PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements.

PubMed

Tang, Yat T; Marshall, Garland R

2011-02-28

Binding affinity prediction is one of the most critical components to computer-aided structure-based drug design. Despite advances in first-principle methods for predicting binding affinity, empirical scoring functions that are fast and only relatively accurate are still widely used in structure-based drug design. With the increasing availability of X-ray crystallographic structures in the Protein Data Bank and continuing application of biophysical methods such as isothermal titration calorimetry to measure thermodynamic parameters contributing to binding free energy, sufficient experimental data exists that scoring functions can now be derived by separating enthalpic (ΔH) and entropic (TΔS) contributions to binding free energy (ΔG). PHOENIX, a scoring function to predict binding affinities of protein-ligand complexes, utilizes the increasing availability of experimental data to improve binding affinity predictions by the following: model training and testing using high-resolution crystallographic data to minimize structural noise, independent models of enthalpic and entropic contributions fitted to thermodynamic parameters assumed to be thermodynamically biased to calculate binding free energy, use of shape and volume descriptors to better capture entropic contributions. A set of 42 descriptors and 112 protein-ligand complexes were used to derive functions using partial least-squares for change of enthalpy (ΔH) and change of entropy (TΔS) to calculate change of binding free energy (ΔG), resulting in a predictive r2 (r(pred)2) of 0.55 and a standard error (SE) of 1.34 kcal/mol. External validation using the 2009 version of the PDBbind "refined set" (n = 1612) resulted in a Pearson correlation coefficient (R(p)) of 0.575 and a mean error (ME) of 1.41 pK(d). Enthalpy and entropy predictions were of limited accuracy individually. However, their difference resulted in a relatively accurate binding free energy. While the development of an accurate and applicable scoring function was an objective of this study, the main focus was evaluation of the use of high-resolution X-ray crystal structures with high-quality thermodynamic parameters from isothermal titration calorimetry for scoring function development. With the increasing application of structure-based methods in molecular design, this study suggests that using high-resolution crystal structures, separating enthalpy and entropy contributions to binding free energy, and including descriptors to better capture entropic contributions may prove to be effective strategies toward rapid and accurate calculation of binding affinity.

Accurate structural and spectroscopic characterization of prebiotic molecules: The neutral and cationic acetyl cyanide and their related species.

PubMed

Bellili, A; Linguerri, R; Hochlaf, M; Puzzarini, C

2015-11-14

In an effort to provide an accurate structural and spectroscopic characterization of acetyl cyanide, its two enolic isomers and the corresponding cationic species, state-of-the-art computational methods, and approaches have been employed. The coupled-cluster theory including single and double excitations together with a perturbative treatment of triples has been used as starting point in composite schemes accounting for extrapolation to the complete basis-set limit as well as core-valence correlation effects to determine highly accurate molecular structures, fundamental vibrational frequencies, and rotational parameters. The available experimental data for acetyl cyanide allowed us to assess the reliability of our computations: structural, energetic, and spectroscopic properties have been obtained with an overall accuracy of about, or better than, 0.001 Å, 2 kcal/mol, 1-10 MHz, and 11 cm(-1) for bond distances, adiabatic ionization potentials, rotational constants, and fundamental vibrational frequencies, respectively. We are therefore confident that the highly accurate spectroscopic data provided herein can be useful for guiding future experimental investigations and/or astronomical observations.

Vfold: a web server for RNA structure and folding thermodynamics prediction.

PubMed

Xu, Xiaojun; Zhao, Peinan; Chen, Shi-Jie

2014-01-01

The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

Light-propagation management in coupled waveguide arrays: Quantitative experimental and theoretical assessment from band structures to functional patterns

NASA Astrophysics Data System (ADS)

Moison, Jean-Marie; Belabas, Nadia; Levenson, Juan Ariel; Minot, Christophe

2012-09-01

We assess the band structure of arrays of coupled optical waveguides both by ab initio calculations and by experiments, with an excellent quantitative agreement without any adjustable physical parameter. The band structures we obtain can deviate strongly from the expectations of the standard coupled mode theory approximation, but we describe them efficiently by a few parameters within an extended coupled mode theory. We also demonstrate that this description is in turn a firm and simple basis for accurate beam management in functional patterns of coupled waveguides, in full accordance with their design.

Surface effect investigation on multipactor in microwave components using the EM-PIC method

NASA Astrophysics Data System (ADS)

Li, Yun; Ye, Ming; He, Yong-Ning; Cui, Wan-Zhao; Wang, Dan

2017-11-01

Multipactor poses a great risk to microwave components in space and its accurate controllable suppression is still lacking. To evaluate the secondary electron emission (SEE) of arbitrary surface states on multipactor, metal samples fabricated with ideal smoothness, random roughness, and micro-structures on the surface are investigated through SEE experiments and multipactor simulations. An accurate quantitative relationship between the SEE parameters and the multipactor discharge threshold in practical components has been established through Electromagnetic Particle-In-Cell (EM-PIC) simulation. Simulation results of microwave components, including the impedance transformer and the coaxial filter, exhibit an intuitive correlation between the critical SEE parameters, varied due to different surface states, and multipactor thresholds. It is demonstrated that it is the surface micro-structures with certain depth and morphology that determine the average yield of secondaries, other than the random surface relieves. Both the random surface relieves and micro-structures have a scattering effect on SEE, and the yield is prone to be identical upon different elevation angles of incident electrons. It possesses a great potential in the optimization and improvement of suppression technology without the exhaustion of the technological parameter.

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.

Combined electrochemical, heat generation, and thermal model for large prismatic lithium-ion batteries in real-time applications

NASA Astrophysics Data System (ADS)

Farag, Mohammed; Sweity, Haitham; Fleckenstein, Matthias; Habibi, Saeid

2017-08-01

Real-time prediction of the battery's core temperature and terminal voltage is very crucial for an accurate battery management system. In this paper, a combined electrochemical, heat generation, and thermal model is developed for large prismatic cells. The proposed model consists of three sub-models, an electrochemical model, heat generation model, and thermal model which are coupled together in an iterative fashion through physicochemical temperature dependent parameters. The proposed parameterization cycles identify the sub-models' parameters separately by exciting the battery under isothermal and non-isothermal operating conditions. The proposed combined model structure shows accurate terminal voltage and core temperature prediction at various operating conditions while maintaining a simple mathematical structure, making it ideal for real-time BMS applications. Finally, the model is validated against both isothermal and non-isothermal drive cycles, covering a broad range of C-rates, and temperature ranges [-25 °C to 45 °C].

Algorithmic detectability threshold of the stochastic block model

NASA Astrophysics Data System (ADS)

Kawamoto, Tatsuro

2018-03-01

The assumption that the values of model parameters are known or correctly learned, i.e., the Nishimori condition, is one of the requirements for the detectability analysis of the stochastic block model in statistical inference. In practice, however, there is no example demonstrating that we can know the model parameters beforehand, and there is no guarantee that the model parameters can be learned accurately. In this study, we consider the expectation-maximization (EM) algorithm with belief propagation (BP) and derive its algorithmic detectability threshold. Our analysis is not restricted to the community structure but includes general modular structures. Because the algorithm cannot always learn the planted model parameters correctly, the algorithmic detectability threshold is qualitatively different from the one with the Nishimori condition.

Efficient and accurate approach to modeling the microstructure and defect properties of LaCoO3

NASA Astrophysics Data System (ADS)

Buckeridge, J.; Taylor, F. H.; Catlow, C. R. A.

2016-04-01

Complex perovskite oxides are promising materials for cathode layers in solid oxide fuel cells. Such materials have intricate electronic, magnetic, and crystalline structures that prove challenging to model accurately. We analyze a wide range of standard density functional theory approaches to modeling a highly promising system, the perovskite LaCoO3, focusing on optimizing the Hubbard U parameter to treat the self-interaction of the B-site cation's d states, in order to determine the most appropriate method to study defect formation and the effect of spin on local structure. By calculating structural and electronic properties for different magnetic states we determine that U =4 eV for Co in LaCoO3 agrees best with available experiments. We demonstrate that the generalized gradient approximation (PBEsol +U ) is most appropriate for studying structure versus spin state, while the local density approximation (LDA +U ) is most appropriate for determining accurate energetics for defect properties.

An Indirect System Identification Technique for Stable Estimation of Continuous-Time Parameters of the Vestibulo-Ocular Reflex (VOR)

NASA Technical Reports Server (NTRS)

Kukreja, Sunil L.; Wallin, Ragnar; Boyle, Richard D.

2013-01-01

The vestibulo-ocular reflex (VOR) is a well-known dual mode bifurcating system that consists of slow and fast modes associated with nystagmus and saccade, respectively. Estimation of continuous-time parameters of nystagmus and saccade models are known to be sensitive to estimation methodology, noise and sampling rate. The stable and accurate estimation of these parameters are critical for accurate disease modelling, clinical diagnosis, robotic control strategies, mission planning for space exploration and pilot safety, etc. This paper presents a novel indirect system identification method for the estimation of continuous-time parameters of VOR employing standardised least-squares with dual sampling rates in a sparse structure. This approach permits the stable and simultaneous estimation of both nystagmus and saccade data. The efficacy of this approach is demonstrated via simulation of a continuous-time model of VOR with typical parameters found in clinical studies and in the presence of output additive noise.

An accurate metric for the spacetime around rotating neutron stars

NASA Astrophysics Data System (ADS)

Pappas, George

2017-04-01

The problem of having an accurate description of the spacetime around rotating neutron stars is of great astrophysical interest. For astrophysical applications, one needs to have a metric that captures all the properties of the spacetime around a rotating neutron star. Furthermore, an accurate appropriately parametrized metric, I.e. a metric that is given in terms of parameters that are directly related to the physical structure of the neutron star, could be used to solve the inverse problem, which is to infer the properties of the structure of a neutron star from astrophysical observations. In this work, we present such an approximate stationary and axisymmetric metric for the exterior of rotating neutron stars, which is constructed using the Ernst formalism and is parametrized by the relativistic multipole moments of the central object. This metric is given in terms of an expansion on the Weyl-Papapetrou coordinates with the multipole moments as free parameters and is shown to be extremely accurate in capturing the physical properties of a neutron star spacetime as they are calculated numerically in general relativity. Because the metric is given in terms of an expansion, the expressions are much simpler and easier to implement, in contrast to previous approaches. For the parametrization of the metric in general relativity, the recently discovered universal 3-hair relations are used to produce a three-parameter metric. Finally, a straightforward extension of this metric is given for scalar-tensor theories with a massless scalar field, which also admit a formulation in terms of an Ernst potential.

Accurate Determination of the Frequency Response Function of Submerged and Confined Structures by Using PZT-Patches†.

PubMed

Presas, Alexandre; Valentin, David; Egusquiza, Eduard; Valero, Carme; Egusquiza, Mònica; Bossio, Matias

2017-03-22

To accurately determine the dynamic response of a structure is of relevant interest in many engineering applications. Particularly, it is of paramount importance to determine the Frequency Response Function (FRF) for structures subjected to dynamic loads in order to avoid resonance and fatigue problems that can drastically reduce their useful life. One challenging case is the experimental determination of the FRF of submerged and confined structures, such as hydraulic turbines, which are greatly affected by dynamic problems as reported in many cases in the past. The utilization of classical and calibrated exciters such as instrumented hammers or shakers to determine the FRF in such structures can be very complex due to the confinement of the structure and because their use can disturb the boundary conditions affecting the experimental results. For such cases, Piezoelectric Patches (PZTs), which are very light, thin and small, could be a very good option. Nevertheless, the main drawback of these exciters is that the calibration as dynamic force transducers (relationship voltage/force) has not been successfully obtained in the past. Therefore, in this paper, a method to accurately determine the FRF of submerged and confined structures by using PZTs is developed and validated. The method consists of experimentally determining some characteristic parameters that define the FRF, with an uncalibrated PZT exciting the structure. These parameters, which have been experimentally determined, are then introduced in a validated numerical model of the tested structure. In this way, the FRF of the structure can be estimated with good accuracy. With respect to previous studies, where only the natural frequencies and mode shapes were considered, this paper discuss and experimentally proves the best excitation characteristic to obtain also the damping ratios and proposes a procedure to fully determine the FRF. The method proposed here has been validated for the structure vibrating in air comparing the FRF experimentally obtained with a calibrated exciter (impact Hammer) and the FRF obtained with the described method. Finally, the same methodology has been applied for the structure submerged and close to a rigid wall, where it is extremely important to not modify the boundary conditions for an accurate determination of the FRF. As experimentally shown in this paper, in such cases, the use of PZTs combined with the proposed methodology gives much more accurate estimations of the FRF than other calibrated exciters typically used for the same purpose. Therefore, the validated methodology proposed in this paper can be used to obtain the FRF of a generic submerged and confined structure, without a previous calibration of the PZT.

Extended Czjzek model applied to NMR parameter distributions in sodium metaphosphate glass

NASA Astrophysics Data System (ADS)

Vasconcelos, Filipe; Cristol, Sylvain; Paul, Jean-François; Delevoye, Laurent; Mauri, Francesco; Charpentier, Thibault; Le Caër, Gérard

2013-06-01

The extended Czjzek model (ECM) is applied to the distribution of NMR parameters of a simple glass model (sodium metaphosphate, NaPO3) obtained by molecular dynamics (MD) simulations. Accurate NMR tensors, electric field gradient (EFG) and chemical shift anisotropy (CSA) are calculated from density functional theory (DFT) within the well-established PAW/GIPAW framework. The theoretical results are compared to experimental high-resolution solid-state NMR data and are used to validate the considered structural model. The distributions of the calculated coupling constant CQ ∝ |Vzz| and the asymmetry parameter ηQ that characterize the quadrupolar interaction are discussed in terms of structural considerations with the help of a simple point charge model. Finally, the ECM analysis is shown to be relevant for studying the distribution of CSA tensor parameters and gives new insight into the structural characterization of disordered systems by solid-state NMR.

Extended Czjzek model applied to NMR parameter distributions in sodium metaphosphate glass.

PubMed

Vasconcelos, Filipe; Cristol, Sylvain; Paul, Jean-François; Delevoye, Laurent; Mauri, Francesco; Charpentier, Thibault; Le Caër, Gérard

2013-06-26

The extended Czjzek model (ECM) is applied to the distribution of NMR parameters of a simple glass model (sodium metaphosphate, NaPO3) obtained by molecular dynamics (MD) simulations. Accurate NMR tensors, electric field gradient (EFG) and chemical shift anisotropy (CSA) are calculated from density functional theory (DFT) within the well-established PAW/GIPAW framework. The theoretical results are compared to experimental high-resolution solid-state NMR data and are used to validate the considered structural model. The distributions of the calculated coupling constant C(Q) is proportional to |V(zz)| and the asymmetry parameter η(Q) that characterize the quadrupolar interaction are discussed in terms of structural considerations with the help of a simple point charge model. Finally, the ECM analysis is shown to be relevant for studying the distribution of CSA tensor parameters and gives new insight into the structural characterization of disordered systems by solid-state NMR.

Anisotropic Effects on Constitutive Model Parameters of Aluminum Alloys

DTIC Science & Technology

2012-01-01

constants are required input to computer codes (LS-DYNA, DYNA3D or SPH ) to accurately simulate fragment impact on structural components made of high...different temperatures. These model constants are required input to computer codes (LS-DYNA, DYNA3D or SPH ) to accurately simulate fragment impact on...ADDRESS(ES) Naval Surface Warfare Center,4104Evans Way Suite 102,Indian Head,MD,20640 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING/MONITORING

Application of nonlinear least-squares regression to ground-water flow modeling, west-central Florida

USGS Publications Warehouse

Yobbi, D.K.

2000-01-01

A nonlinear least-squares regression technique for estimation of ground-water flow model parameters was applied to an existing model of the regional aquifer system underlying west-central Florida. The regression technique minimizes the differences between measured and simulated water levels. Regression statistics, including parameter sensitivities and correlations, were calculated for reported parameter values in the existing model. Optimal parameter values for selected hydrologic variables of interest are estimated by nonlinear regression. Optimal estimates of parameter values are about 140 times greater than and about 0.01 times less than reported values. Independently estimating all parameters by nonlinear regression was impossible, given the existing zonation structure and number of observations, because of parameter insensitivity and correlation. Although the model yields parameter values similar to those estimated by other methods and reproduces the measured water levels reasonably accurately, a simpler parameter structure should be considered. Some possible ways of improving model calibration are to: (1) modify the defined parameter-zonation structure by omitting and/or combining parameters to be estimated; (2) carefully eliminate observation data based on evidence that they are likely to be biased; (3) collect additional water-level data; (4) assign values to insensitive parameters, and (5) estimate the most sensitive parameters first, then, using the optimized values for these parameters, estimate the entire data set.

Toward Improved Force-Field Accuracy through Sensitivity Analysis of Host-Guest Binding Thermodynamics

PubMed Central

Yin, Jian; Fenley, Andrew T.; Henriksen, Niel M.; Gilson, Michael K.

2015-01-01

Improving the capability of atomistic computer models to predict the thermodynamics of noncovalent binding is critical for successful structure-based drug design, and the accuracy of such calculations remains limited by non-optimal force field parameters. Ideally, one would incorporate protein-ligand affinity data into force field parametrization, but this would be inefficient and costly. We now demonstrate that sensitivity analysis can be used to efficiently tune Lennard-Jones parameters of aqueous host-guest systems for increasingly accurate calculations of binding enthalpy. These results highlight the promise of a comprehensive use of calorimetric host-guest binding data, along with existing validation data sets, to improve force field parameters for the simulation of noncovalent binding, with the ultimate goal of making protein-ligand modeling more accurate and hence speeding drug discovery. PMID:26181208

Marginal space learning for efficient detection of 2D/3D anatomical structures in medical images.

PubMed

Zheng, Yefeng; Georgescu, Bogdan; Comaniciu, Dorin

2009-01-01

Recently, marginal space learning (MSL) was proposed as a generic approach for automatic detection of 3D anatomical structures in many medical imaging modalities [1]. To accurately localize a 3D object, we need to estimate nine pose parameters (three for position, three for orientation, and three for anisotropic scaling). Instead of exhaustively searching the original nine-dimensional pose parameter space, only low-dimensional marginal spaces are searched in MSL to improve the detection speed. In this paper, we apply MSL to 2D object detection and perform a thorough comparison between MSL and the alternative full space learning (FSL) approach. Experiments on left ventricle detection in 2D MRI images show MSL outperforms FSL in both speed and accuracy. In addition, we propose two novel techniques, constrained MSL and nonrigid MSL, to further improve the efficiency and accuracy. In many real applications, a strong correlation may exist among pose parameters in the same marginal spaces. For example, a large object may have large scaling values along all directions. Constrained MSL exploits this correlation for further speed-up. The original MSL only estimates the rigid transformation of an object in the image, therefore cannot accurately localize a nonrigid object under a large deformation. The proposed nonrigid MSL directly estimates the nonrigid deformation parameters to improve the localization accuracy. The comparison experiments on liver detection in 226 abdominal CT volumes demonstrate the effectiveness of the proposed methods. Our system takes less than a second to accurately detect the liver in a volume.

Yes, one can obtain better quality structures from routine X-ray data collection.

PubMed

Sanjuan-Szklarz, W Fabiola; Hoser, Anna A; Gutmann, Matthias; Madsen, Anders Østergaard; Woźniak, Krzysztof

2016-01-01

Single-crystal X-ray diffraction structural results for benzidine dihydrochloride, hydrated and protonated N,N,N,N-peri(dimethylamino)naphthalene chloride, triptycene, dichlorodimethyltriptycene and decamethylferrocene have been analysed. A critical discussion of the dependence of structural and thermal parameters on resolution for these compounds is presented. Results of refinements against X-ray data, cut off to different resolutions from the high-resolution data files, are compared to structural models derived from neutron diffraction experiments. The Independent Atom Model (IAM) and the Transferable Aspherical Atom Model (TAAM) are tested. The average differences between the X-ray and neutron structural parameters (with the exception of valence angles defined by H atoms) decrease with the increasing 2θmax angle. The scale of differences between X-ray and neutron geometrical parameters can be significantly reduced when data are collected to the higher, than commonly used, 2θmax diffraction angles (for Mo Kα 2θmax > 65°). The final structural and thermal parameters obtained for the studied compounds using TAAM refinement are in better agreement with the neutron values than the IAM results for all resolutions and all compounds. By using TAAM, it is still possible to obtain accurate results even from low-resolution X-ray data. This is particularly important as TAAM is easy to apply and can routinely be used to improve the quality of structural investigations [Dominiak (2015 ▸). LSDB from UBDB. University of Buffalo, USA]. We can recommend that, in order to obtain more adequate (more accurate and precise) structural and displacement parameters during the IAM model refinement, data should be collected up to the larger diffraction angles, at least, for Mo Kα radiation to 2θmax = 65° (sin θmax/λ < 0.75 Å(-1)). The TAAM approach is a very good option to obtain more adequate results even using data collected to the lower 2θmax angles. Also the results of translation-libration-screw (TLS) analysis and vibrational entropy values are more reliable for 2θmax > 65°.

Simplified rotor load models and fatigue damage estimates for offshore wind turbines.

PubMed

Muskulus, M

2015-02-28

The aim of rotor load models is to characterize and generate the thrust loads acting on an offshore wind turbine. Ideally, the rotor simulation can be replaced by time series from a model with a few parameters and state variables only. Such models are used extensively in control system design and, as a potentially new application area, structural optimization of support structures. Different rotor load models are here evaluated for a jacket support structure in terms of fatigue lifetimes of relevant structural variables. All models were found to be lacking in accuracy, with differences of more than 20% in fatigue load estimates. The most accurate models were the use of an effective thrust coefficient determined from a regression analysis of dynamic thrust loads, and a novel stochastic model in state-space form. The stochastic model explicitly models the quasi-periodic components obtained from rotational sampling of turbulent fluctuations. Its state variables follow a mean-reverting Ornstein-Uhlenbeck process. Although promising, more work is needed on how to determine the parameters of the stochastic model and before accurate lifetime predictions can be obtained without comprehensive rotor simulations. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

An accurate halo model for fitting non-linear cosmological power spectra and baryonic feedback models

NASA Astrophysics Data System (ADS)

Mead, A. J.; Peacock, J. A.; Heymans, C.; Joudaki, S.; Heavens, A. F.

2015-12-01

We present an optimized variant of the halo model, designed to produce accurate matter power spectra well into the non-linear regime for a wide range of cosmological models. To do this, we introduce physically motivated free parameters into the halo-model formalism and fit these to data from high-resolution N-body simulations. For a variety of Λ cold dark matter (ΛCDM) and wCDM models, the halo-model power is accurate to ≃ 5 per cent for k ≤ 10h Mpc-1 and z ≤ 2. An advantage of our new halo model is that it can be adapted to account for the effects of baryonic feedback on the power spectrum. We demonstrate this by fitting the halo model to power spectra from the OWLS (OverWhelmingly Large Simulations) hydrodynamical simulation suite via parameters that govern halo internal structure. We are able to fit all feedback models investigated at the 5 per cent level using only two free parameters, and we place limits on the range of these halo parameters for feedback models investigated by the OWLS simulations. Accurate predictions to high k are vital for weak-lensing surveys, and these halo parameters could be considered nuisance parameters to marginalize over in future analyses to mitigate uncertainty regarding the details of feedback. Finally, we investigate how lensing observables predicted by our model compare to those from simulations and from HALOFIT for a range of k-cuts and feedback models and quantify the angular scales at which these effects become important. Code to calculate power spectra from the model presented in this paper can be found at https://github.com/alexander-mead/hmcode.

Joint probabilistic determination of earthquake location and velocity structure: application to local and regional events

NASA Astrophysics Data System (ADS)

Beucler, E.; Haugmard, M.; Mocquet, A.

2016-12-01

The most widely used inversion schemes to locate earthquakes are based on iterative linearized least-squares algorithms and using an a priori knowledge of the propagation medium. When a small amount of observations is available for moderate events for instance, these methods may lead to large trade-offs between outputs and both the velocity model and the initial set of hypocentral parameters. We present a joint structure-source determination approach using Bayesian inferences. Monte-Carlo continuous samplings, using Markov chains, generate models within a broad range of parameters, distributed according to the unknown posterior distributions. The non-linear exploration of both the seismic structure (velocity and thickness) and the source parameters relies on a fast forward problem using 1-D travel time computations. The a posteriori covariances between parameters (hypocentre depth, origin time and seismic structure among others) are computed and explicitly documented. This method manages to decrease the influence of the surrounding seismic network geometry (sparse and/or azimuthally inhomogeneous) and a too constrained velocity structure by inferring realistic distributions on hypocentral parameters. Our algorithm is successfully used to accurately locate events of the Armorican Massif (western France), which is characterized by moderate and apparently diffuse local seismicity.

Characterization of isolated 1-aza-adamantan-4-one (C9H13NO) from microwave, millimeter-wave and infrared spectroscopy supported by electronic structure calculations

NASA Astrophysics Data System (ADS)

Pirali, O.; Goubet, M.; Boudon, V.; D'Accolti, L.; Fusco, C.; Annese, C.

2017-08-01

We have synthesized 1-aza-adamantan-4-one (C9H13NO) starting from commercial 1,4-cyclohexanedionemonoethylene acetal and tosylmethylisocianide, following a procedure already described in the literature. The high degree of sample purity was demonstrated by gas chromatography and mass spectrometric measurements and its structure evidenced by 1H and 13C NMR spectroscopy. Among numerous interests in physical chemistry, this target molecule is of high relevance for mechanistic evaluation and the synthesis of novel pharmaceutical compounds. We present a thorough spectroscopic study of this molecule by gas phase vibrational and rotational spectroscopy. Accurate vibrational frequencies have been determined from infrared and far-infrared spectra. The pure rotational spectrum of the molecule has been recorded both by cavity-based Fourier transform microwave spectroscopy in the 2-20 GHz region by supersonically expanding the vapor pressure of the warm sample and by room-temperature absorption spectroscopy in the 140-220 GHz range. Accurate sets of rotational and centrifugal distortion parameters of 1-aza-adamantan-4-one in its ground state and in five vibrationally excited states have been derived from these measurements and compared to accurate quantum chemical calculations. The hyperfine parameters have been discussed in terms of molecular structure around the nitrogen quadrupole nucleus.

A new qualitative acoustic emission parameter based on Shannon's entropy for damage monitoring

NASA Astrophysics Data System (ADS)

Chai, Mengyu; Zhang, Zaoxiao; Duan, Quan

2018-02-01

An important objective of acoustic emission (AE) non-destructive monitoring is to accurately identify approaching critical damage and to avoid premature failure by means of the evolutions of AE parameters. One major drawback of most parameters such as count and rise time is that they are strongly dependent on the threshold and other settings employed in AE data acquisition system. This may hinder the correct reflection of original waveform generated from AE sources and consequently bring difficulty for the accurate identification of the critical damage and early failure. In this investigation, a new qualitative AE parameter based on Shannon's entropy, i.e. AE entropy is proposed for damage monitoring. Since it derives from the uncertainty of amplitude distribution of each AE waveform, it is independent of the threshold and other time-driven parameters and can characterize the original micro-structural deformations. Fatigue crack growth test on CrMoV steel and three point bending test on a ductile material are conducted to validate the feasibility and effectiveness of the proposed parameter. The results show that the new parameter, compared to AE amplitude, is more effective in discriminating the different damage stages and identifying the critical damage.

Noise elimination algorithm for modal analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bao, X. X., E-mail: baoxingxian@upc.edu.cn; Li, C. L.; Xiong, C. B.

2015-07-27

Modal analysis is an ongoing interdisciplinary physical issue. Modal parameters estimation is applied to determine the dynamic characteristics of structures under vibration excitation. Modal analysis is more challenging for the measured vibration response signals are contaminated with noise. This study develops a mathematical algorithm of structured low rank approximation combined with the complex exponential method to estimate the modal parameters. Physical experiments using a steel cantilever beam with ten accelerometers mounted, excited by an impulse load, demonstrate that this method can significantly eliminate noise from measured signals and accurately identify the modal frequencies and damping ratios. This study provides amore » fundamental mechanism of noise elimination using structured low rank approximation in physical fields.« less

Parameter identification for structural dynamics based on interval analysis algorithm

NASA Astrophysics Data System (ADS)

Yang, Chen; Lu, Zixing; Yang, Zhenyu; Liang, Ke

2018-04-01

A parameter identification method using interval analysis algorithm for structural dynamics is presented in this paper. The proposed uncertain identification method is investigated by using central difference method and ARMA system. With the help of the fixed memory least square method and matrix inverse lemma, a set-membership identification technology is applied to obtain the best estimation of the identified parameters in a tight and accurate region. To overcome the lack of insufficient statistical description of the uncertain parameters, this paper treats uncertainties as non-probabilistic intervals. As long as we know the bounds of uncertainties, this algorithm can obtain not only the center estimations of parameters, but also the bounds of errors. To improve the efficiency of the proposed method, a time-saving algorithm is presented by recursive formula. At last, to verify the accuracy of the proposed method, two numerical examples are applied and evaluated by three identification criteria respectively.

Inverts permittivity and conductivity with structural constraint in GPR FWI based on truncated Newton method

NASA Astrophysics Data System (ADS)

Ren, Qianci

2018-04-01

Full waveform inversion (FWI) of ground penetrating radar (GPR) is a promising technique to quantitatively evaluate the permittivity and conductivity of near subsurface. However, these two parameters are simultaneously inverted in the GPR FWI, increasing the difficulty to obtain accurate inversion results for both parameters. In this study, I present a structural constrained GPR FWI procedure to jointly invert the two parameters, aiming to force a structural relationship between permittivity and conductivity in the process of model reconstruction. The structural constraint is enforced by a cross-gradient function. In this procedure, the permittivity and conductivity models are inverted alternately at each iteration and updated with hierarchical frequency components in the frequency domain. The joint inverse problem is solved by the truncated Newton method which considering the effect of Hessian operator and using the approximated solution of Newton equation to be the perturbation model in the updating process. The joint inversion procedure is tested by three synthetic examples. The results show that jointly inverting permittivity and conductivity in GPR FWI effectively increases the structural similarities between the two parameters, corrects the structures of parameter models, and significantly improves the accuracy of conductivity model, resulting in a better inversion result than the individual inversion.

Interdependence of spin structure, anion height and electronic structure of BaFe{sub 2}As{sub 2}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sen, Smritijit, E-mail: smritijit.sen@gmail.com; Ghosh, Haranath, E-mail: hng@rrcat.gov.in; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094

2016-05-06

Superconducting as well as other electronic properties of Fe-based superconductors are quite sensitive to the structural parameters specially, on anion height which is intimately related to z{sub As}, the fractional z co-ordinate of As atom. Due to presence of strong magnetic fluctuation in these Fe-based superconductors, optimized structural parameters (lattice parameters a, b, c) including z{sub As} using density functional theory (DFT) under generalized gradient approximation (GGA) does not match experimental values accurately. In this work, we show that the optimized value of z{sub As} is strongly influenced by the spin structures in the orthorhombic phase of BaFe{sub 2}As{sub 2}more » system. We take all possible spin structures for the orthorhombic BaFe{sub 2}As{sub 2} system and then optimize z{sub As}. Using these optimized structures we calculate electronic structures like density of states, band structures etc., for each spin configurations. From these studies we show that the electronic structure, orbital order which is responsible for structural as well as related to nematic transition, are significantly influenced by the spin structures.« less

Cell-accurate optical mapping across the entire developing heart.

PubMed

Weber, Michael; Scherf, Nico; Meyer, Alexander M; Panáková, Daniela; Kohl, Peter; Huisken, Jan

2017-12-29

Organogenesis depends on orchestrated interactions between individual cells and morphogenetically relevant cues at the tissue level. This is true for the heart, whose function critically relies on well-ordered communication between neighboring cells, which is established and fine-tuned during embryonic development. For an integrated understanding of the development of structure and function, we need to move from isolated snap-shot observations of either microscopic or macroscopic parameters to simultaneous and, ideally continuous, cell-to-organ scale imaging. We introduce cell-accurate three-dimensional Ca 2+ -mapping of all cells in the entire electro-mechanically uncoupled heart during the looping stage of live embryonic zebrafish, using high-speed light sheet microscopy and tailored image processing and analysis. We show how myocardial region-specific heterogeneity in cell function emerges during early development and how structural patterning goes hand-in-hand with functional maturation of the entire heart. Our method opens the way to systematic, scale-bridging, in vivo studies of vertebrate organogenesis by cell-accurate structure-function mapping across entire organs.

Cell-accurate optical mapping across the entire developing heart

PubMed Central

Meyer, Alexander M; Panáková, Daniela; Kohl, Peter

2017-01-01

Organogenesis depends on orchestrated interactions between individual cells and morphogenetically relevant cues at the tissue level. This is true for the heart, whose function critically relies on well-ordered communication between neighboring cells, which is established and fine-tuned during embryonic development. For an integrated understanding of the development of structure and function, we need to move from isolated snap-shot observations of either microscopic or macroscopic parameters to simultaneous and, ideally continuous, cell-to-organ scale imaging. We introduce cell-accurate three-dimensional Ca2+-mapping of all cells in the entire electro-mechanically uncoupled heart during the looping stage of live embryonic zebrafish, using high-speed light sheet microscopy and tailored image processing and analysis. We show how myocardial region-specific heterogeneity in cell function emerges during early development and how structural patterning goes hand-in-hand with functional maturation of the entire heart. Our method opens the way to systematic, scale-bridging, in vivo studies of vertebrate organogenesis by cell-accurate structure-function mapping across entire organs. PMID:29286002

Accurate Determination of the Frequency Response Function of Submerged and Confined Structures by Using PZT-Patches †

PubMed Central

Presas, Alexandre; Valentin, David; Egusquiza, Eduard; Valero, Carme; Egusquiza, Mònica; Bossio, Matias

2017-01-01

To accurately determine the dynamic response of a structure is of relevant interest in many engineering applications. Particularly, it is of paramount importance to determine the Frequency Response Function (FRF) for structures subjected to dynamic loads in order to avoid resonance and fatigue problems that can drastically reduce their useful life. One challenging case is the experimental determination of the FRF of submerged and confined structures, such as hydraulic turbines, which are greatly affected by dynamic problems as reported in many cases in the past. The utilization of classical and calibrated exciters such as instrumented hammers or shakers to determine the FRF in such structures can be very complex due to the confinement of the structure and because their use can disturb the boundary conditions affecting the experimental results. For such cases, Piezoelectric Patches (PZTs), which are very light, thin and small, could be a very good option. Nevertheless, the main drawback of these exciters is that the calibration as dynamic force transducers (relationship voltage/force) has not been successfully obtained in the past. Therefore, in this paper, a method to accurately determine the FRF of submerged and confined structures by using PZTs is developed and validated. The method consists of experimentally determining some characteristic parameters that define the FRF, with an uncalibrated PZT exciting the structure. These parameters, which have been experimentally determined, are then introduced in a validated numerical model of the tested structure. In this way, the FRF of the structure can be estimated with good accuracy. With respect to previous studies, where only the natural frequencies and mode shapes were considered, this paper discuss and experimentally proves the best excitation characteristic to obtain also the damping ratios and proposes a procedure to fully determine the FRF. The method proposed here has been validated for the structure vibrating in air comparing the FRF experimentally obtained with a calibrated exciter (impact Hammer) and the FRF obtained with the described method. Finally, the same methodology has been applied for the structure submerged and close to a rigid wall, where it is extremely important to not modify the boundary conditions for an accurate determination of the FRF. As experimentally shown in this paper, in such cases, the use of PZTs combined with the proposed methodology gives much more accurate estimations of the FRF than other calibrated exciters typically used for the same purpose. Therefore, the validated methodology proposed in this paper can be used to obtain the FRF of a generic submerged and confined structure, without a previous calibration of the PZT. PMID:28327501

Retrieving Temperature Anomaly in the Global Subsurface and Deeper Ocean From Satellite Observations

NASA Astrophysics Data System (ADS)

Su, Hua; Li, Wene; Yan, Xiao-Hai

2018-01-01

Retrieving the subsurface and deeper ocean (SDO) dynamic parameters from satellite observations is crucial for effectively understanding ocean interior anomalies and dynamic processes, but it is challenging to accurately estimate the subsurface thermal structure over the global scale from sea surface parameters. This study proposes a new approach based on Random Forest (RF) machine learning to retrieve subsurface temperature anomaly (STA) in the global ocean from multisource satellite observations including sea surface height anomaly (SSHA), sea surface temperature anomaly (SSTA), sea surface salinity anomaly (SSSA), and sea surface wind anomaly (SSWA) via in situ Argo data for RF training and testing. RF machine-learning approach can accurately retrieve the STA in the global ocean from satellite observations of sea surface parameters (SSHA, SSTA, SSSA, SSWA). The Argo STA data were used to validate the accuracy and reliability of the results from the RF model. The results indicated that SSHA, SSTA, SSSA, and SSWA together are useful parameters for detecting SDO thermal information and obtaining accurate STA estimations. The proposed method also outperformed support vector regression (SVR) in global STA estimation. It will be a useful technique for studying SDO thermal variability and its role in global climate system from global-scale satellite observations.

An algorithm for the design and tuning of RF accelerating structures with variable cell lengths

NASA Astrophysics Data System (ADS)

Lal, Shankar; Pant, K. K.

2018-05-01

An algorithm is proposed for the design of a π mode standing wave buncher structure with variable cell lengths. It employs a two-parameter, multi-step approach for the design of the structure with desired resonant frequency and field flatness. The algorithm, along with analytical scaling laws for the design of the RF power coupling slot, makes it possible to accurately design the structure employing a freely available electromagnetic code like SUPERFISH. To compensate for machining errors, a tuning method has been devised to achieve desired RF parameters for the structure, which has been qualified by the successful tuning of a 7-cell buncher to π mode frequency of 2856 MHz with field flatness <3% and RF coupling coefficient close to unity. The proposed design algorithm and tuning method have demonstrated the feasibility of developing an S-band accelerating structure for desired RF parameters with a relatively relaxed machining tolerance of ∼ 25 μm. This paper discusses the algorithm for the design and tuning of an RF accelerating structure with variable cell lengths.

A Study of Al-Mn Transition Edge Sensor Engineering for Stability

DOE Office of Scientific and Technical Information (OSTI.GOV)

George, E. M.; et al.

2013-11-10

The stability of Al-Mn transition edge sensor (TES) bolometers is studied as we vary the engineered TES transition, heat capacity, and/or coupling between the heat capacity and TES. We present thermal structure measurements of each of the 39 designs tested. The data is accurately fit by a two-body bolometer model, which allows us to extract the basic TES parameters that affect device stability. We conclude that parameters affecting device stability can be engineered for optimal device operation, and present the model parameters extracted for the different TES designs.

Structure determination from XAFS using high-accuracy measurements of x-ray mass attenuation coefficients of silver, 11 keV-28 keV, and development of an all-energies approach to local dynamical analysis of bond length, revealing variation of effective thermal contributions across the XAFS spectrum.

PubMed

Tantau, L J; Chantler, C T; Bourke, J D; Islam, M T; Payne, A T; Rae, N A; Tran, C Q

2015-07-08

We use the x-ray extended range technique (XERT) to experimentally determine the mass attenuation coefficient of silver in the x-ray energy range 11 kev-28 kev including the silver K absorption edge. The results are accurate to better than 0.1%, permitting critical tests of atomic and solid state theory. This is one of the most accurate demonstrations of cross-platform accuracy in synchrotron studies thus far. We derive the mass absorption coefficients and the imaginary component of the form factor over this range. We apply conventional XAFS analytic techniques, extended to include error propagation and uncertainty, yielding bond lengths accurate to approximately 0.24% and thermal Debye-Waller parameters accurate to 30%. We then introduce the FDMX technique for accurate analysis of such data across the full XAFS spectrum, built on full-potential theory, yielding a bond length accuracy of order 0.1% and the demonstration that a single Debye parameter is inadequate and inconsistent across the XAFS range. Two effective Debye-Waller parameters are determined: a high-energy value based on the highly-correlated motion of bonded atoms (σ(DW) = 0.1413(21) Å), and an uncorrelated bulk value (σ(DW) = 0.1766(9) Å) in good agreement with that derived from (room-temperature) crystallography.

Near Identifiability of Dynamical Systems

NASA Technical Reports Server (NTRS)

Hadaegh, F. Y.; Bekey, G. A.

1987-01-01

Concepts regarding approximate mathematical models treated rigorously. Paper presents new results in analysis of structural identifiability, equivalence, and near equivalence between mathematical models and physical processes they represent. Helps establish rigorous mathematical basis for concepts related to structural identifiability and equivalence revealing fundamental requirements, tacit assumptions, and sources of error. "Structural identifiability," as used by workers in this field, loosely translates as meaning ability to specify unique mathematical model and set of model parameters that accurately predict behavior of corresponding physical system.

A statistical evaluation and comparison of VISSR Atmospheric Sounder (VAS) data

NASA Technical Reports Server (NTRS)

Jedlovec, G. J.

1984-01-01

In order to account for the temporal and spatial discrepancies between the VAS and rawinsonde soundings, the rawinsonde data were adjusted to a common hour of release where the new observation time corresponded to the satellite scan time. Both the satellite and rawinsonde observations of the basic atmospheric parameters (T Td, and Z) were objectively analyzed to a uniform grid maintaining the same mesoscale structure in each data set. The performance of each retrieval algorithm in producing accurate and representative soundings was evaluated using statistical parameters such as the mean, standard deviation, and root mean square of the difference fields for each parameter and grid level. Horizontal structure was also qualitatively evaluated by examining atmospheric features on constant pressure surfaces. An analysis of the vertical structure of the atmosphere were also performed by looking at colocated and grid mean vertical profiles of both the satellite and rawinsonde data sets. Highlights of these results are presented.

Sensitivity of Space Station alpha joint robust controller to structural modal parameter variations

NASA Technical Reports Server (NTRS)

Kumar, Renjith R.; Cooper, Paul A.; Lim, Tae W.

1991-01-01

The photovoltaic array sun tracking control system of Space Station Freedom is described. A synthesis procedure for determining optimized values of the design variables of the control system is developed using a constrained optimization technique. The synthesis is performed to provide a given level of stability margin, to achieve the most responsive tracking performance, and to meet other design requirements. Performance of the baseline design, which is synthesized using predicted structural characteristics, is discussed and the sensitivity of the stability margin is examined for variations of the frequencies, mode shapes and damping ratios of dominant structural modes. The design provides enough robustness to tolerate a sizeable error in the predicted modal parameters. A study was made of the sensitivity of performance indicators as the modal parameters of the dominant modes vary. The design variables are resynthesized for varying modal parameters in order to achieve the most responsive tracking performance while satisfying the design requirements. This procedure of reoptimization design parameters would be useful in improving the control system performance if accurate model data are provided.

A simulation for gravity fine structure recovery from high-low GRAVSAT SST data

NASA Technical Reports Server (NTRS)

Estes, R. H.; Lancaster, E. R.

1976-01-01

Covariance error analysis techniques were applied to investigate estimation strategies for the high-low SST mission for accurate local recovery of gravitational fine structure, considering the aliasing effects of unsolved for parameters. Surface density blocks of 5 deg x 5 deg and 2 1/2 deg x 2 1/2 deg resolution were utilized to represent the high order geopotential with the drag-free GRAVSAT configured in a nearly circular polar orbit at 250 km. altitude. GEOPAUSE and geosynchronous satellites were considered as high relay spacecraft. It is demonstrated that knowledge of gravitational fine structure can be significantly improved at 5 deg x 5 deg resolution using SST data from a high-low configuration with reasonably accurate orbits for the low GRAVSAT. The gravity fine structure recoverability of the high-low SST mission is compared with the low-low configuration and shown to be superior.

Quantum Monte Carlo for atoms and molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barnett, R.N.

1989-11-01

The diffusion quantum Monte Carlo with fixed nodes (QMC) approach has been employed in studying energy-eigenstates for 1--4 electron systems. Previous work employing the diffusion QMC technique yielded energies of high quality for H{sub 2}, LiH, Li{sub 2}, and H{sub 2}O. Here, the range of calculations with this new approach has been extended to include additional first-row atoms and molecules. In addition, improvements in the previously computed fixed-node energies of LiH, Li{sub 2}, and H{sub 2}O have been obtained using more accurate trial functions. All computations were performed within, but are not limited to, the Born-Oppenheimer approximation. In our computations,more » the effects of variation of Monte Carlo parameters on the QMC solution of the Schroedinger equation were studied extensively. These parameters include the time step, renormalization time and nodal structure. These studies have been very useful in determining which choices of such parameters will yield accurate QMC energies most efficiently. Generally, very accurate energies (90--100% of the correlation energy is obtained) have been computed with single-determinant trail functions multiplied by simple correlation functions. Improvements in accuracy should be readily obtained using more complex trial functions.« less

Structural parameters associated with location of peaks of peripapillary retinal nerve fiber layer thickness in young healthy eyes.

PubMed

Yamashita, Takehiro; Asaoka, Ryo; Kii, Yuya; Terasaki, Hiroto; Murata, Hiroshi; Sakamoto, Taiji

2017-01-01

The location of the peaks of the circumpapillary retinal nerve fiber layer (cpRNFL) thickness is affected by several ocular parameters. In this study, we have generated equations that can determine the peaks of the cpRNFL. This study was a prospective, observational, cross sectional study of 118 healthy right eyes. The axial length, optic disc tilt, superiortemporal (ST)- and inferiortemporal (IT)-peaks of the cpRNFL thickness, and angles of the ST and IT retinal arteries (RA) and veins (RV) were determined. The correlations between the location of the ST- and IT-peaks and ocular structural parameters and the sex, body height and weight were calculated. The best fit equations to generate the location of the ST/IT-peaks were determined using corrected-Akaike Information Criteria. The location of the ST-peak was 0.72+(0.40 x ST-RA)+(0.27 x ST-RV)+(0.14 x height)-(0.47 x papillo-macular-position)-(0.11 x disc tilt) with a coefficient of correlation of 0.61 (P<0.0001). The location of the IT-peak was 21.88+(0.53 x IT-RA)+(0.15 x IT-RV)+(0.041 x corneal thickness)-(1.00 x axial length) with a coefficient of correlation of 0.59 (P<0.0001). The location of ST/IT peaks is determined by different parameters of the ocular structure. These equations allow clinicians to obtain an accurate location of the peaks for a more accurate diagnosis of glaucoma.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Roy, Surajit; Ladpli, Purim; Chang, Fu-Kuo

Accurate interpretation of in-situ piezoelectric sensor signals is a challenging task. This article presents the development of a numerical compensation model based on physical insight to address the influence of structural loads on piezo-sensor signals. The model requires knowledge of in-situ strain and temperature distribution in a structure while acquiring sensor signals. The parameters of the numerical model are obtained using experiments on flat aluminum plate under uniaxial tensile loading. It is shown that the model parameters obtained experimentally can be used for different structures, and sensor layout. Furthermore, the combined effects of load and temperature on the piezo-sensor responsemore » are also investigated and it is observed that both of these factors have a coupled effect on the sensor signals. It is proposed to obtain compensation model parameters under a range of operating temperatures to address this coupling effect. An important outcome of this study is a new load monitoring concept using in-situ piezoelectric sensor signals to track changes in the load paths in a structure.« less

Ellipsometric study of metal-organic chemically vapor deposited III-V semiconductor structures

NASA Technical Reports Server (NTRS)

Alterovitz, Samuel A.; Sekula-Moise, Patricia A.; Sieg, Robert M.; Drotos, Mark N.; Bogner, Nancy A.

1992-01-01

An ellipsometric study of MOCVD-grown layers of AlGaAs and InGaAs in thick films and strained layer complex structures is presented. It is concluded that the ternary composition of thick nonstrained layers can be accurately determined to within experimental errors using numerical algorithms. In the case of complex structures, thickness of all layers and the alloy composition of nonstrained layers can be determined simultaneously, provided that the correlations between parameters is no higher than 0.9.

Microwave spectra and molecular structures of (Z)-pent-2-en-4-ynenitrile and maleonitrile.

PubMed

Halter, R J; Fimmen, R L; McMahon, R J; Peebles, S A; Kuczkowski, R L; Stanton, J F

2001-12-12

Accurate equilibrium structures have been determined for (Z)-pent-2-en-4-ynenitrile (8) and maleonitrile (9) by combining microwave spectroscopy data and ab initio quantum chemistry calculations. The microwave spectra of 10 isotopomers of 8 and 5 isotopomers of 9 were obtained using a pulsed nozzle Fourier transform microwave spectrometer. The ground-state rotational constants were adjusted for vibration-rotation interaction effects calculated from force fields obtained from ab initio calculations. The resultant equilibrium rotational constants were used to determine structures that are in very good agreement with those obtained from high-level ab initio calculations (CCSD(T)/cc-pVTZ). The geometric parameters in 8 and 9 are very similar; they also do not differ significantly from the all-carbon analogue, (Z)-hex-3-ene-1,5-diyne (7), the parent molecule for the Bergman cyclization. A small deviation from linearity about the alkyne and cyano linkages is observed for 7-9 and several related species where accurate equilibrium parameters are available. The data on 7-9 should be of interest to radioastronomy and may provide insights on the formation and interstellar chemistry of unsaturated species such as the cyanopolyynes.

Compound Velocity Synchronizing Control Strategy for Electro-Hydraulic Load Simulator and Its Engineering Application.

PubMed

Han, Songshan; Jiao, Zongxia; Yao, Jianyong; Shang, Yaoxing

2014-09-01

An electro-hydraulic load simulator (EHLS) is a typical case of torque systems with strong external disturbances from hydraulic motion systems. A new velocity synchronizing compensation strategy is proposed in this paper to eliminate motion disturbances, based on theoretical and experimental analysis of a structure invariance method and traditional velocity synchronizing compensation controller (TVSM). This strategy only uses the servo-valve's control signal of motion system and torque feedback of torque system, which could avoid the requirement on the velocity and acceleration signal in the structure invariance method, and effectively achieve a more accurate velocity synchronizing compensation in large loading conditions than a TVSM. In order to facilitate the implementation of this strategy in engineering cases, the selection rules for compensation parameters are proposed. It does not rely on any accurate information of structure parameters. This paper presents the comparison data of an EHLS with various typical operating conditions using three controllers, i.e., closed loop proportional integral derivative (PID) controller, TVSM, and the proposed improved velocity synchronizing controller. Experiments are conducted to confirm that the new strategy performs well against motion disturbances. It is more effective to improve the tracking accuracy and is a more appropriate choice for engineering applications.

Accurately controlled sequential self-folding structures by polystyrene film

NASA Astrophysics Data System (ADS)

Deng, Dongping; Yang, Yang; Chen, Yong; Lan, Xing; Tice, Jesse

2017-08-01

Four-dimensional (4D) printing overcomes the traditional fabrication limitations by designing heterogeneous materials to enable the printed structures evolve over time (the fourth dimension) under external stimuli. Here, we present a simple 4D printing of self-folding structures that can be sequentially and accurately folded. When heated above their glass transition temperature pre-strained polystyrene films shrink along the XY plane. In our process silver ink traces printed on the film are used to provide heat stimuli by conducting current to trigger the self-folding behavior. The parameters affecting the folding process are studied and discussed. Sequential folding and accurately controlled folding angles are achieved by using printed ink traces and angle lock design. Theoretical analyses are done to guide the design of the folding processes. Programmable structures such as a lock and a three-dimensional antenna are achieved to test the feasibility and potential applications of this method. These self-folding structures change their shapes after fabrication under controlled stimuli (electric current) and have potential applications in the fields of electronics, consumer devices, and robotics. Our design and fabrication method provides an easy way by using silver ink printed on polystyrene films to 4D print self-folding structures for electrically induced sequential folding with angular control.

Can the electronegativity equalization method predict spectroscopic properties?

PubMed

Verstraelen, T; Bultinck, P

2015-02-05

The electronegativity equalization method is classically used as a method allowing the fast generation of atomic charges using a set of calibrated parameters and provided knowledge of the molecular structure. Recently, it has started being used for the calculation of other reactivity descriptors and for the development of polarizable and reactive force fields. For such applications, it is of interest to know whether the method, through the inclusion of the molecular geometry in the Taylor expansion of the energy, would also allow sufficiently accurate predictions of spectroscopic data. In this work, relevant quantities for IR spectroscopy are considered, namely the dipole derivatives and the Cartesian Hessian. Despite careful calibration of parameters for this specific task, it is shown that the current models yield insufficiently accurate results. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

CHARMM Force-Fields with Modified Polyphosphate Parameters Allow Stable Simulation of the ATP-Bound Structure of Ca(2+)-ATPase.

PubMed

Komuro, Yasuaki; Re, Suyong; Kobayashi, Chigusa; Muneyuki, Eiro; Sugita, Yuji

2014-09-09

Adenosine triphosphate (ATP) is an indispensable energy source in cells. In a wide variety of biological phenomena like glycolysis, muscle contraction/relaxation, and active ion transport, chemical energy released from ATP hydrolysis is converted to mechanical forces to bring about large-scale conformational changes in proteins. Investigation of structure-function relationships in these proteins by molecular dynamics (MD) simulations requires modeling of ATP in solution and ATP bound to proteins with accurate force-field parameters. In this study, we derived new force-field parameters for the triphosphate moiety of ATP based on the high-precision quantum calculations of methyl triphosphate. We tested our new parameters on membrane-embedded sarcoplasmic reticulum Ca(2+)-ATPase and four soluble proteins. The ATP-bound structure of Ca(2+)-ATPase remains stable during MD simulations, contrary to the outcome in shorter simulations using original parameters. Similar results were obtained with the four ATP-bound soluble proteins. The new force-field parameters were also tested by investigating the range of conformations sampled during replica-exchange MD simulations of ATP in explicit water. Modified parameters allowed a much wider range of conformational sampling compared with the bias toward extended forms with original parameters. A diverse range of structures agrees with the broad distribution of ATP conformations in proteins deposited in the Protein Data Bank. These simulations suggest that the modified parameters will be useful in studies of ATP in solution and of the many ATP-utilizing proteins.

Exploratory Movement Generates Higher-Order Information That Is Sufficient for Accurate Perception of Scaled Egocentric Distance

PubMed Central

Mantel, Bruno; Stoffregen, Thomas A.; Campbell, Alain; Bardy, Benoît G.

2015-01-01

Body movement influences the structure of multiple forms of ambient energy, including optics and gravito-inertial force. Some researchers have argued that egocentric distance is derived from inferential integration of visual and non-visual stimulation. We suggest that accurate information about egocentric distance exists in perceptual stimulation as higher-order patterns that extend across optics and inertia. We formalize a pattern that specifies the egocentric distance of a stationary object across higher-order relations between optics and inertia. This higher-order parameter is created by self-generated movement of the perceiver in inertial space relative to the illuminated environment. For this reason, we placed minimal restrictions on the exploratory movements of our participants. We asked whether humans can detect and use the information available in this higher-order pattern. Participants judged whether a virtual object was within reach. We manipulated relations between body movement and the ambient structure of optics and inertia. Judgments were precise and accurate when the higher-order optical-inertial parameter was available. When only optic flow was available, judgments were poor. Our results reveal that participants perceived egocentric distance from the higher-order, optical-inertial consequences of their own exploratory activity. Analysis of participants’ movement trajectories revealed that self-selected movements were complex, and tended to optimize availability of the optical-inertial pattern that specifies egocentric distance. We argue that accurate information about egocentric distance exists in higher-order patterns of ambient energy, that self-generated movement can generate these higher-order patterns, and that these patterns can be detected and used to support perception of egocentric distance that is precise and accurate. PMID:25856410

A 3D Image Filter for Parameter-Free Segmentation of Macromolecular Structures from Electron Tomograms

PubMed Central

Ali, Rubbiya A.; Landsberg, Michael J.; Knauth, Emily; Morgan, Garry P.; Marsh, Brad J.; Hankamer, Ben

2012-01-01

3D image reconstruction of large cellular volumes by electron tomography (ET) at high (≤5 nm) resolution can now routinely resolve organellar and compartmental membrane structures, protein coats, cytoskeletal filaments, and macromolecules. However, current image analysis methods for identifying in situ macromolecular structures within the crowded 3D ultrastructural landscape of a cell remain labor-intensive, time-consuming, and prone to user-bias and/or error. This paper demonstrates the development and application of a parameter-free, 3D implementation of the bilateral edge-detection (BLE) algorithm for the rapid and accurate segmentation of cellular tomograms. The performance of the 3D BLE filter has been tested on a range of synthetic and real biological data sets and validated against current leading filters—the pseudo 3D recursive and Canny filters. The performance of the 3D BLE filter was found to be comparable to or better than that of both the 3D recursive and Canny filters while offering the significant advantage that it requires no parameter input or optimisation. Edge widths as little as 2 pixels are reproducibly detected with signal intensity and grey scale values as low as 0.72% above the mean of the background noise. The 3D BLE thus provides an efficient method for the automated segmentation of complex cellular structures across multiple scales for further downstream processing, such as cellular annotation and sub-tomogram averaging, and provides a valuable tool for the accurate and high-throughput identification and annotation of 3D structural complexity at the subcellular level, as well as for mapping the spatial and temporal rearrangement of macromolecular assemblies in situ within cellular tomograms. PMID:22479430

The fast and accurate 3D-face scanning technology based on laser triangle sensors

NASA Astrophysics Data System (ADS)

Wang, Jinjiang; Chang, Tianyu; Ge, Baozhen; Tian, Qingguo; Chen, Yang; Kong, Bin

2013-08-01

A laser triangle scanning method and the structure of 3D-face measurement system were introduced. In presented system, a liner laser source was selected as an optical indicated signal in order to scanning a line one times. The CCD image sensor was used to capture image of the laser line modulated by human face. The system parameters were obtained by system calibrated calculated. The lens parameters of image part of were calibrated with machine visual image method and the triangle structure parameters were calibrated with fine wire paralleled arranged. The CCD image part and line laser indicator were set with a linear motor carry which can achieve the line laser scanning form top of the head to neck. For the nose is ledge part and the eyes are sunk part, one CCD image sensor can not obtain the completed image of laser line. In this system, two CCD image sensors were set symmetric at two sides of the laser indicator. In fact, this structure includes two laser triangle measure units. Another novel design is there laser indicators were arranged in order to reduce the scanning time for it is difficult for human to keep static for longer time. The 3D data were calculated after scanning. And further data processing include 3D coordinate refine, mesh calculate and surface show. Experiments show that this system has simply structure, high scanning speed and accurate. The scanning range covers the whole head of adult, the typical resolution is 0.5mm.

Method and apparatus for improved observation of in-situ combustion processes

DOEpatents

Lee, D.O.; Montoya, P.C.; Wayland, J.R. Jr.

Method and apparatus are provided for obtaining accurate dynamic measurements for passage of phase fronts through a core sample in a test fixture. Flow-through grid structures are provided for electrodes to permit data to be obtained before, during and after passage of a front there-through. Such electrodes are incorporated in a test apparatus for obtaining electrical characteristics of the core sample. With the inventive structure a method is provided for measurement of instabilities in a phase front progressing through the medium. Availability of accurate dynamic data representing parameters descriptive of material characteristics before, during and after passage of a front provides a more efficient method for enhanced recovery of oil using a fire flood technique. 6 figures, 2 tables.

The usage of image trigonometry in bone measurements.

PubMed

Dymond, Ian W; Ashforth, James A; Dymond, Graeme F; Spirakis, Thanos; Learmonth, Ian D

2013-01-01

The entire musculo-skeletal system responds dynamically to stresses and strains applied to it. Restoring normal biomechanics contributes to the normal function that ensures that physiological stresses and strains are preserved. Appropriate preoperative planning is mandatory to restore normal biomechanics at reconstructive surgery. Effective preoperative planning depends on the ability to reproducibly make accurate measurements of lengths and angles from plain radiographs. Measurement has become an integral part of orthopaedics to define morphological abnormality, to plan for reconstruction and for comparative research. The most prevalent method of measurement is usually based on lines drawn on radiographs with no accurate reference to the actual geometry of the structures. This two-dimensional projection of an asymmetrical three-dimensional structure leads to inaccuracy and consequently to a compromise in the overall precision of many procedures. In addition it is also difficult to monitor the progression of disease as the exact relationship of the bones and joints to each other, and to prosthetics, cannot be accurately recorded. This paper presents a method of digitally measuring relevant bone parameters in a geometric manner in order to achieve accurate, repeatable measurements.

A Fast Surrogate-facilitated Data-driven Bayesian Approach to Uncertainty Quantification of a Regional Groundwater Flow Model with Structural Error

NASA Astrophysics Data System (ADS)

Xu, T.; Valocchi, A. J.; Ye, M.; Liang, F.

2016-12-01

Due to simplification and/or misrepresentation of the real aquifer system, numerical groundwater flow and solute transport models are usually subject to model structural error. During model calibration, the hydrogeological parameters may be overly adjusted to compensate for unknown structural error. This may result in biased predictions when models are used to forecast aquifer response to new forcing. In this study, we extend a fully Bayesian method [Xu and Valocchi, 2015] to calibrate a real-world, regional groundwater flow model. The method uses a data-driven error model to describe model structural error and jointly infers model parameters and structural error. In this study, Bayesian inference is facilitated using high performance computing and fast surrogate models. The surrogate models are constructed using machine learning techniques to emulate the response simulated by the computationally expensive groundwater model. We demonstrate in the real-world case study that explicitly accounting for model structural error yields parameter posterior distributions that are substantially different from those derived by the classical Bayesian calibration that does not account for model structural error. In addition, the Bayesian with error model method gives significantly more accurate prediction along with reasonable credible intervals.

Transfer Function Identification Using Orthogonal Fourier Transform Modeling Functions

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.

2013-01-01

A method for transfer function identification, including both model structure determination and parameter estimation, was developed and demonstrated. The approach uses orthogonal modeling functions generated from frequency domain data obtained by Fourier transformation of time series data. The method was applied to simulation data to identify continuous-time transfer function models and unsteady aerodynamic models. Model fit error, estimated model parameters, and the associated uncertainties were used to show the effectiveness of the method for identifying accurate transfer function models from noisy data.

Evaluating the effectiveness of the MASW technique in a geologically complex terrain

NASA Astrophysics Data System (ADS)

Anukwu, G. C.; Khalil, A. E.; Abdullah, K. B.

2018-04-01

MASW surveys carried at a number of sites in Pulau Pinang, Malaysia, showed complicated dispersion curves which consequently made the inversion into soil shear velocity model ambiguous. This research work details effort to define the source of these complicated dispersion curves. As a starting point, the complexity of the phase velocity spectrum is assumed to be due to either the surveying parameters or the elastic properties of the soil structures. For the former, the surveying was carried out using different parameters. The complexities were persistent for the different surveying parameters, an indication that the elastic properties of the soil structure could be the reason. In order to exploit this assumption, a synthetic modelling approach was adopted using information from borehole, literature and geologically plausible models. Results suggest that the presence of irregular variation in the stiffness of the soil layers, high stiffness contrast and relatively shallow bedrock, results in a quite complex f-v spectrum, especially at frequencies lower than 20Hz, making it difficult to accurately extract the dispersion curve below this frequency. As such, for MASW technique, especially in complex geological situations as demonstrated, great care should be taken during the data processing and inversion to obtain a model that accurately depicts the subsurface.

Sensitivity and Limitations of Structures from X-ray and Neutron-Based Diffraction Analyses of Transition Metal Oxide Lithium-Battery Electrodes

DOE PAGES

Liu, Hao; Liu, Haodong; Lapidus, Saul H.; ...

2017-06-21

Lithium transition metal oxides are an important class of electrode materials for lithium-ion batteries. Binary or ternary (transition) metal doping brings about new opportunities to improve the electrode’s performance and often leads to more complex stoichiometries and atomic structures than the archetypal LiCoO 2. Rietveld structural analyses of X-ray and neutron diffraction data is a widely-used approach for structural characterization of crystalline materials. But, different structural models and refinement approaches can lead to differing results, and some parameters can be difficult to quantify due to the inherent limitations of the data. Here, through the example of LiNi 0.8Co 0.15Al 0.05Omore » 2 (NCA), we demonstrated the sensitivity of various structural parameters in Rietveld structural analysis to different refinement approaches and structural models, and proposed an approach to reduce refinement uncertainties due to the inexact X-ray scattering factors of the constituent atoms within the lattice. Furthermore, this refinement approach was implemented for electrochemically-cycled NCA samples and yielded accurate structural parameters using only X-ray diffraction data. The present work provides the best practices for performing structural refinement of lithium transition metal oxides.« less

Sensitivity and Limitations of Structures from X-ray and Neutron-Based Diffraction Analyses of Transition Metal Oxide Lithium-Battery Electrodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Hao; Liu, Haodong; Lapidus, Saul H.

Lithium transition metal oxides are an important class of electrode materials for lithium-ion batteries. Binary or ternary (transition) metal doping brings about new opportunities to improve the electrode’s performance and often leads to more complex stoichiometries and atomic structures than the archetypal LiCoO 2. Rietveld structural analyses of X-ray and neutron diffraction data is a widely-used approach for structural characterization of crystalline materials. But, different structural models and refinement approaches can lead to differing results, and some parameters can be difficult to quantify due to the inherent limitations of the data. Here, through the example of LiNi 0.8Co 0.15Al 0.05Omore » 2 (NCA), we demonstrated the sensitivity of various structural parameters in Rietveld structural analysis to different refinement approaches and structural models, and proposed an approach to reduce refinement uncertainties due to the inexact X-ray scattering factors of the constituent atoms within the lattice. Furthermore, this refinement approach was implemented for electrochemically-cycled NCA samples and yielded accurate structural parameters using only X-ray diffraction data. The present work provides the best practices for performing structural refinement of lithium transition metal oxides.« less

Half-blind remote sensing image restoration with partly unknown degradation

NASA Astrophysics Data System (ADS)

Xie, Meihua; Yan, Fengxia

2017-01-01

The problem of image restoration has been extensively studied for its practical importance and theoretical interest. This paper mainly discusses the problem of image restoration with partly unknown kernel. In this model, the degraded kernel function is known but its parameters are unknown. With this model, we should estimate the parameters in Gaussian kernel and the real image simultaneity. For this new problem, a total variation restoration model is put out and an intersect direction iteration algorithm is designed. Peak Signal to Noise Ratio (PSNR) and Structural Similarity Index Measurement (SSIM) are used to measure the performance of the method. Numerical results show that we can estimate the parameters in kernel accurately, and the new method has both much higher PSNR and much higher SSIM than the expectation maximization (EM) method in many cases. In addition, the accuracy of estimation is not sensitive to noise. Furthermore, even though the support of the kernel is unknown, we can also use this method to get accurate estimation.

Orientation estimation of anatomical structures in medical images for object recognition

NASA Astrophysics Data System (ADS)

Bağci, Ulaş; Udupa, Jayaram K.; Chen, Xinjian

2011-03-01

Recognition of anatomical structures is an important step in model based medical image segmentation. It provides pose estimation of objects and information about "where" roughly the objects are in the image and distinguishing them from other object-like entities. In,1 we presented a general method of model-based multi-object recognition to assist in segmentation (delineation) tasks. It exploits the pose relationship that can be encoded, via the concept of ball scale (b-scale), between the binary training objects and their associated grey images. The goal was to place the model, in a single shot, close to the right pose (position, orientation, and scale) in a given image so that the model boundaries fall in the close vicinity of object boundaries in the image. Unlike position and scale parameters, we observe that orientation parameters require more attention when estimating the pose of the model as even small differences in orientation parameters can lead to inappropriate recognition. Motivated from the non-Euclidean nature of the pose information, we propose in this paper the use of non-Euclidean metrics to estimate orientation of the anatomical structures for more accurate recognition and segmentation. We statistically analyze and evaluate the following metrics for orientation estimation: Euclidean, Log-Euclidean, Root-Euclidean, Procrustes Size-and-Shape, and mean Hermitian metrics. The results show that mean Hermitian and Cholesky decomposition metrics provide more accurate orientation estimates than other Euclidean and non-Euclidean metrics.

Geometric dependence of the parasitic components and thermal properties of HEMTs

NASA Astrophysics Data System (ADS)

Vun, Peter V.; Parker, Anthony E.; Mahon, Simon J.; Fattorini, Anthony

2007-12-01

For integrated circuit design up to 50GHz and beyond accurate models of the transistor access structures and intrinsic structures are necessary for prediction of circuit performance. The circuit design process relies on optimising transistor geometry parameters such as unit gate width, number of gates, number of vias and gate-to-gate spacing. So the relationship between electrical and thermal parasitic components in transistor access structures, and transistor geometry is important to understand when developing models for transistors of differing geometries. Current approaches to describing the geometric dependence of models are limited to empirical methods which only describe a finite set of geometries and only include unit gate width and number of gates as variables. A better understanding of the geometric dependence is seen as a way to provide scalable models that remain accurate for continuous variation of all geometric parameters. Understanding the distribution of parasitic elements between the manifold, the terminal fingers, and the reference plane discontinuities is an issue identified as important in this regard. Examination of dc characteristics and thermal images indicates that gate-to-gate thermal coupling and increased thermal conductance at the gate ends, affects the device total thermal conductance. Consequently, a distributed thermal model is proposed which accounts for these effects. This work is seen as a starting point for developing comprehensive scalable models that will allow RF circuit designers to optimise circuit performance parameters such as total die area, maximum output power, power-added-efficiency (PAE) and channel temperature/lifetime.

Thermodynamic stability of RNA structures formed by CNG trinucleotide repeats. Implication for prediction of RNA structure.

PubMed

Broda, Magdalena; Kierzek, Elzbieta; Gdaniec, Zofia; Kulinski, Tadeusz; Kierzek, Ryszard

2005-08-16

Trinucleotide repeat expansion diseases (TREDs) are correlated with elongation of CNG DNA and RNA repeats to pathological level. This paper shows, for the first time, complete data concerning thermodynamic stabilities of RNA with CNG trinucleotide repeats. Our studies include the stability of oligoribonucleotides composed of two to seven of CAG, CCG, CGG, and CUG repeats. The thermodynamic parameters of helix propagation correlated with the presence of multiple N-N mismatches within CNG RNA duplexes were also determined. Moreover, the total stability of CNG RNA hairpins, as well as the contribution of trinucleotide repeats placed only in the stem or loop regions, was evaluated. The improved thermodynamic parameters allow to predict much more accurately the thermodynamic stabilities and structures of CNG RNAs.

Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics

PubMed Central

Xue, Yi; Skrynnikov, Nikolai R

2014-01-01

Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native-like fashion as dictated by the original force field. To validate this approach, we have used the data from solid-state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well-established model protein, ubiquitin. The ensemble-restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid-state chemical shifts, and backbone order parameters. The predictions for 15N R1 relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high-resolution crystallographic data can be viewed as protein-specific empirical corrections to the standard force fields. PMID:24452989

Retrieval with Infrared Atmospheric Sounding Interferometer and Validation during JAIVEx

NASA Technical Reports Server (NTRS)

Zhou, Daniel K.; Liu, Xu; Larar, Allen M.; Smith, William L.; Taylor, Jonathan P.; Schluessel, Peter; Strow, L. Larrabee; Mango, Stephen A.

2008-01-01

A state-of-the-art IR-only retrieval algorithm has been developed with an all-season-global EOF Physical Regression and followed by 1-D Var. Physical Iterative Retrieval for IASI, AIRS, and NAST-I. The benefits of this retrieval are to produce atmospheric structure with a single FOV horizontal resolution (approx. 15 km for IASI and AIRS), accurate profiles above the cloud (at least) or down to the surface, surface parameters, and/or cloud microphysical parameters. Initial case study and validation indicates that surface, cloud, and atmospheric structure (include TBL) are well captured by IASI and AIRS measurements. Coincident dropsondes during the IASI and AIRS overpasses are used to validate atmospheric conditions, and accurate retrievals are obtained with an expected vertical resolution. JAIVEx has provided the data needed to validate the retrieval algorithm and its products which allows us to assess the instrument ability and/or performance. Retrievals with global coverage are under investigation for detailed retrieval assessment. It is greatly desired that these products be used for testing the impact on Atmospheric Data Assimilation and/or Numerical Weather Prediction.

Improved treatment of nucleosides and nucleotides in the OPLS-AA force field

NASA Astrophysics Data System (ADS)

Robertson, Michael J.; Tirado-Rives, Julian; Jorgensen, William L.

2017-09-01

DFT calculations have been used to develop improved descriptions of the torsional energetics for nucleosides and nucleotides in the OPLS-AA force field. Scans of nucleotide dihedral angles (γ, χ, and β) and methyl phosphates provided the bases for the new torsional parameters. In addition, the angle-bending parameters of phosphodiesters and ribose were updated, and adjustments were made to existing carbohydrate torsions to better capture the sugar puckering landscape of ribose. MD simulations of nucleosides with the new parameters demonstrate a significant improvement in the ribose sugar puckering and χ angle distributions. Additionally, energy-minimization of protein-nucleotide crystal structures with the new parameters produced accurate poses.

High-order dynamic modeling and parameter identification of structural discontinuities in Timoshenko beams by using reflection coefficients

NASA Astrophysics Data System (ADS)

Fan, Qiang; Huang, Zhenyu; Zhang, Bing; Chen, Dayue

2013-02-01

Properties of discontinuities, such as bolt joints and cracks in the waveguide structures, are difficult to evaluate by either analytical or numerical methods due to the complexity and uncertainty of the discontinuities. In this paper, the discontinuity in a Timoshenko beam is modeled with high-order parameters and then these parameters are identified by using reflection coefficients at the discontinuity. The high-order model is composed of several one-order sub-models in series and each sub-model consists of inertia, stiffness and damping components in parallel. The order of the discontinuity model is determined based on the characteristics of the reflection coefficient curve and the accuracy requirement of the dynamic modeling. The model parameters are identified through the least-square fitting iteration method, of which the undetermined model parameters are updated in iteration to fit the dynamic reflection coefficient curve with the wave-based one. By using the spectral super-element method (SSEM), simulation cases, including one-order discontinuities on infinite- and finite-beams and a two-order discontinuity on an infinite beam, were employed to evaluate both the accuracy of the discontinuity model and the effectiveness of the identification method. For practical considerations, effects of measurement noise on the discontinuity parameter identification are investigated by adding different levels of noise to the simulated data. The simulation results were then validated by the corresponding experiments. Both the simulation and experimental results show that (1) the one-order discontinuities can be identified accurately with the maximum errors of 6.8% and 8.7%, respectively; (2) and the high-order discontinuities can be identified with the maximum errors of 15.8% and 16.2%, respectively; and (3) the high-order model can predict the complex discontinuity much more accurately than the one-order discontinuity model.

Spatiotemporal dynamics in excitable homogeneous random networks composed of periodically self-sustained oscillation.

PubMed

Qian, Yu; Liu, Fei; Yang, Keli; Zhang, Ge; Yao, Chenggui; Ma, Jun

2017-09-19

The collective behaviors of networks are often dependent on the network connections and bifurcation parameters, also the local kinetics plays an important role in contributing the consensus of coupled oscillators. In this paper, we systematically investigate the influence of network structures and system parameters on the spatiotemporal dynamics in excitable homogeneous random networks (EHRNs) composed of periodically self-sustained oscillation (PSO). By using the dominant phase-advanced driving (DPAD) method, the one-dimensional (1D) Winfree loop is exposed as the oscillation source supporting the PSO, and the accurate wave propagation pathways from the oscillation source to the whole network are uncovered. Then, an order parameter is introduced to quantitatively study the influence of network structures and system parameters on the spatiotemporal dynamics of PSO in EHRNs. Distinct results induced by the network structures and the system parameters are observed. Importantly, the corresponding mechanisms are revealed. PSO influenced by the network structures are induced not only by the change of average path length (APL) of network, but also by the invasion of 1D Winfree loop from the outside linking nodes. Moreover, PSO influenced by the system parameters are determined by the excitation threshold and the minimum 1D Winfree loop. Finally, we confirmed that the excitation threshold and the minimum 1D Winfree loop determined PSO will degenerate as the system size is expanded.

Basic research on design analysis methods for rotorcraft vibrations

NASA Technical Reports Server (NTRS)

Hanagud, S.

1991-01-01

The objective of the present work was to develop a method for identifying physically plausible finite element system models of airframe structures from test data. The assumed models were based on linear elastic behavior with general (nonproportional) damping. Physical plausibility of the identified system matrices was insured by restricting the identification process to designated physical parameters only and not simply to the elements of the system matrices themselves. For example, in a large finite element model the identified parameters might be restricted to the moduli for each of the different materials used in the structure. In the case of damping, a restricted set of damping values might be assigned to finite elements based on the material type and on the fabrication processes used. In this case, different damping values might be associated with riveted, bolted and bonded elements. The method itself is developed first, and several approaches are outlined for computing the identified parameter values. The method is applied first to a simple structure for which the 'measured' response is actually synthesized from an assumed model. Both stiffness and damping parameter values are accurately identified. The true test, however, is the application to a full-scale airframe structure. In this case, a NASTRAN model and actual measured modal parameters formed the basis for the identification of a restricted set of physically plausible stiffness and damping parameters.

Determination of structure parameters in strong-field tunneling ionization theory of molecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao Songfeng; Jin Cheng; College of Physics and Electronic Engineering, Northwest Normal University, Lanzhou, Gansu 730070

2010-03-15

In the strong field molecular tunneling ionization theory of Tong et al. [Phys. Rev. A 66, 033402 (2002)], the ionization rate depends on the asymptotic wave function of the molecular orbital from which the electron is removed. The orbital wave functions obtained from standard quantum chemistry packages in general are not good enough in the asymptotic region. Here we construct a one-electron model potential for several linear molecules using density functional theory. We show that the asymptotic wave function can be improved with an iteration method and after one iteration accurate asymptotic wave functions and structure parameters are determined. Withmore » the new parameters we examine the alignment-dependent tunneling ionization probabilities for several molecules and compare with other calculations and with recent measurements, including ionization from inner molecular orbitals.« less

Application of tire dynamics to aircraft landing gear design analysis

NASA Technical Reports Server (NTRS)

Black, R. J.

1983-01-01

The tire plays a key part in many analyses used for design of aircraft landing gear. Examples include structural design of wheels, landing gear shimmy, brake whirl, chatter and squeal, complex combination of chatter and shimmy on main landing gear (MLG) systems, anti-skid performance, gear walk, and rough terrain loads and performance. Tire parameters needed in the various analyses are discussed. Two tire models are discussed for shimmy analysis, the modified Moreland approach and the von Schlippe-Dietrich approach. It is shown that the Moreland model can be derived from the Von Schlippe-Dietrich model by certain approximations. The remaining analysis areas are discussed in general terms and the tire parameters needed for each are identified. Accurate tire data allows more accurate design analysis and the correct prediction of dynamic performance of aircraft landing gear.

Accurate modeling of defects in graphene transport calculations

NASA Astrophysics Data System (ADS)

Linhart, Lukas; Burgdörfer, Joachim; Libisch, Florian

2018-01-01

We present an approach for embedding defect structures modeled by density functional theory into large-scale tight-binding simulations. We extract local tight-binding parameters for the vicinity of the defect site using Wannier functions. In the transition region between the bulk lattice and the defect the tight-binding parameters are continuously adjusted to approach the bulk limit far away from the defect. This embedding approach allows for an accurate high-level treatment of the defect orbitals using as many as ten nearest neighbors while keeping a small number of nearest neighbors in the bulk to render the overall computational cost reasonable. As an example of our approach, we consider an extended graphene lattice decorated with Stone-Wales defects, flower defects, double vacancies, or silicon substitutes. We predict distinct scattering patterns mirroring the defect symmetries and magnitude that should be experimentally accessible.

Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction

DOE PAGES

Boiteau, Rene M.; Hoyt, David W.; Nicora, Carrie D.; ...

2018-01-17

Here, we introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS 2), and NMR in a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture and then we identify an uncatalogued secondary metabolite in Arabidopsis thaliana. The NMR/MS 2 approach is well suited for discovery ofmore » new metabolites in plant extracts, microbes, soils, dissolved organic matter, food extracts, biofuels, and biomedical samples, facilitating the identification of metabolites that are not present in experimental NMR and MS metabolomics databases.« less

Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boiteau, Rene M.; Hoyt, David W.; Nicora, Carrie D.

Here, we introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS 2), and NMR in a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture and then we identify an uncatalogued secondary metabolite in Arabidopsis thaliana. The NMR/MS 2 approach is well suited for discovery ofmore » new metabolites in plant extracts, microbes, soils, dissolved organic matter, food extracts, biofuels, and biomedical samples, facilitating the identification of metabolites that are not present in experimental NMR and MS metabolomics databases.« less

Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction

PubMed Central

Hoyt, David W.; Nicora, Carrie D.; Kinmonth-Schultz, Hannah A.; Ward, Joy K.

2018-01-01

We introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS2), and NMR into a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter out the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture, and then we identify an uncatalogued secondary metabolite in Arabidopsis thaliana. The NMR/MS2 approach is well suited to the discovery of new metabolites in plant extracts, microbes, soils, dissolved organic matter, food extracts, biofuels, and biomedical samples, facilitating the identification of metabolites that are not present in experimental NMR and MS metabolomics databases. PMID:29342073

QuickFF: A program for a quick and easy derivation of force fields for metal-organic frameworks from ab initio input.

PubMed

Vanduyfhuys, Louis; Vandenbrande, Steven; Verstraelen, Toon; Schmid, Rochus; Waroquier, Michel; Van Speybroeck, Veronique

2015-05-15

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal-organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three-step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal-organic frameworks (MOFs), QuickFF is used to determine force fields for MIL-53(Al) and MOF-5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

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. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Accurate Construction of Photoactivated Localization Microscopy (PALM) Images for Quantitative Measurements

PubMed Central

Coltharp, Carla; Kessler, Rene P.; Xiao, Jie

2012-01-01

Localization-based superresolution microscopy techniques such as Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) have allowed investigations of cellular structures with unprecedented optical resolutions. One major obstacle to interpreting superresolution images, however, is the overcounting of molecule numbers caused by fluorophore photoblinking. Using both experimental and simulated images, we determined the effects of photoblinking on the accurate reconstruction of superresolution images and on quantitative measurements of structural dimension and molecule density made from those images. We found that structural dimension and relative density measurements can be made reliably from images that contain photoblinking-related overcounting, but accurate absolute density measurements, and consequently faithful representations of molecule counts and positions in cellular structures, require the application of a clustering algorithm to group localizations that originate from the same molecule. We analyzed how applying a simple algorithm with different clustering thresholds (tThresh and dThresh) affects the accuracy of reconstructed images, and developed an easy method to select optimal thresholds. We also identified an empirical criterion to evaluate whether an imaging condition is appropriate for accurate superresolution image reconstruction with the clustering algorithm. Both the threshold selection method and imaging condition criterion are easy to implement within existing PALM clustering algorithms and experimental conditions. The main advantage of our method is that it generates a superresolution image and molecule position list that faithfully represents molecule counts and positions within a cellular structure, rather than only summarizing structural properties into ensemble parameters. This feature makes it particularly useful for cellular structures of heterogeneous densities and irregular geometries, and allows a variety of quantitative measurements tailored to specific needs of different biological systems. PMID:23251611

Structural Damage Detection Using Virtual Passive Controllers

NASA Technical Reports Server (NTRS)

Lew, Jiann-Shiun; Juang, Jer-Nan

2001-01-01

This paper presents novel approaches for structural damage detection which uses the virtual passive controllers attached to structures, where passive controllers are energy dissipative devices and thus guarantee the closed-loop stability. The use of the identified parameters of various closed-loop systems can solve the problem that reliable identified parameters, such as natural frequencies of the open-loop system may not provide enough information for damage detection. Only a small number of sensors are required for the proposed approaches. The identified natural frequencies, which are generally much less sensitive to noise and more reliable than the identified natural frequencies, are used for damage detection. Two damage detection techniques are presented. One technique is based on the structures with direct output feedback controllers while the other technique uses the second-order dynamic feedback controllers. A least-squares technique, which is based on the sensitivity of natural frequencies to damage variables, is used for accurately identifying the damage variables.

Optimal structure and parameter learning of Ising models

DOE PAGES

Lokhov, Andrey; Vuffray, Marc Denis; Misra, Sidhant; ...

2018-03-16

Reconstruction of the structure and parameters of an Ising model from binary samples is a problem of practical importance in a variety of disciplines, ranging from statistical physics and computational biology to image processing and machine learning. The focus of the research community shifted toward developing universal reconstruction algorithms that are both computationally efficient and require the minimal amount of expensive data. Here, we introduce a new method, interaction screening, which accurately estimates model parameters using local optimization problems. The algorithm provably achieves perfect graph structure recovery with an information-theoretically optimal number of samples, notably in the low-temperature regime, whichmore » is known to be the hardest for learning. Here, the efficacy of interaction screening is assessed through extensive numerical tests on synthetic Ising models of various topologies with different types of interactions, as well as on real data produced by a D-Wave quantum computer. Finally, this study shows that the interaction screening method is an exact, tractable, and optimal technique that universally solves the inverse Ising problem.« less

Optimal structure and parameter learning of Ising models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lokhov, Andrey; Vuffray, Marc Denis; Misra, Sidhant

Reconstruction of the structure and parameters of an Ising model from binary samples is a problem of practical importance in a variety of disciplines, ranging from statistical physics and computational biology to image processing and machine learning. The focus of the research community shifted toward developing universal reconstruction algorithms that are both computationally efficient and require the minimal amount of expensive data. Here, we introduce a new method, interaction screening, which accurately estimates model parameters using local optimization problems. The algorithm provably achieves perfect graph structure recovery with an information-theoretically optimal number of samples, notably in the low-temperature regime, whichmore » is known to be the hardest for learning. Here, the efficacy of interaction screening is assessed through extensive numerical tests on synthetic Ising models of various topologies with different types of interactions, as well as on real data produced by a D-Wave quantum computer. Finally, this study shows that the interaction screening method is an exact, tractable, and optimal technique that universally solves the inverse Ising problem.« less

Automated palpation for breast tissue discrimination based on viscoelastic biomechanical properties.

PubMed

Tsukune, Mariko; Kobayashi, Yo; Miyashita, Tomoyuki; Fujie, G Masakatsu

2015-05-01

Accurate, noninvasive methods are sought for breast tumor detection and diagnosis. In particular, a need for noninvasive techniques that measure both the nonlinear elastic and viscoelastic properties of breast tissue has been identified. For diagnostic purposes, it is important to select a nonlinear viscoelastic model with a small number of parameters that highly correlate with histological structure. However, the combination of conventional viscoelastic models with nonlinear elastic models requires a large number of parameters. A nonlinear viscoelastic model of breast tissue based on a simple equation with few parameters was developed and tested. The nonlinear viscoelastic properties of soft tissues in porcine breast were measured experimentally using fresh ex vivo samples. Robotic palpation was used for measurements employed in a finite element model. These measurements were used to calculate nonlinear viscoelastic parameters for fat, fibroglandular breast parenchyma and muscle. The ability of these parameters to distinguish the tissue types was evaluated in a two-step statistical analysis that included Holm's pairwise [Formula: see text] test. The discrimination error rate of a set of parameters was evaluated by the Mahalanobis distance. Ex vivo testing in porcine breast revealed significant differences in the nonlinear viscoelastic parameters among combinations of three tissue types. The discrimination error rate was low among all tested combinations of three tissue types. Although tissue discrimination was not achieved using only a single nonlinear viscoelastic parameter, a set of four nonlinear viscoelastic parameters were able to reliably and accurately discriminate fat, breast fibroglandular tissue and muscle.

Finite element analysis of drilling in carbon fiber reinforced polymer composites

NASA Astrophysics Data System (ADS)

Phadnis, V. A.; Roy, A.; Silberschmidt, V. V.

2012-08-01

Carbon fiber reinforced polymer composite (CFRP) laminates are attractive for many applications in the aerospace industry especially as aircraft structural components due to their superior properties. Usually drilling is an important final machining process for components made of composite laminates. In drilling of CFRP, it is an imperative task to determine the maximum critical thrust forces that trigger inter-laminar and intra-laminar damage modes owing to highly anisotropic fibrous media; and negotiate integrity of composite structures. In this paper, a 3D finite element (FE) model of drilling in CFRP composite laminate is developed, which accurately takes into account the dynamic characteristics involved in the process along with the accurate geometrical considerations. A user defined material model is developed to account for accurate though thickness response of composite laminates. The average critical thrust forces and torques obtained using FE analysis, for a set of machining parameters are found to be in good agreement with the experimental results from literature.

Uncertainty analysis of scintillometers methods in measuring sensible heat fluxes of forest ecosystem

NASA Astrophysics Data System (ADS)

Zheng, N.

2017-12-01

Sensible heat flux (H) is one of the driving factors of surface turbulent motion and energy exchange. Therefore, it is particularly important to measure sensible heat flux accurately at the regional scale. However, due to the heterogeneity of the underlying surface, hydrothermal regime, and different weather conditions, it is difficult to estimate the represented flux at the kilometer scale. The scintillometer have been developed into an effective and universal equipment for deriving heat flux at the regional-scale which based on the turbulence effect of light in the atmosphere since the 1980s. The parameter directly obtained by the scintillometer is the structure parameter of the refractive index of air based on the changes of light intensity fluctuation. Combine with parameters such as temperature structure parameter, zero-plane displacement, surface roughness, wind velocity, air temperature and the other meteorological data heat fluxes can be derived. These additional parameters increase the uncertainties of flux because the difference between the actual feature of turbulent motion and the applicable conditions of turbulence theory. Most previous studies often focused on the constant flux layers that are above the rough sub-layers and homogeneous flat surfaces underlying surfaces with suitable weather conditions. Therefore, the criteria and modified forms of key parameters are invariable. In this study, we conduct investment over the hilly area of northern China with different plants, such as cork oak, cedar-black and locust. On the basis of key research on the threshold and modified forms of saturation with different turbulence intensity, modified forms of Bowen ratio with different drying-and-wetting conditions, universal function for the temperature structure parameter under different atmospheric stability, the dominant sources of uncertainty will be determined. The above study is significant to reveal influence mechanism of uncertainty and explore influence degree of uncertainty with quantitative analysis. The study can provide theoretical basis and technical support for accurately measuring sensible heat fluxes of forest ecosystem with scintillometer method, and can also provide work foundation for further study on role of forest ecosystem in energy balance and climate change.

Characterization of structural connections using free and forced response test data

NASA Technical Reports Server (NTRS)

Lawrence, Charles; Huckelbridge, Arthur A.

1989-01-01

The accurate prediction of system dynamic response often has been limited by deficiencies in existing capabilities to characterize connections adequately. Connections between structural components often are complex mechanically, and difficult to accurately model analytically. Improved analytical models for connections are needed to improve system dynamic preditions. A procedure for identifying physical connection properties from free and forced response test data is developed, then verified utilizing a system having both a linear and nonlinear connection. Connection properties are computed in terms of physical parameters so that the physical characteristics of the connections can better be understood, in addition to providing improved input for the system model. The identification procedure is applicable to multi-degree of freedom systems, and does not require that the test data be measured directly at the connection locations.

Measuring of electrical changes induced by in situ combustion through flow-through electrodes in a laboratory sample of core material

DOEpatents

Lee, D.O.; Montoya, P.C.; Wayland, J.R. Jr.

1986-12-09

Method and apparatus are provided for obtaining accurate dynamic measurements for passage of phase fronts through a core sample in a test fixture. Flow-through grid structures are provided for electrodes to permit data to be obtained before, during and after passage of a front there through. Such electrodes are incorporated in a test apparatus for obtaining electrical characteristics of the core sample. With the inventive structure a method is provided for measurement of instabilities in a phase front progressing through the medium. Availability of accurate dynamic data representing parameters descriptive of material characteristics before, during and after passage of a front provides a more efficient method for enhanced recovery of oil using a fire flood technique. 12 figs.

Measuring of electrical changes induced by in situ combustion through flow-through electrodes in a laboratory sample of core material

DOEpatents

Lee, David O.; Montoya, Paul C.; Wayland, Jr., James R.

1986-01-01

Method and apparatus are provided for obtaining accurate dynamic measurements for passage of phase fronts through a core sample in a test fixture. Flow-through grid structures are provided for electrodes to permit data to be obtained before, during and after passage of a front therethrough. Such electrodes are incorporated in a test apparatus for obtaining electrical characteristics of the core sample. With the inventive structure a method is provided for measurement of instabilities in a phase front progressing through the medium. Availability of accurate dynamic data representing parameters descriptive of material characteristics before, during and after passage of a front provides a more efficient method for enhanced recovery of oil using a fire flood technique.

Parameter Estimation for Viscoplastic Material Modeling

NASA Technical Reports Server (NTRS)

Saleeb, Atef F.; Gendy, Atef S.; Wilt, Thomas E.

1997-01-01

A key ingredient in the design of engineering components and structures under general thermomechanical loading is the use of mathematical constitutive models (e.g. in finite element analysis) capable of accurate representation of short and long term stress/deformation responses. In addition to the ever-increasing complexity of recent viscoplastic models of this type, they often also require a large number of material constants to describe a host of (anticipated) physical phenomena and complicated deformation mechanisms. In turn, the experimental characterization of these material parameters constitutes the major factor in the successful and effective utilization of any given constitutive model; i.e., the problem of constitutive parameter estimation from experimental measurements.

Adjoint sensitivity analysis of plasmonic structures using the FDTD method.

PubMed

Zhang, Yu; Ahmed, Osman S; Bakr, Mohamed H

2014-05-15

We present an adjoint variable method for estimating the sensitivities of arbitrary responses with respect to the parameters of dispersive discontinuities in nanoplasmonic devices. Our theory is formulated in terms of the electric field components at the vicinity of perturbed discontinuities. The adjoint sensitivities are computed using at most one extra finite-difference time-domain (FDTD) simulation regardless of the number of parameters. Our approach is illustrated through the sensitivity analysis of an add-drop coupler consisting of a square ring resonator between two parallel waveguides. The computed adjoint sensitivities of the scattering parameters are compared with those obtained using the accurate but computationally expensive central finite difference approach.

A hybrid system identification methodology for wireless structural health monitoring systems based on dynamic substructuring

NASA Astrophysics Data System (ADS)

Dragos, Kosmas; Smarsly, Kay

2016-04-01

System identification has been employed in numerous structural health monitoring (SHM) applications. Traditional system identification methods usually rely on centralized processing of structural response data to extract information on structural parameters. However, in wireless SHM systems the centralized processing of structural response data introduces a significant communication bottleneck. Exploiting the merits of decentralization and on-board processing power of wireless SHM systems, many system identification methods have been successfully implemented in wireless sensor networks. While several system identification approaches for wireless SHM systems have been proposed, little attention has been paid to obtaining information on the physical parameters (e.g. stiffness, damping) of the monitored structure. This paper presents a hybrid system identification methodology suitable for wireless sensor networks based on the principles of component mode synthesis (dynamic substructuring). A numerical model of the monitored structure is embedded into the wireless sensor nodes in a distributed manner, i.e. the entire model is segmented into sub-models, each embedded into one sensor node corresponding to the substructure the sensor node is assigned to. The parameters of each sub-model are estimated by extracting local mode shapes and by applying the equations of the Craig-Bampton method on dynamic substructuring. The proposed methodology is validated in a laboratory test conducted on a four-story frame structure to demonstrate the ability of the methodology to yield accurate estimates of stiffness parameters. Finally, the test results are discussed and an outlook on future research directions is provided.

Sensitivity and Specificity of Eustachian Tube Function Tests in Adults

PubMed Central

Doyle, William J.; Swarts, J. Douglas; Banks, Julianne; Casselbrant, Margaretha L; Mandel, Ellen M; Alper, Cuneyt M.

2013-01-01

Objective Determine if Eustachian Tube (ET) function (ETF) tests can identify ears with physician-diagnosed ET dysfunction (ETD) in a mixed population at high sensitivity and specificity and define the inter-relatedness of ETF test parameters. Methods ETF was evaluated using the Forced-Response, Inflation-Deflation, Valsalva and Sniffing tests in 15 control ears of adult subjects after unilateral myringotomy (Group I) and in 23 ears of 19 adult subjects with ventilation tubes inserted for ETD (Group II). Data were analyzed using logistic regression including each parameter independently and then a step-down Discriminant Analysis including all ETF test parameters to predict group assignment. Factor Analysis operating over all parameters was used to explore relatedness. Results The Discriminant Analysis identified 4 ETF test parameters (Valsalva, ET opening pressure, dilatory efficiency and % positive pressure equilibrated) that together correctly assigned ears to Group II at a sensitivity of 95% and a specificity of 83%. Individual parameters representing the efficiency of ET opening during swallowing showed moderately accurate assignments of ears to their respective groups. Three factors captured approximately 98% of the variance among parameters, the first had negative loadings of the ETF structural parameters, the second had positive loadings of the muscle-assisted ET opening parameters and the third had negative loadings of the muscle-assisted ET opening parameters and positive loadings of the structural parameters. Discussion These results show that ETF tests can correctly assign individual ears to physician-diagnosed ETD with high sensitivity and specificity and that ETF test parameters can be grouped into structural-functional categories. PMID:23868429

Selection of regularization parameter for l1-regularized damage detection

NASA Astrophysics Data System (ADS)

Hou, Rongrong; Xia, Yong; Bao, Yuequan; Zhou, Xiaoqing

2018-06-01

The l1 regularization technique has been developed for structural health monitoring and damage detection through employing the sparsity condition of structural damage. The regularization parameter, which controls the trade-off between data fidelity and solution size of the regularization problem, exerts a crucial effect on the solution. However, the l1 regularization problem has no closed-form solution, and the regularization parameter is usually selected by experience. This study proposes two strategies of selecting the regularization parameter for the l1-regularized damage detection problem. The first method utilizes the residual and solution norms of the optimization problem and ensures that they are both small. The other method is based on the discrepancy principle, which requires that the variance of the discrepancy between the calculated and measured responses is close to the variance of the measurement noise. The two methods are applied to a cantilever beam and a three-story frame. A range of the regularization parameter, rather than one single value, can be determined. When the regularization parameter in this range is selected, the damage can be accurately identified even for multiple damage scenarios. This range also indicates the sensitivity degree of the damage identification problem to the regularization parameter.

Electronic structure, dielectric response, and surface charge distribution of RGD (1FUV) peptide.

PubMed

Adhikari, Puja; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Steinmetz, Nicole F; Podgornik, Rudolf; Ching, Wai-Yim

2014-07-08

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.

Dependence of nuclear quadrupole resonance transitions on the electric field gradient asymmetry parameter for nuclides with half-integer spins

DOE PAGES

Cho, Herman

2016-02-28

Allowed transition energies and eigenstate expansions have been calculated and tabulated in numerical form as functions of the electric field gradient asymmetry parameter for the zero field Hamiltonian of quadrupolar nuclides with I = 3/2,5/2,7/2, and 9/2. These results are essential to interpret nuclear quadrupole resonance (NQR) spectra and extract accurate values of the electric field gradient tensors. Furthermore, applications of NQR methods to studies of electronic structure in heavy element systems are proposed.

Determination of Structural Parameters from EXAFS (Extended X-Ray Absorption Fine Structure): Application to Solutions and Catalysts.

DTIC Science & Technology

1984-05-23

the disorder was accurately known. Inverse Transform To isolate the EAFS contribution due to a single feature in the Fourier transform, the inverse ...is associated with setting the "fold" components to 27 zero in r-space. An inverse transform (real part) of the major feature of the Fig. 4 Fourier...phase of the resulting inverse transform represents only any differences between the material being studied and the reference. This residual is

Finite Element Modelling of a Field-Sensed Magnetic Suspended System for Accurate Proximity Measurement Based on a Sensor Fusion Algorithm with Unscented Kalman Filter

PubMed Central

Chowdhury, Amor; Sarjaš, Andrej

2016-01-01

The presented paper describes accurate distance measurement for a field-sensed magnetic suspension system. The proximity measurement is based on a Hall effect sensor. The proximity sensor is installed directly on the lower surface of the electro-magnet, which means that it is very sensitive to external magnetic influences and disturbances. External disturbances interfere with the information signal and reduce the usability and reliability of the proximity measurements and, consequently, the whole application operation. A sensor fusion algorithm is deployed for the aforementioned reasons. The sensor fusion algorithm is based on the Unscented Kalman Filter, where a nonlinear dynamic model was derived with the Finite Element Modelling approach. The advantage of such modelling is a more accurate dynamic model parameter estimation, especially in the case when the real structure, materials and dimensions of the real-time application are known. The novelty of the paper is the design of a compact electro-magnetic actuator with a built-in low cost proximity sensor for accurate proximity measurement of the magnetic object. The paper successively presents a modelling procedure with the finite element method, design and parameter settings of a sensor fusion algorithm with Unscented Kalman Filter and, finally, the implementation procedure and results of real-time operation. PMID:27649197

Finite Element Modelling of a Field-Sensed Magnetic Suspended System for Accurate Proximity Measurement Based on a Sensor Fusion Algorithm with Unscented Kalman Filter.

PubMed

Chowdhury, Amor; Sarjaš, Andrej

2016-09-15

The presented paper describes accurate distance measurement for a field-sensed magnetic suspension system. The proximity measurement is based on a Hall effect sensor. The proximity sensor is installed directly on the lower surface of the electro-magnet, which means that it is very sensitive to external magnetic influences and disturbances. External disturbances interfere with the information signal and reduce the usability and reliability of the proximity measurements and, consequently, the whole application operation. A sensor fusion algorithm is deployed for the aforementioned reasons. The sensor fusion algorithm is based on the Unscented Kalman Filter, where a nonlinear dynamic model was derived with the Finite Element Modelling approach. The advantage of such modelling is a more accurate dynamic model parameter estimation, especially in the case when the real structure, materials and dimensions of the real-time application are known. The novelty of the paper is the design of a compact electro-magnetic actuator with a built-in low cost proximity sensor for accurate proximity measurement of the magnetic object. The paper successively presents a modelling procedure with the finite element method, design and parameter settings of a sensor fusion algorithm with Unscented Kalman Filter and, finally, the implementation procedure and results of real-time operation.

The impact of experimental measurement errors on long-term viscoelastic predictions. [of structural materials

NASA Technical Reports Server (NTRS)

Tuttle, M. E.; Brinson, H. F.

1986-01-01

The impact of flight error in measured viscoelastic parameters on subsequent long-term viscoelastic predictions is numerically evaluated using the Schapery nonlinear viscoelastic model. Of the seven Schapery parameters, the results indicated that long-term predictions were most sensitive to errors in the power law parameter n. Although errors in the other parameters were significant as well, errors in n dominated all other factors at long times. The process of selecting an appropriate short-term test cycle so as to insure an accurate long-term prediction was considered, and a short-term test cycle was selected using material properties typical for T300/5208 graphite-epoxy at 149 C. The process of selection is described, and its individual steps are itemized.

Realization of a mixed-symmetry superconducting gap in correlated organic metals

NASA Astrophysics Data System (ADS)

Altmeyer, Michaela; Guterding, Daniel; Jeschke, Harald O.; Diehl, Sandra; Methfessel, Torsten; Tutsch, Ulrich; Schubert, Harald; Lang, Michael; Müller, Jens; Huth, Michael; Jourdan, Martin; Elmers, Hans-Joachim; Valenti, Roser

Recent scanning tunneling spectroscopy measurements on the organic charge tranfer salt κ-(BEDT-TTF)2Cu[N(CN)2]Br show clear evidence of a highly anisotropic gap structure. Based on an ab initio derived model Hamiltonian we employ random phase approximation spin fluctuation theory yielding a composite order parameter of (extended) s+dx2-y2 symmetry. Taking explicitly also the shape of the Fermi surface into account we calculate STS spectra that are in excellent agreement to the experimental observations [1]. Moreover we determine the minimal tight binding model to describe the general lattice structure of these compounds accurately and generate a phase diagram for the gap symmetry by varying the hopping parameters. Based on ab initio derived parameter sets we predict the gap symmetry of other superconducting κ charge transfer salts. This work was supported by Deutsche Forschungsgemeinschaft under Grant No. SFB/TR 49.

Ab-initio investigation of Rb substitution in KTP single crystal

NASA Astrophysics Data System (ADS)

Ghoohestani, Marzieh; Arab, Ali; Hashemifar, S. Javad; Sadeghi, Hossein

2018-01-01

The effects of rubidium doping on the structural, electronic, and optical properties of KTiOPO4 (KTP) are investigated in the framework of density functional theory. The equilibrium structural parameters of KTP and RbTiOPO4 (RTP) are calculated within the local density and Perdew-Burke-Ernzerhof (PBE), Wu-Cohen, and PBEsol formulation of generalized gradient approximations. We discuss that PBEsol predicts better equilibrium parameters for the KTP alloy. In addition, the variation of lattice constants and Ti-O-Ti bond angles are evaluated as a function of rubidium concentration. The modern modified Becke-Johnson functional is applied for more accurate band gap determination in the pure and alloyed KTP/RTP compounds. The phenomenological pseudoinversion parameter is calculated for a qualitative understanding of the effect of impurity on a non-linear optical response of KTP. We also analyze the behavior of the dielectric function, dispersive refractive indices, and birefringence of KTP/RTP alloys.

Improving substructure identification accuracy of shear structures using virtual control system

NASA Astrophysics Data System (ADS)

Zhang, Dongyu; Yang, Yang; Wang, Tingqiang; Li, Hui

2018-02-01

Substructure identification is a powerful tool to identify the parameters of a complex structure. Previously, the authors developed an inductive substructure identification method for shear structures. The identification error analysis showed that the identification accuracy of this method is significantly influenced by the magnitudes of two key structural responses near a certain frequency; if these responses are unfavorable, the method cannot provide accurate estimation results. In this paper, a novel method is proposed to improve the substructure identification accuracy by introducing a virtual control system (VCS) into the structure. A virtual control system is a self-balanced system, which consists of some control devices and a set of self-balanced forces. The self-balanced forces counterbalance the forces that the control devices apply on the structure. The control devices are combined with the structure to form a controlled structure used to replace the original structure in the substructure identification; and the self-balance forces are treated as known external excitations to the controlled structure. By optimally tuning the VCS’s parameters, the dynamic characteristics of the controlled structure can be changed such that the original structural responses become more favorable for the substructure identification and, thus, the identification accuracy is improved. A numerical example of 6-story shear structure is utilized to verify the effectiveness of the VCS based controlled substructure identification method. Finally, shake table tests are conducted on a 3-story structural model to verify the efficacy of the VCS to enhance the identification accuracy of the structural parameters.

An improved wavelet neural network medical image segmentation algorithm with combined maximum entropy

NASA Astrophysics Data System (ADS)

Hu, Xiaoqian; Tao, Jinxu; Ye, Zhongfu; Qiu, Bensheng; Xu, Jinzhang

2018-05-01

In order to solve the problem of medical image segmentation, a wavelet neural network medical image segmentation algorithm based on combined maximum entropy criterion is proposed. Firstly, we use bee colony algorithm to optimize the network parameters of wavelet neural network, get the parameters of network structure, initial weights and threshold values, and so on, we can quickly converge to higher precision when training, and avoid to falling into relative extremum; then the optimal number of iterations is obtained by calculating the maximum entropy of the segmented image, so as to achieve the automatic and accurate segmentation effect. Medical image segmentation experiments show that the proposed algorithm can reduce sample training time effectively and improve convergence precision, and segmentation effect is more accurate and effective than traditional BP neural network (back propagation neural network : a multilayer feed forward neural network which trained according to the error backward propagation algorithm.

Neglecting primordial non-Gaussianity threatens future cosmological experiment accuracy

NASA Astrophysics Data System (ADS)

Camera, Stefano; Carbone, Carmelita; Fedeli, Cosimo; Moscardini, Lauro

2015-02-01

Future galaxy redshift surveys aim at probing the clustering of the cosmic large-scale structure with unprecedented accuracy, thus complementing cosmic microwave background experiments in the quest to deliver the most precise and accurate picture ever of our Universe. Analyses of such measurements are usually performed within the context of the so-called vanilla Λ CDM model—the six-parameter phenomenological model which, for instance, emerges from best fits against the recent data obtained by the Planck satellite. Here, we show that such an approach is prone to subtle systematics when the Gaussianity of primordial fluctuations is concerned. In particular, we demonstrate that, if we neglect even a tiny amount of primordial non-Gaussianity—fully consistent with current limits—we shall introduce spurious biases in the reconstruction of cosmological parameters. This is a serious issue that must be properly accounted for in view of accurate (as well as precise) cosmology.

Global assessment of predictability of water availability: A bivariate probabilistic Budyko analysis

NASA Astrophysics Data System (ADS)

Wang, Weiguang; Fu, Jianyu

2018-02-01

Estimating continental water availability is of great importance for water resources management, in terms of maintaining ecosystem integrity and sustaining society development. To more accurately quantify the predictability of water availability, on the basis of univariate probabilistic Budyko framework, a bivariate probabilistic Budyko approach was developed using copula-based joint distribution model for considering the dependence between parameter ω of Wang-Tang's equation and the Normalized Difference Vegetation Index (NDVI), and was applied globally. The results indicate the predictive performance in global water availability is conditional on the climatic condition. In comparison with simple univariate distribution, the bivariate one produces the lower interquartile range under the same global dataset, especially in the regions with higher NDVI values, highlighting the importance of developing the joint distribution by taking into account the dependence structure of parameter ω and NDVI, which can provide more accurate probabilistic evaluation of water availability.

Structural Significance of Lipid Diversity as Studied by Small Angle Neutron and X-ray Scattering

DOE PAGES

Kučerka, Norbert; Heberle, Frederick A.; Pan, Jianjun; ...

2015-09-21

In this paper, we review recent developments in the rapidly growing field of membrane biophysics, with a focus on the structural properties of single lipid bilayers determined by different scattering techniques, namely neutron and X-ray scattering. The need for accurate lipid structural properties is emphasized by the sometimes conflicting results found in the literature, even in the case of the most studied lipid bilayers. Increasingly, accurate and detailed structural models require more experimental data, such as those from contrast varied neutron scattering and X-ray scattering experiments that are jointly refined with molecular dynamics simulations. This experimental and computational approach producesmore » robust bilayer structural parameters that enable insights, for example, into the interplay between collective membrane properties and its components (e.g., hydrocarbon chain length and unsaturation, and lipid headgroup composition). Finally, from model studies such as these, one is better able to appreciate how a real biological membrane can be tuned by balancing the contributions from the lipid’s different moieties (e.g., acyl chains, headgroups, backbones, etc.).« less

Validation tools for image segmentation

NASA Astrophysics Data System (ADS)

Padfield, Dirk; Ross, James

2009-02-01

A large variety of image analysis tasks require the segmentation of various regions in an image. For example, segmentation is required to generate accurate models of brain pathology that are important components of modern diagnosis and therapy. While the manual delineation of such structures gives accurate information, the automatic segmentation of regions such as the brain and tumors from such images greatly enhances the speed and repeatability of quantifying such structures. The ubiquitous need for such algorithms has lead to a wide range of image segmentation algorithms with various assumptions, parameters, and robustness. The evaluation of such algorithms is an important step in determining their effectiveness. Therefore, rather than developing new segmentation algorithms, we here describe validation methods for segmentation algorithms. Using similarity metrics comparing the automatic to manual segmentations, we demonstrate methods for optimizing the parameter settings for individual cases and across a collection of datasets using the Design of Experiment framework. We then employ statistical analysis methods to compare the effectiveness of various algorithms. We investigate several region-growing algorithms from the Insight Toolkit and compare their accuracy to that of a separate statistical segmentation algorithm. The segmentation algorithms are used with their optimized parameters to automatically segment the brain and tumor regions in MRI images of 10 patients. The validation tools indicate that none of the ITK algorithms studied are able to outperform with statistical significance the statistical segmentation algorithm although they perform reasonably well considering their simplicity.

Accurate reconstruction of the optical parameter distribution in participating medium based on the frequency-domain radiative transfer equation

NASA Astrophysics Data System (ADS)

Qiao, Yao-Bin; Qi, Hong; Zhao, Fang-Zhou; Ruan, Li-Ming

2016-12-01

Reconstructing the distribution of optical parameters in the participating medium based on the frequency-domain radiative transfer equation (FD-RTE) to probe the internal structure of the medium is investigated in the present work. The forward model of FD-RTE is solved via the finite volume method (FVM). The regularization term formatted by the generalized Gaussian Markov random field model is used in the objective function to overcome the ill-posed nature of the inverse problem. The multi-start conjugate gradient (MCG) method is employed to search the minimum of the objective function and increase the efficiency of convergence. A modified adjoint differentiation technique using the collimated radiative intensity is developed to calculate the gradient of the objective function with respect to the optical parameters. All simulation results show that the proposed reconstruction algorithm based on FD-RTE can obtain the accurate distributions of absorption and scattering coefficients. The reconstructed images of the scattering coefficient have less errors than those of the absorption coefficient, which indicates the former are more suitable to probing the inner structure. Project supported by the National Natural Science Foundation of China (Grant No. 51476043), the Major National Scientific Instruments and Equipment Development Special Foundation of China (Grant No. 51327803), and the Foundation for Innovative Research Groups of the National Natural Science Foundation of China (Grant No. 51121004).

Modeling and characteristic of the SMT Board Plug connector in high speed optical communication system

NASA Astrophysics Data System (ADS)

Wu, Haoran; Dong, Zhenzhen; Wang, Tanglin; Zhao, Heng; Feng, Junbo; Cui, Naidi; Teng, Jie; Guo, Jin

2015-04-01

Modeling and characteristic of the SMT Board Plug connector, which is used to connect micro optical transceiver to the main board, are proposed and analyzed in this paper. When the high speed signal transfers from the PCB of transceiver to main board through SMT Board Plug connector, the structure and material discontinuity of the connector causes insertion losses and impedance mismatches. This makes the performance of high speed digital system exacerbated. So it is essential to analyze the signal transfer characteristics of the connector and find out what factors affected the signal quality at the design stage of the digital system. To solve this problem, Ansoft's High Frequency Structure Simulator (HFSS), based on the finite element method, was employed to build accurate 3D models, analyze the effects of various structure parameters, and obtain the full-wave characteristics of the SMT Board Plug connectors in this paper. Then an equivalent circuit model was developed. The circuit parameters were extracted precisely in the frequency range of interests by using the curve fitting method in ADS software, and the result was in good agreement with HFSS simulations up to 8GHz with different structure parameters. At last, the measurement results of S-parameter and eye diagram were given and the S-parameters showed good coincidence between the measurement and HFSS simulation up to 4GHz.

Investigation of the Surface Stress in SiC and Diamond Nanocrystals by In-situ High Pressure Powder Diffraction Technique

NASA Technical Reports Server (NTRS)

Palosz, B.; Stelmakh, S.; Grzanka, E.; Gierlotka, S.; Zhao, Y.; Palosz, W.

2003-01-01

The real atomic structure of nanocrystals determines key properties of the materials. For such materials the serious experimental problem lies in obtaining sufficiently accurate measurements of the structural parameters of the crystals, since very small crystals constitute rather a two-phase than a uniform crystallographic phase system. As a result, elastic properties of nanograins may be expected to reflect a dual nature of their structure, with a corresponding set of different elastic property parameters. We studied those properties by in-situ high-pressure powder diffraction technique. For nanocrystalline, even one-phase materials such measurements are particularly difficult to make since determination of the lattice parameters of very small crystals presents a challenge due to inherent limitations of standard elaboration of powder diffractograms. In this investigation we used our methodology of the structural analysis, the 'apparent lattice parameter' (alp) concept. The methodology allowed us to avoid the traps (if applied to nanocrystals) of standard powder diffraction evaluation techniques. The experiments were performed for nanocrystalline Sic and GaN powders using synchrotron sources. We applied both hydrostatic and isostatic pressures in the range of up to 40 GPa. Elastic properties of the samples were examined based on the measurements of a change of the lattice parameters with pressure. The results show a dual nature of the mechanical properties (compressibilities) of the materials, indicating a complex, core-shell structure of the grains.

Thermal transport properties of bulk and monolayer MoS2: an ab-initio approach

NASA Astrophysics Data System (ADS)

Bano, Amreen; Khare, Preeti; Gaur, N. K.

2017-05-01

The transport properties of semiconductors are key to the performance of many solid-state devices (transistors, data storage, thermoelectric cooling and power generation devices, etc). In recent years simulation tools based on first-principles calculations have been greatly improved, being able to obtain the fundamental ground-state properties of materials accurately. The quasi harmonic thermal properties of bulk and monolayer of MoS2 has been computed with ab initio periodic simulations based of density functional theory (DFT). The temperature dependence of bulk modulus, specific heat, thermal expansion and gruneisen parameter have been calculated in our work within the temperature range of 0K to 900K with projected augmented wave (PAW) method using generalized gradient approximation (GGA). Our results show that the optimized lattice parameters are in good agreement with the earlier reported works and also for thermoelastic parameter, i.e. isothermal bulk modulus (B) at 0K indicates that monolayer MoS2 (48.5 GPa)is more compressible than the bulk structure (159.23 GPa). The thermal expansion of monolayer structure is slightly less than the bulk. Similarly, other parameters like heat capacity and gruneisen parameter shows different nature which is due to the confinement of 3 dimensional structure to 2 dimension (2D) for improving its transport characteristics.

Morphology, stoichiometry, and crystal structure control via post-annealing for Pt-ZnO nanograin Schottky barrier interfaces

NASA Astrophysics Data System (ADS)

Chan, Yuet Ching; Yu, Jerry; Ho, Derek

2018-06-01

Nanointerfaces have attracted intensive research effort for advanced electronics due to their unique and tunable semiconducting properties made possible by metal-contacted oxide structures at the nanoscale. Although much work has been on the adjustment of fabrication parameters to achieve high-quality interfaces, little work has experimentally obtained the various correlations between material parameters and Schottky barrier electronic properties to accurately probe the underlying phenomenon. In this work, we investigate the control of Pt-ZnO nanograin interfaces properties by thermal annealing. Specifically, we quantitatively analyze the correlation between material parameters (such as surface morphology, crystallographic structure, and stoichiometry) and Schottky diode parameters (Schottky barrier height, ideality factor, and contact resistance). Results revealed strong dependencies of Schottky barrier characteristics on oxygen vacancies, surface roughness, grain density, d-spacing, and crystallite size. I-V-T data shows that annealing at 600 °C produces a nanograin based interface with the most rectifying diode characteristics. These dependencies, which have not been previously reported holistically, highlight the close relationship between material properties and Schottky barrier characteristics, and are instrumental for the performance optimization of nanostructured metal-semiconductor interfaces in advanced electronic devices.

Melatonin charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone: Molecular structure, DFT studies, thermal analyses, evaluation of biological activity and utility for determination of melatonin in pure and dosage forms

NASA Astrophysics Data System (ADS)

Mohamed, Gehad G.; Hamed, Maher M.; Zaki, Nadia G.; Abdou, Mohamed M.; Mohamed, Marwa El-Badry; Abdallah, Abanoub Mosaad

2017-07-01

A simple, accurate and fast spectrophotometric method for the quantitative determination of melatonin (ML) drug in its pure and pharmaceutical forms was developed based on the formation of its charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electron acceptor. The different conditions for this method were optimized accurately. The Lambert-Beer's law was found to be valid over the concentration range of 4-100 μg mL- 1 ML. The solid form of the CT complex was structurally characterized by means of different spectral methods. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were carried out. The different quantum chemical parameters of the CT complex were calculated. Thermal properties of the CT complex and its kinetic thermodynamic parameters were studied, as well as its antimicrobial and antifungal activities were investigated. Molecular docking studies were performed to predict the binding modes of the CT complex components towards E. coli bacterial RNA and the receptor of breast cancer mutant oxidoreductase.

Melatonin charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone: Molecular structure, DFT studies, thermal analyses, evaluation of biological activity and utility for determination of melatonin in pure and dosage forms.

PubMed

Mohamed, Gehad G; Hamed, Maher M; Zaki, Nadia G; Abdou, Mohamed M; Mohamed, Marwa El-Badry; Abdallah, Abanoub Mosaad

2017-07-05

A simple, accurate and fast spectrophotometric method for the quantitative determination of melatonin (ML) drug in its pure and pharmaceutical forms was developed based on the formation of its charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electron acceptor. The different conditions for this method were optimized accurately. The Lambert-Beer's law was found to be valid over the concentration range of 4-100μgmL -1 ML. The solid form of the CT complex was structurally characterized by means of different spectral methods. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were carried out. The different quantum chemical parameters of the CT complex were calculated. Thermal properties of the CT complex and its kinetic thermodynamic parameters were studied, as well as its antimicrobial and antifungal activities were investigated. Molecular docking studies were performed to predict the binding modes of the CT complex components towards E. coli bacterial RNA and the receptor of breast cancer mutant oxidoreductase. Copyright © 2017 Elsevier B.V. All rights reserved.

Issues in the economic evaluation of influenza vaccination by injection of healthy working adults in the US: a review and decision analysis of ten published studies.

PubMed

Hogan, Thomas J

2012-05-01

The objective was to review recent economic evaluations of influenza vaccination by injection in the US, assess their evidence, and conclude on their collective findings. The literature was searched for economic evaluations of influenza vaccination injection in healthy working adults in the US published since 1995. Ten evaluations described in nine papers were identified. These were synopsized and their results evaluated, the basic structure of all evaluations was ascertained, and sensitivity of outcomes to changes in parameter values were explored using a decision model. Areas to improve economic evaluations were noted. Eight of nine evaluations with credible economic outcomes were favourable to vaccination, representing a statistically significant result compared with a proportion of 50% that would be expected if vaccination and no vaccination were economically equivalent. Evaluations shared a basic structure, but differed considerably with respect to cost components, assumptions, methods, and parameter estimates. Sensitivity analysis indicated that changes in parameter values within the feasible range, individually or simultaneously, could reverse economic outcomes. Given stated misgivings, the methods of estimating influenza reduction ascribed to vaccination must be researched to confirm that they produce accurate and reliable estimates. Research is also needed to improve estimates of the costs per case of influenza illness and the costs of vaccination. Based on their assumptions, the reviewed papers collectively appear to support the economic benefits of influenza vaccination of healthy adults. Yet the underlying assumptions, methods and parameter estimates themselves warrant further research to confirm they are accurate, reliable and appropriate to economic evaluation purposes.

New insights into galaxy structure from GALPHAT- I. Motivation, methodology and benchmarks for Sérsic models

NASA Astrophysics Data System (ADS)

Yoon, Ilsang; Weinberg, Martin D.; Katz, Neal

2011-06-01

We introduce a new galaxy image decomposition tool, GALPHAT (GALaxy PHotometric ATtributes), which is a front-end application of the Bayesian Inference Engine (BIE), a parallel Markov chain Monte Carlo package, to provide full posterior probability distributions and reliable confidence intervals for all model parameters. The BIE relies on GALPHAT to compute the likelihood function. GALPHAT generates scale-free cumulative image tables for the desired model family with precise error control. Interpolation of this table yields accurate pixellated images with any centre, scale and inclination angle. GALPHAT then rotates the image by position angle using a Fourier shift theorem, yielding high-speed, accurate likelihood computation. We benchmark this approach using an ensemble of simulated Sérsic model galaxies over a wide range of observational conditions: the signal-to-noise ratio S/N, the ratio of galaxy size to the point spread function (PSF) and the image size, and errors in the assumed PSF; and a range of structural parameters: the half-light radius re and the Sérsic index n. We characterize the strength of parameter covariance in the Sérsic model, which increases with S/N and n, and the results strongly motivate the need for the full posterior probability distribution in galaxy morphology analyses and later inferences. The test results for simulated galaxies successfully demonstrate that, with a careful choice of Markov chain Monte Carlo algorithms and fast model image generation, GALPHAT is a powerful analysis tool for reliably inferring morphological parameters from a large ensemble of galaxies over a wide range of different observational conditions.

An articulatorily constrained, maximum entropy approach to speech recognition and speech coding

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hogden, J.

Hidden Markov models (HMM`s) are among the most popular tools for performing computer speech recognition. One of the primary reasons that HMM`s typically outperform other speech recognition techniques is that the parameters used for recognition are determined by the data, not by preconceived notions of what the parameters should be. This makes HMM`s better able to deal with intra- and inter-speaker variability despite the limited knowledge of how speech signals vary and despite the often limited ability to correctly formulate rules describing variability and invariance in speech. In fact, it is often the case that when HMM parameter values aremore » constrained using the limited knowledge of speech, recognition performance decreases. However, the structure of an HMM has little in common with the mechanisms underlying speech production. Here, the author argues that by using probabilistic models that more accurately embody the process of speech production, he can create models that have all the advantages of HMM`s, but that should more accurately capture the statistical properties of real speech samples--presumably leading to more accurate speech recognition. The model he will discuss uses the fact that speech articulators move smoothly and continuously. Before discussing how to use articulatory constraints, he will give a brief description of HMM`s. This will allow him to highlight the similarities and differences between HMM`s and the proposed technique.« less

Numerical Convergence in the Dark Matter Halos Properties Using Cosmological Simulations

NASA Astrophysics Data System (ADS)

Mosquera-Escobar, X. E.; Muñoz-Cuartas, J. C.

2017-07-01

Nowadays, the accepted cosmological model is the so called -Cold Dark Matter (CDM). In such model, the universe is considered to be homogeneous and isotropic, composed of diverse components as the dark matter and dark energy, where the latter is the most abundant one. Dark matter plays an important role because it is responsible for the generation of gravitational potential wells, commonly called dark matter halos. At the end, dark matter halos are characterized by a set of parameters (mass, radius, concentration, spin parameter), these parameters provide valuable information for different studies, such as galaxy formation, gravitational lensing, etc. In this work we use the publicly available code Gadget2 to perform cosmological simulations to find to what extent the numerical parameters of the simu- lations, such as gravitational softening, integration time step and force calculation accuracy affect the physical properties of the dark matter halos. We ran a suite of simulations where these parameters were varied in a systematic way in order to explore accurately their impact on the structural parameters of dark matter halos. We show that the variations on the numerical parameters affect the structural pa- rameters of dark matter halos, such as concentration, virial radius, and concentration. We show that these modifications emerged when structures become non- linear (at redshift 2) for the scale of our simulations, such that these variations affected the formation and evolution structure of halos mainly at later cosmic times. As a quantitative result, we propose which would be the most appropriate values for the numerical parameters of the simulations, such that they do not affect the halo properties that are formed. For force calculation accuracy we suggest values smaller or equal to 0.0001, integration time step smaller o equal to 0.005 and for gravitational softening we propose equal to 1/60th of the mean interparticle distance, these values, correspond to the smaller values in the numerical parameters variations. This is an important numerical exercise, since for instance, it is believed that galaxy structural parameters are strongly dependent on dark matter halo structural parameters.

Real-time sensing of fatigue crack damage for information-based decision and control

NASA Astrophysics Data System (ADS)

Keller, Eric Evans

Information-based decision and control for structures that are subject to failure by fatigue cracking is based on the following notion: Maintenance, usage scheduling, and control parameter tuning can be optimized through real time knowledge of the current state of fatigue crack damage. Additionally, if the material properties of a mechanical structure can be identified within a smaller range, then the remaining life prediction of that structure will be substantially more accurate. Information-based decision systems can rely one physical models, estimation of material properties, exact knowledge of usage history, and sensor data to synthesize an accurate snapshot of the current state of damage and the likely remaining life of a structure under given assumed loading. The work outlined in this thesis is structured to enhance the development of information-based decision and control systems. This is achieved by constructing a test facility for laboratory experiments on real-time damage sensing. This test facility makes use of a methodology that has been formulated for fatigue crack model parameter estimation and significantly improves the quality of predictions of remaining life. Specifically, the thesis focuses on development of an on-line fatigue crack damage sensing and life prediction system that is built upon the disciplines of Systems Sciences and Mechanics of Materials. A major part of the research effort has been expended to design and fabricate a test apparatus which allows: (i) measurement and recording of statistical data for fatigue crack growth in metallic materials via different sensing techniques; and (ii) identification of stochastic model parameters for prediction of fatigue crack damage. To this end, this thesis describes the test apparatus and the associated instrumentation based on four different sensing techniques, namely, traveling optical microscopy, ultrasonic flaw detection, Alternating Current Potential Drop (ACPD), and fiber-optic extensometry-based compliance, for crack length measurements.

Temperature-independent fiber-Bragg-grating-based atmospheric pressure sensor

NASA Astrophysics Data System (ADS)

Zhang, Zhiguo; Shen, Chunyan; Li, Luming

2018-03-01

Atmospheric pressure is an important way to achieve a high degree of measurement for modern aircrafts, moreover, it is also an indispensable parameter in the meteorological telemetry system. With the development of society, people are increasingly concerned about the weather. Accurate and convenient atmospheric pressure parameters can provide strong support for meteorological analysis. However, electronic atmospheric pressure sensors currently in application suffer from several shortcomings. After an analysis and discussion, we propose an innovative structural design, in which a vacuum membrane box and a temperature-independent strain sensor based on an equal strength cantilever beam structure and fiber Bragg grating (FBG) sensors are used. We provide experimental verification of that the atmospheric pressure sensor device has the characteristics of a simple structure, lack of an external power supply, automatic temperature compensation, and high sensitivity. The sensor system has good sensitivity, which can be up to 100 nm/MPa, and repeatability. In addition, the device exhibits desired hysteresis.

Integration of neutron time-of-flight single-crystal Bragg peaks in reciprocal space

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schultz, Arthur J; Joergensen, Mads; Wang, Xiaoping

2014-01-01

The intensity of single crystal Bragg peaks obtained by mapping neutron time-of-flight event data into reciprocal space and integrating in various ways are compared. These include spherical integration with a fixed radius, ellipsoid fitting and integrating of the peak intensity and one-dimensional peak profile fitting. In comparison to intensities obtained by integrating in real detector histogram space, the data integrated in reciprocal space results in better agreement factors and more accurate atomic parameters. Furthermore, structure refinement using integrated intensities from one-dimensional profile fitting is demonstrated to be more accurate than simple peak-minus-background integration.

Accurate Cold-Test Model of Helical TWT Slow-Wave Circuits

NASA Technical Reports Server (NTRS)

Kory, Carol L.; Dayton, James A., Jr.

1997-01-01

Recently, a method has been established to accurately calculate cold-test data for helical slow-wave structures using the three-dimensional electromagnetic computer code, MAFIA. Cold-test parameters have been calculated for several helical traveling-wave tube (TWT) slow-wave circuits possessing various support rod configurations, and results are presented here showing excellent agreement with experiment. The helical models include tape thickness, dielectric support shapes and material properties consistent with the actual circuits. The cold-test data from this helical model can be used as input into large-signal helical TWT interaction codes making it possible, for the first time, to design a complete TWT via computer simulation.

Accurate estimation of seismic source parameters of induced seismicity by a combined approach of generalized inversion and genetic algorithm: Application to The Geysers geothermal area, California

NASA Astrophysics Data System (ADS)

Picozzi, M.; Oth, A.; Parolai, S.; Bindi, D.; De Landro, G.; Amoroso, O.

2017-05-01

The accurate determination of stress drop, seismic efficiency, and how source parameters scale with earthquake size is an important issue for seismic hazard assessment of induced seismicity. We propose an improved nonparametric, data-driven strategy suitable for monitoring induced seismicity, which combines the generalized inversion technique together with genetic algorithms. In the first step of the analysis the generalized inversion technique allows for an effective correction of waveforms for attenuation and site contributions. Then, the retrieved source spectra are inverted by a nonlinear sensitivity-driven inversion scheme that allows accurate estimation of source parameters. We therefore investigate the earthquake source characteristics of 633 induced earthquakes (Mw 2-3.8) recorded at The Geysers geothermal field (California) by a dense seismic network (i.e., 32 stations, more than 17.000 velocity records). We find a nonself-similar behavior, empirical source spectra that require an ωγ source model with γ > 2 to be well fit and small radiation efficiency ηSW. All these findings suggest different dynamic rupture processes for smaller and larger earthquakes and that the proportion of high-frequency energy radiation and the amount of energy required to overcome the friction or for the creation of new fractures surface changes with earthquake size. Furthermore, we observe also two distinct families of events with peculiar source parameters that in one case suggests the reactivation of deep structures linked to the regional tectonics, while in the other supports the idea of an important role of steeply dipping faults in the fluid pressure diffusion.

Evaluation of modal pushover-based scaling of one component of ground motion: Tall buildings

USGS Publications Warehouse

Kalkan, Erol; Chopra, Anil K.

2012-01-01

Nonlinear response history analysis (RHA) is now increasingly used for performance-based seismic design of tall buildings. Required for nonlinear RHAs is a set of ground motions selected and scaled appropriately so that analysis results would be accurate (unbiased) and efficient (having relatively small dispersion). This paper evaluates accuracy and efficiency of recently developed modal pushover–based scaling (MPS) method to scale ground motions for tall buildings. The procedure presented explicitly considers structural strength and is based on the standard intensity measure (IM) of spectral acceleration in a form convenient for evaluating existing structures or proposed designs for new structures. Based on results presented for two actual buildings (19 and 52 stories, respectively), it is demonstrated that the MPS procedure provided a highly accurate estimate of the engineering demand parameters (EDPs), accompanied by significantly reduced record-to-record variability of the responses. In addition, the MPS procedure is shown to be superior to the scaling procedure specified in the ASCE/SEI 7-05 document.

A bias correction for covariance estimators to improve inference with generalized estimating equations that use an unstructured correlation matrix.

PubMed

Westgate, Philip M

2013-07-20

Generalized estimating equations (GEEs) are routinely used for the marginal analysis of correlated data. The efficiency of GEE depends on how closely the working covariance structure resembles the true structure, and therefore accurate modeling of the working correlation of the data is important. A popular approach is the use of an unstructured working correlation matrix, as it is not as restrictive as simpler structures such as exchangeable and AR-1 and thus can theoretically improve efficiency. However, because of the potential for having to estimate a large number of correlation parameters, variances of regression parameter estimates can be larger than theoretically expected when utilizing the unstructured working correlation matrix. Therefore, standard error estimates can be negatively biased. To account for this additional finite-sample variability, we derive a bias correction that can be applied to typical estimators of the covariance matrix of parameter estimates. Via simulation and in application to a longitudinal study, we show that our proposed correction improves standard error estimation and statistical inference. Copyright © 2012 John Wiley & Sons, Ltd.

Accurate Vibrational-Rotational Parameters and Infrared Intensities of 1-Bromo-1-fluoroethene: A Joint Experimental Analysis and Ab Initio Study.

PubMed

Pietropolli Charmet, Andrea; Stoppa, Paolo; Giorgianni, Santi; Bloino, Julien; Tasinato, Nicola; Carnimeo, Ivan; Biczysko, Malgorzata; Puzzarini, Cristina

2017-05-04

The medium-resolution gas-phase infrared (IR) spectra of 1-bromo-1-fluoroethene (BrFC═CH 2 , 1,1-C 2 H 2 BrF) were investigated in the range 300-6500 cm -1 , and the vibrational analysis led to the assignment of all fundamentals as well as many overtone and combination bands up to three quanta, thus giving an accurate description of its vibrational structure. Integrated band intensity data were determined with high precision from the measurements of their corresponding absorption cross sections. The vibrational analysis was supported by high-level ab initio investigations. CCSD(T) computations accounting for extrapolation to the complete basis set and core correlation effects were employed to accurately determine the molecular structure and harmonic force field. The latter was then coupled to B2PLYP and MP2 computations in order to account for mechanical and electrical anharmonicities. Second-order perturbative vibrational theory was then applied to the thus obtained hybrid force fields to support the experimental assignment of the IR spectra.

Extracting TSK-type Neuro-Fuzzy model using the Hunting search algorithm

NASA Astrophysics Data System (ADS)

Bouzaida, Sana; Sakly, Anis; M'Sahli, Faouzi

2014-01-01

This paper proposes a Takagi-Sugeno-Kang (TSK) type Neuro-Fuzzy model tuned by a novel metaheuristic optimization algorithm called Hunting Search (HuS). The HuS algorithm is derived based on a model of group hunting of animals such as lions, wolves, and dolphins when looking for a prey. In this study, the structure and parameters of the fuzzy model are encoded into a particle. Thus, the optimal structure and parameters are achieved simultaneously. The proposed method was demonstrated through modeling and control problems, and the results have been compared with other optimization techniques. The comparisons indicate that the proposed method represents a powerful search approach and an effective optimization technique as it can extract the accurate TSK fuzzy model with an appropriate number of rules.

A New Calibration Method for Commercial RGB-D Sensors.

PubMed

Darwish, Walid; Tang, Shenjun; Li, Wenbin; Chen, Wu

2017-05-24

Commercial RGB-D sensors such as Kinect and Structure Sensors have been widely used in the game industry, where geometric fidelity is not of utmost importance. For applications in which high quality 3D is required, i.e., 3D building models of centimeter‑level accuracy, accurate and reliable calibrations of these sensors are required. This paper presents a new model for calibrating the depth measurements of RGB-D sensors based on the structured light concept. Additionally, a new automatic method is proposed for the calibration of all RGB-D parameters, including internal calibration parameters for all cameras, the baseline between the infrared and RGB cameras, and the depth error model. When compared with traditional calibration methods, this new model shows a significant improvement in depth precision for both near and far ranges.

Measuring watershed runoff capability with ERTS data. [Washita River Basin, Oklahoma

NASA Technical Reports Server (NTRS)

Blanchard, B. J.

1974-01-01

Parameters of most equations used to predict runoff from an ungaged area are based on characteristics of the watershed and subject to the biases of a hydrologist. Digital multispectral scanner, MSS, data from ERTS was reduced with the aid of computer programs and a Dicomed display. Multivariate analyses of the MSS data indicate that discrimination between watersheds with different runoff capabilities is possible using ERTS data. Differences between two visible bands of MSS data can be used to more accurately evaluate the parameters than present subjective methods, thus reducing construction cost due to overdesign of flood detention structures.

A Multi-Parameter Approach for Calculating Crack Instability

NASA Technical Reports Server (NTRS)

Zanganeh, M.; Forman, R. G.

2014-01-01

An accurate fracture control analysis of spacecraft pressure systems, boosters, rocket hardware and other critical low-cycle fatigue cases where the fracture toughness highly impacts cycles to failure requires accurate knowledge of the material fracture toughness. However, applicability of the measured fracture toughness values using standard specimens and transferability of the values to crack instability analysis of the realistically complex structures is refutable. The commonly used single parameter Linear Elastic Fracture Mechanics (LEFM) approach which relies on the key assumption that the fracture toughness is a material property would result in inaccurate crack instability predictions. In the past years extensive studies have been conducted to improve the single parameter (K-controlled) LEFM by introducing parameters accounting for the geometry or in-plane constraint effects]. Despite the importance of the thickness (out-of-plane constraint) effects in fracture control problems, the literature is mainly limited to some empirical equations for scaling the fracture toughness data] and only few theoretically based developments can be found. In aerospace hardware where the structure might have only one life cycle and weight reduction is crucial, reducing the design margin of safety by decreasing the uncertainty involved in fracture toughness evaluations would result in lighter hardware. In such conditions LEFM would not suffice and an elastic-plastic analysis would be vital. Multi-parameter elastic plastic crack tip field quantifying developments combined with statistical methods] have been shown to have the potential to be used as a powerful tool for tackling such problems. However, these approaches have not been comprehensively scrutinized using experimental tests. Therefore, in this paper a multi-parameter elastic-plastic approach has been used to study the crack instability problem and the transferability issue by considering the effects of geometrical constraints as well as the thickness. The feasibility of the approach has been examined using a wide range of specimen geometries and thicknesses manufactured from 7075-T7351 aluminum alloy.

Assessing the accuracy of subject-specific, muscle-model parameters determined by optimizing to match isometric strength.

PubMed

DeSmitt, Holly J; Domire, Zachary J

2016-12-01

Biomechanical models are sensitive to the choice of model parameters. Therefore, determination of accurate subject specific model parameters is important. One approach to generate these parameters is to optimize the values such that the model output will match experimentally measured strength curves. This approach is attractive as it is inexpensive and should provide an excellent match to experimentally measured strength. However, given the problem of muscle redundancy, it is not clear that this approach generates accurate individual muscle forces. The purpose of this investigation is to evaluate this approach using simulated data to enable a direct comparison. It is hypothesized that the optimization approach will be able to recreate accurate muscle model parameters when information from measurable parameters is given. A model of isometric knee extension was developed to simulate a strength curve across a range of knee angles. In order to realistically recreate experimentally measured strength, random noise was added to the modeled strength. Parameters were solved for using a genetic search algorithm. When noise was added to the measurements the strength curve was reasonably recreated. However, the individual muscle model parameters and force curves were far less accurate. Based upon this examination, it is clear that very different sets of model parameters can recreate similar strength curves. Therefore, experimental variation in strength measurements has a significant influence on the results. Given the difficulty in accurately recreating individual muscle parameters, it may be more appropriate to perform simulations with lumped actuators representing similar muscles.

