose a method to calibrate the structural parameters of BSVS based on a double-sphere target. The target, consisting of two identical spheres with a known fixed distance, is freely placed in different positions and orientations. Any three non-collinear sphere centres determine a spatial plane whose normal vector under the two camera-coordinate-frames is obtained by means of an intermediate parallel plane calculated by the image points of sphere centres and the depth-scale factors. Hence, the rotation matrix R is solved. The translation vector T is determined using a linear method derived from the epipolar geometry. Furthermore, R and T are refined by nonlinear optimization. We also provide theoretical analysis on the error propagation related to the positional deviation of the sphere image and an approach to mitigate its effect. Computer simulations are conducted to test the performance of the proposed method with respect to the image noise level, target placement times and the depth-scale factor. Experimental results on real data show that the accuracy of measurement is higher than 0.9‰, with a distance of 800 mm and a view field of 250 × 200 mm2. PMID:27420063

  1. Evaluating the Spatio-Temporal Factors that Structure Network Parameters of Plant-Herbivore Interactions

    PubMed Central

    López-Carretero, Antonio; Díaz-Castelazo, Cecilia; Boege, Karina; Rico-Gray, Víctor

    2014-01-01

    Despite the dynamic nature of ecological interactions, most studies on species networks offer static representations of their structure, constraining our understanding of the ecological mechanisms involved in their spatio-temporal stability. This is the first study to evaluate plant-herbivore interaction networks on a small spatio-temporal scale. Specifically, we simultaneously assessed the effect of host plant availability, habitat complexity and seasonality on the structure of plant-herbivore networks in a coastal tropical ecosystem. Our results revealed that changes in the host plant community resulting from seasonality and habitat structure are reflected not only in the herbivore community, but also in the emergent properties (network parameters) of the plant-herbivore interaction network such as connectance, selectiveness and modularity. Habitat conditions and periods that are most stressful favored the presence of less selective and susceptible herbivore species, resulting in increased connectance within networks. In contrast, the high degree of selectivennes (i.e. interaction specialization) and modularity of the networks under less stressful conditions was promoted by the diversification in resource use by herbivores. By analyzing networks at a small spatio-temporal scale we identified the ecological factors structuring this network such as habitat complexity and seasonality. Our research offers new evidence on the role of abiotic and biotic factors in the variation of the properties of species interaction networks. PMID:25340790

  2. The fungal community structure of barley malts from diverse geographical regions correlates with malt quality parameters.

    PubMed

    Kaur, Mandeep; Bowman, John P; Stewart, Doug C; Evans, David E

    2015-12-23

    Malt is a preferred base for fermentations that produce beer or whisky. Barley for malt is grown under diverse environments in different geographical locations. Malt provides an ecological niche for a varied range of microorganisms with both positive and negative effects on its quality for brewing. Little information exists in the literature on the microbial community structure of Australian malt as well as broader global geographical differences in the associated fungal and bacterial communities. The aims of the present study were to compare the bacterial and fungal community structures of Australian commercial malt with its international counterparts originating from different geographical regions using terminal restriction fragment length polymorphism (TRFLP) fingerprinting and clone library analyses of ribosomal RNA genes. Further, the relationship between malt associated microbial communities and conventional malt quality parameters was also compared. Results showed that differences in fungal communities of malts from different geographical location were more pronounced than bacterial communities. TRFLP analysis discriminated high quality commercial malts with low fungal loads from malts deliberately infected with fungal inocula (Fusarium/Penicillium). Malt moisture, beta-amylase, α-amylase and limit dextrinase contents showed significant correlations with fungal community structure. This investigation concluded that fungal community structure was more important to subsequent malt quality outcomes than bacteria.

  3. The fungal community structure of barley malts from diverse geographical regions correlates with malt quality parameters.

    PubMed

    Kaur, Mandeep; Bowman, John P; Stewart, Doug C; Evans, David E

    2015-12-23

    Malt is a preferred base for fermentations that produce beer or whisky. Barley for malt is grown under diverse environments in different geographical locations. Malt provides an ecological niche for a varied range of microorganisms with both positive and negative effects on its quality for brewing. Little information exists in the literature on the microbial community structure of Australian malt as well as broader global geographical differences in the associated fungal and bacterial communities. The aims of the present study were to compare the bacterial and fungal community structures of Australian commercial malt with its international counterparts originating from different geographical regions using terminal restriction fragment length polymorphism (TRFLP) fingerprinting and clone library analyses of ribosomal RNA genes. Further, the relationship between malt associated microbial communities and conventional malt quality parameters was also compared. Results showed that differences in fungal communities of malts from different geographical location were more pronounced than bacterial communities. TRFLP analysis discriminated high quality commercial malts with low fungal loads from malts deliberately infected with fungal inocula (Fusarium/Penicillium). Malt moisture, beta-amylase, α-amylase and limit dextrinase contents showed significant correlations with fungal community structure. This investigation concluded that fungal community structure was more important to subsequent malt quality outcomes than bacteria. PMID:26340674

  4. Microwave, r0 Structural Parameters, Conformational Stability, and Vibrational Assignment of (Chloromethyl)fluorosilane.

    PubMed

    Guirgis, Gamil A; Sawant, Dattatray K; Brenner, Reid E; Deodhar, Bhushan S; Seifert, Nathan A; Geboes, Yannick; Pate, Brooks H; Herrebout, Wouter A; Hickman, Daniel V; Durig, James R

    2015-11-25

    The FT-microwave spectrum (6.5-26 GHz) of (chloromethyl)fluorosilane (ClCH2-SiH2F) has been recorded and 250 transitions for the parent species along with (13)C, (37)Cl, (29)Si, and (30)Si isotopologues have been assigned for trans conformer. Infrared spectra (3100 to 400 cm(-1)) of gas, solid, and the variable temperature (-100 to -60 °C) studies of the infrared spectra of the sample dissolved in xenon have been recorded. Additionally, the variable temperature (-153 to -133 °C) studies of the Raman spectra of the sample dissolved in krypton have been recorded. The enthalpy difference between the trans and gauche conformers in xenon solutions has been determined to be 109 ± 15 cm(-1) (1.47 ± 0.16 kJ mol(-1)), and in krypton solution, the enthalpy difference has been determined to be 97 ± 16 cm(-1) (1.16 ± 0.19 kJ mol(-1)) with the trans conformer as the more stable form. Approximately 46 ± 2% of the trans form is present at ambient temperature. By utilizing the microwave rotational constants of five isotopologues for trans and the structural parameters predicted from MP2(full)/6-311+G(d,p) calculations, adjusted r0 parameters have been obtained for trans conformer. The r0 structural parameter values for the trans form are for the heavy atom distances (Å): Si-F = 1.608 (3); C-Cl = 1.771 (3); Si-C = 1.884 (3); and angles (deg): ∠FSiC = 108.9 (5); ∠ClCSi = 104.9 (5). The results are discussed and compared to some related molecules. PMID:26436757

  5. Effect of chemical fixatives on accurate preservation of Escherichia coli and Bacillus subtilis structure in cells prepared by freeze-substitution

    SciTech Connect

    Graham, L.L.; Beveridge, T.J. )

    1990-04-01

    Five chemical fixatives were evaluated for their ability to accurately preserve bacterial ultrastructure during freeze-substitution of select Escherichia coli and Bacillus subtilis strains. Radioisotopes were specifically incorporated into the peptidoglycan, lipopolysaccharide, and nucleic acids of E. coli SFK11 and W7 and into the peptidoglycan and RNA of B. subtilis 168 and W23. The ease of extraction of radiolabels, as assessed by liquid scintillation counting during all stages of processing for freeze-substitution, was used as an indicator of cell structural integrity and retention of cellular chemical composition. Subsequent visual examination by electron microscopy was used to confirm ultrastructural conformation. The fixatives used were: 2% (wt/vol) osmium tetroxide and 2% (wt/vol) uranyl acetate; 2% (vol/vol) glutaraldehyde and 2% (wt/vol) uranyl acetate; 2% (vol/vol) acrolein and 2% (wt/vol) uranyl acetate; 2% (wt/vol) gallic acid; and 2% (wt/vol) uranyl acetate. All fixatives were prepared in a substitution solvent of anhydrous acetone. Extraction of cellular constituents depended on the chemical fixative used. A combination of 2% osmium tetroxide-2% uranyl acetate or 2% gallic acid alone resulted in optimum fixation as ascertained by least extraction of radiolabels. In both gram-positive and gram-negative organisms, high levels of radiolabel were detected in the processing fluids in which 2% acrolein-2% uranyl acetate, 2% glutaraldehyde-2% uranyl acetate, or 2% uranyl acetate alone were used as fixatives. Ultrastructural variations were observed in cells freeze-substituted in the presence of different chemical fixatives. We recommend the use of osmium tetroxide and uranyl acetate in acetone for routine freeze-substitution of eubacteria, while gallic acid is recommended for use when microanalytical processing necessitates the omission of osmium.

  6. Relationship between global structural parameters and Enzyme Commission hierarchy: implications for function prediction.

    PubMed

    Boareto, Marcelo; Yamagishi, Michel E B; Caticha, Nestor; Leite, Vitor B P

    2012-10-01

    In protein databases there is a substantial number of proteins structurally determined but without function annotation. Understanding the relationship between function and structure can be useful to predict function on a large scale. We have analyzed the similarities in global physicochemical parameters for a set of enzymes which were classified according to the four Enzyme Commission (EC) hierarchical levels. Using relevance theory we introduced a distance between proteins in the space of physicochemical characteristics. This was done by minimizing a cost function of the metric tensor built to reflect the EC classification system. Using an unsupervised clustering method on a set of 1025 enzymes, we obtained no relevant clustering formation compatible with EC classification. The distance distributions between enzymes from the same EC group and from different EC groups were compared by histograms. Such analysis was also performed using sequence alignment similarity as a distance. Our results suggest that global structure parameters are not sufficient to segregate enzymes according to EC hierarchy. This indicates that features essential for function are rather local than global. Consequently, methods for predicting function based on global attributes should not obtain high accuracy in main EC classes prediction without relying on similarities between enzymes from training and validation datasets. Furthermore, these results are consistent with a substantial number of studies suggesting that function evolves fundamentally by recruitment, i.e., a same protein motif or fold can be used to perform different enzymatic functions and a few specific amino acids (AAs) are actually responsible for enzyme activity. These essential amino acids should belong to active sites and an effective method for predicting function should be able to recognize them.

  7. A model-based, Bayesian characterization of subsurface corrosion parameters in composite multi-layered structures

    NASA Astrophysics Data System (ADS)

    Reed, Heather; Hoppe, Wally

    2016-02-01

    Thermographic NDE approaches to detect subsurface corrosion defects of multi-layered structures with composite top layers have proven difficult due to the fact that the thermal conductivity of composite materials is larger in lateral directions (the plane parallel to the surface) than in the through-thickness directions. This causes heat to dissipate faster laterally than through the thickness when a heat source is applied to the surface of the structure, making it difficult for subsurface damage effects to manifest on the surface, where the heat source and inspection typically occur. To address this, a heat induction approach is presented that excites the damaged, metallic bottom layer directly by Joule heating, resulting in more observable damage effects on the surface than what could be expected for traditional thermographic methods on this type of structure. To characterize the subsurface damage parameters (defect location, diameter, and depth), Bayesian inversion of numerically-simulated noisy data, using a high-fidelity, coupled electromagnetic-heat transfer model is employed. Stochastic estimation methods such as Markov chain Monte Carlo (MCMC) allow for quantification of uncertainty surrounding the damage parameters, which is important as this directly translates into uncertainty surrounding the component reliability. However, because thousands of high-fidelity finite element models are computationally costly to evaluate, as is typical in most MCMC methods, the use of Bayesian inversion is rarely feasible in real-time. To address this, a projection-based reduced order modeling (ROM) tracking and interpolation scheme is formulated within the MCMC sampling method for the multi-physics problem, resulting in significant speedup of solution time with little loss of accuracy, enabling near-real time stochastic estimation of damage.

  8. Solid state NMR characterization of structural and motional parameter distributions in polyamidoammonium dendrimers

    NASA Astrophysics Data System (ADS)

    Malyarenko, Dariya Ivanovna

    The characterization of narrow distributions of structural and motional parameters, and their evolution during the broad glass transition, is performed for deuterated PAMAM dendrimer salts using solid state NMR. The broadening of deuteron quadrupole echo (QE) lineshapes is consistent with the presence of narrow hydrogen bond length distribution (σr < 0.25 Å) at the spacer amide and branching tertiary amine sites. The temperature dependent averaging of the experimental lineshapes is explained on the basis of fast planar librations in the dendrimer interior, and fast rotation and intermediate regime libration (in an asymmetric cone) of the dendrimer termini. The amplitudes of libration are temperature dependent and higher for low generation dendrimers, while librational rates show Arrhenius behavior only within the glass transition region. In this region, the width of log-normal distribution of rates increases with temperature at sites associated with chlorine counterions. The largest distributions are still less than one order of magnitude wide, unlike the dendrimer in solution or the linear polymers. Interpenetrated low generations (G < 3), uniform intermediate generations (G = 3-5) with surface network, and backfolded high generations (G > 5), are distinguished by interior and termini dynamics. In the regime of fast motion QE lineshapes are highly sensitive to the presence of narrow structural and motional parameter distributions, and provide constraints on motional geometry independent of rates. The precise characterization of narrow log-normal rate distributions in the intermediate regime can be done using 2H magic angle spinning (MAS). Deuteron inversion-recovery techniques provide quantitative information on the rates of fast motion. For PAMAM salts, the influence of narrow distributions of structural and motional parameters, and fast planar libration, is negligible for distance determination using Rotational Echo Double Resonance (REDOR). The discrimination

  9. Compressive failure modes and parameter optimization of the trabecular structure of biomimetic fully integrated honeycomb plates.

    PubMed

    Chen, Jinxiang; Tuo, Wanyong; Zhang, Xiaoming; He, Chenglin; Xie, Juan; Liu, Chang

    2016-12-01

    To develop lightweight biomimetic composite structures, the compressive failure and mechanical properties of fully integrated honeycomb plates were investigated experimentally and through the finite element method. The results indicated that: fracturing of the fully integrated honeycomb plates primarily occurred in the core layer, including the sealing edge structure. The morphological failures can be classified into two types, namely dislocations and compactions, and were caused primarily by the stress concentrations at the interfaces between the core layer and the upper and lower laminations and secondarily by the disordered short-fiber distribution in the material; although the fully integrated honeycomb plates manufactured in this experiment were imperfect, their mass-specific compressive strength was superior to that of similar biomimetic samples. Therefore, the proposed bio-inspired structure possesses good overall mechanical properties, and a range of parameters, such as the diameter of the transition arc, was defined for enhancing the design of fully integrated honeycomb plates and improving their compressive mechanical properties. PMID:27612711

  10. Identification of Capacitive MEMS Accelerometer Structure Parameters for Human Body Dynamics Measurements

    PubMed Central

    Benevicius, Vincas; Ostasevicius, Vytautas; Gaidys, Rimvydas

    2013-01-01

    Due to their small size, low weight, low cost and low energy consumption, MEMS accelerometers have achieved great commercial success in recent decades. The aim of this research work is to identify a MEMS accelerometer structure for human body dynamics measurements. Photogrammetry was used in order to measure possible maximum accelerations of human body parts and the bandwidth of the digital acceleration signal. As the primary structure the capacitive accelerometer configuration is chosen in such a way that sensing part measures on all three axes as it is 3D accelerometer and sensitivity on each axis is equal. Hill climbing optimization was used to find the structure parameters. Proof-mass displacements were simulated for all the acceleration range that was given by the optimization problem constraints. The final model was constructed in Comsol Multiphysics. Eigenfrequencies were calculated and model's response was found, when vibration stand displacement data was fed into the model as the base excitation law. Model output comparison with experimental data was conducted for all excitation frequencies used during the experiments. PMID:23974151

  11. A simple method for extracting material parameters of multilayered MEMS structures using resonance frequency measurements

    NASA Astrophysics Data System (ADS)

    Sun, Chao; Zhou, Zai-Fa; Li, Wei-Hua; Huang, Qing-An

    2014-07-01

    Multilayered structures are increasingly used in MEMS. Based on the resonant frequency of the doubly-clamped multilayered beam, the Young’s modulus and residual stress for an individual layer have been measured by designing beam test structures for each layer with different widths. Taking into account the buckling or no buckling problem of the multilayered beam, this paper introduces a model for the resonant frequency of the beam. An approach to extract the Young’s modulus and residual stress for the individual layer is developed. The validity of this approach has been studied using finite element modeling. As a multilayered example, test structures for a gold/polysilicon bilayer beam were fabricated. A scanning laser Doppler vibrometer system was used to measure the resonant frequency of the beam. The extracted parameters are that the average value of Young’s modulus of polysilicon and gold are 133.7 GPa and 78.6 GPa with standard deviation being 4.2 GPa and 11.5 GPa, respectively; the average value of residual stress of polysilicon and gold are 13.9 MPa (compressive) and 19.7 MPa (tensile) with standard deviation being 0.47 MPa and 4.4 MPa, respectively.

  12. Identification of capacitive MEMS accelerometer structure parameters for human body dynamics measurements.

    PubMed

    Benevicius, Vincas; Ostasevicius, Vytautas; Gaidys, Rimvydas

    2013-08-22

    Due to their small size, low weight, low cost and low energy consumption, MEMS accelerometers have achieved great commercial success in recent decades. The aim of this research work is to identify a MEMS accelerometer structure for human body dynamics measurements. Photogrammetry was used in order to measure possible maximum accelerations of human body parts and the bandwidth of the digital acceleration signal. As the primary structure the capacitive accelerometer configuration is chosen in such a way that sensing part measures on all three axes as it is 3D accelerometer and sensitivity on each axis is equal. Hill climbing optimization was used to find the structure parameters. Proof-mass displacements were simulated for all the acceleration range that was given by the optimization problem constraints. The final model was constructed in Comsol Multiphysics. Eigenfrequencies were calculated and model's response was found, when vibration stand displacement data was fed into the model as the base excitation law. Model output comparison with experimental data was conducted for all excitation frequencies used during the experiments.

  13. Impact factors and the optimal parameter of acoustic structure quantification in the assessment of liver fibrosis.

    PubMed

    Huang, Yang; Liu, Guang-Jian; Liao, Bing; Huang, Guang-Liang; Liang, Jin-Yu; Zhou, Lu-Yao; Wang, Fen; Li, Wei; Xie, Xiao-Yan; Wang, Wei; Lu, Ming-De

    2015-09-01

    The aims of the present study are to assess the impact factors on acoustic structure quantification (ASQ) ultrasound and find the optimal parameter for the assessment of liver fibrosis. Twenty healthy volunteers underwent ASQ examinations to evaluate impact factors in ASQ image acquisition and analysis. An additional 113 patients with liver diseases underwent standardized ASQ examinations, and the results were compared with histologic staging of liver fibrosis. We found that the right liver displayed lower values of ASQ parameters than the left (p = 0.000-0.021). Receive gain experienced no significant impact except gain 70 (p = 0.193-1.000). With regard to different diameter of involved vessels in regions of interest, the group ≤2.0 mm differed significantly with the group 2.1-5.0 mm (p = 0.000-0.033) and the group >5.0 mm (p = 0.000-0.062). However, the region of interest size (p = 0.438-1.000) and depth (p = 0.072-0.764) had no statistical impact. Good intra- and inter-operator reproducibilities were found in both image acquisitions and offline image analyses. In the liver fibrosis study, the focal disturbance ratio had the highest correlation with histologic fibrosis stage (r = 0.67, p < 0.001). In conclusion, the testing position, receive gain and involved vessels were the main factors in ASQ examinations and focal disturbance ratio was the optimal parameter in the assessment of liver fibrosis. PMID:26055966

  14. Validation of refractive index structure parameter estimation for certain infrared bands.

    PubMed

    Sivaslıgil, Mustafa; Erol, Cemil Berin; Polat, Özgür Murat; Sarı, Hüseyin

    2013-05-10

    Variation of the atmospheric refraction index due to turbulent fluctuations is one of the key factors that affect the performance of electro-optical and infrared systems and sensors. Therefore, any prior knowledge about the degree of variation in the refractive index is critical in the success of field studies such as search and rescue missions, military applications, and remote sensing studies where these systems are used frequently. There are many studies in the literature in which the optical turbulence effects are modeled by estimation of the refractive index structure parameter, C(n)(2), from meteorological data for all levels of the atmosphere. This paper presents a modified approach for bulk-method-based C(n)(2) estimation. According to this approach, conventional wind speed, humidity, and temperature values above the surface by at least two levels are used as input data for Monin-Obukhov similarity theory in the estimation of similarity scaling constants with a finite difference approximation and a bulk-method-based C(n)(2) estimation. Compared with the bulk method, this approach provides the potential for using more than two levels of standard meteorological data, application of the scintillation effects of estimated C(n)(2) on the images, and a much simpler solution than traditional ones due to elimination of the roughness parameters, which are difficult to obtain and which increase the complexity, the execution time, and the number of additional input parameters of the algorithm. As a result of these studies, Atmospheric Turbulence Model Software is developed and the results are validated in comparison to the C(n)(2) model presented by Tunick.

  15. Validation of refractive index structure parameter estimation for certain infrared bands.

    PubMed

    Sivaslıgil, Mustafa; Erol, Cemil Berin; Polat, Özgür Murat; Sarı, Hüseyin

    2013-05-10

    Variation of the atmospheric refraction index due to turbulent fluctuations is one of the key factors that affect the performance of electro-optical and infrared systems and sensors. Therefore, any prior knowledge about the degree of variation in the refractive index is critical in the success of field studies such as search and rescue missions, military applications, and remote sensing studies where these systems are used frequently. There are many studies in the literature in which the optical turbulence effects are modeled by estimation of the refractive index structure parameter, C(n)(2), from meteorological data for all levels of the atmosphere. This paper presents a modified approach for bulk-method-based C(n)(2) estimation. According to this approach, conventional wind speed, humidity, and temperature values above the surface by at least two levels are used as input data for Monin-Obukhov similarity theory in the estimation of similarity scaling constants with a finite difference approximation and a bulk-method-based C(n)(2) estimation. Compared with the bulk method, this approach provides the potential for using more than two levels of standard meteorological data, application of the scintillation effects of estimated C(n)(2) on the images, and a much simpler solution than traditional ones due to elimination of the roughness parameters, which are difficult to obtain and which increase the complexity, the execution time, and the number of additional input parameters of the algorithm. As a result of these studies, Atmospheric Turbulence Model Software is developed and the results are validated in comparison to the C(n)(2) model presented by Tunick. PMID:23669824

  16. Spaceflight effects on structural and some biochemical parameters of Brassica rapa photosynthetic apparatus.

    PubMed

    Adamchuk, N I; Mikhaylenko, N F; Zolotareva, E K; Hilaire, E; Guikema, J A

    1999-07-01

    Chloroplasts play a crucial role in sustaining life on Earth by their dual property in performing the primary fixation of carbon and also in releasing oxygen for use in respiration. Collection of light and its transformation into chemical energy occurs in a thylakoid membrane which is one of the most remarkable transducing systems in the biological world. In order for the light-dependent reactions could take place, a high degree of molecular organization of its constituents is needed. Some results obtained in the framework of the Collaborative Ukrainian Experiment mission (STS-87) which was performed on board of the space shuttle "Columbia" are presented in the given paper. A goal of the study was to obtain data on some parameters of photosynthetic apparatus, namely the chloroplast structure, pigment content and lipid composition of Brassica rapa plants grown in microgravity.

