Comparison of detailed and reduced kinetics mechanisms of silane oxidation in the basis of detonation wave structure problem

NASA Astrophysics Data System (ADS)

Fedorov, A. V.; Tropin, D. A.; Fomin, P. A.

2018-03-01

The paper deals with the problem of the structure of detonation waves in the silane-air mixture within the framework of mathematical model of a nonequilibrium gas dynamics. Detailed kinetic scheme of silane oxidation as well as the newly developed reduced kinetic model of detonation combustion of silane are used. On its basis the detonation wave (DW) structure in stoichiometric silane - air mixture and dependences of Chapman-Jouguet parameters of mixture on stoichiometric ratio between the fuel (silane) and an oxidizer (air) were obtained.

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.

The virtual dissecting room: Creating highly detailed anatomy models for educational purposes.

PubMed

Zilverschoon, Marijn; Vincken, Koen L; Bleys, Ronald L A W

2017-01-01

Virtual 3D models are powerful tools for teaching anatomy. At the present day, there are a lot of different digital anatomy models, most of these commercial applications are based on a 3D model of a human body reconstructed from images with a 1mm intervals. The use of even smaller intervals may result in more details and more realistic appearances of 3D anatomy models. The aim of this study was to create a realistic and highly detailed 3D model of the hand and wrist based on small interval cross-sectional images, suitable for undergraduate and postgraduate teaching purposes with the possibility to perform a virtual dissection in an educational application. In 115 transverse cross-sections from a human hand and wrist, segmentation was done by manually delineating 90 different structures. With the use of Amira the segments were imported and a surface model/polygon model was created, followed by smoothening of the surfaces in Mudbox. In 3D Coat software the smoothed polygon models were automatically retopologied into a quadrilaterals formation and a UV map was added. In Mudbox, the textures from 90 structures were depicted in a realistic way by using photos from real tissue and afterwards height maps, gloss and specular maps were created to add more level of detail and realistic lightning on every structure. Unity was used to build a new software program that would support all the extra map features together with a preferred user interface. A 3D hand model has been created, containing 100 structures (90 at start and 10 extra structures added along the way). The model can be used interactively by changing the transparency, manipulating single or grouped structures and thereby simulating a virtual dissection. This model can be used for a variety of teaching purposes, ranging from undergraduate medical students to residents of hand surgery. Studying the hand and wrist anatomy using this model is cost-effective and not hampered by the limited access to real dissecting facilities. Copyright © 2016 Elsevier Inc. All rights reserved.

Global/local stress analysis of composite panels

NASA Technical Reports Server (NTRS)

Ransom, Jonathan B.; Knight, Norman F., Jr.

1989-01-01

A method for performing a global/local stress analysis is described, and its capabilities are demonstrated. The method employs spline interpolation functions which satisfy the linear plate bending equation to determine displacements and rotations from a global model which are used as boundary conditions for the local model. Then, the local model is analyzed independent of the global model of the structure. This approach can be used to determine local, detailed stress states for specific structural regions using independent, refined local models which exploit information from less-refined global models. The method presented is not restricted to having a priori knowledge of the location of the regions requiring local detailed stress analysis. This approach also reduces the computational effort necessary to obtain the detailed stress state. Criteria for applying the method are developed. The effectiveness of the method is demonstrated using a classical stress concentration problem and a graphite-epoxy blade-stiffened panel with a discontinuous stiffener.

Left Ventricular Trabeculations Decrease the Wall Shear Stress and Increase the Intra-Ventricular Pressure Drop in CFD Simulations

PubMed Central

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

2018-01-01

The aim of the present study is to characterize the hemodynamics of left ventricular (LV) geometries to examine the impact of trabeculae and papillary muscles (PMs) on blood flow using high performance computing (HPC). Five pairs of detailed and smoothed LV endocardium models were reconstructed from high-resolution magnetic resonance images (MRI) of ex-vivo human hearts. The detailed model of one LV pair is characterized only by the PMs and few big trabeculae, to represent state of art level of endocardial detail. The other four detailed models obtained include instead endocardial structures measuring ≥1 mm2 in cross-sectional area. The geometrical characterizations were done using computational fluid dynamics (CFD) simulations with rigid walls and both constant and transient flow inputs on the detailed and smoothed models for comparison. These simulations do not represent a clinical or physiological scenario, but a characterization of the interaction of endocardial structures with blood flow. Steady flow simulations were employed to quantify the pressure drop between the inlet and the outlet of the LVs and the wall shear stress (WSS). Coherent structures were analyzed using the Q-criterion for both constant and transient flow inputs. Our results show that trabeculae and PMs increase the intra-ventricular pressure drop, reduce the WSS and disrupt the dominant single vortex, usually present in the smoothed-endocardium models, generating secondary small vortices. Given that obtaining high resolution anatomical detail is challenging in-vivo, we propose that the effect of trabeculations can be incorporated into smoothed ventricular geometries by adding a porous layer along the LV endocardial wall. Results show that a porous layer of a thickness of 1.2·10−2 m with a porosity of 20 kg/m2 on the smoothed-endocardium ventricle models approximates the pressure drops, vorticities and WSS observed in the detailed models. PMID:29760665

ALAMEDA, a Structural–Functional Model for Faba Bean Crops: Morphological Parameterization and Verification

PubMed Central

RUIZ-RAMOS, MARGARITA; MÍNGUEZ, M. INÉS

2006-01-01

• Background Plant structural (i.e. architectural) models explicitly describe plant morphology by providing detailed descriptions of the display of leaf and stem surfaces within heterogeneous canopies and thus provide the opportunity for modelling the functioning of plant organs in their microenvironments. The outcome is a class of structural–functional crop models that combines advantages of current structural and process approaches to crop modelling. ALAMEDA is such a model. • Methods The formalism of Lindenmayer systems (L-systems) was chosen for the development of a structural model of the faba bean canopy, providing both numerical and dynamic graphical outputs. It was parameterized according to the results obtained through detailed morphological and phenological descriptions that capture the detailed geometry and topology of the crop. The analysis distinguishes between relationships of general application for all sowing dates and stem ranks and others valid only for all stems of a single crop cycle. • Results and Conclusions The results reveal that in faba bean, structural parameterization valid for the entire plant may be drawn from a single stem. ALAMEDA was formed by linking the structural model to the growth model ‘Simulation d'Allongement des Feuilles’ (SAF) with the ability to simulate approx. 3500 crop organs and components of a group of nine plants. Model performance was verified for organ length, plant height and leaf area. The L-system formalism was able to capture the complex architecture of canopy leaf area of this indeterminate crop and, with the growth relationships, generate a 3D dynamic crop simulation. Future development and improvement of the model are discussed. PMID:16390842

Detailed modeling analysis for soot formation and radiation in microgravity gas jet diffusion flames

NASA Technical Reports Server (NTRS)

Ku, Jerry C.; Tong, LI; Greenberg, Paul S.

1995-01-01

Radiation heat transfer in combustion systems has been receiving increasing interest. In the case of hydrocarbon fuels, a significant portion of the radiation comes from soot particles, justifying the need for detailed soot formation model and radiation transfer calculations. For laminar gas jet diffusion flames, results from this project (4/1/91 8/22/95) and another NASA study show that flame shape, soot concentration, and radiation heat fluxes are substantially different under microgravity conditions. Our emphasis is on including detailed soot transport models and a detailed solution for radiation heat transfer, and on coupling them with the flame structure calculations. In this paper, we will discuss the following three specific areas: (1) Comparing two existing soot formation models, and identifying possible improvements; (2) A simple yet reasonably accurate approach to calculating total radiative properties and/or fluxes over the spectral range; and (3) Investigating the convergence of iterations between the flame structure solver and the radiation heat transfer solver.

Beyond textbook illustrations: Hand-held models of ordered DNA and protein structures as 3D supplements to enhance student learning of helical biopolymers.

PubMed

Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

2010-11-01

Textbook illustrations of 3D biopolymers on printed paper, regardless of how detailed and colorful, suffer from its two-dimensionality. For beginners, computer screen display of skeletal models of biopolymers and their animation usually does not provide the at-a-glance 3D perception and details, which can be done by good hand-held models. Here, we report a study on how our students learned more from using our ordered DNA and protein models assembled from colored computer-printouts on transparency film sheets that have useful structural details. Our models (reported in BAMBED 2009), having certain distinguished features, helped our students to grasp various aspects of these biopolymers that they usually find difficult. Quantitative and qualitative learning data from this study are reported. Copyright © 2010 International Union of Biochemistry and Molecular Biology, Inc.

Seeking structural specificity: direct modulation of pentameric ligand-gated ion channels by alcohols and general anesthetics.

PubMed

Howard, Rebecca J; Trudell, James R; Harris, R Adron

2014-01-01

Alcohols and other anesthetic agents dramatically alter neurologic function in a wide range of organisms, yet their molecular sites of action remain poorly characterized. Pentameric ligand-gated ion channels, long implicated in important direct effects of alcohol and anesthetic binding, have recently been illuminated in renewed detail thanks to the determination of atomic-resolution structures of several family members from lower organisms. These structures provide valuable models for understanding and developing anesthetic agents and for allosteric modulation in general. This review surveys progress in this field from function to structure and back again, outlining early evidence for relevant modulation of pentameric ligand-gated ion channels and the development of early structural models for ion channel function and modulation. We highlight insights and challenges provided by recent crystal structures and resulting simulations, as well as opportunities for translation of these newly detailed models back to behavior and therapy.

Seeking Structural Specificity: Direct Modulation of Pentameric Ligand-Gated Ion Channels by Alcohols and General Anesthetics

PubMed Central

Trudell, James R.; Harris, R. Adron

2014-01-01

Alcohols and other anesthetic agents dramatically alter neurologic function in a wide range of organisms, yet their molecular sites of action remain poorly characterized. Pentameric ligand-gated ion channels, long implicated in important direct effects of alcohol and anesthetic binding, have recently been illuminated in renewed detail thanks to the determination of atomic-resolution structures of several family members from lower organisms. These structures provide valuable models for understanding and developing anesthetic agents and for allosteric modulation in general. This review surveys progress in this field from function to structure and back again, outlining early evidence for relevant modulation of pentameric ligand-gated ion channels and the development of early structural models for ion channel function and modulation. We highlight insights and challenges provided by recent crystal structures and resulting simulations, as well as opportunities for translation of these newly detailed models back to behavior and therapy. PMID:24515646

Direct Scaling of Leaf-Resolving Biophysical Models from Leaves to Canopies

NASA Astrophysics Data System (ADS)

Bailey, B.; Mahaffee, W.; Hernandez Ochoa, M.

2017-12-01

Recent advances in the development of biophysical models and high-performance computing have enabled rapid increases in the level of detail that can be represented by simulations of plant systems. However, increasingly detailed models typically require increasingly detailed inputs, which can be a challenge to accurately specify. In this work, we explore the use of terrestrial LiDAR scanning data to accurately specify geometric inputs for high-resolution biophysical models that enables direct up-scaling of leaf-level biophysical processes. Terrestrial LiDAR scans generate "clouds" of millions of points that map out the geometric structure of the area of interest. However, points alone are often not particularly useful in generating geometric model inputs, as additional data processing techniques are required to provide necessary information regarding vegetation structure. A new method was developed that directly reconstructs as many leaves as possible that are in view of the LiDAR instrument, and uses a statistical backfilling technique to ensure that the overall leaf area and orientation distribution matches that of the actual vegetation being measured. This detailed structural data is used to provide inputs for leaf-resolving models of radiation, microclimate, evapotranspiration, and photosynthesis. Model complexity is afforded by utilizing graphics processing units (GPUs), which allows for simulations that resolve scales ranging from leaves to canopies. The model system was used to explore how heterogeneity in canopy architecture at various scales affects scaling of biophysical processes from leaves to canopies.

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

Structural analysis consultation using artificial intelligence

NASA Technical Reports Server (NTRS)

Melosh, R. J.; Marcal, P. V.; Berke, L.

1978-01-01

The primary goal of consultation is definition of the best strategy to deal with a structural engineering analysis objective. The knowledge base to meet the need is designed to identify the type of numerical analysis, the needed modeling detail, and specific analysis data required. Decisions are constructed on the basis of the data in the knowledge base - material behavior, relations between geometry and structural behavior, measures of the importance of time and temperature changes - and user supplied specifics characteristics of the spectrum of analysis types, the relation between accuracy and model detail on the structure, its mechanical loadings, and its temperature states. Existing software demonstrated the feasibility of the approach, encompassing the 36 analysis classes spanning nonlinear, temperature affected, incremental analyses which track the behavior of structural systems.

Development of Multidisciplinary, Multifidelity Analysis, Integration, and Optimization of Aerospace Vehicles

DTIC Science & Technology

2010-02-27

investigated in more detail. The intermediate level of fidelity, though more expensive, is then used to refine the analysis , add geometric detail, and...design stage is used to further refine the analysis , narrowing the design to a handful of options. Figure 1. Integrated Hierarchical Framework. In...computational structural and computational fluid modeling. For the structural analysis tool we used McIntosh Structural Dynamics’ finite element code CNEVAL

Preliminary shuttle structural dynamics modeling design study

NASA Technical Reports Server (NTRS)

1972-01-01

The design and development of a structural dynamics model of the space shuttle are discussed. The model provides for early study of structural dynamics problems, permits evaluation of the accuracy of the structural and hydroelastic analysis methods used on test vehicles, and provides for efficiently evaluating potential cost savings in structural dynamic testing techniques. The discussion is developed around the modes in which major input forces and responses occur and the significant structural details in these modes.

Dynamic model of a micro-tubular solid oxide fuel cell stack including an integrated cooling system

NASA Astrophysics Data System (ADS)

Hering, Martin; Brouwer, Jacob; Winkler, Wolfgang

2017-02-01

A novel dynamic micro-tubular solid oxide fuel cell (MT-SOFC) and stack model including an integrated cooling system is developed using a quasi three-dimensional, spatially resolved, transient thermodynamic, physical and electrochemical model that accounts for the complex geometrical relations between the cells and cooling-tubes. The modeling approach includes a simplified tubular geometry and stack design including an integrated cooling structure, detailed pressure drop and gas property calculations, the electrical and physical constraints of the stack design that determine the current, as well as control strategies for the temperature. Moreover, an advanced heat transfer balance with detailed radiative heat transfer between the cells and the integrated cooling-tubes, convective heat transfer between the gas flows and the surrounding structures and conductive heat transfer between the solid structures inside of the stack, is included. The detailed model can be used as a design basis for the novel MT-SOFC stack assembly including an integrated cooling system, as well as for the development of a dynamic system control strategy. The evaluated best-case design achieves very high electrical efficiency between around 75 and 55% in the entire power density range between 50 and 550 mW /cm2 due to the novel stack design comprising an integrated cooling structure.

Thermodynamic forces in coarse-grained simulations

NASA Astrophysics Data System (ADS)

Noid, William

Atomically detailed molecular dynamics simulations have profoundly advanced our understanding of the structure and interactions in soft condensed phases. Nevertheless, despite dramatic advances in the methodology and resources for simulating atomically detailed models, low-resolution coarse-grained (CG) models play a central and rapidly growing role in science. CG models not only empower researchers to investigate phenomena beyond the scope of atomically detailed simulations, but also to precisely tailor models for specific phenomena. However, in contrast to atomically detailed simulations, which evolve on a potential energy surface, CG simulations should evolve on a free energy surface. Therefore, the forces in CG models should reflect the thermodynamic information that has been eliminated from the CG configuration space. As a consequence of these thermodynamic forces, CG models often demonstrate limited transferability and, moreover, rarely provide an accurate description of both structural and thermodynamic properties. In this talk, I will present a framework that clarifies the origin and impact of these thermodynamic forces. Additionally, I will present computational methods for quantifying these forces and incorporating their effects into CG MD simulations. As time allows, I will demonstrate applications of this framework for liquids, polymers, and interfaces. We gratefully acknowledge the support of the National Science Foundation via CHE 1565631.

Crack propagation modelling for high strength steel welded structural details

NASA Astrophysics Data System (ADS)

Mecséri, B. J.; Kövesdi, B.

2017-05-01

Nowadays the barrier of applying HSS (High Strength Steel) material in bridge structures is their low fatigue strength related to yield strength. This paper focuses on the fatigue behaviour of a structural details (a gusset plate connection) made from NSS and HSS material, which is frequently used in bridges in Hungary. An experimental research program is carried out at the Budapest University of Technology and Economics to investigate the fatigue lifetime of this structural detail type through the same test specimens made from S235 and S420 steel grades. The main aim of the experimental research program is to study the differences in the crack propagation and the fatigue lifetime between normal and high strength steel structures. Based on the observed fatigue crack pattern the main direction and velocity of the crack propagation is determined. In parallel to the tests finite element model (FEM) are also developed, which model can handle the crack propagation. Using the measured strain data in the tests and the calculated values from the FE model, the approximation of the material parameters of the Paris law are calculated step-by-step, and their calculated values are evaluated. The same material properties are determined for NSS and also for HSS specimens as well, and the differences are discussed. In the current paper, the results of the experiments, the calculation method of the material parameters and the calculated values are introduced.

Structural Equation Modeling Diagnostics Using R Package Semdiag and EQS

ERIC Educational Resources Information Center

Yuan, Ke-Hai; Zhang, Zhiyong

2012-01-01

Yuan and Hayashi (2010) introduced 2 scatter plots for model and data diagnostics in structural equation modeling (SEM). However, the generation of the plots requires in-depth understanding of their underlying technical details. This article develops and introduces an R package semdiag for easily drawing the 2 plots. With a model specified in EQS…

Standards for detailed clinical models as the basis for medical data exchange and decision support.

PubMed

Coyle, Joseph F; Mori, Angelo Rossi; Huff, Stanley M

2003-03-01

Detailed clinical models are necessary to exchange medical data between heterogeneous computer systems and to maintain consistency in a longitudinal electronic medical record system. At Intermountain Health Care (IHC), we have a history of designing detailed clinical models. The purpose of this paper is to share our experience and the lessons we have learned over the last 5 years. IHC's newest model is implemented using eXtensible Markup Language (XML) Schema as the formalism, and conforms to the Health Level Seven (HL7) version 3 data types. The centerpiece of the new strategy is the Clinical Event Model, which is a flexible name-value pair data structure that is tightly linked to a coded terminology. We describe IHC's third-generation strategy for representing and implementing detailed clinical models, and discuss the reasons for this design.

Calculation methods study on hot spot stress of new girder structure detail

NASA Astrophysics Data System (ADS)

Liao, Ping; Zhao, Renda; Jia, Yi; Wei, Xing

2017-10-01

To study modeling calculation methods of new girder structure detail's hot spot stress, based on surface extrapolation method among hot spot stress method, a few finite element analysis models of this welded detail were established by finite element software ANSYS. The influence of element type, mesh density, different local modeling methods of the weld toe and extrapolation methods was analyzed on hot spot stress calculation results at the toe of welds. The results show that the difference of the normal stress in the thickness direction and the surface direction among different models is larger when the distance from the weld toe is smaller. When the distance from the toe is greater than 0.5t, the normal stress of solid models, shell models with welds and non-weld shell models tends to be consistent along the surface direction. Therefore, it is recommended that the extrapolated point should be selected outside the 0.5t for new girder welded detail. According to the results of the calculation and analysis, shell models have good grid stability, and extrapolated hot spot stress of solid models is smaller than that of shell models. So it is suggested that formula 2 and solid45 should be carried out during the hot spot stress extrapolation calculation of this welded detail. For each finite element model under different shell modeling methods, the results calculated by formula 2 are smaller than those of the other two methods, and the results of shell models with welds are the largest. Under the same local mesh density, the extrapolated hot spot stress decreases gradually with the increase of the number of layers in the thickness direction of the main plate, and the variation range is within 7.5%.

Structural analysis of β-glucosidase mutants derived from a hyperthermophilic tetrameric structure

PubMed Central

Nakabayashi, Makoto; Kataoka, Misumi; Mishima, Yumiko; Maeno, Yuka; Ishikawa, Kazuhiko

2014-01-01

β-Glucosidase from Pyrococcus furiosus (BGLPf) is a hyperthermophilic tetrameric enzyme which can degrade cellooligosaccharides to glucose under hyperthermophilic conditions and thus holds promise for the saccharification of lignocellulosic biomass at high temperature. Prior to the production of large amounts of this enzyme, detailed information regarding the oligomeric structure of the enzyme is required. Several crystals of BGLPf have been prepared over the past ten years, but its crystal structure had not been solved until recently. In 2011, the first crystal structure of BGLPf was solved and a model was constructed at somewhat low resolution (2.35 Å). In order to obtain more detailed structural data on BGLPf, the relationship between its tetrameric structure and the quality of the crystal was re-examined. A dimeric form of BGLPf was constructed and its crystal structure was solved at a resolution of 1.70 Å using protein-engineering methods. Furthermore, using the high-resolution crystal structural data for the dimeric form, a monomeric form of BGLPf was constructed which retained the intrinsic activity of the tetrameric form. The thermostability of BGLPf is affected by its oligomeric structure. Here, the biophysical and biochemical properties of engineered dimeric and monomeric BGLPfs are reported, which are promising prototype models to apply to the saccharification reaction. Furthermore, details regarding the oligomeric structures of BGLPf and the reasons why the mutations yielded improved crystal structures are discussed. PMID:24598756

Finite Element Model Development For Aircraft Fuselage Structures

NASA Technical Reports Server (NTRS)

Buehrle, Ralph D.; Fleming, Gary A.; Pappa, Richard S.; Grosveld, Ferdinand W.

2000-01-01

The ability to extend the valid frequency range for finite element based structural dynamic predictions using detailed models of the structural components and attachment interfaces is examined for several stiffened aircraft fuselage structures. This extended dynamic prediction capability is needed for the integration of mid-frequency noise control technology. Beam, plate and solid element models of the stiffener components are evaluated. Attachment models between the stiffener and panel skin range from a line along the rivets of the physical structure to a constraint over the entire contact surface. The finite element models are validated using experimental modal analysis results.

Solid-State NMR Studies of Amyloid Materials: A Protocol to Define an Atomic Model of Aβ(1-42) in Amyloid Fibrils.

PubMed

Xiao, Yiling; McElheny, Dan; Hoshi, Minako; Ishii, Yoshitaka

2018-01-01

Intense efforts have been made to understand the molecular structures of misfolded amyloid β (Aβ) in order to gain insight into the pathological mechanism of Alzheimer's disease. Solid-state NMR spectroscopy (SSNMR) is considered a primary tool for elucidating the structures of insoluble and noncrystalline amyloid fibrils and other amyloid assemblies. In this chapter, we describe a detailed protocol to obtain the first atomic model of the 42-residue human Aβ peptide Aβ(1-42) in structurally homogeneous amyloid fibrils from our recent SSNMR study (Nat Struct Mol Biol 22:499-505, 2015). Despite great biological and clinical interest in Aβ(1-42) fibrils, their structural details have been long-elusive until this study. The protocol is divided into four sections. First, the solid-phase peptide synthesis (SPPS) and purification of monomeric Aβ(1-42) is described. We illustrate a controlled incubation method to prompt misfolding of Aβ(1-42) into homogeneous amyloid fibrils in an aqueous solution with fragmented Aβ(1-42) fibrils as seeds. Next, we detail analysis of Aβ(1-42) fibrils by SSNMR to obtain structural restraints. Finally, we describe methods to construct atomic models of Aβ(1-42) fibrils based on SSNMR results through two-stage molecular dynamics calculations.

Absorbable energy monitoring scheme: new design protocol to test vehicle structural crashworthiness.

PubMed

Ofochebe, Sunday M; Enibe, Samuel O; Ozoegwu, Chigbogu G

2016-05-01

In vehicle crashworthiness design optimization detailed system evaluation capable of producing reliable results are basically achieved through high-order numerical computational (HNC) models such as the dynamic finite element model, mesh-free model etc. However the application of these models especially during optimization studies is basically challenged by their inherent high demand on computational resources, conditional stability of the solution process, and lack of knowledge of viable parameter range for detailed optimization studies. The absorbable energy monitoring scheme (AEMS) presented in this paper suggests a new design protocol that attempts to overcome such problems in evaluation of vehicle structure for crashworthiness. The implementation of the AEMS involves studying crash performance of vehicle components at various absorbable energy ratios based on a 2DOF lumped-mass-spring (LMS) vehicle impact model. This allows for prompt prediction of useful parameter values in a given design problem. The application of the classical one-dimensional LMS model in vehicle crash analysis is further improved in the present work by developing a critical load matching criterion which allows for quantitative interpretation of the results of the abstract model in a typical vehicle crash design. The adequacy of the proposed AEMS for preliminary vehicle crashworthiness design is demonstrated in this paper, however its extension to full-scale design-optimization problem involving full vehicle model that shows greater structural detail requires more theoretical development.

Structured Hypermedia Application Development Model (SHADM): A structured Model for Technical Documentation Application Design

DTIC Science & Technology

1991-12-01

effective (19:15) Figure 2 details a flowchart of the basic steps in prototyping. The basic concept behind prototyping is to quickly produce a working...One approach to overcoming this is to structure the document relative to the experience level of the user (14:49). A "novice" or beginner would

Exploring the Subtleties of Inverse Probability Weighting and Marginal Structural Models.

PubMed

Breskin, Alexander; Cole, Stephen R; Westreich, Daniel

2018-05-01

Since being introduced to epidemiology in 2000, marginal structural models have become a commonly used method for causal inference in a wide range of epidemiologic settings. In this brief report, we aim to explore three subtleties of marginal structural models. First, we distinguish marginal structural models from the inverse probability weighting estimator, and we emphasize that marginal structural models are not only for longitudinal exposures. Second, we explore the meaning of the word "marginal" in "marginal structural model." Finally, we show that the specification of a marginal structural model can have important implications for the interpretation of its parameters. Each of these concepts have important implications for the use and understanding of marginal structural models, and thus providing detailed explanations of them may lead to better practices for the field of epidemiology.

Detailed electromagnetic simulation for the structural color of butterfly wings.

PubMed

Lee, R Todd; Smith, Glenn S

2009-07-20

Many species of butterflies exhibit interesting optical phenomena due to structural color. The physical reason for this color is subwavelength features on the surface of a single scale. The exposed surface of a scale is covered with a ridge structure. The fully three-dimensional, periodic, finite-difference time-domain method is used to create a detailed electromagnetic model of a generic ridge. A novel method for presenting the three-dimensional observed color pattern is developed. Using these tools, the change in color that is a result of varying individual features of the scale is explored. Computational models are developed that are similar to three butterflies: Morpho rhetenor, Troides magellanus, and Ancyluris meliboeus.

Cellular structure of lean hydrogen flames in microgravity

NASA Technical Reports Server (NTRS)

Patnaik, G.; Kailasanath, K.

1990-01-01

Detailed, time-dependent, two-dimensional numerical simulations of premixed laminar flames have been used to study the initiation and subsequent development of cellular structures in lean hydrogen-air flames. The model includes detailed hydrogen-oxygen combustion with 24 elementary reactions of eight reactive species and a nitrogen diluent, molecular diffusion of all species, thermal conduction, viscosity, and convection. This model has been used to study the nonlinear evolution of cellular flame structure and shows that cell splitting, as observed in experiments, can be predicted numerically for sufficiently reactive mixtures. The structures that evolved also resembled the cellular structures observed in experiments. The present study shows that the 'cell-split limit' postulated from experimental observations is an intrinsic property of the mixture and that external factors such as heat losses are not necessary to cause this limit.

Inhibitor-based validation of a homology model of the active-site of tripeptidyl peptidase II.

PubMed

De Winter, Hans; Breslin, Henry; Miskowski, Tamara; Kavash, Robert; Somers, Marijke

2005-04-01

A homology model of the active site region of tripeptidyl peptidase II (TPP II) was constructed based on the crystal structures of four subtilisin-like templates. The resulting model was subsequently validated by judging expectations of the model versus observed activities for a broad set of prepared TPP II inhibitors. The structure-activity relationships observed for the prepared TPP II inhibitors correlated nicely with the structural details of the TPP II active site model, supporting the validity of this model and its usefulness for structure-based drug design and pharmacophore searching experiments.

Details of insect wing design and deformation enhance aerodynamic function and flight efficiency.

PubMed

Young, John; Walker, Simon M; Bomphrey, Richard J; Taylor, Graham K; Thomas, Adrian L R

2009-09-18

Insect wings are complex structures that deform dramatically in flight. We analyzed the aerodynamic consequences of wing deformation in locusts using a three-dimensional computational fluid dynamics simulation based on detailed wing kinematics. We validated the simulation against smoke visualizations and digital particle image velocimetry on real locusts. We then used the validated model to explore the effects of wing topography and deformation, first by removing camber while keeping the same time-varying twist distribution, and second by removing camber and spanwise twist. The full-fidelity model achieved greater power economy than the uncambered model, which performed better than the untwisted model, showing that the details of insect wing topography and deformation are important aerodynamically. Such details are likely to be important in engineering applications of flapping flight.

High-Resolution 3D P-Wave Velocity Model in the Trans-European Suture Zone in Poland

NASA Astrophysics Data System (ADS)

Polkowski, M.; Grad, M.; Ostaficzuk, S.

2014-12-01

Poland is located on conjunction of major European tectonic units - the Precambrian East European Craton and the Paleozoic Platform of Central and Western Europe. This conjunction is known as Trans-European Suture Zone (TESZ). Geological and seismic structure under area of Poland is well studied by over one hundred thousand boreholes, over thirty deep seismic refraction and wide angle reflection profiles and other methods: vertical seismic profiling, magnetic, gravity, magnetotelluric, thermal. Compilation of these studies allows creation of detailed, high-resolution 3D P-wave velocity model for entire Earth's crust in the area of Poland. Model provides detailed six layer sediments (Tertiary and Quaternary, Cretaceous, Jurassic, Triassic, Permian, old Paleozoic), consolidated / crystalline crust and uppermost mantle. Continental suturing is a fundamental part of the plate tectonic cycle, and knowing its detailed structure allows understanding plate tectonic cycle. We present a set of crustal cross sections through the TESZ, illustrating differentiation in the structure between Precambrian and Wariscan Europe. National Science Centre Poland provided financial support for this work by NCN grant DEC- 2011/02/A/ST10/00284.

NSTX Disruption Simulations of Detailed Divertor and Passive Plate Models by Vector Potential Transfer from OPERA Global Analysis Results

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

P. H. Titus, S. Avasaralla, A.Brooks, R. Hatcher

2010-09-22

The National Spherical Torus Experiment (NSTX) project is planning upgrades to the toroidal field, plasma current and pulse length. This involves the replacement of the center-stack, including the inner legs of the TF, OH, and inner PF coils. A second neutral beam will also be added. The increased performance of the upgrade requires qualification of the remaining components including the vessel, passive plates, and divertor for higher disruption loads. The hardware needing qualification is more complex than is typically accessible by large scale electromagnetic (EM) simulations of the plasma disruptions. The usual method is to include simplified representations of componentsmore » in the large EM models and attempt to extract forces to apply to more detailed models. This paper describes a more efficient approach of combining comprehensive modeling of the plasma and tokamak conducting structures, using the 2D OPERA code, with much more detailed treatment of individual components using ANSYS electromagnetic (EM) and mechanical analysis. This capture local eddy currents and resulting loads in complex details, and allows efficient non-linear, and dynamic structural analyses.« less

Beyond Textbook Illustrations: Hand-Held Models of Ordered DNA and Protein Structures as 3D Supplements to Enhance Student Learning of Helical Biopolymers

ERIC Educational Resources Information Center

Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

2010-01-01

Textbook illustrations of 3D biopolymers on printed paper, regardless of how detailed and colorful, suffer from its two-dimensionality. For beginners, computer screen display of skeletal models of biopolymers and their animation usually does not provide the at-a-glance 3D perception and details, which can be done by good hand-held models. Here, we…

Sierra Structural Dynamics User's Notes

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

Reese, Garth M.

2015-10-19

Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a users guide to the input for Sierra/SD. Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.

The difference between energy consumption and energy cost: Modelling energy tariff structures for water resource recovery facilities.

PubMed

Aymerich, I; Rieger, L; Sobhani, R; Rosso, D; Corominas, Ll

2015-09-15

The objective of this paper is to demonstrate the importance of incorporating more realistic energy cost models (based on current energy tariff structures) into existing water resource recovery facilities (WRRFs) process models when evaluating technologies and cost-saving control strategies. In this paper, we first introduce a systematic framework to model energy usage at WRRFs and a generalized structure to describe energy tariffs including the most common billing terms. Secondly, this paper introduces a detailed energy cost model based on a Spanish energy tariff structure coupled with a WRRF process model to evaluate several control strategies and provide insights into the selection of the contracted power structure. The results for a 1-year evaluation on a 115,000 population-equivalent WRRF showed monthly cost differences ranging from 7 to 30% when comparing the detailed energy cost model to an average energy price. The evaluation of different aeration control strategies also showed that using average energy prices and neglecting energy tariff structures may lead to biased conclusions when selecting operating strategies or comparing technologies or equipment. The proposed framework demonstrated that for cost minimization, control strategies should be paired with a specific optimal contracted power. Hence, the design of operational and control strategies must take into account the local energy tariff. Copyright © 2015 Elsevier Ltd. All rights reserved.

NMR Crystallography of Enzyme Active Sites: Probing Chemically-Detailed, Three-Dimensional Structure in Tryptophan Synthase

PubMed Central

Dunn, Michael F.

2013-01-01

Conspectus NMR crystallography – the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry – offers unprecedented insight into three-dimensional, chemically-detailed structure. From its initial role in refining diffraction data of organic and inorganic solids, NMR crystallography is now being developed for application to active sites in biomolecules, where it reveals chemically-rich detail concerning the interactions between enzyme site residues and the reacting substrate that is not achievable when X-ray, NMR, or computational methodologies are applied in isolation. For example, typical X-ray crystal structures (1.5 to 2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate, but do not directly identify the protonation state of either. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them, only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but rely on chemical details that must be specified. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which models of the active site can be developed using computational chemistry; these models can be distinguished by comparison of their calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at highest resolution. In this Account, we detail our first steps in the development of NMR crystallography for application to enzyme catalysis. We begin with a brief introduction to NMR crystallography and then define the process that we have employed to probe the active site in the β-subunit of tryptophan synthase with unprecedented atomic-level resolution. This approach has resulted in a novel structural hypothesis for the protonation state of the quinonoid intermediate in tryptophan synthase and its surprising role in directing the next step in the catalysis of L-Trp formation. PMID:23537227

Soft 3D-Printed Phantom of the Human Kidney with Collecting System.

PubMed

Adams, Fabian; Qiu, Tian; Mark, Andrew; Fritz, Benjamin; Kramer, Lena; Schlager, Daniel; Wetterauer, Ulrich; Miernik, Arkadiusz; Fischer, Peer

2017-04-01

Organ models are used for planning and simulation of operations, developing new surgical instruments, and training purposes. There is a substantial demand for in vitro organ phantoms, especially in urological surgery. Animal models and existing simulator systems poorly mimic the detailed morphology and the physical properties of human organs. In this paper, we report a novel fabrication process to make a human kidney phantom with realistic anatomical structures and physical properties. The detailed anatomical structure was directly acquired from high resolution CT data sets of human cadaveric kidneys. The soft phantoms were constructed using a novel technique that combines 3D wax printing and polymer molding. Anatomical details and material properties of the phantoms were validated in detail by CT scan, ultrasound, and endoscopy. CT reconstruction, ultrasound examination, and endoscopy showed that the designed phantom mimics a real kidney's detailed anatomy and correctly corresponds to the targeted human cadaver's upper urinary tract. Soft materials with a tensile modulus of 0.8-1.5 MPa as well as biocompatible hydrogels were used to mimic human kidney tissues. We developed a method of constructing 3D organ models from medical imaging data using a 3D wax printing and molding process. This method is cost-effective means for obtaining a reproducible and robust model suitable for surgical simulation and training purposes.

Imaging the Alpine Fault: preliminary results from a detailed 3D-VSP experiment at the DFDP-2 drill site in Whataroa, New Zealand

NASA Astrophysics Data System (ADS)

Lay, Vera; Bodenburg, Sascha; Buske, Stefan; Townend, John; Kellett, Richard; Savage, Martha; Schmitt, Douglas; Constantinou, Alexis; Eccles, Jennifer; Lawton, Donald; Hall, Kevin; Bertram, Malcolm; Gorman, Andrew

2017-04-01

The plate-bounding Alpine Fault in New Zealand is an 850 km long transpressive continental fault zone that is late in its earthquake cycle. The Deep Fault Drilling Project (DFDP) aims to deliver insight into the geological structure of this fault zone and its evolution by drilling and sampling the Alpine Fault at depth. Previously analysed 2D reflection seismic data image the main Alpine Fault reflector at a depth of 1.5-2.2 km with a dip of approximately 48° to the southeast below the DFDP-2 borehole. Additionally, there are indications of a more complex 3D fault structure with several fault branches which have not yet been clearly imaged in detail. For that reason we acquired a 3D-VSP seismic data set at the DFDP-2 drill site in January 2016. A zero-offset VSP and a walk-away VSP survey were conducted using a Vibroseis source. Within the borehole, a permanently installed "Distributed Acoustic Fibre Optic Cable" (down to 893 m) and a 3C Sercel slimwave tool (down to 400 m) were used to record the seismic wavefield. In addition, an array of 160 three-component receivers with a spacing of 10 m perpendicular and 20 m parallel to the main strike of the Alpine Fault was set up and moved successively along the valley to record reflections from the main Alpine Fault zone over a broad depth range and to derive a detailed 3D tomographic velocity model in the hanging wall. We will show a detailed 3D velocity model derived from first-arrival traveltime tomography. Subsets of the whole data set were analysed separately to estimate the corresponding ray coverage and the reliability of the observed features in the obtained velocity model. By testing various inversion parameters and starting models, we derived a detailed near-surface velocity model that reveals the significance of the old glacial valley structures. Hence, this new 3D model improves the velocity model derived previously from a 2D seismic profile line in that area. Furthermore, processing of the dense 3C data shows clear reflections on both inline and crossline profiles. Correlating single reflection events enables us to identify the origin of reflections recorded in the data and reveal their 3D character. This array data gives strong evidence for reflections coming from the side, possibly from the steeply dipping valley flanks. Finally, the data will be processed using advanced seismic imaging methods to derive a detailed structural image of the valley and the fault zone at depth. Thus, the results will provide a detailed basis for a seismic site characterization at the DFDP-2 drill site, that will be of crucial importance for further structural and geological investigations of the architecture of the Alpine Fault in this area.

Persistent Monitoring of Urban Infrasound Phenomenology-Report 2: Investigation of Structural Infrasound Signals in an Urban Environment

DTIC Science & Technology

2016-11-01

space houses, etc.), and the unique weather environments that occur in the Urban Heat Island. A detailed urban terrain model was developed in a...affected by urban infrastructure (large buildings, roadways, densely space houses, etc.). A detailed urban terrain model was developed ERDC TR-15-5...different points in the model provided insight to complex propagation paths characteristic of urban environments. ERDC TR-15-5; Report 2 20 4

X-ray phase-contrast tomography for high-spatial-resolution zebrafish muscle imaging

NASA Astrophysics Data System (ADS)

Vågberg, William; Larsson, Daniel H.; Li, Mei; Arner, Anders; Hertz, Hans M.

2015-11-01

Imaging of muscular structure with cellular or subcellular detail in whole-body animal models is of key importance for understanding muscular disease and assessing interventions. Classical histological methods for high-resolution imaging methods require excision, fixation and staining. Here we show that the three-dimensional muscular structure of unstained whole zebrafish can be imaged with sub-5 μm detail with X-ray phase-contrast tomography. Our method relies on a laboratory propagation-based phase-contrast system tailored for detection of low-contrast 4-6 μm subcellular myofibrils. The method is demonstrated on 20 days post fertilization zebrafish larvae and comparative histology confirms that we resolve individual myofibrils in the whole-body animal. X-ray imaging of healthy zebrafish show the expected structured muscle pattern while specimen with a dystrophin deficiency (sapje) displays an unstructured pattern, typical of Duchenne muscular dystrophy. The method opens up for whole-body imaging with sub-cellular detail also of other types of soft tissue and in different animal models.

Surprises in low dimensional spin 1/2 magnets - from crystal chemistry to microscopic magnetic models of complex oxides

NASA Astrophysics Data System (ADS)

Rosner, Helge

2011-03-01

A microscopic understanding of the structure-properties relation in crystalline materials is a main goal of modern solid state chemistry and physics. Due to their peculiar magnetism, low dimensional spin 1/2 systems are often highly sensitive to structural details. Seemingly unimportant structural details can be crucial for the magnetic ground state of a compound, especially in the case of competing interactions, frustration and near-degeneracy. Here, we present for selected, complex Cu 2+ systems that a first principles based approach can reliably provide the correct magnetic model, especially in cases where the interpretation of experimental data meets serious difficulties or fails. We demonstrate that the magnetism of low dimensional insulators crucially depends on the magnetically active orbitals which are determined by details of the ligand field of the magnetic cation. Our theoretical results are in very good agreement with thermodynamic and spectroscopic data and provide deep microscopic insight into topical low dimensional magnets.

Cost model relationships between textile manufacturing processes and design details for transport fuselage elements

NASA Technical Reports Server (NTRS)

Metschan, Stephen L.; Wilden, Kurtis S.; Sharpless, Garrett C.; Andelman, Rich M.

1993-01-01

Textile manufacturing processes offer potential cost and weight advantages over traditional composite materials and processes for transport fuselage elements. In the current study, design cost modeling relationships between textile processes and element design details were developed. Such relationships are expected to help future aircraft designers to make timely decisions on the effect of design details and overall configurations on textile fabrication costs. The fundamental advantage of a design cost model is to insure that the element design is cost effective for the intended process. Trade studies on the effects of processing parameters also help to optimize the manufacturing steps for a particular structural element. Two methods of analyzing design detail/process cost relationships developed for the design cost model were pursued in the current study. The first makes use of existing databases and alternative cost modeling methods (e.g. detailed estimating). The second compares design cost model predictions with data collected during the fabrication of seven foot circumferential frames for ATCAS crown test panels. The process used in this case involves 2D dry braiding and resin transfer molding of curved 'J' cross section frame members having design details characteristic of the baseline ATCAS crown design.

Chemokines and their receptors: insights from molecular modeling and crystallography.

PubMed

Kufareva, Irina

2016-10-01

Chemokines are small secreted proteins that direct cell migration in development, immunity, inflammation, and cancer. They do so by binding and activating specific G protein coupled receptors on the surface of migrating cells. Despite the importance of receptor:chemokine interactions, their structural basis remained unclear for a long time. In 2015, the first atomic resolution insights were obtained with the publication of X-ray structures for two distantly related receptors bound to chemokines. In conjunction with experiment-guided molecular modeling, the structures suggest a conserved receptor:chemokine complex architecture, while highlighting the diverse details and functional roles of individual interaction epitopes. Novel findings promote the development and detailed structural interpretation of the canonical two-site hypothesis of receptor:chemokine recognition, and suggest new avenues for pharmacological modulation of chemokine receptors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Flow structure through pool-riffle sequences and a conceptual model for their sustainability in gravel-bed rivers

Treesearch

D. Caamano; P. Goodwin; J. M. Buffington

2010-01-01

Detailed field measurements and simulations of three-dimensional flow structure were used to develop a conceptual model to explain the sustainability of self-formed pool-riffle sequences in gravel-bed rivers. The analysis was conducted at the Red River Wildlife Management Area in Idaho, USA, and enabled characterization of the flow structure through two consecutive...

Problem of the slotted wing : a communication from the Aerodynamic Institute of the Aachen Technical High School

NASA Technical Reports Server (NTRS)

Klemperer, W

1922-01-01

It is to be expected that the advantageous properties, hitherto discovered in many slotted wing sections, depend very largely on the contour of the slot and the structural details of the wing. It is therefore of interest, aside from measurements on wings of constant cross-section along the span, to measure also wing models in which the structural details have already been given practical consideration.

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.

Optimisation and evaluation of pre-design models for offshore wind turbines with jacket support structures and their influence on integrated load simulations

NASA Astrophysics Data System (ADS)

Schafhirt, S.; Kaufer, D.; Cheng, P. W.

2014-12-01

In recent years many advanced load simulation tools, allowing an aero-servo-hydroelastic analyses of an entire offshore wind turbine, have been developed and verified. Nowadays, even an offshore wind turbine with a complex support structure such as a jacket can be analysed. However, the computational effort rises significantly with an increasing level of details. This counts especially for offshore wind turbines with lattice support structures, since those models do naturally have a higher number of nodes and elements than simpler monopile structures. During the design process multiple load simulations are demanded to obtain an optimal solution. In the view of pre-design tasks it is crucial to apply load simulations which keep the simulation quality and the computational effort in balance. The paper will introduce a reference wind turbine model consisting of the REpower5M wind turbine and a jacket support structure with a high level of detail. In total twelve variations of this reference model are derived and presented. Main focus is to simplify the models of the support structure and the foundation. The reference model and the simplified models are simulated with the coupled simulation tool Flex5-Poseidon and analysed regarding frequencies, fatigue loads, and ultimate loads. A model has been found which reaches an adequate increase of simulation speed while holding the results in an acceptable range compared to the reference results.

Aircraft Structural Mass Property Prediction Using Conceptual-Level Structural Analysis

NASA Technical Reports Server (NTRS)

Sexstone, Matthew G.

1998-01-01

This paper describes a methodology that extends the use of the Equivalent LAminated Plate Solution (ELAPS) structural analysis code from conceptual-level aircraft structural analysis to conceptual-level aircraft mass property analysis. Mass property analysis in aircraft structures has historically depended upon parametric weight equations at the conceptual design level and Finite Element Analysis (FEA) at the detailed design level. ELAPS allows for the modeling of detailed geometry, metallic and composite materials, and non-structural mass coupled with analytical structural sizing to produce high-fidelity mass property analyses representing fully configured vehicles early in the design process. This capability is especially valuable for unusual configuration and advanced concept development where existing parametric weight equations are inapplicable and FEA is too time consuming for conceptual design. This paper contrasts the use of ELAPS relative to empirical weight equations and FEA. ELAPS modeling techniques are described and the ELAPS-based mass property analysis process is detailed. Examples of mass property stochastic calculations produced during a recent systems study are provided. This study involved the analysis of three remotely piloted aircraft required to carry scientific payloads to very high altitudes at subsonic speeds. Due to the extreme nature of this high-altitude flight regime, few existing vehicle designs are available for use in performance and weight prediction. ELAPS was employed within a concurrent engineering analysis process that simultaneously produces aerodynamic, structural, and static aeroelastic results for input to aircraft performance analyses. The ELAPS models produced for each concept were also used to provide stochastic analyses of wing structural mass properties. The results of this effort indicate that ELAPS is an efficient means to conduct multidisciplinary trade studies at the conceptual design level.

Aircraft Structural Mass Property Prediction Using Conceptual-Level Structural Analysis

NASA Technical Reports Server (NTRS)

Sexstone, Matthew G.

1998-01-01

This paper describes a methodology that extends the use of the Equivalent LAminated Plate Solution (ELAPS) structural analysis code from conceptual-level aircraft structural analysis to conceptual-level aircraft mass property analysis. Mass property analysis in aircraft structures has historically depended upon parametric weight equations at the conceptual design level and Finite Element Analysis (FEA) at the detailed design level ELAPS allows for the modeling of detailed geometry, metallic and composite materials, and non-structural mass coupled with analytical structural sizing to produce high-fidelity mass property analyses representing fully configured vehicles early in the design process. This capability is especially valuable for unusual configuration and advanced concept development where existing parametric weight equations are inapplicable and FEA is too time consuming for conceptual design. This paper contrasts the use of ELAPS relative to empirical weight equations and FEA. ELAPS modeling techniques are described and the ELAPS-based mass property analysis process is detailed Examples of mass property stochastic calculations produced during a recent systems study are provided This study involved the analysis of three remotely piloted aircraft required to carry scientific payloads to very high altitudes at subsonic speeds. Due to the extreme nature of this high-altitude flight regime,few existing vehicle designs are available for use in performance and weight prediction. ELAPS was employed within a concurrent engineering analysis process that simultaneously produces aerodynamic, structural, and static aeroelastic results for input to aircraft performance analyses. The ELAPS models produced for each concept were also used to provide stochastic analyses of wing structural mass properties. The results of this effort indicate that ELAPS is an efficient means to conduct multidisciplinary trade studies at the conceptual design level.

Semi-Structured Interview Protocol for Constructing Logic Models

ERIC Educational Resources Information Center

Gugiu, P. Cristian; Rodriguez-Campos, Liliana

2007-01-01

This paper details a semi-structured interview protocol that evaluators can use to develop a logic model of a program's services and outcomes. The protocol presents a series of questions, which evaluators can ask of specific program informants, that are designed to: (1) identify key informants basic background and contextual information, (2)…

The effect of a loss of model structural detail due to network skeletonization on contamination warning system design: case studies.