Utility of a novel error-stepping method to improve gradient-based parameter identification by increasing the smoothness of the local objective surface: a case-study of pulmonary mechanics.

PubMed

Docherty, Paul D; Schranz, Christoph; Chase, J Geoffrey; Chiew, Yeong Shiong; Möller, Knut

2014-05-01

Accurate model parameter identification relies on accurate forward model simulations to guide convergence. However, some forward simulation methodologies lack the precision required to properly define the local objective surface and can cause failed parameter identification. The role of objective surface smoothness in identification of a pulmonary mechanics model was assessed using forward simulation from a novel error-stepping method and a proprietary Runge-Kutta method. The objective surfaces were compared via the identified parameter discrepancy generated in a Monte Carlo simulation and the local smoothness of the objective surfaces they generate. The error-stepping method generated significantly smoother error surfaces in each of the cases tested (p<0.0001) and more accurate model parameter estimates than the Runge-Kutta method in three of the four cases tested (p<0.0001) despite a 75% reduction in computational cost. Of note, parameter discrepancy in most cases was limited to a particular oblique plane, indicating a non-intuitive multi-parameter trade-off was occurring. The error-stepping method consistently improved or equalled the outcomes of the Runge-Kutta time-integration method for forward simulations of the pulmonary mechanics model. This study indicates that accurate parameter identification relies on accurate definition of the local objective function, and that parameter trade-off can occur on oblique planes resulting prematurely halted parameter convergence. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Assessing the influence of flight parameters, interferometric processing, slope and canopy density on the accuracy of X-band IFSAR-derived forest canopy height models.

Treesearch

H.-E. Andersen; R.J. McGaughey; S.E. Reutebuch

2008-01-01

High resolution, active remote sensing technologies, such as interferometric synthetic aperture radar (IFSAR) and airborne laser scanning (LIDAR) have the capability to provide forest managers with direct measurements of 3-dimensional forest canopy surface structure. Although LIDAR systems can provide highly accurate measurements of canopy and terrain surfaces, high-...

Numerical analysis of the diffusive mass transport in brain tissues with applications to optical sensors

NASA Astrophysics Data System (ADS)

Neculae, Adrian P.; Otte, Andreas; Curticapean, Dan

2013-03-01

In the brain-cell microenvironment, diffusion plays an important role: apart from delivering glucose and oxygen from the vascular system to brain cells, it also moves informational substances between cells. The brain is an extremely complex structure of interwoven, intercommunicating cells, but recent theoretical and experimental works showed that the classical laws of diffusion, cast in the framework of porous media theory, can deliver an accurate quantitative description of the way molecules are transported through this tissue. The mathematical modeling and the numerical simulations are successfully applied in the investigation of diffusion processes in tissues, replacing the costly laboratory investigations. Nevertheless, modeling must rely on highly accurate information regarding the main parameters (tortuosity, volume fraction) which characterize the tissue, obtained by structural and functional imaging. The usual techniques to measure the diffusion mechanism in brain tissue are the radiotracer method, the real time iontophoretic method and integrative optical imaging using fluorescence microscopy. A promising technique for obtaining the values for characteristic parameters of the transport equation is the direct optical investigation using optical fibers. The analysis of these parameters also reveals how the local geometry of the brain changes with time or under pathological conditions. This paper presents a set of computations concerning the mass transport inside the brain tissue, for different types of cells. By measuring the time evolution of the concentration profile of an injected substance and using suitable fitting procedures, the main parameters characterizing the tissue can be determined. This type of analysis could be an important tool in understanding the functional mechanisms of effective drug delivery in complex structures such as the brain tissue. It also offers possibilities to realize optical imaging methods for in vitro and in vivo measurements using optical fibers. The model also may help in radiotracer biomarker models for the understanding of the mechanism of action of new chemical entities.

Reducing process delays for real-time earthquake parameter estimation - An application of KD tree to large databases for Earthquake Early Warning

NASA Astrophysics Data System (ADS)

Yin, Lucy; Andrews, Jennifer; Heaton, Thomas

2018-05-01

Earthquake parameter estimations using nearest neighbor searching among a large database of observations can lead to reliable prediction results. However, in the real-time application of Earthquake Early Warning (EEW) systems, the accurate prediction using a large database is penalized by a significant delay in the processing time. We propose to use a multidimensional binary search tree (KD tree) data structure to organize large seismic databases to reduce the processing time in nearest neighbor search for predictions. We evaluated the performance of KD tree on the Gutenberg Algorithm, a database-searching algorithm for EEW. We constructed an offline test to predict peak ground motions using a database with feature sets of waveform filter-bank characteristics, and compare the results with the observed seismic parameters. We concluded that large database provides more accurate predictions of the ground motion information, such as peak ground acceleration, velocity, and displacement (PGA, PGV, PGD), than source parameters, such as hypocenter distance. Application of the KD tree search to organize the database reduced the average searching process by 85% time cost of the exhaustive method, allowing the method to be feasible for real-time implementation. The algorithm is straightforward and the results will reduce the overall time of warning delivery for EEW.

Accurate step-hold tracking of smoothly varying periodic and aperiodic probability.

PubMed

Ricci, Matthew; Gallistel, Randy

2017-07-01

Subjects observing many samples from a Bernoulli distribution are able to perceive an estimate of the generating parameter. A question of fundamental importance is how the current percept-what we think the probability now is-depends on the sequence of observed samples. Answers to this question are strongly constrained by the manner in which the current percept changes in response to changes in the hidden parameter. Subjects do not update their percept trial-by-trial when the hidden probability undergoes unpredictable and unsignaled step changes; instead, they update it only intermittently in a step-hold pattern. It could be that the step-hold pattern is not essential to the perception of probability and is only an artifact of step changes in the hidden parameter. However, we now report that the step-hold pattern obtains even when the parameter varies slowly and smoothly. It obtains even when the smooth variation is periodic (sinusoidal) and perceived as such. We elaborate on a previously published theory that accounts for: (i) the quantitative properties of the step-hold update pattern; (ii) subjects' quick and accurate reporting of changes; (iii) subjects' second thoughts about previously reported changes; (iv) subjects' detection of higher-order structure in patterns of change. We also call attention to the challenges these results pose for trial-by-trial updating theories.

Composite laminate failure parameter optimization through four-point flexure experimentation and analysis

DOE PAGES

Nelson, Stacy; English, Shawn; Briggs, Timothy

2016-05-06

Fiber-reinforced composite materials offer light-weight solutions to many structural challenges. In the development of high-performance composite structures, a thorough understanding is required of the composite materials themselves as well as methods for the analysis and failure prediction of the relevant composite structures. However, the mechanical properties required for the complete constitutive definition of a composite material can be difficult to determine through experimentation. Therefore, efficient methods are necessary that can be used to determine which properties are relevant to the analysis of a specific structure and to establish a structure's response to a material parameter that can only be definedmore » through estimation. The objectives of this paper deal with demonstrating the potential value of sensitivity and uncertainty quantification techniques during the failure analysis of loaded composite structures; and the proposed methods are applied to the simulation of the four-point flexural characterization of a carbon fiber composite material. Utilizing a recently implemented, phenomenological orthotropic material model that is capable of predicting progressive composite damage and failure, a sensitivity analysis is completed to establish which material parameters are truly relevant to a simulation's outcome. Then, a parameter study is completed to determine the effect of the relevant material properties' expected variations on the simulated four-point flexural behavior as well as to determine the value of an unknown material property. This process demonstrates the ability to formulate accurate predictions in the absence of a rigorous material characterization effort. Finally, the presented results indicate that a sensitivity analysis and parameter study can be used to streamline the material definition process as the described flexural characterization was used for model validation.« less

Thermodynamic modeling of transcription: sensitivity analysis differentiates biological mechanism from mathematical model-induced effects.

PubMed

Dresch, Jacqueline M; Liu, Xiaozhou; Arnosti, David N; Ay, Ahmet

2010-10-24

Quantitative models of gene expression generate parameter values that can shed light on biological features such as transcription factor activity, cooperativity, and local effects of repressors. An important element in such investigations is sensitivity analysis, which determines how strongly a model's output reacts to variations in parameter values. Parameters of low sensitivity may not be accurately estimated, leading to unwarranted conclusions. Low sensitivity may reflect the nature of the biological data, or it may be a result of the model structure. Here, we focus on the analysis of thermodynamic models, which have been used extensively to analyze gene transcription. Extracted parameter values have been interpreted biologically, but until now little attention has been given to parameter sensitivity in this context. We apply local and global sensitivity analyses to two recent transcriptional models to determine the sensitivity of individual parameters. We show that in one case, values for repressor efficiencies are very sensitive, while values for protein cooperativities are not, and provide insights on why these differential sensitivities stem from both biological effects and the structure of the applied models. In a second case, we demonstrate that parameters that were thought to prove the system's dependence on activator-activator cooperativity are relatively insensitive. We show that there are numerous parameter sets that do not satisfy the relationships proferred as the optimal solutions, indicating that structural differences between the two types of transcriptional enhancers analyzed may not be as simple as altered activator cooperativity. Our results emphasize the need for sensitivity analysis to examine model construction and forms of biological data used for modeling transcriptional processes, in order to determine the significance of estimated parameter values for thermodynamic models. Knowledge of parameter sensitivities can provide the necessary context to determine how modeling results should be interpreted in biological systems.

Electronic Structure, Dielectric Response, and Surface Charge Distribution of RGD (1FUV) Peptide

PubMed Central

Adhikari, Puja; Wen, Amy M.; French, Roger H.; Parsegian, V. Adrian; Steinmetz, Nicole F.; Podgornik, Rudolf; Ching, Wai-Yim

2014-01-01

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor. PMID:25001596

Remote sensing techniques for prediction of watershed runoff

NASA Technical Reports Server (NTRS)

Blanchard, B. J.

1975-01-01

Hydrologic parameters of watersheds for use in mathematical models and as design criteria for flood detention structures are sometimes difficult to quantify using conventional measuring systems. The advent of remote sensing devices developed in the past decade offers the possibility that watershed characteristics such as vegetative cover, soils, soil moisture, etc., may be quantified rapidly and economically. Experiments with visible and near infrared data from the LANDSAT-1 multispectral scanner indicate a simple technique for calibration of runoff equation coefficients is feasible. The technique was tested on 10 watersheds in the Chickasha area and test results show more accurate runoff coefficients were obtained than with conventional methods. The technique worked equally as well using a dry fall scene. The runoff equation coefficients were then predicted for 22 subwatersheds with flood detention structures. Predicted values were again more accurate than coefficients produced by conventional methods.

Application of Differential Evolutionary Optimization Methodology for Parameter Structure Identification in Groundwater Modeling

NASA Astrophysics Data System (ADS)

Chiu, Y.; Nishikawa, T.

2013-12-01

With the increasing complexity of parameter-structure identification (PSI) in groundwater modeling, there is a need for robust, fast, and accurate optimizers in the groundwater-hydrology field. For this work, PSI is defined as identifying parameter dimension, structure, and value. In this study, Voronoi tessellation and differential evolution (DE) are used to solve the optimal PSI problem. Voronoi tessellation is used for automatic parameterization, whereby stepwise regression and the error covariance matrix are used to determine the optimal parameter dimension. DE is a novel global optimizer that can be used to solve nonlinear, nondifferentiable, and multimodal optimization problems. It can be viewed as an improved version of genetic algorithms and employs a simple cycle of mutation, crossover, and selection operations. DE is used to estimate the optimal parameter structure and its associated values. A synthetic numerical experiment of continuous hydraulic conductivity distribution was conducted to demonstrate the proposed methodology. The results indicate that DE can identify the global optimum effectively and efficiently. A sensitivity analysis of the control parameters (i.e., the population size, mutation scaling factor, crossover rate, and mutation schemes) was performed to examine their influence on the objective function. The proposed DE was then applied to solve a complex parameter-estimation problem for a small desert groundwater basin in Southern California. Hydraulic conductivity, specific yield, specific storage, fault conductance, and recharge components were estimated simultaneously. Comparison of DE and a traditional gradient-based approach (PEST) shows DE to be more robust and efficient. The results of this work not only provide an alternative for PSI in groundwater models, but also extend DE applications towards solving complex, regional-scale water management optimization problems.

Machine learnt bond order potential to model metal-organic (Co-C) heterostructures.

PubMed

Narayanan, Badri; Chan, Henry; Kinaci, Alper; Sen, Fatih G; Gray, Stephen K; Chan, Maria K Y; Sankaranarayanan, Subramanian K R S

2017-11-30

A fundamental understanding of the inter-relationships between structure, morphology, atomic scale dynamics, chemistry, and physical properties of mixed metallic-covalent systems is essential to design novel functional materials for applications in flexible nano-electronics, energy storage and catalysis. To achieve such knowledge, it is imperative to develop robust and computationally efficient atomistic models that describe atomic interactions accurately within a single framework. Here, we present a unified Tersoff-Brenner type bond order potential (BOP) for a Co-C system, trained against lattice parameters, cohesive energies, equation of state, and elastic constants of different crystalline phases of cobalt as well as orthorhombic Co 2 C derived from density functional theory (DFT) calculations. The independent BOP parameters are determined using a combination of supervised machine learning (genetic algorithms) and local minimization via the simplex method. Our newly developed BOP accurately describes the structural, thermodynamic, mechanical, and surface properties of both the elemental components as well as the carbide phases, in excellent accordance with DFT calculations and experiments. Using our machine-learnt BOP potential, we performed large-scale molecular dynamics simulations to investigate the effect of metal/carbon concentration on the structure and mechanical properties of porous architectures obtained via self-assembly of cobalt nanoparticles and fullerene molecules. Such porous structures have implications in flexible electronics, where materials with high electrical conductivity and low elastic stiffness are desired. Using unsupervised machine learning (clustering), we identify the pore structure, pore-distribution, and metallic conduction pathways in self-assembled structures at different C/Co ratios. We find that as the C/Co ratio increases, the connectivity between the Co nanoparticles becomes limited, likely resulting in low electrical conductivity; on the other hand, such C-rich hybrid structures are highly flexible (i.e., low stiffness). The BOP model developed in this work is a valuable tool to investigate atomic scale processes, structure-property relationships, and temperature/pressure response of Co-C systems, as well as design organic-inorganic hybrid structures with a desired set of properties.

Modal testing with Asher's method using a Fourier analyzer and curve fitting

NASA Technical Reports Server (NTRS)

Gold, R. R.; Hallauer, W. L., Jr.

1979-01-01

An unusual application of the method proposed by Asher (1958) for structural dynamic and modal testing is discussed. Asher's method has the capability, using the admittance matrix and multiple-shaker sinusoidal excitation, of separating structural modes having indefinitely close natural frequencies. The present application uses Asher's method in conjunction with a modern Fourier analyzer system but eliminates the necessity of exciting the test structure simultaneously with several shakers. Evaluation of this approach with numerically simulated data demonstrated its effectiveness; the parameters of two modes having almost identical natural frequencies were accurately identified. Laboratory evaluation of this approach was inconclusive because of poor experimental input data.

A Structural Molar Volume Model for Oxide Melts Part I: Li2O-Na2O-K2O-MgO-CaO-MnO-PbO-Al2O3-SiO2 Melts—Binary Systems

NASA Astrophysics Data System (ADS)

Thibodeau, Eric; Gheribi, Aimen E.; Jung, In-Ho

2016-04-01

A structural molar volume model was developed to accurately reproduce the molar volume of molten oxides. As the non-linearity of molar volume is related to the change in structure of molten oxides, the silicate tetrahedral Q-species, calculated from the modified quasichemical model with an optimized thermodynamic database, were used as basic structural units in the present model. Experimental molar volume data for unary and binary melts in the Li2O-Na2O-K2O-MgO-CaO-MnO-PbO-Al2O3-SiO2 system were critically evaluated. The molar volumes of unary oxide components and binary Q-species, which are model parameters of the present structural model, were determined to accurately reproduce the experimental data across the entire binary composition in a wide range of temperatures. The non-linear behavior of molar volume and thermal expansivity of binary melt depending on SiO2 content are well reproduced by the present model.

ESR paper on structured reporting in radiology.

PubMed

2018-02-01

Structured reporting is emerging as a key element of optimising radiology's contribution to patient outcomes and ensuring the value of radiologists' work. It is being developed and supported by many national and international radiology societies, based on the recognised need to use uniform language and structure to accurately describe radiology findings. Standardisation of report structures ensures that all relevant areas are addressed. Standardisation of terminology prevents ambiguity in reports and facilitates comparability of reports. The use of key data elements and quantified parameters in structured reports ("radiomics") permits automatic functions (e.g. TNM staging), potential integration with other clinical parameters (e.g. laboratory results), data sharing (e.g. registries, biobanks) and data mining for research, teaching and other purposes. This article outlines the requirements for a successful structured reporting strategy (definition of content and structure, standard terminologies, tools and protocols). A potential implementation strategy is outlined. Moving from conventional prose reports to structured reporting is endorsed as a positive development, and must be an international effort, with international design and adoption of structured reporting templates that can be translated and adapted in local environments as needed. Industry involvement is key to success, based on international data standards and guidelines. • Standardisation of radiology report structure ensures completeness and comparability of reports. • Use of standardised language in reports minimises ambiguity. • Structured reporting facilitates automatic functions, integration with other clinical parameters and data sharing. • International and inter-society cooperation is key to developing successful structured report templates. • Integration with industry providers of radiology-reporting software is also crucial.

Application of viscous and Iwan modal damping models to experimental measurements from bolted structures

DOE PAGES

Deaner, Brandon J.; Allen, Matthew S.; Starr, Michael James; ...

2015-01-20

Measurements are presented from a two-beam structure with several bolted interfaces in order to characterize the nonlinear damping introduced by the joints. The measurements (all at force levels below macroslip) reveal that each underlying mode of the structure is well approximated by a single degree-of-freedom (SDOF) system with a nonlinear mechanical joint. At low enough force levels, the measurements show dissipation that scales as the second power of the applied force, agreeing with theory for a linear viscously damped system. This is attributed to linear viscous behavior of the material and/or damping provided by the support structure. At larger forcemore » levels, the damping is observed to behave nonlinearly, suggesting that damping from the mechanical joints is dominant. A model is presented that captures these effects, consisting of a spring and viscous damping element in parallel with a four-parameter Iwan model. As a result, the parameters of this model are identified for each mode of the structure and comparisons suggest that the model captures the stiffness and damping accurately over a range of forcing levels.« less

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Doherty, Kimberly R., E-mail: kimberly.doherty@quintiles.com; Talbert, Dominique R.; Trusk, Patricia B.

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.more » 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-depth insight towards mechanism of cardiac toxicity. • Testing functional and structural endpoints enhances early cardiac risk assessment.« less

The relationship between dental implant stability and trabecular bone structure using cone-beam computed tomography

PubMed Central

2016-01-01

Purpose The objective of this study was to investigate the relationships between primary implant stability as measured by impact response frequency and the structural parameters of trabecular bone using cone-beam computed tomography(CBCT), excluding the effect of cortical bone thickness. Methods We measured the impact response of a dental implant placed into swine bone specimens composed of only trabecular bone without the cortical bone layer using an inductive sensor. The peak frequency of the impact response spectrum was determined as an implant stability criterion (SPF). The 3D microstructural parameters were calculated from CT images of the bone specimens obtained using both micro-CT and CBCT. Results SPF had significant positive correlations with trabecular bone structural parameters (BV/TV, BV, BS, BSD, Tb.Th, Tb.N, FD, and BS/BV) (P<0.01) while SPF demonstrated significant negative correlations with other microstructural parameters (Tb.Sp, Tb.Pf, and SMI) using micro-CT and CBCT (P<0.01). Conclusions There was an increase in implant stability prediction by combining BV/TV and SMI in the stepwise forward regression analysis. Bone with high volume density and low surface density shows high implant stability. Well-connected thick bone with small marrow spaces also shows high implant stability. The combination of bone density and architectural parameters measured using CBCT can predict the implant stability more accurately than the density alone in clinical diagnoses. PMID:27127692

An Automatic Procedure for Combining Digital Images and Laser Scanner Data

NASA Astrophysics Data System (ADS)

Moussa, W.; Abdel-Wahab, M.; Fritsch, D.

2012-07-01

Besides improving both the geometry and the visual quality of the model, the integration of close-range photogrammetry and terrestrial laser scanning techniques directs at filling gaps in laser scanner point clouds to avoid modeling errors, reconstructing more details in higher resolution and recovering simple structures with less geometric details. Thus, within this paper a flexible approach for the automatic combination of digital images and laser scanner data is presented. Our approach comprises two methods for data fusion. The first method starts by a marker-free registration of digital images based on a point-based environment model (PEM) of a scene which stores the 3D laser scanner point clouds associated with intensity and RGB values. The PEM allows the extraction of accurate control information for the direct computation of absolute camera orientations with redundant information by means of accurate space resection methods. In order to use the computed relations between the digital images and the laser scanner data, an extended Helmert (seven-parameter) transformation is introduced and its parameters are estimated. Precedent to that, in the second method, the local relative orientation parameters of the camera images are calculated by means of an optimized Structure and Motion (SaM) reconstruction method. Then, using the determined transformation parameters results in having absolute oriented images in relation to the laser scanner data. With the resulting absolute orientations we have employed robust dense image reconstruction algorithms to create oriented dense image point clouds, which are automatically combined with the laser scanner data to form a complete detailed representation of a scene. Examples of different data sets are shown and experimental results demonstrate the effectiveness of the presented procedures.

Calibration under uncertainty for finite element models of masonry monuments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Atamturktur, Sezer,; Hemez, Francois,; Unal, Cetin

2010-02-01

Historical unreinforced masonry buildings often include features such as load bearing unreinforced masonry vaults and their supporting framework of piers, fill, buttresses, and walls. The masonry vaults of such buildings are among the most vulnerable structural components and certainly among the most challenging to analyze. The versatility of finite element (FE) analyses in incorporating various constitutive laws, as well as practically all geometric configurations, has resulted in the widespread use of the FE method for the analysis of complex unreinforced masonry structures over the last three decades. However, an FE model is only as accurate as its input parameters, andmore » there are two fundamental challenges while defining FE model input parameters: (1) material properties and (2) support conditions. The difficulties in defining these two aspects of the FE model arise from the lack of knowledge in the common engineering understanding of masonry behavior. As a result, engineers are unable to define these FE model input parameters with certainty, and, inevitably, uncertainties are introduced to the FE model.« less

A three-dimensional bioprinting system for use with a hydrogel-based biomaterial and printing parameter characterization.

PubMed

Song, Seung-Joon; Choi, Jaesoon; Park, Yong-Doo; Lee, Jung-Joo; Hong, So Young; Sun, Kyung

2010-11-01

Bioprinting is an emerging technology for constructing tissue or bioartificial organs with complex three-dimensional (3D) structures. It provides high-precision spatial shape forming ability on a larger scale than conventional tissue engineering methods, and simultaneous multiple components composition ability. Bioprinting utilizes a computer-controlled 3D printer mechanism for 3D biological structure construction. To implement minimal pattern width in a hydrogel-based bioprinting system, a study on printing characteristics was performed by varying printer control parameters. The experimental results showed that printing pattern width depends on associated printer control parameters such as printing flow rate, nozzle diameter, and nozzle velocity. The system under development showed acceptable feasibility of potential use for accurate printing pattern implementation in tissue engineering applications and is another example of novel techniques for regenerative medicine based on computer-aided biofabrication system. © 2010, Copyright the Authors. Artificial Organs © 2010, International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

Approach to quantify human dermal skin aging using multiphoton laser scanning microscopy

NASA Astrophysics Data System (ADS)

Puschmann, Stefan; Rahn, Christian-Dennis; Wenck, Horst; Gallinat, Stefan; Fischer, Frank

2012-03-01

Extracellular skin structures in human skin are impaired during intrinsic and extrinsic aging. Assessment of these dermal changes is conducted by subjective clinical evaluation and histological and molecular analysis. We aimed to develop a new parameter for the noninvasive quantitative determination of dermal skin alterations utilizing the high-resolution three-dimensional multiphoton laser scanning microscopy (MPLSM) technique. To quantify structural differences between chronically sun-exposed and sun-protected human skin, the respective collagen-specific second harmonic generation and the elastin-specific autofluorescence signals were recorded in young and elderly volunteers using the MPLSM technique. After image processing, the elastin-to-collagen ratio (ELCOR) was calculated. Results show that the ELCOR parameter of volar forearm skin significantly increases with age. For elderly volunteers, the ELCOR value calculated for the chronically sun-exposed temple area is significantly augmented compared to the sun-protected upper arm area. Based on the MPLSM technology, we introduce the ELCOR parameter as a new means to quantify accurately age-associated alterations in the extracellular matrix.

Does the choice of the crystal structure influence the results of the periodic DFT calculations? A case of glycine alpha polymorph GIPAW NMR parameters computations.

PubMed

Szeleszczuk, Łukasz; Pisklak, Dariusz Maciej; Zielińska-Pisklak, Monika

2018-05-30

Glycine is a common amino acid with relatively complex chemistry in solid state. Although several polymorphs (α, β, δ, γ, ε) of crystalline glycine are known, for NMR spectroscopy the most important is a polymorph, which is used as a standard for calibration of spectrometer performance and therefore it is intensively studied by both experimental methods and theoretical computation. The great scientific interest in a glycine results in a large number of crystallographic information files (CIFs) deposited in Cambridge Structural Database (CSD). The aim of this study was to evaluate the influence of the chosen crystal structure of α glycine obtained in different crystallographic experimental conditions (temperature, pressure and source of radiation of α glycine) on the results of periodic DFT calculation. For this purpose the total of 136 GIPAW calculations of α glycine NMR parameters were performed, preceded by the four approaches ("SP", "only H", "full", "full+cell") of structure preparation. The analysis of the results of those computations performed on the representative group of 34 structures obtained at various experimental conditions revealed that though the structures were generally characterized by good accuracy (R < 0.05 for most of them) the results of the periodic DFT calculations performed using the unoptimized structures differed significantly. The values of the standard deviations of the studied NMR parameters were in most cases decreasing with the number of optimized parameters. The most accurate results (of the calculations) were in most cases obtained using the structures with solely hydrogen atoms positions optimized. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Reaction Wheel Disturbance Model Extraction Software - RWDMES

NASA Technical Reports Server (NTRS)

Blaurock, Carl

2009-01-01

The RWDMES is a tool for modeling the disturbances imparted on spacecraft by spinning reaction wheels. Reaction wheels are usually the largest disturbance source on a precision pointing spacecraft, and can be the dominating source of pointing error. Accurate knowledge of the disturbance environment is critical to accurate prediction of the pointing performance. In the past, it has been difficult to extract an accurate wheel disturbance model since the forcing mechanisms are difficult to model physically, and the forcing amplitudes are filtered by the dynamics of the reaction wheel. RWDMES captures the wheel-induced disturbances using a hybrid physical/empirical model that is extracted directly from measured forcing data. The empirical models capture the tonal forces that occur at harmonics of the spin rate, and the broadband forces that arise from random effects. The empirical forcing functions are filtered by a physical model of the wheel structure that includes spin-rate-dependent moments (gyroscopic terms). The resulting hybrid model creates a highly accurate prediction of wheel-induced forces. It accounts for variation in disturbance frequency, as well as the shifts in structural amplification by the whirl modes, as the spin rate changes. This software provides a point-and-click environment for producing accurate models with minimal user effort. Where conventional approaches may take weeks to produce a model of variable quality, RWDMES can create a demonstrably high accuracy model in two hours. The software consists of a graphical user interface (GUI) that enables the user to specify all analysis parameters, to evaluate analysis results and to iteratively refine the model. Underlying algorithms automatically extract disturbance harmonics, initialize and tune harmonic models, and initialize and tune broadband noise models. The component steps are described in the RWDMES user s guide and include: converting time domain data to waterfall PSDs (power spectral densities); converting PSDs to order analysis data; extracting harmonics; initializing and simultaneously tuning a harmonic model and a wheel structural model; initializing and tuning a broadband model; and verifying the harmonic/broadband/structural model against the measurement data. Functional operation is through a MATLAB GUI that loads test data, performs the various analyses, plots evaluation data for assessment and refinement of analysis parameters, and exports the data to documentation or downstream analysis code. The harmonic models are defined as specified functions of frequency, typically speed-squared. The reaction wheel structural model is realized as mass, damping, and stiffness matrices (typically from a finite element analysis package) with the addition of a gyroscopic forcing matrix. The broadband noise model is realized as a set of speed-dependent filters. The tuning of the combined model is performed using nonlinear least squares techniques. RWDMES is implemented as a MATLAB toolbox comprising the Fit Manager for performing the model extraction, Data Manager for managing input data and output models, the Gyro Manager for modifying wheel structural models, and the Harmonic Editor for evaluating and tuning harmonic models. This software was validated using data from Goodrich E wheels, and from GSFC Lunar Reconnaissance Orbiter (LRO) wheels. The validation testing proved that RWDMES has the capability to extract accurate disturbance models from flight reaction wheels with minimal user effort.

A sophisticated simulation for the fracture behavior of concrete material using XFEM

NASA Astrophysics Data System (ADS)

Zhai, Changhai; Wang, Xiaomin; Kong, Jingchang; Li, Shuang; Xie, Lili

2017-10-01

The development of a powerful numerical model to simulate the fracture behavior of concrete material has long been one of the dominant research areas in earthquake engineering. A reliable model should be able to adequately represent the discontinuous characteristics of cracks and simulate various failure behaviors under complicated loading conditions. In this paper, a numerical formulation, which incorporates a sophisticated rigid-plastic interface constitutive model coupling cohesion softening, contact, friction and shear dilatation into the XFEM, is proposed to describe various crack behaviors of concrete material. An effective numerical integration scheme for accurately assembling the contribution to the weak form on both sides of the discontinuity is introduced. The effectiveness of the proposed method has been assessed by simulating several well-known experimental tests. It is concluded that the numerical method can successfully capture the crack paths and accurately predict the fracture behavior of concrete structures. The influence of mode-II parameters on the mixed-mode fracture behavior is further investigated to better determine these parameters.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, Stacy; English, Shawn; Briggs, Timothy

Fiber-reinforced composite materials offer light-weight solutions to many structural challenges. In the development of high-performance composite structures, a thorough understanding is required of the composite materials themselves as well as methods for the analysis and failure prediction of the relevant composite structures. However, the mechanical properties required for the complete constitutive definition of a composite material can be difficult to determine through experimentation. Therefore, efficient methods are necessary that can be used to determine which properties are relevant to the analysis of a specific structure and to establish a structure's response to a material parameter that can only be definedmore » through estimation. The objectives of this paper deal with demonstrating the potential value of sensitivity and uncertainty quantification techniques during the failure analysis of loaded composite structures; and the proposed methods are applied to the simulation of the four-point flexural characterization of a carbon fiber composite material. Utilizing a recently implemented, phenomenological orthotropic material model that is capable of predicting progressive composite damage and failure, a sensitivity analysis is completed to establish which material parameters are truly relevant to a simulation's outcome. Then, a parameter study is completed to determine the effect of the relevant material properties' expected variations on the simulated four-point flexural behavior as well as to determine the value of an unknown material property. This process demonstrates the ability to formulate accurate predictions in the absence of a rigorous material characterization effort. Finally, the presented results indicate that a sensitivity analysis and parameter study can be used to streamline the material definition process as the described flexural characterization was used for model validation.« less

Quantifying the influences of spectral resolution on uncertainty in leaf trait estimates through a Bayesian approach to RTM inversion

DOE PAGES

Shiklomanov, Alexey N.; Dietze, Michael C.; Viskari, Toni; ...

2016-06-09

The remote monitoring of plant canopies is critically needed for understanding of terrestrial ecosystem mechanics and biodiversity as well as capturing the short- to long-term responses of vegetation to disturbance and climate change. A variety of orbital, sub-orbital, and field instruments have been used to retrieve optical spectral signals and to study different vegetation properties such as plant biochemistry, nutrient cycling, physiology, water status, and stress. Radiative transfer models (RTMs) provide a mechanistic link between vegetation properties and observed spectral features, and RTM spectral inversion is a useful framework for estimating these properties from spectral data. However, existing approaches tomore » RTM spectral inversion are typically limited by the inability to characterize uncertainty in parameter estimates. Here, we introduce a Bayesian algorithm for the spectral inversion of the PROSPECT 5 leaf RTM that is distinct from past approaches in two important ways: First, the algorithm only uses reflectance and does not require transmittance observations, which have been plagued by a variety of measurement and equipment challenges. Second, the output is not a point estimate for each parameter but rather the joint probability distribution that includes estimates of parameter uncertainties and covariance structure. We validated our inversion approach using a database of leaf spectra together with measurements of equivalent water thickness (EWT) and leaf dry mass per unit area (LMA). The parameters estimated by our inversion were able to accurately reproduce the observed reflectance (RMSE VIS = 0.0063, RMSE NIR-SWIR = 0.0098) and transmittance (RMSE VIS = 0.0404, RMSE NIR-SWIR = 0.0551) for both broadleaved and conifer species. Inversion estimates of EWT and LMA for broadleaved species agreed well with direct measurements (CV EWT = 18.8%, CV LMA = 24.5%), while estimates for conifer species were less accurate (CV EWT = 53.2%, CV LMA = 63.3%). To examine the influence of spectral resolution on parameter uncertainty, we simulated leaf reflectance as observed by ten common remote sensing platforms with varying spectral configurations and performed a Bayesian inversion on the resulting spectra. We found that full-range hyperspectral platforms were able to retrieve all parameters accurately and precisely, while the parameter estimates of multispectral platforms were much less precise and prone to bias at high and low values. We also observed that variations in the width and location of spectral bands influenced the shape of the covariance structure of parameter estimates. Lastly, our Bayesian spectral inversion provides a powerful and versatile framework for future RTM development and single- and multi-instrumental remote sensing of vegetation.« less

Quantifying the influences of spectral resolution on uncertainty in leaf trait estimates through a Bayesian approach to RTM inversion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shiklomanov, Alexey N.; Dietze, Michael C.; Viskari, Toni

The remote monitoring of plant canopies is critically needed for understanding of terrestrial ecosystem mechanics and biodiversity as well as capturing the short- to long-term responses of vegetation to disturbance and climate change. A variety of orbital, sub-orbital, and field instruments have been used to retrieve optical spectral signals and to study different vegetation properties such as plant biochemistry, nutrient cycling, physiology, water status, and stress. Radiative transfer models (RTMs) provide a mechanistic link between vegetation properties and observed spectral features, and RTM spectral inversion is a useful framework for estimating these properties from spectral data. However, existing approaches tomore » RTM spectral inversion are typically limited by the inability to characterize uncertainty in parameter estimates. Here, we introduce a Bayesian algorithm for the spectral inversion of the PROSPECT 5 leaf RTM that is distinct from past approaches in two important ways: First, the algorithm only uses reflectance and does not require transmittance observations, which have been plagued by a variety of measurement and equipment challenges. Second, the output is not a point estimate for each parameter but rather the joint probability distribution that includes estimates of parameter uncertainties and covariance structure. We validated our inversion approach using a database of leaf spectra together with measurements of equivalent water thickness (EWT) and leaf dry mass per unit area (LMA). The parameters estimated by our inversion were able to accurately reproduce the observed reflectance (RMSE VIS = 0.0063, RMSE NIR-SWIR = 0.0098) and transmittance (RMSE VIS = 0.0404, RMSE NIR-SWIR = 0.0551) for both broadleaved and conifer species. Inversion estimates of EWT and LMA for broadleaved species agreed well with direct measurements (CV EWT = 18.8%, CV LMA = 24.5%), while estimates for conifer species were less accurate (CV EWT = 53.2%, CV LMA = 63.3%). To examine the influence of spectral resolution on parameter uncertainty, we simulated leaf reflectance as observed by ten common remote sensing platforms with varying spectral configurations and performed a Bayesian inversion on the resulting spectra. We found that full-range hyperspectral platforms were able to retrieve all parameters accurately and precisely, while the parameter estimates of multispectral platforms were much less precise and prone to bias at high and low values. We also observed that variations in the width and location of spectral bands influenced the shape of the covariance structure of parameter estimates. Lastly, our Bayesian spectral inversion provides a powerful and versatile framework for future RTM development and single- and multi-instrumental remote sensing of vegetation.« less

Electronic properties of doped and defective NiO: A quantum Monte Carlo study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shin, Hyeondeok; Luo, Ye; Ganesh, Panchapakesan

NiO is a canonical Mott (or charge-transfer) insulator and as such is notoriously difficult to describe using density functional theory (DFT) based electronic structure methods. Doped Mott insulators such as NiO are of interest for various applications but rigorous theoretical descriptions are lacking. Here, we use quantum Monte Carlo methods, which very accurately include electron-electron interactions, to examine energetics, charge- and spin-structures of NiO with various point defects, such as vacancies or substitutional doping with potassium. The formation energy of a potassium dopant is significantly lower than for a Ni vacancy, making potassium an attractive monovalent dopant for NiO. Wemore » compare our results with DFT results that include an on-site Hubbard U (DFT+U) to account for correlations and find relatively large discrepancies for defect formation energies as well as for charge and spin redistributions in the presence of point defects. Finally, it is unlikely that single-parameter fixes of DFT may be able to obtain accurate accounts of anything but a single parameter, e.g., band gap; responses that, maybe in addition to the band gap, depend in subtle and complex ways on ground state properties, such as charge and spin densities, are likely to contain quantitative and qualitative errors.« less

Estimating 3D Leaf and Stem Shape of Nursery Paprika Plants by a Novel Multi-Camera Photography System

PubMed Central

Zhang, Yu; Teng, Poching; Shimizu, Yo; Hosoi, Fumiki; Omasa, Kenji

2016-01-01

For plant breeding and growth monitoring, accurate measurements of plant structure parameters are very crucial. We have, therefore, developed a high efficiency Multi-Camera Photography (MCP) system combining Multi-View Stereovision (MVS) with the Structure from Motion (SfM) algorithm. In this paper, we measured six variables of nursery paprika plants and investigated the accuracy of 3D models reconstructed from photos taken by four lens types at four different positions. The results demonstrated that error between the estimated and measured values was small, and the root-mean-square errors (RMSE) for leaf width/length and stem height/diameter were 1.65 mm (R2 = 0.98) and 0.57 mm (R2 = 0.99), respectively. The accuracies of the 3D model reconstruction of leaf and stem by a 28-mm lens at the first and third camera positions were the highest, and the number of reconstructed fine-scale 3D model shape surfaces of leaf and stem is the most. The results confirmed the practicability of our new method for the reconstruction of fine-scale plant model and accurate estimation of the plant parameters. They also displayed that our system is a good system for capturing high-resolution 3D images of nursery plants with high efficiency. PMID:27314348

Electronic properties of doped and defective NiO: A quantum Monte Carlo study

DOE PAGES

Shin, Hyeondeok; Luo, Ye; Ganesh, Panchapakesan; ...

2017-12-28

NiO is a canonical Mott (or charge-transfer) insulator and as such is notoriously difficult to describe using density functional theory (DFT) based electronic structure methods. Doped Mott insulators such as NiO are of interest for various applications but rigorous theoretical descriptions are lacking. Here, we use quantum Monte Carlo methods, which very accurately include electron-electron interactions, to examine energetics, charge- and spin-structures of NiO with various point defects, such as vacancies or substitutional doping with potassium. The formation energy of a potassium dopant is significantly lower than for a Ni vacancy, making potassium an attractive monovalent dopant for NiO. Wemore » compare our results with DFT results that include an on-site Hubbard U (DFT+U) to account for correlations and find relatively large discrepancies for defect formation energies as well as for charge and spin redistributions in the presence of point defects. Finally, it is unlikely that single-parameter fixes of DFT may be able to obtain accurate accounts of anything but a single parameter, e.g., band gap; responses that, maybe in addition to the band gap, depend in subtle and complex ways on ground state properties, such as charge and spin densities, are likely to contain quantitative and qualitative errors.« less

A New Calibration Method for Commercial RGB-D Sensors

PubMed Central

Darwish, Walid; Tang, Shenjun; Li, Wenbin; Chen, Wu

2017-01-01

Commercial RGB-D sensors such as Kinect and Structure Sensors have been widely used in the game industry, where geometric fidelity is not of utmost importance. For applications in which high quality 3D is required, i.e., 3D building models of centimeter-level accuracy, accurate and reliable calibrations of these sensors are required. This paper presents a new model for calibrating the depth measurements of RGB-D sensors based on the structured light concept. Additionally, a new automatic method is proposed for the calibration of all RGB-D parameters, including internal calibration parameters for all cameras, the baseline between the infrared and RGB cameras, and the depth error model. When compared with traditional calibration methods, this new model shows a significant improvement in depth precision for both near and far ranges. PMID:28538695

A New Hybrid Viscoelastic Soft Tissue Model based on Meshless Method for Haptic Surgical Simulation

PubMed Central

Bao, Yidong; Wu, Dongmei; Yan, Zhiyuan; Du, Zhijiang

2013-01-01

This paper proposes a hybrid soft tissue model that consists of a multilayer structure and many spheres for surgical simulation system based on meshless. To improve accuracy of the model, tension is added to the three-parameter viscoelastic structure that connects the two spheres. By using haptic device, the three-parameter viscoelastic model (TPM) produces accurate deformationand also has better stress-strain, stress relaxation and creep properties. Stress relaxation and creep formulas have been obtained by mathematical formula derivation. Comparing with the experimental results of the real pig liver which were reported by Evren et al. and Amy et al., the curve lines of stress-strain, stress relaxation and creep of TPM are close to the experimental data of the real liver. Simulated results show that TPM has better real-time, stability and accuracy. PMID:24339837

Using Plate Finite Elements for Modeling Fillets in Design, Optimization, and Dynamic Analysis

NASA Technical Reports Server (NTRS)

Brown, A. M.; Seugling, R. M.

2003-01-01

A methodology has been developed that allows the use of plate elements instead of numerically inefficient solid elements for modeling structures with 90 degree fillets. The technique uses plate bridges with pseudo Young's modulus (Eb) and thickness (tb) values placed between the tangent points of the fillets. These parameters are obtained by solving two nonlinear simultaneous equations in terms of the independent variables rlt and twallt. These equations are generated by equating the rotation at the tangent point of a bridge system with that of a fillet, where both rotations are derived using beam theory. Accurate surface fits of the solutions are also presented to provide the user with closed-form equations for the parameters. The methodology was verified on the subcomponent level and with a representative filleted structure, where the technique yielded a plate model exhibiting a level of accuracy better than or equal to a high-fidelity solid model and with a 90-percent reduction in the number of DOFs. The application of this method for parametric design studies, optimization, and dynamic analysis should prove extremely beneficial for the finite element practitioner. Although the method does not attempt to produce accurate stresses in the filleted region, it can also be used to obtain stresses elsewhere in the structure for preliminary analysis. A future avenue of study is to extend the theory developed here to other fillet geometries, including fillet angles other than 90 and multifaceted intersections.

Optimization of the GBMV2 implicit solvent force field for accurate simulation of protein conformational equilibria.

PubMed

Lee, Kuo Hao; Chen, Jianhan

2017-06-15

Accurate treatment of solvent environment is critical for reliable simulations of protein conformational equilibria. Implicit treatment of solvation, such as using the generalized Born (GB) class of models arguably provides an optimal balance between computational efficiency and physical accuracy. Yet, GB models are frequently plagued by a tendency to generate overly compact structures. The physical origins of this drawback are relatively well understood, and the key to a balanced implicit solvent protein force field is careful optimization of physical parameters to achieve a sufficient level of cancellation of errors. The latter has been hampered by the difficulty of generating converged conformational ensembles of non-trivial model proteins using the popular replica exchange sampling technique. Here, we leverage improved sampling efficiency of a newly developed multi-scale enhanced sampling technique to re-optimize the generalized-Born with molecular volume (GBMV2) implicit solvent model with the CHARMM36 protein force field. Recursive optimization of key GBMV2 parameters (such as input radii) and protein torsion profiles (via the CMAP torsion cross terms) has led to a more balanced GBMV2 protein force field that recapitulates the structures and stabilities of both helical and β-hairpin model peptides. Importantly, this force field appears to be free of the over-compaction bias, and can generate structural ensembles of several intrinsically disordered proteins of various lengths that seem highly consistent with available experimental data. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Bayesian estimation of the transmissivity spatial structure from pumping test data

NASA Astrophysics Data System (ADS)

Demir, Mehmet Taner; Copty, Nadim K.; Trinchero, Paolo; Sanchez-Vila, Xavier

2017-06-01

Estimating the statistical parameters (mean, variance, and integral scale) that define the spatial structure of the transmissivity or hydraulic conductivity fields is a fundamental step for the accurate prediction of subsurface flow and contaminant transport. In practice, the determination of the spatial structure is a challenge because of spatial heterogeneity and data scarcity. In this paper, we describe a novel approach that uses time drawdown data from multiple pumping tests to determine the transmissivity statistical spatial structure. The method builds on the pumping test interpretation procedure of Copty et al. (2011) (Continuous Derivation method, CD), which uses the time-drawdown data and its time derivative to estimate apparent transmissivity values as a function of radial distance from the pumping well. A Bayesian approach is then used to infer the statistical parameters of the transmissivity field by combining prior information about the parameters and the likelihood function expressed in terms of radially-dependent apparent transmissivities determined from pumping tests. A major advantage of the proposed Bayesian approach is that the likelihood function is readily determined from randomly generated multiple realizations of the transmissivity field, without the need to solve the groundwater flow equation. Applying the method to synthetically-generated pumping test data, we demonstrate that, through a relatively simple procedure, information on the spatial structure of the transmissivity may be inferred from pumping tests data. It is also shown that the prior parameter distribution has a significant influence on the estimation procedure, given the non-uniqueness of the estimation procedure. Results also indicate that the reliability of the estimated transmissivity statistical parameters increases with the number of available pumping tests.

White-light Interferometry using a Channeled Spectrum: II. Calibration Methods, Numerical and Experimental Results

NASA Technical Reports Server (NTRS)

Zhai, Chengxing; Milman, Mark H.; Regehr, Martin W.; Best, Paul K.

2007-01-01

In the companion paper, [Appl. Opt. 46, 5853 (2007)] a highly accurate white light interference model was developed from just a few key parameters characterized in terms of various moments of the source and instrument transmission function. We develop and implement the end-to-end process of calibrating these moment parameters together with the differential dispersion of the instrument and applying them to the algorithms developed in the companion paper. The calibration procedure developed herein is based on first obtaining the standard monochromatic parameters at the pixel level: wavenumber, phase, intensity, and visibility parameters via a nonlinear least-squares procedure that exploits the structure of the model. The pixel level parameters are then combined to obtain the required 'global' moment and dispersion parameters. The process is applied to both simulated scenarios of astrometric observations and to data from the microarcsecond metrology testbed (MAM), an interferometer testbed that has played a prominent role in the development of this technology.

Refinement of Generalized Born Implicit Solvation Parameters for Nucleic Acids and their Complexes with Proteins

PubMed Central

Nguyen, Hai; Pérez, Alberto; Bermeo, Sherry; Simmerling, Carlos

2016-01-01

The Generalized Born (GB) implicit solvent model has undergone significant improvements in accuracy for modeling of proteins and small molecules. However, GB still remains a less widely explored option for nucleic acid simulations, in part because fast GB models are often unable to maintain stable nucleic acid structures, or they introduce structural bias in proteins, leading to difficulty in application of GB models in simulations of protein-nucleic acid complexes. Recently, GB-neck2 was developed to improve the behavior of protein simulations. In an effort to create a more accurate model for nucleic acids, a similar procedure to the development of GB-neck2 is described here for nucleic acids. The resulting parameter set significantly reduces absolute and relative energy error relative to Poisson Boltzmann for both nucleic acids and nucleic acid-protein complexes, when compared to its predecessor GB-neck model. This improvement in solvation energy calculation translates to increased structural stability for simulations of DNA and RNA duplexes, quadruplexes, and protein-nucleic acid complexes. The GB-neck2 model also enables successful folding of small DNA and RNA hairpins to near native structures as determined from comparison with experiment. The functional form and all required parameters are provided here and also implemented in the AMBER software. PMID:26574454

Simulation and Experimental Studies on Grain Selection and Structure Design of the Spiral Selector for Casting Single Crystal Ni-Based Superalloy.

PubMed

Zhang, Hang; Xu, Qingyan

2017-10-27

Grain selection is an important process in single crystal turbine blades manufacturing. Selector structure is a control factor of grain selection, as well as directional solidification (DS). In this study, the grain selection and structure design of the spiral selector were investigated through experimentation and simulation. A heat transfer model and a 3D microstructure growth model were established based on the Cellular automaton-Finite difference (CA-FD) method for the grain selector. Consequently, the temperature field, the microstructure and the grain orientation distribution were simulated and further verified. The average error of the temperature result was less than 1.5%. The grain selection mechanisms were further analyzed and validated through simulations. The structural design specifications of the selector were suggested based on the two grain selection effects. The structural parameters of the spiral selector, namely, the spiral tunnel diameter ( d w ), the spiral pitch ( h b ) and the spiral diameter ( h s ), were studied and the design criteria of these parameters were proposed. The experimental and simulation results demonstrated that the improved selector could accurately and efficiently produce a single crystal structure.

Simulation and Experimental Studies on Grain Selection and Structure Design of the Spiral Selector for Casting Single Crystal Ni-Based Superalloy

PubMed Central

Zhang, Hang; Xu, Qingyan

2017-01-01

Grain selection is an important process in single crystal turbine blades manufacturing. Selector structure is a control factor of grain selection, as well as directional solidification (DS). In this study, the grain selection and structure design of the spiral selector were investigated through experimentation and simulation. A heat transfer model and a 3D microstructure growth model were established based on the Cellular automaton-Finite difference (CA-FD) method for the grain selector. Consequently, the temperature field, the microstructure and the grain orientation distribution were simulated and further verified. The average error of the temperature result was less than 1.5%. The grain selection mechanisms were further analyzed and validated through simulations. The structural design specifications of the selector were suggested based on the two grain selection effects. The structural parameters of the spiral selector, namely, the spiral tunnel diameter (dw), the spiral pitch (hb) and the spiral diameter (hs), were studied and the design criteria of these parameters were proposed. The experimental and simulation results demonstrated that the improved selector could accurately and efficiently produce a single crystal structure. PMID:29077067

Research on the printability of hydrogels in 3D bioprinting

PubMed Central

He, Yong; Yang, FeiFei; Zhao, HaiMing; Gao, Qing; Xia, Bing; Fu, JianZhong

2016-01-01

As the biocompatible materials, hydrogels have been widely used in three- dimensional (3D) bioprinting/organ printing to load cell for tissue engineering. It is important to precisely control hydrogels deposition during printing the mimic organ structures. However, the printability of hydrogels about printing parameters is seldom addressed. In this paper, we systemically investigated the printability of hydrogels from printing lines (one dimensional, 1D structures) to printing lattices/films (two dimensional, 2D structures) and printing 3D structures with a special attention to the accurate printing. After a series of experiments, we discovered the relationships between the important factors such as air pressure, feedrate, or even printing distance and the printing quality of the expected structures. Dumbbell shape was observed in the lattice structures printing due to the hydrogel diffuses at the intersection. Collapses and fusion of adjacent layer would result in the error accumulation at Z direction which was an important fact that could cause printing failure. Finally, we successfully demonstrated a 3D printing hydrogel scaffold through harmonize with all the parameters. The cell viability after printing was compared with the casting and the results showed that our bioprinting method almost had no extra damage to the cells. PMID:27436509

Research on the printability of hydrogels in 3D bioprinting

NASA Astrophysics Data System (ADS)

He, Yong; Yang, Feifei; Zhao, Haiming; Gao, Qing; Xia, Bing; Fu, Jianzhong

2016-07-01

As the biocompatible materials, hydrogels have been widely used in three- dimensional (3D) bioprinting/organ printing to load cell for tissue engineering. It is important to precisely control hydrogels deposition during printing the mimic organ structures. However, the printability of hydrogels about printing parameters is seldom addressed. In this paper, we systemically investigated the printability of hydrogels from printing lines (one dimensional, 1D structures) to printing lattices/films (two dimensional, 2D structures) and printing 3D structures with a special attention to the accurate printing. After a series of experiments, we discovered the relationships between the important factors such as air pressure, feedrate, or even printing distance and the printing quality of the expected structures. Dumbbell shape was observed in the lattice structures printing due to the hydrogel diffuses at the intersection. Collapses and fusion of adjacent layer would result in the error accumulation at Z direction which was an important fact that could cause printing failure. Finally, we successfully demonstrated a 3D printing hydrogel scaffold through harmonize with all the parameters. The cell viability after printing was compared with the casting and the results showed that our bioprinting method almost had no extra damage to the cells.

Hyperfine Structure and Abundances of Heavy Elements in 68 Tauri (HD 27962)

NASA Astrophysics Data System (ADS)

Martinet, S.; Monier, R.

2017-12-01

HD 27962, also known as 68 Tauri, is a Chemically Peculiar Am star member of the Hyades Open Cluster in the local arm of the Galaxy. We have modeled the high resolution SOPHIE (R=75000) spectrum of 68 Tauri using updated model atmosphere and spectrum synthesis to derive chemical abundances in its atmosphere. In particular, we have studied the effect of the inclusion of Hyperfine Structure of various Baryum isotopes on the determination of the Baryum abundance in 68 Tauri. We have also derived new abundances using updated accurate atomic parameters retrieved from the NIST database.

The polarization response in InAs quantum dots: theoretical correlation between composition and electronic properties.

PubMed

Usman, Muhammad; Tasco, Vittorianna; Todaro, Maria Teresa; De Giorgi, Milena; O'Reilly, Eoin P; Klimeck, Gerhard; Passaseo, Adriana

2012-04-27

III-V growth and surface conditions strongly influence the physical structure and resulting optical properties of self-assembled quantum dots (QDs). Beyond the design of a desired active optical wavelength, the polarization response of QDs is of particular interest for optical communications and quantum information science. Previous theoretical studies based on a pure InAs QD model failed to reproduce experimentally observed polarization properties. In this work, multi-million atom simulations are performed in an effort to understand the correlation between chemical composition and polarization properties of QDs. A systematic analysis of QD structural parameters leads us to propose a two-layer composition model, mimicking In segregation and In-Ga intermixing effects. This model, consistent with mostly accepted compositional findings, allows us to accurately fit the experimental PL spectra. The detailed study of QD morphology parameters presented here serves as a tool for using growth dynamics to engineer the strain field inside and around the QD structures, allowing tuning of the polarization response.

An interval model updating strategy using interval response surface models

NASA Astrophysics Data System (ADS)

Fang, Sheng-En; Zhang, Qiu-Hu; Ren, Wei-Xin

2015-08-01

Stochastic model updating provides an effective way of handling uncertainties existing in real-world structures. In general, probabilistic theories, fuzzy mathematics or interval analyses are involved in the solution of inverse problems. However in practice, probability distributions or membership functions of structural parameters are often unavailable due to insufficient information of a structure. At this moment an interval model updating procedure shows its superiority in the aspect of problem simplification since only the upper and lower bounds of parameters and responses are sought. To this end, this study develops a new concept of interval response surface models for the purpose of efficiently implementing the interval model updating procedure. The frequent interval overestimation due to the use of interval arithmetic can be maximally avoided leading to accurate estimation of parameter intervals. Meanwhile, the establishment of an interval inverse problem is highly simplified, accompanied by a saving of computational costs. By this means a relatively simple and cost-efficient interval updating process can be achieved. Lastly, the feasibility and reliability of the developed method have been verified against a numerical mass-spring system and also against a set of experimentally tested steel plates.

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.; ...

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, Sc 2O 3, Y 2O 3 and La 2O 3. 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 withmore » local and semi-local DFT approximations the 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

An evaluation of the predictive capabilities of CTRW and MRMT

NASA Astrophysics Data System (ADS)

Fiori, Aldo; Zarlenga, Antonio; Gotovac, Hrvoje; Jankovic, Igor; Cvetkovic, Vladimir; Dagan, Gedeon

2016-04-01

The prediction capability of two approximate models of non-Fickian transport in highly heterogeneous aquifers is checked by comparison with accurate numerical simulations, for mean uniform flow of velocity U. The two models considered are the MRMT (Multi Rate Mass Transfer) and CTRW (Continuous Time Random Walk) models. Both circumvent the need to solve the flow and transport equations by using proxy models, which provide the BTC μ(x,t) depending on a vector a of unknown 5 parameters. Although underlain by different conceptualisations, the two models have a similar mathematical structure. The proponents of the models suggest using field transport experiments at a small scale to calibrate a, toward predicting transport at larger scale. The strategy was tested with the aid of accurate numerical simulations in two and three dimensions from the literature. First, the 5 parameter values were calibrated by using the simulated μ at a control plane close to the injection one and subsequently using these same parameters for predicting μ at further 10 control planes. It is found that the two methods perform equally well, though the parameters identification is nonunique, with a large set of parameters providing similar fitting. Also, errors in the determination of the mean eulerian velocity may lead to significant shifts of the predicted BTC. It is found that the simulated BTCs satisfy Markovianity: they can be found as n-fold convolutions of a "kernel", in line with the models' main assumption.

Determination of lattice parameters, strain state and composition in semipolar III-nitrides using high resolution X-ray diffraction

NASA Astrophysics Data System (ADS)

Frentrup, Martin; Hatui, Nirupam; Wernicke, Tim; Stellmach, Joachim; Bhattacharya, Arnab; Kneissl, Michael

2013-12-01

In group-III-nitride heterostructures with semipolar or nonpolar crystal orientation, anisotropic lattice and thermal mismatch with the buffer or substrate lead to a complex distortion of the unit cells, e.g., by shearing of the lattice. This makes an accurate determination of lattice parameters, composition, and strain state under assumption of the hexagonal symmetry impossible. In this work, we present a procedure to accurately determine the lattice constants, strain state, and composition of semipolar heterostructures using high resolution X-ray diffraction. An analysis of the unit cell distortion shows that four independent lattice parameters are sufficient to describe this distortion. Assuming only small deviations from an ideal hexagonal structure, a linear expression for the interplanar distances dhkl is derived. It is used to determine the lattice parameters from high resolution X-ray diffraction 2ϑ-ω-scans of multiple on- and off-axis reflections via a weighted least-square fit. The strain and composition of ternary alloys are then evaluated by transforming the elastic parameters (using Hooke's law) from the natural crystal-fixed coordinate system to a layer-based system, given by the in-plane directions and the growth direction. We illustrate our procedure taking an example of (112¯2) AlκGa1-κN epilayers with Al-contents over the entire composition range. We separately identify the in-plane and out-of-plane strains and discuss origins for the observed anisotropy.

Ordinary kriging as a tool to estimate historical daily streamflow records

USGS Publications Warehouse

Farmer, William H.

2016-01-01

Efficient and responsible management of water resources relies on accurate streamflow records. However, many watersheds are ungaged, limiting the ability to assess and understand local hydrology. Several tools have been developed to alleviate this data scarcity, but few provide continuous daily streamflow records at individual streamgages within an entire region. Building on the history of hydrologic mapping, ordinary kriging was extended to predict daily streamflow time series on a regional basis. Pooling parameters to estimate a single, time-invariant characterization of spatial semivariance structure is shown to produce accurate reproduction of streamflow. This approach is contrasted with a time-varying series of variograms, representing the temporal evolution and behavior of the spatial semivariance structure. Furthermore, the ordinary kriging approach is shown to produce more accurate time series than more common, single-index hydrologic transfers. A comparison between topological kriging and ordinary kriging is less definitive, showing the ordinary kriging approach to be significantly inferior in terms of Nash–Sutcliffe model efficiencies while maintaining significantly superior performance measured by root mean squared errors. Given the similarity of performance and the computational efficiency of ordinary kriging, it is concluded that ordinary kriging is useful for first-order approximation of daily streamflow time series in ungaged watersheds.

High-precision measurement of the X-ray Cu Kα spectrum

PubMed Central

Mendenhall, Marcus H.; Henins, Albert; Hudson, Lawrence T.; Szabo, Csilla I.; Windover, Donald; Cline, James P.

2017-01-01

The structure of the X-ray emission lines of the Cu Kα complex has been remeasured on a newly commissioned instrument, in a manner directly traceable to the Système Internationale definition of the meter. In this measurement, the region from 8000 eV to 8100 eV has been covered with a highly precise angular scale, and well-defined system efficiency, providing accurate wavelengths and relative intensities. This measurement updates the standard multi-Lorentzian-fit parameters from Härtwig, Hölzer, et al., and is in modest disagreement with their results for the wavelength of the Kα1 line when compared via quadratic fitting of the peak top; the intensity ratio of Kα1 to Kα2 agrees within the combined error bounds. However, the position of the fitted top of Kα1 is very sensitive to the fit parameters, so it is not believed to be a robust value to quote without further qualification. We also provide accurate intensity and wavelength information for the so-called Kα3,4 “satellite” complex. Supplementary data is provided which gives the entire shape of the spectrum in this region, allowing it to be used directly in cases where simplified, multi-Lorentzian fits to it are not sufficiently accurate. PMID:28757682

Computer Simulation of Microwave Devices

NASA Technical Reports Server (NTRS)

Kory, Carol L.

1997-01-01

The accurate simulation of cold-test results including dispersion, on-axis beam interaction impedance, and attenuation of a helix traveling-wave tube (TWT) slow-wave circuit using the three-dimensional code MAFIA (Maxwell's Equations Solved by the Finite Integration Algorithm) was demonstrated for the first time. Obtaining these results is a critical step in the design of TWT's. A well-established procedure to acquire these parameters is to actually build and test a model or a scale model of the circuit. However, this procedure is time-consuming and expensive, and it limits freedom to examine new variations to the basic circuit. These limitations make the need for computational methods crucial since they can lower costs, reduce tube development time, and lessen limitations on novel designs. Computer simulation has been used to accurately obtain cold-test parameters for several slow-wave circuits. Although the helix slow-wave circuit remains the mainstay of the TWT industry because of its exceptionally wide bandwidth, until recently it has been impossible to accurately analyze a helical TWT using its exact dimensions because of the complexity of its geometrical structure. A new computer modeling technique developed at the NASA Lewis Research Center overcomes these difficulties. The MAFIA three-dimensional mesh for a C-band helix slow-wave circuit is shown.

The heavy atom microwave structure of 2-methyltetrahydrofuran

NASA Astrophysics Data System (ADS)

Van, Vinh; Stahl, Wolfgang; Nguyen, Ha Vinh Lam

2016-11-01

The rotational spectra of 2-methyltetrahydrofuran have been observed using a pulsed molecular beam Fourier transform microwave spectrometer operating in the frequency range 2-26.5 GHz. Conformational analysis using quantum chemical calculations yields two stable conformers; both of them possess an envelope structure. The conformational transformation can occur via two different transition states. The Cremer-Pople notation for five-membered rings is chosen for describing the conformations. Only one conformer with equatorial position of the methyl group is assigned in the experimental spectrum. The fits of its parent species, 13C- and 18O-isotopologues result in highly accurate molecular parameters, and enable the determination of a heavy atom rs structure using Kraitchman's equations. This experimentally determined structure is in excellent agreement with the structure calculated by anharmonic frequency calculations.

Nonlocal electrical detection of spin accumulation generated by anomalous Hall effect in mesoscopic N i81F e19 films

NASA Astrophysics Data System (ADS)

Qin, Chuan; Chen, Shuhan; Cai, Yunjiao; Kandaz, Fatih; Ji, Yi

2017-10-01

Spin accumulation generated by the anomalous Hall effect (AHE) in mesoscopic ferromagnetic N i81F e19 (permalloy, Py) films is detected electrically by a nonlocal method. The reciprocal phenomenon, the inverse spin Hall effect (ISHE), can also be generated and detected all electrically in the same structure. For accurate quantitative analysis, a series of nonlocal AHE/ISHE structures and supplementary structures are fabricated on each sample substrate to account for statistical variations and to accurately determine all essential physical parameters in situ. By exploring Py thicknesses of 4, 8, and 12 nm, the Py spin diffusion length λPy is found to be much shorter than the film thicknesses. The product of λPy and the Py spin Hall angle αSH is determined to be independent of thickness and resistivity: αSHλPy=(0.066 ±0.009 ) nm at 5 K and (0.041 ±0.010 )nm at 295 K. These values are comparable to those obtained from mesoscopic Pt films.

Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops

PubMed Central

Phan, Andy; Mailey, Katherine; Saeki, Jessica; Gu, Xiaobo

2017-01-01

Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites. PMID:28213527

A constrained reconstruction technique of hyperelasticity parameters for breast cancer assessment

NASA Astrophysics Data System (ADS)

Mehrabian, Hatef; Campbell, Gordon; Samani, Abbas

2010-12-01

In breast elastography, breast tissue usually undergoes large compression resulting in significant geometric and structural changes. This implies that breast elastography is associated with tissue nonlinear behavior. In this study, an elastography technique is presented and an inverse problem formulation is proposed to reconstruct parameters characterizing tissue hyperelasticity. Such parameters can potentially be used for tumor classification. This technique can also have other important clinical applications such as measuring normal tissue hyperelastic parameters in vivo. Such parameters are essential in planning and conducting computer-aided interventional procedures. The proposed parameter reconstruction technique uses a constrained iterative inversion; it can be viewed as an inverse problem. To solve this problem, we used a nonlinear finite element model corresponding to its forward problem. In this research, we applied Veronda-Westmann, Yeoh and polynomial models to model tissue hyperelasticity. To validate the proposed technique, we conducted studies involving numerical and tissue-mimicking phantoms. The numerical phantom consisted of a hemisphere connected to a cylinder, while we constructed the tissue-mimicking phantom from polyvinyl alcohol with freeze-thaw cycles that exhibits nonlinear mechanical behavior. Both phantoms consisted of three types of soft tissues which mimic adipose, fibroglandular tissue and a tumor. The results of the simulations and experiments show feasibility of accurate reconstruction of tumor tissue hyperelastic parameters using the proposed method. In the numerical phantom, all hyperelastic parameters corresponding to the three models were reconstructed with less than 2% error. With the tissue-mimicking phantom, we were able to reconstruct the ratio of the hyperelastic parameters reasonably accurately. Compared to the uniaxial test results, the average error of the ratios of the parameters reconstructed for inclusion to the middle and external layers were 13% and 9.6%, respectively. Given that the parameter ratios of the abnormal tissues to the normal ones range from three times to more than ten times, this accuracy is sufficient for tumor classification.

Bayesian approach to estimate AUC, partition coefficient and drug targeting index for studies with serial sacrifice design.

PubMed

Wang, Tianli; Baron, Kyle; Zhong, Wei; Brundage, Richard; Elmquist, William

2014-03-01

The current study presents a Bayesian approach to non-compartmental analysis (NCA), which provides the accurate and precise estimate of AUC 0 (∞) and any AUC 0 (∞) -based NCA parameter or derivation. In order to assess the performance of the proposed method, 1,000 simulated datasets were generated in different scenarios. A Bayesian method was used to estimate the tissue and plasma AUC 0 (∞) s and the tissue-to-plasma AUC 0 (∞) ratio. The posterior medians and the coverage of 95% credible intervals for the true parameter values were examined. The method was applied to laboratory data from a mice brain distribution study with serial sacrifice design for illustration. Bayesian NCA approach is accurate and precise in point estimation of the AUC 0 (∞) and the partition coefficient under a serial sacrifice design. It also provides a consistently good variance estimate, even considering the variability of the data and the physiological structure of the pharmacokinetic model. The application in the case study obtained a physiologically reasonable posterior distribution of AUC, with a posterior median close to the value estimated by classic Bailer-type methods. This Bayesian NCA approach for sparse data analysis provides statistical inference on the variability of AUC 0 (∞) -based parameters such as partition coefficient and drug targeting index, so that the comparison of these parameters following destructive sampling becomes statistically feasible.

Force-field parameters from the SAFT-γ equation of state for use in coarse-grained molecular simulations.

PubMed

Müller, Erich A; Jackson, George

2014-01-01

A description of fluid systems with molecular-based algebraic equations of state (EoSs) and by direct molecular simulation is common practice in chemical engineering and the physical sciences, but the two approaches are rarely closely coupled. The key for an integrated representation is through a well-defined force field and Hamiltonian at the molecular level. In developing coarse-grained intermolecular potential functions for the fluid state, one typically starts with a detailed, bottom-up quantum-mechanical or atomic-level description and then integrates out the unwanted degrees of freedom using a variety of techniques; an iterative heuristic simulation procedure is then used to refine the parameters of the model. By contrast, with a top-down technique, one can use an accurate EoS to link the macroscopic properties of the fluid and the force-field parameters. We discuss the latest developments in a top-down representation of fluids, with a particular focus on a group-contribution formulation of the statistical associating fluid theory (SAFT-γ). The accurate SAFT-γ EoS is used to estimate the parameters of the Mie force field, which can then be used with confidence in direct molecular simulations to obtain thermodynamic, structural, interfacial, and dynamical properties that are otherwise inaccessible from the EoS. This is exemplified for several prototypical fluids and mixtures, including carbon dioxide, hydrocarbons, perfluorohydrocarbons, and aqueous surfactants.

MIA-Clustering: a novel method for segmentation of paleontological material.

PubMed

Dunmore, Christopher J; Wollny, Gert; Skinner, Matthew M

2018-01-01

Paleontological research increasingly uses high-resolution micro-computed tomography (μCT) to study the inner architecture of modern and fossil bone material to answer important questions regarding vertebrate evolution. This non-destructive method allows for the measurement of otherwise inaccessible morphology. Digital measurement is predicated on the accurate segmentation of modern or fossilized bone from other structures imaged in μCT scans, as errors in segmentation can result in inaccurate calculations of structural parameters. Several approaches to image segmentation have been proposed with varying degrees of automation, ranging from completely manual segmentation, to the selection of input parameters required for computational algorithms. Many of these segmentation algorithms provide speed and reproducibility at the cost of flexibility that manual segmentation provides. In particular, the segmentation of modern and fossil bone in the presence of materials such as desiccated soft tissue, soil matrix or precipitated crystalline material can be difficult. Here we present a free open-source segmentation algorithm application capable of segmenting modern and fossil bone, which also reduces subjective user decisions to a minimum. We compare the effectiveness of this algorithm with another leading method by using both to measure the parameters of a known dimension reference object, as well as to segment an example problematic fossil scan. The results demonstrate that the medical image analysis-clustering method produces accurate segmentations and offers more flexibility than those of equivalent precision. Its free availability, flexibility to deal with non-bone inclusions and limited need for user input give it broad applicability in anthropological, anatomical, and paleontological contexts.

