Bayesian Semiparametric Structural Equation Models with Latent Variables

ERIC Educational Resources Information Center

Yang, Mingan; Dunson, David B.

2010-01-01

Structural equation models (SEMs) with latent variables are widely useful for sparse covariance structure modeling and for inferring relationships among latent variables. Bayesian SEMs are appealing in allowing for the incorporation of prior information and in providing exact posterior distributions of unknowns, including the latent variables. In…

Food-web models predict species abundances in response to habitat change.

PubMed

Gotelli, Nicholas J; Ellison, Aaron M

2006-10-01

Plant and animal population sizes inevitably change following habitat loss, but the mechanisms underlying these changes are poorly understood. We experimentally altered habitat volume and eliminated top trophic levels of the food web of invertebrates that inhabit rain-filled leaves of the carnivorous pitcher plant Sarracenia purpurea. Path models that incorporated food-web structure better predicted population sizes of food-web constituents than did simple keystone species models, models that included only autecological responses to habitat volume, or models including both food-web structure and habitat volume. These results provide the first experimental confirmation that trophic structure can determine species abundances in the face of habitat loss.

Array seismological investigation of the South Atlantic 'Superplume'

NASA Astrophysics Data System (ADS)

Hempel, Stefanie; Gassmöller, Rene; Thomas, Christine

2015-04-01

We apply the axisymmetric, spherical Earth spectral elements code AxiSEM to model seismic compressional waves which sample complex `superplume' structures in the lower mantle. High-resolution array seismological stacking techniques are evaluated regarding their capability to resolve large-scale high-density low-velocity bodies including interior structure such as inner upwellings, high density lenses, ultra-low velocity zones (ULVZs), neighboring remnant slabs and adjacent small-scale uprisings. Synthetic seismograms are also computed and processed for models of the Earth resulting from geodynamic modelling of the South Atlantic mantle including plate reconstruction. We discuss the interference and suppression of the resulting seismic signals and implications for a seismic data study in terms of visibility of the South Atlantic `superplume' structure. This knowledge is used to process, invert and interpret our data set of seismic sources from the Andes and the South Sandwich Islands detected at seismic arrays spanning from Ethiopia over Cameroon to South Africa mapping the South Atlantic `superplume' structure including its interior structure. In order too present the model of the South Atlantic `superplume' structure that best fits the seismic data set, we iteratively compute synthetic seismograms while adjusting the model according to the dependencies found in the parameter study.

The factor structure of posttraumatic stress disorder: a literature update, critique of methodology, and agenda for future research.

PubMed

Elhai, Jon D; Palmieri, Patrick A

2011-08-01

We present an update of recent literature (since 2007) exploring the factor structure of posttraumatic stress disorder (PTSD) symptom measures. Research supporting a four-factor emotional numbing model and a four-factor dysphoria model is presented, with these models fitting better than all other models examined. Variables accounting for factor structure differences are reviewed, including PTSD query instructions, type of PTSD measure, extent of trauma exposure, ethnicity, and timing of administration. Methodological and statistical limitations with recent studies are presented. Finally, a research agenda and recommendations are offered to push this research area forward, including suggestions to validate PTSD’s factors against external measures of psychopathology, test moderators of factor structure, and examine heterogeneity of symptom presentations based on factor structure examination.

Bayesian Network Webserver: a comprehensive tool for biological network modeling.

PubMed

Ziebarth, Jesse D; Bhattacharya, Anindya; Cui, Yan

2013-11-01

The Bayesian Network Webserver (BNW) is a platform for comprehensive network modeling of systems genetics and other biological datasets. It allows users to quickly and seamlessly upload a dataset, learn the structure of the network model that best explains the data and use the model to understand relationships between network variables. Many datasets, including those used to create genetic network models, contain both discrete (e.g. genotype) and continuous (e.g. gene expression traits) variables, and BNW allows for modeling hybrid datasets. Users of BNW can incorporate prior knowledge during structure learning through an easy-to-use structural constraint interface. After structure learning, users are immediately presented with an interactive network model, which can be used to make testable hypotheses about network relationships. BNW, including a downloadable structure learning package, is available at http://compbio.uthsc.edu/BNW. (The BNW interface for adding structural constraints uses HTML5 features that are not supported by current version of Internet Explorer. We suggest using other browsers (e.g. Google Chrome or Mozilla Firefox) when accessing BNW). ycui2@uthsc.edu. Supplementary data are available at Bioinformatics online.

SMART Structures User's Guide - Version 3.0

NASA Technical Reports Server (NTRS)

Spangler, Jan L.

1996-01-01

Version 3.0 of the Solid Modeling Aerospace Research Tool (SMART Structures) is used to generate structural models for conceptual and preliminary-level aerospace designs. Features include the generation of structural elements for wings and fuselages, the integration of wing and fuselage structural assemblies, and the integration of fuselage and tail structural assemblies. The highly interactive nature of this software allows the structural engineer to move quickly from a geometry that defines a vehicle's external shape to one that has both external components and internal components which may include ribs, spars, longerons, variable depth ringframes, a floor, a keel, and fuel tanks. The geometry that is output is consistent with FEA requirements and includes integrated wing and empennage carry-through and frame attachments. This report provides a comprehensive description of SMART Structures and how to use it.

Sensitivity of Fit Indices to Misspecification in Growth Curve Models

ERIC Educational Resources Information Center

Wu, Wei; West, Stephen G.

2010-01-01

This study investigated the sensitivity of fit indices to model misspecification in within-individual covariance structure, between-individual covariance structure, and marginal mean structure in growth curve models. Five commonly used fit indices were examined, including the likelihood ratio test statistic, root mean square error of…

Theoretical and software considerations for nonlinear dynamic analysis

NASA Technical Reports Server (NTRS)

Schmidt, R. J.; Dodds, R. H., Jr.

1983-01-01

In the finite element method for structural analysis, it is generally necessary to discretize the structural model into a very large number of elements to accurately evaluate displacements, strains, and stresses. As the complexity of the model increases, the number of degrees of freedom can easily exceed the capacity of present-day software system. Improvements of structural analysis software including more efficient use of existing hardware and improved structural modeling techniques are discussed. One modeling technique that is used successfully in static linear and nonlinear analysis is multilevel substructuring. This research extends the use of multilevel substructure modeling to include dynamic analysis and defines the requirements for a general purpose software system capable of efficient nonlinear dynamic analysis. The multilevel substructuring technique is presented, the analytical formulations and computational procedures for dynamic analysis and nonlinear mechanics are reviewed, and an approach to the design and implementation of a general purpose structural software system is presented.

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

Los Alamos National Laboratory, Mailstop M888, Los Alamos, NM 87545, USA; Lawrence Berkeley National Laboratory, One Cyclotron Road, Building 64R0121, Berkeley, CA 94720, USA; Department of Haematology, University of Cambridge, Cambridge CB2 0XY, England

The PHENIX AutoBuild Wizard is a highly automated tool for iterative model-building, structure refinement and density modification using RESOLVE or TEXTAL model-building, RESOLVE statistical density modification, and phenix.refine structure refinement. Recent advances in the AutoBuild Wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model completion algorithms, and automated solvent molecule picking. Model completion algorithms in the AutoBuild Wizard include loop-building, crossovers between chains in different models of a structure, and side-chain optimization. The AutoBuild Wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 {angstrom} tomore » 3.2 {angstrom}, resulting in a mean R-factor of 0.24 and a mean free R factor of 0.29. The R-factor of the final model is dependent on the quality of the starting electron density, and relatively independent of resolution.« less

Status of DSMT research program

NASA Technical Reports Server (NTRS)

Mcgowan, Paul E.; Javeed, Mehzad; Edighoffer, Harold H.

1991-01-01

The status of the Dynamic Scale Model Technology (DSMT) research program is presented. DSMT is developing scale model technology for large space structures as part of the Control Structure Interaction (CSI) program at NASA Langley Research Center (LaRC). Under DSMT a hybrid-scale structural dynamics model of Space Station Freedom was developed. Space Station Freedom was selected as the focus structure for DSMT since the station represents the first opportunity to obtain flight data on a complex, three-dimensional space structure. Included is an overview of DSMT including the development of the space station scale model and the resulting hardware. Scaling technology was developed for this model to achieve a ground test article which existing test facilities can accommodate while employing realistically scaled hardware. The model was designed and fabricated by the Lockheed Missile and Space Co., and is assembled at LaRc for dynamic testing. Also, results from ground tests and analyses of the various model components are presented along with plans for future subassembly and matted model tests. Finally, utilization of the scale model for enhancing analysis verification of the full-scale space station is also considered.

Distinct families of cis-acting RNA replication elements epsilon from hepatitis B viruses

PubMed Central

Chen, Augustine; Brown, Chris

2012-01-01

The hepadnavirus encapsidation signal, epsilon (ε), is an RNA structure located at the 5′ end of the viral pregenomic RNA. It is essential for viral replication and functions in polymerase protein binding and priming. This structure could also have potential regulatory roles in controlling the expression of viral replicative proteins. In addition to its structure, the primary sequence of this RNA element has crucial functional roles in the viral lifecycle. Although the ε elements in hepadnaviruses share common critical functions, there are some significant differences in mammalian and avian hepadnaviruses, which include both sequence and structural variations.   Here we present several covariance models for ε elements from the Hepadnaviridae. The model building included experimentally determined data from previous studies using chemical probing and NMR analysis. These models have sufficient similarity to comprise a clan. The clan has in common a highly conserved overall structure consisting of a lower-stem, bulge, upper-stem and apical-loop. The models differ in functionally critical regions—notably the two types of avian ε elements have a tetra-loop (UGUU) including a non-canonical UU base pair, while the hepatitis B virus (HBV) epsilon has a tri-loop (UGU). The avian epsilon elements have a less stable dynamic structure in the upper stem. Comparisons between these models and all other Rfam models, and searches of genomes, showed these structures are specific to the Hepadnaviridae. Two family models and the clan are available from the Rfam database. PMID:22418844

The diagram of phase-field crystal structures: an influence of model parameters in a two-mode approximation

NASA Astrophysics Data System (ADS)

Ankudinov, V.; Galenko, P. K.

2017-04-01

Effect of phase-field crystal model (PFC-model) parameters on the structure diagram is analyzed. The PFC-model is taken in a two-mode approximation and the construction of structure diagram follows from the free energy minimization and Maxwell thermodynamic rule. The diagram of structure’s coexistence for three dimensional crystal structures [Body-Centered-Cubic (BCC), Face-Centered-Cubic (FCC) and homogeneous structures] are constructed. An influence of the model parameters, including the stability parameters, are discussed. A question about the structure diagram construction using the two-mode PFC-model with the application to real materials is established.

Design for inadvertent damage in composite laminates

NASA Technical Reports Server (NTRS)

Singhal, Surendra N.; Chamis, Christos C.

1992-01-01

Simplified predictive methods and models to computationally simulate durability and damage in polymer matrix composite materials/structures are described. The models include (1) progressive fracture, (2) progressively damaged structural behavior, (3) progressive fracture in aggressive environments, (4) stress concentrations, and (5) impact resistance. Several examples are included to illustrate applications of the models and to identify significant parameters and sensitivities. Comparisons with limited experimental data are made.

Using Structural Equation Modeling To Fit Models Incorporating Principal Components.

ERIC Educational Resources Information Center

Dolan, Conor; Bechger, Timo; Molenaar, Peter

1999-01-01

Considers models incorporating principal components from the perspectives of structural-equation modeling. These models include the following: (1) the principal-component analysis of patterned matrices; (2) multiple analysis of variance based on principal components; and (3) multigroup principal-components analysis. Discusses fitting these models…

Dynamic analysis of space structures including elastic, multibody, and control behavior

NASA Technical Reports Server (NTRS)

Pinson, Larry; Soosaar, Keto

1989-01-01

The problem is to develop analysis methods, modeling stategies, and simulation tools to predict with assurance the on-orbit performance and integrity of large complex space structures that cannot be verified on the ground. The problem must incorporate large reliable structural models, multi-body flexible dynamics, multi-tier controller interaction, environmental models including 1g and atmosphere, various on-board disturbances, and linkage to mission-level performance codes. All areas are in serious need of work, but the weakest link is multi-body flexible dynamics.

Food-Web Models Predict Species Abundances in Response to Habitat Change

PubMed Central

Gotelli, Nicholas J; Ellison, Aaron M

2006-01-01

Plant and animal population sizes inevitably change following habitat loss, but the mechanisms underlying these changes are poorly understood. We experimentally altered habitat volume and eliminated top trophic levels of the food web of invertebrates that inhabit rain-filled leaves of the carnivorous pitcher plant Sarracenia purpurea. Path models that incorporated food-web structure better predicted population sizes of food-web constituents than did simple keystone species models, models that included only autecological responses to habitat volume, or models including both food-web structure and habitat volume. These results provide the first experimental confirmation that trophic structure can determine species abundances in the face of habitat loss. PMID:17002518

Flight-vehicle materials, structures, and dynamics - Assessment and future directions. Vol. 5 - Structural dynamics and aeroelasticity

NASA Technical Reports Server (NTRS)

Noor, Ahmed K. (Editor); Venneri, Samuel L. (Editor)

1993-01-01

Various papers on flight vehicle materials, structures, and dynamics are presented. Individual topics addressed include: general modeling methods, component modeling techniques, time-domain computational techniques, dynamics of articulated structures, structural dynamics in rotating systems, structural dynamics in rotorcraft, damping in structures, structural acoustics, structural design for control, structural modeling for control, control strategies for structures, system identification, overall assessment of needs and benefits in structural dynamics and controlled structures. Also discussed are: experimental aeroelasticity in wind tunnels, aeroservoelasticity, nonlinear aeroelasticity, aeroelasticity problems in turbomachines, rotary-wing aeroelasticity with application to VTOL vehicles, computational aeroelasticity, structural dynamic testing and instrumentation.

Structural mode significance using INCA. [Interactive Controls Analysis computer program

NASA Technical Reports Server (NTRS)

Bauer, Frank H.; Downing, John P.; Thorpe, Christopher J.

1990-01-01

Structural finite element models are often too large to be used in the design and analysis of control systems. Model reduction techniques must be applied to reduce the structural model to manageable size. In the past, engineers either performed the model order reduction by hand or used distinct computer programs to retrieve the data, to perform the significance analysis and to reduce the order of the model. To expedite this process, the latest version of INCA has been expanded to include an interactive graphical structural mode significance and model order reduction capability.

Defect sink characteristics of specific grain boundary types in 304 stainless steels under high dose neutron environments

DOE PAGES

Field, Kevin G.; Yang, Ying; Busby, Jeremy T.; ...

2015-03-09

Radiation induced segregation (RIS) is a well-studied phenomena which occurs in many structurally relevant nuclear materials including austenitic stainless steels. RIS occurs due to solute atoms preferentially coupling to mobile point defect fluxes that migrate and interact with defect sinks. Here, a 304 stainless steel was neutron irradiated up to 47.1 dpa at 320 °C. Investigations into the RIS response at specific grain boundary types were utilized to determine the sink characteristics of different boundary types as a function of irradiation dose. A rate theory model built on the foundation of the modified inverse Kirkendall (MIK) model is proposed andmore » benchmarked to the experimental results. This model, termed the GiMIK model, includes alterations in the boundary conditions based on grain boundary structure and includes expressions for interstitial binding. This investigation, through experiment and modeling, found specific grain boundary structures exhibit unique defect sink characteristics depending on their local structure. Furthermore, such interactions were found to be consistent across all doses investigated and had larger global implications including precipitation of Ni-Si clusters near different grain boundary types.« less

A Structural Modeling Approach to a Multilevel Random Coefficients Model.

ERIC Educational Resources Information Center

Rovine, Michael J.; Molenaar, Peter C. M.

2000-01-01

Presents a method for estimating the random coefficients model using covariance structure modeling and allowing one to estimate both fixed and random effects. The method is applied to real and simulated data, including marriage data from J. Belsky and M. Rovine (1990). (SLD)

Structure and dynamics of coronal plasmas

NASA Technical Reports Server (NTRS)

Golub, Leon (Principal Investigator)

1996-01-01

Progress for the period July 1995 - June 1996 included work on the differential magnetic field shear in an active region; observations and modeling of the solar chromosphere seen in soft X-ray absorption by NIXT; and modeling magnetic flux emergence. These were the subjects of three papers. The plans for the current year include projects on a converging flux model for point-like brightenings around sunspots, and difficulties in observing coronal structure.

Mantle viscosity structure constrained by joint inversions of seismic velocities and density

NASA Astrophysics Data System (ADS)

Rudolph, M. L.; Moulik, P.; Lekic, V.

2017-12-01

The viscosity structure of Earth's deep mantle affects the thermal evolution of Earth, the ascent of mantle upwellings, sinking of subducted oceanic lithosphere, and the mixing of compositional heterogeneities in the mantle. Modeling the long-wavelength dynamic geoid allows us to constrain the radial viscosity profile of the mantle. Typically, in inversions for the mantle viscosity structure, wavespeed variations are mapped into density variations using a constant- or depth-dependent scaling factor. Here, we use a newly developed joint model of anisotropic Vs, Vp, density and transition zone topographies to generate a suite of solutions for the mantle viscosity structure directly from the seismologically constrained density structure. The density structure used to drive our forward models includes contributions from both thermal and compositional variations, including important contributions from compositionally dense material in the Large Low Velocity Provinces at the base of the mantle. These compositional variations have been neglected in the forward models used in most previous inversions and have the potential to significantly affect large-scale flow and thus the inferred viscosity structure. We use a transdimensional, hierarchical, Bayesian approach to solve the inverse problem, and our solutions for viscosity structure include an increase in viscosity below the base of the transition zone, in the shallow lower mantle. Using geoid dynamic response functions and an analysis of the correlation between the observed geoid and mantle structure, we demonstrate the underlying reason for this inference. Finally, we present a new family of solutions in which the data uncertainty is accounted for using covariance matrices associated with the mantle structure models.

An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization

PubMed Central

Hinckley, Daniel M.; Freeman, Gordon S.; Whitmer, Jonathan K.; de Pablo, Juan J.

2013-01-01

A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model includes anisotropic potentials between bases involved in base stacking and base pair interactions that enable the description of relevant structural properties, including the major and minor grooves. In an improvement over available coarse-grained models, the correct persistence length is recovered for both ssDNA and dsDNA, allowing for simulation of non-canonical structures such as hairpins. DNA melting temperatures, measured for duplexes and hairpins by integrating over free energy surfaces generated using metadynamics simulations, are shown to be in quantitative agreement with experiment for a variety of sequences and conditions. Hybridization rate constants, calculated using forward-flux sampling, are also shown to be in good agreement with experiment. The coarse-grained model presented here is suitable for use in biological and engineering applications, including nucleosome positioning and DNA-templated engineering. PMID:24116642

Modeling the Structure of Helical Assemblies with Experimental Constraints in Rosetta.

PubMed

André, Ingemar

2018-01-01

Determining high-resolution structures of proteins with helical symmetry can be challenging due to limitations in experimental data. In such instances, structure-based protein simulations driven by experimental data can provide a valuable approach for building models of helical assemblies. This chapter describes how the Rosetta macromolecular package can be used to model homomeric protein assemblies with helical symmetry in a range of modeling scenarios including energy refinement, symmetrical docking, comparative modeling, and de novo structure prediction. Data-guided structure modeling of helical assemblies with experimental information from electron density, X-ray fiber diffraction, solid-state NMR, and chemical cross-linking mass spectrometry is also described.

Alignment of the system's chief nursing officer: staff or direct line structure?

PubMed

Kerfoot, Karlene M; Luquire, Rosemary

2012-01-01

The role of the system chief nursing officer nationally and internationally has been traditionally structured as a staff model, a direct line model, or a hybrid that includes parts of each model. The choice of structure should be made after a thorough investigation of what outcomes the system wants this position to accomplish, developing the appropriate structure to achieve these outcomes, and then engaging a chief nursing officer with the skills indicated by the type of structure chosen. This article describes these 3 structures and the support infrastructure necessary for each model.

Optimization of the time series NDVI-rainfall relationship using linear mixed-effects modeling for the anti-desertification area in the Beijing and Tianjin sandstorm source region

NASA Astrophysics Data System (ADS)

Wang, Jin; Sun, Tao; Fu, Anmin; Xu, Hao; Wang, Xinjie

2018-05-01

Degradation in drylands is a critically important global issue that threatens ecosystem and environmental in many ways. Researchers have tried to use remote sensing data and meteorological data to perform residual trend analysis and identify human-induced vegetation changes. However, complex interactions between vegetation and climate, soil units and topography have not yet been considered. Data used in the study included annual accumulated Moderate Resolution Imaging Spectroradiometer (MODIS) 250 m normalized difference vegetation index (NDVI) from 2002 to 2013, accumulated rainfall from September to August, digital elevation model (DEM) and soil units. This paper presents linear mixed-effect (LME) modeling methods for the NDVI-rainfall relationship. We developed linear mixed-effects models that considered the random effects of sample points nested in soil units for nested two-level modeling and single-level modeling of soil units and sample points, respectively. Additionally, three functions, including the exponential function (exp), the power function (power), and the constant plus power function (CPP), were tested to remove heterogeneity, and an additional three correlation structures, including the first-order autoregressive structure [AR(1)], a combination of first-order autoregressive and moving average structures [ARMA(1,1)] and the compound symmetry structure (CS), were used to address the spatiotemporal correlations. It was concluded that the nested two-level model considering both heteroscedasticity with (CPP) and spatiotemporal correlation with [ARMA(1,1)] showed the best performance (AMR = 0.1881, RMSE = 0.2576, adj- R 2 = 0.9593). Variations between soil units and sample points that may have an effect on the NDVI-rainfall relationship should be included in model structures, and linear mixed-effects modeling achieves this in an effective and accurate way.

The impact of structural uncertainty on cost-effectiveness models for adjuvant endocrine breast cancer treatments: the need for disease-specific model standardization and improved guidance.

PubMed

Frederix, Gerardus W J; van Hasselt, Johan G C; Schellens, Jan H M; Hövels, Anke M; Raaijmakers, Jan A M; Huitema, Alwin D R; Severens, Johan L

2014-01-01

Structural uncertainty relates to differences in model structure and parameterization. For many published health economic analyses in oncology, substantial differences in model structure exist, leading to differences in analysis outcomes and potentially impacting decision-making processes. The objectives of this analysis were (1) to identify differences in model structure and parameterization for cost-effectiveness analyses (CEAs) comparing tamoxifen and anastrazole for adjuvant breast cancer (ABC) treatment; and (2) to quantify the impact of these differences on analysis outcome metrics. The analysis consisted of four steps: (1) review of the literature for identification of eligible CEAs; (2) definition and implementation of a base model structure, which included the core structural components for all identified CEAs; (3) definition and implementation of changes or additions in the base model structure or parameterization; and (4) quantification of the impact of changes in model structure or parameterizations on the analysis outcome metrics life-years gained (LYG), incremental costs (IC) and the incremental cost-effectiveness ratio (ICER). Eleven CEA analyses comparing anastrazole and tamoxifen as ABC treatment were identified. The base model consisted of the following health states: (1) on treatment; (2) off treatment; (3) local recurrence; (4) metastatic disease; (5) death due to breast cancer; and (6) death due to other causes. The base model estimates of anastrazole versus tamoxifen for the LYG, IC and ICER were 0.263 years, €3,647 and €13,868/LYG, respectively. In the published models that were evaluated, differences in model structure included the addition of different recurrence health states, and associated transition rates were identified. Differences in parameterization were related to the incidences of recurrence, local recurrence to metastatic disease, and metastatic disease to death. The separate impact of these model components on the LYG ranged from 0.207 to 0.356 years, while incremental costs ranged from €3,490 to €3,714 and ICERs ranged from €9,804/LYG to €17,966/LYG. When we re-analyzed the published CEAs in our framework by including their respective model properties, the LYG ranged from 0.207 to 0.383 years, IC ranged from €3,556 to €3,731 and ICERs ranged from €9,683/LYG to €17,570/LYG. Differences in model structure and parameterization lead to substantial differences in analysis outcome metrics. This analysis supports the need for more guidance regarding structural uncertainty and the use of standardized disease-specific models for health economic analyses of adjuvant endocrine breast cancer therapies. The developed approach in the current analysis could potentially serve as a template for further evaluations of structural uncertainty and development of disease-specific models.

Epidemics in adaptive networks with community structure

NASA Astrophysics Data System (ADS)

Shaw, Leah; Tunc, Ilker

2010-03-01

Models for epidemic spread on static social networks do not account for changes in individuals' social interactions. Recent studies of adaptive networks have modeled avoidance behavior, as non-infected individuals try to avoid contact with infectives. Such models have not generally included realistic social structure. Here we study epidemic spread on an adaptive network with community structure. We model the effect of heterogeneous communities on infection levels and epidemic extinction. We also show how an epidemic can alter the community structure.

Introduction to the special section on mixture modeling in personality assessment.

PubMed

Wright, Aidan G C; Hallquist, Michael N

2014-01-01

Latent variable models offer a conceptual and statistical framework for evaluating the underlying structure of psychological constructs, including personality and psychopathology. Complex structures that combine or compare categorical and dimensional latent variables can be accommodated using mixture modeling approaches, which provide a powerful framework for testing nuanced theories about psychological structure. This special series includes introductory primers on cross-sectional and longitudinal mixture modeling, in addition to empirical examples applying these techniques to real-world data collected in clinical settings. This group of articles is designed to introduce personality assessment scientists and practitioners to a general latent variable framework that we hope will stimulate new research and application of mixture models to the assessment of personality and its pathology.

Transferable atomistic model to describe the energetics of zirconia

NASA Astrophysics Data System (ADS)

Wilson, Mark; Schönberger, Uwe; Finnis, Michael W.

1996-10-01

We have investigated the energies of a number of phases of ZrO2 using models of an increasing degree of sophistication: the simple ionic model, the polarizable ion model, the compressible ion model, and finally a model including quadrupole polarizability of the oxygen ions. The three structures which are observed with increasing temperatures are monoclinic, tetragonal, and cubic (fluorite). Besides these we have studied some hypothetical structures which certain potentials erroneously predict or which occur in other oxides with this stoichiometry, e.g., the α-PbO2 structure and rutile. We have also performed ab initio density functional calculations with the full-potential linear combination of muffin-tin orbitals method to investigate the cubic-tetragonal distortion. A detailed comparison is made between the results using classical potentials, the experimental data, and our own and other ab initio results. The factors which stabilize the various structure are analyzed. We find the only genuinely transferable model is the one including compressible ions and anion polarizability to the quadrupole level.

Uncovering the drivers of host-associated microbiota with joint species distribution modelling.

PubMed

Björk, Johannes R; Hui, Francis K C; O'Hara, Robert B; Montoya, Jose M

2018-06-01

In addition to the processes structuring free-living communities, host-associated microbiota are directly or indirectly shaped by the host. Therefore, microbiota data have a hierarchical structure where samples are nested under one or several variables representing host-specific factors, often spanning multiple levels of biological organization. Current statistical methods do not accommodate this hierarchical data structure and therefore cannot explicitly account for the effect of the host in structuring the microbiota. We introduce a novel extension of joint species distribution models (JSDMs) which can straightforwardly accommodate and discern between effects such as host phylogeny and traits, recorded covariates such as diet and collection site, among other ecological processes. Our proposed methodology includes powerful yet familiar outputs seen in community ecology overall, including (a) model-based ordination to visualize and quantify the main patterns in the data; (b) variance partitioning to assess how influential the included host-specific factors are in structuring the microbiota; and (c) co-occurrence networks to visualize microbe-to-microbe associations. © 2018 John Wiley & Sons Ltd.

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

PubMed Central

Xu, Dong; Zhang, Jian; Roy, Ambrish; Zhang, Yang

2011-01-01

I-TASSER is an automated pipeline for protein tertiary structure prediction using multiple threading alignments and iterative structure assembly simulations. In CASP9 experiments, two new algorithms, QUARK and FG-MD, were added to the I-TASSER pipeline for improving the structural modeling accuracy. QUARK is a de novo structure prediction algorithm used for structure modeling of proteins that lack detectable template structures. For distantly homologous targets, QUARK models are found useful as a reference structure for selecting good threading alignments and guiding the I-TASSER structure assembly simulations. FG-MD is an atomic-level structural refinement program that uses structural fragments collected from the PDB structures to guide molecular dynamics simulation and improve the local structure of predicted model, including hydrogen-bonding networks, torsion angles and steric clashes. Despite considerable progress in both the template-based and template-free structure modeling, significant improvements on protein target classification, domain parsing, model selection, and ab initio folding of beta-proteins are still needed to further improve the I-TASSER pipeline. PMID:22069036

The cross-national structure of mental disorders: results from the World Mental Health Surveys.

PubMed

de Jonge, Peter; Wardenaar, Klaas J; Lim, Carmen C W; Aguilar-Gaxiola, Sergio; Alonso, Jordi; Andrade, Laura Helena; Bunting, Brendan; Chatterji, Somnath; Ciutan, Marius; Gureje, Oye; Karam, Elie G; Lee, Sing; Medina-Mora, Maria Elena; Moskalewicz, Jacek; Navarro-Mateu, Fernando; Pennell, Beth-Ellen; Piazza, Marina; Posada-Villa, José; Torres, Yolanda; Kessler, Ronald C; Scott, Kate

2017-12-19

The patterns of comorbidity among mental disorders have led researchers to model the underlying structure of psychopathology. While studies have suggested a structure including internalizing and externalizing disorders, less is known with regard to the cross-national stability of this model. Moreover, little data are available on the placement of eating disorders, bipolar disorder and psychotic experiences (PEs) in this structure. We evaluated the structure of mental disorders with data from the World Health Organization Composite International Diagnostic Interview, including 15 lifetime mental disorders and six PEs. Respondents (n = 5478-15 499) were included from 10 high-, middle- and lower middle-income countries across the world aged 18 years or older. Confirmatory factor analyses (CFAs) were used to evaluate and compare the fit of different factor structures to the lifetime disorder data. Measurement invariance was evaluated with multigroup CFA (MG-CFA). A second-order model with internalizing and externalizing factors and fear and distress subfactors best described the structure of common mental disorders. MG-CFA showed that this model was stable across countries. Of the uncommon disorders, bipolar disorder and eating disorder were best grouped with the internalizing factor, and PEs with a separate factor. These results indicate that cross-national patterns of lifetime common mental-disorder comorbidity can be explained with a second-order underlying structure that is stable across countries and can be extended to also cover less common mental disorders.

U.S. perspective on technology demonstration experiments for adaptive structures

NASA Technical Reports Server (NTRS)

Aswani, Mohan; Wada, Ben K.; Garba, John A.

1991-01-01

Evaluation of design concepts for adaptive structures is being performed in support of several focused research programs. These include programs such as Precision Segmented Reflector (PSR), Control Structure Interaction (CSI), and the Advanced Space Structures Technology Research Experiment (ASTREX). Although not specifically designed for adaptive structure technology validation, relevant experiments can be performed using the Passive and Active Control of Space Structures (PACOSS) testbed, the Space Integrated Controls Experiment (SPICE), the CSI Evolutionary Model (CEM), and the Dynamic Scale Model Test (DSMT) Hybrid Scale. In addition to the ground test experiments, several space flight experiments have been planned, including a reduced gravity experiment aboard the KC-135 aircraft, shuttle middeck experiments, and the Inexpensive Flight Experiment (INFLEX).

Evaluation of Maximum Radionuclide Groundwater Concentrations for Basement Fill Model. Zion Station Restoration Project

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

Sullivan, T.

2016-05-20

ZionSolutions is in the process of decommissioning the Zion Nuclear Power Station (ZNPS). After decommissioning is completed, the site will contain two reactor Containment Buildings, the Fuel Handling Building and Transfer Canals, Auxiliary Building, Turbine Building, Crib House/Forebay, and a Waste Water Treatment Facility that have been demolished to a depth of 3 feet below grade. Additional below ground structures remaining will include the Main Steam Tunnels and large diameter intake and discharge pipes. These additional structures are not included in the modeling described in this report, but the inventory remaining (expected to be very low) will be included withmore » one of the structures that are modeled as designated in the Zion Station Restoration Project (ZSRP) License Termination Plan (LTP). The remaining underground structures will be backfilled with clean material. The final selection of fill material has not been made.« less

State Education Governance Structures: 2017 Update. 50-State Review

ERIC Educational Resources Information Center

Railey, Hunter

2017-01-01

This 50-State Review provides an overview of governance structures in the states, as well as implications for practice, deep dives into four governance models and examples of other governance models. One appendix, State Education Governance Models by State, is included.

A Taxonomy of Latent Structure Assumptions for Probability Matrix Decomposition Models.

ERIC Educational Resources Information Center

Meulders, Michel; De Boeck, Paul; Van Mechelen, Iven

2003-01-01

Proposed a taxonomy of latent structure assumptions for probability matrix decomposition (PMD) that includes the original PMD model and a three-way extension of the multiple classification latent class model. Simulation study results show the usefulness of the taxonomy. (SLD)

Starting from Scratch: The Evolution of One University's Administrative Structure for Adult Programs

ERIC Educational Resources Information Center

Williams, Carol G.

2012-01-01

Abilene Christian University uses a hybrid governance model. Centralized structures include traditional program departments that supply the faculty and curriculum development for online graduate programs. Decentralized structures include an associate provost and separate student services for the online program.

The NASA High Speed ASE Project: Computational Analyses of a Low-Boom Supersonic Configuration

NASA Technical Reports Server (NTRS)

Silva, Walter A.; DeLaGarza, Antonio; Zink, Scott; Bounajem, Elias G.; Johnson, Christopher; Buonanno, Michael; Sanetrik, Mark D.; Yoo, Seung Y.; Kopasakis, George; Christhilf, David M.;

Querying and Ranking XML Documents.

ERIC Educational Resources Information Center

Schlieder, Torsten; Meuss, Holger

2002-01-01

Discussion of XML, information retrieval, precision, and recall focuses on a retrieval technique that adopts the similarity measure of the vector space model, incorporates the document structure, and supports structured queries. Topics include a query model based on tree matching; structured queries and term-based ranking; and term frequency and…

Ecogeography, genetics, and the evolution of human body form.

PubMed

Roseman, Charles C; Auerbach, Benjamin M

2015-01-01

Genetic resemblances among groups are non-randomly distributed in humans. This population structure may influence the correlations between traits and environmental drivers of natural selection thus complicating the interpretation of the fossil record when modern human variation is used as a referential model. In this paper, we examine the effects of population structure and natural selection on postcranial traits that reflect body size and shape with application to the more general issue of how climate - using latitude as a proxy - has influenced hominin morphological variation. We compare models that include terms reflecting population structure, ascertained from globally distributed microsatellite data, and latitude on postcranial phenotypes derived from skeletal dimensions taken from a large global sample of modern humans. We find that models with a population structure term fit better than a model of natural selection along a latitudinal cline in all cases. A model including both latitude and population structure terms is a good fit to distal limb element lengths and bi-iliac breadth, indicating that multiple evolutionary forces shaped these morphologies. In contrast, a model that included only a population structure term best explained femoral head diameter and the crural index. The results demonstrate that population structure is an important part of human postcranial variation, and that clinally distributed natural selection is not sufficient to explain among-group differentiation. The distribution of human body form is strongly influenced by the contingencies of modern human origins, which calls for new ways to approach problems in the evolution of human variation, past and present. Copyright © 2014 Elsevier Ltd. All rights reserved.

Seven challenges for metapopulation models of epidemics, including households models.

PubMed

Ball, Frank; Britton, Tom; House, Thomas; Isham, Valerie; Mollison, Denis; Pellis, Lorenzo; Scalia Tomba, Gianpaolo

2015-03-01

This paper considers metapopulation models in the general sense, i.e. where the population is partitioned into sub-populations (groups, patches,...), irrespective of the biological interpretation they have, e.g. spatially segregated large sub-populations, small households or hosts themselves modelled as populations of pathogens. This framework has traditionally provided an attractive approach to incorporating more realistic contact structure into epidemic models, since it often preserves analytic tractability (in stochastic as well as deterministic models) but also captures the most salient structural inhomogeneity in contact patterns in many applied contexts. Despite the progress that has been made in both the theory and application of such metapopulation models, we present here several major challenges that remain for future work, focusing on models that, in contrast to agent-based ones, are amenable to mathematical analysis. The challenges range from clarifying the usefulness of systems of weakly-coupled large sub-populations in modelling the spread of specific diseases to developing a theory for endemic models with household structure. They include also developing inferential methods for data on the emerging phase of epidemics, extending metapopulation models to more complex forms of human social structure, developing metapopulation models to reflect spatial population structure, developing computationally efficient methods for calculating key epidemiological model quantities, and integrating within- and between-host dynamics in models. Copyright © 2014 The Authors. Published by Elsevier B.V. All rights reserved.

Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30.

PubMed

Lee, Hasup; Baek, Minkyung; Lee, Gyu Rie; Park, Sangwoo; Seok, Chaok

2017-03-01

Many proteins function as homo- or hetero-oligomers; therefore, attempts to understand and regulate protein functions require knowledge of protein oligomer structures. The number of available experimental protein structures is increasing, and oligomer structures can be predicted using the experimental structures of related proteins as templates. However, template-based models may have errors due to sequence differences between the target and template proteins, which can lead to functional differences. Such structural differences may be predicted by loop modeling of local regions or refinement of the overall structure. In CAPRI (Critical Assessment of PRotein Interactions) round 30, we used recently developed features of the GALAXY protein modeling package, including template-based structure prediction, loop modeling, model refinement, and protein-protein docking to predict protein complex structures from amino acid sequences. Out of the 25 CAPRI targets, medium and acceptable quality models were obtained for 14 and 1 target(s), respectively, for which proper oligomer or monomer templates could be detected. Symmetric interface loop modeling on oligomer model structures successfully improved model quality, while loop modeling on monomer model structures failed. Overall refinement of the predicted oligomer structures consistently improved the model quality, in particular in interface contacts. Proteins 2017; 85:399-407. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

PubMed

Czaplewski, Cezary; Karczynska, Agnieszka; Sieradzan, Adam K; Liwo, Adam

2018-04-30

A server implementation of the UNRES package (http://www.unres.pl) for coarse-grained simulations of protein structures with the physics-based UNRES model, coined a name UNRES server, is presented. In contrast to most of the protein coarse-grained models, owing to its physics-based origin, the UNRES force field can be used in simulations, including those aimed at protein-structure prediction, without ancillary information from structural databases; however, the implementation includes the possibility of using restraints. Local energy minimization, canonical molecular dynamics simulations, replica exchange and multiplexed replica exchange molecular dynamics simulations can be run with the current UNRES server; the latter are suitable for protein-structure prediction. The user-supplied input includes protein sequence and, optionally, restraints from secondary-structure prediction or small x-ray scattering data, and simulation type and parameters which are selected or typed in. Oligomeric proteins, as well as those containing D-amino-acid residues and disulfide links can be treated. The output is displayed graphically (minimized structures, trajectories, final models, analysis of trajectory/ensembles); however, all output files can be downloaded by the user. The UNRES server can be freely accessed at http://unres-server.chem.ug.edu.pl.

Equivalent plate modeling for conceptual design of aircraft wing structures

NASA Technical Reports Server (NTRS)

Giles, Gary L.

1995-01-01

This paper describes an analysis method that generates conceptual-level design data for aircraft wing structures. A key requirement is that this data must be produced in a timely manner so that is can be used effectively by multidisciplinary synthesis codes for performing systems studies. Such a capability is being developed by enhancing an equivalent plate structural analysis computer code to provide a more comprehensive, robust and user-friendly analysis tool. The paper focuses on recent enhancements to the Equivalent Laminated Plate Solution (ELAPS) analysis code that significantly expands the modeling capability and improves the accuracy of results. Modeling additions include use of out-of-plane plate segments for representing winglets and advanced wing concepts such as C-wings along with a new capability for modeling the internal rib and spar structure. The accuracy of calculated results is improved by including transverse shear effects in the formulation and by using multiple sets of assumed displacement functions in the analysis. Typical results are presented to demonstrate these new features. Example configurations include a C-wing transport aircraft, a representative fighter wing and a blended-wing-body transport. These applications are intended to demonstrate and quantify the benefits of using equivalent plate modeling of wing structures during conceptual design.

Evaluating bacterial gene-finding HMM structures as probabilistic logic programs.

PubMed

Mørk, Søren; Holmes, Ian

2012-03-01

Probabilistic logic programming offers a powerful way to describe and evaluate structured statistical models. To investigate the practicality of probabilistic logic programming for structure learning in bioinformatics, we undertook a simplified bacterial gene-finding benchmark in PRISM, a probabilistic dialect of Prolog. We evaluate Hidden Markov Model structures for bacterial protein-coding gene potential, including a simple null model structure, three structures based on existing bacterial gene finders and two novel model structures. We test standard versions as well as ADPH length modeling and three-state versions of the five model structures. The models are all represented as probabilistic logic programs and evaluated using the PRISM machine learning system in terms of statistical information criteria and gene-finding prediction accuracy, in two bacterial genomes. Neither of our implementations of the two currently most used model structures are best performing in terms of statistical information criteria or prediction performances, suggesting that better-fitting models might be achievable. The source code of all PRISM models, data and additional scripts are freely available for download at: http://github.com/somork/codonhmm. Supplementary data are available at Bioinformatics online.

Analysis of structural dynamic data from Skylab. Volume 1: Technical discussion

NASA Technical Reports Server (NTRS)

Demchak, L.; Harcrow, H.

1976-01-01

The results of a study to analyze data and document dynamic program highlights of the Skylab Program are presented. Included are structural model sources, illustration of the analytical models, utilization of models and the resultant derived data, data supplied to organization and subsequent utilization, and specifications of model cycles.

Modeling Smoke Plume-Rise and Dispersion from Southern United States Prescribed Burns with Daysmoke

Treesearch

G L Achtemeier; S L Goodrick; Y Liu; F Garcia-Menendez; Y Hu; M. Odman

2011-01-01

We present Daysmoke, an empirical-statistical plume rise and dispersion model for simulating smoke from prescribed burns. Prescribed fires are characterized by complex plume structure including multiple-core updrafts which makes modeling with simple plume models difficult. Daysmoke accounts for plume structure in a three-dimensional veering/sheering atmospheric...

Probabilistic Structural Analysis Methods (PSAM) for select space propulsion system structural components

NASA Technical Reports Server (NTRS)

Cruse, T. A.

1987-01-01

The objective is the development of several modular structural analysis packages capable of predicting the probabilistic response distribution for key structural variables such as maximum stress, natural frequencies, transient response, etc. The structural analysis packages are to include stochastic modeling of loads, material properties, geometry (tolerances), and boundary conditions. The solution is to be in terms of the cumulative probability of exceedance distribution (CDF) and confidence bounds. Two methods of probability modeling are to be included as well as three types of structural models - probabilistic finite-element method (PFEM); probabilistic approximate analysis methods (PAAM); and probabilistic boundary element methods (PBEM). The purpose in doing probabilistic structural analysis is to provide the designer with a more realistic ability to assess the importance of uncertainty in the response of a high performance structure. Probabilistic Structural Analysis Method (PSAM) tools will estimate structural safety and reliability, while providing the engineer with information on the confidence that should be given to the predicted behavior. Perhaps most critically, the PSAM results will directly provide information on the sensitivity of the design response to those variables which are seen to be uncertain.

Probabilistic Structural Analysis Methods for select space propulsion system structural components (PSAM)

NASA Technical Reports Server (NTRS)

Cruse, T. A.; Burnside, O. H.; Wu, Y.-T.; Polch, E. Z.; Dias, J. B.

1988-01-01

The objective is the development of several modular structural analysis packages capable of predicting the probabilistic response distribution for key structural variables such as maximum stress, natural frequencies, transient response, etc. The structural analysis packages are to include stochastic modeling of loads, material properties, geometry (tolerances), and boundary conditions. The solution is to be in terms of the cumulative probability of exceedance distribution (CDF) and confidence bounds. Two methods of probability modeling are to be included as well as three types of structural models - probabilistic finite-element method (PFEM); probabilistic approximate analysis methods (PAAM); and probabilistic boundary element methods (PBEM). The purpose in doing probabilistic structural analysis is to provide the designer with a more realistic ability to assess the importance of uncertainty in the response of a high performance structure. Probabilistic Structural Analysis Method (PSAM) tools will estimate structural safety and reliability, while providing the engineer with information on the confidence that should be given to the predicted behavior. Perhaps most critically, the PSAM results will directly provide information on the sensitivity of the design response to those variables which are seen to be uncertain.

Participatory modeling and structured decision making

USGS Publications Warehouse

Robinson, Kelly F.; Fuller, Angela K.

2016-01-01

Structured decision making (SDM) provides a framework for making sound decisions even when faced with uncertainty, and is a transparent, defensible, and replicable method used to understand complex problems. A hallmark of SDM is the explicit incorporation of values and science, which often includes participation from multiple stakeholders, helping to garner trust and ultimately result in a decision that is more likely to be implemented. The core steps in the SDM process are used to structure thinking about natural resources management choices, and include: (1) properly defining the problem and the decision context, (2) determining the objectives that help describe the aspirations of the decision maker, (3) devising management actions or alternatives that can achieve those objectives, (4) evaluating the outcomes or consequences of each alternative on each of the objectives, (5) evaluating trade-offs, and (6) implementing the decision. Participatory modeling for SDM includes engaging stakeholders in some or all of the steps of the SDM process listed above. In addition, participatory modeling often is crucial for creating qualitative and quantitative models of how the system works, providing data for these models, and eliciting expert opinion when data are unavailable. In these ways, SDM provides a framework for decision making in natural resources management that includes participation from stakeholder groups throughout the process, including the modeling phase.

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".

Computational Insights into the O2-evolving complex of photosystem II

PubMed Central

Sproviero, Eduardo M.; McEvoy, James P.; Gascón, José A.; Brudvig, Gary W.; Batista, Victor S.

2009-01-01

Mechanistic investigations of the water-splitting reaction of the oxygen-evolving complex (OEC) of photosystem II (PSII) are fundamentally informed by structural studies. Many physical techniques have provided important insights into the OEC structure and function, including X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy as well as mass spectrometry (MS), electron paramagnetic resonance (EPR) spectroscopy and Fourier transform infrared spectroscopy applied in conjunction with mutagenesis studies. However, experimental studies have yet to yield consensus as to the exact configuration of the catalytic metal cluster and its ligation scheme. Computational modeling studies, including density functional (DFT) theory combined with quantum mechanics/molecular mechanics (QM/MM) hybrid methods for explicitly including the influence of the surrounding protein, have proposed chemically satisfactory models of the fully ligated OEC within PSII that are maximally consistent with experimental results. The inorganic core of these models is similar to the crystallographic model upon which they were based but comprises important modifications due to structural refinement, hydration and proteinaceous ligation which improve agreement with a wide range of experimental data. The computational models are useful for rationalizing spectroscopic and crystallographic results and for building a complete structure-based mechanism of water-splitting in PSII as described by the intermediate oxidation states of the OEC. This review summarizes these recent advances in QM/MM modeling of PSII within the context of recent experimental studies. PMID:18483777

Visualization of RNA structure models within the Integrative Genomics Viewer.

PubMed

Busan, Steven; Weeks, Kevin M

2017-07-01

Analyses of the interrelationships between RNA structure and function are increasingly important components of genomic studies. The SHAPE-MaP strategy enables accurate RNA structure probing and realistic structure modeling of kilobase-length noncoding RNAs and mRNAs. Existing tools for visualizing RNA structure models are not suitable for efficient analysis of long, structurally heterogeneous RNAs. In addition, structure models are often advantageously interpreted in the context of other experimental data and gene annotation information, for which few tools currently exist. We have developed a module within the widely used and well supported open-source Integrative Genomics Viewer (IGV) that allows visualization of SHAPE and other chemical probing data, including raw reactivities, data-driven structural entropies, and data-constrained base-pair secondary structure models, in context with linear genomic data tracks. We illustrate the usefulness of visualizing RNA structure in the IGV by exploring structure models for a large viral RNA genome, comparing bacterial mRNA structure in cells with its structure under cell- and protein-free conditions, and comparing a noncoding RNA structure modeled using SHAPE data with a base-pairing model inferred through sequence covariation analysis. © 2017 Busan and Weeks; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Probabilistic structural analysis methods of hot engine structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Hopkins, D. A.

1989-01-01

Development of probabilistic structural analysis methods for hot engine structures is a major activity at Lewis Research Center. Recent activities have focused on extending the methods to include the combined uncertainties in several factors on structural response. This paper briefly describes recent progress on composite load spectra models, probabilistic finite element structural analysis, and probabilistic strength degradation modeling. Progress is described in terms of fundamental concepts, computer code development, and representative numerical results.

CFD-ACE+: a CAD system for simulation and modeling of MEMS

NASA Astrophysics Data System (ADS)

Stout, Phillip J.; Yang, H. Q.; Dionne, Paul; Leonard, Andy; Tan, Zhiqiang; Przekwas, Andrzej J.; Krishnan, Anantha

1999-03-01

Computer aided design (CAD) systems are a key to designing and manufacturing MEMS with higher performance/reliability, reduced costs, shorter prototyping cycles and improved time- to-market. One such system is CFD-ACE+MEMS, a modeling and simulation environment for MEMS which includes grid generation, data visualization, graphical problem setup, and coupled fluidic, thermal, mechanical, electrostatic, and magnetic physical models. The fluid model is a 3D multi- block, structured/unstructured/hybrid, pressure-based, implicit Navier-Stokes code with capabilities for multi- component diffusion, multi-species transport, multi-step gas phase chemical reactions, surface reactions, and multi-media conjugate heat transfer. The thermal model solves the total enthalpy from of the energy equation. The energy equation includes unsteady, convective, conductive, species energy, viscous dissipation, work, and radiation terms. The electrostatic model solves Poisson's equation. Both the finite volume method and the boundary element method (BEM) are available for solving Poisson's equation. The BEM method is useful for unbounded problems. The magnetic model solves for the vector magnetic potential from Maxwell's equations including eddy currents but neglecting displacement currents. The mechanical model is a finite element stress/deformation solver which has been coupled to the flow, heat, electrostatic, and magnetic calculations to study flow, thermal electrostatically, and magnetically included deformations of structures. The mechanical or structural model can accommodate elastic and plastic materials, can handle large non-linear displacements, and can model isotropic and anisotropic materials. The thermal- mechanical coupling involves the solution of the steady state Navier equation with thermoelastic deformation. The electrostatic-mechanical coupling is a calculation of the pressure force due to surface charge on the mechanical structure. Results of CFD-ACE+MEMS modeling of MEMS such as cantilever beams, accelerometers, and comb drives are discussed.

[Primary branch size of Pinus koraiensis plantation: a prediction based on linear mixed effect model].

PubMed

Dong, Ling-Bo; Liu, Zhao-Gang; Li, Feng-Ri; Jiang, Li-Chun

2013-09-01

By using the branch analysis data of 955 standard branches from 60 sampled trees in 12 sampling plots of Pinus koraiensis plantation in Mengjiagang Forest Farm in Heilongjiang Province of Northeast China, and based on the linear mixed-effect model theory and methods, the models for predicting branch variables, including primary branch diameter, length, and angle, were developed. Considering tree effect, the MIXED module of SAS software was used to fit the prediction models. The results indicated that the fitting precision of the models could be improved by choosing appropriate random-effect parameters and variance-covariance structure. Then, the correlation structures including complex symmetry structure (CS), first-order autoregressive structure [AR(1)], and first-order autoregressive and moving average structure [ARMA(1,1)] were added to the optimal branch size mixed-effect model. The AR(1) improved the fitting precision of branch diameter and length mixed-effect model significantly, but all the three structures didn't improve the precision of branch angle mixed-effect model. In order to describe the heteroscedasticity during building mixed-effect model, the CF1 and CF2 functions were added to the branch mixed-effect model. CF1 function improved the fitting effect of branch angle mixed model significantly, whereas CF2 function improved the fitting effect of branch diameter and length mixed model significantly. Model validation confirmed that the mixed-effect model could improve the precision of prediction, as compare to the traditional regression model for the branch size prediction of Pinus koraiensis plantation.

Progressive Damage Analysis of Bonded Composite Joints

NASA Technical Reports Server (NTRS)

Leone, Frank A., Jr.; Girolamo, Donato; Davila, Carlos G.

2012-01-01

The present work is related to the development and application of progressive damage modeling techniques to bonded joint technology. The joint designs studied in this work include a conventional composite splice joint and a NASA-patented durable redundant joint. Both designs involve honeycomb sandwich structures with carbon/epoxy facesheets joined using adhesively bonded doublers.Progressive damage modeling allows for the prediction of the initiation and evolution of damage within a structure. For structures that include multiple material systems, such as the joint designs under consideration, the number of potential failure mechanisms that must be accounted for drastically increases the complexity of the analyses. Potential failure mechanisms include fiber fracture, intraply matrix cracking, delamination, core crushing, adhesive failure, and their interactions. The bonded joints were modeled using highly parametric, explicitly solved finite element models, with damage modeling implemented via custom user-written subroutines. Each ply was discretely meshed using three-dimensional solid elements. Layers of cohesive elements were included between each ply to account for the possibility of delaminations and were used to model the adhesive layers forming the joint. Good correlation with experimental results was achieved both in terms of load-displacement history and the predicted failure mechanism(s).

Parameterization of Model Validating Sets for Uncertainty Bound Optimizations. Revised

NASA Technical Reports Server (NTRS)

Lim, K. B.; Giesy, D. P.

2000-01-01

Given measurement data, a nominal model and a linear fractional transformation uncertainty structure with an allowance on unknown but bounded exogenous disturbances, easily computable tests for the existence of a model validating uncertainty set are given. Under mild conditions, these tests are necessary and sufficient for the case of complex, nonrepeated, block-diagonal structure. For the more general case which includes repeated and/or real scalar uncertainties, the tests are only necessary but become sufficient if a collinearity condition is also satisfied. With the satisfaction of these tests, it is shown that a parameterization of all model validating sets of plant models is possible. The new parameterization is used as a basis for a systematic way to construct or perform uncertainty tradeoff with model validating uncertainty sets which have specific linear fractional transformation structure for use in robust control design and analysis. An illustrative example which includes a comparison of candidate model validating sets is given.

Engineering 3D Models of Tumors and Bone to Understand Tumor-Induced Bone Disease and Improve Treatments.

PubMed

Kwakwa, Kristin A; Vanderburgh, Joseph P; Guelcher, Scott A; Sterling, Julie A

2017-08-01

Bone is a structurally unique microenvironment that presents many challenges for the development of 3D models for studying bone physiology and diseases, including cancer. As researchers continue to investigate the interactions within the bone microenvironment, the development of 3D models of bone has become critical. 3D models have been developed that replicate some properties of bone, but have not fully reproduced the complex structural and cellular composition of the bone microenvironment. This review will discuss 3D models including polyurethane, silk, and collagen scaffolds that have been developed to study tumor-induced bone disease. In addition, we discuss 3D printing techniques used to better replicate the structure of bone. 3D models that better replicate the bone microenvironment will help researchers better understand the dynamic interactions between tumors and the bone microenvironment, ultimately leading to better models for testing therapeutics and predicting patient outcomes.

Ecosystem size structure response to 21st century climate projection: large fish abundance decreases in the central North Pacific and increases in the California Current.

PubMed

Woodworth-Jefcoats, Phoebe A; Polovina, Jeffrey J; Dunne, John P; Blanchard, Julia L

2013-03-01

Output from an earth system model is paired with a size-based food web model to investigate the effects of climate change on the abundance of large fish over the 21st century. The earth system model, forced by the Intergovernmental Panel on Climate Change (IPCC) Special report on emission scenario A2, combines a coupled climate model with a biogeochemical model including major nutrients, three phytoplankton functional groups, and zooplankton grazing. The size-based food web model includes linkages between two size-structured pelagic communities: primary producers and consumers. Our investigation focuses on seven sites in the North Pacific, each highlighting a specific aspect of projected climate change, and includes top-down ecosystem depletion through fishing. We project declines in large fish abundance ranging from 0 to 75.8% in the central North Pacific and increases of up to 43.0% in the California Current (CC) region over the 21st century in response to change in phytoplankton size structure and direct physiological effects. We find that fish abundance is especially sensitive to projected changes in large phytoplankton density and our model projects changes in the abundance of large fish being of the same order of magnitude as changes in the abundance of large phytoplankton. Thus, studies that address only climate-induced impacts to primary production without including changes to phytoplankton size structure may not adequately project ecosystem responses. © 2012 Blackwell Publishing Ltd.

Characterizing Uncertainty and Variability in PBPK Models ...

EPA Pesticide Factsheets

Mode-of-action based risk and safety assessments can rely upon tissue dosimetry estimates in animals and humans obtained from physiologically-based pharmacokinetic (PBPK) modeling. However, risk assessment also increasingly requires characterization of uncertainty and variability; such characterization for PBPK model predictions represents a continuing challenge to both modelers and users. Current practices show significant progress in specifying deterministic biological models and the non-deterministic (often statistical) models, estimating their parameters using diverse data sets from multiple sources, and using them to make predictions and characterize uncertainty and variability. The International Workshop on Uncertainty and Variability in PBPK Models, held Oct 31-Nov 2, 2006, sought to identify the state-of-the-science in this area and recommend priorities for research and changes in practice and implementation. For the short term, these include: (1) multidisciplinary teams to integrate deterministic and non-deterministic/statistical models; (2) broader use of sensitivity analyses, including for structural and global (rather than local) parameter changes; and (3) enhanced transparency and reproducibility through more complete documentation of the model structure(s) and parameter values, the results of sensitivity and other analyses, and supporting, discrepant, or excluded data. Longer-term needs include: (1) theoretic and practical methodological impro

An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization

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

Hinckley, Daniel M.; Freeman, Gordon S.; Whitmer, Jonathan K.

2013-10-14

A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model includes anisotropic potentials between bases involved in base stacking and base pair interactions that enable the description of relevant structural properties, including the major and minor grooves. In an improvement over available coarse-grained models, the correct persistence length is recovered for both ssDNA and dsDNA, allowing for simulation of non-canonical structures such as hairpins. DNA melting temperatures, measured for duplexes and hairpins by integrating over free energy surfaces generated using metadynamics simulations, are shown to be in quantitative agreement with experiment for a variety of sequences and conditions. Hybridizationmore » rate constants, calculated using forward-flux sampling, are also shown to be in good agreement with experiment. The coarse-grained model presented here is suitable for use in biological and engineering applications, including nucleosome positioning and DNA-templated engineering.« less

Methods for evaluating the predictive accuracy of structural dynamic models

NASA Technical Reports Server (NTRS)

Hasselman, Timothy K.; Chrostowski, Jon D.

1991-01-01

Modeling uncertainty is defined in terms of the difference between predicted and measured eigenvalues and eigenvectors. Data compiled from 22 sets of analysis/test results was used to create statistical databases for large truss-type space structures and both pretest and posttest models of conventional satellite-type space structures. Modeling uncertainty is propagated through the model to produce intervals of uncertainty on frequency response functions, both amplitude and phase. This methodology was used successfully to evaluate the predictive accuracy of several structures, including the NASA CSI Evolutionary Structure tested at Langley Research Center. Test measurements for this structure were within + one-sigma intervals of predicted accuracy for the most part, demonstrating the validity of the methodology and computer code.

Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots.

PubMed

Hajdin, Christine E; Bellaousov, Stanislav; Huggins, Wayne; Leonard, Christopher W; Mathews, David H; Weeks, Kevin M

2013-04-02

A pseudoknot forms in an RNA when nucleotides in a loop pair with a region outside the helices that close the loop. Pseudoknots occur relatively rarely in RNA but are highly overrepresented in functionally critical motifs in large catalytic RNAs, in riboswitches, and in regulatory elements of viruses. Pseudoknots are usually excluded from RNA structure prediction algorithms. When included, these pairings are difficult to model accurately, especially in large RNAs, because allowing this structure dramatically increases the number of possible incorrect folds and because it is difficult to search the fold space for an optimal structure. We have developed a concise secondary structure modeling approach that combines SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) experimental chemical probing information and a simple, but robust, energy model for the entropic cost of single pseudoknot formation. Structures are predicted with iterative refinement, using a dynamic programming algorithm. This melded experimental and thermodynamic energy function predicted the secondary structures and the pseudoknots for a set of 21 challenging RNAs of known structure ranging in size from 34 to 530 nt. On average, 93% of known base pairs were predicted, and all pseudoknots in well-folded RNAs were identified.

The Folding Energy Landscape and Free Energy Excitations of Cytochrome c

PubMed Central

Weinkam, Patrick; Zimmermann, Jörg; Romesberg, Floyd E.

2014-01-01

The covalently bound heme cofactor plays a dominant role in the folding of cytochrome c. Due to the complicated inorganic chemistry of the heme, some might consider the folding of cytochrome c to be a special case that follows different principles than those used to describe folding of proteins without cofactors. Recent investigations, however, demonstrate that models which are commonly used to describe folding for many proteins work well for cytochrome c when heme is explicitly introduced and generally provide results that agree with experimental observations. We will first discuss results from simple native structure-based models. These models include attractive interactions between nonadjacent residues only if they are present in the crystal structure at pH 7. Since attractive nonnative contacts are not included in native structure-based models, their energy landscapes can be described as “perfectly funneled.” In other words, native structure-based models are energetically guided towards the native state and contain no energetic traps that would hinder folding. Energetic traps are sources of frustration which cause specific transient intermediates to be populated. Native structure-based models do include repulsion between residues due to excluded volume. Nonenergetic traps can therefore exist if the chain, which cannot cross over itself, must partially unfold in order for folding to proceed. The ability of native structure-based models to capture these type of motions is in part responsible for their successful predictions of folding pathways for many types of proteins. Models without frustration describe well the sequence of folding events for cytochrome c inferred from hydrogen exchange experiments thereby justifying their use as a starting point. At low pH, the folding sequence of cytochrome c deviates from that at pH 7 and from those predicted from models with perfectly funneled energy landscapes. Alternate folding pathways are a result of “chemical frustration.” This frustration arises because some regions of the protein are destabilized more than others due to the heterogeneous distribution of titratable residues that are protonated at low pH. We construct more complex models that include chemical frustration, in addition to the native structure-based terms. These more complex models only modestly perturb the energy landscape which remains overall well funneled. These perturbed models can accurately describe how alternative folding pathways are used at low pH. At alkaline pH, cytochrome c populates distinctly different structural ensembles. For instance, lysine residues are deprotonated and compete for the heme ligation site. The same models that can describe folding at low pH also predict well the structures and relative stabilities of intermediates populated at alkaline pH. PMID:20143816

A discourse on sensitivity analysis for discretely-modeled structures

NASA Technical Reports Server (NTRS)

Adelman, Howard M.; Haftka, Raphael T.

1991-01-01

A descriptive review is presented of the most recent methods for performing sensitivity analysis of the structural behavior of discretely-modeled systems. The methods are generally but not exclusively aimed at finite element modeled structures. Topics included are: selections of finite difference step sizes; special consideration for finite difference sensitivity of iteratively-solved response problems; first and second derivatives of static structural response; sensitivity of stresses; nonlinear static response sensitivity; eigenvalue and eigenvector sensitivities for both distinct and repeated eigenvalues; and sensitivity of transient response for both linear and nonlinear structural response.

Research in structures, structural dynamics and materials, 1989

NASA Technical Reports Server (NTRS)

Hunter, William F. (Compiler); Noor, Ahmed K. (Compiler)

1989-01-01

Topics addressed include: composite plates; buckling predictions; missile launch tube modeling; structural/control systems design; optimization of nonlinear R/C frames; error analysis for semi-analytic displacement; crack acoustic emission; and structural dynamics.

Multiplicity Control in Structural Equation Modeling: Incorporating Parameter Dependencies

ERIC Educational Resources Information Center

Smith, Carrie E.; Cribbie, Robert A.

2013-01-01

When structural equation modeling (SEM) analyses are conducted, significance tests for all important model relationships (parameters including factor loadings, covariances, etc.) are typically conducted at a specified nominal Type I error rate ([alpha]). Despite the fact that many significance tests are often conducted in SEM, rarely is…

A Structural Equation Model of Expertise in College Physics

ERIC Educational Resources Information Center

Taasoobshirazi, Gita; Carr, Martha

2009-01-01

A model of expertise in physics was tested on a sample of 374 college students in 2 different level physics courses. Structural equation modeling was used to test hypothesized relationships among variables linked to expert performance in physics including strategy use, pictorial representation, categorization skills, and motivation, and these…

A Structural Equation Model of Conceptual Change in Physics

ERIC Educational Resources Information Center

Taasoobshirazi, Gita; Sinatra, Gale M.

2011-01-01

A model of conceptual change in physics was tested on introductory-level, college physics students. Structural equation modeling was used to test hypothesized relationships among variables linked to conceptual change in physics including an approach goal orientation, need for cognition, motivation, and course grade. Conceptual change in physics…

Three Approaches to Using Lengthy Ordinal Scales in Structural Equation Models: Parceling, Latent Scoring, and Shortening Scales

ERIC Educational Resources Information Center

Yang, Chongming; Nay, Sandra; Hoyle, Rick H.

2010-01-01

Lengthy scales or testlets pose certain challenges for structural equation modeling (SEM) if all the items are included as indicators of a latent construct. Three general approaches to modeling lengthy scales in SEM (parceling, latent scoring, and shortening) have been reviewed and evaluated. A hypothetical population model is simulated containing…

Text Extraction from Scene Images by Character Appearance and Structure Modeling

PubMed Central

Yi, Chucai; Tian, Yingli

2012-01-01

In this paper, we propose a novel algorithm to detect text information from natural scene images. Scene text classification and detection are still open research topics. Our proposed algorithm is able to model both character appearance and structure to generate representative and discriminative text descriptors. The contributions of this paper include three aspects: 1) a new character appearance model by a structure correlation algorithm which extracts discriminative appearance features from detected interest points of character samples; 2) a new text descriptor based on structons and correlatons, which model character structure by structure differences among character samples and structure component co-occurrence; and 3) a new text region localization method by combining color decomposition, character contour refinement, and string line alignment to localize character candidates and refine detected text regions. We perform three groups of experiments to evaluate the effectiveness of our proposed algorithm, including text classification, text detection, and character identification. The evaluation results on benchmark datasets demonstrate that our algorithm achieves the state-of-the-art performance on scene text classification and detection, and significantly outperforms the existing algorithms for character identification. PMID:23316111

GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors

PubMed Central

Esguerra, Mauricio; Siretskiy, Alexey; Bello, Xabier; Sallander, Jessica; Gutiérrez-de-Terán, Hugo

2016-01-01

GPCR-ModSim (http://open.gpcr-modsim.org) is a centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs). 3D molecular models can be generated from amino acid sequence by homology-modeling techniques, considering different receptor conformations. GPCR-ModSim includes a membrane insertion and molecular dynamics (MD) equilibration protocol, which can be used to refine the generated model or any GPCR structure uploaded to the server, including if desired non-protein elements such as orthosteric or allosteric ligands, structural waters or ions. We herein revise the main characteristics of GPCR-ModSim and present new functionalities. The templates used for homology modeling have been updated considering the latest structural data, with separate profile structural alignments built for inactive, partially-active and active groups of templates. We have also added the possibility to perform multiple-template homology modeling in a unique and flexible way. Finally, our new MD protocol considers a series of distance restraints derived from a recently identified conserved network of helical contacts, allowing for a smoother refinement of the generated models which is particularly advised when there is low homology to the available templates. GPCR- ModSim has been tested on the GPCR Dock 2013 competition with satisfactory results. PMID:27166369

Modeling and Circumventing the Effect of Sediments and Water Column on Receiver Functions

NASA Astrophysics Data System (ADS)

Audet, P.

2017-12-01

Teleseismic P-wave receiver functions are routinely used to resolve crust and mantle structure in various geologic settings. Receiver functions are approximations to the Earth's Green's functions and are composed of various scattered phase arrivals, depending on the complexity of the underlying Earth structure. For simple structure, the dominant arrivals (converted and back-scattered P-to-S phases) are well separated in time and can be reliably used in estimating crustal velocity structure. In the presence of sedimentary layers, strong reverberations typically produce high-amplitude oscillations that contaminate the early part of the wave train and receiver functions can be difficult to interpret in terms of underlying structure. The effect of a water column also limits the interpretability of under-water receiver functions due to the additional acoustic wave propagating within the water column that can contaminate structural arrivals. We perform numerical modeling of teleseismic Green's functions and receiver functions using a reflectivity technique for a range of Earth models that include thin sedimentary layers and overlying water column. These modeling results indicate that, as expected, receiver functions are difficult to interpret in the presence of sediments, but the contaminating effect of the water column is dependent on the thickness of the water layer. To circumvent these effects and recover source-side structure, we propose using an approach based on transfer function modeling that bypasses receiver functions altogether and estimates crustal properties directly from the waveforms (Frederiksen and Delayney, 2015). Using this approach, reasonable assumptions about the properties of the sedimentary layer can be included in forward calculations of the Green's functions that are convolved with radial waveforms to predict vertical waveforms. Exploration of model space using Monte Carlo-style search and least-square waveform misfits can be performed to estimate any model parameter of interest, including those of the sedimentary or water layer. We show how this method can be applied to OBS data using broadband stations from the Cascadia Initiative to recover oceanic plate structure.

Buckling analysis of SMA bonded sandwich structure – using FEM

NASA Astrophysics Data System (ADS)

Katariya, Pankaj V.; Das, Arijit; Panda, Subrata K.

2018-03-01

Thermal buckling strength of smart sandwich composite structure (bonded with shape memory alloy; SMA) examined numerically via a higher-order finite element model in association with marching technique. The excess geometrical distortion of the structure under the elevated environment modeled through Green’s strain function whereas the material nonlinearity counted with the help of marching method. The system responses are computed numerically by solving the generalized eigenvalue equations via a customized MATLAB code. The comprehensive behaviour of the current finite element solutions (minimum buckling load parameter) is established by solving the adequate number of numerical examples including the given input parameter. The current numerical model is extended further to check the influence of various structural parameter of the sandwich panel on the buckling temperature including the SMA effect and reported in details.

Factors Influencing Progressive Failure Analysis Predictions for Laminated Composite Structure

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.

2008-01-01

Progressive failure material modeling methods used for structural analysis including failure initiation and material degradation are presented. Different failure initiation criteria and material degradation models are described that define progressive failure formulations. These progressive failure formulations are implemented in a user-defined material model for use with a nonlinear finite element analysis tool. The failure initiation criteria include the maximum stress criteria, maximum strain criteria, the Tsai-Wu failure polynomial, and the Hashin criteria. The material degradation model is based on the ply-discounting approach where the local material constitutive coefficients are degraded. Applications and extensions of the progressive failure analysis material model address two-dimensional plate and shell finite elements and three-dimensional solid finite elements. Implementation details are described in the present paper. Parametric studies for laminated composite structures are discussed to illustrate the features of the progressive failure modeling methods that have been implemented and to demonstrate their influence on progressive failure analysis predictions.

RACER a Coarse-Grained RNA Model for Capturing Folding Free Energy in Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Cheng, Sara; Bell, David; Ren, Pengyu

RACER is a coarse-grained RNA model that can be used in molecular dynamics simulations to predict native structures and sequence-specific variation of free energy of various RNA structures. RACER is capable of accurate prediction of native structures of duplexes and hairpins (average RMSD of 4.15 angstroms), and RACER can capture sequence-specific variation of free energy in excellent agreement with experimentally measured stabilities (r-squared =0.98). The RACER model implements a new effective non-bonded potential and re-parameterization of hydrogen bond and Debye-Huckel potentials. Insights from the RACER model include the importance of treating pairing and stacking interactions separately in order to distinguish folded an unfolded states and identification of hydrogen-bonding, base stacking, and electrostatic interactions as essential driving forces for RNA folding. Future applications of the RACER model include predicting free energy landscapes of more complex RNA structures and use of RACER for multiscale simulations.

Frequency Response Function Based Damage Identification for Aerospace Structures

NASA Astrophysics Data System (ADS)

Oliver, Joseph Acton

Structural health monitoring technologies continue to be pursued for aerospace structures in the interests of increased safety and, when combined with health prognosis, efficiency in life-cycle management. The current dissertation develops and validates damage identification technology as a critical component for structural health monitoring of aerospace structures and, in particular, composite unmanned aerial vehicles. The primary innovation is a statistical least-squares damage identification algorithm based in concepts of parameter estimation and model update. The algorithm uses frequency response function based residual force vectors derived from distributed vibration measurements to update a structural finite element model through statistically weighted least-squares minimization producing location and quantification of the damage, estimation uncertainty, and an updated model. Advantages compared to other approaches include robust applicability to systems which are heavily damped, large, and noisy, with a relatively low number of distributed measurement points compared to the number of analytical degrees-of-freedom of an associated analytical structural model (e.g., modal finite element model). Motivation, research objectives, and a dissertation summary are discussed in Chapter 1 followed by a literature review in Chapter 2. Chapter 3 gives background theory and the damage identification algorithm derivation followed by a study of fundamental algorithm behavior on a two degree-of-freedom mass-spring system with generalized damping. Chapter 4 investigates the impact of noise then successfully proves the algorithm against competing methods using an analytical eight degree-of-freedom mass-spring system with non-proportional structural damping. Chapter 5 extends use of the algorithm to finite element models, including solutions for numerical issues, approaches for modeling damping approximately in reduced coordinates, and analytical validation using a composite sandwich plate model. Chapter 6 presents the final extension to experimental systems-including methods for initial baseline correlation and data reduction-and validates the algorithm on an experimental composite plate with impact damage. The final chapter deviates from development and validation of the primary algorithm to discuss development of an experimental scaled-wing test bed as part of a collaborative effort for developing structural health monitoring and prognosis technology. The dissertation concludes with an overview of technical conclusions and recommendations for future work.

Probing Xist RNA Structure in Cells Using Targeted Structure-Seq

PubMed Central

Rutenberg-Schoenberg, Michael; Simon, Matthew D.

2015-01-01

The long non-coding RNA (lncRNA) Xist is a master regulator of X-chromosome inactivation in mammalian cells. Models for how Xist and other lncRNAs function depend on thermodynamically stable secondary and higher-order structures that RNAs can form in the context of a cell. Probing accessible RNA bases can provide data to build models of RNA conformation that provide insight into RNA function, molecular evolution, and modularity. To study the structure of Xist in cells, we built upon recent advances in RNA secondary structure mapping and modeling to develop Targeted Structure-Seq, which combines chemical probing of RNA structure in cells with target-specific massively parallel sequencing. By enriching for signals from the RNA of interest, Targeted Structure-Seq achieves high coverage of the target RNA with relatively few sequencing reads, thus providing a targeted and scalable approach to analyze RNA conformation in cells. We use this approach to probe the full-length Xist lncRNA to develop new models for functional elements within Xist, including the repeat A element in the 5’-end of Xist. This analysis also identified new structural elements in Xist that are evolutionarily conserved, including a new element proximal to the C repeats that is important for Xist function. PMID:26646615

Twilight reloaded: the peptide experience

PubMed Central

Weichenberger, Christian X.; Pozharski, Edwin; Rupp, Bernhard

2017-01-01

The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallo­graphic studies of biomolecules with reasonably valid outcomes: that is, models based on properly interpreted electron density. Robust validation has led to major mistakes in the protein part of structure models becoming rare, but some depositions of protein–peptide complex structure models, which generally carry significant interest to the scientific community, still contain erroneous models of the bound peptide ligand. Here, the protein small-molecule ligand validation tool Twilight is updated to include peptide ligands. (i) The primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) a new method used to score peptide-ligand models is presented; (iii) a few instructive and specific examples, including an electron-density-based analysis of peptide-ligand structures that do not contain any ligands, are discussed in detail; (iv) means to avoid such mistakes and the implications for database integrity are discussed and (v) some suggestions as to how journal editors could help to expunge errors from the Protein Data Bank are provided. PMID:28291756

Twilight reloaded: the peptide experience.

PubMed

Weichenberger, Christian X; Pozharski, Edwin; Rupp, Bernhard

2017-03-01

The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallographic studies of biomolecules with reasonably valid outcomes: that is, models based on properly interpreted electron density. Robust validation has led to major mistakes in the protein part of structure models becoming rare, but some depositions of protein-peptide complex structure models, which generally carry significant interest to the scientific community, still contain erroneous models of the bound peptide ligand. Here, the protein small-molecule ligand validation tool Twilight is updated to include peptide ligands. (i) The primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) a new method used to score peptide-ligand models is presented; (iii) a few instructive and specific examples, including an electron-density-based analysis of peptide-ligand structures that do not contain any ligands, are discussed in detail; (iv) means to avoid such mistakes and the implications for database integrity are discussed and (v) some suggestions as to how journal editors could help to expunge errors from the Protein Data Bank are provided.

An automated curation procedure for addressing chemical errors and inconsistencies in public datasets used in QSAR modelling.

PubMed

Mansouri, K; Grulke, C M; Richard, A M; Judson, R S; Williams, A J

2016-11-01

The increasing availability of large collections of chemical structures and associated experimental data provides an opportunity to build robust QSAR models for applications in different fields. One common concern is the quality of both the chemical structure information and associated experimental data. Here we describe the development of an automated KNIME workflow to curate and correct errors in the structure and identity of chemicals using the publicly available PHYSPROP physicochemical properties and environmental fate datasets. The workflow first assembles structure-identity pairs using up to four provided chemical identifiers, including chemical name, CASRNs, SMILES, and MolBlock. Problems detected included errors and mismatches in chemical structure formats, identifiers and various structure validation issues, including hypervalency and stereochemistry descriptions. Subsequently, a machine learning procedure was applied to evaluate the impact of this curation process. The performance of QSAR models built on only the highest-quality subset of the original dataset was compared with the larger curated and corrected dataset. The latter showed statistically improved predictive performance. The final workflow was used to curate the full list of PHYSPROP datasets, and is being made publicly available for further usage and integration by the scientific community.

Chemistry Notes.

ERIC Educational Resources Information Center

School Science Review, 1982

1982-01-01

Discusses laboratory procedures, classroom materials, and demonstrations including: a model for metallic/ionic structures; Friedel-Crafts acylation reaction; aids to teaching crystal structure; a metal displacement project; silver recovery from fixer and silver residues; iodine sublimation; nature of acids; card models for teaching bonding; and…

Bridging gaps: On the performance of airborne LiDAR to model wood mouse-habitat structure relationships in pine forests.

PubMed

Jaime-González, Carlos; Acebes, Pablo; Mateos, Ana; Mezquida, Eduardo T

2017-01-01

LiDAR technology has firmly contributed to strengthen the knowledge of habitat structure-wildlife relationships, though there is an evident bias towards flying vertebrates. To bridge this gap, we investigated and compared the performance of LiDAR and field data to model habitat preferences of wood mouse (Apodemus sylvaticus) in a Mediterranean high mountain pine forest (Pinus sylvestris). We recorded nine field and 13 LiDAR variables that were summarized by means of Principal Component Analyses (PCA). We then analyzed wood mouse's habitat preferences using three different models based on: (i) field PCs predictors, (ii) LiDAR PCs predictors; and (iii) both set of predictors in a combined model, including a variance partitioning analysis. Elevation was also included as a predictor in the three models. Our results indicate that LiDAR derived variables were better predictors than field-based variables. The model combining both data sets slightly improved the predictive power of the model. Field derived variables indicated that wood mouse was positively influenced by the gradient of increasing shrub cover and negatively affected by elevation. Regarding LiDAR data, two LiDAR PCs, i.e. gradients in canopy openness and complexity in forest vertical structure positively influenced wood mouse, although elevation interacted negatively with the complexity in vertical structure, indicating wood mouse's preferences for plots with lower elevations but with complex forest vertical structure. The combined model was similar to the LiDAR-based model and included the gradient of shrub cover measured in the field. Variance partitioning showed that LiDAR-based variables, together with elevation, were the most important predictors and that part of the variation explained by shrub cover was shared. LiDAR derived variables were good surrogates of environmental characteristics explaining habitat preferences by the wood mouse. Our LiDAR metrics represented structural features of the forest patch, such as the presence and cover of shrubs, as well as other characteristics likely including time since perturbation, food availability and predation risk. Our results suggest that LiDAR is a promising technology for further exploring habitat preferences by small mammal communities.

Acoustic Modeling of Lightweight Structures: A Literature Review

NASA Astrophysics Data System (ADS)

Yang, Shasha; Shen, Cheng

2017-10-01

This paper gives an overview of acoustic modeling for three kinds of typical lightweight structures including double-leaf plate system, stiffened single (or double) plate and porous material. Classical models are citied to provide frame work of theoretical modeling for acoustic property of lightweight structures; important research advances derived by our research group and other authors are introduced to describe the current state of art for acoustic research. Finally, remaining problems and future research directions are concluded and prospected briefly

Model for dynamic self-assembled magnetic surface structures

NASA Astrophysics Data System (ADS)

Belkin, M.; Glatz, A.; Snezhko, A.; Aranson, I. S.

2010-07-01

We propose a first-principles model for the dynamic self-assembly of magnetic structures at a water-air interface reported in earlier experiments. The model is based on the Navier-Stokes equation for liquids in shallow water approximation coupled to Newton equations for interacting magnetic particles suspended at a water-air interface. The model reproduces most of the observed phenomenology, including spontaneous formation of magnetic snakelike structures, generation of large-scale vortex flows, complex ferromagnetic-antiferromagnetic ordering of the snake, and self-propulsion of bead-snake hybrids.

High Speed Research Program Structural Acoustics Multi-Year Summary Report

NASA Technical Reports Server (NTRS)

Beier, Theodor H.; Bhat, Waman V.; Rizzi, Stephen A.; Silcox, Richard J.; Simpson, Myles A.

2005-01-01

This report summarizes the work conducted by the Structural Acoustics Integrated Technology Development (ITD) Team under NASA's High Speed Research (HSR) Phase II program from 1993 to 1999. It is intended to serve as a reference for future researchers by documenting the results of the interior noise and sonic fatigue technology development activities conducted during this period. For interior noise, these activities included excitation modeling, structural acoustic response modeling, development of passive treatments and active controls, and prediction of interior noise. For sonic fatigue, these activities included loads prediction, materials characterization, sonic fatigue code development, development of response reduction techniques, and generation of sonic fatigue design requirements. Also included are lessons learned and recommendations for future work.

Update to core reporting practices in structural equation modeling.

PubMed

Schreiber, James B

This paper is a technical update to "Core Reporting Practices in Structural Equation Modeling." 1 As such, the content covered in this paper includes, sample size, missing data, specification and identification of models, estimation method choices, fit and residual concerns, nested, alternative, and equivalent models, and unique issues within the SEM family of techniques. Copyright © 2016 Elsevier Inc. All rights reserved.

The numerics of hydrostatic structured-grid coastal ocean models: State of the art and future perspectives

NASA Astrophysics Data System (ADS)

Klingbeil, Knut; Lemarié, Florian; Debreu, Laurent; Burchard, Hans

2018-05-01

The state of the art of the numerics of hydrostatic structured-grid coastal ocean models is reviewed here. First, some fundamental differences in the hydrodynamics of the coastal ocean, such as the large surface elevation variation compared to the mean water depth, are contrasted against large scale ocean dynamics. Then the hydrodynamic equations as they are used in coastal ocean models as well as in large scale ocean models are presented, including parameterisations for turbulent transports. As steps towards discretisation, coordinate transformations and spatial discretisations based on a finite-volume approach are discussed with focus on the specific requirements for coastal ocean models. As in large scale ocean models, splitting of internal and external modes is essential also for coastal ocean models, but specific care is needed when drying & flooding of intertidal flats is included. As one obvious characteristic of coastal ocean models, open boundaries occur and need to be treated in a way that correct model forcing from outside is transmitted to the model domain without reflecting waves from the inside. Here, also new developments in two-way nesting are presented. Single processes such as internal inertia-gravity waves, advection and turbulence closure models are discussed with focus on the coastal scales. Some overview on existing hydrostatic structured-grid coastal ocean models is given, including their extensions towards non-hydrostatic models. Finally, an outlook on future perspectives is made.

Progressive Damage Modeling of Durable Bonded Joint Technology

NASA Technical Reports Server (NTRS)

Leone, Frank A.; Davila, Carlos G.; Lin, Shih-Yung; Smeltzer, Stan; Girolamo, Donato; Ghose, Sayata; Guzman, Juan C.; McCarville, Duglas A.

2013-01-01

The development of durable bonded joint technology for assembling composite structures for launch vehicles is being pursued for the U.S. Space Launch System. The present work is related to the development and application of progressive damage modeling techniques to bonded joint technology applicable to a wide range of sandwich structures for a Heavy Lift Launch Vehicle. The joint designs studied in this work include a conventional composite splice joint and a NASA-patented Durable Redundant Joint. Both designs involve a honeycomb sandwich with carbon/epoxy facesheets joined with adhesively bonded doublers. Progressive damage modeling allows for the prediction of the initiation and evolution of damage. For structures that include multiple materials, the number of potential failure mechanisms that must be considered increases the complexity of the analyses. Potential failure mechanisms include fiber fracture, matrix cracking, delamination, core crushing, adhesive failure, and their interactions. The joints were modeled using Abaqus parametric finite element models, in which damage was modeled with user-written subroutines. Each ply was meshed discretely, and layers of cohesive elements were used to account for delaminations and to model the adhesive layers. Good correlation with experimental results was achieved both in terms of load-displacement history and predicted failure mechanisms.

Applications of Artificial Neural Networks in Structural Engineering with Emphasis on Continuum Models

NASA Technical Reports Server (NTRS)

Kapania, Rakesh K.; Liu, Youhua

1998-01-01

The use of continuum models for the analysis of discrete built-up complex aerospace structures is an attractive idea especially at the conceptual and preliminary design stages. But the diversity of available continuum models and hard-to-use qualities of these models have prevented them from finding wide applications. In this regard, Artificial Neural Networks (ANN or NN) may have a great potential as these networks are universal approximators that can realize any continuous mapping, and can provide general mechanisms for building models from data whose input-output relationship can be highly nonlinear. The ultimate aim of the present work is to be able to build high fidelity continuum models for complex aerospace structures using the ANN. As a first step, the concepts and features of ANN are familiarized through the MATLAB NN Toolbox by simulating some representative mapping examples, including some problems in structural engineering. Then some further aspects and lessons learned about the NN training are discussed, including the performances of Feed-Forward and Radial Basis Function NN when dealing with noise-polluted data and the technique of cross-validation. Finally, as an example of using NN in continuum models, a lattice structure with repeating cells is represented by a continuum beam whose properties are provided by neural networks.

Exploring Human Diseases and Biological Mechanisms by Protein Structure Prediction and Modeling.

PubMed

Wang, Juexin; Luttrell, Joseph; Zhang, Ning; Khan, Saad; Shi, NianQing; Wang, Michael X; Kang, Jing-Qiong; Wang, Zheng; Xu, Dong

2016-01-01

Protein structure prediction and modeling provide a tool for understanding protein functions by computationally constructing protein structures from amino acid sequences and analyzing them. With help from protein prediction tools and web servers, users can obtain the three-dimensional protein structure models and gain knowledge of functions from the proteins. In this chapter, we will provide several examples of such studies. As an example, structure modeling methods were used to investigate the relation between mutation-caused misfolding of protein and human diseases including epilepsy and leukemia. Protein structure prediction and modeling were also applied in nucleotide-gated channels and their interaction interfaces to investigate their roles in brain and heart cells. In molecular mechanism studies of plants, rice salinity tolerance mechanism was studied via structure modeling on crucial proteins identified by systems biology analysis; trait-associated protein-protein interactions were modeled, which sheds some light on the roles of mutations in soybean oil/protein content. In the age of precision medicine, we believe protein structure prediction and modeling will play more and more important roles in investigating biomedical mechanism of diseases and drug design.

Estimating the Uncertain Mathematical Structure of Hydrological Model via Bayesian Data Assimilation

NASA Astrophysics Data System (ADS)

Bulygina, N.; Gupta, H.; O'Donell, G.; Wheater, H.

2008-12-01

The structure of hydrological model at macro scale (e.g. watershed) is inherently uncertain due to many factors, including the lack of a robust hydrological theory at the macro scale. In this work, we assume that a suitable conceptual model for the hydrologic system has already been determined - i.e., the system boundaries have been specified, the important state variables and input and output fluxes to be included have been selected, and the major hydrological processes and geometries of their interconnections have been identified. The structural identification problem then is to specify the mathematical form of the relationships between the inputs, state variables and outputs, so that a computational model can be constructed for making simulations and/or predictions of system input-state-output behaviour. We show how Bayesian data assimilation can be used to merge both prior beliefs in the form of pre-assumed model equations with information derived from the data to construct a posterior model. The approach, entitled Bayesian Estimation of Structure (BESt), is used to estimate a hydrological model for a small basin in England, at hourly time scales, conditioned on the assumption of 3-dimensional state - soil moisture storage, fast and slow flow stores - conceptual model structure. Inputs to the system are precipitation and potential evapotranspiration, and outputs are actual evapotranspiration and streamflow discharge. Results show the difference between prior and posterior mathematical structures, as well as provide prediction confidence intervals that reflect three types of uncertainty: due to initial conditions, due to input and due to mathematical structure.

Structural bioinformatics of the human spliceosomal proteome

PubMed Central

Korneta, Iga; Magnus, Marcin; Bujnicki, Janusz M.

2012-01-01

In this work, we describe the results of a comprehensive structural bioinformatics analysis of the spliceosomal proteome. We used fold recognition analysis to complement prior data on the ordered domains of 252 human splicing proteins. Examples of newly identified domains include a PWI domain in the U5 snRNP protein 200K (hBrr2, residues 258–338), while examples of previously known domains with a newly determined fold include the DUF1115 domain of the U4/U6 di-snRNP protein 90K (hPrp3, residues 540–683). We also established a non-redundant set of experimental models of spliceosomal proteins, as well as constructed in silico models for regions without an experimental structure. The combined set of structural models is available for download. Altogether, over 90% of the ordered regions of the spliceosomal proteome can be represented structurally with a high degree of confidence. We analyzed the reduced spliceosomal proteome of the intron-poor organism Giardia lamblia, and as a result, we proposed a candidate set of ordered structural regions necessary for a functional spliceosome. The results of this work will aid experimental and structural analyses of the spliceosomal proteins and complexes, and can serve as a starting point for multiscale modeling of the structure of the entire spliceosome. PMID:22573172

Sources of Uncertainty in Predicting Land Surface Fluxes Using Diverse Data and Models

NASA Technical Reports Server (NTRS)

Dungan, Jennifer L.; Wang, Weile; Michaelis, Andrew; Votava, Petr; Nemani, Ramakrishma

2010-01-01

In the domain of predicting land surface fluxes, models are used to bring data from large observation networks and satellite remote sensing together to make predictions about present and future states of the Earth. Characterizing the uncertainty about such predictions is a complex process and one that is not yet fully understood. Uncertainty exists about initialization, measurement and interpolation of input variables; model parameters; model structure; and mixed spatial and temporal supports. Multiple models or structures often exist to describe the same processes. Uncertainty about structure is currently addressed by running an ensemble of different models and examining the distribution of model outputs. To illustrate structural uncertainty, a multi-model ensemble experiment we have been conducting using the Terrestrial Observation and Prediction System (TOPS) will be discussed. TOPS uses public versions of process-based ecosystem models that use satellite-derived inputs along with surface climate data and land surface characterization to produce predictions of ecosystem fluxes including gross and net primary production and net ecosystem exchange. Using the TOPS framework, we have explored the uncertainty arising from the application of models with different assumptions, structures, parameters, and variable definitions. With a small number of models, this only begins to capture the range of possible spatial fields of ecosystem fluxes. Few attempts have been made to systematically address the components of uncertainty in such a framework. We discuss the characterization of uncertainty for this approach including both quantifiable and poorly known aspects.

Engineering 3D Models of Tumors and Bone to Understand Tumor-Induced Bone Disease and Improve Treatments

PubMed Central

Kwakwa, Kristin A.; Vanderburgh, Joseph P.; Guelcher, Scott A.

2018-01-01

Purpose of Review Bone is a structurally unique microenvironment that presents many challenges for the development of 3D models for studying bone physiology and diseases, including cancer. As researchers continue to investigate the interactions within the bone microenvironment, the development of 3D models of bone has become critical. Recent Findings 3D models have been developed that replicate some properties of bone, but have not fully reproduced the complex structural and cellular composition of the bone microenvironment. This review will discuss 3D models including polyurethane, silk, and collagen scaffolds that have been developed to study tumor-induced bone disease. In addition, we discuss 3D printing techniques used to better replicate the structure of bone. Summary 3D models that better replicate the bone microenvironment will help researchers better understand the dynamic interactions between tumors and the bone microenvironment, ultimately leading to better models for testing therapeutics and predicting patient outcomes. PMID:28646444

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.

Integrated smart panel and support structure response

NASA Astrophysics Data System (ADS)

DeGiorgi, Virginia G.

1998-06-01

The performance of smart structures is a complex interaction between active and passive components. Active components, even when non-activated, can have an impact on structural performance and, conversely, structural characteristics of passive components can have a measurable impact on active component performance. The present work is an evaluation of the structural characteristics of an active panel designed for acoustic quieting. The support structure is included in the panel design as evaluated. Finite element methods are used to determine the active panel-support structure response. Two conditions are considered; a hollow unfilled support structure and the same structure filled with a polymer compound. Finite element models were defined so that stiffness values corresponding to the center of individual pistons could be determined. Superelement techniques were used to define mass and stiffness values representative of the combined active and support structure at the center of each piston. Results of interest obtained from the analysis include mode shapes, natural frequencies, and equivalent spring stuffiness for use in structural response models to represent the support structure. The effects on plate motion on piston performance cannot be obtained from this analysis, however mass and stiffness matrices for use in an integrated system model to determine piston head velocities can be obtained from this work.

Quantitative structure-activity relationship of organosulphur compounds as soybean 15-lipoxygenase inhibitors using CoMFA and CoMSIA.

PubMed

Caballero, Julio; Fernández, Michael; Coll, Deysma

2010-12-01

Three-dimensional quantitative structure-activity relationship studies were carried out on a series of 28 organosulphur compounds as 15-lipoxygenase inhibitors using comparative molecular field analysis and comparative molecular similarity indices analysis. Quantitative information on structure-activity relationships is provided for further rational development and direction of selective synthesis. All models were carried out over a training set including 22 compounds. The best comparative molecular field analysis model only included steric field and had a good Q² = 0.789. Comparative molecular similarity indices analysis overcame the comparative molecular field analysis results: the best comparative molecular similarity indices analysis model also only included steric field and had a Q² = 0.894. In addition, this model predicted adequately the compounds contained in the test set. Furthermore, plots of steric comparative molecular similarity indices analysis field allowed conclusions to be drawn for the choice of suitable inhibitors. In this sense, our model should prove useful in future 15-lipoxygenase inhibitor design studies. © 2010 John Wiley & Sons A/S.

HYDROLOGIC EVALUATION OF LANDFILL PERFORMANCE (HELP) MODEL - USER'S GUIDE FOR VERSION 3

EPA Science Inventory

This report documents the solution methods and process descriptions used in the Version 3 of the HELP model. Program documentation including program options, system and operating requirements, file structures, program structure and variable descriptions are provided in a separat...

Comparing Posttraumatic Stress Disorder's Symptom Structure between Deployed and Nondeployed Veterans

ERIC Educational Resources Information Center

Engdahl, Ryan M.; Elhai, Jon D.; Richardson, J. Don; Frueh, B. Christopher

2011-01-01

We tested two empirically validated 4-factor models of posttraumatic stress disorder (PTSD) symptoms using the PTSD Checklist: King, Leskin, King, and Weathers' (1998) model including reexperiencing, avoidance, emotional numbing, and hyperarousal factors, and Simms, Watson, and Doebbeling's (2002) model including reexperiencing, avoidance,…

Modelface: an Application Programming Interface (API) for Homology Modeling Studies Using Modeller Software

PubMed Central

Sakhteman, Amirhossein; Zare, Bijan

2016-01-01

An interactive application, Modelface, was presented for Modeller software based on windows platform. The application is able to run all steps of homology modeling including pdb to fasta generation, running clustal, model building and loop refinement. Other modules of modeler including energy calculation, energy minimization and the ability to make single point mutations in the PDB structures are also implemented inside Modelface. The API is a simple batch based application with no memory occupation and is free of charge for academic use. The application is also able to repair missing atom types in the PDB structures making it suitable for many molecular modeling studies such as docking and molecular dynamic simulation. Some successful instances of modeling studies using Modelface are also reported. PMID:28243276

APPLE - An aeroelastic analysis system for turbomachines and propfans

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Bakhle, Milind A.; Srivastava, R.; Mehmed, Oral

1992-01-01

This paper reviews aeroelastic analysis methods for propulsion elements (advanced propellers, compressors and turbines) being developed and used at NASA Lewis Research Center. These aeroelastic models include both structural and aerodynamic components. The structural models include the typical section model, the beam model with and without disk flexibility, and the finite element blade model with plate bending elements. The aerodynamic models are based on the solution of equations ranging from the two-dimensional linear potential equation for a cascade to the three-dimensional Euler equations for multi-blade configurations. Typical results are presented for each aeroelastic model. Suggestions for further research are indicated. All the available aeroelastic models and analysis methods are being incorporated into a unified computer program named APPLE (Aeroelasticity Program for Propulsion at LEwis).

Model structures amplify uncertainty in predicted soil carbon responses to climate change.

PubMed

Shi, Zheng; Crowell, Sean; Luo, Yiqi; Moore, Berrien

2018-06-04

Large model uncertainty in projected future soil carbon (C) dynamics has been well documented. However, our understanding of the sources of this uncertainty is limited. Here we quantify the uncertainties arising from model parameters, structures and their interactions, and how those uncertainties propagate through different models to projections of future soil carbon stocks. Both the vertically resolved model and the microbial explicit model project much greater uncertainties to climate change than the conventional soil C model, with both positive and negative C-climate feedbacks, whereas the conventional model consistently predicts positive soil C-climate feedback. Our findings suggest that diverse model structures are necessary to increase confidence in soil C projection. However, the larger uncertainty in the complex models also suggests that we need to strike a balance between model complexity and the need to include diverse model structures in order to forecast soil C dynamics with high confidence and low uncertainty.

Exploratory Study of Factors Influencing Job-Related Stress in Japanese Psychiatric Nurses

PubMed Central

Yada, Hironori; Lu, Xi; Omori, Hisamitsu; Abe, Hiroshi; Matsuo, Hisae; Ishida, Yasushi; Katoh, Takahiko

2015-01-01

This study explored the factor structure of psychiatric nurses' job-related stress and examined the specificity of the related stressors using the job stressor scale of the Brief Job Stress Questionnaire (BJSQ). The stressor scale of the BJSQ was administered to 296 nurses and assistant nurses. Answers were examined statistically. Exploratory factor analysis was performed to identify factor structures; two factors (overload and job environment) were valid. Confirmatory factor analysis was conducted to examine the two-factor structure and found 11 items with factor loadings of >0.40 (model 1), 13 items with factor loadings from 0.30 to <0.40 (model 2), and 17 items with factor loadings from 0.20 to <0.30 (model 3) for one factor; model 1 demonstrated the highest goodness of fit. Then, we observed that the two-factor structure (model 1) showed a higher goodness of fit than the original six-factor structure. This differed from subscales based on general workers' job-related stressors, suggesting that the factor structure of psychiatric nurses' job-related stressors is specific. Further steps may be necessary to reduce job-related stress specifically related to overload including attention to many needs of patients and job environment including complex ethical dilemmas in psychiatric nursing. PMID:25922763

Exploratory study of factors influencing job-related stress in Japanese psychiatric nurses.

PubMed

Yada, Hironori; Lu, Xi; Omori, Hisamitsu; Abe, Hiroshi; Matsuo, Hisae; Ishida, Yasushi; Katoh, Takahiko

2015-01-01

This study explored the factor structure of psychiatric nurses' job-related stress and examined the specificity of the related stressors using the job stressor scale of the Brief Job Stress Questionnaire (BJSQ). The stressor scale of the BJSQ was administered to 296 nurses and assistant nurses. Answers were examined statistically. Exploratory factor analysis was performed to identify factor structures; two factors (overload and job environment) were valid. Confirmatory factor analysis was conducted to examine the two-factor structure and found 11 items with factor loadings of >0.40 (model 1), 13 items with factor loadings from 0.30 to <0.40 (model 2), and 17 items with factor loadings from 0.20 to <0.30 (model 3) for one factor; model 1 demonstrated the highest goodness of fit. Then, we observed that the two-factor structure (model 1) showed a higher goodness of fit than the original six-factor structure. This differed from subscales based on general workers' job-related stressors, suggesting that the factor structure of psychiatric nurses' job-related stressors is specific. Further steps may be necessary to reduce job-related stress specifically related to overload including attention to many needs of patients and job environment including complex ethical dilemmas in psychiatric nursing.

Model verification of large structural systems

NASA Technical Reports Server (NTRS)

Lee, L. T.; Hasselman, T. K.

1977-01-01

A methodology was formulated, and a general computer code implemented for processing sinusoidal vibration test data to simultaneously make adjustments to a prior mathematical model of a large structural system, and resolve measured response data to obtain a set of orthogonal modes representative of the test model. The derivation of estimator equations is shown along with example problems. A method for improving the prior analytic model is included.

Structural Relations of Personal and Collective Self-Esteem to Subjective Well-Being: Attachment as Moderator

ERIC Educational Resources Information Center

Simsek, Omer Faruk

2013-01-01

A model indicating that the relationship between collective self-esteem and indicators of subjective well-being, happiness and life satisfaction, was mediated by personal self-esteem was tested by structural equation modeling. The model, including all participants, fitted well to the data. The results suggested that the relationship of collective…

Centrifugal and Numerical Modeling of Buried Structures. Volume 2. Dynamic Soil-Structure Interaction.

DTIC Science & Technology

1987-07-14

RD-RISE 368 CENTRIFUGAL AND NUMERICAL MODELING OF BURIED STRUCTURES 1/3 VOLUME 2 DYNAMIC..(U) COLORADO UNIV AT BOULDER DEPT OF CIVIL ENVIRONMENTAL...20332-6448 ELEMENT NO NO. NO ACCESSION NO 61102F 2302 Cl 11 TITLE (Include Security Classification) (U) Centrifugal and Numerical Modeling of Buried ...were buried in a dry sand and tested in the centrifuge to simulate the effects of gravity-induced overburden stresses which played a major role in

Economic evaluation in chronic pain: a systematic review and de novo flexible economic model.

PubMed

Sullivan, W; Hirst, M; Beard, S; Gladwell, D; Fagnani, F; López Bastida, J; Phillips, C; Dunlop, W C N

2016-07-01

There is unmet need in patients suffering from chronic pain, yet innovation may be impeded by the difficulty of justifying economic value in a field beset by data limitations and methodological variability. A systematic review was conducted to identify and summarise the key areas of variability and limitations in modelling approaches in the economic evaluation of treatments for chronic pain. The results of the literature review were then used to support the development of a fully flexible open-source economic model structure, designed to test structural and data assumptions and act as a reference for future modelling practice. The key model design themes identified from the systematic review included: time horizon; titration and stabilisation; number of treatment lines; choice/ordering of treatment; and the impact of parameter uncertainty (given reliance on expert opinion). Exploratory analyses using the model to compare a hypothetical novel therapy versus morphine as first-line treatments showed cost-effectiveness results to be sensitive to structural and data assumptions. Assumptions about the treatment pathway and choice of time horizon were key model drivers. Our results suggest structural model design and data assumptions may have driven previous cost-effectiveness results and ultimately decisions based on economic value. We therefore conclude that it is vital that future economic models in chronic pain are designed to be fully transparent and hope our open-source code is useful in order to aspire to a common approach to modelling pain that includes robust sensitivity analyses to test structural and parameter uncertainty.

The demographic consequences of growing older and bigger in oyster populations.

PubMed

Moore, Jacob L; Lipcius, Romuald N; Puckett, Brandon; Schreiber, Sebastian J

2016-10-01

Structured population models, particularly size- or age-structured, have a long history of informing conservation and natural resource management. While size is often easier to measure than age and is the focus of many management strategies, age-structure can have important effects on population dynamics that are not captured in size-only models. However, relatively few studies have included the simultaneous effects of both age- and size-structure. To better understand how population structure, particularly that of age and size, impacts restoration and management decisions, we developed and compared a size-structured integral projection model (IPM) and an age- and size-structured IPM, using a population of Crassostrea gigas oysters in the northeastern Pacific Ocean. We analyzed sensitivity of model results across values of local retention that give populations decreasing in size to populations increasing in size. We found that age- and size-structured models yielded the best fit to the demographic data and provided more reliable results about long-term demography. Elasticity analysis showed that population growth rate was most sensitive to changes in the survival of both large (>175 mm shell length) and small (<75 mm shell length) oysters, indicating that a maximum size limit, in addition to a minimum size limit, could be an effective strategy for maintaining a sustainable population. In contrast, the purely size-structured model did not detect the importance of large individuals. Finally, patterns in stable age and stable size distributions differed between populations decreasing in size due to limited local retention and populations increasing in size due to high local retention. These patterns can be used to determine population status and restoration success. The methodology described here provides general insight into the necessity of including both age- and size-structure into modeling frameworks when using population models to inform restoration and management decisions. © 2016 by the Ecological Society of America.

Model-based active control of a continuous structure subjected to moving loads

NASA Astrophysics Data System (ADS)

Stancioiu, D.; Ouyang, H.

2016-09-01

Modelling of a structure is an important preliminary step of structural control. The main objectives of the modelling, which are almost always antagonistic are accuracy and simplicity of the model. The first part of this study focuses on the experimental and theoretical modelling of a structure subjected to the action of one or two decelerating moving carriages modelled as masses. The aim of this part is to obtain a simple but accurate model which will include not only the structure-moving load interaction but also the actuators dynamics. A small scale rig is designed to represent a four-span continuous metallic bridge structure with miniature guiding rails. A series of tests are run subjecting the structure to the action of one or two minicarriages with different loads that were launched along the structure at different initial speeds. The second part is dedicated to model based control design where a feedback controller is designed and tested against the validated model. The study shows that a positive position feedback is able to improve system dynamics but also shows some of the limitations of state- space methods for this type of system.

Flight dynamics simulation modeling and control of a large flexible tiltrotor aircraft

NASA Astrophysics Data System (ADS)

Juhasz, Ondrej

A high order rotorcraft mathematical model is developed and validated against the XV-15 and a Large Civil Tiltrotor (LCTR) concept. The mathematical model is generic and allows for any rotorcraft configuration, from single main rotor helicopters to coaxial and tiltrotor aircraft. Rigid-body and inflow states, as well as flexible wing and blade states are used in the analysis. The separate modeling of each rotorcraft component allows for structural flexibility to be included, which is important when modeling large aircraft where structural modes affect the flight dynamics frequency ranges of interest, generally 1 to 20 rad/sec. Details of the formulation of the mathematical model are given, including derivations of structural, aerodynamic, and inertial loads. The linking of the components of the aircraft is developed using an approach similar to multibody analyses by exploiting a tree topology, but without equations of constraints. Assessments of the effects of wing flexibility are given. Flexibility effects are evaluated by looking at the nature of the couplings between rigid-body modes and wing structural modes and vice versa. The effects of various different forms of structural feedback on aircraft dynamics are analyzed. A proportional-integral feedback on the structural acceleration is deemed to be most effective at both improving the damping and reducing the overall excitation of a structural mode. A model following control architecture is then implemented on full order flexible LCTR models. For this aircraft, the four lowest frequency structural modes are below 20 rad/sec, and are thus needed for control law development and analysis. The impact of structural feedback on both Attitude-Command, Attitude-Hold (ACAH) and Translational Rate Command (TRC) response types are investigated. A rigid aircraft model has optimistic performance characteristics, and a control system designed for a rigid aircraft could potentially destabilize a flexible one. The various control systems are flown in a fixed-base simulator. Pilot inputs and aircraft performance are recorded and analyzed.

Delamination Modeling of Composites for Improved Crash Analysis

NASA Technical Reports Server (NTRS)

Fleming, David C.

1999-01-01

Finite element crash modeling of composite structures is limited by the inability of current commercial crash codes to accurately model delamination growth. Efforts are made to implement and assess delamination modeling techniques using a current finite element crash code, MSC/DYTRAN. Three methods are evaluated, including a straightforward method based on monitoring forces in elements or constraints representing an interface; a cohesive fracture model proposed in the literature; and the virtual crack closure technique commonly used in fracture mechanics. Results are compared with dynamic double cantilever beam test data from the literature. Examples show that it is possible to accurately model delamination propagation in this case. However, the computational demands required for accurate solution are great and reliable property data may not be available to support general crash modeling efforts. Additional examples are modeled including an impact-loaded beam, damage initiation in laminated crushing specimens, and a scaled aircraft subfloor structures in which composite sandwich structures are used as energy-absorbing elements. These examples illustrate some of the difficulties in modeling delamination as part of a finite element crash analysis.

A sampling-based method for ranking protein structural models by integrating multiple scores and features.

PubMed

Shi, Xiaohu; Zhang, Jingfen; He, Zhiquan; Shang, Yi; Xu, Dong

2011-09-01

One of the major challenges in protein tertiary structure prediction is structure quality assessment. In many cases, protein structure prediction tools generate good structural models, but fail to select the best models from a huge number of candidates as the final output. In this study, we developed a sampling-based machine-learning method to rank protein structural models by integrating multiple scores and features. First, features such as predicted secondary structure, solvent accessibility and residue-residue contact information are integrated by two Radial Basis Function (RBF) models trained from different datasets. Then, the two RBF scores and five selected scoring functions developed by others, i.e., Opus-CA, Opus-PSP, DFIRE, RAPDF, and Cheng Score are synthesized by a sampling method. At last, another integrated RBF model ranks the structural models according to the features of sampling distribution. We tested the proposed method by using two different datasets, including the CASP server prediction models of all CASP8 targets and a set of models generated by our in-house software MUFOLD. The test result shows that our method outperforms any individual scoring function on both best model selection, and overall correlation between the predicted ranking and the actual ranking of structural quality.

Thick strings, the liquid crystal blue phase, and cosmological large-scale structure

NASA Technical Reports Server (NTRS)

Luo, Xiaochun; Schramm, David N.

1992-01-01

A phenomenological model based on the liquid crystal blue phase is proposed as a model for a late-time cosmological phase transition. Topological defects, in particular thick strings and/or domain walls, are presented as seeds for structure formation. It is shown that the observed large-scale structure, including quasi-periodic wall structure, can be well fitted in the model without violating the microwave background isotropy bound or the limits from induced gravitational waves and the millisecond pulsar timing. Furthermore, such late-time transitions can produce objects such as quasars at high redshifts. The model appears to work with either cold or hot dark matter.

A Review of Recent Aeroelastic Analysis Methods for Propulsion at NASA Lewis Research Center

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Bakhle, Milind A.; Srivastava, R.; Mehmed, Oral; Stefko, George L.

1993-01-01

This report reviews aeroelastic analyses for propulsion components (propfans, compressors and turbines) being developed and used at NASA LeRC. These aeroelastic analyses include both structural and aerodynamic models. The structural models include a typical section, a beam (with and without disk flexibility), and a finite-element blade model (with plate bending elements). The aerodynamic models are based on the solution of equations ranging from the two-dimensional linear potential equation to the three-dimensional Euler equations for multibladed configurations. Typical calculated results are presented for each aeroelastic model. Suggestions for further research are made. Many of the currently available aeroelastic models and analysis methods are being incorporated in a unified computer program, APPLE (Aeroelasticity Program for Propulsion at LEwis).

Experimental Study of a Hot Structure for a Reentry Vehicle

NASA Technical Reports Server (NTRS)

Pride, Richard A.; Royster, Dick M.; Helms, Bobbie F.

1960-01-01

A large structural model of a reentry vehicle has been built incorporating design concepts applicable to a radiation-cooled vehicle. Thermal-stress alleviating features of the model are discussed. Environmental tests on the model include approximately 100 cycles of loading at room temperature and 33 cycles of combined loading and-heating up to temperatures of 1,6000 F. Measured temperatures are shown for typical parts of the model. Comparisons are made between experimental and calculated deflections and strains. The structure successfully survived the heating and loading environments.

Computer-aided operations engineering with integrated models of systems and operations

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Ryan, Dan; Fleming, Land

1994-01-01

CONFIG 3 is a prototype software tool that supports integrated conceptual design evaluation from early in the product life cycle, by supporting isolated or integrated modeling, simulation, and analysis of the function, structure, behavior, failures and operation of system designs. Integration and reuse of models is supported in an object-oriented environment providing capabilities for graph analysis and discrete event simulation. Integration is supported among diverse modeling approaches (component view, configuration or flow path view, and procedure view) and diverse simulation and analysis approaches. Support is provided for integrated engineering in diverse design domains, including mechanical and electro-mechanical systems, distributed computer systems, and chemical processing and transport systems. CONFIG supports abstracted qualitative and symbolic modeling, for early conceptual design. System models are component structure models with operating modes, with embedded time-related behavior models. CONFIG supports failure modeling and modeling of state or configuration changes that result in dynamic changes in dependencies among components. Operations and procedure models are activity structure models that interact with system models. CONFIG is designed to support evaluation of system operability, diagnosability and fault tolerance, and analysis of the development of system effects of problems over time, including faults, failures, and procedural or environmental difficulties.

Handling Correlations between Covariates and Random Slopes in Multilevel Models

ERIC Educational Resources Information Center

Bates, Michael David; Castellano, Katherine E.; Rabe-Hesketh, Sophia; Skrondal, Anders

2014-01-01

This article discusses estimation of multilevel/hierarchical linear models that include cluster-level random intercepts and random slopes. Viewing the models as structural, the random intercepts and slopes represent the effects of omitted cluster-level covariates that may be correlated with included covariates. The resulting correlations between…

Numerical Modeling of the Lake Mary Road Bridge for Foundation Reuse Assessment

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

Sitek, M. A.; Bojanowski, C.; Lottes, S. A.

This project uses numerical techniques to assess the structural integrity and capacity of the bridge foundations and, as a result, reduces the risk associated with reusing the same foundation for a new superstructure. Nondestructive test methods of different types were used in combination with the numerical modeling and analysis. The onsite tests included visual inspection, tomography, ground penetrating radar, drilling boreholes and coreholes, and the laboratory tests on recovered samples. The results were utilized to identify the current geometry of the structure with foundation, including the hidden geometry of the abutments and piers, and soil and foundation material properties. Thismore » data was used to build the numerical models and run computational analyses on a high performance computer cluster to assess the structural integrity of the bridge and foundations including the suitability of the foundation for reuse with a new superstructure and traffic that will increase the load on the foundations. Computational analysis is more cost-effective and gives an advantage of getting more detailed knowledge about the structural response. It also enables to go beyond non-destructive testing and find the failure conditions without destroying the structure under consideration.« less

Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules.

PubMed

Murrell, Daniel S; Cortes-Ciriano, Isidro; van Westen, Gerard J P; Stott, Ian P; Bender, Andreas; Malliavin, Thérèse E; Glen, Robert C

2015-01-01

In silico predictive models have proved to be valuable for the optimisation of compound potency, selectivity and safety profiles in the drug discovery process. camb is an R package that provides an environment for the rapid generation of quantitative Structure-Property and Structure-Activity models for small molecules (including QSAR, QSPR, QSAM, PCM) and is aimed at both advanced and beginner R users. camb's capabilities include the standardisation of chemical structure representation, computation of 905 one-dimensional and 14 fingerprint type descriptors for small molecules, 8 types of amino acid descriptors, 13 whole protein sequence descriptors, filtering methods for feature selection, generation of predictive models (using an interface to the R package caret), as well as techniques to create model ensembles using techniques from the R package caretEnsemble). Results can be visualised through high-quality, customisable plots (R package ggplot2). Overall, camb constitutes an open-source framework to perform the following steps: (1) compound standardisation, (2) molecular and protein descriptor calculation, (3) descriptor pre-processing and model training, visualisation and validation, and (4) bioactivity/property prediction for new molecules. camb aims to speed model generation, in order to provide reproducibility and tests of robustness. QSPR and proteochemometric case studies are included which demonstrate camb's application.Graphical abstractFrom compounds and data to models: a complete model building workflow in one package.

Evidence for the Continuous Latent Structure of Mania in the Epidemiologic Catchment Area from Multiple Latent Structure and Construct Validation Methodologies

PubMed Central

Prisciandaro, James J.; Roberts, John E.

2011-01-01

Background Although psychiatric diagnostic systems have conceptualized mania as a discrete phenomenon, appropriate latent structure investigations testing this conceptualization are lacking. In contrast to these diagnostic systems, several influential theories of mania have suggested a continuous conceptualization. The present study examined whether mania has a continuous or discrete latent structure using a comprehensive approach including taxometric, information-theoretic latent distribution modeling (ITLDM), and predictive validity methodologies in the Epidemiologic Catchment Area (ECA) study. Methods Eight dichotomous manic symptom items were submitted to a variety of latent structural analyses; including factor analyses, taxometric procedures, and ITLDM; in 10,105 ECA community participants. Additionally, a variety of continuous and discrete models of mania were compared in terms of their relative abilities to predict outcomes (i.e., health service utilization, internalizing and externalizing disorders, and suicidal behavior). Results Taxometric and ITLDM analyses consistently supported a continuous conceptualization of mania. In ITLDM analyses, a continuous model of mania demonstrated 6:52:1 odds over the best fitting latent class model of mania. Factor analyses suggested that the continuous structure of mania was best represented by a single latent factor. Predictive validity analyses demonstrated a consistent superior ability of continuous models of mania relative to discrete models. Conclusions The present study provided three independent lines of support for a continuous conceptualization of mania. The implications of a continuous model of mania are discussed. PMID:20507671

The NASTRAN user's manual

NASA Technical Reports Server (NTRS)

1983-01-01

All information directly associated with problem solving using the NASTRAN program is presented. This structural analysis program uses the finite element approach to structural modeling wherein the distributed finite properties of a structure are represented by a finite element of structural elements which are interconnected at a finite number of grid points, to which loads are applied and for which displacements are calculated. Procedures are described for defining and loading a structural model. Functional references for every card used for structural modeling, the NASTRAN data deck and control cards, problem solution sequences (rigid formats), using the plotting capability, writing a direct matrix abstraction program, and diagnostic messages are explained. A dictionary of mnemonics, acronyms, phrases, and other commonly used NASTRAN terms is included.