  17. Elements of an algorithm for optimizing a parameter-structural neural network

    NASA Astrophysics Data System (ADS)

    Mrówczyńska, Maria

    2016-06-01

    The field of processing information provided by measurement results is one of the most important components of geodetic technologies. The dynamic development of this field improves classic algorithms for numerical calculations in the aspect of analytical solutions that are difficult to achieve. Algorithms based on artificial intelligence in the form of artificial neural networks, including the topology of connections between neurons have become an important instrument connected to the problem of processing and modelling processes. This concept results from the integration of neural networks and parameter optimization methods and makes it possible to avoid the necessity to arbitrarily define the structure of a network. This kind of extension of the training process is exemplified by the algorithm called the Group Method of Data Handling (GMDH), which belongs to the class of evolutionary algorithms. The article presents a GMDH type network, used for modelling deformations of the geometrical axis of a steel chimney during its operation.

  18. Intrahorizon differentiation of the structural-functional parameters of the humic acids from a typical chernozem

    NASA Astrophysics Data System (ADS)

    Chukov, S. N.; Golubkov, M. S.; Ryumin, A. G.

    2010-11-01

    It is shown that some structural-functional parameters of humic acids from the surface (0-5 cm) layer of a typical chernozem differ from those in a deeper (5-20 cm) layer. The Cha-to-Cfa ratio in the surface layer is by 1.7 times lower, and the concentration of free radicals is by almost an order of magnitude lower than that in the layer of 5-20 cm. The stimulating effect of humic acids from the surface layer on the processes of photosynthesis is sharply retarded, whereas their effect on respiration of Chlorella vulgaris is more pronounced. Humic acids from the deeper layer of chernozem have a much stronger stimulating effect on photosynthesis and a very weak stimulating effect of respiration. The concentration of free radicals in humic acids and the activity of physiological processes of photosynthesis in Chlorella vulgaris display a tight correlative relationship.

  19. Two-scale homogenization to determine effective parameters of thin metallic-structured films

    NASA Astrophysics Data System (ADS)

    Marigo, Jean-Jacques; Maurel, Agnès

    2016-08-01

    We present a homogenization method based on matched asymptotic expansion technique to derive effective transmission conditions of thin structured films. The method leads unambiguously to effective parameters of the interface which define jump conditions or boundary conditions at an equivalent zero thickness interface. The homogenized interface model is presented in the context of electromagnetic waves for metallic inclusions associated with Neumann or Dirichlet boundary conditions for transverse electric or transverse magnetic wave polarization. By comparison with full-wave simulations, the model is shown to be valid for thin interfaces up to thicknesses close to the wavelength. We also compare our effective conditions with the two-sided impedance conditions obtained in transmission line theory and to the so-called generalized sheet transition conditions.

  20. Soil air CO2 concentration as an integrative parameter of soil structure

    NASA Astrophysics Data System (ADS)

    Ebeling, Corinna; Gaertig, Thorsten; Fründ, Heinz-Christian

    2015-04-01

    The assessment of soil structure is an important but difficult issue and normally takes place in the laboratory. Typical parameters are soil bulk density, porosity, water or air conductivity or gas diffusivity. All methods are time-consuming. The integrative parameter soil air CO2 concentration ([CO2]) can be used to assess soil structure in situ and in a short time. Several studies highlighted that independent of soil respiration, [CO2] in the soil air increases with decreasing soil aeration. Therefore, [CO2] is a useful indicator of soil aeration. Embedded in the German research project RÜWOLA, which focus on soil protection at forest sites, we investigated soil compaction and recovery of soil structure after harvesting. Therefore, we measured soil air CO2 concentrations continuously and in single measurements and compared the results with the measurements of bulk density, porosity and gas diffusivity. Two test areas were investigated: At test area 1 with high natural regeneration potential (clay content approx. 25 % and soil-pH between 5 and 7), solid-state CO2-sensors using NDIR technology were installed in the wheel track of different aged skidding tracks in 5 and 10 cm soil depths. At area 2 (acidic silty loam, soil-pH between 3.5 and 4), CO2-sensors and water-tension sensors (WatermarkR) were installed in 6 cm soil depth. The results show a low variance of [CO2] in the undisturbed soil with a long term mean from May to June 2014 between 0.2 and 0.5 % [CO2] in both areas. In the wheel tracks [CO2] was consistently higher. The long term mean [CO2] in the 8-year-old-wheel track in test area 1 is 5 times higher than in the reference soil and shows a high variation (mean=2.0 %). The 18-year-old wheel track shows a long-term mean of 1.2 % [CO2]. Furthermore, there were strong fluctuations of [CO2] in the wheel tracks corresponding to precipitation and humidity. Similar results were yielded with single measurements during the vegetation period using a portable

  1. Electronic-Structure Theory of Organic Semiconductors: Charge-Transport Parameters and Metal/Organic Interfaces

    NASA Astrophysics Data System (ADS)

    Coropceanu, Veaceslav; Li, Hong; Winget, Paul; Zhu, Lingyun; Brédas, Jean-Luc

    2013-07-01

    We focus this review on the theoretical description, at the density functional theory level, of two key processes that are common to electronic devices based on organic semiconductors (such as organic light-emitting diodes, field-effect transistors, and solar cells), namely charge transport and charge injection from electrodes. By using representative examples of current interest, our main goal is to introduce some of the reliable theoretical methodologies that can best depict these processes. We first discuss the evaluation of the microscopic parameters that determine charge-carrier transport in organic molecular crystals, i.e., electronic couplings and electron-vibration couplings. We then examine the electronic structure at interfaces between an organic layer and a metal or conducting oxide electrode, with an emphasis on the work-function modifications induced by the organic layer and on the interfacial energy-level alignments.

  2. STRUCTURAL PARAMETERS FOR GLOBULAR CLUSTERS IN THE OUTER HALO OF M31

    SciTech Connect

    Wang Song; Ma Jun

    2012-06-15

    In this paper, we present internal surface brightness profiles, using images in the F606W and F814W filter bands observed with the Advanced Camera for Surveys on the Hubble Space Telescope, for 10 globular clusters (GCs) in the outer halo of M31. Standard King models are fitted to the profiles to derive their structural and dynamical parameters. The results show that, in general, the properties of clusters in M31 and the Milky Way fall in the same regions of parameter spaces. The outer halo GCs of M31 have larger ellipticities than most of the GCs in M31 and the Milky Way. Their large ellipticities may be due to galaxy tides coming from satellite dwarf galaxies of M31 or may be related to the apparently more vigorous accretion or merger history that M31 has experienced. The tight correlation of cluster binding energy E{sub b} with mass M{sub mod} indicates that the 'fundamental plane' does exist for clusters, regardless of their host environments, which is consistent with previous studies.

  3. VizieR Online Data Catalog: Structural parameters of galaxies in CANDELS (van der Wel+, 2012)

    NASA Astrophysics Data System (ADS)

    van der Wel, A.; Bell, E. F.; Haussler, B.; McGrath, E. J.; Chang, Y.-Y.; Guo, Y.; McIntosh, D. H.; Rix, H.-W.; Barden, M.; Cheung, E.; Faber, S. M.; Ferguson, H. C.; Galametz, A.; Grogin, N. A.; Hartley, W.; Kartaltepe, J. S.; Kocevski, D. D.; Koekemoer, A. M.; Lotz, J.; Mozena, M.; Peth, M. A.; Peng, C. Y.

    2012-11-01

    In this paper we describe the measurements of structural parameters of 109533 unique objects in the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS) WFC3/IR data, representing roughly 2/3 of the full survey. Our online materials will be updated with the final 1/3 of the survey once observations have been completed by the end of 2013. A full description of the CANDELS observing program is given by Grogin et al. (2011ApJS..197...35G) and Koekemoer et al. (2011ApJS..197...36K). CANDELS is a WFC3 and parallel ACS, 902 orbit HST imaging survey; here we concentrate on the WFC3 data only, which cover 800arcmin2 and are distributed over five widely separated fields (GOODS-S, GOODS-N, COSMOS, UDS and EGS). In table 1, structural parameters for three fields are summarized, namely, the UDS field (Lawrence et al. 2007MNRAS.379.1599L - see Cat. II/314), the Cosmological Evolution Survey field (COSMOS; Scoville et al. 2007ApJS..172....1S - see Cat. II/284) (both 9'x24' and each at "wide" depth), and the GOODS-South field (GOODS-S; Giavalisco et al. 2004, Cat. II/261); "wide" is over 4'x10' and "deep" is over 7'x10'. The CANDELS observations are augmented by previously obtained WFC3/IR data from the ERS program (Windhorst et al. 2011ApJS..193...27W) in the northern part of the GOODS-S field (4'x9' at a 2 orbit depth in F098M, F125W, and F160W) and the UDF program (Bouwens et al. 2010ApJ...709L.133B) embedded in the GOODS-S deep area (1 pointing with ~15 orbits in F105W and F125W, and 28 orbits in F160W). (2 data files).

  4. Accuracy in Parameter Estimation for Targeted Effects in Structural Equation Modeling: Sample Size Planning for Narrow Confidence Intervals

    ERIC Educational Resources Information Center

    Lai, Keke; Kelley, Ken

    2011-01-01

    In addition to evaluating a structural equation model (SEM) as a whole, often the model parameters are of interest and confidence intervals for those parameters are formed. Given a model with a good overall fit, it is entirely possible for the targeted effects of interest to have very wide confidence intervals, thus giving little information about…

  5. CONDENSED MATTER: STRUCTURE, THERMAL AND MECHANICAL PROPERTIES: A novel approach to topological defects in a vector order parameter system

    NASA Astrophysics Data System (ADS)

    Ren, Ji-Rong; Rong, Shu-Jun; Zhu, Tao

    2009-07-01

    Based on Duan's topological current theory, we propose a novel approach to study the topological properties of topological defects in a two-dimensional complex vector order parameter system. This method shows explicitly the fine topological structure of defects. The branch processes of defects in the vector order parameter system have also been investigated with this method.

  6. A Survey of Compact Star Clusters in the S-W Field of the M 31 Disk. Structural Parameters. Ii

    NASA Astrophysics Data System (ADS)

    Šablevičiūtė, I.; Vansevičius, V.; Kodaira, K.; Narbutis, D.; Stonkutė, R.; Bridžius, A.

    The King and the EFF (Elson, Fall & Freeman 1987) analytical models are employed to determine the structural parameters of star clusters using an 1-D surface brightness profile fitting method. The structural parameters are derived and a catalogue is provided for 51 star cluster candidates from the survey of compact star clusters in the South-West field of the M 31 disk performed by Kodaira et al. (2004).

  7. Infrared and Raman spectra, r0 structural parameters, conformational stability, and vibrational assignment of 2-cyanoethylamine

    NASA Astrophysics Data System (ADS)

    Durig, James R.; Darkhalil, Ikhlas D.; Klaassen, Joshua J.

    2012-09-01

    The infrared spectra (4000-200 cm-1) of the gas and solid and the Raman spectrum (4000-40 cm-1) of the liquid have been recorded. Vibrational fundamentals have been identified for four of the possible five stable conformers and complete vibrational assignments have been made for the Gg and Gt forms where the Capital G is for Gauche for the orientation around the Csbnd C bond and the lower cases g and t for gauche and trans orientation for the amine. These forms are the two lowest energy conformers. Vibrational assignments have been supported by MP2(full)/6-31G(d) ab initio calculations to predict harmonic force constants, fundamental frequencies, infrared intensities, Raman activities, and depolarization ratios. The conformational stabilities have been predicted from ab initio calculations utilizing several different basis sets up to aug-cc-pVTZ for both MP2(full) and density functional theory calculations by the B3LYP method. The enthalpy differences between the Gg and Gt conformers was determined to be 75 cm-1 and for the Gg to Tg form 333 cm-1. The r0 structural parameters have been obtained for the two most stable conformers from predicted parameters from ab initio MP2(full)/6-311+G(d,p) calculations adjusted to fit the previously reported microwave rotational constants. The determined heavy atom structural values for the Gg [Gt] conformer are: the distances (Å) N1sbnd C2 = 1.461(3) [1.453(3)], C2sbnd C3 = 1.535(3) [1.545(3)], C3sbnd C4 = 1.466(3) [1.463(3)], C4tbnd N5 = 1.161(3) [1.161(3)] and angles (°) ∠N1C2C3 = 109.5(5) [116.0(5)], ∠C2C3C4 = 111.1(5) [111.1(5)], ∠C3C4N5 = 177.4(5) [177.0(5)]. These parameters are compared to those estimated from the microwave study. The results are discussed and compared to the corresponding properties of some similar molecules.

  8. Correlation between Parameters of Calcaneal Quantitative Ultrasound and Hip Structural Analysis in Osteoporotic Fracture Patients

    PubMed Central

    Zheng, Hailiang; Li, Ming; Yin, Pengbin; Peng, Ye; Gao, Yuan; Zhang, Lihai; Tang, Peifu

    2015-01-01

    Background Calcaneal quantitative ultrasound (QUS), which is used in the evaluation of osteoporosis, is believed to be intimately associated with the characteristics of the proximal femur. However, the specific associations of calcaneal QUS with characteristics of the hip sub-regions remain unclear. Design A cross-sectional assessment of 53 osteoporotic patients was performed for the skeletal status of the heel and hip. Methods We prospectively enrolled 53 female osteoporotic patients with femoral fractures. Calcaneal QUS, dual energy X-ray absorptiometry (DXA), and hip structural analysis (HSA) were performed for each patient. Femoral heads were obtained during the surgery, and principal compressive trabeculae (PCT) were extracted by a three-dimensional printing technique-assisted method. Pearson’s correlation between QUS measurement with DXA, HSA-derived parameters and Young’s modulus were calculated in order to evaluate the specific association of QUS with the parameters for the hip sub-regions, including the femoral neck, trochanteric and Ward’s areas, and the femoral shaft, respectively. Results Significant correlations were found between estimated BMD (Est.BMD) and BMD of different sub-regions of proximal femur. However, the correlation coefficient of trochanteric area (r = 0.356, p = 0.009) was higher than that of the neck area (r = 0.297, p = 0.031) and total proximal femur (r = 0.291, p = 0.034). Furthermore, the quantitative ultrasound index (QUI) was significantly correlated with the HSA-derived parameters of the trochanteric area (r value: 0.315–0.356, all p<0.05) as well as with the Young’s modulus of PCT from the femoral head (r = 0.589, p<0.001). Conclusion The calcaneal bone had an intimate association with the trochanteric cancellous bone. To a certain extent, the parameters of the calcaneal QUS can reflect the characteristics of the trochanteric area of the proximal hip, although not specifically reflective of those of the femoral neck

  9. Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

    PubMed

    Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

    2012-01-01

    The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications. PMID:22942007

  10. Elliptical trajectory orientation of Lamb wave polarization as a damage localization parameter in aerospace structures

    NASA Astrophysics Data System (ADS)

    Ayers, J.; Owens, C. T.; Swenson, E.; Apetre, N.; Ruzzene, M.; Ghoshal, A.

    2012-05-01

    The ability to measure and quantify the polarization of ultrasonic waves has led to the development of novel non-destructive diagnostic tools, which rely on the sensitivity of polarization to surface roughness, cracks, temperature and residual stresses, among others. In particular, the following paper provides an analytical description of polarized Lamb wave components that yield an elliptical, rotated profile of the particle trajectory. The formulation includes Lamb waves generated by a circular piezoelectric disc, along with descriptions of bi-modal and single mode polarization characteristics. A technique is proposed that utilizes the elliptical orientation as a damage identification parameter for guided wave structural interrogation techniques. The technique is applied to finite element models of aluminum and composite armor-like structures. This analytical formulation is compared to experimental Lamb wave polarization results, where polarized Lamb wave components are extracted from complex, homogenous aluminum specimens using a 3D Scanning Laser Doppler Vibrometry setup. The experimental results show that the proposed technique allows for improved damage characterization.

  11. Structure simulation with calculated NMR parameters - integrating COSMOS into the CCPN framework.

    PubMed

    Schneider, Olaf; Fogh, Rasmus H; Sternberg, Ulrich; Klenin, Konstantin; Kondov, Ivan

    2012-01-01

    The Collaborative Computing Project for NMR (CCPN) has build a software framework consisting of the CCPN data model (with APIs) for NMR related data, the CcpNmr Analysis program and additional tools like CcpNmr FormatConverter. The open architecture allows for the integration of external software to extend the abilities of the CCPN framework with additional calculation methods. Recently, we have carried out the first steps for integrating our software Computer Simulation of Molecular Structures (COSMOS) into the CCPN framework. The COSMOS-NMR force field unites quantum chemical routines for the calculation of molecular properties with a molecular mechanics force field yielding the relative molecular energies. COSMOS-NMR allows introducing NMR parameters as constraints into molecular mechanics calculations. The resulting infrastructure will be made available for the NMR community. As a first application we have tested the evaluation of calculated protein structures using COSMOS-derived 13C Cα and Cβ chemical shifts. In this paper we give an overview of the methodology and a roadmap for future developments and applications.

  12. STEP and STEPSPL: Computer programs for aerodynamic model structure determination and parameter estimation

    NASA Technical Reports Server (NTRS)

    Batterson, J. G.

    1986-01-01

    The successful parametric modeling of the aerodynamics for an airplane operating at high angles of attack or sideslip is performed in two phases. First the aerodynamic model structure must be determined and second the associated aerodynamic parameters (stability and control derivatives) must be estimated for that model. The purpose of this paper is to document two versions of a stepwise regression computer program which were developed for the determination of airplane aerodynamic model structure and to provide two examples of their use on computer generated data. References are provided for the application of the programs to real flight data. The two computer programs that are the subject of this report, STEP and STEPSPL, are written in FORTRAN IV (ANSI l966) compatible with a CDC FTN4 compiler. Both programs are adaptations of a standard forward stepwise regression algorithm. The purpose of the adaptation is to facilitate the selection of a adequate mathematical model of the aerodynamic force and moment coefficients of an airplane from flight test data. The major difference between STEP and STEPSPL is in the basis for the model. The basis for the model in STEP is the standard polynomial Taylor's series expansion of the aerodynamic function about some steady-state trim condition. Program STEPSPL utilizes a set of spline basis functions.

  13. Rings and ribbons in protein structures: Characterization using helical parameters and Ramachandran plots for repeating dipeptides.

    PubMed

    Hayward, Steven; Leader, David P; Al-Shubailly, Fawzia; Milner-White, E James

    2014-02-01

    Helical parameters displayed on a Ramachandran plot allow peptide structures with successive residues having identical main chain conformations to be studied. We investigate repeating dipeptide main chain conformations and present Ramachandran plots encompassing the range of possible structures. Repeating dipeptides fall into the categories: rings, ribbons, and helices. Partial rings occur in the form of "nests" and "catgrips"; many nests are bridged by an oxygen atom hydrogen bonding to the main chain NH groups of alternate residues, an interaction optimized by the ring structure of the nest. A novel recurring feature is identified that we name unpleated β, often situated at the ends of a β-sheet strand. Some are partial rings causing the polypeptide to curve gently away from the sheet; some are straight. They lack β-pleat and almost all incorporate a glycine. An example is the first glycine in the GxxxxGK motif of P-loop proteins. Ribbons in repeating dipeptides can be either flat, as seen in repeated type II and type II' β-turns, or twisted, as in multiple type I and type I' β-turns. Hexa- and octa-peptides in such twisted ribbons occur frequently in proteins, predominantly with type I β-turns, and are the same as the "β-bend ribbons" hitherto identified only in short peptides. One is seen in the GTPase-activating protein for Rho in the active, but not the inactive, form of the enzyme. It forms a β-bend ribbon, which incorporates the catalytic arginine, allowing its side chain guanidino group to approach the active site and enhance enzyme activity.

  14. Parameter estimation of large flexible aerospace structures with application to the control of the Maypole Deployable Reflector

    NASA Technical Reports Server (NTRS)

    Balas, M. J.

    1981-01-01

    Systems such as the Maypole deployable reflector have a distributed parameter nature. The flexible column and hoop structure and the circular antenna of 30-100 meter diameter which it supports are described by partial, rather than ordinary, differential equations. Progress completed in reduced order modelling andd controller design and digital parameter estimation and control is summarized. Topics covered include depolyment and on-orbit operation; quasi-static (steady state) operation; dynamic distributed parameter system; autoregressive moving average identification; frequency domain procedures; direct or implicit active control; adaptive observers; parameter estimation using a linear reinforcement learning factor; feedback control; and reduced order modeling for nonlinear systems.

  15. Simultaneous Joint Inversion of Seismic AVO and Controlled Source Electromagnetic Data by Direct Estimation of Common Parameter Structure

    NASA Astrophysics Data System (ADS)

    Lien, M.

    2012-12-01

    We are concerned with the inverse problem of identifying changes in saturation for monitoring of underground reservoirs with application to CO2 sequestration and oil production monitoring. The inverse problem is at the outset ill-posed, where non-uniqueness and instability issues can lead to large uncertainties in the resulting parameter estimates. Constraining the inversion with a higher degree of information by combining information from different data sets will be important to improve the quality of the model calibration and thereby the reliability of the resulting reservoir predictions. For this, the simultaneous joint inversion of seismic AVO and controlled source electromagnetic (CSEM) data is considered. With simultaneous joint inversion, one secures that the final result from the inversion honors all available data. AVO and CSEM represent different sources of information. The seismic signals provide information about the elastic properties of the reservoir with relatively high spatial resolution, whereas CSEM data probe the electric properties of the subsediments at the extreme low frequency limit. Hence, the coupling of the two data types is not trivial. An increasingly popular approach for simultaneous joint inversion of disparate data sets is structure-coupled joint inversion. Here the coupling of the data sets is obtained by imposing structural dependency between the different geophysical model parameters (i.e. the elastic and electric properties of the reservoir). The idea is that some of the main property changes in the different model parameters are likely to occur over the same interfaces/structures representing e.g. changes in lithology or fluid saturation. We propose a novel approach for structure-coupled joint inversion, where the coupling of the different data sets is obtained by facilitating for estimation of parameter structure directly. The approach is based on a generic method for parameter representation providing a joint relation to a

  16. Retrieval of Vegetation Structural Parameters and 3-D Reconstruction of Forest Canopies Using Ground-Based Echidna® Lidar

    NASA Astrophysics Data System (ADS)

    Strahler, A. H.; Yao, T.; Zhao, F.; Yang, X.; Schaaf, C.; Woodcock, C. E.; Jupp, D. L.; Culvenor, D.; Newnham, G.; Lovell, J.

    2010-12-01

    A ground-based, scanning, near-infrared lidar, the Echidna® validation instrument (EVI), built by CSIRO Australia, retrieves structural parameters of forest stands rapidly and accurately, and by merging multiple scans into a single point cloud, the lidar also provides 3-D stand reconstructions. Echidna lidar technology scans with pulses of light at 1064 nm wavelength and digitizes the full return waveform sufficiently finely to recover and distinguish the differing shapes of return pulses as they are scattered by leaves, trunks, and branches. Deployments in New England in 2007 and the southern Sierra Nevada of California in 2008 tested the ability of the instrument to retrieve mean tree diameter, stem count density (stems/ha), basal area, and above-ground woody biomass from single scans at points beneath the forest canopy. Parameters retrieved from five scans located within six 1-ha stand sites matched manually-measured parameters with values of R2 = 0.94-0.99 in New England and 0.92-0.95 in the Sierra Nevada. Retrieved leaf area index (LAI) values were similar to those of LAI-2000 and hemispherical photography. In New England, an analysis of variance showed that EVI-retrieved values were not significantly different from other methods (power = 0.84 or higher). In the Sierra, R2 = 0.96 and 0.81 for hemispherical photos and LAI-2000, respectively. Foliage profiles, which measure leaf area with canopy height, showed distinctly different shapes for the stands, depending on species composition and age structure. New England stand heights, obtained from foliage profiles, were not significantly different (power = 0.91) from RH100 values observed by LVIS in 2003. Three-dimensional stand reconstruction identifies one or more “hits” along the pulse path coupled with the peak return of each hit expressed as apparent reflectance. Returns are classified as trunk, leaf, or ground returns based on the shape of the return pulse and its location. These data provide a point

  17. The importance of suppressing spin diffusion effects in the accurate determination of the spatial structure of a flexible molecule by nuclear Overhauser effect spectroscopy

    NASA Astrophysics Data System (ADS)

    Khodov, I. A.; Efimov, S. V.; Klochkov, V. V.; Batista de Carvalho, L. A. E.; Kiselev, M. G.