MyPMFs: a simple tool for creating statistical potentials to assess protein structural models.

PubMed

Postic, Guillaume; Hamelryck, Thomas; Chomilier, Jacques; Stratmann, Dirk

2018-05-29

Evaluating the model quality of protein structures that evolve in environments with particular physicochemical properties requires scoring functions that are adapted to their specific residue compositions and/or structural characteristics. Thus, computational methods developed for structures from the cytosol cannot work properly on membrane or secreted proteins. Here, we present MyPMFs, an easy-to-use tool that allows users to train statistical potentials of mean force (PMFs) on the protein structures of their choice, with all parameters being adjustable. We demonstrate its use by creating an accurate statistical potential for transmembrane protein domains. We also show its usefulness to study the influence of the physical environment on residue interactions within protein structures. Our open-source software is freely available for download at https://github.com/bibip-impmc/mypmfs. Copyright © 2018. Published by Elsevier B.V.

Confocal arthroscopy-based patient-specific constitutive models of cartilaginous tissues - II: prediction of reaction force history of meniscal cartilage specimens.

PubMed

Taylor, Zeike A; Kirk, Thomas B; Miller, Karol

2007-10-01

The theoretical framework developed in a companion paper (Part I) is used to derive estimates of mechanical response of two meniscal cartilage specimens. The previously developed framework consisted of a constitutive model capable of incorporating confocal image-derived tissue microstructural data. In the present paper (Part II) fibre and matrix constitutive parameters are first estimated from mechanical testing of a batch of specimens similar to, but independent from those under consideration. Image analysis techniques which allow estimation of tissue microstructural parameters form confocal images are presented. The constitutive model and image-derived structural parameters are then used to predict the reaction force history of the two meniscal specimens subjected to partially confined compression. The predictions are made on the basis of the specimens' individual structural condition as assessed by confocal microscopy and involve no tuning of material parameters. Although the model does not reproduce all features of the experimental curves, as an unfitted estimate of mechanical response the prediction is quite accurate. In light of the obtained results it is judged that more general non-invasive estimation of tissue mechanical properties is possible using the developed framework.

Robust simulation of buckled structures using reduced order modeling

NASA Astrophysics Data System (ADS)

Wiebe, R.; Perez, R. A.; Spottswood, S. M.

2016-09-01

Lightweight metallic structures are a mainstay in aerospace engineering. For these structures, stability, rather than strength, is often the critical limit state in design. For example, buckling of panels and stiffeners may occur during emergency high-g maneuvers, while in supersonic and hypersonic aircraft, it may be induced by thermal stresses. The longstanding solution to such challenges was to increase the sizing of the structural members, which is counter to the ever present need to minimize weight for reasons of efficiency and performance. In this work we present some recent results in the area of reduced order modeling of post- buckled thin beams. A thorough parametric study of the response of a beam to changing harmonic loading parameters, which is useful in exposing complex phenomena and exercising numerical models, is presented. Two error metrics that use but require no time stepping of a (computationally expensive) truth model are also introduced. The error metrics are applied to several interesting forcing parameter cases identified from the parametric study and are shown to yield useful information about the quality of a candidate reduced order model. Parametric studies, especially when considering forcing and structural geometry parameters, coupled environments, and uncertainties would be computationally intractable with finite element models. The goal is to make rapid simulation of complex nonlinear dynamic behavior possible for distributed systems via fast and accurate reduced order models. This ability is crucial in allowing designers to rigorously probe the robustness of their designs to account for variations in loading, structural imperfections, and other uncertainties.

Uniscale multi-view registration using double dog-leg method

NASA Astrophysics Data System (ADS)

Chen, Chao-I.; Sargent, Dusty; Tsai, Chang-Ming; Wang, Yuan-Fang; Koppel, Dan

2009-02-01

3D computer models of body anatomy can have many uses in medical research and clinical practices. This paper describes a robust method that uses videos of body anatomy to construct multiple, partial 3D structures and then fuse them to form a larger, more complete computer model using the structure-from-motion framework. We employ the Double Dog-Leg (DDL) method, a trust-region based nonlinear optimization method, to jointly optimize the camera motion parameters (rotation and translation) and determine a global scale that all partial 3D structures should agree upon. These optimized motion parameters are used for constructing local structures, and the global scale is essential for multi-view registration after all these partial structures are built. In order to provide a good initial guess of the camera movement parameters and outlier free 2D point correspondences for DDL, we also propose a two-stage scheme where multi-RANSAC with a normalized eight-point algorithm is first performed and then a few iterations of an over-determined five-point algorithm is used to polish the results. Our experimental results using colonoscopy video show that the proposed scheme always produces more accurate outputs than the standard RANSAC scheme. Furthermore, since we have obtained many reliable point correspondences, time-consuming and error-prone registration methods like the iterative closest points (ICP) based algorithms can be replaced by a simple rigid-body transformation solver when merging partial structures into a larger model.

Interpretation of Source Parameters from Total Gradient of Gravity and Magnetic Anomalies Caused by Thin Dyke using Nonlinear Global Optimization Technique

NASA Astrophysics Data System (ADS)

Biswas, A.

2016-12-01

A proficient way to deal with appraisal model parameters from total gradient of gravity and magnetic data in light of Very Fast Simulated Annealing (VFSA) has been exhibited. This is the first run through of applying VFSA in deciphering total gradient of potential field information with another detailing estimation brought on because of detached causative sources installed in the subsurface. The model parameters translated here are the amplitude coefficient (k), accurate origin of causative source (x0) depth (z0) and the shape factor (q). The outcome of VFSA improvement demonstrates that it can exceptionally decide all the model parameters when shape variable is fixed. The model parameters assessed by the present strategy, for the most part the shape and depth of the covered structures was observed to be in astounding concurrence with the genuine parameters. The technique has likewise the capability of dodging very uproarious information focuses and enhances the understanding results. Investigation of Histogram and cross-plot examination likewise proposes the translation inside the assessed ambiguity. Inversion of noise-free and noisy synthetic data information for single structures and field information shows the viability of the methodology. The procedure has been carefully and adequately connected to genuine field cases (Leona Anomaly, Senegal for gravity and Pima copper deposit, USA for magnetic) with the nearness of mineral bodies. The present technique can be to a great degree material for mineral investigation or ore bodies of dyke-like structure rooted in the shallow and more deep subsurface. The calculation time for the entire procedure is short.

Linear parameter varying identification of ankle joint intrinsic stiffness during imposed walking movements.

PubMed

Sobhani Tehrani, Ehsan; Jalaleddini, Kian; Kearney, Robert E

2013-01-01

This paper describes a novel model structure and identification method for the time-varying, intrinsic stiffness of human ankle joint during imposed walking (IW) movements. The model structure is based on the superposition of a large signal, linear, time-invariant (LTI) model and a small signal linear-parameter varying (LPV) model. The methodology is based on a two-step algorithm; the LTI model is first estimated using data from an unperturbed IW trial. Then, the LPV model is identified using data from a perturbed IW trial with the output predictions of the LTI model removed from the measured torque. Experimental results demonstrate that the method accurately tracks the continuous-time variation of normal ankle intrinsic stiffness when the joint position changes during the IW movement. Intrinsic stiffness gain decreases from full plantarflexion to near the mid-point of plantarflexion and then increases substantially as the ankle is dosriflexed.

Precisely Tailored DNA Nanostructures and their Theranostic Applications.

PubMed

Zhu, Bing; Wang, Lihua; Li, Jiang; Fan, Chunhai

2017-12-01

A critical challenge in nanotechnology is the limited precision and controllability of the structural parameters, which brings about concerns in uniformity, reproducibility and performance. Self-assembled DNA nanostructures, as a newly emerged type of nano-biomaterials, possess low-nanometer precision, excellent programmability and addressability. They can precisely arrange various molecules and materials to form spatially ordered complex, resulting in unambiguous physical or chemical properties. Because of these, DNA nanostructures have shown great promise in numerous biomedical theranostic applications. In this account, we briefly review the history and advances on construction of DNA nanoarchitectures and superstructures with accurate structural parameters. We focus on recent progress in exploiting these DNA nanostructures as platforms for quantitative biosensing, intracellular diagnosis, imaging, and smart drug delivery. We also discuss key challenges in practical applications. © 2017 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

W-band EPR of vanadyl complexes aggregates on the surface of Al2O3

NASA Astrophysics Data System (ADS)

Mamin, G.; Gafurov, M.; Galukhin, A.; Gracheva, I.; Murzakhanov, F.; Rodionov, A.; Orlinskii, S.

2018-05-01

Structural characterization of metalloporphyrins, asphaltenes and their aggregates in complex systems such as native hydrocarbons is in the focus of scientific and industrial interests since many years. We present W-band (95 GHz) electron paramagnetic resonance (EPR) study in the magnetic field of about 3.4 T and temperature of 100 K for Karmalinskoe oil, asphaltens and asphaltenes deposited on the surface of Al2O3. Features of the obtained spectra are described. Shift to the higher frequencies allows to separate spectrally the contributions from paramagnetic complexes of different origin and define the EPR parameters more accurately comparing to the conventional X-band (9 GHz). Changes of the EPR parameters are tracked. We suggest that the proposed approach can be used for the investigation of structure of vanadyl complexes aggregates in crude oil and their fractions.

Evaluating radiative transfer schemes treatment of vegetation canopy architecture in land surface models

NASA Astrophysics Data System (ADS)

Braghiere, Renato; Quaife, Tristan; Black, Emily

2016-04-01

Incoming shortwave radiation is the primary source of energy driving the majority of the Earth's climate system. The partitioning of shortwave radiation by vegetation into absorbed, reflected, and transmitted terms is important for most of biogeophysical processes, including leaf temperature changes and photosynthesis, and it is currently calculated by most of land surface schemes (LSS) of climate and/or numerical weather prediction models. The most commonly used radiative transfer scheme in LSS is the two-stream approximation, however it does not explicitly account for vegetation architectural effects on shortwave radiation partitioning. Detailed three-dimensional (3D) canopy radiative transfer schemes have been developed, but they are too computationally expensive to address large-scale related studies over long time periods. Using a straightforward one-dimensional (1D) parameterisation proposed by Pinty et al. (2006), we modified a two-stream radiative transfer scheme by including a simple function of Sun zenith angle, so-called "structure factor", which does not require an explicit description and understanding of the complex phenomena arising from the presence of vegetation heterogeneous architecture, and it guarantees accurate simulations of the radiative balance consistently with 3D representations. In order to evaluate the ability of the proposed parameterisation in accurately represent the radiative balance of more complex 3D schemes, a comparison between the modified two-stream approximation with the "structure factor" parameterisation and state-of-art 3D radiative transfer schemes was conducted, following a set of virtual scenarios described in the RAMI4PILPS experiment. These experiments have been evaluating the radiative balance of several models under perfectly controlled conditions in order to eliminate uncertainties arising from an incomplete or erroneous knowledge of the structural, spectral and illumination related canopy characteristics typical of model comparisons with in-situ observations. The structure factor parameters were obtained for each canopy structure through the inversion against direct and diffuse fraction of absorbed photosynthetically active radiation (fAPAR), and albedo PAR. Overall, the modified two-stream approximation consistently showed a good agreement with the RAMI4PILPS reference values under direct and diffuse illumination conditions. It is an efficient and accurate tool to derive PAR absorptance and reflectance for scenarios with different canopy densities, leaf densities and soil background albedos, with especial attention to brighter backgrounds, i.e., snowy. The major difficulty of its applicability in the real world is to acquire the parameterisation parameters from in-situ observations. The derivation of parameters from Digital Hemispherical Photographs (DHP) is highly promising at forest stands scales. DHP provide a permanent record and are a valuable information source for position, size, density, and distribution of canopy gaps. The modified two-stream approximation parameters were derived from gap probability data extracted from DHP obtained in a woody savannah in California, USA. Values of fAPAR and albedo PAR were evaluated against a tree-based vegetation canopy model, MAESPA, which used airborne LiDAR data to define the individual-tree locations, and extract structural information such as tree height and crown diameter. The parameterisation improved the performance of a two-stream approximation by making it achieves comparable results to complex 3D model calculations under observed conditions.

Using radiance predicted by the P3 approximation in a spherical geometry to predict tissue optical properties

NASA Astrophysics Data System (ADS)

Dickey, Dwayne J.; Moore, Ronald B.; Tulip, John

2001-01-01

For photodynamic therapy of solid tumors, such as prostatic carcinoma, to be achieved, an accurate model to predict tissue parameters and light dose must be found. Presently, most analytical light dosimetry models are fluence based and are not clinically viable for tissue characterization. Other methods of predicting optical properties, such as Monet Carlo, are accurate but far too time consuming for clinical application. However, radiance predicted by the P3-Approximation, an anaylitical solution to the transport equation, may be a viable and accurate alternative. The P3-Approximation accurately predicts optical parameters in intralipid/methylene blue based phantoms in a spherical geometry. The optical parameters furnished by the radiance, when introduced into fluence predicted by both P3- Approximation and Grosjean Theory, correlate well with experimental data. The P3-Approximation also predicts the optical properties of prostate tissue, agreeing with documented optical parameters. The P3-Approximation could be the clinical tool necessary to facilitate PDT of solid tumors because of the limited number of invasive measurements required and the speed in which accurate calculations can be performed.

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.

Comparing Molecular Dynamics Force Fields in the Essential Subspace

PubMed Central

Gomez-Puertas, Paulino; Boomsma, Wouter; Lindorff-Larsen, Kresten

2015-01-01

The continued development and utility of molecular dynamics simulations requires improvements in both the physical models used (force fields) and in our ability to sample the Boltzmann distribution of these models. Recent developments in both areas have made available multi-microsecond simulations of two proteins, ubiquitin and Protein G, using a number of different force fields. Although these force fields mostly share a common mathematical form, they differ in their parameters and in the philosophy by which these were derived, and previous analyses showed varying levels of agreement with experimental NMR data. To complement the comparison to experiments, we have performed a structural analysis of and comparison between these simulations, thereby providing insight into the relationship between force-field parameterization, the resulting ensemble of conformations and the agreement with experiments. In particular, our results show that, at a coarse level, many of the motional properties are preserved across several, though not all, force fields. At a finer level of detail, however, there are distinct differences in both the structure and dynamics of the two proteins, which can, together with comparison with experimental data, help to select force fields for simulations of proteins. A noteworthy observation is that force fields that have been reparameterized and improved to provide a more accurate energetic description of the balance between helical and coil structures are difficult to distinguish from their “unbalanced” counterparts in these simulations. This observation implies that simulations of stable, folded proteins, even those reaching 10 microseconds in length, may provide relatively little information that can be used to modify torsion parameters to achieve an accurate balance between different secondary structural elements. PMID:25811178

Effect of Discontinuities and Uncertainties on the Response and Failure of Composite Structures

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.; Perry, Ferman W.; Poteat, Marcia M. (Technical Monitor)

2000-01-01

The overall goal of this research was to assess the effect of discontinuities and uncertainties on the nonlinear response and failure of composite structures subjected to combined mechanical and thermal loads. The four key elements of the study were: (1) development of simple and efficient procedures for the accurate determination of transverse shear and transverse normal stresses in structural sandwiches as well as in unstiffened and stiffened composite panels and shells; (2) study the effects of transverse stresses on the response, damage initiation and propagation in composite and sandwich structures; (3) use of hierarchical sensitivity coefficients to identify the major parameters that affect the response and damage in each of the different levels in the hierarchy (micro-mechanical, layer, panel, subcomponent and component levels); and (4) application of fuzzy set techniques to identify the range and variation of possible responses. The computational models developed were used in conjunction with experiments, to understand the physical phenomena associated with the nonlinear response and failure of composite and sandwich structures. A toolkit was developed for use in conjunction with deterministic analysis programs to help the designer in assessing the effect of uncertainties in the different computational model parameters on the variability of the response quantities.

Voxel-Based 3-D Tree Modeling from Lidar Images for Extracting Tree Structual Information

NASA Astrophysics Data System (ADS)

Hosoi, F.

2014-12-01

Recently, lidar (light detection and ranging) has been used to extracting tree structural information. Portable scanning lidar systems can capture the complex shape of individual trees as a 3-D point-cloud image. 3-D tree models reproduced from the lidar-derived 3-D image can be used to estimate tree structural parameters. We have proposed the voxel-based 3-D modeling for extracting tree structural parameters. One of the tree parameters derived from the voxel modeling is leaf area density (LAD). We refer to the method as the voxel-based canopy profiling (VCP) method. In this method, several measurement points surrounding the canopy and optimally inclined laser beams are adopted for full laser beam illumination of whole canopy up to the internal. From obtained lidar image, the 3-D information is reproduced as the voxel attributes in the 3-D voxel array. Based on the voxel attributes, contact frequency of laser beams on leaves is computed and LAD in each horizontal layer is obtained. This method offered accurate LAD estimation for individual trees and woody canopy trees. For more accurate LAD estimation, the voxel model was constructed by combining airborne and portable ground-based lidar data. The profiles obtained by the two types of lidar complemented each other, thus eliminating blind regions and yielding more accurate LAD profiles than could be obtained by using each type of lidar alone. Based on the estimation results, we proposed an index named laser beam coverage index, Ω, which relates to the lidar's laser beam settings and a laser beam attenuation factor. It was shown that this index can be used for adjusting measurement set-up of lidar systems and also used for explaining the LAD estimation error using different types of lidar systems. Moreover, we proposed a method to estimate woody material volume as another application of the voxel tree modeling. In this method, voxel solid model of a target tree was produced from the lidar image, which is composed of consecutive voxels that filled the outer surface and the interior of the stem and large branches. From the model, the woody material volume of any part of the target tree can be directly calculated easily by counting the number of corresponding voxels and multiplying the result by the per-voxel volume.

Development of a copula-based particle filter (CopPF) approach for hydrologic data assimilation under consideration of parameter interdependence

NASA Astrophysics Data System (ADS)

Fan, Y. R.; Huang, G. H.; Baetz, B. W.; Li, Y. P.; Huang, K.

2017-06-01

In this study, a copula-based particle filter (CopPF) approach was developed for sequential hydrological data assimilation by considering parameter correlation structures. In CopPF, multivariate copulas are proposed to reflect parameter interdependence before the resampling procedure with new particles then being sampled from the obtained copulas. Such a process can overcome both particle degeneration and sample impoverishment. The applicability of CopPF is illustrated with three case studies using a two-parameter simplified model and two conceptual hydrologic models. The results for the simplified model indicate that model parameters are highly correlated in the data assimilation process, suggesting a demand for full description of their dependence structure. Synthetic experiments on hydrologic data assimilation indicate that CopPF can rejuvenate particle evolution in large spaces and thus achieve good performances with low sample size scenarios. The applicability of CopPF is further illustrated through two real-case studies. It is shown that, compared with traditional particle filter (PF) and particle Markov chain Monte Carlo (PMCMC) approaches, the proposed method can provide more accurate results for both deterministic and probabilistic prediction with a sample size of 100. Furthermore, the sample size would not significantly influence the performance of CopPF. Also, the copula resampling approach dominates parameter evolution in CopPF, with more than 50% of particles sampled by copulas in most sample size scenarios.

Parameter space of experimental chaotic circuits with high-precision control parameters.

PubMed

de Sousa, Francisco F G; Rubinger, Rero M; Sartorelli, José C; Albuquerque, Holokx A; Baptista, Murilo S

2016-08-01

We report high-resolution measurements that experimentally confirm a spiral cascade structure and a scaling relationship of shrimps in the Chua's circuit. Circuits constructed using this component allow for a comprehensive characterization of the circuit behaviors through high resolution parameter spaces. To illustrate the power of our technological development for the creation and the study of chaotic circuits, we constructed a Chua circuit and study its high resolution parameter space. The reliability and stability of the designed component allowed us to obtain data for long periods of time (∼21 weeks), a data set from which an accurate estimation of Lyapunov exponents for the circuit characterization was possible. Moreover, this data, rigorously characterized by the Lyapunov exponents, allows us to reassure experimentally that the shrimps, stable islands embedded in a domain of chaos in the parameter spaces, can be observed in the laboratory. Finally, we confirm that their sizes decay exponentially with the period of the attractor, a result expected to be found in maps of the quadratic family.

Hybrid density functional theory band structure engineering in hematite

NASA Astrophysics Data System (ADS)

Pozun, Zachary D.; Henkelman, Graeme

2011-06-01

We present a hybrid density functional theory (DFT) study of doping effects in α-Fe2O3, hematite. Standard DFT underestimates the band gap by roughly 75% and incorrectly identifies hematite as a Mott-Hubbard insulator. Hybrid DFT accurately predicts the proper structural, magnetic, and electronic properties of hematite and, unlike the DFT+U method, does not contain d-electron specific empirical parameters. We find that using a screened functional that smoothly transitions from 12% exact exchange at short ranges to standard DFT at long range accurately reproduces the experimental band gap and other material properties. We then show that the antiferromagnetic symmetry in the pure α-Fe2O3 crystal is broken by all dopants and that the ligand field theory correctly predicts local magnetic moments on the dopants. We characterize the resulting band gaps for hematite doped by transition metals and the p-block post-transition metals. The specific case of Pd doping is investigated in order to correlate calculated doping energies and optical properties with experimentally observed photocatalytic behavior.

Bayesian calibration for electrochemical thermal model of lithium-ion cells

NASA Astrophysics Data System (ADS)

Tagade, Piyush; Hariharan, Krishnan S.; Basu, Suman; Verma, Mohan Kumar Singh; Kolake, Subramanya Mayya; Song, Taewon; Oh, Dukjin; Yeo, Taejung; Doo, Seokgwang

2016-07-01

Pseudo-two dimensional electrochemical thermal (P2D-ECT) model contains many parameters that are difficult to evaluate experimentally. Estimation of these model parameters is challenging due to computational cost and the transient model. Due to lack of complete physical understanding, this issue gets aggravated at extreme conditions like low temperature (LT) operations. This paper presents a Bayesian calibration framework for estimation of the P2D-ECT model parameters. The framework uses a matrix variate Gaussian process representation to obtain a computationally tractable formulation for calibration of the transient model. Performance of the framework is investigated for calibration of the P2D-ECT model across a range of temperatures (333 Ksbnd 263 K) and operating protocols. In the absence of complete physical understanding, the framework also quantifies structural uncertainty in the calibrated model. This information is used by the framework to test validity of the new physical phenomena before incorporation in the model. This capability is demonstrated by introducing temperature dependence on Bruggeman's coefficient and lithium plating formation at LT. With the incorporation of new physics, the calibrated P2D-ECT model accurately predicts the cell voltage with high confidence. The accurate predictions are used to obtain new insights into the low temperature lithium ion cell behavior.

Self-Learning Variable Structure Control for a Class of Sensor-Actuator Systems

PubMed Central

Chen, Sanfeng; Li, Shuai; Liu, Bo; Lou, Yuesheng; Liang, Yongsheng

2012-01-01

Variable structure strategy is widely used for the control of sensor-actuator systems modeled by Euler-Lagrange equations. However, accurate knowledge on the model structure and model parameters are often required for the control design. In this paper, we consider model-free variable structure control of a class of sensor-actuator systems, where only the online input and output of the system are available while the mathematic model of the system is unknown. The problem is formulated from an optimal control perspective and the implicit form of the control law are analytically obtained by using the principle of optimality. The control law and the optimal cost function are explicitly solved iteratively. Simulations demonstrate the effectiveness and the efficiency of the proposed method. PMID:22778633

A Comparison of Three-Dimensional Simulations of Traveling-Wave Tube Cold-Test Characteristics Using CST MICROWAVE STUDIO and MAFIA

NASA Technical Reports Server (NTRS)

Chevalier, C. T.; Herrmann, K. A.; Kory, C. L.; Wilson, J. D.; Cross, A. W.; Williams, W. D. (Technical Monitor)

2001-01-01

Previously, it was shown that MAFIA (solutions of Maxwell's equations by the Finite Integration Algorithm), a three-dimensional simulation code, can be used to produce accurate cold-test characteristics including frequency-phase dispersion, interaction impedance, and attenuation for traveling-wave tube (TWT) slow-wave structures. In an effort to improve user-friendliness and simulation time, a model was developed to compute the cold-test parameters using the electromagnetic field simulation software package CST MICROWAVE STUDIO (MWS). Cold-test parameters were calculated for several slow-wave circuits including a ferruled coupled-cavity, a folded waveguide, and a novel finned-ladder circuit using both MWS and MAFIA. Comparisons indicate that MWS provides more accurate cold-test data with significantly reduced simulation times. Both MAFIA and MWS are based on the finite integration (FI) method; however, MWS has several advantages over MAFIA. First, it has a Windows based interface for PC operation, making it very user-friendly, whereas MAFIA is UNIX based. MWS uses a new Perfect Boundary Approximation (PBA), which increases the accuracy of the simulations by avoiding stair step approximations associated with MAFIA's representation of structures. Finally, MWS includes a Visual Basic for Applications (VBA) compatible macro language that enables the simulation process to be automated and allows for the optimization of user-defined goal functions, such as interaction impedance.

Implications of asymptomatic carriers for infectious disease transmission and control.

PubMed

Chisholm, Rebecca H; Campbell, Patricia T; Wu, Yue; Tong, Steven Y C; McVernon, Jodie; Geard, Nicholas

2018-02-01

For infectious pathogens such as Staphylococcus aureus and Streptococcus pneumoniae , some hosts may carry the pathogen and transmit it to others, yet display no symptoms themselves. These asymptomatic carriers contribute to the spread of disease but go largely undetected and can therefore undermine efforts to control transmission. Understanding the natural history of carriage and its relationship to disease is important for the design of effective interventions to control transmission. Mathematical models of infectious diseases are frequently used to inform decisions about control and should therefore accurately capture the role played by asymptomatic carriers. In practice, incorporating asymptomatic carriers into models is challenging due to the sparsity of direct evidence. This absence of data leads to uncertainty in estimates of model parameters and, more fundamentally, in the selection of an appropriate model structure. To assess the implications of this uncertainty, we systematically reviewed published models of carriage and propose a new model of disease transmission with asymptomatic carriage. Analysis of our model shows how different assumptions about the role of asymptomatic carriers can lead to different conclusions about the transmission and control of disease. Critically, selecting an inappropriate model structure, even when parameters are correctly estimated, may lead to over- or under-estimates of intervention effectiveness. Our results provide a more complete understanding of the role of asymptomatic carriers in transmission and highlight the importance of accurately incorporating carriers into models used to make decisions about disease control.

Accurate and Fully Automatic Hippocampus Segmentation Using Subject-Specific 3D Optimal Local Maps Into a Hybrid Active Contour Model

PubMed Central

Gkontra, Polyxeni; Daras, Petros; Maglaveras, Nicos

2014-01-01

Assessing the structural integrity of the hippocampus (HC) is an essential step toward prevention, diagnosis, and follow-up of various brain disorders due to the implication of the structural changes of the HC in those disorders. In this respect, the development of automatic segmentation methods that can accurately, reliably, and reproducibly segment the HC has attracted considerable attention over the past decades. This paper presents an innovative 3-D fully automatic method to be used on top of the multiatlas concept for the HC segmentation. The method is based on a subject-specific set of 3-D optimal local maps (OLMs) that locally control the influence of each energy term of a hybrid active contour model (ACM). The complete set of the OLMs for a set of training images is defined simultaneously via an optimization scheme. At the same time, the optimal ACM parameters are also calculated. Therefore, heuristic parameter fine-tuning is not required. Training OLMs are subsequently combined, by applying an extended multiatlas concept, to produce the OLMs that are anatomically more suitable to the test image. The proposed algorithm was tested on three different and publicly available data sets. Its accuracy was compared with that of state-of-the-art methods demonstrating the efficacy and robustness of the proposed method. PMID:27170866

Mapping the structural order of laser-induced periodic surface structures in thin polymer films by microfocus beam grazing incidence small-angle X-ray scattering.

PubMed

Martín-Fabiani, Ignacio; Rebollar, Esther; García-Gutiérrez, Mari Cruz; Rueda, Daniel R; Castillejo, Marta; Ezquerra, Tiberio A

2015-02-11

In this work we present an accurate mapping of the structural order of laser-induced periodic surface structures (LIPSS) in spin-coated thin polymer films, via a microfocus beam grazing incidence small-angle X-ray scattering (μGISAXS) scan, GISAXS modeling, and atomic force microscopy imaging all along the scanned area. This combined study has allowed the evaluation of the effects on LIPSS formation due to nonhomogeneous spatial distribution of the laser pulse energy, mapping with micrometric resolution the evolution of the period and degree of structural order of LIPSS across the laser beam diameter in a direction perpendicular to the polarization vector. The experiments presented go one step further toward controlling nanostructure formation in LIPSS through a deep understanding of the parameters that influence this process.

Prospective regularization design in prior-image-based reconstruction

NASA Astrophysics Data System (ADS)

Dang, Hao; Siewerdsen, Jeffrey H.; Webster Stayman, J.

2015-12-01

Prior-image-based reconstruction (PIBR) methods leveraging patient-specific anatomical information from previous imaging studies and/or sequences have demonstrated dramatic improvements in dose utilization and image quality for low-fidelity data. However, a proper balance of information from the prior images and information from the measurements is required (e.g. through careful tuning of regularization parameters). Inappropriate selection of reconstruction parameters can lead to detrimental effects including false structures and failure to improve image quality. Traditional methods based on heuristics are subject to error and sub-optimal solutions, while exhaustive searches require a large number of computationally intensive image reconstructions. In this work, we propose a novel method that prospectively estimates the optimal amount of prior image information for accurate admission of specific anatomical changes in PIBR without performing full image reconstructions. This method leverages an analytical approximation to the implicitly defined PIBR estimator, and introduces a predictive performance metric leveraging this analytical form and knowledge of a particular presumed anatomical change whose accurate reconstruction is sought. Additionally, since model-based PIBR approaches tend to be space-variant, a spatially varying prior image strength map is proposed to optimally admit changes everywhere in the image (eliminating the need to know change locations a priori). Studies were conducted in both an ellipse phantom and a realistic thorax phantom emulating a lung nodule surveillance scenario. The proposed method demonstrated accurate estimation of the optimal prior image strength while achieving a substantial computational speedup (about a factor of 20) compared to traditional exhaustive search. Moreover, the use of the proposed prior strength map in PIBR demonstrated accurate reconstruction of anatomical changes without foreknowledge of change locations in phantoms where the optimal parameters vary spatially by an order of magnitude or more. In a series of studies designed to explore potential unknowns associated with accurate PIBR, optimal prior image strength was found to vary with attenuation differences associated with anatomical change but exhibited only small variations as a function of the shape and size of the change. The results suggest that, given a target change attenuation, prospective patient-, change-, and data-specific customization of the prior image strength can be performed to ensure reliable reconstruction of specific anatomical changes.

Splitting of the neutral mechanical plane depends on the length of the multi-layer structure of flexible electronics.

PubMed

Li, Shuang; Su, Yewang; Li, Rui

2016-06-01

Multi-layer structures with soft (compliant) interlayers have been widely used in flexible electronics and photonics as an effective design for reducing interactions among the hard (stiff) layers and thus avoiding the premature failure of an entire device. The analytic model for bending of such a structure has not been well established due to its complex mechanical behaviour. Here, we present a rational analytic model, without any parameter fitting, to study the bending of a multi-layer structure on a cylinder, which is often regarded as an important approach to mechanical reliability testing of flexible electronics and photonics. For the first time, our model quantitatively reveals that, as the key for accurate strain control, the splitting of the neutral mechanical plane depends not only on the relative thickness of the middle layer, but also on the length-to-thickness ratio of the multi-layer structure. The model accurately captures the key quantities, including the axial strains in the top and bottom layers, the shear strain in the middle layer and the locations of the neutral mechanical planes of the top and bottom layers. The effects of the length of the multi-layer and the thickness of the middle layer are elaborated. This work is very useful for the design of multi-layer structure-based flexible electronics and photonics.

Splitting of the neutral mechanical plane depends on the length of the multi-layer structure of flexible electronics

PubMed Central

Li, Shuang; Li, Rui

2016-01-01

Multi-layer structures with soft (compliant) interlayers have been widely used in flexible electronics and photonics as an effective design for reducing interactions among the hard (stiff) layers and thus avoiding the premature failure of an entire device. The analytic model for bending of such a structure has not been well established due to its complex mechanical behaviour. Here, we present a rational analytic model, without any parameter fitting, to study the bending of a multi-layer structure on a cylinder, which is often regarded as an important approach to mechanical reliability testing of flexible electronics and photonics. For the first time, our model quantitatively reveals that, as the key for accurate strain control, the splitting of the neutral mechanical plane depends not only on the relative thickness of the middle layer, but also on the length-to-thickness ratio of the multi-layer structure. The model accurately captures the key quantities, including the axial strains in the top and bottom layers, the shear strain in the middle layer and the locations of the neutral mechanical planes of the top and bottom layers. The effects of the length of the multi-layer and the thickness of the middle layer are elaborated. This work is very useful for the design of multi-layer structure-based flexible electronics and photonics. PMID:27436977

Dynamics of water confined in lyotropic liquid crystals: Molecular dynamics simulations of the dynamic structure factor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mantha, Sriteja; Yethiraj, Arun

2016-02-24

The properties of water under confinement are of practical and fundamental interest. Here in this work we study the properties of water in the self-assembled lyotropic phases of gemini surfactants with a focus on testing the standard analysis of quasi-elastic neutron scattering (QENS) experiments. In QENS experiments the dynamic structure factor is measured and fit to models to extract the translational diffusion constant, D T , and rotational relaxation time, τ R. We test this procedure by using simulation results for the dynamic structure factor, extracting the dynamic parameters from the fit as is typically done in experiments, and comparingmore » the values to those directly measured in the simulations. We find that the decoupling approximation, where the intermediate scattering function is assumed to be a product of translational and rotational contributions, is quite accurate. The jump-diffusion and isotropic rotation models, however, are not accurate when the degree of confinement is high. In particular, the exponential approximations for the intermediate scattering function fail for highly confined water and the values of D T and τ R can differ from the measured value by as much as a factor of two. Other models have more fit parameters, however, and with the range of energies and wave-vectors accessible to QENS, the typical analysis appears to be the best choice. In the most confined lamellar phase, the dynamics are sufficiently slow that QENS does not access a large enough time scale and neutron spin echo measurements would be a valuable technique in addition to QENS.« less

Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores.

PubMed

Wells, David B; Bhattacharya, Swati; Carr, Rogan; Maffeo, Christopher; Ho, Anthony; Comer, Jeffrey; Aksimentiev, Aleksei

2012-01-01

Molecular dynamics (MD) simulations have become a standard method for the rational design and interpretation of experimental studies of DNA translocation through nanopores. The MD method, however, offers a multitude of algorithms, parameters, and other protocol choices that can affect the accuracy of the resulting data as well as computational efficiency. In this chapter, we examine the most popular choices offered by the MD method, seeking an optimal set of parameters that enable the most computationally efficient and accurate simulations of DNA and ion transport through biological nanopores. In particular, we examine the influence of short-range cutoff, integration timestep and force field parameters on the temperature and concentration dependence of bulk ion conductivity, ion pairing, ion solvation energy, DNA structure, DNA-ion interactions, and the ionic current through a nanopore.

Bayesian estimation of dynamic matching function for U-V analysis in Japan

NASA Astrophysics Data System (ADS)

Kyo, Koki; Noda, Hideo; Kitagawa, Genshiro

2012-05-01

In this paper we propose a Bayesian method for analyzing unemployment dynamics. We derive a Beveridge curve for unemployment and vacancy (U-V) analysis from a Bayesian model based on a labor market matching function. In our framework, the efficiency of matching and the elasticities of new hiring with respect to unemployment and vacancy are regarded as time varying parameters. To construct a flexible model and obtain reasonable estimates in an underdetermined estimation problem, we treat the time varying parameters as random variables and introduce smoothness priors. The model is then described in a state space representation, enabling the parameter estimation to be carried out using Kalman filter and fixed interval smoothing. In such a representation, dynamic features of the cyclic unemployment rate and the structural-frictional unemployment rate can be accurately captured.

Residual Stress Measurement and Calibration for A7N01 Aluminum Alloy Welded Joints by Using Longitudinal Critically Refracted ( LCR) Wave Transmission Method

NASA Astrophysics Data System (ADS)

Zhu, Qimeng; Chen, Jia; Gou, Guoqing; Chen, Hui; Li, Peng; Gao, W.

2016-10-01

Residual stress measurement and control are highly important for the safety of structures of high-speed trains, which is critical for the structure design. The longitudinal critically refracted wave technology is the most widely used method in measuring residual stress with ultrasonic method, but its accuracy is strongly related to the test parameters, namely the flight time at the free-stress condition ( t 0), stress coefficient ( K), and initial stress (σ0) of the measured materials. The difference of microstructure in the weld zone, heat affected zone, and base metal (BM) results in the divergence of experimental parameters. However, the majority of researchers use the BM parameters to determine the residual stress in other zones and ignore the initial stress (σ0) in calibration samples. Therefore, the measured residual stress in different zones is often high in errors and may result in the miscalculation of the safe design of important structures. A serious problem in the ultrasonic estimation of residual stresses requires separation between the microstructure and the acoustoelastic effects. In this paper, the effects of initial stress and microstructure on stress coefficient K and flight time t 0 at free-stress conditions have been studied. The residual stress with or without different corrections was investigated. The results indicated that the residual stresses obtained with correction are more accurate for structure design.

Nonlinear finite element model updating for damage identification of civil structures using batch Bayesian estimation

NASA Astrophysics Data System (ADS)

Ebrahimian, Hamed; Astroza, Rodrigo; Conte, Joel P.; de Callafon, Raymond A.

2017-02-01

This paper presents a framework for structural health monitoring (SHM) and damage identification of civil structures. This framework integrates advanced mechanics-based nonlinear finite element (FE) modeling and analysis techniques with a batch Bayesian estimation approach to estimate time-invariant model parameters used in the FE model of the structure of interest. The framework uses input excitation and dynamic response of the structure and updates a nonlinear FE model of the structure to minimize the discrepancies between predicted and measured response time histories. The updated FE model can then be interrogated to detect, localize, classify, and quantify the state of damage and predict the remaining useful life of the structure. As opposed to recursive estimation methods, in the batch Bayesian estimation approach, the entire time history of the input excitation and output response of the structure are used as a batch of data to estimate the FE model parameters through a number of iterations. In the case of non-informative prior, the batch Bayesian method leads to an extended maximum likelihood (ML) estimation method to estimate jointly time-invariant model parameters and the measurement noise amplitude. The extended ML estimation problem is solved efficiently using a gradient-based interior-point optimization algorithm. Gradient-based optimization algorithms require the FE response sensitivities with respect to the model parameters to be identified. The FE response sensitivities are computed accurately and efficiently using the direct differentiation method (DDM). The estimation uncertainties are evaluated based on the Cramer-Rao lower bound (CRLB) theorem by computing the exact Fisher Information matrix using the FE response sensitivities with respect to the model parameters. The accuracy of the proposed uncertainty quantification approach is verified using a sampling approach based on the unscented transformation. Two validation studies, based on realistic structural FE models of a bridge pier and a moment resisting steel frame, are performed to validate the performance and accuracy of the presented nonlinear FE model updating approach and demonstrate its application to SHM. These validation studies show the excellent performance of the proposed framework for SHM and damage identification even in the presence of high measurement noise and/or way-out initial estimates of the model parameters. Furthermore, the detrimental effects of the input measurement noise on the performance of the proposed framework are illustrated and quantified through one of the validation studies.

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.

Theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis-, and trans-1,2-difluoroethylenes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nozirov, Farhod, E-mail: teobaldk@gmail.com, E-mail: farhod.nozirov@gmail.com; Stachów, Michał, E-mail: michal.stachow@gmail.com; Kupka, Teobald, E-mail: teobaldk@gmail.com, E-mail: farhod.nozirov@gmail.com

2014-04-14

A theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis- and trans-1,2-difluoroethylenes is reported. The results obtained using density functional theory (DFT) combined with large basis sets and gauge-independent atomic orbital calculations were critically compared with experiment and conventional, higher level correlated electronic structure methods. Accurate structural, vibrational, and NMR parameters of difluoroethylenes were obtained using several density functionals combined with dedicated basis sets. B3LYP/6-311++G(3df,2pd) optimized structures of difluoroethylenes closely reproduced experimental geometries and earlier reported benchmark coupled cluster results, while BLYP/6-311++G(3df,2pd) produced accurate harmonic vibrational frequencies. The most accurate vibrations were obtained using B3LYP/6-311++G(3df,2pd)more » with correction for anharmonicity. Becke half and half (BHandH) density functional predicted more accurate {sup 19}F isotropic shieldings and van Voorhis and Scuseria's τ-dependent gradient-corrected correlation functional yielded better carbon shieldings than B3LYP. A surprisingly good performance of Hartree-Fock (HF) method in predicting nuclear shieldings in these molecules was observed. Inclusion of zero-point vibrational correction markedly improved agreement with experiment for nuclear shieldings calculated by HF, MP2, CCSD, and CCSD(T) methods but worsened the DFT results. The threefold improvement in accuracy when predicting {sup 2}J(FF) in 1,1-difluoroethylene for BHandH density functional compared to B3LYP was observed (the deviations from experiment were −46 vs. −115 Hz)« less

A comprehensive study of g-factors, elastic, structural and electronic properties of III-V semiconductors using hybrid-density functional theory

NASA Astrophysics Data System (ADS)

Bastos, Carlos M. O.; Sabino, Fernando P.; Sipahi, Guilherme M.; Da Silva, Juarez L. F.

2018-02-01

Despite the large number of theoretical III-V semiconductor studies reported every year, our atomistic understanding is still limited. The limitations of the theoretical approaches to yield accurate structural and electronic properties on an equal footing, is due to the unphysical self-interaction problem that mainly affects the band gap and spin-orbit splitting (SOC) in semiconductors and, in particular, III-V systems with similar magnitude of the band gap and SOC. In this work, we report a consistent study of the structural and electronic properties of the III-V semiconductors by using the screening hybrid-density functional theory framework, by fitting the α parameters for 12 different III-V compounds, namely, AlN, AlP, AlAs, AlSb, GaN, GaP, GaAs, GaSb, InN, InP, InAs, and InSb, to minimize the deviation between the theoretical and experimental values of the band gap and SOC. Structural relaxation effects were also included. Except for AlP, whose α = 0.127, we obtained α values that ranged from 0.209 to 0.343, which deviate by less than 0.1 from the universal value of 0.25. Our results for the lattice parameter and elastic constants indicate that the fitting of α does not affect those structural parameters when compared with the HSE06 functional, where α = 0.25. Our analysis of the band structure based on the k ṡ p method shows that the effective masses are in agreement with the experimental values, which can be attributed to the simultaneous fitting of the band gap and SOC. Also, we estimate the values of g-factors, extracted directly from the band structure, which are close to experimental results, which indicate that the obtained band structure produced a realistic set of k ṡ p parameters.

Determination of protein secondary structure and solvent accessibility using site-directed fluorescence labeling. Studies of T4 lysozyme using the fluorescent probe monobromobimane.

PubMed

Mansoor, S E; McHaourab, H S; Farrens, D L

1999-12-07

We report an investigation of how much protein structural information could be obtained using a site-directed fluorescence labeling (SDFL) strategy. In our experiments, we used 21 consecutive single-cysteine substitution mutants in T4 lysozyme (residues T115-K135), located in a helix-turn-helix motif. The mutants were labeled with the fluorescent probe monobromobimane and subjected to an array of fluorescence measurements. Thermal stability measurements show that introduction of the label is substantially perturbing only when it is located at buried residue sites. At buried sites (solvent surface accessibility of <40 A(2)), the destabilizations are between 3 and 5.5 kcal/mol, whereas at more exposed sites, DeltaDeltaG values of < or = 1.5 kcal/mol are obtained. Of all the fluorescence parameters that were explored (excitation lambda(max), emission lambda(max), fluorescence lifetime, quantum yield, and steady-state anisotropy), the emission lambda(max) and the steady-state anisotropy values most accurately reflect the solvent surface accessibility at each site as calculated from the crystal structure of cysteine-less T4 lysozyme. The parameters we identify allow the classification of each site as buried, partially buried, or exposed. We find that the variations in these parameters as a function of residue number reflect the sequence-specific secondary structure, the determination of which is a key step for modeling a protein of unknown structure.

Numerical analysis of MHD Casson Navier's slip nanofluid flow yield by rigid rotating disk

NASA Astrophysics Data System (ADS)

Rehman, Khalil Ur; Malik, M. Y.; Zahri, Mostafa; Tahir, M.

2018-03-01

An exertion is perform to report analysis on Casson liquid equipped above the rigid disk for z bar > 0 as a semi-infinite region. The flow of Casson liquid is achieve through rotation of rigid disk with constant angular frequency Ω bar . Magnetic interaction is consider by applying uniform magnetic field normal to the axial direction. The nanosized particles are suspended in the Casson liquid and rotation of disk is manifested with Navier's slip condition, heat generation/absorption and chemical reaction effects. The obtain flow narrating differential equations subject to MHD Casson nanofluid are transformed into ordinary differential system. For this purpose the Von Karman way of scheme is executed. To achieve accurate trends a computational algorithm is develop rather than to go on with usual build-in scheme. The effects logs of involved parameters, namely magnetic field parameter, Casson fluid parameter, slip parameter, thermophoresis and Brownian motion parameters on radial, tangential velocities, temperature, nanoparticles concentration, Nusselt and Sherwood numbers are provided by means of graphical and tabular structures. It is observed that both tangential and radial velocities are decreasing function of Casson fluid parameter.

Ultra-large nonlinear parameter in graphene-silicon waveguide structures.

PubMed

Donnelly, Christine; Tan, Dawn T H

2014-09-22

Mono-layer graphene integrated with optical waveguides is studied for the purpose of maximizing E-field interaction with the graphene layer, for the generation of ultra-large nonlinear parameters. It is shown that the common approach used to minimize the waveguide effective modal area does not accurately predict the configuration with the maximum nonlinear parameter. Both photonic and plasmonic waveguide configurations and graphene integration techniques realizable with today's fabrication tools are studied. Importantly, nonlinear parameters exceeding 10(4) W(-1)/m, two orders of magnitude larger than that in silicon on insulator waveguides without graphene, are obtained for the quasi-TE mode in silicon waveguides incorporating mono-layer graphene in the evanescent part of the optical field. Dielectric loaded surface plasmon polariton waveguides incorporating mono-layer graphene are observed to generate nonlinear parameters as large as 10(5) W(-1)/m, three orders of magnitude larger than that in silicon on insulator waveguides without graphene. The ultra-large nonlinear parameters make such waveguides promising platforms for nonlinear integrated optics at ultra-low powers, and for previously unobserved nonlinear optical effects to be studied in a waveguide platform.

Developing a Graphical User Interface to Automate the Estimation and Prediction of Risk Values for Flood Protective Structures using Artificial Neural Network

NASA Astrophysics Data System (ADS)

Hasan, M.; Helal, A.; Gabr, M.

2014-12-01

In this project, we focus on providing a computer-automated platform for a better assessment of the potential failures and retrofit measures of flood-protecting earth structures, e.g., dams and levees. Such structures play an important role during extreme flooding events as well as during normal operating conditions. Furthermore, they are part of other civil infrastructures such as water storage and hydropower generation. Hence, there is a clear need for accurate evaluation of stability and functionality levels during their service lifetime so that the rehabilitation and maintenance costs are effectively guided. Among condition assessment approaches based on the factor of safety, the limit states (LS) approach utilizes numerical modeling to quantify the probability of potential failures. The parameters for LS numerical modeling include i) geometry and side slopes of the embankment, ii) loading conditions in terms of rate of rising and duration of high water levels in the reservoir, and iii) cycles of rising and falling water levels simulating the effect of consecutive storms throughout the service life of the structure. Sample data regarding the correlations of these parameters are available through previous research studies. We have unified these criteria and extended the risk assessment in term of loss of life through the implementation of a graphical user interface to automate input parameters that divides data into training and testing sets, and then feeds them into Artificial Neural Network (ANN) tool through MATLAB programming. The ANN modeling allows us to predict risk values of flood protective structures based on user feedback quickly and easily. In future, we expect to fine-tune the software by adding extensive data on variations of parameters.

Estimation of Melting Points of Organics.

PubMed

Yalkowsky, Samuel H; Alantary, Doaa

2018-05-01

Unified physicochemical property estimation relationships is a system of empirical and theoretical relationships that relate 20 physicochemical properties of organic molecules to each other and to chemical structure. Melting point is a key parameter in the unified physicochemical property estimation relationships scheme because it is a determinant of several other properties including vapor pressure, and solubility. This review describes the first-principals calculation of the melting points of organic compounds from structure. The calculation is based on the fact that the melting point, T m , is equal to the ratio of the heat of melting, ΔH m , to the entropy of melting, ΔS m . The heat of melting is shown to be an additive constitutive property. However, the entropy of melting is not entirely group additive. It is primarily dependent on molecular geometry, including parameters which reflect the degree of restriction of molecular motion in the crystal to that of the liquid. Symmetry, eccentricity, chirality, flexibility, and hydrogen bonding, each affect molecular freedom in different ways and thus make different contributions to the total entropy of fusion. The relationships of these entropy determining parameters to chemical structure are used to develop a reasonably accurate means of predicting the melting points over 2000 compounds. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

A Three-dimensional Statistical Reconstruction Model of Grapevine (Vitis vinifera) Simulating Canopy Structure Variability within and between Cultivar/Training System Pairs

PubMed Central

Louarn, Gaëtan; Lecoeur, Jérémie; Lebon, Eric

2008-01-01

Background and Aims In grapevine, canopy-structure-related variations in light interception and distribution affect productivity, yield and the quality of the harvested product. A simple statistical model for reconstructing three-dimensional (3D) canopy structures for various cultivar–training system (C × T) pairs has been implemented with special attention paid to balance the time required for model parameterization and accuracy of the representations from organ to stand scales. Such an approach particularly aims at overcoming the weak integration of interplant variability using the usual direct 3D measurement methods. Model This model is original in combining a turbid-medium-like envelope enclosing the volume occupied by vine shoots with the use of discrete geometric polygons representing leaves randomly located within this volume to represent plant structure. Reconstruction rules were adapted to capture the main determinants of grapevine shoot architecture and their variability. Using a simplified set of parameters, it was possible to describe (1) the 3D path of the main shoot, (2) the volume occupied by the foliage around this path and (3) the orientation of individual leaf surfaces. Model parameterization (estimation of the probability distribution for each parameter) was carried out for eight contrasting C × T pairs. Key Results and Conclusions The parameter values obtained in each situation were consistent with our knowledge of grapevine architecture. Quantitative assessments for the generated virtual scenes were carried out at the canopy and plant scales. Light interception efficiency and local variations of light transmittance within and between experimental plots were correctly simulated for all canopies studied. The approach predicted these key ecophysiological variables significantly more accurately than the classical complete digitization method with a limited number of plants. In addition, this model accurately reproduced the characteristics of a wide range of individual digitized plants. Simulated leaf area density and the distribution of light interception among leaves were consistent with measurements. However, at the level of individual organs, the model tended to underestimate light interception. PMID:18202006

Pose-free structure from motion using depth from motion constraints.

PubMed

Zhang, Ji; Boutin, Mireille; Aliaga, Daniel G

2011-10-01

Structure from motion (SFM) is the problem of recovering the geometry of a scene from a stream of images taken from unknown viewpoints. One popular approach to estimate the geometry of a scene is to track scene features on several images and reconstruct their position in 3-D. During this process, the unknown camera pose must also be recovered. Unfortunately, recovering the pose can be an ill-conditioned problem which, in turn, can make the SFM problem difficult to solve accurately. We propose an alternative formulation of the SFM problem with fixed internal camera parameters known a priori. In this formulation, obtained by algebraic variable elimination, the external camera pose parameters do not appear. As a result, the problem is better conditioned in addition to involving much fewer variables. Variable elimination is done in three steps. First, we take the standard SFM equations in projective coordinates and eliminate the camera orientations from the equations. We then further eliminate the camera center positions. Finally, we also eliminate all 3-D point positions coordinates, except for their depths with respect to the camera center, thus obtaining a set of simple polynomial equations of degree two and three. We show that, when there are merely a few points and pictures, these "depth-only equations" can be solved in a global fashion using homotopy methods. We also show that, in general, these same equations can be used to formulate a pose-free cost function to refine SFM solutions in a way that is more accurate than by minimizing the total reprojection error, as done when using the bundle adjustment method. The generalization of our approach to the case of varying internal camera parameters is briefly discussed. © 2011 IEEE

Designing and redesigning medical telecare services: a forces-oriented model.

PubMed

Gortzis, L G

2007-01-01

Medical telecare services' designing and redesigning still remains a challenging issue since it often depends on how a number of socio-technological issues are framed. This work has two key objectives; the former is to theoretically analyze the nature of a telecare environment by developing a model that reveals potential areas of analysis and the latter is to support designing and redesigning medical telecare services by formulating a strategy as well as a number of 'state of the art' guidelines. We have extended Leavitt's diamond to develop a model capable of accurately reflecting the telecare environment building dimensions as well as their interactions. This model depends on the i) technology, ii) collaborators, iii) tasks, iv) structure, v) social forces, and the vi) procedure dimensions. Taking this model as a core element we have proposed a service designing and redesigning strategy formulating, in parallel, six scalable dimension-oriented guidelines. During the two-year period (2003-2005) an enormous amount of data was collected (by active participating in two EU projects, by conducting semistructured interviews, by performing onsite observations as well as by reviewing 78 previous projects) and classified, structuring six guidelines. These guidelines can be considered as the 'state of the art' to support future services' design and redesign. This work considering the telecare environment as a multi-dimensional, operational organization has put the focus on accurate telecare services' design and redesign. The parameters are not limited, by any means, and are drawn from experience of designing services in a variety of telecare domains. The optimal parameter combination must be chosen according to the aim of each telecare procedure. Further research is needed to determine the minimum parameters to support telecare service design.

Thrombus segmentation by texture dynamics from microscopic image sequences

NASA Astrophysics Data System (ADS)

Brieu, Nicolas; Serbanovic-Canic, Jovana; Cvejic, Ana; Stemple, Derek; Ouwehand, Willem; Navab, Nassir; Groher, Martin

2010-03-01

The genetic factors of thrombosis are commonly explored by microscopically imaging the coagulation of blood cells induced by injuring a vessel of mice or of zebrafish mutants. The latter species is particularly interesting since skin transparency permits to non-invasively acquire microscopic images of the scene with a CCD camera and to estimate the parameters characterizing the thrombus development. These parameters are currently determined by manual outlining, which is both error prone and extremely time consuming. Even though a technique for automatic thrombus extraction would be highly valuable for gene analysts, little work can be found, which is mainly due to very low image contrast and spurious structures. In this work, we propose to semi-automatically segment the thrombus over time from microscopic image sequences of wild-type zebrafish larvae. To compensate the lack of valuable spatial information, our main idea consists of exploiting the temporal information by modeling the variations of the pixel intensities over successive temporal windows with a linear Markov-based dynamic texture formalization. We then derive an image from the estimated model parameters, which represents the probability of a pixel to belong to the thrombus. We employ this probability image to accurately estimate the thrombus position via an active contour segmentation incorporating also prior and spatial information of the underlying intensity images. The performance of our approach is tested on three microscopic image sequences. We show that the thrombus is accurately tracked over time in each sequence if the respective parameters controlling prior influence and contour stiffness are correctly chosen.

Improvements to robotics-inspired conformational sampling in rosetta.

PubMed

Stein, Amelie; Kortemme, Tanja

2013-01-01

To accurately predict protein conformations in atomic detail, a computational method must be capable of sampling models sufficiently close to the native structure. All-atom sampling is difficult because of the vast number of possible conformations and extremely rugged energy landscapes. Here, we test three sampling strategies to address these difficulties: conformational diversification, intensification of torsion and omega-angle sampling and parameter annealing. We evaluate these strategies in the context of the robotics-based kinematic closure (KIC) method for local conformational sampling in Rosetta on an established benchmark set of 45 12-residue protein segments without regular secondary structure. We quantify performance as the fraction of sub-Angstrom models generated. While improvements with individual strategies are only modest, the combination of intensification and annealing strategies into a new "next-generation KIC" method yields a four-fold increase over standard KIC in the median percentage of sub-Angstrom models across the dataset. Such improvements enable progress on more difficult problems, as demonstrated on longer segments, several of which could not be accurately remodeled with previous methods. Given its improved sampling capability, next-generation KIC should allow advances in other applications such as local conformational remodeling of multiple segments simultaneously, flexible backbone sequence design, and development of more accurate energy functions.

Improvements to Robotics-Inspired Conformational Sampling in Rosetta

PubMed Central

Stein, Amelie; Kortemme, Tanja

2013-01-01

To accurately predict protein conformations in atomic detail, a computational method must be capable of sampling models sufficiently close to the native structure. All-atom sampling is difficult because of the vast number of possible conformations and extremely rugged energy landscapes. Here, we test three sampling strategies to address these difficulties: conformational diversification, intensification of torsion and omega-angle sampling and parameter annealing. We evaluate these strategies in the context of the robotics-based kinematic closure (KIC) method for local conformational sampling in Rosetta on an established benchmark set of 45 12-residue protein segments without regular secondary structure. We quantify performance as the fraction of sub-Angstrom models generated. While improvements with individual strategies are only modest, the combination of intensification and annealing strategies into a new “next-generation KIC” method yields a four-fold increase over standard KIC in the median percentage of sub-Angstrom models across the dataset. Such improvements enable progress on more difficult problems, as demonstrated on longer segments, several of which could not be accurately remodeled with previous methods. Given its improved sampling capability, next-generation KIC should allow advances in other applications such as local conformational remodeling of multiple segments simultaneously, flexible backbone sequence design, and development of more accurate energy functions. PMID:23704889

Accurate prediction of X-ray pulse properties from a free-electron laser using machine learning

DOE PAGES

Sanchez-Gonzalez, A.; Micaelli, P.; Olivier, C.; ...

2017-06-05

Free-electron lasers providing ultra-short high-brightness pulses of X-ray radiation have great potential for a wide impact on science, and are a critical element for unravelling the structural dynamics of matter. To fully harness this potential, we must accurately know the X-ray properties: intensity, spectrum and temporal profile. Owing to the inherent fluctuations in free-electron lasers, this mandates a full characterization of the properties for each and every pulse. While diagnostics of these properties exist, they are often invasive and many cannot operate at a high-repetition rate. Here, we present a technique for circumventing this limitation. Employing a machine learning strategy,more » we can accurately predict X-ray properties for every shot using only parameters that are easily recorded at high-repetition rate, by training a model on a small set of fully diagnosed pulses. Lastly, this opens the door to fully realizing the promise of next-generation high-repetition rate X-ray lasers.« less

Accurate prediction of X-ray pulse properties from a free-electron laser using machine learning

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanchez-Gonzalez, A.; Micaelli, P.; Olivier, C.

Free-electron lasers providing ultra-short high-brightness pulses of X-ray radiation have great potential for a wide impact on science, and are a critical element for unravelling the structural dynamics of matter. To fully harness this potential, we must accurately know the X-ray properties: intensity, spectrum and temporal profile. Owing to the inherent fluctuations in free-electron lasers, this mandates a full characterization of the properties for each and every pulse. While diagnostics of these properties exist, they are often invasive and many cannot operate at a high-repetition rate. Here, we present a technique for circumventing this limitation. Employing a machine learning strategy,more » we can accurately predict X-ray properties for every shot using only parameters that are easily recorded at high-repetition rate, by training a model on a small set of fully diagnosed pulses. Lastly, this opens the door to fully realizing the promise of next-generation high-repetition rate X-ray lasers.« less

Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.

PubMed

Phan, Andy; Mailey, Katherine; Saeki, Jessica; Gu, Xiaobo; Schroeder, Susan J

2017-05-01

Accurate thermodynamic parameters improve RNA structure predictions and thus accelerate understanding of RNA function and the identification of RNA drug binding sites. Many viral RNA structures, such as internal ribosome entry sites, have internal loops and bulges that are potential drug target sites. Current models used to predict internal loops are biased toward small, symmetric purine loops, and thus poorly predict asymmetric, pyrimidine-rich loops with >6 nucleotides (nt) that occur frequently in viral RNA. This article presents new thermodynamic data for 40 pyrimidine loops, many of which can form UU or protonated CC base pairs. Uracil and protonated cytosine base pairs stabilize asymmetric internal loops. Accurate prediction rules are presented that account for all thermodynamic measurements of RNA asymmetric internal loops. New loop initiation terms for loops with >6 nt are presented that do not follow previous assumptions that increasing asymmetry destabilizes loops. Since the last 2004 update, 126 new loops with asymmetry or sizes greater than 2 × 2 have been measured. These new measurements significantly deepen and diversify the thermodynamic database for RNA. These results will help better predict internal loops that are larger, pyrimidine-rich, and occur within viral structures such as internal ribosome entry sites. © 2017 Phan et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

CTER-rapid estimation of CTF parameters with error assessment.

PubMed

Penczek, Pawel A; Fang, Jia; Li, Xueming; Cheng, Yifan; Loerke, Justus; Spahn, Christian M T

2014-05-01

In structural electron microscopy, the accurate estimation of the Contrast Transfer Function (CTF) parameters, particularly defocus and astigmatism, is of utmost importance for both initial evaluation of micrograph quality and for subsequent structure determination. Due to increases in the rate of data collection on modern microscopes equipped with new generation cameras, it is also important that the CTF estimation can be done rapidly and with minimal user intervention. Finally, in order to minimize the necessity for manual screening of the micrographs by a user it is necessary to provide an assessment of the errors of fitted parameters values. In this work we introduce CTER, a CTF parameters estimation method distinguished by its computational efficiency. The efficiency of the method makes it suitable for high-throughput EM data collection, and enables the use of a statistical resampling technique, bootstrap, that yields standard deviations of estimated defocus and astigmatism amplitude and angle, thus facilitating the automation of the process of screening out inferior micrograph data. Furthermore, CTER also outputs the spatial frequency limit imposed by reciprocal space aliasing of the discrete form of the CTF and the finite window size. We demonstrate the efficiency and accuracy of CTER using a data set collected on a 300kV Tecnai Polara (FEI) using the K2 Summit DED camera in super-resolution counting mode. Using CTER we obtained a structure of the 80S ribosome whose large subunit had a resolution of 4.03Å without, and 3.85Å with, inclusion of astigmatism parameters. Copyright © 2014 Elsevier B.V. All rights reserved.

Tailor-made force fields for crystal-structure prediction.

PubMed

Neumann, Marcus A

2008-08-14

A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

Fluid-structure interaction analysis of the flow through a stenotic aortic valve

NASA Astrophysics Data System (ADS)

Maleki, Hoda; Labrosse, Michel R.; Durand, Louis-Gilles; Kadem, Lyes

2009-11-01

In Europe and North America, aortic stenosis (AS) is the most frequent valvular heart disease and cardiovascular disease after systemic hypertension and coronary artery disease. Understanding blood flow through an aortic stenosis and developing new accurate non-invasive diagnostic parameters is, therefore, of primarily importance. However, simulating such flows is highly challenging. In this study, we considered the interaction between blood flow and the valve leaflets and compared the results obtained in healthy valves with stenotic ones. One effective method to model the interaction between the fluid and the structure is to use Arbitrary Lagrangian-Eulerian (ALE) approach. Our two-dimensional model includes appropriate nonlinear and anisotropic materials. It is loaded during the systolic phase by applying pressure curves to the fluid domain at the inflow. For modeling the calcified stenotic valve, calcium will be added on the aortic side of valve leaflets. Such simulations allow us to determine the effective orifice area of the valve, one of the main parameters used clinically to evaluate the severity of an AS, and to correlate it with changes in the structure of the leaflets.

Toward a better understanding of helicopter stability derivatives

NASA Technical Reports Server (NTRS)

Hansen, R. S.

1982-01-01

An amended six degree of freedom helicopter stability and control derivative model was developed in which body acceleration and control rate derivatives were included in the Taylor series expansion. These additional derivatives were derived from consideration of the effects of the higher order rotor flapping dynamics, which are known to be inadequately represented in the conventional six degree of freedom, quasistatic stability derivative model. The amended model was a substantial improvement over the conventional model, effectively doubling the unsable bandwidth and providing a more accurate representation of the short period and cross axis characteristics. Further investigations assessed the applicability of the two stability derivative model structures for flight test parameter identification. Parameters were identified using simulation data generated from a higher order base line model having sixth order rotor tip path plane dynamics. Three lower order models were identified: one using the conventional stability derivative model structure, a second using the amended six degree of freedom model structure, and a third model having eight degrees of freedom that included a simplified rotor tip path plane tilt representation.

Ab Initio Calculation of XAFS Debye-Waller Factors for Crystalline Materials

NASA Astrophysics Data System (ADS)

Dimakis, Nicholas

2007-02-01

A direct an accurate technique for calculating the thermal X-ray absorption fine structure (XAFS) Debye-Waller factors (DWF) for materials of crystalline structure is presented. Using the Density Functional Theory (DFT) under the hybrid X3LYP functional, a library of MnO spin—optimized clusters are built and their phonon spectrum properties are calculated; these properties in the form of normal mode eigenfrequencies and eigenvectors are in turn used for calculation of the single and multiple scattering XAFS DWF. DWF obtained via this technique are temperature dependent expressions and can be used to substantially reduce the number of fitting parameters when experimental spectra are fitted with a hypothetical structure without any ad hoc assumptions. Due to the high computational demand a hybrid approach of mixing the DFT calculated DWF with the correlated Debye model for inner and outer shells respectively is presented. DFT obtained DWFs are compared with corresponding values from experimental XAFS spectra on manganosite. The cluster size effect and the spin parameter on the DFT calculated DWFs are discussed.

Prediction of Scour below Flip Bucket using Soft Computing Techniques

NASA Astrophysics Data System (ADS)

Azamathulla, H. Md.; Ab Ghani, Aminuddin; Azazi Zakaria, Nor

2010-05-01

The accurate prediction of the depth of scour around hydraulic structure (trajectory spillways) has been based on the experimental studies and the equations developed are mainly empirical in nature. This paper evaluates the performance of the soft computing (intelligence) techiques, Adaptive Neuro-Fuzzy System (ANFIS) and Genetic expression Programming (GEP) approach, in prediction of scour below a flip bucket spillway. The results are very promising, which support the use of these intelligent techniques in prediction of highly non-linear scour parameters.

Realistic absorption coefficient of each individual film in a multilayer architecture

NASA Astrophysics Data System (ADS)

Cesaria, M.; Caricato, A. P.; Martino, M.

2015-02-01

A spectrophotometric strategy, termed multilayer-method (ML-method), is presented and discussed to realistically calculate the absorption coefficient of each individual layer embedded in multilayer architectures without reverse engineering, numerical refinements and assumptions about the layer homogeneity and thickness. The strategy extends in a non-straightforward way a consolidated route, already published by the authors and here termed basic-method, able to accurately characterize an absorbing film covering transparent substrates. The ML-method inherently accounts for non-measurable contribution of the interfaces (including multiple reflections), describes the specific film structure as determined by the multilayer architecture and used deposition approach and parameters, exploits simple mathematics, and has wide range of applicability (high-to-weak absorption regions, thick-to-ultrathin films). Reliability tests are performed on films and multilayers based on a well-known material (indium tin oxide) by deliberately changing the film structural quality through doping, thickness-tuning and underlying supporting-film. Results are found consistent with information obtained by standard (optical and structural) analysis, the basic-method and band gap values reported in the literature. The discussed example-applications demonstrate the ability of the ML-method to overcome the drawbacks commonly limiting an accurate description of multilayer architectures.

Study on Material Parameters Identification of Brain Tissue Considering Uncertainty of Friction Coefficient

NASA Astrophysics Data System (ADS)

Guan, Fengjiao; Zhang, Guanjun; Liu, Jie; Wang, Shujing; Luo, Xu; Zhu, Feng

2017-10-01

Accurate material parameters are critical to construct the high biofidelity finite element (FE) models. However, it is hard to obtain the brain tissue parameters accurately because of the effects of irregular geometry and uncertain boundary conditions. Considering the complexity of material test and the uncertainty of friction coefficient, a computational inverse method for viscoelastic material parameters identification of brain tissue is presented based on the interval analysis method. Firstly, the intervals are used to quantify the friction coefficient in the boundary condition. And then the inverse problem of material parameters identification under uncertain friction coefficient is transformed into two types of deterministic inverse problem. Finally the intelligent optimization algorithm is used to solve the two types of deterministic inverse problems quickly and accurately, and the range of material parameters can be easily acquired with no need of a variety of samples. The efficiency and convergence of this method are demonstrated by the material parameters identification of thalamus. The proposed method provides a potential effective tool for building high biofidelity human finite element model in the study of traffic accident injury.

A volumetric ablation model of EPDM considering complex physicochemical process in porous structure of char layer

NASA Astrophysics Data System (ADS)

Yang, Liu; Xiao-Jing, Yu; Jian-Ming, Ma; Yi-Wen, Guan; Jiang, Li; Qiang, Li; Sa, Yang

2017-06-01

A volumetric ablation model for EPDM (ethylene- propylene-diene monomer) is established in this paper. This model considers the complex physicochemical process in the porous structure of a char layer. An ablation physics model based on a porous structure of a char layer and another model of heterogeneous volumetric ablation char layer physics are then built. In the model, porosity is used to describe the porous structure of a char layer. Gas diffusion and chemical reactions are introduced to the entire porous structure. Through detailed formation analysis, the causes of the compact or loose structure in the char layer and chemical vapor deposition (CVD) reaction between pyrolysis gas and char layer skeleton are introduced. The Arrhenius formula is adopted to determine the methods for calculating carbon deposition rate C which is the consumption rate caused by thermochemical reactions in the char layer, and porosity evolution. The critical porosity value is used as a criterion for char layer porous structure failure under gas flow and particle erosion. This critical porosity value is obtained by fitting experimental parameters and surface porosity of the char layer. Linear ablation and mass ablation rates are confirmed with the critical porosity value. Results of linear ablation and mass ablation rate calculations generally coincide with experimental results, suggesting that the ablation analysis proposed in this paper can accurately reflect practical situations and that the physics and mathematics models built are accurate and reasonable.