PubMed

Davis, Michael J; Janke, Robert

2018-01-04

The effect of limitations in the structural detail available in a network model on contamination warning system (CWS) design was examined in case studies using the original and skeletonized network models for two water distribution systems (WDSs). The skeletonized models were used as proxies for incomplete network models. CWS designs were developed by optimizing sensor placements for worst-case and mean-case contamination events. Designs developed using the skeletonized network models were transplanted into the original network model for evaluation. CWS performance was defined as the number of people who ingest more than some quantity of a contaminant in tap water before the CWS detects the presence of contamination. Lack of structural detail in a network model can result in CWS designs that (1) provide considerably less protection against worst-case contamination events than that obtained when a more complete network model is available and (2) yield substantial underestimates of the consequences associated with a contamination event. Nevertheless, CWSs developed using skeletonized network models can provide useful reductions in consequences for contaminants whose effects are not localized near the injection location. Mean-case designs can yield worst-case performances similar to those for worst-case designs when there is uncertainty in the network model. Improvements in network models for WDSs have the potential to yield significant improvements in CWS designs as well as more realistic evaluations of those designs. Although such improvements would be expected to yield improved CWS performance, the expected improvements in CWS performance have not been quantified previously. The results presented here should be useful to those responsible for the design or implementation of CWSs, particularly managers and engineers in water utilities, and encourage the development of improved network models.

The effect of a loss of model structural detail due to network skeletonization on contamination warning system design: case studies

NASA Astrophysics Data System (ADS)

Davis, Michael J.; Janke, Robert

2018-05-01

The effect of limitations in the structural detail available in a network model on contamination warning system (CWS) design was examined in case studies using the original and skeletonized network models for two water distribution systems (WDSs). The skeletonized models were used as proxies for incomplete network models. CWS designs were developed by optimizing sensor placements for worst-case and mean-case contamination events. Designs developed using the skeletonized network models were transplanted into the original network model for evaluation. CWS performance was defined as the number of people who ingest more than some quantity of a contaminant in tap water before the CWS detects the presence of contamination. Lack of structural detail in a network model can result in CWS designs that (1) provide considerably less protection against worst-case contamination events than that obtained when a more complete network model is available and (2) yield substantial underestimates of the consequences associated with a contamination event. Nevertheless, CWSs developed using skeletonized network models can provide useful reductions in consequences for contaminants whose effects are not localized near the injection location. Mean-case designs can yield worst-case performances similar to those for worst-case designs when there is uncertainty in the network model. Improvements in network models for WDSs have the potential to yield significant improvements in CWS designs as well as more realistic evaluations of those designs. Although such improvements would be expected to yield improved CWS performance, the expected improvements in CWS performance have not been quantified previously. The results presented here should be useful to those responsible for the design or implementation of CWSs, particularly managers and engineers in water utilities, and encourage the development of improved network models.

Detailed p- and s-wave velocity models along the LARSE II transect, Southern California

USGS Publications Warehouse

Murphy, J.M.; Fuis, G.S.; Ryberg, T.; Lutter, W.J.; Catchings, R.D.; Goldman, M.R.

2010-01-01

Structural details of the crust determined from P-wave velocity models can be improved with S-wave velocity models, and S-wave velocities are needed for model-based predictions of strong ground motion in southern California. We picked P- and S-wave travel times for refracted phases from explosive-source shots of the Los Angeles Region Seismic Experiment, Phase II (LARSE II); we developed refraction velocity models from these picks using two different inversion algorithms. For each inversion technique, we calculated ratios of P- to S-wave velocities (VP/VS) where there is coincident P- and S-wave ray coverage.We compare the two VP inverse velocity models to each other and to results from forward modeling, and we compare the VS inverse models. The VS and VP/VS models differ in structural details from the VP models. In particular, dipping, tabular zones of low VS, or high VP/VS, appear to define two fault zones in the central Transverse Ranges that could be parts of a positive flower structure to the San Andreas fault. These two zones are marginally resolved, but their presence in two independent models lends them some credibility. A plot of VS versus VP differs from recently published plots that are based on direct laboratory or down-hole sonic measurements. The difference in plots is most prominent in the range of VP = 3 to 5 km=s (or VS ~ 1:25 to 2:9 km/s), where our refraction VS is lower by a few tenths of a kilometer per second from VS based on direct measurements. Our new VS - VP curve may be useful for modeling the lower limit of VS from a VP model in calculating strong motions from scenario earthquakes.

3-DIMENSIONAL Geometric Survey and Structural Modelling of the Dome of Pisa Cathedral

NASA Astrophysics Data System (ADS)

Aita, D.; Barsotti, R.; Bennati, S.; Caroti, G.; Piemonte, A.

2017-02-01

This paper aims to illustrate the preliminary results of a research project on the dome of Pisa Cathedral (Italy). The final objective of the present research is to achieve a deep understanding of the structural behaviour of the dome, through a detailed knowledge of its geometry and constituent materials, and by taking into account historical and architectural aspects as well. A reliable survey of the dome is the essential starting point for any further investigation and adequate structural modelling. Examination of the status quo on the surveys of the Cathedral dome shows that a detailed survey suitable for structural analysis is in fact lacking. For this reason, high-density and high-precision surveys have been planned, by considering that a different survey output is needed, according both to the type of structural model chosen and purposes to be achieved. Thus, both range-based (laser scanning) and image-based (3D Photogrammetry) survey methodologies have been used. This contribution introduces the first results concerning the shape of the dome derived from surveys. Furthermore, a comparison is made between such survey outputs and those available in the literature.

Epidemic patch models applied to pandemic influenza: contact matrix, stochasticity, robustness of predictions.

PubMed

Lunelli, Antonella; Pugliese, Andrea; Rizzo, Caterina

2009-07-01

Due to the recent emergence of H5N1 virus, the modelling of pandemic influenza has become a relevant issue. Here we present an SEIR model formulated to simulate a possible outbreak in Italy, analysing its structure and, more generally, the effect of including specific details into a model. These details regard population heterogeneities, such as age and spatial distribution, as well as stochasticity, that regulates the epidemic dynamics when the number of infectives is low. We discuss and motivate the specific modelling choices made when building the model and investigate how the model details influence the predicted dynamics. Our analysis may help in deciding which elements of complexity are worth including in the design of a deterministic model for pandemic influenza, in a balance between, on the one hand, keeping the model computationally efficient and the number of parameters low and, on the other hand, maintaining the necessary realistic features.

Multilevel modelling: Beyond the basic applications.

PubMed

Wright, Daniel B; London, Kamala

2009-05-01

Over the last 30 years statistical algorithms have been developed to analyse datasets that have a hierarchical/multilevel structure. Particularly within developmental and educational psychology these techniques have become common where the sample has an obvious hierarchical structure, like pupils nested within a classroom. We describe two areas beyond the basic applications of multilevel modelling that are important to psychology: modelling the covariance structure in longitudinal designs and using generalized linear multilevel modelling as an alternative to methods from signal detection theory (SDT). Detailed code for all analyses is described using packages for the freeware R.

QUIESCENT PROMINENCES IN THE ERA OF ALMA: SIMULATED OBSERVATIONS USING THE 3D WHOLE-PROMINENCE FINE STRUCTURE MODEL

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

Gunár, Stanislav; Heinzel, Petr; Mackay, Duncan H.

2016-12-20

We use the detailed 3D whole-prominence fine structure model to produce the first simulated high-resolution ALMA observations of a modeled quiescent solar prominence. The maps of synthetic brightness temperature and optical thickness shown in the present paper are produced using a visualization method for synthesis of the submillimeter/millimeter radio continua. We have obtained the simulated observations of both the prominence at the limb and the filament on the disk at wavelengths covering a broad range that encompasses the full potential of ALMA. We demonstrate here extent to which the small-scale and large-scale prominence and filament structures will be visible inmore » the ALMA observations spanning both the optically thin and thick regimes. We analyze the relationship between the brightness and kinetic temperature of the prominence plasma. We also illustrate the opportunities ALMA will provide for studying the thermal structure of the prominence plasma from the cores of the cool prominence fine structure to the prominence–corona transition region. In addition, we show that detailed 3D modeling of entire prominences with their numerous fine structures will be important for the correct interpretation of future ALMA observations of prominences.« less

Hierarchical Coarse-Graining Via a Generalized Yvon-Born Green Framework: Many-Body Correlations, Mappings, and Structural Accuracy

NASA Astrophysics Data System (ADS)

Rudzinski, Joseph F.

Atomically-detailed molecular dynamics simulations have emerged as one of the most powerful theoretic tools for studying complex, condensed-phase systems. Despite their ability to provide incredible molecular insight, these simulations are insufficient for investigating complex biological processes, e.g., protein folding or molecular aggregation, on relevant length and time scales. The increasing scope and sophistication of atomically-detailed models has motivated the development of "hierarchical" approaches, which parameterize a low resolution, coarse-grained (CG) model based on simulations of an atomically-detailed model. The utility of hierarchical CG models depends on their ability to accurately incorporate the correct physics of the underlying model. One approach for ensuring this "consistency" between the models is to parameterize the CG model to reproduce the structural ensemble generated by the high resolution model. The many-body potential of mean force is the proper CG energy function for reproducing all structural distributions of the atomically-detailed model, at the CG level of resolution. However, this CG potential is a configuration-dependent free energy function that is generally too complicated to represent or simulate. The multiscale coarse-graining (MS-CG) method employs a generalized Yvon-Born-Green (g-YBG) relation to directly determine a variationally optimal approximation to the many-body potential of mean force. The MS-CG/g-YBG method provides a convenient and transparent framework for investigating the equilibrium structure of the system, at the CG level of resolution. In this work, we investigate the fundamental limitations and approximations of the MS-CG/g-YBG method. Throughout the work, we propose several theoretic constructs to directly relate the MS-CG/g-YBG method to other popular structure-based CG approaches. We investigate the physical interpretation of the MS-CG/g-YBG correlation matrix, the quantity responsible for disentangling the various contributions to the average force on a CG site. We then employ an iterative extension of the MS-CG/g-YBG method that improves the accuracy of a particular set of low order correlation functions relative to the original MS-CG/g-YBG model. We demonstrate that this method provides a powerful framework for identifying the precise source of error in an MS-CG/g-YBG model. We then propose a method for identifying an optimal CG representation, prior to the development of the CG model. We employ these techniques together to demonstrate that in the cases where the MS-CG/g-YBG method fails to determine an accurate model, a fundamental problem likely exists with the chosen CG representation or interaction set. Additionally, we explicitly demonstrate that while the iterative model successfully improves the accuracy of the low order structure, it does so by distorting the higher order structural correlations relative to the underlying model. Finally, we apply these methods to investigate the utility of the MS-CG/g- YBG method for developing models for systems with complex intramolecular structure. Overall, our results demonstrate the power of the g-YBG framework for developing accurate CG models and for investigating the driving forces of equilibrium structures for complex condensed-phase systems. This work also explicitly motivates future development of bottom-up CG methods and highlights some outstanding problems in the field. iii.

Wind-tunnel measurements in the wakes of structures

NASA Technical Reports Server (NTRS)

Woo, H. G. C.; Peterka, J. A.; Cermak, J. E.

1977-01-01

Detailed measurements of longitudinal mean velocity, turbulence intensity, space correlations, and spectra made in the wake of two rectangular scaled models in simulated atmospheric boundary-layer winds are presented. The model buildings were 1:50 scale models of two trailers. Results of a flow visualization study of the wake geometry are analyzed with some singular point theorems. Two hypothetical flow patterns of the detailed wake geometry are proposed. Some preliminary studies of the vortex wake, effects of the model size, model aspect ratios, and boundary layer characteristics on the decay rate and extent of the wake are also presented and discussed.

Titanium and advanced composite structures for a supersonic cruise arrow wing configuration

NASA Technical Reports Server (NTRS)

Turner, M. J.; Hoy, J. M.

1976-01-01

Structural design studies were made, based on current technology and on an estimate of technology to be available in the mid 1980's, to assess the relative merits of structural concepts and materials for an advanced arrow wing configuration cruising at Mach 2.7. Preliminary studies were made to insure compliance of the configuration with general design criteria, integrate the propulsion system with the airframe, and define an efficient structural arrangement. Material and concept selection, detailed structural analysis, structural design and airplane mass analysis were completed based on current technology. Based on estimated future technology, structural sizing for strength and a preliminary assessment of the flutter of a strength designed composite structure were completed. An advanced computerized structural design system was used, in conjunction with a relatively complex finite element model, for detailed analysis and sizing of structural members.

Terrestrial laser scanning to quantify above-ground biomass of structurally complex coastal wetland vegetation

NASA Astrophysics Data System (ADS)

Owers, Christopher J.; Rogers, Kerrylee; Woodroffe, Colin D.

2018-05-01

Above-ground biomass represents a small yet significant contributor to carbon storage in coastal wetlands. Despite this, above-ground biomass is often poorly quantified, particularly in areas where vegetation structure is complex. Traditional methods for providing accurate estimates involve harvesting vegetation to develop mangrove allometric equations and quantify saltmarsh biomass in quadrats. However broad scale application of these methods may not capture structural variability in vegetation resulting in a loss of detail and estimates with considerable uncertainty. Terrestrial laser scanning (TLS) collects high resolution three-dimensional point clouds capable of providing detailed structural morphology of vegetation. This study demonstrates that TLS is a suitable non-destructive method for estimating biomass of structurally complex coastal wetland vegetation. We compare volumetric models, 3-D surface reconstruction and rasterised volume, and point cloud elevation histogram modelling techniques to estimate biomass. Our results show that current volumetric modelling approaches for estimating TLS-derived biomass are comparable to traditional mangrove allometrics and saltmarsh harvesting. However, volumetric modelling approaches oversimplify vegetation structure by under-utilising the large amount of structural information provided by the point cloud. The point cloud elevation histogram model presented in this study, as an alternative to volumetric modelling, utilises all of the information within the point cloud, as opposed to sub-sampling based on specific criteria. This method is simple but highly effective for both mangrove (r2 = 0.95) and saltmarsh (r2 > 0.92) vegetation. Our results provide evidence that application of TLS in coastal wetlands is an effective non-destructive method to accurately quantify biomass for structurally complex vegetation.

An Introductory Classroom Exercise on Protein Molecular Model Visualization and Detailed Analysis of Protein-Ligand Binding

ERIC Educational Resources Information Center

Poeylaut-Palena, Andres, A.; de los Angeles Laborde, Maria

2013-01-01

A learning module for molecular level analysis of protein structure and ligand/drug interaction through the visualization of X-ray diffraction is presented. Using DeepView as molecular model visualization software, students learn about the general concepts of protein structure. This Biochemistry classroom exercise is designed to be carried out by…

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...

Three-Dimensional Geologic Framework Model for a Karst Aquifer System, Hasty and Western Grove Quadrangles, Northern Arkansas

USGS Publications Warehouse

Turner, Kenzie J.; Hudson, Mark R.; Murray, Kyle E.; Mott, David N.

2007-01-01

Understanding ground-water flow in a karst aquifer benefits from a detailed conception of the three-dimensional (3D) geologic framework. Traditional two-dimensional products, such as geologic maps, cross-sections, and structure contour maps, convey a mental picture of the area but a stronger conceptualization can be achieved by constructing a digital 3D representation of the stratigraphic and structural geologic features. In this study, a 3D geologic model was created to better understand a karst aquifer system in the Buffalo National River watershed in northern Arkansas. The model was constructed based on data obtained from recent, detailed geologic mapping for the Hasty and Western Grove 7.5-minute quadrangles. The resulting model represents 11 stratigraphic zones of Ordovician, Mississippian, and Pennsylvanian age. As a result of the highly dissected topography, stratigraphic and structural control from geologic contacts and interpreted structure contours were sufficient for effectively modeling the faults and folds in the model area. Combined with recent dye-tracing studies, the 3D framework model is useful for visualizing the various geologic features and for analyzing the potential control they exert on the ground-water flow regime. Evaluation of the model, by comparison to published maps and cross-sections, indicates that the model accurately reproduces both the surface geology and subsurface geologic features of the area.

An Experimental Approach to Mathematical Modeling in Biology

ERIC Educational Resources Information Center

Ledder, Glenn

2008-01-01

The simplest age-structured population models update a population vector via multiplication by a matrix. These linear models offer an opportunity to introduce mathematical modeling to students of limited mathematical sophistication and background. We begin with a detailed discussion of mathematical modeling, particularly in a biological context.…

Analytical Prediction of the Seismic Response of a Reinforced Concrete Containment Vessel

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

James, R.J.; Rashid, Y.R.; Cherry, J.L.

Under the sponsorship of the Ministry of International Trade and Industry (MITI) of Japan, the Nuclear Power Engineering Corporation (NUPEC) is investigating the seismic behavior of a Reinforced Concrete Containment Vessel (RCCV) through scale-model testing using the high-performance shaking table at the Tadotsu Engineering Laboratory. A series of tests representing design-level seismic ground motions was initially conducted to gather valuable experimental measurements for use in design verification. Additional tests will be conducted with increasing amplifications of the seismic input until a structural failure of the test model occurs. In a cooperative program with NUPEC, the US Nuclear Regulatory Commission (USNRC),more » through Sandia National Laboratories (SNL), is conducting analytical research on the seismic behavior of RCCV structures. As part of this program, pretest analytical predictions of the model tests are being performed. The dynamic time-history analysis utilizes a highly detailed concrete constitutive model applied to a three-dimensional finite element representation of the test structure. This paper describes the details of the analysis model and provides analysis results.« less

Acoustic scaling: A re-evaluation of the acoustic model of Manchester Studio 7

NASA Astrophysics Data System (ADS)

Walker, R.

1984-12-01

The reasons for the reconstruction and re-evaluation of the acoustic scale mode of a large music studio are discussed. The design and construction of the model using mechanical and structural considerations rather than purely acoustic absorption criteria is described and the results obtained are given. The results confirm that structural elements within the studio gave rise to unexpected and unwanted low-frequency acoustic absorption. The results also show that at least for the relatively well understood mechanisms of sound energy absorption physical modelling of the structural and internal components gives an acoustically accurate scale model, within the usual tolerances of acoustic design. The poor reliability of measurements of acoustic absorption coefficients, is well illustrated. The conclusion is reached that such acoustic scale modelling is a valid and, for large scale projects, financially justifiable technique for predicting fundamental acoustic effects. It is not appropriate for the prediction of fine details because such small details are unlikely to be reproduced exactly at a different size without extensive measurements of the material's performance at both scales.

Detailed Velocity and Density models of the Cascadia Subduction Zone from Prestack Full-Waveform Inversion

NASA Astrophysics Data System (ADS)

Fortin, W.; Holbrook, W. S.; Mallick, S.; Everson, E. D.; Tobin, H. J.; Keranen, K. M.

2014-12-01

Understanding the geologic composition of the Cascadia Subduction Zone (CSZ) is critically important in assessing seismic hazards in the Pacific Northwest. Despite being a potential earthquake and tsunami threat to millions of people, key details of the structure and fault mechanisms remain poorly understood in the CSZ. In particular, the position and character of the subduction interface remains elusive due to its relative aseismicity and low seismic reflectivity, making imaging difficult for both passive and active source methods. Modern active-source reflection seismic data acquired as part of the COAST project in 2012 provide an opportunity to study the transition from the Cascadia basin, across the deformation front, and into the accretionary prism. Coupled with advances in seismic inversion methods, this new data allow us to produce detailed velocity models of the CSZ and accurate pre-stack depth migrations for studying geologic structure. While still computationally expensive, current computing clusters can perform seismic inversions at resolutions that match that of the seismic image itself. Here we present pre-stack full waveform inversions of the central seismic line of the COAST survey offshore Washington state. The resultant velocity model is produced by inversion at every CMP location, 6.25 m laterally, with vertical resolution of 0.2 times the dominant seismic frequency. We report a good average correlation value above 0.8 across the entire seismic line, determined by comparing synthetic gathers to the real pre-stack gathers. These detailed velocity models, both Vp and Vs, along with the density model, are a necessary step toward a detailed porosity cross section to be used to determine the role of fluids in the CSZ. Additionally, the P-velocity model is used to produce a pre-stack depth migration image of the CSZ.

HINDERED DIFFUSION OF COAL LIQUIDS

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

Theodore T. Tsotsis; Muhammad Sahimi; Ian A. Webster

1996-01-01

It was the purpose of the project described here to carry out careful and detailed investigations of petroleum and coal asphaltene transport through model porous systems under a broad range of temperature conditions. The experimental studies were to be coupled with detailed, in-depth statistical and molecular dynamics models intended to provide a fundamental understanding of the overall transport mechanisms and a more accurate concept of the asphaltene structure. The following discussion describes some of our accomplishments.

Studies of implicit and explicit solution techniques in transient thermal analysis of structures

NASA Technical Reports Server (NTRS)

Adelman, H. M.; Haftka, R. T.; Robinson, J. C.

1982-01-01

Studies aimed at an increase in the efficiency of calculating transient temperature fields in complex aerospace vehicle structures are reported. The advantages and disadvantages of explicit and implicit algorithms are discussed and a promising set of implicit algorithms with variable time steps, known as GEARIB, is described. Test problems, used for evaluating and comparing various algorithms, are discussed and finite element models of the configurations are described. These problems include a coarse model of the Space Shuttle wing, an insulated frame tst article, a metallic panel for a thermal protection system, and detailed models of sections of the Space Shuttle wing. Results generally indicate a preference for implicit over explicit algorithms for transient structural heat transfer problems when the governing equations are stiff (typical of many practical problems such as insulated metal structures). The effects on algorithm performance of different models of an insulated cylinder are demonstrated. The stiffness of the problem is highly sensitive to modeling details and careful modeling can reduce the stiffness of the equations to the extent that explicit methods may become the best choice. Preliminary applications of a mixed implicit-explicit algorithm and operator splitting techniques for speeding up the solution of the algebraic equations are also described.

Studies of implicit and explicit solution techniques in transient thermal analysis of structures

NASA Astrophysics Data System (ADS)

Adelman, H. M.; Haftka, R. T.; Robinson, J. C.

1982-08-01

Studies aimed at an increase in the efficiency of calculating transient temperature fields in complex aerospace vehicle structures are reported. The advantages and disadvantages of explicit and implicit algorithms are discussed and a promising set of implicit algorithms with variable time steps, known as GEARIB, is described. Test problems, used for evaluating and comparing various algorithms, are discussed and finite element models of the configurations are described. These problems include a coarse model of the Space Shuttle wing, an insulated frame tst article, a metallic panel for a thermal protection system, and detailed models of sections of the Space Shuttle wing. Results generally indicate a preference for implicit over explicit algorithms for transient structural heat transfer problems when the governing equations are stiff (typical of many practical problems such as insulated metal structures). The effects on algorithm performance of different models of an insulated cylinder are demonstrated. The stiffness of the problem is highly sensitive to modeling details and careful modeling can reduce the stiffness of the equations to the extent that explicit methods may become the best choice. Preliminary applications of a mixed implicit-explicit algorithm and operator splitting techniques for speeding up the solution of the algebraic equations are also described.

Use of EBSD Data in Numerical Analyses

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

Becker, R; Wiland, H

2000-01-14

Experimentation, theory and modeling have all played vital roles in defining what is known about microstructural evolution and the effects of microstructure on material properties. Recently, technology has become an enabling factor, allowing significant advances to be made on several fronts. Experimental evidence of crystallographic slip and the basic theory of crystal plasticity were established in the early 20th Century, and the theory and models evolved incrementally over the next 60 years. (Asaro provides a comprehensive review of the mechanisms and basic plasticity models.) During this time modeling was primarily concerned with the average response of polycrystalline aggregates. While somemore » detailed finite element modeling (FEM) with crystal plasticity constitutive relations was done in the early 1980s, such simulations over taxed the capabilities of the available computer hardware. Advances in computer capability led to a flurry of activity in finite element modeling in the next 10 years, increasing understanding of microstructure evolution and pushing the limits of theories and material characterization. Automated Electron Back Scatter Diffraction (EBSD) has produced a similar revolution in material characterization. The data collected is extensive and many questions about the evolution of microstructure and its role in determining mechanic properties can now be addressed. It is also now possible to obtain sufficient information about lattice orientations on a fine enough scale to allow detailed quantitative comparisons of experiments and newly emerging large scale numerical simulations. The insight gained from the coupling of EBSD and FEM studies will provide impetus for further development of microstructure models and theories of microstructure evolution. Early studies connecting EBSD data to finite element models used manual measurements to define initial orientations for the simulation. In one study, manual measurements of the deformed structure were also obtained for comparison with the model predictions. More recent work has taken advantage of automated data collection on deformed specimens as a means of collecting detailed and spatially correlated data for model validation. Although it will not be discussed in detail here, another area in which EBSD data is having a great impact is on recrystallization modeling. EBSD techniques can be used to collect data for quantitative microstructural analysis. This data can be used to infer growth kinetics of specific orientations, and this information can be synthesized into more accurate grain growth or recrystallization models. Another role which EBSD techniques may play is in determining initial structures for recrystallization models. A realistic starting structure is vital for evaluating the models, and attempts at predicting realistic structures with finite element simulations are not yet successful. As methodologies and equipment resolution continue to improve, it is possible that measured structures will serve as input for recrystallization models. Simulations have already been run using information obtained manually from a TEM.« less

SSME structural dynamic model development

NASA Technical Reports Server (NTRS)

Foley, M. J.; Tilley, D. M.; Welch, C. T.

1983-01-01

A mathematical model of the Space Shuttle Main Engine (SSME) as a complete assembly, with detailed emphasis on LOX and High Fuel Turbopumps is developed. The advantages of both complete engine dynamics, and high fidelity modeling are incorporated. Development of this model, some results, and projected applications are discussed.

A NASTRAN model of a large flexible swing-wing bomber. Volume 5: NASTRAN model development-fairing structure

NASA Technical Reports Server (NTRS)

Mock, W. D.; Latham, R. A.

1982-01-01

The NASTRAN model plan for the fairing structure was expanded in detail to generate the NASTRAN model of this substructure. The grid point coordinates, element definitions, material properties, and sizing data for each element were specified. The fairing model was thoroughly checked out for continuity, connectivity, and constraints. The substructure was processed for structural influence coefficients (SIC) point loadings to determine the deflection characteristics of the fairing model. Finally, a demonstration and validation processing of this substructure was accomplished using the NASTRAN finite element program. The bulk data deck, stiffness matrices, and SIC output data were delivered.

A generative, probabilistic model of local protein structure.

PubMed

Boomsma, Wouter; Mardia, Kanti V; Taylor, Charles C; Ferkinghoff-Borg, Jesper; Krogh, Anders; Hamelryck, Thomas

2008-07-01

Despite significant progress in recent years, protein structure prediction maintains its status as one of the prime unsolved problems in computational biology. One of the key remaining challenges is an efficient probabilistic exploration of the structural space that correctly reflects the relative conformational stabilities. Here, we present a fully probabilistic, continuous model of local protein structure in atomic detail. The generative model makes efficient conformational sampling possible and provides a framework for the rigorous analysis of local sequence-structure correlations in the native state. Our method represents a significant theoretical and practical improvement over the widely used fragment assembly technique by avoiding the drawbacks associated with a discrete and nonprobabilistic approach.

Nano-sized Adsorbate Structure Formation in Anisotropic Multilayer System

NASA Astrophysics Data System (ADS)

Kharchenko, Vasyl O.; Kharchenko, Dmitrii O.; Yanovsky, Vladimir V.

2017-05-01

In this article, we study dynamics of adsorbate island formation in a model plasma-condensate system numerically. We derive the generalized reaction-diffusion model for adsorptive multilayer system by taking into account anisotropy in transfer of adatoms between neighbor layers induced by electric field. It will be found that with an increase in the electric field strength, a structural transformation from nano-holes inside adsorbate matrix toward separated nano-sized adsorbate islands on a substrate is realized. Dynamics of adsorbate island sizes and corresponding distributions are analyzed in detail. This study provides an insight into details of self-organization of adatoms into nano-sized adsorbate islands in anisotropic multilayer plasma-condensate systems.

A virtual reality browser for Space Station models

NASA Technical Reports Server (NTRS)

Goldsby, Michael; Pandya, Abhilash; Aldridge, Ann; Maida, James

1993-01-01

The Graphics Analysis Facility at NASA/JSC has created a visualization and learning tool by merging its database of detailed geometric models with a virtual reality system. The system allows an interactive walk-through of models of the Space Station and other structures, providing detailed realistic stereo images. The user can activate audio messages describing the function and connectivity of selected components within his field of view. This paper presents the issues and trade-offs involved in the implementation of the VR system and discusses its suitability for its intended purposes.

Using CONTENT 1.5 to analyze an SIR model for childhood infectious diseases

NASA Astrophysics Data System (ADS)

Su, Rui; He, Daihai

2008-11-01

In this work, we introduce a standard software CONTENT 1.5 for analysis of dynamical systems. A simple model for childhood infectious diseases is used as an example. The detailed steps to obtain the bifurcation structures of the system are given. These bifurcation structures can be used to explain the observed dynamical transition in measles incidences.

Pipelines subject to slow landslide movements: Structural modeling vs field measurement

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

Bruschi, R.; Glavina, S.; Spinazze, M.

1996-12-01

In recent years finite element techniques have been increasingly used to investigate the behavior of buried pipelines subject to soil movements. The use of these tools provides a rational basis for the definition of minimum wall thickness requirements in landslide crossings. Furthermore the design of mitigation measures or monitoring systems which control the development of undesirable strains in the pipe wall over time, requires a detailed structural modeling. The scope of this paper is to discuss the use of dedicated structural modeling with relevant calibration to field measurements. The strain measurements used were regularly gathered from pipe sections, in twomore » different sites over a period of time long enough to record changes of axial strain due to soil movement. Detailed structural modeling of pipeline layout in both sites and for operating conditions, is applied. Numerical simulations show the influence of the distribution of soil movement acting on the pipeline with regards to the state of strain which can be developed in certain locations. The role of soil nature and direction of relative movements in the definition of loads transferred to the pipeline, is also discussed.« less

Oscillating water column structural model

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

Copeland, Guild; Bull, Diana L; Jepsen, Richard Alan

2014-09-01

An oscillating water column (OWC) wave energy converter is a structure with an opening to the ocean below the free surface, i.e. a structure with a moonpool. Two structural models for a non-axisymmetric terminator design OWC, the Backward Bent Duct Buoy (BBDB) are discussed in this report. The results of this structural model design study are intended to inform experiments and modeling underway in support of the U.S. Department of Energy (DOE) initiated Reference Model Project (RMP). A detailed design developed by Re Vision Consulting used stiffeners and girders to stabilize the structure against the hydrostatic loads experienced by amore » BBDB device. Additional support plates were added to this structure to account for loads arising from the mooring line attachment points. A simplified structure was designed in a modular fashion. This simplified design allows easy alterations to the buoyancy chambers and uncomplicated analysis of resulting changes in buoyancy.« less

A New Generation of Los Alamos Opacity Tables

DOE PAGES

Colgan, James Patrick; Kilcrease, David Parker; Magee, Jr., Norman H.; ...

2016-01-26

We present a new, publicly available, set of Los Alamos OPLIB opacity tables for the elements hydrogen through zinc. Our tables are computed using the Los Alamos ATOMIC opacity and plasma modeling code, and make use of atomic structure calculations that use fine-structure detail for all the elements considered. Our equation-of-state (EOS) model, known as ChemEOS, is based on the minimization of free energy in a chemical picture and appears to be a reasonable and robust approach to determining atomic state populations over a wide range of temperatures and densities. In this paper we discuss in detail the calculations thatmore » we have performed for the 30 elements considered, and present some comparisons of our monochromatic opacities with measurements and other opacity codes. We also use our new opacity tables in solar modeling calculations and compare and contrast such modeling with previous work.« less

Analysis of shell-type structures subjected to time-dependent mechanical and thermal loading

NASA Technical Reports Server (NTRS)

Simitses, George J.

1990-01-01

The development of a general mathematical model and solution methodologies for analyzing structural response of thin, metallic shell-like structures under dynamic and/or static thermomechanical loads is examined. In the mathematical model, geometric as well as material-type of nonlinearities are considered. Traditional as well as novel approaches are reported and detailed applications are presented in the appendices. The emphasis for the mathematical model, the related solution schemes, and the applications, is on thermal viscoelastic and viscoplastic phenomena, which can predict creep and ratchetting.

Analysis of shell-type structures subjected to time-dependent mechanical and thermal loading

NASA Technical Reports Server (NTRS)

Simitses, G. J.

1991-01-01

This report deals with the development of a general mathematical model and solution methodology for analyzing the structural response of thin, metallic shell-like structures under dynamic and/or static thermomechanical loads. In the mathematical model, geometric as well as the material-type of nonlinearities are considered. Traditional as well as novel approaches are reported and detailed applications are presented in the appendices. The emphasis for the mathematical model, the related solution schemes, and the applications, is on thermal viscoelastic and viscoplastic phenomena, which can predict creep and ratchetting.

Spatially structured superinfection and the evolution of disease virulence.

PubMed

Caraco, Thomas; Glavanakov, Stephan; Li, Shengua; Maniatty, William; Szymanski, Boleslaw K

2006-06-01

When pathogen strains differing in virulence compete for hosts, spatial structuring of disease transmission can govern both evolved levels of virulence and patterns in strain coexistence. We develop a spatially detailed model of superinfection, a form of contest competition between pathogen strains; the probability of superinfection depends explicitly on the difference in levels of virulence. We apply methods of adaptive dynamics to address the interplay of spatial dynamics and evolution. The mean-field approximation predicts evolution to criticality; any small increase in virulence capable of dynamical persistence is favored. Both pair approximation and simulation of the detailed model indicate that spatial structure constrains disease virulence. Increased spatial clustering reduces the maximal virulence capable of single-strain persistence and, more importantly, reduces the convergent-stable virulence level under strain competition. The spatially detailed model predicts that increasing the probability of superinfection, for given difference in virulence, increases the likelihood of between-strain coexistence. When strains differing in virulence can coexist ecologically, our results may suggest policies for managing diseases with localized transmission. Comparing equilibrium densities from the pair approximation, we find that introducing a more virulent strain into a host population infected by a less virulent strain can sometimes reduce total host mortality and increase global host density.

Detailed temporal structure of communication networks in groups of songbirds.

PubMed

Stowell, Dan; Gill, Lisa; Clayton, David

2016-06-01

Animals in groups often exchange calls, in patterns whose temporal structure may be influenced by contextual factors such as physical location and the social network structure of the group. We introduce a model-based analysis for temporal patterns of animal call timing, originally developed for networks of firing neurons. This has advantages over cross-correlation analysis in that it can correctly handle common-cause confounds and provides a generative model of call patterns with explicit parameters for the influences between individuals. It also has advantages over standard Markovian analysis in that it incorporates detailed temporal interactions which affect timing as well as sequencing of calls. Further, a fitted model can be used to generate novel synthetic call sequences. We apply the method to calls recorded from groups of domesticated zebra finch (Taeniopygia guttata) individuals. We find that the communication network in these groups has stable structure that persists from one day to the next, and that 'kernels' reflecting the temporal range of influence have a characteristic structure for a calling individual's effect on itself, its partner and on others in the group. We further find characteristic patterns of influences by call type as well as by individual. © 2016 The Authors.

Free-falling Crystals: Biological Macromolecular Crystal Growth Studies in Low Earth Orbit

NASA Technical Reports Server (NTRS)

Judge, Russell A.; Snell, E. H.; Pusey, M. L.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Spacecraft orbiting the earth experience a reduced acceleration environment due to being in a state of continuous free-fall. This state colloquially termed microgravity, has produced improved X-ray diffraction quality crystals of biological macromolecules. Improvements in X-ray diffraction resolution (detail) or signal to noise, provide greater detail in the three-dimensional molecular structure providing information about the molecule, how it works, how to improve its function or how to impede it. Greater molecular detail obtained by crystallization in microgravity, has important implications for structural biology. In this article we examine the theories behind macromolecule crystal quality improvement in microgravity using results obtained from studies with the model protein, chicken egg white lysozyme.

Vector Autoregression, Structural Equation Modeling, and Their Synthesis in Neuroimaging Data Analysis

PubMed Central

Chen, Gang; Glen, Daniel R.; Saad, Ziad S.; Hamilton, J. Paul; Thomason, Moriah E.; Gotlib, Ian H.; Cox, Robert W.

2011-01-01

Vector autoregression (VAR) and structural equation modeling (SEM) are two popular brain-network modeling tools. VAR, which is a data-driven approach, assumes that connected regions exert time-lagged influences on one another. In contrast, the hypothesis-driven SEM is used to validate an existing connectivity model where connected regions have contemporaneous interactions among them. We present the two models in detail and discuss their applicability to FMRI data, and interpretational limits. We also propose a unified approach that models both lagged and contemporaneous effects. The unifying model, structural vector autoregression (SVAR), may improve statistical and explanatory power, and avoids some prevalent pitfalls that can occur when VAR and SEM are utilized separately. PMID:21975109

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.

Creation of anatomical models from CT data

NASA Astrophysics Data System (ADS)

Alaytsev, Innokentiy K.; Danilova, Tatyana V.; Manturov, Alexey O.; Mareev, Gleb O.; Mareev, Oleg V.

2018-04-01

Computed tomography is a great source of biomedical data because it allows a detailed exploration of complex anatomical structures. Some structures are not visible on CT scans, and some are hard to distinguish due to partial volume effect. CT datasets require preprocessing before using them as anatomical models in a simulation system. The work describes segmentation and data transformation methods for an anatomical model creation from the CT data. The result models may be used for visual and haptic rendering and drilling simulation in a virtual surgery system.

International Space Station 2A Array Modal Analysis

NASA Technical Reports Server (NTRS)

Laible, Michael; Fitzpatrick, Kristin; Grygier, Michael

2012-01-01

On December 9th 2009, the International Space Station (ISS) 2A solar array mast experienced prolonged longeron shadowing during a Soyuz undocking. Analytical reconstruction of induced thermal and dynamic structural loads showed an exceedance of the mast buckling limit. Possible structural damage to the solar array mast could have occurred during this event. A Low fidelity video survey of the 2A mast showed no obvious damage of the mast longerons or battens. The decision was made to conduct an on-orbit dynamic test of the 2A array on December 18th, 2009. The test included thruster pluming on the array while photogrammetry data was recorded. The test was similar to other Dedicated Thruster Firings (DTFs) that were performed to measure structural frequency and damping of a solar array. Results of the DTF indicated lower frequency mast modes than model predictions, thus leading to speculation of mast damage. A detailed nonlinear analysis was performed on the 2A array model to assess possible solutions to modal differences. The setup of the parametric nonlinear trade study included the use of a detailed array model and the reduced mass and stiffness matrices of the entire ISS being applied to the array interface. The study revealed that the array attachment structure is nonlinear and thus was the source of error in the model prediction of mast modes. In addition, a detailed study was performed to determine mast mode sensitivity to mast longeron damage. This sensitivity study was performed to assess if the ISS program has sufficient instrumentation for mast damage detection.

Parametric representation of weld fillets using shell finite elements—a proposal based on minimum stiffness and inertia errors

NASA Astrophysics Data System (ADS)

Echer, L.; Marczak, R. J.

2018-02-01

The objective of the present work is to introduce a methodology capable of modelling welded components for structural stress analysis. The modelling technique was based on the recommendations of the International Institute of Welding; however, some geometrical features of the weld fillet were used as design parameters in an optimization problem. Namely, the weld leg length and thickness of the shell elements representing the weld fillet were optimized in such a way that the first natural frequencies were not changed significantly when compared to a reference result. Sequential linear programming was performed for T-joint structures corresponding to two different structural details: with and without full penetration weld fillets. Both structural details were tested in scenarios of various plate thicknesses and depths. Once the optimal parameters were found, a modelling procedure was proposed for T-shaped components. Furthermore, the proposed modelling technique was extended for overlapped welded joints. The results obtained were compared to well-established methodologies presented in standards and in the literature. The comparisons included results for natural frequencies, total mass and structural stress. By these comparisons, it was observed that some established practices produce significant errors in the overall stiffness and inertia. The methodology proposed herein does not share this issue and can be easily extended to other types of structure.

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.

Hardware-Based Non-Optimum Factors for Launch Vehicle Structural Design

NASA Technical Reports Server (NTRS)

Wu, K. Chauncey; Cerro, Jeffrey A.

2010-01-01

During aerospace vehicle conceptual and preliminary design, empirical non-optimum factors are typically applied to predicted structural component weights to account for undefined manufacturing and design details. Non-optimum factors are developed here for 32 aluminum-lithium 2195 orthogrid panels comprising the liquid hydrogen tank barrel of the Space Shuttle External Tank using measured panel weights and manufacturing drawings. Minimum values for skin thickness, axial and circumferential blade stiffener thickness and spacing, and overall panel thickness are used to estimate individual panel weights. Panel non-optimum factors computed using a coarse weights model range from 1.21 to 1.77, and a refined weights model (including weld lands and skin and stiffener transition details) yields non-optimum factors of between 1.02 and 1.54. Acreage panels have an average 1.24 non-optimum factor using the coarse model, and 1.03 with the refined version. The observed consistency of these acreage non-optimum factors suggests that relatively simple models can be used to accurately predict large structural component weights for future launch vehicles.

The thermal structure of the magnetized solar transition region

NASA Technical Reports Server (NTRS)

Mok, Y.; Van Hoven, G.

1993-01-01

The detailed thermal structure of the magnetized solar transition region, as measured by its differential emission measure DEM(T), is unknown. Proposals have been made that envision a significant lower-temperature contribution to the energy balance from cross-field (ion) heat flux. In this paper, we describe a self-consistent 2D MHD simulation (including the full effects of anisotropic thermal conduction) of a conceptual model due to Athay (1990). We display the detailed irregular thermal and magnetic structure of the transition region and demonstrate that the predicted DEM agrees with observations, particularly in the T less than 10 exp 5 K regime where previous theories had difficulty.

An accurate nonlinear finite element analysis and test correlation of a stiffened composite wing panel

NASA Astrophysics Data System (ADS)

Davis, D. D., Jr.; Krishnamurthy, T.; Stroud, W. J.; McCleary, S. L.

1991-05-01

State-of-the-art nonlinear finite element analysis techniques are evaluated by applying them to a realistic aircraft structural component. A wing panel from the V-22 tiltrotor aircraft is chosen because it is a typical modern aircraft structural component for which there is experimental data for comparison of results. From blueprints and drawings, a very detailed finite element model containing 2284 9-node Assumed Natural-Coordinate Strain elements was generated. A novel solution strategy which accounts for geometric nonlinearity through the use of corotating element reference frames and nonlinear strain-displacement relations is used to analyze this detailed model. Results from linear analyses using the same finite element model are presented in order to illustrate the advantages and costs of the nonlinear analysis as compared with the more traditional linear analysis.

An accurate nonlinear finite element analysis and test correlation of a stiffened composite wing panel

NASA Technical Reports Server (NTRS)

Davis, D. D., Jr.; Krishnamurthy, T.; Stroud, W. J.; Mccleary, S. L.

1991-01-01

State-of-the-art nonlinear finite element analysis techniques are evaluated by applying them to a realistic aircraft structural component. A wing panel from the V-22 tiltrotor aircraft is chosen because it is a typical modern aircraft structural component for which there is experimental data for comparison of results. From blueprints and drawings, a very detailed finite element model containing 2284 9-node Assumed Natural-Coordinate Strain elements was generated. A novel solution strategy which accounts for geometric nonlinearity through the use of corotating element reference frames and nonlinear strain-displacement relations is used to analyze this detailed model. Results from linear analyses using the same finite element model are presented in order to illustrate the advantages and costs of the nonlinear analysis as compared with the more traditional linear analysis.

Insights into DNA-mediated interparticle interactions from a coarse-grained model

NASA Astrophysics Data System (ADS)

Ding, Yajun; Mittal, Jeetain

2014-11-01

DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system in metastable amorphous states. Therefore, it is vital to explore the molecular details of particle assembly processes in order to understand the underlying mechanisms. Molecular simulations based on coarse-grained models can provide a convenient route to explore these details. Most of the currently available coarse-grained models of DNA-functionalized particles ignore key chemical and structural details of DNA behavior. These models therefore are limited in scope for studying experimental phenomena. In this paper, we present a new coarse-grained model of DNA-functionalized particles which incorporates some of the desired features of DNA behavior. The coarse-grained DNA model used here provides explicit DNA representation (at the nucleotide level) and complementary interactions between Watson-Crick base pairs, which lead to the formation of single-stranded hairpin and double-stranded DNA. Aggregation between multiple complementary strands is also prevented in our model. We study interactions between two DNA-functionalized particles as a function of DNA grafting density, lengths of the hybridizing and non-hybridizing parts of DNA, and temperature. The calculated free energies as a function of pair distance between particles qualitatively resemble experimental measurements of DNA-mediated pair interactions.

ACOSS FIVE (Active Control of Space Structures). Phase 1A

DTIC Science & Technology

1982-03-01

The control design MKUCTUKAL MOOC L PtRFOHMANCl MÜDtL DISTURBANCE MODEL I ’ II Q|S£) XM=) STATE SPACE MODEL KEDUCED MODELS (HAC... library ) whose detailed numerical procedures, structural reduction, eigen-computations, etc., are implemented dif- ferently than in NASTRAN. SPAR was...i-i. rCappesser ..ctn. ..ir. A. .^llliars i /ui N. t-t. i.yer orlva ..rlin^ton, ^\\ 22209 o j i c e 7 11 \\ttn. iULO Library

A Protein in the palm of your hand through augmented reality.

PubMed

Berry, Colin; Board, Jason

2014-01-01

Understanding of proteins and other biological macromolecules must be based on an appreciation of their 3-dimensional shape and the fine details of their structure. Conveying these details in a clear and stimulating fashion can present challenges using conventional approaches and 2-dimensional monitors and projectors. Here we describe a method for the production of 3-D interactive images of protein structures that can be manipulated in real time through the use of augmented reality software. Users first see a real-time image of themselves using the computer's camera, then, when they hold up a trigger image, a model of a molecule appears automatically in the video. This model rotates and translates in space in response to movements of the trigger card. The system described has been optimized to allow customization for the display of user-selected structures to create engaging, educational visualizations to explore 3-D structures. Copyright © 2014 The International Union of Biochemistry and Molecular Biology.

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

Structure prediction and analysis of MxaF from obligate, facultative and restricted facultative methylobacterium.

PubMed

Singh, Raghvendra Pratap; Singh, Ram Nageena; Srivastava, Manish K; Srivastava, Alok Kumar; Kumar, Sudheer; Dubey, Ramesh Chandra; Sharma, Arun Kumar

2012-01-01

Methylobacteria are ubiquitous in the biosphere which are capable of growing on C1 compounds such as formate, formaldehyde, methanol and methylamine as well as on a wide range of multi-carbon growth substrates such as C2, C3 and C4 compounds due to the methylotrophic enzymes methanol dehydrogenase (MDH). MDH is performing these functions with the help of a key protein mxaF. Unfortunately, detailed structural analysis and homology modeling of mxaF is remains undefined. Hence, the objective of this research is the characterization and three dimensional modeling of mxaF protein from three different methylotrophs by using I-TASSER server. The predicted model were further optimize and validate by Profile 3D, Errat, Verifiy3-D and PROCHECK server. Predicted and best evaluated models have been successfully deposited to PMDB database with PMDB ID PM0077505, PM0077506 and PM0077507. Active site identification revealed 11, 13 and 14 putative functional site residues in respected models. It may play a major role during protein-protein, and protein-cofactor interactions. This study can provide us an ab-initio and detail information to understand the structure, mechanism of action and regulation of mxaF protein.

Structure prediction and analysis of MxaF from obligate, facultative and restricted facultative methylobacterium

PubMed Central

Singh, Raghvendra Pratap; Singh, Ram Nageena; Srivastava, Manish K; Srivastava, Alok Kumar; Kumar, Sudheer; Dubey, Ramesh Chandra; Sharma, Arun Kumar

2012-01-01

Methylobacteria are ubiquitous in the biosphere which are capable of growing on C1 compounds such as formate, formaldehyde, methanol and methylamine as well as on a wide range of multi-carbon growth substrates such as C2, C3 and C4 compounds due to the methylotrophic enzymes methanol dehydrogenase (MDH). MDH is performing these functions with the help of a key protein mxaF. Unfortunately, detailed structural analysis and homology modeling of mxaF is remains undefined. Hence, the objective of this research is the characterization and three dimensional modeling of mxaF protein from three different methylotrophs by using I-TASSER server. The predicted model were further optimize and validate by Profile 3D, Errat, Verifiy3-D and PROCHECK server. Predicted and best evaluated models have been successfully deposited to PMDB database with PMDB ID PM0077505, PM0077506 and PM0077507. Active site identification revealed 11, 13 and 14 putative functional site residues in respected models. It may play a major role during protein-protein, and protein-cofactor interactions. This study can provide us an ab-initio and detail information to understand the structure, mechanism of action and regulation of mxaF protein. PMID:23275704

Design of a Model Execution Framework: Repetitive Object-Oriented Simulation Environment (ROSE)

NASA Technical Reports Server (NTRS)

Gray, Justin S.; Briggs, Jeffery L.