NASA/Howard University Large Space Structures Institute

NASA Technical Reports Server (NTRS)

Broome, T. H., Jr.

1984-01-01

Basic research on the engineering behavior of large space structures is presented. Methods of structural analysis, control, and optimization of large flexible systems are examined. Topics of investigation include the Load Correction Method (LCM) modeling technique, stabilization of flexible bodies by feedback control, mathematical refinement of analysis equations, optimization of the design of structural components, deployment dynamics, and the use of microprocessors in attitude and shape control of large space structures. Information on key personnel, budgeting, support plans and conferences is included.

On the role of minicomputers in structural design

NASA Technical Reports Server (NTRS)

Storaasli, O. O.

1977-01-01

Results are presented of exploratory studies on the use of a minicomputer in conjunction with large-scale computers to perform structural design tasks, including data and program management, use of interactive graphics, and computations for structural analysis and design. An assessment is made of minicomputer use for the structural model definition and checking and for interpreting results. Included are results of computational experiments demonstrating the advantages of using both a minicomputer and a large computer to solve a large aircraft structural design problem.

Modeling Composite Laminate Crushing for Crash Analysis

NASA Technical Reports Server (NTRS)

Fleming, David C.; Jones, Lisa (Technical Monitor)

2002-01-01

Crash modeling of composite structures remains limited in application and has not been effectively demonstrated as a predictive tool. While the global response of composite structures may be well modeled, when composite structures act as energy-absorbing members through direct laminate crushing the modeling accuracy is greatly reduced. The most efficient composite energy absorbing structures, in terms of energy absorbed per unit mass, are those that absorb energy through a complex progressive crushing response in which fiber and matrix fractures on a small scale dominate the behavior. Such failure modes simultaneously include delamination of plies, failure of the matrix to produce fiber bundles, and subsequent failure of fiber bundles either in bending or in shear. In addition, the response may include the significant action of friction, both internally (between delaminated plies or fiber bundles) or externally (between the laminate and the crushing surface). A figure shows the crushing damage observed in a fiberglass composite tube specimen, illustrating the complexity of the response. To achieve a finite element model of such complex behavior is an extremely challenging problem. A practical crushing model based on detailed modeling of the physical mechanisms of crushing behavior is not expected in the foreseeable future. The present research describes attempts to model composite crushing behavior using a novel hybrid modeling procedure. Experimental testing is done is support of the modeling efforts, and a test specimen is developed to provide data for validating laminate crushing models.

Shock Structure Analysis and Aerodynamics in a Weakly Ionized Gas Flow

NASA Technical Reports Server (NTRS)

Saeks, R.; Popovic, S.; Chow, A. S.

2006-01-01

The structure of a shock wave propagating through a weakly ionized gas is analyzed using an electrofluid dynamics model composed of classical conservation laws and Gauss Law. A viscosity model is included to correctly model the spatial scale of the shock structure, and quasi-neutrality is not assumed. A detailed analysis of the structure of a shock wave propagating in a weakly ionized gas is presented, together with a discussion of the physics underlying the key features of the shock structure. A model for the flow behind a shock wave propagating through a weakly ionized gas is developed and used to analyze the effect of the ionization on the aerodynamics and performance of a two-dimensional hypersonic lifting body.

Computer-aided design of microvasculature systems for use in vascular scaffold production.

PubMed

Mondy, William Lafayette; Cameron, Don; Timmermans, Jean-Pierre; De Clerck, Nora; Sasov, Alexander; Casteleyn, Christophe; Piegl, Les A

2009-09-01

In vitro biomedical engineering of intact, functional vascular networks, which include capillary structures, is a prerequisite for adequate vascular scaffold production. Capillary structures are necessary since they provide the elements and compounds for the growth, function and maintenance of 3D tissue structures. Computer-aided modeling of stereolithographic (STL) micro-computer tomographic (micro-CT) 3D models is a technique that enables us to mimic the design of vascular tree systems containing capillary beds, found in tissues. In our first paper (Mondy et al 2009 Tissue Eng. at press), using micro-CT, we studied the possibility of using vascular tissues to produce data capable of aiding the design of vascular tree scaffolding, which would help in the reverse engineering of a complete vascular tree system including capillary bed structures. In this paper, we used STL models of large datasets of computer-aided design (CAD) data of vascular structures which contained capillary structures that mimic those in the dermal layers of rabbit skin. Using CAD software we created from 3D STL models a bio-CAD design for the development of capillary-containing vascular tree scaffolding for skin. This method is designed to enhance a variety of therapeutic protocols including, but not limited to, organ and tissue repair, systemic disease mediation and cell/tissue transplantation therapy. Our successful approach to in vitro vasculogenesis will allow the bioengineering of various other types of 3D tissue structures, and as such greatly expands the potential applications of biomedical engineering technology into the fields of biomedical research and medicine.

The impact of lianas on the carbon cycle of tropical forests: a modeling study using the Ecosystem Demography model

NASA Astrophysics Data System (ADS)

di Porcia e Brugnera, M.; Longo, M.; Verbeek, H.

2017-12-01

Lianas are an important component of tropical forests, constituting up to 40% of the woody stems and about 35% of the woody species. Tropical forests have been experiencing large-scale structural changes, including an increase in liana abundance and biomass. This may eventually reduce the projected carbon sink of tropical forests. Despite their crucial role no single terrestrial ecosystem model has included lianas so far. Here, we present the very first implementation of lianas in the Ecosystem Demography model (ED2). ED2 is able to represent the competition for water and light between different vegetation types at the regional level. Our new implementation of ED2 is hence suitable to address important questions such as the impact of lianas on the tropical forest carbon balance. We validated the model against forest inventory and eddy covariance flux data at a dry seasonal site (Barro Colorado Island, Panama), and at a wet rainforest site (Paracou, French Guiana). The model was able to represent size structure and carbon accumulation rates. We also evaluated the impact of the unique allocation strategy of lianas on their competitive ability. Lianas invest only a small fraction of their carbon for structural tissues when compared to trees. As a result, lianas benefit from an extra amount of available carbon, however the trade-offs of low allocation on structural tissues are not yet well understood. We are currently investigating a number of hypotheses, including the possibility for lianas to have high turnover rates for leaves and fine roots, or to have high mortality rates due to the loss of structural support when trees die. As such our model allows us to get a better understanding of the role of lianas in the tropical forest carbon cycle.

Structural Test Laboratory | Water Power | NREL

Science.gov Websites

Structural Test Laboratory Structural Test Laboratory NREL engineers design and configure structural components can validate models, demonstrate system reliability, inform design margins, and assess , including mass and center of gravity, to ensure compliance with design goals Dynamic Characterization Use

A systematic review of lumped-parameter equivalent circuit models for real-time estimation of lithium-ion battery states

NASA Astrophysics Data System (ADS)

Nejad, S.; Gladwin, D. T.; Stone, D. A.

2016-06-01

This paper presents a systematic review for the most commonly used lumped-parameter equivalent circuit model structures in lithium-ion battery energy storage applications. These models include the Combined model, Rint model, two hysteresis models, Randles' model, a modified Randles' model and two resistor-capacitor (RC) network models with and without hysteresis included. Two variations of the lithium-ion cell chemistry, namely the lithium-ion iron phosphate (LiFePO4) and lithium nickel-manganese-cobalt oxide (LiNMC) are used for testing purposes. The model parameters and states are recursively estimated using a nonlinear system identification technique based on the dual Extended Kalman Filter (dual-EKF) algorithm. The dynamic performance of the model structures are verified using the results obtained from a self-designed pulsed-current test and an electric vehicle (EV) drive cycle based on the New European Drive Cycle (NEDC) profile over a range of operating temperatures. Analysis on the ten model structures are conducted with respect to state-of-charge (SOC) and state-of-power (SOP) estimation with erroneous initial conditions. Comparatively, both RC model structures provide the best dynamic performance, with an outstanding SOC estimation accuracy. For those cell chemistries with large inherent hysteresis levels (e.g. LiFePO4), the RC model with only one time constant is combined with a dynamic hysteresis model to further enhance the performance of the SOC estimator.

Instrumentation, digital image correlation, and modeling to monitor bridge behavior and condition assessment.

DOT National Transportation Integrated Search

2015-06-01

Bridge managers have historically relied on visual inspection reports and field observation, including : photographs, to assess bridge health. The inclusion of instrumentation, including strain gauges, along : with a structural model can enhance brid...

The Structure of Phonological Processing and Its Relationship to Basic Reading

ERIC Educational Resources Information Center

Nelson, Jason M.; Lindstrom, Jennifer H.; Lindstrom, Will; Denis, Daniel

2012-01-01

We investigated various structural models of phonological processing and the relationship of phonological processing abilities to basic reading. Data were collected on 116 kindergarten and first grade students. The specific ability model, which included phonological awareness, phonological memory, and rapid automatized naming as separate…

Banking Structure and Monetary Policy: New Wine in Old Bottles.

ERIC Educational Resources Information Center

Hacche, John

1989-01-01

Provides an extension of the basic banking model used in introductory economics courses. This expanded model introduces the concept of banking capital and reserves, and includes the relationship existing between current issues and banking structure and money supply growth. Provides worksheet exercises and answers. (LS)

Computational Modeling of Airway and Pulmonary Vascular Structure and Function: Development of a “Lung Physiome”

PubMed Central

Tawhai, M. H.; Clark, A. R.; Donovan, G. M.; Burrowes, K. S.

2011-01-01

Computational models of lung structure and function necessarily span multiple spatial and temporal scales, i.e., dynamic molecular interactions give rise to whole organ function, and the link between these scales cannot be fully understood if only molecular or organ-level function is considered. Here, we review progress in constructing multiscale finite element models of lung structure and function that are aimed at providing a computational framework for bridging the spatial scales from molecular to whole organ. These include structural models of the intact lung, embedded models of the pulmonary airways that couple to model lung tissue, and models of the pulmonary vasculature that account for distinct structural differences at the extra- and intra-acinar levels. Biophysically based functional models for tissue deformation, pulmonary blood flow, and airway bronchoconstriction are also described. The development of these advanced multiscale models has led to a better understanding of complex physiological mechanisms that govern regional lung perfusion and emergent heterogeneity during bronchoconstriction. PMID:22011236

Structural analysis of light aircraft using NASTRAN

NASA Technical Reports Server (NTRS)

Wilkinson, M. T.; Bruce, A. C.

1973-01-01

An application of NASTRAN to the structural analysis of light aircraft was conducted to determine the cost effectiveness. A model of the Baby Ace D model homebuilt aircraft was used. The NASTRAN model of the aircraft consists of 193 grid points connected by 352 structural members. All members are either rod or beam elements, including bending of unsymmetrical cross sections and torsion of noncircular cross sections. The aerodynamic loads applied to the aircraft were in accordance with FAA regulations governing the utility category aircraft.

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields.

PubMed

Whitford, Paul C; Noel, Jeffrey K; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y; Onuchic, José N

2009-05-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Go) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase, and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a C(alpha) structure-based model and an all-atom empirical forcefield. Key findings include: (1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature, (2) folding mechanisms are robust to variations of the energetic parameters, (3) protein folding free-energy barriers can be manipulated through parametric modifications, (4) the global folding mechanisms in a C(alpha) model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model, and (5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Because this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function.

An All-atom Structure-Based Potential for Proteins: Bridging Minimal Models with All-atom Empirical Forcefields

PubMed Central

Whitford, Paul C.; Noel, Jeffrey K.; Gosavi, Shachi; Schug, Alexander; Sanbonmatsu, Kevin Y.; Onuchic, José N.

2012-01-01

Protein dynamics take place on many time and length scales. Coarse-grained structure-based (Gō) models utilize the funneled energy landscape theory of protein folding to provide an understanding of both long time and long length scale dynamics. All-atom empirical forcefields with explicit solvent can elucidate our understanding of short time dynamics with high energetic and structural resolution. Thus, structure-based models with atomic details included can be used to bridge our understanding between these two approaches. We report on the robustness of folding mechanisms in one such all-atom model. Results for the B domain of Protein A, the SH3 domain of C-Src Kinase and Chymotrypsin Inhibitor 2 are reported. The interplay between side chain packing and backbone folding is explored. We also compare this model to a Cα structure-based model and an all-atom empirical forcefield. Key findings include 1) backbone collapse is accompanied by partial side chain packing in a cooperative transition and residual side chain packing occurs gradually with decreasing temperature 2) folding mechanisms are robust to variations of the energetic parameters 3) protein folding free energy barriers can be manipulated through parametric modifications 4) the global folding mechanisms in a Cα model and the all-atom model agree, although differences can be attributed to energetic heterogeneity in the all-atom model 5) proline residues have significant effects on folding mechanisms, independent of isomerization effects. Since this structure-based model has atomic resolution, this work lays the foundation for future studies to probe the contributions of specific energetic factors on protein folding and function. PMID:18837035

Tropical Pacific moisture variability: Its detection, synoptic structure and consequences in the general circulation

NASA Technical Reports Server (NTRS)

Mcguirk, James P.

1990-01-01

Satellite data analysis tools are developed and implemented for the diagnosis of atmospheric circulation systems over the tropical Pacific Ocean. The tools include statistical multi-variate procedures, a multi-spectral radiative transfer model, and the global spectral forecast model at NMC. Data include in-situ observations; satellite observations from VAS (moisture, infrared and visible) NOAA polar orbiters (including Tiros Operational Satellite System (TOVS) multi-channel sounding data and OLR grids) and scanning multichannel microwave radiometer (SMMR); and European Centre for Medium Weather Forecasts (ECHMWF) analyses. A primary goal is a better understanding of the relation between synoptic structures of the area, particularly tropical plumes, and the general circulation, especially the Hadley circulation. A second goal is the definition of the quantitative structure and behavior of all Pacific tropical synoptic systems. Finally, strategies are examined for extracting new and additional information from existing satellite observations. Although moisture structure is emphasized, thermal patterns are also analyzed. Both horizontal and vertical structures are studied and objective quantitative results are emphasized.

Research and development program for non-linear structural modeling with advanced time-temperature dependent constitutive relationships

NASA Technical Reports Server (NTRS)

Walker, K. P.

1981-01-01

Results of a 20-month research and development program for nonlinear structural modeling with advanced time-temperature constitutive relationships are reported. The program included: (1) the evaluation of a number of viscoplastic constitutive models in the published literature; (2) incorporation of three of the most appropriate constitutive models into the MARC nonlinear finite element program; (3) calibration of the three constitutive models against experimental data using Hastelloy-X material; and (4) application of the most appropriate constitutive model to a three dimensional finite element analysis of a cylindrical combustor liner louver test specimen to establish the capability of the viscoplastic model to predict component structural response.

Model-based Approaches for the Determination of Lipid Bilayer Structure from Small-Angle Neutron and X-ray Scattering Data

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

Heberle, Frederick A; Pan, Jianjun; Standaert, Robert F

2012-01-01

Some of our recent work has resulted in the detailed structures of fully hydrated, fluid phase phosphatidylcholine (PC) and phosphatidylglycerol (PG) bilayers. These structures were obtained from the joint refinement of small-angle neutron and X-ray data using the scattering density profile (SDP) models developed by Ku erka et al. (Ku erka et al. 2012; Ku erka et al. 2008). In this review, we first discuss models for the standalone analysis of neutron or X-ray scattering data from bilayers, and assess the strengths and weaknesses inherent in these models. In particular, it is recognized that standalone data do not contain enoughmore » information to fully resolve the structure of inherently disordered fluid bilayers, and therefore may not provide a robust determination of bilayer structural parameters, including the much sought after area per lipid. We then discuss the development of matter density-based models (including the SDP model) that allow for the joint refinement of different contrast neutron and X-ray data sets, as well as the implementation of local volume conservation in the unit cell (i.e., ideal packing). Such models provide natural definitions of bilayer thicknesses (most importantly the hydrophobic and Luzzati thicknesses) in terms of Gibbs dividing surfaces, and thus allow for the robust determination of lipid areas through equivalent slab relationships between bilayer thickness and lipid volume. In the final section of this review, we discuss some of the significant findings/features pertaining to structures of PC and PG bilayers as determined from SDP model analyses.« less

Airloads, wakes, and aeroelasticity

NASA Technical Reports Server (NTRS)

Johnson, Wayne

1990-01-01

Fundamental considerations regarding the theory of modeling of rotary wing airloads, wakes, and aeroelasticity are presented. The topics covered are: airloads and wakes, including lifting-line theory, wake models and nonuniform inflow, free wake geometry, and blade-vortex interaction; aerodynamic and wake models for aeroelasticity, including two-dimensional unsteady aerodynamics and dynamic inflow; and airloads and structural dynamics, including comprehensive airload prediction programs. Results of calculations and correlations are presented.

Variable Complexity Optimization of Composite Structures

NASA Technical Reports Server (NTRS)

Haftka, Raphael T.

2002-01-01

The use of several levels of modeling in design has been dubbed variable complexity modeling. The work under the grant focused on developing variable complexity modeling strategies with emphasis on response surface techniques. Applications included design of stiffened composite plates for improved damage tolerance, the use of response surfaces for fitting weights obtained by structural optimization, and design against uncertainty using response surface techniques.

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

NASA Astrophysics Data System (ADS)

Snodin, Benedict E. K.; Randisi, Ferdinando; Mosayebi, Majid; Šulc, Petr; Schreck, John S.; Romano, Flavio; Ouldridge, Thomas E.; Tsukanov, Roman; Nir, Eyal; Louis, Ard A.; Doye, Jonathan P. K.

2015-06-01

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na+] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

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

Snodin, Benedict E. K., E-mail: benedict.snodin@chem.ox.ac.uk; Mosayebi, Majid; Schreck, John S.

2015-06-21

We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na{sup +}] = 0.5M), so that it can be used for a range of salt concentrations including thosemore » corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.« less

NMR and NQR parameters of ethanol crystal

NASA Astrophysics Data System (ADS)

Milinković, M.; Bilalbegović, G.

2012-04-01

Electric field gradients and chemical shielding tensors of the stable monoclinic crystal phase of ethanol are computed. The projector-augmented wave (PAW) and gauge-including projector-augmented wave (GIPAW) models in the periodic plane-wave density functional theory are used. The crystal data from X-ray measurements, as well as the structures where either all atomic, or only hydrogen atom positions are optimized in the density functional theory are analyzed. These structural models are also studied by including the semi-empirical van der Waals correction to the density functional theory. Infrared spectra of these five crystal models are calculated.

Application of partial differential equation modeling of the control/structural dynamics of flexible spacecraft

NASA Technical Reports Server (NTRS)

Taylor, Lawrence W., Jr.; Rajiyah, H.

1991-01-01

Partial differential equations for modeling the structural dynamics and control systems of flexible spacecraft are applied here in order to facilitate systems analysis and optimization of these spacecraft. Example applications are given, including the structural dynamics of SCOLE, the Solar Array Flight Experiment, the Mini-MAST truss, and the LACE satellite. The development of related software is briefly addressed.

Static Aeroelastic Analysis with an Inviscid Cartesian Method

NASA Technical Reports Server (NTRS)

Rodriguez, David L.; Aftosmis, Michael J.; Nemec, Marian; Smith, Stephen C.

2014-01-01

An embedded-boundary Cartesian-mesh flow solver is coupled with a three degree-offreedom structural model to perform static, aeroelastic analysis of complex aircraft geometries. The approach solves the complete system of aero-structural equations using a modular, loosely-coupled strategy which allows the lower-fidelity structural model to deform the highfidelity CFD model. The approach uses an open-source, 3-D discrete-geometry engine to deform a triangulated surface geometry according to the shape predicted by the structural model under the computed aerodynamic loads. The deformation scheme is capable of modeling large deflections and is applicable to the design of modern, very-flexible transport wings. The interface is modular so that aerodynamic or structural analysis methods can be easily swapped or enhanced. This extended abstract includes a brief description of the architecture, along with some preliminary validation of underlying assumptions and early results on a generic 3D transport model. The final paper will present more concrete cases and validation of the approach. Preliminary results demonstrate convergence of the complete aero-structural system and investigate the accuracy of the approximations used in the formulation of the structural model.

Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles

PubMed Central

Schneidman-Duhovny, Dina; Hammel, Michal

2018-01-01

Small-angle X-ray scattering (SAXS) is an increasingly common and useful technique for structural characterization of molecules in solution. A SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. SAXS profiles can be utilized in a variety of molecular modeling applications, such as comparing solution and crystal structures, structural characterization of flexible proteins, assembly of multi-protein complexes, and modeling of missing regions in the high-resolution structure. Here, we describe protocols for modeling atomic structures based on SAXS profiles. The first protocol is for comparing solution and crystal structures including modeling of missing regions and determination of the oligomeric state. The second protocol performs multi-state modeling by finding a set of conformations and their weights that fit the SAXS profile starting from a single-input structure. The third protocol is for protein-protein docking based on the SAXS profile of the complex. We describe the underlying software, followed by demonstrating their application on interleukin 33 (IL33) with its primary receptor ST2 and DNA ligase IV-XRCC4 complex. PMID:29605933

Structural weights analysis of advanced aerospace vehicles using finite element analysis

NASA Technical Reports Server (NTRS)

Bush, Lance B.; Lentz, Christopher A.; Rehder, John J.; Naftel, J. Chris; Cerro, Jeffrey A.

1989-01-01

A conceptual/preliminary level structural design system has been developed for structural integrity analysis and weight estimation of advanced space transportation vehicles. The system includes a three-dimensional interactive geometry modeler, a finite element pre- and post-processor, a finite element analyzer, and a structural sizing program. Inputs to the system include the geometry, surface temperature, material constants, construction methods, and aerodynamic and inertial loads. The results are a sized vehicle structure capable of withstanding the static loads incurred during assembly, transportation, operations, and missions, and a corresponding structural weight. An analysis of the Space Shuttle external tank is included in this paper as a validation and benchmark case of the system.

Learning to Predict Combinatorial Structures

NASA Astrophysics Data System (ADS)

Vembu, Shankar

2009-12-01

The major challenge in designing a discriminative learning algorithm for predicting structured data is to address the computational issues arising from the exponential size of the output space. Existing algorithms make different assumptions to ensure efficient, polynomial time estimation of model parameters. For several combinatorial structures, including cycles, partially ordered sets, permutations and other graph classes, these assumptions do not hold. In this thesis, we address the problem of designing learning algorithms for predicting combinatorial structures by introducing two new assumptions: (i) The first assumption is that a particular counting problem can be solved efficiently. The consequence is a generalisation of the classical ridge regression for structured prediction. (ii) The second assumption is that a particular sampling problem can be solved efficiently. The consequence is a new technique for designing and analysing probabilistic structured prediction models. These results can be applied to solve several complex learning problems including but not limited to multi-label classification, multi-category hierarchical classification, and label ranking.

A Robust Bayesian Approach for Structural Equation Models with Missing Data

ERIC Educational Resources Information Center

Lee, Sik-Yum; Xia, Ye-Mao

2008-01-01

In this paper, normal/independent distributions, including but not limited to the multivariate t distribution, the multivariate contaminated distribution, and the multivariate slash distribution, are used to develop a robust Bayesian approach for analyzing structural equation models with complete or missing data. In the context of a nonlinear…

Microwave Diffraction Techniques from Macroscopic Crystal Models

ERIC Educational Resources Information Center

Murray, William Henry

1974-01-01

Discusses the construction of a diffractometer table and four microwave models which are built of styrofoam balls with implanted metallic reflecting spheres and designed to simulate the structures of carbon (graphite structure), sodium chloride, tin oxide, and palladium oxide. Included are samples of Bragg patterns and computer-analysis results.…

Structural Equation Modeling Reporting Practices for Language Assessment

ERIC Educational Resources Information Center

Ockey, Gary J.; Choi, Ikkyu

2015-01-01

Studies that use structural equation modeling (SEM) techniques are increasingly encountered in the language assessment literature. This popularity has created the need for a set of guidelines that can indicate what should be included in a research report and make it possible for research consumers to judge the appropriateness of the…

Mastodon

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

Coleman, Justin Leigh; Veeraraghavan, Swetha; Bolisetti, Chandrakanth

MASTODON has the capability to model stochastic nonlinear soil-structure interaction (NLSSI) in a dynamic probabilistic risk assessment framework. The NLSSI simulations include structural dynamics, time integration, dynamic porous media flow, nonlinear hysteretic soil constitutive models, geometric nonlinearities (gapping, sliding, and uplift). MASTODON is also the MOOSE based master application for dynamic PRA of external hazards.

Definition of ground test for verification of large space structure control

NASA Technical Reports Server (NTRS)

Seltzer, S. M.; Doane, G. B., III

1985-01-01

Directions regarding the analytical models were received. A counter balance arm with weights was added at the top of the ASTROMAST to offset the arm with the gimbals. In addition to this model, three more models were requested from MSFC: structure as in the revised model with the addition of lumped masses at bays 46 and 91 of the ASTROMAST; cantilevered cruciform structure with lumped masses at bays 46 and 91, and an all up cruciform structure with lumped masses at bays 46 and 91. Figures for each model and their corresponding natural frequencies and general mode shapes associated with these frequencies are included. The drawbar in use in the cruciform models must be incorporated into the antenna and ASTROMAST models. The total tensile load carrying capability of the ASTROMAST is approximately 840 pounds.

Leadership Models.

ERIC Educational Resources Information Center

Freeman, Thomas J.

This paper discusses six different models of organizational structure and leadership, including the scalar chain or pyramid model, the continuum model, the grid model, the linking pin model, the contingency model, and the circle or democratic model. Each model is examined in a separate section that describes the model and its development, lists…

Unified constitutive models for high-temperature structural applications

NASA Technical Reports Server (NTRS)

Lindholm, U. S.; Chan, K. S.; Bodner, S. R.; Weber, R. M.; Walker, K. P.

1988-01-01

Unified constitutive models are characterized by the use of a single inelastic strain rate term for treating all aspects of inelastic deformation, including plasticity, creep, and stress relaxation under monotonic or cyclic loading. The structure of this class of constitutive theory pertinent for high temperature structural applications is first outlined and discussed. The effectiveness of the unified approach for representing high temperature deformation of Ni-base alloys is then evaluated by extensive comparison of experimental data and predictions of the Bodner-Partom and the Walker models. The use of the unified approach for hot section structural component analyses is demonstrated by applying the Walker model in finite element analyses of a benchmark notch problem and a turbine blade problem.

1T Pixel Using Floating-Body MOSFET for CMOS Image Sensors.

PubMed

Lu, Guo-Neng; Tournier, Arnaud; Roy, François; Deschamps, Benoît

2009-01-01

We present a single-transistor pixel for CMOS image sensors (CIS). It is a floating-body MOSFET structure, which is used as photo-sensing device and source-follower transistor, and can be controlled to store and evacuate charges. Our investigation into this 1T pixel structure includes modeling to obtain analytical description of conversion gain. Model validation has been done by comparing theoretical predictions and experimental results. On the other hand, the 1T pixel structure has been implemented in different configurations, including rectangular-gate and ring-gate designs, and variations of oxidation parameters for the fabrication process. The pixel characteristics are presented and discussed.

Dynamics of Rotating Multi-component Turbomachinery Systems

NASA Technical Reports Server (NTRS)

Lawrence, Charles

1993-01-01

The ultimate objective of turbomachinery vibration analysis is to predict both the overall, as well as component dynamic response. To accomplish this objective requires complete engine structural models, including multistages of bladed disk assemblies, flexible rotor shafts and bearings, and engine support structures and casings. In the present approach each component is analyzed as a separate structure and boundary information is exchanged at the inter-component connections. The advantage of this tactic is that even though readily available detailed component models are utilized, accurate and comprehensive system response information may be obtained. Sample problems, which include a fixed base rotating blade and a blade on a flexible rotor, are presented.

Using decision trees to understand structure in missing data

PubMed Central

Tierney, Nicholas J; Harden, Fiona A; Harden, Maurice J; Mengersen, Kerrie L

2015-01-01

Objectives Demonstrate the application of decision trees—classification and regression trees (CARTs), and their cousins, boosted regression trees (BRTs)—to understand structure in missing data. Setting Data taken from employees at 3 different industrial sites in Australia. Participants 7915 observations were included. Materials and methods The approach was evaluated using an occupational health data set comprising results of questionnaires, medical tests and environmental monitoring. Statistical methods included standard statistical tests and the ‘rpart’ and ‘gbm’ packages for CART and BRT analyses, respectively, from the statistical software ‘R’. A simulation study was conducted to explore the capability of decision tree models in describing data with missingness artificially introduced. Results CART and BRT models were effective in highlighting a missingness structure in the data, related to the type of data (medical or environmental), the site in which it was collected, the number of visits, and the presence of extreme values. The simulation study revealed that CART models were able to identify variables and values responsible for inducing missingness. There was greater variation in variable importance for unstructured as compared to structured missingness. Discussion Both CART and BRT models were effective in describing structural missingness in data. CART models may be preferred over BRT models for exploratory analysis of missing data, and selecting variables important for predicting missingness. BRT models can show how values of other variables influence missingness, which may prove useful for researchers. Conclusions Researchers are encouraged to use CART and BRT models to explore and understand missing data. PMID:26124509

An enhanced beam model for constrained layer damping and a parameter study of damping contribution

NASA Astrophysics Data System (ADS)

Xie, Zhengchao; Shepard, W. Steve, Jr.

2009-01-01

An enhanced analytical model is presented based on an extension of previous models for constrained layer damping (CLD) in beam-like structures. Most existing CLD models are based on the assumption that shear deformation in the core layer is the only source of damping in the structure. However, previous research has shown that other types of deformation in the core layer, such as deformations from longitudinal extension and transverse compression, can also be important. In the enhanced analytical model developed here, shear, extension, and compression deformations are all included. This model can be used to predict the natural frequencies and modal loss factors. The numerical study shows that compared to other models, this enhanced model is accurate in predicting the dynamic characteristics. As a result, the model can be accepted as a general computation model. With all three types of damping included and the formulation used here, it is possible to study the impact of the structure's geometry and boundary conditions on the relative contribution of each type of damping. To that end, the relative contributions in the frequency domain for a few sample cases are presented.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

NASA Astrophysics Data System (ADS)

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-01

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.

PubMed

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-07

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

PubMed

Rodriguez, Abel; Schmidler, Scott C

The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key "gap" parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence-structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples.

Structural Equation Modeling: A Framework for Ocular and Other Medical Sciences Research

PubMed Central

Christ, Sharon L.; Lee, David J.; Lam, Byron L.; Diane, Zheng D.

2017-01-01

Structural equation modeling (SEM) is a modeling framework that encompasses many types of statistical models and can accommodate a variety of estimation and testing methods. SEM has been used primarily in social sciences but is increasingly used in epidemiology, public health, and the medical sciences. SEM provides many advantages for the analysis of survey and clinical data, including the ability to model latent constructs that may not be directly observable. Another major feature is simultaneous estimation of parameters in systems of equations that may include mediated relationships, correlated dependent variables, and in some instances feedback relationships. SEM allows for the specification of theoretically holistic models because multiple and varied relationships may be estimated together in the same model. SEM has recently expanded by adding generalized linear modeling capabilities that include the simultaneous estimation of parameters of different functional form for outcomes with different distributions in the same model. Therefore, mortality modeling and other relevant health outcomes may be evaluated. Random effects estimation using latent variables has been advanced in the SEM literature and software. In addition, SEM software has increased estimation options. Therefore, modern SEM is quite general and includes model types frequently used by health researchers, including generalized linear modeling, mixed effects linear modeling, and population average modeling. This article does not present any new information. It is meant as an introduction to SEM and its uses in ocular and other health research. PMID:24467557

Effects of parceling on model selection: Parcel-allocation variability in model ranking.

PubMed

Sterba, Sonya K; Rights, Jason D

2017-03-01

Research interest often lies in comparing structural model specifications implying different relationships among latent factors. In this context parceling is commonly accepted, assuming the item-level measurement structure is well known and, conservatively, assuming items are unidimensional in the population. Under these assumptions, researchers compare competing structural models, each specified using the same parcel-level measurement model. However, little is known about consequences of parceling for model selection in this context-including whether and when model ranking could vary across alternative item-to-parcel allocations within-sample. This article first provides a theoretical framework that predicts the occurrence of parcel-allocation variability (PAV) in model selection index values and its consequences for PAV in ranking of competing structural models. These predictions are then investigated via simulation. We show that conditions known to manifest PAV in absolute fit of a single model may or may not manifest PAV in model ranking. Thus, one cannot assume that low PAV in absolute fit implies a lack of PAV in ranking, and vice versa. PAV in ranking is shown to occur under a variety of conditions, including large samples. To provide an empirically supported strategy for selecting a model when PAV in ranking exists, we draw on relationships between structural model rankings in parcel- versus item-solutions. This strategy employs the across-allocation modal ranking. We developed software tools for implementing this strategy in practice, and illustrate them with an example. Even if a researcher has substantive reason to prefer one particular allocation, investigating PAV in ranking within-sample still provides an informative sensitivity analysis. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Characterizing uncertainty and variability in physiologically based pharmacokinetic models: state of the science and needs for research and implementation.

PubMed

Barton, Hugh A; Chiu, Weihsueh A; Setzer, R Woodrow; Andersen, Melvin E; Bailer, A John; Bois, Frédéric Y; Dewoskin, Robert S; Hays, Sean; Johanson, Gunnar; Jones, Nancy; Loizou, George; Macphail, Robert C; Portier, Christopher J; Spendiff, Martin; Tan, Yu-Mei

2007-10-01

Physiologically based pharmacokinetic (PBPK) models are used in mode-of-action based risk and safety assessments to estimate internal dosimetry in animals and humans. When used in risk assessment, these models can provide a basis for extrapolating between species, doses, and exposure routes or for justifying nondefault values for uncertainty factors. Characterization of uncertainty and variability is increasingly recognized as important for risk assessment; this represents a continuing challenge for both PBPK modelers and users. Current practices show significant progress in specifying deterministic biological models and nondeterministic (often statistical) models, estimating parameters using diverse data sets from multiple sources, using them to make predictions, and characterizing uncertainty and variability of model parameters and predictions. The International Workshop on Uncertainty and Variability in PBPK Models, held 31 Oct-2 Nov 2006, identified the state-of-the-science, needed changes in practice and implementation, and research priorities. For the short term, these include (1) multidisciplinary teams to integrate deterministic and nondeterministic/statistical models; (2) broader use of sensitivity analyses, including for structural and global (rather than local) parameter changes; and (3) enhanced transparency and reproducibility through improved documentation of model structure(s), parameter values, sensitivity and other analyses, and supporting, discrepant, or excluded data. Longer-term needs include (1) theoretical and practical methodological improvements for nondeterministic/statistical modeling; (2) better methods for evaluating alternative model structures; (3) peer-reviewed databases of parameters and covariates, and their distributions; (4) expanded coverage of PBPK models across chemicals with different properties; and (5) training and reference materials, such as cases studies, bibliographies/glossaries, model repositories, and enhanced software. The multidisciplinary dialogue initiated by this Workshop will foster the collaboration, research, data collection, and training necessary to make characterizing uncertainty and variability a standard practice in PBPK modeling and risk assessment.

Modeling and analysis of pinhole occulter experiment: Initial study phase

NASA Technical Reports Server (NTRS)

Vandervoort, R. J.

1985-01-01

The feasibility of using a generic simulation, TREETOPS, to simulate the Pinhole/Occulter Facility (P/OF) to be tested on the space shuttle was demonstrated. The baseline control system was used to determine the pointing performance of the P/OF. The task included modeling the structure as a three body problem (shuttle-instrument pointing system- P/OP) including the flexibility of the 32 meter P/OF boom. Modeling of sensors, actuators, and control algorithms was also required. Detailed mathematical models for the structure, sensors, and actuators are presented, as well as the control algorithm and corresponding design procedure. Closed loop performance using this controller and computer listings for the simulator are also given.

Structural, Thermal, and Optical Performance (STOP) Modeling and Results for the James Webb Space Telescope Integrated Science Instrument Module

NASA Technical Reports Server (NTRS)

Gracey, Renee; Bartoszyk, Andrew; Cofie, Emmanuel; Comber, Brian; Hartig, George; Howard, Joseph; Sabatke, Derek; Wenzel, Greg; Ohl, Raymond

2016-01-01

The James Webb Space Telescope includes the Integrated Science Instrument Module (ISIM) element that contains four science instruments (SI) including a Guider. We performed extensive structural, thermal, and optical performance(STOP) modeling in support of all phases of ISIM development. In this paper, we focus on modeling and results associated with test and verification. ISIMs test program is bound by ground environments, mostly notably the 1g and test chamber thermal environments. This paper describes STOP modeling used to predict ISIM system performance in 0g and at various on-orbit temperature environments. The predictions are used to project results obtained during testing to on-orbit performance.

Structural Damage Detection Using Changes in Natural Frequencies: Theory and Applications

NASA Astrophysics Data System (ADS)

He, K.; Zhu, W. D.

2011-07-01

A vibration-based method that uses changes in natural frequencies of a structure to detect damage has advantages over conventional nondestructive tests in detecting various types of damage, including loosening of bolted joints, using minimum measurement data. Two major challenges associated with applications of the vibration-based damage detection method to engineering structures are addressed: accurate modeling of structures and the development of a robust inverse algorithm to detect damage, which are defined as the forward and inverse problems, respectively. To resolve the forward problem, new physics-based finite element modeling techniques are developed for fillets in thin-walled beams and for bolted joints, so that complex structures can be accurately modeled with a reasonable model size. To resolve the inverse problem, a logistical function transformation is introduced to convert the constrained optimization problem to an unconstrained one, and a robust iterative algorithm using a trust-region method, called the Levenberg-Marquardt method, is developed to accurately detect the locations and extent of damage. The new methodology can ensure global convergence of the iterative algorithm in solving under-determined system equations and deal with damage detection problems with relatively large modeling error and measurement noise. The vibration-based damage detection method is applied to various structures including lightning masts, a space frame structure and one of its components, and a pipeline. The exact locations and extent of damage can be detected in the numerical simulation where there is no modeling error and measurement noise. The locations and extent of damage can be successfully detected in experimental damage detection.

Modeling and experimental study of resistive switching in vertically aligned carbon nanotubes

NASA Astrophysics Data System (ADS)

Ageev, O. A.; Blinov, Yu F.; Ilina, M. V.; Ilin, O. I.; Smirnov, V. A.

2016-08-01

Model of the resistive switching in vertically aligned carbon nanotube (VA CNT) taking into account the processes of deformation, polarization and piezoelectric charge accumulation have been developed. Origin of hysteresis in VA CNT-based structure is described. Based on modeling results the VACNTs-based structure has been created. The ration resistance of high-resistance to low-resistance states of the VACNTs-based structure amounts 48. The correlation the modeling results with experimental studies is shown. The results can be used in the development nanoelectronics devices based on VA CNTs, including the nonvolatile resistive random-access memory.

Modelling the social and structural determinants of tuberculosis: opportunities and challenges

PubMed Central

Boccia, D.; Dodd, P. J.; Lönnroth, K.; Dowdy, D. W.; Siroka, A.; Kimerling, M. E.; White, R. G.; Houben, R. M. G. J.

2017-01-01

INTRODUCTION: Despite the close link between tuberculosis (TB) and poverty, most mathematical models of TB have not addressed underlying social and structural determinants. OBJECTIVE: To review studies employing mathematical modelling to evaluate the epidemiological impact of the structural determinants of TB. METHODS: We systematically searched PubMed and personal libraries to identify eligible articles. We extracted data on the modelling techniques employed, research question, types of structural determinants modelled and setting. RESULTS: From 232 records identified, we included eight articles published between 2008 and 2015; six employed population-based dynamic TB transmission models and two non-dynamic analytic models. Seven studies focused on proximal TB determinants (four on nutritional status, one on wealth, one on indoor air pollution, and one examined overcrowding, socioeconomic and nutritional status), and one focused on macro-economic influences. CONCLUSIONS: Few modelling studies have attempted to evaluate structural determinants of TB, resulting in key knowledge gaps. Despite the challenges of modelling such a complex system, models must broaden their scope to remain useful for policy making. Given the intersectoral nature of the interrelations between structural determinants and TB outcomes, this work will require multidisciplinary collaborations. A useful starting point would be to focus on developing relatively simple models that can strengthen our knowledge regarding the potential effect of the structural determinants on TB outcomes. PMID:28826444

Quantitative structure-retention relationship studies for taxanes including epimers and isomeric metabolites in ultra fast liquid chromatography.

PubMed

Dong, Pei-Pei; Ge, Guang-Bo; Zhang, Yan-Yan; Ai, Chun-Zhi; Li, Guo-Hui; Zhu, Liang-Liang; Luan, Hong-Wei; Liu, Xing-Bao; Yang, Ling

2009-10-16

Seven pairs of epimers and one pair of isomeric metabolites of taxanes, each pair of which have similar structures but different retention behaviors, together with additional 13 taxanes with different substitutions were chosen to investigate the quantitative structure-retention relationship (QSRR) of taxanes in ultra fast liquid chromatography (UFLC). Monte Carlo variable selection (MCVS) method was adopted to choose descriptors. The selected four descriptors were used to build QSRR model with multi-linear regression (MLR) and artificial neural network (ANN) modeling techniques. Both linear and nonlinear models show good predictive ability, of which ANN model was better with the determination coefficient R(2) for training, validation and test set being 0.9892, 0.9747 and 0.9840, respectively. The results of 100 times' leave-12-out cross validation showed the robustness of this model. All the isomers can be correctly differentiated by this model. According to the selected descriptors, the three dimensional structural information was critical for recognition of epimers. Hydrophobic interaction was the uppermost factor for retention in UFLC. Molecules' polarizability and polarity properties were also closely correlated with retention behaviors. This QSRR model will be useful for separation and identification of taxanes including epimers and metabolites from botanical or biological samples.

Long-Term Structural Health Monitoring System for a High-Speed Railway Bridge Structure.

PubMed

Ding, You-Liang; Wang, Gao-Xin; Sun, Peng; Wu, Lai-Yi; Yue, Qing

2015-01-01

Nanjing Dashengguan Bridge, which serves as the shared corridor crossing Yangtze River for both Beijing-Shanghai high-speed railway and Shanghai-Wuhan-Chengdu railway, is the first 6-track high-speed railway bridge with the longest span throughout the world. In order to ensure safety and detect the performance deterioration during the long-time service of the bridge, a Structural Health Monitoring (SHM) system has been implemented on this bridge by the application of modern techniques in sensing, testing, computing, and network communication. The SHM system includes various sensors as well as corresponding data acquisition and transmission equipment for automatic data collection. Furthermore, an evaluation system of structural safety has been developed for the real-time condition assessment of this bridge. The mathematical correlation models describing the overall structural behavior of the bridge can be obtained with the support of the health monitoring system, which includes cross-correlation models for accelerations, correlation models between temperature and static strains of steel truss arch, and correlation models between temperature and longitudinal displacements of piers. Some evaluation results using the mean value control chart based on mathematical correlation models are presented in this paper to show the effectiveness of this SHM system in detecting the bridge's abnormal behaviors under the varying environmental conditions such as high-speed trains and environmental temperature.

Evaluating the roles of detailed endocardial structures on right ventricular haemodynamics by means of CFD simulations.

PubMed

Sacco, Federica; Paun, Bruno; Lehmkuhl, Oriol; Iles, Tinen L; Iaizzo, Paul A; Houzeaux, Guillaume; Vázquez, Mariano; Butakoff, Constantine; Aguado-Sierra, Jazmin

2018-06-11

Computational modelling plays an important role in right ventricular (RV) haemodynamic analysis. However, current approaches employ smoothed ventricular anatomies. The aim of this study is to characterise RV haemodynamics including detailed endocardial structures like trabeculae, moderator band and papillary muscles (PMs). Four paired detailed and smoothed RV endocardium models (two male and two female) were reconstructed from ex-vivo human hearts high-resolution magnetic resonance images (MRI). Detailed models include structures with ≥1 mm 2 cross-sectional area. Haemodynamic characterisation was done by computational fluid dynamics (CFD) simulations with steady and transient inflows, using high performance computing (HPC). The differences between the flows in smoothed and detailed models were assessed using Q-criterion for vorticity quantification, the pressure drop between inlet and outlet, and the wall shear stress (WSS). Results demonstrated that detailed endocardial structures increase the degree of intra-ventricular pressure drop, decrease the WSS and disrupt the dominant vortex creating secondary small vortices. Increasingly turbulent blood flow was observed in the detailed RVs. Female RVs were less trabeculated and presented lower pressure drops than the males. In conclusion, neglecting endocardial structures in RV haemodynamic models may lead to inaccurate conclusions about the pressures, stresses, and blood flow behaviour in the cavity. This article is protected by copyright. All rights reserved.

Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

PubMed

Park, Hahnbeom; Lee, Gyu Rie; Heo, Lim; Seok, Chaok

2014-01-01

Protein loop modeling is a tool for predicting protein local structures of particular interest, providing opportunities for applications involving protein structure prediction and de novo protein design. Until recently, the majority of loop modeling methods have been developed and tested by reconstructing loops in frameworks of experimentally resolved structures. In many practical applications, however, the protein loops to be modeled are located in inaccurate structural environments. These include loops in model structures, low-resolution experimental structures, or experimental structures of different functional forms. Accordingly, discrepancies in the accuracy of the structural environment assumed in development of the method and that in practical applications present additional challenges to modern loop modeling methods. This study demonstrates a new strategy for employing a hybrid energy function combining physics-based and knowledge-based components to help tackle this challenge. The hybrid energy function is designed to combine the strengths of each energy component, simultaneously maintaining accurate loop structure prediction in a high-resolution framework structure and tolerating minor environmental errors in low-resolution structures. A loop modeling method based on global optimization of this new energy function is tested on loop targets situated in different levels of environmental errors, ranging from experimental structures to structures perturbed in backbone as well as side chains and template-based model structures. The new method performs comparably to force field-based approaches in loop reconstruction in crystal structures and better in loop prediction in inaccurate framework structures. This result suggests that higher-accuracy predictions would be possible for a broader range of applications. The web server for this method is available at http://galaxy.seoklab.org/loop with the PS2 option for the scoring function.

Modeling and tachometer feedback in the control of an experimental single link flexible structure

NASA Technical Reports Server (NTRS)

Garcia, Ephrahim; Inman, Daniel J.

1990-01-01

In this work a formulation for the modeling of a single link flexible structure will be introduced that includes the effects of dynamic interaction between the actuator and structure. These effects are the rotational modal participation factors for the structure's vibratory motion that occurs at the slewing axis. It will be shown, both theoretically and experimentally, that this dynamic interaction can be advantageous for vibration suppression of the flexible modes of the system during slewing positioning maneuvers.

Methodology for analysis and simulation of large multidisciplinary problems

NASA Technical Reports Server (NTRS)

Russell, William C.; Ikeda, Paul J.; Vos, Robert G.

1989-01-01

The Integrated Structural Modeling (ISM) program is being developed for the Air Force Weapons Laboratory and will be available for Air Force work. Its goal is to provide a design, analysis, and simulation tool intended primarily for directed energy weapons (DEW), kinetic energy weapons (KEW), and surveillance applications. The code is designed to run on DEC (VMS and UNIX), IRIS, Alliant, and Cray hosts. Several technical disciplines are included in ISM, namely structures, controls, optics, thermal, and dynamics. Four topics from the broad ISM goal are discussed. The first is project configuration management and includes two major areas: the software and database arrangement and the system model control. The second is interdisciplinary data transfer and refers to exchange of data between various disciplines such as structures and thermal. Third is a discussion of the integration of component models into one system model, i.e., multiple discipline model synthesis. Last is a presentation of work on a distributed processing computing environment.

Dark matter self-interactions and small scale structure

NASA Astrophysics Data System (ADS)

Tulin, Sean; Yu, Hai-Bo

2018-02-01

We review theories of dark matter (DM) beyond the collisionless paradigm, known as self-interacting dark matter (SIDM), and their observable implications for astrophysical structure in the Universe. Self-interactions are motivated, in part, due to the potential to explain long-standing (and more recent) small scale structure observations that are in tension with collisionless cold DM (CDM) predictions. Simple particle physics models for SIDM can provide a universal explanation for these observations across a wide range of mass scales spanning dwarf galaxies, low and high surface brightness spiral galaxies, and clusters of galaxies. At the same time, SIDM leaves intact the success of ΛCDM cosmology on large scales. This report covers the following topics: (1) small scale structure issues, including the core-cusp problem, the diversity problem for rotation curves, the missing satellites problem, and the too-big-to-fail problem, as well as recent progress in hydrodynamical simulations of galaxy formation; (2) N-body simulations for SIDM, including implications for density profiles, halo shapes, substructure, and the interplay between baryons and self-interactions; (3) semi-analytic Jeans-based methods that provide a complementary approach for connecting particle models with observations; (4) merging systems, such as cluster mergers (e.g., the Bullet Cluster) and minor infalls, along with recent simulation results for mergers; (5) particle physics models, including light mediator models and composite DM models; and (6) complementary probes for SIDM, including indirect and direct detection experiments, particle collider searches, and cosmological observations. We provide a summary and critical look for all current constraints on DM self-interactions and an outline for future directions.

CELSS scenario analysis: Breakeven calculations

NASA Technical Reports Server (NTRS)

Mason, R. M.

1980-01-01

A model of the relative mass requirements of food production components in a controlled ecological life support system (CELSS) based on regenerative concepts is described. Included are a discussion of model scope, structure, and example calculations. Computer programs for cultivar and breakeven calculations are also included.

Investigating the Relationships among Metacognitive Strategy Training, Willingness to Read English Medical Texts, and Reading Comprehension Ability Using Structural Equation Modeling

ERIC Educational Resources Information Center

Hassanpour, Masoumeh; Ghonsooly, Behzad; Nooghabi, Mehdi Jabbari; Shafiee, Mohammad Naser

2017-01-01

This quasi-experimental study examined the relationship between students' metacognitive awareness and willingness to read English medical texts. So, a model was proposed and tested using structural equation modeling (SEM) with R software. Participants included 98 medical students of two classes. One class was assigned as the control group and the…

Relaxations of fluorouracil tautomers by decorations of fullerene-like SiCs: DFT studies

NASA Astrophysics Data System (ADS)

Kouchaki, Alireza; Gülseren, Oğuz; Hadipour, Nasser; Mirzaei, Mahmoud

2016-06-01

Decorations of silicon carbide (SiC) fullerene-like nanoparticles by fluorouracil (FU) and its tautomers are investigated through density functional theory (DFT) calculations. Two models of fullerene-like particles including Si12C8 and Si8C12 are constructed to be counterparts of decorated hybrid structures, FU@Si12C8 and FU@Si8C12, respectively. The initial models including original FU and tautomeric structures and SiC nanoparticles are individually optimized and then combined for further optimizations in the hybrid forms. Covalent bonds are observed for FU@Si12C8 hybrids, whereas non-covalent interactions are seen for FU@Si8C12 ones. The obtained properties indicated that Si12C8 model could be considered as a better counterpart for interactions with FU structures than Si8C12 model. The results also showed significant effects of interactions on the properties of atoms close to the interacting regions in nanoparticles. Finally, the tautomeric structures show different behaviors in interactions with SiC nanoparticles, in which the SiC nanoparticles could be employed to detect the situations of tautomeric processes for FU structures.

Synthetic Modifications In the Frequency Domain for Finite Element Model Update and Damage Detection

DTIC Science & Technology

2017-09-01

Sensitivity-based finite element model updating and structural damage detection has been limited by the number of modes available in a vibration test and...increase the number of modes and corresponding sensitivity data by artificially constraining the structure under test, producing a large number of... structural modifications to the measured data, including both springs-to-ground and mass modifications. This is accomplished with frequency domain

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

PubMed

Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

2012-07-01

The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

A Statistical Model for Estimation of Fish Density Including Correlation in Size, Space, Time and between Species from Research Survey Data

PubMed Central

Bastardie, Francois

2014-01-01

Trawl survey data with high spatial and seasonal coverage were analysed using a variant of the Log Gaussian Cox Process (LGCP) statistical model to estimate unbiased relative fish densities. The model estimates correlations between observations according to time, space, and fish size and includes zero observations and over-dispersion. The model utilises the fact the correlation between numbers of fish caught increases when the distance in space and time between the fish decreases, and the correlation between size groups in a haul increases when the difference in size decreases. Here the model is extended in two ways. Instead of assuming a natural scale size correlation, the model is further developed to allow for a transformed length scale. Furthermore, in the present application, the spatial- and size-dependent correlation between species was included. For cod (Gadus morhua) and whiting (Merlangius merlangus), a common structured size correlation was fitted, and a separable structure between the time and space-size correlation was found for each species, whereas more complex structures were required to describe the correlation between species (and space-size). The within-species time correlation is strong, whereas the correlations between the species are weaker over time but strong within the year. PMID:24911631

Current advancements and challenges in soil-root interactions modelling

NASA Astrophysics Data System (ADS)

Schnepf, Andrea; Huber, Katrin; Abesha, Betiglu; Meunier, Felicien; Leitner, Daniel; Roose, Tiina; Javaux, Mathieu; Vanderborght, Jan; Vereecken, Harry

2015-04-01

Roots change their surrounding soil chemically, physically and biologically. This includes changes in soil moisture and solute concentration, the exudation of organic substances into the rhizosphere, increased growth of soil microorganisms, or changes in soil structure. The fate of water and solutes in the root zone is highly determined by these root-soil interactions. Mathematical models of soil-root systems in combination with non-invasive techniques able to characterize root systems are a promising tool to understand and predict the behaviour of water and solutes in the root zone. With respect to different fields of applications, predictive mathematical models can contribute to the solution of optimal control problems in plant recourse efficiency. This may result in significant gains in productivity, efficiency and environmental sustainability in various land use activities. Major challenges include the coupling of model parameters of the relevant processes with the surrounding environment such as temperature, nutrient concentration or soil water content. A further challenge is the mathematical description of the different spatial and temporal scales involved. This includes in particular the branched structures formed by root systems or the external mycelium of mycorrhizal fungi. Here, reducing complexity as well as bridging between spatial scales is required. Furthermore, the combination of experimental and mathematical techniques may advance the field enormously. Here, the use of root system, soil and rhizosphere models is presented through a number of modelling case studies, including image based modelling of phosphate uptake by a root with hairs, model-based optimization of root architecture for phosphate uptake from soil, upscaling of rhizosphere models, modelling root growth in structured soil, and the effect of root hydraulic architecture on plant water uptake efficiency and drought resistance.

Current Advancements and Challenges in Soil-Root Interactions Modelling

NASA Astrophysics Data System (ADS)

Schnepf, A.; Huber, K.; Abesha, B.; Meunier, F.; Leitner, D.; Roose, T.; Javaux, M.; Vanderborght, J.; Vereecken, H.

2014-12-01

Roots change their surrounding soil chemically, physically and biologically. This includes changes in soil moisture and solute concentration, the exudation of organic substances into the rhizosphere, increased growth of soil microorganisms, or changes in soil structure. The fate of water and solutes in the root zone is highly determined by these root-soil interactions. Mathematical models of soil-root systems in combination with non-invasive techniques able to characterize root systems are a promising tool to understand and predict the behaviour of water and solutes in the root zone. With respect to different fields of applications, predictive mathematical models can contribute to the solution of optimal control problems in plant recourse efficiency. This may result in significant gains in productivity, efficiency and environmental sustainability in various land use activities. Major challenges include the coupling of model parameters of the relevant processes with the surrounding environment such as temperature, nutrient concentration or soil water content. A further challenge is the mathematical description of the different spatial and temporal scales involved. This includes in particular the branched structures formed by root systems or the external mycelium of mycorrhizal fungi. Here, reducing complexity as well as bridging between spatial scales is required. Furthermore, the combination of experimental and mathematical techniques may advance the field enormously. Here, the use of root system, soil and rhizosphere models is presented through a number of modelling case studies, including image based modelling of phosphate uptake by a root with hairs, model-based optimization of root architecture for phosphate uptake from soil, upscaling of rhizosphere models, modelling root growth in structured soil, and the effect of root hydraulic architecture on plant water uptake efficiency and drought resistance.

Experimental and operational modal analysis of a laboratory scale model of a tripod support structure.

NASA Astrophysics Data System (ADS)

Luczak, M. M.; Mucchi, E.; Telega, J.

2016-09-01

The goal of the research is to develop a vibration-based procedure for the identification of structural failures in a laboratory scale model of a tripod supporting structure of an offshore wind turbine. In particular, this paper presents an experimental campaign on the scale model tested in two stages. Stage one encompassed the model tripod structure tested in air. The second stage was done in water. The tripod model structure allows to investigate the propagation of a circumferential representative crack of a cylindrical upper brace. The in-water test configuration included the tower with three bladed rotor. The response of the structure to the different waves loads were measured with accelerometers. Experimental and operational modal analysis was applied to identify the dynamic properties of the investigated scale model for intact and damaged state with different excitations and wave patterns. A comprehensive test matrix allows to assess the differences in estimated modal parameters due to damage or as potentially introduced by nonlinear structural response. The presented technique proves to be effective for detecting and assessing the presence of representative cracks.

Lessons from making the Structural Classification of Proteins (SCOP) and their implications for protein structure modelling.

PubMed

Andreeva, Antonina

2016-06-15

The Structural Classification of Proteins (SCOP) database has facilitated the development of many tools and algorithms and it has been successfully used in protein structure prediction and large-scale genome annotations. During the development of SCOP, numerous exceptions were found to topological rules, along with complex evolutionary scenarios and peculiarities in proteins including the ability to fold into alternative structures. This article reviews cases of structural variations observed for individual proteins and among groups of homologues, knowledge of which is essential for protein structure modelling. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

Construction typification as the tool for optimizing the functioning of a robotized manufacturing system

NASA Astrophysics Data System (ADS)

Gwiazda, A.; Banas, W.; Sekala, A.; Foit, K.; Hryniewicz, P.; Kost, G.