Modeling structured population dynamics using data from unmarked individuals

USGS Publications Warehouse

Grant, Evan H. Campbell; Zipkin, Elise; Thorson, James T.; See, Kevin; Lynch, Heather J.; Kanno, Yoichiro; Chandler, Richard; Letcher, Benjamin H.; Royle, J. Andrew

2014-01-01

The study of population dynamics requires unbiased, precise estimates of abundance and vital rates that account for the demographic structure inherent in all wildlife and plant populations. Traditionally, these estimates have only been available through approaches that rely on intensive mark–recapture data. We extended recently developed N-mixture models to demonstrate how demographic parameters and abundance can be estimated for structured populations using only stage-structured count data. Our modeling framework can be used to make reliable inferences on abundance as well as recruitment, immigration, stage-specific survival, and detection rates during sampling. We present a range of simulations to illustrate the data requirements, including the number of years and locations necessary for accurate and precise parameter estimates. We apply our modeling framework to a population of northern dusky salamanders (Desmognathus fuscus) in the mid-Atlantic region (USA) and find that the population is unexpectedly declining. Our approach represents a valuable advance in the estimation of population dynamics using multistate data from unmarked individuals and should additionally be useful in the development of integrated models that combine data from intensive (e.g., mark–recapture) and extensive (e.g., counts) data sources.

Automation methodologies and large-scale validation for G W : Towards high-throughput G W calculations

NASA Astrophysics Data System (ADS)

van Setten, M. J.; Giantomassi, M.; Gonze, X.; Rignanese, G.-M.; Hautier, G.

2017-10-01

The search for new materials based on computational screening relies on methods that accurately predict, in an automatic manner, total energy, atomic-scale geometries, and other fundamental characteristics of materials. Many technologically important material properties directly stem from the electronic structure of a material, but the usual workhorse for total energies, namely density-functional theory, is plagued by fundamental shortcomings and errors from approximate exchange-correlation functionals in its prediction of the electronic structure. At variance, the G W method is currently the state-of-the-art ab initio approach for accurate electronic structure. It is mostly used to perturbatively correct density-functional theory results, but is, however, computationally demanding and also requires expert knowledge to give accurate results. Accordingly, it is not presently used in high-throughput screening: fully automatized algorithms for setting up the calculations and determining convergence are lacking. In this paper, we develop such a method and, as a first application, use it to validate the accuracy of G0W0 using the PBE starting point and the Godby-Needs plasmon-pole model (G0W0GN @PBE) on a set of about 80 solids. The results of the automatic convergence study utilized provide valuable insights. Indeed, we find correlations between computational parameters that can be used to further improve the automatization of G W calculations. Moreover, we find that G0W0GN @PBE shows a correlation between the PBE and the G0W0GN @PBE gaps that is much stronger than that between G W and experimental gaps. However, the G0W0GN @PBE gaps still describe the experimental gaps more accurately than a linear model based on the PBE gaps. With this paper, we hence show that G W can be made automatic and is more accurate than using an empirical correction of the PBE gap, but that, for accurate predictive results for a broad class of materials, an improved starting point or some type of self-consistency is necessary.

Green-ampt infiltration parameters in riparian buffers

Treesearch

L.M. Stahr; D.E. Eisenhauer; M.J. Helmers; Mike G. Dosskey; T.G. Franti

2004-01-01

Riparian buffers can improve surface water quality by filtering contaminants from runoff before they enter streams. Infiltration is an important process in riparian buffers. Computer models are often used to assess the performance of riparian buffers. Accurate prediction of infiltration by these models is dependent upon accurate estimates of infiltration parameters....

The spatial gradients in the solar wind and IMF in the vicinity of the first Lagrangian point

NASA Astrophysics Data System (ADS)

Lai, H.; Russell, C. T.; Riley, P.

2017-12-01

To verify the accuracy of predicted solar wind conditions at L1, we need to know how accurate our measurements are as well as the spatial gradients of solar wind properties since the data are not obtained precisely at the L1 point. With ACE, Wind, and DSCOVR currently taking measurements in the vicinity of L1, we first need to test whether their responses to the solar wind are the same and if not, to determine which data are most accurate. Secondly, we need to study the coherency scales of the solar wind properties, which determine the scale over which the measurements can be accurately extrapolated. By comparing the measurements during large solar wind structures (e.g. CMEs), we find that the magnetic fields from all spacecraft are measured accurately, but the plasma parameters can be significantly different from one spacecraft to another. By examining the sum of magnetic and plasma thermal pressure across tangential discontinuities, we find that the density and temperature measurements from Wind and DSCOVR do show pressure continuity as expected while ACE does not. Since plasma data from DSCOVR have a greater variability about the mean and have many data gaps, we believe that data from Wind should be used whenever available. We find that strength of the magnetic field and zero levels of the various magnetometers are consistent, but the direction of the magnetic field can change significantly in the cross-flow direction. Thus, over the separation distance of spacecraft near L1, large changes in the IMF direction can appear between spacecraft even though the IMF is accurately measured. In contrast, the plasma parameters, when measured accurately, are spatially uniform over about 100Re and may be extrapolated well. Our results can also be applied to improving future space weather mission design. A constellation of cubesats with magnetometers would be needed to determine the IMF impinging on the magnetosphere. Fewer plasma instruments are needed to determine the impinging solar wind conditions, but they should be more accurate than the current detectors.

Physically based model for extracting dual permeability parameters using non-Newtonian fluids

NASA Astrophysics Data System (ADS)

Abou Najm, M. R.; Basset, C.; Stewart, R. D.; Hauswirth, S.

2017-12-01

Dual permeability models are effective for the assessment of flow and transport in structured soils with two dominant structures. The major challenge to those models remains in the ability to determine appropriate and unique parameters through affordable, simple, and non-destructive methods. This study investigates the use of water and a non-Newtonian fluid in saturated flow experiments to derive physically-based parameters required for improved flow predictions using dual permeability models. We assess the ability of these two fluids to accurately estimate the representative pore sizes in dual-domain soils, by determining the effective pore sizes of macropores and micropores. We developed two sub-models that solve for the effective macropore size assuming either cylindrical (e.g., biological pores) or planar (e.g., shrinkage cracks and fissures) pore geometries, with the micropores assumed to be represented by a single effective radius. Furthermore, the model solves for the percent contribution to flow (wi) corresponding to the representative macro and micro pores. A user-friendly solver was developed to numerically solve the system of equations, given that relevant non-Newtonian viscosity models lack forms conducive to analytical integration. The proposed dual-permeability model is a unique attempt to derive physically based parameters capable of measuring dual hydraulic conductivities, and therefore may be useful in reducing parameter uncertainty and improving hydrologic model predictions.

Stochastic filtering for damage identification through nonlinear structural finite element model updating

NASA Astrophysics Data System (ADS)

Astroza, Rodrigo; Ebrahimian, Hamed; Conte, Joel P.

2015-03-01

This paper describes a novel framework that combines advanced mechanics-based nonlinear (hysteretic) finite element (FE) models and stochastic filtering techniques to estimate unknown time-invariant parameters of nonlinear inelastic material models used in the FE model. Using input-output data recorded during earthquake events, the proposed framework updates the nonlinear FE model of the structure. The updated FE model can be directly used for damage identification and further used for damage prognosis. To update the unknown time-invariant parameters of the FE model, two alternative stochastic filtering methods are used: the extended Kalman filter (EKF) and the unscented Kalman filter (UKF). A three-dimensional, 5-story, 2-by-1 bay reinforced concrete (RC) frame is used to verify the proposed framework. The RC frame is modeled using fiber-section displacement-based beam-column elements with distributed plasticity and is subjected to the ground motion recorded at the Sylmar station during the 1994 Northridge earthquake. The results indicate that the proposed framework accurately estimate the unknown material parameters of the nonlinear FE model. The UKF outperforms the EKF when the relative root-mean-square error of the recorded responses are compared. In addition, the results suggest that the convergence of the estimate of modeling parameters is smoother and faster when the UKF is utilized.

Free-decay time-domain modal identification for large space structures

NASA Technical Reports Server (NTRS)

Kim, Hyoung M.; Vanhorn, David A.; Doiron, Harold H.

1992-01-01

Concept definition studies for the Modal Identification Experiment (MIE), a proposed space flight experiment for the Space Station Freedom (SSF), have demonstrated advantages and compatibility of free-decay time-domain modal identification techniques with the on-orbit operational constraints of large space structures. Since practical experience with modal identification using actual free-decay responses of large space structures is very limited, several numerical and test data reduction studies were conducted. Major issues and solutions were addressed, including closely-spaced modes, wide frequency range of interest, data acquisition errors, sampling delay, excitation limitations, nonlinearities, and unknown disturbances during free-decay data acquisition. The data processing strategies developed in these studies were applied to numerical simulations of the MIE, test data from a deployable truss, and launch vehicle flight data. Results of these studies indicate free-decay time-domain modal identification methods can provide accurate modal parameters necessary to characterize the structural dynamics of large space structures.

Bayesian Modal Estimation of the Four-Parameter Item Response Model in Real, Realistic, and Idealized Data Sets.

PubMed

Waller, Niels G; Feuerstahler, Leah

2017-01-01

In this study, we explored item and person parameter recovery of the four-parameter model (4PM) in over 24,000 real, realistic, and idealized data sets. In the first analyses, we fit the 4PM and three alternative models to data from three Minnesota Multiphasic Personality Inventory-Adolescent form factor scales using Bayesian modal estimation (BME). Our results indicated that the 4PM fits these scales better than simpler item Response Theory (IRT) models. Next, using the parameter estimates from these real data analyses, we estimated 4PM item parameters in 6,000 realistic data sets to establish minimum sample size requirements for accurate item and person parameter recovery. Using a factorial design that crossed discrete levels of item parameters, sample size, and test length, we also fit the 4PM to an additional 18,000 idealized data sets to extend our parameter recovery findings. Our combined results demonstrated that 4PM item parameters and parameter functions (e.g., item response functions) can be accurately estimated using BME in moderate to large samples (N ⩾ 5, 000) and person parameters can be accurately estimated in smaller samples (N ⩾ 1, 000). In the supplemental files, we report annotated [Formula: see text] code that shows how to estimate 4PM item and person parameters in [Formula: see text] (Chalmers, 2012 ).

Determination of Littlest Higgs Model Parameters at the ILC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Conley, John A.; Hewett, JoAnne; Le, My Phuong

2005-07-27

We examine the effects of the extended gauge sector of the Littlest Higgs model in high energy e{sup +}e{sup -} collisions. We find that the search reach in e{sup +}e{sup -} {yields} f{bar f} at a {radical}s = 500 GeV International Linear Collider covers essentially the entire parameter region where the Littlest Higgs model is relevant to the gauge hierarchy problem. In addition, we show that this channel provides an accurate determination of the fundamental model parameters, to the precision of a few percent, provided that the LHC measures the mass of the heavy neutral gauge .eld. Additionally, we showmore » that the couplings of the extra gauge bosons to the light Higgs can be observed from the process e{sup +}e{sup -} {yields} Zh for a significant region of the parameter space. This allows for confirmation of the structure of the cancellation of the Higgs mass quadratic divergence and would verify the little Higgs mechanism.« less

Numerical simulations of catastrophic disruption: Recent results

NASA Technical Reports Server (NTRS)

Benz, W.; Asphaug, E.; Ryan, E. V.

1994-01-01

Numerical simulations have been used to study high velocity two-body impacts. In this paper, a two-dimensional Largrangian finite difference hydro-code and a three-dimensional smooth particle hydro-code (SPH) are described and initial results reported. These codes can be, and have been, used to make specific predictions about particular objects in our solar system. But more significantly, they allow us to explore a broad range of collisional events. Certain parameters (size, time) can be studied only over a very restricted range within the laboratory; other parameters (initial spin, low gravity, exotic structure or composition) are difficult to study at all experimentally. The outcomes of numerical simulations lead to a more general and accurate understanding of impacts in their many forms.

Low Velocity Earth-Penetration Test and Analysis

NASA Technical Reports Server (NTRS)

Fasanella, Edwin L.; Jones, Yvonne; Knight, Norman F., Jr.; Kellas, Sotiris

2001-01-01

Modeling and simulation of structural impacts into soil continue to challenge analysts to develop accurate material models and detailed analytical simulations to predict the soil penetration event. This paper discusses finite element modeling of a series of penetrometer drop tests into soft clay. Parametric studies are performed with penetrometers of varying diameters, masses, and impact speeds to a maximum of 45 m/s. Parameters influencing the simulation such as the contact penalty factor and the material model representing the soil are also studied. An empirical relationship between key parameters is developed and is shown to correlate experimental and analytical results quite well. The results provide preliminary design guidelines for Earth impact that may be useful for future space exploration sample return missions.

Dependence of nuclear quadrupole resonance transitions on the electric field gradient asymmetry parameter for nuclides with half-integer spins

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cho, Herman

2016-09-01

Allowed transition energies and eigenstate expansions have been calculated and tabulated in numerical form as functions of the electric field gradient asymmetry parameter for the zero field Hamiltonian of quadrupolar nuclides with I = 3/2, 5/2, 7/2, and 9/2. These results may be used to interpret nuclear quadrupole resonance (NQR) spectra and extract accurate values of the electric field gradient tensors. Applications of NQR methods to studies of electronic structure in heavy element systems are proposed. This material is based upon work supported by the U.S. Department of Energy Office of Science, Office of Basic Energy Sciences, Heavy Element Chemistrymore » program.« less

Influence of Drilling Parameters on Torque during Drilling of GFRP Composites Using Response Surface Methodology

NASA Astrophysics Data System (ADS)

Mohan, N. S.; Kulkarni, S. M.

2018-01-01

Polymer based composites have marked their valuable presence in the area of aerospace, defense and automotive industry. Components made of composite, are assembled to main structure by fastener, which require accurate, precise high quality holes to be drilled. Drilling the hole in composite with accuracy require control over various processes parameters viz., speed, feed, drill bit size and thickens of specimen. TRIAC VMC machining center is used to drill the hole and to relate the cutting and machining parameters on the torque. MINITAB 14 software is used to analyze the collected data. As a function of cutting and specimen parameters this method could be useful for predicting torque parameters. The purpose of this work is to investigate the effect of drilling parameters to get low torque value. Results show that thickness of specimen and drill bit size are significant parameters influencing the torque and spindle speed and feed rate have least influence and overlaid plot indicates a feasible and low region of torque is observed for medium to large sized drill bits for the range of spindle speed selected. Response surface contour plots indicate the sensitivity of the drill size and specimen thickness to the torque.

Experimental Identification and Characterization of Multirotor UAV Propulsion

NASA Astrophysics Data System (ADS)

Kotarski, Denis; Krznar, Matija; Piljek, Petar; Simunic, Nikola

2017-07-01

In this paper, an experimental procedure for the identification and characterization of multirotor Unmanned Aerial Vehicle (UAV) propulsion is presented. Propulsion configuration needs to be defined precisely in order to achieve required flight performance. Based on the accurate dynamic model and empirical measurements of multirotor propulsion physical parameters, it is possible to design diverse configurations with different characteristics for various purposes. As a case study, we investigated design considerations for a micro indoor multirotor which is suitable for control algorithm implementation in structured environment. It consists of open source autopilot, sensors for indoor flight, “take off the shelf” propulsion components and frame. The series of experiments were conducted to show the process of parameters identification and the procedure for analysis and propulsion characterization. Additionally, we explore battery performance in terms of mass and specific energy. Experimental results show identified and estimated propulsion parameters through which blade element theory is verified.

Control of DNA-Functionalized Nanoparticle Assembly

NASA Astrophysics Data System (ADS)

Olvera de La Cruz, Monica

Directed crystallization of a large variety of nanoparticles, including proteins, via DNA hybridization kinetics has led to unique materials with a broad range of crystal symmetries. The nanoparticles are functionalized with DNA chains that link neighboring functionalized units. The shape of the nanoparticle, the DNA length, the sequence of the hybridizing DNA linker and the grafting density determine the crystal symmetries and lattice spacing. By carefully selecting these parameters one can, in principle, achieve all the symmetries found for both atomic and colloidal crystals of asymmetric shapes as well as new symmetries, and drive transitions between them. A scale-accurate coarse-grained model with explicit DNA chains provides the design parameters, including degree of hybridization, to achieve specific crystal structures. The model also provides surface energy values to determine the shape of defect-free single crystals with macroscopic anisotropic properties, as well as the parameters to develop colloidal models that reproduce both the shape of single crystals and their growth kinetics.

The Impact of Model and Rainfall Forcing Errors on Characterizing Soil Moisture Uncertainty in Land Surface Modeling

NASA Technical Reports Server (NTRS)

Maggioni, V.; Anagnostou, E. N.; Reichle, R. H.

2013-01-01

The contribution of rainfall forcing errors relative to model (structural and parameter) uncertainty in the prediction of soil moisture is investigated by integrating the NASA Catchment Land Surface Model (CLSM), forced with hydro-meteorological data, in the Oklahoma region. Rainfall-forcing uncertainty is introduced using a stochastic error model that generates ensemble rainfall fields from satellite rainfall products. The ensemble satellite rain fields are propagated through CLSM to produce soil moisture ensembles. Errors in CLSM are modeled with two different approaches: either by perturbing model parameters (representing model parameter uncertainty) or by adding randomly generated noise (representing model structure and parameter uncertainty) to the model prognostic variables. Our findings highlight that the method currently used in the NASA GEOS-5 Land Data Assimilation System to perturb CLSM variables poorly describes the uncertainty in the predicted soil moisture, even when combined with rainfall model perturbations. On the other hand, by adding model parameter perturbations to rainfall forcing perturbations, a better characterization of uncertainty in soil moisture simulations is observed. Specifically, an analysis of the rank histograms shows that the most consistent ensemble of soil moisture is obtained by combining rainfall and model parameter perturbations. When rainfall forcing and model prognostic perturbations are added, the rank histogram shows a U-shape at the domain average scale, which corresponds to a lack of variability in the forecast ensemble. The more accurate estimation of the soil moisture prediction uncertainty obtained by combining rainfall and parameter perturbations is encouraging for the application of this approach in ensemble data assimilation systems.

Modal identification of structures by a novel approach based on FDD-wavelet method

NASA Astrophysics Data System (ADS)

Tarinejad, Reza; Damadipour, Majid

2014-02-01

An important application of system identification in structural dynamics is the determination of natural frequencies, mode shapes and damping ratios during operation which can then be used for calibrating numerical models. In this paper, the combination of two advanced methods of Operational Modal Analysis (OMA) called Frequency Domain Decomposition (FDD) and Continuous Wavelet Transform (CWT) based on novel cyclic averaging of correlation functions (CACF) technique are used for identification of dynamic properties. By using this technique, the autocorrelation of averaged correlation functions is used instead of original signals. Integration of FDD and CWT methods is used to overcome their deficiency and take advantage of the unique capabilities of these methods. The FDD method is able to accurately estimate the natural frequencies and mode shapes of structures in the frequency domain. On the other hand, the CWT method is in the time-frequency domain for decomposition of a signal at different frequencies and determines the damping coefficients. In this paper, a new formulation applied to the wavelet transform of the averaged correlation function of an ambient response is proposed. This application causes to accurate estimation of damping ratios from weak (noise) or strong (earthquake) vibrations and long or short duration record. For this purpose, the modified Morlet wavelet having two free parameters is used. The optimum values of these two parameters are obtained by employing a technique which minimizes the entropy of the wavelet coefficients matrix. The capabilities of the novel FDD-Wavelet method in the system identification of various dynamic systems with regular or irregular distribution of mass and stiffness are illustrated. This combined approach is superior to classic methods and yields results that agree well with the exact solutions of the numerical models.

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

DOE PAGES

Ray, Jaideep; Lefantzi, Sophia; Arunajatesan, Srinivasan; ...

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.

Effects of Combined Loads on the Nonlinear Response and Residual Strength of Damaged Stiffened Shells

NASA Technical Reports Server (NTRS)

Starnes, James H., Jr.; Rose, Cheryl A.; Rankin, Charles C.

1996-01-01

The results of an analytical study of the nonlinear response of stiffened fuselage shells with long cracks are presented. The shells are modeled with a hierarchical modeling strategy and analyzed with a nonlinear shell analysis code that maintains the shell in a nonlinear equilibrium state while the crack is grown. The analysis accurately accounts for global and local structural response phenomena. Results are presented for various combinations of internal pressure and mechanical loads, and the effects of crack orientation on the shell response are described. The effects of combined loading conditions and the effects of varying structural parameters on the stress-intensity factors associated with a crack are presented.

Electronic structure and optical band gap determination of NiFe2O4.

PubMed

Meinert, Markus; Reiss, Günter

2014-03-19

In a theoretical study we investigate the electronic structure and band gap of the inverse spinel ferrite NiFe2O4. The experimental optical absorption spectrum is accurately reproduced by fitting the Tran-Blaha parameter in the modified Becke-Johnson potential. The accuracy of the commonly applied Tauc plot to find the optical gap is assessed based on the computed spectra and we find that this approach can lead to a misinterpretation of the experimental data. The minimum gap of NiFe2O4 is found to be a 1.53 eV wide indirect gap, which is located in the minority spin channel.

Design and Validation of 3D Printed Complex Bone Models with Internal Anatomic Fidelity for Surgical Training and Rehearsal.

PubMed

Unger, Bertram J; Kraut, Jay; Rhodes, Charlotte; Hochman, Jordan

2014-01-01

Physical models of complex bony structures can be used for surgical skills training. Current models focus on surface rendering but suffer from a lack of internal accuracy due to limitations in the manufacturing process. We describe a technique for generating internally accurate rapid-prototyped anatomical models with solid and hollow structures from clinical and microCT data using a 3D printer. In a face validation experiment, otolaryngology residents drilled a cadaveric bone and its corresponding printed model. The printed bone models were deemed highly realistic representations across all measured parameters and the educational value of the models was strongly appreciated.

Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

PubMed

Song, Yinglei; Liu, Chunmei; Malmberg, Russell; Pan, Fangfang; Cai, Liming

2005-01-01

Searching genomes for RNA secondary structure with computational methods has become an important approach to the annotation of non-coding RNAs. However, due to the lack of efficient algorithms for accurate RNA structure-sequence alignment, computer programs capable of fast and effectively searching genomes for RNA secondary structures have not been available. In this paper, a novel RNA structure profiling model is introduced based on the notion of a conformational graph to specify the consensus structure of an RNA family. Tree decomposition yields a small tree width t for such conformation graphs (e.g., t = 2 for stem loops and only a slight increase for pseudo-knots). Within this modelling framework, the optimal alignment of a sequence to the structure model corresponds to finding a maximum valued isomorphic subgraph and consequently can be accomplished through dynamic programming on the tree decomposition of the conformational graph in time O(k(t)N(2)), where k is a small parameter; and N is the size of the projiled RNA structure. Experiments show that the application of the alignment algorithm to search in genomes yields the same search accuracy as methods based on a Covariance model with a significant reduction in computation time. In particular; very accurate searches of tmRNAs in bacteria genomes and of telomerase RNAs in yeast genomes can be accomplished in days, as opposed to months required by other methods. The tree decomposition based searching tool is free upon request and can be downloaded at our site h t t p ://w.uga.edu/RNA-informatics/software/index.php.

The impulsive hard X-rays from solar flares

NASA Technical Reports Server (NTRS)

Leach, J.

1984-01-01

A technique for determining the physical arrangement of a solar flare during the impulsive phase was developed based upon a nonthermal model interpretation of the emitted hard X-rays. Accurate values are obtained for the flare parameters, including those which describe the magnetic field structure and the beaming of the energetic electrons, parameters which have hitherto been mostly inaccessible. The X-ray intensity height structure can be described readily with a single expression based upon a semi-empirical fit to the results from many models. Results show that the degree of linear polarization of the X-rays from a flaring loop does not exceed 25 percent and can easily and naturally be as low as the polarization expected from a thermal model. This is a highly significant result in that it supersedes those based upon less thorough calculations of the electron beam dynamics and requires that a reevaluation of hopes of using polarization measurements to discriminate between categories of flare models.

Impact of Parameter Variation in Fabrication of Nanostructure by Atomic Force Microscopy Nanolithography

PubMed Central

Dehzangi, Arash; Larki, Farhad; Hutagalung, Sabar D.; Goodarz Naseri, Mahmood; Majlis, Burhanuddin Y.; Navasery, Manizheh; Hamid, Norihan Abdul; Noor, Mimiwaty Mohd

2013-01-01

In this letter, we investigate the fabrication of Silicon nanostructure patterned on lightly doped (1015 cm−3) p-type silicon-on-insulator by atomic force microscope nanolithography technique. The local anodic oxidation followed by two wet etching steps, potassium hydroxide etching for silicon removal and hydrofluoric etching for oxide removal, are implemented to reach the structures. The impact of contributing parameters in oxidation such as tip materials, applying voltage on the tip, relative humidity and exposure time are studied. The effect of the etchant concentration (10% to 30% wt) of potassium hydroxide and its mixture with isopropyl alcohol (10%vol. IPA ) at different temperatures on silicon surface are expressed. For different KOH concentrations, the effect of etching with the IPA admixture and the effect of the immersing time in the etching process on the structure are investigated. The etching processes are accurately optimized by 30%wt. KOH +10%vol. IPA in appropriate time, temperature, and humidity. PMID:23776479

Higher-dimensional Wannier functions of multiparameter Hamiltonians

NASA Astrophysics Data System (ADS)

Hanke, Jan-Philipp; Freimuth, Frank; Blügel, Stefan; Mokrousov, Yuriy

2015-05-01

When using Wannier functions to study the electronic structure of multiparameter Hamiltonians H(k ,λ ) carrying a dependence on crystal momentum k and an additional periodic parameter λ , one usually constructs several sets of Wannier functions for a set of values of λ . We present the concept of higher-dimensional Wannier functions (HDWFs), which provide a minimal and accurate description of the electronic structure of multiparameter Hamiltonians based on a single set of HDWFs. The obstacle of nonorthogonality of Bloch functions at different λ is overcome by introducing an auxiliary real space, which is reciprocal to the parameter λ . We derive a generalized interpolation scheme and emphasize the essential conceptual and computational simplifications in using the formalism, for instance, in the evaluation of linear response coefficients. We further implement the necessary machinery to construct HDWFs from ab initio within the full potential linearized augmented plane-wave method (FLAPW). We apply our implementation to accurately interpolate the Hamiltonian of a one-dimensional magnetic chain of Mn atoms in two important cases of λ : (i) the spin-spiral vector q and (ii) the direction of the ferromagnetic magnetization m ̂. Using the generalized interpolation of the energy, we extract the corresponding values of magnetocrystalline anisotropy energy, Heisenberg exchange constants, and spin stiffness, which compare very well with the values obtained from direct first principles calculations. For toy models we demonstrate that the method of HDWFs can also be used in applications such as the virtual crystal approximation, ferroelectric polarization, and spin torques.

Stress Wave Scattering: Friend or Enemy of Non Destructive Testing of Concrete?

NASA Astrophysics Data System (ADS)

Aggelis, Dimitrios G.; Shiotani, Tomoki; Philippidis, Theodore P.; Polyzos, Demosthenes

Cementitious materials are by definition inhomogeneous containing cement paste, sand, aggregates as well as air voids. Wave propagation in such a material is characterized by scattering phenomena. Damage in the form of micro or macro cracks certainly enhances scattering influence. Its most obvious manifestation is the velocity variation with frequency and excessive attenuation. The influence becomes stronger with increased mis-match of elastic properties of constituent materials and higher crack content. Therefore, in many cases of large concrete structures, field application of stress waves is hindered since attenuation makes the acquisition of reliable signals troublesome. However, measured wave parameters, combined with investigation with scattering theory can reveal much about the internal condition and supply information that cannot be obtained in any other way. The size and properties of the scatterers leave their signature on the dispersion and attenuation curves making thus the characterization more accurate in case of damage assessment, repair evaluation as well as composition inspection. In this paper, three indicative cases of scattering influence are presented. Namely, the interaction of actual distributed damage, as well as the repair material injected in an old concrete structure with the wave parameters. Other cases are the influence of light plastic inclusions in hardened mortar and the influence of sand and water content in the examination of fresh concrete. In all the above cases, scattering seems to complicate the propagation behavior but also offers the way for a more accurate characterization of the quality of the material.

Documentation for assessment of modal pushover-based scaling procedure for nonlinear response history analysis of "ordinary standard" bridges

USGS Publications Warehouse

Kalkan, Erol; Kwong, Neal S.

2010-01-01

The earthquake engineering profession is increasingly utilizing nonlinear response history analyses (RHA) to evaluate seismic performance of existing structures and proposed designs of new structures. One of the main ingredients of nonlinear RHA is a set of ground-motion records representing the expected hazard environment for the structure. When recorded motions do not exist (as is the case for the central United States), or when high-intensity records are needed (as is the case for San Francisco and Los Angeles), ground motions from other tectonically similar regions need to be selected and scaled. The modal-pushover-based scaling (MPS) procedure recently was developed to determine scale factors for a small number of records, such that the scaled records provide accurate and efficient estimates of 'true' median structural responses. The adjective 'accurate' refers to the discrepancy between the benchmark responses and those computed from the MPS procedure. The adjective 'efficient' refers to the record-to-record variability of responses. Herein, the accuracy and efficiency of the MPS procedure are evaluated by applying it to four types of existing 'ordinary standard' bridges typical of reinforced-concrete bridge construction in California. These bridges are the single-bent overpass, multi span bridge, curved-bridge, and skew-bridge. As compared to benchmark analyses of unscaled records using a larger catalog of ground motions, it is demonstrated that the MPS procedure provided an accurate estimate of the engineering demand parameters (EDPs) accompanied by significantly reduced record-to-record variability of the responses. Thus, the MPS procedure is a useful tool for scaling ground motions as input to nonlinear RHAs of 'ordinary standard' bridges.

Coarse-Grained Descriptions of Dynamics for Networks with Both Intrinsic and Structural Heterogeneities

PubMed Central

Bertalan, Tom; Wu, Yan; Laing, Carlo; Gear, C. William; Kevrekidis, Ioannis G.

2017-01-01

Finding accurate reduced descriptions for large, complex, dynamically evolving networks is a crucial enabler to their simulation, analysis, and ultimately design. Here, we propose and illustrate a systematic and powerful approach to obtaining good collective coarse-grained observables—variables successfully summarizing the detailed state of such networks. Finding such variables can naturally lead to successful reduced dynamic models for the networks. The main premise enabling our approach is the assumption that the behavior of a node in the network depends (after a short initial transient) on the node identity: a set of descriptors that quantify the node properties, whether intrinsic (e.g., parameters in the node evolution equations) or structural (imparted to the node by its connectivity in the particular network structure). The approach creates a natural link with modeling and “computational enabling technology” developed in the context of Uncertainty Quantification. In our case, however, we will not focus on ensembles of different realizations of a problem, each with parameters randomly selected from a distribution. We will instead study many coupled heterogeneous units, each characterized by randomly assigned (heterogeneous) parameter value(s). One could then coin the term Heterogeneity Quantification for this approach, which we illustrate through a model dynamic network consisting of coupled oscillators with one intrinsic heterogeneity (oscillator individual frequency) and one structural heterogeneity (oscillator degree in the undirected network). The computational implementation of the approach, its shortcomings and possible extensions are also discussed. PMID:28659781

Precomputing upscaled hydraulic conductivity for complex geological structures

NASA Astrophysics Data System (ADS)

Mariethoz, G.; Jha, S. K.; George, M.; Maheswarajah, S.; John, V.; De Re, D.; Smith, M.

2013-12-01

3D geological models are built to capture the geological heterogeneity at a fine scale. However groundwater modellers are often interested in the hydraulic conductivity (K) values at a much coarser scale to reduce the numerical burden. Upscaling is used to assign conductivity to large volumes, which necessarily causes a loss of information. Recent literature has shown that the connectivity in the channelized structures is an important feature that needs to be taken into account for accurate upscaling. In this work we study the effect of channel parameters, e.g. width, sinuosity, connectivity etc. on the upscaled values of the hydraulic conductivity and the associated uncertainty. We devise a methodology that derives correspondences between a lithological description and the equivalent hydraulic conductivity at a larger scale. The method uses multiple-point geostatistics simulations (MPS) and parameterizes the 3D structures by introducing continuous rotation and affinity parameters. Additional statistical characterization is obtained by transition probabilities and connectivity measures. Equivalent hydraulic conductivity is then estimated by solving a flow problem for the entire heterogeneous domain by applying steady state flow in horizontal and vertical directions. This is systematically performed for many random realisations of the small scale structures to enable a probability distribution for the equivalent upscaled hydraulic conductivity. This process allows deriving systematic relationships between a given depositional environment and precomputed equivalent parameters. A modeller can then exploit the prior knowledge of the depositional environment and expected geological heterogeneity to bypass the step of generating small-scale models, and directly work with upscaled values.

A Vision-Based Self-Calibration Method for Robotic Visual Inspection Systems

PubMed Central

Yin, Shibin; Ren, Yongjie; Zhu, Jigui; Yang, Shourui; Ye, Shenghua

2013-01-01

A vision-based robot self-calibration method is proposed in this paper to evaluate the kinematic parameter errors of a robot using a visual sensor mounted on its end-effector. This approach could be performed in the industrial field without external, expensive apparatus or an elaborate setup. A robot Tool Center Point (TCP) is defined in the structural model of a line-structured laser sensor, and aligned to a reference point fixed in the robot workspace. A mathematical model is established to formulate the misalignment errors with kinematic parameter errors and TCP position errors. Based on the fixed point constraints, the kinematic parameter errors and TCP position errors are identified with an iterative algorithm. Compared to the conventional methods, this proposed method eliminates the need for a robot-based-frame and hand-to-eye calibrations, shortens the error propagation chain, and makes the calibration process more accurate and convenient. A validation experiment is performed on an ABB IRB2400 robot. An optimal configuration on the number and distribution of fixed points in the robot workspace is obtained based on the experimental results. Comparative experiments reveal that there is a significant improvement of the measuring accuracy of the robotic visual inspection system. PMID:24300597

Anisotropic Effects on Constitutive Model Parameters of Aluminum Alloys

NASA Astrophysics Data System (ADS)

Brar, Nachhatter; Joshi, Vasant

2011-06-01

Simulation of low velocity impact on structures or high velocity penetration in armor materials heavily rely on constitutive material models. The model constants are required input to computer codes (LS-DYNA, DYNA3D or SPH) to accurately simulate fragment impact on structural components made of high strength 7075-T651 aluminum alloys. Johnson-Cook model constants determined for Al7075-T651 alloy bar material failed to simulate correctly the penetration into 1' thick Al-7075-T651plates. When simulations go well beyond minor parameter tweaking and experimental results are drastically different it is important to determine constitutive parameters from the actual material used in impact/penetration experiments. To investigate anisotropic effects on the yield/flow stress of this alloy we performed quasi-static and high strain rate tensile tests on specimens fabricated in the longitudinal, transverse, and thickness directions of 1' thick Al7075-T651 plate. Flow stresses at a strain rate of ~1100/s in the longitudinal and transverse direction are similar around 670MPa and decreases to 620 MPa in the thickness direction. These data are lower than the flow stress of 760 MPa measured in Al7075-T651 bar stock.

Convergence in parameters and predictions using computational experimental design.

PubMed

Hagen, David R; White, Jacob K; Tidor, Bruce

2013-08-06

Typically, biological models fitted to experimental data suffer from significant parameter uncertainty, which can lead to inaccurate or uncertain predictions. One school of thought holds that accurate estimation of the true parameters of a biological system is inherently problematic. Recent work, however, suggests that optimal experimental design techniques can select sets of experiments whose members probe complementary aspects of a biochemical network that together can account for its full behaviour. Here, we implemented an experimental design approach for selecting sets of experiments that constrain parameter uncertainty. We demonstrated with a model of the epidermal growth factor-nerve growth factor pathway that, after synthetically performing a handful of optimal experiments, the uncertainty in all 48 parameters converged below 10 per cent. Furthermore, the fitted parameters converged to their true values with a small error consistent with the residual uncertainty. When untested experimental conditions were simulated with the fitted models, the predicted species concentrations converged to their true values with errors that were consistent with the residual uncertainty. This paper suggests that accurate parameter estimation is achievable with complementary experiments specifically designed for the task, and that the resulting parametrized models are capable of accurate predictions.

Environmental effects on natural frequencies of the San Pietro bell tower in Perugia, Italy, and their removal for structural performance assessment

NASA Astrophysics Data System (ADS)

Ubertini, Filippo; Comanducci, Gabriele; Cavalagli, Nicola; Laura Pisello, Anna; Luigi Materazzi, Annibale; Cotana, Franco

2017-01-01

Continuously identified natural frequencies of vibration can provide unique information for low-cost automated condition assessment of civil constructions and infrastructures. However, the effects of changes in environmental parameters, such as temperature and humidity, need to be effectively investigated and accurately removed from identified frequency data for an effective performance assessment. This task is particularly challenging in the case of historical constructions that are typically massive and heterogeneous masonry structures characterized by complex variations of materials' properties with varying environmental parameters and by a differential heat conduction process where thermal capacity plays a major role. While there is abundance of documented monitoring data highlighting correlations between environmental parameters and natural frequencies in the case of new structures, such as long-span bridges, similar studies for historical constructions are still missing, with only a few literature works occasionally reporting increments in natural frequencies with increasing temperature of construction materials due to the closure of internal micro-cracks in the mortar layers caused by thermal expansion. In order to gain some knowledge on the effects of changes in temperature and humidity on the natural frequencies of slender masonry buildings, the paper focuses on the case study of an Italian monumental bell tower that has been monitored by the authors for more than nine months. Correlations between natural frequencies and environmental parameters are investigated in detail and the predictive capabilities of linear statistical regressive models based on the use of several environmental continuous monitoring sensors are assessed. At the end, three basic mechanisms governing environmentally-induced changes in the dynamic behavior of the tower are identified and essential information is achieved on the optimal location and minimum number of environmental sensors that are necessary in a structural health monitoring perspective.

Correlation of RNA secondary structure statistics with thermodynamic stability and applications to folding.

PubMed

Wu, Johnny C; Gardner, David P; Ozer, Stuart; Gutell, Robin R; Ren, Pengyu

2009-08-28

The accurate prediction of the secondary and tertiary structure of an RNA with different folding algorithms is dependent on several factors, including the energy functions. However, an RNA higher-order structure cannot be predicted accurately from its sequence based on a limited set of energy parameters. The inter- and intramolecular forces between this RNA and other small molecules and macromolecules, in addition to other factors in the cell such as pH, ionic strength, and temperature, influence the complex dynamics associated with transition of a single stranded RNA to its secondary and tertiary structure. Since all of the factors that affect the formation of an RNAs 3D structure cannot be determined experimentally, statistically derived potential energy has been used in the prediction of protein structure. In the current work, we evaluate the statistical free energy of various secondary structure motifs, including base-pair stacks, hairpin loops, and internal loops, using their statistical frequency obtained from the comparative analysis of more than 50,000 RNA sequences stored in the RNA Comparative Analysis Database (rCAD) at the Comparative RNA Web (CRW) Site. Statistical energy was computed from the structural statistics for several datasets. While the statistical energy for a base-pair stack correlates with experimentally derived free energy values, suggesting a Boltzmann-like distribution, variation is observed between different molecules and their location on the phylogenetic tree of life. Our statistical energy values calculated for several structural elements were utilized in the Mfold RNA-folding algorithm. The combined statistical energy values for base-pair stacks, hairpins and internal loop flanks result in a significant improvement in the accuracy of secondary structure prediction; the hairpin flanks contribute the most.

The structure of binding curves and practical identifiability of equilibrium ligand-binding parameters

PubMed Central

Middendorf, Thomas R.

2017-01-01

A critical but often overlooked question in the study of ligands binding to proteins is whether the parameters obtained from analyzing binding data are practically identifiable (PI), i.e., whether the estimates obtained from fitting models to noisy data are accurate and unique. Here we report a general approach to assess and understand binding parameter identifiability, which provides a toolkit to assist experimentalists in the design of binding studies and in the analysis of binding data. The partial fraction (PF) expansion technique is used to decompose binding curves for proteins with n ligand-binding sites exactly and uniquely into n components, each of which has the form of a one-site binding curve. The association constants of the PF component curves, being the roots of an n-th order polynomial, may be real or complex. We demonstrate a fundamental connection between binding parameter identifiability and the nature of these one-site association constants: all binding parameters are identifiable if the constants are all real and distinct; otherwise, at least some of the parameters are not identifiable. The theory is used to construct identifiability maps from which the practical identifiability of binding parameters for any two-, three-, or four-site binding curve can be assessed. Instructions for extending the method to generate identifiability maps for proteins with more than four binding sites are also given. Further analysis of the identifiability maps leads to the simple rule that the maximum number of structurally identifiable binding parameters (shown in the previous paper to be equal to n) will also be PI only if the binding curve line shape contains n resolved components. PMID:27993951

A Combined High and Low Cycle Fatigue Model for Life Prediction of Turbine Blades

PubMed Central

Yue, Peng; Yu, Zheng-Yong; Wang, Qingyuan

2017-01-01

Combined high and low cycle fatigue (CCF) generally induces the failure of aircraft gas turbine attachments. Based on the aero-engine load spectrum, accurate assessment of fatigue damage due to the interaction of high cycle fatigue (HCF) resulting from high frequency vibrations and low cycle fatigue (LCF) from ground-air-ground engine cycles is of critical importance for ensuring structural integrity of engine components, like turbine blades. In this paper, the influence of combined damage accumulation on the expected CCF life are investigated for turbine blades. The CCF behavior of a turbine blade is usually studied by testing with four load-controlled parameters, including high cycle stress amplitude and frequency, and low cycle stress amplitude and frequency. According to this, a new damage accumulation model is proposed based on Miner’s rule to consider the coupled damage due to HCF-LCF interaction by introducing the four load parameters. Five experimental datasets of turbine blade alloys and turbine blades were introduced for model validation and comparison between the proposed Miner, Manson-Halford, and Trufyakov-Kovalchuk models. Results show that the proposed model provides more accurate predictions than others with lower mean and standard deviation values of model prediction errors. PMID:28773064

A Combined High and Low Cycle Fatigue Model for Life Prediction of Turbine Blades.

PubMed

Zhu, Shun-Peng; Yue, Peng; Yu, Zheng-Yong; Wang, Qingyuan

2017-06-26

Combined high and low cycle fatigue (CCF) generally induces the failure of aircraft gas turbine attachments. Based on the aero-engine load spectrum, accurate assessment of fatigue damage due to the interaction of high cycle fatigue (HCF) resulting from high frequency vibrations and low cycle fatigue (LCF) from ground-air-ground engine cycles is of critical importance for ensuring structural integrity of engine components, like turbine blades. In this paper, the influence of combined damage accumulation on the expected CCF life are investigated for turbine blades. The CCF behavior of a turbine blade is usually studied by testing with four load-controlled parameters, including high cycle stress amplitude and frequency, and low cycle stress amplitude and frequency. According to this, a new damage accumulation model is proposed based on Miner's rule to consider the coupled damage due to HCF-LCF interaction by introducing the four load parameters. Five experimental datasets of turbine blade alloys and turbine blades were introduced for model validation and comparison between the proposed Miner, Manson-Halford, and Trufyakov-Kovalchuk models. Results show that the proposed model provides more accurate predictions than others with lower mean and standard deviation values of model prediction errors.

Nuclear ground-state masses and deformations: FRDM(2012)

DOE PAGES

Moller, P.; Sierk, A. J.; Ichikawa, T.; ...

2016-03-25

Here, we tabulate the atomic mass excesses and binding energies, ground-state shell-plus-pairing corrections, ground-state microscopic corrections, and nuclear ground-state deformations of 9318 nuclei ranging from 16O to A=339. The calculations are based on the finite-range droplet macroscopic and the folded-Yukawa single-particle microscopic nuclear-structure models, which are completely specified. Relative to our FRDM(1992) mass table in Möller et al. (1995), the results are obtained in the same model, but with considerably improved treatment of deformation and fewer of the approximations that were necessary earlier, due to limitations in computer power. The more accurate execution of the model and the more extensivemore » and more accurate experimental mass data base now available allow us to determine one additional macroscopic-model parameter, the density-symmetry coefficient LL, which was not varied in the previous calculation, but set to zero. Because we now realize that the FRDM is inaccurate for some highly deformed shapes occurring in fission, because some effects are derived in terms of perturbations around a sphere, we only adjust its macroscopic parameters to ground-state masses.« less

Compact perturbative expressions for neutrino oscillations in matter

DOE PAGES

Denton, Peter B.; Minakata, Hisakazu; Parke, Stephen J.

2016-06-08

We further develop and extend a recent perturbative framework for neutrino oscillations in uniform matter density so that the resulting oscillation probabilities are accurate for the complete matter potential versus baseline divided by neutrino energy plane. This extension also gives the exact oscillation probabilities in vacuum for all values of baseline divided by neutrino energy. The expansion parameter used is related to the ratio of the solar to the atmosphericmore » $$\\Delta m^2$$ scales but with a unique choice of the atmospheric $$\\Delta m^2$$ such that certain first-order effects are taken into account in the zeroth-order Hamiltonian. Using a mixing matrix formulation, this framework has the exceptional feature that the neutrino oscillation probability in matter has the same structure as in vacuum, to all orders in the expansion parameter. It also contains all orders in the matter potential and $$\\sin\\theta_{13}$$. It facilitates immediate physical interpretation of the analytic results, and makes the expressions for the neutrino oscillation probabilities extremely compact and very accurate even at zeroth order in our perturbative expansion. Furthermore, the first and second order results are also given which improve the precision by approximately two or more orders of magnitude per perturbative order.« less

A new, high-precision measurement of the X-ray Cu K α spectrum

NASA Astrophysics Data System (ADS)

Mendenhall, Marcus H.; Cline, James P.; Henins, Albert; Hudson, Lawrence T.; Szabo, Csilla I.; Windover, Donald

2016-03-01

One of the primary measurement issues addressed with NIST Standard Reference Materials (SRMs) for powder diffraction is that of line position. SRMs for this purpose are certified with respect to lattice parameter, traceable to the SI through precise measurement of the emission spectrum of the X-ray source. Therefore, accurate characterization of the emission spectrum is critical to a minimization of the error bounds on the certified parameters. The presently accepted sources for the SI traceable characterization of the Cu K α emission spectrum are those of Härtwig, Hölzer et al., published in the 1990s. The structure of the X-ray emission lines of the Cu K α complex has been remeasured on a newly commissioned double-crystal instrument, with six-bounce Si (440) optics, in a manner directly traceable to the SI definition of the meter. In this measurement, the entire region from 8020 eV to 8100 eV has been covered with a highly precise angular scale and well-defined system efficiency, providing accurate wavelengths and relative intensities. This measurement is in modest disagreement with reference values for the wavelength of the Kα1 line, and strong disagreement for the wavelength of the Kα2 line.

Comprehensive Study of Z-Cut Highly Integrated LiNbO3 Optical Modulator with Adjustable Chirp Parameters

NASA Astrophysics Data System (ADS)

Palodiya, Vikram; Raghuwanshi, Sanjeev Kumar

2017-12-01

In this paper, the domain inversion is used in a simple fashion to improve the performance of a Z-cut highly integrated LiNbO3 optical modulator (LNOM). The Z-cut modulator having ≤ 3 V switching voltage and bandwidth of 15 GHz for an external modulator in which traveling-wave electrode length L_{m} imposed the modulating voltage, the product of V_π and L_{m} is fixed for a given electro-optic material (EOM). An investigation to achieve a low V_π by both magnitude of the electro-optic coefficient (EOC) for a wide variety of EOMs has been reported. The Sellmeier equation (SE) for the extraordinary index of congruent LiNbO3 is derived. The predictions related to phase matching are accurate between room temperature and 250 °C and wavelength ranging from 0.4 to 5 μm. The SE predicts more accurate refractive indices (RI) at long wavelengths. The different overlaps between the waveguides for the Z-cut structure are shown to yield a chirp parameter that can able to adjust 0-0.7. Theoretical results are perfectly verified by simulated results.

Labeling Projections on Published Maps

USGS Publications Warehouse

Snyder, John P.

1987-01-01

To permit accurate scaling on a map, and to use the map as a source of accurate positions in the transfer of data, certain parameters - such as the standard parallels selected for a conic projection - must be stated on the map. This information is often missing on published maps. Three current major world atlases are evaluated with respect to map projection identification. The parameters essential for the projections used in these three atlases are discussed and listed. These parameters should be stated on any map based on the same projection.

Linking lipid architecture to bilayer structure and mechanics using self-consistent field modelling.

PubMed

Pera, H; Kleijn, J M; Leermakers, F A M

2014-02-14

To understand how lipid architecture determines the lipid bilayer structure and its mechanics, we implement a molecularly detailed model that uses the self-consistent field theory. This numerical model accurately predicts parameters such as Helfrichs mean and Gaussian bending modulus kc and k̄ and the preferred monolayer curvature J(0)(m), and also delivers structural membrane properties like the core thickness, and head group position and orientation. We studied how these mechanical parameters vary with system variations, such as lipid tail length, membrane composition, and those parameters that control the lipid tail and head group solvent quality. For the membrane composition, negatively charged phosphatidylglycerol (PG) or zwitterionic, phosphatidylcholine (PC), and -ethanolamine (PE) lipids were used. In line with experimental findings, we find that the values of kc and the area compression modulus kA are always positive. They respond similarly to parameters that affect the core thickness, but differently to parameters that affect the head group properties. We found that the trends for k̄ and J(0)(m) can be rationalised by the concept of Israelachivili's surfactant packing parameter, and that both k̄ and J(0)(m) change sign with relevant parameter changes. Although typically k̄ < 0, membranes can form stable cubic phases when the Gaussian bending modulus becomes positive, which occurs with membranes composed of PC lipids with long tails. Similarly, negative monolayer curvatures appear when a small head group such as PE is combined with long lipid tails, which hints towards the stability of inverse hexagonal phases at the cost of the bilayer topology. To prevent the destabilisation of bilayers, PG lipids can be mixed into these PC or PE lipid membranes. Progressive loading of bilayers with PG lipids lead to highly charged membranes, resulting in J(0)(m) > 0, especially at low ionic strengths. We anticipate that these changes lead to unstable membranes as these become vulnerable to pore formation or disintegration into lipid disks.

Validity of the Born approximation for beyond Gaussian weak lensing observables

DOE PAGES

Petri, Andrea; Haiman, Zoltan; May, Morgan

2017-06-06

Accurate forward modeling of weak lensing (WL) observables from cosmological parameters is necessary for upcoming galaxy surveys. Because WL probes structures in the nonlinear regime, analytical forward modeling is very challenging, if not impossible. Numerical simulations of WL features rely on ray tracing through the outputs of N-body simulations, which requires knowledge of the gravitational potential and accurate solvers for light ray trajectories. A less accurate procedure, based on the Born approximation, only requires knowledge of the density field, and can be implemented more efficiently and at a lower computational cost. In this work, we use simulations to show thatmore » deviations of the Born-approximated convergence power spectrum, skewness and kurtosis from their fully ray-traced counterparts are consistent with the smallest nontrivial O(Φ 3) post-Born corrections (so-called geodesic and lens-lens terms). Our results imply a cancellation among the larger O(Φ 4) (and higher order) terms, consistent with previous analytic work. We also find that cosmological parameter bias induced by the Born-approximated power spectrum is negligible even for a LSST-like survey, once galaxy shape noise is considered. When considering higher order statistics such as the κ skewness and kurtosis, however, we find significant bias of up to 2.5σ. Using the LensTools software suite, we show that the Born approximation saves a factor of 4 in computing time with respect to the full ray tracing in reconstructing the convergence.« less

Theoretical Clues to the Ultraviolet Diversity of Type Ia Supernovae

NASA Astrophysics Data System (ADS)

Brown, Peter J.; Baron, E.; Milne, Peter; Roming, Peter W. A.; Wang, Lifan

2015-08-01

The effect of metallicity on the observed light of Type Ia supernovae (SNe Ia) could lead to systematic errors as the absolute magnitudes of local and distant SNe Ia are compared to measure luminosity distances and determine cosmological parameters. The UV light may be especially sensitive to metallicity, though different modeling methods disagree as to the magnitude, wavelength dependence, and even the sign of the effect. The outer density structure, 56Ni, and to a lesser degree asphericity, also impact the UV. We compute synthetic photometry of various metallicity-dependent models and compare to UV/optical photometry from the Swift Ultra-Violet/Optical Telescope. We find that the scatter in the mid-UV to near-UV colors is larger than predicted by changes in metallicity alone and is not consistent with reddening. We demonstrate that a recently employed method to determine relative abundances using UV spectra can be done using UVOT photometry, but we warn that accurate results require an accurate model of the cause of the variations. The abundance of UV photometry now available should provide constraints on models that typically rely on UV spectroscopy for constraining metallicity, density, and other parameters. Nevertheless, UV spectroscopy for a variety of supernova explosions is still needed to guide the creation of accurate models. A better understanding of the influences affecting the UV is important for using SNe Ia as cosmological probes, as the UV light may test whether SNe Ia are significantly affected by evolutionary effects.

Validity of the Born approximation for beyond Gaussian weak lensing observables

NASA Astrophysics Data System (ADS)

Petri, Andrea; Haiman, Zoltán; May, Morgan

2017-06-01

Accurate forward modeling of weak lensing (WL) observables from cosmological parameters is necessary for upcoming galaxy surveys. Because WL probes structures in the nonlinear regime, analytical forward modeling is very challenging, if not impossible. Numerical simulations of WL features rely on ray tracing through the outputs of N -body simulations, which requires knowledge of the gravitational potential and accurate solvers for light ray trajectories. A less accurate procedure, based on the Born approximation, only requires knowledge of the density field, and can be implemented more efficiently and at a lower computational cost. In this work, we use simulations to show that deviations of the Born-approximated convergence power spectrum, skewness and kurtosis from their fully ray-traced counterparts are consistent with the smallest nontrivial O (Φ3) post-Born corrections (so-called geodesic and lens-lens terms). Our results imply a cancellation among the larger O (Φ4) (and higher order) terms, consistent with previous analytic work. We also find that cosmological parameter bias induced by the Born-approximated power spectrum is negligible even for a LSST-like survey, once galaxy shape noise is considered. When considering higher order statistics such as the κ skewness and kurtosis, however, we find significant bias of up to 2.5 σ . Using the LensTools software suite, we show that the Born approximation saves a factor of 4 in computing time with respect to the full ray tracing in reconstructing the convergence.

A validated approach for modeling collapse of steel structures

NASA Astrophysics Data System (ADS)

Saykin, Vitaliy Victorovich

A civil engineering structure is faced with many hazardous conditions such as blasts, earthquakes, hurricanes, tornadoes, floods, and fires during its lifetime. Even though structures are designed for credible events that can happen during a lifetime of the structure, extreme events do happen and cause catastrophic failures. Understanding the causes and effects of structural collapse is now at the core of critical areas of national need. One factor that makes studying structural collapse difficult is the lack of full-scale structural collapse experimental test results against which researchers could validate their proposed collapse modeling approaches. The goal of this work is the creation of an element deletion strategy based on fracture models for use in validated prediction of collapse of steel structures. The current work reviews the state-of-the-art of finite element deletion strategies for use in collapse modeling of structures. It is shown that current approaches to element deletion in collapse modeling do not take into account stress triaxiality in vulnerable areas of the structure, which is important for proper fracture and element deletion modeling. The report then reviews triaxiality and its role in fracture prediction. It is shown that fracture in ductile materials is a function of triaxiality. It is also shown that, depending on the triaxiality range, different fracture mechanisms are active and should be accounted for. An approach using semi-empirical fracture models as a function of triaxiality are employed. The models to determine fracture initiation, softening and subsequent finite element deletion are outlined. This procedure allows for stress-displacement softening at an integration point of a finite element in order to subsequently remove the element. This approach avoids abrupt changes in the stress that would create dynamic instabilities, thus making the results more reliable and accurate. The calibration and validation of these models are shown. The calibration is performed using a particle swarm optimization algorithm to establish accurate parameters when calibrated to circumferentially notched tensile coupons. It is shown that consistent, accurate predictions are attained using the chosen models. The variation of triaxiality in steel material during plastic hardening and softening is reported. The range of triaxiality in steel structures undergoing collapse is investigated in detail and the accuracy of the chosen finite element deletion approaches is discussed. This is done through validation of different structural components and structural frames undergoing severe fracture and collapse.

A standard model eye with micro scale multilayer structure for ophthalmic optical coherence tomography equipment

NASA Astrophysics Data System (ADS)

Cao, Zhenggang; Ding, Zengqian; Hu, Zhixiong; Wen, Tao; Qiao, Wen; Liu, Wenli

2016-10-01

Optical coherence tomography (OCT) has been widely applied in diagnosis of eye diseases during the last 20 years. Differing from traditional two-dimension imaging technologies, OCT could also provide cross-sectional information of target tissues simultaneously and precisely. As well known, axial resolution is one of the most critical parameters impacting the OCT image quality, which determines whether an accurate diagnosis could be obtained. Therefore, it is important to evaluate the axial resolution of an OCT equipment. Phantoms always play an important role in the standardization and validation process. Here, a standard model eye with micro-scale multilayer structure was custom designed and manufactured. Mimicking a real human eye, analyzing the physical characteristic of layer structures of retina and cornea in-depth, appropriate materials were selected by testing the scattering coefficient of PDMS phantoms with difference concentration of TiO2 or BaSO4 particles. An artificial retina and cornea with multilayer-films which have a thickness of 10 to 60 micrometers for each layer were fabricated using spin coating technology. Considering key parameters of the standard model eye need to be traceable as well as accurate, the optical refractive index and layer structure thicknesses of phantoms were verified by utilizing Thickness Monitoring System. Consequently, a standard OCT model eye was obtained after the retinal or corneal phantom was embedded into a water-filled model eye which has been fabricated by 3D printing technology to simulate ocular dispersion and emmetropic refraction. The eye model was manufactured with a transparent resin to simulate realistic ophthalmic testing environment, and most key optical elements including cornea, lens and vitreous body were realized. By investigating with a research and a clinical OCT system respectively, the OCT model eye was demonstrated with similar physical properties as natural eye, and the multilayer film measurement provided an effective method to rapidly evaluate the axial resolution of ophthalmic OCT devices.

Rail inspection system based on iGPS

NASA Astrophysics Data System (ADS)

Fu, Xiaoyan; Wang, Mulan; Wen, Xiuping

2018-05-01

Track parameters include gauge, super elevation, cross level and so on, which could be calculated through the three-dimensional coordinates of the track. The rail inspection system based on iGPS (indoor/infrared GPS) was composed of base station, receiver, rail inspection frame, wireless communication unit, display and control unit and data processing unit. With the continuous movement of the inspection frame, the system could accurately inspect the coordinates of rail; realize the intelligent detection and precision measurement. According to principle of angle intersection measurement, the inspection model was structured, and detection process was given.

Communication: Analytic continuation of the virial series through the critical point using parametric approximants.

PubMed

Barlow, Nathaniel S; Schultz, Andrew J; Weinstein, Steven J; Kofke, David A

2015-08-21

The mathematical structure imposed by the thermodynamic critical point motivates an approximant that synthesizes two theoretically sound equations of state: the parametric and the virial. The former is constructed to describe the critical region, incorporating all scaling laws; the latter is an expansion about zero density, developed from molecular considerations. The approximant is shown to yield an equation of state capable of accurately describing properties over a large portion of the thermodynamic parameter space, far greater than that covered by each treatment alone.

A non-asymptotic homogenization theory for periodic electromagnetic structures.

PubMed

Tsukerman, Igor; Markel, Vadim A

2014-08-08

Homogenization of electromagnetic periodic composites is treated as a two-scale problem and solved by approximating the fields on both scales with eigenmodes that satisfy Maxwell's equations and boundary conditions as accurately as possible. Built into this homogenization methodology is an error indicator whose value characterizes the accuracy of homogenization. The proposed theory allows one to define not only bulk, but also position-dependent material parameters (e.g. in proximity to a physical boundary) and to quantify the trade-off between the accuracy of homogenization and its range of applicability to various illumination conditions.

Combination of complex momentum representation and Green's function methods in relativistic mean-field theory

NASA Astrophysics Data System (ADS)

Shi, Min; Niu, Zhong-Ming; Liang, Haozhao

2018-06-01

We have combined the complex momentum representation method with the Green's function method in the relativistic mean-field framework to establish the RMF-CMR-GF approach. This new approach is applied to study the halo structure of 74Ca. All the continuum level density of concerned resonant states are calculated accurately without introducing any unphysical parameters, and they are independent of the choice of integral contour. The important single-particle wave functions and densities for the halo phenomenon in 74Ca are discussed in detail.

Bending of an Infinite beam on a base with two parameters in the absence of a part of the base

NASA Astrophysics Data System (ADS)

Aleksandrovskiy, Maxim; Zaharova, Lidiya

2018-03-01

Currently, in connection with the rapid development of high-rise construction and the improvement of joint operation of high-rise structures and bases models, the questions connected with the use of various calculation methods become topical. The rigor of analytical methods is capable of more detailed and accurate characterization of the structures behavior, which will affect the reliability of objects and can lead to a reduction in their cost. In the article, a model with two parameters is used as a computational model of the base that can effectively take into account the distributive properties of the base by varying the coefficient reflecting the shift parameter. The paper constructs the effective analytical solution of the problem of a beam of infinite length interacting with a two-parameter voided base. Using the Fourier integral equations, the original differential equation is reduced to the Fredholm integral equation of the second kind with a degenerate kernel, and all the integrals are solved analytically and explicitly, which leads to an increase in the accuracy of the computations in comparison with the approximate methods. The paper consider the solution of the problem of a beam loaded with a concentrated force applied at the point of origin with a fixed value of the length of the dip section. The paper gives the analysis of the obtained results values for various parameters of coefficient taking into account cohesion of the ground.

A multi-mode real-time terrain parameter estimation method for wheeled motion control of mobile robots

NASA Astrophysics Data System (ADS)

Li, Yuankai; Ding, Liang; Zheng, Zhizhong; Yang, Qizhi; Zhao, Xingang; Liu, Guangjun

2018-05-01

For motion control of wheeled planetary rovers traversing on deformable terrain, real-time terrain parameter estimation is critical in modeling the wheel-terrain interaction and compensating the effect of wheel slipping. A multi-mode real-time estimation method is proposed in this paper to achieve accurate terrain parameter estimation. The proposed method is composed of an inner layer for real-time filtering and an outer layer for online update. In the inner layer, sinkage exponent and internal frictional angle, which have higher sensitivity than that of the other terrain parameters to wheel-terrain interaction forces, are estimated in real time by using an adaptive robust extended Kalman filter (AREKF), whereas the other parameters are fixed with nominal values. The inner layer result can help synthesize the current wheel-terrain contact forces with adequate precision, but has limited prediction capability for time-variable wheel slipping. To improve estimation accuracy of the result from the inner layer, an outer layer based on recursive Gauss-Newton (RGN) algorithm is introduced to refine the result of real-time filtering according to the innovation contained in the history data. With the two-layer structure, the proposed method can work in three fundamental estimation modes: EKF, REKF and RGN, making the method applicable for flat, rough and non-uniform terrains. Simulations have demonstrated the effectiveness of the proposed method under three terrain types, showing the advantages of introducing the two-layer structure.

Tailoring Spin Textures in Complex Oxide Micromagnets

DOE PAGES

Lee, Michael S.; Wynn, Thomas A.; Folven, Erik; ...

2016-09-12

Engineered topological spin textures with submicron dimensions in magnetic materials have emerged in recent years as the building blocks for various spin-based memory devices. Examples of these magnetic configurations include magnetic skyrmions, vortices, and domain walls. Here in this paper, we show the ability to control and characterize the evolution of spin textures in complex oxide micromagnets as a function of temperature through the delicate balance of fundamental materials parameters, micromagnet geometries, and epitaxial strain. These results demonstrate that in order to fully describe the observed spin textures, it is necessary to account for the spatial variation of the magneticmore » parameters within the micromagnet. This study provides the framework to accurately characterize such structures, leading to efficient design of spin-based memory devices based on complex oxide thin films.« less

New optical package and algorithms for accurate estimation and interactive recording of the cloud cover information over land and sea

NASA Astrophysics Data System (ADS)

Krinitskiy, Mikhail; Sinitsyn, Alexey; Gulev, Sergey

2014-05-01

Cloud fraction is a critical parameter for the accurate estimation of short-wave and long-wave radiation - one of the most important surface fluxes over sea and land. Massive estimates of the total cloud cover as well as cloud amount for different layers of clouds are available from visual observations, satellite measurements and reanalyses. However, these data are subject of different uncertainties and need continuous validation against highly accurate in-situ measurements. Sky imaging with high resolution fish eye camera provides an excellent opportunity for collecting cloud cover data supplemented with additional characteristics hardly available from routine visual observations (e.g. structure of cloud cover under broken cloud conditions, parameters of distribution of cloud dimensions). We present operational automatic observational package which is based on fish eye camera taking sky images with high resolution (up to 1Hz) in time and a spatial resolution of 968x648px. This spatial resolution has been justified as an optimal by several sensitivity experiments. For the use of the package at research vessel when the horizontal positioning becomes critical, a special extension of the hardware and software to the package has been developed. These modules provide the explicit detection of the optimal moment for shooting. For the post processing of sky images we developed a software realizing the algorithm of the filtering of sunburn effect in case of small and moderate could cover and broken cloud conditions. The same algorithm accurately quantifies the cloud fraction by analyzing color mixture for each point and introducing the so-called "grayness rate index" for every pixel. The accuracy of the algorithm has been tested using the data collected during several campaigns in 2005-2011 in the North Atlantic Ocean. The collection of images included more than 3000 images for different cloud conditions supplied with observations of standard parameters. The system is fully autonomous and has a block for digital data collection at the hard disk. The system has been tested for a wide range of open ocean cloud conditions and we will demonstrate some pilot results of data processing and physical interpretation of fractional cloud cover estimation.

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 values were largely development-stage independent. The authors suggest that the high level of parameter stability observed in GREENLAB can be used to conduct comparisons among genotypes and, ultimately, genetic analyses. PMID:17158141

Relativistic quasiparticle band structures of Mg2Si, Mg2Ge, and Mg2Sn: Consistent parameterization and prediction of Seebeck coefficients

NASA Astrophysics Data System (ADS)

Shi, Guangsha; Kioupakis, Emmanouil

2018-02-01

We apply density functional and many-body perturbation theory calculations to consistently determine and parameterize the relativistic quasiparticle band structures of Mg2Si, Mg2Ge, and Mg2Sn, and predict the Seebeck coefficient as a function of doping and temperature. The quasiparticle band gaps, including spin-orbit coupling effects, are determined to be 0.728 eV, 0.555 eV, and 0.142 eV for Mg2Si, Mg2Ge, and Mg2Sn, respectively. The inclusion of the semicore electrons of Mg, Ge, and Sn in the valence is found to be important for the accurate determination of the band gaps of Mg2Ge and Mg2Sn. We also developed a Luttinger-Kohn Hamiltonian and determined a set of band parameters to model the near-edge relativistic quasiparticle band structure consistently for all three compounds that can be applied for thermoelectric device simulations. Our calculated values for the Seebeck coefficient of all three compounds are in good agreement with the available experimental data for a broad range of temperatures and carrier concentrations. Our results indicate that quasiparticle corrections are necessary for the accurate determination of Seebeck coefficients at high temperatures at which bipolar transport becomes important.

Spectrally formulated user-defined element in conventional finite element environment for wave motion analysis in 2-D composite structures

NASA Astrophysics Data System (ADS)

Khalili, Ashkan; Jha, Ratneshwar; Samaratunga, Dulip

2016-11-01

Wave propagation analysis in 2-D composite structures is performed efficiently and accurately through the formulation of a User-Defined Element (UEL) based on the wavelet spectral finite element (WSFE) method. The WSFE method is based on the first-order shear deformation theory which yields accurate results for wave motion at high frequencies. The 2-D WSFE model is highly efficient computationally and provides a direct relationship between system input and output in the frequency domain. The UEL is formulated and implemented in Abaqus (commercial finite element software) for wave propagation analysis in 2-D composite structures with complexities. Frequency domain formulation of WSFE leads to complex valued parameters, which are decoupled into real and imaginary parts and presented to Abaqus as real values. The final solution is obtained by forming a complex value using the real number solutions given by Abaqus. Five numerical examples are presented in this article, namely undamaged plate, impacted plate, plate with ply drop, folded plate and plate with stiffener. Wave motions predicted by the developed UEL correlate very well with Abaqus simulations. The results also show that the UEL largely retains computational efficiency of the WSFE method and extends its ability to model complex features.

disLocate: tools to rapidly quantify local intermolecular structure to assess two-dimensional order in self-assembled systems.

PubMed

Bumstead, Matt; Liang, Kunyu; Hanta, Gregory; Hui, Lok Shu; Turak, Ayse

2018-01-24

Order classification is particularly important in photonics, optoelectronics, nanotechnology, biology, and biomedicine, as self-assembled and living systems tend to be ordered well but not perfectly. Engineering sets of experimental protocols that can accurately reproduce specific desired patterns can be a challenge when (dis)ordered outcomes look visually similar. Robust comparisons between similar samples, especially with limited data sets, need a finely tuned ensemble of accurate analysis tools. Here we introduce our numerical Mathematica package disLocate, a suite of tools to rapidly quantify the spatial structure of a two-dimensional dispersion of objects. The full range of tools available in disLocate give different insights into the quality and type of order present in a given dispersion, accessing the translational, orientational and entropic order. The utility of this package allows for researchers to extract the variation and confidence range within finite sets of data (single images) using different structure metrics to quantify local variation in disorder. Containing all metrics within one package allows for researchers to easily and rapidly extract many different parameters simultaneously, allowing robust conclusions to be drawn on the order of a given system. Quantifying the experimental trends which produce desired morphologies enables engineering of novel methods to direct self-assembly.

Structural, optoelectronic, and thermoelectric properties of AZn13 (A=Na, K, Ca, Sr, Ba) compounds

NASA Astrophysics Data System (ADS)

Basit, Abdul; Murtaza, G.; Mahmood, Asif; Yar, Abdullah; Muhammad, S.

2016-08-01

We report the structural, electronic, optical, and thermoelectric properties of the five cubic alkali-earth transition-metals AZn13 (A-Na, K, Ca, Sr, Ba) using density functional theory. Structural properties, electronic structures and optical behaviors are calculated explicitly via highly accurate contemporary full potential-linearized augmented plane wave (FP-LAPW) method. The investigated ground state data of these materials is quite close to the experimental information. The modified Becke-Johnson (mBJ) predicts the intermetallic nature of AZn13 (A-Na, K, Ca, Sr, Ba) materials. The complex dielectric function of these intermetallic compounds has been calculated and the observed noticeable peaks are examined through mBJ. With the help of complex dielectric function, the other important optical parameters like reflectivities, conductivities and refractive indices of AZn13 (A-Na, K, Ca, Sr, Ba) have been calculated as a function of energy. The optical response suggests that AZn13 (A-Na, K, Ca, Sr, Ba) compounds can be used for the optoelectronic devices. Further, the thermoelectric properties have been calculated through BoltzTraP program, the calculated values for different thermoelectric parameters recommend that these AZn13 (A-Na, K, Ca, Sr, Ba) materials are the suitable candidates for thermoelectric applications.