    2016-02-01

    Two-dimensional nuclear Overhauser effect spectroscopy is applied to the elucidation of conformation distribution of small molecules in solution. An essential influence of the nonlinear multistep magnetization transfer (spin diffusion) on the NMR-based analysis of conformers distribution for small druglike molecules in solution was revealed. Therefore, the spin diffusion should be eliminated from the obtained NMR data in order to obtain accurate results. Efficiency of QUIET-NOESY spectroscopy in solving the problem of accurate determination of inter-proton distances in a small molecule was shown in a study of ibuprofen. Although it requires much experimental time, this technique was found to be helpful to solve the spin diffusion problem.

  18. Constraining the Galactic structure parameters with the XSTPS-GAC and SDSS photometric surveys

    NASA Astrophysics Data System (ADS)

    Chen, B.-Q.; Liu, X.-W.; Yuan, H.-B.; Robin, A. C.; Huang, Y.; Xiang, M.-S.; Wang, C.; Ren, J.-J.; Tian, Z.-J.; Zhang, H.-W.

    2016-10-01

    Photometric data from the Xuyi Schmidt Telescope Photometric Survey of the Galactic Anticentre (XSTPS-GAC) and the Sloan Digital Sky Survey (SDSS) are used to derive the global structure parameters of the smooth components of the Milky Way. The data, which cover nearly 11,000 deg2 sky area and the full range of Galactic latitude, allow us to construct a globally representative Galactic model. The number density distribution of Galactic halo stars is fitted with an oblate spheroid that decays by power law. The best-fit yields an axis ratio and a power law index κ = 0.65 and p = 2.79, respectively. The r-band differential star counts of three dwarf samples are then fitted with a Galactic model. The best-fit model yielded by a Markov Chain Monte Carlo analysis has thin and thick disk scale heights and lengths of H1 = 322 pc and L1 =2343 pc, H2 =794 pc and L2 =3638 pc, a local thick-to-thin disk density ratio of f2 =11 per cent, and a local density ratio of the oblate halo to the thin disk of fh =0.16 per cent. The measured star count distribution, which is in good agreement with the above model for most of the sky area, shows a number of statistically significant large scale overdensities, including some of the previously known substructures, such as the Virgo overdensity and the so-called "north near structure", and a new feature between 150°

  19. Genetic structure and forensic parameters of 38 Indels for human identification purposes in eight Mexican populations.

    PubMed

    Martínez-Cortés, G; Gusmão, L; Pereira, R; Salcido, V H; Favela-Mendoza, A F; Muñoz-Valle, J F; Inclán-Sánchez, A; López-Hernández, L B; Rangel-Villalobos, H

    2015-07-01

    Insertion-deletions for human identification purposes (HID-Indels) offer advantages to solve particular forensic situations and complex paternity cases. In Mexico, admixed population known as Mestizos is the largest (∼90%), plus a number of Amerindian groups (∼10%), which have not been studied with HID-Indels. For this reason, allele frequencies and forensic parameters for 38 HID-Indels were estimated in 531 unrelated individuals from one Amerindian (Purépecha) and seven Mestizo populations from different regions of the country. Genotype distribution was in agreement with Hardy-Weinberg expectations in almost all loci/populations. The linkage disequilibrium (LD) test did not reveal possible associations between loci pairs in all eight Mexican populations. The combined power of discrimination was high in all populations (PD >99.99999999998%). However, the power of exclusion of the 38 HID-Indel system (PE >99.6863%) was reduced regarding most of autosomal STR kits. The assessment of genetic structure (AMOVA) and relationships between populations (FST) demonstrated significant differences among Mexican populations, mainly of the Purépecha Amerindian group. Among Mexican-Mestizos, three population clusters consistent with geography were defined: (i) North-West region: Chihuahua, Sinaloa, and Jalisco; (ii) Central-Southern region: Mexico City, Veracruz and Yucatan; (iii) South region: Chiapas. In brief, this report validates the inclusion of the 38 HID-Indel system in forensic casework and paternity cases in seven Mexican-Mestizo populations from different regions, and in one Mexican Amerindian group.

  20. Applications of the theory of optimal control of distributed-parameter systems to structural optimization

    NASA Technical Reports Server (NTRS)

    Armand, J. P.

    1972-01-01

    An extension of classical methods of optimal control theory for systems described by ordinary differential equations to distributed-parameter systems described by partial differential equations is presented. An application is given involving the minimum-mass design of a simply-supported shear plate with a fixed fundamental frequency of vibration. An optimal plate thickness distribution in analytical form is found. The case of a minimum-mass design of an elastic sandwich plate whose fundamental frequency of free vibration is fixed. Under the most general conditions, the optimization problem reduces to the solution of two simultaneous partial differential equations involving the optimal thickness distribution and the modal displacement. One equation is the uniform energy distribution expression which was found by Ashley and McIntosh for the optimal design of one-dimensional structures with frequency constraints, and by Prager and Taylor for various design criteria in one and two dimensions. The second equation requires dynamic equilibrium at the preassigned vibration frequency.

  1. Effects of Jet Opening Angle and Velocity Structure on Blazar Parameters

    NASA Astrophysics Data System (ADS)

    Wiita, P. J.; Gopal-Krishna; Dhurde, S.; Sircar, P.

    2008-06-01

    We had earlier shown that for a constant velocity jet the discrepancy between the low speeds (β) indicated by VLBI knot motions and the high Doppler factors (δ) inferred from emission of TeV photons could be reconciled if ultrarelativistic jets possessed modest opening angles. Here we evaluate the (flux-weighted) viewing angles of the jet and the apparent β and δ values of the radio knots on parsec scales. The influence of the jet opening angle on these radio knot parameters are found for the usually considered types of relativistic nuclear jets: those with uniform bulk speeds and those where the bulk Lorentz factor of the flow decreases with distance from the jet axis, known as ``spine--sheath'' flows. For both types of jet velocity structures the expectation value of the jet orientation angle at first falls dramatically with increases in the (central) jet Lorentz factor, but for extremely relativistic jets it levels off at a fraction of the opening angle. The effective values of the apparent speeds and Doppler factors of the knots always decline substantially with increasing jet opening angle. The rarity of highly superluminal parsec-scale radio components in TeV blazars can be understood if their jets are both highly relativistic and intrinsically weaker, so probably less well collimated, than the jets in ordinary blazars.

  2. Nonlinear FE simulations of structural behavior parameters of reinforced concrete beam with epoxy-bonded FRP

    NASA Astrophysics Data System (ADS)

    Sasmal, Saptarshi; Kalidoss, S.

    2015-05-01

    In the present study, investigations on fiber-reinforced plastic (FRP) plated-reinforced concrete (RC) beam are carried out. Numerical investigations are performed by using a nonlinear finite element analysis by incorporating cracking and crushing of concrete. The numerical models developed in the present study are validated with the results obtained from the experiment under monotonic load using the servo-hydraulic actuator in displacement control mode. Further, the validated numerical models are used to evaluate the influence of different parameters. It is found from the investigations that increase in the elastic modulus of adhesive layer and CFRP laminate increases the interfacial stresses whereas increase in laminate modulus decreases the displacement and reinforcement strain of the beam. It is also observed that increase in the adhesive layer can largely reduce the interfacial stresses, whereas increase in laminate thickness increases it. However, increase in laminate thickness decreases the displacement and reinforcement strain of the beam significantly. It is mention worthy that increase in laminate length reduces the interfacial stresses, whereas CFRP width change does not affect the interfacial stresses. The study will be useful for the design and practicing engineers for arriving at the FRP-based strengthening schemes for RC structures judiciously.

  3. Effect of operating parameters and reactor structure on moderate temperature dry desulfurization

    SciTech Connect

    Jie Zhang; Changfu You; Haiying Qi; Bo Hou; Changhe Chen; Xuchang Xu

    2006-07-01

    A moderate temperature dry desulfurization process at 600-800 C was studied in a pilot-scale circulating fluidized bed flue gas desulfurization (CFB-FGD) experimental facility. The desulfurization efficiency was investigated for various operating parameters. Structural improvements in key parts of the CFB-FGD system, i.e., the cyclone separator and the distributor, were made to improve the desulfurization efficiency and flow resistance. The experimental results show that the desulfurization efficiency increased rapidly with increasing temperature above 600 C due to enhanced gas diffusion and the shift of the equilibrium for the carbonate reaction. The sorbent sulfated gradually after quick carbonation of the sorbent with a long particle residence time necessary to realize a high desulfurization ratio. A reduced solids concentration in the bed reduced the particle residence time and the desulfurization efficiency. A single-stage cyclone separator produced no improvement in the desulfurization efficiency compared with a two-stage cyclone separator. Compared with a wind cap distributor, a large hole distributor reduced the flow resistance which reduced the desulfurization efficiency due to the reduced bed pressure drop and worsened bed fluidization. The desulfurization efficiency can be improved by increasing the collection efficiency of fine particles to prolong their residence time and by improving the solids concentration distribution to increase the gas-solid contact surface area. 16 refs., 9 figs.

  4. Optical properties, structural parameters, and bonding of highly textured rocksalt tantalum nitride films

    SciTech Connect

    Matenoglou, G. M.; Koutsokeras, L. E.; Lekka, Ch. E.; Patsalas, P.; Abadias, G.; Camelio, S.; Evangelakis, G. A.; Kosmidis, C.

    2008-12-15

    Tantalum nitride is an interesting solid with exceptional properties and it might be considered as a representative model system of the d{sup 3}s{sup 2} transition metal nitrides. In this work highly textured, stoichiometric, rocksalt TaN(111) films have been grown on Si(100) by pulsed laser deposition. The films were under a triaxial stress, which has been determined by the sin{sup 2} {psi} method. The stress-free lattice parameter was found to be 0.433{+-}0.001 nm, a value which has been also determined by ab initio calculations within the local spin density approximation. The optical properties of TaN have been studied using spectroscopic ellipsometry and detailed band structure calculations. The electron conductivity of TaN is due to the Ta 5dt{sub 2g} band that intercepts the Fermi level and is the source of intraband absorption. The plasma energies of fully dense rocksalt TaN were found to be 9.45 and 9.7 eV based on the experimental results and ab initio calculations, respectively. Additional optical absorption bands were also observed around 1.9 and 7.3 eV and attributed to be due to crystal field splitting of the Ta 5d band (t{sub 2g}{yields}e{sub g} transition) and the N p{yields}Ta d interband transition, respectively.

  5. Photometric and Structural Parameters of Globular Clusters Towards the Galactic Bulge: Results from VVV and More

    NASA Astrophysics Data System (ADS)

    Cohen, Roger; Mauro, Francesco; Moni Bidin, Christian; Geisler, Douglas

    2016-01-01

    Globular clusters (GCs) located towards the Galactic bulge have been systematically excluded from most ground- and space-based photometric surveys due to severe total and differential extinction. Recent discoveries based on near-infrared imaging imply that these clusters hold valuable keys to Galactic formation and evolution, including double horizontal branches and density profiles which differ significantly from results based on optical integrated light. We present results based on wide-field near-infrared PSF photometry of bulge GCs from the Vista Variables in the Via Lactea (VVV) survey, leveraged together with results from a plethora of other sources: Near-IR photometry of well-studied GCs, deep space-based optical imaging, and recent observations from ground-based adaptive optics facilities. The results include new calibrations of distance- and reddening-independent photometric metallicity indicators, the first broad tests of multiple sets of evolutionary models against homogenous photometry in the near-IR, and the first number density-based structural parameters for many poorly studied bulge GCs.

  6. The Globular Cluster System of NGC 5128: Ages, Metallicities, Kinematics and Structural Parameters

    NASA Astrophysics Data System (ADS)

    Woodley, K. A.; Gómez, M.

    2010-10-01

    We review our recent studies of the globular cluster system of NGC 5128. First, we have obtained low-resolution, high signal-to-noise spectroscopy of 72 globular clusters using Gemini-S/GMOS to obtain the ages, metallicities, and the level of alpha enrichment of the metal-poor and metal-rich globular cluster subpopulations. Second, we have explored the rotational signature and velocity dispersion of the galaxy's halo using over 560 globular clusters with radial velocity measurements. We have also compared the dependence of these properties on galactocentric distance and globular cluster age and metallicity. Using globular clusters as tracer objects, we have analyzed the mass, and mass-to-light ratio of NGC 5128. Last, we have measured the structural parameters, such as half-light radii, of over 570 globular clusters from a superb 1.2-square-degree Magellan/IMACS image. We will present the findings of these studies and discuss the connection to the formation and evolution of NGC 5128.

  7. Experimental study on detonation parameters and cellular structures of fuel cloud

    NASA Astrophysics Data System (ADS)

    Xie, Li-Feng; Li, Bin; Zhang, Yu-Lei

    2012-04-01

    In this paper, detonation parameters of fuel cloud, such as propylene oxide (PO), isopropyl nitrate (IPN), hexane, 90# oil and decane were measured in a self-designed and constructed vertical shock tube. Results show that the detonation pressure and velocity of PO increase to a peak value and then decrease smoothly with increasing equivalence ratio. Several nitrate sensitizers were added into PO to make fuel mixtures, and test results indicated that the additives can efficiently enhance detonation velocity and pressure of fuel cloud and one type of additive n-propyl nitrate (NPN) played the best in the improvement. The critical initiation energy that directly initiated detonation of all the test liquid fuel clouds showed a U-shape curve relationship with equivalence ratios. The optimum concentration lies on the rich-fuel side ( ϕ > 1). The critical initiation energy is closely related to molecular structure and volatility of fuels. IPN and PO have similar critical values while that of alkanes are larger. Detonation cell sizes of PO were respectively investigated at 25°C, 35°C and 50°C with smoked foil technique. The cell width shows a U-shape curve relationship with equivalence ratios at all temperatures. The minimal cell width also lies on the rich-fuel side ( ϕ > 1). The cell width of PO vapor is slightly larger than that of PO cloud. Therefore, the detonation reaction of PO at normal temperature is controlled by gas phase reaction.

  8. Effect of operating parameters and reactor structure on moderate temperature dry desulfurization.

    PubMed

    Zhang, Jie; You, Changfu; Qi, Haiying; Hou, Bo; Chen, Changhe; Xu, Xuchang

    2006-07-01

    A moderate temperature dry desulfurization process at 600-800 degrees C was studied in a pilot-scale circulating fluidized bed flue gas desulfurization (CFB-FGD) experimental facility. The desulfurization efficiency was investigated for various operating parameters, such as bed temperature, CO2 concentration, and solids concentration. In addition, structural improvements in key parts of the CFB-FGD system, i.e., the cyclone separator and the distributor, were made to improve the desulfurization efficiency and flow resistance. The experimental results show that the desulfurization efficiency increased rapidly with increasing temperature above 600 degrees C due to enhanced gas diffusion and the shift of the equilibrium for the carbonate reaction. The sorbent sulfated gradually after quick carbonation of the sorbent with a long particle residence time necessary to realize a high desulfurization ratio. A reduced solids concentration in the bed reduced the particle residence time and the desulfurization efficiency. A single-stage cyclone separator produced no improvement in the desulfurization efficiency compared with a two-stage cyclone separator. Compared with a wind cap distributor, a large hole distributor reduced the flow resistance which reduced the desulfurization efficiency due to the reduced bed pressure drop and worsened bed fluidization. The desulfurization efficiency can be improved by increasing the collection efficiency of fine particles to prolong their residence time and by improving the solids concentration distribution to increase the gas-solid contact surface area.

  9. Phytoplankton abundance and structural parameters of the critically endangered protected area Vaya Lake (Bulgaria)

    PubMed Central

    Dimitrova, Ralits; Nenova, Elena; Uzunov, Blagoy; Shishiniova, Maria; Stoyneva, Maya

    2014-01-01

    Vaya (Ramsar site, protected area and Natura 2000 site) is the biggest natural lake in Bulgaria and the shallowest Black Sea coastal lake, which during the last decades has undergone significant changes and was included as critically endangered in the Red List of Bulgarian Wetlands. Our studies were conducted during the summer and autumn months of three years – 2004–2006. The paper presents results on the phytoplankton abundance (numbers, biomass and carbon content) in combination with the indices of species diversity, evenness and dominance. Phytoplankton abundance was extremely high (average values of 1135 × 106 cells/L for the quantity and of 46 mg/L for the biomass) and increased in the end of the studied period (years 2005–2006), when decrease of species diversity and increase of the dominance index values were detected. The carbon content of the phytoplankton was at an average value of 9.7 mg/L and also increased from 2004 to 2006. Cyanoprokaryota dominated in the formation of the total carbon content of the phytoplankton, in its numbers (88%–97.8%), and in the biomass (62%–87.9%). All data on phytoplankton abundance and structural parameters in Vaya confirm the hypertrophic status of the lake and reflect the general negative trend in its development. PMID:26019571

  10. Calibration of the Mixing-Length Free Parameter for White Dwarf Structures

    NASA Astrophysics Data System (ADS)

    Tremblay, P.-E.; Ludwig, H.-G.; Freytag, B.; Fontaine, G.; Steffen, M.; Brassard, P.

    2015-06-01

    We present a comparison of our grid of 3D radiation-hydrodynamical simulations for 70 pure-hydrogen DA white dwarfs, in the surface gravity range 7.0 ≤log g≤ 9.0, with 1D envelope models based on the mixing-length theory (MLT) for convection. We perform a calibration of the mixing-length parameter for the lower part of the convection zone. The 3D simulations are often restricted to the upper convective layers, and in those cases, we rely on the asymptotic entropy value of the adiabatic 3D upflows to calibrate 1D envelopes. Our results can be applied to 1D structure calculations, and in particular for pulsation and convective mixing studies. We demonstrate that while the 1D MLT only provides a bottom boundary of the convection zone based on the Schwarzschild criterion, the 3D stratifications are more complex. There is a large overshoot region below the convective layers that is likely critical for chemical diffusion applications.

  11. Revisiting Melton: Analyzing the correlation structure of geomorphological and climatological parameters

    NASA Astrophysics Data System (ADS)

    Carothers, R. A.; Sangireddy, H.; Passalacqua, P.

    2013-12-01

    In his expansive 1957 study of over 80 basins in Arizona, Colorado, New Mexico, and Utah, Mark Melton measured key morphometric, soil, land cover, and climatic parameters [Melton, 1957]. He identified correlations between morphological parameters and climatic regimes in an attempt to characterize the geomorphology of the basin as a function of climate and vegetation. Using modern techniques such as high resolution digital terrain models in combination with high spatial resolution weather station records, vector soil maps, seamless raster geological data, and land cover vector maps, we revisit Melton's 1957 dataset with the following hypotheses: (1) Patterns of channelization carry strong, codependent signatures in the form of statistical correlations of rainfall variability, soil type, and vegetation patterns. (2) Channelization patterns reflect the erosion processes on sub-catchment scale and the subsequent processes of vegetation recovery and gullying. In order to characterize various topographic and climatic parameters, we obtain elevation and land cover data from the USGS National Elevation dataset, climate data from the Western Regional Climate Center and PRISM climate group database, and soil type from the USDA STATSGO soil database. We generate a correlative high resolution database on vegetation, soil cover, lithology, and climatology for the basins identified by Melton in his 1957 study. Using the GeoNet framework developed by Passalacqua et al. [2010], we extract various morphological parameters such as slope, drainage density, and stream frequency. We also calculate metrics for patterns of channelization such as number of channelized pixels in a basin and channel head density. In order to understand the correlation structure between climate and morphological variables, we compute the Pearson's correlation coefficient similar to Melton's analysis and also explore other statistical procedures to characterize the feedbacks between these variables. By

  12. Deriving structural parameters of semi-resolved star clusters. FitClust: a program for crowded fields

    NASA Astrophysics Data System (ADS)

    Narbutis, D.; Semionov, D.; Stonkutė, R.; de Meulenaer, P.; Mineikis, T.; Bridžius, A.; Vansevičius, V.

    2014-09-01

    Context. An automatic tool to derive structural parameters of semi-resolved star clusters located in crowded stellar fields in nearby galaxies is needed for homogeneous processing of archival frames. Aims: We have developed a program that automatically derives the structural parameters of star clusters and estimates errors by accounting for individual stars and variable sky background. Methods: Models of observed frames consist of the cluster's surface brightness distribution, convolved with a point spread function; the stars, represented by the same point spread function; and a smoothly variable sky background. The cluster's model is fitted within a large radius by using the Levenberg-Marquardt and Markov chain Monte Carlo algorithms to derive structural parameters, the flux of the cluster, and individual fluxes of all well-resolved stars. Results: FitClust, a program to derive structural parameters of semi-resolved clusters in crowded stellar fields, was developed and is available for free use. The program was tested on simulated cluster frames, and was used to measure clusters of the M31 galaxy in Subaru Suprime-Cam frames. Conclusions: Accounting for bright resolved stars and variable sky background significantly improves the accuracy of derived structural parameters of star clusters. However, their uncertainty remains dominated by the stochastic noise of unresolved stars.

  13. Statistical error analysis of surface-structure parameters determined by low-energy electron and positron diffraction: Data errors

    NASA Astrophysics Data System (ADS)

    Duke, C. B.; Lazarides, A.; Paton, A.; Wang, Y. R.

    1995-11-01

    An error-analysis procedure that gives statistically significant error estimates for surface-structure parameters extracted from analyses of measured low-energy electron and positron diffraction (LEED and LEPD) intensities is proposed. This procedure is applied to a surface-structure analysis of Cu(100) in which experimental data are simulated by adding Gaussian-distributed random errors to the calculated intensities for relaxed surface structures. Quantitative expressions for the variances in the surface-structural parameters are given and shown to obey the expected scaling laws for Gaussian errors in the experimental data. The procedure is shown to describe rigorously parameter errors in the limit that the errors in the measured intensities are described by uncorrelated Gaussian statistics. The analysis is valid for structure determinations that are of sufficient quality to admit errors that have magnitudes within the region of convergence of a linear theory that relates perturbations of diffracted intensities to perturbations in structural parameters. It is compared with previously proposed error-estimation techniques used in LEED, LEPD, and x-ray intensity analyses.

  14. An Improved Method of Parameter Identification and Damage Detection in Beam Structures under Flexural Vibration Using Wavelet Multi-Resolution Analysis

    PubMed Central

    Ravanfar, Seyed Alireza; Abdul Razak, Hashim; Ismail, Zubaidah; Monajemi, Hooman

    2015-01-01

    This paper reports on a two-step approach for optimally determining the location and severity of damage in beam structures under flexural vibration. The first step focuses on damage location detection. This is done by defining the damage index called relative wavelet packet entropy (RWPE). The damage severities of the model in terms of loss of stiffness are assessed in the second step using the inverse solution of equations of motion of a structural system in the wavelet domain. For this purpose, the connection coefficient of the scaling function to convert the equations of motion in the time domain into the wavelet domain is applied. Subsequently, the dominant components based on the relative energies of the wavelet packet transform (WPT) components of the acceleration responses are defined. To obtain the best estimation of the stiffness parameters of the model, the least squares error minimization is used iteratively over the dominant components. Then, the severity of the damage is evaluated by comparing the stiffness parameters of the identified model before and after the occurrence of damage. The numerical and experimental results demonstrate that the proposed method is robust and effective for the determination of damage location and accurate estimation of the loss in stiffness due to damage. PMID:26371005

  15. An Improved Method of Parameter Identification and Damage Detection in Beam Structures under Flexural Vibration Using Wavelet Multi-Resolution Analysis.