2008-01-01

The ROSE framework was designed to facilitate complex system analyses. It completely divorces the model execution process from the model itself. By doing so ROSE frees the modeler to develop a library of standard modeling processes such as Design of Experiments, optimizers, parameter studies, and sensitivity studies which can then be applied to any of their available models. The ROSE framework accomplishes this by means of a well defined API and object structure. Both the API and object structure are presented here with enough detail to implement ROSE in any object-oriented language or modeling tool.

The simulation approach to lipid-protein interactions.

PubMed

Paramo, Teresa; Garzón, Diana; Holdbrook, Daniel A; Khalid, Syma; Bond, Peter J

2013-01-01

The interactions between lipids and proteins are crucial for a range of biological processes, from the folding and stability of membrane proteins to signaling and metabolism facilitated by lipid-binding proteins. However, high-resolution structural details concerning functional lipid/protein interactions are scarce due to barriers in both experimental isolation of native lipid-bound complexes and subsequent biophysical characterization. The molecular dynamics (MD) simulation approach provides a means to complement available structural data, yielding dynamic, structural, and thermodynamic data for a protein embedded within a physiologically realistic, modelled lipid environment. In this chapter, we provide a guide to current methods for setting up and running simulations of membrane proteins and soluble, lipid-binding proteins, using standard atomistically detailed representations, as well as simplified, coarse-grained models. In addition, we outline recent studies that illustrate the power of the simulation approach in the context of biologically relevant lipid/protein interactions.

Three-Dimensional Integrated Survey for Building Investigations.

PubMed

Costantino, Domenica; Angelini, Maria Giuseppa

2015-11-01

The study shows the results of a survey aimed to represent a building collapse and the feasibility of the modellation as a support of structure analysis. An integrated survey using topographic, photogrammetric, and terrestrial laser techniques was carried out to obtain a three-dimensional (3D) model of the building, plans and prospects, and the particulars of the collapsed area. Authors acquired, by a photogrammetric survey, information about regular parties of the structure; while using laser scanner data they reconstructed a set of more interesting architectural details and areas with higher surface curvature. Specifically, the process of texture provided a detailed 3D structure of the areas under investigation. The analysis of the data acquired resulted to be very useful both in identifying the causes of the disaster and also in helping the reconstruction of the collapsed corner showing the contribution that the integrated surveys can give in preserving architectural and historic heritage. © 2015 American Academy of Forensic Sciences.

A new debate for Turkish physicians: e-detailing.

PubMed

Ventura, Keti; Baybars, Miray; Dedeoglu, Ayla Ozhan

2012-01-01

The study presents an empirical analysis of the attitudes of Turkish physicians towards e-detailing practices compared to face-to-face detailing. The findings reveal that although physicians have positive attitudes toward e-detailing, on some points they are still undecided and/or have doubts. The structural model revealed that affect, convenience, and informative content influence their attitude in a positive manner, whereas the personal interaction was found to be a negative factor. Physicians' age and frequency of calls received from representatives are moderators. The present study can be seen as an addition to pharmaceutical marketing, an underresearched study field in Turkey, and e-detailing particularly.

Architecture with GIDEON, A Program for Design in Structural DNA Nanotechnology

PubMed Central

Birac, Jeffrey J.; Sherman, William B.; Kopatsch, Jens; Constantinou, Pamela E.; Seeman, Nadrian C.

2012-01-01

We present geometry based design strategies for DNA nanostructures. The strategies have been implemented with GIDEON – a Graphical Integrated Development Environment for OligoNucleotides. GIDEON has a highly flexible graphical user interface that facilitates the development of simple yet precise models, and the evaluation of strains therein. Models are built on a simple model of undistorted B-DNA double-helical domains. Simple point and click manipulations of the model allow the minimization of strain in the phosphate-backbone linkages between these domains and the identification of any steric clashes that might occur as a result. Detailed analysis of 3D triangles yields clear predictions of the strains associated with triangles of different sizes. We have carried out experiments that confirm that 3D triangles form well only when their geometrical strain is less than 4% deviation from the estimated relaxed structure. Thus geometry-based techniques alone, without energetic considerations, can be used to explain general trends in DNA structure formation. We have used GIDEON to build detailed models of double crossover and triple crossover molecules, evaluating the non-planarity associated with base tilt and junction mis-alignments. Computer modeling using a graphical user interface overcomes the limited precision of physical models for larger systems, and the limited interaction rate associated with earlier, command-line driven software. PMID:16630733

The Stability and Structure of Lean Hydrogen-Air Flames: Effects of Gravity

DTIC Science & Technology

1990-05-17

INTRODUCTION ................................................................................................. 1 MULTIDIMENSIONAL FLAME MODEL ...combustion, molecular diffusion between the reactants, intermediates, and products, thermal conduction, convection, and gravity. Such a detailed model allows...instabil- ity, generally called the Rayleigh-Taylor instability5 . A numerical model of the premixed hydrogen flame that includes all the physical

Incremental Testing of the Community Multiscale Air Quality (CMAQ) Modeling System Version 4.7

EPA Science Inventory

This paper describes the scientific and structural updates to the latest release of the Community Multiscale Air Quality (CMAQ) modeling system version 4.7 (v4.7) and points the reader to additional resources for further details. The model updates were evaluated relative to obse...

Applications of the hybrid coordinate method to the TOPS autopilot

NASA Technical Reports Server (NTRS)

Fleischer, G. E.

1978-01-01

Preliminary results are presented from the application of the hybrid coordinate method to modeling TOPS (thermoelectric outer planet spacecraft) structural dynamics. Computer simulated responses of the vehicle are included which illustrate the interaction of relatively flexible appendages with an autopilot control system. Comparisons were made between simplified single-axis models of the control loop, with spacecraft flexibility represented by hinged rigid bodies, and a very detailed three-axis spacecraft model whose flexible portions are described by modal coordinates. While single-axis system, root loci provided reasonable qualitative indications of stability margins in this case, they were quantitatively optimistic when matched against responses of the detailed model.

Finite element analysis of helicopter structures

NASA Technical Reports Server (NTRS)

Rich, M. J.

1978-01-01

Application of the finite element analysis is now being expanded to three dimensional analysis of mechanical components. Examples are presented for airframe, mechanical components, and composite structure calculations. Data are detailed on the increase of model size, computer usage, and the effect on reducing stress analysis costs. Future applications for use of finite element analysis for helicopter structures are projected.

Thermodynamically Feasible Kinetic Models of Reaction Networks

PubMed Central

Ederer, Michael; Gilles, Ernst Dieter

2007-01-01

The dynamics of biological reaction networks are strongly constrained by thermodynamics. An holistic understanding of their behavior and regulation requires mathematical models that observe these constraints. However, kinetic models may easily violate the constraints imposed by the principle of detailed balance, if no special care is taken. Detailed balance demands that in thermodynamic equilibrium all fluxes vanish. We introduce a thermodynamic-kinetic modeling (TKM) formalism that adapts the concepts of potentials and forces from irreversible thermodynamics to kinetic modeling. In the proposed formalism, the thermokinetic potential of a compound is proportional to its concentration. The proportionality factor is a compound-specific parameter called capacity. The thermokinetic force of a reaction is a function of the potentials. Every reaction has a resistance that is the ratio of thermokinetic force and reaction rate. For mass-action type kinetics, the resistances are constant. Since it relies on the thermodynamic concept of potentials and forces, the TKM formalism structurally observes detailed balance for all values of capacities and resistances. Thus, it provides an easy way to formulate physically feasible, kinetic models of biological reaction networks. The TKM formalism is useful for modeling large biological networks that are subject to many detailed balance relations. PMID:17208985

Coupling a distributed hydrological model with detailed forest structural information for large-scale global change impact assessment

NASA Astrophysics Data System (ADS)

Eisner, Stephanie; Huang, Shaochun; Majasalmi, Titta; Bright, Ryan; Astrup, Rasmus; Beldring, Stein

2017-04-01

Forests are recognized for their decisive effect on landscape water balance with structural forest characteristics as stand density or species composition determining energy partitioning and dominant flow paths. However, spatial and temporal variability in forest structure is often poorly represented in hydrological modeling frameworks, in particular in regional to large scale hydrological modeling and impact analysis. As a common practice, prescribed land cover classes (including different generic forest types) are linked to parameter values derived from literature, or parameters are determined by calibration. While national forest inventory (NFI) data provide comprehensive, detailed information on hydrologically relevant forest characteristics, their potential to inform hydrological simulation over larger spatial domains is rarely exploited. In this study we present a modeling framework that couples the distributed hydrological model HBV with forest structural information derived from the Norwegian NFI and multi-source remote sensing data. The modeling framework, set up for the entire of continental Norway at 1 km spatial resolution, is explicitly designed to study the combined and isolated impacts of climate change, forest management and land use change on hydrological fluxes. We use a forest classification system based on forest structure rather than biomes which allows to implicitly account for impacts of forest management on forest structural attributes. In the hydrological model, different forest classes are represented by three parameters: leaf area index (LAI), mean tree height and surface albedo. Seasonal cycles of LAI and surface albedo are dynamically simulated to make the framework applicable under climate change conditions. Based on a hindcast for the pilot regions Nord-Trøndelag and Sør-Trøndelag, we show how forest management has affected regional hydrological fluxes during the second half of the 20th century as contrasted to climate variability.

Technoeconomic Modeling of Battery Energy Storage in SAM

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

DiOrio, Nicholas; Dobos, Aron; Janzou, Steven

Detailed comprehensive lead-acid and lithium-ion battery models have been integrated with photovoltaic models in an effort to allow System Advisor Model (SAM) to offer the ability to predict the performance and economic benefit of behind the meter storage. In a system with storage, excess PV energy can be saved until later in the day when PV production has fallen, or until times of peak demand when it is more valuable. Complex dispatch strategies can be developed to leverage storage to reduce energy consumption or power demand based on the utility rate structure. This document describes the details of the batterymore » performance and economic models in SAM.« less

Smart wing wind tunnel model design

NASA Astrophysics Data System (ADS)

Martin, Christopher A.; Jasmin, Larry; Flanagan, John S.; Appa, Kari; Kudva, Jayanth N.

1997-05-01

To verify the predicted benefits of the smart wing concept, two 16% scale wind tunnel models, one conventional and the other incorporating smart wing design features, were designed, fabricated and tested. Meticulous design of the two models was essential to: (1) ensure the required factor of safety of four for operation in the NASA Langley TDT wind tunnel, (2) efficiently integrate the smart actuation systems, (3) quantify the performance improvements, and (4) facilitate eventual scale-up to operational aircraft. Significant challenges were encountered in designing the attachment of the shape memory alloy control surfaces to the wing box, integration of the SMA torque tube in the wing structure, and development of control mechanisms to protect the model and the tunnel in the event of failure of the smart systems. In this paper, detailed design of the two models are presented. First, dynamic scaling of the models based on the geometry and structural details of the full- scale aircraft is presented. Next, results of the stress, divergence and flutter analyses are summarized. Finally some of the challenges of integrating the smart actuators with the model are highlighted.

Structure and dynamics of complex liquid water: Molecular dynamics simulation

NASA Astrophysics Data System (ADS)

S, Indrajith V.; Natesan, Baskaran

2015-06-01

We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.

3D WHOLE-PROMINENCE FINE STRUCTURE MODELING

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

Gunár, Stanislav; Mackay, Duncan H.

2015-04-20

We present the first 3D whole-prominence fine structure model. The model combines a 3D magnetic field configuration of an entire prominence obtained from nonlinear force-free field simulations, with a detailed description of the prominence plasma. The plasma is located in magnetic dips in hydrostatic equilibrium and is distributed along multiple fine structures within the 3D magnetic model. Through the use of a novel radiative transfer visualization technique for the Hα line such plasma-loaded magnetic field model produces synthetic images of the modeled prominence comparable with high-resolution observations. This allows us for the first time to use a single technique tomore » consistently study, in both emission on the limb and absorption against the solar disk, the fine structures of prominences/filaments produced by a magnetic field model.« less

a Historical Timber Frame Model for Diagnosis and Documentation Before Building Restoration

NASA Astrophysics Data System (ADS)

Koehl, M.; Viale, A.; Reeb, S.

2013-09-01

The aim of the project that is described in this paper was to define a four-level timber frame survey mode of a historical building: the so-called "Andlau's Seigniory", Alsace, France. This historical building (domain) was built in the late XVIth century and is now in a stage of renovation in order to become a heritage interpretation centre. The used measurement methods combine Total Station measurements, Photogrammetry and 3D Terrestrial Laser scanner. Different modelling workflows were tested and compared according to the data acquisition method, but also according to the characteristics of the reconstructed model in terms of accuracy and level of detail. 3D geometric modelling of the entire structure was performed including modelling the degree of detail adapted to the needs. The described 3D timber framework exists now in different versions, from a theoretical and geometrical one up to a very detailed one, in which measurements and evaluation of deformation by time are potentially allowed. The virtually generated models involving archaeologists, architects, historians and specialists in historical crafts, are intended to be used during the four stages of the project: (i) knowledge of the current state of needs for diagnosis and understanding of former construction techniques; (ii) preparation and evaluation of restoration steps; (iii) knowledge and documentation concerning the archaeological object; (iv) transmission and dissemination of knowledge through the implementation of museum animations. Among the generated models we can also find a documentation of the site in the form of virtual tours created from panoramic photographs before and during the restoration works. Finally, the timber framework model was structured and integrated into a 3D GIS, where the association of descriptive and complementary digital documents was possible. Both offer tools leading to the diagnosis, the understanding of the structure, knowledge dissemination, documentation and the creation of educational activities. The integration of these measurements in a historical information system will lead to the creation of an interactive model and the creation of a digital visual display unit for consultation. It will be offered to any public to understand interactively the art of constructing a Renaissance structure, with detailed photos, descriptive texts and graphics. The 3D digital model of the framework will be used directly in the interpretation path, within the space dedicated to "Seigniory" of Andlau. An interactive touch-screen will be installed. It will incorporate several levels of playgrounds (playful, evocative and teaching). In a virtual way, it will deal with the different stages of building a wooden framework and clarify the art of construction.

Three Dimensional Modeling via Photographs for Documentation of a Village Bath

NASA Astrophysics Data System (ADS)

Balta, H. B.; Hamamcioglu-Turan, M.; Ocali, O.

2013-07-01

The aim of this study is supporting the conceptual discussions of architectural restoration with three dimensional modeling of monuments based on photogrammetric survey. In this study, a 16th century village bath in Ulamış, Seferihisar, and Izmir is modeled for documentation. Ulamış is one of the historical villages within which Turkish population first settled in the region of Seferihisar - Urla. The methodology was tested on an antique monument; a bath with a cubical form. Within the limits of this study, only the exterior of the bath was modeled. The presentation scale for the bath was determined as 1 / 50, considering the necessities of designing structural interventions and architectural ones within the scope of a restoration project. The three dimensional model produced is a realistic document presenting the present situation of the ruin. Traditional plan, elevation and perspective drawings may be produced from the model, in addition to the realistic textured renderings and wireframe representations. The model developed in this study provides opportunity for presenting photorealistic details of historical morphologies in scale. Compared to conventional drawings, the renders based on the 3d models provide an opportunity for conceiving architectural details such as color, material and texture. From these documents, relatively more detailed restitution hypothesis can be developed and intervention decisions can be taken. Finally, the principles derived from the case study can be used for 3d documentation of historical structures with irregular surfaces.

On the numerical modeling of sliding beams: A comparison of different approaches

NASA Astrophysics Data System (ADS)

Steinbrecher, Ivo; Humer, Alexander; Vu-Quoc, Loc

2017-11-01

The transient analysis of sliding beams represents a challenging problem of structural mechanics. Typically, the sliding motion superimposed by large flexible deformation requires numerical methods as, e.g., finite elements, to obtain approximate solutions. By means of the classical sliding spaghetti problem, the present paper provides a guideline to the numerical modeling with conventional finite element codes. For this purpose, two approaches, one using solid elements and one using beam elements, respectively, are employed in the analysis, and the characteristics of each approach are addressed. The contact formulation realizing the interaction of the beam with its support demands particular attention in the context of sliding structures. Additionally, the paper employs the sliding-beam formulation as a third approach, which avoids the numerical difficulties caused by the large sliding motion through a suitable coordinate transformation. The present paper briefly outlines the theoretical fundamentals of the respective approaches for the modeling of sliding structures and gives a detailed comparison by means of the sliding spaghetti serving as a representative example. The specific advantages and limitations of the different approaches with regard to accuracy and computational efficiency are discussed in detail. Through the comparison, the sliding-beam formulation, which proves as an effective approach for the modeling, can be validated for the general problem of a sliding structure subjected to large deformation.

KINETIC MODELING OF COUNTERFLOW DIFFUSION FLAMES OF BUTADIENE. (R828193)

EPA Science Inventory

A comprehensive, semi-detailed kinetic scheme was used to simulate the chemical structures of counterflow diffusion and fuel-rich premixed 1,3-butadiene flames, to better understand the formation of polycyclic aromatic hydrocarbons (PAH). The results showed that model predicti...

Computational Biochemistry-Enzyme Mechanisms Explored.

PubMed

Culka, Martin; Gisdon, Florian J; Ullmann, G Matthias

2017-01-01

Understanding enzyme mechanisms is a major task to achieve in order to comprehend how living cells work. Recent advances in biomolecular research provide huge amount of data on enzyme kinetics and structure. The analysis of diverse experimental results and their combination into an overall picture is, however, often challenging. Microscopic details of the enzymatic processes are often anticipated based on several hints from macroscopic experimental data. Computational biochemistry aims at creation of a computational model of an enzyme in order to explain microscopic details of the catalytic process and reproduce or predict macroscopic experimental findings. Results of such computations are in part complementary to experimental data and provide an explanation of a biochemical process at the microscopic level. In order to evaluate the mechanism of an enzyme, a structural model is constructed which can be analyzed by several theoretical approaches. Several simulation methods can and should be combined to get a reliable picture of the process of interest. Furthermore, abstract models of biological systems can be constructed combining computational and experimental data. In this review, we discuss structural computational models of enzymatic systems. We first discuss various models to simulate enzyme catalysis. Furthermore, we review various approaches how to characterize the enzyme mechanism both qualitatively and quantitatively using different modeling approaches. © 2017 Elsevier Inc. All rights reserved.

Electron microscopy study of gold nanoparticles deposited on transition metal oxides.

PubMed

Akita, Tomoki; Kohyama, Masanori; Haruta, Masatake

2013-08-20

Many researchers have investigated the catalytic performance of gold nanoparticles (GNPs) supported on metal oxides for various catalytic reactions of industrial importance. These studies have consistently shown that the catalytic activity and selectivity depend on the size of GNPs, the kind of metal oxide supports, and the gold/metal oxide interface structure. Although researchers have proposed several structural models for the catalytically active sites and have identified the specific electronic structures of GNPs induced by the quantum effect, recent experimental and theoretical studies indicate that the perimeter around GNPs in contact with the metal oxide supports acts as an active site in many reactions. Thus, it is of immense importance to investigate the detailed structures of the perimeters and the contact interfaces of gold/metal oxide systems by using electron microscopy at an atomic scale. This Account describes our investigation, at the atomic scale using electron microscopy, of GNPs deposited on metal oxides. In particular, high-resolution transmission electron microscopy (HRTEM) and high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) are valuable tools to observe local atomic structures, as has been successfully demonstrated for various nanoparticles, surfaces, and material interfaces. TEM can be applied to real powder catalysts as received without making special specimens, in contrast to what is typically necessary to observe bulk materials. For precise structure analyses at an atomic scale, model catalysts prepared by using well-defined single-crystalline substrates are also adopted for TEM observations. Moreover, aberration-corrected TEM, which has high spatial resolution under 0.1 nm, is a promising tool to observe the interface structure between GNPs and metal oxide supports including oxygen atoms at the interfaces. The oxygen atoms in particular play an important role in the behavior of gold/metal oxide interfaces, because they may participate in catalytic reaction steps. Detailed information about the interfacial structures between GNPs and metal oxides provides valuable structure models for theoretical calculations which can elucidate the local electronic structure effective for activating a reactant molecule. Based on our observations with HRTEM and HAADF-STEM, we report the detailed structure of gold/metal oxide interfaces.

Integration of ground-based laser scanner and aerial digital photogrammetry for topographic modelling of Vesuvio volcano

NASA Astrophysics Data System (ADS)

Pesci, Arianna; Fabris, Massimo; Conforti, Dario; Loddo, Fabiana; Baldi, Paolo; Anzidei, Marco

2007-05-01

This work deals with the integration of different surveying methodologies for the definition of very accurate Digital Terrain Models (DTM) and/or Digital Surface Models (DSM): in particular, the aerial digital photogrammetry and the terrestrial laser scanning were used to survey the Vesuvio volcano, allowing the total coverage of the internal cone and surroundings (the whole surveyed area was about 3 km × 3 km). The possibility to reach a very high precision, especially from the laser scanner data set, allowed a detailed description of the morphology of the volcano. The comparisons of models obtained in repeated surveys allow a detailed map of residuals providing a data set that can be used for detailed studies of the morphological evolution. Moreover, the reflectivity information, highly correlated to materials properties, allows for the measurement and quantification of some morphological variations in areas where structural discontinuities and displacements are present.

Grazing-incidence small angle x-ray scattering studies of nanoscale polymer gratings

NASA Astrophysics Data System (ADS)

Doxastakis, Manolis; Suh, Hyo Seon; Chen, Xuanxuan; Rincon Delgadillo, Paulina A.; Wan, Lingshu; Williamson, Lance; Jiang, Zhang; Strzalka, Joseph; Wang, Jin; Chen, Wei; Ferrier, Nicola; Ramirez-Hernandez, Abelardo; de Pablo, Juan J.; Gronheid, Roel; Nealey, Paul

2015-03-01

Grazing-Incidence Small Angle X-ray Scattering (GISAXS) offers the ability to probe large sample areas, providing three-dimensional structural information at high detail in a thin film geometry. In this study we exploit the application of GISAXS to structures formed at one step of the LiNe (Liu-Nealey) flow using chemical patterns for directed self-assembly of block copolymer films. Experiments conducted at the Argonne National Laboratory provided scattering patterns probing film characteristics at both parallel and normal directions to the surface. We demonstrate the application of new computational methods to construct models based on scattering measured. Such analysis allows for extraction of structural characteristics at unprecedented detail.

Simulation study of disruption characteristics in KSTAR

NASA Astrophysics Data System (ADS)

Lee, Jongkyu; Kim, J. Y.; Kessel, C. E.; Poli, F.

2012-10-01

A detailed simulation study of disruption in KSTAR had been performed using the Tokamak Simulation Code(TSC) [1] during the initial design phase of KSTAR [2]. Recently, however, a partial modification in the structure of passive plate was made in relation to reduce eddy current and increase the efficiency of control of vertical position. A substantial change can then occur in disruption characteristics and plasma behavior during disruption due to changes in passive plate structure. Because of this, growth rate of vertical instability is expected to be increased and eddy current and its associated electomagnetic force are expected to be reduced. To check this in more detail, a new simulation study is here given with modified passive plate structure of KSTAR. In particular, modeling of vertical disruption that is vertical displacement event (VDE) was carried out. We calculated vertical growth rate for a drift phase of plasma and electromagnetic force acting on PFC structures and compared the results between in a new model and an old model. [4pt] [1] S.C. Jardin, N. Pomphrey and J. Delucia, J. Comp. Phys. 66, 481 (1986).[0pt] [2] J.Y. Kim, S.Y. Cho and KSTAR Team, Disruption load analysis on KSTAR PFC structures, J. Accel. Plasma Res. 5, 149 (2000).

Systems definition study for shuttle demonstration flights of large space structures. Volume 3: Thermal analyses

NASA Technical Reports Server (NTRS)

1979-01-01

the development of large space structure technology is discussed. A detailed thermal analysis of a model space fabricated 1 meter beam is presented. Alternative thermal coatings are evaluated, and deflections, stresses, and stiffness variations resulting from flight orientations and solar conditions are predicted.

EIT intensity noise spectroscopy power-broadening and level structure

NASA Astrophysics Data System (ADS)

Snider, Charles; Crescimanno, Michael; Oleary, Shannon

2011-05-01

One particularly interesting (and potentially technologically useful) characteristic of EIT coherence as viewed through intensity noise spectroscopy is its power-broadening resistant features. We detail a connection between the power broadening behavior and the underlying level structure by solving a more realistic quantum optics scenario modeled on recent experiments.

The design and development of a two-dimensional adaptive truss structure

NASA Technical Reports Server (NTRS)

Kuwao, Fumihiro; Motohashi, Shoichi; Yoshihara, Makoto; Takahara, Kenichi; Natori, Michihiro

1987-01-01

The functional model of a two dimensional adaptive truss structure which can purposefully change its geometrical configuration is introduced. The details of design and fabrication such as kinematic analysis, dynamic characteristics analysis and some test results are presented for the demonstration of this two dimensional truss concept.

Predicting climate change: Uncertainties and prospects for surmounting them

NASA Astrophysics Data System (ADS)

Ghil, Michael

2008-03-01

General circulation models (GCMs) are among the most detailed and sophisticated models of natural phenomena in existence. Still, the lack of robust and efficient subgrid-scale parametrizations for GCMs, along with the inherent sensitivity to initial data and the complex nonlinearities involved, present a major and persistent obstacle to narrowing the range of estimates for end-of-century warming. Estimating future changes in the distribution of climatic extrema is even more difficult. Brute-force tuning the large number of GCM parameters does not appear to help reduce the uncertainties. Andronov and Pontryagin (1937) proposed structural stability as a way to evaluate model robustness. Unfortunately, many real-world systems proved to be structurally unstable. We illustrate these concepts with a very simple model for the El Niño--Southern Oscillation (ENSO). Our model is governed by a differential delay equation with a single delay and periodic (seasonal) forcing. Like many of its more or less detailed and realistic precursors, this model exhibits a Devil's staircase. We study the model's structural stability, describe the mechanisms of the observed instabilities, and connect our findings to ENSO phenomenology. In the model's phase-parameter space, regions of smooth dependence on parameters alternate with rough, fractal ones. We then apply the tools of random dynamical systems and stochastic structural stability to the circle map and a torus map. The effect of noise with compact support on these maps is fairly intuitive: it is the most robust structures in phase-parameter space that survive the smoothing introduced by the noise. The nature of the stochastic forcing matters, thus suggesting that certain types of stochastic parametrizations might be better than others in achieving GCM robustness. This talk represents joint work with M. Chekroun, E. Simonnet and I. Zaliapin.

Continuum modeling of three-dimensional truss-like space structures

NASA Technical Reports Server (NTRS)

Nayfeh, A. H.; Hefzy, M. S.

1978-01-01

A mathematical and computational analysis capability has been developed for calculating the effective mechanical properties of three-dimensional periodic truss-like structures. Two models are studied in detail. The first, called the octetruss model, is a three-dimensional extension of a two-dimensional model, and the second is a cubic model. Symmetry considerations are employed as a first step to show that the specific octetruss model has four independent constants and that the cubic model has two. The actual values of these constants are determined by averaging the contributions of each rod element to the overall structure stiffness. The individual rod member contribution to the overall stiffness is obtained by a three-dimensional coordinate transformation. The analysis shows that the effective three-dimensional elastic properties of both models are relatively close to each other.

A Model for the Creation of Human-Generated Metadata within Communities

ERIC Educational Resources Information Center

Brasher, Andrew; McAndrew, Patrick

2005-01-01

This paper considers situations for which detailed metadata descriptions of learning resources are necessary, and focuses on human generation of such metadata. It describes a model which facilitates human production of good quality metadata by the development and use of structured vocabularies. Using examples, this model is applied to single and…

Structure and dynamics of human vimentin intermediate filament dimer and tetramer in explicit and implicit solvent models.

PubMed

Qin, Zhao; Buehler, Markus J

2011-01-01

Intermediate filaments, in addition to microtubules and microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells, and play an important role in mechanotransduction as well as in providing mechanical stability to cells at large stretch. The molecular structures, mechanical and dynamical properties of the intermediate filament basic building blocks, the dimer and the tetramer, however, have remained elusive due to persistent experimental challenges owing to the large size and fibrillar geometry of this protein. We have recently reported an atomistic-level model of the human vimentin dimer and tetramer, obtained through a bottom-up approach based on structural optimization via molecular simulation based on an implicit solvent model (Qin et al. in PLoS ONE 2009 4(10):e7294, 9). Here we present extensive simulations and structural analyses of the model based on ultra large-scale atomistic-level simulations in an explicit solvent model, with system sizes exceeding 500,000 atoms and simulations carried out at 20 ns time-scales. We report a detailed comparison of the structural and dynamical behavior of this large biomolecular model with implicit and explicit solvent models. Our simulations confirm the stability of the molecular model and provide insight into the dynamical properties of the dimer and tetramer. Specifically, our simulations reveal a heterogeneous distribution of the bending stiffness along the molecular axis with the formation of rather soft and highly flexible hinge-like regions defined by non-alpha-helical linker domains. We report a comparison of Ramachandran maps and the solvent accessible surface area between implicit and explicit solvent models, and compute the persistence length of the dimer and tetramer structure of vimentin intermediate filaments for various subdomains of the protein. Our simulations provide detailed insight into the dynamical properties of the vimentin dimer and tetramer intermediate filament building blocks, which may guide the development of novel coarse-grained models of intermediate filaments, and could also help in understanding assembly mechanisms.

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

Structural pierce into molecular mechanism underlying Clostridium perfringens Epsilon toxin function.

PubMed

Khalili, Saeed; Jahangiri, Abolfazl; Hashemi, Zahra Sadat; Khalesi, Bahman; Mard-Soltani, Maysam; Amani, Jafar

2017-03-01

Epsilon toxin of the Clostridium perfringens garnered a lot of attention due to its potential for toxicity in humans, extreme potency for cytotoxicity in mice and lack of any approved therapeutics prescribed for human. However, the intricacies of the Epsilon toxin action mechanism are yet to be understood. In this regard, various in silico tools have been exploited to model and refine the 3D structure of the toxin and its two receptors. The receptor proteins were embedded into designed lipid membranes within an aqueous and ionized environment. Thereafter, the modeled structures subjected to series of consecutive molecular dynamics runs to achieve the most natural like coordination for each model. Ultimately, protein-protein interaction analyses were performed to understand the probable action mechanism. The obtained results successfully confirmed the accuracy of employed methods to achieve high quality models for the toxin and its receptors within their lipid bilayers. Molecular dynamics analyses lead the structures to a more native like coordination. Moreover, the results of previous empirical studies were confirmed, while new insights for action mechanisms including the detailed roles of Hepatitis A virus cellular receptor 1 (HAVCR1) and Myelin and lymphocyte protein (MAL) proteins were achieved. In light of previous and our observations, we suggested novel models which elucidated the existing interplay between potential players of Epsilon toxin action mechanism with detailed structural evidences. These models would pave the way to have more robust understanding of the Epsilon toxin biology, more precise vaccine construction and more successful drug (inhibitor) design. Copyright © 2017 Elsevier Ltd. All rights reserved.

Are Models Easier to Understand than Code? An Empirical Study on Comprehension of Entity-Relationship (ER) Models vs. Structured Query Language (SQL) Code

ERIC Educational Resources Information Center

Sanchez, Pablo; Zorrilla, Marta; Duque, Rafael; Nieto-Reyes, Alicia

2011-01-01

Models in Software Engineering are considered as abstract representations of software systems. Models highlight relevant details for a certain purpose, whereas irrelevant ones are hidden. Models are supposed to make system comprehension easier by reducing complexity. Therefore, models should play a key role in education, since they would ease the…

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.

Permanent magnet design methodology

NASA Technical Reports Server (NTRS)

Leupold, Herbert A.

1991-01-01

Design techniques developed for the exploitation of high energy magnetically rigid materials such as Sm-Co and Nd-Fe-B have resulted in a revolution in kind rather than in degree in the design of a variety of electron guidance structures for ballistic and aerospace applications. Salient examples are listed. Several prototype models were developed. These structures are discussed in some detail: permanent magnet solenoids, transverse field sources, periodic structures, and very high field structures.

The calculation of theoretical chromospheric models and the interpretation of the solar spectrum

NASA Technical Reports Server (NTRS)

Avrett, Eugene H.

1994-01-01

Since the early 1970s we have been developing the extensive computer programs needed to construct models of the solar atmosphere and to calculate detailed spectra for use in the interpretation of solar observations. This research involves two major related efforts: work by Avrett and Loeser on the Pandora computer program for non-LTE modeling of the solar atmosphere including a wide range of physical processes, and work by Kurucz on the detailed synthesis of the solar spectrum based on opacity data for over 58 million atomic and molecular lines. Our goals are to determine models of the various features observed on the sun (sunspots, different components of quiet and active regions, and flares) by means of physically realistic models, and to calculate detailed spectra at all wavelengths that match observations of those features. These two goals are interrelated: discrepancies between calculated and observed spectra are used to determine improvements in the structure of the models, and in the detailed physical processes used in both the model calculations and the spectrum calculations. The atmospheric models obtained in this way provide not only the depth variation of various atmospheric parameters, but also a description of the internal physical processes that are responsible for nonradiative heating, and for solar activity in general.

The calculation of theoretical chromospheric models and the interpretation of solar spectra from rockets and spacecraft

NASA Technical Reports Server (NTRS)

Avrett, Eugene H.

1993-01-01

Since the early 1970s we have been developing the extensive computer programs needed to construct models of the solar atmosphere and to calculate detailed spectra for use in the interpretation of solar observations. This research involves two major related efforts: work by Avrett and Loeser on the Pandora computer program for non-LTE modeling of the solar atmosphere including a wide range of physical processes, and work by Kurucz on the detailed synthesis of the solar spectrum based on opacity data for over 58 million atomic and molecular lines. Our goals are to determine models of the various features observed on the Sun (sunspots, different components of quiet and active regions, and flares) by means of physically realistic models, and to calculate detailed spectra at all wavelengths that match observations of those features. These two goals are interrelated: discrepancies between calculated and observed spectra are used to determine improvements in the structure of the models, and in the detailed physical processes used in both the model calculations and the spectrum calculations. The atmospheric models obtained in this way provide not only the depth variation of various atmospheric parameters, but also a description of the internal physical processes that are responsible for non-radiative heating, and for solar activity in general.

The General Aggression Model.

PubMed

Allen, Johnie J; Anderson, Craig A; Bushman, Brad J

2018-02-01

The General Aggression Model (GAM) is a comprehensive, integrative, framework for understanding aggression. It considers the role of social, cognitive, personality, developmental, and biological factors on aggression. Proximate processes of GAM detail how person and situation factors influence cognitions, feelings, and arousal, which in turn affect appraisal and decision processes, which in turn influence aggressive or nonaggressive behavioral outcomes. Each cycle of the proximate processes serves as a learning trial that affects the development and accessibility of aggressive knowledge structures. Distal processes of GAM detail how biological and persistent environmental factors can influence personality through changes in knowledge structures. GAM has been applied to understand aggression in many contexts including media violence effects, domestic violence, intergroup violence, temperature effects, pain effects, and the effects of global climate change. Copyright © 2017 Elsevier Ltd. All rights reserved.

Elucidating nitric oxide synthase domain interactions by molecular dynamics.

PubMed

Hollingsworth, Scott A; Holden, Jeffrey K; Li, Huiying; Poulos, Thomas L

2016-02-01

Nitric oxide synthase (NOS) is a multidomain enzyme that catalyzes the production of nitric oxide (NO) by oxidizing L-Arg to NO and L-citrulline. NO production requires multiple interdomain electron transfer steps between the flavin mononucleotide (FMN) and heme domain. Specifically, NADPH-derived electrons are transferred to the heme-containing oxygenase domain via the flavin adenine dinucleotide (FAD) and FMN containing reductase domains. While crystal structures are available for both the reductase and oxygenase domains of NOS, to date there is no atomic level structural information on domain interactions required for the final FMN-to-heme electron transfer step. Here, we evaluate a model of this final electron transfer step for the heme-FMN-calmodulin NOS complex based on the recent biophysical studies using a 105-ns molecular dynamics trajectory. The resulting equilibrated complex structure is very stable and provides a detailed prediction of interdomain contacts required for stabilizing the NOS output state. The resulting equilibrated complex model agrees well with previous experimental work and provides a detailed working model of the final NOS electron transfer step required for NO biosynthesis. © 2015 The Protein Society.

Multipeak low-temperature behavior of specific heat capacity in frustrated magnetic systems: An exact theoretical analysis

NASA Astrophysics Data System (ADS)

Jurčišinová, E.; Jurčišin, M.

2018-05-01

We investigate in detail the process of formation of the multipeak low-temperature structure in the behavior of the specific heat capacity in frustrated magnetic systems in the framework of the exactly solvable antiferromagnetic spin-1 /2 Ising model with the multisite interaction in the presence of the external magnetic field on the kagome-like Husimi lattice. The behavior of the entropy of the model is studied and exact values of the residual entropies of all ground states are found. It is shown that the multipeak structure in the behavior of the specific heat capacity is related to the formation of the multilevel hierarchical ordering in the system of all ground states of the model. Direct relation between the maximal number of peaks in the specific heat capacity behavior and the number of independent interactions in studied frustrated magnetic system is identified. The mechanism of the formation of the multipeak structure in the specific heat capacity is described and studied in detail, and it is generalized to frustrated magnetic systems with arbitrary numbers of independent interactions.

Different structures of monoclinic martensitic phases in titanium nickelide

NASA Astrophysics Data System (ADS)

Voronin, V. I.; Naish, V. E.; Novoselova, T. V.; Pushin, V. G.; Sagaradze, I. V.

2000-03-01

The detailed theoretical and experimental analysis has been undertaken to bring to light the true structure of the monoclinic phase in titanium nickelide (NiTi). Theoretical models for such a phase have been proposed to describe the experimental data. In addition to the well-known B19‧ phase two more structures - new monoclinic M phase with Cm space group and triclinic phase with P1 space group - have been produced and analyzed in detail. Diffraction patterns have been obtained from different NiTi samples by using the neutron diffractometer IVV2 at different temperatures. From the refinement by DBWS-9411 program all these neutron patterns have been decoded successfully. The proposed new structures and stereotype B19‧ one agree with correspondent experimental data and the agreement is quite good.

A generic simulation model to assess the performance of sterilization services in health establishments.

PubMed

Di Mascolo, Maria; Gouin, Alexia

2013-03-01

The work presented here is with a view to improving performance of sterilization services in hospitals. We carried out a survey in a large number of health establishments in the Rhône-Alpes region in France. Based on the results of this survey and a detailed study of a specific service, we have built a generic model. The generic nature of the model relies on a common structure with a high level of detail. This model can be used to improve the performance of a specific sterilization service and/or to dimension its resources. It can also serve for quantitative comparison of performance indicators of various sterilization services.

Studying the Microanatomy of the Heart in Three Dimensions: A Practical Update

PubMed Central

Jarvis, Jonathan C.; Stephenson, Robert

2013-01-01

The structure and function of the heart needs to be understood in three dimensions. We give a brief historical summary of the methods by which such an understanding has been sought, and some practical details of the relatively new technique of micro-CT with iodine contrast enhancement in samples from rat and rabbit. We discuss how the improved anatomical detail available in fixed cadaveric hearts will enhance our ability to model and to understand the integrated function of the cardiomyocytes, conducting tissues, and fibrous supporting structures that generate the pumping function of the heart. PMID:24400272

Robustness of atomistic Gō models in predicting native-like folding intermediates

NASA Astrophysics Data System (ADS)

Estácio, S. G.; Fernandes, C. S.; Krobath, H.; Faísca, P. F. N.; Shakhnovich, E. I.

2012-08-01

Gō models are exceedingly popular tools in computer simulations of protein folding. These models are native-centric, i.e., they are directly constructed from the protein's native structure. Therefore, it is important to understand up to which extent the atomistic details of the native structure dictate the folding behavior exhibited by Gō models. Here we address this challenge by performing exhaustive discrete molecular dynamics simulations of a Gō potential combined with a full atomistic protein representation. In particular, we investigate the robustness of this particular type of Gō models in predicting the existence of intermediate states in protein folding. We focus on the N47G mutational form of the Spc-SH3 folding domain (x-ray structure) and compare its folding pathway with that of alternative native structures produced in silico. Our methodological strategy comprises equilibrium folding simulations, structural clustering, and principal component analysis.

Modelling and Holographic Visualization of Space Radiation-Induced DNA Damage

NASA Technical Reports Server (NTRS)

Plante, Ianik

2017-01-01

Space radiation is composed by a mixture of ions of different energies. Among these, heavy inos are of particular importance because their health effects are poorly understood. In. the recent years, a software named RITRACKS (Relativistic Ion Tracks) was developed to simulate the detailed radiation track structure, several DNA models and DNA damage. As the DNA structure is complex due to packing, it is difficult to the damage using a regular computer screen.

Creating a Structurally Realistic Finite Element Geometric Model of a Cardiomyocyte to Study the Role of Cellular Architecture in Cardiomyocyte Systems Biology.

PubMed

Rajagopal, Vijay; Bass, Gregory; Ghosh, Shouryadipta; Hunt, Hilary; Walker, Cameron; Hanssen, Eric; Crampin, Edmund; Soeller, Christian

2018-04-18

With the advent of three-dimensional (3D) imaging technologies such as electron tomography, serial-block-face scanning electron microscopy and confocal microscopy, the scientific community has unprecedented access to large datasets at sub-micrometer resolution that characterize the architectural remodeling that accompanies changes in cardiomyocyte function in health and disease. However, these datasets have been under-utilized for investigating the role of cellular architecture remodeling in cardiomyocyte function. The purpose of this protocol is to outline how to create an accurate finite element model of a cardiomyocyte using high resolution electron microscopy and confocal microscopy images. A detailed and accurate model of cellular architecture has significant potential to provide new insights into cardiomyocyte biology, more than experiments alone can garner. The power of this method lies in its ability to computationally fuse information from two disparate imaging modalities of cardiomyocyte ultrastructure to develop one unified and detailed model of the cardiomyocyte. This protocol outlines steps to integrate electron tomography and confocal microscopy images of adult male Wistar (name for a specific breed of albino rat) rat cardiomyocytes to develop a half-sarcomere finite element model of the cardiomyocyte. The procedure generates a 3D finite element model that contains an accurate, high-resolution depiction (on the order of ~35 nm) of the distribution of mitochondria, myofibrils and ryanodine receptor clusters that release the necessary calcium for cardiomyocyte contraction from the sarcoplasmic reticular network (SR) into the myofibril and cytosolic compartment. The model generated here as an illustration does not incorporate details of the transverse-tubule architecture or the sarcoplasmic reticular network and is therefore a minimal model of the cardiomyocyte. Nevertheless, the model can already be applied in simulation-based investigations into the role of cell structure in calcium signaling and mitochondrial bioenergetics, which is illustrated and discussed using two case studies that are presented following the detailed protocol.

Model tool to describe chemical structures in XML format utilizing structural fragments and chemical ontology.

PubMed

Sankar, Punnaivanam; Alain, Krief; Aghila, Gnanasekaran

2010-05-24

We have developed a model structure-editing tool, ChemEd, programmed in JAVA, which allows drawing chemical structures on a graphical user interface (GUI) by selecting appropriate structural fragments defined in a fragment library. The terms representing the structural fragments are organized in fragment ontology to provide a conceptual support. ChemEd describes the chemical structure in an XML document (ChemFul) with rich semantics explicitly encoding the details of the chemical bonding, the hybridization status, and the electron environment around each atom. The document can be further processed through suitable algorithms and with the support of external chemical ontologies to generate understandable reports about the functional groups present in the structure and their specific environment.

Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

PubMed

Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M; Schulten, Klaus; Roux, Benoît

2015-10-01

The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with the consensus model of the resting state VSD and the spin-spin distance histograms from ESR/DEER experiments on T4 lysozyme are accurately reproduced.

Data Mining of Macromolecular Structures.

PubMed

van Beusekom, Bart; Perrakis, Anastassis; Joosten, Robbie P

2016-01-01

The use of macromolecular structures is widespread for a variety of applications, from teaching protein structure principles all the way to ligand optimization in drug development. Applying data mining techniques on these experimentally determined structures requires a highly uniform, standardized structural data source. The Protein Data Bank (PDB) has evolved over the years toward becoming the standard resource for macromolecular structures. However, the process selecting the data most suitable for specific applications is still very much based on personal preferences and understanding of the experimental techniques used to obtain these models. In this chapter, we will first explain the challenges with data standardization, annotation, and uniformity in the PDB entries determined by X-ray crystallography. We then discuss the specific effect that crystallographic data quality and model optimization methods have on structural models and how validation tools can be used to make informed choices. We also discuss specific advantages of using the PDB_REDO databank as a resource for structural data. Finally, we will provide guidelines on how to select the most suitable protein structure models for detailed analysis and how to select a set of structure models suitable for data mining.

Research status of wave energy conversion (WEC) device of raft structure

NASA Astrophysics Data System (ADS)

Dong, Jianguo; Gao, Jingwei; Tao, Liang; Zheng, Peng

2017-10-01

This paper has briefly described the concept of wave energy generation and six typical conversion devices. As for raft structure, detailed analysis is provided from its development process to typical devices. Taking the design process and working principle of Plamis as an example, the general principle of raft structure is briefly described. After that, a variety of raft structure models are introduced. Finally, the advantages and disadvantages, and development trend of raft structure are pointed out.

A Cervico-Thoraco-Lumbar Multibody Dynamic Model for the Estimation of Joint Loads and Muscle Forces.

PubMed

Khurelbaatar, Tsolmonbaatar; Kim, Kyungsoo; Hyuk Kim, Yoon

2015-11-01

Computational musculoskeletal models have been developed to predict mechanical joint loads on the human spine, such as the forces and moments applied to vertebral and facet joints and the forces that act on ligaments and muscles because of difficulties in the direct measurement of joint loads. However, many whole-spine models lack certain elements. For example, the detailed facet joints in the cervical region or the whole spine region may not be implemented. In this study, a detailed cervico-thoraco-lumbar multibody musculoskeletal model with all major ligaments, separated structures of facet contact and intervertebral disk joints, and the rib cage was developed. The model was validated by comparing the intersegmental rotations, ligament tensile forces, facet joint contact forces, compressive and shear forces on disks, and muscle forces were to those reported in previous experimental and computational studies both by region (cervical, thoracic, or lumbar regions) and for the whole model. The comparisons demonstrated that our whole spine model is consistent with in vitro and in vivo experimental studies and with computational studies. The model developed in this study can be used in further studies to better understand spine structures and injury mechanisms of spinal disorders.

Magnetic basement and crustal structure in the Arabia-Eurasia collision zone from a combined gravity and magnetic model

NASA Astrophysics Data System (ADS)

Mousavi, Naeim; Ebbing, Jörg

2017-04-01

In this study, we investigate the magnetic basement and crustal structure in the region of Iran by inverse and forward modeling of aeromagnetic data and gravity data. The main focus is on the definition of the magnetic top basement. The combination of multiple shallow magnetic sources and an assumed shallow Curie isotherm depth beneath the Iranian Plateau creates a complex magnetic architecture over the area. Qualitative analysis, including pseudo gravity, wavelength filtering and upward continuation allowed a first separation of probable deep and shallow features, like the Sanandaj Sirjan zone, Urumieh Dokhtar Magmatic Assemblage, Kopet Dagh structural unit and Central Iran domain. In the second step, we apply inverse modeling to generate an estimate of the top basement geometry. The initial model was established from top basement to (a) constant depth of 25 km and (b) Moho depth. The inversion result was used as starting model for more detailed modelling in 3D to evaluate the effect of susceptibility heterogeneities in the crust. Subsequently, the model was modified with respect to tectonic and geological characterization of the region. Further modification of model in regards more details of susceptibility distribution was led to separating upper crust to different magnetic domains. In addition, we refined the top basement geometry by using terrestrial gravity observation as well. The best fitting model is consistent with the Curie isotherm depth as the base of magnetization. The Curie isotherm was derived from independent geophysical-petrological model.

EIA model documentation: World oil refining logistics demand model,``WORLD`` reference manual. Version 1.1

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

Not Available

1994-04-11

This manual is intended primarily for use as a reference by analysts applying the WORLD model to regional studies. It also provides overview information on WORLD features of potential interest to managers and analysts. Broadly, the manual covers WORLD model features in progressively increasing detail. Section 2 provides an overview of the WORLD model, how it has evolved, what its design goals are, what it produces, and where it can be taken with further enhancements. Section 3 reviews model management covering data sources, managing over-optimization, calibration and seasonality, check-points for case construction and common errors. Section 4 describes in detailmore » the WORLD system, including: data and program systems in overview; details of mainframe and PC program control and files;model generation, size management, debugging and error analysis; use with different optimizers; and reporting and results analysis. Section 5 provides a detailed description of every WORLD model data table, covering model controls, case and technology data. Section 6 goes into the details of WORLD matrix structure. It provides an overview, describes how regional definitions are controlled and defines the naming conventions for-all model rows, columns, right-hand sides, and bounds. It also includes a discussion of the formulation of product blending and specifications in WORLD. Several Appendices supplement the main sections.« less

Development and testing of a fast conceptual river water quality model.