High Frequency Electromagnetic Impedance Measurements for Characterization, Monitoring and Verification Efforts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Ki Ha; Becker, Alex; Framgos, William

1999-06-01

Non-invasive, high-resolution imaging of the shallow subsurface is needed for delineation of buried waste, detection of unexploded ordinance, verification and monitoring of containment structures, and other environmental applications. Electromagnetic measurements at frequencies between 1 and 100 MHz are important for such applications, because the induction number of many targets is small and the ability to determine the dielectric permittivity in addition to electrical conductivity of the subsurface is possible. Earlier workers were successful in developing systems for detecting anomalous areas, but no quantifiable information was accurately determined. For high-resolution imaging, accurate measurements are necessary so the field data can bemore » mapped into the space of the subsurface parameters. We are developing a non-invasive method for accurately imaging the electrical conductivity and dielectric permittivity of the shallow subsurface using the plane wave impedance approach. Electric and magnetic sensors are being tested in a known area against theoretical predictions, thereby insuring that the data collected with the high-frequency impedance (HFI) system will support high-resolution, multi-dimensional imaging techniques.« less

High-Frequency Electromagnetic Impedance Measurements for Characterization, Monitoring and Verification Efforts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Ki Ha; Becker, Alex; Tseng, Hung-Wen

2002-11-20

Non-invasive, high-resolution imaging of the shallow subsurface is needed for delineation of buried waste, detection of unexploded ordinance, verification and monitoring of containment structures, and other environmental applications. Electromagnetic (EM) measurements at frequencies between 1 and 100 MHz are important for such applications, because the induction number of many targets is small and the ability to determine the dielectric permittivity in addition to electrical conductivity of the subsurface is possible. Earlier workers were successful in developing systems for detecting anomalous areas, but no quantifiable information was accurately determined. For high-resolution imaging, accurate measurements are necessary so the field data canmore » be mapped into the space of the subsurface parameters. We are developing a non-invasive method for accurately mapping the electrical conductivity and dielectric permittivity of the shallow subsurface using the EM impedance approach (Frangos, 2001; Lee and Becker, 2001; Song et al., 2002). Electric and magnetic sensors are being tested in a known area against theoretical predictions, thereby insuring that the data collected with the high-frequency impedance (HFI) system will support high-resolution, multi-dimensional imaging techniques.« less

High-Frequency Electromagnetic Impedance Measurements for Characterization, Monitoring, and Verification Efforts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Ki Ha; Becker, Alex

2000-06-01

Non-invasive, high-resolution imaging of the shallow subsurface is needed for delineation of buried waste, detection of unexploded ordinance, verification and monitoring of containment structures, and other environmental applications. Electromagnetic measurements at frequencies between 1 and 100 MHz are important for such applications, because the induction number of many targets is small and the ability to determine the dielectric permittivity in addition to electrical conductivity of the subsurface is possible. Earlier workers were successful in developing systems for detecting anomalous areas, but no quantifiable information was accurately determined. For high-resolution imaging, accurate measurements are necessary so the field data can bemore » mapped into the space of the subsurface parameters. We are developing a non-invasive method for accurately imaging the electrical conductivity and dielectric permittivity of the shallow subsurface using the plane wave impedance approach (Song et al., 1997). Electric and magnetic sensors are being tested in a known area against theoretical predictions, thereby insuring that the data collected with the high-frequency impedance (HFI) system will support high-resolution, multi-dimensional imaging techniques.« less

High-Frequency Electromagnetic Impedance Measurements for Characterization, Monitoring and Verification Efforts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Ki Ha; Becker, Alex; Tseng, Hung-Wen

2001-06-10

Non-invasive, high-resolution imaging of the shallow subsurface is needed for delineation of buried waste, detection of unexploded ordinance, verification and monitoring of containment structures, and other environmental applications. Electromagnetic (EM) measurements at frequencies between 1 and 100 MHz are important for such applications, because the induction number of many targets is small and the ability to determine the dielectric permittivity in addition to electrical conductivity of the subsurface is possible. Earlier workers were successful in developing systems for detecting anomalous areas, but no quantifiable information was accurately determined. For high-resolution imaging, accurate measurements are necessary so the field data canmore » be mapped into the space of the subsurface parameters. We are developing a non-invasive method for accurately mapping the electrical conductivity and dielectric permittivity of the shallow subsurface using the EM impedance approach (Frangos, 2001; Lee and Becker, 2001). Electric and magnetic sensors are being tested in a known area against theoretical predictions, thereby insuring that the data collected with the high-frequency impedance (HFI) system will support high-resolution, multi-dimensional imaging techniques.« less

Structure, dynamics and bifurcations of discrete solitons in trapped ion crystals

NASA Astrophysics Data System (ADS)

Landa, H.; Reznik, B.; Brox, J.; Mielenz, M.; Schaetz, T.

2013-09-01

We study discrete solitons (kinks) accessible in the state-of-the-art trapped ion experiments, considering zigzag crystals and quasi-three-dimensional configurations, both theoretically and experimentally. We first extend the theoretical understanding of different phenomena predicted and recently experimentally observed in the structure and dynamics of these topological excitations. Employing tools from topological degree theory, we analyze bifurcations of crystal configurations in dependence on the trapping parameters, and investigate the formation of kink configurations and the transformations of kinks between different structures. This allows us to accurately define and calculate the effective potential experienced by solitons within the Wigner crystal, and study how this (so-called Peierls-Nabarro) potential gets modified to a non-periodic globally trapping potential in certain parameter regimes. The kinks' rest mass (energy) and spectrum of modes are computed and the dynamics of linear and nonlinear kink oscillations are analyzed. We also present novel, experimentally observed, configurations of kinks incorporating a large-mass defect realized by an embedded molecular ion, and of pairs of interacting kinks stable for long times, offering the perspective for exploring and exploiting complex collective nonlinear excitations, controllable on the quantum level.

Ubiquitous human upper-limb motion estimation using wearable sensors.

PubMed

Zhang, Zhi-Qiang; Wong, Wai-Choong; Wu, Jian-Kang

2011-07-01

Human motion capture technologies have been widely used in a wide spectrum of applications, including interactive game and learning, animation, film special effects, health care, navigation, and so on. The existing human motion capture techniques, which use structured multiple high-resolution cameras in a dedicated studio, are complicated and expensive. With the rapid development of microsensors-on-chip, human motion capture using wearable microsensors has become an active research topic. Because of the agility in movement, upper-limb motion estimation has been regarded as the most difficult problem in human motion capture. In this paper, we take the upper limb as our research subject and propose a novel ubiquitous upper-limb motion estimation algorithm, which concentrates on modeling the relationship between upper-arm movement and forearm movement. A link structure with 5 degrees of freedom (DOF) is proposed to model the human upper-limb skeleton structure. Parameters are defined according to Denavit-Hartenberg convention, forward kinematics equations are derived, and an unscented Kalman filter is deployed to estimate the defined parameters. The experimental results have shown that the proposed upper-limb motion capture and analysis algorithm outperforms other fusion methods and provides accurate results in comparison to the BTS optical motion tracker.

A clustering algorithm for determining community structure in complex networks

NASA Astrophysics Data System (ADS)

Jin, Hong; Yu, Wei; Li, ShiJun

2018-02-01

Clustering algorithms are attractive for the task of community detection in complex networks. DENCLUE is a representative density based clustering algorithm which has a firm mathematical basis and good clustering properties allowing for arbitrarily shaped clusters in high dimensional datasets. However, this method cannot be directly applied to community discovering due to its inability to deal with network data. Moreover, it requires a careful selection of the density parameter and the noise threshold. To solve these issues, a new community detection method is proposed in this paper. First, we use a spectral analysis technique to map the network data into a low dimensional Euclidean Space which can preserve node structural characteristics. Then, DENCLUE is applied to detect the communities in the network. A mathematical method named Sheather-Jones plug-in is chosen to select the density parameter which can describe the intrinsic clustering structure accurately. Moreover, every node on the network is meaningful so there were no noise nodes as a result the noise threshold can be ignored. We test our algorithm on both benchmark and real-life networks, and the results demonstrate the effectiveness of our algorithm over other popularity density based clustering algorithms adopted to community detection.

Structural tuning of photoluminescence in nanoporous anodic alumina by hard anodization in oxalic and malonic acids

PubMed Central

2012-01-01

We report on an exhaustive and systematic study about the photoluminescent properties of nanoporous anodic alumina membranes fabricated by the one-step anodization process under hard conditions in oxalic and malonic acids. This optical property is analysed as a function of several parameters (i.e. hard anodization voltage, pore diameter, membrane thickness, annealing temperature and acid electrolyte). This analysis makes it possible to tune the photoluminescent behaviour at will simply by modifying the structural characteristics of these membranes. This structural tuning ability is of special interest in such fields as optoelectronics, in which an accurate design of the basic nanostructures (e.g. microcavities, resonators, filters, supports, etc.) yields the control over their optical properties and, thus, upon the performance of the nanodevices derived from them (biosensors, interferometers, selective filters, etc.) PMID:22515214

Studies of HZE particle interactions and transport for space radiation protection purposes

NASA Technical Reports Server (NTRS)

Townsend, Lawrence W.; Wilson, John W.; Schimmerling, Walter; Wong, Mervyn

1987-01-01

The main emphasis is on developing general methods for accurately predicting high-energy heavy ion (HZE) particle interactions and transport for use by researchers in mission planning studies, in evaluating astronaut self-shielding factors, and in spacecraft shield design and optimization studies. The two research tasks are: (1) to develop computationally fast and accurate solutions to the Boltzmann (transport) equation; and (2) to develop accurate HZE interaction models, from fundamental physical considerations, for use as inputs into these transport codes. Accurate solutions to the HZE transport problem have been formulated through a combination of analytical and numerical techniques. In addition, theoretical models for the input interaction parameters are under development: stopping powers, nuclear absorption cross sections, and fragmentation parameters.

Self-recalibration of a robot-assisted structured-light-based measurement system.

PubMed

Xu, Jing; Chen, Rui; Liu, Shuntao; Guan, Yong

2017-11-10

The structured-light-based measurement method is widely employed in numerous fields. However, for industrial inspection, to achieve complete scanning of a work piece and overcome occlusion, the measurement system needs to be moved to different viewpoints. Moreover, frequent reconfiguration of the measurement system may be needed based on the size of the measured object, making the self-recalibration of extrinsic parameters indispensable. To this end, this paper proposes an automatic self-recalibration and reconstruction method, wherein a robot arm is employed to move the measurement system for complete scanning; the self-recalibration is achieved using fundamental matrix calculations and point cloud registration without the need for an accurate calibration gauge. Experimental results demonstrate the feasibility and accuracy of our method.

Microfluidic 3D cell culture: potential application for tissue-based bioassays

PubMed Central

Li, XiuJun (James); Valadez, Alejandra V.; Zuo, Peng; Nie, Zhihong

2014-01-01

Current fundamental investigations of human biology and the development of therapeutic drugs, commonly rely on two-dimensional (2D) monolayer cell culture systems. However, 2D cell culture systems do not accurately recapitulate the structure, function, physiology of living tissues, as well as highly complex and dynamic three-dimensional (3D) environments in vivo. The microfluidic technology can provide micro-scale complex structures and well-controlled parameters to mimic the in vivo environment of cells. The combination of microfluidic technology with 3D cell culture offers great potential for in vivo-like tissue-based applications, such as the emerging organ-on-a-chip system. This article will review recent advances in microfluidic technology for 3D cell culture and their biological applications. PMID:22793034

Ab-initio investigations for opto-electronic response of (Cd, Zn)Ga2Te4: Promising solar PV materials

NASA Astrophysics Data System (ADS)

Sahariya, Jagrati; Soni, Amit; Kumar, Pancham

2018-04-01

In this paper, the first principle calculations are performed to analyze the structural, electronic and optical behavior of promising solar materials (Cd,Zn)Ga2Te4. To perform these calculations we have used one of the most accurate Full Potential Linearized Augmented Plane Wave (FP-LAPW) method. The ground state properties of these compounds are confirmed over here after proper examination of energy and charge convergence using Perdew-Burke-Ernzerhof (PBE-sol) exchange correlation potential. The investigations performed such as energy band structure, Density of States (DOS), optical parameters like complex dielectric function and absorption co-efficient are discussed over here to understand the overall response of the chosen system.

The circuit parameters measurement of the SABALAN-I plasma focus facility and comparison with Lee Model

NASA Astrophysics Data System (ADS)

Karimi, F. S.; Saviz, S.; Ghoranneviss, M.; Salem, M. K.; Aghamir, F. M.

The circuit parameters are investigated in a Mather-type plasma focus device. The experiments are performed in the SABALAN-I plasma focus facility (2 kJ, 20 kV, 10 μF). A 12-turn Rogowski coil is built and used to measure the time derivative of discharge current (dI/dt). The high pressure test has been performed in this work, as alternative technique to short circuit test to determine the machine circuit parameters and calibration factor of the Rogowski coil. The operating parameters are calculated by two methods and the results show that the relative error of determined parameters by method I, are very low in comparison to method II. Thus the method I produces more accurate results than method II. The high pressure test is operated with this assumption that no plasma motion and the circuit parameters may be estimated using R-L-C theory given that C0 is known. However, for a plasma focus, even at highest permissible pressure it is found that there is significant motion, so that estimated circuit parameters not accurate. So the Lee Model code is used in short circuit mode to generate the computed current trace for fitting to the current waveform was integrated from current derivative signal taken with Rogowski coil. Hence, the dynamics of plasma is accounted for into the estimation and the static bank parameters are determined accurately.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Newsom, R. K.; Sivaraman, C.; Shippert, T. R.

Wind speed and direction, together with pressure, temperature, and relative humidity, are the most fundamental atmospheric state parameters. Accurate measurement of these parameters is crucial for numerical weather prediction. Vertically resolved wind measurements in the atmospheric boundary layer are particularly important for modeling pollutant and aerosol transport. Raw data from a scanning coherent Doppler lidar system can be processed to generate accurate height-resolved measurements of wind speed and direction in the atmospheric boundary layer.

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

PubMed Central

2014-01-01

Background Accurate estimation of parameters of biochemical models is required to characterize the dynamics of molecular processes. This problem is intimately linked to identifying the most informative experiments for accomplishing such tasks. While significant progress has been made, effective experimental strategies for parameter identification and for distinguishing among alternative network topologies remain unclear. We approached these questions in an unbiased manner using a unique community-based approach in the context of the DREAM initiative (Dialogue for Reverse Engineering Assessment of Methods). We created an in silico test framework under which participants could probe a network with hidden parameters by requesting a range of experimental assays; results of these experiments were simulated according to a model of network dynamics only partially revealed to participants. Results We proposed two challenges; in the first, participants were given the topology and underlying biochemical structure of a 9-gene regulatory network and were asked to determine its parameter values. In the second challenge, participants were given an incomplete topology with 11 genes and asked to find three missing links in the model. In both challenges, a budget was provided to buy experimental data generated in silico with the model and mimicking the features of different common experimental techniques, such as microarrays and fluorescence microscopy. Data could be bought at any stage, allowing participants to implement an iterative loop of experiments and computation. Conclusions A total of 19 teams participated in this competition. The results suggest that the combination of state-of-the-art parameter estimation and a varied set of experimental methods using a few datasets, mostly fluorescence imaging data, can accurately determine parameters of biochemical models of gene regulation. However, the task is considerably more difficult if the gene network topology is not completely defined, as in challenge 2. Importantly, we found that aggregating independent parameter predictions and network topology across submissions creates a solution that can be better than the one from the best-performing submission. PMID:24507381

Monte Carlo modeling of the Siemens Optifocus multileaf collimator.

PubMed

Laliena, Victor; García-Romero, Alejandro

2015-05-01

We have developed a new component module for the BEAMnrc software package, called SMLC, which models the tongue-and-groove structure of the Siemens Optifocus multileaf collimator. The ultimate goal is to perform accurate Monte Carlo simulations of the IMRT treatments carried out with Optifocus. SMLC has been validated by direct geometry checks and by comparing quantitatively the results of simulations performed with it and with the component module VARMLC. Measurements and Monte Carlo simulations of absorbed dose distributions of radiation fields sensitive to the tongue-and-groove effect have been performed to tune the free parameters of SMLC. The measurements cannot be accurately reproduced with VARMLC. Finally, simulations of a typical IMRT field showed that SMLC improves the agreement with experimental measurements with respect to VARMLC in clinically relevant cases. 87.55. K. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Automated adaptive inference of phenomenological dynamical models.

PubMed

Daniels, Bryan C; Nemenman, Ilya

2015-08-21

Dynamics of complex systems is often driven by large and intricate networks of microscopic interactions, whose sheer size obfuscates understanding. With limited experimental data, many parameters of such dynamics are unknown, and thus detailed, mechanistic models risk overfitting and making faulty predictions. At the other extreme, simple ad hoc models often miss defining features of the underlying systems. Here we develop an approach that instead constructs phenomenological, coarse-grained models of network dynamics that automatically adapt their complexity to the available data. Such adaptive models produce accurate predictions even when microscopic details are unknown. The approach is computationally tractable, even for a relatively large number of dynamical variables. Using simulated data, it correctly infers the phase space structure for planetary motion, avoids overfitting in a biological signalling system and produces accurate predictions for yeast glycolysis with tens of data points and over half of the interacting species unobserved.

Application of double-hybrid density functionals to charge transfer in N-substituted pentacenequinones.

PubMed

Sancho-García, J C

2012-05-07

A set of N-heteroquinones, deriving from oligoacenes, have been recently proposed as n-type organic semiconductors with high electron mobilities in thin-film transistors. Generally speaking, this class of compounds self-assembles in neighboring π-stacks linked by weak hydrogen bonds. We aim at theoretically characterizing here the sequential charge transport (hopping) process expected to take place across these arrays of molecules. To do so, we need to accurately address the preferred packing of these materials simultaneously to single-molecule properties related to charge-transfer events, carefully employing dispersion-corrected density functional theory methods to accurately extract the key molecular parameters governing this phenomenon at the nanoscale. This study confirms the great deal of interest around these compounds, since controlled functionalization of model molecules (i.e., pentacene) allows to efficiently tune the corresponding charge mobilities, and the capacity of modern quantum-chemical methods to predict it after rationalizing the underlying structure-property relationships.

Automated adaptive inference of phenomenological dynamical models

PubMed Central

Daniels, Bryan C.; Nemenman, Ilya

2015-01-01

Dynamics of complex systems is often driven by large and intricate networks of microscopic interactions, whose sheer size obfuscates understanding. With limited experimental data, many parameters of such dynamics are unknown, and thus detailed, mechanistic models risk overfitting and making faulty predictions. At the other extreme, simple ad hoc models often miss defining features of the underlying systems. Here we develop an approach that instead constructs phenomenological, coarse-grained models of network dynamics that automatically adapt their complexity to the available data. Such adaptive models produce accurate predictions even when microscopic details are unknown. The approach is computationally tractable, even for a relatively large number of dynamical variables. Using simulated data, it correctly infers the phase space structure for planetary motion, avoids overfitting in a biological signalling system and produces accurate predictions for yeast glycolysis with tens of data points and over half of the interacting species unobserved. PMID:26293508

Analytical model of diffuse reflectance spectrum of skin tissue

NASA Astrophysics Data System (ADS)

Lisenko, S. A.; Kugeiko, M. M.; Firago, V. A.; Sobchuk, A. N.

2014-01-01

We have derived simple analytical expressions that enable highly accurate calculation of diffusely reflected light signals of skin in the spectral range from 450 to 800 nm at a distance from the region of delivery of exciting radiation. The expressions, taking into account the dependence of the detected signals on the refractive index, transport scattering coefficient, absorption coefficient and anisotropy factor of the medium, have been obtained in the approximation of a two-layer medium model (epidermis and dermis) for the same parameters of light scattering but different absorption coefficients of layers. Numerical experiments on the retrieval of the skin biophysical parameters from the diffuse reflectance spectra simulated by the Monte Carlo method show that commercially available fibre-optic spectrophotometers with a fixed distance between the radiation source and detector can reliably determine the concentration of bilirubin, oxy- and deoxyhaemoglobin in the dermis tissues and the tissue structure parameter characterising the size of its effective scatterers. We present the examples of quantitative analysis of the experimental data, confirming the correctness of estimates of biophysical parameters of skin using the obtained analytical expressions.

Exciton scattering approach for optical spectra calculations in branched conjugated macromolecules

NASA Astrophysics Data System (ADS)

Li, Hao; Wu, Chao; Malinin, Sergey V.; Tretiak, Sergei; Chernyak, Vladimir Y.

2016-12-01

The exciton scattering (ES) technique is a multiscale approach based on the concept of a particle in a box and developed for efficient calculations of excited-state electronic structure and optical spectra in low-dimensional conjugated macromolecules. Within the ES method, electronic excitations in molecular structure are attributed to standing waves representing quantum quasi-particles (excitons), which reside on the graph whose edges and nodes stand for the molecular linear segments and vertices, respectively. Exciton propagation on the linear segments is characterized by the exciton dispersion, whereas exciton scattering at the branching centers is determined by the energy-dependent scattering matrices. Using these ES energetic parameters, the excitation energies are then found by solving a set of generalized "particle in a box" problems on the graph that represents the molecule. Similarly, unique energy-dependent ES dipolar parameters permit calculations of the corresponding oscillator strengths, thus, completing optical spectra modeling. Both the energetic and dipolar parameters can be extracted from quantum-chemical computations in small molecular fragments and tabulated in the ES library for further applications. Subsequently, spectroscopic modeling for any macrostructure within a considered molecular family could be performed with negligible numerical effort. We demonstrate the ES method application to molecular families of branched conjugated phenylacetylenes and ladder poly-para-phenylenes, as well as structures with electron donor and acceptor chemical substituents. Time-dependent density functional theory (TD-DFT) is used as a reference model for electronic structure. The ES calculations accurately reproduce the optical spectra compared to the reference quantum chemistry results, and make possible to predict spectra of complex macromolecules, where conventional electronic structure calculations are unfeasible.

Characterizing the Background Corona with SDO/AIA

NASA Technical Reports Server (NTRS)

Napier, Kate; Alexander, Caroline; Winebarger, Amy

2014-01-01

Characterizing the nature of the solar coronal background would enable scientists to more accurately determine plasma parameters, and may lead to a better understanding of the coronal heating problem. Because scientists study the 3D structure of the Sun in 2D, any line-of-sight includes both foreground and background material, and thus, the issue of background subtraction arises. By investigating the intensity values in and around an active region, using multiple wavelengths collected from the Atmospheric Imaging Assembly (AIA) on the Solar Dynamics Observatory (SDO) over an eight-hour period, this project aims to characterize the background as smooth or structured. Different methods were employed to measure the true coronal background and create minimum intensity images. These were then investigated for the presence of structure. The background images created were found to contain long-lived structures, including coronal loops, that were still present in all of the wavelengths, 131, 171, 193, 211, and 335 A. The intensity profiles across the active region indicate that the background is much more structured than previously thought.

Thermoelectric properties of AgSbTe₂ from first-principles calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rezaei, Nafiseh; Akbarzadeh, Hadi; Hashemifar, S. Javad, E-mail: hashemifar@cc.iut.ac.ir

2014-09-14

The structural, electronic, and transport properties of AgSbTe₂ are studied by using full-relativistic first-principles electronic structure calculation and semiclassical description of transport parameters. The results indicate that, within various exchange-correlation functionals, the cubic Fd3⁻m and trigonal R3⁻m structures of AgSbTe₂ are more stable than two other considered structures. The computed Seebeck coefficients at different values of the band gap and carrier concentration are accurately compared with the available experimental data to speculate a band gap of about 0.1–0.35 eV for AgSbTe₂ compound, in agreement with our calculated electronic structure within the hybrid HSE (Heyd-Scuseria-Ernzerhof) functional. By calculating the semiclassical Seebeckmore » coefficient, electrical conductivity, and electronic part of thermal conductivity, we present the theoretical upper limit of the thermoelectric figure of merit of AgSbTe₂ as a function of temperature and carrier concentration.« less

STEAM: a software tool based on empirical analysis for micro electro mechanical systems

NASA Astrophysics Data System (ADS)

Devasia, Archana; Pasupuleti, Ajay; Sahin, Ferat

2006-03-01

In this research a generalized software framework that enables accurate computer aided design of MEMS devices is developed. The proposed simulation engine utilizes a novel material property estimation technique that generates effective material properties at the microscopic level. The material property models were developed based on empirical analysis and the behavior extraction of standard test structures. A literature review is provided on the physical phenomena that govern the mechanical behavior of thin films materials. This survey indicates that the present day models operate under a wide range of assumptions that may not be applicable to the micro-world. Thus, this methodology is foreseen to be an essential tool for MEMS designers as it would develop empirical models that relate the loading parameters, material properties, and the geometry of the microstructures with its performance characteristics. This process involves learning the relationship between the above parameters using non-parametric learning algorithms such as radial basis function networks and genetic algorithms. The proposed simulation engine has a graphical user interface (GUI) which is very adaptable, flexible, and transparent. The GUI is able to encompass all parameters associated with the determination of the desired material property so as to create models that provide an accurate estimation of the desired property. This technique was verified by fabricating and simulating bilayer cantilevers consisting of aluminum and glass (TEOS oxide) in our previous work. The results obtained were found to be very encouraging.

Baryon acoustic oscillations in 2D: Modeling redshift-space power spectrum from perturbation theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taruya, Atsushi; Institute for the Physics and Mathematics of the Universe, University of Tokyo, Kashiwa, Chiba 277-8568; Nishimichi, Takahiro

2010-09-15

We present an improved prescription for the matter power spectrum in redshift space taking proper account of both nonlinear gravitational clustering and redshift distortion, which are of particular importance for accurately modeling baryon acoustic oscillations (BAOs). Contrary to the models of redshift distortion phenomenologically introduced but frequently used in the literature, the new model includes the corrections arising from the nonlinear coupling between the density and velocity fields associated with two competitive effects of redshift distortion, i.e., Kaiser and Finger-of-God effects. Based on the improved treatment of perturbation theory for gravitational clustering, we compare our model predictions with the monopolemore » and quadrupole power spectra of N-body simulations, and an excellent agreement is achieved over the scales of BAOs. Potential impacts on constraining dark energy and modified gravity from the redshift-space power spectrum are also investigated based on the Fisher-matrix formalism, particularly focusing on the measurements of the Hubble parameter, angular diameter distance, and growth rate for structure formation. We find that the existing phenomenological models of redshift distortion produce a systematic error on measurements of the angular diameter distance and Hubble parameter by 1%-2%, and the growth-rate parameter by {approx}5%, which would become non-negligible for future galaxy surveys. Correctly modeling redshift distortion is thus essential, and the new prescription for the redshift-space power spectrum including the nonlinear corrections can be used as an accurate theoretical template for anisotropic BAOs.« less

A feasibility study for using ABS plastic and a low-cost 3D printer for patient-specific brachytherapy mould design.

PubMed

Harris, Benjamin D; Nilsson, Sanna; Poole, Christopher M

2015-09-01

This feasibility study aims to determine if a low-cost 3D printer (BitsFromBytes 3D Touch) with ABS plastic can print custom mould structures and catheter channels defined in a brachytherapy treatment planning system (Nucletron Oncentra) for patient-specific treatment. Printer accuracy was evaluated through physical measurement, and print quality was investigated by adjusting print parameters (print speed, layer thickness, percentage infill). Catheter positioning and reproducibility were measured over repeated insertions. ABS plastic water equivalency was investigated by comparing Ir-192 HDR source dose distributions, measured with radiochromic film, in ABS plastic and in water. Structures and catheter channels were printed accurately to within 0.5 mm laterally and 1 mm in the vertical print direction. Adjusting print parameters could reduce print time, albeit with reduced print quality. 3.5 mm channel diameters allowed for easy catheter insertion. Catheter positioning was reproducible to within 0.5 mm but, because of catheter flex within the channel, was on average 1 mm offset from defined TPS positions. This offset could be accounted for by repeating the treatment planning CT scan with the printed mould positioned on the patient. Dose attenuation in ABS plastic and in water was equivalent to within the measurement limitations. While clinical uses for this particular low-cost printer and ABS plastic are limited by print size restrictions and non-certification for biocompatibility, it has been demonstrated that a low-cost 3D printer set-up can accurately create custom moulds and catheter channels potentially acceptable for clinical use.

High Resolution Tsunami Modeling and Assessment of Harbor Resilience; Case Study in Istanbul

NASA Astrophysics Data System (ADS)

Cevdet Yalciner, Ahmet; Aytore, Betul; Gokhan Guler, Hasan; Kanoglu, Utku; Duzgun, Sebnem; Zaytsev, Andrey; Arikawa, Taro; Tomita, Takashi; Ozer Sozdinler, Ceren; Necmioglu, Ocal; Meral Ozel, Nurcan

2014-05-01

Ports and harbors are the major vulnerable coastal structures under tsunami attack. Resilient harbors against tsunami impacts are essential for proper, efficient and successful rescue operations and reduction of the loss of life and property by tsunami disasters. There are several critical coastal structures as such in the Marmara Sea. Haydarpasa and Yenikapi ports are located in the Marmara Sea coast of Istanbul. These two ports are selected as the sites of numerical experiments to test their resilience under tsunami impact. Cargo, container and ro-ro handlings, and short/long distance passenger transfers are the common services in both ports. Haydarpasa port has two breakwaters with the length of three kilometers in total. Yenikapi port has one kilometer long breakwater. The accurate resilience analysis needs high resolution tsunami modeling and careful assessment of the site. Therefore, building data with accurate coordinates of their foot prints and elevations are obtained. The high resolution bathymetry and topography database with less than 5m grid size is developed for modeling. The metadata of the several types of structures and infrastructure of the ports and environs are processed. Different resistances for the structures/buildings/infrastructures are controlled by assigning different friction coefficients in a friction matrix. Two different tsunami conditions - high expected and moderate expected - are selected for numerical modeling. The hybrid tsunami simulation and visualization codes NAMI DANCE, STOC-CADMAS System are utilized to solve all necessary tsunami parameters and obtain the spatial and temporal distributions of flow depth, current velocity, inundation distance and maximum water level in the study domain. Finally, the computed critical values of tsunami parameters are evaluated and structural performance of the port components are discussed in regard to a better resilience. ACKNOWLEDGEMENTS: Support by EU 603839 ASTARTE Project, UDAP-Ç-12-14 of AFAD, 108Y227 and 113M556 of TUBITAK, RAPSODI (CONCERT_Dis-021) of CONCERT-Japan Joint Call, Earthquake and Tsunami Disaster Mitigation in The Marmara Region and Disaster Education in Turkey Japan-Turkey Joint Research Project by SATREPS, 2011K140210 of DPT, Istanbul Metropolitan Municipality are acknowledged.

Parameter extraction using global particle swarm optimization approach and the influence of polymer processing temperature on the solar cell parameters

NASA Astrophysics Data System (ADS)

Kumar, S.; Singh, A.; Dhar, A.

2017-08-01

The accurate estimation of the photovoltaic parameters is fundamental to gain an insight of the physical processes occurring inside a photovoltaic device and thereby to optimize its design, fabrication processes, and quality. A simulative approach of accurately determining the device parameters is crucial for cell array and module simulation when applied in practical on-field applications. In this work, we have developed a global particle swarm optimization (GPSO) approach to estimate the different solar cell parameters viz., ideality factor (η), short circuit current (Isc), open circuit voltage (Voc), shunt resistant (Rsh), and series resistance (Rs) with wide a search range of over ±100 % for each model parameter. After validating the accurateness and global search power of the proposed approach with synthetic and noisy data, we applied the technique to the extract the PV parameters of ZnO/PCDTBT based hybrid solar cells (HSCs) prepared under different annealing conditions. Further, we examine the variation of extracted model parameters to unveil the physical processes occurring when different annealing temperatures are employed during the device fabrication and establish the role of improved charge transport in polymer films from independent FET measurements. The evolution of surface morphology, optical absorption, and chemical compositional behaviour of PCDTBT co-polymer films as a function of processing temperature has also been captured in the study and correlated with the findings from the PV parameters extracted using GPSO approach.

State-space models’ dirty little secrets: even simple linear Gaussian models can have estimation problems

NASA Astrophysics Data System (ADS)

Auger-Méthé, Marie; Field, Chris; Albertsen, Christoffer M.; Derocher, Andrew E.; Lewis, Mark A.; Jonsen, Ian D.; Mills Flemming, Joanna

2016-05-01

State-space models (SSMs) are increasingly used in ecology to model time-series such as animal movement paths and population dynamics. This type of hierarchical model is often structured to account for two levels of variability: biological stochasticity and measurement error. SSMs are flexible. They can model linear and nonlinear processes using a variety of statistical distributions. Recent ecological SSMs are often complex, with a large number of parameters to estimate. Through a simulation study, we show that even simple linear Gaussian SSMs can suffer from parameter- and state-estimation problems. We demonstrate that these problems occur primarily when measurement error is larger than biological stochasticity, the condition that often drives ecologists to use SSMs. Using an animal movement example, we show how these estimation problems can affect ecological inference. Biased parameter estimates of a SSM describing the movement of polar bears (Ursus maritimus) result in overestimating their energy expenditure. We suggest potential solutions, but show that it often remains difficult to estimate parameters. While SSMs are powerful tools, they can give misleading results and we urge ecologists to assess whether the parameters can be estimated accurately before drawing ecological conclusions from their results.

MARE2DEM: a 2-D inversion code for controlled-source electromagnetic and magnetotelluric data

NASA Astrophysics Data System (ADS)

Key, Kerry

2016-10-01

This work presents MARE2DEM, a freely available code for 2-D anisotropic inversion of magnetotelluric (MT) data and frequency-domain controlled-source electromagnetic (CSEM) data from onshore and offshore surveys. MARE2DEM parametrizes the inverse model using a grid of arbitrarily shaped polygons, where unstructured triangular or quadrilateral grids are typically used due to their ease of construction. Unstructured grids provide significantly more geometric flexibility and parameter efficiency than the structured rectangular grids commonly used by most other inversion codes. Transmitter and receiver components located on topographic slopes can be tilted parallel to the boundary so that the simulated electromagnetic fields accurately reproduce the real survey geometry. The forward solution is implemented with a goal-oriented adaptive finite-element method that automatically generates and refines unstructured triangular element grids that conform to the inversion parameter grid, ensuring accurate responses as the model conductivity changes. This dual-grid approach is significantly more efficient than the conventional use of a single grid for both the forward and inverse meshes since the more detailed finite-element meshes required for accurate responses do not increase the memory requirements of the inverse problem. Forward solutions are computed in parallel with a highly efficient scaling by partitioning the data into smaller independent modeling tasks consisting of subsets of the input frequencies, transmitters and receivers. Non-linear inversion is carried out with a new Occam inversion approach that requires fewer forward calls. Dense matrix operations are optimized for memory and parallel scalability using the ScaLAPACK parallel library. Free parameters can be bounded using a new non-linear transformation that leaves the transformed parameters nearly the same as the original parameters within the bounds, thereby reducing non-linear smoothing effects. Data balancing normalization weights for the joint inversion of two or more data sets encourages the inversion to fit each data type equally well. A synthetic joint inversion of marine CSEM and MT data illustrates the algorithm's performance and parallel scaling on up to 480 processing cores. CSEM inversion of data from the Middle America Trench offshore Nicaragua demonstrates a real world application. The source code and MATLAB interface tools are freely available at http://mare2dem.ucsd.edu.

Analysis of Air Traffic Track Data with the AutoBayes Synthesis System

NASA Technical Reports Server (NTRS)

Schumann, Johann Martin Philip; Cate, Karen; Lee, Alan G.

2010-01-01

The Next Generation Air Traffic System (NGATS) is aiming to provide substantial computer support for the air traffic controllers. Algorithms for the accurate prediction of aircraft movements are of central importance for such software systems but trajectory prediction has to work reliably in the presence of unknown parameters and uncertainties. We are using the AutoBayes program synthesis system to generate customized data analysis algorithms that process large sets of aircraft radar track data in order to estimate parameters and uncertainties. In this paper, we present, how the tasks of finding structure in track data, estimation of important parameters in climb trajectories, and the detection of continuous descent approaches can be accomplished with compact task-specific AutoBayes specifications. We present an overview of the AutoBayes architecture and describe, how its schema-based approach generates customized analysis algorithms, documented C/C++ code, and detailed mathematical derivations. Results of experiments with actual air traffic control data are discussed.

Aircraft to aircraft intercomparison during SEMAPHORE

NASA Astrophysics Data System (ADS)

Lambert, Dominique; Durand, Pierre

1998-10-01

During the Structure des Echanges Mer-Atmosphère, Propriétés des Hétérogénéités Océaniques: Recherche Expérimentale (SEMAPHORE) experiment, performed in the Azores region in 1993, two French research aircraft were simultaneously used for in situ measurements in the atmospheric boundary layer. We present the results obtained from one intercomparison flight between the two aircraft. The mean parameters generally agree well, although the temperature has to be slightly shifted in order to be in agreement for the two aircraft. A detailed comparison of the turbulence parameters revealed no bias. The agreement is good for variances and is satisfactory for fluxes and skewness. A thorough study of the errors involved in flux computation revealed that the greatest accuracy is obtained for latent heat flux. Errors in sensible heat flux are considerably greater, and the worst results are obtained for momentum flux. The latter parameter, however, is more accurate than expected from previous parameterizations.

Effect of Helical Slow-Wave Circuit Variations on TWT Cold-Test Characteristics

NASA Technical Reports Server (NTRS)

Kory, Carol L.; Dayton, J. A., Jr.

1998-01-01

Recent advances in the state of the art of computer modeling offer the possibility for the first time to evaluate the effect that slow-wave structure parameter variations, such as manufacturing tolerances, have on the cold-test characteristics of helical traveling-wave tubes (TWT's). This will enable manufacturers to determine the cost effectiveness of controlling the dimensions of the component parts of the TWT, which is almost impossible to do experimentally without building a large number of tubes and controlling several parameters simultaneously. The computer code MAFIA is used in this analysis to determine the effect on dispersion and on-axis interaction impedance of several helical slow-wave circuit parameter variations, including thickness and relative dielectric constant of the support rods, tape width, and height of the metallized films deposited on the dielectric rods. Previous computer analyzes required so many approximations that accurate determinations of the effect of many relevant dimensions on tube performance were practically impossible.

Effect of Helical Slow-Wave Circuit Variations on TWT Cold-Test Characteristics

NASA Technical Reports Server (NTRS)

Kory, Carol L.; Dayton, James A., Jr.

1997-01-01

Recent advances in the state of the art of computer modeling offer the possibility for the first time to evaluate the effect that slow-wave structure parameter variations, such as manufacturing tolerances, have on the cold-test characteristics of helical traveling-wave tubes (TWT's). This will enable manufacturers to determine the cost effectiveness of controlling the dimensions of the component parts of the TWT, which is almost impossible to do experimentally without building a large number of tubes and controlling several parameters simultaneously. The computer code MAFIA is used in this analysis to determine the effect on dispersion and on-axis interaction impedance of several helical slow-wave circuit parameter variations, including thickness and relative dielectric constant of the support rods, tape width, and height of the metallized films deposited on the dielectric rods. Previous computer analyses required so many approximations that accurate determinations of the effect of many relevant dimensions on tube performance were practically impossible.

Effect of Helical Slow-Wave Circuit Variations on TWT Cold-Test Characteristics

NASA Technical Reports Server (NTRS)

Kory, Carol L.; Dayton, James A., Jr.

1998-01-01

Recent advances in the state of the art of computer modeling offer the possibility for the first time to evaluate the effect that slow-wave structure parameter variations, such'as manufacturing tolerances, have on the cold-test characteristics of helical traveling-wave tubes (TWT's). This will enable manufacturers to determine the cost effectiveness of controlling the dimensions of the component parts of the TWT, which is almost impossible to do experimentally without building a large number of tubes and controlling several parameters simultaneously. The computer code MAxwell's equations by the Finite Integration Algorithm (MAFIA) is used in this analysis to determine the effect on dispersion and on-axis interaction impedance of several helical slow-wave circuit parameter variations, including thickness and relative dielectric constant of the support rods, tape width, and height of the metallized films deposited on the dielectric rods. Previous computer analyzes required so many approximations that accurate determinations of the effect of many relevant dimensions on tube performance were practically impossible.

Factors Predictive of Improved Abdominal Ultrasound Visualization after Oral Administration of Simethicone.

PubMed

Marsico, Maria; Gabbani, Tommaso; Casseri, Tommaso; Biagini, Maria Rosa

2016-11-01

Ultrasonography is a non-invasive, accurate and low-cost technique used to study the upper abdomen, but it has reduced reliability in the study of the pancreas and retroperitoneum. Simethicone is a well-known emulsifying agent that has been used to improve ultrasonographic visualization. The aim of this study was to identify anthropometric parameters that are able to predict a good response to simethicone in improving ultrasonographic visualization of abdominal structures. One hundred twenty-seven patients were recruited. After basal examination, their anthropometric parameters were collected. Patients with an incomplete upper abdominal examination because of gastrointestinal gas have greater body mass index, waist circumference and abdominal wall thickness. In our study, the best anthropometric parameter for identifying patients with poor visualization at abdominal ultrasound examination is waist circumference. Using a cutoff of 84 cm, we can identify patients with poor visibility at abdominal ultrasound examination (group B) with a sensitivity of 90%. Copyright © 2016 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sousa, Francisco F. G. de; Rubinger, Rero M.; Sartorelli, José C., E-mail: sartorelli@if.usp.br

We report high-resolution measurements that experimentally confirm a spiral cascade structure and a scaling relationship of shrimps in the Chua's circuit. Circuits constructed using this component allow for a comprehensive characterization of the circuit behaviors through high resolution parameter spaces. To illustrate the power of our technological development for the creation and the study of chaotic circuits, we constructed a Chua circuit and study its high resolution parameter space. The reliability and stability of the designed component allowed us to obtain data for long periods of time (∼21 weeks), a data set from which an accurate estimation of Lyapunov exponentsmore » for the circuit characterization was possible. Moreover, this data, rigorously characterized by the Lyapunov exponents, allows us to reassure experimentally that the shrimps, stable islands embedded in a domain of chaos in the parameter spaces, can be observed in the laboratory. Finally, we confirm that their sizes decay exponentially with the period of the attractor, a result expected to be found in maps of the quadratic family.« less

Lung vessel segmentation in CT images using graph-cuts

NASA Astrophysics Data System (ADS)

Zhai, Zhiwei; Staring, Marius; Stoel, Berend C.

2016-03-01

Accurate lung vessel segmentation is an important operation for lung CT analysis. Filters that are based on analyzing the eigenvalues of the Hessian matrix are popular for pulmonary vessel enhancement. However, due to their low response at vessel bifurcations and vessel boundaries, extracting lung vessels by thresholding the vesselness is not sufficiently accurate. Some methods turn to graph-cuts for more accurate segmentation, as it incorporates neighbourhood information. In this work, we propose a new graph-cuts cost function combining appearance and shape, where CT intensity represents appearance and vesselness from a Hessian-based filter represents shape. Due to the amount of voxels in high resolution CT scans, the memory requirement and time consumption for building a graph structure is very high. In order to make the graph representation computationally tractable, those voxels that are considered clearly background are removed from the graph nodes, using a threshold on the vesselness map. The graph structure is then established based on the remaining voxel nodes, source/sink nodes and the neighbourhood relationship of the remaining voxels. Vessels are segmented by minimizing the energy cost function with the graph-cuts optimization framework. We optimized the parameters used in the graph-cuts cost function and evaluated the proposed method with two manually labeled sub-volumes. For independent evaluation, we used 20 CT scans of the VESSEL12 challenge. The evaluation results of the sub-volume data show that the proposed method produced a more accurate vessel segmentation compared to the previous methods, with F1 score 0.76 and 0.69. In the VESSEL12 data-set, our method obtained a competitive performance with an area under the ROC curve of 0.975, especially among the binary submissions.

BEYOND ELLIPSE(S): ACCURATELY MODELING THE ISOPHOTAL STRUCTURE OF GALAXIES WITH ISOFIT AND CMODEL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ciambur, B. C., E-mail: bciambur@swin.edu.au

2015-09-10

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,more » 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.« less

Seismic source parameters of the induced seismicity at The Geysers geothermal area, California, by a generalized inversion approach

NASA Astrophysics Data System (ADS)

Picozzi, Matteo; Oth, Adrien; Parolai, Stefano; Bindi, Dino; De Landro, Grazia; Amoroso, Ortensia

2017-04-01

The accurate determination of stress drop, seismic efficiency and how source parameters scale with earthquake size is an important for seismic hazard assessment of induced seismicity. We propose an improved non-parametric, data-driven strategy suitable for monitoring induced seismicity, which combines the generalized inversion technique together with genetic algorithms. In the first step of the analysis the generalized inversion technique allows for an effective correction of waveforms for the attenuation and site contributions. Then, the retrieved source spectra are inverted by a non-linear sensitivity-driven inversion scheme that allows accurate estimation of source parameters. We therefore investigate the earthquake source characteristics of 633 induced earthquakes (ML 2-4.5) recorded at The Geysers geothermal field (California) by a dense seismic network (i.e., 32 stations of the Lawrence Berkeley National Laboratory Geysers/Calpine surface seismic network, more than 17.000 velocity records). We find for most of the events a non-selfsimilar behavior, empirical source spectra that requires ωγ source model with γ > 2 to be well fitted and small radiation efficiency ηSW. All these findings suggest different dynamic rupture processes for smaller and larger earthquakes, and that the proportion of high frequency energy radiation and the amount of energy required to overcome the friction or for the creation of new fractures surface changes with the earthquake size. Furthermore, we observe also two distinct families of events with peculiar source parameters that, in one case suggests the reactivation of deep structures linked to the regional tectonics, while in the other supports the idea of an important role of steeply dipping fault in the fluid pressure diffusion.

Neural network river forecasting through baseflow separation and binary-coded swarm optimization

NASA Astrophysics Data System (ADS)

Taormina, Riccardo; Chau, Kwok-Wing; Sivakumar, Bellie

2015-10-01

The inclusion of expert knowledge in data-driven streamflow modeling is expected to yield more accurate estimates of river quantities. Modular models (MMs) designed to work on different parts of the hydrograph are preferred ways to implement such approach. Previous studies have suggested that better predictions of total streamflow could be obtained via modular Artificial Neural Networks (ANNs) trained to perform an implicit baseflow separation. These MMs fit separately the baseflow and excess flow components as produced by a digital filter, and reconstruct the total flow by adding these two signals at the output. The optimization of the filter parameters and ANN architectures is carried out through global search techniques. Despite the favorable premises, the real effectiveness of such MMs has been tested only on a few case studies, and the quality of the baseflow separation they perform has never been thoroughly assessed. In this work, we compare the performance of MM against global models (GMs) for nine different gaging stations in the northern United States. Binary-coded swarm optimization is employed for the identification of filter parameters and model structure, while Extreme Learning Machines, instead of ANN, are used to drastically reduce the large computational times required to perform the experiments. The results show that there is no evidence that MM outperform global GM for predicting the total flow. In addition, the baseflow produced by the MM largely underestimates the actual baseflow component expected for most of the considered gages. This occurs because the values of the filter parameters maximizing overall accuracy do not reflect the geological characteristics of the river basins. The results indeed show that setting the filter parameters according to expert knowledge results in accurate baseflow separation but lower accuracy of total flow predictions, suggesting that these two objectives are intrinsically conflicting rather than compatible.

On the analysis of very small samples of Gaussian repeated measurements: an alternative approach.

PubMed

Westgate, Philip M; Burchett, Woodrow W

2017-03-15

The analysis of very small samples of Gaussian repeated measurements can be challenging. First, due to a very small number of independent subjects contributing outcomes over time, statistical power can be quite small. Second, nuisance covariance parameters must be appropriately accounted for in the analysis in order to maintain the nominal test size. However, available statistical strategies that ensure valid statistical inference may lack power, whereas more powerful methods may have the potential for inflated test sizes. Therefore, we explore an alternative approach to the analysis of very small samples of Gaussian repeated measurements, with the goal of maintaining valid inference while also improving statistical power relative to other valid methods. This approach uses generalized estimating equations with a bias-corrected empirical covariance matrix that accounts for all small-sample aspects of nuisance correlation parameter estimation in order to maintain valid inference. Furthermore, the approach utilizes correlation selection strategies with the goal of choosing the working structure that will result in the greatest power. In our study, we show that when accurate modeling of the nuisance correlation structure impacts the efficiency of regression parameter estimation, this method can improve power relative to existing methods that yield valid inference. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Fractional viscoelasticity of soft elastomers and auxetic foams

NASA Astrophysics Data System (ADS)

Solheim, Hannah; Stanisauskis, Eugenia; Miles, Paul; Oates, William

2018-03-01

Dielectric elastomers are commonly implemented in adaptive structures due to their unique capabilities for real time control of a structure's shape, stiffness, and damping. These active polymers are often used in applications where actuator control or dynamic tunability are important, making an accurate understanding of the viscoelastic behavior critical. This challenge is complicated as these elastomers often operate over a broad range of deformation rates. Whereas research has demonstrated success in applying a nonlinear viscoelastic constitutive model to characterize the behavior of Very High Bond (VHB) 4910, robust predictions of the viscoelastic response over the entire range of time scales is still a significant challenge. An alternative formulation for viscoelastic modeling using fractional order calculus has shown significant improvement in predictive capabilities. While fractional calculus has been explored theoretically in the field of linear viscoelasticity, limited experimental validation and statistical evaluation of the underlying phenomena have been considered. In the present study, predictions across several orders of magnitude in deformation rates are validated against data using a single set of model parameters. Moreover, we illustrate the fractional order is material dependent by running complementary experiments and parameter estimation on the elastomer VHB 4949 as well as an auxetic foam. All results are statistically validated using Bayesian uncertainty methods to obtain posterior densities for the fractional order as well as the hyperelastic parameters.

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.

Multiscale metrologies for process optimization of carbon nanotube polymer composites

DOE PAGES

Natarajan, Bharath; Orloff, Nathan D.; Ashkar, Rana; ...

2016-07-18

Carbon nanotube (CNT) polymer nanocomposites are attractive multifunctional materials with a growing range of commercial applications. With the increasing demand for these materials, it is imperative to develop and validate methods for on-line quality control and process monitoring during production. In this work, a novel combination of characterization techniques is utilized, that facilitates the non-invasive assessment of CNT dispersion in epoxy produced by the scalable process of calendering. First, the structural parameters of these nanocomposites are evaluated across multiple length scales (10 -10 m to 10 -3 m) using scanning gallium-ion microscopy, transmission electron microscopy and small-angle neutron scattering. Then,more » a non-contact resonant microwave cavity perturbation (RCP) technique is employed to accurately measure the AC electrical conductivity of the nanocomposites. Quantitative correlations between the conductivity and structural parameters find the RCP measurements to be sensitive to CNT mass fraction, spatial organization and, therefore, the processing parameters. These results, and the non-contact nature and speed of RCP measurements identify this technique as being ideally suited for quality control of CNT nanocomposites in a nanomanufacturing environment. In conclusion, when validated by the multiscale characterization suite, RCP may be broadly applicable in the production of hybrid functional materials, such as graphene, gold nanorod, and carbon black nanocomposites.« less

Influence of the volume and density functions within geometric models for estimating trunk inertial parameters.

PubMed

Wicke, Jason; Dumas, Genevieve A

2010-02-01

The geometric method combines a volume and a density function to estimate body segment parameters and has the best opportunity for developing the most accurate models. In the trunk, there are many different tissues that greatly differ in density (e.g., bone versus lung). Thus, the density function for the trunk must be particularly sensitive to capture this diversity, such that accurate inertial estimates are possible. Three different models were used to test this hypothesis by estimating trunk inertial parameters of 25 female and 24 male college-aged participants. The outcome of this study indicates that the inertial estimates for the upper and lower trunk are most sensitive to the volume function and not very sensitive to the density function. Although it appears that the uniform density function has a greater influence on inertial estimates in the lower trunk region than in the upper trunk region, this is likely due to the (overestimated) density value used. When geometric models are used to estimate body segment parameters, care must be taken in choosing a model that can accurately estimate segment volumes. Researchers wanting to develop accurate geometric models should focus on the volume function, especially in unique populations (e.g., pregnant or obese individuals).

Experimental design and efficient parameter estimation in preclinical pharmacokinetic studies.

PubMed

Ette, E I; Howie, C A; Kelman, A W; Whiting, B

1995-05-01

Monte Carlo simulation technique used to evaluate the effect of the arrangement of concentrations on the efficiency of estimation of population pharmacokinetic parameters in the preclinical setting is described. Although the simulations were restricted to the one compartment model with intravenous bolus input, they provide the basis of discussing some structural aspects involved in designing a destructive ("quantic") preclinical population pharmacokinetic study with a fixed sample size as is usually the case in such studies. The efficiency of parameter estimation obtained with sampling strategies based on the three and four time point designs were evaluated in terms of the percent prediction error, design number, individual and joint confidence intervals coverage for parameter estimates approaches, and correlation analysis. The data sets contained random terms for both inter- and residual intra-animal variability. The results showed that the typical population parameter estimates for clearance and volume were efficiently (accurately and precisely) estimated for both designs, while interanimal variability (the only random effect parameter that could be estimated) was inefficiently (inaccurately and imprecisely) estimated with most sampling schedules of the two designs. The exact location of the third and fourth time point for the three and four time point designs, respectively, was not critical to the efficiency of overall estimation of all population parameters of the model. However, some individual population pharmacokinetic parameters were sensitive to the location of these times.

Dynamic Modeling from Flight Data with Unknown Time Skews

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.

2016-01-01

A method for estimating dynamic model parameters from flight data with unknown time skews is described and demonstrated. The method combines data reconstruction, nonlinear optimization, and equation-error parameter estimation in the frequency domain to accurately estimate both dynamic model parameters and the relative time skews in the data. Data from a nonlinear F-16 aircraft simulation with realistic noise, instrumentation errors, and arbitrary time skews were used to demonstrate the approach. The approach was further evaluated using flight data from a subscale jet transport aircraft, where the measured data were known to have relative time skews. Comparison of modeling results obtained from time-skewed and time-synchronized data showed that the method accurately estimates both dynamic model parameters and relative time skew parameters from flight data with unknown time skews.

An equation of state for high pressure-temperature liquids (RTpress) with application to MgSiO3 melt

NASA Astrophysics Data System (ADS)

Wolf, Aaron S.; Bower, Dan J.

2018-05-01

The thermophysical properties of molten silicates at extreme conditions are crucial for understanding the early evolution of Earth and other massive rocky planets, which is marked by giant impacts capable of producing deep magma oceans. Cooling and crystallization of molten mantles are sensitive to the densities and adiabatic profiles of high-pressure molten silicates, demanding accurate Equation of State (EOS) models to predict the early evolution of planetary interiors. Unfortunately, EOS modeling for liquids at high P-T conditions is difficult due to constantly evolving liquid structure. The Rosenfeld-Tarazona (RT) model provides a physically sensible and accurate description of liquids but is limited to constant volume heating paths (Rosenfeld and Tarazona, 1998). We develop a high P-T EOS for liquids, called RTpress, which uses a generalized Rosenfeld-Tarazona model as a thermal perturbation to isothermal and adiabatic reference compression curves. This approach provides a thermodynamically consistent EOS which remains accurate over a large P-T range and depends on a limited number of physically meaningful parameters that can be determined empirically from either simulated or experimental datasets. As a first application, we model MgSiO3 melt representing a simplified rocky mantle chemistry. The model parameters are fitted to the MD simulations of both Spera et al. (2011) and de Koker and Stixrude (2009), recovering pressures, volumes, and internal energies to within 0.6 GPa, 0.1 Å3 , and 6 meV per atom on average (for the higher resolution data set), as well as accurately predicting liquid densities and temperatures from shock-wave experiments on MgSiO3 glass. The fitted EOS is used to determine adiabatic thermal profiles, revealing the approximate thermal structure of a fully molten magma ocean like that of the early Earth. These adiabats, which are in strong agreement for both fitted models, are shown to be sufficiently steep to produce either a center-outwards or bottom-up style of crystallization, depending on the curvature of the mantle melting curve (liquidus), with a high-curvature model yielding crystallization at depths of roughly 80 GPa (Stixrude et al., 2009) whereas a nearly-flat experimentally determined liquidus implies bottom-up crystallization (Andrault et al., 2011).

Registration of knee joint surfaces for the in vivo study of joint injuries based on magnetic resonance imaging

NASA Astrophysics Data System (ADS)

Cheng, Rita W. T.; Habib, Ayman F.; Frayne, Richard; Ronsky, Janet L.

2006-03-01

In-vivo quantitative assessments of joint conditions and health status can help to increase understanding of the pathology of osteoarthritis, a degenerative joint disease that affects a large population each year. Magnetic resonance imaging (MRI) provides a non-invasive and accurate means to assess and monitor joint properties, and has become widely used for diagnosis and biomechanics studies. Quantitative analyses and comparisons of MR datasets require accurate alignment of anatomical structures, thus image registration becomes a necessary procedure for these applications. This research focuses on developing a registration technique for MR knee joint surfaces to allow quantitative study of joint injuries and health status. It introduces a novel idea of translating techniques originally developed for geographic data in the field of photogrammetry and remote sensing to register 3D MR data. The proposed algorithm works with surfaces that are represented by randomly distributed points with no requirement of known correspondences. The algorithm performs matching locally by identifying corresponding surface elements, and solves for the transformation parameters relating the surfaces by minimizing normal distances between them. This technique was used in three applications to: 1) register temporal MR data to verify the feasibility of the algorithm to help monitor diseases, 2) quantify patellar movement with respect to the femur based on the transformation parameters, and 3) quantify changes in contact area locations between the patellar and femoral cartilage at different knee flexion angles. The results indicate accurate registration and the proposed algorithm can be applied for in-vivo study of joint injuries with MRI.

Manufacturing and advanced characterization of sub-25nm diameter CD-AFM probes with sub-10nm tip edges radius

NASA Astrophysics Data System (ADS)

Foucher, Johann; Filippov, Pavel; Penzkofer, Christian; Irmer, Bernd; Schmidt, Sebastian W.

2013-04-01

Atomic force microscopy (AFM) is increasingly used in the semiconductor industry as a versatile monitoring tool for highly critical lithography and etching process steps. Applications range from the inspection of the surface roughness of new materials, over accurate depth measurements to the determination of critical dimension structures. The aim to address the rapidly growing demands on measurement uncertainty and throughput more and more shifts the focus of attention to the AFM tip, which represents the crucial link between AFM tool and the sample to be monitored. Consequently, in order to reach the AFM tool's full potential, the performance of the AFM tip has to be considered as a determining parameter. Currently available AFM tips made from silicon are generally limited by their diameter, radius, and sharpness, considerably restricting the AFM measurement capabilities on sub-30nm spaces. In addition to that, there's lack of adequate characterization structures to accurately characterize sub-25nm tip diameters. Here, we present and discuss a recently introduced AFM tip design (T-shape like design) with precise tip diameters down to 15nm and tip radii down to 5nm fabricated from amorphous, high density diamond-like carbon (HDC/DLC) using electron beam induced processing (EBIP). In addition to that advanced design, we propose a new characterizer structure, which allows for accurate characterization and design control of sub-25nm tip diameters and sub-10nm tip edges radii. We demonstrate the potential advantages of combining a small tip shape design, i.e. tip diameter and tip edge radius, and an advanced tip characterizer for the semiconductor industry by the measurement of advanced lithography patterns.

Geometries and properties of bimetallic phosphido-bridged complex Cp(CO) 2W(μ-PPh 2)W(CO) 5 and Cp(CO) 3W(μ-PPh 2)W(CO) 5

NASA Astrophysics Data System (ADS)

Wang, Fang; Yang, Hongmei; Yang, Zuoyin; Zhang, Jingchang; Cao, Weiliang

2007-01-01

Complete geometry optimizations were carried out by HF and DFT methods to study the molecular structure of binuclear transition-metal compounds (Cp(CO) 3W(μ-PPh 2)W(CO) 5) (I) and (Cp(CO) 2W(μ-PPh 2)W(CO) 5) (II). A comparison of the experimental data and calculated structural parameters demonstrates that the most accurate geometry parameters are predicted by the MPW1PW91/LANL2DZ among the three DFT methods. Topological properties of molecular charge distributions were analyzed with the theory of atoms in molecules. (3, -1) critical points, namely bond critical point, were found between the two tungsten atoms, and between W1 and C10 in complex II, which confirms the existence of the metal-metal bond and a semi-bridging CO between the two tungsten atoms. The result provided a theoretical guidance of detailed study on the binuclear phosphido-bridged complex containing transition metal-metal bond, which could be useful in the further study of the heterobimetallic phosphido-bridged complexes.

Food structure: Its formation and relationships with other properties.

PubMed

Joardder, Mohammad U H; Kumar, Chandan; Karim, M A

2017-04-13

Food materials are complex in nature as it has heterogeneous, amorphous, hygroscopic and porous properties. During processing, microstructure of food materials changes which significantly affects other properties of food. An appropriate understanding of the microstructure of the raw food material and its evolution during processing is critical in order to understand and accurately describe dehydration processes and quality anticipation. This review critically assesses the factors that influence the modification of microstructure in the course of drying of fruits and vegetables. The effect of simultaneous heat and mass transfer on microstructure in various drying methods is investigated. Effects of changes in microstructure on other functional properties of dried foods are discussed. After an extensive review of the literature, it is found that development of food structure significantly depends on fresh food properties and process parameters. Also, modification of microstructure influences the other properties of final product. An enhanced understanding of the relationships between food microstructure, drying process parameters and final product quality will facilitate the energy efficient optimum design of the food processor in order to achieve high-quality food.

Stochastic subspace identification for operational modal analysis of an arch bridge

NASA Astrophysics Data System (ADS)

Loh, Chin-Hsiung; Chen, Ming-Che; Chao, Shu-Hsien

2012-04-01

In this paer the application of output-only system identification technique, known as Stochastic Subspace Identification (SSI) algorithms, for civil infrastructures is carried out. The ability of covariance driven stochastic subspace identification (SSI-COV) was proved through the analysis of the ambient data of an arch bridge under operational condition. A newly developed signal processing technique, Singular Spectrum analysis (SSA), capable to smooth noisy signals, is adopted for pre-processing the recorded data before the SSI. The conjunction of SSA and SSICOV provides a useful criterion for the system order determination. With the aim of estimating accurate modal parameters of the structure in off-line analysis, a stabilization diagram is constructed by plotting the identified poles of the system with increasing the size of data Hankel matrix. Identification task of a real structure, Guandu Bridge, is carried out to identify the system natural frequencies and mode shapes. The uncertainty of the identified model parameters from output-only measurement of the bridge under operation condition, such as temperature and traffic loading conditions, is discussed.

Metallic coatings of microelectromechanical structures at low temperatures: Stress, elasticity, and nonlinear dissipation

NASA Astrophysics Data System (ADS)

Collin, E.; Kofler, J.; Lakhloufi, S.; Pairis, S.; Bunkov, Yu. M.; Godfrin, H.

2010-06-01

We present mechanical measurements performed at low temperatures on cantilever-based microelectromechanical structures coated with a metallic layer. Two very different coatings are presented in order to illustrate the capabilities of the present approach, namely (soft) aluminum and (hard) niobium oxide. The temperature is used as a control parameter to access materials properties. We benefit from low temperature techniques to extract a phase-resolved measurement of the first mechanical resonance mode in cryogenic vacuum. By repeating the experiment on the same samples, after multiple metallic depositions, we can determine accurately the contribution of the coating layers to the mechanical properties in terms of surface stress, additional mass, additional elasticity, and damping. Analytic theoretical expressions are derived and used to fit the data. Taking advantage of the extremely broad dynamic range provided by the technique, we can measure the anelasticity of the thin metallic film. The key parameters describing the metals' dynamics are analyzed in an original way in order to provide new experimental grounds for future theoretical modelings of the underlying mechanisms.

Effect of spin-orbit and on-site Coulomb interactions on the electronic structure and lattice dynamics of uranium monocarbide

NASA Astrophysics Data System (ADS)

Wdowik, U. D.; Piekarz, P.; Legut, D.; Jagło, G.

2016-08-01

Uranium monocarbide, a potential fuel material for the generation IV reactors, is investigated within density functional theory. Its electronic, magnetic, elastic, and phonon properties are analyzed and discussed in terms of spin-orbit interaction and localized versus itinerant behavior of the 5 f electrons. The localization of the 5 f states is tuned by varying the local Coulomb repulsion interaction parameter. We demonstrate that the theoretical electronic structure, elastic constants, phonon dispersions, and their densities of states can reproduce accurately the results of x-ray photoemission and bremsstrahlung isochromat measurements as well as inelastic neutron scattering experiments only when the 5 f states experience the spin-orbit interaction and simultaneously remain partially localized. The partial localization of the 5 f electrons could be represented by a moderate value of the on-site Coulomb interaction parameter of about 2 eV. The results of the present studies indicate that both strong electron correlations and spin-orbit effects are crucial for realistic theoretical description of the ground-state properties of uranium carbide.

Advective transport in heterogeneous aquifers: Are proxy models predictive?

NASA Astrophysics Data System (ADS)

Fiori, A.; Zarlenga, A.; Gotovac, H.; Jankovic, I.; Volpi, E.; Cvetkovic, V.; Dagan, G.

2015-12-01

We examine the prediction capability of two approximate models (Multi-Rate Mass Transfer (MRMT) and Continuous Time Random Walk (CTRW)) of non-Fickian transport, by comparison with accurate 2-D and 3-D numerical simulations. Both nonlocal in time approaches circumvent the need to solve the flow and transport equations by using proxy models to advection, providing the breakthrough curves (BTC) at control planes at any x, depending on a vector of five unknown parameters. Although underlain by different mechanisms, the two models have an identical structure in the Laplace Transform domain and have the Markovian property of independent transitions. We show that also the numerical BTCs enjoy the Markovian property. Following the procedure recommended in the literature, along a practitioner perspective, we first calibrate the parameters values by a best fit with the numerical BTC at a control plane at x1, close to the injection plane, and subsequently use it for prediction at further control planes for a few values of σY2≤8. Due to a similar structure and Markovian property, the two methods perform equally well in matching the numerical BTC. The identified parameters are generally not unique, making their identification somewhat arbitrary. The inverse Gaussian model and the recently developed Multi-Indicator Model (MIM), which does not require any fitting as it relates the BTC to the permeability structure, are also discussed. The application of the proxy models for prediction requires carrying out transport field tests of large plumes for a long duration.

Flexible Force Field Parameterization through Fitting on the Ab Initio-Derived Elastic Tensor

PubMed Central

2017-01-01

Constructing functional forms and their corresponding force field parameters for the metal–linker interface of metal–organic frameworks is challenging. We propose fitting these parameters on the elastic tensor, computed from ab initio density functional theory calculations. The advantage of this top-down approach is that it becomes evident if functional forms are missing when components of the elastic tensor are off. As a proof-of-concept, a new flexible force field for MIL-47(V) is derived. Negative thermal expansion is observed and framework flexibility has a negligible effect on adsorption and transport properties for small guest molecules. We believe that this force field parametrization approach can serve as a useful tool for developing accurate flexible force field models that capture the correct mechanical behavior of the full periodic structure. PMID:28661672

Developing a molecular dynamics force field for both folded and disordered protein states.

PubMed

Robustelli, Paul; Piana, Stefano; Shaw, David E

2018-05-07

Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB- disp , should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields. Copyright © 2018 the Author(s). Published by PNAS.

An adaptive extended finite element method for the analysis of agglomeration of colloidal particles in a flowing fluid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Choi, Young Joon; Jorshari, Razzi Movassaghi; Djilali, Ned

2015-03-10

Direct numerical simulations of the flow-nanoparticle interaction in a colloidal suspension are presented using an extended finite element method (XFEM) in which the dynamics of the nanoparticles is solved in a fully-coupled manner with the flow. The method is capable of accurately describing solid-fluid interfaces without the need of boundary-fitted meshes to investigate the dynamics of particles in complex flows. In order to accurately compute the high interparticle shear stresses and pressures while minimizing computing costs, an adaptive meshing technique is incorporated with the fluid-structure interaction algorithm. The particle-particle interaction at the microscopic level is modeled using the Lennard-Jones (LJ)more » potential and the corresponding potential parameters are determined by a scaling procedure. The study is relevant to the preparation of inks used in the fabrication of catalyst layers for fuel cells. In this paper, we are particularly interested in investigating agglomeration of the nanoparticles under external shear flow in a sliding bi-periodic Lees-Edwards frame. The results indicate that the external shear has a crucial impact on the structure formation of colloidal particles in a suspension.« less

Challenges in first-principles NPT molecular dynamics of soft porous crystals: A case study on MIL-53(Ga)

NASA Astrophysics Data System (ADS)

Haigis, Volker; Belkhodja, Yacine; Coudert, François-Xavier; Vuilleumier, Rodolphe; Boutin, Anne

2014-08-01

Soft porous crystals present a challenge to molecular dynamics simulations with flexible size and shape of the simulation cell (i.e., in the NPT ensemble), since their framework responds very sensitively to small external stimuli. Hence, all interactions have to be described very accurately in order to obtain correct equilibrium structures. Here, we report a methodological study on the nanoporous metal-organic framework MIL-53(Ga), which undergoes a large-amplitude transition between a narrow- and a large-pore phase upon a change in temperature. Since this system has not been investigated by density functional theory (DFT)-based NPT simulations so far, we carefully check the convergence of the stress tensor with respect to computational parameters. Furthermore, we demonstrate the importance of dispersion interactions and test two different ways of incorporating them into the DFT framework. As a result, we propose two computational schemes which describe accurately the narrow- and the large-pore phase of the material, respectively. These schemes can be used in future work on the delicate interplay between adsorption in the nanopores and structural flexibility of the host material.

s -wave scattering length of a Gaussian potential

NASA Astrophysics Data System (ADS)

Jeszenszki, Peter; Cherny, Alexander Yu.; Brand, Joachim

2018-04-01

We provide accurate expressions for the s -wave scattering length for a Gaussian potential well in one, two, and three spatial dimensions. The Gaussian potential is widely used as a pseudopotential in the theoretical description of ultracold-atomic gases, where the s -wave scattering length is a physically relevant parameter. We first describe a numerical procedure to compute the value of the s -wave scattering length from the parameters of the Gaussian, but find that its accuracy is limited in the vicinity of singularities that result from the formation of new bound states. We then derive simple analytical expressions that capture the correct asymptotic behavior of the s -wave scattering length near the bound states. Expressions that are increasingly accurate in wide parameter regimes are found by a hierarchy of approximations that capture an increasing number of bound states. The small number of numerical coefficients that enter these expressions is determined from accurate numerical calculations. The approximate formulas combine the advantages of the numerical and approximate expressions, yielding an accurate and simple description from the weakly to the strongly interacting limit.