    PubMed

    Ravanfar, Seyed Alireza; Razak, Hashim Abdul; Ismail, Zubaidah; Monajemi, Hooman

    2015-01-01

    This paper reports on a two-step approach for optimally determining the location and severity of damage in beam structures under flexural vibration. The first step focuses on damage location detection. This is done by defining the damage index called relative wavelet packet entropy (RWPE). The damage severities of the model in terms of loss of stiffness are assessed in the second step using the inverse solution of equations of motion of a structural system in the wavelet domain. For this purpose, the connection coefficient of the scaling function to convert the equations of motion in the time domain into the wavelet domain is applied. Subsequently, the dominant components based on the relative energies of the wavelet packet transform (WPT) components of the acceleration responses are defined. To obtain the best estimation of the stiffness parameters of the model, the least squares error minimization is used iteratively over the dominant components. Then, the severity of the damage is evaluated by comparing the stiffness parameters of the identified model before and after the occurrence of damage. The numerical and experimental results demonstrate that the proposed method is robust and effective for the determination of damage location and accurate estimation of the loss in stiffness due to damage. PMID:26371005

  16. An Improved Method of Parameter Identification and Damage Detection in Beam Structures under Flexural Vibration Using Wavelet Multi-Resolution Analysis.

    PubMed

    Ravanfar, Seyed Alireza; Razak, Hashim Abdul; Ismail, Zubaidah; Monajemi, Hooman

    2015-09-09

    This paper reports on a two-step approach for optimally determining the location and severity of damage in beam structures under flexural vibration. The first step focuses on damage location detection. This is done by defining the damage index called relative wavelet packet entropy (RWPE). The damage severities of the model in terms of loss of stiffness are assessed in the second step using the inverse solution of equations of motion of a structural system in the wavelet domain. For this purpose, the connection coefficient of the scaling function to convert the equations of motion in the time domain into the wavelet domain is applied. Subsequently, the dominant components based on the relative energies of the wavelet packet transform (WPT) components of the acceleration responses are defined. To obtain the best estimation of the stiffness parameters of the model, the least squares error minimization is used iteratively over the dominant components. Then, the severity of the damage is evaluated by comparing the stiffness parameters of the identified model before and after the occurrence of damage. The numerical and experimental results demonstrate that the proposed method is robust and effective for the determination of damage location and accurate estimation of the loss in stiffness due to damage.

  17. Reliability analysis of structural ceramic components using a three-parameter Weibull distribution

    NASA Technical Reports Server (NTRS)

    Duffy, Stephen F.; Powers, Lynn M.; Starlinger, Alois

    1992-01-01

    Described here are nonlinear regression estimators for the three-parameter Weibull distribution. Issues relating to the bias and invariance associated with these estimators are examined numerically using Monte Carlo simulation methods. The estimators were used to extract parameters from sintered silicon nitride failure data. A reliability analysis was performed on a turbopump blade utilizing the three-parameter Weibull distribution and the estimates from the sintered silicon nitride data.

  18. Theoretical studies of the local structure and EPR parameters for Cu2+ centers in disodium malonate trihydrate single crystal

    NASA Astrophysics Data System (ADS)

    Chao-Ying, Li; Ying, Huang; Xue-Mei, Zheng

    2015-01-01

    The electron paramagnetic resonance (EPR) parameters (g factors gxx, gyy, gzz and hyperfine structure constants Axx, Ayy, Azz) of the two Cu2+ centers in disodium malonate trihydrate (DSMT) single crystal are theoretically interpreted using the high order perturbation formulas of these parameters for a 3d9 ions in rhombically elongated octahedra. In the calculation, the rhombic crystal-field parameters are determined from the superposition model and the admixture of d-orbitals in the ground state wave function are taking account, the results show that although the admixture of the | d z 2 > state to the ground state wave function is small, it should not be neglected in calculations of the EPR parameters. The theoretical EPR parameters show good agreement with the observed values. The results are discussed.

  19. Quantitative Genetics and Functional–Structural Plant Growth Models: Simulation of Quantitative Trait Loci Detection for Model Parameters and Application to Potential Yield Optimization

    PubMed Central

    Letort, Véronique; Mahe, Paul; Cournède, Paul-Henry; de Reffye, Philippe; Courtois, Brigitte

    2008-01-01

    Background and Aims Prediction of phenotypic traits from new genotypes under untested environmental conditions is crucial to build simulations of breeding strategies to improve target traits. Although the plant response to environmental stresses is characterized by both architectural and functional plasticity, recent attempts to integrate biological knowledge into genetics models have mainly concerned specific physiological processes or crop models without architecture, and thus may prove limited when studying genotype × environment interactions. Consequently, this paper presents a simulation study introducing genetics into a functional–structural growth model, which gives access to more fundamental traits for quantitative trait loci (QTL) detection and thus to promising tools for yield optimization. Methods The GREENLAB model was selected as a reasonable choice to link growth model parameters to QTL. Virtual genes and virtual chromosomes were defined to build a simple genetic model that drove the settings of the species-specific parameters of the model. The QTL Cartographer software was used to study QTL detection of simulated plant traits. A genetic algorithm was implemented to define the ideotype for yield maximization based on the model parameters and the associated allelic combination. Key Results and Conclusions By keeping the environmental factors constant and using a virtual population with a large number of individuals generated by a Mendelian genetic model, results for an ideal case could be simulated. Virtual QTL detection was compared in the case of phenotypic traits – such as cob weight – and when traits were model parameters, and was found to be more accurate in the latter case. The practical interest of this approach is illustrated by calculating the parameters (and the corresponding genotype) associated with yield optimization of a GREENLAB maize model. The paper discusses the potentials of GREENLAB to represent environment × genotype

  20. VLTI/AMBER observations of cold giant stars: atmospheric structures and fundamental parameters

    NASA Astrophysics Data System (ADS)

    Arroyo-Torres, B.; Martí-Vidal, I.; Marcaide, J. M.; Wittkowski, M.; Guirado, J. C.; Hauschildt, P. H.; Quirrenbach, A.; Fabregat, J.

    2014-06-01

    Aims: The main goal of this research is to determine the angular size and the atmospheric structures of cool giant stars (ɛ Oct, β Peg, NU Pav, ψ Peg, and γ Hya) and to compare them with hydrostatic stellar model atmospheres, to estimate the fundamental parameters, and to obtain a better understanding of the circumstellar environment. Methods: We conducted spectro-interferometric observations of ɛ Oct, β Peg, NU Pav, and ψ Peg in the near-infrared K band (2.13-2.47 μm), and γ Hya (1.9-2.47 μm) with the VLTI/AMBER instrument at medium spectral resolution (~1500). To obtain the fundamental parameters, we compared our data with hydrostatic atmosphere models (PHOENIX). Results: We estimated the Rosseland angular diameters of ɛ Oct, β Peg, NU Pav, ψ Peg, and γ Hya to be 11.66±1.50 mas, 16.87±1.00 mas, 13.03±1.75 mas, 6.31±0.35 mas, and 3.78±0.65 mas, respectively. Together with distances and bolometric fluxes (obtained from the literature), we estimated radii, effective temperatures, and luminosities of our targets. In the β Peg visibility, we observed a molecular layer of CO with a size similar to that modeled with PHOENIX. However, there is an additional slope in absorption starting around 2.3 μm. This slope is possibly due to a shell of H2O that is not modeled with PHOENIX (the size of the layer increases to about 5% with respect to the near-continuum level). The visibility of ψ Peg shows a low increase in the CO bands, compatible with the modeling of the PHOENIX model. The visibility data of ɛ Oct, NU Pav, and γ Hya show no increase in molecular bands. Conclusions: The spectra and visibilities predicted by the PHOENIX atmospheres agree with the spectra and the visibilities observed in our stars (except for β Peg). This indicates that the opacity of the molecular bands is adequately included in the model, and the atmospheres of our targets have an extension similar to the modeled atmospheres. The atmosphere of β Peg is more extended than

  1. The unique structural parameters of the underlying host galaxies in blue compact dwarfs

    SciTech Connect

    Janowiecki, Steven; Salzer, John J. E-mail: slaz@astro.indiana.edu

    2014-10-01

    The nature of possible evolutionary pathways between various types of dwarf galaxies is still not fully understood. Blue compact dwarf galaxies (BCDs) provide a unique window into dwarf galaxy formation and evolution and are often thought of as an evolutionary stage between different classes of dwarf galaxies. In this study we use deep optical and near-infrared observations of the underlying hosts of BCDs in order to study the structural differences between different types of dwarf galaxies. When compared with dwarf irregular galaxies of similar luminosities, we find that the underlying hosts of BCDs have significantly more concentrated light distributions, with smaller scale lengths and brighter central surface brightnesses. We demonstrate here that the underlying hosts of BCDs are distinct from the broad continuum of typical dwarf irregular galaxies, and that it is unlikely that most dwarf irregular galaxies can transform into a BCD or vice versa. Furthermore, we find that the starburst in a BCD only brightens it on average by ∼0.8 mag (factor of two), in agreement with other studies. It appears that a BCD is a long-lived and distinct type of dwarf galaxy that exhibits an exceptionally concentrated matter distribution. We suggest that it is this compact mass distribution that enables the strong star formation events that characterize this class of dwarf galaxy, that the compactness of the underlying host can be used as a distinguishing parameter between BCDs and other dwarf galaxies, and that it can also be used to identify BCDs which are not currently experiencing an intense starburst event.

  2. [The kinetic parameters of retainment and release of deposited in human tissue structures calcium].

    PubMed

    Ermakova, I P; Potanina, T V; Pronchenko, I A; Larina, I M; Sevast'ianov, V I

    2014-11-01

    The analysis of retainment and release kinetics of deposited in tissue structures calcium was made in the hypercalcemic conditions in 28 healthy volunteers (22 males and 6 females) of the age of 33 ± 6.5 years via drip infusion (Groups 1, 2) and in 9 individuals (3 males and 6 females) in 12 trials via stream infusion (Group 3). By the end of each hour after the termination of calcium infusion the amount of calcium retained in tissues was calculated (Mtis./kg); the parameters of its binding (specific buffer volume--β3 sp, association constant--Ka, number of binding centers--n) were established using the Langmuir and Scetchard coordinates. The Group 1 volunteers (n = = 12) showed a section of positive cooperativity (a direct regression on Sketchard coordinates, Hill coefficient 3.36 ± 1.63) and 2 sections of the consecutive calcium separation from one set of noninteracting centers. 5 volunteers of Group 2 and 8 volunteers of Group 3 demonstrated a slight calcium delivery to tissues after 1 hour of observation which then followed for 2 volunteers of Group 2 and for 2 volunteers of Group 3. Other volunteers of Groups 2 and 3 showed a release of tissue-deposited calcium via the mechanism of the consecutive separation from one set of noninteracting centers with βsp 3 times less and Ka 7 times higher than with the calcium infusion. The excretion of calcium in urine was the highest in Group 1 and the lowest in Group 3. The [Ca2+] and Mtis./kg values were normalized in Groups 1 and 2 the next morning and in Group 3 after 2-3 hours of observation. An assumption was made about the relationship between the tissue and kidney [Ca2+] normalizing mechanisms with hypercalcemia.

  3. Effect of Scintillometer Height on Structure Parameter of the Refractive Index of Air Measurements

    NASA Astrophysics Data System (ADS)

    Gowda, P. H.; Howell, T. A.; Hartogensis, O.; Basu, S.; Scanlon, B. R.

    2009-12-01

    Scintillometers measure amount of scintillations by emitting a beam of light over a horizontal path and expresses as the atmospheric turbulence structure parameter as the refractive index of air (Cn2). Cn2 represents the turbulent strength of the atmosphere and describes the ability of the atmosphere to transport heat and humidity. The main objective of this study was to evaluate the effect of scintillometer height on Cn2 measurements and on the estimation of latent heat fluxes. The study was conducted during the 2009 summer growing season in the USDA-ARS Conservation and Production Research Laboratory (CPRL) at Bushland [350 11' N, 1020 06' W; 1,170 m elevation MSL], Texas. Field experiment consisted of two steps: (1) cross-calibration of scintillometers and (2) measurement of Cn2 at different heights. In the first step, three large aperture scintillometers (LAS) were deployed across two large lysimeter fields with bare soil surfaces. During the 3-week cross-calibration period, all three scintillometers were installed at a 2-m height with a path length of 420 m. Cn2 was monitored at a 1-min interval and averaged for 15-min periods. Cn2 measurements were synchronized with weather station and weighing lysimeter measurements. After the cross-calibration period, scintillometers were installed at 2-, 2.5- and 3-m heights, and Cn2 measurements were continued for another 3-week period. In addition to the Cn2 measurements, net radiation (Rn) and soil heat fluxes (G) were measured in both lysimeter fields. Cn2 values were corrected for inner scale dependence before cross calibration and estimation of sensible heat fluxes. Measurements of wind speed, air temperature, and relative humidity were used with Cn2 data to derive sensible heat fluxes. Latent heat fluxes were estimated as a residual from the energy balance and compared with lysimeter data. Results of cross calibration and effects of scintillometer height on the estimation of latent heat fluxes were reported and

  4. [Genetic demographic parameters of the marriage structure of the Yevpatoria population].

    PubMed

    Atramentova, L A; Meshcheriakova, I P

    2007-03-01

    Records on marriages contracted in the city of Yevpatoria, Ukraine in 1960/1961, 1985, 1993, and 1994/1995 were used to determine some parameters of the city population structure. The coefficients of correlation with respect to the age of marriage in reproductive-age couples contracting marriages in these years were 0.77, 0.81, and 0.80, respectively. Women that contracted marriages at reproductively unfavorable ages (under 20 and over 30 years) in the respective years constituted 28.3, 40.6, and 45.4% of the total sample. The proportions of interethnic marriages in these years were 39.4, 43.9, and 46.6%. The proportion of Slavs decreased from 94 to 91% during 35 years, but the proportion of Ukrainians increased from 23.1 to 26.5%. The proportion of other ethnic groups (Tatars, Armenians, Karaites, Poles, Germans, etc.) increased from 3 to 8.6%. The marriage contingency with respect to ethnicity (K = 0.26 in 1960/1961, K = 0.22 in 1985, and K = 0.28 in 1994/1995) was higher than with respect to education (K = 0.18 in 1985 and K = 0.23 in 1993) or occupation (K = 0.18 in 1960/1961, K = 0.17 in 1985, and K = 0.23 in 1994/1995). The marriage assortativeness with respect to ethnicity was the highest in ethnic minorities (A' = 55.1%); that with respect to education, in persons who had higher or primary education (A' = 40.1% and A'= 78.0%, respectively); and that with respect to occupation, in students, military personnel, and production workers (60.6, 58.7, and 30.9%).

  5. Structural parameters and blue stragglers in Sagittarius dwarf spheroidal galaxy globular clusters

    NASA Astrophysics Data System (ADS)

    Salinas, Ricardo; Jílková, Lucie; Carraro, Giovanni; Catelan, Márcio; Amigo, Pía.

    2012-04-01

    We present BV photometry of four Sagittarius dwarf spheroidal galaxy globular clusters: Arp 2, NGC 5634, Palomar 12 and Terzan 8, obtained with the Danish Telescope at ESO La Silla. We measure the structural parameters of the clusters using a King profile fitting, obtaining the first reliable measurements of the tidal radius of Arp 2 and Terzan 8. These two clusters are remarkably extended and with low concentrations; with a concentration of only c= 0.41 ± 0.02, Terzan 8 is less concentrated than any cluster in our Galaxy. Blue stragglers are identified in the four clusters, and their spatial distribution is compared to those of horizontal branch and red giant branch stars. The blue straggler properties do not provide evidence of mass segregation in Terzan 8, while Arp 2 probably shares the same status, although with less confidence. In the case of NGC 5634 and Palomar 12, blue stragglers are significantly less populous, and their analysis suggests that the two clusters have probably undergone mass segregation. References: (1) Peterson (1976); (2) Kron, Hewitt & Wasserman (1984); (3) Chernoff & Djorgovski (1989); (4) Trager, Djorgovski & King (1993); (5) Trager et al. (1995); (6) Rosenberg et al. (1998); (7) Mackey & Gilmore (2003b); (8) McLaughlin & van der Marel (2005) and (9) Carballo-Bello et al. (2012).

  6. Accurate monotone cubic interpolation

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1991-01-01

    Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.

  7. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  8. The Combination of Laser Scanning and Structure from Motion Technology for Creation of Accurate Exterior and Interior Orthophotos of ST. Nicholas Baroque Church

    NASA Astrophysics Data System (ADS)

    Koska, B.; Křemen, T.

    2013-02-01

    Terrestrial laser scanning technology is used for creation of building documentation and 3D building model from its emerging at the turn of the millennium. Photogrammetry has even longer tradition in this field. Both technologies have some technical limitations if they are used for creation of a façade or even an interior orthophoto, but combination of both technologies seems profitable. Laser scanning can be used for creation of an accurate 3D model and photogrammetry for consequent application of high quality colour information. Both technologies were used in synergy to create the building plans, 2D drawing documentation of facades and interior views and the orthophotos of St. Nicholas Baroque church in Prague. The case study is described in details in the paper.

  9. The Model Parameter Estimation Experiment (MOPEX): Its structure, connection to other international initiatives and future directions

    SciTech Connect

    Wagener, T; Hogue, T; Schaake, J; Duan, Q; Gupta, H; Andreassian, V; Hall, A; Leavesley, G

    2006-05-08

    The Model Parameter Estimation Experiment (MOPEX) is an international project aimed at developing enhanced techniques for the a priori estimation of parameters in hydrologic models and in land surface parameterization schemes connected to atmospheric models. The MOPEX science strategy involves: database creation, a priori parameter estimation methodology development, parameter refinement or calibration, and the demonstration of parameter transferability. A comprehensive MOPEX database has been developed that contains historical hydrometeorological data and land surface characteristics data for many hydrologic basins in the United States (US) and in other countries. This database is being continuously expanded to include basins from various hydroclimatic regimes throughout the world. MOPEX research has largely been driven by a series of international workshops that have brought interested hydrologists and land surface modelers together to exchange knowledge and experience in developing and applying parameter estimation techniques. With its focus on parameter estimation, MOPEX plays an important role in the international context of other initiatives such as GEWEX, PUB and PILPS. This paper outlines the MOPEX initiative, discusses its role in the scientific community and briefly states future directions.

  10. The Model Parameter Estimation Experiment (MOPEX): Its structure, connection to other international initiatives and future directions

    USGS Publications Warehouse

    Wagener, T.; Hogue, T.; Schaake, J.; Duan, Q.; Gupta, H.; Andreassian, V.; Hall, A.; Leavesley, G.

    2006-01-01

    The Model Parameter Estimation Experiment (MOPEX) is an international project aimed at developing enhanced techniques for the a priori estimation of parameters in hydrological models and in land surface parameterization schemes connected to atmospheric models. The MOPEX science strategy involves: database creation, a priori parameter estimation methodology development, parameter refinement or calibration, and the demonstration of parameter transferability. A comprehensive MOPEX database has been developed that contains historical hydrometeorological data and land surface characteristics data for many hydrological basins in the United States (US) and in other countries. This database is being continuously expanded to include basins from various hydroclimatic regimes throughout the world. MOPEX research has largely been driven by a series of international workshops that have brought interested hydrologists and land surface modellers together to exchange knowledge and experience in developing and applying parameter estimation techniques. With its focus on parameter estimation, MOPEX plays an important role in the international context of other initiatives such as GEWEX, HEPEX, PUB and PILPS. This paper outlines the MOPEX initiative, discusses its role in the scientific community, and briefly states future directions.

  11. Analysis of the structural parameters that influence gas production from the Devonian shale. Annual progress report, 1979-1980

    SciTech Connect

    Negus-de Wys, J.; Dixon, J. M.; Evans, M. A.; Lee, K. D.; Ruotsala, J. E.; Wilson, T. H.; Williams, R. T.

    1980-10-01

    The executive study presents the results and progress of efforts toward understanding shale gas production from the Devonian shale in Appalachia. A correlation was found between the geochemical parameters of the shale in eastern Kentucky and shale gas production there. Tasks on resource inventory tasks and shale characterization include regional structure studies, production studies, geophysical studies, structure studies, fracture density and orientation, and fracture studies. (DLC)

  12. Theoretical studies of the EPR parameters and local structures for Cu2+-doped cobalt ammonium phosphate hexahydrate

    NASA Astrophysics Data System (ADS)

    Li, Chao-Ying; Liu, Shi-Fei; Fu, Jin-Xian

    2015-11-01

    High-order perturbation formulas for a 3d9 ion in rhombically elongated octahedral was applied to calculate the electron paramagnetic resonance (EPR) parameters (the g factors, gi, and the hyperfine structure constants Ai, i = x, y, z) of the rhombic Cu2+ center in CoNH4PO4.6H2O. In the calculations, the required crystal-field parameters are estimated from the superposition model which enables correlation of the crystal-field parameters and hence the EPR parameters with the local structure of the rhombic Cu2+ center. Based on the calculations, the ligand octahedral (i.e. [Cu(H2O)6]2+ cluster) are found to experience the local bond length variations ΔZ (≈0.213 Å) and δr (≈0.132 Å) along axial and perpendicular directions due to the Jahn-Teller effect. Theoretical EPR parameters based on the above local structure are in good agreement with the observed values; the results are discussed.

  13. Constraints on Source Parameters on Deep Moonquakes and Lunar Interior Structure

    NASA Astrophysics Data System (ADS)

    Yamada, R.; Araki, H.; Noda, H.; Matsumoto, K.

    2014-12-01

    The NASA Apollo mission realized the first and only seismic network on the Moon consisting of 4 seismic stations (Apollo 12, 14, 15 and 16). The seismic recording obtained by the network revealed that the most active lunar seismic events occurred in the lunar deep region at about 700 to 1200 km depth, which are called as deep moonquakes (e.g., Nakamura, 2005). The deep moonquakes repeatedly occur at the identical source with lunar tidal period depending on the relative positions of the Moon, the Earth and the Sun (e.g., Lammlein, 1977). On the other hand, the occurrence mechanism of the deep moonquakes is still unclear because we do not yet understand the source parameters such as focal mechanism, seismic moment and source spectrum. Yamada et al. (2013) analyzed the seismic data from Apollo 12 station to derive seismic moment distribution for active 15 deep moonquakes and showed that the seismic moments were different source by source. However, we found that the amplitudes of deep moonquakes observed at Apollo 15 and 16 stations cannot be well explained by our seismic moment distribution derived from the Apollo 12 data (Yamada et al., 2014). The higher seismic quality factors of S-wave are required to explain attenuation of amplitude of the deep moonquakes. This discrepancy may be also due to assumption of constant radiation pattern (strike dip, slip) in our previous studies. The amplitude of seismic event is determined from seismic moment, radiation pattern and lunar interior structure through which the seismic rays pass. Nakamura (1978) indicated that the radiation pattern varies with time by analyzing of the ratio of amplitudes of the same deep event observed at two stations. In this study, we investigate possible radiation pattern and seismic quality factor and seismic moments so as to explain the amplitude ratios of the same deep event observed at three stations (Apollo12, 15 and 16) and absolute amplitude of the deep events at each station using Markov

  14. [Theoretical Investigation of the Electron Paramagnetic Resonance Parameters and Local Structures for Zinc Phosphate Glass Doped with VO2+].