2015-11-01

Process of workcell designing is limited by different constructional requirements. They are related to technological parameters of manufactured element, to specifications of purchased elements of a workcell and to technical characteristics of a workcell scene. This shows the complexity of the design-constructional process itself. The results of such approach are individually designed workcell suitable to the specific location and specific production cycle. Changing this parameters one must rebuild the whole configuration of a workcell. Taking into consideration this it is important to elaborate the base of typical elements of a robot kinematic chain that could be used as the tool for building Virtual modelling of kinematic chains of industrial robots requires several preparatory phase. Firstly, it is important to create a database element, which will be models of industrial robot arms. These models could be described as functional primitives that represent elements between components of the kinematic pairs and structural members of industrial robots. A database with following elements is created: the base kinematic pairs, the base robot structural elements, the base of the robot work scenes. The first of these databases includes kinematic pairs being the key component of the manipulator actuator modules. Accordingly, as mentioned previously, it includes the first stage rotary pair of fifth stage. This type of kinematic pairs was chosen due to the fact that it occurs most frequently in the structures of industrial robots. Second base consists of structural robot elements therefore it allows for the conversion of schematic structures of kinematic chains in the structural elements of the arm of industrial robots. It contains, inter alia, the structural elements such as base, stiff members - simple or angular units. They allow converting recorded schematic three-dimensional elements. Last database is a database of scenes. It includes elements of both simple and complex: simple models of technological equipment, conveyors models, models of the obstacles and like that. Using these elements it could be formed various production spaces (robotized workcells), in which it is possible to virtually track the operation of an industrial robot arm modelled in the system.

Centrifuge Rotor Models: A Comparison of the Euler-Lagrange and the Bond Graph Modeling Approach

NASA Technical Reports Server (NTRS)

Granda, Jose J.; Ramakrishnan, Jayant; Nguyen, Louis H.

2006-01-01

A viewgraph presentation on centrifuge rotor models with a comparison using Euler-Lagrange and bond graph methods is shown. The topics include: 1) Objectives; 2) MOdeling Approach Comparisons; 3) Model Structures; and 4) Application.

Structural insights into SAM domain-mediated tankyrase oligomerization.

PubMed

DaRosa, Paul A; Ovchinnikov, Sergey; Xu, Wenqing; Klevit, Rachel E

2016-09-01

Tankyrase 1 (TNKS1; a.k.a. ARTD5) and tankyrase 2 (TNKS2; a.k.a ARTD6) are highly homologous poly(ADP-ribose) polymerases (PARPs) that function in a wide variety of cellular processes including Wnt signaling, Src signaling, Akt signaling, Glut4 vesicle translocation, telomere length regulation, and centriole and spindle pole maturation. Tankyrase proteins include a sterile alpha motif (SAM) domain that undergoes oligomerization in vitro and in vivo. However, the SAM domains of TNKS1 and TNKS2 have not been structurally characterized and the mode of oligomerization is not yet defined. Here we model the SAM domain-mediated oligomerization of tankyrase. The structural model, supported by mutagenesis and NMR analysis, demonstrates a helical, homotypic head-to-tail polymer that facilitates TNKS self-association. Furthermore, we show that TNKS1 and TNKS2 can form (TNKS1 SAM-TNKS2 SAM) hetero-oligomeric structures mediated by their SAM domains. Though wild-type tankyrase proteins have very low solubility, model-based mutations of the SAM oligomerization interface residues allowed us to obtain soluble TNKS proteins. These structural insights will be invaluable for the functional and biophysical characterization of TNKS1/2, including the role of TNKS oligomerization in protein poly(ADP-ribosyl)ation (PARylation) and PARylation-dependent ubiquitylation. © 2016 The Protein Society.

Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights.

PubMed

Shimizu, Masahiro; Noguchi, Yasunori; Sakiyama, Yukari; Kawakami, Hironori; Katayama, Tsutomu; Takada, Shoji

2016-12-13

Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.

The Factor Structure and Screening Utility of the Social Interaction Anxiety Scale

ERIC Educational Resources Information Center

Rodebaugh, Thomas L.; Woods, Carol M.; Heimberg, Richard G.; Liebowitz, Michael R.; Schneier, Franklin R.

2006-01-01

The widely used Social Interaction Anxiety Scale (SIAS; R. P. Mattick & J. C. Clarke, 1998) possesses favorable psychometric properties, but questions remain concerning its factor structure and item properties. Analyses included 445 people with social anxiety disorder and 1,689 undergraduates. Simple unifactorial models fit poorly, and models that…

Teacher's Corner: Structural Equation Modeling with the Sem Package in R

ERIC Educational Resources Information Center

Fox, John

2006-01-01

R is free, open-source, cooperatively developed software that implements the S statistical programming language and computing environment. The current capabilities of R are extensive, and it is in wide use, especially among statisticians. The sem package provides basic structural equation modeling facilities in R, including the ability to fit…

Vibro-Acoustic FE Analyses of the Saab 2000 Aircraft

NASA Technical Reports Server (NTRS)

Green, Inge S.

1992-01-01

A finite element model of the Saab 2000 fuselage structure and interior cavity has been created in order to compute the noise level in the passenger cabin due to propeller noise. Areas covered in viewgraph format include the following: coupled acoustic/structural noise; data base creation; frequency response analysis; model validation; and planned analyses.

Electronic band structures and optical properties of type-II superlattice photodetectors with interfacial effect.

PubMed

Qiao, Peng-Fei; Mou, Shin; Chuang, Shun Lien

2012-01-30

The electronic band structures and optical properties of type-II superlattice (T2SL) photodetectors in the mid-infrared (IR) range are investigated. We formulate a rigorous band structure model using the 8-band k · p method to include the conduction and valence band mixing. After solving the 8 × 8 Hamiltonian and deriving explicitly the new momentum matrix elements in terms of envelope functions, optical transition rates are obtained through the Fermi's golden rule under various doping and injection conditions. Optical measurements on T2SL photodetectors are compared with our model and show good agreement. Our modeling results of quantum structures connect directly to the device-level design and simulation. The predicted doping effect is readily applicable to the optimization of photodetectors. We further include interfacial (IF) layers to study the significance of their effect. Optical properties of T2SLs are expected to have a large tunable range by controlling the thickness and material composition of the IF layers. Our model provides an efficient tool for the designs of novel photodetectors.

Foot Type Biomechanics Part 2: are structure and anthropometrics related to function?

PubMed

Mootanah, Rajshree; Song, Jinsup; Lenhoff, Mark W; Hafer, Jocelyn F; Backus, Sherry I; Gagnon, David; Deland, Jonathan T; Hillstrom, Howard J

2013-03-01

Many foot pathologies are associated with specific foot types. If foot structure and function are related, measurement of either could assist with differential diagnosis of pedal pathologies. Biomechanical measures of foot structure and function are related in asymptomatic healthy individuals. Sixty-one healthy subjects' left feet were stratified into cavus (n=12), rectus (n=27) and planus (n=22) foot types. Foot structure was assessed by malleolar valgus index, arch height index, and arch height flexibility. Anthropometrics (height and weight), age, and walking speed were measured. Foot function was assessed by center of pressure excursion index, peak plantar pressure, maximum force, and gait pattern parameters. Foot structure and anthropometric variables were entered into stepwise linear regression models to identify predictors of function. Measures of foot structure and anthropometrics explained 10-37% of the model variance (adjusted R(2)) for gait pattern parameters. When walking speed was included, the adjusted R(2) increased to 45-77% but foot structure was no longer a factor. Foot structure and anthropometrics predicted 7-47% of the model variance for plantar pressure and 16-64% for maximum force parameters. All multivariate models were significant (p<0.05), supporting acceptance of the hypothesis. Foot structure and function are related in asymptomatic healthy individuals. The structural parameters employed are basic measurements that do not require ionizing radiation and could be used in a clinical setting. Further research is needed to identify additional predictive parameters (plantar soft tissue characteristics, skeletal alignment, and neuromuscular control) and to include individuals with pathology. Copyright © 2012. Published by Elsevier B.V.

Foot Type Biomechanics Part 2: Are structure and anthropometrics related to function?

PubMed Central

Mootanah, Rajshree; Song, Jinsup; Lenhoff, Mark W.; Hafer, Jocelyn F.; Backus, Sherry I.; Gagnon, David; Deland, Jonathan T.; Hillstrom, Howard J.

2013-01-01

Background Many foot pathologies are associated with specific foot types. If foot structure and function are related, measurement of either could assist with differential diagnosis of pedal pathologies. Hypothesis Biomechanical measures of foot structure and function are related in asymptomatic healthy individuals. Methods Sixty-one healthy subjects' left feet were stratified into cavus (n = 12), rectus (n = 27) and planus (n = 22) foot types. Foot structure was assessed by malleolar valgus index, arch height index, and arch height flexibility. Anthropometrics (height and weight), age, and walking speed were measured. Foot function was assessed by center of pressure excursion index, peak plantar pressure, maximum force, and gait pattern parameters. Foot structure and anthropometric variables were entered into stepwise linear regression models to identify predictors of function. Results Measures of foot structure and anthropometrics explained 10–37% of the model variance (adjusted R2) for gait pattern parameters. When walking speed was included, the adjusted R2 increased to 45–77% but foot structure was no longer a factor. Foot structure and anthropometrics predicted 7–47% of the model variance for plantar pressure and 16–64% for maximum force parameters. All multivariate models were significant (p < 0.05), supporting acceptance of the hypothesis. Discussion and conclusion Foot structure and function are related in asymptomatic healthy individuals. The structural parameters employed are basic measurements that do not require ionizing radiation and could be used in a clinical setting. Further research is needed to identify additional predictive parameters (plantar soft tissue characteristics, skeletal alignment, and neuromuscular control) and to include individuals with pathology. PMID:23107624

Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations.

PubMed

Subbotina, Julia; Yarov-Yarovoy, Vladimir; Lees-Miller, James; Durdagi, Serdar; Guo, Jiqing; Duff, Henry J; Noskov, Sergei Yu

2010-11-01

The hERG1 gene (Kv11.1) encodes a voltage-gated potassium channel. Mutations in this gene lead to one form of the Long QT Syndrome (LQTS) in humans. Promiscuous binding of drugs to hERG1 is known to alter the structure/function of the channel leading to an acquired form of the LQTS. Expectably, creation and validation of reliable 3D model of the channel have been a key target in molecular cardiology and pharmacology for the last decade. Although many models were built, they all were limited to pore domain. In this work, a full model of the hERG1 channel is developed which includes all transmembrane segments. We tested a template-driven de-novo design with ROSETTA-membrane modeling using side-chain placements optimized by subsequent molecular dynamics (MD) simulations. Although backbone templates for the homology modeled parts of the pore and voltage sensors were based on the available structures of KvAP, Kv1.2 and Kv1.2-Kv2.1 chimera channels, the missing parts are modeled de-novo. The impact of several alignments on the structure of the S4 helix in the voltage-sensing domain was also tested. Herein, final models are evaluated for consistency to the reported structural elements discovered mainly on the basis of mutagenesis and electrophysiology. These structural elements include salt bridges and close contacts in the voltage-sensor domain; and the topology of the extracellular S5-pore linker compared with that established by toxin foot-printing and nuclear magnetic resonance studies. Implications of the refined hERG1 model to binding of blockers and channels activators (potent new ligands for channel activations) are discussed. © 2010 Wiley-Liss, Inc.

Structural elements and organization of the ancestral translational machinery

NASA Technical Reports Server (NTRS)

Rein, R.; Srinivasan, S.; Mcdonald, J.; Raghunathan, G.; Shibata, M.

1987-01-01

The molecular mechanisms of the primitive translational apparatus are discussed in the framework of present-day protein biosynthesis. The structural necessities of an early adaptor and the multipoint recognition properties of such an adaptor are investigated on the basis of structure/function relationships found in a contemporary system and a molecular model of the contemporary transpeptidation complex. A model of the tRNA(Tyr)-tyrosyl tRNA synthetase complex including the positioning of the disordered region is proposed; the model is used to illustrate the required recognition properties of the ancestor aminoacyl synthetase.

Analytical modeling of the structureborne noise path on a small twin-engine aircraft

NASA Technical Reports Server (NTRS)

Cole, J. E., III; Stokes, A. Westagard; Garrelick, J. M.; Martini, K. F.

1988-01-01

The structureborne noise path of a six passenger twin-engine aircraft is analyzed. Models of the wing and fuselage structures as well as the interior acoustic space of the cabin are developed and used to evaluate sensitivity to structural and acoustic parameters. Different modeling approaches are used to examine aspects of the structureborne path. These approaches are guided by a number of considerations including the geometry of the structures, the frequency range of interest, and the tractability of the computations. Results of these approaches are compared with experimental data.

The NASTRAN user's manual (level 17.0)

NASA Technical Reports Server (NTRS)

1979-01-01

NASTRAN embodies a lumped element approach, wherein the distributed physical properties of a structure are represented by a model consisting of a finite number of idealized substructures or elements that are interconnected at a finite of grid points, to which loads are applied. All input and output data pertain to the idealized structural model. The general procedures for defining structural models are described and instructions are given for each of the bulk data cards and case control cards. Additional information on the case control cards and use of parameters is included for each rigid format.

Protein docking by the interface structure similarity: how much structure is needed?

PubMed

Sinha, Rohita; Kundrotas, Petras J; Vakser, Ilya A

2012-01-01

The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities. The size of the structure involved in the alignment is important for the success in modeling. This paper describes a systematic large-scale study to find the optimal definition/size of the interfaces for the structure alignment-based docking applications. The results showed that structural areas corresponding to the cutoff values <12 Å across the interface inadequately represent structural details of the interfaces. With the increase of the cutoff beyond 12 Å, the success rate for the benchmark set of 99 protein complexes, did not increase significantly for higher accuracy models, and decreased for lower-accuracy models. The 12 Å cutoff was optimal in our interface alignment-based docking, and a likely best choice for the large-scale (e.g., on the scale of the entire genome) applications to protein interaction networks. The results provide guidelines for the docking approaches, including high-throughput applications to modeled structures.

Mechanical constraints on fault geometries and structural styles in extensional geologic settings

NASA Astrophysics Data System (ADS)

Hughes, A. N.

2017-12-01

The geologic structures that accommodate crustal extension in various tectonic environments, including rifts basins, passive margins, and gravitational collapse systems, exhibit a wide range of geometric styles. While several previous studies have focused on the mechanical controls on crustal-scale rift margin geometry, less attention has been paid to the role of mechanics in the style of the individual structures or groups of structures that deform the brittle upper crust. The main modes of extensional structures that have been observed—including parallel fault arrays, half-grabens, grabens, and core complexes—inherently imply mechanical conditions that favor their formation, but an exhaustive evaluation of the circumstances that favor the creation of each of these primary types has yet to be explored, and thus is the focus of this study. This issue is addressed through the construction of a series of 2D forward mechanical models using the discrete element modeling approach. With the intent of representing the wide range of realistic geologic circumstances in which these structures form, a suite of models were constructed by varying parameters such as rock section thickness and strength properties, detachment zone friction, thickness, and dip, extension rate, and various boundary conditions such as erosion and syntectonic sedimentation. The results of these models were then evaluated in order to identify the combinations of parameters that favor the development of each of the main structural styles. Furthermore, the ability to interrogate the stress and strain fields in the models helps shed light on the specific mechanisms that give rise to these different manifestations of extensional strain. Application of these insights to interpretations of extensional structures in rift basins will help to provide a useful framework for understanding the connection between the observed structural style in a region and the conditions that gave rise to its occurrence.

Boussinesq Modeling for Inlets, Harbors, and Structures (Bouss-2D)

DTIC Science & Technology

2015-10-30

a wide variety of coastal and ocean engineering and naval architecture problems, including: transformation of waves over small to medium spatial...and outputs, and GIS data used in modeling. Recent applications include: Pillar Point Harbor, Oyster Point Marina, CA; Mouth of Columbia River

Vibrations and structureborne noise in space station

NASA Technical Reports Server (NTRS)

Vaicaitis, R.

1985-01-01

Theoretical models were developed capable of predicting structural response and noise transmission to random point mechanical loads. Fiber reinforced composite and aluminum materials were considered. Cylindrical shells and circular plates were taken as typical representatives of structural components for space station habitability modules. Analytical formulations include double wall and single wall constructions. Pressurized and unpressurized models were considered. Parametric studies were conducted to determine the effect on structural response and noise transmission due to fiber orientation, point load location, damping in the core and the main load carrying structure, pressurization, interior acoustic absorption, etc. These analytical models could serve as preliminary tools for assessing noise related problems, for space station applications.

Effects of damping on mode shapes, volume 1

NASA Technical Reports Server (NTRS)

Gates, R. M.

1977-01-01

Displacement, velocity, and acceleration admittances were calculated for a realistic NASTRAN structural model of space shuttle for three conditions: liftoff, maximum dynamic pressure and end of solid rocket booster burn. The realistic model of the orbiter, external tank, and solid rocket motors included the representation of structural joint transmissibilities by finite stiffness and damping elements. Methods developed to incorporate structural joints and their damping characteristics into a finite element model of the space shuttle, to determine the point damping parameters required to produce realistic damping in the primary modes, and to calculate the effect of distributed damping on structural resonances through the calculation of admittances.

Six-degree-of-freedom aircraft simulation with mixed-data structure using the applied dynamics simulation language, ADSIM

NASA Technical Reports Server (NTRS)

Savaglio, Clare

1989-01-01

A realistic simulation of an aircraft in the flight using the AD 100 digital computer is presented. The implementation of three model features is specifically discussed: (1) a large aerodynamic data base (130,00 function values) which is evaluated using function interpolation to obtain the aerodynamic coefficients; (2) an option to trim the aircraft in longitudinal flight; and (3) a flight control system which includes a digital controller. Since the model includes a digital controller the simulation implements not only continuous time equations but also discrete time equations, thus the model has a mixed-data structure.

Representing functions/procedures and processes/structures for analysis of effects of failures on functions and operations

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Leifker, Daniel B.

1991-01-01

Current qualitative device and process models represent only the structure and behavior of physical systems. However, systems in the real world include goal-oriented activities that generally cannot be easily represented using current modeling techniques. An extension of a qualitative modeling system, known as functional modeling, which captures goal-oriented activities explicitly is proposed and how they may be used to support intelligent automation and fault management is shown.

Empirically evaluating decision-analytic models.

PubMed

Goldhaber-Fiebert, Jeremy D; Stout, Natasha K; Goldie, Sue J

2010-08-01

Model-based cost-effectiveness analyses support decision-making. To augment model credibility, evaluation via comparison to independent, empirical studies is recommended. We developed a structured reporting format for model evaluation and conducted a structured literature review to characterize current model evaluation recommendations and practices. As an illustration, we applied the reporting format to evaluate a microsimulation of human papillomavirus and cervical cancer. The model's outputs and uncertainty ranges were compared with multiple outcomes from a study of long-term progression from high-grade precancer (cervical intraepithelial neoplasia [CIN]) to cancer. Outcomes included 5 to 30-year cumulative cancer risk among women with and without appropriate CIN treatment. Consistency was measured by model ranges overlapping study confidence intervals. The structured reporting format included: matching baseline characteristics and follow-up, reporting model and study uncertainty, and stating metrics of consistency for model and study results. Structured searches yielded 2963 articles with 67 meeting inclusion criteria and found variation in how current model evaluations are reported. Evaluation of the cervical cancer microsimulation, reported using the proposed format, showed a modeled cumulative risk of invasive cancer for inadequately treated women of 39.6% (30.9-49.7) at 30 years, compared with the study: 37.5% (28.4-48.3). For appropriately treated women, modeled risks were 1.0% (0.7-1.3) at 30 years, study: 1.5% (0.4-3.3). To support external and projective validity, cost-effectiveness models should be iteratively evaluated as new studies become available, with reporting standardized to facilitate assessment. Such evaluations are particularly relevant for models used to conduct comparative effectiveness analyses.

Modelling the effect of temperament on BMI through appetite reactivity and self-regulation in eating: a Structural Equation Modelling approach in young adolescents.

PubMed

Godefroy, V; Trinchera, L; Romo, L; Rigal, N

2016-04-01

Appetitive traits and general temperament traits have both been correlated with adiposity and obesity in children. However, very few studies have tested structural models to identify the links between temperament, appetitive traits and adiposity in children. A validated structural model would help suggesting mechanisms to explain the impact of temperament on body mass index (BMI). In this study, we used Rothbart's heuristic definition of temperament as a starting point to define four appetitive traits, including two appetite reactivity dimensions (Appetite Arousal and Appetite Persistence) and two dimensions of self-regulation in eating (Self-regulation In Eating Without Hunger and Self-regulation in Eating Speed). We conducted a cross-sectional study in young adolescents to validate a structural model including these four appetitive traits, Effortful Control (a general temperament trait) and adiposity. A questionnaire assessing the four appetitive trait dimensions and Effortful Control was completed by adolescents from 10 to 14 years old (n=475), and their BMI-for-age was calculated (n=441). In total, 74% of the study participants were normal weight, 26% were overweight and 8% were obese. We then used structural equation modelling to test the structural model. We identified a well-fitting structural model (Comparative Fit Index=0.91; Root Mean Square Error of Approximation=0.04) that supports the hypothesis that Effortful Control impacts both dimensions of self-regulation in eating, which in turn are linked with both appetite reactivity dimensions. Moreover, Appetite Persistence is the only appetitive trait that was significantly related to adiposity (B=0.12; P<0.05). Our model shows that Effortful Control is related to adiposity through the mediation of an individual's 'eating temperament' (appetite reactivity and self-regulation in eating). Results suggest that young adolescents who exhibit high appetite reactivity but a low level of self-regulation in eating are at higher risk for excess adiposity.

Using SAS PROC CALIS to fit Level-1 error covariance structures of latent growth models.

PubMed

Ding, Cherng G; Jane, Ten-Der

2012-09-01

In the present article, we demonstrates the use of SAS PROC CALIS to fit various types of Level-1 error covariance structures of latent growth models (LGM). Advantages of the SEM approach, on which PROC CALIS is based, include the capabilities of modeling the change over time for latent constructs, measured by multiple indicators; embedding LGM into a larger latent variable model; incorporating measurement models for latent predictors; and better assessing model fit and the flexibility in specifying error covariance structures. The strength of PROC CALIS is always accompanied with technical coding work, which needs to be specifically addressed. We provide a tutorial on the SAS syntax for modeling the growth of a manifest variable and the growth of a latent construct, focusing the documentation on the specification of Level-1 error covariance structures. Illustrations are conducted with the data generated from two given latent growth models. The coding provided is helpful when the growth model has been well determined and the Level-1 error covariance structure is to be identified.

Stability and growth of continental shields in mantle convection models including recurrent melt production

NASA Astrophysics Data System (ADS)

de Smet, J. H.; van den Berg, A. P.; Vlaar, N. J.

1998-10-01

The long-term growth and stability of compositionally layered continental upper mantle has been investigated by numerical modelling. We present the first numerical model of a convecting mantle including differentiation through partial melting resulting in a stable compositionally layered continental upper mantle structure. This structure includes a continental root extending to a depth of about 200 km. The model covers the upper mantle including the crust and incorporates physical features important for the study of the continental upper mantle during secular cooling of the Earth since the Archaean. Among these features are: a partial melt generation mechanism allowing consistent recurrent melting, time-dependent non-uniform radiogenic heat production, and a temperature- and pressure-dependent rheology. The numerical results reveal a long-term growth mechanism of the continental compositional root. This mechanism operates through episodical injection of small diapiric upwellings from the deep layer of undepleted mantle into the continental root which consists of compositionally distinct depleted mantle material. Our modelling results show the layered continental structure to remain stable during at least 1.5 Ga. After this period mantle differentiation through partial melting ceases due to the prolonged secular cooling and small-scale instabilities set in through continental delamination. This stable period of 1.5 Ga is related to a number of limitations in our model. By improving on these limitations in the future this stable period will be extended to more realistic values.

Factor Structure of the Wechsler Intelligence Scale for Children: Fourth Edition in Children with ADHD.

PubMed

Thaler, Nicholas S; Barchard, Kimberly A; Parke, Elyse; Jones, W Paul; Etcoff, Lewis M; Allen, Daniel N

2015-12-01

Recent evidence suggests that the factor structure of the Wechsler Intelligence Scale for Children-Fourth Edition (WISC-IV) is better explained by a five-factor model rather than the four-factor model in the standardization sample. The current study examined the WISC-IV's factor structure in a sample of children with ADHD. Participants included 314 children and adolescents who were diagnosed with ADHD. Confirmatory factor analysis was conducted on the 10 core subtests of the WISC-IV, and three models were examined including two based on Cattell-Horn-Carroll (CHC) theory. A five-factor model consisting of Gc, Gf, Gv, Gsm, and Gs factors provided the best fit for the data. The Perceptual Reasoning factor identified in the original four-factor model split into the two CHC factors, Gf and Gv, and cross-loaded the Symbol Search subtest onto the Gv factor. A five-factor model based on CHC theory provided superior fit for the WISC-IV in children with ADHD, as has been found with the standardization sample. © The Author(s) 2012.

Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation

PubMed Central

Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E.

2014-01-01

This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand the structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as means to sample conformational space for a better understanding of the relevance of a given model. From this discussion, the major limitations with modeling, in general, were highlighted. These are the difficult issues in sampling conformational space effectively—the multiple minima or conformational sampling problems—and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These are discussed in detail in this unit. PMID:18428877

Molecular modeling of nucleic Acid structure: electrostatics and solvation.

PubMed

Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

2014-12-19

This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. Copyright © 2014 John Wiley & Sons, Inc.

Modelling Size Structured Food Webs Using a Modified Niche Model with Two Predator Traits

PubMed Central

Klecka, Jan

2014-01-01

The structure of food webs is frequently described using phenomenological stochastic models. A prominent example, the niche model, was found to produce artificial food webs resembling real food webs according to a range of summary statistics. However, the size structure of food webs generated by the niche model and real food webs has not yet been rigorously compared. To fill this void, I use a body mass based version of the niche model and compare prey-predator body mass allometry and predator-prey body mass ratios predicted by the model to empirical data. The results show that the model predicts weaker size structure than observed in many real food webs. I introduce a modified version of the niche model which allows to control the strength of size-dependence of predator-prey links. In this model, optimal prey body mass depends allometrically on predator body mass and on a second trait, such as foraging mode. These empirically motivated extensions of the model allow to represent size structure of real food webs realistically and can be used to generate artificial food webs varying in several aspects of size structure in a controlled way. Hence, by explicitly including the role of species traits, this model provides new opportunities for simulating the consequences of size structure for food web dynamics and stability. PMID:25119999

75 FR 31731 - Airworthiness Directives; Bombardier, Inc. Model BD-700-1A10 and BD-700-1A11 Airplanes

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-04

... turbine imbalance. Such imbalance could potentially result in RAT structural failure (including blade... turbine imbalance. Such imbalance could potentially result in RAT structural failure (including blade... reported cases of balance washer screw failure on similar RATs [ram air turbines]/air driven generators...

A multiscale model of placental oxygen exchange: The effect of villous tree structure on exchange efficiency.

PubMed

Lin, Mabelle; Mauroy, Benjamin; James, Joanna L; Tawhai, Merryn H; Clark, Alys R

2016-11-07

The placenta is critical to fetal health during pregnancy as it supplies oxygen and nutrients to maintain life. It has a complex structure, and alterations to this structure across spatial scales are associated with several pregnancy complications, including intrauterine growth restriction (IUGR). The relationship between placental structure and its efficiency as an oxygen exchanger is not well understood in normal or pathological pregnancies. Here we present a computational framework that predicts oxygen transport in the placenta which accounts for blood and oxygen transport in the space around a placental functional unit (the villous tree). The model includes the well-defined branching structure of the largest villous tree branches, as well as a smoothed representation of the small terminal villi that comprise the placenta's gas exchange interfaces. The model demonstrates that oxygen exchange is sensitive to villous tree geometry, including the villous branch length and volume, which are seen to change in IUGR. This is because, to be an efficient exchanger, the architecture of the villous tree must provide a balance between maximising the surface area available for exchange, and the opposing condition of allowing sufficient maternal blood flow to penetrate into the space surrounding the tree. The model also predicts an optimum oxygen exchange when the branch angle is 24 °, as villous branches and TBs are spread out sufficiently to channel maternal blood flow deep into the placental tissue for oxygen exchange without being shunted directly into the DVs. Without concurrent change in the branch length and angles, the model predicts that the number of branching generations has a small influence on oxygen exchange. The modelling framework is presented in 2D for simplicity but is extendible to 3D or to incorporate the high-resolution imaging data that is currently evolving to better quantify placental structure. Copyright © 2016 Elsevier Ltd. All rights reserved.

An integrated geophysical study of north African and Mediterranean lithospheric structure

NASA Astrophysics Data System (ADS)

Dial, Paul Joseph

1998-07-01

This dissertation utilizes gravity and seismic waveform modeling techniques to: (1) determine models of lithospheric structure across northern African through gravity modeling and (2) determine lithospheric and crustal structure and seismic wave propagation characteristics across northern Africa and the Mediterranean region. The purpose of the gravity investigation was to construct models of lithospheric structure across northern Africa through the analysis of gravity data constrained by previous geological and geophysical studies. Three lithospheric models were constructed from Bouguer gravity data using computer modeling, and the gravity data was wavelength-filtered to investigate the relative depth and extent of the structures associated with the major anomalies. In the Atlas Mountains area, the resulting earth models showed slightly greater crustal thickness than those of previous studies if a low density mantle region is not included in the models. However, if a low density mantle region (density = 3.25 g/cm3) was included beneath the Atlas, the earth models showed little crustal thickening (38 km), in accord with previous seismic studies. The second portion of the research consisted of seismic waveform modeling of regional and teleseismic events to determine crustal and lithospheric structure across northern Africa and the Mediterranean. A total of 174 seismograms (145 at regional distances (200--1400 km) and 29 with epicentral distances exceeding 1900 km) were modeled using 1-D velocity models and a reflectivity code. At regional distances from four stations surrounding the western Mediterranean basin (MAL, TOL, PTO and AQU) and one station near the Red Sea (HLW), 1-D velocity models can satisfactorily model the relative amplitudes of both the Pnl and surface wave portions of the seismograms. Modeling of propagation paths greater than 1900 km was also conducted across northern Africa and the Mediterranean. The results indicate that the S-wave velocity model of Corchete et al. (1995) is more appropriate for the Iberian Peninsula, southwestern Mediterranean basin and northwest African coast than the other models tested. This model was better able to predict both the timing and amplitudes of the observed Sn and surface wave components on the observed seismograms. (Abstract shortened by UMI.)

Polar semiconductor heterojunction structure energy band diagram considerations

NASA Astrophysics Data System (ADS)

Lin, Shuxun; Wen, Cheng P.; Wang, Maojun; Hao, Yilong

2016-03-01

The unique nature of built-in electric field induced positive/negative charge pairs of polar semiconductor heterojunction structure has led to a more realistic device model for hexagonal III-nitride HEMT. In this modeling approach, the distribution of charge carriers is dictated by the electrostatic potential profile instead of Femi statistics. The proposed device model is found suitable to explain peculiar properties of GaN HEMT structures, including: (1) Discrepancy in measured conventional linear transmission line model (LTLM) sheet resistance and contactless sheet resistance of GaN HEMT with thin barrier layer. (2) Below bandgap radiation from forward biased Nickel Schottky barrier diode on GaN HEMT structure. (3) GaN HEMT barrier layer doping has negligible effect on transistor channel sheet charge density.

Analytical coupled-wave model for photonic crystal surface-emitting quantum cascade lasers.

PubMed

Wang, Zhixin; Liang, Yong; Yin, Xuefan; Peng, Chao; Hu, Weiwei; Faist, Jérôme

2017-05-15

An analytical coupled-wave model is developed for surface-emitting photonic-crystal quantum cascade lasers (PhC-QCLs). This model provides an accurate and efficient analysis of full three-dimensional device structure with large-area cavity size. Various laser properties of interest including the band structure, mode frequency, cavity loss, mode intensity profile, and far field pattern (FFP), as well as their dependence on PhC structures and cavity size, are investigated. Comparison with numerical simulations confirms the accuracy and validity of our model. The calculated FFP and polarization profile well explain the previously reported experimental results. In particular, we reveal the possibility of switching the lasing modes and generating single-lobed FFP by properly tuning PhC structures.

The role of stand history in assessing forest impacts

USGS Publications Warehouse

Dale, V.H.; Doyle, T.W.

1987-01-01

Air pollution, harvesting practices, and natural disturbances can affect the growth of trees and forest development. To make predictions about anthropogenic impacts on forests, we need to understand how these factors affect tree growth. In this study the effect of disturbance history on tree growth and stand structure was examined by using a computer model of forest development. The model was run under the climatic conditions of east Tennessee, USA, and the results compared to stand structure and tree growth data from a yellow poplar-white oak forest. Basal area growth and forest biomass were more accurately projected when rough approximations of the thinning and fire history typical of the measured plots were included in the simulation model. Stand history can influence tree growth rates and forest structure and should be included in any attempt to assess forest impacts.

Computer-Aided Geometry Modeling

NASA Technical Reports Server (NTRS)

Shoosmith, J. N. (Compiler); Fulton, R. E. (Compiler)

1984-01-01

Techniques in computer-aided geometry modeling and their application are addressed. Mathematical modeling, solid geometry models, management of geometric data, development of geometry standards, and interactive and graphic procedures are discussed. The applications include aeronautical and aerospace structures design, fluid flow modeling, and gas turbine design.

A new modal-based approach for modelling the bump foil structure in the simultaneous solution of foil-air bearing rotor dynamic problems

NASA Astrophysics Data System (ADS)

Bin Hassan, M. F.; Bonello, P.

2017-05-01

Recently-proposed techniques for the simultaneous solution of foil-air bearing (FAB) rotor dynamic problems have been limited to a simple bump foil model in which the individual bumps were modelled as independent spring-damper (ISD) subsystems. The present paper addresses this limitation by introducing a modal model of the bump foil structure into the simultaneous solution scheme. The dynamics of the corrugated bump foil structure are first studied using the finite element (FE) technique. This study is experimentally validated using a purpose-made corrugated foil structure. Based on the findings of this study, it is proposed that the dynamics of the full foil structure, including bump interaction and foil inertia, can be represented by a modal model comprising a limited number of modes. This full foil structure modal model (FFSMM) is then adapted into the rotordynamic FAB problem solution scheme, instead of the ISD model. Preliminary results using the FFSMM under static and unbalance excitation conditions are proven to be reliable by comparison against the corresponding ISD foil model results and by cross-correlating different methods for computing the deflection of the full foil structure. The rotor-bearing model is also validated against experimental and theoretical results in the literature.

Preliminary results on the dynamics of large and flexible space structures in Halo orbits

NASA Astrophysics Data System (ADS)

Colagrossi, Andrea; Lavagna, Michèle

2017-05-01

The global exploration roadmap suggests, among other ambitious future space programmes, a possible manned outpost in lunar vicinity, to support surface operations and further astronaut training for longer and deeper space missions and transfers. In particular, a Lagrangian point orbit location - in the Earth- Moon system - is suggested for a manned cis-lunar infrastructure; proposal which opens an interesting field of study from the astrodynamics perspective. Literature offers a wide set of scientific research done on orbital dynamics under the Three-Body Problem modelling approach, while less of it includes the attitude dynamics modelling as well. However, whenever a large space structure (ISS-like) is considered, not only the coupled orbit-attitude dynamics should be modelled to run more accurate analyses, but the structural flexibility should be included too. The paper, starting from the well-known Circular Restricted Three-Body Problem formulation, presents some preliminary results obtained by adding a coupled orbit-attitude dynamical model and the effects due to the large structure flexibility. In addition, the most relevant perturbing phenomena, such as the Solar Radiation Pressure (SRP) and the fourth-body (Sun) gravity, are included in the model as well. A multi-body approach has been preferred to represent possible configurations of the large cis-lunar infrastructure: interconnected simple structural elements - such as beams, rods or lumped masses linked by springs - build up the space segment. To better investigate the relevance of the flexibility effects, the lumped parameters approach is compared with a distributed parameters semi-analytical technique. A sensitivity analysis of system dynamics, with respect to different configurations and mechanical properties of the extended structure, is also presented, in order to highlight drivers for the lunar outpost design. Furthermore, a case study for a large and flexible space structure in Halo orbits around one of the Earth-Moon collinear Lagrangian points, L1 or L2, is discussed to point out some relevant outcomes for the potential implementation of such a mission.

Error modeling and sensitivity analysis of a parallel robot with SCARA(selective compliance assembly robot arm) motions

NASA Astrophysics Data System (ADS)

Chen, Yuzhen; Xie, Fugui; Liu, Xinjun; Zhou, Yanhua

2014-07-01

Parallel robots with SCARA(selective compliance assembly robot arm) motions are utilized widely in the field of high speed pick-and-place manipulation. Error modeling for these robots generally simplifies the parallelogram structures included by the robots as a link. As the established error model fails to reflect the error feature of the parallelogram structures, the effect of accuracy design and kinematic calibration based on the error model come to be undermined. An error modeling methodology is proposed to establish an error model of parallel robots with parallelogram structures. The error model can embody the geometric errors of all joints, including the joints of parallelogram structures. Thus it can contain more exhaustively the factors that reduce the accuracy of the robot. Based on the error model and some sensitivity indices defined in the sense of statistics, sensitivity analysis is carried out. Accordingly, some atlases are depicted to express each geometric error's influence on the moving platform's pose errors. From these atlases, the geometric errors that have greater impact on the accuracy of the moving platform are identified, and some sensitive areas where the pose errors of the moving platform are extremely sensitive to the geometric errors are also figured out. By taking into account the error factors which are generally neglected in all existing modeling methods, the proposed modeling method can thoroughly disclose the process of error transmission and enhance the efficacy of accuracy design and calibration.

Multi-Group Covariance and Mean Structure Modeling of the Relationship between the WAIS-III Common Factors and Sex and Educational Attainment in Spain

ERIC Educational Resources Information Center

Dolan, Conor V.; Colom, Roberto; Abad, Francisco J.; Wicherts, Jelte M.; Hessen, David J.; van de Sluis, Sophie

2006-01-01

We investigated sex effects and the effects of educational attainment (EA) on the covariance structure of the WAIS-III in a subsample of the Spanish standardization data. We fitted both first order common factor models and second order common factor models. The latter include general intelligence ("g") as a second order common factor.…

DEM modeling of flexible structures against granular material avalanches

NASA Astrophysics Data System (ADS)

Lambert, Stéphane; Albaba, Adel; Nicot, François; Chareyre, Bruno

2016-04-01

This article presents the numerical modeling of flexible structures intended to contain avalanches of granular and coarse material (e.g. rock slide, a debris slide). The numerical model is based on a discrete element method (YADE-Dem). The DEM modeling of both the flowing granular material and the flexible structure are detailed before presenting some results. The flowing material consists of a dry polydisperse granular material accounting for the non-sphericity of real materials. The flexible structure consists in a metallic net hanged on main cables, connected to the ground via anchors, on both sides of the channel, including dissipators. All these components were modeled as flexible beams or wires, with mechanical parameters defined from literature data. The simulation results are presented with the aim of investigating the variability of the structure response depending on different parameters related to the structure (inclination of the fence, with/without brakes, mesh size opening), but also to the channel (inclination). Results are then compared with existing recommendations in similar fields.

Propulsion System Dynamic Modeling for the NASA Supersonic Concept Vehicle: AeroPropulsoServoElasticity

NASA Technical Reports Server (NTRS)

Kopasakis, George; Connolly, Joseph; Seidel, Jonathan

2014-01-01

A summary of the propulsion system modeling under NASA's High Speed Project (HSP) AeroPropulsoServoElasticity (APSE) task is provided with a focus on the propulsion system for the low-boom supersonic configuration developed by Lockheed Martin and referred to as the N+2 configuration. This summary includes details on the effort to date to develop computational models for the various propulsion system components. The objective of this paper is to summarize the model development effort in this task, while providing more detail in the modeling areas that have not been previously published. The purpose of the propulsion system modeling and the overall APSE effort is to develop an integrated dynamic vehicle model to conduct appropriate unsteady analysis of supersonic vehicle performance. This integrated APSE system model concept includes the propulsion system model, and the vehicle structural-aerodynamics model. The development to date of such a preliminary integrated model will also be summarized in this report.propulsion system dynamics, the structural dynamics, and aerodynamics.

Modelling of high-frequency structure-borne sound transmission on FEM grids using the Discrete Flow Mapping technique

NASA Astrophysics Data System (ADS)

Hartmann, Timo; Tanner, Gregor; Xie, Gang; Chappell, David; Bajars, Janis

2016-09-01

Dynamical Energy Analysis (DEA) combined with the Discrete Flow Mapping technique (DFM) has recently been introduced as a mesh-based high frequency method modelling structure borne sound for complex built-up structures. This has proven to enhance vibro-acoustic simulations considerably by making it possible to work directly on existing finite element meshes circumventing time-consuming and costly re-modelling strategies. In addition, DFM provides detailed spatial information about the vibrational energy distribution within a complex structure in the mid-to-high frequency range. We will present here progress in the development of the DEA method towards handling complex FEM-meshes including Rigid Body Elements. In addition, structure borne transmission paths due to spot welds are considered. We will present applications for a car floor structure.

Moving beyond Watson-Crick models of coarse grained DNA dynamics.

PubMed

Linak, Margaret C; Tourdot, Richard; Dorfman, Kevin D

2011-11-28

DNA produces a wide range of structures in addition to the canonical B-form of double-stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed an experimentally parameterized, coarse-grained model that incorporates such bonds. The model reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures. We demonstrate the utility of the model by simulating the folding of a thrombin aptamer, which contains G-quartets, and strand invasion during triplex formation. Our results highlight the importance of including Hoogsteen bonding in coarse-grained models of DNA.

Static shape control for flexible structures

NASA Technical Reports Server (NTRS)

Rodriguez, G.; Scheid, R. E., Jr.

1986-01-01

An integrated methodology is described for defining static shape control laws for large flexible structures. The techniques include modeling, identifying and estimating the control laws of distributed systems characterized in terms of infinite dimensional state and parameter spaces. The models are expressed as interconnected elliptic partial differential equations governing a range of static loads, with the capability of analyzing electromagnetic fields around antenna systems. A second-order analysis is carried out for statistical errors, and model parameters are determined by maximizing an appropriate defined likelihood functional which adjusts the model to observational data. The parameter estimates are derived from the conditional mean of the observational data, resulting in a least squares superposition of shape functions obtained from the structural model.

Modern CACSD using the Robust-Control Toolbox

NASA Technical Reports Server (NTRS)

Chiang, Richard Y.; Safonov, Michael G.

1989-01-01

The Robust-Control Toolbox is a collection of 40 M-files which extend the capability of PC/PRO-MATLAB to do modern multivariable robust control system design. Included are robust analysis tools like singular values and structured singular values, robust synthesis tools like continuous/discrete H(exp 2)/H infinity synthesis and Linear Quadratic Gaussian Loop Transfer Recovery methods and a variety of robust model reduction tools such as Hankel approximation, balanced truncation and balanced stochastic truncation, etc. The capabilities of the toolbox are described and illustated with examples to show how easily they can be used in practice. Examples include structured singular value analysis, H infinity loop-shaping and large space structure model reduction.

Code System to Calculate Tornado-Induced Flow Material Transport.

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

ANDRAE, R. W.

1999-11-18

Version: 00 TORAC models tornado-induced flows, pressures, and material transport within structures. Its use is directed toward nuclear fuel cycle facilities and their primary release pathway, the ventilation system. However, it is applicable to other structures and can model other airflow pathways within a facility. In a nuclear facility, this network system could include process cells, canyons, laboratory offices, corridors, and offgas systems. TORAC predicts flow through a network system that also includes ventilation system components such as filters, dampers, ducts, and blowers. These ventilation system components are connected to the rooms and corridors of the facility to form amore » complete network for moving air through the structure and, perhaps, maintaining pressure levels in certain areas. The material transport capability in TORAC is very basic and includes convection, depletion, entrainment, and filtration of material.« less

An Investigation of the Connection between Outdoor Orientation and Thriving

ERIC Educational Resources Information Center

Rude, Wally James; Bobilya, Andrew J.; Bell, Brent J.

2017-01-01

This study explored the contribution of outdoor orientation experiences to student thriving. Participants included 295 first-year college students from three institutions across North America. A thriving model was tested using structural equation modeling and included the following variables: outdoor orientation, thriving, involvement,…

Automated Generation of Finite-Element Meshes for Aircraft Conceptual Design

NASA Technical Reports Server (NTRS)

Li, Wu; Robinson, Jay

2016-01-01

This paper presents a novel approach for automated generation of fully connected finite-element meshes for all internal structural components and skins of a given wing-body geometry model, controlled by a few conceptual-level structural layout parameters. Internal structural components include spars, ribs, frames, and bulkheads. Structural layout parameters include spar/rib locations in wing chordwise/spanwise direction and frame/bulkhead locations in longitudinal direction. A simple shell thickness optimization problem with two load conditions is used to verify versatility and robustness of the automated meshing process. The automation process is implemented in ModelCenter starting from an OpenVSP geometry and ending with a NASTRAN 200 solution. One subsonic configuration and one supersonic configuration are used for numerical verification. Two different structural layouts are constructed for each configuration and five finite-element meshes of different sizes are generated for each layout. The paper includes various comparisons of solutions of 20 thickness optimization problems, as well as discussions on how the optimal solutions are affected by the stress constraint bound and the initial guess of design variables.

ProTSAV: A protein tertiary structure analysis and validation server.

PubMed

Singh, Ankita; Kaushik, Rahul; Mishra, Avinash; Shanker, Asheesh; Jayaram, B

2016-01-01

Quality assessment of predicted model structures of proteins is as important as the protein tertiary structure prediction. A highly efficient quality assessment of predicted model structures directs further research on function. Here we present a new server ProTSAV, capable of evaluating predicted model structures based on some popular online servers and standalone tools. ProTSAV furnishes the user with a single quality score in case of individual protein structure along with a graphical representation and ranking in case of multiple protein structure assessment. The server is validated on ~64,446 protein structures including experimental structures from RCSB and predicted model structures for CASP targets and from public decoy sets. ProTSAV succeeds in predicting quality of protein structures with a specificity of 100% and a sensitivity of 98% on experimentally solved structures and achieves a specificity of 88%and a sensitivity of 91% on predicted protein structures of CASP11 targets under 2Å.The server overcomes the limitations of any single server/method and is seen to be robust in helping in quality assessment. ProTSAV is freely available at http://www.scfbio-iitd.res.in/software/proteomics/protsav.jsp. Copyright © 2015 Elsevier B.V. All rights reserved.

A general modeling framework for describing spatially structured population dynamics

USGS Publications Warehouse

Sample, Christine; Fryxell, John; Bieri, Joanna; Federico, Paula; Earl, Julia; Wiederholt, Ruscena; Mattsson, Brady; Flockhart, Tyler; Nicol, Sam; Diffendorfer, James E.; Thogmartin, Wayne E.; Erickson, Richard A.; Norris, D. Ryan

2017-01-01

Variation in movement across time and space fundamentally shapes the abundance and distribution of populations. Although a variety of approaches model structured population dynamics, they are limited to specific types of spatially structured populations and lack a unifying framework. Here, we propose a unified network-based framework sufficiently novel in its flexibility to capture a wide variety of spatiotemporal processes including metapopulations and a range of migratory patterns. It can accommodate different kinds of age structures, forms of population growth, dispersal, nomadism and migration, and alternative life-history strategies. Our objective was to link three general elements common to all spatially structured populations (space, time and movement) under a single mathematical framework. To do this, we adopt a network modeling approach. The spatial structure of a population is represented by a weighted and directed network. Each node and each edge has a set of attributes which vary through time. The dynamics of our network-based population is modeled with discrete time steps. Using both theoretical and real-world examples, we show how common elements recur across species with disparate movement strategies and how they can be combined under a unified mathematical framework. We illustrate how metapopulations, various migratory patterns, and nomadism can be represented with this modeling approach. We also apply our network-based framework to four organisms spanning a wide range of life histories, movement patterns, and carrying capacities. General computer code to implement our framework is provided, which can be applied to almost any spatially structured population. This framework contributes to our theoretical understanding of population dynamics and has practical management applications, including understanding the impact of perturbations on population size, distribution, and movement patterns. By working within a common framework, there is less chance that comparative analyses are colored by model details rather than general principles

Structural Analysis of Chemokine Receptor–Ligand Interactions

PubMed Central

2017-01-01

This review focuses on the construction and application of structural chemokine receptor models for the elucidation of molecular determinants of chemokine receptor modulation and the structure-based discovery and design of chemokine receptor ligands. A comparative analysis of ligand binding pockets in chemokine receptors is presented, including a detailed description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures, and their implication for modeling molecular interactions of chemokine receptors with small-molecule ligands, peptide ligands, and large antibodies and chemokines. These studies demonstrate how the integration of new structural information on chemokine receptors with extensive structure–activity relationship and site-directed mutagenesis data facilitates the prediction of the structure of chemokine receptor–ligand complexes that have not been crystallized. Finally, a review of structure-based ligand discovery and design studies based on chemokine receptor crystal structures and homology models illustrates the possibilities and challenges to find novel ligands for chemokine receptors. PMID:28165741

On the analytical modeling of the nonlinear vibrations of pretensioned space structures

NASA Technical Reports Server (NTRS)

Housner, J. M.; Belvin, W. K.

1983-01-01

Pretensioned structures are receiving considerable attention as candidate large space structures. A typical example is a hoop-column antenna. The large number of preloaded members requires efficient analytical methods for concept validation and design. Validation through analyses is especially important since ground testing may be limited due to gravity effects and structural size. The present investigation has the objective to present an examination of the analytical modeling of pretensioned members undergoing nonlinear vibrations. Two approximate nonlinear analysis are developed to model general structural arrangements which include beam-columns and pretensioned cables attached to a common nucleus, such as may occur at a joint of a pretensioned structure. Attention is given to structures undergoing nonlinear steady-state oscillations due to sinusoidal excitation forces. Three analyses, linear, quasi-linear, and nonlinear are conducted and applied to study the response of a relatively simple cable stiffened structure.

Time-varying volatility in Malaysian stock exchange: An empirical study using multiple-volatility-shift fractionally integrated model

NASA Astrophysics Data System (ADS)

Cheong, Chin Wen

2008-02-01

This article investigated the influences of structural breaks on the fractionally integrated time-varying volatility model in the Malaysian stock markets which included the Kuala Lumpur composite index and four major sectoral indices. A fractionally integrated time-varying volatility model combined with sudden changes is developed to study the possibility of structural change in the empirical data sets. Our empirical results showed substantial reduction in fractional differencing parameters after the inclusion of structural change during the Asian financial and currency crises. Moreover, the fractionally integrated model with sudden change in volatility performed better in the estimation and specification evaluations.

Identification and calibration of the structural model of historical masonry building damaged during the 2016 Italian earthquakes: The case study of Palazzo del Podestà in Montelupone

NASA Astrophysics Data System (ADS)

Catinari, Federico; Pierdicca, Alessio; Clementi, Francesco; Lenci, Stefano

2017-11-01

The results of an ambient-vibration based investigation conducted on the "Palazzo del Podesta" in Montelupone (Italy) is presented. The case study was damaged during the 20I6 Italian earthquakes that stroke the central part of the Italy. The assessment procedure includes full-scale ambient vibration testing, modal identification from ambient vibration responses, finite element modeling and dynamic-based identification of the uncertain structural parameters of the model. A very good match between theoretical and experimental modal parameters was reached and the model updating has been performed identifying some structural parameters.

Reanalysis, compatibility and correlation in analysis of modified antenna structures

NASA Technical Reports Server (NTRS)

Levy, R.

1989-01-01

A simple computational procedure is synthesized to process changes in the microwave-antenna pathlength-error measure when there are changes in the antenna structure model. The procedure employs structural modification reanalysis methods combined with new extensions of correlation analysis to provide the revised rms pathlength error. Mainframe finite-element-method processing of the structure model is required only for the initial unmodified structure, and elementary postprocessor computations develop and deal with the effects of the changes. Several illustrative computational examples are included. The procedure adapts readily to processing spectra of changes for parameter studies or sensitivity analyses.

Lunar regolith and structure mechanics

NASA Technical Reports Server (NTRS)

Barnes, Frank; Ko, Hon-Yim; Sture, Stein; Carter, Tyrone R.; Evenson, Kraig A.; Nathan, Mark P.; Perkins, Steve W.

1991-01-01

The topics are presented in viewgraph form and include the following: modeling of regolith-structure interaction in extraterrestrial constructed facilities; densification of lunar soil simulant; and vibration assisted penetration of lunar soil simulant.

A semi-empirical model relating micro structure to acoustic properties of bimodal porous material

NASA Astrophysics Data System (ADS)

Mosanenzadeh, Shahrzad Ghaffari; Doutres, Olivier; Naguib, Hani E.; Park, Chul B.; Atalla, Noureddine

2015-01-01

Complex morphology of open cell porous media makes it difficult to link microstructural parameters and acoustic behavior of these materials. While morphology determines the overall sound absorption and noise damping effectiveness of a porous structure, little is known on the influence of microstructural configuration on the macroscopic properties. In the present research, a novel bimodal porous structure was designed and developed solely for modeling purposes. For the developed porous structure, it is possible to have direct control on morphological parameters and avoid complications raised by intricate pore geometries. A semi-empirical model is developed to relate microstructural parameters to macroscopic characteristics of porous material using precise characterization results based on the designed bimodal porous structures. This model specifically links macroscopic parameters including static airflow resistivity ( σ ) , thermal characteristic length ( Λ ' ) , viscous characteristic length ( Λ ) , and dynamic tortuosity ( α ∞ ) to microstructural factors such as cell wall thickness ( 2 t ) and reticulation rate ( R w ) . The developed model makes it possible to design the morphology of porous media to achieve optimum sound absorption performance based on the application in hand. This study makes the base for understanding the role of microstructural geometry and morphological factors on the overall macroscopic parameters of porous materials specifically for acoustic capabilities. The next step is to include other microstructural parameters as well to generalize the developed model. In the present paper, pore size was kept constant for eight categories of bimodal foams to study the effect of secondary porous structure on macroscopic properties and overall acoustic behavior of porous media.

Parametric Dependencies in Aero-Elastic, Articulated, Flapping Flight

NASA Astrophysics Data System (ADS)

Willis, D. J.; Persson, P.; Peraire, J.; Breuer, K. S.

2006-11-01

Aero-elastic coupling and wing articulation both play a vital role in the generation of lift and propulsion in birds, bats and fish. We present results from a computational study that employs several tools of varying fidelity to explore the role of flexible structures on the performance and efficiency of bird and bat flight mechanics. The tools (both 2-D and 3-D) include a Wake only ``Betz'' analysis following the work of Hall, Pigott and Hall (J. Aircaft, 1998), a potential flow model coupled to a free-vortex wake (Willis, Peraire & White, AIAA 2005-0854), and lastly, a discontinuous Galerkin solver (Persson & Peraire, AIAA 2006-0113) for the full Navier-Stokes equations. Structural models include springs, beams and membranes to represent compliant biological structures. The results demonstrate the changes in efficiency that can be achieved by different parametric variations in the flight behavior, including the effects of increasing kinematic degrees of freedom (e.g. articulated wings) and the effect of compliance in wing and skeletal structures.

Hydrodynamic Modeling for Channel and Shoreline Stabilization at Rhodes Point, Smith Island, MD

DTIC Science & Technology

2016-11-01

shorelines. Both Alternatives included the same revetment structure for protecting the south shoreline. The Coastal Modeling System (CMS, including CMS...ER D C/ CH L TR -1 6- 17 Coastal Inlets Research Program Hydrodynamic Modeling for Channel and Shoreline Stabilization at Rhodes Point...acwc.sdp.sirsi.net/client/default. Coastal Inlets Research Program ERDC/CHL TR-16-17 November 2016 Hydrodynamic Modeling for Channel and Shoreline

The effect of row structure on soil moisture retrieval accuracy from passive microwave data.

PubMed

Xingming, Zheng; Kai, Zhao; Yangyang, Li; Jianhua, Ren; Yanling, Ding

2014-01-01

Row structure causes the anisotropy of microwave brightness temperature (TB) of soil surface, and it also can affect soil moisture retrieval accuracy when its influence is ignored in the inversion model. To study the effect of typical row structure on the retrieved soil moisture and evaluate if there is a need to introduce this effect into the inversion model, two ground-based experiments were carried out in 2011. Based on the observed C-band TB, field soil and vegetation parameters, row structure rough surface assumption (Q p model and discrete model), including the effect of row structure, and flat rough surface assumption (Q p model), ignoring the effect of row structure, are used to model microwave TB of soil surface. Then, soil moisture can be retrieved, respectively, by minimizing the difference of the measured and modeled TB. The results show that soil moisture retrieval accuracy based on the row structure rough surface assumption is approximately 0.02 cm(3)/cm(3) better than the flat rough surface assumption for vegetated soil, as well as 0.015 cm(3)/cm(3) better for bare and wet soil. This result indicates that the effect of row structure cannot be ignored for accurately retrieving soil moisture of farmland surface when C-band is used.

An integrated study of structures, aerodynamics and controls on the forward swept wing X-29A and the oblique wing research aircraft

NASA Technical Reports Server (NTRS)

Dawson, Kenneth S.; Fortin, Paul E.

1987-01-01

The results of an integrated study of structures, aerodynamics, and controls using the STARS program on two advanced airplane configurations are presented. Results for the X-29A include finite element modeling, free vibration analyses, unsteady aerodynamic calculations, flutter/divergence analyses, and an aeroservoelastic controls analysis. Good correlation is shown between STARS results and various other verified results. The tasks performed on the Oblique Wing Research Aircraft include finite element modeling and free vibration analyses.

An Aeroelastic Analysis of a Thin Flexible Membrane

NASA Technical Reports Server (NTRS)

Scott, Robert C.; Bartels, Robert E.; Kandil, Osama A.

2007-01-01

Studies have shown that significant vehicle mass and cost savings are possible with the use of ballutes for aero-capture. Through NASA's In-Space Propulsion program, a preliminary examination of ballute sensitivity to geometry and Reynolds number was conducted, and a single-pass coupling between an aero code and a finite element solver was used to assess the static aeroelastic effects. There remain, however, a variety of open questions regarding the dynamic aeroelastic stability of membrane structures for aero-capture, with the primary challenge being the prediction of the membrane flutter onset. The purpose of this paper is to describe and begin addressing these issues. The paper includes a review of the literature associated with the structural analysis of membranes and membrane utter. Flow/structure analysis coupling and hypersonic flow solver options are also discussed. An approach is proposed for tackling this problem that starts with a relatively simple geometry and develops and evaluates analysis methods and procedures. This preliminary study considers a computationally manageable 2-dimensional problem. The membrane structural models used in the paper include a nonlinear finite-difference model for static and dynamic analysis and a NASTRAN finite element membrane model for nonlinear static and linear normal modes analysis. Both structural models are coupled with a structured compressible flow solver for static aeroelastic analysis. For dynamic aeroelastic analyses, the NASTRAN normal modes are used in the structured compressible flow solver and 3rd order piston theories were used with the finite difference membrane model to simulate utter onset. Results from the various static and dynamic aeroelastic analyses are compared.

Customizing G Protein-coupled receptor models for structure-based virtual screening.