An automatic scaling method for obtaining the trace and parameters from oblique ionogram based on hybrid genetic algorithm

NASA Astrophysics Data System (ADS)

Song, Huan; Hu, Yaogai; Jiang, Chunhua; Zhou, Chen; Zhao, Zhengyu; Zou, Xianjian

2016-12-01

Scaling oblique ionogram plays an important role in obtaining ionospheric structure at the midpoint of oblique sounding path. The paper proposed an automatic scaling method to extract the trace and parameters of oblique ionogram based on hybrid genetic algorithm (HGA). The extracted 10 parameters come from F2 layer and Es layer, such as maximum observation frequency, critical frequency, and virtual height. The method adopts quasi-parabolic (QP) model to describe F2 layer's electron density profile that is used to synthesize trace. And it utilizes secant theorem, Martyn's equivalent path theorem, image processing technology, and echoes' characteristics to determine seven parameters' best fit values, and three parameter's initial values in QP model to set up their searching spaces which are the needed input data of HGA. Then HGA searches the three parameters' best fit values from their searching spaces based on the fitness between the synthesized trace and the real trace. In order to verify the performance of the method, 240 oblique ionograms are scaled and their results are compared with manual scaling results and the inversion results of the corresponding vertical ionograms. The comparison results show that the scaling results are accurate or at least adequate 60-90% of the time.

Test of Parameterized Post-Newtonian Gravity with Galaxy-scale Strong Lensing Systems

NASA Astrophysics Data System (ADS)

Cao, Shuo; Li, Xiaolei; Biesiada, Marek; Xu, Tengpeng; Cai, Yongzhi; Zhu, Zong-Hong

2017-01-01

Based on a mass-selected sample of galaxy-scale strong gravitational lenses from the SLACS, BELLS, LSD, and SL2S surveys and using a well-motivated fiducial set of lens-galaxy parameters, we tested the weak-field metric on kiloparsec scales and found a constraint on the post-Newtonian parameter γ ={0.995}-0.047+0.037 under the assumption of a flat ΛCDM universe with parameters taken from Planck observations. General relativity (GR) predicts exactly γ = 1. Uncertainties concerning the total mass density profile, anisotropy of the velocity dispersion, and the shape of the light profile combine to systematic uncertainties of ˜25%. By applying a cosmological model-independent method to the simulated future LSST data, we found a significant degeneracy between the PPN γ parameter and the spatial curvature of the universe. Setting a prior on the cosmic curvature parameter -0.007 < Ωk < 0.006, we obtained the constraint on the PPN parameter that γ ={1.000}-0.0025+0.0023. We conclude that strong lensing systems with measured stellar velocity dispersions may serve as another important probe to investigate validity of the GR, if the mass-dynamical structure of the lensing galaxies is accurately constrained in future lens surveys.

A New Energy-Critical Plane Damage Parameter for Multiaxial Fatigue Life Prediction of Turbine Blades.

PubMed

Yu, Zheng-Yong; Zhu, Shun-Peng; Liu, Qiang; Liu, Yunhan

2017-05-08

As one of fracture critical components of an aircraft engine, accurate life prediction of a turbine blade to disk attachment is significant for ensuring the engine structural integrity and reliability. Fatigue failure of a turbine blade is often caused under multiaxial cyclic loadings at high temperatures. In this paper, considering different failure types, a new energy-critical plane damage parameter is proposed for multiaxial fatigue life prediction, and no extra fitted material constants will be needed for practical applications. Moreover, three multiaxial models with maximum damage parameters on the critical plane are evaluated under tension-compression and tension-torsion loadings. Experimental data of GH4169 under proportional and non-proportional fatigue loadings and a case study of a turbine disk-blade contact system are introduced for model validation. Results show that model predictions by Wang-Brown (WB) and Fatemi-Socie (FS) models with maximum damage parameters are conservative and acceptable. For the turbine disk-blade contact system, both of the proposed damage parameters and Smith-Watson-Topper (SWT) model show reasonably acceptable correlations with its field number of flight cycles. However, life estimations of the turbine blade reveal that the definition of the maximum damage parameter is not reasonable for the WB model but effective for both the FS and SWT models.

A New Energy-Critical Plane Damage Parameter for Multiaxial Fatigue Life Prediction of Turbine Blades

PubMed Central

Yu, Zheng-Yong; Zhu, Shun-Peng; Liu, Qiang; Liu, Yunhan

2017-01-01

As one of fracture critical components of an aircraft engine, accurate life prediction of a turbine blade to disk attachment is significant for ensuring the engine structural integrity and reliability. Fatigue failure of a turbine blade is often caused under multiaxial cyclic loadings at high temperatures. In this paper, considering different failure types, a new energy-critical plane damage parameter is proposed for multiaxial fatigue life prediction, and no extra fitted material constants will be needed for practical applications. Moreover, three multiaxial models with maximum damage parameters on the critical plane are evaluated under tension-compression and tension-torsion loadings. Experimental data of GH4169 under proportional and non-proportional fatigue loadings and a case study of a turbine disk-blade contact system are introduced for model validation. Results show that model predictions by Wang-Brown (WB) and Fatemi-Socie (FS) models with maximum damage parameters are conservative and acceptable. For the turbine disk-blade contact system, both of the proposed damage parameters and Smith-Watson-Topper (SWT) model show reasonably acceptable correlations with its field number of flight cycles. However, life estimations of the turbine blade reveal that the definition of the maximum damage parameter is not reasonable for the WB model but effective for both the FS and SWT models. PMID:28772873

The Shock Pulse Index and Its Application in the Fault Diagnosis of Rolling Element Bearings

PubMed Central

Sun, Peng; Liao, Yuhe; Lin, Jin

2017-01-01

The properties of the time domain parameters of vibration signals have been extensively studied for the fault diagnosis of rolling element bearings (REBs). Parameters like kurtosis and Envelope Harmonic-to-Noise Ratio are the most widely applied in this field and some important progress has been made. However, since only one-sided information is contained in these parameters, problems still exist in practice when the signals collected are of complicated structure and/or contaminated by strong background noises. A new parameter, named Shock Pulse Index (SPI), is proposed in this paper. It integrates the mutual advantages of both the parameters mentioned above and can help effectively identify fault-related impulse components under conditions of interference of strong background noises, unrelated harmonic components and random impulses. The SPI optimizes the parameters of Maximum Correlated Kurtosis Deconvolution (MCKD), which is used to filter the signals under consideration. Finally, the transient information of interest contained in the filtered signal can be highlighted through demodulation with the Teager Energy Operator (TEO). Fault-related impulse components can therefore be extracted accurately. Simulations show the SPI can correctly indicate the fault impulses under the influence of strong background noises, other harmonic components and aperiodic impulse and experiment analyses verify the effectiveness and correctness of the proposed method. PMID:28282883

Line Narrowing Parameter Measurement by Modulation Spectroscopy

NASA Technical Reports Server (NTRS)

Dharamsi, Amin N.

1998-01-01

Accurate Characterization of Oxygen A-Band Line Parameters by Wavelength Modulation Spectroscopy with tunable diode lasers is an ongoing research at Old Dominion University, under sponsorship from NASA Langley research Center. The work proposed here will be undertaken under the guidance of Dr. William Chu and Dr. Lamont Poole of the Aerosol Research Branch at NASA Langley-Research Center in Hampton, Virginia. The research was started about two years ago and utilizes wavelength modulation absorption spectroscopy with higher harmonic detection, a technique that we developed at Old Dominion University, to obtain the absorption line characteristics of the Oxygen A-band rovibronic lines. Accurate characterization of this absorption band is needed for processing of data that will be obtained in experiments such as the NASA Stratospheric Aerosol and Gas Experiment III (SAGE III) as part of the US Mission to Planet Earth. The research work for Summer Fellowship undertook a measurement of the Dicke line-narrowing parameters of the Oxygen A-Band lines by using wavelength modulation spectroscopy. Our previous theoretical results had indicated that such a measurement could be done sensitively and in a convenient fashion by using this type of spectroscopy. In particular, theoretical results had indicated that the signal magnitude would depend on pressure in a manner that was very sensitive to the narrowing parameter. One of the major tasks undertaken during the summer of 1998 was to establish experimentally that these theoretical predictions were correct. This was done successfully and the results of the work are being prepared for publication. Experimental Results were obtained in which the magnitude of the signal was measured as a function of pressure, for various harmonic detection orders (N = 1, 2, 3, 4, 5). A comparison with theoretical results was made, and it was shown that the agreement between theory and experiment was very good. More importantly, however, it was shown that the measurement was yielded a very sensitive technique for obtaining the narrowing parameter that describes the deviation of Oxygen A-band lines from the Voigt profile. In particular, it was seen that the best fits were obtained consistently when the narrowing parameter value used was 0.022 1/cm, 1/Atm, Previous work, upon which the current work was based has resulted in several accurate measurements of properties of particular lines of the Oxygen A band. For example, this work has resulted in the measurement of the collision cross sections of several lines including the RQ(13,14) and the RR(15,15) lines. A major achievement of achievement of the work was also the demonstration that the technique we have developed can accurately probe the structure of the absorption lineshape function. In particular, the method we have developed is very well suited for experimentally probing the characteristics of lines in their wings. This work was accepted for publication in the Journal of Applied Physics, and is scheduled to appear in the December 15, 1998 issue.

On the Calculation of Uncertainty Statistics with Error Bounds for CFD Calculations Containing Random Parameters and Fields

NASA Technical Reports Server (NTRS)

Barth, Timothy J.

2016-01-01

This chapter discusses the ongoing development of combined uncertainty and error bound estimates for computational fluid dynamics (CFD) calculations subject to imposed random parameters and random fields. An objective of this work is the construction of computable error bound formulas for output uncertainty statistics that guide CFD practitioners in systematically determining how accurately CFD realizations should be approximated and how accurately uncertainty statistics should be approximated for output quantities of interest. Formal error bounds formulas for moment statistics that properly account for the presence of numerical errors in CFD calculations and numerical quadrature errors in the calculation of moment statistics have been previously presented in [8]. In this past work, hierarchical node-nested dense and sparse tensor product quadratures are used to calculate moment statistics integrals. In the present work, a framework has been developed that exploits the hierarchical structure of these quadratures in order to simplify the calculation of an estimate of the quadrature error needed in error bound formulas. When signed estimates of realization error are available, this signed error may also be used to estimate output quantity of interest probability densities as a means to assess the impact of realization error on these density estimates. Numerical results are presented for CFD problems with uncertainty to demonstrate the capabilities of this framework.

Multilayer integral method for simulation of eddy currents in thin volumes of arbitrary geometry produced by MRI gradient coils.

PubMed

Sanchez Lopez, Hector; Freschi, Fabio; Trakic, Adnan; Smith, Elliot; Herbert, Jeremy; Fuentes, Miguel; Wilson, Stephen; Liu, Limei; Repetto, Maurizio; Crozier, Stuart

2014-05-01

This article aims to present a fast, efficient and accurate multi-layer integral method (MIM) for the evaluation of complex spatiotemporal eddy currents in nonmagnetic and thin volumes of irregular geometries induced by arbitrary arrangements of gradient coils. The volume of interest is divided into a number of layers, wherein the thickness of each layer is assumed to be smaller than the skin depth and where one of the linear dimensions is much smaller than the remaining two dimensions. The diffusion equation of the current density is solved both in time-harmonic and transient domain. The experimentally measured magnetic fields produced by the coil and the induced eddy currents as well as the corresponding time-decay constants were in close agreement with the results produced by the MIM. Relevant parameters such as power loss and force induced by the eddy currents in a split cryostat were simulated using the MIM. The proposed method is capable of accurately simulating the current diffusion process inside thin volumes, such as the magnet cryostat. The method permits the priori-calculation of optimal pre-emphasis parameters. The MIM enables unified designs of gradient coil-magnet structures for an optimal mitigation of deleterious eddy current effects. Copyright © 2013 Wiley Periodicals, Inc.

Influence of Thunderstorms on the Structure of the Ionosphere using Composite Analysis

NASA Astrophysics Data System (ADS)

Nava, O.; Sutherland, E.

2017-12-01

It is well known in the amateur (ham) radio community that thunderstorms have a significant influence on local and long-distance high-frequency (HF) communications. This study aims to characterize the structure of the ionosphere in response to strong convective activity and cloud electrification. Superposed Epoch Analysis is applied to surface weather observations and ionosonde data at Eglin Air Force Base, Florida from August 2014 to July 2017. Preliminary results indicate that thunderstorms significantly modify the structure of the ionosphere, generating statistically different measurements of several key parameters (e.g., foEs, hmF2, ITEC) compared to clear-sky observations. Seasonal and diurnal influences between the thunderstorm and clear sky cases are also explored. Accurate characterization of the ionosphere in response to thunderstorms has important implications for the effective use of HF communications in civilian and military operations, to include emergency services, aviation, amateur radio, and over-the-horizon radar.

Spectroscopic study on deuterated benzenes. II. High-resolution laser spectroscopy and rotational structure in the S{sub 1} state

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kunishige, Sachi; Katori, Toshiharu; Baba, Masaaki, E-mail: baba@kuchem.kyoto-u.ac.jp

High-resolution spectra of the S{sub 1}←S{sub 0} transition in jet-cooled deuterated benzenes were observed using pulse dye amplification of single-mode laser light and mass-selective resonance enhanced multiphoton ionization (REMPI) detection. The vibrational and rotational structures were accurately analyzed for the vibronic levels in the S{sub 1} state. The degenerate 6{sup 1} levels of C{sub 6}H{sub 6} or C{sub 6}D{sub 6} are split into 6a{sup 1} and 6b{sup 1} in many of deuterated benzenes. The rigid-rotor rotational constants were assessed and found to be slightly different between 6a and 6b because of different mean molecular structures. Their rotational levels are significantlymore » shifted by Coriolis interactions. It was found that the Coriolis parameter proportionally changed with the number of substituted D atoms.« less

Investigation of the structural behavior of the blades of a darrieus wind turbine†

NASA Astrophysics Data System (ADS)

Rosen, A.; Abramovich, H.

1985-06-01

A theoretical model in which account is taken of the non-linear, non-planar structural behavior of the curved blades of a Darrieus wind turbine is described. This model is simpler and needs less computational effort than some other models, but is still accurate enough for most engineering purposes. By using the present method, it is possible to treat any blade geometry, any structural, mass and aerodynamic blade properties distribution and any combination of boundary conditions. The model is used in order to calculate the blade behavior under the influence of concentrated loads, gravity loads and centrifugal loads. In order to verify the theoretical model, predictions are compared with experimental results which are obtained from tests with small models of curved blades. Usually the agreement between the theoretical and experimental results is very good. The influence of different parameters on blade behavior is presented and discussed.

A shock absorber model for structure-borne noise analyses

NASA Astrophysics Data System (ADS)

Benaziz, Marouane; Nacivet, Samuel; Thouverez, Fabrice

2015-08-01

Shock absorbers are often responsible for undesirable structure-borne noise in cars. The early numerical prediction of this noise in the automobile development process can save time and money and yet remains a challenge for industry. In this paper, a new approach to predicting shock absorber structure-borne noise is proposed; it consists in modelling the shock absorber and including the main nonlinear phenomena responsible for discontinuities in the response. The model set forth herein features: compressible fluid behaviour, nonlinear flow rate-pressure relations, valve mechanical equations and rubber mounts. The piston, base valve and complete shock absorber model are compared with experimental results. Sensitivity of the shock absorber response is evaluated and the most important parameters are classified. The response envelope is also computed. This shock absorber model is able to accurately reproduce local nonlinear phenomena and improves our state of knowledge on potential noise sources within the shock absorber.

The ambivalent effect of lattice structure on a spatial game

NASA Astrophysics Data System (ADS)

Zhang, Hui; Gao, Meng; Li, Zizhen; Maa, Zhihui; Wang, Hailong

2011-06-01

The evolution of cooperation is studied in lattice-structured populations, in which each individual who adopts one of the following strategies ‘always defect' (ALLD), ‘tit-for-tat' (TFT), and ‘always cooperate' (ALLC) plays the repeated Prisoner's Dilemma game with its neighbors according to an asynchronous update rule. Computer simulations are applied to analyse the dynamics depending on major parameters. Mathematical analyses based on invasion probability analysis, mean-field approximation, as well as pair approximation are also used. We find that the lattice structure promotes the evolution of cooperation compared with a non-spatial population, this is also confirmed by invasion probability analysis in one dimension. Meanwhile, it also inhibits the evolution of cooperation due to the advantage of being spiteful, which indicates the key role of specific life-history assumptions. Mean-field approximation fails to predict the outcome of computer simulations. Pair approximation is accurate in two dimensions but fails in one dimension.

Estimation of Dynamic Systems for Gene Regulatory Networks from Dependent Time-Course Data.

PubMed

Kim, Yoonji; Kim, Jaejik

2018-06-15

Dynamic system consisting of ordinary differential equations (ODEs) is a well-known tool for describing dynamic nature of gene regulatory networks (GRNs), and the dynamic features of GRNs are usually captured through time-course gene expression data. Owing to high-throughput technologies, time-course gene expression data have complex structures such as heteroscedasticity, correlations between genes, and time dependence. Since gene experiments typically yield highly noisy data with small sample size, for a more accurate prediction of the dynamics, the complex structures should be taken into account in ODE models. Hence, this study proposes an ODE model considering such data structures and a fast and stable estimation method for the ODE parameters based on the generalized profiling approach with data smoothing techniques. The proposed method also provides statistical inference for the ODE estimator and it is applied to a zebrafish retina cell network.

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

NASA Astrophysics Data System (ADS)

Kim, Jeongnim; Baczewski, Andrew D.; Beaudet, Todd D.; Benali, Anouar; Chandler Bennett, M.; Berrill, Mark A.; Blunt, Nick S.; Josué Landinez Borda, Edgar; Casula, Michele; Ceperley, David M.; Chiesa, Simone; Clark, Bryan K.; Clay, Raymond C., III; Delaney, Kris T.; Dewing, Mark; Esler, Kenneth P.; Hao, Hongxia; Heinonen, Olle; Kent, Paul R. C.; Krogel, Jaron T.; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M. Graham; Luo, Ye; Malone, Fionn D.; Martin, Richard M.; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A.; Mitas, Lubos; Morales, Miguel A.; Neuscamman, Eric; Parker, William D.; Pineda Flores, Sergio D.; Romero, Nichols A.; Rubenstein, Brenda M.; Shea, Jacqueline A. R.; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F.; Townsend, Joshua P.; Tubman, Norm M.; Van Der Goetz, Brett; Vincent, Jordan E.; ChangMo Yang, D.; Yang, Yubo; Zhang, Shuai; Zhao, Luning

2018-05-01

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater–Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids.

PubMed

Kim, Jeongnim; Baczewski, Andrew T; Beaudet, Todd D; Benali, Anouar; Bennett, M Chandler; Berrill, Mark A; Blunt, Nick S; Borda, Edgar Josué Landinez; Casula, Michele; Ceperley, David M; Chiesa, Simone; Clark, Bryan K; Clay, Raymond C; Delaney, Kris T; Dewing, Mark; Esler, Kenneth P; Hao, Hongxia; Heinonen, Olle; Kent, Paul R C; Krogel, Jaron T; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M Graham; Luo, Ye; Malone, Fionn D; Martin, Richard M; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A; Mitas, Lubos; Morales, Miguel A; Neuscamman, Eric; Parker, William D; Pineda Flores, Sergio D; Romero, Nichols A; Rubenstein, Brenda M; Shea, Jacqueline A R; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F; Townsend, Joshua P; Tubman, Norm M; Van Der Goetz, Brett; Vincent, Jordan E; Yang, D ChangMo; Yang, Yubo; Zhang, Shuai; Zhao, Luning

2018-05-16

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program's capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

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.

Performance Evaluation and Improvement of Ferroelectric Field-Effect Transistor Memory

NASA Astrophysics Data System (ADS)

Yu, Hyung Suk

Flash memory is reaching scaling limitations rapidly due to reduction of charge in floating gates, charge leakage and capacitive coupling between cells which cause threshold voltage fluctuations, short retention times, and interference. Many new memory technologies are being considered as alternatives to flash memory in an effort to overcome these limitations. Ferroelectric Field-Effect Transistor (FeFET) is one of the main emerging candidates because of its structural similarity to conventional FETs and fast switching speed. Nevertheless, the performance of FeFETs have not been systematically compared and analyzed against other competing technologies. In this work, we first benchmark the intrinsic performance of FeFETs and other memories by simulations in order to identify the strengths and weaknesses of FeFETs. To simulate realistic memory applications, we compare memories on an array structure. For the comparisons, we construct an accurate delay model and verify it by benchmarking against exact HSPICE simulations. Second, we propose an accurate model for FeFET memory window since the existing model has limitations. The existing model assumes symmetric operation voltages but it is not valid for the practical asymmetric operation voltages. In this modeling, we consider practical operation voltages and device dimensions. Also, we investigate realistic changes of memory window over time and retention time of FeFETs. Last, to improve memory window and subthreshold swing, we suggest nonplanar junctionless structures for FeFETs. Using the suggested structures, we study the dimensional dependences of crucial parameters like memory window and subthreshold swing and also analyze key interference mechanisms.

Band gap characterization of ternary BBi1-xNx (0≤x≤1) alloys using modified Becke-Johnson (mBJ) potential

NASA Astrophysics Data System (ADS)

Yalcin, Battal G.

2015-04-01

The semi-local Becke-Johnson (BJ) exchange-correlation potential and its modified form proposed by Tran and Blaha have attracted a lot of interest recently because of the surprisingly accurate band gaps they can deliver for many semiconductors and insulators (e.g., sp semiconductors, noble-gas solids, and transition-metal oxides). The structural and electronic properties of ternary alloys BBi1-xNx (0≤x≤1) in zinc-blende phase have been reported in this study. The results of the studied binary compounds (BN and BBi) and ternary alloys BBi1-xNx structures are presented by means of density functional theory. The exchange and correlation effects are taken into account by using the generalized gradient approximation (GGA) functional of Wu and Cohen (WC) which is an improved form of the most popular Perdew-Burke-Ernzerhof (PBE). For electronic properties the modified Becke-Johnson (mBJ) potential, which is more accurate than standard semi-local LDA and PBE calculations, has been chosen. Geometric optimization has been implemented before the volume optimization calculations for all the studied alloys structure. The obtained equilibrium lattice constants of the studied binary compounds are in coincidence with experimental works. And, the variation of the lattice parameter of ternary alloys BBi1-xNx almost perfectly matches with Vegard's law. The spin-orbit interaction (SOI) has been also considered for structural and electronic calculations and the results are compared to those of non-SOI calculations.

Application of a data assimilation method via an ensemble Kalman filter to reactive urea hydrolysis transport modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Juxiu Tong; Bill X. Hu; Hai Huang

2014-03-01

With growing importance of water resources in the world, remediations of anthropogenic contaminations due to reactive solute transport become even more important. A good understanding of reactive rate parameters such as kinetic parameters is the key to accurately predicting reactive solute transport processes and designing corresponding remediation schemes. For modeling reactive solute transport, it is very difficult to estimate chemical reaction rate parameters due to complex processes of chemical reactions and limited available data. To find a method to get the reactive rate parameters for the reactive urea hydrolysis transport modeling and obtain more accurate prediction for the chemical concentrations,more » we developed a data assimilation method based on an ensemble Kalman filter (EnKF) method to calibrate reactive rate parameters for modeling urea hydrolysis transport in a synthetic one-dimensional column at laboratory scale and to update modeling prediction. We applied a constrained EnKF method to pose constraints to the updated reactive rate parameters and the predicted solute concentrations based on their physical meanings after the data assimilation calibration. From the study results we concluded that we could efficiently improve the chemical reactive rate parameters with the data assimilation method via the EnKF, and at the same time we could improve solute concentration prediction. The more data we assimilated, the more accurate the reactive rate parameters and concentration prediction. The filter divergence problem was also solved in this study.« less

Characterising molecules for fundamental physics: an accurate spectroscopic model of methyltrioxorhenium derived from new infrared and millimetre-wave measurements.

PubMed

Asselin, Pierre; Berger, Yann; Huet, Thérèse R; Margulès, Laurent; Motiyenko, Roman; Hendricks, Richard J; Tarbutt, Michael R; Tokunaga, Sean K; Darquié, Benoît

2017-02-08

Precise spectroscopic analysis of polyatomic molecules enables many striking advances in physical chemistry and fundamental physics. We use several new high-resolution spectroscopic devices to improve our understanding of the rotational and rovibrational structure of methyltrioxorhenium (MTO), the achiral parent of a family of large oxorhenium compounds that are ideal candidate species for a planned measurement of parity violation in chiral molecules. Using millimetre-wave and infrared spectroscopy in a pulsed supersonic jet, a cryogenic buffer gas cell, and room temperature absorption cells, we probe the ground state and the Re[double bond, length as m-dash]O antisymmetric and symmetric stretching excited states of both CH 3 187 ReO 3 and CH 3 185 ReO 3 isotopologues in the gas phase with unprecedented precision. By extending the rotational spectra to the 150-300 GHz range, we characterize the ground state rotational and hyperfine structure up to J = 43 and K = 41, resulting in refinements to the rotational, quartic and hyperfine parameters, and the determination of sextic parameters and a centrifugal distortion correction to the quadrupolar hyperfine constant. We obtain rovibrational data for temperatures between 6 and 300 K in the 970-1015 cm -1 range, at resolutions down to 8 MHz and accuracies of 30 MHz. We use these data to determine more precise excited-state rotational, Coriolis and quartic parameters, as well as the ground-state centrifugal distortion parameter D K of the 187 Re isotopologue. We also account for hyperfine structure in the rovibrational transitions and hence determine the upper state rhenium atom quadrupole coupling constant eQq'.

Estimating stellar effective temperatures and detected angular parameters using stochastic particle swarm optimization

NASA Astrophysics Data System (ADS)

Zhang, Chuan-Xin; Yuan, Yuan; Zhang, Hao-Wei; Shuai, Yong; Tan, He-Ping

2016-09-01

Considering features of stellar spectral radiation and sky surveys, we established a computational model for stellar effective temperatures, detected angular parameters and gray rates. Using known stellar flux data in some bands, we estimated stellar effective temperatures and detected angular parameters using stochastic particle swarm optimization (SPSO). We first verified the reliability of SPSO, and then determined reasonable parameters that produced highly accurate estimates under certain gray deviation levels. Finally, we calculated 177 860 stellar effective temperatures and detected angular parameters using data from the Midcourse Space Experiment (MSX) catalog. These derived stellar effective temperatures were accurate when we compared them to known values from literatures. This research makes full use of catalog data and presents an original technique for studying stellar characteristics. It proposes a novel method for calculating stellar effective temperatures and detecting angular parameters, and provides theoretical and practical data for finding information about radiation in any band.

Simple method for quick estimation of aquifer hydrogeological parameters

NASA Astrophysics Data System (ADS)

Ma, C.; Li, Y. Y.

2017-08-01

Development of simple and accurate methods to determine the aquifer hydrogeological parameters was of importance for groundwater resources assessment and management. Aiming at the present issue of estimating aquifer parameters based on some data of the unsteady pumping test, a fitting function of Theis well function was proposed using fitting optimization method and then a unitary linear regression equation was established. The aquifer parameters could be obtained by solving coefficients of the regression equation. The application of the proposed method was illustrated, using two published data sets. By the error statistics and analysis on the pumping drawdown, it showed that the method proposed in this paper yielded quick and accurate estimates of the aquifer parameters. The proposed method could reliably identify the aquifer parameters from long distance observed drawdowns and early drawdowns. It was hoped that the proposed method in this paper would be helpful for practicing hydrogeologists and hydrologists.

Treatment of atomic and molecular line blanketing by opacity sampling. [atmospheric optics - stellar atmospheres

NASA Technical Reports Server (NTRS)

Johnson, H. R.; Krupp, B. M.

1975-01-01

An opacity sampling (OS) technique for treating the radiative opacity of large numbers of atomic and molecular lines in cool stellar atmospheres is presented. Tests were conducted and results show that the structure of atmospheric models is accurately fixed by the use of 1000 frequency points, and 500 frequency points is often adequate. The effects of atomic and molecular lines are separately studied. A test model computed by using the OS method agrees very well with a model having identical atmospheric parameters computed by the giant line (opacity distribution function) method.

A non-asymptotic homogenization theory for periodic electromagnetic structures

PubMed Central

Tsukerman, Igor; Markel, Vadim A.

2014-01-01

Homogenization of electromagnetic periodic composites is treated as a two-scale problem and solved by approximating the fields on both scales with eigenmodes that satisfy Maxwell's equations and boundary conditions as accurately as possible. Built into this homogenization methodology is an error indicator whose value characterizes the accuracy of homogenization. The proposed theory allows one to define not only bulk, but also position-dependent material parameters (e.g. in proximity to a physical boundary) and to quantify the trade-off between the accuracy of homogenization and its range of applicability to various illumination conditions. PMID:25104912

TAP score: torsion angle propensity normalization applied to local protein structure evaluation

PubMed Central

Tosatto, Silvio CE; Battistutta, Roberto

2007-01-01

Background Experimentally determined protein structures may contain errors and require validation. Conformational criteria based on the Ramachandran plot are mainly used to distinguish between distorted and adequately refined models. While the readily available criteria are sufficient to detect totally wrong structures, establishing the more subtle differences between plausible structures remains more challenging. Results A new criterion, called TAP score, measuring local sequence to structure fitness based on torsion angle propensities normalized against the global minimum and maximum is introduced. It is shown to be more accurate than previous methods at estimating the validity of a protein model in terms of commonly used experimental quality parameters on two test sets representing the full PDB database and a subset of obsolete PDB structures. Highly selective TAP thresholds are derived to recognize over 90% of the top experimental structures in the absence of experimental information. Both a web server and an executable version of the TAP score are available at . Conclusion A novel procedure for energy normalization (TAP) has significantly improved the possibility to recognize the best experimental structures. It will allow the user to more reliably isolate problematic structures in the context of automated experimental structure determination. PMID:17504537

Accurate acoustic power measurement for low-intensity focused ultrasound using focal axial vibration velocity

NASA Astrophysics Data System (ADS)

Tao, Chenyang; Guo, Gepu; Ma, Qingyu; Tu, Juan; Zhang, Dong; Hu, Jimin

2017-07-01

Low-intensity focused ultrasound is a form of therapy that can have reversible acoustothermal effects on biological tissue, depending on the exposure parameters. The acoustic power (AP) should be chosen with caution for the sake of safety. To recover the energy of counteracted radial vibrations at the focal point, an accurate AP measurement method using the focal axial vibration velocity (FAVV) is proposed in explicit formulae and is demonstrated experimentally using a laser vibrometer. The experimental APs for two transducers agree well with theoretical calculations and numerical simulations, showing that AP is proportional to the square of the FAVV, with a fixed power gain determined by the physical parameters of the transducers. The favorable results suggest that the FAVV can be used as a valuable parameter for non-contact AP measurement, providing a new strategy for accurate power control for low-intensity focused ultrasound in biomedical engineering.

An automated method of tuning an attitude estimator

NASA Technical Reports Server (NTRS)

Mason, Paul A. C.; Mook, D. Joseph

1995-01-01

Attitude determination is a major element of the operation and maintenance of a spacecraft. There are several existing methods of determining the attitude of a spacecraft. One of the most commonly used methods utilizes the Kalman filter to estimate the attitude of the spacecraft. Given an accurate model of a system and adequate observations, a Kalman filter can produce accurate estimates of the attitude. If the system model, filter parameters, or observations are inaccurate, the attitude estimates may be degraded. Therefore, it is advantageous to develop a method of automatically tuning the Kalman filter to produce the accurate estimates. In this paper, a three-axis attitude determination Kalman filter, which uses only magnetometer measurements, is developed and tested using real data. The appropriate filter parameters are found via the Process Noise Covariance Estimator (PNCE). The PNCE provides an optimal criterion for determining the best filter parameters.

Laser diode absorption spectroscopy for accurate CO(2) line parameters at 2 microm: consequences for space-based DIAL measurements and potential biases.

PubMed

Joly, Lilian; Marnas, Fabien; Gibert, Fabien; Bruneau, Didier; Grouiez, Bruno; Flamant, Pierre H; Durry, Georges; Dumelie, Nicolas; Parvitte, Bertrand; Zéninari, Virginie

2009-10-10

Space-based active sensing of CO(2) concentration is a very promising technique for the derivation of CO(2) surface fluxes. There is a need for accurate spectroscopic parameters to enable accurate space-based measurements to address global climatic issues. New spectroscopic measurements using laser diode absorption spectroscopy are presented for the preselected R30 CO(2) absorption line ((20(0)1)(III)<--(000) band) and four others. The line strength, air-broadening halfwidth, and its temperature dependence have been investigated. The results exhibit significant improvement for the R30 CO(2) absorption line: 0.4% on the line strength, 0.15% on the air-broadening coefficient, and 0.45% on its temperature dependence. Analysis of potential biases of space-based DIAL CO(2) mixing ratio measurements associated to spectroscopic parameter uncertainties are presented.

Elastic Response and Failure Studies of Multi-Wall Carbon Nanotube Twisted Yarns

NASA Technical Reports Server (NTRS)

Gates, Thomas S.; Jefferson, Gail D.; Frankland, Sarah-Jane V.

2007-01-01

Experimental data on the stress-strain behavior of a polymer multiwall carbon nanotube (MWCNT) yarn composite are used to motivate an initial study in multi-scale modeling of strength and stiffness. Atomistic and continuum length scale modeling methods are outlined to illustrate the range of parameters required to accurately model behavior. The carbon nanotubes yarns are four-ply, twisted, and combined with an elastomer to form a single-layer, unidirectional composite. Due to this textile structure, the yarn is a complicated system of unique geometric relationships subjected to combined loads. Experimental data illustrate the local failure modes induced by static, tensile tests. Key structure-property relationships are highlighted at each length scale indicating opportunities for parametric studies to assist the selection of advantageous material development and manufacturing methods.

Chemical vapor deposition modeling for high temperature materials

NASA Technical Reports Server (NTRS)

Gokoglu, Suleyman A.

1992-01-01

The formalism for the accurate modeling of chemical vapor deposition (CVD) processes has matured based on the well established principles of transport phenomena and chemical kinetics in the gas phase and on surfaces. The utility and limitations of such models are discussed in practical applications for high temperature structural materials. Attention is drawn to the complexities and uncertainties in chemical kinetics. Traditional approaches based on only equilibrium thermochemistry and/or transport phenomena are defended as useful tools, within their validity, for engineering purposes. The role of modeling is discussed within the context of establishing the link between CVD process parameters and material microstructures/properties. It is argued that CVD modeling is an essential part of designing CVD equipment and controlling/optimizing CVD processes for the production and/or coating of high performance structural materials.

Improved Model for Predicting the Free Energy Contribution of Dinucleotide Bulges to RNA Duplex Stability.

PubMed

Tomcho, Jeremy C; Tillman, Magdalena R; Znosko, Brent M

2015-09-01

Predicting the secondary structure of RNA is an intermediate in predicting RNA three-dimensional structure. Commonly, determining RNA secondary structure from sequence uses free energy minimization and nearest neighbor parameters. Current algorithms utilize a sequence-independent model to predict free energy contributions of dinucleotide bulges. To determine if a sequence-dependent model would be more accurate, short RNA duplexes containing dinucleotide bulges with different sequences and nearest neighbor combinations were optically melted to derive thermodynamic parameters. These data suggested energy contributions of dinucleotide bulges were sequence-dependent, and a sequence-dependent model was derived. This model assigns free energy penalties based on the identity of nucleotides in the bulge (3.06 kcal/mol for two purines, 2.93 kcal/mol for two pyrimidines, 2.71 kcal/mol for 5'-purine-pyrimidine-3', and 2.41 kcal/mol for 5'-pyrimidine-purine-3'). The predictive model also includes a 0.45 kcal/mol penalty for an A-U pair adjacent to the bulge and a -0.28 kcal/mol bonus for a G-U pair adjacent to the bulge. The new sequence-dependent model results in predicted values within, on average, 0.17 kcal/mol of experimental values, a significant improvement over the sequence-independent model. This model and new experimental values can be incorporated into algorithms that predict RNA stability and secondary structure from sequence.

Three-dimensional measurement of femur based on structured light scanning

NASA Astrophysics Data System (ADS)

Li, Jie; Ouyang, Jianfei; Qu, Xinghua

2009-12-01

Osteometry is fundamental to study the human skeleton. It has been widely used in palaeoanthropology, bionics, and criminal investigation for more than 200 years. The traditional osteometry is a simple 1-dimensional measurement that can only get 1D size of the bones in manual step-by-step way, even though there are more than 400 parameters to be measured. For today's research and application it is significant and necessary to develop an advanced 3-dimensional osteometry technique. In this paper a new 3D osteometry is presented, which focuses on measurement of the femur, the largest tubular bone in human body. 3D measurement based on the structured light scanning is developed to create fast and precise measurement of the entire body of the femur. The cloud data and geometry model of the sample femur is established in mathematic, accurate and fast way. More than 30 parameters are measured and compared with each other. The experiment shows that the proposed method can meet traditional osteometry and obtain all 1D geometric parameters of the bone at the same time by the mathematics model, such as trochanter-lateral condyle length, superior breadth of shaft, and collo-diaphyseal angle, etc. In the best way, many important geometric parameters that are very difficult to measure by existing osteometry, such as volume, surface area, and curvature of the bone, can be obtained very easily. The overall measuring error is less than 0.1mm.

Sci—Thur AM: YIS - 11: Estimation of Bladder-Wall Cumulative Dose in Multi-Fraction Image-Based Gynaecological Brachytherapy Using Deformable Point Set Registration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zakariaee, R; Brown, C J; Hamarneh, G

2014-08-15

Dosimetric parameters based on dose-volume histograms (DVH) of contoured structures are routinely used to evaluate dose delivered to target structures and organs at risk. However, the DVH provides no information on the spatial distribution of the dose in situations of repeated fractions with changes in organ shape or size. The aim of this research was to develop methods to more accurately determine geometrically localized, cumulative dose to the bladder wall in intracavitary brachytherapy for cervical cancer. The CT scans and treatment plans of 20 cervical cancer patients were used. Each patient was treated with five high-dose-rate (HDR) brachytherapy fractions ofmore » 600cGy prescribed dose. The bladder inner and outer surfaces were delineated using MIM Maestro software (MIM Software Inc.) and were imported into MATLAB (MathWorks) as 3-dimensional point clouds constituting the “bladder wall”. A point-set registration toolbox for MATLAB, Coherent Point Drift (CPD), was used to non-rigidly transform the bladder-wall points from four of the fractions to the coordinate system of the remaining (reference) fraction, which was chosen to be the emptiest bladder for each patient. The doses were accumulated on the reference fraction and new cumulative dosimetric parameters were calculated. The LENT-SOMA toxicity scores of these patients were studied against the cumulative dose parameters. Based on this study, there was no significant correlation between the toxicity scores and the determined cumulative dose parameters.« less

Three-dimensional measurement of femur based on structured light scanning

NASA Astrophysics Data System (ADS)

Li, Jie; Ouyang, Jianfei; Qu, Xinghua

2010-03-01

Osteometry is fundamental to study the human skeleton. It has been widely used in palaeoanthropology, bionics, and criminal investigation for more than 200 years. The traditional osteometry is a simple 1-dimensional measurement that can only get 1D size of the bones in manual step-by-step way, even though there are more than 400 parameters to be measured. For today's research and application it is significant and necessary to develop an advanced 3-dimensional osteometry technique. In this paper a new 3D osteometry is presented, which focuses on measurement of the femur, the largest tubular bone in human body. 3D measurement based on the structured light scanning is developed to create fast and precise measurement of the entire body of the femur. The cloud data and geometry model of the sample femur is established in mathematic, accurate and fast way. More than 30 parameters are measured and compared with each other. The experiment shows that the proposed method can meet traditional osteometry and obtain all 1D geometric parameters of the bone at the same time by the mathematics model, such as trochanter-lateral condyle length, superior breadth of shaft, and collo-diaphyseal angle, etc. In the best way, many important geometric parameters that are very difficult to measure by existing osteometry, such as volume, surface area, and curvature of the bone, can be obtained very easily. The overall measuring error is less than 0.1mm.

First Principles Investigation of Fluorine Based Strontium Series of Perovskites

NASA Astrophysics Data System (ADS)

Erum, Nazia; Azhar Iqbal, Muhammad

2016-11-01

Density functional theory is used to explore structural, elastic, and mechanical properties of SrLiF3, SrNaF3, SrKF3 and SrRbF3 fluoroperovskite compounds by means of an ab-initio Full Potential-Linearized Augmented Plane Wave (FP-LAPW) method. Several lattice parameters are employed to obtain accurate equilibrium volume (Vo). The resultant quantities include ground state energy, elastic constants, shear modulus, bulk modulus, young's modulus, cauchy's pressure, poisson's ratio, shear constant, ratio of elastic anisotropy factor, kleinman's parameter, melting temperature, and lame's coefficient. The calculated structural parameters via DFT as well as analytical methods are found to be consistent with experimental findings. Chemical bonding is used to investigate corresponding chemical trends which authenticate combination of covalent-ionic behavior. Furthermore electron density plots as well as elastic and mechanical properties are reported for the first time which reveals that fluorine based strontium series of perovskites are mechanically stable and posses weak resistance towards shear deformation as compared to resistance towards unidirectional compression while brittleness and ionic behavior is dominated in them which decreases from SrLiF3 to SrRbF3. Calculated cauchy's pressure, poisson's ratio and B/G ratio also proves ionic nature in these compounds. The present methodology represents an effective and influential approach to calculate the whole set of elastic and mechanical parameters which would support to understand various physical phenomena and empower device engineers for implementing these materials in numerous applications.

Fast automated analysis of strong gravitational lenses with convolutional neural networks.

PubMed

Hezaveh, Yashar D; Levasseur, Laurence Perreault; Marshall, Philip J

2017-08-30

Quantifying image distortions caused by strong gravitational lensing-the formation of multiple images of distant sources due to the deflection of their light by the gravity of intervening structures-and estimating the corresponding matter distribution of these structures (the 'gravitational lens') has primarily been performed using maximum likelihood modelling of observations. This procedure is typically time- and resource-consuming, requiring sophisticated lensing codes, several data preparation steps, and finding the maximum likelihood model parameters in a computationally expensive process with downhill optimizers. Accurate analysis of a single gravitational lens can take up to a few weeks and requires expert knowledge of the physical processes and methods involved. Tens of thousands of new lenses are expected to be discovered with the upcoming generation of ground and space surveys. Here we report the use of deep convolutional neural networks to estimate lensing parameters in an extremely fast and automated way, circumventing the difficulties that are faced by maximum likelihood methods. We also show that the removal of lens light can be made fast and automated using independent component analysis of multi-filter imaging data. Our networks can recover the parameters of the 'singular isothermal ellipsoid' density profile, which is commonly used to model strong lensing systems, with an accuracy comparable to the uncertainties of sophisticated models but about ten million times faster: 100 systems in approximately one second on a single graphics processing unit. These networks can provide a way for non-experts to obtain estimates of lensing parameters for large samples of data.

Integrated experimental and theoretical approach for the structural characterization of Hg2+ aqueous solutions

NASA Astrophysics Data System (ADS)

D'Angelo, Paola; Migliorati, Valentina; Mancini, Giordano; Barone, Vincenzo; Chillemi, Giovanni

2008-02-01

The structural and dynamic properties of the solvated Hg2+ ion in aqueous solution have been investigated by a combined experimental-theoretical approach employing x-ray absorption spectroscopy and molecular dynamics (MD) simulations. This method allows one to perform a quantitative analysis of the x-ray absorption near-edge structure (XANES) spectra of ionic solutions using a proper description of the thermal and structural fluctuations. XANES spectra have been computed starting from the MD trajectory, without carrying out any minimization in the structural parameter space. The XANES experimental data are accurately reproduced by a first-shell heptacoordinated cluster only if the second hydration shell is included in the calculations. These results confirm at the same time the existence of a sevenfold first hydration shell for the Hg2+ ion in aqueous solution and the reliability of the potentials used in the MD simulations. The combination of MD and XANES is found to be very helpful to get important new insights into the quantitative estimation of structural properties of disordered systems.

An approximate methods approach to probabilistic structural analysis

NASA Technical Reports Server (NTRS)

Mcclung, R. C.; Millwater, H. R.; Wu, Y.-T.; Thacker, B. H.; Burnside, O. H.

1989-01-01

A major research and technology program in Probabilistic Structural Analysis Methods (PSAM) is currently being sponsored by the NASA Lewis Research Center with Southwest Research Institute as the prime contractor. This program is motivated by the need to accurately predict structural response in an environment where the loadings, the material properties, and even the structure may be considered random. The heart of PSAM is a software package which combines advanced structural analysis codes with a fast probability integration (FPI) algorithm for the efficient calculation of stochastic structural response. The basic idea of PAAM is simple: make an approximate calculation of system response, including calculation of the associated probabilities, with minimal computation time and cost, based on a simplified representation of the geometry, loads, and material. The deterministic solution resulting should give a reasonable and realistic description of performance-limiting system responses, although some error will be inevitable. If the simple model has correctly captured the basic mechanics of the system, however, including the proper functional dependence of stress, frequency, etc. on design parameters, then the response sensitivities calculated may be of significantly higher accuracy.

Deriving stellar parameters with the SME software package

NASA Astrophysics Data System (ADS)

Piskunov, N.

2017-09-01

Photometry and spectroscopy are complementary tools for deriving accurate stellar parameters. Here I present one of the popular packages for stellar spectroscopy called SME with the emphasis on the latest developments and error assessment for the derived parameters.

Structural, dynamical & electronic properties of CaCuO{sub 2}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Agrawal, B.K.; Agrawal, S.

1994-12-31

The scalar relativistic version of an accurate first principles full potential self- consistent linearized muffin tin orbital (LMTO) method has been employed for describing the physical properties of the parent system of the high-Tc oxide superconductors, i.e., CaCuO2. The presently employed modified version of the LMTO method is quite fast and goes beyond the usual LMTO-ASA method in the sense that it permits a completely general shape of the potential and the charge density. Also, in contrast to LMTO-ASA, the present method is also capable of treating distorted lattice structures accurately. The calculated values of the lattice parameters of puremore » CaCuO2 lie within 3% of the experimentally measured values for the Sr-doped system Ca(.86)Sr(.14)CuO(2). The computed electronic structures and the density of states is quite similar to those of the other oxide superconductors, except of their three- dimensional character because of the presence of strong coupling between the closely spaced CuO2 layers. The van Hove singularity peak appears slightly below the Fermi level and a small concentration of oxygenation /or/ substitutional doping may pin it as the Fermi level. The calculated frequencies for some symmetric frozen phonons for undoped CaCuO2 are quite near to the measured data for the Sr-doped CaCuO2.« less

Structural, dynamical and electronic properties of CaCuO2

NASA Technical Reports Server (NTRS)

Agrawal, Bal K.; Agrawal, Savitri

1995-01-01

The scalar relativistic version of an accurate first principles full potential self-consistent linearized muffin tin orbital (LMTO) method has been employed for describing the physical properties of the parent system of the high-T(sub c) oxide superconductors, i.e., CaCuO2. The presently employed modified version of the LMTO method is quite fast and goes beyond the usual LMTO ASA method in the sense that it permits a completely general shape of the potential and the charge density. Also, in contrast to LMTO ASA, the present method is also capable of treating distorted lattice structures accurately. The calculated values of the lattice parameters of pure CaCuO2 lie within 3% of the experimentally measured values for the Sr-doped system Ca(0.86)Sr(0.14)CuO(2). The computed electronic structures and the density of states is quite similar to those of the other oxide superconductors, except of their three- dimensional character because of the presence of strong coupling between the closely spaced CuO2 layers. The van Hove singularity peak appears slightly below the Fermi level and a small concentration of oxygenation /or/ substitutional doping may pin it at the Fermi level. The calculated frequencies for some symmetric frozen phonons for undoped CaCuO2 are quite near to the measured data for the Sr-doped CaCuO2.

Ab Initio High Pressure and Temperature Investigation on Cubic PbMoO3 Perovskite

NASA Astrophysics Data System (ADS)

Dar, Sajad Ahmad; Srivastava, Vipul; Sakalle, Umesh Kumar

2017-12-01

A combined high pressure and temperature investigation on recently reported cubic perovskite PbMoO3 have been performed within the most accurate density functional theory (DFT). The structure was found stable in cubic paramagnetic phase. The DFT calculated analytical and experimental lattice constant were found in good agreement. The analytical tolerance factor as well as the elastic properties further verifies the cubic stability for PbMoO3. The spin polarized electronic band structure and density of states presented metallic nature with symmetry in up and down states. The insignificant magnetic moment also confirms the paramagnetic nature for the compound. The high pressure elastic and mechanical study up to 35 GPa reveal the structural stability of the material in this pressure range. The compound was found to establish a ductile nature. The electrical conductivity obtained from the band structure results show a decreasing trend with increasing temperature. The temperature dependence of thermodynamic parameters such as specific heat ( C v), thermal expansion ( α) has also been evaluated.

Sensitivity Analysis of an ENteric Immunity SImulator (ENISI)-Based Model of Immune Responses to Helicobacter pylori Infection

PubMed Central

Alam, Maksudul; Deng, Xinwei; Philipson, Casandra; Bassaganya-Riera, Josep; Bisset, Keith; Carbo, Adria; Eubank, Stephen; Hontecillas, Raquel; Hoops, Stefan; Mei, Yongguo; Abedi, Vida; Marathe, Madhav

2015-01-01

Agent-based models (ABM) are widely used to study immune systems, providing a procedural and interactive view of the underlying system. The interaction of components and the behavior of individual objects is described procedurally as a function of the internal states and the local interactions, which are often stochastic in nature. Such models typically have complex structures and consist of a large number of modeling parameters. Determining the key modeling parameters which govern the outcomes of the system is very challenging. Sensitivity analysis plays a vital role in quantifying the impact of modeling parameters in massively interacting systems, including large complex ABM. The high computational cost of executing simulations impedes running experiments with exhaustive parameter settings. Existing techniques of analyzing such a complex system typically focus on local sensitivity analysis, i.e. one parameter at a time, or a close “neighborhood” of particular parameter settings. However, such methods are not adequate to measure the uncertainty and sensitivity of parameters accurately because they overlook the global impacts of parameters on the system. In this article, we develop novel experimental design and analysis techniques to perform both global and local sensitivity analysis of large-scale ABMs. The proposed method can efficiently identify the most significant parameters and quantify their contributions to outcomes of the system. We demonstrate the proposed methodology for ENteric Immune SImulator (ENISI), a large-scale ABM environment, using a computational model of immune responses to Helicobacter pylori colonization of the gastric mucosa. PMID:26327290

Sensitivity Analysis of an ENteric Immunity SImulator (ENISI)-Based Model of Immune Responses to Helicobacter pylori Infection.

PubMed

Alam, Maksudul; Deng, Xinwei; Philipson, Casandra; Bassaganya-Riera, Josep; Bisset, Keith; Carbo, Adria; Eubank, Stephen; Hontecillas, Raquel; Hoops, Stefan; Mei, Yongguo; Abedi, Vida; Marathe, Madhav

2015-01-01

Agent-based models (ABM) are widely used to study immune systems, providing a procedural and interactive view of the underlying system. The interaction of components and the behavior of individual objects is described procedurally as a function of the internal states and the local interactions, which are often stochastic in nature. Such models typically have complex structures and consist of a large number of modeling parameters. Determining the key modeling parameters which govern the outcomes of the system is very challenging. Sensitivity analysis plays a vital role in quantifying the impact of modeling parameters in massively interacting systems, including large complex ABM. The high computational cost of executing simulations impedes running experiments with exhaustive parameter settings. Existing techniques of analyzing such a complex system typically focus on local sensitivity analysis, i.e. one parameter at a time, or a close "neighborhood" of particular parameter settings. However, such methods are not adequate to measure the uncertainty and sensitivity of parameters accurately because they overlook the global impacts of parameters on the system. In this article, we develop novel experimental design and analysis techniques to perform both global and local sensitivity analysis of large-scale ABMs. The proposed method can efficiently identify the most significant parameters and quantify their contributions to outcomes of the system. We demonstrate the proposed methodology for ENteric Immune SImulator (ENISI), a large-scale ABM environment, using a computational model of immune responses to Helicobacter pylori colonization of the gastric mucosa.

Seismic velocity structure of the crust and upper mantle beneath the Texas-Gulf of Mexico margin from joint inversion of Ps and Sp receiver functions and surface wave dispersion

NASA Astrophysics Data System (ADS)

Agrawal, M.; Pulliam, J.; Sen, M. K.

2013-12-01

The seismic structure beneath Texas Gulf Coast Plain (GCP) is determined via velocity analysis of stacked common conversion point (CCP) Ps and Sp receiver functions and surface wave dispersion. The GCP is a portion of a ocean-continental transition zone, or 'passive margin', where seismic imaging of lithospheric Earth structure via passive seismic techniques has been rare. Seismic data from a temporary array of 22 broadband stations, spaced 16-20 km apart, on a ~380-km-long profile from Matagorda Island, a barrier island in the Gulf of Mexico, to Johnson City, Texas were employed to construct a coherent image of the crust and uppermost mantle. CCP stacking was applied to data from teleseismic earthquakes to enhance the signal-to-noise ratios of converted phases, such as Ps phases. An inaccurate velocity model, used for time-to-depth conversion in CCP stacking, may produce higher errors, especially in a region of substantial lateral velocity variations. An accurate velocity model is therefore essential to constructing high quality depth-domain images. To find accurate velocity P- and S-wave models, we applied a joint modeling approach that searches for best-fitting models via simulated annealing. This joint inversion approach, which we call 'multi objective optimization in seismology' (MOOS), simultaneously models Ps receiver functions, Sp receiver functions and group velocity surface wave dispersion curves after assigning relative weights for each objective function. Weights are computed from the standard deviations of the data. Statistical tools such as the posterior parameter correlation matrix and posterior probability density (PPD) function are used to evaluate the constraints that each data type places on model parameters. They allow us to identify portions of the model that are well or poorly constrained.

Effects of LiDAR point density, sampling size and height threshold on estimation accuracy of crop biophysical parameters.

PubMed

Luo, Shezhou; Chen, Jing M; Wang, Cheng; Xi, Xiaohuan; Zeng, Hongcheng; Peng, Dailiang; Li, Dong

2016-05-30

Vegetation leaf area index (LAI), height, and aboveground biomass are key biophysical parameters. Corn is an important and globally distributed crop, and reliable estimations of these parameters are essential for corn yield forecasting, health monitoring and ecosystem modeling. Light Detection and Ranging (LiDAR) is considered an effective technology for estimating vegetation biophysical parameters. However, the estimation accuracies of these parameters are affected by multiple factors. In this study, we first estimated corn LAI, height and biomass (R² = 0.80, 0.874 and 0.838, respectively) using the original LiDAR data (7.32 points/m²), and the results showed that LiDAR data could accurately estimate these biophysical parameters. Second, comprehensive research was conducted on the effects of LiDAR point density, sampling size and height threshold on the estimation accuracy of LAI, height and biomass. Our findings indicated that LiDAR point density had an important effect on the estimation accuracy for vegetation biophysical parameters, however, high point density did not always produce highly accurate estimates, and reduced point density could deliver reasonable estimation results. Furthermore, the results showed that sampling size and height threshold were additional key factors that affect the estimation accuracy of biophysical parameters. Therefore, the optimal sampling size and the height threshold should be determined to improve the estimation accuracy of biophysical parameters. Our results also implied that a higher LiDAR point density, larger sampling size and height threshold were required to obtain accurate corn LAI estimation when compared with height and biomass estimations. In general, our results provide valuable guidance for LiDAR data acquisition and estimation of vegetation biophysical parameters using LiDAR data.

Probabilistic seismic demand analysis using advanced ground motion intensity measures

USGS Publications Warehouse

Tothong, P.; Luco, N.

2007-01-01

One of the objectives in performance-based earthquake engineering is to quantify the seismic reliability of a structure at a site. For that purpose, probabilistic seismic demand analysis (PSDA) is used as a tool to estimate the mean annual frequency of exceeding a specified value of a structural demand parameter (e.g. interstorey drift). This paper compares and contrasts the use, in PSDA, of certain advanced scalar versus vector and conventional scalar ground motion intensity measures (IMs). One of the benefits of using a well-chosen IM is that more accurate evaluations of seismic performance are achieved without the need to perform detailed ground motion record selection for the nonlinear dynamic structural analyses involved in PSDA (e.g. record selection with respect to seismic parameters such as earthquake magnitude, source-to-site distance, and ground motion epsilon). For structural demands that are dominated by a first mode of vibration, using inelastic spectral displacement (Sdi) can be advantageous relative to the conventionally used elastic spectral acceleration (Sa) and the vector IM consisting of Sa and epsilon (??). This paper demonstrates that this is true for ordinary and for near-source pulse-like earthquake records. The latter ground motions cannot be adequately characterized by either Sa alone or the vector of Sa and ??. For structural demands with significant higher-mode contributions (under either of the two types of ground motions), even Sdi (alone) is not sufficient, so an advanced scalar IM that additionally incorporates higher modes is used.

Structure determination of Ba5AlF13 by coupling electron, synchrotron and neutron powder diffraction, solid-state NMR and ab initio calculations.

PubMed

Martineau, Charlotte; Allix, Mathieu; Suchomel, Matthew R; Porcher, Florence; Vivet, François; Legein, Christophe; Body, Monique; Massiot, Dominique; Taulelle, Francis; Fayon, Franck

2016-10-04

The room temperature structure of Ba 5 AlF 13 has been investigated by coupling electron, synchrotron and neutron powder diffraction, solid-state high-resolution NMR ( 19 F and 27 Al) and first principles calculations. An initial structural model has been obtained from electron and synchrotron powder diffraction data, and its main features have been confirmed by one- and two-dimensional NMR measurements. However, DFT GIPAW calculations of the 19 F isotropic shieldings revealed an inaccurate location of one fluorine site (F3, site 8a), which exhibited unusual long F-Ba distances. The atomic arrangement was reinvestigated using neutron powder diffraction data. Subsequent Fourier maps showed that this fluorine atom occupies a crystallographic site of lower symmetry (32e) with partial occupancy (25%). GIPAW computations of the NMR parameters validate the refined structural model, ruling out the presence of local static disorder and indicating that the partial occupancy of this F site reflects a local motional process. Visualisation of the dynamic process was then obtained from the Rietveld refinement of neutron diffraction data using an anharmonic description of the displacement parameters to account for the thermal motion of the mobile fluorine. The whole ensemble of powder diffraction and NMR data, coupled with first principles calculations, allowed drawing an accurate structural model of Ba 5 AlF 13 , including site-specific dynamical disorder in the fluorine sub-network.

Density functional theory molecular modeling, chemical synthesis, and antimicrobial behaviour of selected benzimidazole derivatives

NASA Astrophysics Data System (ADS)

Marinescu, Maria; Tudorache, Diana Gabriela; Marton, George Iuliu; Zalaru, Christina-Marie; Popa, Marcela; Chifiriuc, Mariana-Carmen; Stavarache, Cristina-Elena; Constantinescu, Catalin

2017-02-01

Eco-friendly, one-pot, solvent-free synthesis of biologically active 2-substituted benzimidazoles is presented and discussed herein. Novel N-Mannich bases are synthesized from benzimidazoles, secondary amines and formaldehyde, and their structures are confirmed by 1H nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR), and elemental analysis. All benzimidazole derivatives are evaluated by qualitative and quantitative methods against 9 bacterial strains. The largest microbicide and anti-biofilm effect is observed for the 2-(1-hydroxyethyl)-compounds. Density functional theory (DFT) modeling of the molecular structure and frontier molecular orbitals, i.e. highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO/LUMO), is accomplished by using the GAMESS 2012 software. Antimicrobial activity is correlated with the electronic parameters (chemical hardness, electronic chemical potential, global electrophilicity index), Mullikan atomic charges and geometric parameters of the benzimidazole compounds. The planarity of the compound, symmetry of the molecule, and the presence of a nucleophilic group, are advantages for a high antimicrobial activity. Finally, we briefly show that further accurate processing of such compounds into thin films and hybrid structures, e.g. by laser ablation matrix-assisted pulsed laser evaporation and/or laser-induced forward transfer, may indeed provide simple and environmental friendly, state-of-the-art solutions for antimicrobial coatings.

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

PubMed

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

2014-10-01

This study investigates the hypothesis that structured light reflectance imaging with high spatial frequency patterns [Formula: see text] can be used to quantitatively map the anisotropic scattering phase function distribution [Formula: see text] in turbid media. Monte Carlo simulations were used in part to establish a semi-empirical model of demodulated reflectance ([Formula: see text]) in terms of dimensionless scattering [Formula: see text] and [Formula: see text], a metric of the first two moments of the [Formula: see text] distribution. Experiments completed in tissue-simulating phantoms showed that simultaneous analysis of [Formula: see text] spectra sampled at multiple [Formula: see text] in the frequency range [0.05-0.5] [Formula: see text] allowed accurate estimation of both [Formula: see text] in the relevant tissue range [0.4-1.8] [Formula: see text], and [Formula: see text] in the range [1.4-1.75]. Pilot measurements of a healthy volunteer exhibited [Formula: see text]-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.

Exploratory Bifactor Analysis: The Schmid-Leiman Orthogonalization and Jennrich-Bentler Analytic Rotations

PubMed Central

Mansolf, Maxwell; Reise, Steven P.

2017-01-01

Analytic bifactor rotations (Jennrich & Bentler, 2011, 2012) have been recently developed and made generally available, but are not well understood. The Jennrich-Bentler analytic bifactor rotations (bi-quartimin and bi-geomin) are an alternative to, and arguably an improvement upon, the less technically sophisticated Schmid-Leiman orthogonalization (Schmid & Leiman, 1957). We review the technical details that underlie the Schmid-Leiman and Jennrich-Bentler bifactor rotations, using simulated data structures to illustrate important features and limitations. For the Schmid-Leiman, we review the problem of inaccurate parameter estimates caused by the linear dependencies, sometimes called “proportionality constraints,” that are required to expand a p correlated factors solution into a (p+1) (bi)factor space. We also review the complexities involved when the data depart from perfect cluster structure (e.g., item cross-loading on group factors). For the Jennrich-Bentler rotations, we describe problems in parameter estimation caused by departures from perfect cluster structure. In addition, we illustrate the related problems of: (a) solutions that are not invariant under different starting values (i.e., local minima problems); and, (b) group factors collapsing onto the general factor. Recommendations are made for substantive researchers including examining all local minima and applying multiple exploratory techniques in an effort to identify an accurate model. PMID:27612521

High Performance, Robust Control of Flexible Space Structures: MSFC Center Director's Discretionary Fund

NASA Technical Reports Server (NTRS)

Whorton, M. S.

1998-01-01

Many spacecraft systems have ambitious objectives that place stringent requirements on control systems. Achievable performance is often limited because of difficulty of obtaining accurate models for flexible space structures. To achieve sufficiently high performance to accomplish mission objectives may require the ability to refine the control design model based on closed-loop test data and tune the controller based on the refined model. A control system design procedure is developed based on mixed H2/H(infinity) optimization to synthesize a set of controllers explicitly trading between nominal performance and robust stability. A homotopy algorithm is presented which generates a trajectory of gains that may be implemented to determine maximum achievable performance for a given model error bound. Examples show that a better balance between robustness and performance is obtained using the mixed H2/H(infinity) design method than either H2 or mu-synthesis control design. A second contribution is a new procedure for closed-loop system identification which refines parameters of a control design model in a canonical realization. Examples demonstrate convergence of the parameter estimation and improved performance realized by using the refined model for controller redesign. These developments result in an effective mechanism for achieving high-performance control of flexible space structures.

Correlation matrix renormalization theory for correlated-electron materials with application to the crystalline phases of atomic hydrogen

DOE PAGES

Zhao, Xin; Liu, Jun; Yao, Yong-Xin; ...

2018-01-23

Developing accurate and computationally efficient methods to calculate the electronic structure and total energy of correlated-electron materials has been a very challenging task in condensed matter physics and materials science. Recently, we have developed a correlation matrix renormalization (CMR) method which does not assume any empirical Coulomb interaction U parameters and does not have double counting problems in the ground-state total energy calculation. The CMR method has been demonstrated to be accurate in describing both the bonding and bond breaking behaviors of molecules. In this study, we extend the CMR method to the treatment of electron correlations in periodic solidmore » systems. By using a linear hydrogen chain as a benchmark system, we show that the results from the CMR method compare very well with those obtained recently by accurate quantum Monte Carlo (QMC) calculations. We also study the equation of states of three-dimensional crystalline phases of atomic hydrogen. We show that the results from the CMR method agree much better with the available QMC data in comparison with those from density functional theory and Hartree-Fock calculations.« less

Correlation matrix renormalization theory for correlated-electron materials with application to the crystalline phases of atomic hydrogen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Xin; Liu, Jun; Yao, Yong-Xin

Developing accurate and computationally efficient methods to calculate the electronic structure and total energy of correlated-electron materials has been a very challenging task in condensed matter physics and materials science. Recently, we have developed a correlation matrix renormalization (CMR) method which does not assume any empirical Coulomb interaction U parameters and does not have double counting problems in the ground-state total energy calculation. The CMR method has been demonstrated to be accurate in describing both the bonding and bond breaking behaviors of molecules. In this study, we extend the CMR method to the treatment of electron correlations in periodic solidmore » systems. By using a linear hydrogen chain as a benchmark system, we show that the results from the CMR method compare very well with those obtained recently by accurate quantum Monte Carlo (QMC) calculations. We also study the equation of states of three-dimensional crystalline phases of atomic hydrogen. We show that the results from the CMR method agree much better with the available QMC data in comparison with those from density functional theory and Hartree-Fock calculations.« less

High-Frequency Electromagnetic Impedance Measurements for Characterization, Monitoring and Verification Efforts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Ki Ha; Becker, Alex; Tseng, Hung-Wen

2004-06-16

Non-invasive, high-resolution imaging of the shallow subsurface is needed for delineation of buried waste, detection of unexploded ordinance, verification and monitoring of containment structures, and other environmental applications. Electromagnetic (EM) measurements at frequencies between 0.1 and 100 MHz are important for such applications, because the induction number of many targets is small and the ability to determine the dielectric permittivity in addition to electrical conductivity of the subsurface is possible. Earlier workers were successful in developing systems for detecting anomalous areas, but no quantifiable information was accurately determined. For high-resolution imaging, accurate measurements are necessary so the field data canmore » be mapped into the space of the subsurface parameters. We are developing a non-invasive method for accurately mapping the electrical conductivity and dielectric permittivity of the shallow subsurface using the EM impedance approach (Frangos, 2001; Lee and Becker, 2001; Song et al., 2002, Tseng et al., 2003). Electric and magnetic sensors are being tested and calibrated on sea water and in a known area against theoretical predictions, thereby insuring that the data collected with the high-frequency impedance (HFI) system will support high-resolution, multi-dimensional imaging techniques.« less

Fast 3D registration of multimodality tibial images with significant structural mismatch

NASA Astrophysics Data System (ADS)

Rajapakse, C. S.; Wald, M. J.; Magland, J.; Zhang, X. H.; Liu, X. S.; Guo, X. E.; Wehrli, F. W.

2009-02-01

Recently, micro-magnetic resonance imaging (μMRI) in conjunction with micro-finite element analysis has shown great potential in estimating mechanical properties - stiffness and elastic moduli - of bone in patients at risk of osteoporosis. Due to limited spatial resolution and signal-to-noise ratio achievable in vivo, the validity of estimated properties is often established by comparison to those derived from high-resolution micro-CT (μCT) images of cadaveric specimens. For accurate comparison of mechanical parameters derived from μMR and μCT images, analyzed 3D volumes have to be closely matched. The alignment of the micro structure (and the cortex) is often hampered by the fundamental differences of μMR and μCT images and variations in marrow content and cortical bone thickness. Here we present an intensity cross-correlation based registration algorithm coupled with segmentation for registering 3D tibial specimen images acquired by μMRI and μCT in the context of finite-element modeling to assess the bone's mechanical constants. The algorithm first generates three translational and three rotational parameters required to align segmented μMR and CT images from sub regions with high micro-structural similarities. These transformation parameters are then used to register the grayscale μMR and μCT images, which include both the cortex and trabecular bone. The intensity crosscorrelation maximization based registration algorithm described here is suitable for 3D rigid-body image registration applications where through-plane rotations are known to be relatively small. The close alignment of the resulting images is demonstrated quantitatively based on a voxel-overlap measure and qualitatively using visual inspection of the micro structure.

Delay-induced depinning of localized structures in a spatially inhomogeneous Swift-Hohenberg model

NASA Astrophysics Data System (ADS)

Tabbert, Felix; Schelte, Christian; Tlidi, Mustapha; Gurevich, Svetlana V.