    PubMed

    Li, Chao-ying; Yuang, Xian-Kai; Tu, Qiu; Wang, Wei-yang; Zheng, Xue-mei

    2015-07-01

    As an important model system, 3d(1) ions (VO2+, V4+ et al) have been extensively investigated by means of electron paramagnetic resonance (EPR), and many experimental results of EPR parameters were also measured. The optical absorption and EPR parameters (g factors g||, g⊥ and hyperfine structure constants A||, A⊥) of a tetragonal V4+ center in zinc phosphate glass are theoretically investigated, using the perturbation formulas for a 3d(1) ion in tetragonally compressed octahedra. Since the spin-orbit coupling parameter r (150 cm(-1)) of ligand O2- is close to that ξp(0) (≈248 cm(-1)) of the central 3d(1) ion in zinc phosphate glass doped VO2+, the effect of the spin-orbit coupling parameter ξp(0) on the EPR spectra and optical absorption spectra should be taken into account. In this work, the relationship between the EPR parameters as well as the optical absorption spectra and the local structure of the impurity center are established based on the superposition model. By fitting the calculated EPR parameters and optical absorption spectra for V4+ center in zinc phosphate glass to the experimental data, the local structure parameters of [VO6](8-) cluster are obtained. According to the investigation, the magnitudes of the metal-ligand distances parallel and perpendicular to the C4-axis of [VO6](8-) cluster are, respectively, R|| ≈ 0.175 nm and R⊥ ≈ 0.197 nm, the local structure around the V4+ ions possesses a compressed tetragonal distortion along C4 axis. Theoretical results of EPR parameters and optical absorption spectra are in good agreement with experimental data, the validity of the calculated results has also been discussed. Thus, perturbation method is effective to the studies the EPR parameters and optical spectra of transition-metal 3d ions in crystals. In addition, based on the studies of the hyperfine structure constants (All and A1), one can found that the large value of kappa indicates a large contribution to the hyperfine constant by the

  15. An improved filtering method based on EEMD and wavelet-threshold for modal parameter identification of hydraulic structure

    NASA Astrophysics Data System (ADS)

    Zhang, Yan; Lian, Jijian; Liu, Fang

    2016-02-01

    Modal parameter identification is a core issue in the health monitoring and damage detection of hydraulic structures. The parameters are mainly obtained from the measured vibrational response under ambient excitation. However, the response signal is mixed with noise and interference signals, which will cover the structure vibration information; therefore, the parameter cannot be identified. This paper proposes an improved filtering method based on an ensemble empirical mode decomposition (EEMD) and wavelet threshold method. A 'noise index' is presented to estimate the noise degree of the components decomposed by the EEMD, and this index is related to the wavelet threshold calculation. In addition, the improved filtering method combined with an eigensystem realization algorithm (ERA) and a singular entropy (SE) is applied to an operational modal identification of a roof overflow powerhouse with a bulb tubular unit.

  16. Investigations of the EPR Parameters and Local Lattice Structure for the Rhombic Cu2+ Centre in TZSH Crystal

    NASA Astrophysics Data System (ADS)

    Li, Chao-Ying; Liu, Shi-Fei; Fu, Jin-Xian

    2016-03-01

    The electron paramagnetic resonance (EPR) parameters [i.e. g factors gi (i=x, y, z) and hyperfine structure constants Ai] and the local lattice structure for the Cu2+ centre in Tl2Zn(SO4)2·6H2O (TZSH) crystal were theoretically investigated by utilising the perturbation formulae of these parameters for a 3d9 ion under rhombically elongated octahedra. In the calculations, the admixture of d orbitals in the ground state and the ligand orbital and spin-orbit coupling interactions are taken into account based on the cluster approach. The theoretical EPR parameters show good agreement with the observed values, and the Cu2+-H2O bond lengths are obtained as follows: Rx≈1.98 Å, Ry≈2.09 Å, Rz≈2.32 Å. The results are discussed.

  17. Reliability analysis of structural ceramic components using a three-parameter Weibull distribution

    NASA Technical Reports Server (NTRS)

    Duffy, Stephen F.; Powers, Lynn M.; Starlinger, Alois

    1992-01-01

    Described here are nonlinear regression estimators for the three-Weibull distribution. Issues relating to the bias and invariance associated with these estimators are examined numerically using Monte Carlo simulation methods. The estimators were used to extract parameters from sintered silicon nitride failure data. A reliability analysis was performed on a turbopump blade utilizing the three-parameter Weibull distribution and the estimates from the sintered silicon nitride data.

  18. Structural investigations of {beta}-CaAlF{sub 5} by coupling powder XRD, NMR, EPR and spectroscopic parameter calculations

    SciTech Connect

    Body, M. . E-mail: monique.body@univ-lemans.fr; Silly, G.; Legein, C.; Buzare, J.-Y.; Calvayrac, F.; Blaha, P.

    2005-12-15

    {beta}-CaAlF{sub 5} was synthesized by solid-state reaction. The precise structure was refined from X-ray powder diffraction data in the monoclinic space group P2{sub 1}/c with lattice constants a=5.3361A, b=9.8298A, c=7.3271A, and {beta}=109.91{sup o} (Z=4). The structure exhibits isolated chains of AlF{sub 6}{sup 3-} octahedra sharing opposite corners.{sup 19}F and {sup 27}Al solid state NMR spectra were recorded using MAS and SATRAS techniques. An EPR spectrum was recorded for {beta}-CaAlF{sub 5}:Cr{sup 3+}. The experimental spectra were simulated in order to extract the NMR and EPR parameter values. Five fluorine sites and one low symmetry aluminium site were found in agreement with the refined structure. These parameters were calculated using empirical and ab-initio methods. The agreement obtained between the calculated {sup 19}F chemical shift values, {sup 27}Al quadrupolar parameters, Cr{sup 3+} EPR fine structure parameters and the experimental results demonstrates the complementarity of XRD, magnetic resonance experiments and theoretical methodologies.

  19. Variance in water chemistry parameters in isolated wetlands of Florida, USA, and relationships with macroinvertebrate and diatom community structure

    EPA Science Inventory

    Eighty small isolated wetlands throughout Florida were sampled in 2005 to explore within-site variability of water chemistry parameters and relate water chemistry to macroinvertebrate and diatom community structure. Three samples or measures of water were collected within each si...

  20. High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure.

    PubMed

    Darby, B J; Todd, T C; Herman, M A

    2013-11-01

    Nematodes are abundant consumers in grassland soils, but more sensitive and specific methods of enumeration are needed to improve our understanding of how different nematode species affect, and are affected by, ecosystem processes. High-throughput amplicon sequencing is used to enumerate microbial and invertebrate communities at a high level of taxonomic resolution, but the method requires validation against traditional specimen-based morphological identifications. To investigate the consistency between these approaches, we enumerated nematodes from a 25-year field experiment using both morphological and molecular identification techniques in order to determine the long-term effects of annual burning and nitrogen enrichment on soil nematode communities. Family-level frequencies based on amplicon sequencing were not initially consistent with specimen-based counts, but correction for differences in rRNA gene copy number using a genetic algorithm improved quantitative accuracy. Multivariate analysis of corrected sequence-based abundances of nematode families was consistent with, but not identical to, analysis of specimen-based counts. In both cases, herbivores, fungivores and predator/omnivores generally were more abundant in burned than nonburned plots, while bacterivores generally were more abundant in nonburned or nitrogen-enriched plots. Discriminate analysis of sequence-based abundances identified putative indicator species representing each trophic group. We conclude that high-throughput amplicon sequencing can be a valuable method for characterizing nematode communities at high taxonomic resolution as long as rRNA gene copy number variation is accounted for and accurate sequence databases are available. PMID:24103081

  1. High-throughput amplicon sequencing of rRNA genes requires a copy number correction to accurately reflect the effects of management practices on soil nematode community structure.

    PubMed

    Darby, B J; Todd, T C; Herman, M A

    2013-11-01

    Nematodes are abundant consumers in grassland soils, but more sensitive and specific methods of enumeration are needed to improve our understanding of how different nematode species affect, and are affected by, ecosystem processes. High-throughput amplicon sequencing is used to enumerate microbial and invertebrate communities at a high level of taxonomic resolution, but the method requires validation against traditional specimen-based morphological identifications. To investigate the consistency between these approaches, we enumerated nematodes from a 25-year field experiment using both morphological and molecular identification techniques in order to determine the long-term effects of annual burning and nitrogen enrichment on soil nematode communities. Family-level frequencies based on amplicon sequencing were not initially consistent with specimen-based counts, but correction for differences in rRNA gene copy number using a genetic algorithm improved quantitative accuracy. Multivariate analysis of corrected sequence-based abundances of nematode families was consistent with, but not identical to, analysis of specimen-based counts. In both cases, herbivores, fungivores and predator/omnivores generally were more abundant in burned than nonburned plots, while bacterivores generally were more abundant in nonburned or nitrogen-enriched plots. Discriminate analysis of sequence-based abundances identified putative indicator species representing each trophic group. We conclude that high-throughput amplicon sequencing can be a valuable method for characterizing nematode communities at high taxonomic resolution as long as rRNA gene copy number variation is accounted for and accurate sequence databases are available.

  2. Accurate determination of optical bandgap and lattice parameters of Zn{sub 1-x}Mg{sub x}O epitaxial films (0{<=}x{<=}0.3) grown by plasma-assisted molecular beam epitaxy on a-plane sapphire

    SciTech Connect

    Laumer, Bernhard; Schuster, Fabian; Stutzmann, Martin; Bergmaier, Andreas; Dollinger, Guenther; Eickhoff, Martin

    2013-06-21

    Zn{sub 1-x}Mg{sub x}O epitaxial films with Mg concentrations 0{<=}x{<=}0.3 were grown by plasma-assisted molecular beam epitaxy on a-plane sapphire substrates. Precise determination of the Mg concentration x was performed by elastic recoil detection analysis. The bandgap energy was extracted from absorption measurements with high accuracy taking electron-hole interaction and exciton-phonon complexes into account. From these results a linear relationship between bandgap energy and Mg concentration is established for x{<=}0.3. Due to alloy disorder, the increase of the photoluminescence emission energy with Mg concentration is less pronounced. An analysis of the lattice parameters reveals that the epitaxial films grow biaxially strained on a-plane sapphire.

  3. GlycoMinestruct: a new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features

    PubMed Central

    Li, Fuyi; Li, Chen; Revote, Jerico; Zhang, Yang; Webb, Geoffrey I.; Li, Jian; Song, Jiangning; Lithgow, Trevor

    2016-01-01

    Glycosylation plays an important role in cell-cell adhesion, ligand-binding and subcellular recognition. Current approaches for predicting protein glycosylation are primarily based on sequence-derived features, while little work has been done to systematically assess the importance of structural features to glycosylation prediction. Here, we propose a novel bioinformatics method called GlycoMinestruct(http://glycomine.erc.monash.edu/Lab/GlycoMine_Struct/) for improved prediction of human N- and O-linked glycosylation sites by combining sequence and structural features in an integrated computational framework with a two-step feature-selection strategy. Experiments indicated that GlycoMinestruct outperformed NGlycPred, the only predictor that incorporated both sequence and structure features, achieving AUC values of 0.941 and 0.922 for N- and O-linked glycosylation, respectively, on an independent test dataset. We applied GlycoMinestruct to screen the human structural proteome and obtained high-confidence predictions for N- and O-linked glycosylation sites. GlycoMinestruct can be used as a powerful tool to expedite the discovery of glycosylation events and substrates to facilitate hypothesis-driven experimental studies. PMID:27708373

  4. Assessment of structural model and parameter uncertainty with a multi-model system for soil water balance models

    NASA Astrophysics Data System (ADS)

    Michalik, Thomas; Multsch, Sebastian; Frede, Hans-Georg; Breuer, Lutz

    2016-04-01

    Water for agriculture is strongly limited in arid and semi-arid regions and often of low quality in terms of salinity. The application of saline waters for irrigation increases the salt load in the rooting zone and has to be managed by leaching to maintain a healthy soil, i.e. to wash out salts by additional irrigation. Dynamic simulation models are helpful tools to calculate the root zone water fluxes and soil salinity content in order to investigate best management practices. However, there is little information on structural and parameter uncertainty for simulations regarding the water and salt balance of saline irrigation. Hence, we established a multi-model system with four different models (AquaCrop, RZWQM, SWAP, Hydrus1D/UNSATCHEM) to analyze the structural and parameter uncertainty by using the Global Likelihood and Uncertainty Estimation (GLUE) method. Hydrus1D/UNSATCHEM and SWAP were set up with multiple sets of different implemented functions (e.g. matric and osmotic stress for root water uptake) which results in a broad range of different model structures. The simulations were evaluated against soil water and salinity content observations. The posterior distribution of the GLUE analysis gives behavioral parameters sets and reveals uncertainty intervals for parameter uncertainty. Throughout all of the model sets, most parameters accounting for the soil water balance show a low uncertainty, only one or two out of five to six parameters in each model set displays a high uncertainty (e.g. pore-size distribution index in SWAP and Hydrus1D/UNSATCHEM). The differences between the models and model setups reveal the structural uncertainty. The highest structural uncertainty is observed for deep percolation fluxes between the model sets of Hydrus1D/UNSATCHEM (~200 mm) and RZWQM (~500 mm) that are more than twice as high for the latter. The model sets show a high variation in uncertainty intervals for deep percolation as well, with an interquartile range (IQR) of

  5. Parameter estimation techniques based on optimizing goodness-of-fit statistics for structural reliability

    NASA Technical Reports Server (NTRS)

    Starlinger, Alois; Duffy, Stephen F.; Palko, Joseph L.

    1993-01-01

    New methods are presented that utilize the optimization of goodness-of-fit statistics in order to estimate Weibull parameters from failure data. It is assumed that the underlying population is characterized by a three-parameter Weibull distribution. Goodness-of-fit tests are based on the empirical distribution function (EDF). The EDF is a step function, calculated using failure data, and represents an approximation of the cumulative distribution function for the underlying population. Statistics (such as the Kolmogorov-Smirnov statistic and the Anderson-Darling statistic) measure the discrepancy between the EDF and the cumulative distribution function (CDF). These statistics are minimized with respect to the three Weibull parameters. Due to nonlinearities encountered in the minimization process, Powell's numerical optimization procedure is applied to obtain the optimum value of the EDF. Numerical examples show the applicability of these new estimation methods. The results are compared to the estimates obtained with Cooper's nonlinear regression algorithm.

  6. Structure-property relationships of carboxymethyl hydroxypropyl guar gum in water and a hyperentanglement parameter.

    PubMed

    Szopinski, Daniel; Kulicke, Werner-Michael; Luinstra, Gerrit A

    2015-03-30

    The viscoelastic properties of carboxymethyl hydroxypropyl guar gum (CMHPG) in aqueous solution were determined as function of concentration and of molecular weight, using SEC/MALLS/dRI and viscometry. The chain is more rigid as in native guar as was deduced from the molecular parameter in dilute solution. Superstructures are formed in moderately concentrated solutions as is shown from the comparison of steady state shear and small amplitude oscillatory shear (SAOS) experiments. The shear rate dependent viscosity of CMHPG can satisfactorily be described by the Carreau-Yasuda model with the rheological parameters (η0, λ0, n, b) obtained from the evaluation of viscosity data. A quantitative hyperentanglement parameter is introduced to account for the differences in responses in shear and SAOS experiments. PMID:25563956

  7. High frequency 3-component waveform inversion for source and structural parameters. Final report, 31 December 1993--30 June 1998

    SciTech Connect

    Harvey, D.J.; Lavehio, A.L.

    1998-09-01

    The authors present the results of three studies to develop and verify techniques to classify weak seismic events. (1) The method and results of full waveform inversion for both detailed source parameters and structure parameters are described. Input data were seismograms from industrial explosions in Eastern Kazakhstan recorded by the NRDC seismic network in 1987. Very good fits were produced between the synthetic seismograms and the observed data on all three components simultaneously and for P-wave, Rayleigh wave, and Love wave. They interpreted some of the inverted source parameters as characteristic of several different types of industrial surface mining operations. (2) The same technique was used to determine detailed source and structure parameters using an event that is highly relevant to nuclear monitoring. They determined that a salt mine collapse near Solikamsk, the Ural Mountains on 5 January 1995 was most likely a mine collapse instead of an underground explosions. (3) This study was carried out jointly by the Seismology Group of the University of Colorado and the Russian team from the Int`l Institute of Earthquake Prediction Theory and Math. Geophysics. They developed a new technique to identify a seismic event based on simultaneous inversion of surface wave amplitude spectra and signs of first motions of body wave. They applied this technique to several events near the Chinese test site at Lop Nor and demonstrated significant differences in source parameters characterizing explosions and natural earthquakes in this region.

  8. Effect of glass structure on spin Hamiltonian parameters: Cu doped tellurite glasses

    NASA Astrophysics Data System (ADS)

    Ramamoorthy, Raj Kumar; Bhatnagar, Anil K.

    2015-06-01

    Cu-doped glasses with compositions [(70TeO2-(30-x)ZnO-xPbO)0.98- (CuO)0.02] (x = 5, 10, 15, 20) were prepared using the melt quenching technique and characterized by EPR. Cu2+ ions are found to be in distorted oxygen octahedral cage and their corresponding spin Hamiltonian (splitting) parameters are deduced for all glasses as a function of increasing PbO. Finally, effect of the matrix on spin Hamiltonian parameters of Cu2+ ions are correlated with the help of EPR and earlier Raman analysis.

  9. Effect of glass structure on spin Hamiltonian parameters: Cu doped tellurite glasses

    SciTech Connect

    Ramamoorthy, Raj Kumar; Bhatnagar, Anil K.

    2015-06-24

    Cu-doped glasses with compositions [(70TeO{sub 2}−(30−x)ZnO−xPbO){sub 0.98}− (CuO){sub 0.02}] (x = 5, 10, 15, 20) were prepared using the melt quenching technique and characterized by EPR. Cu{sup 2+} ions are found to be in distorted oxygen octahedral cage and their corresponding spin Hamiltonian (splitting) parameters are deduced for all glasses as a function of increasing PbO. Finally, effect of the matrix on spin Hamiltonian parameters of Cu{sup 2+} ions are correlated with the help of EPR and earlier Raman analysis.

  10. Study on variability of modal parameters of concrete structure: humidity and moisture effect

    NASA Astrophysics Data System (ADS)

    Zhou, W.; Li, H.; Nasser, H.

    2008-03-01

    The complex external environment for civil engineering structures results in the structural vibration properties varying with external conditions, such as humidity and temperature. For the vibration-based structural health monitoring techniques, for example damage identification, modal updating etc., above characteristics will result in the vibration-based techniques invalid. Other researchers have reported that modal frequencies varied significantly due to temperature change, but the humidity affect structural vibration properties in another manner. This paper discusses the variation of frequencies and mode shapes with respect to humidity and temperature changes for concrete structures, for which the changing of moisture will affect the density of materials, and the changing of temperature will affect the stiffness of structures. This paper models these two factors with finite element model approach based on the theoretical analysis, and numerical results obtained on the FE model of a concrete bridge deck are reported.

  11. The Identification of Nanoscale Structures According to a Parameters of Acoustic Structuroscopy Method

    NASA Astrophysics Data System (ADS)

    Ababkov, N. V.; Smirnov, A. N.; Bykova, N. V.

    2016-04-01

    The fracture surface of a destroyed steam turbine rotor is studied by acoustic structuroscopy method. The structural-phase state of the metal of the destroyed rotor of a steam turbine is studied using the methods of electron microscopy. It was established that in the areas of control, where the values of the acoustic characteristics have significant differences from the rest of the metal, detected nanocrystalline structure. The possibility of determining the structure of the nanoscale metal by acoustic structuroscopy is shown.

  12. Scaling up the Single Transducer Thickness-Independent Ultrasonic Imaging Method for Accurate Characterization of Microstructural Gradients in Monolithic and Composite Tubular Structures

    NASA Technical Reports Server (NTRS)

    Roth, Don J.; Carney, Dorothy V.; Baaklini, George Y.; Bodis, James R.; Rauser, Richard W.

    1998-01-01

    Ultrasonic velocity/time-of-flight imaging that uses back surface reflections to gauge volumetric material quality is highly suited for quantitative characterization of microstructural gradients including those due to pore fraction, density, fiber fraction, and chemical composition variations. However, a weakness of conventional pulse-echo ultrasonic velocity/time-of-flight imaging is that the image shows the effects of thickness as well as microstructural variations unless the part is uniformly thick. This limits this imaging method's usefulness in practical applications. Prior studies have described a pulse-echo time-of-flight-based ultrasonic imaging method that requires using a single transducer in combination with a reflector plate placed behind samples that eliminates the effect of thickness variation in the image. In those studies, this method was successful at isolating ultrasonic variations due to material microstructure in plate-like samples of silicon nitride, metal matrix composite, and polymer matrix composite. In this study, the method is engineered for inspection of more complex-shaped structures-those having (hollow) tubular/curved geometry. The experimental inspection technique and results are described as applied to (1) monolithic mullite ceramic and polymer matrix composite 'proof-of-concept' tubular structures that contain machined patches of various depths and (2) as-manufactured monolithic silicon nitride ceramic and silicon carbide/silicon carbide composite tubular structures that might be used in 'real world' applications.

  13. Insights in the electronic structure and redox reaction energy in LiFePO{sub 4} battery material from an accurate Tran-Blaha modified Becke Johnson potential

    SciTech Connect

    Araujo, Rafael B.; Almeida, J. de S; Ferreira da Silva, A.; Ahuja, Rajeev

    2015-09-28

    The main goals of this paper are to investigate the accuracy of the Tran-Blaha modified Becke Johnson (TB-mBJ) potential to predict the electronic structure of lithium iron phosphate and the related redox reaction energy with the lithium deintercalation process. The computed electronic structures show that the TB-mBJ method is able to partially localize Fe-3d electrons in LiFePO{sub 4} and FePO{sub 4} which usually is a problem for the generalized gradient approximation (GGA) due to the self interaction error. The energy band gap is also improved by the TB-mBJ calculations in comparison with the GGA results. It turned out, however, that the redox reaction energy evaluated by the TB-mBJ technique is not in good agreement with the measured one. It is speculated that this disagreement in the computed redox energy and the experimental value is due to the lack of a formal expression to evaluate the exchange and correlation energy. Therefore, the TB-mBJ is an efficient method to improve the prediction of the electronic structures coming form the standard GGA functional in LiFePO{sub 4} and FePO{sub 4}. However, it does not appear to have the same efficiency for evaluating the redox reaction energies for the investigated system.

  14. Distinguishing the effects of model structural error and parameter uncertainty on predictions of pesticide leaching under climate change

    NASA Astrophysics Data System (ADS)

    Steffens, K.; Larsbo, M.; Moeys, J.; Jarvis, N.; Lewan, E.

    2012-04-01

    Studying climate change impacts on pesticide leaching is laced with various sources of uncertainty, which must be assessed in as detailed way as possible in order to understand the reliability of predictions of pesticide leaching under current and future climate conditions. One dilemma in this respect is the difficulty in separating the effects of model structural error from parameter uncertainty. An example of the former is that most of the commonly-used pesticide transport models only consider temperature-dependent degradation, whereas temperature also influences transport in soils through its effect on sorption and diffusion. Especially for climate impact assessments of pesticide leaching, the processes and parameters that depend on soil temperature and moisture should be carefully considered. Two functions, one describing temperature-dependent sorption and one for temperature-dependent diffusion, were therefore introduced as options into the process-oriented 1D pesticide fate and transport model MACRO5.2, which resulted in four structurally different versions of the MACRO-model. The aims of the study were to assess (i) the uncertainty related to model structure in relation to parameter uncertainty and (ii) the importance of these sources of uncertainty in long-term predictions of leaching in the perspective of climate change. A case study for leaching of the mobile herbicide Bentazone was performed in a two-step procedure. First, acceptable parameter sets were identified by evaluating model performance using the Nash-Sutcliff criteria against comprehensive data from a one-year field experiment on a clay soil in Lanna (Southern Sweden). Eight sensitive and uncertain parameters were sampled from uniform distributions in a Monte-Carlo approach, separately for each of the four model versions. In a second step, each model-version with its particular ensemble of different acceptable parameter combinations was used to predict leaching for a present (1970-1999) and a

  15. Validation of HFCS-I on Calculation of High-Frequency Parameters of Helical Slow-Wave Structures

    NASA Astrophysics Data System (ADS)

    Zhu, Xiaofang; Yang, Zhonghai; Li, Bin; Li, Jianqing; Xu, Li

    2010-02-01

    To validate HFCS-I, a newly developed design tool for high frequency circuits of microwave tubes, the high-frequency parameters (including dispersion, interaction impedance and attenuation constant) of a typical helical slow-wave structure (SWS) for millimetre wave travelling-wave tube are calculated by HFCS-I and MAFIA. Both the direct calculation method and the Non-Resonant Perturbation (NRP) technique are adopted to get the interaction impedance. The obtained high-frequency parameters from HFCS-I and MAFIA are compared in detail and the consistency has proved the reliability and validity of HFCS-I.