PubMed

de Graaf, Chris; Rognan, Didier

2009-01-01

This review will focus on the construction, refinement, and validation of G Protein-coupled receptor models for the purpose of structure-based virtual screening. Practical tips and tricks derived from concrete modeling and virtual screening exercises to overcome the problems and pitfalls associated with the different steps of the receptor modeling workflow will be presented. These examples will not only include rhodopsin-like (class A), but also secretine-like (class B), and glutamate-like (class C) receptors. In addition, the review will present a careful comparative analysis of current crystal structures and their implication on homology modeling. The following themes will be discussed: i) the use of experimental anchors in guiding the modeling procedure; ii) amino acid sequence alignments; iii) ligand binding mode accommodation and binding cavity expansion; iv) proline-induced kinks in transmembrane helices; v) binding mode prediction and virtual screening by receptor-ligand interaction fingerprint scoring; vi) extracellular loop modeling; vii) virtual filtering schemes. Finally, an overview of several successful structure-based screening shows that receptor models, despite structural inaccuracies, can be efficiently used to find novel ligands.

Canopy structural complexity predicts forest canopy light absorption at continental scales

NASA Astrophysics Data System (ADS)

Atkins, J. W.; Fahey, R. T.; Hardiman, B. S.; Gough, C. M.

2017-12-01

Understanding how the physical structure of forest canopies influence light acquisition is a long-standing area of inquiry fundamental to advancing understanding of many areas of the physical sciences, including the modeling and interpretation of biogeochemical cycles. Conventional measures of forest canopy structure employed in earth system models are often limited to leaf area index (LAI)—a measure of the quantity of leaves in the canopy. However, more novel multi-dimensional measures of canopy structural complexity (CSC) that describe the arrangement of vegetation are now possible because of technological advances, and may improve modeled estimates of canopy light absorption. During 2016 and 2017, we surveyed forests at sites from across the eastern, southern, and midwestern United States using portable canopy LiDAR (PCL). This survey included 14 National Ecological Observation Network (NEON), Long-Term Ecological Research Network (LTER,) Ameriflux, and University affiliated sites. Our findings show that a composite model including CSC parameters and LAI explains 96.8% of the variance in light acquisition, measured as the fraction of photosynthetically absorbed radiation (fPAR) at the continental scale, and improvement of 12% over an LAI only model. Under high light sky conditions, measures of CSC are more strongly coupled with light acquisition than under low light, possibly because light scattering partially decouples CSC from canopy light absorption under low, predominately diffuse light conditions. We conclude that scalable estimates of CSC metrics may improve continent-wide estimates of canopy light absorption and, therefore, carbon uptake, with implications for remote sensing and earth system modeling.

Hierarchical modeling and inference in ecology: The analysis of data from populations, metapopulations and communities

USGS Publications Warehouse

Royle, J. Andrew; Dorazio, Robert M.

2008-01-01

A guide to data collection, modeling and inference strategies for biological survey data using Bayesian and classical statistical methods. This book describes a general and flexible framework for modeling and inference in ecological systems based on hierarchical models, with a strict focus on the use of probability models and parametric inference. Hierarchical models represent a paradigm shift in the application of statistics to ecological inference problems because they combine explicit models of ecological system structure or dynamics with models of how ecological systems are observed. The principles of hierarchical modeling are developed and applied to problems in population, metapopulation, community, and metacommunity systems. The book provides the first synthetic treatment of many recent methodological advances in ecological modeling and unifies disparate methods and procedures. The authors apply principles of hierarchical modeling to ecological problems, including * occurrence or occupancy models for estimating species distribution * abundance models based on many sampling protocols, including distance sampling * capture-recapture models with individual effects * spatial capture-recapture models based on camera trapping and related methods * population and metapopulation dynamic models * models of biodiversity, community structure and dynamics.

Model reduction in integrated controls-structures design

NASA Technical Reports Server (NTRS)

Maghami, Peiman G.

1993-01-01

It is the objective of this paper to present a model reduction technique developed for the integrated controls-structures design of flexible structures. Integrated controls-structures design problems are typically posed as nonlinear mathematical programming problems, where the design variables consist of both structural and control parameters. In the solution process, both structural and control design variables are constantly changing; therefore, the dynamic characteristics of the structure are also changing. This presents a problem in obtaining a reduced-order model for active control design and analysis which will be valid for all design points within the design space. In other words, the frequency and number of the significant modes of the structure (modes that should be included) may vary considerably throughout the design process. This is also true as the locations and/or masses of the sensors and actuators change. Moreover, since the number of design evaluations in the integrated design process could easily run into thousands, any feasible order-reduction method should not require model reduction analysis at every design iteration. In this paper a novel and efficient technique for model reduction in the integrated controls-structures design process, which addresses these issues, is presented.

A new 3D immersed boundary method for non-Newtonian fluid-structure-interaction with application

NASA Astrophysics Data System (ADS)

Zhu, Luoding

2017-11-01

Motivated by fluid-structure-interaction (FSI) phenomena in life sciences (e.g., motions of sperm and cytoskeleton in complex fluids), we introduce a new immersed boundary method for FSI problems involving non-Newtonian fluids in three dimensions. The non-Newtonian fluids are modelled by the FENE-P model (including the Oldroyd-B model as an especial case) and numerically solved by a lattice Boltzmann scheme (the D3Q7 model). The fluid flow is modelled by the lattice Boltzmann equations and numerically solved by the D3Q19 model. The deformable structure and the fluid-structure-interaction are handled by the immersed boundary method. As an application, we study a FSI toy problem - interaction of an elastic plate (flapped at its leading edge and restricted nowhere else) with a non-Newtonian fluid in a 3D flow. Thanks to the support of NSF-DMS support under research Grant 1522554.

Mixture models with entropy regularization for community detection in networks

NASA Astrophysics Data System (ADS)

Chang, Zhenhai; Yin, Xianjun; Jia, Caiyan; Wang, Xiaoyang

2018-04-01

Community detection is a key exploratory tool in network analysis and has received much attention in recent years. NMM (Newman's mixture model) is one of the best models for exploring a range of network structures including community structure, bipartite and core-periphery structures, etc. However, NMM needs to know the number of communities in advance. Therefore, in this study, we have proposed an entropy regularized mixture model (called EMM), which is capable of inferring the number of communities and identifying network structure contained in a network, simultaneously. In the model, by minimizing the entropy of mixing coefficients of NMM using EM (expectation-maximization) solution, the small clusters contained little information can be discarded step by step. The empirical study on both synthetic networks and real networks has shown that the proposed model EMM is superior to the state-of-the-art methods.

Bridge-in-a-backpack(TM) : task 3.2: investigating soil - structure interaction - modeling and experimental results of steel arches.

DOT National Transportation Integrated Search

2015-07-01

This report includes fulfillment of Task 3.2 of a multi-task contract to further enhance concrete filled FRP tubes, or : the Bridge in a Backpack. Task 3 is an investigation of soil-structure interaction for the FRP tubes. Task 3.2 is the : modeling ...

Bridge-in-a-backpack(TM) task 3.3 : investigate soil-structure interaction-modeling and experimental results of concrete filled FRP tube arches.

DOT National Transportation Integrated Search

2015-12-01

This report includes fulfillment of Task 3.3 of a multi-task contract to further enhance concrete filled FRP tubes, or : the Bridge in a Backpack. Task 3 is an investigation of soil-structure interaction for the FRP tubes. Task 3.3 is the : modeling ...

A Model of Sexual Abuse's Effects on Suicidal Behavior and Delinquency: The Role of Emotions as Mediating Factors

ERIC Educational Resources Information Center

Sigfusdottir, Inga Dora; Asgeirsdottir, Bryndis Bjork; Gudjonsson, Gisli H.; Sigurdsson, Jon Fridrik

2008-01-01

Drawing on Agnew's general strain theory, we examined whether depressed mood and anger mediated the effects of sexual abuse on suicidal behavior and delinquency. Participants included 9,113 students attending high schools in Iceland. Structural equation modeling showed that, while controlling for family structure and parental education, being…

Adhesive in the buckling failure of corrugated fiberboard : a finite element investigation

Treesearch

Adeeb A. Rahman; Said M. Abubakr

1998-01-01

This research study proposed to include the glue material in a finite element model that represents the actual geometry and material properties of a corrugated fiberboard. The model is a detailed representation of the different components of the structure (adhesive, linerboard, medium) to perform buckling analysis of corrugated structures under compressive loads. The...

School Attendance Problems and Youth Psychopathology: Structural Cross-Lagged Regression Models in Three Longitudinal Data Sets

ERIC Educational Resources Information Center

Wood, Jeffrey J.; Lynne-Landsman, Sarah D.; Langer, David A.; Wood, Patricia A.; Clark, Shaunna L.; Eddy, J. Mark; Ialongo, Nick

2012-01-01

This study tests a model of reciprocal influences between absenteeism and youth psychopathology using 3 longitudinal datasets (Ns = 20,745, 2,311, and 671). Participants in 1st through 12th grades were interviewed annually or biannually. Measures of psychopathology include self-, parent-, and teacher-report questionnaires. Structural cross-lagged…

Proximal and Distal Outcomes of Organizational Socialization among New Teachers: A Mediation Analysis

ERIC Educational Resources Information Center

Tengku Ariffin, Tengku Faekah; Awang Hashim, Rosna; Yusof, Norhafezah

2014-01-01

This study was designed to examine the relationship between socialization experience and the task performance of new teachers. It proposed to do this by testing a structural model. In explicating the relationship between the two constructs, teacher engagement in workplace learning activities and wellbeing were included in the structural model as…

Understanding the Impact of Trauma Exposure on Posttraumatic Stress Symptomatology: A Structural Equation Modeling Approach

ERIC Educational Resources Information Center

Chen, Wei; Wang, Long; Zhang, Xing-Li; Shi, Jian-Nong

2012-01-01

The objective of this study was to investigate the impact of trauma exposure on the posttraumatic stress symptomatology (PTSS) of children who resided near the epicenter of the 2008 Wenchuan earthquake. The mechanisms of this impact were explored via structural equation models with self-esteem and coping strategies included as mediators. The…

Structure Prediction of the Second Extracellular Loop in G-Protein-Coupled Receptors

PubMed Central

Kmiecik, Sebastian; Jamroz, Michal; Kolinski, Michal

2014-01-01

G-protein-coupled receptors (GPCRs) play key roles in living organisms. Therefore, it is important to determine their functional structures. The second extracellular loop (ECL2) is a functionally important region of GPCRs, which poses significant challenge for computational structure prediction methods. In this work, we evaluated CABS, a well-established protein modeling tool for predicting ECL2 structure in 13 GPCRs. The ECL2s (with between 13 and 34 residues) are predicted in an environment of other extracellular loops being fully flexible and the transmembrane domain fixed in its x-ray conformation. The modeling procedure used theoretical predictions of ECL2 secondary structure and experimental constraints on disulfide bridges. Our approach yielded ensembles of low-energy conformers and the most populated conformers that contained models close to the available x-ray structures. The level of similarity between the predicted models and x-ray structures is comparable to that of other state-of-the-art computational methods. Our results extend other studies by including newly crystallized GPCRs. PMID:24896119

A generic model for the shallow velocity structure of volcanoes

NASA Astrophysics Data System (ADS)

Lesage, Philippe; Heap, Michael J.; Kushnir, Alexandra

2018-05-01

The knowledge of the structure of volcanoes and of the physical properties of volcanic rocks is of paramount importance to the understanding of volcanic processes and the interpretation of monitoring observations. However, the determination of these structures by geophysical methods suffers limitations including a lack of resolution and poor precision. Laboratory experiments provide complementary information on the physical properties of volcanic materials and their behavior as a function of several parameters including pressure and temperature. Nevertheless combined studies and comparisons of field-based geophysical and laboratory-based physical approaches remain scant in the literature. Here, we present a meta-analysis which compares 44 seismic velocity models of the shallow structure of eleven volcanoes, laboratory velocity measurements on about one hundred rock samples from five volcanoes, and seismic well-logs from deep boreholes at two volcanoes. The comparison of these measurements confirms the strong variability of P- and S-wave velocities, which reflects the diversity of volcanic materials. The values obtained from laboratory experiments are systematically larger than those provided by seismic models. This discrepancy mainly results from scaling problems due to the difference between the sampled volumes. The averages of the seismic models are characterized by very low velocities at the surface and a strong velocity increase at shallow depth. By adjusting analytical functions to these averages, we define a generic model that can describe the variations in P- and S-wave velocities in the first 500 m of andesitic and basaltic volcanoes. This model can be used for volcanoes where no structural information is available. The model can also account for site time correction in hypocenter determination as well as for site and path effects that are commonly observed in volcanic structures.

The Quality and Validation of Structures from Structural Genomics

PubMed Central

Domagalski, Marcin J.; Zheng, Heping; Zimmerman, Matthew D.; Dauter, Zbigniew; Wlodawer, Alexander; Minor, Wladek

2014-01-01

Quality control of three-dimensional structures of macromolecules is a critical step to ensure the integrity of structural biology data, especially those produced by structural genomics centers. Whereas the Protein Data Bank (PDB) has proven to be a remarkable success overall, the inconsistent quality of structures reveals a lack of universal standards for structure/deposit validation. Here, we review the state-of-the-art methods used in macromolecular structure validation, focusing on validation of structures determined by X-ray crystallography. We describe some general protocols used in the rebuilding and re-refinement of problematic structural models. We also briefly discuss some frontier areas of structure validation, including refinement of protein–ligand complexes, automation of structure redetermination, and the use of NMR structures and computational models to solve X-ray crystal structures by molecular replacement. PMID:24203341

A multiphysics and multiscale model for low frequency electromagnetic direct-chill casting

NASA Astrophysics Data System (ADS)

Košnik, N.; Guštin, A. Z.; Mavrič, B.; Šarler, B.

2016-03-01

Simulation and control of macrosegregation, deformation and grain size in low frequency electromagnetic (EM) direct-chill casting (LFEMC) is important for downstream processing. Respectively, a multiphysics and multiscale model is developed for solution of Lorentz force, temperature, velocity, concentration, deformation and grain structure of LFEMC processed aluminum alloys, with focus on axisymmetric billets. The mixture equations with lever rule, linearized phase diagram, and stationary thermoelastic solid phase are assumed, together with EM induction equation for the field imposed by the coil. Explicit diffuse approximate meshless solution procedure [1] is used for solving the EM field, and the explicit local radial basis function collocation method [2] is used for solving the coupled transport phenomena and thermomechanics fields. Pressure-velocity coupling is performed by the fractional step method [3]. The point automata method with modified KGT model is used to estimate the grain structure [4] in a post-processing mode. Thermal, mechanical, EM and grain structure outcomes of the model are demonstrated. A systematic study of the complicated influences of the process parameters can be investigated by the model, including intensity and frequency of the electromagnetic field. The meshless solution framework, with the implemented simplest physical models, will be further extended by including more sophisticated microsegregation and grain structure models, as well as a more realistic solid and solid-liquid phase rheology.

Experimental application of OMA solutions on the model of industrial structure

NASA Astrophysics Data System (ADS)

Mironov, A.; Mironovs, D.

2017-10-01

It is very important and sometimes even vital to maintain reliability of industrial structures. High quality control during production and structural health monitoring (SHM) in exploitation provides reliable functioning of large, massive and remote structures, like wind generators, pipelines, power line posts, etc. This paper introduces a complex of technological and methodical solutions for SHM and diagnostics of industrial structures, including those that are actuated by periodic forces. Solutions were verified on a wind generator scaled model with integrated system of piezo-film deformation sensors. Simultaneous and multi-patch Operational Modal Analysis (OMA) approaches were implemented as methodical means for structural diagnostics and monitoring. Specially designed data processing algorithms provide objective evaluation of structural state modification.

QSAR modeling based on structure-information for properties of interest in human health.

PubMed

Hall, L H; Hall, L M

2005-01-01

The development of QSAR models based on topological structure description is presented for problems in human health. These models are based on the structure-information approach to quantitative biological modeling and prediction, in contrast to the mechanism-based approach. The structure-information approach is outlined, starting with basic structure information developed from the chemical graph (connection table). Information explicit in the connection table (element identity and skeletal connections) leads to significant (implicit) structure information that is useful for establishing sound models of a wide range of properties of interest in drug design. Valence state definition leads to relationships for valence state electronegativity and atom/group molar volume. Based on these important aspects of molecules, together with skeletal branching patterns, both the electrotopological state (E-state) and molecular connectivity (chi indices) structure descriptors are developed and described. A summary of four QSAR models indicates the wide range of applicability of these structure descriptors and the predictive quality of QSAR models based on them: aqueous solubility (5535 chemically diverse compounds, 938 in external validation), percent oral absorption (%OA, 417 therapeutic drugs, 195 drugs in external validation testing), AMES mutagenicity (2963 compounds including 290 therapeutic drugs, 400 in external validation), fish toxicity (92 substituted phenols, anilines and substituted aromatics). These models are established independent of explicit three-dimensional (3-D) structure information and are directly interpretable in terms of the implicit structure information useful to the drug design process.

Long-Term Structural Health Monitoring System for a High-Speed Railway Bridge Structure

PubMed Central

Wu, Lai-Yi

2015-01-01

Nanjing Dashengguan Bridge, which serves as the shared corridor crossing Yangtze River for both Beijing-Shanghai high-speed railway and Shanghai-Wuhan-Chengdu railway, is the first 6-track high-speed railway bridge with the longest span throughout the world. In order to ensure safety and detect the performance deterioration during the long-time service of the bridge, a Structural Health Monitoring (SHM) system has been implemented on this bridge by the application of modern techniques in sensing, testing, computing, and network communication. The SHM system includes various sensors as well as corresponding data acquisition and transmission equipment for automatic data collection. Furthermore, an evaluation system of structural safety has been developed for the real-time condition assessment of this bridge. The mathematical correlation models describing the overall structural behavior of the bridge can be obtained with the support of the health monitoring system, which includes cross-correlation models for accelerations, correlation models between temperature and static strains of steel truss arch, and correlation models between temperature and longitudinal displacements of piers. Some evaluation results using the mean value control chart based on mathematical correlation models are presented in this paper to show the effectiveness of this SHM system in detecting the bridge's abnormal behaviors under the varying environmental conditions such as high-speed trains and environmental temperature. PMID:26451387

The Interiors of Jupiter and Saturn

NASA Astrophysics Data System (ADS)

Helled, Ravit

2018-05-01

Probing the interiors of the giant planets in our Solar System is not an easy task. This requires a set of observations combined with theoretical models that are used to infer the planetary composition and its depth dependence. The masses of Jupiter and Saturn are 318 and 96 Earth masses, respectively, and since a few decades, we know that they mostly consist of hydrogen and helium. It is the mass of heavy elements (all elements heavier than helium) that is not well determined, as well as its distribution within the planets. While the heavy elements are not the dominating materials in Jupiter and Saturn, they are the key for our understanding of their formation and evolution histories. The planetary internal structure is inferred to fit the available observational constraints including the planetary masses, radii, 1-bar temperatures, rotation rates, and gravitational fields. Then, using theoretical equations of states (EOSs) for hydrogen, helium, their mixtures, and heavier elements (typically rocks and/or ices), a structure model is developed. However, there is no unique solution for the planetary structure, and the results depend on the used EOSs and the model assumptions imposed by the modeler. Standard interior models of Jupiter and Saturn include three main regions: (1) the central region (core) that consists of heavy elements, (2) an inner metallic hydrogen envelope that is helium rich, and (3) an outer molecular hydrogen envelope depleted with helium. The distribution of heavy elements can be either homogenous or discontinuous between the two envelopes. Major model assumptions that can affect the derived internal structure include the number of layers, the heat transport mechanism within the planet (and its entropy), the nature of the core (compact vs. diluted), and the location/pressure where the envelopes are divided. Alternative structure models assume a less distinct division between the layers and/or a less non-homogenous distribution of the heavy elements. The fact that the behavior of hydrogen at high pressures and temperatures in not perfectly known, and that helium separates from hydrogen at the deep interior add sources of uncertainties to the interior model. Today, with accurate measurements of the gravitational fields of Jupiter and Saturn from the Juno and Cassini missions, structure models can be further constrained. At the same time, these measurements introduce new challenges and open question for planetary modelers.

The Theory of Planned Behavior as a Model of Heavy Episodic Drinking Among College Students

PubMed Central

Collins, Susan E.; Carey, Kate B.

2008-01-01

This study provided a simultaneous, confirmatory test of the theory of planned behavior (TPB) in predicting heavy episodic drinking (HED) among college students. It was hypothesized that past HED, drinking attitudes, subjective norms and drinking refusal self-efficacy would predict intention, which would in turn predict future HED. Participants consisted of 131 college drinkers (63% female) who reported having engaged in HED in the previous two weeks. Participants were recruited and completed questionnaires within the context of a larger intervention study (see Collins & Carey, 2005). Latent factor structural equation modeling was used to test the ability of the TPB to predict HED. Chi-square tests and fit indices indicated good fit for the final structural models. Self-efficacy and attitudes but not subjective norms significantly predicted baseline intention, and intention and past HED predicted future HED. Contrary to hypotheses, however, a structural model excluding past HED provided a better fit than a model including it. Although further studies must be conducted before a definitive conclusion is reached, a TPB model excluding past behavior, which is arguably more parsimonious and theory driven, may provide better prediction of HED among college drinkers than a model including past behavior. PMID:18072832

An "age"-structured model of hematopoietic stem cell organization with application to chronic myeloid leukemia.

PubMed

Roeder, Ingo; Herberg, Maria; Horn, Matthias

2009-04-01

Previously, we have modeled hematopoietic stem cell organization by a stochastic, single cell-based approach. Applications to different experimental systems demonstrated that this model consistently explains a broad variety of in vivo and in vitro data. A major advantage of the agent-based model (ABM) is the representation of heterogeneity within the hematopoietic stem cell population. However, this advantage comes at the price of time-consuming simulations if the systems become large. One example in this respect is the modeling of disease and treatment dynamics in patients with chronic myeloid leukemia (CML), where the realistic number of individual cells to be considered exceeds 10(6). To overcome this deficiency, without losing the representation of the inherent heterogeneity of the stem cell population, we here propose to approximate the ABM by a system of partial differential equations (PDEs). The major benefit of such an approach is its independence from the size of the system. Although this mean field approach includes a number of simplifying assumptions compared to the ABM, it retains the key structure of the model including the "age"-structure of stem cells. We show that the PDE model qualitatively and quantitatively reproduces the results of the agent-based approach.

In silico modeling to predict drug-induced phospholipidosis

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

Choi, Sydney S.; Kim, Jae S.; Valerio, Luis G., E-mail: luis.valerio@fda.hhs.gov

2013-06-01

Drug-induced phospholipidosis (DIPL) is a preclinical finding during pharmaceutical drug development that has implications on the course of drug development and regulatory safety review. A principal characteristic of drugs inducing DIPL is known to be a cationic amphiphilic structure. This provides evidence for a structure-based explanation and opportunity to analyze properties and structures of drugs with the histopathologic findings for DIPL. In previous work from the FDA, in silico quantitative structure–activity relationship (QSAR) modeling using machine learning approaches has shown promise with a large dataset of drugs but included unconfirmed data as well. In this study, we report the constructionmore » and validation of a battery of complementary in silico QSAR models using the FDA's updated database on phospholipidosis, new algorithms and predictive technologies, and in particular, we address high performance with a high-confidence dataset. The results of our modeling for DIPL include rigorous external validation tests showing 80–81% concordance. Furthermore, the predictive performance characteristics include models with high sensitivity and specificity, in most cases above ≥ 80% leading to desired high negative and positive predictivity. These models are intended to be utilized for regulatory toxicology applied science needs in screening new drugs for DIPL. - Highlights: • New in silico models for predicting drug-induced phospholipidosis (DIPL) are described. • The training set data in the models is derived from the FDA's phospholipidosis database. • We find excellent predictivity values of the models based on external validation. • The models can support drug screening and regulatory decision-making on DIPL.« less

Constitutive modeling and control of 1D smart composite structures

NASA Astrophysics Data System (ADS)

Briggs, Jonathan P.; Ostrowski, James P.; Ponte-Castaneda, Pedro

1998-07-01

Homogenization techniques for determining effective properties of composite materials may provide advantages for control of stiffness and strain in systems using hysteretic smart actuators embedded in a soft matrix. In this paper, a homogenized model of a 1D composite structure comprised of shape memory alloys and a rubber-like matrix is presented. With proportional and proportional/integral feedback, using current as the input state and global strain as an error state, implementation scenarios include the use of tractions on the boundaries and a nonlinear constitutive law for the matrix. The result is a simple model which captures the nonlinear behavior of the smart composite material system and is amenable to experiments with various control paradigms. The success of this approach in the context of the 1D model suggests that the homogenization method may prove useful in investigating control of more general smart structures. Applications of such materials could include active rehabilitation aids, e.g. wrist braces, as well as swimming/undulating robots, or adaptive molds for manufacturing processes.

Experimental analysis and constitutive modelling of steel of A-IIIN strength class

NASA Astrophysics Data System (ADS)

Kruszka, Leopold; Janiszewski, Jacek

2015-09-01

Fundamentally important is the better understanding of behaviour of new building steels under impact loadings, including plastic deformations. Results of the experimental analysis in wide range of strain rates in compression at room temperature, as well as constitutive modelling for and B500SP structural steels of new A-IIIN Polish strength class, examined dynamically by split Hopkinson pressure bar technique at high strain rates, are presented in table and graphic forms. Dynamic mechanical characteristics of compressive strength for tested building structural steel are determined as well as dynamic mechanical properties of this material are compared with 18G2-b steel of A-II strength class, including effects of the shape of tested specimens, i.e. their slenderness. The paper focuses the attention on those experimental tests, their interpretation, and constitutive semi-empirical modelling of the behaviour of tested steels based on Johnson-Cook's model. Obtained results of analyses presented here are used for designing and numerical simulations of reinforced concrete protective structures.

Modeling our understanding of the His-Purkinje system.

PubMed

Vigmond, Edward J; Stuyvers, Bruno D

2016-01-01

The His-Purkinje System (HPS) is responsible for the rapid electric conduction in the ventricles. It relays electrical impulses from the atrioventricular node to the muscle cells and, thus, coordinates the contraction of ventricles in order to ensure proper cardiac pump function. The HPS has been implicated in the genesis of ventricular tachycardia and fibrillation as a source of ectopic beats, as well as forming distinct portions of reentry circuitry. Despite its importance, it remains much less well characterized, structurally and functionally, than the myocardium. Notably, important differences exist with regard to cell structure and electrophysiology, including ion channels, intracellular calcium handling, and gap junctions. Very few computational models address the HPS, and the majority of organ level modeling studies omit it. This review will provide an overview of our current knowledge of structure and function (including electrophysiology) of the HPS. We will review the most recent advances in modeling of the system from the single cell to the organ level, with considerations for relevant interspecies distinctions. Copyright © 2015 Elsevier Ltd. All rights reserved.

Modeling process-structure-property relationships for additive manufacturing

NASA Astrophysics Data System (ADS)

Yan, Wentao; Lin, Stephen; Kafka, Orion L.; Yu, Cheng; Liu, Zeliang; Lian, Yanping; Wolff, Sarah; Cao, Jian; Wagner, Gregory J.; Liu, Wing Kam

2018-02-01

This paper presents our latest work on comprehensive modeling of process-structure-property relationships for additive manufacturing (AM) materials, including using data-mining techniques to close the cycle of design-predict-optimize. To illustrate the processstructure relationship, the multi-scale multi-physics process modeling starts from the micro-scale to establish a mechanistic heat source model, to the meso-scale models of individual powder particle evolution, and finally to the macro-scale model to simulate the fabrication process of a complex product. To link structure and properties, a highefficiency mechanistic model, self-consistent clustering analyses, is developed to capture a variety of material response. The model incorporates factors such as voids, phase composition, inclusions, and grain structures, which are the differentiating features of AM metals. Furthermore, we propose data-mining as an effective solution for novel rapid design and optimization, which is motivated by the numerous influencing factors in the AM process. We believe this paper will provide a roadmap to advance AM fundamental understanding and guide the monitoring and advanced diagnostics of AM processing.

Workshop on the Tectonic Evolution of Greenstone Belts (supplement containing abstracts of invited talks and late abstracts)

NASA Technical Reports Server (NTRS)

1986-01-01

Topics addressed include: greenstone belt tectonics, thermal constaints, geological structure, rock components, crustal accretion model, geological evolution, synsedimentary deformation, Archean structures and geological faults.

General Retarded Contact Self-energies in and beyond the Non-equilibrium Green's Functions Method

NASA Astrophysics Data System (ADS)

Kubis, Tillmann; He, Yu; Andrawis, Robert; Klimeck, Gerhard

2016-03-01

Retarded contact self-energies in the framework of nonequilibrium Green's functions allow to model the impact of lead structures on the device without explicitly including the leads in the actual device calculation. Most of the contact self-energy algorithms are limited to homogeneous or periodic, semi-infinite lead structures. In this work, the complex absorbing potential method is extended to solve retarded contact self-energies for arbitrary lead structures, including irregular and randomly disordered leads. This method is verified for regular leads against common approaches and on physically equivalent, but numerically different irregular leads. Transmission results on randomly alloyed In0.5Ga0.5As structures show the importance of disorder in the leads. The concept of retarded contact self-energies is expanded to model passivation of atomically resolved surfaces without explicitly increasing the device's Hamiltonian.

Measurement Model Specification Error in LISREL Structural Equation Models.

ERIC Educational Resources Information Center

Baldwin, Beatrice; Lomax, Richard

This LISREL study examines the robustness of the maximum likelihood estimates under varying degrees of measurement model misspecification. A true model containing five latent variables (two endogenous and three exogenous) and two indicator variables per latent variable was used. Measurement model misspecification considered included errors of…

Evaluation of integration methods for hybrid simulation of complex structural systems through collapse

NASA Astrophysics Data System (ADS)

Del Carpio R., Maikol; Hashemi, M. Javad; Mosqueda, Gilberto

2017-10-01

This study examines the performance of integration methods for hybrid simulation of large and complex structural systems in the context of structural collapse due to seismic excitations. The target application is not necessarily for real-time testing, but rather for models that involve large-scale physical sub-structures and highly nonlinear numerical models. Four case studies are presented and discussed. In the first case study, the accuracy of integration schemes including two widely used methods, namely, modified version of the implicit Newmark with fixed-number of iteration (iterative) and the operator-splitting (non-iterative) is examined through pure numerical simulations. The second case study presents the results of 10 hybrid simulations repeated with the two aforementioned integration methods considering various time steps and fixed-number of iterations for the iterative integration method. The physical sub-structure in these tests consists of a single-degree-of-freedom (SDOF) cantilever column with replaceable steel coupons that provides repeatable highlynonlinear behavior including fracture-type strength and stiffness degradations. In case study three, the implicit Newmark with fixed-number of iterations is applied for hybrid simulations of a 1:2 scale steel moment frame that includes a relatively complex nonlinear numerical substructure. Lastly, a more complex numerical substructure is considered by constructing a nonlinear computational model of a moment frame coupled to a hybrid model of a 1:2 scale steel gravity frame. The last two case studies are conducted on the same porotype structure and the selection of time steps and fixed number of iterations are closely examined in pre-test simulations. The generated unbalance forces is used as an index to track the equilibrium error and predict the accuracy and stability of the simulations.

Traffic Circle Model

DOT National Transportation Integrated Search

1971-05-01

The report describes a dynamic model of a traffic circle which has been implemented on a CRT display terminal. The model includes sufficient parameters to allow changes in the structure of the traffic circle, the frequency of traffic introduced to th...

Data-assisted protein structure modeling by global optimization in CASP12.

PubMed

Joo, Keehyoung; Heo, Seungryong; Joung, InSuk; Hong, Seung Hwan; Lee, Sung Jong; Lee, Jooyoung

2018-03-01

In CASP12, 2 types of data-assisted protein structure modeling were experimented. Either SAXS experimental data or cross-linking experimental data was provided for a selected number of CASP12 targets that the CASP12 predictor could utilize for better protein structure modeling. We devised 2 separate energy terms for SAXS data and cross-linking data to drive the model structures into more native-like structures that satisfied the given experimental data as much as possible. In CASP11, we successfully performed protein structure modeling using simulated sparse and ambiguously assigned NOE data and/or correct residue-residue contact information, where the only energy term that folded the protein into its native structure was the term which was originated from the given experimental data. However, the 2 types of experimental data provided in CASP12 were far from being sufficient enough to fold the target protein into its native structure because SAXS data provides only the overall shape of the molecule and the cross-linking contact information provides only very low-resolution distance information. For this reason, we combined the SAXS or cross-linking energy term with our regular modeling energy function that includes both the template energy term and the de novo energy terms. By optimizing the newly formulated energy function, we obtained protein models that fit better with provided SAXS data than the X-ray structure of the target. However, the improvement of the model relative to the 1 modeled without the SAXS data, was not significant. Consistent structural improvement was achieved by incorporating cross-linking data into the protein structure modeling. © 2018 Wiley Periodicals, Inc.

Structurally Controlled Geothermal Systems in the Central Cascades Arc-Backarc Regime, Oregon

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

Wannamaker, Philip E.

The goal of this project has been to analyze available magnetotelluric (MT) geophysical surveys, structural geology based on mapping and LiDAR, and fluid geochemical data, to identify high-temperature fluid upwellings, critically stressed rock volumes, and other evidence of structurally-controlled geothermal resources. Data were to be integrated to create conceptual models of volcanic-hosted geothermal resources along the Central Cascades arc segment, especially in the vicinity of Mt. Jefferson to Three Sisters. LiDAR data sets available at Oregon State University (OSU) allowed detailed structural geology modeling through forest canopy. Copious spring and well fluid chemistries, including isotopes, were modeled using Geo-T andmore » TOUGHREACT software.« less

Initial dynamic load estimates during configuration design

NASA Technical Reports Server (NTRS)

Schiff, Daniel

1987-01-01

This analysis includes the structural response to shock and vibration and evaluates the maximum deflections and material stresses and the potential for the occurrence of elastic instability, fatigue and fracture. The required computations are often performed by means of finite element analysis (FEA) computer programs in which the structure is simulated by a finite element model which may contain thousands of elements. The formulation of a finite element model can be time consuming, and substantial additional modeling effort may be necessary if the structure requires significant changes after initial analysis. Rapid methods for obtaining rough estimates of the structural response to shock and vibration are presented for the purpose of providing guidance during the initial mechanical design configuration stage.

Recent Developments in Smart Adaptive Structures for Solar Sailcraft

NASA Technical Reports Server (NTRS)

Whorton, M. S.; Kim, Y. K.; Oakley, J.; Adetona, O.; Keel, L. H.

2007-01-01

The "Smart Adaptive Structures for Solar Sailcraft" development activity at MSFC has investigated issues associated with understanding how to model and scale the subsystem and multi-body system dynamics of a gossamer solar sailcraft with the objective of designing sailcraft attitude control systems. This research and development activity addressed three key tasks that leveraged existing facilities and core competencies of MSFC to investigate dynamics and control issues of solar sails. Key aspects of this effort included modeling and testing of a 30 m deployable boom; modeling of the multi-body system dynamics of a gossamer sailcraft; investigation of control-structures interaction for gossamer sailcraft; and development and experimental demonstration of adaptive control technologies to mitigate control-structures interaction.

System Model for MEMS based Laser Ultrasonic Receiver

NASA Technical Reports Server (NTRS)

Wilson, William C.

2002-01-01

A need has been identified for more advanced nondestructive Evaluation technologies for assuring the integrity of airframe structures, wiring, etc. Laser ultrasonic inspection instruments have been shown to detect flaws in structures. However, these instruments are generally too bulky to be used in the confined spaces that are typical of aerospace vehicles. Microsystems technology is one key to reducing the size of current instruments and enabling increased inspection coverage in areas that were previously inaccessible due to instrument size and weight. This paper investigates the system modeling of a Micro OptoElectroMechanical System (MOEMS) based laser ultrasonic receiver. The system model is constructed in software using MATLAB s dynamical simulator, Simulink. The optical components are modeled using geometrical matrix methods and include some image processing. The system model includes a test bench which simulates input stimuli and models the behavior of the material under test.

The Relation Between Rotation Deformity and Nerve Root Stress in Lumbar Scoliosis

NASA Astrophysics Data System (ADS)

Kim, Ho-Joong; Lee, Hwan-Mo; Moon, Seong-Hwan; Chun, Heoung-Jae; Kang, Kyoung-Tak

Even though several finite element models of lumbar spine were introduced, there has been no model including the neural structure. Therefore, the authors made the novel lumbar spine finite element model including neural structure. Using this model, we investigated the relation between the deformity pattern and nerve root stress. Two lumbar models with different types of curve pattern (lateral bending and lateral bending with rotation curve) were made. In the model of lateral bending curves without rotation, the principal compressive nerve root stress on the concave side was greater than the principal tensile stress on the convex side at the apex vertebra. Contrarily, in the lateral bending curve with rotational deformity, the nerve stress on the convex side was higher than that on the concave side. Therefore, this study elicit that deformity pattern could have significantly influence on the nerve root stress in the lumbar spine.

A Review of the Combination of Experimental Measurements and Fibril-Reinforced Modeling for Investigation of Articular Cartilage and Chondrocyte Response to Loading

PubMed Central

Wilson, Wouter; Isaksson, Hanna; Jurvelin, Jukka S.; Herzog, Walter; Korhonen, Rami K.

2013-01-01

The function of articular cartilage depends on its structure and composition, sensitively impaired in disease (e.g. osteoarthritis, OA). Responses of chondrocytes to tissue loading are modulated by the structure. Altered cell responses as an effect of OA may regulate cartilage mechanotransduction and cell biosynthesis. To be able to evaluate cell responses and factors affecting the onset and progression of OA, local tissue and cell stresses and strains in cartilage need to be characterized. This is extremely challenging with the presently available experimental techniques and therefore computational modeling is required. Modern models of articular cartilage are inhomogeneous and anisotropic, and they include many aspects of the real tissue structure and composition. In this paper, we provide an overview of the computational applications that have been developed for modeling the mechanics of articular cartilage at the tissue and cellular level. We concentrate on the use of fibril-reinforced models of cartilage. Furthermore, we introduce practical considerations for modeling applications, including also experimental tests that can be combined with the modeling approach. At the end, we discuss the prospects for patient-specific models when aiming to use finite element modeling analysis and evaluation of articular cartilage function, cellular responses, failure points, OA progression, and rehabilitation. PMID:23653665

Integrated analysis of engine structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1981-01-01

The need for light, durable, fuel efficient, cost effective aircraft requires the development of engine structures which are flexible, made from advaced materials (including composites), resist higher temperatures, maintain tighter clearances and have lower maintenance costs. The formal quantification of any or several of these requires integrated computer programs (multilevel and/or interdisciplinary analysis programs interconnected) for engine structural analysis/design. Several integrated analysis computer prorams are under development at Lewis Reseach Center. These programs include: (1) COBSTRAN-Composite Blade Structural Analysis, (2) CODSTRAN-Composite Durability Structural Analysis, (3) CISTRAN-Composite Impact Structural Analysis, (4) STAEBL-StruTailoring of Engine Blades, and (5) ESMOSS-Engine Structures Modeling Software System. Three other related programs, developed under Lewis sponsorship, are described.

Computer support for physiological cell modelling using an ontology on cell physiology.

PubMed

Takao, Shimayoshi; Kazuhiro, Komurasaki; Akira, Amano; Takeshi, Iwashita; Masanori, Kanazawa; Tetsuya, Matsuda

2006-01-01

The development of electrophysiological whole cell models to support the understanding of biological mechanisms is increasing rapidly. Due to the complexity of biological systems, comprehensive cell models, which are composed of many imported sub-models of functional elements, can get quite complicated as well, making computer modification difficult. Here, we propose a computer support to enhance structural changes of cell models, employing the markup languages CellML and our original PMSML (physiological model structure markup language), in addition to a new ontology for cell physiological modelling. In particular, a method to make references from CellML files to the ontology and a method to assist manipulation of model structures using markup languages together with the ontology are reported. Using these methods three software utilities, including a graphical model editor, are implemented. Experimental results proved that these methods are effective for the modification of electrophysiological models.

Modelling Spatial Dependence Structures Between Climate Variables by Combining Mixture Models with Copula Models

NASA Astrophysics Data System (ADS)

Khan, F.; Pilz, J.; Spöck, G.

2017-12-01

Spatio-temporal dependence structures play a pivotal role in understanding the meteorological characteristics of a basin or sub-basin. This further affects the hydrological conditions and consequently will provide misleading results if these structures are not taken into account properly. In this study we modeled the spatial dependence structure between climate variables including maximum, minimum temperature and precipitation in the Monsoon dominated region of Pakistan. For temperature, six, and for precipitation four meteorological stations have been considered. For modelling the dependence structure between temperature and precipitation at multiple sites, we utilized C-Vine, D-Vine and Student t-copula models. For temperature, multivariate mixture normal distributions and for precipitation gamma distributions have been used as marginals under the copula models. A comparison was made between C-Vine, D-Vine and Student t-copula by observational and simulated spatial dependence structure to choose an appropriate model for the climate data. The results show that all copula models performed well, however, there are subtle differences in their performances. The copula models captured the patterns of spatial dependence structures between climate variables at multiple meteorological sites, however, the t-copula showed poor performance in reproducing the dependence structure with respect to magnitude. It was observed that important statistics of observed data have been closely approximated except of maximum values for temperature and minimum values for minimum temperature. Probability density functions of simulated data closely follow the probability density functions of observational data for all variables. C and D-Vines are better tools when it comes to modelling the dependence between variables, however, Student t-copulas compete closely for precipitation. Keywords: Copula model, C-Vine, D-Vine, Spatial dependence structure, Monsoon dominated region of Pakistan, Mixture models, EM algorithm.

A benchmark testing ground for integrating homology modeling and protein docking.

PubMed

Bohnuud, Tanggis; Luo, Lingqi; Wodak, Shoshana J; Bonvin, Alexandre M J J; Weng, Zhiping; Vajda, Sandor; Schueler-Furman, Ora; Kozakov, Dima

2017-01-01

Protein docking procedures carry out the task of predicting the structure of a protein-protein complex starting from the known structures of the individual protein components. More often than not, however, the structure of one or both components is not known, but can be derived by homology modeling on the basis of known structures of related proteins deposited in the Protein Data Bank (PDB). Thus, the problem is to develop methods that optimally integrate homology modeling and docking with the goal of predicting the structure of a complex directly from the amino acid sequences of its component proteins. One possibility is to use the best available homology modeling and docking methods. However, the models built for the individual subunits often differ to a significant degree from the bound conformation in the complex, often much more so than the differences observed between free and bound structures of the same protein, and therefore additional conformational adjustments, both at the backbone and side chain levels need to be modeled to achieve an accurate docking prediction. In particular, even homology models of overall good accuracy frequently include localized errors that unfavorably impact docking results. The predicted reliability of the different regions in the model can also serve as a useful input for the docking calculations. Here we present a benchmark dataset that should help to explore and solve combined modeling and docking problems. This dataset comprises a subset of the experimentally solved 'target' complexes from the widely used Docking Benchmark from the Weng Lab (excluding antibody-antigen complexes). This subset is extended to include the structures from the PDB related to those of the individual components of each complex, and hence represent potential templates for investigating and benchmarking integrated homology modeling and docking approaches. Template sets can be dynamically customized by specifying ranges in sequence similarity and in PDB release dates, or using other filtering options, such as excluding sets of specific structures from the template list. Multiple sequence alignments, as well as structural alignments of the templates to their corresponding subunits in the target are also provided. The resource is accessible online or can be downloaded at http://cluspro.org/benchmark, and is updated on a weekly basis in synchrony with new PDB releases. Proteins 2016; 85:10-16. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Fluid-structure interaction including volumetric coupling with homogenised subdomains for modeling respiratory mechanics.

PubMed

Yoshihara, Lena; Roth, Christian J; Wall, Wolfgang A

2017-04-01

In this article, a novel approach is presented for combining standard fluid-structure interaction with additional volumetric constraints to model fluid flow into and from homogenised solid domains. The proposed algorithm is particularly interesting for investigations in the field of respiratory mechanics as it enables the mutual coupling of airflow in the conducting part and local tissue deformation in the respiratory part of the lung by means of a volume constraint. In combination with a classical monolithic fluid-structure interaction approach, a comprehensive model of the human lung can be established that will be useful to gain new insights into respiratory mechanics in health and disease. To illustrate the validity and versatility of the novel approach, three numerical examples including a patient-specific lung model are presented. The proposed algorithm proves its capability of computing clinically relevant airflow distribution and tissue strain data at a level of detail that is not yet achievable, neither with current imaging techniques nor with existing computational models. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

TED Study of Si(113) Surfaces

NASA Astrophysics Data System (ADS)

Suzuki, T.; Minoda, H.; Tanishiro, Y.; Yagi, K.

A TED study of Si(113) surfaces was carried out. Reflections from the 3 × 2 reconstruction were seen at room temperature, while half-order reflections were very faint. The surface showed the phase transition between the 3 × 1 and the disordered (rough) structures at about 930°C. The (113) surface structure at room temperature was analyzed using TED intensity. Four kinds of structure models proposed previously, including both the 3 × 1 and the 3 × 2 reconstructed structures, were examined. The R-factors calculated using the energy-optimized atomic coordinates are not sufficiently small. After minimization of the R-factors, Dabrowski's 3 × 2 structure model is most agreeable, while Ranke's 3 × 1 and 3 × 2 structure models are not to be excluded. STM observation showed that the surface is composed of small domains of the 3 × 2 structure.

New Tools Being Developed for Engine- Airframe Blade-Out Structural Simulations

NASA Technical Reports Server (NTRS)

Lawrence, Charles

2003-01-01

One of the primary concerns of aircraft structure designers is the accurate simulation of the blade-out event. This is required for the aircraft to pass Federal Aviation Administration (FAA) certification and to ensure that the aircraft is safe for operation. Typically, the most severe blade-out occurs when a first-stage fan blade in a high-bypass gas turbine engine is released. Structural loading results from both the impact of the blade onto the containment ring and the subsequent instantaneous unbalance of the rotating components. Reliable simulations of blade-out are required to ensure structural integrity during flight as well as to guarantee successful blade-out certification testing. The loads generated by these analyses are critical to the design teams for several components of the airplane structures including the engine, nacelle, strut, and wing, as well as the aircraft fuselage. Currently, a collection of simulation tools is used for aircraft structural design. Detailed high-fidelity simulation tools are used to capture the structural loads resulting from blade loss, and then these loads are used as input into an overall system model that includes complete structural models of both the engines and the airframe. The detailed simulation (shown in the figure) includes the time-dependent trajectory of the lost blade and its interactions with the containment structure, and the system simulation includes the lost blade loadings and the interactions between the rotating turbomachinery and the remaining aircraft structural components. General-purpose finite element structural analysis codes are typically used, and special provisions are made to include transient effects from the blade loss and rotational effects resulting from the engine s turbomachinery. To develop and validate these new tools with test data, the NASA Glenn Research Center has teamed with GE Aircraft Engines, Pratt & Whitney, Boeing Commercial Aircraft, Rolls-Royce, and MSC.Software.

Ask Questions to Encourage Questions Asked

ERIC Educational Resources Information Center

belcastro, sarah-marie

2017-01-01

We delineate some types of structured practice (modeling, requests, feedback, and space-making) that help students learn to pose appropriate questions and to initiate exploration of those questions. Developing skills requires practice, so we suggest ways to embed structured practice into existing class sessions. Including structured practice is…

Modeling human target acquisition in ground-to-air weapon systems

NASA Technical Reports Server (NTRS)

Phatak, A. V.; Mohr, R. L.; Vikmanis, M.; Wei, K. C.

1982-01-01

The problems associated with formulating and validating mathematical models for describing and predicting human target acquisition response are considered. In particular, the extension of the human observer model to include the acquisition phase as well as the tracking segment is presented. Relationship of the Observer model structure to the more complex Standard Optimal Control model formulation and to the simpler Transfer Function/Noise representation is discussed. Problems pertinent to structural identifiability and the form of the parameterization are elucidated. A systematic approach toward the identification of the observer acquisition model parameters from ensemble tracking error data is presented.

Finite Element Models and Properties of a Stiffened Floor-Equipped Composite Cylinder

NASA Technical Reports Server (NTRS)

Grosveld, Ferdinand W.; Schiller, Noah H.; Cabell, Randolph H.

2010-01-01

Finite element models were developed of a floor-equipped, frame and stringer stiffened composite cylinder including a coarse finite element model of the structural components, a coarse finite element model of the acoustic cavities above and below the beam-supported plywood floor, and two dense models consisting of only the structural components. The report summarizes the geometry, the element properties, the material and mechanical properties, the beam cross-section characteristics, the beam element representations and the boundary conditions of the composite cylinder models. The expressions used to calculate the group speeds for the cylinder components are presented.

A dynamic social systems model for considering structural factors in HIV prevention and detection

PubMed Central

Latkin, Carl; Weeks, Margaret; Glasman, Laura; Galletly, Carol; Albarracin, Dolores

2010-01-01

We present a model for HIV-related behaviors that emphasizes the dynamic and social nature of the structural factors that influence HIV prevention and detection. Key structural dimensions of the model include resources, science and technology, formal social control, informal social influences and control, social interconnectedness, and settings. These six dimensions can be conceptualized on macro, meso, and micro levels. Given the inherent complexity of structural factors and their interrelatedness, HIV prevention interventions may focus on different levels and dimensions. We employ a systems perspective to describe the interconnected and dynamic processes of change among social systems and their components. The topics of HIV testing and safer injection facilities are analyzed using this structural framework. Finally, we discuss methodological issues in the development and evaluation of structural interventions for HIV prevention and detection. PMID:20838871

Optical interferometer testbed

NASA Technical Reports Server (NTRS)

Blackwood, Gary H.

1991-01-01

Viewgraphs on optical interferometer testbed presented at the MIT Space Research Engineering Center 3rd Annual Symposium are included. Topics covered include: space-based optical interferometer; optical metrology; sensors and actuators; real time control hardware; controlled structures technology (CST) design methodology; identification for MIMO control; FEM/ID correlation for the naked truss; disturbance modeling; disturbance source implementation; structure design: passive damping; low authority control; active isolation of lightweight mirrors on flexible structures; open loop transfer function of mirror; and global/high authority control.

Transition mixing study empirical model report

NASA Technical Reports Server (NTRS)

Srinivasan, R.; White, C.

1988-01-01

The empirical model developed in the NASA Dilution Jet Mixing Program has been extended to include the curvature effects of transition liners. This extension is based on the results of a 3-D numerical model generated under this contract. The empirical model results agree well with the numerical model results for all tests cases evaluated. The empirical model shows faster mixing rates compared to the numerical model. Both models show drift of jets toward the inner wall of a turning duct. The structure of the jets from the inner wall does not exhibit the familiar kidney-shaped structures observed for the outer wall jets or for jets injected in rectangular ducts.

Finite-rate chemistry effects upon convective and radiative heating of an atmospheric entry vehicle. [reentry aerothermochemistry

NASA Technical Reports Server (NTRS)

Guillermo, P.

1975-01-01

A mathematical model of the aerothermochemical environment along the stagnation line of a planetary return spacecraft using an ablative thermal protection system was developed and solved for conditions typical of atmospheric entry from planetary missions. The model, implemented as a FORTRAN 4 computer program, was designed to predict viscous, reactive and radiative coupled shock layer structure and the resulting body heating rates. The analysis includes flow field coupling with the ablator surface, binary diffusion, coupled line and continuum radiative and equilibrium or finite rate chemistry effects. The gas model used includes thermodynamic, transport, kinetic and radiative properties of air and ablation product species, including 19 chemical species and 16 chemical reactions. Specifically, the impact of nonequilibrium chemistry effects upon stagnation line shock layer structure and body heating rates was investigated.

A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins

PubMed Central

Vallat, Brinda Kizhakke; Pillardy, Jaroslaw; Elber, Ron

2010-01-01

The first step in homology modeling is to identify a template protein for the target sequence. The template structure is used in later phases of the calculation to construct an atomically detailed model for the target. We have built from the Protein Data Bank a large-scale learning set that includes tens of millions of pair matches that can be either a true template or a false one. Discriminatory learning (learning from positive and negative examples) is employed to train a decision tree. Each branch of the tree is a mathematical programming model. The decision tree is tested on an independent set from PDB entries and on the sequences of CASP7. It provides significant enrichment of true templates (between 50-100 percent) when compared to PSI-BLAST. The model is further verified by building atomically detailed structures for each of the tentative true templates with modeller. The probability that a true match does not yield an acceptable structural model (within 6Å RMSD from the native structure), decays linearly as a function of the TM structural-alignment score. PMID:18300226

The inverse niche model for food webs with parasites

USGS Publications Warehouse

Warren, Christopher P.; Pascual, Mercedes; Lafferty, Kevin D.; Kuris, Armand M.

2010-01-01

Although parasites represent an important component of ecosystems, few field and theoretical studies have addressed the structure of parasites in food webs. We evaluate the structure of parasitic links in an extensive salt marsh food web, with a new model distinguishing parasitic links from non-parasitic links among free-living species. The proposed model is an extension of the niche model for food web structure, motivated by the potential role of size (and related metabolic rates) in structuring food webs. The proposed extension captures several properties observed in the data, including patterns of clustering and nestedness, better than does a random model. By relaxing specific assumptions, we demonstrate that two essential elements of the proposed model are the similarity of a parasite's hosts and the increasing degree of parasite specialization, along a one-dimensional niche axis. Thus, inverting one of the basic rules of the original model, the one determining consumers' generality appears critical. Our results support the role of size as one of the organizing principles underlying niche space and food web topology. They also strengthen the evidence for the non-random structure of parasitic links in food webs and open the door to addressing questions concerning the consequences and origins of this structure.

Bearing-Load Modeling and Analysis Study for Mechanically Connected Structures

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.

2006-01-01

Bearing-load response for a pin-loaded hole is studied within the context of two-dimensional finite element analyses. Pin-loaded-hole configurations are representative of mechanically connected structures, such as a stiffener fastened to a rib of an isogrid panel, that are idealized as part of a larger structural component. Within this context, the larger structural component may be idealized as a two-dimensional shell finite element model to identify load paths and high stress regions. Finite element modeling and analysis aspects of a pin-loaded hole are considered in the present paper including the use of linear and nonlinear springs to simulate the pin-bearing contact condition. Simulating pin-connected structures within a two-dimensional finite element analysis model using nonlinear spring or gap elements provides an effective way for accurate prediction of the local effective stress state and peak forces.

Social inheritance can explain the structure of animal social networks

PubMed Central

Ilany, Amiyaal; Akçay, Erol

2016-01-01

The social network structure of animal populations has major implications for survival, reproductive success, sexual selection and pathogen transmission of individuals. But as of yet, no general theory of social network structure exists that can explain the diversity of social networks observed in nature, and serve as a null model for detecting species and population-specific factors. Here we propose a simple and generally applicable model of social network structure. We consider the emergence of network structure as a result of social inheritance, in which newborns are likely to bond with maternal contacts, and via forming bonds randomly. We compare model output with data from several species, showing that it can generate networks with properties such as those observed in real social systems. Our model demonstrates that important observed properties of social networks, including heritability of network position or assortative associations, can be understood as consequences of social inheritance. PMID:27352101

The discovery of the alpha-helix and beta-sheet, the principal structural features of proteins.

PubMed

Eisenberg, David

2003-09-30

PNAS papers by Linus Pauling, Robert Corey, and Herman Branson in the spring of 1951 proposed the alpha-helix and the beta-sheet, now known to form the backbones of tens of thousands of proteins. They deduced these fundamental building blocks from properties of small molecules, known both from crystal structures and from Pauling's resonance theory of chemical bonding that predicted planar peptide groups. Earlier attempts by others to build models for protein helices had failed both by including nonplanar peptides and by insisting on helices with an integral number of units per turn. In major respects, the Pauling-Corey-Branson models were astoundingly correct, including bond lengths that were not surpassed in accuracy for >40 years. However, they did not consider the hand of the helix or the possibility of bent sheets. They also proposed structures and functions that have not been found, including the gamma-helix.

The discovery of the -helix and -sheet, the principal structural features of proteins

NASA Astrophysics Data System (ADS)

Eisenberg, David

2003-09-01

PNAS papers by Linus Pauling, Robert Corey, and Herman Branson in the spring of 1951 proposed the -helix and the -sheet, now known to form the backbones of tens of thousands of proteins. They deduced these fundamental building blocks from properties of small molecules, known both from crystal structures and from Pauling's resonance theory of chemical bonding that predicted planar peptide groups. Earlier attempts by others to build models for protein helices had failed both by including nonplanar peptides and by insisting on helices with an integral number of units per turn. In major respects, the Pauling-Corey-Branson models were astoundingly correct, including bond lengths that were not surpassed in accuracy for >40 years. However, they did not consider the hand of the helix or the possibility of bent sheets. They also proposed structures and functions that have not been found, including the -helix.

The folding energy landscape and free energy excitations of cytochrome c.

PubMed

Weinkam, Patrick; Zimmermann, Jörg; Romesberg, Floyd E; Wolynes, Peter G

2010-05-18

The covalently bound heme cofactor plays a dominant role in the folding of cytochrome c. Because of the complicated inorganic chemistry of the heme, some might consider the folding of cytochrome c to be a special case, following principles different from those used to describe the folding of proteins without cofactors. Recent investigations, however, demonstrate that common models describing folding for many proteins work well for cytochrome c when heme is explicitly introduced, generally providing results that agree with experimental observations. In this Account, we first discuss results from simple native structure-based models. These models include attractive interactions between nonadjacent residues only if they are present in the crystal structure at pH 7. Because attractive nonnative contacts are not included in native structure-based models, their energy landscapes can be described as "perfectly funneled". In other words, native structure-based models are energetically guided towards the native state and contain no energetic traps that would hinder folding. Energetic traps are denoted sources of "frustration", which cause specific transient intermediates to be populated. Native structure-based models do, however, include repulsion between residues due to excluded volume. Nonenergetic traps can therefore exist if the chain, which cannot cross over itself, must partially unfold so that folding can proceed. The ability of native structure-based models to capture this kind of motion is partly responsible for their successful predictions of folding pathways for many types of proteins. Models without frustration describe the sequence of folding events for cytochrome c well (as inferred from hydrogen-exchange experiments), thereby justifying their use as a starting point. At low pH, the experimentally observed folding sequence of cytochrome c deviates from that at pH 7 and from models with perfectly funneled energy landscapes. Here, alternate folding pathways are a result of "chemical frustration". This frustration arises because some regions of the protein are destabilized more than others due to the heterogeneous distribution of titratable residues that are protonated at low pH. Beginning with native structure-based terms, we construct more complex models by adding chemical frustration. These more complex models only modestly perturb the energy landscape, which remains, overall, well funneled. These perturbed models can accurately describe how alternative folding pathways are used at low pH. At alkaline pH, cytochrome c populates distinctly different structural ensembles. For instance, lysine residues are deprotonated and compete for the heme ligation site. The same models that can describe folding at low pH also predict well the structures and relative stabilities of intermediates populated at alkaline pH. The success of models based on funneled energy landscapes suggest that cytochrome c folding is driven primarily by native contacts. The presence of heme appears to add chemical complexity to the folding process, but it does not require fundamental modification of the general principles used to describe folding. Moreover, its added complexity provides a valuable means of probing the folding energy landscape in greater detail than is possible with simpler systems.

Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data.

PubMed

Roy Choudhury, Amrita; Sikorska, Emilia; van den Boom, Johannes; Bayer, Peter; Popenda, Łukasz; Szutkowski, Kosma; Jurga, Stefan; Bonomi, Massimiliano; Sali, Andrej; Zhukov, Igor; Passamonti, Sabina; Novič, Marjana

2015-01-01

We present a 3D model of the four transmembrane (TM) helical regions of bilitranslocase (BTL), a structurally uncharacterized protein that transports organic anions across the cell membrane. The model was computed by considering helix-helix interactions as primary constraints, using Monte Carlo simulations. The interactions between the TM2 and TM3 segments have been confirmed by Förster resonance energy transfer (FRET) spectroscopy and nuclear magnetic resonance (NMR) spectroscopy, increasing our confidence in the model. Several insights into the BTL transport mechanism were obtained by analyzing the model. For example, the observed cis-trans Leu-Pro peptide bond isomerization in the TM3 fragment may indicate a key conformational change during anion transport by BTL. Our structural model of BTL may facilitate further studies, including drug discovery.

Modeling Fission Product Sorption in Graphite Structures

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

Szlufarska, Izabela; Morgan, Dane; Allen, Todd

2013-04-08

The goal of this project is to determine changes in adsorption and desorption of fission products to/from nuclear-grade graphite in response to a changing chemical environment. First, the project team will employ principle calculations and thermodynamic analysis to predict stability of fission products on graphite in the presence of structural defects commonly observed in very high- temperature reactor (VHTR) graphites. Desorption rates will be determined as a function of partial pressure of oxygen and iodine, relative humidity, and temperature. They will then carry out experimental characterization to determine the statistical distribution of structural features. This structural information will yield distributionsmore » of binding sites to be used as an input for a sorption model. Sorption isotherms calculated under this project will contribute to understanding of the physical bases of the source terms that are used in higher-level codes that model fission product transport and retention in graphite. The project will include the following tasks: Perform structural characterization of the VHTR graphite to determine crystallographic phases, defect structures and their distribution, volume fraction of coke, and amount of sp2 versus sp3 bonding. This information will be used as guidance for ab initio modeling and as input for sorptivity models; Perform ab initio calculations of binding energies to determine stability of fission products on the different sorption sites present in nuclear graphite microstructures. The project will use density functional theory (DFT) methods to calculate binding energies in vacuum and in oxidizing environments. The team will also calculate stability of iodine complexes with fission products on graphite sorption sites; Model graphite sorption isotherms to quantify concentration of fission products in graphite. The binding energies will be combined with a Langmuir isotherm statistical model to predict the sorbed concentration of fission products on each type of graphite site. The model will include multiple simultaneous adsorbing species, which will allow for competitive adsorption effects between different fission product species and O and OH (for modeling accident conditions).« less

A strand graph semantics for DNA-based computation

PubMed Central

Petersen, Rasmus L.; Lakin, Matthew R.; Phillips, Andrew

2015-01-01

DNA nanotechnology is a promising approach for engineering computation at the nanoscale, with potential applications in biofabrication and intelligent nanomedicine. DNA strand displacement is a general strategy for implementing a broad range of nanoscale computations, including any computation that can be expressed as a chemical reaction network. Modelling and analysis of DNA strand displacement systems is an important part of the design process, prior to experimental realisation. As experimental techniques improve, it is important for modelling languages to keep pace with the complexity of structures that can be realised experimentally. In this paper we present a process calculus for modelling DNA strand displacement computations involving rich secondary structures, including DNA branches and loops. We prove that our calculus is also sufficiently expressive to model previous work on non-branching structures, and propose a mapping from our calculus to a canonical strand graph representation, in which vertices represent DNA strands, ordered sites represent domains, and edges between sites represent bonds between domains. We define interactions between strands by means of strand graph rewriting, and prove the correspondence between the process calculus and strand graph behaviours. Finally, we propose a mapping from strand graphs to an efficient implementation, which we use to perform modelling and simulation of DNA strand displacement systems with rich secondary structure. PMID:27293306

Quantitative structure-activity relationship modeling on in vitro endocrine effects and metabolic stability involving 26 selected brominated flame retardants.

PubMed

Harju, Mikael; Hamers, Timo; Kamstra, Jorke H; Sonneveld, Edwin; Boon, Jan P; Tysklind, Mats; Andersson, Patrik L

2007-04-01

In this work, quantitative structure-activity relationships (QSARs) were developed to aid human and environmental risk assessment processes for brominated flame retardants (BFRs). Brominated flame retardants, such as the high-production-volume chemicals polybrominated diphenyl ethers (PBDEs), tetrabromobisphenol A, and hexabromocyclododecane, have been identified as potential endocrine disruptors. Quantitative structure-activity relationship models were built based on the in vitro potencies of 26 selected BFRs. The in vitro assays included interactions with, for example, androgen, progesterone, estrogen, and dioxin (aryl hydrocarbon) receptor, plus competition with thyroxine for its plasma carrier protein (transthyretin), inhibition of estradiol sulfation via sulfotransferase, and finally, rate of metabolization. The QSAR modeling, a number of physicochemical parameters were calculated describing the electronic, lipophilic, and structural characteristics of the molecules. These include frontier molecular orbitals, molecular charges, polarities, log octanol/water partitioning coefficient, and two- and three-dimensional molecularproperties. Experimental properties were included and measured for PBDEs, such as their individual ultraviolet spectra (200-320 nm) and retention times on three different high-performance liquid chromatography columns and one nonpolar gas chromatography column. Quantitative structure-activity relationship models based on androgen antagonism and metabolic degradation rates generally gave similar results, suggesting that lower-brominated PBDEs with bromine substitutions in ortho positions and bromine-free meta- and para positions had the highest potencies and metabolic degradation rates. Predictions made for the constituents of the technical flame retardant Bromkal 70-5DE found BDE 17 to be a potent androgen antagonist and BDE 66, which is a relevant PBDE in environmental samples, to be only a weak antagonist.

A nonlinear interface model applied to masonry structures

NASA Astrophysics Data System (ADS)

Lebon, Frédéric; Raffa, Maria Letizia; Rizzoni, Raffaella

2015-12-01

In this paper, a new imperfect interface model is presented. The model includes finite strains, micro-cracks and smooth roughness. The model is consistently derived by coupling a homogenization approach for micro-cracked media and arguments of asymptotic analysis. The model is applied to brick/mortar interfaces. Numerical results are presented.

76 FR 8316 - Special Conditions: Gulfstream Model GVI Airplane; Interaction of Systems and Structures

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-14

... considered in isolation but should be included in the overall safety evaluation of the airplane. These... forced structural vibrations (oscillatory failures) must not produce loads that could result in...

Development and application of a comprehensive simulation model to evaluate impacts of watershed structures and irrigation water use on streamflow and groundwater: The case of Wet Walnut Creek Watershed, Kansas, USA

USGS Publications Warehouse

Ramireddygari, S.R.; Sophocleous, M.A.; Koelliker, J.K.; Perkins, S.P.; Govindaraju, R.S.

2000-01-01

This paper presents the results of a comprehensive modeling study of surface and groundwater systems, including stream-aquifer interactions, for the Wet Walnut Creek Watershed in west-central Kansas. The main objective of this study was to assess the impacts of watershed structures and irrigation water use on streamflow and groundwater levels, which in turn affect availability of water for the Cheyenne Bottoms Wildlife Refuge Management area. The surface-water flow model, POTYLDR, and the groundwater flow model, MODFLOW, were combined into an integrated, watershed-scale, continuous simulation model. Major revisions and enhancements were made to the POTYLDR and MODFLOW models for simulating the detailed hydrologic budget for the Wet Walnut Creek Watershed. The computer simulation model was calibrated and verified using historical streamflow records (at Albert and Nekoma gaging stations), reported irrigation water use, observed water-level elevations in watershed structure pools, and groundwater levels in the alluvial aquifer system. To assess the impact of watershed structures and irrigation water use on streamflow and groundwater levels, a number of hypothetical management scenarios were simulated under various operational criteria for watershed structures and different annual limits on water use for irrigation. A standard 'base case' was defined to allow comparative analysis of the results of different scenarios. The simulated streamflows showed that watershed structures decrease both streamflows and groundwater levels in the watershed. The amount of water used for irrigation has a substantial effect on the total simulated streamflow and groundwater levels, indicating that irrigation is a major budget item for managing water resources in the watershed. (C) 2000 Elsevier Science B.V.This paper presents the results of a comprehensive modeling study of surface and groundwater systems, including stream-aquifer interactions, for the Wet Walnut Creek Watershed in west-central Kansas. The main objective of this study was to assess the impacts of watershed structures and irrigation water use on streamflow and groundwater levels, which in turn affect availability of water for the Cheyenne Bottoms Wildlife Refuge Management area. The surface-water flow model, POTYLDR, and the groundwater flow model, MODFLOW, were combined into an integrated, watershed-scale, continuous simulation model. Major revisions and enhancements were made to the POTYLDR and MODFLOW models for simulating the detailed hydrologic budget for the Wet Walnut Creek Watershed. The computer simulation model was calibrated and verified using historical streamflow records (at Albert and Nekoma gaging stations), reported irrigation water use, observed water-level elevations in watershed structure pools, and groundwater levels in the alluvial aquifer system. To assess the impact of watershed structures and irrigation water use on streamflow and groundwater levels, a number of hypothetical management scenarios were simulated under various operational criteria for watershed structures and different annual limits on water use for irrigation. A standard `base case' was defined to allow comparative analysis of the results of different scenarios. The simulated streamflows showed that watershed structures decrease both streamflows and groundwater levels in the watershed. The amount of water used for irrigation has a substantial effect on the total simulated streamflow and groundwater levels, indicating that irrigation is a major budget item for managing water resources in the watershed.A comprehensive simulation model that combines the surface water flow model POTYLDR and the groundwater flow model MODFLOW was used to study the impacts of watershed structures (e.g., dams) and irrigation water use (including stream-aquifer interactions) on streamflow and groundwater. The model was revised, enhanced, calibrated, and verified, then applied to evaluate the hydrologic budget for Wet Wal

Correlation of finite-element structural dynamic analysis with measured free vibration characteristics for a full-scale helicopter fuselage

NASA Technical Reports Server (NTRS)

Kenigsberg, I. J.; Dean, M. W.; Malatino, R.

1974-01-01

The correlation achieved with each program provides the material for a discussion of modeling techniques developed for general application to finite-element dynamic analyses of helicopter airframes. Included are the selection of static and dynamic degrees of freedom, cockpit structural modeling, and the extent of flexible-frame modeling in the transmission support region and in the vicinity of large cut-outs. The sensitivity of predicted results to these modeling assumptions are discussed. Both the Sikorsky Finite-Element Airframe Vibration analysis Program (FRAN/Vibration Analysis) and the NASA Structural Analysis Program (NASTRAN) have been correlated with data taken in full-scale vibration tests of a modified CH-53A helicopter.

Influence of an asymmetric ring on the modeling of an orthogonally stiffened cylindrical shell

NASA Technical Reports Server (NTRS)

Rastogi, Naveen; Johnson, Eric R.

1994-01-01

Structural models are examined for the influence of a ring with an asymmetrical cross section on the linear elastic response of an orthogonally stiffened cylindrical shell subjected to internal pressure. The first structural model employs classical theory for the shell and stiffeners. The second model employs transverse shear deformation theories for the shell and stringer and classical theory for the ring. Closed-end pressure vessel effects are included. Interacting line load intensities are computed in the stiffener-to-skin joints for an example problem having the dimensions of the fuselage of a large transport aircraft. Classical structural theory is found to exaggerate the asymmetric response compared to the transverse shear deformation theory.

CFD-PBM coupled simulation of a nanobubble generator with honeycomb structure

NASA Astrophysics Data System (ADS)

Ren, F.; Noda, N. A.; Ueda, T.; Sano, Y.; Takase, Y.; Umekage, T.; Yonezawa, Y.; Tanaka, H.

2018-06-01

In recent years, nanobubble technologies have drawn great attention due to their wide applications in many fields of science and technology. The nitrogen nanobubble water circulation can be used to slow the progressions of oxidation and spoilage for the seafood long- term storage. From previous studies, a kind of honeycomb structure for high-efficiency nanobubble generation has been proposed. In this paper, the bubbly flow in the honeycomb structure was studied. The numerical simulations of honeycomb structure were performed by using a computational fluid dynamics–population balance model (CFD-PBM) coupled model. The numerical model was based on the Eulerian multiphase model and the population balance model (PBM) was used to calculate the gas bubble size distribution. The bubble coalescence and breakage were included. Considering the effect of bubble diameter on the fluid flow, the phase interactions were coupled with the PBM. The bubble size distributions in the honeycomb structure under different work conditions were predicted. The experimental results were compared with the simulation predictions.

Effects of model structural uncertainty on carbon cycle projections: biological nitrogen fixation as a case study

NASA Astrophysics Data System (ADS)

Wieder, William R.; Cleveland, Cory C.; Lawrence, David M.; Bonan, Gordon B.

2015-04-01

Uncertainties in terrestrial carbon (C) cycle projections increase uncertainty of potential climate feedbacks. Efforts to improve model performance often include increased representation of biogeochemical processes, such as coupled carbon-nitrogen (N) cycles. In doing so, models are becoming more complex, generating structural uncertainties in model form that reflect incomplete knowledge of how to represent underlying processes. Here, we explore structural uncertainties associated with biological nitrogen fixation (BNF) and quantify their effects on C cycle projections. We find that alternative plausible structures to represent BNF result in nearly equivalent terrestrial C fluxes and pools through the twentieth century, but the strength of the terrestrial C sink varies by nearly a third (50 Pg C) by the end of the twenty-first century under a business-as-usual climate change scenario representative concentration pathway 8.5. These results indicate that actual uncertainty in future C cycle projections may be larger than previously estimated, and this uncertainty will limit C cycle projections until model structures can be evaluated and refined.

Recovery of Weak Factor Loadings When Adding the Mean Structure in Confirmatory Factor Analysis: A Simulation Study

PubMed Central

Ximénez, Carmen

2016-01-01

This article extends previous research on the recovery of weak factor loadings in confirmatory factor analysis (CFA) by exploring the effects of adding the mean structure. This issue has not been examined in previous research. This study is based on the framework of Yung and Bentler (1999) and aims to examine the conditions that affect the recovery of weak factor loadings when the model includes the mean structure, compared to analyzing the covariance structure alone. A simulation study was conducted in which several constraints were defined for one-, two-, and three-factor models. Results show that adding the mean structure improves the recovery of weak factor loadings and reduces the asymptotic variances for the factor loadings, particularly for the models with a smaller number of factors and a small sample size. Therefore, under certain circumstances, modeling the means should be seriously considered for covariance models containing weak factor loadings. PMID:26779071

Prediction of biodegradability from chemical structure: Modeling or ready biodegradation test data

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

Loonen, H.; Lindgren, F.; Hansen, B.

1999-08-01

Biodegradation data were collected and evaluated for 894 substances with widely varying chemical structures. All data were determined according to the Japanese Ministry of International Trade and Industry (MITI) I test protocol. The MITI I test is a screening test for ready biodegradability and has been described by Organization for Economic Cooperation and Development (OECD) test guideline 301 C and European Union (EU) test guideline C4F. The chemicals were characterized by a set of 127 predefined structural fragments. This data set was used to develop a model for the prediction of the biodegradability of chemicals under standardized OECD and EUmore » ready biodegradation test conditions. Partial least squares (PLS) discriminant analysis was used for the model development. The model was evaluated by means of internal cross-validation and repeated external validation. The importance of various structural fragments and fragment interactions was investigated. The most important fragments include the presence of a long alkyl chain; hydroxy, ester, and acid groups (enhancing biodegradation); and the presence of one or more aromatic rings and halogen substituents (regarding biodegradation). More than 85% of the model predictions were correct for using the complete data set. The not readily biodegradable predictions were slightly better than the readily biodegradable predictions (86 vs 84%). The average percentage of correct predictions from four external validation studies was 83%. Model optimization by including fragment interactions improve the model predicting capabilities to 89%. It can be concluded that the PLS model provides predictions of high reliability for a diverse range of chemical structures. The predictions conform to the concept of readily biodegradable (or not readily biodegradable) as defined by OECD and EU test guidelines.« less

Advances in parameter estimation techniques applied to flexible structures

NASA Technical Reports Server (NTRS)

Maben, Egbert; Zimmerman, David C.

1994-01-01

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

System requirements specification for SMART structures mode

NASA Technical Reports Server (NTRS)

1992-01-01

Specified here are the functional and informational requirements for software modules which address the geometric and data modeling needs of the aerospace structural engineer. The modules are to be included as part of the Solid Modeling Aerospace Research Tool (SMART) package developed for the Vehicle Analysis Branch (VAB) at the NASA Langley Research Center (LaRC). The purpose is to precisely state what the SMART Structures modules will do, without consideration of how it will be done. Each requirement is numbered for reference in development and testing.

Transform methods for precision continuum and control models of flexible space structures

NASA Technical Reports Server (NTRS)

Lupi, Victor D.; Turner, James D.; Chun, Hon M.

1991-01-01

An open loop optimal control algorithm is developed for general flexible structures, based on Laplace transform methods. A distributed parameter model of the structure is first presented, followed by a derivation of the optimal control algorithm. The control inputs are expressed in terms of their Fourier series expansions, so that a numerical solution can be easily obtained. The algorithm deals directly with the transcendental transfer functions from control inputs to outputs of interest, and structural deformation penalties, as well as penalties on control effort, are included in the formulation. The algorithm is applied to several structures of increasing complexity to show its generality.

Demonstrating the Uneven Importance of Fine-Scale Forest Structure on Snow Distributions using High Resolution Modeling

NASA Astrophysics Data System (ADS)

Broxton, P. D.; Harpold, A. A.; van Leeuwen, W.; Biederman, J. A.

2016-12-01

Quantifying the amount of snow in forested mountainous environments, as well as how it may change due to warming and forest disturbance, is critical given its importance for water supply and ecosystem health. Forest canopies affect snow accumulation and ablation in ways that are difficult to observe and model. Furthermore, fine-scale forest structure can accentuate or diminish the effects of forest-snow interactions. Despite decades of research demonstrating the importance of fine-scale forest structure (e.g. canopy edges and gaps) on snow, we still lack a comprehensive understanding of where and when forest structure has the largest impact on snowpack mass and energy budgets. Here, we use a hyper-resolution (1 meter spatial resolution) mass and energy balance snow model called the Snow Physics and Laser Mapping (SnowPALM) model along with LIDAR-derived forest structure to determine where spatial variability of fine-scale forest structure has the largest influence on large scale mass and energy budgets. SnowPALM was set up and calibrated at sites representing diverse climates in New Mexico, Arizona, and California. Then, we compared simulations at different model resolutions (i.e. 1, 10, and 100 m) to elucidate the effects of including versus not including information about fine scale canopy structure. These experiments were repeated for different prescribed topographies (i.e. flat, 30% slope north, and south-facing) at each site. Higher resolution simulations had more snow at lower canopy cover, with the opposite being true at high canopy cover. Furthermore, there is considerable scatter, indicating that different canopy arrangements can lead to different amounts of snow, even when the overall canopy coverage is the same. This modeling is contributing to the development of a high resolution machine learning algorithm called the Snow Water Artificial Network (SWANN) model to generate predictions of snow distributions over much larger domains, which has implications for improving land surface models that do not currently resolve or parameterize fine-scale canopy structure. In addition, these findings have implications for understanding the potential of different forest management strategies (i.e. thinning) based on local topography and climate to maximize the amount and retention of snow.

An Overview of Psycholinguistic Reading Theory.

ERIC Educational Resources Information Center

Hayes, Christopher G.

In the most adequate psycholinguistic model of the reading process the proficient silent reader decodes directly from graphic surface structure into deep structure, with no decoding into oral surface structure. Three cue systems used by all proficient readers include graphic cues (letters and words), syntactic cues (the grammatical arrangement of…

Architecture of dermatophyte cell Walls: Electron microscopic and biochemical analysis

NASA Technical Reports Server (NTRS)

Nozawa, Y.; Kitajima, Y.

1984-01-01

A review with 83 references on the cell wall structure of dermatophytes is presented. Topics discussed include separation and preparation of cell walls; microstructure of cell walls by electron microscopy; chemical composition of cell walls; structural model of cell walls; and morphological structure of cell walls.

Numerical model a graphene component for the sensing of weak electromagnetic signals

NASA Astrophysics Data System (ADS)

Nasswettrova, A.; Fiala, P.; Nešpor, D.; Drexler, P.; Steinbauer, M.

2015-05-01

The paper discusses a numerical model and provides an analysis of a graphene coaxial line suitable for sub-micron sensors of magnetic fields. In relation to the presented concept, the target areas and disciplines include biology, medicine, prosthetics, and microscopic solutions for modern actuators or SMART elements. The proposed numerical model is based on an analysis of a periodic structure with high repeatability, and it exploits a graphene polymer having a basic dimension in nanometers. The model simulates the actual random motion in the structure as the source of spurious signals and considers the pulse propagation along the structure; furthermore, the model also examines whether and how the pulse will be distorted at the beginning of the line, given the various ending versions. The results of the analysis are necessary for further use of the designed sensing devices based on graphene structures.

External validation of structure-biodegradation relationship (SBR) models for predicting the biodegradability of xenobiotics.

PubMed

Devillers, J; Pandard, P; Richard, B

2013-01-01

Biodegradation is an important mechanism for eliminating xenobiotics by biotransforming them into simple organic and inorganic products. Faced with the ever growing number of chemicals available on the market, structure-biodegradation relationship (SBR) and quantitative structure-biodegradation relationship (QSBR) models are increasingly used as surrogates of the biodegradation tests. Such models have great potential for a quick and cheap estimation of the biodegradation potential of chemicals. The Estimation Programs Interface (EPI) Suite™ includes different models for predicting the potential aerobic biodegradability of organic substances. They are based on different endpoints, methodologies and/or statistical approaches. Among them, Biowin 5 and 6 appeared the most robust, being derived from the largest biodegradation database with results obtained only from the Ministry of International Trade and Industry (MITI) test. The aim of this study was to assess the predictive performances of these two models from a set of 356 chemicals extracted from notification dossiers including compatible biodegradation data. Another set of molecules with no more than four carbon atoms and substituted by various heteroatoms and/or functional groups was also embodied in the validation exercise. Comparisons were made with the predictions obtained with START (Structural Alerts for Reactivity in Toxtree). Biowin 5 and Biowin 6 gave satisfactorily prediction results except for the prediction of readily degradable chemicals. A consensus model built with Biowin 1 allowed the diminution of this tendency.

Using the Past in the Class: Learning from Historical Models of Cell Membranes.

ERIC Educational Resources Information Center

Johnson, Cameron; Luft, Julie A.

2001-01-01

Including historical events and cultural contexts to enrich science teaching helps students understand the human aspect of science. Describes a sample lesson that includes the historical milestones that led to our current understanding of the structure of cell membranes. Examines the development and use of scientific models within the historical…

Health Promotion Behavior of Chinese International Students in Korea Including Acculturation Factors: A Structural Equation Model.

PubMed

Kim, Sun Jung; Yoo, Il Young

2016-03-01

The purpose of this study was to explain the health promotion behavior of Chinese international students in Korea using a structural equation model including acculturation factors. A survey using self-administered questionnaires was employed. Data were collected from 272 Chinese students who have resided in Korea for longer than 6 months. The data were analyzed using structural equation modeling. The p value of final model is .31. The fitness parameters of the final model such as goodness of fit index, adjusted goodness of fit index, normed fit index, non-normed fit index, and comparative fit index were more than .95. Root mean square of residual and root mean square error of approximation also met the criteria. Self-esteem, perceived health status, acculturative stress and acculturation level had direct effects on health promotion behavior of the participants and the model explained 30.0% of variance. The Chinese students in Korea with higher self-esteem, perceived health status, acculturation level, and lower acculturative stress reported higher health promotion behavior. The findings can be applied to develop health promotion strategies for this population. Copyright © 2016. Published by Elsevier B.V.

Emergent structure-function relations in emphysema and asthma.

PubMed

Winkler, Tilo; Suki, Béla

2011-01-01

Structure-function relationships in the respiratory system are often a result of the emergence of self-organized patterns or behaviors that are characteristic of certain respiratory diseases. Proper description of such self-organized behavior requires network models that include nonlinear interactions among different parts of the system. This review focuses on 2 models that exhibit self-organized behavior: a network model of the lung parenchyma during the progression of emphysema that is driven by mechanical force-induced breakdown, and an integrative model of bronchoconstriction in asthma that describes interactions among airways within the bronchial tree. Both models suggest that the transition from normal to pathologic states is a nonlinear process that includes a tipping point beyond which interactions among the system components are reinforced by positive feedback, further promoting the progression of pathologic changes. In emphysema, the progressive destruction of tissue is irreversible, while in asthma, it is possible to recover from a severe bronchoconstriction. These concepts may have implications for pulmonary medicine. Specifically, we suggest that structure-function relationships emerging from network behavior across multiple scales should be taken into account when the efficacy of novel treatments or drug therapy is evaluated. Multiscale, computational, network models will play a major role in this endeavor.

Accurate force field for molybdenum by machine learning large materials data

NASA Astrophysics Data System (ADS)

Chen, Chi; Deng, Zhi; Tran, Richard; Tang, Hanmei; Chu, Iek-Heng; Ong, Shyue Ping

2017-09-01

In this work, we present a highly accurate spectral neighbor analysis potential (SNAP) model for molybdenum (Mo) developed through the rigorous application of machine learning techniques on large materials data sets. Despite Mo's importance as a structural metal, existing force fields for Mo based on the embedded atom and modified embedded atom methods do not provide satisfactory accuracy on many properties. We will show that by fitting to the energies, forces, and stress tensors of a large density functional theory (DFT)-computed dataset on a diverse set of Mo structures, a Mo SNAP model can be developed that achieves close to DFT accuracy in the prediction of a broad range of properties, including elastic constants, melting point, phonon spectra, surface energies, grain boundary energies, etc. We will outline a systematic model development process, which includes a rigorous approach to structural selection based on principal component analysis, as well as a differential evolution algorithm for optimizing the hyperparameters in the model fitting so that both the model error and the property prediction error can be simultaneously lowered. We expect that this newly developed Mo SNAP model will find broad applications in large and long-time scale simulations.

Vibrations and structureborne noise in space station

NASA Technical Reports Server (NTRS)

Vaicaitis, R.; Lyrintzis, C. S.; Bofilios, D. A.

1987-01-01

Analytical models were developed to predict vibrations and structureborne noise generation of cylindrical and rectangular acoustic enclosures. These models are then used to determine structural vibration levels and interior noise to random point input forces. The guidelines developed could provide preliminary information on acoustical and vibrational environments in space station habitability modules under orbital operations. The structural models include single wall monocoque shell, double wall shell, stiffened orthotropic shell, descretely stiffened flat panels, and a coupled system composed of a cantilever beam structure and a stiffened sidewall. Aluminum and fiber reinforced composite materials are considered for single and double wall shells. The end caps of the cylindrical enclosures are modeled either as single or double wall circular plates. Sound generation in the interior space is calculated by coupling the structural vibrations to the acoustic field in the enclosure. Modal methods and transfer matrix techniques are used to obtain structural vibrations. Parametric studies are performed to determine the sensitivity of interior noise environment to changes in input, geometric and structural conditions.

Ab initio solution of macromolecular crystal structures without direct methods.

PubMed

McCoy, Airlie J; Oeffner, Robert D; Wrobel, Antoni G; Ojala, Juha R M; Tryggvason, Karl; Lohkamp, Bernhard; Read, Randy J

2017-04-04

The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure. Instead, likelihood-based methods allow a continuum of applications depending predictably on the quality of the model and the resolution of the data. Unexpectedly, our understanding of the signal-to-noise ratio in molecular replacement leads to the finding that, with data to sufficiently high resolution, fragments as small as single atoms of elements usually found in proteins can yield ab initio solutions of macromolecular structures, including some that elude traditional direct methods.

Scaled Tank Test Design and Results for the Aquantis 2.5 MW Ocean Current Generation Device

DOE Data Explorer

Swales, Henry; Kils, Ole; Coakley, David B.; Sites, Eric; Mayer, Tyler

2015-06-03

Aquantis 2.5 MW Ocean Current Generation Device, Tow Tank Dynamic Rig Structural Analysis Results. This is the detailed documentation for scaled device testing in a tow tank, including models, drawings, presentations, cost of energy analysis, and structural analysis. This dataset also includes specific information on drivetrain, roller bearing, blade fabrication, mooring, and rotor characteristics.

Frame junction vibration transmission with a modified frame deformation model.

PubMed

Moore, J A

1990-12-01

A previous paper dealt with vibration transmission through junctions of connected frame members where the allowed frame deformations included bending, torsion, and longitudinal motions [J.A. Moore, J. Acoust. Soc. Am. 88, 2766-2776 (1990)]. In helicopter and aircraft structures the skin panels can constitute a high impedance connection along the length of the frames that effectively prohibits in-plane motion at the elevation of the skin panels. This has the effect of coupling in-plane bending and torsional motions within the frame. This paper discusses the transmission behavior through frame junctions that accounts for the in-plane constraint in idealized form by assuming that the attached skin panels completely prohibit inplane motion in the frames. Also, transverse shear deformation is accounted for in describing the relatively deep web frame constructions common in aircraft structures. Longitudinal motion in the frames is not included in the model. Transmission coefficient predictions again show the importance of out-of-plane bending deformation to the transmission of vibratory energy in an aircraft structure. Comparisons are shown with measured vibration transmission data along the framing in the overhead of a helicopter airframe, with good agreement. The frame junction description has been implemented within a general purpose statistical energy analysis (SEA) computer code in modeling the entire airframe structure including skin panels.

MOD Tool (Microwave Optics Design Tool)

NASA Technical Reports Server (NTRS)

Katz, Daniel S.; Borgioli, Andrea; Cwik, Tom; Fu, Chuigang; Imbriale, William A.; Jamnejad, Vahraz; Springer, Paul L.

1999-01-01

The Jet Propulsion Laboratory (JPL) is currently designing and building a number of instruments that operate in the microwave and millimeter-wave bands. These include MIRO (Microwave Instrument for the Rosetta Orbiter), MLS (Microwave Limb Sounder), and IMAS (Integrated Multispectral Atmospheric Sounder). These instruments must be designed and built to meet key design criteria (e.g., beamwidth, gain, pointing) obtained from the scientific goals for the instrument. These criteria are frequently functions of the operating environment (both thermal and mechanical). To design and build instruments which meet these criteria, it is essential to be able to model the instrument in its environments. Currently, a number of modeling tools exist. Commonly used tools at JPL include: FEMAP (meshing), NASTRAN (structural modeling), TRASYS and SINDA (thermal modeling), MACOS/IMOS (optical modeling), and POPO (physical optics modeling). Each of these tools is used by an analyst, who models the instrument in one discipline. The analyst then provides the results of this modeling to another analyst, who continues the overall modeling in another discipline. There is a large reengineering task in place at JPL to automate and speed-up the structural and thermal modeling disciplines, which does not include MOD Tool. The focus of MOD Tool (and of this paper) is in the fields unique to microwave and millimeter-wave instrument design. These include initial design and analysis of the instrument without thermal or structural loads, the automation of the transfer of this design to a high-end CAD tool, and the analysis of the structurally deformed instrument (due to structural and/or thermal loads). MOD Tool is a distributed tool, with a database of design information residing on a server, physical optics analysis being performed on a variety of supercomputer platforms, and a graphical user interface (GUI) residing on the user's desktop computer. The MOD Tool client is being developed using Tcl/Tk, which allows the user to work on a choice of platforms (PC, Mac, or Unix) after downloading the Tcl/Tk binary, which is readily available on the web. The MOD Tool server is written using Expect, and it resides on a Sun workstation. Client/server communications are performed over a socket, where upon a connection from a client to the server, the server spawns a child which is be dedicated to communicating with that client. The server communicates with other machines, such as supercomputers using Expect with the username and password being provided by the user on the client.

PROCRU: A model for analyzing crew procedures in approach to landing

NASA Technical Reports Server (NTRS)

Baron, S.; Muralidharan, R.; Lancraft, R.; Zacharias, G.

1980-01-01

A model for analyzing crew procedures in approach to landing is developed. The model employs the information processing structure used in the optimal control model and in recent models for monitoring and failure detection. Mechanisms are added to this basic structure to model crew decision making in this multi task environment. Decisions are based on probability assessments and potential mission impact (or gain). Sub models for procedural activities are included. The model distinguishes among external visual, instrument visual, and auditory sources of information. The external visual scene perception models incorporate limitations in obtaining information. The auditory information channel contains a buffer to allow for storage in memory until that information can be processed.

The Interplay between Radiation Pressure and the Photoelectric Instability in Optically Thin Disks of Gas and Dust

NASA Astrophysics Data System (ADS)

Richert, Alexander J. W.; Lyra, Wladimir; Kuchner, Marc J.

2018-03-01

In optically thin disks, dust grains are photoelectrically stripped of electrons by starlight, heating nearby gas and possibly creating a dust clumping instability—the photoelectric instability (PeI)—that significantly alters global disk structure. In the current work, we use the Pencil Code to perform the first numerical models of the PeI that include stellar radiation pressure on dust grains in order to explore the parameter regime in which the instability operates. In some models with low gas and dust surface densities, we see a variety of dust structures, including sharp concentric rings. In the most gas- and dust-rich models, nonaxisymmetric clumps, arcs, and spiral arms emerge that represent dust surface density enhancements of factors of ∼5–20. In one high gas surface density model, we include a large, low-order gas viscosity and find that it observably smooths the structures that form in the gas and dust, suggesting that resolved images of a given disk may be useful for deriving constraints on the effective viscosity of its gas. Our models show that radiation pressure does not preclude the formation of complex structure from the PeI, but the qualitative manifestation of the PeI depends strongly on the parameters of the system. The PeI may provide an explanation for unusual disk morphologies, such as the moving blobs of the AU Mic disk, the asymmetric dust distribution of the 49 Ceti disk, and the rings and arcs found in the HD 141569A disk.

Studies in turbulence

NASA Technical Reports Server (NTRS)

Gatski, Thomas B. (Editor); Sarkar, Sutanu (Editor); Speziale, Charles G. (Editor)

1992-01-01

Various papers on turbulence are presented. Individual topics addressed include: modeling the dissipation rate in rotating turbulent flows, mapping closures for turbulent mixing and reaction, understanding turbulence in vortex dynamics, models for the structure and dynamics of near-wall turbulence, complexity of turbulence near a wall, proper orthogonal decomposition, propagating structures in wall-bounded turbulence flows. Also discussed are: constitutive relation in compressible turbulence, compressible turbulence and shock waves, direct simulation of compressible turbulence in a shear flow, structural genesis in wall-bounded turbulence flows, vortex lattice structure of turbulent shear slows, etiology of shear layer vortices, trilinear coordinates in fluid mechanics.

Recursive formulae and performance comparisons for first mode dynamics of periodic structures

NASA Astrophysics Data System (ADS)

Hobeck, Jared D.; Inman, Daniel J.

2017-05-01

Periodic structures are growing in popularity especially in the energy harvesting and metastructures communities. Common types of these unique structures are referred to in the literature as zigzag, orthogonal spiral, fan-folded, and longitudinal zigzag structures. Many of these studies on periodic structures have two competing goals in common: (a) minimizing natural frequency, and (b) minimizing mass or volume. These goals suggest that no single design is best for all applications; therefore, there is a need for design optimization and comparison tools which first require efficient easy-to-implement models. All available structural dynamics models for these types of structures do provide exact analytical solutions; however, they are complex requiring tedious implementation and providing more information than necessary for practical applications making them computationally inefficient. This paper presents experimentally validated recursive models that are able to very accurately and efficiently predict the dynamics of the four most common types of periodic structures. The proposed modeling technique employs a combination of static deflection formulae and Rayleigh’s Quotient to estimate the first mode shape and natural frequency of periodic structures having any number of beams. Also included in this paper are the results of an extensive experimental validation study which show excellent agreement between model prediction and measurement. Lastly, the proposed models are used to evaluate the performance of each type of structure. Results of this performance evaluation reveal key advantages and disadvantages associated with each type of structure.

The contrasting response of Hadley circulation to different meridional structure of sea surface temperature in CMIP5

NASA Astrophysics Data System (ADS)

Feng, Juan; Li, Jianping; Zhu, Jianlei; Li, Yang; Li, Fei

2018-02-01

The response of the Hadley circulation (HC) to the sea surface temperature (SST) is determined by the meridional structure of SST and varies according to the changing nature of this meridional structure. The capability of the models from the phase 5 of the Coupled Model Intercomparison Project (CMIP5) is utilized to represent the contrast response of the HC to different meridional SST structures. To evaluate the responses, the variations of HC and SST were linearly decomposed into two components: the equatorially asymmetric (HEA for HC, and SEA for SST) and equatorially symmetric (HES for HC, and SES for SST) components. The result shows that the climatological features of HC and tropical SST (including the spatial structures and amplitude) are reasonably simulated in all the models. However, the response contrast of HC to different SST meridional structures shows uncertainties among models. This may be due to the fact that the long-term temporal variabilities of HEA, HES, and SEA are limited reproduced in the models, although the spatial structures of their long-term variabilities are relatively reasonably simulated. These results indicate that the performance of the CMIP5 models to simulate long-term temporal variability of different meridional SST structures and related HC variations plays a fundamental role in the successful reproduction of the response of HC to different meridional SST structures.

Vision-based stress estimation model for steel frame structures with rigid links

NASA Astrophysics Data System (ADS)

Park, Hyo Seon; Park, Jun Su; Oh, Byung Kwan

2017-07-01

This paper presents a stress estimation model for the safety evaluation of steel frame structures with rigid links using a vision-based monitoring system. In this model, the deformed shape of a structure under external loads is estimated via displacements measured by a motion capture system (MCS), which is a non-contact displacement measurement device. During the estimation of the deformed shape, the effective lengths of the rigid link ranges in the frame structure are identified. The radius of the curvature of the structural member to be monitored is calculated using the estimated deformed shape and is employed to estimate stress. Using MCS in the presented model, the safety of a structure can be assessed gauge-freely. In addition, because the stress is directly extracted from the radius of the curvature obtained from the measured deformed shape, information on the loadings and boundary conditions of the structure are not required. Furthermore, the model, which includes the identification of the effective lengths of the rigid links, can consider the influences of the stiffness of the connection and support on the deformation in the stress estimation. To verify the applicability of the presented model, static loading tests for a steel frame specimen were conducted. By comparing the stress estimated by the model with the measured stress, the validity of the model was confirmed.

Conceptual Model for Basement and Surface Structure Relationships in an Oblique Collision, Sawtooth Range, MT

NASA Astrophysics Data System (ADS)

Palu, J. M.; Burberry, C. M.

2014-12-01

The reactivation potential of pre-existing basement structures affects the geometry of subsequent deformation structures. A conceptual model depicting the results of these interactions can be applied to multiple fold-thrust systems and lead to valuable deformation predictions. These predictions include the potential for hydrocarbon traps or seismic risk in an actively deforming area. The Sawtooth Range, Montana, has been used as a study area. A model for the development of structures close to the Augusta Syncline in the Sawtooth Range is being developed using: 1) an ArcGIS map of the basement structures of the belt based on analysis of geophysical data indicating gravity anomalies and aeromagnetic lineations, seismic data indicating deformation structures, and well logs for establishing lithologies, previously collected by others and 2) an ArcGIS map of the surface deformation structures of the belt based on interpretation of remote sensing images and verification through the collection of surface field data indicating stress directions and age relationships, resulting in a conceptual model based on the understanding of the interaction of the two previous maps including statistical correlations of data and development of balanced cross-sections using Midland Valley's 2D/3D Move software. An analysis of the model will then indicate viable deformation paths where prominent basement structures influenced subsequently developed deformation structures and reactivated faults. Preliminary results indicate that the change in orientation of thrust faults observed in the Sawtooth Range, from a NNW-SSE orientation near the Gibson Reservoir to a WNW-ESE trend near Haystack Butte correlates with pre-existing deformation structures lying within the Great Falls Tectonic Zone. The Scapegoat-Bannatyne trend appears to be responsible for this orientation change and rather than being a single feature, may be composed of up to 4 NE-SW oriented basement strike-slip faults. This indicates that the pre-existing basement features have a profound effect on the geometry of the later deformation. This conceptual model can also be applied to other deformed belts to provide a prediction for the potential hydrocarbon trap locations of the belt as well as their seismic risk.

Bayesian nonlinear structural FE model and seismic input identification for damage assessment of civil structures

NASA Astrophysics Data System (ADS)

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

2017-09-01

A methodology is proposed to update mechanics-based nonlinear finite element (FE) models of civil structures subjected to unknown input excitation. The approach allows to jointly estimate unknown time-invariant model parameters of a nonlinear FE model of the structure and the unknown time histories of input excitations using spatially-sparse output response measurements recorded during an earthquake event. The unscented Kalman filter, which circumvents the computation of FE response sensitivities with respect to the unknown model parameters and unknown input excitations by using a deterministic sampling approach, is employed as the estimation tool. The use of measurement data obtained from arrays of heterogeneous sensors, including accelerometers, displacement sensors, and strain gauges is investigated. Based on the estimated FE model parameters and input excitations, the updated nonlinear FE model can be interrogated to detect, localize, classify, and assess damage in the structure. Numerically simulated response data of a three-dimensional 4-story 2-by-1 bay steel frame structure with six unknown model parameters subjected to unknown bi-directional horizontal seismic excitation, and a three-dimensional 5-story 2-by-1 bay reinforced concrete frame structure with nine unknown model parameters subjected to unknown bi-directional horizontal seismic excitation are used to illustrate and validate the proposed methodology. The results of the validation studies show the excellent performance and robustness of the proposed algorithm to jointly estimate unknown FE model parameters and unknown input excitations.

Development of a rotorcraft. Propulsion dynamics interface analysis, volume 2

NASA Technical Reports Server (NTRS)

Hull, R.

1982-01-01

A study was conducted to establish a coupled rotor/propulsion analysis that would be applicable to a wide range of rotorcraft systems. The effort included the following tasks: (1) development of a model structure suitable for simulating a wide range of rotorcraft configurations; (2) defined a methodology for parameterizing the model structure to represent a particular rotorcraft; (3) constructing a nonlinear coupled rotor/propulsion model as a test case to use in analyzing coupled system dynamics; and (4) an attempt to develop a mostly linear coupled model derived from the complete nonlinear simulations. Documentation of the computer models developed is presented.

Improving the accuracy of macromolecular structure refinement at 7 Å resolution.

PubMed

Brunger, Axel T; Adams, Paul D; Fromme, Petra; Fromme, Raimund; Levitt, Michael; Schröder, Gunnar F

2012-06-06

In X-ray crystallography, molecular replacement and subsequent refinement is challenging at low resolution. We compared refinement methods using synchrotron diffraction data of photosystem I at 7.4 Å resolution, starting from different initial models with increasing deviations from the known high-resolution structure. Standard refinement spoiled the initial models, moving them further away from the true structure and leading to high R(free)-values. In contrast, DEN refinement improved even the most distant starting model as judged by R(free), atomic root-mean-square differences to the true structure, significance of features not included in the initial model, and connectivity of electron density. The best protocol was DEN refinement with initial segmented rigid-body refinement. For the most distant initial model, the fraction of atoms within 2 Å of the true structure improved from 24% to 60%. We also found a significant correlation between R(free) values and the accuracy of the model, suggesting that R(free) is useful even at low resolution. Copyright © 2012 Elsevier Ltd. All rights reserved.

System identification of smart structures using a wavelet neuro-fuzzy model

NASA Astrophysics Data System (ADS)

Mitchell, Ryan; Kim, Yeesock; El-Korchi, Tahar

2012-11-01

This paper proposes a complex model of smart structures equipped with magnetorheological (MR) dampers. Nonlinear behavior of the structure-MR damper systems is represented by the use of a wavelet-based adaptive neuro-fuzzy inference system (WANFIS). The WANFIS is developed through the integration of wavelet transforms, artificial neural networks, and fuzzy logic theory. To evaluate the effectiveness of the WANFIS model, a three-story building employing an MR damper under a variety of natural hazards is investigated. An artificial earthquake is used for training the input-output mapping of the WANFIS model. The artificial earthquake is generated such that the characteristics of a variety of real recorded earthquakes are included. It is demonstrated that this new WANFIS approach is effective in modeling nonlinear behavior of the structure-MR damper system subjected to a variety of disturbances while resulting in shorter training times in comparison with an adaptive neuro-fuzzy inference system (ANFIS) model. Comparison with high fidelity data proves the viability of the proposed approach in a structural health monitoring setting, and it is validated using known earthquake signals such as El-Centro, Kobe, Northridge, and Hachinohe.

Single-molecule FRET-Rosetta reveals RNA structural rearrangements during human telomerase catalysis

PubMed Central

Parks, Joseph W.; Kappel, Kalli; Das, Rhiju; Stone, Michael D.

2017-01-01

Maintenance of telomeres by telomerase permits continuous proliferation of rapidly dividing cells, including the majority of human cancers. Despite its direct biomedical significance, the architecture of the human telomerase complex remains unknown. Generating homogeneous telomerase samples has presented a significant barrier to developing improved structural models. Here we pair single-molecule Förster resonance energy transfer (smFRET) measurements with Rosetta modeling to map the conformations of the essential telomerase RNA core domain within the active ribonucleoprotein. FRET-guided modeling places the essential pseudoknot fold distal to the active site on a protein surface comprising the C-terminal element, a domain that shares structural homology with canonical polymerase thumb domains. An independently solved medium-resolution structure of Tetrahymena telomerase provides a blind test of our modeling methodology and sheds light on the structural homology of this domain across diverse organisms. Our smFRET-Rosetta models reveal nanometer-scale rearrangements within the RNA core domain during catalysis. Taken together, our FRET data and pseudoatomic molecular models permit us to propose a possible mechanism for how RNA core domain rearrangement is coupled to template hybrid elongation. PMID:28096444

Dressing the Coronal Magnetic Extrapolations of Active Regions with a Parameterized Thermal Structure

NASA Astrophysics Data System (ADS)

Nita, Gelu M.; Viall, Nicholeen M.; Klimchuk, James A.; Loukitcheva, Maria A.; Gary, Dale E.; Kuznetsov, Alexey A.; Fleishman, Gregory D.

2018-01-01

The study of time-dependent solar active region (AR) morphology and its relation to eruptive events requires analysis of imaging data obtained in multiple wavelength domains with differing spatial and time resolution, ideally in combination with 3D physical models. To facilitate this goal, we have undertaken a major enhancement of our IDL-based simulation tool, GX_Simulator, previously developed for modeling microwave and X-ray emission from flaring loops, to allow it to simulate quiescent emission from solar ARs. The framework includes new tools for building the atmospheric model and enhanced routines for calculating emission that include new wavelengths. In this paper, we use our upgraded tool to model and analyze an AR and compare the synthetic emission maps with observations. We conclude that the modeled magneto-thermal structure is a reasonably good approximation of the real one.

Structural analysis of a Petri net model of oxidative stress in atherosclerosis.

PubMed

Kozak, Adam; Formanowicz, Dorota; Formanowicz, Piotr

2018-06-01

Atherosclerosis is a complex process of gathering sub-endothelial plaques decreasing lumen of the blood vessels. This disorder affects people of all ages, but its progression is asymptomatic for many years. It is regulated by many typical and atypical factors including the immune system response, a chronic kidney disease, a diet rich in lipids, a local inflammatory process and a local oxidative stress that is here one of the key factors. In this study, a Petri net model of atherosclerosis regulation is presented. This model includes also some information about stoichiometric relationships between its components and covers all mentioned factors. For the model, a structural analysis based on invariants was made and biological conclusions are presented. Since the model contains inhibitor arcs, a heuristic method for analysis of such cases is presented. This method can be used to extend the concept of feasible t -invariants.

Conformational analysis of α-helical polypeptide included L-proline residue by high-resolution solid-state NMR measurement and quantum chemical calculation

NASA Astrophysics Data System (ADS)

Souma, Hiroyuki; Shoji, Akira; Kurosu, Hiromichi

2008-10-01

We challenged the problem about the stabilization mechanism of an α-helix formation for polypeptides containing L-proline (Pro) residue. We computed the optimized structure of α-helical poly( L-alanine) molecules including a Pro residue, H-(Ala) 8-Pro-(Ala) 9-OH, based on the molecular orbital calculation with density functional theory, B3LYP/6-31G(d) and the 13C and 15N chemical shift values based on the GIAO-CHF method with B3LYP/6-311G(d,p), respectively. It was found that two kinds of optimized structures, 'Bent structure' and 'Included α-helix structure', were preferred structures in H-(Ala) 8-Pro-(Ala) 9-OH. In addition, based on the precise 13C and 15N chemical shift data of the simple model, we successfully analyzed the secondary structure of well-defined synthetic polypeptide H-(Phe-Leu-Ala) 3-Phe C-Pro-Ala N-(Phe-Leu-Ala) 2-OH (FLA-11P), the secondary structure of which was proven to the 'Included α-helix structure'.

Environmental modeling and recognition for an autonomous land vehicle

NASA Technical Reports Server (NTRS)

Lawton, D. T.; Levitt, T. S.; Mcconnell, C. C.; Nelson, P. C.

1987-01-01

An architecture for object modeling and recognition for an autonomous land vehicle is presented. Examples of objects of interest include terrain features, fields, roads, horizon features, trees, etc. The architecture is organized around a set of data bases for generic object models and perceptual structures, temporary memory for the instantiation of object and relational hypotheses, and a long term memory for storing stable hypotheses that are affixed to the terrain representation. Multiple inference processes operate over these databases. Researchers describe these particular components: the perceptual structure database, the grouping processes that operate over this, schemas, and the long term terrain database. A processing example that matches predictions from the long term terrain model to imagery, extracts significant perceptual structures for consideration as potential landmarks, and extracts a relational structure to update the long term terrain database is given.

8th Annual Glycoscience Symposium: Integrating Models of Plant Cell Wall Structure, Biosynthesis and Assembly

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

Azadi, Paratoo

2015-09-24

The Complex Carbohydrate Research Center (CCRC) of the University of Georgia holds a symposium yearly that highlights a broad range of carbohydrate research topics. The 8th Annual Georgia Glycoscience Symposium entitled “Integrating Models of Plant Cell Wall Structure, Biosynthesis and Assembly” was held on April 7, 2014 at the CCRC. The focus of symposium was on the role of glycans in plant cell wall structure and synthesis. The goal was to have world leaders in conjunction with graduate students, postdoctoral fellows and research scientists to propose the newest plant cell wall models. The symposium program closely followed the DOE’s missionmore » and was specifically designed to highlight chemical and biochemical structures and processes important for the formation and modification of renewable plant cell walls which serve as the basis for biomaterial and biofuels. The symposium was attended by both senior investigators in the field as well as students including a total attendance of 103, which included 80 faculty/research scientists, 11 graduate students and 12 Postdoctoral students.« less

Probabilistic Structural Analysis Methods (PSAM) for select space propulsion system components, part 2

NASA Technical Reports Server (NTRS)

1991-01-01

The technical effort and computer code enhancements performed during the sixth year of the Probabilistic Structural Analysis Methods program are summarized. Various capabilities are described to probabilistically combine structural response and structural resistance to compute component reliability. A library of structural resistance models is implemented in the Numerical Evaluations of Stochastic Structures Under Stress (NESSUS) code that included fatigue, fracture, creep, multi-factor interaction, and other important effects. In addition, a user interface was developed for user-defined resistance models. An accurate and efficient reliability method was developed and was successfully implemented in the NESSUS code to compute component reliability based on user-selected response and resistance models. A risk module was developed to compute component risk with respect to cost, performance, or user-defined criteria. The new component risk assessment capabilities were validated and demonstrated using several examples. Various supporting methodologies were also developed in support of component risk assessment.

User-Defined Material Model for Progressive Failure Analysis

NASA Technical Reports Server (NTRS)

Knight, Norman F. Jr.; Reeder, James R. (Technical Monitor)

2006-01-01

An overview of different types of composite material system architectures and a brief review of progressive failure material modeling methods used for structural analysis including failure initiation and material degradation are presented. Different failure initiation criteria and material degradation models are described that define progressive failure formulations. These progressive failure formulations are implemented in a user-defined material model (or UMAT) for use with the ABAQUS/Standard1 nonlinear finite element analysis tool. The failure initiation criteria include the maximum stress criteria, maximum strain criteria, the Tsai-Wu failure polynomial, and the Hashin criteria. The material degradation model is based on the ply-discounting approach where the local material constitutive coefficients are degraded. Applications and extensions of the progressive failure analysis material model address two-dimensional plate and shell finite elements and three-dimensional solid finite elements. Implementation details and use of the UMAT subroutine are described in the present paper. Parametric studies for composite structures are discussed to illustrate the features of the progressive failure modeling methods that have been implemented.

Studying Turbulence Using Numerical Simulation Databases. Part 6; Proceedings of the 1996 Summer Program

NASA Technical Reports Server (NTRS)

1996-01-01

Topics considered include: New approach to turbulence modeling; Second moment closure analysis of the backstep flow database; Prediction of the backflow and recovery regions in the backward facing step at various Reynolds numbers; Turbulent flame propagation in partially premixed flames; Ensemble averaged dynamic modeling. Also included a study of the turbulence structures of wall-bounded shear flows; Simulation and modeling of the elliptic streamline flow.

Chip level modeling of LSI devices

NASA Technical Reports Server (NTRS)

Armstrong, J. R.

1984-01-01

The advent of Very Large Scale Integration (VLSI) technology has rendered the gate level model impractical for many simulation activities critical to the design automation process. As an alternative, an approach to the modeling of VLSI devices at the chip level is described, including the specification of modeling language constructs important to the modeling process. A model structure is presented in which models of the LSI devices are constructed as single entities. The modeling structure is two layered. The functional layer in this structure is used to model the input/output response of the LSI chip. A second layer, the fault mapping layer, is added, if fault simulations are required, in order to map the effects of hardware faults onto the functional layer. Modeling examples for each layer are presented. Fault modeling at the chip level is described. Approaches to realistic functional fault selection and defining fault coverage for functional faults are given. Application of the modeling techniques to single chip and bit slice microprocessors is discussed.

3D Numerical simulation of bed morphological responses to complex in-streamstructures

NASA Astrophysics Data System (ADS)

Xu, Y.; Liu, X.

2017-12-01

In-stream structures are widely used in stream restoration for both hydraulic and ecologicalpurposes. The geometries of the structures are usually designed to be extremely complex andirregular, so as to provide nature-like physical habitat. The aim of this study is to develop anumerical model to accurately predict the bed-load transport and the morphological changescaused by the complex in-stream structures. This model is developed in the platform ofOpenFOAM. In the hydrodynamics part, it utilizes different turbulence models to capture thedetailed turbulence information near the in-stream structures. The technique of immersedboundary method (IBM) is efficiently implemented in the model to describe the movable bendand the rigid solid body of in-stream structures. With IBM, the difficulty of mesh generation onthe complex geometry is greatly alleviated, and the bed surface deformation is able to becoupled in to flow system. This morphodynamics model is firstly validated by simple structures,such as the morphology of the scour in log-vane structure. Then it is applied in a more complexstructure, engineered log jams (ELJ), which consists of multiple logs piled together. Thenumerical results including turbulence flow information and bed morphological responses areevaluated against the experimental measurement within the exact same flow condition.

Structural testing and analysis of a braided, inflatable fabric torus structure

NASA Astrophysics Data System (ADS)

Young, Andrew C.; Davids, William G.; Whitney, Daniel J.; Clapp, Joshua D.; Goupee, Andrew J.

2017-10-01

Inflatable structural members have military, disaster relief, aerospace and other important applications as they possess low mass, can be stored in a relatively small volume and have significant load-carrying capacity once pressurized. Of particular interest to the present research is the Hypersonic Inflatable Aerodynamic Decelerator (HIAD) structure under development by NASA. In order to make predictions about the structural response of the HIAD system, it is necessary to understand the response of individual inflatable tori composing the HIAD structure. These inflatable members present unique challenges to structural testing and modeling due to their internal inflation pressure and relative compliance. Structural testing was performed on a braided, inflatable, toroidal structural member with axial reinforcing cords. The internal inflation pressure, magnitude of enforced displacement and loading methodology were varied. In-plane and out-of-plane experimental results were compared to model predictions using a three dimensional, corotational, flexibility-based fiber-beam finite element model including geometric and material nonlinearities, as well as the effects of inflation pressure. It was found that in order to approximate the load-deformation response observed in experimentation it is necessary to carefully control the test and model boundary conditions and loading scheme.

A perspective on coherent structures and conceptual models for turbulent boundary layer physics

NASA Technical Reports Server (NTRS)

Robinson, Stephen K.

1990-01-01

Direct numerical simulations of turbulent boundary layers have been analyzed to develop a unified conceptual model for the kinematics of coherent motions in low Reynolds number canonical turbulent boundary layers. All classes of coherent motions are considered in the model, including low-speed streaks, ejections and sweeps, vortical structures, near-wall and outer-region shear layers, sublayer pockets, and large-scale outer-region eddies. The model reflects the conclusions from the study of the simulated boundary layer that vortical structures are directly associated with the production of turbulent shear stresses, entrainment, dissipation of turbulence kinetic energy, and the fluctuating pressure field. These results, when viewed from the perspective of the large body of published work on the subject of coherent motions, confirm that vortical structures may be considered the central dynamic element in the maintenance of turbulence in the canonical boundary layer. Vortical structures serve as a framework on which to construct a unified picture of boundary layer structure, providing a means to relate the many known structural elements in a consistent way.

Structure prediction of the second extracellular loop in G-protein-coupled receptors.

PubMed

Kmiecik, Sebastian; Jamroz, Michal; Kolinski, Michal

2014-06-03

G-protein-coupled receptors (GPCRs) play key roles in living organisms. Therefore, it is important to determine their functional structures. The second extracellular loop (ECL2) is a functionally important region of GPCRs, which poses significant challenge for computational structure prediction methods. In this work, we evaluated CABS, a well-established protein modeling tool for predicting ECL2 structure in 13 GPCRs. The ECL2s (with between 13 and 34 residues) are predicted in an environment of other extracellular loops being fully flexible and the transmembrane domain fixed in its x-ray conformation. The modeling procedure used theoretical predictions of ECL2 secondary structure and experimental constraints on disulfide bridges. Our approach yielded ensembles of low-energy conformers and the most populated conformers that contained models close to the available x-ray structures. The level of similarity between the predicted models and x-ray structures is comparable to that of other state-of-the-art computational methods. Our results extend other studies by including newly crystallized GPCRs. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Goal importance within planned behaviour theory as 'the' predictor of study behaviour in college.