PubMed

Keupers, Ingrid; Willems, Patrick

2017-04-15

Modern, model based river quality management strongly relies on river water quality models to simulate the temporal and spatial evolution of pollutant concentrations in the water body. Such models are typically constructed by extending detailed hydrodynamic models with a component describing the advection-diffusion and water quality transformation processes in a detailed, physically based way. This approach is too computational time demanding, especially when simulating long time periods that are needed for statistical analysis of the results or when model sensitivity analysis, calibration and validation require a large number of model runs. To overcome this problem, a structure identification method to set up a conceptual river water quality model has been developed. Instead of calculating the water quality concentrations at each water level and discharge node, the river branch is divided into conceptual reservoirs based on user information such as location of interest and boundary inputs. These reservoirs are modelled as Plug Flow Reactor (PFR) and Continuously Stirred Tank Reactor (CSTR) to describe advection and diffusion processes. The same water quality transformation processes as in the detailed models are considered but with adjusted residence times based on the hydrodynamic simulation results and calibrated to the detailed water quality simulation results. The developed approach allows for a much faster calculation time (factor 10 5 ) without significant loss of accuracy, making it feasible to perform time demanding scenario runs. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

ScrumPy: metabolic modelling with Python.

PubMed

Poolman, M G

2006-09-01

ScrumPy is a software package used for the definition and analysis of metabolic models. It is written using the Python programming language that is also used as a user interface. ScrumPy has features for both kinetic and structural modelling, but the emphasis is on structural modelling and those features of most relevance to analysis of large (genome-scale) models. The aim is at describing ScrumPy's functionality to readers with some knowledge of metabolic modelling, but implementation, programming and other computational details are omitted. ScrumPy is released under the Gnu Public Licence, and available for download from http://mudshark.brookes.ac.uk/ ScrumPy.

Multistep modeling of protein structure: application to bungarotoxin

NASA Technical Reports Server (NTRS)

Srinivasan, S.; Shibata, M.; Rein, R.

1986-01-01

Modelling of bungarotoxin in atomic details is presented in this article. The model-building procedure utilizes the low-resolution crystal coordinates of the c-alpha atoms of bungarotoxin, sequence homology within the neurotoxin family, as well as high-resolution x-ray diffraction data of cobratoxin and erabutoxin. Our model-building procedure involves: (a) principles of comparative modelling, (b) embedding procedures of distance geometry, and (c) use of molecular mechanics for optimizing packing. The model is not only consistent with the c-alpha coordinates of crystal structure, but also agrees with solution conformational features of the triple-stranded beta sheet as observed by NOE measurements.

LOD 1 VS. LOD 2 - Preliminary Investigations Into Differences in Mobile Rendering Performance

NASA Astrophysics Data System (ADS)

Ellul, C.; Altenbuchner, J.

2013-09-01

The increasing availability, size and detail of 3D City Model datasets has led to a challenge when rendering such data on mobile devices. Understanding the limitations to the usability of such models on these devices is particularly important given the broadening range of applications - such as pollution or noise modelling, tourism, planning, solar potential - for which these datasets and resulting visualisations can be utilized. Much 3D City Model data is created by extrusion of 2D topographic datasets, resulting in what is known as Level of Detail (LoD) 1 buildings - with flat roofs. However, in the UK the National Mapping Agency (the Ordnance Survey, OS) is now releasing test datasets to Level of Detail (LoD) 2 - i.e. including roof structures. These datasets are designed to integrate with the LoD 1 datasets provided by the OS, and provide additional detail in particular on larger buildings and in town centres. The availability of such integrated datasets at two different Levels of Detail permits investigation into the impact of the additional roof structures (and hence the display of a more realistic 3D City Model) on rendering performance on a mobile device. This paper describes preliminary work carried out to investigate this issue, for the test area of the city of Sheffield (in the UK Midlands). The data is stored in a 3D spatial database as triangles and then extracted and served as a web-based data stream which is queried by an App developed on the mobile device (using the Android environment, Java and OpenGL for graphics). Initial tests have been carried out on two dataset sizes, for the city centre and a larger area, rendering the data onto a tablet to compare results. Results of 52 seconds for rendering LoD 1 data, and 72 seconds for LoD 1 mixed with LoD 2 data, show that the impact of LoD 2 is significant.

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

Upper Mantle Velocity Structure beneath the Northeastern Philippine Sea Constrained by Waveform Modeling of P Triplicated Phases

NASA Astrophysics Data System (ADS)

Cho, S.; Rhie, J.; Lee, S. H.; Kim, S.; Kang, T. S.

2017-12-01

A study on the detailed velocity structures of the stagnant Pacific slab is important to understand the complex processes happening in the upper mantle. Although waveform modeling of P triplicated phases can reveal the detailed velocity structures especially for the discontinuities, the regions where the method can be applied are limited due to uneven distribution of earthquakes and stations. In this study, we used waveforms generated by two deep earthquakes near Izu-Bonin Trench and recorded by stations in South Korea. These event-station pairs are appropriate to study the upper mantle structures beneath the northeastern Philippine Sea, where no previous results by triplicated waveform modeling have been reported. In this region, the subducting Pacific slab seems to hit the 660 km discontinuity and become stagnant. We applied the reflectivity method to calculate waveforms and found the best fitting model by trial-and-error and manual inspection. In general, our best model is similar to M3.11, which is widely accepted 1D model for the regions where the stagnant slab exists and the 660 km discontinuity is depressed by the slab. The most noticeable feature of our model is that P wave velocities of inside and above the slab are considerably higher and lower than ones for M3.11, respectively. This specific velocity model is necessary to explain arrivals of two distinct phases identified in observed waveforms; one refracts inside the slab and the other reflects on the upper boundary of the slab. To understand the cause of the differences between our model and M3.11, further studies including thermal and mechanical modelling of the slab in this region will be recommended.

Detailed Geological Modelling in Urban Areas focused on Structures relevant to the Near Surface Groundwater Flow in the context of Climatic Changes

NASA Astrophysics Data System (ADS)

Bach, T.; Pallesen, T. M.; Jensen, N. P.; Mielby, S.; Sandersen, P.; Kristensen, M.

2015-12-01

This case demonstrates a practical example from the city of Odense (DK) where new geological modeling techniques has been developed and used in the software GeoScene3D, to create a detailed voxel model of the anthropogenic layer. The voxel model has been combined with a regional hydrostratigraphic layer model. The case is part of a pilot project partly financed by VTU (Foundation for Development of Technology in the Danish Water Sector) and involves many different datatypes such as borehole information, geophysical data, human related elements (landfill, pipelines, basements, roadbeds etc). In the last few years, there has been increased focus on detailed geological modeling in urban areas. The models serve as important input to hydrological models. This focus is partly due to climate changes as high intensity rainfalls are seen more often than in the past, and water recharge is a topic too. In urban areas, this arises new challenges. There is a need of a high level of detailed geological knowledge for the uppermost zone of the soil, which typically are problematic due to practically limitations, especially when using geological layer models. Furthermore, to accommodate the need of a high detail, all relevant available data has to be used in the modeling process. Human activity has deeply changed the soil layers, e.g. by constructions as roadbeds, buildings with basements, pipelines, landfill etc. These elements can act as barriers or pathways regarding surface near groundwater flow and can attribute to local flooding or mobilization and transport of contaminants etc. A geological voxel model is built by small boxes (a voxel). Each box can contain several parameters, ex. lithology, transmissivity or contaminant concentration. Human related elements can be implemented using tools, which gives the modeler advanced options for making detailed small-scale models. This case demonstrates the workflow and the resulting geological model for the pilot area.

An Exploration of the Nanoworld with LEGO Bricks

ERIC Educational Resources Information Center

Campbell, Dean J.; Miller, Josiah D.; Bannon, Stephen J.; Obermaier, Lauren M.

2011-01-01

LEGO bricks can be used for a number of demonstrations of chemical structures and properties, especially at the nanoscale level. These bricks can also be used to model instrumentation that probes these structures and properties. Detailed resources about many of these demonstrations are located on the extensive Web site "Exploring the Nanoworld…

Renormalizable group field theory beyond melonic diagrams: An example in rank four

NASA Astrophysics Data System (ADS)

Carrozza, Sylvain; Lahoche, Vincent; Oriti, Daniele

2017-09-01

We prove the renormalizability of a gauge-invariant, four-dimensional group field theory (GFT) model on SU(2), whose defining interactions correspond to necklace bubbles (found also in the context of new large-N expansions of tensor models), rather than melonic ones, which are not renormalizable in this case. The respective scaling of different interactions in the vicinity of the Gaussian fixed point is determined by the renormalization group itself. This is possible because the appropriate notion of canonical dimension of the GFT coupling constants takes into account the detailed combinatorial structure of the individual interaction terms. This is one more instance of the peculiarity (and greater mathematical richness) of GFTs with respect to ordinary local quantum field theories. We also explore the renormalization group flow of the model at the nonperturbative level, using functional renormalization group methods, and identify a nontrivial fixed point in various truncations. This model is expected to have a similar structure of divergences as the GFT models of 4D quantum gravity, thus paving the way to more detailed investigations on them.

Mechanical Properties of Nanostructured Materials Determined Through Molecular Modeling Techniques

NASA Technical Reports Server (NTRS)

Clancy, Thomas C.; Gates, Thomas S.

2005-01-01

The potential for gains in material properties over conventional materials has motivated an effort to develop novel nanostructured materials for aerospace applications. These novel materials typically consist of a polymer matrix reinforced with particles on the nanometer length scale. In this study, molecular modeling is used to construct fully atomistic models of a carbon nanotube embedded in an epoxy polymer matrix. Functionalization of the nanotube which consists of the introduction of direct chemical bonding between the polymer matrix and the nanotube, hence providing a load transfer mechanism, is systematically varied. The relative effectiveness of functionalization in a nanostructured material may depend on a variety of factors related to the details of the chemical bonding and the polymer structure at the nanotube-polymer interface. The objective of this modeling is to determine what influence the details of functionalization of the carbon nanotube with the polymer matrix has on the resulting mechanical properties. By considering a range of degree of functionalization, the structure-property relationships of these materials is examined and mechanical properties of these models are calculated using standard techniques.

Basement-involved faults and deep structures in the West Philippine Basin: constrains from gravity field

NASA Astrophysics Data System (ADS)

Wang, Gang; Jiang, Suhua; Li, Sanzhong; Zhang, Huixuan; Lei, Jianping; Gao, Song; Zhao, Feiyu

2017-06-01

To reveal the basement-involved faults and deep structures of the West Philippine Basin (WPB), the gravitational responses caused by these faults are observed and analyzed based on the latest spherical gravity model: WGM2012 Model. By mapping the free-air and Bouguer gravity anomalies, several main faults and some other linear structures are located and observed in the WPB. Then, by conducting a 2D discrete multi-scale wavelet decomposition, the Bouguer anomalies are decomposed into the first- to eighth-order detail and approximation fields (the first- to eighth-order Details and Approximations). The first- to third-order Details reflect detailed and localized geological information of the crust at different depths, and of which the higher-order reflects gravity field of the deeper depth. The first- to fourth-order Approximations represent the regional gravity fields at different depths of the crust, respectively. The fourth-order Approximation represents the regional gravity fluctuation caused by the density inhomogeneity of Moho interface. Therefore, taking the fourth-order Approximation as input, and adopting Parker-Oldenburg interactive inversion, We calculated the depth of Moho interface in the WPB. Results show that the Moho interface depth in the WPB ranges approximately from 8 to 12 km, indicating that there is typical oceanic crust in the basin. In the Urdaneta Plateau and the Benham Rise, the Moho interface depths are about 14 and 16 km, respectively, which provides a piece of evidence to support that the Banham Rise could be a transitional crust caused by a large igneous province. The second-order vertical derivative and the horizontal derivatives in direction 0° and 90° are computed based on the data of the third-order Detail, and most of the basement-involved faults and structures in the WPB, such as the Central Basin Fault Zone, the Gagua Ridge, the Luzon-Okinawa Fault Zone, and the Mindanao Fault Zone are interpreted by the gravity derivatives.

Institutional Approaches to Innovation and Change: A Review of the Esman Model of Institution Building.

ERIC Educational Resources Information Center

Bhola, H. S.

The definitional and conceptual structure of the Esman model of institution building is described in great detail, emphasizing its philosophic and process assumptions and its latent dynamics. The author systematically critiques the Esman model in terms of its (1) specificity to the universe of institution building, (2) generalizability across…

Langley's CSI evolutionary model: Phase 2

NASA Technical Reports Server (NTRS)

Horta, Lucas G.; Reaves, Mercedes C.; Elliott, Kenny B.; Belvin, W. Keith; Teter, John E.

1995-01-01

Phase 2 testbed is part of a sequence of laboratory models, developed at NASA Langley Research Center, to enhance our understanding on how to model, control, and design structures for space applications. A key problem with structures that must perform in space is the appearance of unwanted vibrations during operations. Instruments, design independently by different scientists, must share the same vehicle causing them to interact with each other. Once in space, these problems are difficult to correct and therefore, prediction via analysis design, and experiments is very important. Phase 2 laboratory model and its predecessors are designed to fill a gap between theory and practice and to aid in understanding important aspects in modeling, sensor and actuator technology, ground testing techniques, and control design issues. This document provides detailed information on the truss structure and its main components, control computer architecture, and structural models generated along with corresponding experimental results.

Optical systems integrated modeling

NASA Technical Reports Server (NTRS)

Shannon, Robert R.; Laskin, Robert A.; Brewer, SI; Burrows, Chris; Epps, Harlan; Illingworth, Garth; Korsch, Dietrich; Levine, B. Martin; Mahajan, Vini; Rimmer, Chuck

1992-01-01

An integrated modeling capability that provides the tools by which entire optical systems and instruments can be simulated and optimized is a key technology development, applicable to all mission classes, especially astrophysics. Many of the future missions require optical systems that are physically much larger than anything flown before and yet must retain the characteristic sub-micron diffraction limited wavefront accuracy of their smaller precursors. It is no longer feasible to follow the path of 'cut and test' development; the sheer scale of these systems precludes many of the older techniques that rely upon ground evaluation of full size engineering units. The ability to accurately model (by computer) and optimize the entire flight system's integrated structural, thermal, and dynamic characteristics is essential. Two distinct integrated modeling capabilities are required. These are an initial design capability and a detailed design and optimization system. The content of an initial design package is shown. It would be a modular, workstation based code which allows preliminary integrated system analysis and trade studies to be carried out quickly by a single engineer or a small design team. A simple concept for a detailed design and optimization system is shown. This is a linkage of interface architecture that allows efficient interchange of information between existing large specialized optical, control, thermal, and structural design codes. The computing environment would be a network of large mainframe machines and its users would be project level design teams. More advanced concepts for detailed design systems would support interaction between modules and automated optimization of the entire system. Technology assessment and development plans for integrated package for initial design, interface development for detailed optimization, validation, and modeling research are presented.

Interactions in the Dark Sector of Cosmology

NASA Astrophysics Data System (ADS)

Bean, Rachel

The success of modern cosmology hinges on two dramatic augmentations beyond the minimalist assumption of baryonic matter interacting gravitationally through general relativity. The first assumption is that there must exist either new gravitational dynamics or a new component of the cosmic energy budget - dark matter - that allows structure to form and accounts for weak lensing and galactic rotation curves. The second assumption is that a further dynamical modification or energy component - dark energy - exists, driving late-time cosmic acceleration. The need for these is now firmly established through a host of observations, which have raised crucial questions, and present a deep challenge to fundamental physics. The central theme of this proposal is the detailed understanding of the nature of the dark sector through the inevitable interactions between its individual components and with the visible universe. Such interactions can be crucial to a given model's viability, affecting its capability to reproduce the cosmic expansion history; the detailed predictions or structure formation; the gravitational dynamics on astrophysical and solar system scales; the stability of the microphysical model, and its ultimate consistency. While many models are consistent with cosmology on the coarsest scales, as is often the case, the devil may lie in the details. In this proposal we plan a comprehensive analysis of these details, focusing on the interactions within the dark sector and between it and visible matter, and on how these interactions affect the observational and theoretical consistency of models. Since it is unlikely that there will be a silver bullet allowing us to isolate the cause of cosmic acceleration, it is critical to develop a coherent view of the landscape of proposed models, extract clear predictions, and determine what combination of experiments and observations might allow us to test these predictions.

Problems in Catalytic Oxidation of Hydrocarbons and Detailed Simulation of Combustion Processes

NASA Astrophysics Data System (ADS)

Xin, Yuxuan

This dissertation research consists of two parts, with Part I on the kinetics of catalytic oxidation of hydrocarbons and Part II on aspects on the detailed simulation of combustion processes. In Part I, the catalytic oxidation of C1--C3 hydrocarbons, namely methane, ethane, propane and ethylene, was investigated for lean hydrocarbon-air mixtures over an unsupported Pd-based catalyst, from 600 to 800 K and under atmospheric pressure. In Chapter 2, the experimental facility of wire microcalorimetry and simulation configuration were described in details. In Chapter 3 and 4, the oxidation rate of C1--C 3 hydrocarbons is demonstrated to be determined by the dissociative adsorption of hydrocarbons. A detailed surface kinetics model is proposed with deriving the rate coefficient of hydrocarbon dissociative adsorption from the wire microcalorimetry data. In Part II, four fundamental studies were conducted through detailed combustion simulations. In Chapter 5, self-accelerating hydrogen-air flames are studied via two-dimensional detailed numerical simulation (DNS). The increase in the global flame velocity is shown to be caused by the increase of flame surface area, and the fractal structure of the flame front is demonstrated by the box-counting method. In Chapter 6, skeletal reaction models for butane combustion are derived by using directed relation graph (DRG) and DRG-aided sensitivity analysis (DRGASA), and uncertainty minimization by polynomial chaos expansion (MUM-PCE) mothodes. The dependence of model uncertainty is subjected to the completeness of the model. In Chapter 7, a systematic strategy is proposed to reduce the cost of the multicomponent diffusion model by accurately accounting for the species whose diffusivity is important to the global responses of the combustion systems, and approximating those of less importance by the mixture-averaged model. The reduced model is validated in an n-heptane mechanism with 88 species. In Chapter 8, the influence of Soret diffusion on the n-heptane/air flames is investigated numerically. In the unstretched flames, Soret diffusion primarily affects the chemical kinetics embedded in the flame structure and the net effect is small; while in the stretched flames, its impact is mainly through those of n-heptane and the secondary fuel, H2, in modifying the flame temperature, with substantial effects.

Synthesis-atomic structure-properties relationships in metallic nanoparticles by total scattering experiments and 3D computer simulations: case of Pt-Ru nanoalloy catalysts

NASA Astrophysics Data System (ADS)

Prasai, Binay; Ren, Yang; Shan, Shiyao; Zhao, Yinguang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian; Petkov, Valeri

2015-04-01

An approach to determining the 3D atomic structure of metallic nanoparticles (NPs) in fine detail and using the unique knowledge obtained for rationalizing their synthesis and properties targeted for optimization is described and exemplified on Pt-Ru alloy NPs of importance to the development of devices for clean energy conversion such as fuel cells. In particular, PtxRu100-x alloy NPs, where x = 31, 49 and 75, are synthesized by wet chemistry and activated catalytically by a post-synthesis treatment involving heating under controlled N2-H2 atmosphere. So-activated NPs are evaluated as catalysts for gas-phase CO oxidation and ethanol electro-oxidation reactions taking place in fuel cells. Both as-synthesized and activated NPs are characterized structurally by total scattering experiments involving high-energy synchrotron X-ray diffraction coupled to atomic pair distribution functions (PDFs) analysis. 3D structure models both for as-synthesized and activated NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modelling Sutton-Chen method. Models are refined against the experimental PDF data by reverse Monte Carlo simulations and analysed in terms of prime structural characteristics such as metal-to-metal bond lengths, bond angles and first coordination numbers for Pt and Ru atoms. Analysis indicates that, though of a similar type, the atomic structure of as-synthesized and respective activated NPs differ in several details of importance to NP catalytic properties. Structural characteristics of activated NPs and data for their catalytic activity are compared side by side and strong evidence found that electronic effects, indicated by significant changes in Pt-Pt and Ru-Ru metal bond lengths at NP surface, and practically unrecognized so far atomic ensemble effects, indicated by distinct stacking of atomic layers near NP surface and prevalence of particular configurations of Pt and Ru atoms in these layers, contribute to the observed enhancement of the catalytic activity of PtxRu100-x alloy NPs at x ~ 50. Implications of so-established relationships between the atomic structure and catalytic activity of Pt-Ru alloy NPs on efforts aimed at improving further the latter by tuning-up the former are discussed and the usefulness of detailed NP structure studies to advancing science and technology of metallic NPs - exemplified.An approach to determining the 3D atomic structure of metallic nanoparticles (NPs) in fine detail and using the unique knowledge obtained for rationalizing their synthesis and properties targeted for optimization is described and exemplified on Pt-Ru alloy NPs of importance to the development of devices for clean energy conversion such as fuel cells. In particular, PtxRu100-x alloy NPs, where x = 31, 49 and 75, are synthesized by wet chemistry and activated catalytically by a post-synthesis treatment involving heating under controlled N2-H2 atmosphere. So-activated NPs are evaluated as catalysts for gas-phase CO oxidation and ethanol electro-oxidation reactions taking place in fuel cells. Both as-synthesized and activated NPs are characterized structurally by total scattering experiments involving high-energy synchrotron X-ray diffraction coupled to atomic pair distribution functions (PDFs) analysis. 3D structure models both for as-synthesized and activated NPs are built by molecular dynamics simulations based on the archetypal for current theoretical modelling Sutton-Chen method. Models are refined against the experimental PDF data by reverse Monte Carlo simulations and analysed in terms of prime structural characteristics such as metal-to-metal bond lengths, bond angles and first coordination numbers for Pt and Ru atoms. Analysis indicates that, though of a similar type, the atomic structure of as-synthesized and respective activated NPs differ in several details of importance to NP catalytic properties. Structural characteristics of activated NPs and data for their catalytic activity are compared side by side and strong evidence found that electronic effects, indicated by significant changes in Pt-Pt and Ru-Ru metal bond lengths at NP surface, and practically unrecognized so far atomic ensemble effects, indicated by distinct stacking of atomic layers near NP surface and prevalence of particular configurations of Pt and Ru atoms in these layers, contribute to the observed enhancement of the catalytic activity of PtxRu100-x alloy NPs at x ~ 50. Implications of so-established relationships between the atomic structure and catalytic activity of Pt-Ru alloy NPs on efforts aimed at improving further the latter by tuning-up the former are discussed and the usefulness of detailed NP structure studies to advancing science and technology of metallic NPs - exemplified. Electronic supplementary information (ESI) available: XRD patterns, TEM and 3D structure modelling methodology. See DOI: 10.1039/c5nr00800j

Goal Structuring Notation in a Radiation Hardening Assurance Case for COTS-Based Spacecraft

NASA Technical Reports Server (NTRS)

Witulski, A.; Austin, R.; Evans, J.; Mahadevan, N.; Karsai, G.; Sierawski, B.; LaBel, K.; Reed, R.

2016-01-01

The attached presentation is a summary of how mission assurance is supported by model-based representations of spacecraft systems that can define sub-system functionality and interfacing, reliability parameters, as well as detailing a new paradigm for assurance, a model-centric and not document-centric process.

Structural dynamic testing of composite propfan blades for a cruise missile wind tunnel model

NASA Technical Reports Server (NTRS)

Elgin, Stephen D.; Sutliff, Thomas J.

1993-01-01

The Naval Weapons Center at China Lake, California is currently evaluating a counter rotating propfan system as a means of propulsion for the next generation of cruise missiles. The details and results of a structural dynamic test program are presented for scale model graphite-epoxy composite propfan blades. These blades are intended for use on a cruise missile wind tunnel model. Both dynamic characteristics and strain operating limits of the blades are presented. Complications associated with high strain level fatigue testing methods are also discussed.

Mass Conservation in Modeling Moisture Diffusion in Multi-Layer Carbon Composite Structures

NASA Technical Reports Server (NTRS)

Nurge, Mark A.; Youngquist, Robert C.; Starr, Stanley O.

2009-01-01

Moisture diffusion in multi-layer carbon composite structures is difficult to model using finite difference methods due to the discontinuity in concentrations between adjacent layers of differing materials. Applying a mass conserving approach at these boundaries proved to be effective at accurately predicting moisture uptake for a sample exposed to a fixed temperature and relative humidity. Details of the model developed are presented and compared with actual moisture uptake data gathered over 130 days from a graphite epoxy composite sandwich coupon with a Rohacell foam core.

Quadtree of TIN: a new algorithm of dynamic LOD

NASA Astrophysics Data System (ADS)

Zhang, Junfeng; Fei, Lifan; Chen, Zhen

2009-10-01

Currently, Real-time visualization of large-scale digital elevation model mainly employs the regular structure of GRID based on quadtree and triangle simplification methods based on irregular triangulated network (TIN). TIN is a refined means to express the terrain surface in the computer science, compared with GRID. However, the data structure of TIN model is complex, and is difficult to realize view-dependence representation of level of detail (LOD) quickly. GRID is a simple method to realize the LOD of terrain, but contains more triangle count. A new algorithm, which takes full advantage of the two methods' merit, is presented in this paper. This algorithm combines TIN with quadtree structure to realize the view-dependence LOD controlling over the irregular sampling point sets, and holds the details through the distance of viewpoint and the geometric error of terrain. Experiments indicate that this approach can generate an efficient quadtree triangulation hierarchy over any irregular sampling point sets and achieve dynamic and visual multi-resolution performance of large-scale terrain at real-time.

Physics Based Model for Cryogenic Chilldown and Loading. Part IV: Code Structure

NASA Technical Reports Server (NTRS)

Luchinsky, D. G.; Smelyanskiy, V. N.; Brown, B.

2014-01-01

This is the fourth report in a series of technical reports that describe separated two-phase flow model application to the cryogenic loading operation. In this report we present the structure of the code. The code consists of five major modules: (1) geometry module; (2) solver; (3) material properties; (4) correlations; and finally (5) stability control module. The two key modules - solver and correlations - are further divided into a number of submodules. Most of the physics and knowledge databases related to the properties of cryogenic two-phase flow are included into the cryogenic correlations module. The functional form of those correlations is not well established and is a subject of extensive research. Multiple parametric forms for various correlations are currently available. Some of them are included into correlations module as will be described in details in a separate technical report. Here we describe the overall structure of the code and focus on the details of the solver and stability control modules.

Structural history of Maxwell Montes, Venus: Implications for Venusian mountain belt formation

NASA Astrophysics Data System (ADS)

Keep, Myra; Hansen, Vicki L.

1994-12-01

Models for Venusian mountain belt formation are important for understanding planetary geodynamic mechanisms. A range of data sets at various scales must be considered in geodynamic modelling. Long wavelength data, such as gravity and geoid to topography ratios, need constraints from smaller-scale observations of the surface. Pre-Magellan images of the Venusian surface were not of high enough resolution to observe details of surface deformation. High-resolution Magellan images of Maxwell Montes and the other deformation belts allow us to determine the nature of surfce deformation. With these images we can begin to understand the constraints that surface deformation places on planetary dynamic models. Maxwell Montes and three other deformation belts (Akna, Freyja, and Danu montes) surround the highland plateau Lakshmi Planum in Venus, northern hemisphere. Maxwell, the highest of these belts, stands 11 km above mean planetary radius. We present a detailed structural and kinematic study of Maxwell Montes. Key observations include (1) dominant structural fabrics are broadly distributed and show little change in spacing relative to elevation changes of several kilometers; (2) the spacing, wavelength, and inferred amplitude of mapped structures are small, (3) interpreted extensional structures occur only in areas of steep slope, with no extension at the highest topographic levels; and (4) deformation terminates abruptly at the base of steep slopes. One implication of these observations is that topography is independent of thin-skinned, broadly distributed, Maxwell deformation. Maxwell is apparently stable, with no observed extensional collapse. We propose a ``deformation-from-below'' model for Maxwell, in which the crust deforms passively over structurally imbricated and thickened lower crust. This model may have implications for the other deformation belts.

Structural history of Maxwell Montes, Venus: Implications for Venusian mountain belt formation

NASA Astrophysics Data System (ADS)

Keep, Myra; Hansen, Vicki L.

1994-12-01

Models for Venusian mountain belt formation are important for understanding planetary geodynamic mechanisms. A range of data sets at various scales must be considered in geodynamic modelling. Long wavelength data, such as gravity and geoid to topography ratios, need constraints from smaller-scale observations of the surface. Pre-Magellan images of the Venusian surface were not of high enough resolution to observe details of surface deformation. High-resolution Magellan images of Maxwell Montes and the other deformation belts allow us to determine the nature of surface deformation. With these images we can begin to understand the constraints that surface deformation places on planetary dynamic models. Maxwell Montes and three other deformation belts (Akna, Freyja, and Danu montes) surround the highland plateau Lakshmi Planum in Venus' northern hemisphere. Maxwell, the highest of these belts, stands 11 km above mean planetary radius. We present a detailed structural and kinematic study of Maxwell Montes. Key observations include (1) dominant structure fabrics are broadly distributed and show little change in spacing relative to elevation changes of several kilometers; (2) the spacing, wavelength and inferred amplitude of mapped structures are small; (3) interpreted extensional structures occur only in areas of steep slope, with no extension at the highest topographic levels; and (4) deformation terminates abruptly at the base of steep slopes. One implications of these observations is that topography is independent of thin-skinned, broadly distributed, Maxwell deformation. Maxwell is apparently stable, with no observed extensional collapse. We propose a 'deformation-from-below' model for Maxwell, in which the crust deforms passively over structurally imbricated and thickened lower crust. This model may have implications for the other deformation belts.

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.

Bi-directional evolutionary structural optimization for strut-and-tie modelling of three-dimensional structural concrete

NASA Astrophysics Data System (ADS)

Shobeiri, Vahid; Ahmadi-Nedushan, Behrouz

2017-12-01

This article presents a method for the automatic generation of optimal strut-and-tie models in reinforced concrete structures using a bi-directional evolutionary structural optimization method. The methodology presented is developed for compliance minimization relying on the Abaqus finite element software package. The proposed approach deals with the generation of truss-like designs in a three-dimensional environment, addressing the design of corbels and joints as well as bridge piers and pile caps. Several three-dimensional examples are provided to show the capabilities of the proposed framework in finding optimal strut-and-tie models in reinforced concrete structures and verifying its efficiency to cope with torsional actions. Several issues relating to the use of the topology optimization for strut-and-tie modelling of structural concrete, such as chequerboard patterns, mesh-dependency and multiple load cases, are studied. In the last example, a design procedure for detailing and dimensioning of the strut-and-tie models is given according to the American Concrete Institute (ACI) 318-08 provisions.

High-resolution subject-specific mitral valve imaging and modeling: experimental and computational methods.

PubMed

Toma, Milan; Bloodworth, Charles H; Einstein, Daniel R; Pierce, Eric L; Cochran, Richard P; Yoganathan, Ajit P; Kunzelman, Karyn S

2016-12-01

The diversity of mitral valve (MV) geometries and multitude of surgical options for correction of MV diseases necessitates the use of computational modeling. Numerical simulations of the MV would allow surgeons and engineers to evaluate repairs, devices, procedures, and concepts before performing them and before moving on to more costly testing modalities. Constructing, tuning, and validating these models rely upon extensive in vitro characterization of valve structure, function, and response to change due to diseases. Micro-computed tomography ([Formula: see text]CT) allows for unmatched spatial resolution for soft tissue imaging. However, it is still technically challenging to obtain an accurate geometry of the diastolic MV. We discuss here the development of a novel technique for treating MV specimens with glutaraldehyde fixative in order to minimize geometric distortions in preparation for [Formula: see text]CT scanning. The technique provides a resulting MV geometry which is significantly more detailed in chordal structure, accurate in leaflet shape, and closer to its physiological diastolic geometry. In this paper, computational fluid-structure interaction (FSI) simulations are used to show the importance of more detailed subject-specific MV geometry with 3D chordal structure to simulate a proper closure validated against [Formula: see text]CT images of the closed valve. Two computational models, before and after use of the aforementioned technique, are used to simulate closure of the MV.

Multidisciplinary Aerodynamic-Structural Shape Optimization Using Deformation (MASSOUD)

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2000-01-01

This paper presents a multidisciplinary shape parameterization approach. The approach consists of two basic concepts: (1) parameterizing the shape perturbations rather than the geometry itself and (2) performing the shape deformation by means of the soft object animation algorithms used in computer graphics. Because the formulation presented in this paper is independent of grid topology, we can treat computational fluid dynamics and finite element grids in the same manner. The proposed approach is simple, compact, and efficient. Also, the analytical sensitivity derivatives are easily computed for use in a gradient-based optimization. This algorithm is suitable for low-fidelity (e.g., linear aerodynamics and equivalent laminate plate structures) and high-fidelity (e.g., nonlinear computational fluid dynamics and detailed finite element modeling) analysis tools. This paper contains the implementation details of parameterizing for planform, twist, dihedral, thickness, camber, and free-form surface. Results are presented for a multidisciplinary application consisting of nonlinear computational fluid dynamics, detailed computational structural mechanics, and a simple performance module.

Multidisciplinary Aerodynamic-Structural Shape Optimization Using Deformation (MASSOUD)

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2000-01-01

This paper presents a multidisciplinary shape parameterization approach. The approach consists of two basic concepts: (1) parameterizing the shape perturbations rather than the geometry itself and (2) performing the shape deformation by means of the soft object animation algorithms used in computer graphics. Because the formulation presented in this paper is independent of grid topology, we can treat computational fluid dynamics and finite element grids in a similar manner. The proposed approach is simple, compact, and efficient. Also, the analytical sensitivity derivatives are easily computed for use in a gradient-based optimization. This algorithm is suitable for low-fidelity (e.g., linear aerodynamics and equivalent laminated plate structures) and high-fidelity (e.g., nonlinear computational fluid dynamics and detailed finite element modeling analysis tools. This paper contains the implementation details of parameterizing for planform, twist, dihedral, thickness, camber, and free-form surface. Results are presented for a multidisciplinary design optimization application consisting of nonlinear computational fluid dynamics, detailed computational structural mechanics, and a simple performance module.

Vortex Filaments in Grids for Scalable, Fine Smoke Simulation.

PubMed

Meng, Zhang; Weixin, Si; Yinling, Qian; Hanqiu, Sun; Jing, Qin; Heng, Pheng-Ann

2015-01-01

Vortex modeling can produce attractive visual effects of dynamic fluids, which are widely applicable for dynamic media, computer games, special effects, and virtual reality systems. However, it is challenging to effectively simulate intensive and fine detailed fluids such as smoke with fast increasing vortex filaments and smoke particles. The authors propose a novel vortex filaments in grids scheme in which the uniform grids dynamically bridge the vortex filaments and smoke particles for scalable, fine smoke simulation with macroscopic vortex structures. Using the vortex model, their approach supports the trade-off between simulation speed and scale of details. After computing the whole velocity, external control can be easily exerted on the embedded grid to guide the vortex-based smoke motion. The experimental results demonstrate the efficiency of using the proposed scheme for a visually plausible smoke simulation with macroscopic vortex structures.

Controllable morphology of flux avalanches in microstructured superconductors

NASA Astrophysics Data System (ADS)

Motta, M.; Colauto, F.; Vestgârden, J. I.; Fritzsche, J.; Timmermans, M.; Cuppens, J.; Attanasio, C.; Cirillo, C.; Moshchalkov, V. V.; Van de Vondel, J.; Johansen, T. H.; Ortiz, W. A.; Silhanek, A. V.

2014-04-01

The morphology of abrupt bursts of magnetic flux into superconducting films with engineered periodic pinning centers (antidots) has been investigated. Guided flux avalanches of thermomagnetic origin develop a treelike structure, with the main trunk perpendicular to the borders of the sample, while secondary branches follow well-defined directions determined by the geometrical details of the underlying periodic pinning landscape. Strikingly, we demonstrate that in a superconductor with relatively weak random pinning the morphology of such flux avalanches can be fully controlled by proper combinations of lattice symmetry and antidot geometry. Moreover, the resulting flux patterns can be reproduced, to the finest details, by simulations based on a phenomenological thermomagnetic model. In turn, this model can be used to predict such complex structures and to estimate physical variables of more difficult experimental access, such as the local values of temperature and electric field.

Development of Residential Prototype Building Models and Analysis System for Large-Scale Energy Efficiency Studies Using EnergyPlus

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

Mendon, Vrushali V.; Taylor, Zachary T.

ABSTRACT: Recent advances in residential building energy efficiency and codes have resulted in increased interest in detailed residential building energy models using the latest energy simulation software. One of the challenges of developing residential building models to characterize new residential building stock is to allow for flexibility to address variability in house features like geometry, configuration, HVAC systems etc. Researchers solved this problem in a novel way by creating a simulation structure capable of creating fully-functional EnergyPlus batch runs using a completely scalable residential EnergyPlus template system. This system was used to create a set of thirty-two residential prototype buildingmore » models covering single- and multifamily buildings, four common foundation types and four common heating system types found in the United States (US). A weighting scheme with detailed state-wise and national weighting factors was designed to supplement the residential prototype models. The complete set is designed to represent a majority of new residential construction stock. The entire structure consists of a system of utility programs developed around the core EnergyPlus simulation engine to automate the creation and management of large-scale simulation studies with minimal human effort. The simulation structure and the residential prototype building models have been used for numerous large-scale studies, one of which is briefly discussed in this paper.« less

InterPred: A pipeline to identify and model protein-protein interactions.

PubMed

Mirabello, Claudio; Wallner, Björn

2017-06-01

Protein-protein interactions (PPI) are crucial for protein function. There exist many techniques to identify PPIs experimentally, but to determine the interactions in molecular detail is still difficult and very time-consuming. The fact that the number of PPIs is vastly larger than the number of individual proteins makes it practically impossible to characterize all interactions experimentally. Computational approaches that can bridge this gap and predict PPIs and model the interactions in molecular detail are greatly needed. Here we present InterPred, a fully automated pipeline that predicts and model PPIs from sequence using structural modeling combined with massive structural comparisons and molecular docking. A key component of the method is the use of a novel random forest classifier that integrate several structural features to distinguish correct from incorrect protein-protein interaction models. We show that InterPred represents a major improvement in protein-protein interaction detection with a performance comparable or better than experimental high-throughput techniques. We also show that our full-atom protein-protein complex modeling pipeline performs better than state of the art protein docking methods on a standard benchmark set. In addition, InterPred was also one of the top predictors in the latest CAPRI37 experiment. InterPred source code can be downloaded from http://wallnerlab.org/InterPred Proteins 2017; 85:1159-1170. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

High-resolution protein design with backbone freedom.

PubMed

Harbury, P B; Plecs, J J; Tidor, B; Alber, T; Kim, P S

1998-11-20

Recent advances in computational techniques have allowed the design of precise side-chain packing in proteins with predetermined, naturally occurring backbone structures. Because these methods do not model protein main-chain flexibility, they lack the breadth to explore novel backbone conformations. Here the de novo design of a family of alpha-helical bundle proteins with a right-handed superhelical twist is described. In the design, the overall protein fold was specified by hydrophobic-polar residue patterning, whereas the bundle oligomerization state, detailed main-chain conformation, and interior side-chain rotamers were engineered by computational enumerations of packing in alternate backbone structures. Main-chain flexibility was incorporated through an algebraic parameterization of the backbone. The designed peptides form alpha-helical dimers, trimers, and tetramers in accord with the design goals. The crystal structure of the tetramer matches the designed structure in atomic detail.

Bayes Forest: a data-intensive generator of morphological tree clones

PubMed Central

Järvenpää, Marko; Åkerblom, Markku; Raumonen, Pasi; Kaasalainen, Mikko

2017-01-01

Abstract Detailed and realistic tree form generators have numerous applications in ecology and forestry. For example, the varying morphology of trees contributes differently to formation of landscapes, natural habitats of species, and eco-physiological characteristics of the biosphere. Here, we present an algorithm for generating morphological tree “clones” based on the detailed reconstruction of the laser scanning data, statistical measure of similarity, and a plant growth model with simple stochastic rules. The algorithm is designed to produce tree forms, i.e., morphological clones, similar (and not identical) in respect to tree-level structure, but varying in fine-scale structural detail. Although we opted for certain choices in our algorithm, individual parts may vary depending on the application, making it a general adaptable pipeline. Namely, we showed that a specific multipurpose procedural stochastic growth model can be algorithmically adjusted to produce the morphological clones replicated from the target experimentally measured tree. For this, we developed a statistical measure of similarity (structural distance) between any given pair of trees, which allows for the comprehensive comparing of the tree morphologies by means of empirical distributions describing the geometrical and topological features of a tree. Finally, we developed a programmable interface to manipulate data required by the algorithm. Our algorithm can be used in a variety of applications for exploration of the morphological potential of the growth models (both theoretical and experimental), arising in all sectors of plant science research. PMID:29020742

Evolution of physician-hospital alignment models: a case study of comanagement.

PubMed

Sowers, Kevin W; Newman, Paul R; Langdon, Jeffrey C

2013-06-01

Recently, quality, financial, and regulatory demands have driven physicians to seek alignment opportunities with hospitals. The motivation for alignment on the part of physicians and hospitals is now accelerating because the new paradigm under healthcare reform requires an increased focus on improving quality, cost, and efficiency. We (1) identify the key drivers for physician-hospital alignment models; (2) summarize comanagement as a physician-hospital alignment model; and (3) explore a detailed case study of comanagement as an option to better align physicians with hospital goals on quality, safety, and outcomes. A Medline abstract review was performed that identified 45 references that discuss options for physician-hospital alignment. None of the articles identified provide a detailed example of successful alignment structures. A detailed case study of a successful comanagement alignment program is reviewed. The key drivers for alignment are inpatient growth rates, declining reimbursements, and the opportunity to improve quality, decrease costs, and increase efficiency. Two general strategies of alignment involve noneconomic and/or economic integration. In our example, comanagement with economic integration was chosen as the preferred structure for physician-hospital alignment. The choice of structure will vary depending on the existing relationships and governance of the hospital and the physicians in the targeted area of focus. The measure of success in building physician-hospital alignment is measured in improvements in care for the patient, reduced cost of care delivery, and improved relations between physicians and hospital leadership.

A multi-objective programming model for assessment the GHG emissions in MSW management

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

Mavrotas, George, E-mail: mavrotas@chemeng.ntua.gr; Skoulaxinou, Sotiria; Gakis, Nikos

2013-09-15

Highlights: • The multi-objective multi-period optimization model. • The solution approach for the generation of the Pareto front with mathematical programming. • The very detailed description of the model (decision variables, parameters, equations). • The use of IPCC 2006 guidelines for landfill emissions (first order decay model) in the mathematical programming formulation. - Abstract: In this study a multi-objective mathematical programming model is developed for taking into account GHG emissions for Municipal Solid Waste (MSW) management. Mathematical programming models are often used for structure, design and operational optimization of various systems (energy, supply chain, processes, etc.). The last twenty yearsmore » they are used all the more often in Municipal Solid Waste (MSW) management in order to provide optimal solutions with the cost objective being the usual driver of the optimization. In our work we consider the GHG emissions as an additional criterion, aiming at a multi-objective approach. The Pareto front (Cost vs. GHG emissions) of the system is generated using an appropriate multi-objective method. This information is essential to the decision maker because he can explore the trade-offs in the Pareto curve and select his most preferred among the Pareto optimal solutions. In the present work a detailed multi-objective, multi-period mathematical programming model is developed in order to describe the waste management problem. Apart from the bi-objective approach, the major innovations of the model are (1) the detailed modeling considering 34 materials and 42 technologies, (2) the detailed calculation of the energy content of the various streams based on the detailed material balances, and (3) the incorporation of the IPCC guidelines for the CH{sub 4} generated in the landfills (first order decay model). The equations of the model are described in full detail. Finally, the whole approach is illustrated with a case study referring to the application of the model in a Greek region.« less

Conceptual Design and Structural Optimization of NASA Environmentally Responsible Aviation (ERA) Hybrid Wing Body Aircraft

NASA Technical Reports Server (NTRS)

Quinlan, Jesse R.; Gern, Frank H.

2016-01-01

Simultaneously achieving the fuel consumption and noise reduction goals set forth by NASA's Environmentally Responsible Aviation (ERA) project requires innovative and unconventional aircraft concepts. In response, advanced hybrid wing body (HWB) aircraft concepts have been proposed and analyzed as a means of meeting these objectives. For the current study, several HWB concepts were analyzed using the Hybrid wing body Conceptual Design and structural optimization (HCDstruct) analysis code. HCDstruct is a medium-fidelity finite element based conceptual design and structural optimization tool developed to fill the critical analysis gap existing between lower order structural sizing approaches and detailed, often finite element based sizing methods for HWB aircraft concepts. Whereas prior versions of the tool used a half-model approach in building the representative finite element model, a full wing-tip-to-wing-tip modeling capability was recently added to HCDstruct, which alleviated the symmetry constraints at the model centerline in place of a free-flying model and allowed for more realistic center body, aft body, and wing loading and trim response. The latest version of HCDstruct was applied to two ERA reference cases, including the Boeing Open Rotor Engine Integration On an HWB (OREIO) concept and the Boeing ERA-0009H1 concept, and results agreed favorably with detailed Boeing design data and related Flight Optimization System (FLOPS) analyses. Following these benchmark cases, HCDstruct was used to size NASA's ERA HWB concepts and to perform a related scaling study.

A combined experimental and theoretical spectroscopic protocol for determination of the structure of heterogeneous catalysts: developing the information content of the resonance Raman spectra of M1 MoVO x .

PubMed

Kubas, Adam; Noak, Johannes; Trunschke, Annette; Schlögl, Robert; Neese, Frank; Maganas, Dimitrios

2017-09-01

Absorption and multiwavelength resonance Raman spectroscopy are widely used to investigate the electronic structure of transition metal centers in coordination compounds and extended solid systems. In combination with computational methodologies that have predictive accuracy, they define powerful protocols to study the spectroscopic response of catalytic materials. In this work, we study the absorption and resonance Raman spectra of the M1 MoVO x catalyst. The spectra were calculated by time-dependent density functional theory (TD-DFT) in conjunction with the independent mode displaced harmonic oscillator model (IMDHO), which allows for detailed bandshape predictions. For this purpose cluster models with up to 9 Mo and V metallic centers are considered to represent the bulk structure of MoVO x . Capping hydrogens were used to achieve valence saturation at the edges of the cluster models. The construction of model structures was based on a thorough bonding analysis which involved conventional DFT and local coupled cluster (DLPNO-CCSD(T)) methods. Furthermore the relationship of cluster topology to the computed spectral features is discussed in detail. It is shown that due to the local nature of the involved electronic transitions, band assignment protocols developed for molecular systems can be applied to describe the calculated spectral features of the cluster models as well. The present study serves as a reference for future applications of combined experimental and computational protocols in the field of solid-state heterogeneous catalysis.

3D basin structure of the Santa Clara Valley constrained by ambient noise tomography

NASA Astrophysics Data System (ADS)

Cho, H.; Lee, S. J.; Rhie, J.; Kim, S.

2017-12-01

The basin structure is an important factor controls the intensity and duration of ground shaking due to earthquake. Thus it is important to study the basin structure for better understanding seismic hazard and also improving the earthquake preparedness. An active source seismic survey is the most appropriate method to determine the basin structure in detail but its applicability, especially in urban areas, is limited. In this study, we tested the potential of an ambient noise tomography, which can be a cheaper and more easily applicable method compared to a traditional active source survey, to construct the velocity model of the basin. Our testing region is the Santa Clara Valley, which is one of the major urban sedimentary basins in the States. We selected this region because continuous seismic recordings and well defined velocity models are available. Continuous seismic recordings of 6 months from short-period array of Santa Clara Valley Seismic Experiment are cross-correlated with 1 hour time window. And the fast marching method and the subspace method are jointly applied to construct 2-D group velocity maps between 0.2 - 4.0 Hz. Then, shear wave velocity model of the Santa Clara Valley is calculated up to 5 km depth using bayesian inversion technique. Although our model cannot depict the detailed structures, it is roughly comparable with the velocity model of the US Geological Survey, which is constrained by active seismic surveys and field researches. This result indicate that an ambient noise tomography can be a replacement, at least in part, of an active seismic survey to construct the velocity model of the basin.

A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations

PubMed Central

Alberini, Giulio; Benfenati, Fabio

2017-01-01

Tight-junctions between epithelial cells of biological barriers are specialized molecular structures that regulate the flux of solutes across the barrier, parallel to cell walls. The tight-junction backbone is made of strands of transmembrane proteins from the claudin family, but the molecular mechanism of its function is still not completely understood. Recently, the crystal structure of a mammalian claudin-15 was reported, displaying for the first time the detailed features of transmembrane and extracellular domains. Successively, a structural model of claudin-15-based paracellular channels has been proposed, suggesting a putative assembly that illustrates how claudins associate in the same cell (via cis interactions) and across adjacent cells (via trans interactions). Although very promising, the model offers only a static conformation, with residues missing in the most important extracellular regions and potential steric clashes. Here we present detailed atomic models of paracellular single and double pore architectures, obtained from the putative assembly and refined via structural modeling and all-atom molecular dynamics simulations in double membrane bilayer and water environment. Our results show an overall stable configuration of the complex with a fluctuating pore size. Extracellular residue loops in trans interaction are able to form stable contacts and regulate the size of the pore, which displays a stationary radius of 2.5–3.0 Å at the narrowest region. The side-by-side interactions of the cis configuration are preserved via stable hydrogen bonds, already predicted by cysteine crosslinking experiments. Overall, this work introduces an improved version of the claudin-15-based paracellular channel model that strengthens its validity and that can be used in further computational studies to understand the structural features of tight-junctions regulation. PMID:28863193

Sierra/SD User's Notes.