  16. A Case Study on the Application of a Structured Experimental Method for Optimal Parameter Design of a Complex Control System

    NASA Technical Reports Server (NTRS)

    Torres-Pomales, Wilfredo

    2015-01-01

    This report documents a case study on the application of Reliability Engineering techniques to achieve an optimal balance between performance and robustness by tuning the functional parameters of a complex non-linear control system. For complex systems with intricate and non-linear patterns of interaction between system components, analytical derivation of a mathematical model of system performance and robustness in terms of functional parameters may not be feasible or cost-effective. The demonstrated approach is simple, structured, effective, repeatable, and cost and time efficient. This general approach is suitable for a wide range of systems.

  17. Corticothalamic dynamics: Structure of parameter space, spectra, instabilities, and reduced model

    NASA Astrophysics Data System (ADS)

    Roberts, J. A.; Robinson, P. A.

    2012-01-01

    Linear instabilities are analyzed in a physiologically based mean-field corticothalamic model and a reduced-parameter model derived from it. In both models, the stable zone corresponding to normal arousal states is bounded by a series of surfaces demarcating the onsets of instabilities. The stable zone is found to depend on delay and rate parameters, whose values have a simple relationship to the number of instabilities and dominant frequencies on the stable zone's boundary. The dominant frequencies of linear activity inside the stable zone are found to lie in clearly delineated regions, each corresponding to an instability surface on its boundary and having approximately the same dominant frequency. These regions are ordered in parameter space according to their dominant frequencies, and an instability associated with the intrathalamic loop is shown to have the highest frequency that can become unstable. This reveals an important role for the thalamus in controlling the stability and bandwidth of dynamics in the corticothalamic system as a whole. The reduced model is found to agree well with the full model in a wide region of parameter space and, thus, is a useful guide to the full model's dynamics.

  18. Influence of Spatial Resolution on SiC Industrial Foam's Structural Parameters Obtained by X-ray Microtomography

    NASA Astrophysics Data System (ADS)

    Nagata, Rodrigo; Appoloni, Carlos R.; Marques, Leonardo C.; Fernandes, Jaquiel S.

    2011-08-01

    X-rays microtomography is a non-destructive technique that generates digital images of samples' internal structure by attenuation of an X-rays beam. The samples' structural parameters are obtained from these images by specific software analysis. This means that the image quality is essential to perform a suitable structural characterization. The spatial resolution is one of the main parameters that contribute to image quality. In this work the influence of spatial resolution for industrial SiC ceramic foam's analysis was evaluated. The samples' pore density was 60 pores per inch (ppi). This kind of foam can operate at high temperatures, which allow them to be used as liquid metal filters, heat exchangers or composite of rocket nozzles, for example. The measurements were performed with a SkyScan microtomograph, model 1172. It was operated at 50 kV and 60 kV high voltage for measurements with 24.8 μm and 2.5 μm spatial resolution, respectively. The total porosity and the pore size distribution were the structural parameters studied. They were obtained by Imago software. The total porosity results were statistically equivalent for both resolutions, but the comparison of the microtomographic images datasets and pore size distributions of both resolutions showed differences that enhances the importance of the spatial resolution for a complete characterization of the sample internal microstructure.

  19. Structure and electrical characterization of gallium arsenide nanowires with different V/III ratio growth parameters

    SciTech Connect

    Muhammad, R.; Ahamad, R.; Ibrahim, Z.; Othaman, Z.

    2014-03-05

    Gallium arsenide (GaAs) nanowires were grown vertically on GaAs(111)B substrate by gold-assisted using metal-organic chemical vapour deposition. Field-emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM) and conductivity atomic force microscopy (CAFM) analysis were carried out to investigate the effects of V/III ratio on structural properties and current-voltage changes in the wires. Results show that GaAs NWs grow preferably in the wurtzite crystal structure than zinc blende crystal structure with increasing V/III ratio. Additionally, CAFM studies have revealed that zincblende nanowires indicate ohmic characteristic compared to oscillation current occurred for wurtzite structures. The GaAs NWs with high quality structures are needed in solar cells technology for trapping energy that directly converts of sunlight into electricity with maximum capacity.

  20. Fullwaveform inversion for structure and source parameters using regional data recorded in eastern Kazakhstan. Final report, 1 September 1990-1 September 1992

    SciTech Connect

    Harvey, D.J.

    1993-04-01

    We have completed a study which was aimed at obtaining fundamental understanding of regional wave propagation by attempting to match synthetic seismograms with real data. The first part of this study involved the identification and analysis of a set of local and regional seismic events recorded near the former Soviet test site at Semipalatinsk. We then applied full waveform inversion in the 0.5 to 1 Hertz frequency band to selected events to extract source and structure parameters. We found that for certain source-receiver paths we could do an excellent job of matching complete seismograms on radial and vertical components up to a frequency of one Hertz including P, S and Rg phases using shallow explosion sources. For other source-receiver paths the fits were not so good using shallow explosion sources, however we obtained good fits on all three components by assuming a 5 km deep earth source. These results indicate that waveform inversion can be used to discriminate small shallow explosions from small relatively shallow earthquakes and that structural effects can be accurately modeled in this region up to a frequency of 1 Hertz.... Regional events, Source discrimination, Waveform inversion, Waveform modeling.

  1. Identification of the structure parameters using short-time non-stationary stochastic excitation

    NASA Astrophysics Data System (ADS)

    Jarczewska, Kamila; Koszela, Piotr; Śniady, PaweŁ; Korzec, Aleksandra

    2011-07-01

    In this paper, we propose an approach to the flexural stiffness or eigenvalue frequency identification of a linear structure using a non-stationary stochastic excitation process. The idea of the proposed approach lies within time domain input-output methods. The proposed method is based on transforming the dynamical problem into a static one by integrating the input and the output signals. The output signal is the structure reaction, i.e. structure displacements due to the short-time, irregular load of random type. The systems with single and multiple degrees of freedom, as well as continuous systems are considered.

  2. The reduced order model problem in distributed parameter systems adaptive identification and control. [large space structures

    NASA Technical Reports Server (NTRS)

    Johnson, C. R., Jr.; Lawrence, D.

    1981-01-01

    The basic assumption that a large space structure can be decoupled preceding the application of reduced order active control was considered and alternative solutions to the control of such structures (in contrast to the strict modal control) were investigated. The transfer function matrix from the actuators to the sensors was deemed to be a reasonable candidate. More refined models from multivariable systems theory were studied and recent results in the multivariable control field were compared with respect to theoretical deficiencies and likely problems in application to large space structures.

  3. Effects of correlated parameters and uncertainty in electronic-structure-based chemical kinetic modelling.

    PubMed

    Sutton, Jonathan E; Guo, Wei; Katsoulakis, Markos A; Vlachos, Dionisios G

    2016-04-01

    Kinetic models based on first principles are becoming common place in heterogeneous catalysis because of their ability to interpret experimental data, identify the rate-controlling step, guide experiments and predict novel materials. To overcome the tremendous computational cost of estimating parameters of complex networks on metal catalysts, approximate quantum mechanical calculations are employed that render models potentially inaccurate. Here, by introducing correlative global sensitivity analysis and uncertainty quantification, we show that neglecting correlations in the energies of species and reactions can lead to an incorrect identification of influential parameters and key reaction intermediates and reactions. We rationalize why models often underpredict reaction rates and show that, despite the uncertainty being large, the method can, in conjunction with experimental data, identify influential missing reaction pathways and provide insights into the catalyst active site and the kinetic reliability of a model. The method is demonstrated in ethanol steam reforming for hydrogen production for fuel cells. PMID:27001728

  4. Effects of correlated parameters and uncertainty in electronic-structure-based chemical kinetic modelling

    NASA Astrophysics Data System (ADS)

    Sutton, Jonathan E.; Guo, Wei; Katsoulakis, Markos A.; Vlachos, Dionisios G.

    2016-04-01

    Kinetic models based on first principles are becoming common place in heterogeneous catalysis because of their ability to interpret experimental data, identify the rate-controlling step, guide experiments and predict novel materials. To overcome the tremendous computational cost of estimating parameters of complex networks on metal catalysts, approximate quantum mechanical calculations are employed that render models potentially inaccurate. Here, by introducing correlative global sensitivity analysis and uncertainty quantification, we show that neglecting correlations in the energies of species and reactions can lead to an incorrect identification of influential parameters and key reaction intermediates and reactions. We rationalize why models often underpredict reaction rates and show that, despite the uncertainty being large, the method can, in conjunction with experimental data, identify influential missing reaction pathways and provide insights into the catalyst active site and the kinetic reliability of a model. The method is demonstrated in ethanol steam reforming for hydrogen production for fuel cells.

  5. A theoretical study of the influence of technological friction stir welding parameters on weld structures

    NASA Astrophysics Data System (ADS)

    Astafurov, Sergey; Shilko, Evgeny; Kolubaev, Evgeny; Psakhie, Sergey

    2015-10-01

    Computer simulation by the movable cellular automaton method was performed to study the dynamics of friction stir welding of duralumin plates. It was shown that the ratio of the rotation rate to the translational velocity of the rotating tool has a great influence on the quality of the welded joint. A suitably chosen ratio of these parameters combined with an additional ultrasonic impact reduces considerably the porosity and the amount of microcracks in the weld.

  6. Relativistic Calculating the Spectral Lines Hyperfine Structure Parameters for Heavy Ions

    SciTech Connect

    Khetselius, O. Yu.

    2008-10-22

    The energies and constants of the hyperfine structure, derivatives of the one-electron characteristics on nuclear radius, nuclear electric quadrupole, magnetic dipole moments for some Li-like multicharged ions are calculated.

  7. Vegetation structure determination using LIDAR data and the forest growth parameters

    NASA Astrophysics Data System (ADS)

    Rybansky, M.; Brenova, M.; Cermak, J.; van Genderen, J.; Sivertun, Å.

    2016-06-01

    The goal of this paper is to identify the main vegetation factors in the terrain, which are important for the analysis of forest structure. Such an analysis is important for forestry, rescue operations management during crises situations and disasters such as fires, storms, earthquakes and military analysis (transportation, cover, concealment, etc.). For the forest structure determination, both LIDAR and the forest growth prediction analysis were used. As main results, the vegetation height, tree spacing and stem diameters were determined

  8. Mathematical model relating uniaxial compressive behavior of manufactured sand mortar to MIP-derived pore structure parameters.

    PubMed

    Tian, Zhenghong; Bu, Jingwu

    2014-01-01

    The uniaxial compression response of manufactured sand mortars proportioned using different water-cement ratio and sand-cement ratio is examined. Pore structure parameters such as porosity, threshold diameter, mean diameter, and total amounts of macropores, as well as shape and size of micropores are quantified by using mercury intrusion porosimetry (MIP) technique. Test results indicate that strains at peak stress and compressive strength decreased with the increasing sand-cement ratio due to insufficient binders to wrap up entire sand. A compression stress-strain model of normal concrete extending to predict the stress-strain relationships of manufactured sand mortar is verified and agreed well with experimental data. Furthermore, the stress-strain model constant is found to be influenced by threshold diameter, mean diameter, shape, and size of micropores. A mathematical model relating stress-strain model constants to the relevant pore structure parameters of manufactured sand mortar is developed.

  9. Mathematical Model Relating Uniaxial Compressive Behavior of Manufactured Sand Mortar to MIP-Derived Pore Structure Parameters

    PubMed Central

    Tian, Zhenghong; Bu, Jingwu

    2014-01-01

    The uniaxial compression response of manufactured sand mortars proportioned using different water-cement ratio and sand-cement ratio is examined. Pore structure parameters such as porosity, threshold diameter, mean diameter, and total amounts of macropores, as well as shape and size of micropores are quantified by using mercury intrusion porosimetry (MIP) technique. Test results indicate that strains at peak stress and compressive strength decreased with the increasing sand-cement ratio due to insufficient binders to wrap up entire sand. A compression stress-strain model of normal concrete extending to predict the stress-strain relationships of manufactured sand mortar is verified and agreed well with experimental data. Furthermore, the stress-strain model constant is found to be influenced by threshold diameter, mean diameter, shape, and size of micropores. A mathematical model relating stress-strain model constants to the relevant pore structure parameters of manufactured sand mortar is developed. PMID:25133257

  10. Fermi surface and order parameter driven vortex lattice structure transitions in twin-free YBa2Cu3O7.

    PubMed

    White, J S; Hinkov, V; Heslop, R W; Lycett, R J; Forgan, E M; Bowell, C; Strässle, S; Abrahamsen, A B; Laver, M; Dewhurst, C D; Kohlbrecher, J; Gavilano, J L; Mesot, J; Keimer, B; Erb, A

    2009-03-01

    We report on small-angle neutron scattering studies of the intrinsic vortex lattice (VL) structure in detwinned YBa2Cu3O7 at 2 K, and in fields up to 10.8 T. Because of the suppressed pinning to twin-domain boundaries, a new distorted hexagonal VL structure phase is stabilized at intermediate fields. It is separated from a low-field hexagonal phase of different orientation and distortion by a first-order transition at 2.0(2) T that is probably driven by Fermi surface effects. We argue that another first-order transition at 6.7(2) T, into a rhombic structure with a distortion of opposite sign, marks a crossover from a regime where Fermi surface anisotropy is dominant, to one where the VL structure and distortion is controlled by the order-parameter anisotropy. PMID:19392554

  11. The Devil is in the Details: Using X-Ray Computed Tomography to Develop Accurate 3D Grain Characteristics and Bed Structure Metrics for Gravel Bed Rivers

    NASA Astrophysics Data System (ADS)

    Voepel, H.; Hodge, R. A.; Leyland, J.; Sear, D. A.; Ahmed, S. I.

    2014-12-01

    Uncertainty for bedload estimates in gravel bed rivers is largely driven by our inability to characterize the arrangement and orientation of the sediment grains within the bed. The characteristics of the surface structure are produced by the water working of grains, which leads to structural differences in bedforms through differential patterns of grain sorting, packing, imbrication, mortaring and degree of bed armoring. Until recently the technical and logistical difficulties of characterizing the arrangement of sediment in 3D have prohibited a full understanding of how grains interact with stream flow and the feedback mechanisms that exist. Micro-focus X-ray CT has been used for non-destructive 3D imaging of grains within a series of intact sections of river bed taken from key morphological units (see Figure 1). Volume, center of mass, points of contact, protrusion and spatial orientation of individual surface grains are derived from these 3D images, which in turn, facilitates estimates of 3D static force properties at the grain-scale such as pivoting angles, buoyancy and gravity forces, and grain exposure. By aggregating representative samples of grain-scale properties of localized interacting sediment into overall metrics, we can compare and contrast bed stability at a macro-scale with respect to stream bed morphology. Understanding differences in bed stability through representative metrics derived at the grain-scale will ultimately lead to improved bedload estimates with reduced uncertainty and increased understanding of interactions between grain-scale properties on channel morphology. Figure 1. CT-Scans of a water worked gravel-filled pot. a. 3D rendered scan showing the outer mesh, and b. the same pot with the mesh removed. c. vertical change in porosity of the gravels sampled in 5mm volumes. Values are typical of those measured in the field and lab. d. 2-D slices through the gravels at 20% depth from surface (porosity = 0.35), and e. 75% depth from

  12. Accurate Optical Reference Catalogs

    NASA Astrophysics Data System (ADS)

    Zacharias, N.

    2006-08-01

    Current and near future all-sky astrometric catalogs on the ICRF are reviewed with the emphasis on reference star data at optical wavelengths for user applications. The standard error of a Hipparcos Catalogue star position is now about 15 mas per coordinate. For the Tycho-2 data it is typically 20 to 100 mas, depending on magnitude. The USNO CCD Astrograph Catalog (UCAC) observing program was completed in 2004 and reductions toward the final UCAC3 release are in progress. This all-sky reference catalogue will have positional errors of 15 to 70 mas for stars in the 10 to 16 mag range, with a high degree of completeness. Proper motions for the about 60 million UCAC stars will be derived by combining UCAC astrometry with available early epoch data, including yet unpublished scans of the complete set of AGK2, Hamburg Zone astrograph and USNO Black Birch programs. Accurate positional and proper motion data are combined in the Naval Observatory Merged Astrometric Dataset (NOMAD) which includes Hipparcos, Tycho-2, UCAC2, USNO-B1, NPM+SPM plate scan data for astrometry, and is supplemented by multi-band optical photometry as well as 2MASS near infrared photometry. The Milli-Arcsecond Pathfinder Survey (MAPS) mission is currently being planned at USNO. This is a micro-satellite to obtain 1 mas positions, parallaxes, and 1 mas/yr proper motions for all bright stars down to about 15th magnitude. This program will be supplemented by a ground-based program to reach 18th magnitude on the 5 mas level.

  13. Band-structure calculations of noble-gas and alkali halide solids using accurate Kohn-Sham potentials with self-interaction correction

    SciTech Connect

    Li, Y.; Krieger, J.B. ); Norman, M.R. ); Iafrate, G.J. )

    1991-11-15

    The optimized-effective-potential (OEP) method and a method developed recently by Krieger, Li, and Iafrate (KLI) are applied to the band-structure calculations of noble-gas and alkali halide solids employing the self-interaction-corrected (SIC) local-spin-density (LSD) approximation for the exchange-correlation energy functional. The resulting band gaps from both calculations are found to be in fair agreement with the experimental values. The discrepancies are typically within a few percent with results that are nearly the same as those of previously published orbital-dependent multipotential SIC calculations, whereas the LSD results underestimate the band gaps by as much as 40%. As in the LSD---and it is believed to be the case even for the exact Kohn-Sham potential---both the OEP and KLI predict valence-band widths which are narrower than those of experiment. In all cases, the KLI method yields essentially the same results as the OEP.

  14. Parameter splitting in dark energy: is dark energy the same in the background and in the cosmic structures?

    NASA Astrophysics Data System (ADS)

    Bernal, José Luis; Verde, Licia; Cuesta, Antonio J.

    2016-02-01

    We perform an empirical consistency test of General Relativity/dark energy by disentangling expansion history and growth of structure constraints. We replace each late-universe parameter that describes the behavior of dark energy with two meta-parameters: one describing geometrical information in cosmological probes, and the other controlling the growth of structure. If the underlying model (a standard wCDM cosmology with General Relativity) is correct, that is under the null hypothesis, the two meta-parameters coincide. If they do not, it could indicate a failure of the model or systematics in the data. We present a global analysis using state-of-the-art cosmological data sets which points in the direction that cosmic structures prefer a weaker growth than that inferred by background probes. This result could signify inconsistencies of the model, the necessity of extensions to it or the presence of systematic errors in the data. We examine all these possibilities. The fact that the result is mostly driven by a specific sub-set of galaxy clusters abundance data, points to the need of a better understanding of this probe.

  15. Magnetic and atomic structure parameters of Sc-doped barium hexagonal ferrites

    NASA Astrophysics Data System (ADS)

    Yang, Aria; Chen, Yajie; Chen, Zhaohui; Vittoria, Carmine; Harris, V. G.

    2008-04-01

    Scandium-doped M-type barium hexagonal ferrites of the composition BaFe12-xScxO19 are well suited for low frequency microwave device applications such as isolators and circulators. A series of Sc-doped M-type barium hexagonal ferrite powders (x =0-1.2) were prepared by conventional ceramic processing techniques. The resulting powders were verified to be pure phase and maintain the nominal chemical stoichiometry by x-ray diffraction and energy dispersive x-ray spectroscopy, respectively. Static magnetic measurements indicated that both saturation magnetization and uniaxial magnetocrystalline anisotropy field decreased with increasing concentration of scandium. Extended x-ray absorption fine structure measurements were carried out to clarify the correlation between the magnetic and atomic structure properties. It is found that the substituted Sc has a strong preference for the bipyramidal site. Nevertheless, the substitution did not introduce additional atomic structural disorder into the barium hexagonal structure. The structural study provided important evidence to quantitatively explain the change in dc and microwave magnetic properties due to Sc ion doping.

  16. Improved segmentation of deep brain grey matter structures using magnetization transfer (MT) parameter maps

    PubMed Central

    Helms, Gunther; Draganski, Bogdan; Frackowiak, Richard; Ashburner, John; Weiskopf, Nikolaus

    2009-01-01

    Basal ganglia and brain stem nuclei are involved in the pathophysiology of various neurological and neuropsychiatric disorders. Currently available structural T1-weighted (T1w) magnetic resonance images do not provide sufficient contrast for reliable automated segmentation of various subcortical grey matter structures. We use a novel, semi-quantitative magnetization transfer (MT) imaging protocol that overcomes limitations in T1w images, which are mainly due to their sensitivity to the high iron content in subcortical grey matter. We demonstrate improved automated segmentation of putamen, pallidum, pulvinar and substantia nigra using MT images. A comparison with segmentation of high-quality T1w images was performed in 49 healthy subjects. Our results show that MT maps are highly suitable for automated segmentation, and so for multi-subject morphometric studies with a focus on subcortical structures. PMID:19344771

  17. Determination by spaceborne backscatter lidar of the structural parameters of atmospheric scattering layers.

    PubMed

    Chazette, P; Pelon, J; Mégie, G

    2001-07-20

    Spaceborne active lidar systems are under development to give new insight into the vertical distribution of clouds and aerosols in the atmosphere and to provide new information on variables required for improvement of forecast models and for understanding the radiative and dynamic processes that are linked to the dynamics of climate change. However, when they are operated from space, lidar systems are limited by atmospheric backscattered signals that have low signal-to-noise ratios (SNRs) on optically thin targets. Therefore specific methods of analysis have to be developed to ensure accurate determination of the geometric and optical properties of scattering layers in the atmosphere. A first approach to retrieving the geometric properties of semitransparent cloud and aerosol layers is presented as a function of false-alarm and no-detection probabilities for a given SNR. Simulations show that the geometric properties of thin cirrus clouds and the altitude of the top of the unstable atmospheric boundary layer can be retrieved with standard deviations smaller than 150 m for a vertical resolution of the lidar system in the 50-100-m range and a SNR of 3. The altitudes of the top of dense clouds are retrieved with a precision in altitude of better than 50 m, as this retrieval corresponds to a higher SNR value. Such methods have an important potential application to future spaceborne lidar missions.

  18. Sampling of Stochastic Input Parameters for Rockfall Calculations and for Structural Response Calculations Under Vibratory Ground Motion

    SciTech Connect

    M. Gross

    2004-09-01

    The purpose of this scientific analysis is to define the sampled values of stochastic (random) input parameters for (1) rockfall calculations in the lithophysal and nonlithophysal zones under vibratory ground motions, and (2) structural response calculations for the drip shield and waste package under vibratory ground motions. This analysis supplies: (1) Sampled values of ground motion time history and synthetic fracture pattern for analysis of rockfall in emplacement drifts in nonlithophysal rock (Section 6.3 of ''Drift Degradation Analysis'', BSC 2004 [DIRS 166107]); (2) Sampled values of ground motion time history and rock mechanical properties category for analysis of rockfall in emplacement drifts in lithophysal rock (Section 6.4 of ''Drift Degradation Analysis'', BSC 2004 [DIRS 166107]); (3) Sampled values of ground motion time history and metal to metal and metal to rock friction coefficient for analysis of waste package and drip shield damage to vibratory motion in ''Structural Calculations of Waste Package Exposed to Vibratory Ground Motion'' (BSC 2004 [DIRS 167083]) and in ''Structural Calculations of Drip Shield Exposed to Vibratory Ground Motion'' (BSC 2003 [DIRS 163425]). The sampled values are indices representing the number of ground motion time histories, number of fracture patterns and rock mass properties categories. These indices are translated into actual values within the respective analysis and model reports or calculations. This report identifies the uncertain parameters and documents the sampled values for these parameters. The sampled values are determined by GoldSim V6.04.007 [DIRS 151202] calculations using appropriate distribution types and parameter ranges. No software development or model development was required for these calculations. The calculation of the sampled values allows parameter uncertainty to be incorporated into the rockfall and structural response calculations that support development of the seismic scenario for the

  19. Motion and vibration control of a slewing flexible structure by SMA actuators and parameter sensitivity analysis

    NASA Astrophysics Data System (ADS)

    Janzen, F. C.; Tusset, A. M.; Piccirillo, V.; Balthazar, J. M.; Brasil, R. M. L. R. F.