PubMed

Sideridis, G D; Kaissidis-Rodafinos, A

2001-12-01

The theory of planned behaviour has been rarely used for the explanation of student study behaviour and achievement. Although successful, the theory has been criticised for not including important cognitions, so goal importance was added in the present study. Goal importance refers to the weight-importance an individual assigns towards achieving a specific goal (Hollenbeck & Williams, 1987). The purpose of Study 1 was to explain the study behaviour habits of first year college students, using a) Ajzen and Madden's (1986) theory of planned behaviour, and b) planned behaviour with the addition of goal importance. The purpose of Study 2 was to replicate the findings of Study 1. The sample of Study 1 included 149 first year students of an American College located in northern Greece. Study 2 included 85 first year students of the same institution. The students in Study 1 were given a questionnaire four weeks prior to the end of the spring 1998 semester, and those in Study 2 in the autumn of 1998, including all elements of the theory of planned behaviour and goal importance. The data were modelled using Covariance Structural Modelling (CSM) and EQS 5.7b (Bentler, 1998). The planned behaviour model was not well supported in Study 1 providing a Comparative Fit Index (CFI) of.83. However, when goal importance was included in the equation, the resulting structural model produced a CFI of.94. The final structural model of Study 1 was re-tested with the sample of Study 2 and produced a CFI =.95. Findings suggest that goal importance is the causal agent in directing all elements necessary to achieve high levels of study behaviour. Future studies should examine the role of goal importance with other behaviours as well.

A novel use of structural equation models to examine factors associated with prediabetes among adults aged 50 years and older: National Health and Nutrition Examination Survey 2001-2006.

PubMed

Bardenheier, Barbara H; Bullard, Kai McKeever; Caspersen, Carl J; Cheng, Yiling J; Gregg, Edward W; Geiss, Linda S

2013-09-01

To use structural modeling to test a hypothesized model of causal pathways related with prediabetes among older adults in the U.S. Cross-sectional study of 2,230 older adults (≥ 50 years) without diabetes included in the morning fasting sample of the 2001-2006 National Health and Nutrition Examination Surveys. Demographic data included age, income, marital status, race/ethnicity, and education. Behavioral data included physical activity (metabolic equivalent hours per week for vigorous or moderate muscle strengthening, walking/biking, and house/yard work), and poor diet (refined grains, red meat, added sugars, solid fats, and high-fat dairy). Structural-equation modeling was performed to examine the interrelationships among these variables with family history of diabetes, high blood pressure, BMI, large waist (waist circumference: women, ≥ 35 inches; men, ≥ 40 inches), triglycerides ≥ 200 mg/dL, and total and HDL (≥ 60 mg/dL) cholesterol. After dropping BMI and total cholesterol, our best-fit model included three single factors: socioeconomic position (SEP), physical activity, and poor diet. Large waist had the strongest direct effect on prediabetes (0.279), followed by male sex (0.270), SEP (-0.157), high blood pressure (0.122), family history of diabetes (0.070), and age (0.033). Physical activity had direct effects on HDL (0.137), triglycerides (-0.136), high blood pressure (-0.132), and large waist (-0.067); poor diet had direct effects on large waist (0.146) and triglycerides (0.148). Our results confirmed that, while including factors known to be associated with high risk of developing prediabetes, large waist circumference had the strongest direct effect. The direct effect of SEP on prediabetes suggests mediation by some unmeasured factor(s).

Nonlinear transient analysis via energy minimization

NASA Technical Reports Server (NTRS)

Kamat, M. P.; Knight, N. F., Jr.

1978-01-01

The formulation basis for nonlinear transient analysis of finite element models of structures using energy minimization is provided. Geometric and material nonlinearities are included. The development is restricted to simple one and two dimensional finite elements which are regarded as being the basic elements for modeling full aircraft-like structures under crash conditions. The results indicate the effectiveness of the technique as a viable tool for this purpose.

Protocol and Demonstrations of Probabilistic Reliability Assessment for Structural Health Monitoring Systems (Preprint)

DTIC Science & Technology

2011-11-01

assessment to quality of localization/characterization estimates. This protocol includes four critical components: (1) a procedure to identify the...critical factors impacting SHM system performance; (2) a multistage or hierarchical approach to SHM system validation; (3) a model -assisted evaluation...Lindgren, E. A ., Buynak, C. F., Steffes, G., Derriso, M., “ Model -assisted Probabilistic Reliability Assessment for Structural Health Monitoring

Simple Model with Time-Varying Fine-Structure ``Constant''

NASA Astrophysics Data System (ADS)

Berman, M. S.

2009-10-01

Extending the original version written in colaboration with L.A. Trevisan, we study the generalisation of Dirac's LNH, so that time-variation of the fine-structure constant, due to varying electrical and magnetic permittivities is included along with other variations (cosmological and gravitational ``constants''), etc. We consider the present Universe, and also an inflationary scenario. Rotation of the Universe is a given possibility in this model.

The Impact of Using Model of Marzano Gain Students the Ability to Configure an Integrated Conceptual Structure in Islamic Concepts

ERIC Educational Resources Information Center

Alkhateeb, Omar

2015-01-01

The study aimed that the impact of using model of Marzano gain students the ability to configure an integrated conceptual structure in Islamic concepts the Sample included studious (120) student students the first year where of college of the educational sciences study in, two branches be organized in their choice was complete random among seven…

The topography of Ceres and implications for the formation of linear surface structures

NASA Astrophysics Data System (ADS)

Buczkowski, D.; Otto, K.; Ruesch, O.; Scully, J. E. C.; Williams, D. A.; Mest, S. C.; Schenk, P.; Jaumann, R.; Nathues, A.; Preusker, F.; Park, R. S.; Raymond, C. A.; Russell, C. T.

2015-12-01

NASA's Dawn spacecraft began orbiting the dwarf planet Ceres in April 2015. Framing Camera data from the Approach (1.3 km/px) and Survey (415 m/px) orbits include digital terrain models derived from processing stereo images. These models have supported various scientific studies of the surface. The eastern hemisphere of Ceres is topographically higher than the western hemisphere. Some of linear structures on Ceres (which include grooves, pit crater chains, fractures and troughs) appear to be radial to the large basins Urvara and Yalode, and most likely formed due to impact processes. However, set of regional linear structures (RLS) that do not have any obvious relationship to impact craters are found on the eastern hemisphere topographic high region. Many of the longer RLS are comprised of smaller structures that have linked together, suggestive of en echelon fractures. Polygonal craters, theorized to form when pervasive subsurface fracturing affects crater formation [1], are widespread on Ceres [2], and those proximal to the RLS have straight crater rims aligned with the grooves and troughs, suggesting that the RLS are fracture systems. A cross-section of one RLS is displayed in FC images of the Occator crater wall. Comparing these images to the digital terrain models show 1) that the structure dips ~60º and 2) there is downward motion on the hanging wall, implying normal faulting. The digital terrain models also reveal the presence of numerous positive relief features with sub-circular shapes. These dome-like features have been tentatively interpreted as volcanic/magmatic features [3]; other possibilities include salt domes. Analog models of domal uplift in areas of regional extension [4] predict patterns of linear structures similar to those observed in the RLS near Occator. Utilizing topography data provided by the Ceres digital terrain models, we assess the relationship between the RLS and nearby domes and topographic high regions to determine the mechanism by which the RLS may have formed. [1] Thomas, P.C. et al. (1999) Icarus, doi: 10.1006/icar.1999.6121 [2] Otto et al. (2015) EPSC2015-284 [3] Ruesch et al. [this meeting] [4] Sims et al. (2013) AAPG Bulletin, doi: 10.1306/02101209136

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

Faulds, James

We conducted a comprehensive analysis of the structural controls of geothermal systems within the Great Basin and adjacent regions. Our main objectives were to: 1) Produce a catalogue of favorable structural environments and models for geothermal systems. 2) Improve site-specific targeting of geothermal resources through detailed studies of representative sites, which included innovative techniques of slip tendency analysis of faults and 3D modeling. 3) Compare and contrast the structural controls and models in different tectonic settings. 4) Synthesize data and develop methodologies for enhancement of exploration strategies for conventional and EGS systems, reduction in the risk of drilling non-productive wells,more » and selecting the best EGS sites.« less

Dynamical structure factor of the J1-J2 Heisenberg model in one dimension: The variational Monte Carlo approach

NASA Astrophysics Data System (ADS)

Ferrari, Francesco; Parola, Alberto; Sorella, Sandro; Becca, Federico

2018-06-01

The dynamical spin structure factor is computed within a variational framework to study the one-dimensional J1-J2 Heisenberg model. Starting from Gutzwiller-projected fermionic wave functions, the low-energy spectrum is constructed from two-spinon excitations. The direct comparison with Lanczos calculations on small clusters demonstrates the excellent description of both gapless and gapped (dimerized) phases, including incommensurate structures for J2/J1>0.5 . Calculations on large clusters show how the intensity evolves when increasing the frustrating ratio and give an unprecedented accurate characterization of the dynamical properties of (nonintegrable) frustrated spin models.

Integrating data from multiple sources for insights into demographic processes: Simulation studies and proof of concept for hierarchical change-in-ratio models.

PubMed

Nilsen, Erlend B; Strand, Olav

2018-01-01

We developed a model for estimating demographic rates and population abundance based on multiple data sets revealing information about population age- and sex structure. Such models have previously been described in the literature as change-in-ratio models, but we extend the applicability of the models by i) using time series data allowing the full temporal dynamics to be modelled, by ii) casting the model in an explicit hierarchical modelling framework, and by iii) estimating parameters based on Bayesian inference. Based on sensitivity analyses we conclude that the approach developed here is able to obtain estimates of demographic rate with high precision whenever unbiased data of population structure are available. Our simulations revealed that this was true also when data on population abundance are not available or not included in the modelling framework. Nevertheless, when data on population structure are biased due to different observability of different age- and sex categories this will affect estimates of all demographic rates. Estimates of population size is particularly sensitive to such biases, whereas demographic rates can be relatively precisely estimated even with biased observation data as long as the bias is not severe. We then use the models to estimate demographic rates and population abundance for two Norwegian reindeer (Rangifer tarandus) populations where age-sex data were available for all harvested animals, and where population structure surveys were carried out in early summer (after calving) and late fall (after hunting season), and population size is counted in winter. We found that demographic rates were similar regardless whether we include population count data in the modelling, but that the estimated population size is affected by this decision. This suggest that monitoring programs that focus on population age- and sex structure will benefit from collecting additional data that allow estimation of observability for different age- and sex classes. In addition, our sensitivity analysis suggests that focusing monitoring towards changes in demographic rates might be more feasible than monitoring abundance in many situations where data on population age- and sex structure can be collected.

The effects of temperature and diet on age grading and population age structure determination in Drosophila.

PubMed

Aw, Wen C; Ballard, J William O

2013-10-01

The age structure of natural population is of interest in physiological, life history and ecological studies but it is often difficult to determine. One methodological problem is that samples may need to be invasively sampled preventing subsequent taxonomic curation. A second problem is that it can be very expensive to accurately determine the age structure of given population because large sample sizes are often necessary. In this study, we test the effects of temperature (17 °C, 23 °C and 26 °C) and diet (standard cornmeal and low calorie diet) on the accuracy of the non-invasive, inexpensive and high throughput near-infrared spectroscopy (NIRS) technique to determine the age of Drosophila flies. Composite and simplified calibration models were developed for each sex. Independent sets for each temperature and diet treatments with flies not involved in calibration model were then used to validate the accuracy of the calibration models. The composite NIRS calibration model was generated by including flies reared under all temperatures and diets. This approach permits rapid age measurement and age structure determination in large population of flies as less than or equal to 9 days, or more than 9 days old with 85-97% and 64-99% accuracy, respectively. The simplified calibration models were generated by including flies reared at 23 °C on standard diet. Low accuracy rates were observed when simplified calibration models were used to identify (a) Drosophila reared at 17 °C and 26 °C and (b) 23 °C with low calorie diet. These results strongly suggest that appropriate calibration models need to be developed in the laboratory before this technique can be reliably used in field. These calibration models should include the major environmental variables that change across space and time in the particular natural population to be studied. Copyright © 2013 Elsevier Ltd. All rights reserved.

From calls to communities: a model for time-varying social networks

NASA Astrophysics Data System (ADS)

Laurent, Guillaume; Saramäki, Jari; Karsai, Márton

2015-11-01

Social interactions vary in time and appear to be driven by intrinsic mechanisms that shape the emergent structure of social networks. Large-scale empirical observations of social interaction structure have become possible only recently, and modelling their dynamics is an actual challenge. Here we propose a temporal network model which builds on the framework of activity-driven time-varying networks with memory. The model integrates key mechanisms that drive the formation of social ties - social reinforcement, focal closure and cyclic closure, which have been shown to give rise to community structure and small-world connectedness in social networks. We compare the proposed model with a real-world time-varying network of mobile phone communication, and show that they share several characteristics from heterogeneous degrees and weights to rich community structure. Further, the strong and weak ties that emerge from the model follow similar weight-topology correlations as real-world social networks, including the role of weak ties.

Achilles tendons from decorin- and biglycan-null mouse models have inferior mechanical and structural properties predicted by an image-based empirical damage model

PubMed Central

Gordon, J.A.; Freedman, B.R.; Zuskov, A.; Iozzo, R.V.; Birk, D.E.; Soslowsky, L.J.

2015-01-01

Achilles tendons are a common source of pain and injury, and their pathology may originate from aberrant structure function relationships. Small leucine rich proteoglycans (SLRPs) influence mechanical and structural properties in a tendon-specific manner. However, their roles in the Achilles tendon have not been defined. The objective of this study was to evaluate the mechanical and structural differences observed in mouse Achilles tendons lacking class I SLRPs; either decorin or biglycan. In addition, empirical modeling techniques based on mechanical and image-based measures were employed. Achilles tendons from decorin-null (Dcn−/−) and biglycan-null (Bgn−/−) C57BL/6 female mice (N=102) were used. Each tendon underwent a dynamic mechanical testing protocol including simultaneous polarized light image capture to evaluate both structural and mechanical properties of each Achilles tendon. An empirical damage model was adapted for application to genetic variation and for use with image based structural properties to predict tendon dynamic mechanical properties. We found that Achilles tendons lacking decorin and biglycan had inferior mechanical and structural properties that were age dependent; and that simple empirical models, based on previously described damage models, were predictive of Achilles tendon dynamic modulus in both decorin- and biglycan-null mice. PMID:25888014

Achilles tendons from decorin- and biglycan-null mouse models have inferior mechanical and structural properties predicted by an image-based empirical damage model.

PubMed

Gordon, J A; Freedman, B R; Zuskov, A; Iozzo, R V; Birk, D E; Soslowsky, L J

2015-07-16

Achilles tendons are a common source of pain and injury, and their pathology may originate from aberrant structure function relationships. Small leucine rich proteoglycans (SLRPs) influence mechanical and structural properties in a tendon-specific manner. However, their roles in the Achilles tendon have not been defined. The objective of this study was to evaluate the mechanical and structural differences observed in mouse Achilles tendons lacking class I SLRPs; either decorin or biglycan. In addition, empirical modeling techniques based on mechanical and image-based measures were employed. Achilles tendons from decorin-null (Dcn(-/-)) and biglycan-null (Bgn(-/-)) C57BL/6 female mice (N=102) were used. Each tendon underwent a dynamic mechanical testing protocol including simultaneous polarized light image capture to evaluate both structural and mechanical properties of each Achilles tendon. An empirical damage model was adapted for application to genetic variation and for use with image based structural properties to predict tendon dynamic mechanical properties. We found that Achilles tendons lacking decorin and biglycan had inferior mechanical and structural properties that were age dependent; and that simple empirical models, based on previously described damage models, were predictive of Achilles tendon dynamic modulus in both decorin- and biglycan-null mice. Copyright © 2015 Elsevier Ltd. All rights reserved.

Geometrically nonlinear analysis of laminated elastic structures

NASA Technical Reports Server (NTRS)

Reddy, J. N.

1984-01-01

Laminated composite plates and shells that can be used to model automobile bodies, aircraft wings and fuselages, and pressure vessels among many other were analyzed. The finite element method, a numerical technique for engineering analysis of structures, is used to model the geometry and approximate the solution. Various alternative formulations for analyzing laminated plates and shells are developed and their finite element models are tested for accuracy and economy in computation. These include the shear deformation laminate theory and degenerated 3-D elasticity theory for laminates.

Investigation of Structural Dynamics in a 2-Meter Square Solar Sail Model Including Axial Load Effects

NASA Technical Reports Server (NTRS)

Holland, D. B.; Virgin, L. N.; Belvin, W. K.

2003-01-01

This paper presents a parameter study of the effect of boom axial loading on the global dynamics of a 2-meter solar sail scale model. The experimental model used is meant for building expertise in finite element analysis and experimental execution, not as a predecessor to any planned flight mission or particular design concept. The results here are to demonstrate the ability to predict and measure structural dynamics and mode shapes in the presence of axial loading.

Peridynamics with LAMMPS : a user guide.

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

Lehoucq, Richard B.; Silling, Stewart Andrew; Seleson, Pablo

Peridynamics is a nonlocal extension of classical continuum mechanics. The discrete peridynamic model has the same computational structure as a molecular dynamics model. This document provides a brief overview of the peridynamic model of a continuum, then discusses how the peridynamic model is discretized within LAMMPS. An example problem is also included.

Common quandaries and their practical solutions in Bayesian network modeling

Treesearch

Bruce G. Marcot

2017-01-01

Use and popularity of Bayesian network (BN) modeling has greatly expanded in recent years, but many common problems remain. Here, I summarize key problems in BN model construction and interpretation,along with suggested practical solutions. Problems in BN model construction include parameterizing probability values, variable definition, complex network structures,...

SubductionGenerator: A program to build three-dimensional plate configurations

NASA Astrophysics Data System (ADS)

Jadamec, M. A.; Kreylos, O.; Billen, M. I.; Turcotte, D. L.; Knepley, M.

2016-12-01

Geologic, geochemical, and geophysical data from subduction zones indicate that a two-dimensional paradigm for plate tectonic boundaries is no longer adequate to explain the observations. Many open source software packages exist to simulate the viscous flow of the Earth, such as the dynamics of subduction. However, there are few open source programs that generate the three-dimensional model input. We present an open source software program, SubductionGenerator, that constructs the three-dimensional initial thermal structure and plate boundary structure. A 3D model mesh and tectonic configuration are constructed based on a user specified model domain, slab surface, seafloor age grid file, and shear zone surface. The initial 3D thermal structure for the plates and mantle within the model domain is then constructed using a series of libraries within the code that use a half-space cooling model, plate cooling model, and smoothing functions. The code maps the initial 3D thermal structure and the 3D plate interface onto the mesh nodes using a series of libraries including a k-d tree to increase efficiency. In this way, complicated geometries and multiple plates with variable thickness can be built onto a multi-resolution finite element mesh with a 3D thermal structure and 3D isotropic shear zones oriented at any angle with respect to the grid. SubductionGenerator is aimed at model set-ups more representative of the earth, which can be particularly challenging to construct. Examples include subduction zones where the physical attributes vary in space, such as slab dip and temperature, and overriding plate temperature and thickness. Thus, the program can been used to construct initial tectonic configurations for triple junctions and plate boundary corners.

Insights into drug metabolism by cytochromes P450 from modelling studies of CYP2D6-drug interactions

PubMed Central

Maréchal, J-D; Kemp, C A; Roberts, G C K; Paine, M J I; Wolf, C R; Sutcliffe, M J

2008-01-01

The cytochromes P450 (CYPs) comprise a vast superfamily of enzymes found in virtually all life forms. In mammals, xenobiotic metabolizing CYPs provide crucial protection from the effects of exposure to a wide variety of chemicals, including environmental toxins and therapeutic drugs. Ideally, the information on the possible metabolism by CYPs required during drug development would be obtained from crystal structures of all the CYPs of interest. For some years only crystal structures of distantly related bacterial CYPs were available and homology modelling techniques were used to bridge the gap and produce structural models of human CYPs, and thereby obtain useful functional information. A significant step forward in the reliability of these models came seven years ago with the first crystal structure of a mammalian CYP, rabbit CYP2C5, followed by the structures of six human enzymes, CYP1A2, CYP2A6, CYP2C8, CYP2C9, CYP2D6 and CYP3A4, and a second rabbit enzyme, CYP2B4. In this review we describe as a case study the evolution of a CYP2D6 model, leading to the validation of the model as an in silico tool for predicting binding and metabolism. This work has led directly to the successful design of CYP2D6 mutants with novel activity—including creating a testosterone hydroxylase, converting quinidine from inhibitor to substrate, creating a diclofenac hydroxylase and creating a dextromethorphan O-demethylase. Our modelling-derived hypothesis-driven integrated interdisciplinary studies have given key insight into the molecular determinants of CYP2D6 and other important drug metabolizing enzymes. PMID:18026129

Models for Rational Decision Making. Analysis of Literature and Selected Bibliography. Analysis and Bibliography Series, No. 6.

ERIC Educational Resources Information Center

Hall, John S.

This review analyzes the trend in educational decision making to replace hierarchical authority structures with more rational models for decision making drawn from management science. Emphasis is also placed on alternatives to a hierarchical decision-making model, including governing models, union models, and influence models. A 54-item…

Bayesian Analysis of Multidimensional Item Response Theory Models: A Discussion and Illustration of Three Response Style Models

ERIC Educational Resources Information Center

Leventhal, Brian C.; Stone, Clement A.

2018-01-01

Interest in Bayesian analysis of item response theory (IRT) models has grown tremendously due to the appeal of the paradigm among psychometricians, advantages of these methods when analyzing complex models, and availability of general-purpose software. Possible models include models which reflect multidimensionality due to designed test structure,…

Molecular structure and gas chromatographic retention behavior of the components of Ylang-Ylang oil.

PubMed

Olivero, J; Gracia, T; Payares, P; Vivas, R; Díaz, D; Daza, E; Geerlings, P

1997-05-01

Using quantitative structure-retention relationships (QSRR) methodologies the Kovats gas chromatographic retention indices for both apolar (DB-1) and polar (DB-Wax) columns for 48 compounds from Ylang-Ylang essential oil were empirically predicted from calculated and experimental data on molecular structure. Topological, geometric, and electronic descriptors were obtained for model generation. Relationships between descriptors and the retention data reported were established by linear multiple regression, giving equations that can be used to predict the Kovats indices for compounds present in essential oils, both in DB-1 and DB-Wax columns. Factor analysis was performed to interpret the meaning of the descriptors included in the models. The prediction model for the DB-1 column includes descriptors such as Randic's first-order connectivity index (1X), the molecular surface (MSA), the sum of the atomic charge on all the hydrogens (QH), Randic's third-order connectivity index (3X) and the molecular electronegativity (chi). The prediction model for the DB-Wax column includes the first three descriptors mentioned for the DB-1 column (1X, MSA and QH) and the most negative charge (MNC), the global softness (S), and the difference between Randic's and Kier and Hall's third-order connectivity indexes (3X-3XV).

Simple Models for Tough Concepts

ERIC Educational Resources Information Center

Cavagnoi, Richard M.; Barnett, Thomas

1976-01-01

Describes the construction of teaching models made from a variety of materials such as poker chips and cardboard that illustrate many chemical phenomena, including subatomic particles, molecular structure, solvation and dissociation, and enzyme-substrate interactions. (MLH)

The NASA/Industry Design Analysis Methods for Vibrations (DAMVIBS) Program - A government overview. [of rotorcraft technology development using finite element method

NASA Technical Reports Server (NTRS)

Kvaternik, Raymond G.

1992-01-01

An overview is presented of government contributions to the program called Design Analysis Methods for Vibrations (DAMV) which attempted to develop finite-element-based analyses of rotorcraft vibrations. NASA initiated the program with a finite-element modeling program for the CH-47D tandem-rotor helicopter. The DAMV program emphasized four areas including: airframe finite-element modeling, difficult components studies, coupled rotor-airframe vibrations, and airframe structural optimization. Key accomplishments of the program include industrywide standards for modeling metal and composite airframes, improved industrial designs for vibrations, and the identification of critical structural contributors to airframe vibratory responses. The program also demonstrated the value of incorporating secondary modeling details to improving correlation, and the findings provide the basis for an improved finite-element-based dynamics design-analysis capability.

Computational Methods for Structural Mechanics and Dynamics, part 1

NASA Technical Reports Server (NTRS)

Stroud, W. Jefferson (Editor); Housner, Jerrold M. (Editor); Tanner, John A. (Editor); Hayduk, Robert J. (Editor)

1989-01-01

The structural analysis methods research has several goals. One goal is to develop analysis methods that are general. This goal of generality leads naturally to finite-element methods, but the research will also include other structural analysis methods. Another goal is that the methods be amenable to error analysis; that is, given a physical problem and a mathematical model of that problem, an analyst would like to know the probable error in predicting a given response quantity. The ultimate objective is to specify the error tolerances and to use automated logic to adjust the mathematical model or solution strategy to obtain that accuracy. A third goal is to develop structural analysis methods that can exploit parallel processing computers. The structural analysis methods research will focus initially on three types of problems: local/global nonlinear stress analysis, nonlinear transient dynamics, and tire modeling.

Jennifer van Rij | NREL

Science.gov Websites

Jennifer.Vanrij@nrel.gov | 303-384-7180 Jennifer's expertise is in developing computational modeling methods for collaboratively developing numerical modeling methods to simulate the hydrodynamic, structural dynamic, power -elastic interactions. Her other diverse work experiences include developing numerical modeling methods for

Probing the structure of Leishmania major DHFR TS and structure based virtual screening of peptide library for the identification of anti-leishmanial leads.

PubMed

Rajasekaran, Rajalakshmi; Chen, Yi-Ping Phoebe

2012-09-01

Leishmaniasis, a multi-faceted ethereal disease is considered to be one of the World's major communicable diseases that demands exhaustive research and control measures. The substantial data on these protozoan parasites has not been utilized completely to develop potential therapeutic strategies against Leishmaniasis. Dihydrofolate reductase thymidylate synthase (DHFR-TS) plays a major role in the infective state of the parasite and hence the DHFR-TS based drugs remains of much interest to researchers working on Leishmaniasis. Although, crystal structures of DHFR-TS from different species including Plasmodium falciparum and Trypanosoma cruzi are available, the experimentally determined structure of the Leishmania major DHFR-TS has not yet been reported in the Protein Data Bank. A high quality three dimensional structure of L.major DHFR-TS has been modeled through the homology modeling approach. Carefully refined and the energy minimized structure of the modeled protein was validated using a number of structure validation programs to confirm its structure quality. The modeled protein structure was used in the process of structure based virtual screening to figure out a potential lead structure against DHFR TS. The lead molecule identified has a binding affinity of 0.51 nM and clearly follows drug like properties.

MARC calculations for the second WIPP structural benchmark problem

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

Morgan, H.S.

1981-05-01

This report describes calculations made with the MARC structural finite element code for the second WIPP structural benchmark problem. Specific aspects of problem implementation such as element choice, slip line modeling, creep law implementation, and thermal-mechanical coupling are discussed in detail. Also included are the computational results specified in the benchmark problem formulation.

Population Genetics of Boise Basin Bull Trout (Salvelinus confluentus)

Treesearch

A.R. Whiteley; P. Spruell; F.W. Allendorf

2003-01-01

We analyzed the population genetic structure of bull trout (Salvelinus confluentus) in the Boise River Basin, Idaho. We determined the influence of contemporary (including anthropogenic) and historic factors on genetic structure, taking into accountexisting data on bull trout habitat patches in this basin. We tested three models of the organization of genetic structure...

Multi-Layer Identification of Highly-Potent ABCA1 Up-Regulators Targeting LXRβ Using Multiple QSAR Modeling, Structural Similarity Analysis, and Molecular Docking.

PubMed

Chen, Meimei; Yang, Fafu; Kang, Jie; Yang, Xuemei; Lai, Xinmei; Gao, Yuxing

2016-11-29

In this study, in silico approaches, including multiple QSAR modeling, structural similarity analysis, and molecular docking, were applied to develop QSAR classification models as a fast screening tool for identifying highly-potent ABCA1 up-regulators targeting LXRβ based on a series of new flavonoids. Initially, four modeling approaches, including linear discriminant analysis, support vector machine, radial basis function neural network, and classification and regression trees, were applied to construct different QSAR classification models. The statistics results indicated that these four kinds of QSAR models were powerful tools for screening highly potent ABCA1 up-regulators. Then, a consensus QSAR model was developed by combining the predictions from these four models. To discover new ABCA1 up-regulators at maximum accuracy, the compounds in the ZINC database that fulfilled the requirement of structural similarity of 0.7 compared to known potent ABCA1 up-regulator were subjected to the consensus QSAR model, which led to the discovery of 50 compounds. Finally, they were docked into the LXRβ binding site to understand their role in up-regulating ABCA1 expression. The excellent binding modes and docking scores of 10 hit compounds suggested they were highly-potent ABCA1 up-regulators targeting LXRβ. Overall, this study provided an effective strategy to discover highly potent ABCA1 up-regulators.

IN SILICO MODELLING OF HAZARDOUS ENDPOINTS: CURRENT PROBLEMS AND PROSPECTIVES

EPA Science Inventory

The primary hurdles for Quantitative Structure-Activity Relationships (QSARs) to overcome their acceptance for regulatory purposes will be discussed. They include (a) the development of more mechanistic representations of chemical structure, (b) the classification of toxicity pa...

Sculpting Cells with Play Doh.

ERIC Educational Resources Information Center

Way, Virginia A.

1982-01-01

Suggests using Play Doh to mold models of the nucleus, mitochondria, and inner cellular structures. Students can conceptualize the cell's structures as three-dimensional even though they appear two-dimensional under a microscope. Includes instructions for preparing homemade dough. (Author/JN)

Surface generation and editing operations applied to structural support of aerospace vehicle fuselages. M.S. Thesis

NASA Technical Reports Server (NTRS)

Schwartz, Susan K.

1992-01-01

The Solid Modeling Aerospace Research Tool (SMART) is a computer aided design tool used in aerospace vehicle design. Modeling of structural components using SMART includes the representation of the transverse or cross-wise elements of a vehicle's fuselage, ringframes, and bulkheads. Ringframes are placed along a vehicle's fuselage to provide structural support and maintain the shape of the fuselage. Bulkheads are also used to maintain shape, but are placed at locations where substantial structural support is required. Given a Bezier curve representation of a cross sectional cut through a vehicle's fuselage and/or an internal tank, this project produces a first-guess Bezier patch representation of a ringframe or bulkhead at the cross-sectional position. The grid produced is later used in the structural analysis of the vehicle. The graphical display of the generated patches allows the user to edit patch control points in real time. Constraints considered in the patch generation include maintaining 'square-like' patches and placement of longitudinal, or lengthwise along the fuselage, structural elements called longerons.

Unifying error structures in commonly used biotracer mixing models.

PubMed

Stock, Brian C; Semmens, Brice X

2016-10-01

Mixing models are statistical tools that use biotracers to probabilistically estimate the contribution of multiple sources to a mixture. These biotracers may include contaminants, fatty acids, or stable isotopes, the latter of which are widely used in trophic ecology to estimate the mixed diet of consumers. Bayesian implementations of mixing models using stable isotopes (e.g., MixSIR, SIAR) are regularly used by ecologists for this purpose, but basic questions remain about when each is most appropriate. In this study, we describe the structural differences between common mixing model error formulations in terms of their assumptions about the predation process. We then introduce a new parameterization that unifies these mixing model error structures, as well as implicitly estimates the rate at which consumers sample from source populations (i.e., consumption rate). Using simulations and previously published mixing model datasets, we demonstrate that the new error parameterization outperforms existing models and provides an estimate of consumption. Our results suggest that the error structure introduced here will improve future mixing model estimates of animal diet. © 2016 by the Ecological Society of America.

Construction of a 3D model of nattokinase, a novel fibrinolytic enzyme from Bacillus natto. A novel nucleophilic catalytic mechanism for nattokinase.

PubMed

Zheng, Zhong-liang; Zuo, Zhen-yu; Liu, Zhi-gang; Tsai, Keng-chang; Liu, Ai-fu; Zou, Guo-lin

2005-01-01

A three-dimensional structural model of nattokinase (NK) from Bacillus natto was constructed by homology modeling. High-resolution X-ray structures of Subtilisin BPN' (SB), Subtilisin Carlsberg (SC), Subtilisin E (SE) and Subtilisin Savinase (SS), four proteins with sequential, structural and functional homology were used as templates. Initial models of NK were built by MODELLER and analyzed by the PROCHECK programs. The best quality model was chosen for further refinement by constrained molecular dynamics simulations. The overall quality of the refined model was evaluated. The refined model NKC1 was analyzed by different protein analysis programs including PROCHECK for the evaluation of Ramachandran plot quality, PROSA for testing interaction energies and WHATIF for the calculation of packing quality. This structure was found to be satisfactory and also stable at room temperature as demonstrated by a 300ps long unconstrained molecular dynamics (MD) simulation. Further docking analysis promoted the coming of a new nucleophilic catalytic mechanism for NK, which is induced by attacking of hydroxyl rich in catalytic environment and locating of S221.

Value: A Framework for Radiation Oncology

PubMed Central

Teckie, Sewit; McCloskey, Susan A.; Steinberg, Michael L.

2014-01-01

In the current health care system, high costs without proportional improvements in quality or outcome have prompted widespread calls for change in how we deliver and pay for care. Value-based health care delivery models have been proposed. Multiple impediments exist to achieving value, including misaligned patient and provider incentives, information asymmetries, convoluted and opaque cost structures, and cultural attitudes toward cancer treatment. Radiation oncology as a specialty has recently become a focus of the value discussion. Escalating costs secondary to rapidly evolving technologies, safety breaches, and variable, nonstandardized structures and processes of delivering care have garnered attention. In response, we present a framework for the value discussion in radiation oncology and identify approaches for attaining value, including economic and structural models, process improvements, outcome measurement, and cost assessment. PMID:25113759

FE Modelling of the Fluid-Structure-Acoustic Interaction for the Vocal Folds Self-Oscillation

NASA Astrophysics Data System (ADS)

Švancara, Pavel; Horáček, J.; Hrůza, V.

The flow induced self-oscillation of the human vocal folds in interaction with acoustic processes in the simplified vocal tract model was explored by three-dimensional (3D) finite element (FE) model. Developed FE model includes vocal folds pretension before phonation, large deformations of the vocal fold tissue, vocal folds contact, fluid-structure interaction, morphing the fluid mesh according the vocal folds motion (Arbitrary Lagrangian-Eulerian approach), unsteady viscous compressible airflow described by the Navier-Stokes equations and airflow separation during the glottis closure. Iterative partitioned approach is used for modelling the fluid-structure interaction. Computed results prove that the developed model can be used for simulation of the vocal folds self-oscillation and resulting acoustic waves. The developed model enables to numerically simulate an influence of some pathological changes in the vocal fold tissue on the voice production.

Exploring the measurement structure of the Gambling Related Cognitions Scale (GRCS) in treatment-seekers: A Bayesian structural equation modelling approach.

PubMed

Smith, David; Woodman, Richard; Drummond, Aaron; Battersby, Malcolm

2016-03-30

Knowledge of a problem gambler's underlying gambling related cognitions plays an important role in treatment planning. The Gambling Related Cognitions Scale (GRCS) is therefore frequently used in clinical settings for screening and evaluation of treatment outcomes. However, GRCS validation studies have generated conflicting results regarding its latent structure using traditional confirmatory factor analyses (CFA). This may partly be due to the rigid constraints imposed on cross-factor loadings with traditional CFA. The aim of this investigation was to determine whether a Bayesian structural equation modelling (BSEM) approach to examination of the GRCS factor structure would better replicate substantive theory and also inform model re-specifications. Participants were 454 treatment-seekers at first presentation to a gambling treatment centre between January 2012 and December 2014. Model fit indices were well below acceptable standards for CFA. In contrast, the BSEM model which included small informative priors for the residual covariance matrix in addition to cross-loadings produced excellent model fit for the original hypothesised factor structure. The results also informed re-specification of the CFA model which provided more reasonable model fit. These conclusions have implications that should be useful to both clinicians and researchers evaluating measurement models relating to gambling related cognitions in treatment-seekers. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Likelihood analysis of spatial capture-recapture models for stratified or class structured populations

USGS Publications Warehouse

Royle, J. Andrew; Sutherland, Christopher S.; Fuller, Angela K.; Sun, Catherine C.

2015-01-01

We develop a likelihood analysis framework for fitting spatial capture-recapture (SCR) models to data collected on class structured or stratified populations. Our interest is motivated by the necessity of accommodating the problem of missing observations of individual class membership. This is particularly problematic in SCR data arising from DNA analysis of scat, hair or other material, which frequently yields individual identity but fails to identify the sex. Moreover, this can represent a large fraction of the data and, given the typically small sample sizes of many capture-recapture studies based on DNA information, utilization of the data with missing sex information is necessary. We develop the class structured likelihood for the case of missing covariate values, and then we address the scaling of the likelihood so that models with and without class structured parameters can be formally compared regardless of missing values. We apply our class structured model to black bear data collected in New York in which sex could be determined for only 62 of 169 uniquely identified individuals. The models containing sex-specificity of both the intercept of the SCR encounter probability model and the distance coefficient, and including a behavioral response are strongly favored by log-likelihood. Estimated population sex ratio is strongly influenced by sex structure in model parameters illustrating the importance of rigorous modeling of sex differences in capture-recapture models.

Accounting for age Structure in Ponderosa Pine Ecosystem Analyses: Integrating Management, Disturbance Histories and Observations with the BIOME-BGC Model

NASA Astrophysics Data System (ADS)

Hibbard, K. A.; Law, B.; Thornton, P.

2003-12-01

Disturbance and management regimes in forested ecosystems have been recently highlighted as important factors contributing to quantification of carbon stocks and fluxes. Disturbance events, such as stand-replacing fires and current management regimes that emphasize understory and tree thinning are primary suspects influencing ecosystem processes, including net ecosystem productivity (NEP) in forests of the Pacific Northwest. Several recent analyses have compared simulated to measured component stocks and fluxes of carbon in Ponderosa Pine (Pinus ponderosa var. Laws) at 12 sites ranging from 9 to 300 years in central Oregon (Law et al. 2001, Law et al. 2003) using the BIOME-BGC model. Major emphases on ecosystem model developments include improving allocation logic, integrating ecosystem processes with disturbance such as fire and including nitrogen in biogeochemical cycling. In Law et al. (2001, 2003), field observations prompted BIOME-BGC improvements including dynamic allocation of carbon to fine root mass through the life of a stand. A sequence of simulations was also designed to represent both management and disturbance histories for each site, however, current age structure of each sites wasn't addressed. Age structure, or cohort management has largely been ignored by ecosystem models, however, some studies have sought to incorporate stand age with disturbance and management (e.g. Hibbard et al. 2003). In this analyses, we regressed tree ages against height (R2 = 0.67) to develop a proportional distribution of age structure for each site. To preserve the integrity of the comparison between Law et al. (2003) and this study, we maintained the same timing of harvest, however, based on the distribution of age structures, we manipulated the amount of removal. Harvest by Law et al. (2003) was set at stand-replacement (99%) levels to simulate clear-cutting and reflecting the average top 10% of the age in each plot. For the young sites, we set removal at 73%, 51% and 61% for sites averaging 9,16 and 23 years, respectively. It was assumed that changes in long-term pools (e.g. soil C) were negligible within these timeframes. In Law et al. (2003), the model performed well for old and mature sites, however, model simulations of the younger sites (9-50Y) were weak compared to NEP estimates from observations. Error for the young plots in Law et al. (2003) ranged from 150 - >400% of observed NEP. By accounting for the observed age structure through harvest removal, model error from this study ranged from 20-90% in young plots. This study is one of a few that have sought to account for age structure in simulating ecosystem dynamics and processes.

Ion-acoustic and electron-acoustic type nonlinear waves in dusty plasmas

NASA Astrophysics Data System (ADS)

Volosevich, A.-V.; Meister, C.-V.

2003-04-01

In the present work, two three-dimensional nonlinear theoretical models of electrostatic solitary waves are investigated within the frame of magnetohydrodynamics. Both times, a multi-component plasma is considered, which consists of hot electrons with a rather flexible distribution function, hot ions with Boltzmann-type distribution, and (negatively as well as positively charged) dust. Additionally, cold ion beams are taken into account in the model to study ion-acoustic structures (IAS), and cold electron beams are included into the model to investigate electron-acoustic structures (EAS). The numerical results of the considered theoretical models allow to make the following conclusions: 1) Electrostatic structures with negative potential (of rarefaction type) are formed both in the IAS model and in the EAS model, but structures with negative potential (of compressional type) are formed in the IAS model only. 2) The intervals of various plasma parameters (velocities of ion and electron beams, temperatures, densities of the plasma components, ions' masses), for which the existence of IAS and EAS solitary waves and structures is possible, are calculated. 3) Further, the parameters of the electrostatic structures (wave amplitudes, scales along and perpendicular to the magnetic field, velocities) are estimated. 4) The application of the present numerical simulation for multi-component plasmas to various astrophysical systems under different physical conditions is discussed.

SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines

PubMed Central

2014-01-01

Background It is important to predict the quality of a protein structural model before its native structure is known. The method that can predict the absolute local quality of individual residues in a single protein model is rare, yet particularly needed for using, ranking and refining protein models. Results We developed a machine learning tool (SMOQ) that can predict the distance deviation of each residue in a single protein model. SMOQ uses support vector machines (SVM) with protein sequence and structural features (i.e. basic feature set), including amino acid sequence, secondary structures, solvent accessibilities, and residue-residue contacts to make predictions. We also trained a SVM model with two new additional features (profiles and SOV scores) on 20 CASP8 targets and found that including them can only improve the performance when real deviations between native and model are higher than 5Å. The SMOQ tool finally released uses the basic feature set trained on 85 CASP8 targets. Moreover, SMOQ implemented a way to convert predicted local quality scores into a global quality score. SMOQ was tested on the 84 CASP9 single-domain targets. The average difference between the residue-specific distance deviation predicted by our method and the actual distance deviation on the test data is 2.637Å. The global quality prediction accuracy of the tool is comparable to other good tools on the same benchmark. Conclusion SMOQ is a useful tool for protein single model quality assessment. Its source code and executable are available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/. PMID:24776231

SMOQ: a tool for predicting the absolute residue-specific quality of a single protein model with support vector machines.

PubMed

Cao, Renzhi; Wang, Zheng; Wang, Yiheng; Cheng, Jianlin

2014-04-28

It is important to predict the quality of a protein structural model before its native structure is known. The method that can predict the absolute local quality of individual residues in a single protein model is rare, yet particularly needed for using, ranking and refining protein models. We developed a machine learning tool (SMOQ) that can predict the distance deviation of each residue in a single protein model. SMOQ uses support vector machines (SVM) with protein sequence and structural features (i.e. basic feature set), including amino acid sequence, secondary structures, solvent accessibilities, and residue-residue contacts to make predictions. We also trained a SVM model with two new additional features (profiles and SOV scores) on 20 CASP8 targets and found that including them can only improve the performance when real deviations between native and model are higher than 5Å. The SMOQ tool finally released uses the basic feature set trained on 85 CASP8 targets. Moreover, SMOQ implemented a way to convert predicted local quality scores into a global quality score. SMOQ was tested on the 84 CASP9 single-domain targets. The average difference between the residue-specific distance deviation predicted by our method and the actual distance deviation on the test data is 2.637Å. The global quality prediction accuracy of the tool is comparable to other good tools on the same benchmark. SMOQ is a useful tool for protein single model quality assessment. Its source code and executable are available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/.

Methods for evaluating the predictive accuracy of structural dynamic models

NASA Technical Reports Server (NTRS)

Hasselman, T. K.; Chrostowski, Jon D.

1990-01-01

Uncertainty of frequency response using the fuzzy set method and on-orbit response prediction using laboratory test data to refine an analytical model are emphasized with respect to large space structures. Two aspects of the fuzzy set approach were investigated relative to its application to large structural dynamics problems: (1) minimizing the number of parameters involved in computing possible intervals; and (2) the treatment of extrema which may occur in the parameter space enclosed by all possible combinations of the important parameters of the model. Extensive printer graphics were added to the SSID code to help facilitate model verification, and an application of this code to the LaRC Ten Bay Truss is included in the appendix to illustrate this graphics capability.

Coherent dynamic structure factors of strongly coupled plasmas: A generalized hydrodynamic approach

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

Luo, Di; Hu, GuangYue; Gong, Tao

2016-05-15

A generalized hydrodynamic fluctuation model is proposed to simplify the calculation of the dynamic structure factor S(ω, k) of non-ideal plasmas using the fluctuation-dissipation theorem. In this model, the kinetic and correlation effects are both included in hydrodynamic coefficients, which are considered as functions of the coupling strength (Γ) and collision parameter (kλ{sub ei}), where λ{sub ei} is the electron-ion mean free path. A particle-particle particle-mesh molecular dynamics simulation code is also developed to simulate the dynamic structure factors, which are used to benchmark the calculation of our model. A good agreement between the two different approaches confirms the reliabilitymore » of our model.« less

Improvements in mode-based waveform modeling and application to Eurasian velocity structure

NASA Astrophysics Data System (ADS)

Panning, M. P.; Marone, F.; Kim, A.; Capdeville, Y.; Cupillard, P.; Gung, Y.; Romanowicz, B.

2006-12-01

We introduce several recent improvements to mode-based 3D and asymptotic waveform modeling and examine how to integrate them with numerical approaches for an improved model of upper-mantle structure under eastern Eurasia. The first step in our approach is to create a large-scale starting model including shear anisotropy using Nonlinear Asymptotic Coupling Theory (NACT; Li and Romanowicz, 1995), which models the 2D sensitivity of the waveform to the great-circle path between source and receiver. We have recently improved this approach by implementing new crustal corrections which include a non-linear correction for the difference between the average structure of several large regions from the global model with further linear corrections to account for the local structure along the path between source and receiver (Marone and Romanowicz, 2006; Panning and Romanowicz, 2006). This model is further refined using a 3D implementation of Born scattering (Capdeville, 2005). We have made several recent improvements to this method, in particular introducing the ability to represent perturbations to discontinuities. While the approach treats all sensitivity as linear perturbations to the waveform, we have also experimented with a non-linear modification analogous to that used in the development of NACT. This allows us to treat large accumulated phase delays determined from a path-average approximation non-linearly, while still using the full 3D sensitivity of the Born approximation. Further refinement of shallow regions of the model is obtained using broadband forward finite-difference waveform modeling. We are also integrating a regional Spectral Element Method code into our tomographic modeling, allowing us to move beyond many assumptions inherent in the analytic mode-based approaches, while still taking advantage of their computational efficiency. Illustrations of the effects of these increasingly sophisticated steps will be presented.

Is Small Still Beautiful for the Strengths and Difficulties Questionnaire? Novel Findings Using Exploratory Structural Equation Modeling.

PubMed

Garrido, Luis Eduardo; Barrada, Juan Ramón; Aguasvivas, José Armando; Martínez-Molina, Agustín; Arias, Víctor B; Golino, Hudson F; Legaz, Eva; Ferrís, Gloria; Rojo-Moreno, Luis

2018-06-01

During the present decade a large body of research has employed confirmatory factor analysis (CFA) to evaluate the factor structure of the Strengths and Difficulties Questionnaire (SDQ) across multiple languages and cultures. However, because CFA can produce strongly biased estimations when the population cross-loadings differ meaningfully from zero, it may not be the most appropriate framework to model the SDQ responses. With this in mind, the current study sought to assess the factorial structure of the SDQ using the more flexible exploratory structural equation modeling approach. Using a large-scale Spanish sample composed of 67,253 youths aged between 10 and 18 years ( M = 14.16, SD = 1.07), the results showed that CFA provided a severely biased and overly optimistic assessment of the underlying structure of the SDQ. In contrast, exploratory structural equation modeling revealed a generally weak factorial structure, including questionable indicators with large cross-loadings, multiple error correlations, and significant wording variance. A subsequent Monte Carlo study showed that sample sizes greater than 4,000 would be needed to adequately recover the SDQ loading structure. The findings from this study prevent recommending the SDQ as a screening tool and suggest caution when interpreting previous results in the literature based on CFA modeling.

Coach simplified structure modeling and optimization study based on the PBM method

NASA Astrophysics Data System (ADS)

Zhang, Miaoli; Ren, Jindong; Yin, Ying; Du, Jian

2016-09-01

For the coach industry, rapid modeling and efficient optimization methods are desirable for structure modeling and optimization based on simplified structures, especially for use early in the concept phase and with capabilities of accurately expressing the mechanical properties of structure and with flexible section forms. However, the present dimension-based methods cannot easily meet these requirements. To achieve these goals, the property-based modeling (PBM) beam modeling method is studied based on the PBM theory and in conjunction with the characteristics of coach structure of taking beam as the main component. For a beam component of concrete length, its mechanical characteristics are primarily affected by the section properties. Four section parameters are adopted to describe the mechanical properties of a beam, including the section area, the principal moments of inertia about the two principal axles, and the torsion constant of the section. Based on the equivalent stiffness strategy, expressions for the above section parameters are derived, and the PBM beam element is implemented in HyperMesh software. A case is realized using this method, in which the structure of a passenger coach is simplified. The model precision is validated by comparing the basic performance of the total structure with that of the original structure, including the bending and torsion stiffness and the first-order bending and torsional modal frequencies. Sensitivity analysis is conducted to choose design variables. The optimal Latin hypercube experiment design is adopted to sample the test points, and polynomial response surfaces are used to fit these points. To improve the bending and torsion stiffness and the first-order torsional frequency and taking the allowable maximum stresses of the braking and left turning conditions as constraints, the multi-objective optimization of the structure is conducted using the NSGA-II genetic algorithm on the ISIGHT platform. The result of the Pareto solution set is acquired, and the selection strategy of the final solution is discussed. The case study demonstrates that the mechanical performances of the structure can be well-modeled and simulated by PBM beam. Because of the merits of fewer parameters and convenience of use, this method is suitable to be applied in the concept stage. Another merit is that the optimization results are the requirements for the mechanical performance of the beam section instead of those of the shape and dimensions, bringing flexibility to the succeeding design.

From Data-Sharing to Model-Sharing: SCEC and the Development of Earthquake System Science (Invited)

NASA Astrophysics Data System (ADS)

Jordan, T. H.

2009-12-01

Earthquake system science seeks to construct system-level models of earthquake phenomena and use them to predict emergent seismic behavior—an ambitious enterprise that requires high degree of interdisciplinary, multi-institutional collaboration. This presentation will explore model-sharing structures that have been successful in promoting earthquake system science within the Southern California Earthquake Center (SCEC). These include disciplinary working groups to aggregate data into community models; numerical-simulation working groups to investigate system-specific phenomena (process modeling) and further improve the data models (inverse modeling); and interdisciplinary working groups to synthesize predictive system-level models. SCEC has developed a cyberinfrastructure, called the Community Modeling Environment, that can distribute the community models; manage large suites of numerical simulations; vertically integrate the hardware, software, and wetware needed for system-level modeling; and promote the interactions among working groups needed for model validation and refinement. Various socio-scientific structures contribute to successful model-sharing. Two of the most important are “communities of trust” and collaborations between government and academic scientists on mission-oriented objectives. The latter include improvements of earthquake forecasts and seismic hazard models and the use of earthquake scenarios in promoting public awareness and disaster management.

Fast Geometric Consensus Approach for Protein Model Quality Assessment

PubMed Central

Adamczak, Rafal; Pillardy, Jaroslaw; Vallat, Brinda K.

2011-01-01

Abstract Model quality assessment (MQA) is an integral part of protein structure prediction methods that typically generate multiple candidate models. The challenge lies in ranking and selecting the best models using a variety of physical, knowledge-based, and geometric consensus (GC)-based scoring functions. In particular, 3D-Jury and related GC methods assume that well-predicted (sub-)structures are more likely to occur frequently in a population of candidate models, compared to incorrectly folded fragments. While this approach is very successful in the context of diversified sets of models, identifying similar substructures is computationally expensive since all pairs of models need to be superimposed using MaxSub or related heuristics for structure-to-structure alignment. Here, we consider a fast alternative, in which structural similarity is assessed using 1D profiles, e.g., consisting of relative solvent accessibilities and secondary structures of equivalent amino acid residues in the respective models. We show that the new approach, dubbed 1D-Jury, allows to implicitly compare and rank N models in O(N) time, as opposed to quadratic complexity of 3D-Jury and related clustering-based methods. In addition, 1D-Jury avoids computationally expensive 3D superposition of pairs of models. At the same time, structural similarity scores based on 1D profiles are shown to correlate strongly with those obtained using MaxSub. In terms of the ability to select the best models as top candidates 1D-Jury performs on par with other GC methods. Other potential applications of the new approach, including fast clustering of large numbers of intermediate structures generated by folding simulations, are discussed as well. PMID:21244273

Low Energy Nuclear Structure Modeling: Can It Be Improved?

NASA Astrophysics Data System (ADS)

Stone, Jirina R.

Since the discovery of the atomic nucleus in 1911 generations of physicists have devoted enormous effort to understand low energy nuclear structure. Properties of nuclei in their ground state, including mass, binding energy and shape, provide vital input to many areas of sub-atomic physics as well as astrophysics and cosmology. Low energy excited states are equally important for understanding nuclear dynamics. Yet, no consensus exists as to what is the best path to a theory which would not only consistently reproduce a wide variety of experimental data but also have enough predictive power to yield credible predictions in areas where data are still missing. In this contribution some of the main obstacles preventing building such a theory are discussed. These include modification of the free nucleon-nucleon force in the nuclear environment and effects of the sub-nucleon (quark) structure of the nucleon. Selected classes of nuclear models, mean-field, shell and ab-initio models are briefly outlined. Finally, suggestions are made for, at least partial, progress that can be achieved with the quark-meson coupling model, as reported in recent publication [1].

Integration of system identification and finite element modelling of nonlinear vibrating structures

NASA Astrophysics Data System (ADS)

Cooper, Samson B.; DiMaio, Dario; Ewins, David J.

2018-03-01

The Finite Element Method (FEM), Experimental modal analysis (EMA) and other linear analysis techniques have been established as reliable tools for the dynamic analysis of engineering structures. They are often used to provide solutions to small and large structures and other variety of cases in structural dynamics, even those exhibiting a certain degree of nonlinearity. Unfortunately, when the nonlinear effects are substantial or the accuracy of the predicted response is of vital importance, a linear finite element model will generally prove to be unsatisfactory. As a result, the validated linear FE model requires further enhancement so that it can represent and predict the nonlinear behaviour exhibited by the structure. In this paper, a pragmatic approach to integrating test-based system identification and FE modelling of a nonlinear structure is presented. This integration is based on three different phases: the first phase involves the derivation of an Underlying Linear Model (ULM) of the structure, the second phase includes experiment-based nonlinear identification using measured time series and the third phase covers augmenting the linear FE model and experimental validation of the nonlinear FE model. The proposed case study is demonstrated on a twin cantilever beam assembly coupled with a flexible arch shaped beam. In this case, polynomial-type nonlinearities are identified and validated with force-controlled stepped-sine test data at several excitation levels.

Structure and Binding of Ionic Clusters in Th and Zr Chloride Melts

NASA Astrophysics Data System (ADS)

Akdeniz, Z.; Tosi, M. P.

2001-11-01

We discuss microscopic ionic models for the structure and the binding of small clusters which may exist as structural units in molten ThCl4 and ZrCl4 and in their mixtures with alkali halides according to Raman scattering studies of Photiadis and Papatheodorou. The models are adjusted to the two isolated tetrahedral molecules. Appreciably higher ionicity is found for ThCl4 than for ZrCl4, and this fact underlies the strikingly different behaviour of the two systems in the dense liquid state -in particular, a molecular-type structure for molten ZrCl4 against a structure including charged oligomers in molten ThCl4.

Damage Tolerance of Large Shell Structures

NASA Technical Reports Server (NTRS)

Minnetyan, L.; Chamis, C. C.

1999-01-01

Progressive damage and fracture of large shell structures is investigated. A computer model is used for the assessment of structural response, progressive fracture resistance, and defect/damage tolerance characteristics. Critical locations of a stiffened conical shell segment are identified. Defective and defect-free computer models are simulated to evaluate structural damage/defect tolerance. Safe pressurization levels are assessed for the retention of structural integrity at the presence of damage/ defects. Damage initiation, growth, accumulation, and propagation to fracture are included in the simulations. Damage propagation and burst pressures for defective and defect-free shells are compared to evaluate damage tolerance. Design implications with regard to defect and damage tolerance of a large steel pressure vessel are examined.

Incompletely Mixed Surface Transient Storage Zones at River Restoration Structures: Modeling Implications

NASA Astrophysics Data System (ADS)

Endreny, T. A.; Robinson, J.

2012-12-01

River restoration structures, also known as river steering deflectors, are designed to reduce bank shear stress by generating wake zones between the bank and the constricted conveyance region. There is interest in characterizing the surface transient storage (STS) and associated biogeochemical processing in the STS zones around these structures to quantify the ecosystem benefits of river restoration. This research explored how the hydraulics around river restoration structures prohibits application of transient storage models designed for homogenous, completely mixed STS zones. We used slug and constant rate injections of a conservative tracer in a 3rd order river in Onondaga County, NY over the course of five experiments at varying flow regimes. Recovered breakthrough curves spanned a transect including the main channel and wake zone at a j-hook restoration structure. We noted divergent patterns of peak solute concentration and times within the wake zone regardless of transect location within the structure. Analysis reveals an inhomogeneous STS zone which is frequently still loading tracer after the main channel has peaked. The breakthrough curve loading patterns at the restoration structure violated the assumptions of simplified "random walk" 2 zone transient storage models which seek to identify representative STS zones and zone locations. Use of structure-scale Weiner filter based multi-rate mass transfer models to characterize STS zones residence times are similarly dependent on a representative zone location. Each 2 zone model assumes 1 zone is a completely mixed STS zone and the other a completely mixed main channel. Our research reveals limits to simple application of the recently developed 2 zone models, and raises important questions about the measurement scale necessary to identify critical STS properties at restoration sites. An explanation for the incompletely mixed STS zone may be the distinct hydraulics at restoration sites, including a constrained high velocity conveyance region closely abutting a wake zone that receives periodic disruption from the upstream structure shearing vortices.igure 1. River restoration j-hook with blue dye revealing main channel and edge of wake zone with multiple surface transient storage zones.