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

Munday, Lynn Brendon; Day, David M.; Bunting, Gregory

Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a users guide to the input for Sierra/SD. Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.

Peridynamics with LAMMPS : a user guide.

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

Lehoucq, Richard B.; Silling, Stewart Andrew; Plimpton, Steven James

2008-01-01

Peridynamics is a nonlocal formulation of continuum mechanics. The discrete peridynamic model has the same computational structure as a molecular dynamic model. This document details the implementation of a discrete peridynamic model within the LAMMPS molecular dynamic code. This document provides a brief overview of the peridynamic model of a continuum, then discusses how the peridynamic model is discretized, and overviews the LAMMPS implementation. A nontrivial example problem is also included.

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.

Application of structured analysis to a telerobotic system

NASA Technical Reports Server (NTRS)

Dashman, Eric; Mclin, David; Harrison, F. W.; Soloway, Donald; Young, Steven

1990-01-01

The analysis and evaluation of a multiple arm telerobotic research and demonstration system developed by the NASA Intelligent Systems Research Laboratory (ISRL) is described. Structured analysis techniques were used to develop a detailed requirements model of an existing telerobotic testbed. Performance models generated during this process were used to further evaluate the total system. A commercial CASE tool called Teamwork was used to carry out the structured analysis and development of the functional requirements model. A structured analysis and design process using the ISRL telerobotic system as a model is described. Evaluation of this system focused on the identification of bottlenecks in this implementation. The results demonstrate that the use of structured methods and analysis tools can give useful performance information early in a design cycle. This information can be used to ensure that the proposed system meets its design requirements before it is built.

An adaptive Bayesian inversion for upper-mantle structure using surface waves and scattered body waves

NASA Astrophysics Data System (ADS)

Eilon, Zachary; Fischer, Karen M.; Dalton, Colleen A.

2018-07-01

We present a methodology for 1-D imaging of upper-mantle structure using a Bayesian approach that incorporates a novel combination of seismic data types and an adaptive parametrization based on piecewise discontinuous splines. Our inversion algorithm lays the groundwork for improved seismic velocity models of the lithosphere and asthenosphere by harnessing the recent expansion of large seismic arrays and computational power alongside sophisticated data analysis. Careful processing of P- and S-wave arrivals isolates converted phases generated at velocity gradients between the mid-crust and 300 km depth. This data is allied with ambient noise and earthquake Rayleigh wave phase velocities to obtain detailed VS and VP velocity models. Synthetic tests demonstrate that converted phases are necessary to accurately constrain velocity gradients, and S-p phases are particularly important for resolving mantle structure, while surface waves are necessary for capturing absolute velocities. We apply the method to several stations in the northwest and north-central United States, finding that the imaged structure improves upon existing models by sharpening the vertical resolution of absolute velocity profiles, offering robust uncertainty estimates, and revealing mid-lithospheric velocity gradients indicative of thermochemical cratonic layering. This flexible method holds promise for increasingly detailed understanding of the upper mantle.

An adaptive Bayesian inversion for upper mantle structure using surface waves and scattered body waves

NASA Astrophysics Data System (ADS)

Eilon, Zachary; Fischer, Karen M.; Dalton, Colleen A.

2018-04-01

We present a methodology for 1-D imaging of upper mantle structure using a Bayesian approach that incorporates a novel combination of seismic data types and an adaptive parameterisation based on piecewise discontinuous splines. Our inversion algorithm lays the groundwork for improved seismic velocity models of the lithosphere and asthenosphere by harnessing the recent expansion of large seismic arrays and computational power alongside sophisticated data analysis. Careful processing of P- and S-wave arrivals isolates converted phases generated at velocity gradients between the mid-crust and 300 km depth. This data is allied with ambient noise and earthquake Rayleigh wave phase velocities to obtain detailed VS and VP velocity models. Synthetic tests demonstrate that converted phases are necessary to accurately constrain velocity gradients, and S-p phases are particularly important for resolving mantle structure, while surface waves are necessary for capturing absolute velocities. We apply the method to several stations in the northwest and north-central United States, finding that the imaged structure improves upon existing models by sharpening the vertical resolution of absolute velocity profiles, offering robust uncertainty estimates, and revealing mid-lithospheric velocity gradients indicative of thermochemical cratonic layering. This flexible method holds promise for increasingly detailed understanding of the upper mantle.

Structural diversity in the dandelion (Taraxacum officinale) polyphenol oxidase family results in different responses to model substrates.

PubMed

Dirks-Hofmeister, Mareike E; Singh, Ratna; Leufken, Christine M; Inlow, Jennifer K; Moerschbacher, Bruno M

2014-01-01

Polyphenol oxidases (PPOs) are ubiquitous type-3 copper enzymes that catalyze the oxygen-dependent conversion of o-diphenols to the corresponding quinones. In most plants, PPOs are present as multiple isoenzymes that probably serve distinct functions, although the precise relationship between sequence, structure and function has not been addressed in detail. We therefore compared the characteristics and activities of recombinant dandelion PPOs to gain insight into the structure-function relationships within the plant PPO family. Phylogenetic analysis resolved the 11 isoenzymes of dandelion into two evolutionary groups. More detailed in silico and in vitro analyses of four representative PPOs covering both phylogenetic groups were performed. Molecular modeling and docking predicted differences in enzyme-substrate interactions, providing a structure-based explanation for grouping. One amino acid side chain positioned at the entrance to the active site (position HB2+1) potentially acts as a "selector" for substrate binding. In vitro activity measurements with the recombinant, purified enzymes also revealed group-specific differences in kinetic parameters when the selected PPOs were presented with five model substrates. The combination of our enzyme kinetic measurements and the in silico docking studies therefore indicate that the physiological functions of individual PPOs might be defined by their specific interactions with different natural substrates.

A Score of the Ability of a Three-Dimensional Protein Model to Retrieve Its Own Sequence as a Quantitative Measure of Its Quality and Appropriateness

PubMed Central

Martínez-Castilla, León P.; Rodríguez-Sotres, Rogelio

2010-01-01

Background Despite the remarkable progress of bioinformatics, how the primary structure of a protein leads to a three-dimensional fold, and in turn determines its function remains an elusive question. Alignments of sequences with known function can be used to identify proteins with the same or similar function with high success. However, identification of function-related and structure-related amino acid positions is only possible after a detailed study of every protein. Folding pattern diversity seems to be much narrower than sequence diversity, and the amino acid sequences of natural proteins have evolved under a selective pressure comprising structural and functional requirements acting in parallel. Principal Findings The approach described in this work begins by generating a large number of amino acid sequences using ROSETTA [Dantas G et al. (2003) J Mol Biol 332:449–460], a program with notable robustness in the assignment of amino acids to a known three-dimensional structure. The resulting sequence-sets showed no conservation of amino acids at active sites, or protein-protein interfaces. Hidden Markov models built from the resulting sequence sets were used to search sequence databases. Surprisingly, the models retrieved from the database sequences belonged to proteins with the same or a very similar function. Given an appropriate cutoff, the rate of false positives was zero. According to our results, this protocol, here referred to as Rd.HMM, detects fine structural details on the folding patterns, that seem to be tightly linked to the fitness of a structural framework for a specific biological function. Conclusion Because the sequence of the native protein used to create the Rd.HMM model was always amongst the top hits, the procedure is a reliable tool to score, very accurately, the quality and appropriateness of computer-modeled 3D-structures, without the need for spectroscopy data. However, Rd.HMM is very sensitive to the conformational features of the models' backbone. PMID:20830209

The Morphology and Uniformity of Circumstellar OH/H2O Masers around OH/IR Stars

NASA Astrophysics Data System (ADS)

Felli, Derek Sean

Even though low mass stars ( 8 solar masses), the more massive stars drive the chemical evolution of galaxies from which the next generation of stars and planets can form. Understanding mass loss of asymptotic giant branch stars contributes to our understanding of the chemical evolution of the galaxy, stellar populations, and star formation history. Stars with mass 8 solar masses go supernova. In both cases, these stars enrich their environments with elements heavier than simple hydrogen and helium molecules. While some general info about how stars die and form planetary nebulae are known, specific details are missing due to a lack of high-resolution observations and analysis of the intermediate stages. For example, we know that mass loss in stars creates morphologically diverse planetary nebulae, but we do not know the uniformity of these processes, and therefore lack detailed models to better predict how spherically symmetric stars form asymmetric nebulae. We have selected a specific group of late-stage stars and observed them at different scales to reveal the uniformity of mass loss through different layers close to the star. This includes observing nearby masers that trace the molecular shell structure around these stars. This study revealed detailed structure that was analyzed for uniformity to place constraints on how the mass loss processes behave in models. These results will feed into our ability to create more detailed models to better predict the chemical evolution of the next generation of stars and planets.

Soft modes in the perceptron model for jamming.

NASA Astrophysics Data System (ADS)

Franz, Silvio

I will show how a well known neural network model \\x9Dthe perceptro provides a simple solvable model of glassy behavior and jamming. The glassy minima of the energy function of this model can be studied in full analytic detail. This allows the identification of two kind of soft modes the first ones associated to the existence a marginal glass phase and a hierarchical structure of the energy landscape, the second ones associated to isostaticity and marginality of jamming. These results highlight the universality of the spectrum of normal modes in disordered systems, and open the way toward a detailed analytical understanding of the vibrational spectrum of low-temperature glasses. This work was supported by a Grant from the Simons Foundation (454941 to Silvio Franz).

Modeling Progressive Failure of Bonded Joints Using a Single Joint Finite Element

NASA Technical Reports Server (NTRS)

Stapleton, Scott E.; Waas, Anthony M.; Bednarcyk, Brett A.

2010-01-01

Enhanced finite elements are elements with an embedded analytical solution which can capture detailed local fields, enabling more efficient, mesh-independent finite element analysis. In the present study, an enhanced finite element is applied to generate a general framework capable of modeling an array of joint types. The joint field equations are derived using the principle of minimum potential energy, and the resulting solutions for the displacement fields are used to generate shape functions and a stiffness matrix for a single joint finite element. This single finite element thus captures the detailed stress and strain fields within the bonded joint, but it can function within a broader structural finite element model. The costs associated with a fine mesh of the joint can thus be avoided while still obtaining a detailed solution for the joint. Additionally, the capability to model non-linear adhesive constitutive behavior has been included within the method, and progressive failure of the adhesive can be modeled by using a strain-based failure criteria and re-sizing the joint as the adhesive fails. Results of the model compare favorably with experimental and finite element results.

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.

PubMed

Molloy, Kevin; Shehu, Amarda

2013-01-01

Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajectories is central to understanding the relationship between protein dynamics and function. Computational approaches that build on the Molecular Dynamics framework are in principle able to model transition trajectories at great detail but also at considerable computational cost. Methods that delay consideration of dynamics and focus instead on elucidating energetically-credible conformational paths connecting two functionally-relevant structures provide a complementary approach. Effective sampling-based path planning methods originating in robotics have been recently proposed to produce conformational paths. These methods largely model short peptides or address large proteins by simplifying conformational space. We propose a robotics-inspired method that connects two given structures of a protein by sampling conformational paths. The method focuses on small- to medium-size proteins, efficiently modeling structural deformations through the use of the molecular fragment replacement technique. In particular, the method grows a tree in conformational space rooted at the start structure, steering the tree to a goal region defined around the goal structure. We investigate various bias schemes over a progress coordinate for balance between coverage of conformational space and progress towards the goal. A geometric projection layer promotes path diversity. A reactive temperature scheme allows sampling of rare paths that cross energy barriers. Experiments are conducted on small- to medium-size proteins of length up to 214 amino acids and with multiple known functionally-relevant states, some of which are more than 13Å apart of each-other. Analysis reveals that the method effectively obtains conformational paths connecting structural states that are significantly different. A detailed analysis on the depth and breadth of the tree suggests that a soft global bias over the progress coordinate enhances sampling and results in higher path diversity. The explicit geometric projection layer that biases the exploration away from over-sampled regions further increases coverage, often improving proximity to the goal by forcing the exploration to find new paths. The reactive temperature scheme is shown effective in increasing path diversity, particularly in difficult structural transitions with known high-energy barriers.

Elastomeric Structural Attachment Concepts for Aircraft Flap Noise Reduction - Challenges and Approaches to Hyperelastic Structural Modeling and Analysis

NASA Technical Reports Server (NTRS)

Sreekantamurthy, Thammaiah; Turner, Travis L.; Moore, James B.; Su, Ji

2014-01-01

Airframe noise is a significant part of the overall noise of transport aircraft during the approach and landing phases of flight. Airframe noise reduction is currently emphasized under the Environmentally Responsible Aviation (ERA) and Fixed Wing (FW) Project goals of NASA. A promising concept for trailing-edge-flap noise reduction is a flexible structural element or link that connects the side edges of the deployable flap to the adjacent main-wing structure. The proposed solution is distinguished by minimization of the span-wise extent of the structural link, thereby minimizing the aerodynamic load on the link structure at the expense of increased deformation requirement. Development of such a flexible structural link necessitated application of hyperelastic materials, atypical structural configurations and novel interface hardware. The resulting highly-deformable structural concept was termed the FLEXible Side Edge Link (FLEXSEL) concept. Prediction of atypical elastomeric deformation responses from detailed structural analysis was essential for evaluating feasible concepts that met the design constraints. The focus of this paper is to describe the many challenges encountered with hyperelastic finite element modeling and the nonlinear structural analysis of evolving FLEXSEL concepts. Detailed herein is the nonlinear analysis of FLEXSEL concepts that emerged during the project which include solid-section, foamcore, hollow, extended-span and pre-stressed concepts. Coupon-level analysis performed on elastomeric interface joints, which form a part of the FLEXSEL topology development, are also presented.

Structure-guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm.

PubMed

Maximova, Tatiana; Plaku, Erion; Shehu, Amarda

2016-07-07

Proteins are macromolecules in perpetual motion, switching between structural states to modulate their function. A detailed characterization of the precise yet complex relationship between protein structure, dynamics, and function requires elucidating transitions between functionally-relevant states. Doing so challenges both wet and dry laboratories, as protein dynamics involves disparate temporal scales. In this paper we present a novel, sampling-based algorithm to compute transition paths. The algorithm exploits two main ideas. First, it leverages known structures to initialize its search and define a reduced conformation space for rapid sampling. This is key to address the insufficient sampling issue suffered by sampling-based algorithms. Second, the algorithm embeds samples in a nearest-neighbor graph where transition paths can be efficiently computed via queries. The algorithm adapts the probabilistic roadmap framework that is popular in robot motion planning. In addition to efficiently computing lowest-cost paths between any given structures, the algorithm allows investigating hypotheses regarding the order of experimentally-known structures in a transition event. This novel contribution is likely to open up new venues of research. Detailed analysis is presented on multiple-basin proteins of relevance to human disease. Multiscaling and the AMBER ff14SB force field are used to obtain energetically-credible paths at atomistic detail.

Shape control of large space structures

NASA Technical Reports Server (NTRS)

Hagan, M. T.

1982-01-01

A survey has been conducted to determine the types of control strategies which have been proposed for controlling the vibrations in large space structures. From this survey several representative control strategies were singled out for detailed analyses. The application of these strategies to a simplified model of a large space structure has been simulated. These simulations demonstrate the implementation of the control algorithms and provide a basis for a preliminary comparison of their suitability for large space structure control.

Perceptual category learning and visual processing: An exercise in computational cognitive neuroscience.

PubMed

Cantwell, George; Riesenhuber, Maximilian; Roeder, Jessica L; Ashby, F Gregory

2017-05-01

The field of computational cognitive neuroscience (CCN) builds and tests neurobiologically detailed computational models that account for both behavioral and neuroscience data. This article leverages a key advantage of CCN-namely, that it should be possible to interface different CCN models in a plug-and-play fashion-to produce a new and biologically detailed model of perceptual category learning. The new model was created from two existing CCN models: the HMAX model of visual object processing and the COVIS model of category learning. Using bitmap images as inputs and by adjusting only a couple of learning-rate parameters, the new HMAX/COVIS model provides impressively good fits to human category-learning data from two qualitatively different experiments that used different types of category structures and different types of visual stimuli. Overall, the model provides a comprehensive neural and behavioral account of basal ganglia-mediated learning. Copyright © 2017 Elsevier Ltd. All rights reserved.

Anisotropy of fluctuation dynamics of proteins with an elastic network model.

PubMed Central

Atilgan, A R; Durell, S R; Jernigan, R L; Demirel, M C; Keskin, O; Bahar, I

2001-01-01

Fluctuations about the native conformation of proteins have proven to be suitably reproduced with a simple elastic network model, which has shown excellent agreement with a number of different properties for a wide variety of proteins. This scalar model simply investigates the magnitudes of motion of individual residues in the structure. To use the elastic model approach further for developing the details of protein mechanisms, it becomes essential to expand this model to include the added details of the directions of individual residue fluctuations. In this paper a new tool is presented for this purpose and applied to the retinol-binding protein, which indicates enhanced flexibility in the region of entry to the ligand binding site and for the portion of the protein binding to its carrier protein. PMID:11159421

3D Simulations of Convection: From the Sun Toward Evolved Stars

NASA Astrophysics Data System (ADS)

Höfner, Susanne

2018-04-01

Basic physical considerations and detailed numerical simulations predict a dramatic increase in the sizes of convection cells during late phases of stellar evolution. The recent progress in high-angular-resolution techniques has made it possible to observe surface structures on several nearby giants and supergiants for a wide range of wavelengths. Such observations provide much-needed checkpoints for convection theory, in addition to the detailed comparisons of models and observations for the sun. In this talk I will give an overview of current 3D convection models for different types of stars and discuss related observable phenomena.

The structure and dipole moment of globular proteins in solution and crystalline states: use of NMR and X-ray databases for the numerical calculation of dipole moment.

PubMed

Takashima, S

2001-04-05

The large dipole moment of globular proteins has been well known because of the detailed studies using dielectric relaxation and electro-optical methods. The search for the origin of these dipolemoments, however, must be based on the detailed knowledge on protein structure with atomic resolutions. At present, we have two sources of information on the structure of protein molecules: (1) x-ray databases obtained in crystalline state; (2) NMR databases obtained in solution state. While x-ray databases consist of only one model, NMR databases, because of the fluctuation of the protein folding in solution, consist of a number of models, thus enabling the computation of dipole moment repeated for all these models. The aim of this work, using these databases, is the detailed investigation on the interdependence between the structure and dipole moment of protein molecules. The dipole moment of protein molecules has roughly two components: one dipole moment is due to surface charges and the other, core dipole moment, is due to polar groups such as N--H and C==O bonds. The computation of surface charge dipole moment consists of two steps: (A) calculation of the pK shifts of charged groups for electrostatic interactions and (B) calculation of the dipole moment using the pK corrected for electrostatic shifts. The dipole moments of several proteins were computed using both NMR and x-ray databases. The dipole moments of these two sets of calculations are, with a few exceptions, in good agreement with one another and also with measured dipole moments.

Modelling of double air-bridged structured inductor implemented by a GaAs integrated passive device manufacturing process

NASA Astrophysics Data System (ADS)

Li, Yang; Yao, Zhao; Zhang, Chun-Wei; Fu, Xiao-Qian; Li, Zhi-Ming; Li, Nian-Qiang; Wang, Cong

2017-05-01

In order to provide excellent performance and show the development of a complicated structure in a module and system, this paper presents a double air-bridge-structured symmetrical differential inductor based on integrated passive device technology. Corresponding to the proposed complicated structure, a new manufacturing process fabricated on a high-resistivity GaAs substrate is described in detail. Frequency-independent physical models are presented with lump elements and the results of skin effect-based measurements. Finally, some key features of the inductor are compared; good agreement between the measurements and modeled circuit fully verifies the validity of the proposed modeling approach. Meanwhile, we also present a comparison of different coil turns for inductor performance. The proposed work can provide a good solution for the design, fabrication, modeling, and practical application of radio-frequency modules and systems.

29 CFR 1926.1000 - Rollover protective structures (ROPS) for material handling equipment.

Code of Federal Regulations, 2013 CFR

2013-07-01

... two times the weight of the prime mover applied at the point of impact. (i) The design objective shall..., if any; (3) Machine make, model, or series number that the structure is designed to fit. (f) Machines... performance criteria detailed in §§ 1926.1001 and 1926.1002, as applicable or shall be designed, fabricated...

29 CFR 1926.1000 - Rollover protective structures (ROPS) for material handling equipment.

Code of Federal Regulations, 2010 CFR

2010-07-01

... two times the weight of the prime mover applied at the point of impact. (i) The design objective shall..., if any; (3) Machine make, model, or series number that the structure is designed to fit. (f) Machines... performance criteria detailed in §§ 1926.1001 and 1926.1002, as applicable or shall be designed, fabricated...

29 CFR 1926.1000 - Rollover protective structures (ROPS) for material handling equipment.

Code of Federal Regulations, 2014 CFR

2014-07-01

... two times the weight of the prime mover applied at the point of impact. (i) The design objective shall..., if any; (3) Machine make, model, or series number that the structure is designed to fit. (f) Machines... performance criteria detailed in §§ 1926.1001 and 1926.1002, as applicable or shall be designed, fabricated...

29 CFR 1926.1000 - Rollover protective structures (ROPS) for material handling equipment.

Code of Federal Regulations, 2011 CFR

2011-07-01

... two times the weight of the prime mover applied at the point of impact. (i) The design objective shall..., if any; (3) Machine make, model, or series number that the structure is designed to fit. (f) Machines... performance criteria detailed in §§ 1926.1001 and 1926.1002, as applicable or shall be designed, fabricated...

29 CFR 1926.1000 - Rollover protective structures (ROPS) for material handling equipment.

Code of Federal Regulations, 2012 CFR

2012-07-01

... two times the weight of the prime mover applied at the point of impact. (i) The design objective shall..., if any; (3) Machine make, model, or series number that the structure is designed to fit. (f) Machines... performance criteria detailed in §§ 1926.1001 and 1926.1002, as applicable or shall be designed, fabricated...

Modeling a ball screw/ball nut in substructuring

NASA Technical Reports Server (NTRS)

Butler, Thomas G.

1991-01-01

In the particular NASTRAN application discussed here, a nut was attached to a stationary structure. The object of the analysis was to determine the vibration characteristics of the whole structure for various configurations; i.e., the evaluation of the mode shapes and frequencies when parts were moved to different mating positions. Details of the analysis are given.

Make Your Own Working Models of Heart Valves!

ERIC Educational Resources Information Center

Hudson, Margaret L.

2014-01-01

Heart valves play a vital role in efficient circulation of the blood, and the details of their physical structure are related crucially to their function. However, it can be challenging for the learner to make the mental connection between anatomical structures of valves and the changing pressure gradients that the valves experience and come to an…

Computer Program Re-layers Engineering Drawings

NASA Technical Reports Server (NTRS)

Crosby, Dewey C., III

1990-01-01

RULCHK computer program aids in structuring layers of information pertaining to part or assembly designed with software described in article "Software for Drawing Design Details Concurrently" (MFS-28444). Checks and optionally updates structure of layers for part. Enables designer to construct model and annotate its documentation without burden of manually layering part to conform to standards at design time.

Kinetics and mechanism of soot formation in hydrocarbon combustion

NASA Technical Reports Server (NTRS)

Frenklach, Michael

1990-01-01

The focus of this work was on kinetic modeling. The specific objectives were: detailed modeling of soot formation in premixed flames, elucidation of the effects of fuel structure on the pathway to soot, and the development of a numerical technique for accurate modeling of soot particle coagulation and surface growth. Those tasks were successfully completed and are briefly summarized.

Impact of Machine-Translated Text on Entity and Relationship Extraction

DTIC Science & Technology

2014-12-01

20 1 1. Introduction Using social network analysis tools is an important asset in...semantic modeling software to automatically build detailed network models from unstructured text. Contour imports unstructured text and then maps the text...onto an existing ontology of frames at the sentence level, using FrameNet, a structured language model, and through Semantic Role Labeling ( SRL

Structural modeling and optimization of a joined-wing configuration of a High-Altitude Long-Endurance (HALE) aircraft

NASA Astrophysics Data System (ADS)

Kaloyanova, Valentina B.

Recent research trends have indicated an interest in High-Altitude, Long-Endurance (HALE) aircraft as a low-cost alternative to certain space missions, such as telecommunication relay, environmental sensing and military reconnaissance. HALE missions require a light vehicle flying at low speed in the stratosphere at altitudes of 60,000-80,000 ft, with a continuous loiter time of up to several days. To provide high lift and low drag at these high altitudes, where the air density is low, the wing area should be increased, i.e., high-aspect-ratio wings are necessary. Due to its large span and lightweight, the wing structure is very flexible. To reduce the structural deformation, and increase the total lift in a long-spanned wing, a sensorcraft model with a joined-wing configuration, proposed by AFRL, is employed. The joined-wing encompasses a forward wing, which is swept back with a positive dihedral angle, and connected with an aft wing, which is swept forward. The joined-wing design combines structural strength, high aerodynamic performance and efficiency. As a first step to study the joined-wing structural behavior an 1-D approximation model is developed. The 1-D approximation is a simple structural model created using ANSYS BEAM4 elements to present a possible approach for the aerodynamics-structure coupling. The pressure loads from the aerodynamic analysis are integrated numerically to obtain the resultant aerodynamic forces and moments (spanwise lift and pitching moment distributions, acting at the aerodynamic center). These are applied on the 1-D structural model. A linear static analysis is performed under this equivalent load, and the deformed shape of the 1-D model is used to obtain the deformed shape of the actual 3-D joined wing, i.e. deformed aerodynamic surface grid. To date in the existing studies, only simplified structural models have been examined. In the present work, in addition to the simple 1-D beam model, a semi-monocoque structural model is developed. All stringers, skin panels, ribs and spars are represented by appropriate elements in a finite-element model. Also, the model accounts for the fuel weight and sensorcraft antennae housed within the wings. Linear and nonlinear static analyses under the aerodynamic load are performed. The stress distribution in the wing as well as deformation is explored. Starting with a structural model with uniform mass distribution, a design optimization is performed to achieve a fully stressed design. As the joined-wing structure is prone to buckling, after the design optimization is complete linear and nonlinear bucking analyses are performed to study the global joined-wing structural instability, the load magnitude at which it is expected to occur, and the buckling mode. The buckled shape of the aft wing (which is subjected to compression) is found to resemble that of a fixed-pinned column. The linear buckling analysis overestimates the buckling load. However, even the nonlinear buckling analysis results in a load factor higher than 3, i.e. the wing structure is buckling safe under its current loading conditions. As the region of the joint has a very complicated geometry that has adverse effects in the flow and stress behavior an independent, more finely meshed model (submodel) of the joint region is generated and analyzed. A detailed discussion of the stress distribution obtained in the joint region via the submodeling technique is presented in this study as well. It is found out that compared to its structural response, the joint adverse effects are much more pronounced in its aerodynamic response, so it is suggested for future studies the geometry of the joint to be optimized based on its aerodynamic performance. As this design and analysis study is aimed towards developing a realistic structural representation of the innovative joined-wing configuration, in addition to the "global", or upper-level optimization, a local level design optimization is performed as well. At the lower (local) level detailed models of wing structural panels are used to compute more complex failure modes and to design the details that are not included in the upper (global) level model. Proper coordination between local skin-stringer panel models and the global joined-wing model prevents inconsistency between the upper- (global) and lower- (local) level design models. (Abstract shortened by UMI.)

Detailed low-energy electron diffraction analysis of the (4×4) surface structure of C60 on Cu(111): Seven-atom-vacancy reconstruction

NASA Astrophysics Data System (ADS)

Xu, Geng; Shi, Xing-Qiang; Zhang, R. Q.; Pai, Woei Wu; Jeng, H. T.; Van Hove, M. A.

2012-08-01

A detailed and exhaustive structural analysis by low-energy electron diffraction (LEED) is reported for the C60-induced reconstruction of Cu(111), in the system Cu(111) + (4 × 4)-C60. A wide LEED energy range allows enhanced sensitivity to the crucial C60-metal interface that is buried below the 7-Å-thick molecular layer. The analysis clearly favors a seven-Cu-atom vacancy model (with Pendry R-factor Rp = 0.376) over a one-Cu-atom vacancy model (Rp = 0.608) and over nonreconstructed models (Rp = 0.671 for atop site and Rp = 0.536 for hcp site). The seven-Cu-atom vacancy forms a (4 × 4) lattice of bowl-like holes. In each hole, a C60 molecule can nestle by forming strong bonds (shorter than 2.30 Å) between 15 C atoms of the molecule and 12 Cu atoms of the outermost and second Cu layers.

Simulation Study of Structure and Properties of Plasma Liners for the PLX- α Project

NASA Astrophysics Data System (ADS)

Samulyak, Roman; Shih, Wen; Hsu, Scott; PLX-Alpha Team

2017-10-01

Detailed numerical studies of the propagation and merger of high-Mach-number plasma jets and the formation and implosion of plasma liners have been performed using the FronTier code in support of the Plasma Liner Experiment-ALPHA (PLX- α) project. Physics models include radiation, physical diffusion, plasma-EOS models, and an anisotropic diffusion model that mimics deviations from fully collisional hydrodynamics in outer layers of plasma jets. Detailed structure and non-uniformity of plasma liners of due to primary and secondary shock waves have been studies as well as averaged quantities of ram pressure and Mach number. Synthetic data from simulations have been compared with available experimental data from a multi-chord interferometer and survey and high-resolution spectrometers. Numerical studies of the sensitivity of liner properties to experimental errors in the initial masses of jets and the synchronization of plasma gun valves have also been performed. Supported by the ARPA-E ALPHA program.

Micro-structurally detailed model of a therapeutic hydrogel injectate in a rat biventricular cardiac geometry for computational simulations

PubMed Central

Sirry, Mazin S.; Davies, Neil H.; Kadner, Karen; Dubuis, Laura; Saleh, Muhammad G.; Meintjes, Ernesta M.; Spottiswoode, Bruce S.; Zilla, Peter; Franz, Thomas

2013-01-01

Biomaterial injection based therapies have showed cautious success in restoration of cardiac function and prevention of adverse remodelling into heart failure after myocardial infarction (MI). However, the underlying mechanisms are not well understood. Computational studies utilised simplified representations of the therapeutic myocardial injectates. Wistar rats underwent experimental infarction followed by immediate injection of polyethylene glycol hydrogel in the infarct region. Hearts were explanted, cryo-sectioned and the region with the injectate histologically analysed. Histological micrographs were used to reconstruct the dispersed hydrogel injectate. Cardiac magnetic resonance imaging (CMRI) data from a healthy rat were used to obtain an end-diastolic biventricular geometry which was subsequently adjusted and combined with the injectate model. The computational geometry of the injectate exhibited microscopic structural details found the in situ. The combination of injectate and cardiac geometry provides realistic geometries for multiscale computational studies of intra-myocardial injectate therapies for the rat model that has been widely used for MI research. PMID:23682845

Memory-efficient RNA energy landscape exploration

PubMed Central

Mann, Martin; Kucharík, Marcel; Flamm, Christoph; Wolfinger, Michael T.

2014-01-01

Motivation: Energy landscapes provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions. Higher abstraction levels based on a macro-state decomposition of the landscape enable the study of larger systems; however, they are still restricted by huge memory requirements of exact approaches. Results: We present a highly parallelizable local enumeration scheme that enables the computation of exact macro-state transition models with highly reduced memory requirements. The approach is evaluated on RNA secondary structure landscapes using a gradient basin definition for macro-states. Furthermore, we demonstrate the need for exact transition models by comparing two barrier-based approaches, and perform a detailed investigation of gradient basins in RNA energy landscapes. Availability and implementation: Source code is part of the C++ Energy Landscape Library available at http://www.bioinf.uni-freiburg.de/Software/. Contact: mmann@informatik.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24833804

Introducing DeBRa: a detailed breast model for radiological studies

NASA Astrophysics Data System (ADS)

Ma, Andy K. W.; Gunn, Spencer; Darambara, Dimitra G.

2009-07-01

Currently, x-ray mammography is the method of choice in breast cancer screening programmes. As the mammography technology moves from 2D imaging modalities to 3D, conventional computational phantoms do not have sufficient detail to support the studies of these advanced imaging systems. Studies of these 3D imaging systems call for a realistic and sophisticated computational model of the breast. DeBRa (Detailed Breast model for Radiological studies) is the most advanced, detailed, 3D computational model of the breast developed recently for breast imaging studies. A DeBRa phantom can be constructed to model a compressed breast, as in film/screen, digital mammography and digital breast tomosynthesis studies, or a non-compressed breast as in positron emission mammography and breast CT studies. Both the cranial-caudal and mediolateral oblique views can be modelled. The anatomical details inside the phantom include the lactiferous duct system, the Cooper ligaments and the pectoral muscle. The fibroglandular tissues are also modelled realistically. In addition, abnormalities such as microcalcifications, irregular tumours and spiculated tumours are inserted into the phantom. Existing sophisticated breast models require specialized simulation codes. Unlike its predecessors, DeBRa has elemental compositions and densities incorporated into its voxels including those of the explicitly modelled anatomical structures and the noise-like fibroglandular tissues. The voxel dimensions are specified as needed by any study and the microcalcifications are embedded into the voxels so that the microcalcification sizes are not limited by the voxel dimensions. Therefore, DeBRa works with general-purpose Monte Carlo codes. Furthermore, general-purpose Monte Carlo codes allow different types of imaging modalities and detector characteristics to be simulated with ease. DeBRa is a versatile and multipurpose model specifically designed for both x-ray and γ-ray imaging studies.

Geotechnical centrifuge use at University of Cambridge Geotechnical Centre, August-September 1991

NASA Astrophysics Data System (ADS)

Gilbert, Paul A.

1992-01-01

A geotechnical centrifuge applies elevated acceleration to small-scale soil models to simulate body forces and stress levels characteristic of full-size soil structures. Since the constitutive behavior of soil is stress level development, the centrifuge offers considerable advantage in studying soil structures using models. Several experiments were observed and described in relative detail, including experiments in soil dynamics and liquefaction study, an experiment investigation leaning towers on soft foundations, and an experiment investigating migration of hot pollutants through soils.

Modeling protein structure at near atomic resolutions with Gorgon.

PubMed

Baker, Matthew L; Abeysinghe, Sasakthi S; Schuh, Stephen; Coleman, Ross A; Abrams, Austin; Marsh, Michael P; Hryc, Corey F; Ruths, Troy; Chiu, Wah; Ju, Tao

2011-05-01

Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure. Copyright © 2011 Elsevier Inc. All rights reserved.

Modified chloride diffusion model for concrete under the coupling effect of mechanical load and chloride salt environment

NASA Astrophysics Data System (ADS)

Lei, Mingfeng; Lin, Dayong; Liu, Jianwen; Shi, Chenghua; Ma, Jianjun; Yang, Weichao; Yu, Xiaoniu

2018-03-01

For the purpose of investigating lining concrete durability, this study derives a modified chloride diffusion model for concrete based on the odd continuation of boundary conditions and Fourier transform. In order to achieve this, the linear stress distribution on a sectional structure is considered, detailed procedures and methods are presented for model verification and parametric analysis. Simulation results show that the chloride diffusion model can reflect the effects of linear stress distribution of the sectional structure on the chloride diffusivity with reliable accuracy. Along with the natural environmental characteristics of practical engineering structures, reference value ranges of model parameters are provided. Furthermore, a chloride diffusion model is extended for the consideration of multi-factor coupling of linear stress distribution, chloride concentration and diffusion time. Comparison between model simulation and typical current research results shows that the presented model can produce better considerations with a greater universality.

Combining 3d Volume and Mesh Models for Representing Complicated Heritage Buildings

NASA Astrophysics Data System (ADS)

Tsai, F.; Chang, H.; Lin, Y.-W.

2017-08-01

This study developed a simple but effective strategy to combine 3D volume and mesh models for representing complicated heritage buildings and structures. The idea is to seamlessly integrate 3D parametric or polyhedral models and mesh-based digital surfaces to generate a hybrid 3D model that can take advantages of both modeling methods. The proposed hybrid model generation framework is separated into three phases. Firstly, after acquiring or generating 3D point clouds of the target, these 3D points are partitioned into different groups. Secondly, a parametric or polyhedral model of each group is generated based on plane and surface fitting algorithms to represent the basic structure of that region. A "bare-bones" model of the target can subsequently be constructed by connecting all 3D volume element models. In the third phase, the constructed bare-bones model is used as a mask to remove points enclosed by the bare-bones model from the original point clouds. The remaining points are then connected to form 3D surface mesh patches. The boundary points of each surface patch are identified and these boundary points are projected onto the surfaces of the bare-bones model. Finally, new meshes are created to connect the projected points and original mesh boundaries to integrate the mesh surfaces with the 3D volume model. The proposed method was applied to an open-source point cloud data set and point clouds of a local historical structure. Preliminary results indicated that the reconstructed hybrid models using the proposed method can retain both fundamental 3D volume characteristics and accurate geometric appearance with fine details. The reconstructed hybrid models can also be used to represent targets in different levels of detail according to user and system requirements in different applications.

Fluorescence probing of T box antiterminator RNA: Insights into riboswitch discernment of the tRNA discriminator base

PubMed Central

Means, John A.; Simson, Crystal M.; Zhou, Shu; Rachford, Aaron A.; Rack, Jeffrey J.; Hines, Jennifer V.

2009-01-01

The T box transcription antitermination riboswitch is one of the main regulatory mechanisms utilized by Gram-positive bacteria to regulate genes that are involved in amino acid metabolism. The details of the antitermination event, including the role that Mg2+ plays, in this riboswitch have not been completely elucidated. In these studies, details of the antitermination event were investigated utilizing 2-aminopurine to monitor structural changes of a model antiterminator RNA when it was bound to model tRNA. Based on the results of these fluorescence studies, the model tRNA binds the model antiterminator RNA via an induced fit. This binding is enhanced by the presence of Mg2+, facilitating the complete base pairing of the model tRNA acceptor end with the complementary bases in the model antiterminator bulge. PMID:19755116

The Cognitive Spiral: Creative Thinking and Cognitive Processing.

ERIC Educational Resources Information Center

Ebert, Edward S., II

1994-01-01

The lack of a common understanding of the construct of creative thinking is noted, and the cognitive spiral model is presented, which conceptualizes creative thinking as an integral component of all cognitive processing. This article details the synthesis of a definition and the structure of a model of cognitive processing. (Author/DB)

A Critical Comparison of Psychometric Models for Measuring Achievement. Methodology Project.

ERIC Educational Resources Information Center

Choppin, Bruce; And Others

A detailed description of five latent structure models of achievement measurement is presented. The first project paper, by David L. McArthur, analyzes the history of mental testing to show how conventional item analysis procedures were developed, and how dissatisfaction with them has led to fragmentation. The range of distinct conceptual and…

Assessing Intelligence in Children and Youth Living in the Netherlands

ERIC Educational Resources Information Center

Hurks, Petra P. M.; Bakker, Helen

2016-01-01

In this article, we briefly describe the history of intelligence test use with children and youth in the Netherlands, explain which models of intelligence guide decisions about test use, and detail how intelligence tests are currently being used in Dutch school settings. Empirically supported and theoretical models studying the structure of human…

MCA-NMF: Multimodal Concept Acquisition with Non-Negative Matrix Factorization

PubMed Central

Mangin, Olivier; Filliat, David; ten Bosch, Louis; Oudeyer, Pierre-Yves

2015-01-01

In this paper we introduce MCA-NMF, a computational model of the acquisition of multimodal concepts by an agent grounded in its environment. More precisely our model finds patterns in multimodal sensor input that characterize associations across modalities (speech utterances, images and motion). We propose this computational model as an answer to the question of how some class of concepts can be learnt. In addition, the model provides a way of defining such a class of plausibly learnable concepts. We detail why the multimodal nature of perception is essential to reduce the ambiguity of learnt concepts as well as to communicate about them through speech. We then present a set of experiments that demonstrate the learning of such concepts from real non-symbolic data consisting of speech sounds, images, and motions. Finally we consider structure in perceptual signals and demonstrate that a detailed knowledge of this structure, named compositional understanding can emerge from, instead of being a prerequisite of, global understanding. An open-source implementation of the MCA-NMF learner as well as scripts and associated experimental data to reproduce the experiments are publicly available. PMID:26489021

An experimental and kinetic modeling study on dimethyl carbonate (DMC) pyrolysis and combustion

DOE PAGES

Sun, Wenyu; Yang, Bin; Hansen, Nils; ...

2015-12-08

Because of the absence of C–C bonds and the large oxygen content in its molecular structure, dimethyl carbonate (DMC) is a promising oxygenated additive or substitute for hydrocarbon fuels. In order to understand its chemical oxidation and combustion kinetics, flow reactor pyrolysis at different pressures (40, 200 and 1040 mbar) and low-pressure laminar premixed flames with different equivalence ratios (1.0 and 1.5) were investigated. Mole fraction profiles of many reaction intermediates and products were obtained within estimated experimental uncertainties. From theoretical calculations and estimations, a detailed kinetic model for DMC pyrolysis and high-temperature combustion consisting of 257 species and 1563more » reactions was developed. The performance of the kinetic model was then analyzed using detailed chemical composition information, primarily from the present measurements. In addition, it was examined against the chemical structure of an opposed-flow diffusion flame, relying on global combustion properties such as the ignition delay times and laminar burning velocities. Furthermore, these extended comparisons yielded overall satisfactory agreement, demonstrating the applicability of the present model over a wide range of high-temperature conditions.« less

Structure and dynamics of the coronal magnetic field

NASA Technical Reports Server (NTRS)

VanHoven, Gerard; Schnack, Dalton D.

1996-01-01

The last few years have seen a marked increase in the sophistication of models of the solar corona. This has been brought about by a confluence of three key elements. First, the collection of high-resolution observations of the Sun, both in space and time, has grown tremendously. The SOHO (Solar Heliospheric Observatory) mission is providing additional correlated high-resolution magnetic, white-light and spectroscopic observations. Second, the power and availability of supercomputers has made two- and three-dimensional modeling routine. Third, the sophistication of the models themselves, both in their geometrical realism and in the detailed physics that has been included, has improved significantly. The support from our current Space Physics Theory grant has allowed us to exploit this confluence of capabilities. We have carried out direct comparisons between observations and models of the solar corona. The agreement between simulated coronal structure and observations has verified that the models are mature enough for detailed analysis, as we will describe. The development of this capability is especially timely, since observations obtained from three space missions that are underway (Ulysses, WIND and SOHO) offer an opportunity for significant advances in our understanding of the corona and heliosphere. Through this interplay of observations and theory we can improve our understanding of the Sun. Our achievements thus far include progress modeling the large-scale structure of the solar corona, three-dimensional models of active region fields, development of emerging flux and current, formation and evolution of coronal loops, and coronal heating by current filaments.

Comparing large-scale computational approaches to epidemic modeling: agent-based versus structured metapopulation models.

PubMed

Ajelli, Marco; Gonçalves, Bruno; Balcan, Duygu; Colizza, Vittoria; Hu, Hao; Ramasco, José J; Merler, Stefano; Vespignani, Alessandro

2010-06-29

In recent years large-scale computational models for the realistic simulation of epidemic outbreaks have been used with increased frequency. Methodologies adapt to the scale of interest and range from very detailed agent-based models to spatially-structured metapopulation models. One major issue thus concerns to what extent the geotemporal spreading pattern found by different modeling approaches may differ and depend on the different approximations and assumptions used. We provide for the first time a side-by-side comparison of the results obtained with a stochastic agent-based model and a structured metapopulation stochastic model for the progression of a baseline pandemic event in Italy, a large and geographically heterogeneous European country. The agent-based model is based on the explicit representation of the Italian population through highly detailed data on the socio-demographic structure. The metapopulation simulations use the GLobal Epidemic and Mobility (GLEaM) model, based on high-resolution census data worldwide, and integrating airline travel flow data with short-range human mobility patterns at the global scale. The model also considers age structure data for Italy. GLEaM and the agent-based models are synchronized in their initial conditions by using the same disease parameterization, and by defining the same importation of infected cases from international travels. The results obtained show that both models provide epidemic patterns that are in very good agreement at the granularity levels accessible by both approaches, with differences in peak timing on the order of a few days. The relative difference of the epidemic size depends on the basic reproductive ratio, R0, and on the fact that the metapopulation model consistently yields a larger incidence than the agent-based model, as expected due to the differences in the structure in the intra-population contact pattern of the approaches. The age breakdown analysis shows that similar attack rates are obtained for the younger age classes. The good agreement between the two modeling approaches is very important for defining the tradeoff between data availability and the information provided by the models. The results we present define the possibility of hybrid models combining the agent-based and the metapopulation approaches according to the available data and computational resources.

Heterogeneous structure and surface tension effects on mechanical response in pulmonary acinus: A finite element analysis.

PubMed

Koshiyama, Kenichiro; Nishimoto, Keisuke; Ii, Satoshi; Sera, Toshihiro; Wada, Shigeo

2018-01-20

The pulmonary acinus is a dead-end microstructure that consists of ducts and alveoli. High-resolution micro-CT imaging has recently provided detailed anatomical information of a complete in vivo acinus, but relating its mechanical response with its detailed acinar structure remains challenging. This study aimed to investigate the mechanical response of acinar tissue in a whole acinus for static inflation using computational approaches. We performed finite element analysis of a whole acinus for static inflation. The acinar structure model was generated based on micro-CT images of an intact acinus. A continuum mechanics model of the lung parenchyma was used for acinar tissue material model, and surface tension effects were explicitly included. An anisotropic mechanical field analysis based on a stretch tensor was combined with a curvature-based local structure analysis. The airspace of the acinus exhibited nonspherical deformation as a result of the anisotropic deformation of acinar tissue. A strain hotspot occurred at the ridge-shaped region caused by a rod-like deformation of acinar tissue on the ridge. The local structure becomes bowl-shaped for inflation and, without surface tension effects, the surface of the bowl-shaped region primarily experiences isotropic deformation. Surface tension effects suppressed the increase in airspace volume and inner surface area, while facilitating anisotropic deformation on the alveolar surface. In the lungs, the heterogeneous acinar structure and surface tension induce anisotropic deformation at the acinar and alveolar scales. Further research is needed on structural variation of acini, inter-acini connectivity, or dynamic behavior to understand multiscale lung mechanics. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Consensus Model of Human Apolipoprotein A-I in its Monomeric and Lipid-free State

PubMed Central

Melchior, John T.; Walker, Ryan G.; Cooke, Allison L.; Morris, Jamie; Castleberry, Mark; Thompson, Thomas B.; Jones, Martin K.; Song, Hyun D.; Rye, Kerry-Anne; Oda, Mike N.; Sorci-Thomas, Mary G.; Thomas, Michael J.; Heinecke, Jay W.; Mei, Xiaohu; Atkinson, David; Segrest, Jere P.; Lund-Katz, Sissel; Phillips, Michael C.; Davidson, W. Sean

2017-01-01

Apolipoprotein (apo)A-I is an organizing scaffold protein that is critical to high density lipoprotein (HDL) structure and metabolism, likely mediating many of its cardioprotective properties. However, HDL biogenesis is poorly understood as lipid-free apoA-I has been notoriously resistant to high resolution structural study. Published models from low resolution techniques share certain features but vary considerably in shape and secondary structure. To tackle this central issue in lipoprotein biology, we assembled an unprecedented team of lipoprotein structural biologists and set out to build a consensus model of monomeric lipid-free human apoA-I. Combining novel and published cross-link constraints, small angle X-ray scattering (SAXS), hydrogen-deuterium exchange (H-DX) and crystallography data, we propose a time averaged model consistent with much of the experimental data published over the last 40 years. The model provides a long sought platform for understanding and testing details of HDL biogenesis, structure and function. PMID:29131142

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.

Space-based Scintillation Nowcasting with the Communications/Navigation Outage Forecast System

NASA Astrophysics Data System (ADS)

Groves, K.; Starks, M.; Beach, T.; Basu, S.