    2015-11-01

    This work presents two approaches to the problem of vibration and positioning control of a flexible structural beam driven by a DC motor. The position is controlled by the current applied to the DC motor armature. A Shape Memory Alloy (SMA) actuator controls vibrations of the flexible structural beam. The State Dependent Riccati Equation (SDRE) technique is used to provide a control action which uses sub-optimal control and system local stability search. The robustness of these two controllers is tested by sensitivity analysis to parametric uncertainties. Numerical simulations results are presented to demonstrate the effectiveness of the proposed control strategy.

  20. Generalized parity relations for large space structures with uncertain parameters. M.S. Thesis

    NASA Technical Reports Server (NTRS)

    Dutilloy, J. R.

    1986-01-01

    The generalized parity relations method is a technique that can be used to detect sensor and actuator failures on a large space structure. A model of a grid structure was used to evaluate the performance of these relations. It shows their relative sensitivity to modeling errors. A method using sensor outputs and actuator inputs is required for the design of the generalized parity relations. Three different estimators are studied. The last estimator can generate relations optimized for the detection of a particular failure which are interesting when the level of sensor noise is high.

  1. Material properties of evolutionary diverse spider silks described by variation in a single structural parameter

    NASA Astrophysics Data System (ADS)

    Madurga, Rodrigo; Plaza, Gustavo R.; Blackledge, Todd A.; Guinea, Gustavo. V.; Elices, Manuel; Pérez-Rigueiro, José

    2016-01-01

    Spider major ampullate gland silks (MAS) vary greatly in material properties among species but, this variation is shown here to be confined to evolutionary shifts along a single universal performance trajectory. This reveals an underlying design principle that is maintained across large changes in both spider ecology and silk chemistry. Persistence of this design principle becomes apparent after the material properties are defined relative to the true alignment parameter, which describes the orientation and stretching of the protein chains in the silk fiber. Our results show that the mechanical behavior of all Entelegynae major ampullate silk fibers, under any conditions, are described by this single parameter that connects the sequential action of three deformation micromechanisms during stretching: stressing of protein-protein hydrogen bonds, rotation of the β-nanocrystals and growth of the ordered fraction. Conservation of these traits for over 230 million years is an indication of the optimal design of the material and gives valuable clues for the production of biomimetic counterparts based on major ampullate spider silk.

  2. Material properties of evolutionary diverse spider silks described by variation in a single structural parameter

    PubMed Central

    Madurga, Rodrigo; Plaza, Gustavo R.; Blackledge, Todd A.; Guinea, Gustavo.V.; Elices, Manuel; Pérez-Rigueiro, José

    2016-01-01

    Spider major ampullate gland silks (MAS) vary greatly in material properties among species but, this variation is shown here to be confined to evolutionary shifts along a single universal performance trajectory. This reveals an underlying design principle that is maintained across large changes in both spider ecology and silk chemistry. Persistence of this design principle becomes apparent after the material properties are defined relative to the true alignment parameter, which describes the orientation and stretching of the protein chains in the silk fiber. Our results show that the mechanical behavior of all Entelegynae major ampullate silk fibers, under any conditions, are described by this single parameter that connects the sequential action of three deformation micromechanisms during stretching: stressing of protein-protein hydrogen bonds, rotation of the β-nanocrystals and growth of the ordered fraction. Conservation of these traits for over 230 million years is an indication of the optimal design of the material and gives valuable clues for the production of biomimetic counterparts based on major ampullate spider silk. PMID:26755434

  3. Hunting for hydrogen: random structure searching and prediction of NMR parameters of hydrous wadsleyite† †Electronic supplementary information (ESI) available: Further information on the structures generated by AIRSS, alternative structural models, supercell calculations, total enthalpies of all computed structures and further information on 1H/2H NMR parameters. Example input and all raw output files from AIRSS and CASTEP NMR calculations are also included. See DOI: 10.1039/c6cp01529h Click here for additional data file.

    PubMed Central

    Moran, Robert F.; McKay, David; Pickard, Chris J.; Berry, Andrew J.; Griffin, John M.

    2016-01-01

    The structural chemistry of materials containing low levels of nonstoichiometric hydrogen is difficult to determine, and producing structural models is challenging where hydrogen has no fixed crystallographic site. Here we demonstrate a computational approach employing ab initio random structure searching (AIRSS) to generate a series of candidate structures for hydrous wadsleyite (β-Mg2SiO4 with 1.6 wt% H2O), a high-pressure mineral proposed as a repository for water in the Earth's transition zone. Aligning with previous experimental work, we solely consider models with Mg3 (over Mg1, Mg2 or Si) vacancies. We adapt the AIRSS method by starting with anhydrous wadsleyite, removing a single Mg2+ and randomly placing two H+ in a unit cell model, generating 819 candidate structures. 103 geometries were then subjected to more accurate optimisation under periodic DFT. Using this approach, we find the most favourable hydration mechanism involves protonation of two O1 sites around the Mg3 vacancy. The formation of silanol groups on O3 or O4 sites (with loss of stable O1–H hydroxyls) coincides with an increase in total enthalpy. Importantly, the approach we employ allows observables such as NMR parameters to be computed for each structure. We consider hydrous wadsleyite (∼1.6 wt%) to be dominated by protonated O1 sites, with O3/O4–H silanol groups present as defects, a model that maps well onto experimental studies at higher levels of hydration (J. M. Griffin et al., Chem. Sci., 2013, 4, 1523). The AIRSS approach adopted herein provides the crucial link between atomic-scale structure and experimental studies. PMID:27020937

  4. Multiscale structures of lipids in foods as parameters affecting fatty acid bioavailability and lipid metabolism.

    PubMed

    Michalski, M C; Genot, C; Gayet, C; Lopez, C; Fine, F; Joffre, F; Vendeuvre, J L; Bouvier, J; Chardigny, J M; Raynal-Ljutovac, K

    2013-10-01

    On a nutritional standpoint, lipids are now being studied beyond their energy content and fatty acid (FA) profiles. Dietary FA are building blocks of a huge diversity of more complex molecules such as triacylglycerols (TAG) and phospholipids (PL), themselves organised in supramolecular structures presenting different thermal behaviours. They are generally embedded in complex food matrixes. Recent reports have revealed that molecular and supramolecular structures of lipids and their liquid or solid state at the body temperature influence both the digestibility and metabolism of dietary FA. The aim of the present review is to highlight recent knowledge on the impact on FA digestion, absorption and metabolism of: (i) the intramolecular structure of TAG; (ii) the nature of the lipid molecules carrying FA; (iii) the supramolecular organization and physical state of lipids in native and formulated food products and (iv) the food matrix. Further work should be accomplished now to obtain a more reliable body of evidence and integrate these data in future dietary recommendations. Additionally, innovative lipid formulations in which the health beneficial effects of either native or recomposed structures of lipids will be taken into account can be foreseen.

  5. EVOLUTION OF BRIGHTEST CLUSTER GALAXY STRUCTURAL PARAMETERS IN THE LAST {approx}6 Gyr: FEEDBACK PROCESSES VERSUS MERGER EVENTS

    SciTech Connect

    Ascaso, B.; Aguerri, J. A. L.; Varela, J.; Cava, A.; Moles, M.

    2011-01-10

    We present results on the evolution of the structural parameters of two samples of brightest cluster galaxies (BCGs) in the last 6 Gyr. The nearby sample of BCGs consists of 69 galaxies from the WINGS survey spanning a redshift range of 0.04 < z < 0.07. The intermediate-redshift (0.3 < z < 0.6) sample is formed by 20 BCGs extracted from the Hubble Space Telescope archive. Both samples have similar spatial resolution and their host clusters have similar X-ray luminosities. We report an increase in the size of the BCGs from intermediate to local redshift. However, we do not detect any variation in the Sersic shape parameter in both samples. These results prove to be robust since the observed tendencies are model independent. We also obtain significant correlations between some of the BCG parameters and the main properties of the host clusters. More luminous, larger, and centrally located BCGs are located in more massive and dominant galaxy clusters. These facts indicate that the host galaxy cluster has played an important role in the formation of their BCGs. We discuss the possible mechanisms that can explain the observed evolution of the structural parameters of the BCGs. We conclude that the main mechanisms that can explain the increase in size and the non-evolution in the Sersic shape parameter of the BCGs in the last 6 Gyr are feedback processes. This result disagrees with semi-analytical simulation results supporting the idea that merging processes are the main mechanism responsible for the evolution of the BCGs up until the present epoch.

  6. Method for accurate growth of vertical-cavity surface-emitting lasers

    DOEpatents

    Chalmers, S.A.; Killeen, K.P.; Lear, K.L.

    1995-03-14

    The authors report a method for accurate growth of vertical-cavity surface-emitting lasers (VCSELs). The method uses a single reflectivity spectrum measurement to determine the structure of the partially completed VCSEL at a critical point of growth. This information, along with the extracted growth rates, allows imprecisions in growth parameters to be compensated for during growth of the remaining structure, which can then be completed with very accurate critical dimensions. Using this method, they can now routinely grow lasing VCSELs with Fabry-Perot cavity resonance wavelengths controlled to within 0.5%. 4 figs.

  7. Method for accurate growth of vertical-cavity surface-emitting lasers

    DOEpatents

    Chalmers, Scott A.; Killeen, Kevin P.; Lear, Kevin L.

    1995-01-01

    We report a method for accurate growth of vertical-cavity surface-emitting lasers (VCSELs). The method uses a single reflectivity spectrum measurement to determine the structure of the partially completed VCSEL at a critical point of growth. This information, along with the extracted growth rates, allows imprecisions in growth parameters to be compensated for during growth of the remaining structure, which can then be completed with very accurate critical dimensions. Using this method, we can now routinely grow lasing VCSELs with Fabry-Perot cavity resonance wavelengths controlled to within 0.5%.

  8. An articulated statistical shape model for accurate hip joint segmentation.

    PubMed

    Kainmueller, Dagmar; Lamecker, Hans; Zachow, Stefan; Hege, Hans-Christian

    2009-01-01

    In this paper we propose a framework for fully automatic, robust and accurate segmentation of the human pelvis and proximal femur in CT data. We propose a composite statistical shape model of femur and pelvis with a flexible hip joint, for which we extend the common definition of statistical shape models as well as the common strategy for their adaptation. We do not analyze the joint flexibility statistically, but model it explicitly by rotational parameters describing the bent in a ball-and-socket joint. A leave-one-out evaluation on 50 CT volumes shows that image driven adaptation of our composite shape model robustly produces accurate segmentations of both proximal femur and pelvis. As a second contribution, we evaluate a fine grain multi-object segmentation method based on graph optimization. It relies on accurate initializations of femur and pelvis, which our composite shape model can generate. Simultaneous optimization of both femur and pelvis yields more accurate results than separate optimizations of each structure. Shape model adaptation and graph based optimization are embedded in a fully automatic framework. PMID:19964159

  9. Studies on Pidotimod Enantiomers With Chiralpak-IA: Crystal Structure, Thermodynamic Parameters and Molecular Docking.

    PubMed

    Dou, Xiaorui; Su, Xin; Wang, Yue; Chen, Yadong; Shen, Weiyang

    2015-11-01

    Pidotimod, a synthetic dipeptide, has two chiral centers with biological and immunological activity. Its enantiomers were characterized by x-ray crystallographic analysis. A chiral stationary phase (CSP) Chiralpak-IA based on amylose derivatized with tris-(3, 5-dimethylphenyl carbamate) was used to separate pidotimod enantiomers. The mobile phase was prepared in a ratio of 35:65:0.2 of methyl-tert-butyl-ether and acetonitrile trifluoroaceticacid. In addition, thermodynamics and molecular docking methods were used to explain the enantioseparation mechanism by Chiralpak-IA. Thermodynamic studies were carried out from 10 to 45 °C. In general, both retention and enantioselectivity decreased as the temperature increased. Thermodynamic parameters indicate that the interaction force between the pidotimod enantiomer (4S, 2'R) and IA CSP is stronger and their complex model is more stable. According to GOLD molecular docking simulation, Van der Waals force is the leading cause of pidotimod enantiomers separation by IA CSP.

  10. Effect of preparation parameters on the microporous structure of Ni/SiO{sub 2} catalysts

    SciTech Connect

    Castillon, F.F.; Bodganchikova, N.; Fuentes, S.; Avalos, M.

    1996-12-31

    In this work the authors report the synthesis of Ni/SiO{sub 2} catalysts promoted by group 2 (IIA) cations (calcium and barium) which are currently used as hydrogenation catalysts. The effect of the preparation parameters-aging, base agent, and type of cation, on the surface area of catalysts--is evaluated. Catalysts were prepared by precipitation of the precursor silicic acid, along with nickel nitrate and calcium and barium carbonates, with NaOH, NH{sub 4}OH and Na{sub 2}CO{sub 3} as precipitating agents. Catalysts were characterized by diffuse reflectance spectra (DRS) and by BET-surface area measurements. Results are discussed in terms of sol-gel chemistry.

  11. Effects of structure parameters on the sensor performance of photonic crystal fiber

    NASA Astrophysics Data System (ADS)

    Xiao, Rui; Rong, Zhen; Pang, Yuanfeng; Bo, Xiaochen

    2015-02-01

    A simple and compact sensor based on a photonic crystal fiber (PCF) for the in-situ detection of fluorescence signals with high sensitivity is demonstrated. Several different kinds of PCF probes are studied. The effect of PCF parameters on sensitivity and the guiding mechanisms are analyzed, and the performance of PCF probes is experimentally evaluated by measuring the fluorescence signal of Cy3 dye. In addition, the detection sensitivity of the hollow-core PCF probe and the flat-tippedmulti-mode fiber probe is compared. The experimental results show that the hollow-core PCF probe provides a greater than five-fold increase in detection sensitivity compared with direct measurements by a flat-tippedmulti-mode fiber probe, which shows its potential for wide applications to in-situ detection in the medical, forensic, biological, geological, and environmental fields with high sensitivity.

  12. Humidity's influence on visible region refractive index structure parameter C(n)(2).

    PubMed

    Chang, Mark P J L; Font, Carlos O; Gilbreath, G Charmaine; Oh, Eun

    2007-05-01

    In the near-infrared and visible bandpasses optical propagation theory conventionally assumes that humidity does not contribute to the effects of atmospheric turbulence on optical beams. While this assumption may be reasonable for dry locations, we demonstrate that there is an unequivocal effect owing to the presence of humidity upon the strength of turbulence parameter, C(n)(2), from data collected in the Chesapeake Bay area over 100 m length horizontal propagation paths. We describe and apply a novel technique, Hilbert phase analysis, to the relative humidity, temperature, and C(n)(2) data to show the contribution of the relevant climate variable to C(n)(2) as a function of time.

  13. Mapping magnetized geologic structures from space: The effect of orbital and body parameters

    NASA Technical Reports Server (NTRS)

    Schnetzler, C. C.; Taylor, P. T.; Langel, R. A.

    1984-01-01

    When comparing previous satellite magnetometer missions (such as MAGSAT) with proposed new programs (for example, Geopotential Research Mission, GRM) it is important to quantify the difference in scientific information obtained. The ability to resolve separate magnetic blocks (simulating geological units) is used as a parameter for evaluating the expected geologic information from each mission. The effect of satellite orbital altitude on the ability to resolve two magnetic blocks with varying separations is evaluated and quantified. A systematic, nonlinear, relationship exists between resolution and distance between magnetic blocks as a function of orbital altitude. The proposed GRM would provide an order-of-magnitude greater anomaly resolution than the earlier MAGSAT mission for widely separated bodies. The resolution achieved at any particular altitude varies depending on the location of the bodies and orientation.

  14. Housing land transaction data and structural econometric estimation of preference parameters for urban economic simulation models

    PubMed Central

    Caruso, Geoffrey; Cavailhès, Jean; Peeters, Dominique; Thomas, Isabelle; Frankhauser, Pierre; Vuidel, Gilles

    2015-01-01

    This paper describes a dataset of 6284 land transactions prices and plot surfaces in 3 medium-sized cities in France (Besançon, Dijon and Brest). The dataset includes road accessibility as obtained from a minimization algorithm, and the amount of green space available to households in the neighborhood of the transactions, as evaluated from a land cover dataset. Further to the data presentation, the paper describes how these variables can be used to estimate the non-observable parameters of a residential choice function explicitly derived from a microeconomic model. The estimates are used by Caruso et al. (2015) to run a calibrated microeconomic urban growth simulation model where households are assumed to trade-off accessibility and local green space amenities. PMID:26958606

  15. Studies on Pidotimod Enantiomers With Chiralpak-IA: Crystal Structure, Thermodynamic Parameters and Molecular Docking.

    PubMed

    Dou, Xiaorui; Su, Xin; Wang, Yue; Chen, Yadong; Shen, Weiyang

    2015-11-01

    Pidotimod, a synthetic dipeptide, has two chiral centers with biological and immunological activity. Its enantiomers were characterized by x-ray crystallographic analysis. A chiral stationary phase (CSP) Chiralpak-IA based on amylose derivatized with tris-(3, 5-dimethylphenyl carbamate) was used to separate pidotimod enantiomers. The mobile phase was prepared in a ratio of 35:65:0.2 of methyl-tert-butyl-ether and acetonitrile trifluoroaceticacid. In addition, thermodynamics and molecular docking methods were used to explain the enantioseparation mechanism by Chiralpak-IA. Thermodynamic studies were carried out from 10 to 45 °C. In general, both retention and enantioselectivity decreased as the temperature increased. Thermodynamic parameters indicate that the interaction force between the pidotimod enantiomer (4S, 2'R) and IA CSP is stronger and their complex model is more stable. According to GOLD molecular docking simulation, Van der Waals force is the leading cause of pidotimod enantiomers separation by IA CSP. PMID:26340373

  16. Estimating Geophysical Parameters From Gravity Data

    NASA Technical Reports Server (NTRS)

    Sjogren, William L.; Wimberly, Ravenel N.

    1988-01-01

    ORBSIM program developed for accurate extraction of parameters of geophysical models from Doppler-radio-tracking data acquired from orbiting planetary spacecraft. Model of proposed planetary structure used in numerical integration along simulated trajectories of spacecraft around primary body. Written in FORTRAN 77.

  17. Modelling the effect of structural QSAR parameters on skin penetration using genetic programming

    NASA Astrophysics Data System (ADS)

    Chung, K. K.; Do, D. Q.

    2010-09-01

    In order to model relationships between chemical structures and biological effects in quantitative structure-activity relationship (QSAR) data, an alternative technique of artificial intelligence computing—genetic programming (GP)—was investigated and compared to the traditional method—statistical. GP, with the primary advantage of generating mathematical equations, was employed to model QSAR data and to define the most important molecular descriptions in QSAR data. The models predicted by GP agreed with the statistical results, and the most predictive models of GP were significantly improved when compared to the statistical models using ANOVA. Recently, artificial intelligence techniques have been applied widely to analyse QSAR data. With the capability of generating mathematical equations, GP can be considered as an effective and efficient method for modelling QSAR data.

  18. EFFECT OF DEXTRAN-graft-POLYACRYLAMIDE INTERNAL STRUCTURE ON FLOCCULATION PROCESS PARAMETERS

    SciTech Connect

    Bezugla, T.; Kutsevol, N.; Shyichuk, A.; Ziolkowska, D.

    2008-08-28

    Dextran-graft-Polyacrylamide copolymers (D-g-PAA) of brush-like architecture were tested as flocculation aids in the model kaolin suspensions. Due to expanded conformation the D-g-PAA copolymers are more effective flocculants than individual PAA with close molecular mass. The internal structure of D-g-PAA copolymers which is determined by number and length of grafted PAA chains, the distance between grafts, etc., has the significant influence on flocculation behavior of such polymers.

  19. Effects of Forest Disturbances on Forest Structural Parameters Retrieval from Lidar Waveform Data

    NASA Technical Reports Server (NTRS)

    Ranson, K, Lon; Sun, G.

    2011-01-01

    The effect of forest disturbance on the lidar waveform and the forest biomass estimation was demonstrated by model simulation. The results show that the correlation between stand biomass and the lidar waveform indices changes when the stand spatial structure changes due to disturbances rather than the natural succession. This has to be considered in developing algorithms for regional or global mapping of biomass from lidar waveform data.

  20. Cirrus structure and radiative parameters from airborne lidar and spectral radiometer observations - The 28 October 1986 FIRE study

    NASA Technical Reports Server (NTRS)

    Spinhirne, James D.; Hart, William D.

    1990-01-01

    A description is presented of cirrus based on results from a FIRE observation flight in central Wisconsin on October 28, 1986. Cirrus structure and radiative parameters as determined by the ER-2 lidar and imaging spectral radiometers are presented. From the lidar observations a complex structure was shown with differing cloud layers extending over six kilometers of altitude range. Both thin and dense cirrus layers were present and mixed phase clouds were found at lower altitudes. As indicated by the cloud structure, precipitation of crystals from high, but vertically thin, layers produces a significant fraction of the lower cirrus. Multiple layers should be considered as normal for cirrus formations. It is noted that the cloud height is an important factor for satellite cloud retrievals and cloud climatology.

  1. Effect of anodization parameters on the structural morphology of titanium in fluoride containing electrolytes

    SciTech Connect

    Indira, K.; Ningshen, S.; Mudali, U. Kamachi; Rajendran, N.

    2012-09-15

    In the present work, formation of titania nanopores on titanium substrate was investigated in aqueous (sulphuric acid) and neutral organic (glycerol) electrolytes containing different concentrations of HF (0.1-0.2 M). The surface morphology, topography and phase structures were analyzed using scanning electron microscopy, atomic force microscopy and X-ray diffraction techniques, respectively. Under optimized electrolyte conditions, titania nanopore is obtained with the average pore diameter of 64 nm and 84 nm for aqueous and organic electrolytes, respectively. Atomic force microscope investigation shows that the porous layer forms under a competition of titania formation and oxide dissolution up to a limiting thickness of {approx} 75 nm and 100 nm respectively for aqueous and organic electrolytes. The porous structure was observed at 0.15 M HF concentration. It was found that depending on the electrolytes the pore diameter alters and also its concentration effected the porous structures formation. Compared to aqueous electrolytes, organic electrolytes showed larger diameter pores. From the X-ray diffraction measurement it is evident that the as prepared titania nanopores are amorphous in nature, whereas the anodized heat treated titania nanopores are in anatase phase. - Highlights: Black-Right-Pointing-Pointer Aqueous and organic electrolytes were used to synthesize nanoporous titania. Black-Right-Pointing-Pointer The surface morphology varies with various concentrations of HF. Black-Right-Pointing-Pointer Nanopores were formed at optimum HF concentration of 0.15 M. Black-Right-Pointing-Pointer Nanopore diameter was found to be affected by the electrolyte used.