Inferring global upper-mantle shear attenuation structure by waveform tomography using the spectral element method

NASA Astrophysics Data System (ADS)

Karaoǧlu, Haydar; Romanowicz, Barbara

2018-06-01

We present a global upper-mantle shear wave attenuation model that is built through a hybrid full-waveform inversion algorithm applied to long-period waveforms, using the spectral element method for wavefield computations. Our inversion strategy is based on an iterative approach that involves the inversion for successive updates in the attenuation parameter (δ Q^{-1}_μ) and elastic parameters (isotropic velocity VS, and radial anisotropy parameter ξ) through a Gauss-Newton-type optimization scheme that employs envelope- and waveform-type misfit functionals for the two steps, respectively. We also include source and receiver terms in the inversion steps for attenuation structure. We conducted a total of eight iterations (six for attenuation and two for elastic structure), and one inversion for updates to source parameters. The starting model included the elastic part of the relatively high-resolution 3-D whole mantle seismic velocity model, SEMUCB-WM1, which served to account for elastic focusing effects. The data set is a subset of the three-component surface waveform data set, filtered between 400 and 60 s, that contributed to the construction of the whole-mantle tomographic model SEMUCB-WM1. We applied strict selection criteria to this data set for the attenuation iteration steps, and investigated the effect of attenuation crustal structure on the retrieved mantle attenuation structure. While a constant 1-D Qμ model with a constant value of 165 throughout the upper mantle was used as starting model for attenuation inversion, we were able to recover, in depth extent and strength, the high-attenuation zone present in the depth range 80-200 km. The final 3-D model, SEMUCB-UMQ, shows strong correlation with tectonic features down to 200-250 km depth, with low attenuation beneath the cratons, stable parts of continents and regions of old oceanic crust, and high attenuation along mid-ocean ridges and backarcs. Below 250 km, we observe strong attenuation in the southwestern Pacific and eastern Africa, while low attenuation zones fade beneath most of the cratons. The strong negative correlation of Q^{-1}_μ and VS anomalies at shallow upper-mantle depths points to a common dominant origin for the two, likely due to variations in thermal structure. A comparison with two other global upper-mantle attenuation models shows promising consistency. As we updated the elastic 3-D model in alternate iterations, we found that the VS part of the model was stable, while the ξ structure evolution was more pronounced, indicating that it may be important to include 3-D attenuation effects when inverting for ξ, possibly due to the influence of dispersion corrections on this less well-constrained parameter.

Synthetic, multi-layer, self-oscillating vocal fold model fabrication.

PubMed

Murray, Preston R; Thomson, Scott L

2011-12-02

Sound for the human voice is produced via flow-induced vocal fold vibration. The vocal folds consist of several layers of tissue, each with differing material properties. Normal voice production relies on healthy tissue and vocal folds, and occurs as a result of complex coupling between aerodynamic, structural dynamic, and acoustic physical phenomena. Voice disorders affect up to 7.5 million annually in the United States alone and often result in significant financial, social, and other quality-of-life difficulties. Understanding the physics of voice production has the potential to significantly benefit voice care, including clinical prevention, diagnosis, and treatment of voice disorders. Existing methods for studying voice production include in vivo experimentation using human and animal subjects, in vitro experimentation using excised larynges and synthetic models, and computational modeling. Owing to hazardous and difficult instrument access, in vivo experiments are severely limited in scope. Excised larynx experiments have the benefit of anatomical and some physiological realism, but parametric studies involving geometric and material property variables are limited. Further, they are typically only able to be vibrated for relatively short periods of time (typically on the order of minutes). Overcoming some of the limitations of excised larynx experiments, synthetic vocal fold models are emerging as a complementary tool for studying voice production. Synthetic models can be fabricated with systematic changes to geometry and material properties, allowing for the study of healthy and unhealthy human phonatory aerodynamics, structural dynamics, and acoustics. For example, they have been used to study left-right vocal fold asymmetry, clinical instrument development, laryngeal aerodynamics, vocal fold contact pressure, and subglottal acoustics (a more comprehensive list can be found in Kniesburges et al.) Existing synthetic vocal fold models, however, have either been homogenous (one-layer models) or have been fabricated using two materials of differing stiffness (two-layer models). This approach does not allow for representation of the actual multi-layer structure of the human vocal folds that plays a central role in governing vocal fold flow-induced vibratory response. Consequently, one- and two-layer synthetic vocal fold models have exhibited disadvantages such as higher onset pressures than what are typical for human phonation (onset pressure is the minimum lung pressure required to initiate vibration), unnaturally large inferior-superior motion, and lack of a "mucosal wave" (a vertically-traveling wave that is characteristic of healthy human vocal fold vibration). In this paper, fabrication of a model with multiple layers of differing material properties is described. The model layers simulate the multi-layer structure of the human vocal folds, including epithelium, superficial lamina propria (SLP), intermediate and deep lamina propria (i.e., ligament; a fiber is included for anterior-posterior stiffness), and muscle (i.e., body) layers. Results are included that show that the model exhibits improved vibratory characteristics over prior one- and two-layer synthetic models, including onset pressure closer to human onset pressure, reduced inferior-superior motion, and evidence of a mucosal wave.

Compound Structure-Independent Activity Prediction in High-Dimensional Target Space.

PubMed

Balfer, Jenny; Hu, Ye; Bajorath, Jürgen

2014-08-01

Profiling of compound libraries against arrays of targets has become an important approach in pharmaceutical research. The prediction of multi-target compound activities also represents an attractive task for machine learning with potential for drug discovery applications. Herein, we have explored activity prediction in high-dimensional target space. Different types of models were derived to predict multi-target activities. The models included naïve Bayesian (NB) and support vector machine (SVM) classifiers based upon compound structure information and NB models derived on the basis of activity profiles, without considering compound structure. Because the latter approach can be applied to incomplete training data and principally depends on the feature independence assumption, SVM modeling was not applicable in this case. Furthermore, iterative hybrid NB models making use of both activity profiles and compound structure information were built. In high-dimensional target space, NB models utilizing activity profile data were found to yield more accurate activity predictions than structure-based NB and SVM models or hybrid models. An in-depth analysis of activity profile-based models revealed the presence of correlation effects across different targets and rationalized prediction accuracy. Taken together, the results indicate that activity profile information can be effectively used to predict the activity of test compounds against novel targets. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Spectral damping scaling factors for shallow crustal earthquakes in active tectonic regions

USGS Publications Warehouse

Rezaeian, Sanaz; Bozorgnia, Yousef; Idriss, I.M.; Campbell, Kenneth; Abrahamson, Norman; Silva, Walter

2012-01-01

Ground motion prediction equations (GMPEs) for elastic response spectra, including the Next Generation Attenuation (NGA) models, are typically developed at a 5% viscous damping ratio. In reality, however, structural and non-structural systems can have damping ratios other than 5%, depending on various factors such as structural types, construction materials, level of ground motion excitations, among others. This report provides the findings of a comprehensive study to develop a new model for a Damping Scaling Factor (DSF) that can be used to adjust the 5% damped spectral ordinates predicted by a GMPE to spectral ordinates with damping ratios between 0.5 to 30%. Using the updated, 2011 version of the NGA database of ground motions recorded in worldwide shallow crustal earthquakes in active tectonic regions (i.e., the NGA-West2 database), dependencies of the DSF on variables including damping ratio, spectral period, moment magnitude, source-to-site distance, duration, and local site conditions are examined. The strong influence of duration is captured by inclusion of both magnitude and distance in the DSF model. Site conditions are found to have less significant influence on DSF and are not included in the model. The proposed model for DSF provides functional forms for the median value and the logarithmic standard deviation of DSF. This model is heteroscedastic, where the variance is a function of the damping ratio. Damping Scaling Factor models are developed for the “average” horizontal ground motion components, i.e., RotD50 and GMRotI50, as well as the vertical component of ground motion.

Orbital maneuvering engine feed system coupled stability investigation

NASA Technical Reports Server (NTRS)

Kahn, D. R.; Schuman, M. D.; Hunting, J. K.; Fertig, K. W.

1975-01-01

A digital computer model used to analyze and predict engine feed system coupled instabilities over a frequency range of 10 to 1000 Hz was developed and verified. The analytical approach to modeling the feed system hydrodynamics, combustion dynamics, chamber dynamics, and overall engineering model structure is described and the governing equations in each of the technical areas are presented. This is followed by a description of the generalized computer model, including formulation of the discrete subprograms and their integration into an overall engineering model structure. The operation and capabilities of the engineering model were verified by comparing the model's theoretical predictions with experimental data from an OMS-type engine with a known feed system/engine chugging history.

Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration

PubMed Central

Miller, Thomas F.

2017-01-01

We present a coarse-grained simulation model that is capable of simulating the minute-timescale dynamics of protein translocation and membrane integration via the Sec translocon, while retaining sufficient chemical and structural detail to capture many of the sequence-specific interactions that drive these processes. The model includes accurate geometric representations of the ribosome and Sec translocon, obtained directly from experimental structures, and interactions parameterized from nearly 200 μs of residue-based coarse-grained molecular dynamics simulations. A protocol for mapping amino-acid sequences to coarse-grained beads enables the direct simulation of trajectories for the co-translational insertion of arbitrary polypeptide sequences into the Sec translocon. The model reproduces experimentally observed features of membrane protein integration, including the efficiency with which polypeptide domains integrate into the membrane, the variation in integration efficiency upon single amino-acid mutations, and the orientation of transmembrane domains. The central advantage of the model is that it connects sequence-level protein features to biological observables and timescales, enabling direct simulation for the mechanistic analysis of co-translational integration and for the engineering of membrane proteins with enhanced membrane integration efficiency. PMID:28328943

Road safety forecasts in five European countries using structural time series models.

PubMed

Antoniou, Constantinos; Papadimitriou, Eleonora; Yannis, George

2014-01-01

Modeling road safety development is a complex task and needs to consider both the quantifiable impact of specific parameters as well as the underlying trends that cannot always be measured or observed. The objective of this research is to apply structural time series models for obtaining reliable medium- to long-term forecasts of road traffic fatality risk using data from 5 countries with different characteristics from all over Europe (Cyprus, Greece, Hungary, Norway, and Switzerland). Two structural time series models are considered: (1) the local linear trend model and the (2) latent risk time series model. Furthermore, a structured decision tree for the selection of the applicable model for each situation (developed within the Road Safety Data, Collection, Transfer and Analysis [DaCoTA] research project, cofunded by the European Commission) is outlined. First, the fatality and exposure data that are used for the development of the models are presented and explored. Then, the modeling process is presented, including the model selection process, introduction of intervention variables, and development of mobility scenarios. The forecasts using the developed models appear to be realistic and within acceptable confidence intervals. The proposed methodology is proved to be very efficient for handling different cases of data availability and quality, providing an appropriate alternative from the family of structural time series models in each country. A concluding section providing perspectives and directions for future research is presented.

Molecular Phylogenetics and Systematics of the Bivalve Family Ostreidae Based on rRNA Sequence-Structure Models and Multilocus Species Tree

PubMed Central

Salvi, Daniele; Macali, Armando; Mariottini, Paolo

2014-01-01

The bivalve family Ostreidae has a worldwide distribution and includes species of high economic importance. Phylogenetics and systematic of oysters based on morphology have proved difficult because of their high phenotypic plasticity. In this study we explore the phylogenetic information of the DNA sequence and secondary structure of the nuclear, fast-evolving, ITS2 rRNA and the mitochondrial 16S rRNA genes from the Ostreidae and we implemented a multi-locus framework based on four loci for oyster phylogenetics and systematics. Sequence-structure rRNA models aid sequence alignment and improved accuracy and nodal support of phylogenetic trees. In agreement with previous molecular studies, our phylogenetic results indicate that none of the currently recognized subfamilies, Crassostreinae, Ostreinae, and Lophinae, is monophyletic. Single gene trees based on Maximum likelihood (ML) and Bayesian (BA) methods and on sequence-structure ML were congruent with multilocus trees based on a concatenated (ML and BA) and coalescent based (BA) approaches and consistently supported three main clades: (i) Crassostrea, (ii) Saccostrea, and (iii) an Ostreinae-Lophinae lineage. Therefore, the subfamily Crassotreinae (including Crassostrea), Saccostreinae subfam. nov. (including Saccostrea and tentatively Striostrea) and Ostreinae (including Ostreinae and Lophinae taxa) are recognized. Based on phylogenetic and biogeographical evidence the Asian species of Crassostrea from the Pacific Ocean are assigned to Magallana gen. nov., whereas an integrative taxonomic revision is required for the genera Ostrea and Dendostrea. This study pointed out the suitability of the ITS2 marker for DNA barcoding of oyster and the relevance of using sequence-structure rRNA models and features of the ITS2 folding in molecular phylogenetics and taxonomy. The multilocus approach allowed inferring a robust phylogeny of Ostreidae providing a broad molecular perspective on their systematics. PMID:25250663

Molecular phylogenetics and systematics of the bivalve family Ostreidae based on rRNA sequence-structure models and multilocus species tree.

PubMed

Salvi, Daniele; Macali, Armando; Mariottini, Paolo

2014-01-01

The bivalve family Ostreidae has a worldwide distribution and includes species of high economic importance. Phylogenetics and systematic of oysters based on morphology have proved difficult because of their high phenotypic plasticity. In this study we explore the phylogenetic information of the DNA sequence and secondary structure of the nuclear, fast-evolving, ITS2 rRNA and the mitochondrial 16S rRNA genes from the Ostreidae and we implemented a multi-locus framework based on four loci for oyster phylogenetics and systematics. Sequence-structure rRNA models aid sequence alignment and improved accuracy and nodal support of phylogenetic trees. In agreement with previous molecular studies, our phylogenetic results indicate that none of the currently recognized subfamilies, Crassostreinae, Ostreinae, and Lophinae, is monophyletic. Single gene trees based on Maximum likelihood (ML) and Bayesian (BA) methods and on sequence-structure ML were congruent with multilocus trees based on a concatenated (ML and BA) and coalescent based (BA) approaches and consistently supported three main clades: (i) Crassostrea, (ii) Saccostrea, and (iii) an Ostreinae-Lophinae lineage. Therefore, the subfamily Crassostreinae (including Crassostrea), Saccostreinae subfam. nov. (including Saccostrea and tentatively Striostrea) and Ostreinae (including Ostreinae and Lophinae taxa) are recognized [corrected]. Based on phylogenetic and biogeographical evidence the Asian species of Crassostrea from the Pacific Ocean are assigned to Magallana gen. nov., whereas an integrative taxonomic revision is required for the genera Ostrea and Dendostrea. This study pointed out the suitability of the ITS2 marker for DNA barcoding of oyster and the relevance of using sequence-structure rRNA models and features of the ITS2 folding in molecular phylogenetics and taxonomy. The multilocus approach allowed inferring a robust phylogeny of Ostreidae providing a broad molecular perspective on their systematics.

Aircraft wing structural design optimization based on automated finite element modelling and ground structure approach

NASA Astrophysics Data System (ADS)

Yang, Weizhu; Yue, Zhufeng; Li, Lei; Wang, Peiyan

2016-01-01

An optimization procedure combining an automated finite element modelling (AFEM) technique with a ground structure approach (GSA) is proposed for structural layout and sizing design of aircraft wings. The AFEM technique, based on CATIA VBA scripting and PCL programming, is used to generate models automatically considering the arrangement of inner systems. GSA is used for local structural topology optimization. The design procedure is applied to a high-aspect-ratio wing. The arrangement of the integral fuel tank, landing gear and control surfaces is considered. For the landing gear region, a non-conventional initial structural layout is adopted. The positions of components, the number of ribs and local topology in the wing box and landing gear region are optimized to obtain a minimum structural weight. Constraints include tank volume, strength, buckling and aeroelastic parameters. The results show that the combined approach leads to a greater weight saving, i.e. 26.5%, compared with three additional optimizations based on individual design approaches.

Preserving Lagrangian Structure in Nonlinear Model Reduction with Application to Structural Dynamics

DOE PAGES

Carlberg, Kevin; Tuminaro, Ray; Boggs, Paul

2015-03-11

Our work proposes a model-reduction methodology that preserves Lagrangian structure and achieves computational efficiency in the presence of high-order nonlinearities and arbitrary parameter dependence. As such, the resulting reduced-order model retains key properties such as energy conservation and symplectic time-evolution maps. We focus on parameterized simple mechanical systems subjected to Rayleigh damping and external forces, and consider an application to nonlinear structural dynamics. To preserve structure, the method first approximates the system's “Lagrangian ingredients''---the Riemannian metric, the potential-energy function, the dissipation function, and the external force---and subsequently derives reduced-order equations of motion by applying the (forced) Euler--Lagrange equation with thesemore » quantities. Moreover, from the algebraic perspective, key contributions include two efficient techniques for approximating parameterized reduced matrices while preserving symmetry and positive definiteness: matrix gappy proper orthogonal decomposition and reduced-basis sparsification. Our results for a parameterized truss-structure problem demonstrate the practical importance of preserving Lagrangian structure and illustrate the proposed method's merits: it reduces computation time while maintaining high accuracy and stability, in contrast to existing nonlinear model-reduction techniques that do not preserve structure.« less

Preserving Lagrangian Structure in Nonlinear Model Reduction with Application to Structural Dynamics

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

Carlberg, Kevin; Tuminaro, Ray; Boggs, Paul

Our work proposes a model-reduction methodology that preserves Lagrangian structure and achieves computational efficiency in the presence of high-order nonlinearities and arbitrary parameter dependence. As such, the resulting reduced-order model retains key properties such as energy conservation and symplectic time-evolution maps. We focus on parameterized simple mechanical systems subjected to Rayleigh damping and external forces, and consider an application to nonlinear structural dynamics. To preserve structure, the method first approximates the system's “Lagrangian ingredients''---the Riemannian metric, the potential-energy function, the dissipation function, and the external force---and subsequently derives reduced-order equations of motion by applying the (forced) Euler--Lagrange equation with thesemore » quantities. Moreover, from the algebraic perspective, key contributions include two efficient techniques for approximating parameterized reduced matrices while preserving symmetry and positive definiteness: matrix gappy proper orthogonal decomposition and reduced-basis sparsification. Our results for a parameterized truss-structure problem demonstrate the practical importance of preserving Lagrangian structure and illustrate the proposed method's merits: it reduces computation time while maintaining high accuracy and stability, in contrast to existing nonlinear model-reduction techniques that do not preserve structure.« less

A Practical Approach to Governance and Optimization of Structured Data Elements.

PubMed

Collins, Sarah A; Gesner, Emily; Morgan, Steven; Mar, Perry; Maviglia, Saverio; Colburn, Doreen; Tierney, Diana; Rocha, Roberto

2015-01-01

Definition and configuration of clinical content in an enterprise-wide electronic health record (EHR) implementation is highly complex. Sharing of data definitions across applications within an EHR implementation project may be constrained by practical limitations, including time, tools, and expertise. However, maintaining rigor in an approach to data governance is important for sustainability and consistency. With this understanding, we have defined a practical approach for governance of structured data elements to optimize data definitions given limited resources. This approach includes a 10 step process: 1) identification of clinical topics, 2) creation of draft reference models for clinical topics, 3) scoring of downstream data needs for clinical topics, 4) prioritization of clinical topics, 5) validation of reference models for clinical topics, and 6) calculation of gap analyses of EHR compared against reference model, 7) communication of validated reference models across project members, 8) requested revisions to EHR based on gap analysis, 9) evaluation of usage of reference models across project, and 10) Monitoring for new evidence requiring revisions to reference model.

A structural analysis of an ocean going patrol boat subjected to planning loads

NASA Technical Reports Server (NTRS)

Clark, James H.; Lafreniere, Robert; Stoodt, Robert; Wiedenheft, John

1987-01-01

A static structural analysis of an ocean going patrol vessel subjected to hydrodynamic planning loads is discussed. The analysis required the development of a detailed model that included hull plating, five structural bulkheads, longitudinal and transverse stiffners, and a coarse representation of the superstructure. The finite element model was developed from fabrication drawings using the Navy computer aided design system. Various stress and displacement contours are shown for the entire hull. Because several critical areas appeared to be overstressed, these areas were remeshed for detail and are presented for completeness.

Methanol clusters (CH3OH)n: putative global minimum-energy structures from model potentials and dispersion-corrected density functional theory.

PubMed

Kazachenko, Sergey; Bulusu, Satya; Thakkar, Ajit J

2013-06-14

Putative global minima are reported for methanol clusters (CH3OH)n with n ≤ 15. The predictions are based on global optimization of three intermolecular potential energy models followed by local optimization and single-point energy calculations using two variants of dispersion-corrected density functional theory. Recurring structural motifs include folded and/or twisted rings, folded rings with a short branch, and stacked rings. Many of the larger structures are stabilized by weak C-H···O bonds.

Threading structural model of the manganese-stabilizing protein PsbO reveals presence of two possible beta-sandwich domains.

PubMed

Pazos, F; Heredia, P; Valencia, A; de las Rivas, J

2001-12-01

The manganese-stabilizing protein (PsbO) is an essential component of photosystem II (PSII) and is present in all oxyphotosynthetic organisms. PsbO allows correct water splitting and oxygen evolution by stabilizing the reactions driven by the manganese cluster. Despite its important role, its structure and detailed functional mechanism are still unknown. In this article we propose a structural model based on fold recognition and molecular modeling. This model has additional support from a study of the distribution of characteristics of the PsbO sequence family, such as the distribution of conserved, apolar, tree-determinants, and correlated positions. Our threading results consistently showed PsbO as an all-beta (beta) protein, with two homologous beta domains of approximately 120 amino acids linked by a flexible Proline-Glycine-Glycine (PGG) motif. These features are compatible with a general elongated and flexible architecture, in which the two domains form a sandwich-type structure with Greek key topology. The first domain is predicted to include 8 to 9 beta-strands, the second domain 6 to 7 beta-strands. An Ig-like beta-sandwich structure was selected as a template to build the 3-D model. The second domain has, between the strands, long-loops rich in Pro and Gly that are difficult to model. One of these long loops includes a highly conserved region (between P148 and P174) and a short alpha-helix (between E181 and N188)). These regions are characteristic parts of PsbO and show that the second domain is not so similar to the template. Overall, the model was able to account for much of the experimental data reported by several authors, and it would allow the detection of key residues and regions that are proposed in this article as essential for the structure and function of PsbO. Copyright 2001 Wiley-Liss, Inc.

Development of a design basis tornado and structural design criteria for the Nevada Test Site, Nevada. Final report

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

McDonald, J.R.; Minor, J.E.; Mehta, K.C.

1975-06-01

In order to evaluate the ability of critical facilities at the Nevada Test Site to withstand the possible damaging effects of extreme winds and tornadoes, parameters for the effects of tornadoes and extreme winds and structural design criteria for the design and evaluation of structures were developed. The meteorological investigations conducted are summarized, and techniques used for developing the combined tornado and extreme wind risk model are discussed. The guidelines for structural design include methods for calculating pressure distributions on walls and roofs of structures and methods for accommodating impact loads from wind-driven missiles. Calculations for determining the design loadsmore » for an example structure are included. (LCL)« less

77 FR 6945 - Special Conditions: Learjet Inc., Learjet Model LJ-200-1A10; Interaction of Systems and Structures

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-10

... the system responses and performances. They cannot be considered in isolation but should be included... maintained. (iv) Failures of the system that result in forced structural vibrations (oscillatory failures...

Matrix Management: An Organizational Alternative for Libraries.

ERIC Educational Resources Information Center

Johnson, Peggy

1990-01-01

Describes various organizational structures and models, presents matrix management as an alternative to traditional hierarchical structures, and suggests matrix management as an appropriate organizational alternative for academic libraries. Benefits that are discussed include increased flexibility, a higher level of professional independence, and…

Protein Structure and Function Prediction Using I-TASSER

PubMed Central

Yang, Jianyi; Zhang, Yang

2016-01-01

I-TASSER is a hierarchical protocol for automated protein structure prediction and structure-based function annotation. Starting from the amino acid sequence of target proteins, I-TASSER first generates full-length atomic structural models from multiple threading alignments and iterative structural assembly simulations followed by atomic-level structure refinement. The biological functions of the protein, including ligand-binding sites, enzyme commission number, and gene ontology terms, are then inferred from known protein function databases based on sequence and structure profile comparisons. I-TASSER is freely available as both an on-line server and a stand-alone package. This unit describes how to use the I-TASSER protocol to generate structure and function prediction and how to interpret the prediction results, as well as alternative approaches for further improving the I-TASSER modeling quality for distant-homologous and multi-domain protein targets. PMID:26678386

Simultaneous optimization of biomolecular energy function on features from small molecules and macromolecules

PubMed Central

Park, Hahnbeom; Bradley, Philip; Greisen, Per; Liu, Yuan; Mulligan, Vikram Khipple; Kim, David E.; Baker, David; DiMaio, Frank

2017-01-01

Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking, have been parameterized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data. The energy function improves performance in a wide range of protein structure prediction challenges, including monomeric structure prediction, protein-protein and protein-ligand docking, protein sequence design, and prediction of the free energy changes by mutation, while reasonably recapitulating small-molecule thermodynamic properties. PMID:27766851

GPCR-I-TASSER: A hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome

PubMed Central

Zhang, Jian; Yang, Jianyi; Jang, Richard; Zhang, Yang

2015-01-01

SUMMARY Experimental structure determination remains very difficult for G protein-coupled receptors (GPCRs). We propose a new hybrid protocol to construct GPCR structure models that integrates experimental mutagenesis data with ab initio transmembrane (TM) helix assembly simulations. The method was tested on 24 known GPCRs where the ab initio TM-helix assembly procedure constructed the correct fold for 20 cases. When combined with weak-homology and sparse mutagenesis restraints, the method generated correct folds for all the tested cases with an average C-alpha RMSD 2.4 Å in the TM-regions. The new hybrid protocol was applied to model all 1026 GPCRs in the human genome, where 923 have a high confidence score that are expected to have correct folds; these contain many pharmaceutically important families with no previously solved structures, including Trace amine, Prostanoids, Releasing hormones, Melanocortins, Vasopressin and Neuropeptide Y receptors. The results demonstrate new progress on genome-wide structure modeling of transmembrane proteins. PMID:26190572

Supercoil Formation During DNA Melting

NASA Astrophysics Data System (ADS)

Sayar, Mehmet; Avsaroglu, Baris; Kabakcioglu, Alkan

2009-03-01

Supercoil formation plays a key role in determining the structure-function relationship in DNA. Biological and technological processes, such as protein synthesis, polymerase chain reaction, and microarrays relys on separation of the two strands in DNA, which is coupled to the unwinding of the supercoiled structure. This problem has been studied theoretically via Peyrard-Bishop and Poland-Scheraga type models, which include a simple representation of the DNA structural properties. In recent years, computational models, which provide a more realtistic representaion of DNA molecule, have been used to study the melting behavior of short DNA chains. Here, we will present a new coarse-grained model of DNA which is capable of simulating sufficiently long DNA chains for studying the supercoil formation during melting, without sacrificing the local structural properties. Our coarse-grained model successfully reproduces the local geometry of the DNA molecule, such as the 3'-5' directionality, major-minor groove structure, and the helical pitch. We will present our initial results on the dynamics of supercoiling during DNA melting.

Photogrammetric Modeling and Image-Based Rendering for Rapid Virtual Environment Creation

DTIC Science & Technology

2004-12-01

area and different methods have been proposed. Pertinent methods include: Camera Calibration , Structure from Motion, Stereo Correspondence, and Image...Based Rendering 1.1.1 Camera Calibration Determining the 3D structure of a model from multiple views becomes simpler if the intrinsic (or internal...can introduce significant nonlinearities into the image. We have found that camera calibration is a straightforward process which can simplify the

Force on Force Modeling with Formal Task Structures and Dynamic Geometry

DTIC Science & Technology

2017-03-24

task framework, derived using the MMF methodology to structure a complex mission. It further demonstrated the integration of effects from a range of...application methodology was intended to support a combined developmental testing (DT) and operational testing (OT) strategy for selected systems under test... methodology to develop new or modify existing Models and Simulations (M&S) to: • Apply data from multiple, distributed sources (including test

Lattice Modeling of Early-Age Behavior of Structural Concrete.

PubMed

Pan, Yaming; Prado, Armando; Porras, Rocío; Hafez, Omar M; Bolander, John E

2017-02-25

The susceptibility of structural concrete to early-age cracking depends on material composition, methods of processing, structural boundary conditions, and a variety of environmental factors. Computational modeling offers a means for identifying primary factors and strategies for reducing cracking potential. Herein, lattice models are shown to be adept at simulating the thermal-hygral-mechanical phenomena that influence early-age cracking. In particular, this paper presents a lattice-based approach that utilizes a model of cementitious materials hydration to control the development of concrete properties, including stiffness, strength, and creep resistance. The approach is validated and used to simulate early-age cracking in concrete bridge decks. Structural configuration plays a key role in determining the magnitude and distribution of stresses caused by volume instabilities of the concrete material. Under restrained conditions, both thermal and hygral effects are found to be primary contributors to cracking potential.

Modeling structural change in spatial system dynamics: A Daisyworld example.

PubMed

Neuwirth, C; Peck, A; Simonović, S P

2015-03-01

System dynamics (SD) is an effective approach for helping reveal the temporal behavior of complex systems. Although there have been recent developments in expanding SD to include systems' spatial dependencies, most applications have been restricted to the simulation of diffusion processes; this is especially true for models on structural change (e.g. LULC modeling). To address this shortcoming, a Python program is proposed to tightly couple SD software to a Geographic Information System (GIS). The approach provides the required capacities for handling bidirectional and synchronized interactions of operations between SD and GIS. In order to illustrate the concept and the techniques proposed for simulating structural changes, a fictitious environment called Daisyworld has been recreated in a spatial system dynamics (SSD) environment. The comparison of spatial and non-spatial simulations emphasizes the importance of considering spatio-temporal feedbacks. Finally, practical applications of structural change models in agriculture and disaster management are proposed.

Recent developments in broadly applicable structure-biodegradability relationships.

PubMed

Jaworska, Joanna S; Boethling, Robert S; Howard, Philip H

2003-08-01

Biodegradation is one of the most important processes influencing concentration of a chemical substance after its release to the environment. It is the main process for removal of many chemicals from the environment and therefore is an important factor in risk assessments. This article reviews available methods and models for predicting biodegradability of organic chemicals from structure. The first section of the article briefly discusses current needs for biodegradability estimation methods related to new and existing chemicals and in the context of multimedia exposure models. Following sections include biodegradation test methods and endpoints used in modeling, with special attention given to the Japanese Ministry of International Trade and Industry test; a primer on modeling, describing the various approaches that have been used in the structure/biodegradability relationship work, and contrasting statistical and mechanistic approaches; and recent developments in structure/biodegradability relationships, divided into group contribution, chemometric, and artificial intelligence approaches.

Cognitive Abilities Explain Wording Effects in the Rosenberg Self-Esteem Scale.

PubMed

Gnambs, Timo; Schroeders, Ulrich

2017-12-01

There is consensus that the 10 items of the Rosenberg Self-Esteem Scale (RSES) reflect wording effects resulting from positively and negatively keyed items. The present study examined the effects of cognitive abilities on the factor structure of the RSES with a novel, nonparametric latent variable technique called local structural equation models. In a nationally representative German large-scale assessment including 12,437 students competing measurement models for the RSES were compared: a bifactor model with a common factor and a specific factor for all negatively worded items had an optimal fit. Local structural equation models showed that the unidimensionality of the scale increased with higher levels of reading competence and reasoning, while the proportion of variance attributed to the negatively keyed items declined. Wording effects on the factor structure of the RSES seem to represent a response style artifact associated with cognitive abilities.

Lattice Modeling of Early-Age Behavior of Structural Concrete

PubMed Central

Pan, Yaming; Prado, Armando; Porras, Rocío; Hafez, Omar M.; Bolander, John E.

2017-01-01

The susceptibility of structural concrete to early-age cracking depends on material composition, methods of processing, structural boundary conditions, and a variety of environmental factors. Computational modeling offers a means for identifying primary factors and strategies for reducing cracking potential. Herein, lattice models are shown to be adept at simulating the thermal-hygral-mechanical phenomena that influence early-age cracking. In particular, this paper presents a lattice-based approach that utilizes a model of cementitious materials hydration to control the development of concrete properties, including stiffness, strength, and creep resistance. The approach is validated and used to simulate early-age cracking in concrete bridge decks. Structural configuration plays a key role in determining the magnitude and distribution of stresses caused by volume instabilities of the concrete material. Under restrained conditions, both thermal and hygral effects are found to be primary contributors to cracking potential. PMID:28772590

Impacts of insect disturbance on the structure, composition, and functioning of oak-pine forests

NASA Astrophysics Data System (ADS)

Medvigy, D.; Schafer, K. V.; Clark, K. L.

2011-12-01

Episodic disturbance is an essential feature of terrestrial ecosystems, and strongly modulates their structure, composition, and functioning. However, dynamic global vegetation models that are commonly used to make ecosystem and terrestrial carbon budget predictions rarely have an explicit representation of disturbance. One reason why disturbance is seldom included is that disturbance tends to operate on spatial scales that are much smaller than typical model resolutions. In response to this problem, the Ecosystem Demography model 2 (ED2) was developed as a way of tracking the fine-scale heterogeneity arising from disturbances. In this study, we used ED2 to simulate an oak-pine forest that experiences episodic defoliation by gypsy moth (Lymantria dispar L). The model was carefully calibrated against site-level data, and then used to simulate changes in ecosystem composition, structure, and functioning on century time scales. Compared to simulations that include gypsy moth defoliation, we show that simulations that ignore defoliation events lead to much larger ecosystem carbon stores and a larger fraction of deciduous trees relative to evergreen trees. Furthermore, we find that it is essential to preserve the fine-scale nature of the disturbance. Attempts to "smooth out" the defoliation event over an entire grid cells led to large biases in ecosystem structure and functioning.

Functional and structural insights into novel DREB1A transcription factors in common wheat (Triticum aestivum L.): A molecular modeling approach.

PubMed

Kumar, Anuj; Kumar, Sanjay; Kumar, Upendra; Suravajhala, Prashanth; Gajula, M N V Prasad

2016-10-01

Triticum aestivum L. known as common wheat is one of the most important cereal crops feeding a large and growing population. Various environmental stress factors including drought, high salinity and heat etc. adversely affect wheat production in a significant manner. Dehydration-responsive element-binding (DREB1A) factors, a class of transcription factors (TF) play an important role in combating drought stress. It is known that DREB1A specifically interacts with the dehydration responsive elements (DRE/CRT) inducing expression of genes involved in environmental stress tolerance in plants. Despite its critical interplay in plants, the structural and functional aspects of DREB1A TF in wheat remain unresolved. Previous studies showed that wheat DREBs (DREB1 and DREB2) were isolated using various methods including yeast two-hybrid screens but no extensive structural models were reported. In this study, we made an extensive in silico study to gain insight into DREB1A TF and reported the location of novel DREB1A in wheat chromosomes. We inferred the three-dimensional structural model of DREB1A using homology modelling and further evaluated them using molecular dynamics(MD) simulations yielding refined modelled structures. Our biochemical function predictions suggested that the wheat DREB1A orthologs have similar biochemical functions and pathways to that of AtDREB1A. In conclusion, the current study presents a structural perspective of wheat DREB1A and helps in understanding the molecular basis for the mechanism of DREB1A in response to environmental stress. Copyright © 2016 Elsevier Ltd. All rights reserved.

Integration of QUARK and I-TASSER for ab initio protein structure prediction in CASP11

PubMed Central

Zhang, Wenxuan; Yang, Jianyi; He, Baoji; Walker, Sara Elizabeth; Zhang, Hongjiu; Govindarajoo, Brandon; Virtanen, Jouko; Xue, Zhidong; Shen, Hong-Bin; Zhang, Yang

2015-01-01

We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score=0.736 and RMSD=2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. PMID:26370505

Integration of QUARK and I-TASSER for Ab Initio Protein Structure Prediction in CASP11.

PubMed

Zhang, Wenxuan; Yang, Jianyi; He, Baoji; Walker, Sara Elizabeth; Zhang, Hongjiu; Govindarajoo, Brandon; Virtanen, Jouko; Xue, Zhidong; Shen, Hong-Bin; Zhang, Yang

2016-09-01

We tested two pipelines developed for template-free protein structure prediction in the CASP11 experiment. First, the QUARK pipeline constructs structure models by reassembling fragments of continuously distributed lengths excised from unrelated proteins. Five free-modeling (FM) targets have the model successfully constructed by QUARK with a TM-score above 0.4, including the first model of T0837-D1, which has a TM-score = 0.736 and RMSD = 2.9 Å to the native. Detailed analysis showed that the success is partly attributed to the high-resolution contact map prediction derived from fragment-based distance-profiles, which are mainly located between regular secondary structure elements and loops/turns and help guide the orientation of secondary structure assembly. In the Zhang-Server pipeline, weakly scoring threading templates are re-ordered by the structural similarity to the ab initio folding models, which are then reassembled by I-TASSER based structure assembly simulations; 60% more domains with length up to 204 residues, compared to the QUARK pipeline, were successfully modeled by the I-TASSER pipeline with a TM-score above 0.4. The robustness of the I-TASSER pipeline can stem from the composite fragment-assembly simulations that combine structures from both ab initio folding and threading template refinements. Despite the promising cases, challenges still exist in long-range beta-strand folding, domain parsing, and the uncertainty of secondary structure prediction; the latter of which was found to affect nearly all aspects of FM structure predictions, from fragment identification, target classification, structure assembly, to final model selection. Significant efforts are needed to solve these problems before real progress on FM could be made. Proteins 2016; 84(Suppl 1):76-86. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Solar plus: Optimization of distributed solar PV through battery storage and dispatchable load in residential buildings

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

O'Shaughnessy, Eric; Cutler, Dylan; Ardani, Kristen

As utility electricity rates evolve, pairing solar photovoltaic (PV) systems with battery storage has potential to ensure the value proposition of residential solar by mitigating economic uncertainty. In addition to batteries, load control technologies can reshape customer load profiles to optimize PV system use. The combination of PV, energy storage, and load control provides an integrated approach to PV deployment, which we call 'solar plus'. The U.S. National Renewable Energy Laboratory's Renewable Energy Optimization (REopt) model is utilized to evaluate cost-optimal technology selection, sizing, and dispatch in residential buildings under a variety of rate structures and locations. The REopt modelmore » is extended to include a controllable or 'smart' domestic hot water heater model and smart air conditioner model. We find that the solar plus approach improves end user economics across a variety of rate structures - especially those that are challenging for PV - including lower grid export rates, non-coincident time-of-use structures, and demand charges.« less

Solar plus: Optimization of distributed solar PV through battery storage and dispatchable load in residential buildings

DOE PAGES

O'Shaughnessy, Eric; Cutler, Dylan; Ardani, Kristen; ...

2018-01-11

As utility electricity rates evolve, pairing solar photovoltaic (PV) systems with battery storage has potential to ensure the value proposition of residential solar by mitigating economic uncertainty. In addition to batteries, load control technologies can reshape customer load profiles to optimize PV system use. The combination of PV, energy storage, and load control provides an integrated approach to PV deployment, which we call 'solar plus'. The U.S. National Renewable Energy Laboratory's Renewable Energy Optimization (REopt) model is utilized to evaluate cost-optimal technology selection, sizing, and dispatch in residential buildings under a variety of rate structures and locations. The REopt modelmore » is extended to include a controllable or 'smart' domestic hot water heater model and smart air conditioner model. We find that the solar plus approach improves end user economics across a variety of rate structures - especially those that are challenging for PV - including lower grid export rates, non-coincident time-of-use structures, and demand charges.« less

Dry wind tunnel system

NASA Technical Reports Server (NTRS)

Chen, Ping-Chih (Inventor)

2013-01-01

This invention is a ground flutter testing system without a wind tunnel, called Dry Wind Tunnel (DWT) System. The DWT system consists of a Ground Vibration Test (GVT) hardware system, a multiple input multiple output (MIMO) force controller software, and a real-time unsteady aerodynamic force generation software, that is developed from an aerodynamic reduced order model (ROM). The ground flutter test using the DWT System operates on a real structural model, therefore no scaled-down structural model, which is required by the conventional wind tunnel flutter test, is involved. Furthermore, the impact of the structural nonlinearities on the aeroelastic stability can be included automatically. Moreover, the aeroservoelastic characteristics of the aircraft can be easily measured by simply including the flight control system in-the-loop. In addition, the unsteady aerodynamics generated computationally is interference-free from the wind tunnel walls. Finally, the DWT System can be conveniently and inexpensively carried out as a post GVT test with the same hardware, only with some possible rearrangement of the shakers and the inclusion of additional sensors.

Active vibration absorber for CSI evolutionary model: Design and experimental results

NASA Technical Reports Server (NTRS)

Bruner, Anne M.; Belvin, W. Keith; Horta, Lucas G.; Juang, Jer-Nan

1991-01-01

The development of control of large flexible structures technology must include practical demonstration to aid in the understanding and characterization of controlled structures in space. To support this effort, a testbed facility was developed to study practical implementation of new control technologies under realistic conditions. The design is discussed of a second order, acceleration feedback controller which acts as an active vibration absorber. This controller provides guaranteed stability margins for collocated sensor/actuator pairs in the absence of sensor/actuator dynamics and computational time delay. The primary performance objective considered is damping augmentation of the first nine structural modes. Comparison of experimental and predicted closed loop damping is presented, including test and simulation time histories for open and closed loop cases. Although the simulation and test results are not in full agreement, robustness of this design under model uncertainty is demonstrated. The basic advantage of this second order controller design is that the stability of the controller is model independent.

Does the concept of Clar's aromatic sextet work for dicationic forms of polycyclic aromatic hydrocarbons?--testing the model against charged systems in singlet and triplet states.

PubMed

Dominikowska, Justyna; Palusiak, Marcin

2011-07-07

The concept of Clar's π-electron aromatic sextet was tested against a set of polycyclic aromatic hydrocarbons in neutral and doubly charged forms. Systems containing different types of rings (in the context of Clar's concept) were chosen, including benzene, naphthalene, anthracene, phenanthrene and triphenylene. In the case of dicationic structures both singlet and triplet states were considered. It was found that for singlet state dicationic structures the concept of aromatic sextet could be applied and the local aromaticity could be discussed in the context of that model, whereas in the case of triplet state dicationic structures Clar's model rather failed. Different aromaticity indices based on various properties of molecular systems were applied for the purpose of the studies. The discussion about the interdependence between the values of different aromaticity indices applied to neutral and charged systems in singlet and triplet states is also included. This journal is © the Owner Societies 2011

Roll Damping Derivatives from Generalized Lifting-Surface Theory and Wind Tunnel Forced-Oscillation Tests

NASA Technical Reports Server (NTRS)

Pototzky, Anthony S; Murphy, Patrick C.

2014-01-01

Improving aerodynamic models for adverse loss-of-control conditions in flight is an area being researched under the NASA Aviation Safety Program. Aerodynamic models appropriate for loss of control conditions require a more general mathematical representation to predict nonlinear unsteady behaviors. As more general aerodynamic models are studied that include nonlinear higher order effects, the possibility of measurements that confound aerodynamic and structural responses are probable. In this study an initial step is taken to look at including structural flexibility in analysis of rigid-body forced-oscillation testing that accounts for dynamic rig, sting and balance flexibility. Because of the significant testing required and associated costs in a general study, it makes sense to capitalize on low cost analytical methods where possible, especially where structural flexibility can be accounted for by a low cost method. This paper provides an initial look at using linear lifting surface theory applied to rigid-body aircraft roll forced-oscillation tests.

The hierarchical structure of childhood personality in five countries: continuity from early childhood to early adolescence.

PubMed

Tackett, Jennifer L; Slobodskaya, Helena R; Mar, Raymond A; Deal, James; Halverson, Charles F; Baker, Spencer R; Pavlopoulos, Vassilis; Besevegis, Elias

2012-08-01

Childhood personality is a rapidly growing area of investigation within individual differences research. One understudied topic is the universality of the hierarchical structure of childhood personality. In the present investigation, parents rated the personality characteristics of 3,751 children from 5 countries and 4 age groups. The hierarchical structure of childhood personality was examined for 1-, 2-, 3-, 4-, and 5-factor models across country (Canada, China, Greece, Russia, and the United States) and age group (3-5, 6-8, 9-11, and 12-14 years of age). Many similarities were noted across both country and age. The Five-Factor Model was salient beginning in early childhood (ages 3-5). Deviations across groups and from adult findings are noted, including the prominent role of antagonism in childhood personality and the high covariation between Conscientiousness and intellect. Future directions, including the need for more explicit attempts to merge temperament and personality models, are discussed. © 2011 The Authors. Journal of Personality © 2011, Wiley Periodicals, Inc.

Trajectory-Based Loads for the Ares I-X Test Flight Vehicle

NASA Technical Reports Server (NTRS)

Vause, Roland F.; Starr, Brett R.

2011-01-01

In trajectory-based loads, the structural engineer treats each point on the trajectory as a load case. Distributed aero, inertial, and propulsion forces are developed for the structural model which are equivalent to the integrated values of the trajectory model. Free-body diagrams are then used to solve for the internal forces, or loads, that keep the applied aero, inertial, and propulsion forces in dynamic equilibrium. There are several advantages to using trajectory-based loads. First, consistency is maintained between the integrated equilibrium equations of the trajectory analysis and the distributed equilibrium equations of the structural analysis. Second, the structural loads equations are tied to the uncertainty model for the trajectory systems analysis model. Atmosphere, aero, propulsion, mass property, and controls uncertainty models all feed into the dispersions that are generated for the trajectory systems analysis model. Changes in any of these input models will affect structural loads response. The trajectory systems model manages these inputs as well as the output from the structural model over thousands of dispersed cases. Large structural models with hundreds of thousands of degrees of freedom would execute too slowly to be an efficient part of several thousand system analyses. Trajectory-based loads provide a means for the structures discipline to be included in the integrated systems analysis. Successful applications of trajectory-based loads methods for the Ares I-X vehicle are covered in this paper. Preliminary design loads were based on 2000 trajectories using Monte Carlo dispersions. Range safety loads were tied to 8423 malfunction turn trajectories. In addition, active control system loads were based on 2000 preflight trajectories using Monte Carlo dispersions.

Andreev reflection enhancement in semiconductor-superconductor structures

NASA Astrophysics Data System (ADS)

Bouscher, Shlomi; Winik, Roni; Hayat, Alex

2018-02-01

We develop a theoretical approach for modeling a wide range of semiconductor-superconductor structures with arbitrary potential barriers and a spatially dependent superconducting order parameter. We demonstrate asymmetry in the conductance spectrum as a result of a Schottky barrier shape. We further show that the Andreev reflection process can be significantly enhanced through resonant tunneling with appropriate barrier configuration, which can incorporate the Schottky barrier as a contributing component of the device. Moreover, we show that resonant tunneling can be achieved in superlattice structures as well. These theoretically demonstrated effects along with our modeling approach enable much more efficient Cooper pair injection into semiconductor-superconductor structures, including superconducting optoelectronic devices.

Some aspects of algorithm performance and modeling in transient analysis of structures

NASA Technical Reports Server (NTRS)

Adelman, H. M.; Haftka, R. T.; Robinson, J. C.

1981-01-01

The status of an effort to increase the efficiency of calculating transient temperature fields in complex aerospace vehicle structures is described. The advantages and disadvantages of explicit algorithms with variable time steps, known as the GEAR package, is described. Four test problems, used for evaluating and comparing various algorithms, were selected and finite-element models of the configurations are described. These problems include a space shuttle frame component, an insulated cylinder, a metallic panel for a thermal protection system, and a model of the wing of the space shuttle orbiter. Results generally indicate a preference for implicit over explicit algorithms for solution of transient structural heat transfer problems when the governing equations are stiff (typical of many practical problems such as insulated metal structures).

Plate and butt-weld stresses beyond elastic limit, material and structural modeling

NASA Technical Reports Server (NTRS)

Verderaime, V.

1991-01-01

Ultimate safety factors of high performance structures depend on stress behavior beyond the elastic limit, a region not too well understood. An analytical modeling approach was developed to gain fundamental insights into inelastic responses of simple structural elements. Nonlinear material properties were expressed in engineering stresses and strains variables and combined with strength of material stress and strain equations similar to numerical piece-wise linear method. Integrations are continuous which allows for more detailed solutions. Included with interesting results are the classical combined axial tension and bending load model and the strain gauge conversion to stress beyond the elastic limit. Material discontinuity stress factors in butt-welds were derived. This is a working-type document with analytical methods and results applicable to all industries of high reliability structures.

A systematic literature review of PTSD's latent structure in the Diagnostic and Statistical Manual of Mental Disorders: DSM-IV to DSM-5.

PubMed

Armour, Cherie; Műllerová, Jana; Elhai, Jon D

2016-03-01

The factor structure of posttraumatic stress disorder (PTSD) has been widely researched, but consensus regarding the exact number and nature of factors is yet to be reached. The aim of the current study was to systematically review the extant literature on PTSD's latent structure in the Diagnostic and Statistical Manual of Mental Disorders (DSM) in order to identify the best-fitting model. One hundred and twelve research papers published after 1994 using confirmatory factor analysis and DSM-based measures of PTSD were included in the review. In the DSM-IV literature, four-factor models received substantial support, but the five-factor Dysphoric arousal model demonstrated the best fit, regardless of gender, measurement instrument or trauma type. The recently proposed DSM-5 PTSD model was found to be a good representation of PTSD's latent structure, but studies analysing the six- and seven-factor models suggest that the DSM-5 PTSD factor structure may need further alterations. Copyright © 2015 Elsevier Ltd. All rights reserved.

Molecular modeling of the AhR structure and interactions can shed light on ligand-dependent activation and transformation mechanisms.

PubMed

Bonati, Laura; Corrada, Dario; Tagliabue, Sara Giani; Motta, Stefano

2017-02-01

Molecular modeling has given important contributions to elucidation of the main stages in the AhR signal transduction pathway. Despite the lack of experimentally determined structures of the AhR functional domains, information derived from homologous systems has been exploited for modeling their structure and interactions. Homology models of the AhR PASB domain have provided information on the binding cavity and contributed to elucidate species-specific differences in ligand binding. Molecular Docking simulations of the ligand binding process have given insights into differences in binding of diverse agonists, antagonists, and selective AhR modulators, and their application to virtual screening of large databases of compounds have allowed identification of novel AhR ligands. Recently available structural information on protein-protein and protein-DNA complexes of other bHLH-PAS systems has opened the way for modeling the AhR:ARNT dimer structure and investigating the mechanisms of AhR transformation and DNA binding. Future research directions should include simulation of the protein dynamics to obtain a more reliable description of intermolecular interactions involved in signal transmission.

Overview of refinement procedures within REFMAC5: utilizing data from different sources.

PubMed

Kovalevskiy, Oleg; Nicholls, Robert A; Long, Fei; Carlon, Azzurra; Murshudov, Garib N

2018-03-01

Refinement is a process that involves bringing into agreement the structural model, available prior knowledge and experimental data. To achieve this, the refinement procedure optimizes a posterior conditional probability distribution of model parameters, including atomic coordinates, atomic displacement parameters (B factors), scale factors, parameters of the solvent model and twin fractions in the case of twinned crystals, given observed data such as observed amplitudes or intensities of structure factors. A library of chemical restraints is typically used to ensure consistency between the model and the prior knowledge of stereochemistry. If the observation-to-parameter ratio is small, for example when diffraction data only extend to low resolution, the Bayesian framework implemented in REFMAC5 uses external restraints to inject additional information extracted from structures of homologous proteins, prior knowledge about secondary-structure formation and even data obtained using different experimental methods, for example NMR. The refinement procedure also generates the `best' weighted electron-density maps, which are useful for further model (re)building. Here, the refinement of macromolecular structures using REFMAC5 and related tools distributed as part of the CCP4 suite is discussed.

Space Shuttle Main Engine structural analysis and data reduction/evaluation. Volume 6: Primary nozzle diffuser analysis

NASA Technical Reports Server (NTRS)

Foley, Michael J.

1989-01-01

The primary nozzle diffuser routes fuel from the main fuel valve on the Space Shuttle Main Engine (SSME) to the nozzle coolant inlet mainfold, main combustion chamber coolant inlet mainfold, chamber coolant valve, and the augmented spark igniters. The diffuser also includes the fuel system purge check valve connection. A static stress analysis was performed on the diffuser because no detailed analysis was done on this part in the past. Structural concerns were in the area of the welds because approximately 10 percent are in areas inaccessible by X-ray testing devices. Flow dynamics and thermodynamics were not included in the analysis load case. Constant internal pressure at maximum SSME power was used instead. A three-dimensional, finite element method was generated using ANSYS version 4.3A on the Lockheed VAX 11/785 computer to perform the stress computations. IDEAS Supertab on a Sun 3/60 computer was used to create the finite element model. Rocketdyne drawing number RS009156 was used for the model interpretation. The flight diffuser is denoted as -101. A description of the model, boundary conditions/load case, material properties, structural analysis/results, and a summary are included for documentation.

Detection of Earthquake-Induced Damage in a Framed Structure Using a Finite Element Model Updating Procedure

PubMed Central

Kim, Seung-Nam; Park, Taewon; Lee, Sang-Hyun

2014-01-01

Damage of a 5-story framed structure was identified from two types of measured data, which are frequency response functions (FRF) and natural frequencies, using a finite element (FE) model updating procedure. In this study, a procedure to determine the appropriate weightings for different groups of observations was proposed. In addition, a modified frame element which included rotational springs was used to construct the FE model for updating to represent concentrated damage at the member ends (a formulation for plastic hinges in framed structures subjected to strong earthquakes). The results of the model updating and subsequent damage detection when the rotational springs (RS model) were used were compared with those obtained using the conventional frame elements (FS model). Comparisons indicated that the RS model gave more accurate results than the FS model. That is, the errors in the natural frequencies of the updated models were smaller, and the identified damage showed clearer distinctions between damaged and undamaged members and was more consistent with observed damage. PMID:24574888

Nitrate removal in stream ecosystems measured by 15N addition experiments: Total uptake

USGS Publications Warehouse

Hall, R.O.; Tank, J.L.; Sobota, D.J.; Mulholland, P.J.; O'Brien, J. M.; Dodds, W.K.; Webster, J.R.; Valett, H.M.; Poole, G.C.; Peterson, B.J.; Meyer, J.L.; McDowell, W.H.; Johnson, S.L.; Hamilton, S.K.; Grimm, N. B.; Gregory, S.V.; Dahm, Clifford N.; Cooper, L.W.; Ashkenas, L.R.; Thomas, S.M.; Sheibley, R.W.; Potter, J.D.; Niederlehner, B.R.; Johnson, L.T.; Helton, A.M.; Crenshaw, C.M.; Burgin, A.J.; Bernot, M.J.; Beaulieu, J.J.; Arangob, C.P.

2009-01-01

We measured uptake length of 15NO-3 in 72 streams in eight regions across the United States and Puerto Rico to develop quantitative predictive models on controls of NO-3 uptake length. As part of the Lotic Intersite Nitrogen eXperiment II project, we chose nine streams in each region corresponding to natural (reference), suburban-urban, and agricultural land uses. Study streams spanned a range of human land use to maximize variation in NO-3 concentration, geomorphology, and metabolism. We tested a causal model predicting controls on NO-3 uptake length using structural equation modeling. The model included concomitant measurements of ecosystem metabolism, hydraulic parameters, and nitrogen concentration. We compared this structural equation model to multiple regression models which included additional biotic, catchment, and riparian variables. The structural equation model explained 79% of the variation in log uptake length (S Wtot). Uptake length increased with specific discharge (Q/w) and increasing NO-3 concentrations, showing a loss in removal efficiency in streams with high NO-3 concentration. Uptake lengths shortened with increasing gross primary production, suggesting autotrophic assimilation dominated NO-3 removal. The fraction of catchment area as agriculture and suburban-urban land use weakly predicted NO-3 uptake in bivariate regression, and did improve prediction in a set of multiple regression models. Adding land use to the structural equation model showed that land use indirectly affected NO-3 uptake lengths via directly increasing both gross primary production and NO-3 concentration. Gross primary production shortened SWtot, while increasing NO-3 lengthened SWtot resulting in no net effect of land use on NO- 3 removal. ?? 2009.

Report of the wwPDB Small-Angle Scattering Task Force: data requirements for biomolecular modeling and the PDB.

PubMed

Trewhella, Jill; Hendrickson, Wayne A; Kleywegt, Gerard J; Sali, Andrej; Sato, Mamoru; Schwede, Torsten; Svergun, Dmitri I; Tainer, John A; Westbrook, John; Berman, Helen M

2013-06-04

This report presents the conclusions of the July 12-13, 2012 meeting of the Small-Angle Scattering Task Force of the worldwide Protein Data Bank (wwPDB; Berman et al., 2003) at Rutgers University in New Brunswick, New Jersey. The task force includes experts in small-angle scattering (SAS), crystallography, data archiving, and molecular modeling who met to consider questions regarding the contributions of SAS to modern structural biology. Recognizing there is a rapidly growing community of structural biology researchers acquiring and interpreting SAS data in terms of increasingly sophisticated molecular models, the task force recommends that (1) a global repository is needed that holds standard format X-ray and neutron SAS data that is searchable and freely accessible for download; (2) a standard dictionary is required for definitions of terms for data collection and for managing the SAS data repository; (3) options should be provided for including in the repository SAS-derived shape and atomistic models based on rigid-body refinement against SAS data along with specific information regarding the uniqueness and uncertainty of the model, and the protocol used to obtain it; (4) criteria need to be agreed upon for assessment of the quality of deposited SAS data and the accuracy of SAS-derived models, and the extent to which a given model fits the SAS data; (5) with the increasing diversity of structural biology data and models being generated, archiving options for models derived from diverse data will be required; and (6) thought leaders from the various structural biology disciplines should jointly define what to archive in the PDB and what complementary archives might be needed, taking into account both scientific needs and funding. Copyright © 2013 Elsevier Ltd. All rights reserved.

Multi-model inference for incorporating trophic and climate uncertainty into stock assessments

NASA Astrophysics Data System (ADS)

Ianelli, James; Holsman, Kirstin K.; Punt, André E.; Aydin, Kerim

2016-12-01

Ecosystem-based fisheries management (EBFM) approaches allow a broader and more extensive consideration of objectives than is typically possible with conventional single-species approaches. Ecosystem linkages may include trophic interactions and climate change effects on productivity for the relevant species within the system. Presently, models are evolving to include a comprehensive set of fishery and ecosystem information to address these broader management considerations. The increased scope of EBFM approaches is accompanied with a greater number of plausible models to describe the systems. This can lead to harvest recommendations and biological reference points that differ considerably among models. Model selection for projections (and specific catch recommendations) often occurs through a process that tends to adopt familiar, often simpler, models without considering those that incorporate more complex ecosystem information. Multi-model inference provides a framework that resolves this dilemma by providing a means of including information from alternative, often divergent models to inform biological reference points and possible catch consequences. We apply an example of this approach to data for three species of groundfish in the Bering Sea: walleye pollock, Pacific cod, and arrowtooth flounder using three models: 1) an age-structured "conventional" single-species model, 2) an age-structured single-species model with temperature-specific weight at age, and 3) a temperature-specific multi-species stock assessment model. The latter two approaches also include consideration of alternative future climate scenarios, adding another dimension to evaluate model projection uncertainty. We show how Bayesian model-averaging methods can be used to incorporate such trophic and climate information to broaden single-species stock assessments by using an EBFM approach that may better characterize uncertainty.