2008-12-01

The Air Force Research Laboratory's Communication/Navigation Outage Forecast System (C/NOFS) fuses ground- and space-based data in a near real-time physics-based model aimed at forecasting and nowcasting equatorial scintillations and their impacts on satellite communications and navigation. A key component of the system is the C/NOFS satellite that was launched into a low-inclination (13°) elliptical orbit (400 km x 850 km) in April 2008. The satellite contains six sensors to measure space environment parameters including electron density and temperature, ion density and drift, electric and magnetic fields and neutral wind, as well as a tri-band radio beacon transmitting at 150 MHz, 400 MHz and 1067 MHz. Scintillation nowcasts are derived from measuring the one-dimensional in situ electron density fluctuations and subsequently modeling the propagation environment for satellite-to-ground radio links. The modeling process requires a number of simplifying assumptions regarding the three-dimensional structure of the ionosphere and the results are readily validated by comparisons with ground-based measurements of the satellite's tri-band beacon signals. In mid-September 2008 a campaign to perform detailed analyses of space-based scintillation nowcasts with numerous ground observations was conducted in the vicinity of Kwajalein Atoll, Marshall Islands. To maximize the collection of ground-truth data, the ALTAIR radar was employed to obtain detailed information on the spatial structure of the ionosphere during the campaign and to aid the improvement of space-based nowcasting algorithms. A comparison of these results will be presented; it appears that detailed information on the electron density structure is a limiting factor in modeling the scintillation environment from in situ observations.

Design Through Manufacturing: The Solid Model - Finite Element Analysis Interface

NASA Technical Reports Server (NTRS)

Rubin, Carol

2003-01-01

State-of-the-art computer aided design (CAD) presently affords engineers the opportunity to create solid models of machine parts which reflect every detail of the finished product. Ideally, these models should fulfill two very important functions: (1) they must provide numerical control information for automated manufacturing of precision parts, and (2) they must enable analysts to easily evaluate the stress levels (using finite element analysis - FEA) for all structurally significant parts used in space missions. Today's state-of-the-art CAD programs perform function (1) very well, providing an excellent model for precision manufacturing. But they do not provide a straightforward and simple means of automating the translation from CAD to FEA models, especially for aircraft-type structures. The research performed during the fellowship period investigated the transition process from the solid CAD model to the FEA stress analysis model with the final goal of creating an automatic interface between the two. During the period of the fellowship a detailed multi-year program for the development of such an interface was created. The ultimate goal of this program will be the development of a fully parameterized automatic ProE/FEA translator for parts and assemblies, with the incorporation of data base management into the solution, and ultimately including computational fluid dynamics and thermal modeling in the interface.

Design of robotic cells based on relative handling modules with use of SolidWorks system

NASA Astrophysics Data System (ADS)

Gaponenko, E. V.; Anciferov, S. I.

2018-05-01

The article presents a diagramed engineering solution for a robotic cell with six degrees of freedom for machining of complex details, consisting of the base with a tool installation module and a detail machining module made as parallel structure mechanisms. The output links of the detail machining module and the tool installation module can move along X-Y-Z coordinate axes each. A 3D-model of the complex is designed in the SolidWorks system. It will be used further for carrying out engineering calculations and mathematical analysis and obtaining all required documentation.

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.

High quantum efficiency photocathode simulation for the investigation of novel structured designs

DOE PAGES

MacPhee, A. G.; Nagel, S. R.; Bell, P. M.; ...

2014-09-02

A computer model in CST Studio Suite has been developed to evaluate several novel geometrically enhanced photocathode designs. This work was aimed at identifying a structure that would increase the total electron yield by a factor of two or greater in the 1–30 keV range. The modeling software was used to simulate the electric field and generate particle tracking for several potential structures. The final photocathode structure has been tailored to meet a set of detector performance requirements, namely, a spatial resolution of <40 μm and a temporal spread of 1–10 ps. As a result, we present the details ofmore » the geometrically enhanced photocathode model and resulting static field and electron emission characteristics.« less

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.

In situ AFM imaging of apolipoprotein A-I directly derived from plasma HDL.

PubMed

Gan, Chaoye; Wang, Zhexuan; Chen, Yong

2017-04-01

The major apolipoproteins of plasma lipoproteins play vital roles in the structural integrity and physiological functions of lipoproteins. More than ten structural models of apolipoprotein A-I (apoA-I), the major apolipoprotein of high-density lipoprotein (HDL), have been developed successively. In these models, apoA-I was supposed to organize in a ring-shaped form. To date, however, there is no direct evidence under physiological condition. Here, atomic force microscopy (AFM) was used to in situ visualize the organization of apoA-I, which was exposed via depletion of the lipid component of plasma HDL pre-immobilized on functionalized mica sheets. For the first time, the ring-shaped coarse structure and three detailed structures (crescent-shaped, gapped "O"-shaped, and parentheses-shaped structures, respectively) of apoA-I in plasma HDL, which have the ability of binding scavenger receptors, were directly observed and quantitatively measured by AFM. The three detailed structures probably represent the different extents to which the lipid component of HDL was depleted. Data on lipid depletion of HDL may provide clues to understand lipid insertion of HDL. These data provide important information for the understanding of the structure/maturation of plasma HDL. Moreover, they suggest a powerful method for directly visualizing the major apolipoproteins of plasma lipoproteins or the protein component of lipoprotein-like lipid-protein complexes. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of multicrystal pump–probe data sets. I. Expressions for the RATIO model

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

Fournier, Bertrand; Coppens, Philip

2014-08-30

The RATIO method in time-resolved crystallography [Coppenset al.(2009).J. Synchrotron Rad.16, 226–230] was developed for use with Laue pump–probe diffraction data to avoid complex corrections due to wavelength dependence of the intensities. The application of the RATIO method in processing/analysis prior to structure refinement requires an appropriate ratio model for modeling the light response. The assessment of the accuracy of pump–probe time-resolved structure refinements based on the observed ratios was discussed in a previous paper. In the current paper, a detailed ratio model is discussed, taking into account both geometric and thermal light-induced changes.

Structure and information in spatial segregation

PubMed Central

2017-01-01

Ethnoracial residential segregation is a complex, multiscalar phenomenon with immense moral and economic costs. Modeling the structure and dynamics of segregation is a pressing problem for sociology and urban planning, but existing methods have limitations. In this paper, we develop a suite of methods, grounded in information theory, for studying the spatial structure of segregation. We first advance existing profile and decomposition methods by posing two related regionalization methods, which allow for profile curves with nonconstant spatial scale and decomposition analysis with nonarbitrary areal units. We then formulate a measure of local spatial scale, which may be used for both detailed, within-city analysis and intercity comparisons. These methods highlight detailed insights in the structure and dynamics of urban segregation that would be otherwise easy to miss or difficult to quantify. They are computationally efficient, applicable to a broad range of study questions, and freely available in open source software. PMID:29078323

Structure and information in spatial segregation.

PubMed

Chodrow, Philip S

2017-10-31

Ethnoracial residential segregation is a complex, multiscalar phenomenon with immense moral and economic costs. Modeling the structure and dynamics of segregation is a pressing problem for sociology and urban planning, but existing methods have limitations. In this paper, we develop a suite of methods, grounded in information theory, for studying the spatial structure of segregation. We first advance existing profile and decomposition methods by posing two related regionalization methods, which allow for profile curves with nonconstant spatial scale and decomposition analysis with nonarbitrary areal units. We then formulate a measure of local spatial scale, which may be used for both detailed, within-city analysis and intercity comparisons. These methods highlight detailed insights in the structure and dynamics of urban segregation that would be otherwise easy to miss or difficult to quantify. They are computationally efficient, applicable to a broad range of study questions, and freely available in open source software. Published under the PNAS license.

3D printing of preclinical X-ray computed tomographic data sets.

PubMed

Doney, Evan; Krumdick, Lauren A; Diener, Justin M; Wathen, Connor A; Chapman, Sarah E; Stamile, Brian; Scott, Jeremiah E; Ravosa, Matthew J; Van Avermaete, Tony; Leevy, W Matthew

2013-03-22

Three-dimensional printing allows for the production of highly detailed objects through a process known as additive manufacturing. Traditional, mold-injection methods to create models or parts have several limitations, the most important of which is a difficulty in making highly complex products in a timely, cost-effective manner.(1) However, gradual improvements in three-dimensional printing technology have resulted in both high-end and economy instruments that are now available for the facile production of customized models.(2) These printers have the ability to extrude high-resolution objects with enough detail to accurately represent in vivo images generated from a preclinical X-ray CT scanner. With proper data collection, surface rendering, and stereolithographic editing, it is now possible and inexpensive to rapidly produce detailed skeletal and soft tissue structures from X-ray CT data. Even in the early stages of development, the anatomical models produced by three-dimensional printing appeal to both educators and researchers who can utilize the technology to improve visualization proficiency. (3, 4) The real benefits of this method result from the tangible experience a researcher can have with data that cannot be adequately conveyed through a computer screen. The translation of pre-clinical 3D data to a physical object that is an exact copy of the test subject is a powerful tool for visualization and communication, especially for relating imaging research to students, or those in other fields. Here, we provide a detailed method for printing plastic models of bone and organ structures derived from X-ray CT scans utilizing an Albira X-ray CT system in conjunction with PMOD, ImageJ, Meshlab, Netfabb, and ReplicatorG software packages.

Strategy for the management of substance use disorders in the State of Punjab: Developing a structural model of state-level de-addiction services in the health sector (the “Punjab model”)

PubMed Central

Basu, Debasish; Avasthi, Ajit

2015-01-01

Background: Substance use disorders are believed to have become rampant in the State of Punjab, causing substantive loss to the person, the family, the society, and the state. The situation is likely to worsen further if a structured, government-level, state-wide de-addiction service is not put into place. Aims: The aim was to describe a comprehensive structural model of de-addiction service in the State of Punjab (the “Pyramid model” or “Punjab model”), which is primarily concerned with demand reduction, particularly that part which is concerned with identification, treatment, and aftercare of substance users. Materials and Methods: At the behest of the Punjab Government, this model was developed by the authors after a detailed study of the current scenario, critical and exhaustive look at the existing guidelines, policies, books, web resources, government documents, and the like in this area, a check of the ground reality in terms of existing infrastructural and manpower resources, and keeping pragmatism and practicability in mind. Several rounds of meetings with the government officials and other important stakeholders helped to refine the model further. Results: Our model envisages structural innovation and renovations within the existing state healthcare infrastructure. We formulated a “Pyramid model,” later renamed as “Punjab model,” where there is a broad community base for early identification and outpatient level treatment at the primary care level, both outpatient and inpatient care at the secondary care level, and comprehensive management for more difficult cases at the tertiary care level. A separate de-addiction system for the prisons was also developed. Each of these structural elements was described and refined in details, with the aim of uniform, standardized, and easily accessible care across the state. Conclusions: If the “Punjab model” succeeds, it can provide useful models for other states or even at the national level. PMID:25657452

Considerations for Reporting Finite Element Analysis Studies in Biomechanics

PubMed Central

Erdemir, Ahmet; Guess, Trent M.; Halloran, Jason; Tadepalli, Srinivas C.; Morrison, Tina M.

2012-01-01

Simulation-based medicine and the development of complex computer models of biological structures is becoming ubiquitous for advancing biomedical engineering and clinical research. Finite element analysis (FEA) has been widely used in the last few decades to understand and predict biomechanical phenomena. Modeling and simulation approaches in biomechanics are highly interdisciplinary, involving novice and skilled developers in all areas of biomedical engineering and biology. While recent advances in model development and simulation platforms offer a wide range of tools to investigators, the decision making process during modeling and simulation has become more opaque. Hence, reliability of such models used for medical decision making and for driving multiscale analysis comes into question. Establishing guidelines for model development and dissemination is a daunting task, particularly with the complex and convoluted models used in FEA. Nonetheless, if better reporting can be established, researchers will have a better understanding of a model’s value and the potential for reusability through sharing will be bolstered. Thus, the goal of this document is to identify resources and considerate reporting parameters for FEA studies in biomechanics. These entail various levels of reporting parameters for model identification, model structure, simulation structure, verification, validation, and availability. While we recognize that it may not be possible to provide and detail all of the reporting considerations presented, it is possible to establish a level of confidence with selective use of these parameters. More detailed reporting, however, can establish an explicit outline of the decision-making process in simulation-based analysis for enhanced reproducibility, reusability, and sharing. PMID:22236526

Improving Predictions of Tree Drought Mortality in the Community Land Model Using Hydraulic Physiology Theory and its Effects on Carbon Metabolism

NASA Astrophysics Data System (ADS)

McNellis, B.; Hudiburg, T. W.

2017-12-01

Tree mortality due to drought is predicted to have increasing impacts on ecosystem structure and function during the 21st century. Models can attempt to predict which forests are most at risk from drought, but novel environments may preclude analysis that relies on past observations. The inclusion of more mechanistic detail may reduce uncertainty in predictions, but can also compound model complexity, especially in global models. The Community Land Model version 5 (CLM5), itself a component of the Community Earth System Model (CESM), has recently integrated cohort-based demography into its dynamic vegetation component and is in the process of coupling this demography to a model of plant hydraulic physiology (FATES-Hydro). Previous treatment of drought stress and plant mortality within CLM has been relatively broad, but a detailed hydraulics module represents a key step towards accurate mortality prognosis. Here, we examine the structure of FATES-Hydro with respect to two key physiological attributes: tissue osmotic potentials and embolism refilling. Specifically, we ask how FATES-Hydro captures mechanistic realism within each attribute and how much support there is within the physiological literature for its further elaboration within the model structure. Additionally, connections to broader aspects of carbon metabolism within FATES are explored to better resolve emergent consequences of drought stress on ecosystem function and tree demographics. An on-going field experiment in managed stands of Pinus ponderosa and mixed conifers is assessed for model parameterization and performance across PNW forests, with important implications for future forest management strategy.

Seaway Information System Management and Control Requirements

DOT National Transportation Integrated Search

1973-10-01

This report examines in detail the control and information system requirements of the St. Lawrence Seaway development program in terms of the needs of the vessel traffic controllers and the management users. Structural control models of Seaway operat...

Model systems in heterogeneous catalysis: towards the design and understanding of structure and electronic properties.

PubMed

Pan, Q; Li, L; Shaikhutdinov, S; Fujimori, Y; Hollerer, M; Sterrer, M; Freund, H-J

2018-05-29

We discuss in this paper two case studies related to nano-particle catalyst systems. One concerns a model system for the Cr/SiO2 Phillips catalyst for ethylene polymerization and here we present XPS data to complement the previously published TPD, IRAS and reactivity studies to elucidate the electronic structure of the system in some detail. The second case study provides additional information on Au nano-particles supported on ultrathin MgO(100)/Ag(100) films where we had observed a specific activity of the particle's rim at the metal-oxide interface with respect to CO2 activation and oxalate formation, obviously connected to electron transfer through the MgO film from the metal substrate underneath. Here we present XPS and Auger data, which allows detailed analysis of the observed chemical shifts. This analysis corroborates previous findings deduced via STM.

3-Dimensional Geologic Modeling Applied to the Structural Characterization of Geothermal Systems: Astor Pass, Nevada, USA

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

Siler, Drew L; Faulds, James E; Mayhew, Brett

2013-04-16

Geothermal systems in the Great Basin, USA, are controlled by a variety of fault intersection and fault interaction areas. Understanding the specific geometry of the structures most conducive to broad-scale geothermal circulation is crucial to both the mitigation of the costs of geothermal exploration (especially drilling) and to the identification of geothermal systems that have no surface expression (blind systems). 3-dimensional geologic modeling is a tool that can elucidate the specific stratigraphic intervals and structural geometries that host geothermal reservoirs. Astor Pass, NV USA lies just beyond the northern extent of the dextral Pyramid Lake fault zone near the boundarymore » between two distinct structural domains, the Walker Lane and the Basin and Range, and exhibits characteristics of each setting. Both northwest-striking, left-stepping dextral faults of the Walker Lane and kinematically linked northerly striking normal faults associated with the Basin and Range are present. Previous studies at Astor Pass identified a blind geothermal system controlled by the intersection of west-northwest and north-northwest striking dextral-normal faults. Wells drilled into the southwestern quadrant of the fault intersection yielded 94°C fluids, with geothermometers suggesting a maximum reservoir temperature of 130°C. A 3-dimensional model was constructed based on detailed geologic maps and cross-sections, 2-dimensional seismic data, and petrologic analysis of the cuttings from three wells in order to further constrain the structural setting. The model reveals the specific geometry of the fault interaction area at a level of detail beyond what geologic maps and cross-sections can provide.« less

Foreign body impact event damage formation in composite structures

NASA Technical Reports Server (NTRS)

Bucinell, Ronald B.

1994-01-01

This report discusses a methodology that can be used to assess the effect of foreign body impacts on composite structural integrity. The described effort focuses on modeling the effect of a central impact on a 5 3/4 inch filament wound test article. The discussion will commence with details of the material modeling that was used to establish the input properties for the analytical model. This discussion is followed by an overview of the impact assessment methodology. The progress on this effort to date is reviewed along with a discussion of tasks that have yet to be completed.

NREL Software Aids Offshore Wind Turbine Designs (Fact Sheet)

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

Not Available

2013-10-01

NREL researchers are supporting offshore wind power development with computer models that allow detailed analyses of both fixed and floating offshore wind turbines. While existing computer-aided engineering (CAE) models can simulate the conditions and stresses that a land-based wind turbine experiences over its lifetime, offshore turbines require the additional considerations of variations in water depth, soil type, and wind and wave severity, which also necessitate the use of a variety of support-structure types. NREL's core wind CAE tool, FAST, models the additional effects of incident waves, sea currents, and the foundation dynamics of the support structures.

Modeling an electric motor in 1-D

NASA Technical Reports Server (NTRS)

Butler, Thomas G.

1991-01-01

Quite often the dynamicist will be faced with having an electric drive motor as a link in the elastic path of a structure such that the motor's characteristics must be taken into account to properly represent the dynamics of the primary structure. He does not want to model it so accurately that he could get detailed stress and displacements in the motor proper, but just sufficiently to represent its inertia loading and elastic behavior from its mounting bolts to its drive coupling. Described here is how the rotor and stator of such a motor can be adequately modeled as a colinear pair of beams.

qPIPSA: Relating enzymatic kinetic parameters and interaction fields

PubMed Central

Gabdoulline, Razif R; Stein, Matthias; Wade, Rebecca C

2007-01-01

Background The simulation of metabolic networks in quantitative systems biology requires the assignment of enzymatic kinetic parameters. Experimentally determined values are often not available and therefore computational methods to estimate these parameters are needed. It is possible to use the three-dimensional structure of an enzyme to perform simulations of a reaction and derive kinetic parameters. However, this is computationally demanding and requires detailed knowledge of the enzyme mechanism. We have therefore sought to develop a general, simple and computationally efficient procedure to relate protein structural information to enzymatic kinetic parameters that allows consistency between the kinetic and structural information to be checked and estimation of kinetic constants for structurally and mechanistically similar enzymes. Results We describe qPIPSA: quantitative Protein Interaction Property Similarity Analysis. In this analysis, molecular interaction fields, for example, electrostatic potentials, are computed from the enzyme structures. Differences in molecular interaction fields between enzymes are then related to the ratios of their kinetic parameters. This procedure can be used to estimate unknown kinetic parameters when enzyme structural information is available and kinetic parameters have been measured for related enzymes or were obtained under different conditions. The detailed interaction of the enzyme with substrate or cofactors is not modeled and is assumed to be similar for all the proteins compared. The protein structure modeling protocol employed ensures that differences between models reflect genuine differences between the protein sequences, rather than random fluctuations in protein structure. Conclusion Provided that the experimental conditions and the protein structural models refer to the same protein state or conformation, correlations between interaction fields and kinetic parameters can be established for sets of related enzymes. Outliers may arise due to variation in the importance of different contributions to the kinetic parameters, such as protein stability and conformational changes. The qPIPSA approach can assist in the validation as well as estimation of kinetic parameters, and provide insights into enzyme mechanism. PMID:17919319

Metrology of deep trench etched memory structures using 3D scatterometry

NASA Astrophysics Data System (ADS)

Reinig, Peter; Dost, Rene; Moert, Manfred; Hingst, Thomas; Mantz, Ulrich; Moffitt, Jasen; Shakya, Sushil; Raymond, Christopher J.; Littau, Mike

2005-05-01

Scatterometry is receiving considerable attention as an emerging optical metrology in the silicon industry. One area of progress in deploying these powerful measurements in process control is performing measurements on real device structures, as opposed to limiting scatterometry measurements to periodic structures, such as line-space gratings, placed in the wafer scribe. In this work we will discuss applications of 3D scatterometry to the measurement of advanced trench memory devices. This is a challenging and complex scatterometry application that requires exceptionally high-performance computational abilities. In order to represent the physical device, the relatively tall structures require a high number of slices in the rigorous coupled wave analysis (RCWA) theoretical model. This is complicated further by the presence of an amorphous silicon hard mask on the surface, which is highly sensitive to reflectance scattering and therefore needs to be modeled in detail. The overall structure is comprised of several layers, with the trenches presenting a complex bow-shape sidewall that must be measured. Finally, the double periodicity in the structures demands significantly greater computational capabilities. Our results demonstrate that angular scatterometry is sensitive to the key parameters of interest. The influence of further model parameters and parameter cross correlations have to be carefully taken into account. Profile results obtained by non-library optimization methods compare favorably with cross-section SEM images. Generating a model library suitable for process control, which is preferred for precision, presents numerical throughput challenges. Details will be discussed regarding library generation approaches and strategies for reducing the numerical overhead. Scatterometry and SEM results will be compared, leading to conclusions about the feasibility of this advanced application.

What determines the spectrum of protein native state structures?

PubMed

Lezon, Timothy R; Banavar, Jayanth R; Lesk, Arthur M; Maritan, Amos

2006-05-01

We present a brief summary of the key factors underlying protein structure, as developed in the investigations of Pauling, Ramachandran, and Rose. We then outline a simplified physical model of proteins that focuses on geometry and symmetry. Although this model superficially appears unrelated to the detailed chemical descriptions commonly applied to proteins, we show that it captures the essential elements of the chemistry and provides a unified framework for understanding the common characteristics of folded proteins. We suggest that the spectrum of protein native state structures is determined by geometry and symmetry and the role of the sequence is to choose its native state structure from this predetermined menu. 2006 Wiley-Liss, Inc.

Structure of turbulent non-premixed flames modeled with two-step chemistry

NASA Technical Reports Server (NTRS)

Chen, J. H.; Mahalingam, S.; Puri, I. K.; Vervisch, L.

1992-01-01

Direct numerical simulations of turbulent diffusion flames modeled with finite-rate, two-step chemistry, A + B yields I, A + I yields P, were carried out. A detailed analysis of the turbulent flame structure reveals the complex nature of the penetration of various reactive species across two reaction zones in mixture fraction space. Due to this two zone structure, these flames were found to be robust, resisting extinction over the parameter ranges investigated. As in single-step computations, mixture fraction dissipation rate and the mixture fraction were found to be statistically correlated. Simulations involving unequal molecular diffusivities suggest that the small scale mixing process and, hence, the turbulent flame structure is sensitive to the Schmidt number.

LETTER TO THE EDITOR: Bicomplexes and conservation laws in non-Abelian Toda models

NASA Astrophysics Data System (ADS)

Gueuvoghlanian, E. P.

2001-08-01

A bicomplex structure is associated with the Leznov-Saveliev equation of integrable models. The linear problem associated with the zero-curvature condition is derived in terms of the bicomplex linear equation. The explicit example of a non-Abelian conformal affine Toda model is discussed in detail and its conservation laws are derived from the zero-curvature representation of its equation of motion.

Simulation of Weld Mechanical Behavior to Include Welding-Induced Residual Stress and Distortion: Coupling of SYSWELD and Abaqus Codes

DTIC Science & Technology

2015-11-01

induced residual stresses and distortions from weld simulations in the SYSWELD software code in structural Finite Element Analysis ( FEA ) simulations...performed in the Abaqus FEA code is presented. The translation of these results is accomplished using a newly developed Python script. Full details of...Local Weld Model in Structural FEA ....................................................15 CONCLUSIONS

Spatial Data Structures for Robotic Vehicle Route Planning

DTIC Science & Technology

1988-12-01

goal will be realized in an intelligent Spatial Data Structure Development System (SDSDS) intended for use by Terrain Analysis applications...from the user the details of representation and to permit the infrastructure itself to decide which representations will be most efficient or effective ...to intelligently predict performance of algorithmic sequences and thereby optimize the application (within the accuracy of the prediction models). The

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.

Immersed boundary-finite element model of fluid-structure interaction in the aortic root

NASA Astrophysics Data System (ADS)

Flamini, Vittoria; DeAnda, Abe; Griffith, Boyce E.

2016-04-01

It has long been recognized that aortic root elasticity helps to ensure efficient aortic valve closure, but our understanding of the functional importance of the elasticity and geometry of the aortic root continues to evolve as increasingly detailed in vivo imaging data become available. Herein, we describe a fluid-structure interaction model of the aortic root, including the aortic valve leaflets, the sinuses of Valsalva, the aortic annulus, and the sinotubular junction, that employs a version of Peskin's immersed boundary (IB) method with a finite element description of the structural elasticity. As in earlier work, we use a fiber-based model of the valve leaflets, but this study extends earlier IB models of the aortic root by employing an incompressible hyperelastic model of the mechanics of the sinuses and ascending aorta using a constitutive law fit to experimental data from human aortic root tissue. In vivo pressure loading is accounted for by a backward displacement method that determines the unloaded configuration of the root model. Our model yields realistic cardiac output at physiological pressures, with low transvalvular pressure differences during forward flow, minimal regurgitation during valve closure, and realistic pressure loads when the valve is closed during diastole. Further, results from high-resolution computations indicate that although the detailed leaflet and root kinematics show some grid sensitivity, our IB model of the aortic root nonetheless produces essentially grid-converged flow rates and pressures at practical grid spacings for the high Reynolds number flows of the aortic root. These results thereby clarify minimum grid resolutions required by such models when used as stand-alone models of the aortic valve as well as when used to provide models of the outflow valves in models of left-ventricular fluid dynamics.

Mechanism of variable structural colour in the neon tetra: quantitative evaluation of the Venetian blind model.

PubMed

Yoshioka, S; Matsuhana, B; Tanaka, S; Inouye, Y; Oshima, N; Kinoshita, S

2011-01-06

The structural colour of the neon tetra is distinguishable from those of, e.g., butterfly wings and bird feathers, because it can change in response to the light intensity of the surrounding environment. This fact clearly indicates the variability of the colour-producing microstructures. It has been known that an iridophore of the neon tetra contains a few stacks of periodically arranged light-reflecting platelets, which can cause multilayer optical interference phenomena. As a mechanism of the colour variability, the Venetian blind model has been proposed, in which the light-reflecting platelets are assumed to be tilted during colour change, resulting in a variation in the spacing between the platelets. In order to quantitatively evaluate the validity of this model, we have performed a detailed optical study of a single stack of platelets inside an iridophore. In particular, we have prepared a new optical system that can simultaneously measure both the spectrum and direction of the reflected light, which are expected to be closely related to each other in the Venetian blind model. The experimental results and detailed analysis are found to quantitatively verify the model.

Applications of Parallel Computation in Micro-Mechanics and Finite Element Method

NASA Technical Reports Server (NTRS)

Tan, Hui-Qian

1996-01-01

This project discusses the application of parallel computations related with respect to material analyses. Briefly speaking, we analyze some kind of material by elements computations. We call an element a cell here. A cell is divided into a number of subelements called subcells and all subcells in a cell have the identical structure. The detailed structure will be given later in this paper. It is obvious that the problem is "well-structured". SIMD machine would be a better choice. In this paper we try to look into the potentials of SIMD machine in dealing with finite element computation by developing appropriate algorithms on MasPar, a SIMD parallel machine. In section 2, the architecture of MasPar will be discussed. A brief review of the parallel programming language MPL also is given in that section. In section 3, some general parallel algorithms which might be useful to the project will be proposed. And, combining with the algorithms, some features of MPL will be discussed in more detail. In section 4, the computational structure of cell/subcell model will be given. The idea of designing the parallel algorithm for the model will be demonstrated. Finally in section 5, a summary will be given.

Tornado Damage Assessment: Reconstructing the Wind Through Debris Tracking and Treefall Pattern Analysis

NASA Astrophysics Data System (ADS)

Godfrey, C. M.; Peterson, C. J.; Lombardo, F.

2017-12-01

Efforts to enhance the resilience of communities to tornadoes requires an understanding of the interconnected nature of debris and damage propagation in both the built and natural environment. A first step toward characterizing the interconnectedness of these elements within a given community involves detailed post-event surveys of tornado damage. Such damage surveys immediately followed the 22 January 2017 EF3 tornadoes in the southern Georgia towns of Nashville and Albany. After assigning EF-scale ratings to impacted structures, the authors geotagged hundreds of pieces of debris scattered around selected residential structures and outbuildings in each neighborhood and paired each piece of debris with its source structure. Detailed information on trees in the vicinity of the structures supplements the debris data, including the species, dimensions, location, fall direction, and level of damage. High-resolution satellite imagery helps to identify the location and fall direction of hundreds of additional forest trees. These debris and treefall patterns allow an estimation of the near-surface wind field using a Rankine vortex model coupled with both a tree stability model and an infrastructure fragility model that simulates debris flight. Comparisons between the modeled damage and the actual treefall and debris field show remarkable similarities for a selected set of vortex parameters, indicating the viability of this approach for estimating enhanced Fujita scale levels, determining the near-surface wind field of a tornado during its passage through a neighborhood, and identifying how debris may contribute to the overall risk from tornadoes.

Pathways towards instability in financial networks

NASA Astrophysics Data System (ADS)

Bardoscia, Marco; Battiston, Stefano; Caccioli, Fabio; Caldarelli, Guido

2017-02-01

Following the financial crisis of 2007-2008, a deep analogy between the origins of instability in financial systems and complex ecosystems has been pointed out: in both cases, topological features of network structures influence how easily distress can spread within the system. However, in financial network models, the details of how financial institutions interact typically play a decisive role, and a general understanding of precisely how network topology creates instability remains lacking. Here we show how processes that are widely believed to stabilize the financial system, that is, market integration and diversification, can actually drive it towards instability, as they contribute to create cyclical structures which tend to amplify financial distress, thereby undermining systemic stability and making large crises more likely. This result holds irrespective of the details of how institutions interact, showing that policy-relevant analysis of the factors affecting financial stability can be carried out while abstracting away from such details.

Pathways towards instability in financial networks

PubMed Central

Bardoscia, Marco; Battiston, Stefano; Caccioli, Fabio; Caldarelli, Guido

2017-01-01

Following the financial crisis of 2007–2008, a deep analogy between the origins of instability in financial systems and complex ecosystems has been pointed out: in both cases, topological features of network structures influence how easily distress can spread within the system. However, in financial network models, the details of how financial institutions interact typically play a decisive role, and a general understanding of precisely how network topology creates instability remains lacking. Here we show how processes that are widely believed to stabilize the financial system, that is, market integration and diversification, can actually drive it towards instability, as they contribute to create cyclical structures which tend to amplify financial distress, thereby undermining systemic stability and making large crises more likely. This result holds irrespective of the details of how institutions interact, showing that policy-relevant analysis of the factors affecting financial stability can be carried out while abstracting away from such details. PMID:28221338

Pathways towards instability in financial networks.

PubMed

Bardoscia, Marco; Battiston, Stefano; Caccioli, Fabio; Caldarelli, Guido

2017-02-21

Following the financial crisis of 2007-2008, a deep analogy between the origins of instability in financial systems and complex ecosystems has been pointed out: in both cases, topological features of network structures influence how easily distress can spread within the system. However, in financial network models, the details of how financial institutions interact typically play a decisive role, and a general understanding of precisely how network topology creates instability remains lacking. Here we show how processes that are widely believed to stabilize the financial system, that is, market integration and diversification, can actually drive it towards instability, as they contribute to create cyclical structures which tend to amplify financial distress, thereby undermining systemic stability and making large crises more likely. This result holds irrespective of the details of how institutions interact, showing that policy-relevant analysis of the factors affecting financial stability can be carried out while abstracting away from such details.

GPACC program cost work breakdown structure-dictionary. General purpose aft cargo carrier study, volume 3

NASA Technical Reports Server (NTRS)

1985-01-01

The results of detailed cost estimates and economic analysis performed on the updated Model 101 configuration of the general purpose Aft Cargo Carrier (ACC) are given. The objective of this economic analysis is to provide the National Aeronautics and Space Administration (NASA) with information on the economics of using the ACC on the Space Transportation System (STS). The detailed cost estimates for the ACC are presented by a work breakdown structure (WBS) to ensure that all elements of cost are considered in the economic analysis and related subsystem trades. Costs reported by WBS provide NASA with a basis for comparing competing designs and provide detailed cost information that can be used to forecast phase C/D planning for new projects or programs derived from preliminary conceptual design studies. The scope covers all STS and STS/ACC launch vehicle cost impacts for delivering payloads to a 160 NM low Earth orbit (LEO).

Basic Modeling of the Solar Atmosphere and Spectrum

NASA Technical Reports Server (NTRS)

Avrett, Eugene H.; Wagner, William J. (Technical Monitor)

2000-01-01

During the last three years we have continued the development of extensive computer programs for constructing realistic models of the solar atmosphere and for calculating detailed spectra to use in the interpretation of solar observations. This research involves two major interrelated efforts: work by Avrett and Loeser on the Pandora computer program for optically thick non-LTE modeling of the solar atmosphere including a wide range of physical processes, and work by Kurucz on the detailed high-resolution synthesis of the solar spectrum using data for over 58 million atomic and molecular lines. Our objective is to construct atmospheric models from which the calculated spectra agree as well as possible with high-and low-resolution observations over a wide wavelength range. Such modeling leads to an improved understanding of the physical processes responsible for the structure and behavior of the atmosphere.

Integrating prior information into microwave tomography Part 1: Impact of detail on image quality.

PubMed

Kurrant, Douglas; Baran, Anastasia; LoVetri, Joe; Fear, Elise

2017-12-01

The authors investigate the impact that incremental increases in the level of detail of patient-specific prior information have on image quality and the convergence behavior of an inversion algorithm in the context of near-field microwave breast imaging. A methodology is presented that uses image quality measures to characterize the ability of the algorithm to reconstruct both internal structures and lesions embedded in fibroglandular tissue. The approach permits key aspects that impact the quality of reconstruction of these structures to be identified and quantified. This provides insight into opportunities to improve image reconstruction performance. Patient-specific information is acquired using radar-based methods that form a regional map of the breast. This map is then incorporated into a microwave tomography algorithm. Previous investigations have demonstrated the effectiveness of this approach to improve image quality when applied to data generated with two-dimensional (2D) numerical models. The present study extends this work by generating prior information that is customized to vary the degree of structural detail to facilitate the investigation of the role of prior information in image formation. Numerical 2D breast models constructed from magnetic resonance (MR) scans, and reconstructions formed with a three-dimensional (3D) numerical breast model are used to assess if trends observed for the 2D results can be extended to 3D scenarios. For the blind reconstruction scenario (i.e., no prior information), the breast surface is not accurately identified and internal structures are not clearly resolved. A substantial improvement in image quality is achieved by incorporating the skin surface map and constraining the imaging domain to the breast. Internal features within the breast appear in the reconstructed image. However, it is challenging to discriminate between adipose and glandular regions and there are inaccuracies in both the structural properties of the glandular region and the dielectric properties reconstructed within this structure. Using a regional map with a skin layer only marginally improves this situation. Increasing the structural detail in the prior information to include internal features leads to reconstructions for which the interface that delineates the fat and gland regions can be inferred. Different features within the glandular region corresponding to tissues with varying relative permittivity values, such as a lesion embedded within glandular structure, emerge in the reconstructed images. Including knowledge of the breast surface and skin layer leads to a substantial improvement in image quality compared to the blind case, but the images have limited diagnostic utility for applications such as tumor response tracking. The diagnostic utility of the reconstruction technique is improved considerably when patient-specific structural information is used. This qualitative observation is supported quantitatively with image metrics. © 2017 American Association of Physicists in Medicine.

Predicting temperate forest stand types using only structural profiles from discrete return airborne lidar

NASA Astrophysics Data System (ADS)

Fedrigo, Melissa; Newnham, Glenn J.; Coops, Nicholas C.; Culvenor, Darius S.; Bolton, Douglas K.; Nitschke, Craig R.

2018-02-01

Light detection and ranging (lidar) data have been increasingly used for forest classification due to its ability to penetrate the forest canopy and provide detail about the structure of the lower strata. In this study we demonstrate forest classification approaches using airborne lidar data as inputs to random forest and linear unmixing classification algorithms. Our results demonstrated that both random forest and linear unmixing models identified a distribution of rainforest and eucalypt stands that was comparable to existing ecological vegetation class (EVC) maps based primarily on manual interpretation of high resolution aerial imagery. Rainforest stands were also identified in the region that have not previously been identified in the EVC maps. The transition between stand types was better characterised by the random forest modelling approach. In contrast, the linear unmixing model placed greater emphasis on field plots selected as endmembers which may not have captured the variability in stand structure within a single stand type. The random forest model had the highest overall accuracy (84%) and Cohen's kappa coefficient (0.62). However, the classification accuracy was only marginally better than linear unmixing. The random forest model was applied to a region in the Central Highlands of south-eastern Australia to produce maps of stand type probability, including areas of transition (the 'ecotone') between rainforest and eucalypt forest. The resulting map provided a detailed delineation of forest classes, which specifically recognised the coalescing of stand types at the landscape scale. This represents a key step towards mapping the structural and spatial complexity of these ecosystems, which is important for both their management and conservation.

Structural response of 1/20-scale models of the Clinch River Breeder Reactor to a simulated hypothetical core-disruptive accident

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

Romander, C M; Cagliostro, D J

Five experiments were performed to help evaluate the structural integrity of the reactor vessel and head design and to verify code predictions. In the first experiment (SM 1), a detailed model of the head was loaded statically to determine its stiffness. In the remaining four experiments (SM 2 to SM 5), models of the vessel and head were loaded dynamically under a simulated 661 MW-s hypothetical core disruptive accident (HCDA). Models SM 2 to SM 4, each of increasing complexity, systematically showed the effects of upper internals structures, a thermal liner, core support platform, and torospherical bottom on vessel response.more » Model SM 5, identical to SM 4 but more heavily instrumented, demonstrated experimental reproducibility and provided more comprehensive data. The models consisted of a Ni 200 vessel and core barrel, a head with shielding and simulated component masses, and an upper internals structure (UIS).« less

RCrane: semi-automated RNA model building.

PubMed

Keating, Kevin S; Pyle, Anna Marie

2012-08-01

RNA crystals typically diffract to much lower resolutions than protein crystals. This low-resolution diffraction results in unclear density maps, which cause considerable difficulties during the model-building process. These difficulties are exacerbated by the lack of computational tools for RNA modeling. Here, RCrane, a tool for the partially automated building of RNA into electron-density maps of low or intermediate resolution, is presented. This tool works within Coot, a common program for macromolecular model building. RCrane helps crystallographers to place phosphates and bases into electron density and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides. RCrane then allows the crystallographer to review the newly built structure and select alternative backbone conformations where desired. This tool can also be used to automatically correct the backbone structure of previously built nucleotides. These automated corrections can fix incorrect sugar puckers, steric clashes and other structural problems.

Diffusion paths formation for Cu + ions in superionic Cu 6PS 5I single crystals studied in terms of structural phase transition

NASA Astrophysics Data System (ADS)

Gągor, A.; Pietraszko, A.; Kaynts, D.

2005-11-01

In order to understand the structural transformations leading to high ionic conductivity of Cu + ions in Cu 6PS 5I argyrodite compound, the detailed structure analysis based on single-crystal X-ray diffraction has been performed. Below the phase transition at T=(144-169) K Cu 6PS 5I belongs to monoclinic, ferroelastic phase (space group Cc) with ordered copper sublattice. Above Tc delocalization of copper ions begins and crystal changes the symmetry to cubic superstructure with space group F-43 c ( a'=19.528 Å, z=32). Finally, above T1=274 K increasing disordering of the Cu + ions heightens the symmetry to F-43 m ( a=9.794 Å, z=4). In this work, the final structural model of two cubic phases is presented including the detailed temperature evolution of positions and site occupation factors of copper ions ( R1=0.0397 for F-43 c phase, and 0.0245 for F-43 m phase). Possible diffusion paths for the copper ions are represented by means of the atomic displacement factors and split model. The structural results coincide well with the previously reported non-Arrhenius behavior of conductivity and indicate significant change in conduction mechanism.

Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex*

PubMed Central

Shi, Yi; Fernandez-Martinez, Javier; Tjioe, Elina; Pellarin, Riccardo; Kim, Seung Joong; Williams, Rosemary; Schneidman-Duhovny, Dina; Sali, Andrej; Rout, Michael P.; Chait, Brian T.

2014-01-01

Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope. PMID:25161197

Finite Element Model Development and Validation for Aircraft Fuselage Structures

NASA Technical Reports Server (NTRS)

Buehrle, Ralph D.; Fleming, Gary A.; Pappa, Richard S.; Grosveld, Ferdinand W.

2000-01-01

The ability to extend the valid frequency range for finite element based structural dynamic predictions using detailed models of the structural components and attachment interfaces is examined for several stiffened aircraft fuselage structures. This extended dynamic prediction capability is needed for the integration of mid-frequency noise control technology. Beam, plate and solid element models of the stiffener components are evaluated. Attachment models between the stiffener and panel skin range from a line along the rivets of the physical structure to a constraint over the entire contact surface. The finite element models are validated using experimental modal analysis results. The increased frequency range results in a corresponding increase in the number of modes, modal density and spatial resolution requirements. In this study, conventional modal tests using accelerometers are complemented with Scanning Laser Doppler Velocimetry and Electro-Optic Holography measurements to further resolve the spatial response characteristics. Whenever possible, component and subassembly modal tests are used to validate the finite element models at lower levels of assembly. Normal mode predictions for different finite element representations of components and assemblies are compared with experimental results to assess the most accurate techniques for modeling aircraft fuselage type structures.

Graph theoretical model of a sensorimotor connectome in zebrafish.

PubMed

Stobb, Michael; Peterson, Joshua M; Mazzag, Borbala; Gahtan, Ethan

2012-01-01

Mapping the detailed connectivity patterns (connectomes) of neural circuits is a central goal of neuroscience. The best quantitative approach to analyzing connectome data is still unclear but graph theory has been used with success. We present a graph theoretical model of the posterior lateral line sensorimotor pathway in zebrafish. The model includes 2,616 neurons and 167,114 synaptic connections. Model neurons represent known cell types in zebrafish larvae, and connections were set stochastically following rules based on biological literature. Thus, our model is a uniquely detailed computational representation of a vertebrate connectome. The connectome has low overall connection density, with 2.45% of all possible connections, a value within the physiological range. We used graph theoretical tools to compare the zebrafish connectome graph to small-world, random and structured random graphs of the same size. For each type of graph, 100 randomly generated instantiations were considered. Degree distribution (the number of connections per neuron) varied more in the zebrafish graph than in same size graphs with less biological detail. There was high local clustering and a short average path length between nodes, implying a small-world structure similar to other neural connectomes and complex networks. The graph was found not to be scale-free, in agreement with some other neural connectomes. An experimental lesion was performed that targeted three model brain neurons, including the Mauthner neuron, known to control fast escape turns. The lesion decreased the number of short paths between sensory and motor neurons analogous to the behavioral effects of the same lesion in zebrafish. This model is expandable and can be used to organize and interpret a growing database of information on the zebrafish connectome.

Effects of topography and crustal heterogeneities on the source estimation of LP event at Kilauea volcano

USGS Publications Warehouse

Cesca, S.; Battaglia, J.; Dahm, T.; Tessmer, E.; Heimann, S.; Okubo, P.

2008-01-01

The main goal of this study is to improve the modelling of the source mechanism associated with the generation of long period (LP) signals in volcanic areas. Our intent is to evaluate the effects that detailed structural features of the volcanic models play in the generation of LP signal and the consequent retrieval of LP source characteristics. In particular, effects associated with the presence of topography and crustal heterogeneities are here studied in detail. We focus our study on a LP event observed at Kilauea volcano, Hawaii, in 2001 May. A detailed analysis of this event and its source modelling is accompanied by a set of synthetic tests, which aim to evaluate the effects of topography and the presence of low velocity shallow layers in the source region. The forward problem of Green's function generation is solved numerically following a pseudo-spectral approach, assuming different 3-D models. The inversion is done in the frequency domain and the resulting source mechanism is represented by the sum of two time-dependent terms: a full moment tensor and a single force. Synthetic tests show how characteristic velocity structures, associated with shallow sources, may be partially responsible for the generation of the observed long-lasting ringing waveforms. When applying the inversion technique to Kilauea LP data set, inversions carried out for different crustal models led to very similar source geometries, indicating a subhorizontal cracks. On the other hand, the source time function and its duration are significantly different for different models. These results support the indication of a strong influence of crustal layering on the generation of the LP signal, while the assumption of homogeneous velocity model may bring to misleading results. ?? 2008 The Authors Journal compilation ?? 2008 RAS.

The School Counseling Program Implementation Survey: Initial Instrument Development and Exploratory Factor Analysis

ERIC Educational Resources Information Center

Clemens, Elysia V.; Carey, John C.; Harrington, Karen M.

2010-01-01

This article details the initial development of the School Counseling Program Implementation Survey and psychometric results including reliability and factor structure. An exploratory factor analysis revealed a three-factor model that accounted for 54% of the variance of the intercorrelation matrix and a two-factor model that accounted for 47% of…

76 FR 63159 - Airworthiness Directives; Airbus Model A330-243F Airplanes Equipped With Rolls Royce Trent 700...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-12

... Airworthiness Directives; Airbus Model A330-243F Airplanes Equipped With Rolls Royce Trent 700 Series Engines... Branch, ANM-116, Transport Airplane Directorate, FAA, 1601 Lind Avenue, SW., Renton, Washington 98057... assemblies and along the beam structure of the right and left engine thrust reversers, detailed inspection...

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

NASA Technical Reports Server (NTRS)

Kopasakis, George; Connolly, Joseph W.; Seiel, Jonathan

2016-01-01

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 Dynamic Modeling of the NASA Supersonic Concept Vehicle for AeroPropulsoServoElasticity

NASA Technical Reports Server (NTRS)

Kopasakis, George; Connolly, Joseph W.; 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 lowboom 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.

Order within disorder: The atomic structure of ion-beam sputtered amorphous tantala (a-Ta₂O₅)

DOE PAGES

Bassiri, Riccardo; Liou, Franklin; Abernathy, Matthew R.; ...

2015-03-01

Amorphous tantala (a-Ta₂O₅) is a technologically important material often used in high-performance coatings. Understanding this material at the atomic level provides a way to further improve performance. This work details extended X-ray absorption fine structure measurements of a-Ta₂O₅ coatings, where high-quality experimental data and theoretical fits have allowed a detailed interpretation of the nearest-neighbor distributions. It was found that the tantalum atom is surrounded by four shells of atoms in sequence; oxygen, tantalum, oxygen, and tantalum. A discussion is also included on how these models can be interpreted within the context of published crystalline Ta₂O₅ and other a-T₂O₅ studies.

Requirements and principles for the implementation and construction of large-scale geographic information systems

NASA Technical Reports Server (NTRS)

Smith, Terence R.; Menon, Sudhakar; Star, Jeffrey L.; Estes, John E.

1987-01-01

This paper provides a brief survey of the history, structure and functions of 'traditional' geographic information systems (GIS), and then suggests a set of requirements that large-scale GIS should satisfy, together with a set of principles for their satisfaction. These principles, which include the systematic application of techniques from several subfields of computer science to the design and implementation of GIS and the integration of techniques from computer vision and image processing into standard GIS technology, are discussed in some detail. In particular, the paper provides a detailed discussion of questions relating to appropriate data models, data structures and computational procedures for the efficient storage, retrieval and analysis of spatially-indexed data.

Proton channel models

PubMed Central

Pupo, Amaury; Baez-Nieto, David; Martínez, Agustín; Latorre, Ramón; González, Carlos

2014-01-01

Voltage-gated proton channels are integral membrane proteins with the capacity to permeate elementary particles in a voltage and pH dependent manner. These proteins have been found in several species and are involved in various physiological processes. Although their primary topology is known, lack of details regarding their structures in the open conformation has limited analyses toward a deeper understanding of the molecular determinants of their function and regulation. Consequently, the function-structure relationships have been inferred based on homology models. In the present work, we review the existing proton channel models, their assumptions, predictions and the experimental facts that support them. Modeling proton channels is not a trivial task due to the lack of a close homolog template. Hence, there are important differences between published models. This work attempts to critically review existing proton channel models toward the aim of contributing to a better understanding of the structural features of these proteins. PMID:24755912

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.

Coarse-Grained Structural Modeling of Molecular Motors Using Multibody Dynamics

PubMed Central

Parker, David; Bryant, Zev; Delp, Scott L.

2010-01-01

Experimental and computational approaches are needed to uncover the mechanisms by which molecular motors convert chemical energy into mechanical work. In this article, we describe methods and software to generate structurally realistic models of molecular motor conformations compatible with experimental data from different sources. Coarse-grained models of molecular structures are constructed by combining groups of atoms into a system of rigid bodies connected by joints. Contacts between rigid bodies enforce excluded volume constraints, and spring potentials model system elasticity. This simplified representation allows the conformations of complex molecular motors to be simulated interactively, providing a tool for hypothesis building and quantitative comparisons between models and experiments. In an example calculation, we have used the software to construct atomically detailed models of the myosin V molecular motor bound to its actin track. The software is available at www.simtk.org. PMID:20428469

An approach for modeling thermal destruction of hazardous wastes in circulating fluidized bed incinerator.