  2. Integrative modeling of small artery structure and function uncovers critical parameters for diameter regulation.

    PubMed

    VanBavel, Ed; Tuna, Bilge Guvenc

    2014-01-01

    Organ perfusion is regulated by vasoactivity and structural adaptation of small arteries and arterioles. These resistance vessels are sensitive to pressure, flow and a range of vasoactive stimuli. Several strongly interacting control loops exist. As an example, the myogenic response to a change of pressure influences the endothelial shear stress, thereby altering the contribution of shear-dependent dilation to the vascular tone. In addition, acute responses change the stimulus for structural adaptation and vice versa. Such control loops are able to maintain resistance vessels in a functional and stable state, characterized by regulated wall stress, shear stress, matched active and passive biomechanics and presence of vascular reserve. In this modeling study, four adaptation processes are identified that together with biomechanical properties effectuate such integrated regulation: control of tone, smooth muscle cell length adaptation, eutrophic matrix rearrangement and trophic responses. Their combined action maintains arteries in their optimal state, ready to cope with new challenges, allowing continuous long-term vasoregulation. The exclusion of any of these processes results in a poorly regulated state and in some cases instability of vascular structure.

  3. Community Structure of Macrobiota and Environmental Parameters in Shallow Water Hydrothermal Vents off Kueishan Island, Taiwan.

    PubMed

    Chan, Benny Kwok Kan; Wang, Teng-Wei; Chen, Pin-Chen; Lin, Chia-Wei; Chan, Tin-Yam; Tsang, Ling Ming

    2016-01-01

    Hydrothermal vents represent a unique habitat in the marine ecosystem characterized with high water temperature and toxic acidic chemistry. Vents are distributed at depths ranging from a few meters to several thousand meters. The biological communities of shallow-water vents have, however, been insufficiently studied in most biogeographic areas. We attempted to characterize the macrofauna and macroflora community inhabiting the shallow-water vents off Kueishan Island, Taiwan, to identify the main abiotic factors shaping the community structure and the species distribution. We determined that positively buoyant vent fluid exhibits a more pronounced negative impact to species on the surface water than on the bottom layer. Species richness increased with horizontal distance from the vent, and continuing for a distance of 2000 m, indicating that the vent fluid may exert a negative impact over several kilometers. The community structure off Kueishan Island displayed numerous transitions along the horizontal gradient, which were broadly congruent with changes in environmental conditions. Combination of variation in Ca2+, Cl-, temperature, pH and depth were revealed to show the strongest correlation with the change in benthic community structure, suggesting multiple factors of vent fluid were influencing the associated fauna. Only the vent crabs of Kueishan Island may have an obligated relationship with vents and inhabit the vent mouths because other fauna found nearby are opportunistic taxa that are more tolerant to acidic and toxic environments. PMID:26849440

  4. Community Structure of Macrobiota and Environmental Parameters in Shallow Water Hydrothermal Vents off Kueishan Island, Taiwan.

    PubMed

    Chan, Benny Kwok Kan; Wang, Teng-Wei; Chen, Pin-Chen; Lin, Chia-Wei; Chan, Tin-Yam; Tsang, Ling Ming

    2016-01-01

    Hydrothermal vents represent a unique habitat in the marine ecosystem characterized with high water temperature and toxic acidic chemistry. Vents are distributed at depths ranging from a few meters to several thousand meters. The biological communities of shallow-water vents have, however, been insufficiently studied in most biogeographic areas. We attempted to characterize the macrofauna and macroflora community inhabiting the shallow-water vents off Kueishan Island, Taiwan, to identify the main abiotic factors shaping the community structure and the species distribution. We determined that positively buoyant vent fluid exhibits a more pronounced negative impact to species on the surface water than on the bottom layer. Species richness increased with horizontal distance from the vent, and continuing for a distance of 2000 m, indicating that the vent fluid may exert a negative impact over several kilometers. The community structure off Kueishan Island displayed numerous transitions along the horizontal gradient, which were broadly congruent with changes in environmental conditions. Combination of variation in Ca2+, Cl-, temperature, pH and depth were revealed to show the strongest correlation with the change in benthic community structure, suggesting multiple factors of vent fluid were influencing the associated fauna. Only the vent crabs of Kueishan Island may have an obligated relationship with vents and inhabit the vent mouths because other fauna found nearby are opportunistic taxa that are more tolerant to acidic and toxic environments.

  5. Community Structure of Macrobiota and Environmental Parameters in Shallow Water Hydrothermal Vents off Kueishan Island, Taiwan

    PubMed Central

    Chan, Benny Kwok Kan; Wang, Teng-Wei; Chen, Pin-Chen; Lin, Chia-Wei; Chan, Tin-Yam; Tsang, Ling Ming

    2016-01-01

    Hydrothermal vents represent a unique habitat in the marine ecosystem characterized with high water temperature and toxic acidic chemistry. Vents are distributed at depths ranging from a few meters to several thousand meters. The biological communities of shallow-water vents have, however, been insufficiently studied in most biogeographic areas. We attempted to characterize the macrofauna and macroflora community inhabiting the shallow-water vents off Kueishan Island, Taiwan, to identify the main abiotic factors shaping the community structure and the species distribution. We determined that positively buoyant vent fluid exhibits a more pronounced negative impact to species on the surface water than on the bottom layer. Species richness increased with horizontal distance from the vent, and continuing for a distance of 2000 m, indicating that the vent fluid may exert a negative impact over several kilometers. The community structure off Kueishan Island displayed numerous transitions along the horizontal gradient, which were broadly congruent with changes in environmental conditions. Combination of variation in Ca2+, Cl-, temperature, pH and depth were revealed to show the strongest correlation with the change in benthic community structure, suggesting multiple factors of vent fluid were influencing the associated fauna. Only the vent crabs of Kueishan Island may have an obligated relationship with vents and inhabit the vent mouths because other fauna found nearby are opportunistic taxa that are more tolerant to acidic and toxic environments. PMID:26849440

  6. A new method for measuring the imaginary part of refractive index structure parameter in the urban surface layer

    NASA Astrophysics Data System (ADS)

    Yuan, R.; Luo, T.; Sun, J.; Zeng, Z.; Fu, Y.

    2014-08-01

    Atmospheric refractive index consists of both the real and the imaginary parts. The intensity of refractive index fluctuation is usually expressed as the refractive index structure parameter, whose real part reflects the strength of the atmospheric turbulence while the imaginary part reflects the absorption in the light path. The large aperture scintillometer (LAS) is often used to measure the structure parameter of the real part of atmospheric refractive index, and the sensible and latent heat fluxes can further be obtained, while the influence of the imaginary part is ignored, or thought to be a noise. Based on the expression for the spectrum of the logarithmic light intensity fluctuation caused by the imaginary part of refractive index, new expressions for the logarithmic intensity fluctuation variance and the structure function related to the imaginary part of refractive index are derived. Then a simple expression for the imaginary part of the atmospheric refractive index structure parameter (ARISP) is obtained. It can be conveniently used to measure the imaginary part of the ARISP from LAS. Experiments of light propagation were performed in the urban surface layer and the imaginary part of the ARISP was calculated. The experimental results showed a good agreement with the presented theory. The results also suggested that, the imaginary part of ARISP shows a different variation from the real part of ARISP. For the light with the wavelength of 0.62 μm, the variation of the imaginary part of ARISP is related to both the turbulent transport process and the spatial distribution characteristics of aerosols. Based on the theoretical analysis, it can be expected that the method presented in this study can be applied to measuring the imaginary part of the ARISP caused by the trace gas, if the light wavelength is selected within the corresponding gas absorption region.

  7. A new method for measuring the imaginary part of the atmospheric refractive index structure parameter in the urban surface layer

    NASA Astrophysics Data System (ADS)

    Yuan, R.; Luo, T.; Sun, J.; Zeng, Z.; Ge, C.; Fu, Y.

    2015-03-01

    The atmospheric refractive index consists of both real and imaginary parts. The intensity of refractive index fluctuations is generally expressed as the refractive index structure parameter, with the real part reflecting the strength of atmospheric turbulence and the imaginary part reflecting absorption in the light path. A large aperture scintillometer (LAS) is often used to measure the structure parameter of the real part of the atmospheric refractive index, from which the sensible and latent heat fluxes can further be obtained, whereas the influence of the imaginary part is ignored or considered noise. In this theoretical analysis study, the relationship between logarithmic light intensity variance and the atmospheric refractive index structure parameter (ARISP), as well as that between the logarithmic light intensity structure function and the ARISP, is derived. Additionally, a simple expression for the imaginary part of the ARISP is obtained which can be conveniently used to determine the imaginary part of the ARISP from LAS measurements. Moreover, these relationships provide a new method for estimating the outer scale of turbulence. Light propagation experiments were performed in the urban surface layer, from which the imaginary part of the ARISP was calculated. The experimental results showed good agreement with the presented theory. The results also suggest that the imaginary part of the ARISP exhibits a different diurnal variation from that of the real part. For the wavelength of light used (0.62 μm), the variation of the imaginary part of the ARISP is related to both the turbulent transport process and the spatial distribution characteristics of aerosols.

  8. On how to avoid input and structural uncertainties corrupt the inference of hydrological parameters using a Bayesian framework

    NASA Astrophysics Data System (ADS)

    Hernández, Mario R.; Francés, Félix

    2015-04-01

    One phase of the hydrological models implementation process, significantly contributing to the hydrological predictions uncertainty, is the calibration phase in which values of the unknown model parameters are tuned by optimizing an objective function. An unsuitable error model (e.g. Standard Least Squares or SLS) introduces noise into the estimation of the parameters. The main sources of this noise are the input errors and the hydrological model structural deficiencies. Thus, the biased calibrated parameters cause the divergence model phenomenon, where the errors variance of the (spatially and temporally) forecasted flows far exceeds the errors variance in the fitting period, and provoke the loss of part or all of the physical meaning of the modeled processes. In other words, yielding a calibrated hydrological model which works well, but not for the right reasons. Besides, an unsuitable error model yields a non-reliable predictive uncertainty assessment. Hence, with the aim of prevent all these undesirable effects, this research focuses on the Bayesian joint inference (BJI) of both the hydrological and error model parameters, considering a general additive (GA) error model that allows for correlation, non-stationarity (in variance and bias) and non-normality of model residuals. As hydrological model, it has been used a conceptual distributed model called TETIS, with a particular split structure of the effective model parameters. Bayesian inference has been performed with the aid of a Markov Chain Monte Carlo (MCMC) algorithm called Dream-ZS. MCMC algorithm quantifies the uncertainty of the hydrological and error model parameters by getting the joint posterior probability distribution, conditioned on the observed flows. The BJI methodology is a very powerful and reliable tool, but it must be used correctly this is, if non-stationarity in errors variance and bias is modeled, the Total Laws must be taken into account. The results of this research show that the

  9. Parameter Optimization and Field Validation of the Functional–Structural Model GREENLAB for Maize at Different Population Densities

    PubMed Central

    Ma, Yuntao; Wen, Meiping; Guo, Yan; Li, Baoguo; Cournède, Paul-Henry; de Reffye, Philippe

    2008-01-01

    Background and Aims Plant population density (PPD) influences plant growth greatly. Functional–structural plant models such as GREENLAB can be used to simulate plant development and growth and PPD effects on plant functioning and architectural behaviour can be investigated. This study aims to evaluate the ability of GREENLAB to predict maize growth and development at different PPDs. Methods Two field experiments were conducted on irrigated fields in the North China Plain with a block design of four replications. Each experiment included three PPDs: 2·8, 5·6 and 11·1 plants m−2. Detailed observations were made on the dimensions and fresh biomass of above-ground plant organs for each phytomer throughout the seasons. Growth stage-specific target files (a description of plant organ weight and dimension according to plant topological structure) were established from the measured data required for GREENLAB parameterization. Parameter optimization was conducted using a generalized least square method for the entire growth cycles for all PPDs and years. Data from in situ plant digitization were used to establish geometrical symbol files for organs that were then applied to translate model output directly into 3-D representation for each time step of the model execution. Key Results The analysis indicated that the parameter values of organ sink variation function, and the values of most of the relative sink strength parameters varied little among years and PPDs, but the biomass production parameter, computed plant projection surface and internode relative sink strength varied with PPD. Simulations of maize plant growth based on the fitted parameters were reasonably good as indicated by the linearity and slopes similar to unity for the comparison of simulated and observed values. Based on the parameter values fitted from different PPDs, shoot (including vegetative and reproductive parts of the plant) and cob fresh biomass for other PPDs were simulated. Three

  10. Short Time Impulse Response Function (STIRF) for automatic evaluation of the variation of the dynamic parameters of reinforced concrete framed structures during strong earthquakes.

    NASA Astrophysics Data System (ADS)

    Carlo Ponzo, Felice; Ditommaso, Rocco

    2015-04-01

    This study presents an innovative strategy for automatic evaluation of the variable fundamental frequency and related damping factor of nonlinear structures during strong motion phases. Most of methods for damage detection are based on the assessment of the variations of the dynamic parameters characterizing the monitored structure. A crucial aspect of these methods is the automatic and accurate estimation of both structural eigen-frequencies and related damping factors also during the nonlinear behaviour. A new method, named STIRF (Short-Time Impulse Response Function - STIRF), based on the nonlinear interferometric analysis combined with the Fourier Transform (FT) here is proposed in order to allow scientists and engineers to characterize frequencies and damping variations of a monitored structure. The STIRF approach helps to overcome some limitation derived from the use of techniques based on simple Fourier Transform. These latter techniques provide good results when the response of the monitored system is stationary, but fails when the system exhibits a non-stationary, time-varying behaviour: even non-stationary input, soil-foundation and/or adjacent structures interaction phenomena can show the inadequacy of classic techniques to analysing the nonlinear and/or non-stationary behaviour of structures. In fact, using this kind of approach it is possible to improve some of the existing methods for the automatic damage detection providing stable results also during the strong motion phase. Results are consistent with those expected if compared with other techniques. The main advantage derived from the use of the proposed approach (STIRF) for Structural Health Monitoring is based on the simplicity of the interpretation of the nonlinear variations of the fundamental frequency and the related equivalent viscous damping factor. The proposed methodology has been tested on both numerical and experimental models also using data retrieved from shaking table tests. Based on

  11. A theoretical DFT study on the structural parameters and azide-tetrazole equilibrium in substituted azidothiazole systems

    NASA Astrophysics Data System (ADS)

    Abu-Eittah, Rafie H.; El-Kelany, Khaled E.

    2012-12-01

    Azido-tetrazole equilibrium is sensitive to: substitution, solvent, temperature and phase. In this work, the effects of the type and position of substitution on the thiazole ring of azidothiazoles on its structural parameters and on the azido-tetrazole equilibrium have been theoretically investigated using the density functional procedures at the B3LYP/6-311G∗∗ level of theory. This study includes the investigation of the equilibrium geometry, the transformation of the trans-conformer to the cis one then the ring closure to the tetrazole isomer. The transition states of the two steps were located, confirmed and the structural parameters were calculated. In all the steps of calculations, geometry optimization was considered. The results obtained indicate that substitution by: -NO2 and -CN group shifts the equilibrium to the azide side and in some cases the tetrazole isomer is not obtained. On the other hand, substitution by: -NH2 and -OH groups shifts the equilibrium to the tetrazole side and in some cases the azide isomer is not obtained and if formed changes spontaneously to the tetrazole isomer. The decisive parameters which determine the position of the equilibrium are: charge density on atoms N3 and N8, rearrangement of bond length and bond angles during the process of cyclization and variation of dipole moment as a result of cyclization. Results of this work indicate that substitution on C5 is more efficient than substitution on C4 of the thiazole ring.

  12. Developing Accurate Spatial Maps of Cotton Fiber Quality Parameters

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Awareness of the importance of cotton fiber quality (Gossypium, L. sps.) has increased as advances in spinning technology require better quality cotton fiber. Recent advances in geospatial information sciences allow an improved ability to study the extent and causes of spatial variability in fiber p...

  13. [Structural state of the pancreas and coprogram parameters for assessment patients with chronic pancreatitis after cholecystectomy].

    PubMed

    Babinets', L S; Nazarchuk, N V; Kytsaĭ, K Iu

    2014-11-01

    Reviewed by a structural condition of the pancreas by ultrasound and scores from the Marseille-Cambridge classification in patients with chronic biliary pancreatitis, including those who had a history of cholecystectomy. Found that after cholecystectomy gland size decreased slightly, but significantly fibrosis is increased. Chronic inflammation and fibrosis of the gland leads to inhibition of both acinar and ductal secretory function, leads to its external and internal secretion deficiency. In assessing coprogram found that most patients with CP present with signs of exocrine insufficiency, including steatorrhea and kreatorrhea that are most pronounced in patients with CP after open cholecystectomy.

  14. Structural parameters and their effects on the electronic transport properties in aperiodic superlattice profile

    NASA Astrophysics Data System (ADS)

    Bendahma, F.; Djelti, R.; Bentata, S.

    2016-08-01

    The aperiodic GaAs/AlxGa1-xAs superlattices (SL) with trimer disorder have been studied in this paper. The transfer-matrix technique and the exact Airy function formalism have been used to determine the miniband structure, the transmission coefficient, the resonance energy and resonant tunneling time (RTT). Although the disorder localizes the states on average, our numerical calculations show that the localization length of the states becomes more extended when the disorder is correlated (trimer case). We have also found that the RTT is of the order of several femtoseconds.

  15. Estimating forest LAI profiles and structural parameters using a ground-based laser called 'Echidna'.

    PubMed

    Jupp, David L B; Culvenor, D S; Lovell, J L; Newnham, G J; Strahler, A H; Woodcock, C E

    2009-02-01

    There are many techniques for measuring leaf area index (LAI) and forest canopy foliage profiles but their accuracy is questionable. This paper briefly reviews current methods of estimating forest LAI and presents a novel, ground-based laser system, Echidna that can make a wide range of measurements of forest structure, including LAI. Here, use of the system to provide field data and derived gap probabilities in the form of a 'hemispherical photograph with range' is demonstrated. The results show consistency and reproducibility and do not depend on special conditions for the natural light field. PMID:19203942

  16. Influence of position and parameters of inhomogeneities on vortex structure in long Josephson junctions

    NASA Astrophysics Data System (ADS)

    Andreeva, O. Yu; Boyadjiev, T. L.; Shukrinov, Yu M.

    2008-10-01

    Numerical experiment results on long Josephson junction with one and two rectangular inhomogeneities in the barrier layer are presented. We demonstrate the efiect of the shifting of the inhomogeneity and the value of the Josephson current on the vortex structure. The disappearance of mixed fluxon-antifluxon states is shown when the position of inhomogeneity shifted to the end of the junction. A change of the amplitude of Josephson current at the end makes a strong efiect on the stability of the fluxon states and smoothes the maximums of the dependence 'critical current-magnetic field'.

  17. Bone structural parameters, dosimetry, and relative radiation risk in the beagle skeleton

    SciTech Connect

    Polig, E.; Jee, W.S. )

    1989-10-01

    A variety of morphometric and histomorphometric parameters such as the mass of bone and marrow, bone surface areas, percentage of bone volume, percentage of the surface that is trabecular, and percentage of surfaces that are forming and resting are calculated for all major parts of the beagle skeleton. The total bone surface of the beagle is estimated at 2.9 m2 with 53.7% of the surface area being associated with trabecular bone. There are about 4.5 x 10(9) bone-lining cells and about 1 x 10(9) osteoblasts. From the fractional retention in each part of the skeleton, the initial surface concentration of 239Pu after a single injection of 592 Bq/kg body wt (0.016 microCi/kg) on resting surfaces and at sites of bone formation is calculated for various values of the affinity ratios of trabecular/cortical and forming/resting surfaces. These estimated concentrations then yield dose rates as well as cumulative and collective doses to bone-lining cells and osteoblasts in the different parts of the skeleton. On the assumption that the relative risk of tumor induction is proportional to the collective dose to either bone-lining cells or osteoblasts, the frequency of tumor occurrence is calculated and compared to observed frequencies. Both hypotheses yield approximate agreement with experimental data for different ratios of trabecular/cortical radiation sensitivity, although the differences between some bones are statistically significant.

  18. Mexican mestizo population sub-structure: effects on genetic and forensic statistical parameters.

    PubMed

    Noris, Gino; Santana, Carla; Meraz-Ríos, Marco Antonio; de Lourdes Munoz, María; Majluf-Cruz, Abraham; Magaña, Jonathan J; Granados, Julio; Quezada, Rosa; Revilla, María Cristina; Martínez-Salas, Sergio; Xihuitl, Salvador; Martínez de la Escalera, Gonzalo; Díaz-Badillo, Alvaro; Calderon-Aranda, Emma S; Gómez, Rocío

    2012-12-01

    Since Mexican mestizos are an admixed population, it is necessary to determine the effects that the substructure of the population has on genetic and forensic parameters. With this aim, a study was performed with 15 STR loci (CODIS plus D2S1338 and D19S433) on 1,640 unrelated Mexican mestizos. We determine allele and genotypic frequencies observing departure from Hardy-Weinberg expectation (12 out of 15 loci, with an excess of homozygotes, Fis > 0), as well as pairs of loci in an apparent linkage disequilibrium (13 of 92 loci). We conducted a test for genetic population stratification, the results show that the Mexican mestizo population is substructured into three subgroups, which are in HW and linkage equilibrium. The combination of the 15 loci in the whole population has high forensic efficiency with the capacity to genetically discriminate one individual in one quintillion (1/10(18)). Our data potentially validates the use of these 15 STR loci to establish forensic identity and parentage testing for legal purposes, and offers a powerful tool for genetic variation analysis. However, given that the population is stratified, we highly recommend applying a correction with the inbreeding coefficient in calculations of paternity and forensic studies to avoid erroneous assumptions.

  19. Estimation of the refractive index structure parameter from single-level daytime routine weather data.

    PubMed

    van de Boer, A; Moene, A F; Graf, A; Simmer, C; Holtslag, A A M

    2014-09-10

    Atmospheric scintillations cause difficulties for applications where an undistorted propagation of electromagnetic radiation is essential. These scintillations are related to turbulent fluctuations of temperature and humidity that are in turn related to surface heat fluxes. We developed an approach that quantifies these scintillations by estimating C(n(2)) from surface fluxes that are derived from single-level routine weather data. In contrast to previous methods that are biased to dry and warm air, our method is directly applicable to several land surface types, environmental conditions, wavelengths, and measurement heights (lookup tables for a limited number of site-specific parameters are provided). The approach allows for an efficient evaluation of the performance of, e.g., infrared imaging systems, laser geodetic systems, and ground-to-satellite optical communication systems. We tested our approach for two grass fields in central and southern Europe, and for a wheat field in central Europe. Although there are uncertainties in the flux estimates, the impact on C(n(2)) is shown to be rather small. The C(n(2)) daytime estimates agree well with values determined from eddy covariance measurements for the application to the three fields. However, some adjustments were needed for the approach for the grass in southern Europe because of non-negligible boundary-layer processes that occur in addition to surface-layer processes.

  20. Probing NMR parameters, structure and dynamics of 5-nitroimidazole derivatives. Density functional study of prototypical radiosensitizers.

    PubMed

    Ramalho, Teodorico C; Bühl, Michael

    2005-02-01

    The 15N chemical shifts of metronidazole (1), secnidazole (2), nimorazole (3) and tinidazole (4), radiosensitizers based on the 5-nitroimidazole motif, are reported. A detailed computational study of 1 is presented, calling special attention to the performance of various theoretical methods in reproducing the 13C and 15N data observed in solution. The most sophisticated approach involves density functional-based Car-Parrinello molecular dynamics simulations (CPMD) of 1 in aqueous solution (BP86 level) and averaging chemical shifts over snapshots from the trajectory. In the NMR calculations for these snapshots (performed at the B3LYP level), a small number of discrete water molecules are retained, and the remaining bulk solution effects are included via a polarizable continuum model (PCM). A similarly good accord with experiment is obtained from much less involved, static geometry optimization and NMR computation of pristine 1 employing a PCM approach. Solvent effects on delta(15N), which are of the order of up to 20 ppm, are not due to changes in geometric parameters upon solvation, but arise from the direct response of the electronic wavefunction to the presence of the solvent, which can be represented by discrete molecules and/or the dielectric bulk. PMID:15558660