2017-03-01

We report on the dynamics of localized structures in an inhomogeneous Swift-Hohenberg model describing pattern formation in the transverse plane of an optical cavity. This real order parameter equation is valid close to the second-order critical point associated with bistability. The optical cavity is illuminated by an inhomogeneous spatial Gaussian pumping beam and subjected to time-delayed feedback. The Gaussian injection beam breaks the translational symmetry of the system by exerting an attracting force on the localized structure. We show that the localized structure can be pinned to the center of the inhomogeneity, suppressing the delay-induced drift bifurcation that has been reported in the particular case where the injection is homogeneous, assuming a continuous wave operation. Under an inhomogeneous spatial pumping beam, we perform the stability analysis of localized solutions to identify different instability regimes induced by time-delayed feedback. In particular, we predict the formation of two-arm spirals, as well as oscillating and depinning dynamics caused by the interplay of an attracting inhomogeneity and destabilizing time-delayed feedback. The transition from oscillating to depinning solutions is investigated by means of numerical continuation techniques. Analytically, we use an order parameter approach to derive a normal form of the delay-induced Hopf bifurcation leading to an oscillating solution. Additionally we model the interplay of an attracting inhomogeneity and destabilizing time delay by describing the localized solution as an overdamped particle in a potential well generated by the inhomogeneity. In this case, the time-delayed feedback acts as a driving force. Comparing results from the later approach with the full Swift-Hohenberg model, we show that the approach not only provides an instructive description of the depinning dynamics, but also is numerically accurate throughout most of the parameter regime.

Bayesian approach to analyzing holograms of colloidal particles.

PubMed

Dimiduk, Thomas G; Manoharan, Vinothan N

2016-10-17

We demonstrate a Bayesian approach to tracking and characterizing colloidal particles from in-line digital holograms. We model the formation of the hologram using Lorenz-Mie theory. We then use a tempered Markov-chain Monte Carlo method to sample the posterior probability distributions of the model parameters: particle position, size, and refractive index. Compared to least-squares fitting, our approach allows us to more easily incorporate prior information about the parameters and to obtain more accurate uncertainties, which are critical for both particle tracking and characterization experiments. Our approach also eliminates the need to supply accurate initial guesses for the parameters, so it requires little tuning.

Evaluation of confidence intervals for a steady-state leaky aquifer model

USGS Publications Warehouse

Christensen, S.; Cooley, R.L.

1999-01-01

The fact that dependent variables of groundwater models are generally nonlinear functions of model parameters is shown to be a potentially significant factor in calculating accurate confidence intervals for both model parameters and functions of the parameters, such as the values of dependent variables calculated by the model. The Lagrangian method of Vecchia and Cooley [Vecchia, A.V. and Cooley, R.L., Water Resources Research, 1987, 23(7), 1237-1250] was used to calculate nonlinear Scheffe-type confidence intervals for the parameters and the simulated heads of a steady-state groundwater flow model covering 450 km2 of a leaky aquifer. The nonlinear confidence intervals are compared to corresponding linear intervals. As suggested by the significant nonlinearity of the regression model, linear confidence intervals are often not accurate. The commonly made assumption that widths of linear confidence intervals always underestimate the actual (nonlinear) widths was not correct. Results show that nonlinear effects can cause the nonlinear intervals to be asymmetric and either larger or smaller than the linear approximations. Prior information on transmissivities helps reduce the size of the confidence intervals, with the most notable effects occurring for the parameters on which there is prior information and for head values in parameter zones for which there is prior information on the parameters.The fact that dependent variables of groundwater models are generally nonlinear functions of model parameters is shown to be a potentially significant factor in calculating accurate confidence intervals for both model parameters and functions of the parameters, such as the values of dependent variables calculated by the model. The Lagrangian method of Vecchia and Cooley was used to calculate nonlinear Scheffe-type confidence intervals for the parameters and the simulated heads of a steady-state groundwater flow model covering 450 km2 of a leaky aquifer. The nonlinear confidence intervals are compared to corresponding linear intervals. As suggested by the significant nonlinearity of the regression model, linear confidence intervals are often not accurate. The commonly made assumption that widths of linear confidence intervals always underestimate the actual (nonlinear) widths was not correct. Results show that nonlinear effects can cause the nonlinear intervals to be asymmetric and either larger or smaller than the linear approximations. Prior information on transmissivities helps reduce the size of the confidence intervals, with the most notable effects occurring for the parameters on which there is prior information and for head values in parameter zones for which there is prior information on the parameters.

A new powerful parameterization tool for managing groundwater resources and predicting land subsidence in Las Vegas Valley

NASA Astrophysics Data System (ADS)

Zhang, M.; Nunes, V. D.; Burbey, T. J.; Borggaard, J.

2012-12-01

More than 1.5 m of subsidence has been observed in Las Vegas Valley since 1935 as a result of groundwater pumping that commenced in 1905 (Bell, 2002). The compaction of the aquifer system has led to several large subsidence bowls and deleterious earth fissures. The highly heterogeneous aquifer system with its variably thick interbeds makes predicting the magnitude and location of subsidence extremely difficult. Several numerical groundwater flow models of the Las Vegas basin have been previously developed; however none of them have been able to accurately simulate the observed subsidence patterns or magnitudes because of inadequate parameterization. To better manage groundwater resources and predict future subsidence we have updated and developed a more accurate groundwater management model for Las Vegas Valley by developing a new adjoint parameter estimation package (APE) that is used in conjunction with UCODE along with MODFLOW and the SUB (subsidence) and HFB (horizontal flow barrier) packages. The APE package is used with UCODE to automatically identify suitable parameter zonations and inversely calculate parameter values from hydraulic head and subsidence measurements, which are highly sensitive to both elastic (Ske) and inelastic (Skv) storage coefficients. With the advent of InSAR (Interferometric synthetic aperture radar), distributed spatial and temporal subsidence measurements can be obtained, which greatly enhance the accuracy of parameter estimation. This automation process can remove user bias and provide a far more accurate and robust parameter zonation distribution. The outcome of this work yields a more accurate and powerful tool for managing groundwater resources in Las Vegas Valley to date.

Analysis of several methods and inertial sensors locations to assess gait parameters in able-bodied subjects.

PubMed

Ben Mansour, Khaireddine; Rezzoug, Nasser; Gorce, Philippe

2015-10-01

The purpose of this paper was to determine which types of inertial sensors and which advocated locations should be used for reliable and accurate gait event detection and temporal parameter assessment in normal adults. In addition, we aimed to remove the ambiguity found in the literature of the definition of the initial contact (IC) from the lumbar accelerometer. Acceleration and angular velocity data was gathered from the lumbar region and the distal edge of each shank. This data was evaluated in comparison to an instrumented treadmill and an optoelectronic system during five treadmill speed sessions. The lumbar accelerometer showed that the peak of the anteroposterior component was the most accurate for IC detection. Similarly, the valley that followed the peak of the vertical component was the most precise for terminal contact (TC) detection. Results based on ANOVA and Tukey tests showed that the set of inertial methods was suitable for temporal gait assessment and gait event detection in able-bodied subjects. For gait event detection, an exception was found with the shank accelerometer. The tool was suitable for temporal parameters assessment, despite the high root mean square error on the detection of IC (RMSEIC) and TC (RMSETC). The shank gyroscope was found to be as accurate as the kinematic method since the statistical tests revealed no significant difference between the two techniques for the RMSE off all gait events and temporal parameters. The lumbar and shank accelerometers were the most accurate alternative to the shank gyroscope for gait event detection and temporal parameters assessment, respectively. Copyright © 2015. Published by Elsevier B.V.

Hyoid bone development: An assessment of optimal CT scanner parameters and 3D volume rendering techniques

PubMed Central

Cotter, Meghan M.; Whyms, Brian J.; Kelly, Michael P.; Doherty, Benjamin M.; Gentry, Lindell R.; Bersu, Edward T.; Vorperian, Houri K.

2015-01-01

The hyoid bone anchors and supports the vocal tract. Its complex shape is best studied in three dimensions, but it is difficult to capture on computed tomography (CT) images and three-dimensional volume renderings. The goal of this study was to determine the optimal CT scanning and rendering parameters to accurately measure the growth and developmental anatomy of the hyoid and to determine whether it is feasible and necessary to use these parameters in the measurement of hyoids from in vivo CT scans. Direct linear and volumetric measurements of skeletonized hyoid bone specimens were compared to corresponding CT images to determine the most accurate scanning parameters and three-dimensional rendering techniques. A pilot study was undertaken using in vivo scans from a retrospective CT database to determine feasibility of quantifying hyoid growth. Scanning parameters and rendering technique affected accuracy of measurements. Most linear CT measurements were within 10% of direct measurements; however, volume was overestimated when CT scans were acquired with a slice thickness greater than 1.25 mm. Slice-by-slice thresholding of hyoid images decreased volume overestimation. The pilot study revealed that the linear measurements tested correlate with age. A fine-tuned rendering approach applied to small slice thickness CT scans produces the most accurate measurements of hyoid bones. However, linear measurements can be accurately assessed from in vivo CT scans at a larger slice thickness. Such findings imply that investigation into the growth and development of the hyoid bone, and the vocal tract as a whole, can now be performed using these techniques. PMID:25810349

Hyoid Bone Development: An Assessment Of Optimal CT Scanner Parameters and Three-Dimensional Volume Rendering Techniques.

PubMed

Cotter, Meghan M; Whyms, Brian J; Kelly, Michael P; Doherty, Benjamin M; Gentry, Lindell R; Bersu, Edward T; Vorperian, Houri K

2015-08-01

The hyoid bone anchors and supports the vocal tract. Its complex shape is best studied in three dimensions, but it is difficult to capture on computed tomography (CT) images and three-dimensional volume renderings. The goal of this study was to determine the optimal CT scanning and rendering parameters to accurately measure the growth and developmental anatomy of the hyoid and to determine whether it is feasible and necessary to use these parameters in the measurement of hyoids from in vivo CT scans. Direct linear and volumetric measurements of skeletonized hyoid bone specimens were compared with corresponding CT images to determine the most accurate scanning parameters and three-dimensional rendering techniques. A pilot study was undertaken using in vivo scans from a retrospective CT database to determine feasibility of quantifying hyoid growth. Scanning parameters and rendering technique affected accuracy of measurements. Most linear CT measurements were within 10% of direct measurements; however, volume was overestimated when CT scans were acquired with a slice thickness greater than 1.25 mm. Slice-by-slice thresholding of hyoid images decreased volume overestimation. The pilot study revealed that the linear measurements tested correlate with age. A fine-tuned rendering approach applied to small slice thickness CT scans produces the most accurate measurements of hyoid bones. However, linear measurements can be accurately assessed from in vivo CT scans at a larger slice thickness. Such findings imply that investigation into the growth and development of the hyoid bone, and the vocal tract as a whole, can now be performed using these techniques. © 2015 Wiley Periodicals, Inc.

Validation of Bayesian analysis of compartmental kinetic models in medical imaging.

PubMed

Sitek, Arkadiusz; Li, Quanzheng; El Fakhri, Georges; Alpert, Nathaniel M

2016-10-01

Kinetic compartmental analysis is frequently used to compute physiologically relevant quantitative values from time series of images. In this paper, a new approach based on Bayesian analysis to obtain information about these parameters is presented and validated. The closed-form of the posterior distribution of kinetic parameters is derived with a hierarchical prior to model the standard deviation of normally distributed noise. Markov chain Monte Carlo methods are used for numerical estimation of the posterior distribution. Computer simulations of the kinetics of F18-fluorodeoxyglucose (FDG) are used to demonstrate drawing statistical inferences about kinetic parameters and to validate the theory and implementation. Additionally, point estimates of kinetic parameters and covariance of those estimates are determined using the classical non-linear least squares approach. Posteriors obtained using methods proposed in this work are accurate as no significant deviation from the expected shape of the posterior was found (one-sided P>0.08). It is demonstrated that the results obtained by the standard non-linear least-square methods fail to provide accurate estimation of uncertainty for the same data set (P<0.0001). The results of this work validate new methods for a computer simulations of FDG kinetics. Results show that in situations where the classical approach fails in accurate estimation of uncertainty, Bayesian estimation provides an accurate information about the uncertainties in the parameters. Although a particular example of FDG kinetics was used in the paper, the methods can be extended for different pharmaceuticals and imaging modalities. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Development of a quantum mechanics-based free-energy perturbation method: use in the calculation of relative solvation free energies.

PubMed

Reddy, M Rami; Singh, U C; Erion, Mark D

2004-05-26

Free-energy perturbation (FEP) is considered the most accurate computational method for calculating relative solvation and binding free-energy differences. Despite some success in applying FEP methods to both drug design and lead optimization, FEP calculations are rarely used in the pharmaceutical industry. One factor limiting the use of FEP is its low throughput, which is attributed in part to the dependence of conventional methods on the user's ability to develop accurate molecular mechanics (MM) force field parameters for individual drug candidates and the time required to complete the process. In an attempt to find an FEP method that could eventually be automated, we developed a method that uses quantum mechanics (QM) for treating the solute, MM for treating the solute surroundings, and the FEP method for computing free-energy differences. The thread technique was used in all transformations and proved to be essential for the successful completion of the calculations. Relative solvation free energies for 10 structurally diverse molecular pairs were calculated, and the results were in close agreement with both the calculated results generated by conventional FEP methods and the experimentally derived values. While considerably more CPU demanding than conventional FEP methods, this method (QM/MM-based FEP) alleviates the need for development of molecule-specific MM force field parameters and therefore may enable future automation of FEP-based calculations. Moreover, calculation accuracy should be improved over conventional methods, especially for calculations reliant on MM parameters derived in the absence of experimental data.

Data mining spacecraft telemetry: towards generic solutions to automatic health monitoring and status characterisation

NASA Astrophysics Data System (ADS)

Royer, P.; De Ridder, J.; Vandenbussche, B.; Regibo, S.; Huygen, R.; De Meester, W.; Evans, D. J.; Martinez, J.; Korte-Stapff, M.

2016-07-01

We present the first results of a study aimed at finding new and efficient ways to automatically process spacecraft telemetry for automatic health monitoring. The goal is to reduce the load on the flight control team while extending the "checkability" to the entire telemetry database, and provide efficient, robust and more accurate detection of anomalies in near real time. We present a set of effective methods to (a) detect outliers in the telemetry or in its statistical properties, (b) uncover and visualise special properties of the telemetry and (c) detect new behavior. Our results are structured around two main families of solutions. For parameters visiting a restricted set of signal values, i.e. all status parameters and about one third of all the others, we focus on a transition analysis, exploiting properties of Poincare plots. For parameters with an arbitrarily high number of possible signal values, we describe the statistical properties of the signal via its Kernel Density Estimate. We demonstrate that this allows for a generic and dynamic approach of the soft-limit definition. Thanks to a much more accurate description of the signal and of its time evolution, we are more sensitive and more responsive to outliers than the traditional checks against hard limits. Our methods were validated on two years of Venus Express telemetry. They are generic for assisting in health monitoring of any complex system with large amounts of diagnostic sensor data. Not only spacecraft systems but also present-day astronomical observatories can benefit from them.

Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law

PubMed Central

Yan, Rui; Edwards, Thomas J.; Pankratz, Logan M.; Kuhn, Richard J.; Lanman, Jason K.; Liu, Jun; Jiang, Wen

2015-01-01

Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer-Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples. PMID:26433027

Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law.

PubMed

Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

2015-11-01

Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer-Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples. Copyright © 2015 Elsevier Inc. All rights reserved.

Quantifying Transmission Heterogeneity Using Both Pathogen Phylogenies and Incidence Time Series

PubMed Central

Li, Lucy M.; Grassly, Nicholas C.; Fraser, Christophe

2017-01-01

Abstract Heterogeneity in individual-level transmissibility can be quantified by the dispersion parameter k of the offspring distribution. Quantifying heterogeneity is important as it affects other parameter estimates, it modulates the degree of unpredictability of an epidemic, and it needs to be accounted for in models of infection control. Aggregated data such as incidence time series are often not sufficiently informative to estimate k. Incorporating phylogenetic analysis can help to estimate k concurrently with other epidemiological parameters. We have developed an inference framework that uses particle Markov Chain Monte Carlo to estimate k and other epidemiological parameters using both incidence time series and the pathogen phylogeny. Using the framework to fit a modified compartmental transmission model that includes the parameter k to simulated data, we found that more accurate and less biased estimates of the reproductive number were obtained by combining epidemiological and phylogenetic analyses. However, k was most accurately estimated using pathogen phylogeny alone. Accurately estimating k was necessary for unbiased estimates of the reproductive number, but it did not affect the accuracy of reporting probability and epidemic start date estimates. We further demonstrated that inference was possible in the presence of phylogenetic uncertainty by sampling from the posterior distribution of phylogenies. Finally, we used the inference framework to estimate transmission parameters from epidemiological and genetic data collected during a poliovirus outbreak. Despite the large degree of phylogenetic uncertainty, we demonstrated that incorporating phylogenetic data in parameter inference improved the accuracy and precision of estimates. PMID:28981709

Thermodynamics of acid-base dissociation of several cathinones and 1-phenylethylamine, studied by an accurate capillary electrophoresis method free from the Joule heating impact.

PubMed

Nowak, Paweł Mateusz; Woźniakiewicz, Michał; Mitoraj, Mariusz; Sagan, Filip; Kościelniak, Paweł

2018-03-02

Capillary electrophoresis is often used to the determination of the acid-base dissociation/deprotonation constant (pK a ), and the more advanced thermodynamic quantities describing this process (ΔH°, -TΔS°). Remarkably, it is commonly overlooked that due to insufficient dissipation of Joule heating the accuracy of parameters determined using a standard approach may be questionable. In this work we show an effective method allowing to enhance reliability of these parameters, and to estimate the magnitude of errors. It relies on finding a relationship between electrophoretic mobility and actual temperature, and performing pK a determination with the corrected mobility values. It has been employed to accurately examine the thermodynamics of acid-base dissociation of several amine compounds - known for their strong dependency of pK a on temperature: six cathinones (2-methylmethcathinone, 3-methylmethcathinone, 4-methylmethcathinone, α-pyrrolidinovalerophenone, methylenedioxypyrovalerone, and ephedrone); and structurally similar 1-phenylethylamine. The average pK a error caused by Joule heating noted at 25 °C was relatively small - 0.04-0.05 pH unit, however, a more significant inaccuracy was observed in the enthalpic and, in particular, entropic terms. An alternative correction method has also been proposed, simpler and faster, but not such effective in correcting ΔH°/-TΔS° terms. The corrected thermodynamic data have been interpreted with the aid of theoretical calculations, on a ground of the enthalpy-entropy relationships and the most probable structural effects accounting for them. Finally, we have demonstrated that the thermal dependencies of electrophoretic mobility, modelled during the correction procedure, may be directly used to find optimal temperature providing a maximal separation efficiency. Copyright © 2018 Elsevier B.V. All rights reserved.

MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes.

PubMed

Zhu, Huaiqiu; Hu, Gang-Qing; Yang, Yi-Fan; Wang, Jin; She, Zhen-Su

2007-03-16

Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among genomes. It continues to be interesting to develop new ab initio algorithms which not only accurately predict genes, but also facilitate comparative studies of prokaryotic genomes. This paper describes a new prokaryotic genefinding algorithm based on a comprehensive statistical model of protein coding Open Reading Frames (ORFs) and Translation Initiation Sites (TISs). The former is based on a linguistic "Entropy Density Profile" (EDP) model of coding DNA sequence and the latter comprises several relevant features related to the translation initiation. They are combined to form a so-called Multivariate Entropy Distance (MED) algorithm, MED 2.0, that incorporates several strategies in the iterative program. The iterations enable us to develop a non-supervised learning process and to obtain a set of genome-specific parameters for the gene structure, before making the prediction of genes. Results of extensive tests show that MED 2.0 achieves a competitive high performance in the gene prediction for both 5' and 3' end matches, compared to the current best prokaryotic gene finders. The advantage of the MED 2.0 is particularly evident for GC-rich genomes and archaeal genomes. Furthermore, the genome-specific parameters given by MED 2.0 match with the current understanding of prokaryotic genomes and may serve as tools for comparative genomic studies. In particular, MED 2.0 is shown to reveal divergent translation initiation mechanisms in archaeal genomes while making a more accurate prediction of TISs compared to the existing gene finders and the current GenBank annotation.

A Bayesian Network Based Global Sensitivity Analysis Method for Identifying Dominant Processes in a Multi-physics Model

NASA Astrophysics Data System (ADS)

Dai, H.; Chen, X.; Ye, M.; Song, X.; Zachara, J. M.

2016-12-01

Sensitivity analysis has been an important tool in groundwater modeling to identify the influential parameters. Among various sensitivity analysis methods, the variance-based global sensitivity analysis has gained popularity for its model independence characteristic and capability of providing accurate sensitivity measurements. However, the conventional variance-based method only considers uncertainty contribution of single model parameters. In this research, we extended the variance-based method to consider more uncertainty sources and developed a new framework to allow flexible combinations of different uncertainty components. We decompose the uncertainty sources into a hierarchical three-layer structure: scenario, model and parametric. Furthermore, each layer of uncertainty source is capable of containing multiple components. An uncertainty and sensitivity analysis framework was then constructed following this three-layer structure using Bayesian network. Different uncertainty components are represented as uncertain nodes in this network. Through the framework, variance-based sensitivity analysis can be implemented with great flexibility of using different grouping strategies for uncertainty components. The variance-based sensitivity analysis thus is improved to be able to investigate the importance of an extended range of uncertainty sources: scenario, model, and other different combinations of uncertainty components which can represent certain key model system processes (e.g., groundwater recharge process, flow reactive transport process). For test and demonstration purposes, the developed methodology was implemented into a test case of real-world groundwater reactive transport modeling with various uncertainty sources. The results demonstrate that the new sensitivity analysis method is able to estimate accurate importance measurements for any uncertainty sources which were formed by different combinations of uncertainty components. The new methodology can provide useful information for environmental management and decision-makers to formulate policies and strategies.

DOE Office of Scientific and Technical Information (OSTI.GOV)

de Hatten, Xavier; Cournia, Zoe; Huc, Ivan

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostaticmore » potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1'-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C{sub 2}-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1 {micro}s MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline-1'-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 {micro}s MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Hatten, Xavier; Cournia, Zoe; Smith, Jeremy C

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostaticmore » potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1{prime}-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C2-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1{micro}s MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline{prime}-1-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 s MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.« less

Analysis of energy-based algorithms for RNA secondary structure prediction

PubMed Central

2012-01-01

Background RNA molecules play critical roles in the cells of organisms, including roles in gene regulation, catalysis, and synthesis of proteins. Since RNA function depends in large part on its folded structures, much effort has been invested in developing accurate methods for prediction of RNA secondary structure from the base sequence. Minimum free energy (MFE) predictions are widely used, based on nearest neighbor thermodynamic parameters of Mathews, Turner et al. or those of Andronescu et al. Some recently proposed alternatives that leverage partition function calculations find the structure with maximum expected accuracy (MEA) or pseudo-expected accuracy (pseudo-MEA) methods. Advances in prediction methods are typically benchmarked using sensitivity, positive predictive value and their harmonic mean, namely F-measure, on datasets of known reference structures. Since such benchmarks document progress in improving accuracy of computational prediction methods, it is important to understand how measures of accuracy vary as a function of the reference datasets and whether advances in algorithms or thermodynamic parameters yield statistically significant improvements. Our work advances such understanding for the MFE and (pseudo-)MEA-based methods, with respect to the latest datasets and energy parameters. Results We present three main findings. First, using the bootstrap percentile method, we show that the average F-measure accuracy of the MFE and (pseudo-)MEA-based algorithms, as measured on our largest datasets with over 2000 RNAs from diverse families, is a reliable estimate (within a 2% range with high confidence) of the accuracy of a population of RNA molecules represented by this set. However, average accuracy on smaller classes of RNAs such as a class of 89 Group I introns used previously in benchmarking algorithm accuracy is not reliable enough to draw meaningful conclusions about the relative merits of the MFE and MEA-based algorithms. Second, on our large datasets, the algorithm with best overall accuracy is a pseudo MEA-based algorithm of Hamada et al. that uses a generalized centroid estimator of base pairs. However, between MFE and other MEA-based methods, there is no clear winner in the sense that the relative accuracy of the MFE versus MEA-based algorithms changes depending on the underlying energy parameters. Third, of the four parameter sets we considered, the best accuracy for the MFE-, MEA-based, and pseudo-MEA-based methods is 0.686, 0.680, and 0.711, respectively (on a scale from 0 to 1 with 1 meaning perfect structure predictions) and is obtained with a thermodynamic parameter set obtained by Andronescu et al. called BL* (named after the Boltzmann likelihood method by which the parameters were derived). Conclusions Large datasets should be used to obtain reliable measures of the accuracy of RNA structure prediction algorithms, and average accuracies on specific classes (such as Group I introns and Transfer RNAs) should be interpreted with caution, considering the relatively small size of currently available datasets for such classes. The accuracy of the MEA-based methods is significantly higher when using the BL* parameter set of Andronescu et al. than when using the parameters of Mathews and Turner, and there is no significant difference between the accuracy of MEA-based methods and MFE when using the BL* parameters. The pseudo-MEA-based method of Hamada et al. with the BL* parameter set significantly outperforms all other MFE and MEA-based algorithms on our large data sets. PMID:22296803

Analysis of energy-based algorithms for RNA secondary structure prediction.

PubMed

Hajiaghayi, Monir; Condon, Anne; Hoos, Holger H

2012-02-01

RNA molecules play critical roles in the cells of organisms, including roles in gene regulation, catalysis, and synthesis of proteins. Since RNA function depends in large part on its folded structures, much effort has been invested in developing accurate methods for prediction of RNA secondary structure from the base sequence. Minimum free energy (MFE) predictions are widely used, based on nearest neighbor thermodynamic parameters of Mathews, Turner et al. or those of Andronescu et al. Some recently proposed alternatives that leverage partition function calculations find the structure with maximum expected accuracy (MEA) or pseudo-expected accuracy (pseudo-MEA) methods. Advances in prediction methods are typically benchmarked using sensitivity, positive predictive value and their harmonic mean, namely F-measure, on datasets of known reference structures. Since such benchmarks document progress in improving accuracy of computational prediction methods, it is important to understand how measures of accuracy vary as a function of the reference datasets and whether advances in algorithms or thermodynamic parameters yield statistically significant improvements. Our work advances such understanding for the MFE and (pseudo-)MEA-based methods, with respect to the latest datasets and energy parameters. We present three main findings. First, using the bootstrap percentile method, we show that the average F-measure accuracy of the MFE and (pseudo-)MEA-based algorithms, as measured on our largest datasets with over 2000 RNAs from diverse families, is a reliable estimate (within a 2% range with high confidence) of the accuracy of a population of RNA molecules represented by this set. However, average accuracy on smaller classes of RNAs such as a class of 89 Group I introns used previously in benchmarking algorithm accuracy is not reliable enough to draw meaningful conclusions about the relative merits of the MFE and MEA-based algorithms. Second, on our large datasets, the algorithm with best overall accuracy is a pseudo MEA-based algorithm of Hamada et al. that uses a generalized centroid estimator of base pairs. However, between MFE and other MEA-based methods, there is no clear winner in the sense that the relative accuracy of the MFE versus MEA-based algorithms changes depending on the underlying energy parameters. Third, of the four parameter sets we considered, the best accuracy for the MFE-, MEA-based, and pseudo-MEA-based methods is 0.686, 0.680, and 0.711, respectively (on a scale from 0 to 1 with 1 meaning perfect structure predictions) and is obtained with a thermodynamic parameter set obtained by Andronescu et al. called BL* (named after the Boltzmann likelihood method by which the parameters were derived). Large datasets should be used to obtain reliable measures of the accuracy of RNA structure prediction algorithms, and average accuracies on specific classes (such as Group I introns and Transfer RNAs) should be interpreted with caution, considering the relatively small size of currently available datasets for such classes. The accuracy of the MEA-based methods is significantly higher when using the BL* parameter set of Andronescu et al. than when using the parameters of Mathews and Turner, and there is no significant difference between the accuracy of MEA-based methods and MFE when using the BL* parameters. The pseudo-MEA-based method of Hamada et al. with the BL* parameter set significantly outperforms all other MFE and MEA-based algorithms on our large data sets.

RNA Thermodynamic Structural Entropy

PubMed Central

Garcia-Martin, Juan Antonio; Clote, Peter

2015-01-01

Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner’99 and Turner’04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http://bioinformatics.bc.edu/clotelab/RNAentropy, including source code and ancillary programs. PMID:26555444

RNA Thermodynamic Structural Entropy.

PubMed

Garcia-Martin, Juan Antonio; Clote, Peter

2015-01-01

Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http://bioinformatics.bc.edu/clotelab/RNAentropy, including source code and ancillary programs.

Coordinated Hard Sphere Mixture (CHaSM): A fast approximate model for oxide and silicate melts at extreme conditions

NASA Astrophysics Data System (ADS)

Wolf, A. S.; Asimow, P. D.; Stevenson, D. J.

2015-12-01

Recent first-principles calculations (e.g. Stixrude, 2009; de Koker, 2013), shock-wave experiments (Mosenfelder, 2009), and diamond-anvil cell investigations (Sanloup, 2013) indicate that silicate melts undergo complex structural evolution at high pressure. The observed increase in cation-coordination (e.g. Karki, 2006; 2007) induces higher compressibilities and lower adiabatic thermal gradients in melts as compared with their solid counterparts. These properties are crucial for understanding the evolution of impact-generated magma oceans, which are dominated by the poorly understood behavior of silicates at mantle pressures and temperatures (e.g. Stixrude et al. 2009). Probing these conditions is difficult for both theory and experiment, especially given the large compositional space (MgO-SiO2-FeO-Al2O3-etc). We develop a new model to understand and predict the behavior of oxide and silicate melts at extreme P-T conditions (Wolf et al., 2015). The Coordinated Hard Sphere Mixture (CHaSM) extends the Hard Sphere mixture model, accounting for the range of coordination states for each cation in the liquid. Using approximate analytic expressions for the hard sphere model, this fast statistical method compliments classical and first-principles methods, providing accurate thermodynamic and structural property predictions for melts. This framework is applied to the MgO system, where model parameters are trained on a collection of crystal polymorphs, producing realistic predictions of coordination evolution and the equation of state of MgO melt over a wide P-T range. Typical Mg-coordination numbers are predicted to evolve continuously from 5.25 (0 GPa) to 8.5 (250 GPa), comparing favorably with first-principles Molecular Dynamics (MD) simulations. We begin extending the model to a simplified mantle chemistry using empirical potentials (generally accurate over moderate pressure ranges, <~30 GPa), yielding predictions rooted in statistical representations of melt structure that compare well with more time-consuming classical MD calculations. This approach also sheds light on the universality of the increasing Grüneisen parameter trend for liquids (opposite that of solids), which directly reflects their progressive evolution toward more compact solid-like structures upon compression.

UMAT Implementation of Coupled, Multilevel, Structural Deformation and Damage Analysis of General Hereditary Materials

NASA Technical Reports Server (NTRS)

Arnold, S. M.; Saleeb, A. F.; Wilt, T. E.; Trowbridge, D.

2000-01-01

Extensive research efforts have been made over the years on the phenomenological representations of constitutive material behavior in the inelastic analysis and life assessment of structures composed of advanced monolithic and composite (CMC, MMC, and PMC) materials. Recently, emphasis has been placed on concurrently addressing three important and related areas of constitutive and degradation modeling; i.e. (i) mathematical formulation, (ii) algorithmic developments for the updating (integrating) of external (e.g. stress) and internal state variable, as well as (iii) parameter estimation for the characterization of the specific model. This concurrent perspective has resulted in; i) the formulation of a fully-associative viscoelastoplastic model (GVIPS), (ii) development of an efficient implicit integration and it's associative, symmetric, consistent tangent stiffness matrix algorithm for integration of the underlying rate flow/evolutionary equations, and iii) a robust, stand-alone, Constitutive Material Parameter Estimator (COMPARE) for automatically characterizing the various time-dependent, nonlinear, material models. Furthermore, to provide a robust multi-scale framework for the deformation and life analysis of structures composed of composite materials, NASA Glenn has aggressively pursued the development of a sufficiently general, accurate, and efficient micromechanics approach known as the generalized method of cells (GMC). This work has resulted in the development of MAC/GMC, a stand-alone micromechanics analysis tool that can easily and accurately design/analyze multiphase (composite) materials subjected to complex histories. MAC/GMC admits generalized, physically based, deformation and damage models for each constituent and provides "closed-form" expressions for the macroscopic composite response in terms of the properties, size, shape, distribution, and response of the individual constituents or phases that comprise the material. Consequently, MAC/GMC can be incorporated directly into a structural finite element code like ABAQUS for cost-effective, micromechanics based, large-scale component design and analysis. Our primary objective here is to report on these recent works conducted over the past decade, in the context of their incorporation into ABAQUS through the various user subroutines. Representative results will be shown to demonstrate the features of the developed schemes.

Bone volume fraction and structural parameters for estimation of mechanical stiffness and failure load of human cancellous bone samples; in-vitro comparison of ultrasound transit time spectroscopy and X-ray μCT.

PubMed

Alomari, Ali Hamed; Wille, Marie-Luise; Langton, Christian M

2018-02-01

Conventional mechanical testing is the 'gold standard' for assessing the stiffness (N mm -1 ) and strength (MPa) of bone, although it is not applicable in-vivo since it is inherently invasive and destructive. The mechanical integrity of a bone is determined by its quantity and quality; being related primarily to bone density and structure respectively. Several non-destructive, non-invasive, in-vivo techniques have been developed and clinically implemented to estimate bone density, both areal (dual-energy X-ray absorptiometry (DXA)) and volumetric (quantitative computed tomography (QCT)). Quantitative ultrasound (QUS) parameters of velocity and attenuation are dependent upon both bone quantity and bone quality, although it has not been possible to date to transpose one particular QUS parameter into separate estimates of quantity and quality. It has recently been shown that ultrasound transit time spectroscopy (UTTS) may provide an accurate estimate of bone density and hence quantity. We hypothesised that UTTS also has the potential to provide an estimate of bone structure and hence quality. In this in-vitro study, 16 human femoral bone samples were tested utilising three techniques; UTTS, micro computed tomography (μCT), and mechanical testing. UTTS was utilised to estimate bone volume fraction (BV/TV) and two novel structural parameters, inter-quartile range of the derived transit time (UTTS-IQR) and the transit time of maximum proportion of sonic-rays (TTMP). μCT was utilised to derive BV/TV along with several bone structure parameters. A destructive mechanical test was utilised to measure the stiffness and strength (failure load) of the bone samples. BV/TV was calculated from the derived transit time spectrum (TTS); the correlation coefficient (R 2 ) with μCT-BV/TV was 0.885. For predicting mechanical stiffness and strength, BV/TV derived by both μCT and UTTS provided the strongest correlation with mechanical stiffness (R 2 =0.567 and 0.618 respectively) and mechanical strength (R 2 =0.747 and 0.736 respectively). When respective structural parameters were incorporated to BV/TV, multiple regression analysis indicated that none of the μCT histomorphometric parameters could improve the prediction of mechanical stiffness and strength, while for UTTS, adding TTMP to BV/TV increased the prediction of mechanical stiffness to R 2 =0.711 and strength to R 2 =0.827. It is therefore envisaged that UTTS may have the ability to estimate BV/TV along with providing an improved prediction of osteoporotic fracture risk, within routine clinical practice in the future. Copyright © 2017 Elsevier Inc. All rights reserved.

Cosmological structure formation in Decaying Dark Matter models

NASA Astrophysics Data System (ADS)

Cheng, Dalong; Chu, M.-C.; Tang, Jiayu

2015-07-01

The standard cold dark matter (CDM) model predicts too many and too dense small structures. We consider an alternative model that the dark matter undergoes two-body decays with cosmological lifetime τ into only one type of massive daughters with non-relativistic recoil velocity Vk. This decaying dark matter model (DDM) can suppress the structure formation below its free-streaming scale at time scale comparable to τ. Comparing with warm dark matter (WDM), DDM can better reduce the small structures while being consistent with high redshfit observations. We study the cosmological structure formation in DDM by performing self-consistent N-body simulations and point out that cosmological simulations are necessary to understand the DDM structures especially on non-linear scales. We propose empirical fitting functions for the DDM suppression of the mass function and the concentration-mass relation, which depend on the decay parameters lifetime τ, recoil velocity Vk and redshift. The fitting functions lead to accurate reconstruction of the the non-linear power transfer function of DDM to CDM in the framework of halo model. Using these results, we set constraints on the DDM parameter space by demanding that DDM does not induce larger suppression than the Lyman-α constrained WDM models. We further generalize and constrain the DDM models to initial conditions with non-trivial mother fractions and show that the halo model predictions are still valid after considering a global decayed fraction. Finally, we point out that the DDM is unlikely to resolve the disagreement on cluster numbers between the Planck primary CMB prediction and the Sunyaev-Zeldovich (SZ) effect number count for τ ~ H0-1.

Enhanced multimaterial 4D printing with active hinges

NASA Astrophysics Data System (ADS)

Akbari, Saeed; Hosein Sakhaei, Amir; Kowsari, Kavin; Yang, Bill; Serjouei, Ahmad; Yuanfang, Zhang; Ge, Qi

2018-06-01

Despite great progress in four-dimensional (4D) printing, i.e. three-dimensional (3D) printing of active (stimuli-responsive) materials, the relatively low actuation force of the 4D printed structures often impedes their engineering applications. In this study, we use multimaterial inkjet 3D printing technology to fabricate shape memory structures, including a morphing wing flap and a deployable structure, which consist of active and flexible hinges joining rigid (non-active) parts. The active hinges, printed from a shape memory polymer (SMP), lock the structure into a second temporary shape during a thermomechanical programming process, while the flexible hinges, printed from an elastomer, effectively increase the actuation force and the load-bearing capacity of the printed structure as reflected in the recovery ratio. A broad range of mechanical properties such as modulus and failure strain can be achieved for both active and flexible hinges by varying the composition of the two base materials, i.e. the SMP and the elastomer, to accommodate large deformation induced during programming step, and enhance the recovery in the actuating step. To find the important design parameters, including local deformation, shape fixity and recovery ratio, we conduct high fidelity finite element simulations, which are able to accurately predict the nonlinear deformation of the printed structures. In addition, a coupled thermal-electrical finite element analysis was performed to model the heat transfer within the active hinges during the localized Joule heating process. The model predictions showed good agreement with the measured temperature data and were used to find the major parameters affecting temperature distribution including the applied voltage and the convection rate.

Seasonal extreme value statistics for precipitation in Germany

NASA Astrophysics Data System (ADS)

Fischer, Madlen; Rust, Henning W.; Ulbrich, Uwe

2013-04-01

Extreme precipitation has a strong influence on environment, society and economy. It leads to large damage due to floods, mudslides, increased erosion or hail. While standard annual return levels are important for hydrological structures, seasonaly resolved return levels provide additional information for risk managment, e.g., for the agricultural sector. For 1208 stations in Germany, we calculate monthly resolved return levels. Instead of estimating parameters separately for every month in the year, we use a non-stationary approach and benefit from smoothly varying return levels throughout the year. This natural approach is more suitable to characterise seasonal variability of extreme precipitation and leads to more accurate return level estimates. Harmonic functions of different orders are used to describe the seasonal variation of GEV parameters and crossvalidation is used to determine a suitable model forall stations. Finally particularly vulnerable regions and associated month are investigated in more detail.

Theoretical study of the crystal-field energy levels and two-photon absorption intensities of Tb3+ in cubic host lattices.

PubMed

Duan, Chang-Kui; Tanner, Peter A

2011-03-17

Published two photon excitation (TPE) intensities for the cubic elpasolite systems Cs(2)NaTbX(6) (X = Cl, F) have been simulated by a calculation of two photon absorption (TPA) intensities which takes into account electric dipole transitions involving the detailed crystal-field structure of 4f(7)5d intermediate states, as well as the interactions of the 4f(7) core with the d-electron. The intensity calculation employed parameters from an energy level calculation which not only presented an accurate fit, but also yielded parameters consistent with those from other lanthanide ions. The calculated intensities were used to confirm or adjust the previous assignments of energy levels, resulting in some minor revisions. Generally, the TPA intensity simulations were in better agreement with experimental data for the fluoride, rather than the chloride, system and possible reasons for this are given.

A Knowledge Database on Thermal Control in Manufacturing Processes

NASA Astrophysics Data System (ADS)

Hirasawa, Shigeki; Satoh, Isao

A prototype version of a knowledge database on thermal control in manufacturing processes, specifically, molding, semiconductor manufacturing, and micro-scale manufacturing has been developed. The knowledge database has search functions for technical data, evaluated benchmark data, academic papers, and patents. The database also displays trends and future roadmaps for research topics. It has quick-calculation functions for basic design. This paper summarizes present research topics and future research on thermal control in manufacturing engineering to collate the information to the knowledge database. In the molding process, the initial mold and melt temperatures are very important parameters. In addition, thermal control is related to many semiconductor processes, and the main parameter is temperature variation in wafers. Accurate in-situ temperature measurment of wafers is important. And many technologies are being developed to manufacture micro-structures. Accordingly, the knowledge database will help further advance these technologies.

X-Ray diffraction on large single crystals using a powder diffractometer

DOE PAGES

Jesche, A.; Fix, M.; Kreyssig, A.; ...

2016-06-16

Information on the lattice parameter of single crystals with known crystallographic structure allows for estimations of sample quality and composition. In many cases it is sufficient to determine one lattice parameter or the lattice spacing along a certain, high- symmetry direction, e.g. in order to determine the composition in a substitution series by taking advantage of Vegard’s rule. Here we present a guide to accurate measurements of single crystals with dimensions ranging from 200 μm up to several millimeter using a standard powder diffractometer in Bragg-Brentano geometry. The correction of the error introduced by the sample height and the optimizationmore » of the alignment are discussed in detail. Finally, in particular for single crystals with a plate-like habit, the described procedure allows for measurement of the lattice spacings normal to the plates with high accuracy on a timescale of minutes.« less

Angle-domain common-image gathers from anisotropic Gaussian beam migration and its application to anisotropy-induced imaging errors analysis

NASA Astrophysics Data System (ADS)

Han, Jianguang; Wang, Yun; Yu, Changqing; Chen, Peng

2017-02-01

An approach for extracting angle-domain common-image gathers (ADCIGs) from anisotropic Gaussian beam prestack depth migration (GB-PSDM) is presented in this paper. The propagation angle is calculated in the process of migration using the real-value traveltime information of Gaussian beam. Based on the above, we further investigate the effects of anisotropy on GB-PSDM, where the corresponding ADCIGs are extracted to assess the quality of migration images. The test results of the VTI syncline model and the TTI thrust sheet model show that anisotropic parameters ɛ, δ, and tilt angle 𝜃, have a great influence on the accuracy of the migrated image in anisotropic media, and ignoring any one of them will cause obvious imaging errors. The anisotropic GB-PSDM with the true anisotropic parameters can obtain more accurate seismic images of subsurface structures in anisotropic media.

Full-direct method for imaging pharmacokinetic parameters in dynamic fluorescence molecular tomography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Guanglei, E-mail: guangleizhang@bjtu.edu.cn; Department of Biomedical Engineering, School of Computer and Information Technology, Beijing Jiaotong University, Beijing 100044; Pu, Huangsheng

2015-02-23

Images of pharmacokinetic parameters (also known as parametric images) in dynamic fluorescence molecular tomography (FMT) can provide three-dimensional metabolic information for biological studies and drug development. However, the ill-posed nature of FMT and the high temporal variation of fluorophore concentration together make it difficult to obtain accurate parametric images in small animals in vivo. In this letter, we present a method to directly reconstruct the parametric images from the boundary measurements based on hybrid FMT/X-ray computed tomography (XCT) system. This method can not only utilize structural priors obtained from the XCT system to mitigate the ill-posedness of FMT but alsomore » make full use of the temporal correlations of boundary measurements to model the high temporal variation of fluorophore concentration. The results of numerical simulation and mouse experiment demonstrate that the proposed method leads to significant improvements in the reconstruction quality of parametric images.« less

Aerogel Track Morphology: Measurement, Three Dimensional Reconstruction and Particle Location using Confocal Laser Scanning Microscopy

NASA Technical Reports Server (NTRS)

Kearsley, A. T.; Ball, A. D.; Wozniakiewicz, P. A.; Graham, G. A.; Burchell, M. J.; Cole, M. J.; Horz, F.; See, T. H.

2007-01-01

The Stardust spacecraft returned the first undoubted samples of cometary dust, with many grains embedded in the silica aerogel collector . Although many tracks contain one or more large terminal particles of a wide range of mineral compositions , there is also abundant material along the track walls. To help interpret the full particle size, structure and mass, both experimental simulation of impact by shots and numerical modeling of the impact process have been attempted. However, all approaches require accurate and precise measurement of impact track size parameters such as length, width and volume of specific portions. To make such measurements is not easy, especially if extensive aerogel fracturing and discoloration has occurred. In this paper we describe the application and limitations of laser confocal imagery for determination of aerogel track parameters, and for the location of particle remains.

Bond Ellipticity Alternation: An Accurate Descriptor of the Nonlinear Optical Properties of π-Conjugated Chromophores.

PubMed

Lopes, Thiago O; Machado, Daniel F Scalabrini; Risko, Chad; Brédas, Jean-Luc; de Oliveira, Heibbe C B

2018-03-15

Well-defined structure-property relationships offer a conceptual basis to afford a priori design principles to develop novel π-conjugated molecular and polymer materials for nonlinear optical (NLO) applications. Here, we introduce the bond ellipticity alternation (BEA) as a robust parameter to assess the NLO characteristics of organic chromophores and illustrate its effectiveness in the case of streptocyanines. BEA is based on the symmetry of the electron density, a physical observable that can be determined from experimental X-ray electron densities or from quantum-chemical calculations. Through comparisons to the well-established bond-length alternation and π-bond order alternation parameters, we demonstrate the generality of BEA to foreshadow NLO characteristics and underline that, in the case of large electric fields, BEA is a more reliable descriptor. Hence, this study introduces BEA as a prominent descriptor of organic chromophores of interest for NLO applications.

Mining method selection by integrated AHP and PROMETHEE method.

PubMed

Bogdanovic, Dejan; Nikolic, Djordje; Ilic, Ivana

2012-03-01

Selecting the best mining method among many alternatives is a multicriteria decision making problem. The aim of this paper is to demonstrate the implementation of an integrated approach that employs AHP and PROMETHEE together for selecting the most suitable mining method for the "Coka Marin" underground mine in Serbia. The related problem includes five possible mining methods and eleven criteria to evaluate them. Criteria are accurately chosen in order to cover the most important parameters that impact on the mining method selection, such as geological and geotechnical properties, economic parameters and geographical factors. The AHP is used to analyze the structure of the mining method selection problem and to determine weights of the criteria, and PROMETHEE method is used to obtain the final ranking and to make a sensitivity analysis by changing the weights. The results have shown that the proposed integrated method can be successfully used in solving mining engineering problems.

Physiological motion modeling for organ-mounted robots.

PubMed

Wood, Nathan A; Schwartzman, David; Zenati, Marco A; Riviere, Cameron N

2017-12-01

Organ-mounted robots passively compensate heartbeat and respiratory motion. In model-guided procedures, this motion can be a significant source of information that can be used to aid in localization or to add dynamic information to static preoperative maps. Models for estimating periodic motion are proposed for both position and orientation. These models are then tested on animal data and optimal orders are identified. Finally, methods for online identification are demonstrated. Models using exponential coordinates and Euler-angle parameterizations are as accurate as models using quaternion representations, yet require a quarter fewer parameters. Models which incorporate more than four cardiac or three respiration harmonics are no more accurate. Finally, online methods estimate model parameters as accurately as offline methods within three respiration cycles. These methods provide a complete framework for accurately modelling the periodic deformation of points anywhere on the surface of the heart in a closed chest. Copyright © 2017 John Wiley & Sons, Ltd.

Development of interatomic potential of Ge(1- x - y )Si x Sn y ternary alloy semiconductors for classical lattice dynamics simulation

NASA Astrophysics Data System (ADS)

Tomita, Motohiro; Ogasawara, Masataka; Terada, Takuya; Watanabe, Takanobu

2018-04-01

We provide the parameters of Stillinger-Weber potentials for GeSiSn ternary mixed systems. These parameters can be used in molecular dynamics (MD) simulations to reproduce phonon properties and thermal conductivities. The phonon dispersion relation is derived from the dynamical structure factor, which is calculated by the space-time Fourier transform of atomic trajectories in an MD simulation. The phonon properties and thermal conductivities of GeSiSn ternary crystals calculated using these parameters mostly reproduced both the findings of previous experiments and earlier calculations made using MD simulations. The atomic composition dependence of these properties in GeSiSn ternary crystals obtained by previous studies (both experimental and theoretical) and the calculated data were almost exactly reproduced by our proposed parameters. Moreover, the results of the MD simulation agree with the previous calculations made using a time-independent phonon Boltzmann transport equation with complicated scattering mechanisms. These scattering mechanisms are very important in complicated nanostructures, as they allow the heat-transfer properties to be more accurately calculated by MD simulations. This work enables us to predict the phonon- and heat-related properties of bulk group IV alloys, especially ternary alloys.

An improved estimator for the hydration of fat-free mass from in vivo measurements subject to additive technical errors.

PubMed

Kinnamon, Daniel D; Lipsitz, Stuart R; Ludwig, David A; Lipshultz, Steven E; Miller, Tracie L

2010-04-01

The hydration of fat-free mass, or hydration fraction (HF), is often defined as a constant body composition parameter in a two-compartment model and then estimated from in vivo measurements. We showed that the widely used estimator for the HF parameter in this model, the mean of the ratios of measured total body water (TBW) to fat-free mass (FFM) in individual subjects, can be inaccurate in the presence of additive technical errors. We then proposed a new instrumental variables estimator that accurately estimates the HF parameter in the presence of such errors. In Monte Carlo simulations, the mean of the ratios of TBW to FFM was an inaccurate estimator of the HF parameter, and inferences based on it had actual type I error rates more than 13 times the nominal 0.05 level under certain conditions. The instrumental variables estimator was accurate and maintained an actual type I error rate close to the nominal level in all simulations. When estimating and performing inference on the HF parameter, the proposed instrumental variables estimator should yield accurate estimates and correct inferences in the presence of additive technical errors, but the mean of the ratios of TBW to FFM in individual subjects may not.

Under-sampling trajectory design for compressed sensing based DCE-MRI.

PubMed

Liu, Duan-duan; Liang, Dong; Zhang, Na; Liu, Xin; Zhang, Yuan-ting

2013-01-01

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) needs high temporal and spatial resolution to accurately estimate quantitative parameters and characterize tumor vasculature. Compressed Sensing (CS) has the potential to accomplish this mutual importance. However, the randomness in CS under-sampling trajectory designed using the traditional variable density (VD) scheme may translate to uncertainty in kinetic parameter estimation when high reduction factors are used. Therefore, accurate parameter estimation using VD scheme usually needs multiple adjustments on parameters of Probability Density Function (PDF), and multiple reconstructions even with fixed PDF, which is inapplicable for DCE-MRI. In this paper, an under-sampling trajectory design which is robust to the change on PDF parameters and randomness with fixed PDF is studied. The strategy is to adaptively segment k-space into low-and high frequency domain, and only apply VD scheme in high-frequency domain. Simulation results demonstrate high accuracy and robustness comparing to VD design.

Kalman filter data assimilation: targeting observations and parameter estimation.

PubMed

Bellsky, Thomas; Kostelich, Eric J; Mahalov, Alex

2014-06-01

This paper studies the effect of targeted observations on state and parameter estimates determined with Kalman filter data assimilation (DA) techniques. We first provide an analytical result demonstrating that targeting observations within the Kalman filter for a linear model can significantly reduce state estimation error as opposed to fixed or randomly located observations. We next conduct observing system simulation experiments for a chaotic model of meteorological interest, where we demonstrate that the local ensemble transform Kalman filter (LETKF) with targeted observations based on largest ensemble variance is skillful in providing more accurate state estimates than the LETKF with randomly located observations. Additionally, we find that a hybrid ensemble Kalman filter parameter estimation method accurately updates model parameters within the targeted observation context to further improve state estimation.

Kalman filter data assimilation: Targeting observations and parameter estimation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bellsky, Thomas, E-mail: bellskyt@asu.edu; Kostelich, Eric J.; Mahalov, Alex

2014-06-15

This paper studies the effect of targeted observations on state and parameter estimates determined with Kalman filter data assimilation (DA) techniques. We first provide an analytical result demonstrating that targeting observations within the Kalman filter for a linear model can significantly reduce state estimation error as opposed to fixed or randomly located observations. We next conduct observing system simulation experiments for a chaotic model of meteorological interest, where we demonstrate that the local ensemble transform Kalman filter (LETKF) with targeted observations based on largest ensemble variance is skillful in providing more accurate state estimates than the LETKF with randomly locatedmore » observations. Additionally, we find that a hybrid ensemble Kalman filter parameter estimation method accurately updates model parameters within the targeted observation context to further improve state estimation.« less

Inference of reactive transport model parameters using a Bayesian multivariate approach

NASA Astrophysics Data System (ADS)

Carniato, Luca; Schoups, Gerrit; van de Giesen, Nick

2014-08-01

Parameter estimation of subsurface transport models from multispecies data requires the definition of an objective function that includes different types of measurements. Common approaches are weighted least squares (WLS), where weights are specified a priori for each measurement, and weighted least squares with weight estimation (WLS(we)) where weights are estimated from the data together with the parameters. In this study, we formulate the parameter estimation task as a multivariate Bayesian inference problem. The WLS and WLS(we) methods are special cases in this framework, corresponding to specific prior assumptions about the residual covariance matrix. The Bayesian perspective allows for generalizations to cases where residual correlation is important and for efficient inference by analytically integrating out the variances (weights) and selected covariances from the joint posterior. Specifically, the WLS and WLS(we) methods are compared to a multivariate (MV) approach that accounts for specific residual correlations without the need for explicit estimation of the error parameters. When applied to inference of reactive transport model parameters from column-scale data on dissolved species concentrations, the following results were obtained: (1) accounting for residual correlation between species provides more accurate parameter estimation for high residual correlation levels whereas its influence for predictive uncertainty is negligible, (2) integrating out the (co)variances leads to an efficient estimation of the full joint posterior with a reduced computational effort compared to the WLS(we) method, and (3) in the presence of model structural errors, none of the methods is able to identify the correct parameter values.

Evolutionary model selection and parameter estimation for protein-protein interaction network based on differential evolution algorithm

PubMed Central

Huang, Lei; Liao, Li; Wu, Cathy H.

2016-01-01

Revealing the underlying evolutionary mechanism plays an important role in understanding protein interaction networks in the cell. While many evolutionary models have been proposed, the problem about applying these models to real network data, especially for differentiating which model can better describe evolutionary process for the observed network urgently remains as a challenge. The traditional way is to use a model with presumed parameters to generate a network, and then evaluate the fitness by summary statistics, which however cannot capture the complete network structures information and estimate parameter distribution. In this work we developed a novel method based on Approximate Bayesian Computation and modified Differential Evolution (ABC-DEP) that is capable of conducting model selection and parameter estimation simultaneously and detecting the underlying evolutionary mechanisms more accurately. We tested our method for its power in differentiating models and estimating parameters on the simulated data and found significant improvement in performance benchmark, as compared with a previous method. We further applied our method to real data of protein interaction networks in human and yeast. Our results show Duplication Attachment model as the predominant evolutionary mechanism for human PPI networks and Scale-Free model as the predominant mechanism for yeast PPI networks. PMID:26357273

Spectral estimation of received phase in the presence of amplitude scintillation

NASA Technical Reports Server (NTRS)

Vilnrotter, V. A.; Brown, D. H.; Hurd, W. J.

1988-01-01

A technique is demonstrated for obtaining the spectral parameters of the received carrier phase in the presence of carrier amplitude scintillation, by means of a digital phased locked loop. Since the random amplitude fluctuations generate time-varying loop characteristics, straightforward processing of the phase detector output does not provide accurate results. The method developed here performs a time-varying inverse filtering operation on the corrupted observables, thus recovering the original phase process and enabling accurate estimation of its underlying parameters.

Real Time Spectroscopic Ellipsometry Analysis of First Stage CuIn1−xGaxSe2 Growth: Indium-Gallium Selenide Co-Evaporation

PubMed Central

Pradhan, Puja; Aryal, Puruswottam; Attygalle, Dinesh; Ibdah, Abdel-Rahman; Koirala, Prakash; Li, Jian; Bhandari, Khagendra P.; Liyanage, Geethika K.; Ellingson, Randy J.; Heben, Michael J.; Marsillac, Sylvain; Collins, Robert W.; Podraza, Nikolas J.

2018-01-01

Real time spectroscopic ellipsometry (RTSE) has been applied for in-situ monitoring of the first stage of copper indium-gallium diselenide (CIGS) thin film deposition by the three-stage co-evaporation process used for fabrication of high efficiency thin film photovoltaic (PV) devices. The first stage entails the growth of indium-gallium selenide (In1−xGax)2Se3 (IGS) on a substrate of Mo-coated soda lime glass maintained at a temperature of 400 °C. This is a critical stage of CIGS deposition because a large fraction of the final film thickness is deposited, and as a result precise compositional control is desired in order to achieve the optimum performance of the resulting CIGS solar cell. RTSE is sensitive to monolayer level film growth processes and can provide accurate measurements of bulk and surface roughness layer thicknesses. These in turn enable accurate measurements of the bulk layer optical response in the form of the complex dielectric function ε = ε1 − iε2, spectra. Here, RTSE has been used to obtain the (ε1, ε2) spectra at the measurement temperature of 400 °C for IGS thin films of different Ga contents (x) deduced from different ranges of accumulated bulk layer thickness during the deposition process. Applying an analytical expression in common for each of the (ε1, ε2) spectra of these IGS films, oscillator parameters have been obtained in the best fits and these parameters in turn have been fitted with polynomials in x. From the resulting database of polynomial coefficients, the (ε1, ε2) spectra can be generated for any composition of IGS from the single parameter, x. The results have served as an RTSE fingerprint for IGS composition and have provided further structural information beyond simply thicknesses, for example information related to film density and grain size. The deduced IGS structural evolution and the (ε1, ε2) spectra have been interpreted as well in relation to observations from scanning electron microscopy, X-ray diffractometry and energy-dispersive X-ray spectroscopy profiling analyses. Overall the structural, optical and compositional analysis possible by RTSE has assisted in understanding the growth and properties of three stage CIGS absorbers for solar cells and shows future promise for enhancing cell performance through monitoring and control. PMID:29337931

Real Time Spectroscopic Ellipsometry Analysis of First Stage CuIn1-xGaxSe₂ Growth: Indium-Gallium Selenide Co-Evaporation.

PubMed

Pradhan, Puja; Aryal, Puruswottam; Attygalle, Dinesh; Ibdah, Abdel-Rahman; Koirala, Prakash; Li, Jian; Bhandari, Khagendra P; Liyanage, Geethika K; Ellingson, Randy J; Heben, Michael J; Marsillac, Sylvain; Collins, Robert W; Podraza, Nikolas J

2018-01-16

Real time spectroscopic ellipsometry (RTSE) has been applied for in-situ monitoring of the first stage of copper indium-gallium diselenide (CIGS) thin film deposition by the three-stage co-evaporation process used for fabrication of high efficiency thin film photovoltaic (PV) devices. The first stage entails the growth of indium-gallium selenide (In 1- x Ga x )₂Se₃ (IGS) on a substrate of Mo-coated soda lime glass maintained at a temperature of 400 °C. This is a critical stage of CIGS deposition because a large fraction of the final film thickness is deposited, and as a result precise compositional control is desired in order to achieve the optimum performance of the resulting CIGS solar cell. RTSE is sensitive to monolayer level film growth processes and can provide accurate measurements of bulk and surface roughness layer thicknesses. These in turn enable accurate measurements of the bulk layer optical response in the form of the complex dielectric function ε = ε₁ - iε₂, spectra. Here, RTSE has been used to obtain the (ε₁, ε₂) spectra at the measurement temperature of 400 °C for IGS thin films of different Ga contents ( x ) deduced from different ranges of accumulated bulk layer thickness during the deposition process. Applying an analytical expression in common for each of the (ε₁, ε₂) spectra of these IGS films, oscillator parameters have been obtained in the best fits and these parameters in turn have been fitted with polynomials in x . From the resulting database of polynomial coefficients, the (ε₁, ε₂) spectra can be generated for any composition of IGS from the single parameter, x . The results have served as an RTSE fingerprint for IGS composition and have provided further structural information beyond simply thicknesses, for example information related to film density and grain size. The deduced IGS structural evolution and the (ε₁, ε₂) spectra have been interpreted as well in relation to observations from scanning electron microscopy, X-ray diffractometry and energy-dispersive X-ray spectroscopy profiling analyses. Overall the structural, optical and compositional analysis possible by RTSE has assisted in understanding the growth and properties of three stage CIGS absorbers for solar cells and shows future promise for enhancing cell performance through monitoring and control.

The Sensitivity of Glacial Isostatic Adjustment in West Antarctica to Lateral Variations in Earth Structure

NASA Astrophysics Data System (ADS)

Nield, G.; Whitehouse, P. L.; Blank, B.; van der Wal, W.; O'Donnell, J. P.; Stuart, G. W.; Lloyd, A. J.; Wiens, D.

2017-12-01

Accurate models of Glacial Isostatic Adjustment (GIA) are required for correcting satellite measurements of ice-mass change and for interpretation of geodetic data at the location of present and former ice sheets. Global models of GIA tend to adopt a 1-D representation of Earth structure, varying in the radial direction only. In some regions rheological parameters may differ significantly from this global average leading to bias in model predictions of present-day deformation, geoid change rates and sea-level change. The advancement of 3-D GIA modelling techniques in recent years has led to improvements in the representation of the Earth via the incorporation of laterally varying structure. This study investigates the influence of 3-D Earth structure on deformation rates in West Antarctica using a finite element GIA model with power-law rheology. We utilise datasets of seismic velocity and temperature for the crust and upper mantle with the aim of determining a data-driven Earth model, and consider the differences when compared to deformation predicted from an equivalent 1-D Earth structure.

Characterizing the True Background Corona with SDO/AIA

NASA Technical Reports Server (NTRS)

Napier, Kate; Winebarger, Amy; Alexander, Caroline

2014-01-01

Characterizing the nature of the solar coronal background would enable scientists to more accurately determine plasma parameters, and may lead to a better understanding of the coronal heating problem. Because scientists study the 3D structure of the Sun in 2D, any line of sight includes both foreground and background material, and thus, the issue of background subtraction arises. By investigating the intensity values in and around an active region, using multiple wavelengths collected from the Atmospheric Imaging Assembly (AIA) on the Solar Dynamics Observatory (SDO) over an eight-hour period, this project aims to characterize the background as smooth or structured. Different methods were employed to measure the true coronal background and create minimum intensity images. These were then investigated for the presence of structure. The background images created were found to contain long-lived structures, including coronal loops, that were still present in all of the wavelengths, 193 Angstroms,171 Angstroms,131 Angstroms, and 211 Angstroms. The intensity profiles across the active region indicate that the background is much more structured than previously thought.

First-and Second-Order Displacement Transfer Functions for Structural Shape Calculations Using Analytically Predicted Surface Strains

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2012-01-01

New first- and second-order displacement transfer functions have been developed for deformed shape calculations of nonuniform cross-sectional beam structures such as aircraft wings. The displacement transfer functions are expressed explicitly in terms of beam geometrical parameters and surface strains (uniaxial bending strains) obtained at equally spaced strain stations along the surface of the beam structure. By inputting the measured or analytically calculated surface strains into the displacement transfer functions, one could calculate local slopes, deflections, and cross-sectional twist angles of the nonuniform beam structure for mapping the overall structural deformed shapes for visual display. The accuracy of deformed shape calculations by the first- and second-order displacement transfer functions are determined by comparing these values to the analytically predicted values obtained from finite element analyses. This comparison shows that the new displacement transfer functions could quite accurately calculate the deformed shapes of tapered cantilever tubular beams with different tapered angles. The accuracy of the present displacement transfer functions also are compared to those of the previously developed displacement transfer functions.

Evaluating Thermodynamic Integration Performance of the New Amber Molecular Dynamics Package and Assess Potential Halogen Bonds of Enoyl-ACP Reductase (FabI) Benzimidazole Inhibitors

PubMed Central

Su, Pin-Chih; Johnson, Michael E.

2015-01-01

Thermodynamic integration (TI) can provide accurate binding free energy insights in a lead optimization program, but its high computational expense has limited its usage. In the effort of developing an efficient and accurate TI protocol for FabI inhibitors lead optimization program, we carefully compared TI with different Amber molecular dynamics (MD) engines (sander and pmemd), MD simulation lengths, the number of intermediate states and transformation steps, and the Lennard-Jones and Coulomb Softcore potentials parameters in the one-step TI, using eleven benzimidazole inhibitors in complex with Francisella tularensis enoyl acyl reductase (FtFabI). To our knowledge, this is the first study to extensively test the new AMBER MD engine, pmemd, on TI and compare the parameters of the Softcore potentials in the one-step TI in a protein-ligand binding system. The best performing model, the one-step pmemd TI, using 6 intermediate states and 1 ns MD simulations, provides better agreement with experimental results (RMSD = 0.52 kcal/mol) than the best performing implicit solvent method, QM/MM-GBSA from our previous study (RMSD = 3.00 kcal/mol), while maintaining similar efficiency. Briefly, we show the optimized TI protocol to be highly accurate and affordable for the FtFabI system. This approach can be implemented in a larger scale benzimidazole scaffold lead optimization against FtFabI. Lastly, the TI results here also provide structure-activity relationship insights, and suggest the para-halogen in benzimidazole compounds might form a weak halogen bond with FabI, which is a well-known halogen bond favoring enzyme. PMID:26666582

Evaluating thermodynamic integration performance of the new amber molecular dynamics package and assess potential halogen bonds of enoyl-ACP reductase (FabI) benzimidazole inhibitors.

PubMed

Su, Pin-Chih; Johnson, Michael E

2016-04-05

Thermodynamic integration (TI) can provide accurate binding free energy insights in a lead optimization program, but its high computational expense has limited its usage. In the effort of developing an efficient and accurate TI protocol for FabI inhibitors lead optimization program, we carefully compared TI with different Amber molecular dynamics (MD) engines (sander and pmemd), MD simulation lengths, the number of intermediate states and transformation steps, and the Lennard-Jones and Coulomb Softcore potentials parameters in the one-step TI, using eleven benzimidazole inhibitors in complex with Francisella tularensis enoyl acyl reductase (FtFabI). To our knowledge, this is the first study to extensively test the new AMBER MD engine, pmemd, on TI and compare the parameters of the Softcore potentials in the one-step TI in a protein-ligand binding system. The best performing model, the one-step pmemd TI, using 6 intermediate states and 1 ns MD simulations, provides better agreement with experimental results (RMSD = 0.52 kcal/mol) than the best performing implicit solvent method, QM/MM-GBSA from our previous study (RMSD = 3.00 kcal/mol), while maintaining similar efficiency. Briefly, we show the optimized TI protocol to be highly accurate and affordable for the FtFabI system. This approach can be implemented in a larger scale benzimidazole scaffold lead optimization against FtFabI. Lastly, the TI results here also provide structure-activity relationship insights, and suggest the parahalogen in benzimidazole compounds might form a weak halogen bond with FabI, which is a well-known halogen bond favoring enzyme. © 2015 Wiley Periodicals, Inc.

Computational measurement of joint space width and structural parameters in normal hips.

PubMed

Nishii, Takashi; Shiomi, Toshiyuki; Sakai, Takashi; Takao, Masaki; Yoshikawa, Hideki; Sugano, Nobuhiko

2012-05-01

Joint space width (JSW) of hip joints on radiographs in normal population may vary by related factors, but previous investigations were insufficient due to limitations of sources of radiographs, inclusion of subjects with osteoarthritis, and manual measurement techniques. We investigated influential factors on JSW using semiautomatic computational software on pelvic radiographs in asymptomatic subjects without radiological osteoarthritic findings. Global and local JSW at the medial, middle, and lateral compartments, and the hip structural parameters were measured in asymptomatic, normal 150 cases (300 hips), using a customized computational software. Reliability of measurement in global and local JSWs was high with intraobserver reproducibility (intraclass correlation coefficient) ranging from 0.957 to 0.993 and interobserver reproducibility ranging from 0.925 to 0.985. There were significant differences among three local JSWs, with the largest JSW at the lateral compartment. Global and medial local JSWs were significantly larger in the right hip, and global, medial and middle local JSWs were significantly smaller in women. Global and local JSWs were inversely correlated with CE angle and positively correlated with horizontal distance of the head center, but not correlated with body mass index in men and women. They were positively correlated with age and inversely correlated with vertical distance of the head center only in men. There were interindividual variations of JSW in normal population, depending on sites of the weight-bearing area, side, gender, age, and hip structural parameters. For accurate diagnosis and assessment of hip osteoarthritis, consideration of those influential factors other than degenerative change is important.

Evaluation of non-rigid registration parameters for atlas-based segmentation of CT images of human cochlea

NASA Astrophysics Data System (ADS)

Elfarnawany, Mai; Alam, S. Riyahi; Agrawal, Sumit K.; Ladak, Hanif M.

2017-02-01

Cochlear implant surgery is a hearing restoration procedure for patients with profound hearing loss. In this surgery, an electrode is inserted into the cochlea to stimulate the auditory nerve and restore the patient's hearing. Clinical computed tomography (CT) images are used for planning and evaluation of electrode placement, but their low resolution limits the visualization of internal cochlear structures. Therefore, high resolution micro-CT images are used to develop atlas-based segmentation methods to extract these nonvisible anatomical features in clinical CT images. Accurate registration of the high and low resolution CT images is a prerequisite for reliable atlas-based segmentation. In this study, we evaluate and compare different non-rigid B-spline registration parameters using micro-CT and clinical CT images of five cadaveric human cochleae. The varying registration parameters are cost function (normalized correlation (NC), mutual information and mean square error), interpolation method (linear, windowed-sinc and B-spline) and sampling percentage (1%, 10% and 100%). We compare the registration results visually and quantitatively using the Dice similarity coefficient (DSC), Hausdorff distance (HD) and absolute percentage error in cochlear volume. Using MI or MSE cost functions and linear or windowed-sinc interpolation resulted in visually undesirable deformation of internal cochlear structures. Quantitatively, the transforms using 100% sampling percentage yielded the highest DSC and smallest HD (0.828+/-0.021 and 0.25+/-0.09mm respectively). Therefore, B-spline registration with cost function: NC, interpolation: B-spline and sampling percentage: moments 100% can be the foundation of developing an optimized atlas-based segmentation algorithm of intracochlear structures in clinical CT images.

Estimating winter wheat phenological parameters: Implications for crop modeling

USDA-ARS?s Scientific Manuscript database

Crop parameters, such as the timing of developmental events, are critical for accurate simulation results in crop simulation models, yet uncertainty often exists in determining the parameters. Factors contributing to the uncertainty include: a) sources of variation within a plant (i.e., within diffe...