PubMed

Patil, M P; Sonolikar, R L

2008-10-01

This paper presents a detailed computational fluid dynamics (CFD) based approach for modeling thermal destruction of hazardous wastes in a circulating fluidized bed (CFB) incinerator. The model is based on Eular - Lagrangian approach in which gas phase (continuous phase) is treated in a Eularian reference frame, whereas the waste particulate (dispersed phase) is treated in a Lagrangian reference frame. The reaction chemistry hasbeen modeled through a mixture fraction/ PDF approach. The conservation equations for mass, momentum, energy, mixture fraction and other closure equations have been solved using a general purpose CFD code FLUENT4.5. Afinite volume method on a structured grid has been used for solution of governing equations. The model provides detailed information on the hydrodynamics (gas velocity, particulate trajectories), gas composition (CO, CO2, O2) and temperature inside the riser. The model also allows different operating scenarios to be examined in an efficient manner.

ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

PubMed Central

Schöneberg, Johannes; Noé, Frank

2013-01-01

We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics. PMID:24040218

Structure of shock compressed model basaltic glass: Insights from O K-edge X-ray Raman scattering and high-resolution 27Al NMR spectroscopy

NASA Astrophysics Data System (ADS)

Lee, Sung Keun; Park, Sun Young; Kim, Hyo-Im; Tschauner, Oliver; Asimow, Paul; Bai, Ligang; Xiao, Yuming; Chow, Paul

2012-03-01

The detailed atomic structures of shock compressed basaltic glasses are not well understood. Here, we explore the structures of shock compressed silicate glass with a diopside-anorthite eutectic composition (Di64An36), a common Fe-free model basaltic composition, using oxygen K-edge X-ray Raman scattering and high- resolution 27Al solid-state NMR spectroscopy and report previously unknown details of shock-induced changes in the atomic configurations. A topologically driven densification of the Di64An36 glass is indicated by the increase in oxygen K-edge energy for the glass upon shock compression. The first experimental evidence of the increase in the fraction of highly coordinated Al in shock compressed glass is found in the 27Al NMR spectra. This unambiguous evidence of shock-induced changes in Al coordination environments provides atomistic insights into shock compression in basaltic glasses and allows us to microscopically constrain the magnitude of impact events or relevant processes involving natural basalts on Earth and planetary surfaces.

Atomistic Free Energy Model for Nucleic Acids: Simulations of Single-Stranded DNA and the Entropy Landscape of RNA Stem-Loop Structures.

PubMed

Mak, Chi H

2015-11-25

While single-stranded (ss) segments of DNAs and RNAs are ubiquitous in biology, details about their structures have only recently begun to emerge. To study ssDNA and RNAs, we have developed a new Monte Carlo (MC) simulation using a free energy model for nucleic acids that has the atomisitic accuracy to capture fine molecular details of the sugar-phosphate backbone. Formulated on the basis of a first-principle calculation of the conformational entropy of the nucleic acid chain, this free energy model correctly reproduced both the long and short length-scale structural properties of ssDNA and RNAs in a rigorous comparison against recent data from fluorescence resonance energy transfer, small-angle X-ray scattering, force spectroscopy and fluorescence correlation transport measurements on sequences up to ∼100 nucleotides long. With this new MC algorithm, we conducted a comprehensive investigation of the entropy landscape of small RNA stem-loop structures. From a simulated ensemble of ∼10(6) equilibrium conformations, the entropy for the initiation of different size RNA hairpin loops was computed and compared against thermodynamic measurements. Starting from seeded hairpin loops, constrained MC simulations were then used to estimate the entropic costs associated with propagation of the stem. The numerical results provide new direct molecular insights into thermodynaimc measurement from macroscopic calorimetry and melting experiments.

The Presence of Turbulent and Ordered Local Structure within the ICME Shock-sheath and Its Contribution to Forbush Decrease

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

Shaikh, Zubair; Bhaskar, Ankush; Raghav, Anil, E-mail: raghavanil1984@gmail.com

The transient interplanetary disturbances evoke short-time cosmic-ray flux decrease, which is known as Forbush decrease. The traditional model and understanding of Forbush decrease suggest that the sub-structure of an interplanetary counterpart of coronal mass ejection (ICME) independently contributes to cosmic-ray flux decrease. These sub-structures, shock-sheath, and magnetic cloud (MC) manifest as classical two-step Forbush decrease. The recent work by Raghav et al. has shown multi-step decreases and recoveries within the shock-sheath. However, this cannot be explained by the ideal shock-sheath barrier model. Furthermore, they suggested that local structures within the ICME’s sub-structure (MC and shock-sheath) could explain this deviation ofmore » the FD profile from the classical FD. Therefore, the present study attempts to investigate the cause of multi-step cosmic-ray flux decrease and respective recovery within the shock-sheath in detail. A 3D-hodogram method is utilized to obtain more details regarding the local structures within the shock-sheath. This method unambiguously suggests the formation of small-scale local structures within the ICME (shock-sheath and even in MC). Moreover, the method could differentiate the turbulent and ordered interplanetary magnetic field (IMF) regions within the sub-structures of ICME. The study explicitly suggests that the turbulent and ordered IMF regions within the shock-sheath do influence cosmic-ray variations differently.« less

Modeling filtration and fouling with a microstructured membrane filter

NASA Astrophysics Data System (ADS)

Cummings, Linda; Sanaei, Pejman

2017-11-01

Membrane filters find widespread use in diverse applications such as A/C systems and water purification. While the details of the filtration process may vary significantly, the broad challenge of efficient filtration is the same: to achieve finely-controlled separation at low power consumption. The obvious resolution to the challenge would appear simple: use the largest pore size consistent with the separation requirement. However, the membrane characteristics (and hence the filter performance) are far from constant over its lifetime: the particles removed from the feed are deposited within and on the membrane filter, fouling it and degrading the performance over time. The processes by which this occurs are complex, and depend on several factors, including: the internal structure of the membrane and the type of particles in the feed. We present a model for fouling of a simple microstructured membrane, and investigate how the details of the microstructure affect the filtration efficiency. Our idealized membrane consists of bifurcating pores, arranged in a layered structure, so that the number (and size) of pores changes in the depth of the membrane. In particular, we address how the details of the membrane microstructure affect the filter lifetime, and the total throughput. NSF DMS 1615719.

MIST: An Open Source Environmental Modelling Programming Language Incorporating Easy to Use Data Parallelism.

NASA Astrophysics Data System (ADS)

Bellerby, Tim

2014-05-01

Model Integration System (MIST) is open-source environmental modelling programming language that directly incorporates data parallelism. The language is designed to enable straightforward programming structures, such as nested loops and conditional statements to be directly translated into sequences of whole-array (or more generally whole data-structure) operations. MIST thus enables the programmer to use well-understood constructs, directly relating to the mathematical structure of the model, without having to explicitly vectorize code or worry about details of parallelization. A range of common modelling operations are supported by dedicated language structures operating on cell neighbourhoods rather than individual cells (e.g.: the 3x3 local neighbourhood needed to implement an averaging image filter can be simply accessed from within a simple loop traversing all image pixels). This facility hides details of inter-process communication behind more mathematically relevant descriptions of model dynamics. The MIST automatic vectorization/parallelization process serves both to distribute work among available nodes and separately to control storage requirements for intermediate expressions - enabling operations on very large domains for which memory availability may be an issue. MIST is designed to facilitate efficient interpreter based implementations. A prototype open source interpreter is available, coded in standard FORTRAN 95, with tools to rapidly integrate existing FORTRAN 77 or 95 code libraries. The language is formally specified and thus not limited to FORTRAN implementation or to an interpreter-based approach. A MIST to FORTRAN compiler is under development and volunteers are sought to create an ANSI-C implementation. Parallel processing is currently implemented using OpenMP. However, parallelization code is fully modularised and could be replaced with implementations using other libraries. GPU implementation is potentially possible.

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.

Interface structure between tetraglyme and graphite

NASA Astrophysics Data System (ADS)

Minato, Taketoshi; Araki, Yuki; Umeda, Kenichi; Yamanaka, Toshiro; Okazaki, Ken-ichi; Onishi, Hiroshi; Abe, Takeshi; Ogumi, Zempachi

2017-09-01

Clarification of the details of the interface structure between liquids and solids is crucial for understanding the fundamental processes of physical functions. Herein, we investigate the structure of the interface between tetraglyme and graphite and propose a model for the interface structure based on the observation of frequency-modulation atomic force microscopy in liquids. The ordering and distorted adsorption of tetraglyme on graphite were observed. It is found that tetraglyme stably adsorbs on graphite. Density functional theory calculations supported the adsorption structure. In the liquid phase, there is a layered structure of the molecular distribution with an average distance of 0.60 nm between layers.

Structural and functional analysis of a novel psychrophilic β-mannanase from Glaciozyma antarctica PI12

NASA Astrophysics Data System (ADS)

Parvizpour, Sepideh; Razmara, Jafar; Ramli, Aizi Nor Mazila; Md Illias, Rosli; Shamsir, Mohd Shahir

2014-06-01

The structure of a novel psychrophilic β-mannanase enzyme from Glaciozyma antarctica PI12 yeast has been modelled and analysed in detail. To our knowledge, this is the first attempt to model a psychrophilic β-mannanase from yeast. To this end, a 3D structure of the enzyme was first predicted using a threading method because of the low sequence identity (<30 %) using MODELLER9v12 and simulated using GROMACS at varying low temperatures for structure refinement. Comparisons with mesophilic and thermophilic mannanases revealed that the psychrophilic mannanase contains longer loops and shorter helices, increases in the number of aromatic and hydrophobic residues, reductions in the number of hydrogen bonds and salt bridges and numerous amino acid substitutions on the surface that increased the flexibility and its efficiency for catalytic reactions at low temperatures.

Automated design optimization of supersonic airplane wing structures under dynamic constraints

NASA Technical Reports Server (NTRS)

Fox, R. L.; Miura, H.; Rao, S. S.

1972-01-01

The problems of the preliminary and first level detail design of supersonic aircraft wings are stated as mathematical programs and solved using automated optimum design techniques. The problem is approached in two phases: the first is a simplified equivalent plate model in which the envelope, planform and structural parameters are varied to produce a design, the second is a finite element model with fixed configuration in which the material distribution is varied. Constraints include flutter, aeroelastically computed stresses and deflections, natural frequency and a variety of geometric limitations.

Developments to the Sylvan stand structure model to describe wood quality changes in southern bottomland hardwood forests because of forest management

Treesearch

Ian R. Scott

2009-01-01

Growth models can produce a wealth of detailed information that is often very difficult to perceive because it is frequently presented either as summary tables, stand view or landscape view visualizations. We have developed new tools for use with the Sylvan model (Larsen 1994) that allow the analysis of wood-quality changes as a consequence of forest management....

YAH-63 Helicopter Crashworthiness Simulation and Analysis

DTIC Science & Technology

1983-02-01

had dual 6.00-6 tires and wheels with full caster attachment to a support strut which incorporated a shimmy damper, self- centering device, and swivel...modeled in detail. Each struo- "tural member, link, and wheel of the nose and main landing gears was modeled and th. shook strut properties were derived...COMPARISON ....................... 80 6.1 KRASH Model Modifications ................. 80 6.2 Comparison of Overall Structural Response. 82 6.3 Landing

Three-Dimensional Anisotropic Acoustic and Elastic Full-Waveform Seismic Inversion

NASA Astrophysics Data System (ADS)

Warner, M.; Morgan, J. V.

2013-12-01

Three-dimensional full-waveform inversion is a high-resolution, high-fidelity, quantitative, seismic imaging technique that has advanced rapidly within the oil and gas industry. The method involves the iterative improvement of a starting model using a series of local linearized updates to solve the full non-linear inversion problem. During the inversion, forward modeling employs the full two-way three-dimensional heterogeneous anisotropic acoustic or elastic wave equation to predict the observed raw field data, wiggle-for-wiggle, trace-by-trace. The method is computationally demanding; it is highly parallelized, and runs on large multi-core multi-node clusters. Here, we demonstrate what can be achieved by applying this newly practical technique to several high-density 3D seismic datasets that were acquired to image four contrasting sedimentary targets: a gas cloud above an oil reservoir, a radially faulted dome, buried fluvial channels, and collapse structures overlying an evaporate sequence. We show that the resulting anisotropic p-wave velocity models match in situ measurements in deep boreholes, reproduce detailed structure observed independently on high-resolution seismic reflection sections, accurately predict the raw seismic data, simplify and sharpen reverse-time-migrated reflection images of deeper horizons, and flatten Kirchhoff-migrated common-image gathers. We also show that full-elastic 3D full-waveform inversion of pure pressure data can generate a reasonable shear-wave velocity model for one of these datasets. For two of the four datasets, the inclusion of significant transversely isotropic anisotropy with a vertical axis of symmetry was necessary in order to fit the kinematics of the field data properly. For the faulted dome, the full-waveform-inversion p-wave velocity model recovers the detailed structure of every fault that can be seen on coincident seismic reflection data. Some of the individual faults represent high-velocity zones, some represent low-velocity zones, some have more-complex internal structure, and some are visible merely as offsets between two regions with contrasting velocity. Although this has not yet been demonstrated quantitatively for this dataset, it seems likely that at least some of this fine structure in the recovered velocity model is related to the detailed lithology, strain history and fluid properties within the individual faults. We have here applied this technique to seismic data that were acquired by the extractive industries, however this inversion scheme is immediately scalable and applicable to a much wider range of problems given sufficient quality and density of observed data. Potential targets range from shallow magma chambers beneath active volcanoes, through whole-crustal sections across plate boundaries, to regional and whole-Earth models.

Biologically Inspired, Anisoptropic Flexible Wing for Optimal Flapping Flight

DTIC Science & Technology

2013-01-31

Anisotropic Flexible Wing for Optimal Flapping Flight FA9550-07-1-0547 Sb. GRANT NUMBER Sc. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Sd. PROJECT NUMBER...anisotropic structural flexibility ; c) Conducted coordinated experimental and computational modeling to determine the roles of aerodynamic loading, wing inertia...and structural flexibility and elasticity; and d) Developed surrogate tools for flapping wing MA V design and optimization. Detailed research

Modifiability Tactics

DTIC Science & Technology

2007-09-01

The Pattern Understood in Terms of Tactics 44 13.4 Variants 44 14 Microkernel Pattern 45 14.1 Problem 45 14.2 Solution 45 14.3 The Pattern...Figure 12: Model-View-Controller Pattern Structure 42 Figure 13: Presentation-Abstraction-Control Pattern Structure 43 Figure 14: Microkernel ...Presentation- Abstraction- Control X X X X Microkernel X X X X X Reflection X X Each pattern is described in more detail in the

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.

Brain and Behavioral Pathology in an Animal Model of Wernicke’s Encephalopathy and Wernicke-Korsakoff Syndrome

PubMed Central

Vetreno, Ryan P.; Ramos, Raddy L.; Anzalone, Steven; Savage, Lisa M.

2012-01-01

Animal models provide the opportunity for in-depth and experimental investigation into the anatomical and physiological underpinnings of human neurological disorders. Rodent models of thiamine deficiency have yielded significant insight into the structural, neurochemical and cognitive deficits associated with thiamine deficiency as well as proven useful toward greater understanding of memory function in the intact brain. In this review, we discuss the anatomical, neurochemical and behavioral changes that occur during the acute and chronic phases of thiamine deficiency and describe how rodent models of Wernicke-Korsakoff Syndrome aid in developing a more detailed picture of brain structures involved in learning and memory. PMID:22192411

Brain and behavioral pathology in an animal model of Wernicke's encephalopathy and Wernicke-Korsakoff Syndrome.

PubMed

Vetreno, Ryan P; Ramos, Raddy L; Anzalone, Steven; Savage, Lisa M

2012-02-03

Animal models provide the opportunity for in-depth and experimental investigation into the anatomical and physiological underpinnings of human neurological disorders. Rodent models of thiamine deficiency have yielded significant insight into the structural, neurochemical and cognitive deficits associated with thiamine deficiency as well as proven useful toward greater understanding of memory function in the intact brain. In this review, we discuss the anatomical, neurochemical and behavioral changes that occur during the acute and chronic phases of thiamine deficiency and describe how rodent models of Wernicke-Korsakoff Syndrome aid in developing a more detailed picture of brain structures involved in learning and memory. Copyright © 2011 Elsevier B.V. All rights reserved.

Calibrating White Dwarf Asteroseismic Fitting Techniques

NASA Astrophysics Data System (ADS)

Castanheira, B. G.; Romero, A. D.; Bischoff-Kim, A.

2017-03-01

The main goal of looking for intrinsic variability in stars is the unique opportunity to study their internal structure. Once we have extracted independent modes from the data, it appears to be a simple matter of comparing the period spectrum with those from theoretical model grids to learn the inner structure of that star. However, asteroseismology is much more complicated than this simple description. We must account not only for observational uncertainties in period determination, but most importantly for the limitations of the model grids, coming from the uncertainties in the constitutive physics, and of the fitting techniques. In this work, we will discuss results of numerical experiments where we used different independently calculated model grids (white dwarf cooling models WDEC and fully evolutionary LPCODE-PUL) and fitting techniques to fit synthetic stars. The advantage of using synthetic stars is that we know the details of their interior structure so we can assess how well our models and fitting techniques are able to the recover the interior structure, as well as the stellar parameters.

Design of footbridge with double curvature made of UHPC

NASA Astrophysics Data System (ADS)

Kněž, P.; Tej, P.; Čítek, D.; Kolísko, J.

2017-09-01

This paper presents design of footbridge with double curvature made of UHPC. The structure is designed as a single-span bridge. The span of the bridge is 10.00 m, and the width of the deck is 1.50 m. The thickness of shell structure is 0.03 m for walls and 0.045 m for deck. The main structure of the bridge is one arch shell structure with sidewalls made of UHPC with dispersed steel fibers with conventional reinforcement only at anchoring areas. The structure was designed on the basis of the numerical model. Model was subsequently clarified on the basis of the first test elements. Paper presents detailed course on design of the bridge and presentation will contain also installation in landscape and results of static and dynamic loading tests.

Identification of Historical Veziragasi Aqueduct Using the Operational Modal Analysis

PubMed Central

Ercan, E.; Nuhoglu, A.

2014-01-01

This paper describes the results of a model updating study conducted on a historical aqueduct, called Veziragasi, in Turkey. The output-only modal identification results obtained from ambient vibration measurements of the structure were used to update a finite element model of the structure. For the purposes of developing a solid model of the structure, the dimensions of the structure, defects, and material degradations in the structure were determined in detail by making a measurement survey. For evaluation of the material properties of the structure, nondestructive and destructive testing methods were applied. The modal analysis of the structure was calculated by FEM. Then, a nondestructive dynamic test as well as operational modal analysis was carried out and dynamic properties were extracted. The natural frequencies and corresponding mode shapes were determined from both theoretical and experimental modal analyses and compared with each other. A good harmony was attained between mode shapes, but there were some differences between natural frequencies. The sources of the differences were introduced and the FEM model was updated by changing material parameters and boundary conditions. Finally, the real analytical model of the aqueduct was put forward and the results were discussed. PMID:24511287

Weak lensing shear and aperture mass from linear to non-linear scales

NASA Astrophysics Data System (ADS)

Munshi, Dipak; Valageas, Patrick; Barber, Andrew J.

2004-05-01

We describe the predictions for the smoothed weak lensing shear, γs, and aperture mass,Map, of two simple analytical models of the density field: the minimal tree model and the stellar model. Both models give identical results for the statistics of the three-dimensional density contrast smoothed over spherical cells and only differ by the detailed angular dependence of the many-body density correlations. We have shown in previous work that they also yield almost identical results for the probability distribution function (PDF) of the smoothed convergence, κs. We find that the two models give rather close results for both the shear and the positive tail of the aperture mass. However, we note that at small angular scales (θs<~ 2 arcmin) the tail of the PDF, , for negative Map shows a strong variation between the two models, and the stellar model actually breaks down for θs<~ 0.4 arcmin and Map < 0. This shows that the statistics of the aperture mass provides a very precise probe of the detailed structure of the density field, as it is sensitive to both the amplitude and the detailed angular behaviour of the many-body correlations. On the other hand, the minimal tree model shows good agreement with numerical simulations over all the scales and redshifts of interest, while both models provide a good description of the PDF, , of the smoothed shear components. Therefore, the shear and the aperture mass provide robust and complementary tools to measure the cosmological parameters as well as the detailed statistical properties of the density field.

Simulation Studies of Forest Structure using 3D Lidar and Radar Models

NASA Technical Reports Server (NTRS)

Sun, Guoqing; Ranson, K. Jon; Koetz, Benjamin; Liu, Dawei

2007-01-01

The use of lidars and radars to measure forest structure attributes such as height and biomass are being considered for future Earth Observation missions. Large footprint lidar makes a direct measurement of the heights of scatterers in the illuminated footprint and can yield information about the vertical profile of the canopy. Synthetic Aperture Radar (SAR) is known to sense the canopy volume, especially at longer wavelengths and is useful for estimating biomass. Interferometric SAR (InSAR) has been shown to yield forest canopy height information. For example, the height of scattering phase retrieved from InSAR data is considered to be correlated with the three height and the spatial structure of the forest stand. There is much interest in exploiting these technologies separately and together to get important information for carbon cycle and ecosystem science. More detailed information of the electromagnetic radiation interactions within forest canopies is needed. And backscattering models can be of much utility here. As part of a NASA funded project to explore data fusion, a three-dimensional (3D) coherent radar backscattering model and a 3D lidar backscatter models were used to investigate the use of large footprint lidar, SAR and InSAR for characterizing realistic forest scenes. For this paper, we use stem maps and other forest measurements to develop a realistic spatial structure of a spruce-hemlock forest canopy found in Maine, USA. The radar and lidar models used measurements of the 3D forest scene as input and simulated the coherent radar backscattering signature and 1064nm energy backscatter, respectively. The relationships of backscatter derived forest structure were compared with field measurements. In addition, we also had detailed airborne lidar (Laser Imaging Vegetation Sensor, LVIS) data available over the stem map sites that was used to study the accuracies of tree height derived from modeled SAR backscatter and the scattering phase center retrieved from the simulated InSAR data will be compared with the height indices, or other structure parameters derived from the lidar data. These results will address the possible synergies between lidar and radar in data in terms of forest structural information.

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method

PubMed Central

2013-01-01

Background Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajectories is central to understanding the relationship between protein dynamics and function. Computational approaches that build on the Molecular Dynamics framework are in principle able to model transition trajectories at great detail but also at considerable computational cost. Methods that delay consideration of dynamics and focus instead on elucidating energetically-credible conformational paths connecting two functionally-relevant structures provide a complementary approach. Effective sampling-based path planning methods originating in robotics have been recently proposed to produce conformational paths. These methods largely model short peptides or address large proteins by simplifying conformational space. Methods We propose a robotics-inspired method that connects two given structures of a protein by sampling conformational paths. The method focuses on small- to medium-size proteins, efficiently modeling structural deformations through the use of the molecular fragment replacement technique. In particular, the method grows a tree in conformational space rooted at the start structure, steering the tree to a goal region defined around the goal structure. We investigate various bias schemes over a progress coordinate for balance between coverage of conformational space and progress towards the goal. A geometric projection layer promotes path diversity. A reactive temperature scheme allows sampling of rare paths that cross energy barriers. Results and conclusions Experiments are conducted on small- to medium-size proteins of length up to 214 amino acids and with multiple known functionally-relevant states, some of which are more than 13Å apart of each-other. Analysis reveals that the method effectively obtains conformational paths connecting structural states that are significantly different. A detailed analysis on the depth and breadth of the tree suggests that a soft global bias over the progress coordinate enhances sampling and results in higher path diversity. The explicit geometric projection layer that biases the exploration away from over-sampled regions further increases coverage, often improving proximity to the goal by forcing the exploration to find new paths. The reactive temperature scheme is shown effective in increasing path diversity, particularly in difficult structural transitions with known high-energy barriers. PMID:24565158

An implicit divalent counterion force field for RNA molecular dynamics

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

Henke, Paul S.; Mak, Chi H., E-mail: cmak@usc.edu; Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089

How to properly account for polyvalent counterions in a molecular dynamics simulation of polyelectrolytes such as nucleic acids remains an open question. Not only do counterions such as Mg{sup 2+} screen electrostatic interactions, they also produce attractive intrachain interactions that stabilize secondary and tertiary structures. Here, we show how a simple force field derived from a recently reported implicit counterion model can be integrated into a molecular dynamics simulation for RNAs to realistically reproduce key structural details of both single-stranded and base-paired RNA constructs. This divalent counterion model is computationally efficient. It works with existing atomistic force fields, or coarse-grainedmore » models may be tuned to work with it. We provide optimized parameters for a coarse-grained RNA model that takes advantage of this new counterion force field. Using the new model, we illustrate how the structural flexibility of RNA two-way junctions is modified under different salt conditions.« less

Nonlinear Pressurization and Modal Analysis Procedure for Dynamic Modeling of Inflatable Structures

NASA Technical Reports Server (NTRS)

Smalley, Kurt B.; Tinker, Michael L.; Saxon, Jeff (Technical Monitor)

2002-01-01

An introduction and set of guidelines for finite element dynamic modeling of nonrigidized inflatable structures is provided. A two-step approach is presented, involving 1) nonlinear static pressurization of the structure and updating of the stiffness matrix and 2) hear normal modes analysis using the updated stiffness. Advantages of this approach are that it provides physical realism in modeling of pressure stiffening, and it maintains the analytical convenience of a standard bear eigensolution once the stiffness has been modified. Demonstration of the approach is accomplished through the creation and test verification of an inflated cylinder model using a large commercial finite element code. Good frequency and mode shape comparisons are obtained with test data and previous modeling efforts, verifying the accuracy of the technique. Problems encountered in the application of the approach, as well as their solutions, are discussed in detail.

Numerical modelling of electromagnetic loads on fusion device structures

NASA Astrophysics Data System (ADS)

Bettini, Paolo; Furno Palumbo, Maurizio; Specogna, Ruben

2014-03-01

In magnetic confinement fusion devices, during abnormal operations (disruptions) the plasma begins to move rapidly towards the vessel wall in a vertical displacement event (VDE), producing plasma current asymmetries, vessel eddy currents and open field line halo currents, each of which can exert potentially damaging forces upon the vessel and in-vessel components. This paper presents a methodology to estimate electromagnetic loads, on three-dimensional conductive structures surrounding the plasma, which arise from the interaction of halo-currents associated to VDEs with a magnetic field of the order of some Tesla needed for plasma confinement. Lorentz forces, calculated by complementary formulations, are used as constraining loads in a linear static structural analysis carried out on a detailed model of the mechanical structures of a representative machine.

Structural Diversity in the Dandelion (Taraxacum officinale) Polyphenol Oxidase Family Results in Different Responses to Model Substrates

PubMed Central

Dirks-Hofmeister, Mareike E.; Singh, Ratna; Leufken, Christine M.; Inlow, Jennifer K.; Moerschbacher, Bruno M.

2014-01-01

Polyphenol oxidases (PPOs) are ubiquitous type-3 copper enzymes that catalyze the oxygen-dependent conversion of o-diphenols to the corresponding quinones. In most plants, PPOs are present as multiple isoenzymes that probably serve distinct functions, although the precise relationship between sequence, structure and function has not been addressed in detail. We therefore compared the characteristics and activities of recombinant dandelion PPOs to gain insight into the structure–function relationships within the plant PPO family. Phylogenetic analysis resolved the 11 isoenzymes of dandelion into two evolutionary groups. More detailed in silico and in vitro analyses of four representative PPOs covering both phylogenetic groups were performed. Molecular modeling and docking predicted differences in enzyme-substrate interactions, providing a structure-based explanation for grouping. One amino acid side chain positioned at the entrance to the active site (position HB2+1) potentially acts as a “selector” for substrate binding. In vitro activity measurements with the recombinant, purified enzymes also revealed group-specific differences in kinetic parameters when the selected PPOs were presented with five model substrates. The combination of our enzyme kinetic measurements and the in silico docking studies therefore indicate that the physiological functions of individual PPOs might be defined by their specific interactions with different natural substrates. PMID:24918587

Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane.

PubMed

Zhang, Mingzhen; Zheng, Jie; Nussinov, Ruth; Ma, Buyong

2016-09-15

Dysfunction of Bax, a pro-apoptotic regulator of cellular metabolism is implicated in neurodegenerative diseases and cancer. We have constructed the first atomistic models of the Bax oligomeric pore consisting with experimental residue-residue distances. The models are stable, capturing well double electron-electron resonance (DEER) spectroscopy measurements and provide structural details in line with the DEER data. Comparison with the latest experimental results revealed that our models agree well with both Bax and Bak pores, pointed to a converged structural arrangement for Bax and Bak pore formation. Using multi-scale molecular dynamics simulations, we probed mutational effects on Bax transformation from monomer → dimer → membrane pore formation at atomic resolution. We observe that two cancer-related mutations, G40E and S118I, allosterically destabilize the monomer and stabilize an off-pathway swapped dimer, preventing productive pore formation. This observation suggests a mechanism whereby the mutations may work mainly by over-stabilizing the monomer → dimer transformation toward an unproductive off-pathway swapped-dimer state. Our observations point to misfolded Bax states, shedding light on the molecular mechanism of Bax mutation-elicited cancer. Most importantly, the structure of the Bax pore facilitates future study of releases cytochrome C in atomic detail.

Fluid-Structure Interaction Analysis of Ruptured Mitral Chordae Tendineae.

PubMed

Toma, Milan; Bloodworth, Charles H; Pierce, Eric L; Einstein, Daniel R; Cochran, Richard P; Yoganathan, Ajit P; Kunzelman, Karyn S

2017-03-01

The chordal structure is a part of mitral valve geometry that has been commonly neglected or simplified in computational modeling due to its complexity. However, these simplifications cannot be used when investigating the roles of individual chordae tendineae in mitral valve closure. For the first time, advancements in imaging, computational techniques, and hardware technology make it possible to create models of the mitral valve without simplifications to its complex geometry, and to quickly run validated computer simulations that more realistically capture its function. Such simulations can then be used for a detailed analysis of chordae-related diseases. In this work, a comprehensive model of a subject-specific mitral valve with detailed chordal structure is used to analyze the distinct role played by individual chordae in closure of the mitral valve leaflets. Mitral closure was simulated for 51 possible chordal rupture points. Resultant regurgitant orifice area and strain change in the chordae at the papillary muscle tips were then calculated to examine the role of each ruptured chorda in the mitral valve closure. For certain subclassifications of chordae, regurgitant orifice area was found to trend positively with ruptured chordal diameter, and strain changes correlated negatively with regurgitant orifice area. Further advancements in clinical imaging modalities, coupled with the next generation of computational techniques will enable more physiologically realistic simulations.

Fluid-Structure Interaction Analysis of Ruptured Mitral Chordae Tendineae

PubMed Central

Toma, Milan; Bloodworth, Charles H.; Pierce, Eric L.; Einstein, Daniel R.; Cochran, Richard P.; Yoganathan, Ajit P.; Kunzelman, Karyn S.

2016-01-01

The chordal structure is a part of mitral valve geometry that has been commonly neglected or simplified in computational modeling due to its complexity. However, these simplifications cannot be used when investigating the roles of individual chordae tendineae in mitral valve closure. For the first time, advancements in imaging, computational techniques, and hardware technology make it possible to create models of the mitral valve without simplifications to its complex geometry, and to quickly run validated computer simulations that more realistically capture its function. Such simulations can then be used for a detailed analysis of chordae-related diseases. In this work, a comprehensive model of a subject-specific mitral valve with detailed chordal structure is used to analyze the distinct role played by individual chordae in closure of the mitral valve leaflets. Mitral closure was simulated for 51 possible chordal rupture points. Resultant regurgitant orifice area and strain change in the chordae at the papillary muscle tips were then calculated to examine the role of each ruptured chorda in the mitral valve closure. For certain subclassifications of chordae, regurgitant orifice area was found to trend positively with ruptured chordal diameter, and strain changes correlated negatively with regurgitant orifice area. Further advancements in clinical imaging modalities, coupled with the next generation of computational techniques will enable more physiologically realistic simulations. PMID:27624659

Oncogenic Mutations Differentially Affect Bax Monomer, Dimer, and Oligomeric Pore Formation in the Membrane

NASA Astrophysics Data System (ADS)

Zhang, Mingzhen; Zheng, Jie; Nussinov, Ruth; Ma, Buyong

2016-09-01

Dysfunction of Bax, a pro-apoptotic regulator of cellular metabolism is implicated in neurodegenerative diseases and cancer. We have constructed the first atomistic models of the Bax oligomeric pore consisting with experimental residue-residue distances. The models are stable, capturing well double electron-electron resonance (DEER) spectroscopy measurements and provide structural details in line with the DEER data. Comparison with the latest experimental results revealed that our models agree well with both Bax and Bak pores, pointed to a converged structural arrangement for Bax and Bak pore formation. Using multi-scale molecular dynamics simulations, we probed mutational effects on Bax transformation from monomer → dimer → membrane pore formation at atomic resolution. We observe that two cancer-related mutations, G40E and S118I, allosterically destabilize the monomer and stabilize an off-pathway swapped dimer, preventing productive pore formation. This observation suggests a mechanism whereby the mutations may work mainly by over-stabilizing the monomer → dimer transformation toward an unproductive off-pathway swapped-dimer state. Our observations point to misfolded Bax states, shedding light on the molecular mechanism of Bax mutation-elicited cancer. Most importantly, the structure of the Bax pore facilitates future study of releases cytochrome C in atomic detail.

Relativistic opacities for astrophysical applications

DOE PAGES

Fontes, Christopher John; Fryer, Christopher Lee; Hungerford, Aimee L.; ...

2015-06-29

Here, we report on the use of the Los Alamos suite of relativistic atomic physics codes to generate radiative opacities for the modeling of astrophysically relevant plasmas under local thermodynamic equilibrium (LTE) conditions. The atomic structure calculations are carried out in fine-structure detail, including full configuration interaction. Three example applications are considered: iron opacities at conditions relevant to the base of the solar convection zone, nickel opacities for the modeling of stellar envelopes, and samarium opacities for the modeling of light curves produced by neutron star mergers. In the first two examples, comparisons are made between opacities that are generatedmore » with the fully and semi-relativistic capabilities in the Los Alamos suite of codes. As expected for these highly charged, iron-peak ions, the two methods produce reasonably similar results, providing confidence that the numerical methods have been correctly implemented. However, discrepancies greater than 10% are observed for nickel and investigated in detail. In the final application, the relativistic capability is used in a preliminary investigation of the complicated absorption spectrum associated with cold lanthanide elements.« less

Automated adaptive inference of phenomenological dynamical models.

PubMed

Daniels, Bryan C; Nemenman, Ilya

2015-08-21

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

Similarity measure and domain adaptation in multiple mixture model clustering: An application to image processing.

PubMed

Leong, Siow Hoo; Ong, Seng Huat

2017-01-01

This paper considers three crucial issues in processing scaled down image, the representation of partial image, similarity measure and domain adaptation. Two Gaussian mixture model based algorithms are proposed to effectively preserve image details and avoids image degradation. Multiple partial images are clustered separately through Gaussian mixture model clustering with a scan and select procedure to enhance the inclusion of small image details. The local image features, represented by maximum likelihood estimates of the mixture components, are classified by using the modified Bayes factor (MBF) as a similarity measure. The detection of novel local features from MBF will suggest domain adaptation, which is changing the number of components of the Gaussian mixture model. The performance of the proposed algorithms are evaluated with simulated data and real images and it is shown to perform much better than existing Gaussian mixture model based algorithms in reproducing images with higher structural similarity index.

Similarity measure and domain adaptation in multiple mixture model clustering: An application to image processing

PubMed Central

Leong, Siow Hoo

2017-01-01

This paper considers three crucial issues in processing scaled down image, the representation of partial image, similarity measure and domain adaptation. Two Gaussian mixture model based algorithms are proposed to effectively preserve image details and avoids image degradation. Multiple partial images are clustered separately through Gaussian mixture model clustering with a scan and select procedure to enhance the inclusion of small image details. The local image features, represented by maximum likelihood estimates of the mixture components, are classified by using the modified Bayes factor (MBF) as a similarity measure. The detection of novel local features from MBF will suggest domain adaptation, which is changing the number of components of the Gaussian mixture model. The performance of the proposed algorithms are evaluated with simulated data and real images and it is shown to perform much better than existing Gaussian mixture model based algorithms in reproducing images with higher structural similarity index. PMID:28686634

Automated adaptive inference of phenomenological dynamical models

PubMed Central

Daniels, Bryan C.; Nemenman, Ilya

2015-01-01

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

Extended Graph-Based Models for Enhanced Similarity Search in Cavbase.

PubMed

Krotzky, Timo; Fober, Thomas; Hüllermeier, Eyke; Klebe, Gerhard

2014-01-01

To calculate similarities between molecular structures, measures based on the maximum common subgraph are frequently applied. For the comparison of protein binding sites, these measures are not fully appropriate since graphs representing binding sites on a detailed atomic level tend to get very large. In combination with an NP-hard problem, a large graph leads to a computationally demanding task. Therefore, for the comparison of binding sites, a less detailed coarse graph model is used building upon so-called pseudocenters. Consistently, a loss of structural data is caused since many atoms are discarded and no information about the shape of the binding site is considered. This is usually resolved by performing subsequent calculations based on additional information. These steps are usually quite expensive, making the whole approach very slow. The main drawback of a graph-based model solely based on pseudocenters, however, is the loss of information about the shape of the protein surface. In this study, we propose a novel and efficient modeling formalism that does not increase the size of the graph model compared to the original approach, but leads to graphs containing considerably more information assigned to the nodes. More specifically, additional descriptors considering surface characteristics are extracted from the local surface and attributed to the pseudocenters stored in Cavbase. These properties are evaluated as additional node labels, which lead to a gain of information and allow for much faster but still very accurate comparisons between different structures.

Structure of 8B from elastic and inelastic 7Be+p scattering

NASA Astrophysics Data System (ADS)

Mitchell, J. P.; Rogachev, G. V.; Johnson, E. D.; Baby, L. T.; Kemper, K. W.; Moro, A. M.; Peplowski, P.; Volya, A. S.; Wiedenhöver, I.

2013-05-01

Background: Detailed experimental knowledge of the level structure of light weakly bound nuclei is necessary to guide the development of new theoretical approaches that combine nuclear structure with reaction dynamics.Purpose: The resonant structure of 8B is studied in this work.Method: Excitation functions for elastic and inelastic 7Be+p scattering were measured using a 7Be rare isotope beam. Excitation energies ranging between 1.6 and 3.4 MeV were investigated. An R-matrix analysis of the excitation functions was performed.Results: New low-lying resonances at 1.9, 2.54, and 3.3 MeV in 8B are reported with spin-parity assignment 0+, 2+, and 1+, respectively. Comparison to the time-dependent continuum shell (TDCSM) model and ab initio no-core shell model/resonating-group method (NCSM/RGM) calculations is performed. This work is a more detailed analysis of the data first published as a Rapid Communication. J. P. Mitchell, G. V. Rogachev, E. D. Johnson, L. T. Baby, K. W. Kemper , [Phys. Rev. CPRVCAN0556-281310.1103/PhysRevC.82.011601 82, 011601(R) (2010)].Conclusions: Identification of the 0+, 2+, 1+ states that were predicted by some models at relatively low energy but never observed experimentally is an important step toward understanding the structure of 8B. Their identification was aided by having both elastic and inelastic scattering data. Direct comparison of the cross sections and phase shifts predicted by the TDCSM and ab initio no-core shell model coupled with the resonating group method is of particular interest and provides a good test for these theoretical approaches.

Strengthening the weak link: Built Environment modelling for loss analysis

NASA Astrophysics Data System (ADS)

Millinship, I.

2012-04-01

Methods to analyse insured losses from a range of natural perils, including pricing by primary insurers and catastrophe modelling by reinsurers, typically lack sufficient exposure information. Understanding the hazard intensity in terms of spatial severity and frequency is only the first step towards quantifying the risk of a catastrophic event. For any given event we need to know: Are any structures affected? What type of buildings are they? How much damaged occurred? How much will the repairs cost? To achieve this, detailed exposure information is required to assess the likely damage and to effectively calculate the resultant loss. Modelling exposures in the Built Environment therefore plays as important a role in understanding re/insurance risk as characterising the physical hazard. Across both primary insurance books and aggregated reinsurance portfolios, the location of a property (a risk) and its monetary value is typically known. Exactly what that risk is in terms of detailed property descriptors including structure type and rebuild cost - and therefore its vulnerability to loss - is often omitted. This data deficiency is a primary source of variations between modelled losses and the actual claims value. Built Environment models are therefore required at a high resolution to describe building attributes that relate vulnerability to property damage. However, national-scale household-level datasets are often not computationally practical in catastrophe models and data must be aggregated. In order to provide more accurate risk analysis, we have developed and applied a methodology for Built Environment modelling for incorporation into a range of re/insurance applications, including operational models for different international regions and different perils and covering residential, commercial and industry exposures. Illustrated examples are presented, including exposure modelling suitable for aggregated reinsurance analysis for the UK and bespoke high resolution modelling for industrial sites in Germany. A range of attributes are included following detailed claims analysis and engineering research with property type, age and condition identified as important differentiators of damage from flood, wind and freeze events.

Theoretical calculations of oxygen relaxation in YBa2Cu3O6+x ceramics

NASA Astrophysics Data System (ADS)

Mi, Y.; Schaller, R.; Sathish, S.; Benoit, W.

1991-12-01

A two-dimensional theoretical model of stress-induced point-defect relaxation in a layered structure is presented, with a detailed discussion of the special case of YBa2Cu3O6+x. The experimental results of oxygen relaxation in YBa2Cu3O6+x can be explained qualitatively by this model.

Hand-Held Model of a Sarcomere to Illustrate the Sliding Filament Mechanism in Muscle Contraction

ERIC Educational Resources Information Center

Jittivadhna, Karnyupha; Ruenwongsa, Pintip; Panijpan, Bhinyo

2009-01-01

From our teaching of the contractile unit of the striated muscle, we have found limitations in using textbook illustrations of sarcomere structure and its related dynamic molecular physiological details. A hand-held model of a striated muscle sarcomere made from common items has thus been made by us to enhance students' understanding of the…

Large space telescope engineering scale model optical design

NASA Technical Reports Server (NTRS)

Facey, T. A.

1973-01-01

The objective is to develop the detailed design and tolerance data for the LST engineering scale model optical system. This will enable MSFC to move forward to the optical element procurement phase and also to evaluate tolerances, manufacturing requirements, assembly/checkout procedures, reliability, operational complexity, stability requirements of the structure and thermal system, and the flexibility to change and grow.

The Structure and Dynamics of the Solar Corona and Inner Heliosphere-First Quarter First Year Progress Report

NASA Technical Reports Server (NTRS)

Mikic, Zoran; Grebowsky, J. (Technical Monitor)

2000-01-01

This report details progress during the first quarter of the first year of our Sun-Earth Connections Theory Program (SECTP) contract. Science Applications International Corporation (SAIC) and the University of California, Irvine (UCI) have conducted research into theoretical modeling of active regions, the solar corona, and the inner heliosphere, using the MHD model.

The University Next Door: Developing a Centralized Unit That Strategically Cultivates Community Engagement at an Urban University

ERIC Educational Resources Information Center

Holton, Valerie L.; Early, Jennifer L.; Resler, Meghan; Trussell, Audrey; Howard, Catherine

2016-01-01

Using Kotter's model of change as a framework, this case study will describe the structure and efforts of a centralized unit within an urban, research university to deepen and extend the institutionalization of community engagement. The change model will be described along with details about the implemented strategies and practices that fall…

Simulation of Electric Propulsion Thrusters

DTIC Science & Technology

2011-01-01

and operational lifetime. The second area of modelling activity concerns the plumes produced by electric thrusters. Detailed information on the plumes ...to reproduce the in-orbit space environment using ground-based laboratory facilities. Device modelling also plays an important role in plume ...of the numerical analysis of other aspects of thruster design, such as thermal and structural processes, is omitted here. There are two fundamental

Melt Flow before Crystal Seeding in Cz Si Growth with Transversal MF

NASA Astrophysics Data System (ADS)

Iizuka, Masaya; Mukaiyama, Yuji; Demina, S. E.; Kalaev, V. V.

2017-06-01

Industrial Cz growth of Si crystal of 300 mm and higher diameter usually requires DC magnetic fields (MFs) to suppress turbulence in the melt. We present 3D unsteady analysis of melt turbulent convection in an industrial Cz system coupled with the effect of the transversal MF for different argon gas flow rates for the stage before crystal seeding. We have performed detailed 2D axisymmetric modeling of global heat transfer in the whole Cz furnace. Radiative heat fluxes obtained in 2D modeling have been used in detailed 3D steady and unsteady modeling of crystallization zone. LES method is applied as a predictive approach for modeling of turbulent flow of silicon melt. We have obtained flow structure and temperature distribution in the melt, which were different from previously reported data. We have observed a well-fixed dark spike which includes low temperature melt area on the melt free surface in MF cases. These results indicates that MF and argon flow rate conditions are important to achieve stable positioning of the dark spike on the melt free surface for optimized crystal seeding without uncontrollable meltdown and single crystal structure loss.

Interfacial distribution of mucus under forced expiration in a double bifurcation model

NASA Astrophysics Data System (ADS)

Rajendran, Rahul; Banerjee, Arindam

2017-11-01

Mucus is removed from the lung airways by the rhythmic beating of cilia and the mucus interaction with the turbulent core airflow generated during a cough or forced expiration. The quantity and quality of mucus are adversely altered, impairing mucociliary clearance under chronic pulmonary conditions. Existing studies on airflow induced mucus clearance have established a functional relationship between the airflow rate, mucus properties, flow bias, breathing frequency and clearance; however, the impact of airway branching, gravity, and characterization of primary and secondary flows have not been studied. The focus of the current investigation is the detailed understanding of air-mucus two-phase flow mechanism under steady expiratory airflow in a double bifurcation model. The effect of different airflow rates and mucus viscosities on the flow morphology, mucus layer thickness, mucus clearance and pressure drop across the model will be discussed. The impact of in-plane and out-of-plane configurations of the bifurcation model on the primary and secondary flow structures as well as the mucus distribution will be addressed. In addition, a detailed comparison of the flow structures in the mucus-lined airways, and its corresponding dry wall (no mucus lining) case will be presented.

Mechanical Design Studies of the MQXF Long Model Quadrupole for the HiLumi LHC

DOE PAGES

Pan, Heng; Anderssen, Eric; Ambrosio, Giorgio; ...

2016-12-20

The Large Hadron Collider Luminosity upgrade (HiLumi) program requires new low-β triplet quadrupole magnets, called MQXF, in the Interaction Region (IR) to increase the LHC peak and integrated luminosity. The MQXF magnets, designed and fabricated in collaboration between CERN and the U.S. LARP, will all have the same cross section. The MQXF long model, referred as MQXFA, is a quadrupole using the Nb3Sn superconducting technology with 150 mm aperture and a 4.2 m magnetic length and is the first long prototype of the final MQXF design. The MQXFA magnet is based on the previous LARP HQ and MQXFS designs. Inmore » this paper we present the baseline design of the MQXFA structure with detailed 3D numerical analysis. A detailed tolerance analysis of the baseline case has been performed by using a 3D finite element model, which allows fast computation of structures modelled with actual tolerances. Tolerance sensitivity of each component is discussed to verify the actual tolerances to be achieved by vendors. In conclusion, tolerance stack-up analysis is presented in the end of this paper.« less

Development of a thermal and structural model for a NASTRAN finite-element analysis of a hypersonic wing test structure

NASA Technical Reports Server (NTRS)

Lameris, J.

1984-01-01

The development of a thermal and structural model for a hypersonic wing test structure using the NASTRAN finite-element method as its primary analytical tool is described. A detailed analysis was defined to obtain the temperature and thermal stress distribution in the whole wing as well as the five upper and lower root panels. During the development of the models, it was found that the thermal application of NASTRAN and the VIEW program, used for the generation of the radiation exchange coefficients, were definicent. Although for most of these deficiencies solutions could be found, the existence of one particular deficiency in the current thermal model prevented the final computation of the temperature distributions. A SPAR analysis of a single bay of the wing, using data converted from the original NASTRAN model, indicates that local temperature-time distributions can be obtained with good agreement with the test data. The conversion of the NASTRAN thermal model into a SPAR model is recommended to meet the immediate goal of obtaining an accurate thermal stress distribution.

Experimental evidence and structural modeling of nonstoichiometric (010) surfaces coexisting in hydroxyapatite nano-crystals.

PubMed

Ospina, C A; Terra, J; Ramirez, A J; Farina, M; Ellis, D E; Rossi, A M

2012-01-01

High-resolution transmission electron microscopy (HRTEM) and ab initio quantum-mechanical calculations of electronic structure were combined to investigate the structure of the hydroxyapatite (HA) (010) surface, which plays an important role in HA interactions with biological media. HA was synthesized by in vitro precipitation at 37°C. HRTEM images revealed thin elongated rod nanoparticles with preferential growth along the [001] direction and terminations parallel to the (010) plane. The focal series reconstruction (FSR) technique was applied to develop an atomic-scale structural model of the high-resolution images. The HRTEM simulations identified the coexistence of two structurally distinct terminations for (010) surfaces: a rather flat Ca(II)-terminated surface and a zig-zag structure with open OH channels. Density functional theory (DFT) was applied in a periodic slab plane-wave pseudopotential approach to refine details of atomic coordination and bond lengths of Ca(I) and Ca(II) sites in hydrated HA (010) surfaces, starting from the HRTEM model. Copyright © 2011 Elsevier B.V. All rights reserved.

Failure mechanisms in energy-absorbing composite structures

NASA Astrophysics Data System (ADS)

Johnson, Alastair F.; David, Matthew

2010-11-01

Quasi-static tests are described for determination of the energy-absorption properties of composite crash energy-absorbing segment elements under axial loads. Detailed computer tomography scans of failed specimens were used to identify local compression crush failure mechanisms at the crush front. These mechanisms are important for selecting composite materials for energy-absorbing structures, such as helicopter and aircraft sub-floors. Finite element models of the failure processes are described that could be the basis for materials selection and future design procedures for crashworthy structures.

Effects of potentization in aqueous solutions.

PubMed

Schulte, J

1999-10-01

Over the past two decades, research into structure formation and structure conservation in water has created a significant interest among the homeopathy research community. The formation of sustained static and dynamic structures in aqueous solutions is thought to be synonymous with the possible storage of information in associated liquids. Prominent models and experiments considering this possibility are presented in this paper, and some of their subtleties, which were not given much room in the respective original publications, will be elucidated in more detail here.

Insights from Molecular Dynamics Simulations: Structural Basis for the V567D Mutation-Induced Instability of Zebrafish Alpha-Dystroglycan and Comparison with the Murine Model

PubMed Central

Pirolli, Davide; Sciandra, Francesca; Bozzi, Manuela; Giardina, Bruno; Brancaccio, Andrea; De Rosa, Maria Cristina

2014-01-01

A missense amino acid mutation of valine to aspartic acid in 567 position of alpha-dystroglycan (DG), identified in dag1-mutated zebrafish, results in a reduced transcription and a complete absence of the protein. Lacking experimental structural data for zebrafish DG domains, the detailed mechanism for the observed mutation-induced destabilization of the DG complex and membrane damage, remained unclear. With the aim to contribute to a better clarification of the structure-function relationships featuring the DG complex, three-dimensional structural models of wild-type and mutant (V567D) C-terminal domain of alpha-DG from zebrafish were constructed by a template-based modelling approach. We then ran extensive molecular dynamics (MD) simulations to reveal the structural and dynamic properties of the C-terminal domain and to evaluate the effect of the single mutation on alpha-DG stability. A comparative study has been also carried out on our previously generated model of murine alpha-DG C-terminal domain including the I591D mutation, which is topologically equivalent to the V567D mutation found in zebrafish. Trajectories from MD simulations were analyzed in detail, revealing extensive structural disorder involving multiple beta-strands in the mutated variant of the zebrafish protein whereas local effects have been detected in the murine protein. A biochemical analysis of the murine alpha-DG mutant I591D confirmed a pronounced instability of the protein. Taken together, the computational and biochemical analysis suggest that the V567D/I591D mutation, belonging to the G beta-strand, plays a key role in inducing a destabilization of the alpha-DG C-terminal Ig-like domain that could possibly affect and propagate to the entire DG complex. The structural features herein identified may be of crucial help to understand the molecular basis of primary dystroglycanopathies. PMID:25078606

Insights from molecular dynamics simulations: structural basis for the V567D mutation-induced instability of zebrafish alpha-dystroglycan and comparison with the murine model.

PubMed

Pirolli, Davide; Sciandra, Francesca; Bozzi, Manuela; Giardina, Bruno; Brancaccio, Andrea; De Rosa, Maria Cristina

2014-01-01

A missense amino acid mutation of valine to aspartic acid in 567 position of alpha-dystroglycan (DG), identified in dag1-mutated zebrafish, results in a reduced transcription and a complete absence of the protein. Lacking experimental structural data for zebrafish DG domains, the detailed mechanism for the observed mutation-induced destabilization of the DG complex and membrane damage, remained unclear. With the aim to contribute to a better clarification of the structure-function relationships featuring the DG complex, three-dimensional structural models of wild-type and mutant (V567D) C-terminal domain of alpha-DG from zebrafish were constructed by a template-based modelling approach. We then ran extensive molecular dynamics (MD) simulations to reveal the structural and dynamic properties of the C-terminal domain and to evaluate the effect of the single mutation on alpha-DG stability. A comparative study has been also carried out on our previously generated model of murine alpha-DG C-terminal domain including the I591D mutation, which is topologically equivalent to the V567D mutation found in zebrafish. Trajectories from MD simulations were analyzed in detail, revealing extensive structural disorder involving multiple beta-strands in the mutated variant of the zebrafish protein whereas local effects have been detected in the murine protein. A biochemical analysis of the murine alpha-DG mutant I591D confirmed a pronounced instability of the protein. Taken together, the computational and biochemical analysis suggest that the V567D/I591D mutation, belonging to the G beta-strand, plays a key role in inducing a destabilization of the alpha-DG C-terminal Ig-like domain that could possibly affect and propagate to the entire DG complex. The structural features herein identified may be of crucial help to understand the molecular basis of primary dystroglycanopathies.

Structural response of 1/20-scale models of the Clinch River Breeder Reactor to a simulated hypothetical core disruptive accident. Technical report 4

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

Romander, C. M.; Cagliostro, D. J.

Five experiments were performed to help evaluate the structural integrity of the reactor vessel and head design and to verify code predictions. In the first experiment (SM 1), a detailed model of the head was loaded statically to determine its stiffness. In the remaining four experiments (SM 2 to SM 5), models of the vessel and head were loaded dynamically under a simulated 661 MW-sec hypothetical core disruptive accident (HCDA). Models SM 2 to SM 4, each of increasing complexity, systematically showed the effects of upper internals structures, a thermal liner, core support platform, and torospherical bottom on vessel response.more » Model SM 5, identical to SM 4 but more heavily instrumented, demonstrated experimental reproducibility and provided more comprehensive data. The models consisted of a Ni 200 vessel and core barrel, a head with shielding and simulated component masses, an upper internals structure (UIS), and, in the more complex models SM 4 and SM 5, a Ni 200 thermal liner and core support structure. Water simulated the liquid sodium coolant and a low-density explosive simulated the HCDA loads.« less

Velocity and Attenuation Structure of the Earth's Inner Core Boundary From Semi-Automatic Waveform Modeling

NASA Astrophysics Data System (ADS)

Jin, J.; Song, X.; Sun, D.; Helmberger, D. V.

2013-12-01

The structure of the Earth's inner core boundary (ICB) is complex. Hemispherical differences and local variations of velocity and attenuation structures, as well as the ICB topography have been reported in previous studies. We are using an automatic waveform modeling method to improve the resolution of the ICB structures. The full waveforms of triplicated PKP phases at distance ranges from 120 to 165 degrees are used to model the lowermost 200 km of the outer core and the uppermost 600km of the inner core. Given a 1D velocity and attenuation model, synthetic seismograms are generated by Generalized Ray Theory. We are also experimenting 2D synthetic methods (WKM, AXISEM, and 2D FD) for 2D models (in the mantle and the inner core). The source time function is determined by observed seismic data. We use neighborhood algorithm to search for a group of models that minimize the misfit between predictions and observations. Tests on synthetic data show the efficiency of this method in resolving detailed velocity and attenuation structures of the ICB simultaneously. We are analyzing seismic record sections at dense arrays along different paths and will report our modeling and inversion results in the meeting.

Caring for Us, Caring about People.

ERIC Educational Resources Information Center

Morris, Robert

1992-01-01

Proposes an alternative conceptual framework for social work practice. Describes the present model as lacking a clear, easily articulated identity. Details social problems, including family structure changes, mental illness, physical disability, delinquency, and poverty. Provides key steps to alleviating these problems, emphasizing more active…

Inferring Epidemic Contact Structure from Phylogenetic Trees

PubMed Central

Leventhal, Gabriel E.; Kouyos, Roger; Stadler, Tanja; von Wyl, Viktor; Yerly, Sabine; Böni, Jürg; Cellerai, Cristina; Klimkait, Thomas; Günthard, Huldrych F.; Bonhoeffer, Sebastian

2012-01-01

Contact structure is believed to have a large impact on epidemic spreading and consequently using networks to model such contact structure continues to gain interest in epidemiology. However, detailed knowledge of the exact contact structure underlying real epidemics is limited. Here we address the question whether the structure of the contact network leaves a detectable genetic fingerprint in the pathogen population. To this end we compare phylogenies generated by disease outbreaks in simulated populations with different types of contact networks. We find that the shape of these phylogenies strongly depends on contact structure. In particular, measures of tree imbalance allow us to quantify to what extent the contact structure underlying an epidemic deviates from a null model contact network and illustrate this in the case of random mixing. Using a phylogeny from the Swiss HIV epidemic, we show that this epidemic has a significantly more unbalanced tree than would be expected from random mixing. PMID:22412361

The Interaction of Global Biochemical Cycles

NASA Technical Reports Server (NTRS)

Moore, B., III; Dastoor, M. N.

1984-01-01

The global biosphere in an exceedingly complex system. To gain an understanding of its structure and dynamic features, it is necessary not only to increase the knowledge about the detailed processes but also to develop models of how global interactions take place. Attempts to analyze the detailed physical, chemical and biological processes in this context need to be guided by an advancement of understanding of the latter. It is necessary to develop a strategy of data gathering that severs both these purposes simultaneously. The following papers deal with critical aspects in the global cycles of carbon, nitrogen, phosphorus and sulfur in details as well as the cycle of water and the flow of energy in the Earth's environment. The objective is to set partly the foundation for the development of mathematical models that allow exploration of the coupled dynamics of the global cycles of carbon, nitrogen, phosphorus, sulfur, as well as energy and water flux.

A global/local analysis method for treating details in structural design

NASA Technical Reports Server (NTRS)

Aminpour, Mohammad A.; Mccleary, Susan L.; Ransom, Jonathan B.

1993-01-01

A method for analyzing global/local behavior of plate and shell structures is described. In this approach, a detailed finite element model of the local region is incorporated within a coarser global finite element model. The local model need not be nodally compatible (i.e., need not have a one-to-one nodal correspondence) with the global model at their common boundary; therefore, the two models may be constructed independently. The nodal incompatibility of the models is accounted for by introducing appropriate constraint conditions into the potential energy in a hybrid variational formulation. The primary advantage of this method is that the need for transition modeling between global and local models is eliminated. Eliminating transition modeling has two benefits. First, modeling efforts are reduced since tedious and complex transitioning need not be performed. Second, errors due to the mesh distortion, often unavoidable in mesh transitioning, are minimized by avoiding distorted elements beyond what is needed to represent the geometry of the component. The method is applied reduced to a plate loaded in tension and transverse bending. The plate has a central hole, and various hole sixes and shapes are studied. The method is also applied to a composite laminated fuselage panel with a crack emanating from a window in the panel. While this method is applied herein to global/local problems, it is also applicable to the coupled analysis of independently modeled components as well as adaptive refinement.

Magnetic Doppler imaging of Ap stars

NASA Astrophysics Data System (ADS)

Silvester, J.; Wade, G. A.; Kochukhov, O.; Landstreet, J. D.; Bagnulo, S.

2008-04-01

Historically, the magnetic field geometries of the chemically peculiar Ap stars were modelled in the context of a simple dipole field. However, with the acquisition of increasingly sophisticated diagnostic data, it has become clear that the large-scale field topologies exhibit important departures from this simple model. Recently, new high-resolution circular and linear polarisation spectroscopy has even hinted at the presence of strong, small-scale field structures, which were completely unexpected based on earlier modelling. This project investigates the detailed structure of these strong fossil magnetic fields, in particular the large-scale field geometry, as well as small scale magnetic structures, by mapping the magnetic and chemical surface structure of a selected sample of Ap stars. These maps will be used to investigate the relationship between the local field vector and local surface chemistry, looking for the influence the field may have on the various chemical transport mechanisms (i.e., diffusion, convection and mass loss). This will lead to better constraints on the origin and evolution, as well as refining the magnetic field model for Ap stars. Mapping will be performed using high resolution and signal-to-noise ratio time-series of spectra in both circular and linear polarisation obtained using the new-generation ESPaDOnS (CFHT, Mauna Kea, Hawaii) and NARVAL spectropolarimeters (Pic du Midi Observatory). With these data we will perform tomographic inversion of Doppler-broadened Stokes IQUV Zeeman profiles of a large variety of spectral lines using the INVERS10 magnetic Doppler imaging code, simultaneously recovering the detailed surface maps of the vector magnetic field and chemical abundances.

A combined experimental and theoretical spectroscopic protocol for determination of the structure of heterogeneous catalysts: developing the information content of the resonance Raman spectra of M1 MoVOx † †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc01771e Click here for additional data file.

PubMed Central

Kubas, Adam; Noak, Johannes

2017-01-01

Absorption and multiwavelength resonance Raman spectroscopy are widely used to investigate the electronic structure of transition metal centers in coordination compounds and extended solid systems. In combination with computational methodologies that have predictive accuracy, they define powerful protocols to study the spectroscopic response of catalytic materials. In this work, we study the absorption and resonance Raman spectra of the M1 MoVOx catalyst. The spectra were calculated by time-dependent density functional theory (TD-DFT) in conjunction with the independent mode displaced harmonic oscillator model (IMDHO), which allows for detailed bandshape predictions. For this purpose cluster models with up to 9 Mo and V metallic centers are considered to represent the bulk structure of MoVOx. Capping hydrogens were used to achieve valence saturation at the edges of the cluster models. The construction of model structures was based on a thorough bonding analysis which involved conventional DFT and local coupled cluster (DLPNO-CCSD(T)) methods. Furthermore the relationship of cluster topology to the computed spectral features is discussed in detail. It is shown that due to the local nature of the involved electronic transitions, band assignment protocols developed for molecular systems can be applied to describe the calculated spectral features of the cluster models as well. The present study serves as a reference for future applications of combined experimental and computational protocols in the field of solid-state heterogeneous catalysis. PMID:28989667

Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.

PubMed

Shi, Yi; Fernandez-Martinez, Javier; Tjioe, Elina; Pellarin, Riccardo; Kim, Seung Joong; Williams, Rosemary; Schneidman-Duhovny, Dina; Sali, Andrej; Rout, Michael P; Chait, Brian T

2014-11-01

Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼ 600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

High Accuracy 3D Processing of Satellite Imagery

NASA Technical Reports Server (NTRS)

Gruen, A.; Zhang, L.; Kocaman, S.

2007-01-01

Automatic DSM/DTM generation reproduces not only general features, but also detailed features of the terrain relief. Height accuracy of around 1 pixel in cooperative terrain. RMSE values of 1.3-1.5 m (1.0-2.0 pixels) for IKONOS and RMSE values of 2.9-4.6 m (0.5-1.0 pixels) for SPOT5 HRS. For 3D city modeling, the manual and semi-automatic feature extraction capability of SAT-PP provides a good basis. The tools of SAT-PP allowed the stereo-measurements of points on the roofs in order to generate a 3D city model with CCM The results show that building models with main roof structures can be successfully extracted by HRSI. As expected, with Quickbird more details are visible.

Absorption line studies of reflection from horizontally inhomogeneous layers. [in cloudy planetary atmospheres

NASA Technical Reports Server (NTRS)

Appleby, J. F.; Van Blerkom, D. J.

1975-01-01

The article details an inhomogeneous reflecting layer (IRFL) model designed to survey absorption line behavior from a Squires-like cloud cover (which is characterized by convection cell structure). Computational problems and procedures are discussed in detail. The results show trends usually opposite to those predicted by a simple reflecting layer model. Per cent equivalent width variations for the tower model are usually somewhat greater for weak than for relatively strong absorption lines, with differences of a factor of about two or three. IRFL equivalent width variations do not differ drastically as a function of geometry when the total volume of absorbing gas is held constant. The IRFL results are in many instances consistent with observed equivalent width variations of Jupiter, Saturn, and Venus.

Analysis of Gas-Particle Flows through Multi-Scale Simulations

NASA Astrophysics Data System (ADS)

Gu, Yile

Multi-scale structures are inherent in gas-solid flows, which render the modeling efforts challenging. On one hand, detailed simulations where the fine structures are resolved and particle properties can be directly specified can account for complex flow behaviors, but they are too computationally expensive to apply for larger systems. On the other hand, coarse-grained simulations demand much less computations but they necessitate constitutive models which are often not readily available for given particle properties. The present study focuses on addressing this issue, as it seeks to provide a general framework through which one can obtain the required constitutive models from detailed simulations. To demonstrate the viability of this general framework in which closures can be proposed for different particle properties, we focus on the van der Waals force of interaction between particles. We start with Computational Fluid Dynamics (CFD) - Discrete Element Method (DEM) simulations where the fine structures are resolved and van der Waals force between particles can be directly specified, and obtain closures for stress and drag that are required for coarse-grained simulations. Specifically, we develop a new cohesion model that appropriately accounts for van der Waals force between particles to be used for CFD-DEM simulations. We then validate this cohesion model and the CFD-DEM approach by showing that it can qualitatively capture experimental results where the addition of small particles to gas fluidization reduces bubble sizes. Based on the DEM and CFD-DEM simulation results, we propose stress models that account for the van der Waals force between particles. Finally, we apply machine learning, specifically neural networks, to obtain a drag model that captures the effects from fine structures and inter-particle cohesion. We show that this novel approach using neural networks, which can be readily applied for other closures other than drag here, can take advantage of the large amount of data generated from simulations, and therefore offer superior modeling performance over traditional approaches.

Large-scale shell-model calculation with core excitations for neutron-rich nuclei beyond 132Sn

NASA Astrophysics Data System (ADS)

Jin, Hua; Hasegawa, Munetake; Tazaki, Shigeru; Kaneko, Kazunari; Sun, Yang

2011-10-01

The structure of neutron-rich nuclei with a few nucleons beyond 132Sn is investigated by means of large-scale shell-model calculations. For a considerably large model space, including neutron core excitations, a new effective interaction is determined by employing the extended pairing-plus-quadrupole model with monopole corrections. The model provides a systematical description for energy levels of A=133-135 nuclei up to high spins and reproduces available data of electromagnetic transitions. The structure of these nuclei is analyzed in detail, with emphasis of effects associated with core excitations. The results show evidence of hexadecupole correlation in addition to octupole correlation in this mass region. The suggested feature of magnetic rotation in 135Te occurs in the present shell-model calculation.

Building and evaluation of a structured representation of pharmacokinetics information presented in SPCs: from existing conceptual views of pharmacokinetics associated with natural language processing to object-oriented design.

PubMed

Duclos-Cartolano, Catherine; Venot, Alain

2003-01-01

Develop a detailed representation of pharmacokinetics (PK), derived from the information in Summaries of Product Characteristics (SPCs), for use in computerized systems to help practitioners in pharmaco-therapeutic reasoning. Available knowledge about PK was studied to identify main PK concepts and organize them in a preliminary generic model. The information from 1950 PK SPC-texts in the French language was studied using a morpho-syntactic analyzer. It produced a list of candidate terms (CTs) from which those describing main PK concepts were selected. The contexts in which they occurred were explored to discover co-occurring CTs. The regrouping according to CT semantic types led to a detailed object-oriented model of PK. The model was evaluated. A random sample of 100 PK texts structured according to the model was judged for completeness and semantic accuracy by 8 experts who were blinded to other experts' responses. The PK text file contained about 300000 words, and the morpho-syntactic analysis extracted 17520 different CTs. The context of 592 CTs was studied and used to deduce the PK model. It consists of four entities: the information about the real PK process, the experimental protocol, the mathematical modeling, and the influence of factors causing variation. Experts judged that the PK model represented the information in 100 sample PK texts completely in 89% of cases and nearly completely in the other 11%. There was no distortion of meaning in 98% of cases and little distortion in the remainder. The PK model seems to be applicable to all SPCs and can be used to retranscribe legal information from PK sections of SPCs into structured databases.

Building and Evaluation of a Structured Representation of Pharmacokinetics Information Presented in SPCs: From Existing Conceptual Views of Pharmacokinetics Associated with Natural Language Processing to Object-oriented Design

PubMed Central

Duclos-Cartolano, Catherine; Venot, Alain

2003-01-01

Objective: Develop a detailed representation of pharmacokinetics (PK), derived from the information in Summaries of Product Characteristics (SPCs), for use in computerized systems to help practitioners in pharmaco-therapeutic reasoning. Methods: Available knowledge about PK was studied to identify main PK concepts and organize them in a preliminary generic model. The information from 1,950 PK SPC-texts in the French language was studied using a morpho-syntactic analyzer. It produced a list of candidate terms (CTs) from which those describing main PK concepts were selected. The contexts in which they occurred were explored to discover co-occurring CTs. The regrouping according to CT semantic types led to a detailed object-oriented model of PK. The model was evaluated. A random sample of 100 PK texts structured according to the model was judged for completeness and semantic accuracy by 8 experts who were blinded to other experts’ responses. Results: The PK text file contained about 300,000 words, and the morpho-syntactic analysis extracted 17,520 different CTs. The context of 592 CTs was studied and used to deduce the PK model. It consists of four entities: the information about the real PK process, the experimental protocol, the mathematical modeling, and the influence of factors causing variation. Experts judged that the PK model represented the information in 100 sample PK texts completely in 89% of cases and nearly completely in the other 11%. There was no distortion of meaning in 98% of cases and little distortion in the remainder. Conclusion: The PK model seems to be applicable to all SPCs and can be used to retranscribe legal information from PK sections of SPCs into structured databases. PMID:12626375

Computational studies of transthoracic and transvenous defibrillation in a detailed 3-D human thorax model.

PubMed

Jorgenson, D B; Haynor, D R; Bardy, G H; Kim, Y

1995-02-01

A method for constructing and solving detailed patient-specific 3-D finite element models of the human thorax is presented for use in defibrillation studies. The method utilizes the patient's own X-ray CT scan and a simplified meshing scheme to quickly and efficiently generate a model typically composed of approximately 400,000 elements. A parameter sensitivity study on one human thorax model to examine the effects of variation in assigned tissue resistivity values, level of anatomical detail included in the model, and number of CT slices used to produce the model is presented. Of the seven tissue types examined, the average left ventricular (LV) myocardial voltage gradient was most sensitive to the values of myocardial and blood resistivity. Incorrectly simplifying the model, for example modeling the heart as a homogeneous structure by ignoring the blood in the chambers, caused the average LV myocardial voltage gradient to increase by 12%. The sensitivity of the model to variations in electrode size and position was also examined. Small changes (< 2.0 cm) in electrode position caused average LV myocardial voltage gradient values to increase by up to 12%. We conclude that patient-specific 3-D finite element modeling of human thoracic electric fields is feasible and may reduce the empiric approach to insertion of implantable defibrillators and improve transthoracic defibrillation techniques.

Structural model constructing for optical handwritten character recognition

NASA Astrophysics Data System (ADS)

Khaustov, P. A.; Spitsyn, V. G.; Maksimova, E. I.

2017-02-01

The article is devoted to the development of the algorithms for optical handwritten character recognition based on the structural models constructing. The main advantage of these algorithms is the low requirement regarding the number of reference images. The one-pass approach to a thinning of the binary character representation has been proposed. This approach is based on the joint use of Zhang-Suen and Wu-Tsai algorithms. The effectiveness of the proposed approach is confirmed by the results of the experiments. The article includes the detailed description of the structural model constructing algorithm’s steps. The proposed algorithm has been implemented in character processing application and has been approved on MNIST handwriting characters database. Algorithms that could be used in case of limited reference images number were used for the comparison.

The active engagement model of applied ethics as a structure for ethical reflection in the context of course-based service learning.

PubMed

Nesbit, Kathryn C; Jensen, Gail M; Delany, Clare

2018-01-01

The purpose of this case report is to explore the active engagement model as a tool to illuminate the ethical reflections of student physical therapists in the context of service learning in a developing country. The study participants were a convenience sample of six students. The study design is a case report using a phenomenological perspective. Data were collected from students' narrative writing and semi-structured interviews. The steps of the active engagement model provided the structural framework for student responses. The analysis process included open coding, selective coding, and member checking. Results showed the emergence of two main themes: 1) gathering rich detail and 2) developing independent moral identity. Students' descriptions of their relationships were detailed and included explanations about the complexities of the sociocultural context. Independent and deliberate agency was evident by the students' preparedness to be collaborative, to raise ethical questions, to identify ethically important aspects of their practice and to describe their professional roles. The students noted that the use of the model increased their engagement in the ethical decision-making process and their recognition of ethical questions. This case report illustrates attributes of the active engagement model which have implications for teaching ethical reflection: scaffolding for ethical reflection, use of narrative for reflection, reflection in action, and illumination of relevant themes. Each of these attributes leads to the development of meaningful ethical reflection. The attributes of this model shown by this case report have potential applications to teaching ethical reflection.

Direct numerical simulation of flow around a surface-mounted finite square cylinder at low Reynolds numbers

NASA Astrophysics Data System (ADS)

Zhang, Di; Cheng, Liang; An, Hongwei; Zhao, Ming

2017-04-01

With the aid of direct numerical simulation, this paper presents a detailed investigation on the flow around a finite square cylinder at a fixed aspect ratio (AR) of 4 and six Reynolds numbers (Re = 50, 100, 150, 250, 500, and 1000). It is found that the mean streamwise vortex structure is also affected by Re, apart from the AR value. Three types of mean streamwise vortices have been identified and analyzed in detail, namely, "Quadrupole Type" at Re = 50 and Re = 100, "Six-Vortices Type" at Re = 150 and Re = 250, and "Dipole Type" at Re = 500 and Re = 1000. It is the first time that the "Six-Vortices Type" mean streamwise vortices are reported, which is considered as a transitional structure between the other two types. Besides, three kinds of spanwise vortex-shedding models have been observed in this study, namely, "Hairpin Vortex Model" at Re = 150, "C and Reverse-C and Hairpin Vortex Model (Symmetric Shedding)" at Re = 250, and "C and Reverse-C and Hairpin Vortex Model (Symmetric/Antisymmetric Shedding)" at Re = 500 and Re = 1000. The newly proposed "C and Reverse-C and Hairpin Vortex Model" shares some similarities with "Wang's Model" [H. F. Wang and Y. Zhou, "The finite-length square cylinder near wake," J. Fluid Mech. 638, 453-490 (2009)] but differs in aspects such as the absence of the connection line near the free-end and the "C-Shape" vortex structure in the early stage of the formation of the spanwise vortex.

Relative resolution: A hybrid formalism for fluid mixtures.

PubMed

Chaimovich, Aviel; Peter, Christine; Kremer, Kurt

2015-12-28

We show here that molecular resolution is inherently hybrid in terms of relative separation. While nearest neighbors are characterized by a fine-grained (geometrically detailed) model, other neighbors are characterized by a coarse-grained (isotropically simplified) model. We notably present an analytical expression for relating the two models via energy conservation. This hybrid framework is correspondingly capable of retrieving the structural and thermal behavior of various multi-component and multi-phase fluids across state space.

Relative resolution: A hybrid formalism for fluid mixtures

NASA Astrophysics Data System (ADS)

Chaimovich, Aviel; Peter, Christine; Kremer, Kurt

2015-12-01

We show here that molecular resolution is inherently hybrid in terms of relative separation. While nearest neighbors are characterized by a fine-grained (geometrically detailed) model, other neighbors are characterized by a coarse-grained (isotropically simplified) model. We notably present an analytical expression for relating the two models via energy conservation. This hybrid framework is correspondingly capable of retrieving the structural and thermal behavior of various multi-component and multi-phase fluids across state space.

A Geophysical Inversion Model Enhancement Technique Based on the Blind Deconvolution

NASA Astrophysics Data System (ADS)

Zuo, B.; Hu, X.; Li, H.

2011-12-01

A model-enhancement technique is proposed to enhance the geophysical inversion model edges and details without introducing any additional information. Firstly, the theoretic correctness of the proposed geophysical inversion model-enhancement technique is discussed. An inversion MRM (model resolution matrix) convolution approximating PSF (Point Spread Function) method is designed to demonstrate the correctness of the deconvolution model enhancement method. Then, a total-variation regularization blind deconvolution geophysical inversion model-enhancement algorithm is proposed. In previous research, Oldenburg et al. demonstrate the connection between the PSF and the geophysical inverse solution. Alumbaugh et al. propose that more information could be provided by the PSF if we return to the idea of it behaving as an averaging or low pass filter. We consider the PSF as a low pass filter to enhance the inversion model basis on the theory of the PSF convolution approximation. Both the 1D linear and the 2D magnetotelluric inversion examples are used to analyze the validity of the theory and the algorithm. To prove the proposed PSF convolution approximation theory, the 1D linear inversion problem is considered. It shows the ratio of convolution approximation error is only 0.15%. The 2D synthetic model enhancement experiment is presented. After the deconvolution enhancement, the edges of the conductive prism and the resistive host become sharper, and the enhancement result is closer to the actual model than the original inversion model according the numerical statistic analysis. Moreover, the artifacts in the inversion model are suppressed. The overall precision of model increases 75%. All of the experiments show that the structure details and the numerical precision of inversion model are significantly improved, especially in the anomalous region. The correlation coefficient between the enhanced inversion model and the actual model are shown in Fig. 1. The figure illustrates that more information and details structure of the actual model are enhanced through the proposed enhancement algorithm. Using the proposed enhancement method can help us gain a clearer insight into the results of the inversions and help make better informed decisions.

Simplified and refined structural modeling for economical flutter analysis and design

NASA Technical Reports Server (NTRS)

Ricketts, R. H.; Sobieszczanski, J.

1977-01-01

A coordinated use of two finite-element models of different levels of refinement is presented to reduce the computer cost of the repetitive flutter analysis commonly encountered in structural resizing to meet flutter requirements. One model, termed a refined model (RM), represents a high degree of detail needed for strength-sizing and flutter analysis of an airframe. The other model, called a simplified model (SM), has a relatively much smaller number of elements and degrees-of-freedom. A systematic method of deriving an SM from a given RM is described. The method consists of judgmental and numerical operations to make the stiffness and mass of the SM elements equivalent to the corresponding substructures of RM. The structural data are automatically transferred between the two models. The bulk of analysis is performed on the SM with periodical verifications carried out by analysis of the RM. In a numerical example of a supersonic cruise aircraft with an arrow wing, this approach permitted substantial savings in computer costs and acceleration of the job turn-around.

Approaches to the structural modelling of insect wings.

PubMed Central

Wootton, R J; Herbert, R C; Young, P G; Evans, K E

2003-01-01

Insect wings lack internal muscles, and the orderly, necessary deformations which they undergo in flight and folding are in part remotely controlled, in part encoded in their structure. This factor is crucial in understanding their complex, extremely varied morphology. Models have proved particularly useful in clarifying the facilitation and control of wing deformation. Their development has followed a logical sequence from conceptual models through physical and simple analytical to numerical models. All have value provided their limitations are realized and constant comparisons made with the properties and mechanical behaviour of real wings. Numerical modelling by the finite element method is by far the most time-consuming approach, but has real potential in analysing the adaptive significance of structural details and interpreting evolutionary trends. Published examples are used to review the strengths and weaknesses of each category of model, and a summary is given of new work using finite element modelling to investigate the vibration properties and response to impact of hawkmoth wings. PMID:14561349

Energy modeling. Volume 2: Inventory and details of state energy models

NASA Astrophysics Data System (ADS)

Melcher, A. G.; Underwood, R. G.; Weber, J. C.; Gist, R. L.; Holman, R. P.; Donald, D. W.

1981-05-01

An inventory of energy models developed by or for state governments is presented, and certain models are discussed in depth. These models address a variety of purposes such as: supply or demand of energy or of certain types of energy; emergency management of energy; and energy economics. Ten models are described. The purpose, use, and history of the model is discussed, and information is given on the outputs, inputs, and mathematical structure of the model. The models include five models dealing with energy demand, one of which is econometric and four of which are econometric-engineering end-use models.

PENGEOM-A general-purpose geometry package for Monte Carlo simulation of radiation transport in material systems defined by quadric surfaces

NASA Astrophysics Data System (ADS)

Almansa, Julio; Salvat-Pujol, Francesc; Díaz-Londoño, Gloria; Carnicer, Artur; Lallena, Antonio M.; Salvat, Francesc

2016-02-01

The Fortran subroutine package PENGEOM provides a complete set of tools to handle quadric geometries in Monte Carlo simulations of radiation transport. The material structure where radiation propagates is assumed to consist of homogeneous bodies limited by quadric surfaces. The PENGEOM subroutines (a subset of the PENELOPE code) track particles through the material structure, independently of the details of the physics models adopted to describe the interactions. Although these subroutines are designed for detailed simulations of photon and electron transport, where all individual interactions are simulated sequentially, they can also be used in mixed (class II) schemes for simulating the transport of high-energy charged particles, where the effect of soft interactions is described by the random-hinge method. The definition of the geometry and the details of the tracking algorithm are tailored to optimize simulation speed. The use of fuzzy quadric surfaces minimizes the impact of round-off errors. The provided software includes a Java graphical user interface for editing and debugging the geometry definition file and for visualizing the material structure. Images of the structure are generated by using the tracking subroutines and, hence, they describe the geometry actually passed to the simulation code.

F-RAG: Generating Atomic Coordinates from RNA Graphs by Fragment Assembly.

PubMed

Jain, Swati; Schlick, Tamar

2017-11-24

Coarse-grained models represent attractive approaches to analyze and simulate ribonucleic acid (RNA) molecules, for example, for structure prediction and design, as they simplify the RNA structure to reduce the conformational search space. Our structure prediction protocol RAGTOP (RNA-As-Graphs Topology Prediction) represents RNA structures as tree graphs and samples graph topologies to produce candidate graphs. However, for a more detailed study and analysis, construction of atomic from coarse-grained models is required. Here we present our graph-based fragment assembly algorithm (F-RAG) to convert candidate three-dimensional (3D) tree graph models, produced by RAGTOP into atomic structures. We use our related RAG-3D utilities to partition graphs into subgraphs and search for structurally similar atomic fragments in a data set of RNA 3D structures. The fragments are edited and superimposed using common residues, full atomic models are scored using RAGTOP's knowledge-based potential, and geometries of top scoring models is optimized. To evaluate our models, we assess all-atom RMSDs and Interaction Network Fidelity (a measure of residue interactions) with respect to experimentally solved structures and compare our results to other fragment assembly programs. For a set of 50 RNA structures, we obtain atomic models with reasonable geometries and interactions, particularly good for RNAs containing junctions. Additional improvements to our protocol and databases are outlined. These results provide a good foundation for further work on RNA structure prediction and design applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Crustal insights from gravity and aeromagnetic analysis: Central North Slope, Alaska

USGS Publications Warehouse

Saltus, R.W.; Potter, C.J.; Phillips, J.D.

2006-01-01

Aeromagnetic and gravity data are processed and interpreted to reveal deep and shallow information about the crustal structure of the central North Slope, Alaska. Regional aeromagnetic anomalies primarily reflect deep crustal features. Regional gravity anomalies are more complex and require detailed analysis. We constrain our geophysical models with seismic data and interpretations along two transects including the Trans-Alaska Crustal Transect. Combined geophysical analysis reveals a remarkable heterogeneity of the pre-Mississippian basement. In the central North Slope, pre-Mississippian basement consists of two distinct geophysical domains. To the southwest, the basement is dense and highly magnetic; this basement is likely mafic and mechanically strong, possibly acting as a buttress to basement involvement in Brooks Range thrusting. To the northeast, the central North Slope basement consists of lower density, moderately magnetic rocks with several discrete regions (intrusions?) of more magnetic rocks. A conjugate set of geophysical trends, northwest-southeast and southwest-northeast, may be a factor in the crustal response to tectonic compression in this domain. High-resolution gravity and aeromagnetic data, where available, reflect details of shallow fault and fold structure. The maps and profile models in this report should provide useful guidelines and complementary information for regional structural studies, particularly in combination with detailed seismic reflection interpretations. Future challenges include collection of high-resolution gravity and aeromagnetic data for the entire North Slope as well as additional deep crustal information from seismic, drilling, and other complementary methods. Copyrights ?? 2006. The American Association of Petroleum Geologists. All rights reserved.

Advanced Model Compounds for Understanding Acid-Catalyzed Lignin Depolymerization: Identification of Renewable Aromatics and a Lignin-Derived Solvent.

PubMed

Lahive, Ciaran W; Deuss, Peter J; Lancefield, Christopher S; Sun, Zhuohua; Cordes, David B; Young, Claire M; Tran, Fanny; Slawin, Alexandra M Z; de Vries, Johannes G; Kamer, Paul C J; Westwood, Nicholas J; Barta, Katalin

2016-07-20

The development of fundamentally new approaches for lignin depolymerization is challenged by the complexity of this aromatic biopolymer. While overly simplified model compounds often lack relevance to the chemistry of lignin, the direct use of lignin streams poses significant analytical challenges to methodology development. Ideally, new methods should be tested on model compounds that are complex enough to mirror the structural diversity in lignin but still of sufficiently low molecular weight to enable facile analysis. In this contribution, we present a new class of advanced (β-O-4)-(β-5) dilinkage models that are highly realistic representations of a lignin fragment. Together with selected β-O-4, β-5, and β-β structures, these compounds provide a detailed understanding of the reactivity of various types of lignin linkages in acid catalysis in conjunction with stabilization of reactive intermediates using ethylene glycol. The use of these new models has allowed for identification of novel reaction pathways and intermediates and led to the characterization of new dimeric products in subsequent lignin depolymerization studies. The excellent correlation between model and lignin experiments highlights the relevance of this new class of model compounds for broader use in catalysis studies. Only by understanding the reactivity of the linkages in lignin at this level of detail can fully optimized lignin depolymerization strategies be developed.

Fast flexible modeling of RNA structure using internal coordinates.

PubMed

Flores, Samuel Coulbourn; Sherman, Michael A; Bruns, Christopher M; Eastman, Peter; Altman, Russ Biagio

2011-01-01

Modeling the structure and dynamics of large macromolecules remains a critical challenge. Molecular dynamics (MD) simulations are expensive because they model every atom independently, and are difficult to combine with experimentally derived knowledge. Assembly of molecules using fragments from libraries relies on the database of known structures and thus may not work for novel motifs. Coarse-grained modeling methods have yielded good results on large molecules but can suffer from difficulties in creating more detailed full atomic realizations. There is therefore a need for molecular modeling algorithms that remain chemically accurate and economical for large molecules, do not rely on fragment libraries, and can incorporate experimental information. RNABuilder works in the internal coordinate space of dihedral angles and thus has time requirements proportional to the number of moving parts rather than the number of atoms. It provides accurate physics-based response to applied forces, but also allows user-specified forces for incorporating experimental information. A particular strength of RNABuilder is that all Leontis-Westhof basepairs can be specified as primitives by the user to be satisfied during model construction. We apply RNABuilder to predict the structure of an RNA molecule with 160 bases from its secondary structure, as well as experimental information. Our model matches the known structure to 10.2 Angstroms RMSD and has low computational expense.

Risk Management and Physical Modelling for Mountainous Natural Hazards

NASA Astrophysics Data System (ADS)

Lehning, Michael; Wilhelm, Christian

Population growth and climate change cause rapid changes in mountainous regions resulting in increased risks of floods, avalanches, debris flows and other natural hazards. Xevents are of particular concern, since attempts to protect against them result in exponentially growing costs. In this contribution, we suggest an integral risk management approach to dealing with natural hazards that occur in mountainous areas. Using the example of a mountain pass road, which can be protected from the danger of an avalanche by engineering (galleries) and/or organisational (road closure) measures, we show the advantage of an optimal combination of both versus the traditional approach, which is to rely solely on engineering structures. Organisational measures become especially important for Xevents because engineering structures cannot be designed for those events. However, organisational measures need a reliable and objective forecast of the hazard. Therefore, we further suggest that such forecasts should be developed using physical numerical modelling. We present the status of current approaches to using physical modelling to predict snow cover stability for avalanche warnings and peak runoff from mountain catchments for flood warnings. While detailed physical models can already predict peak runoff reliably, they are only used to support avalanche warnings. With increased process knowledge and computer power, current developments should lead to a enhanced role for detailed physical models in natural mountain hazard prediction.

The influence of the side-chain sequence on the structure-activity correlations of immunomodulatory branched polypeptides. Synthesis and conformational analysis of new model polypeptides.

PubMed

Mezö, G; Hudecz, F; Kajtár, J; Szókán, G; Szekerke, M

1989-10-01

New branched polypeptides were synthesized for a detailed study of the influence of the side-chain structure on the conformation and biological properties. The first subset of polypeptides were prepared by coupling of tetrapeptides to poly[L-Lys]. These polymers contain either DL-Ala3-X [poly[Lys-(X-DL-Ala3)n

United States Air Force Graduate Student Research Program. Program Management Report

DTIC Science & Technology

1988-12-01

PRELIMINARY STRUCTURAL DESIGN/OPTIMIZATION by Richard A. Swift ABSTRACT Finite element analysis for use in structural design has advanced to the point where...Plates Subjected Gregory Schoeppner to Low Velocity Impact *** Same Report as Prof. William Wolfe * 57 Finite Element Analysis for Preliminary Richard...and dynamic load conditions using both radial and bias- ply tires. A detailed three-dimensional finite - element model of the wheel was generated for

On the Electronic Structure of Cu Chlorophyllin and Its Breakdown Products: A Carbon K-Edge X-ray Absorption Spectroscopy Study.

PubMed

Witte, Katharina; Mantouvalou, Ioanna; Sánchez-de-Armas, Rocío; Lokstein, Heiko; Lebendig-Kuhla, Janina; Jonas, Adrian; Roth, Friedrich; Kanngießer, Birgit; Stiel, Holger

2018-02-15

Using near-edge X-ray absorption fine structure (NEXAFS) spectroscopy, the carbon backbone of sodium copper chlorophyllin (SCC), a widely used chlorophyll derivative, and its breakdown products are analyzed to elucidate their electronic structure and physicochemical properties. Using various sample preparation methods and complementary spectroscopic methods (including UV/Vis, X-ray photoelectron spectroscopy), a comprehensive insight into the SCC breakdown process is presented. The experimental results are supported by density functional theory calculations, allowing a detailed assignment of characteristic NEXAFS features to specific C bonds. SCC can be seen as a model system for the large group of porphyrins; thus, this work provides a novel and detailed description of the electronic structure of the carbon backbone of those molecules and their breakdown products. The achieved results also promise prospective optical pump/X-ray probe investigations of dynamic processes in chlorophyll-containing photosynthetic complexes to be analyzed more precisely.

Automated method for relating regional pulmonary structure and function: integration of dynamic multislice CT and thin-slice high-resolution CT

NASA Astrophysics Data System (ADS)

Tajik, Jehangir K.; Kugelmass, Steven D.; Hoffman, Eric A.

1993-07-01

We have developed a method utilizing x-ray CT for relating pulmonary perfusion to global and regional anatomy, allowing for detailed study of structure to function relationships. A thick slice, high temporal resolution mode is used to follow a bolus contrast agent for blood flow evaluation and is fused with a high spatial resolution, thin slice mode to obtain structure- function detail. To aid analysis of blood flow, we have developed a software module, for our image analysis package (VIDA), to produce the combined structure-function image. Color coded images representing blood flow, mean transit time, regional tissue content, regional blood volume, regional air content, etc. are generated and imbedded in the high resolution volume image. A text file containing these values along with a voxel's 3-D coordinates is also generated. User input can be minimized to identifying the location of the pulmonary artery from which the input function to a blood flow model is derived. Any flow model utilizing one input and one output function can be easily added to a user selectable list. We present examples from our physiologic based research findings to demonstrate the strengths of combining dynamic CT and HRCT relative to other scanning modalities to uniquely characterize pulmonary normal and pathophysiology.

Investigating the Structural Impact of the Glutamine Repeat in Huntingtin Assembly

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

Perevozchikova, Tatiana; Stanley, Christopher B; McWilliams-Koeppen, Helen P

2014-01-01

Acquiring detailed structural information about the various aggregation states of the huntingtin-exon1 protein (Htt-exon1) is crucial not only for identifying the true nature of the neurotoxic species responsible for Huntington s disease (HD) but also for designing effective therapeutics. Using time-resolved small-angle neutron scattering (TR-SANS), we followed the conformational changes that occurred during fibrillization of the pathologic form of Htt-exon1 (NtQ42P10) and compared the results with those obtained for the wild-type (NtQ22P10). Our results show that the aggregation pathway of NtQ22P10 is very different from that of NtQ42P10, as the initial steps require a monomer to 7-mer transition stage. Inmore » contrast, the earliest species identified for NtQ42P10 are monomer and dimer. The divergent pathways ultimately result in NtQ22P10 fibrils that possess a pack- ing arrangement consistent with the common amyloid sterical zipper model, whereas NtQ42P10 fibrils present a better fit to the Perutz b-helix structural model. The structural details obtained by TR-SANS should help to delineate the key mechanisms that underpin Htt-exon1 aggregation leading to HD.« less

Inferring a District-Based Hierarchical Structure of Social Contacts from Census Data

PubMed Central

Yu, Zhiwen; Liu, Jiming; Zhu, Xianjun

2015-01-01

Researchers have recently paid attention to social contact patterns among individuals due to their useful applications in such areas as epidemic evaluation and control, public health decisions, chronic disease research and social network research. Although some studies have estimated social contact patterns from social networks and surveys, few have considered how to infer the hierarchical structure of social contacts directly from census data. In this paper, we focus on inferring an individual’s social contact patterns from detailed census data, and generate various types of social contact patterns such as hierarchical-district-structure-based, cross-district and age-district-based patterns. We evaluate newly generated contact patterns derived from detailed 2011 Hong Kong census data by incorporating them into a model and simulation of the 2009 Hong Kong H1N1 epidemic. We then compare the newly generated social contact patterns with the mixing patterns that are often used in the literature, and draw the following conclusions. First, the generation of social contact patterns based on a hierarchical district structure allows for simulations at different district levels. Second, the newly generated social contact patterns reflect individuals social contacts. Third, the newly generated social contact patterns improve the accuracy of the SEIR-based epidemic model. PMID:25679787

Multiscale molecular dynamics simulation approaches to the structure and dynamics of viruses.

PubMed

Huber, Roland G; Marzinek, Jan K; Holdbrook, Daniel A; Bond, Peter J

2017-09-01

Viral pathogens are a significant source of human morbidity and mortality, and have a major impact on societies and economies around the world. One of the challenges inherent in targeting these pathogens with drugs is the tight integration of the viral life cycle with the host's cellular machinery. However, the reliance of the virus on the host cell replication machinery is also an opportunity for therapeutic targeting, as successful entry- and exit-inhibitors have demonstrated. An understanding of the extracellular and intracellular structure and dynamics of the virion - as well as of the entry and exit pathways in host and vector cells - is therefore crucial to the advancement of novel antivirals. In recent years, advances in computing architecture and algorithms have begun to allow us to use simulations to study the structure and dynamics of viral ultrastructures at various stages of their life cycle in atomistic or near-atomistic detail. In this review, we outline specific challenges and solutions that have emerged to allow for structurally detailed modelling of viruses in silico. We focus on the history and state of the art of atomistic and coarse-grained approaches to simulate the dynamics of the large, macromolecular structures associated with viral infection, and on their usefulness in explaining and expanding upon experimental data. We discuss the types of interactions that need to be modeled to describe major components of the virus particle and advances in modelling techniques that allow for the treatment of these systems, highlighting recent key simulation studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Computational Simulation of the Activation Cycle of Gα Subunit in the G Protein Cycle Using an Elastic Network Model

PubMed Central

Kim, Min Hyeok; Kim, Young Jin; Kim, Hee Ryung; Jeon, Tae-Joon; Choi, Jae Boong; Chung, Ka Young; Kim, Moon Ki

2016-01-01

Agonist-activated G protein-coupled receptors (GPCRs) interact with GDP-bound G protein heterotrimers (Gαβγ) promoting GDP/GTP exchange, which results in dissociation of Gα from the receptor and Gβγ. The GTPase activity of Gα hydrolyzes GTP to GDP, and the GDP-bound Gα interacts with Gβγ, forming a GDP-bound G protein heterotrimer. The G protein cycle is allosterically modulated by conformational changes of the Gα subunit. Although biochemical and biophysical methods have elucidated the structure and dynamics of Gα, the precise conformational mechanisms underlying the G protein cycle are not fully understood yet. Simulation methods could help to provide additional details to gain further insight into G protein signal transduction mechanisms. In this study, using the available X-ray crystal structures of Gα, we simulated the entire G protein cycle and described not only the steric features of the Gα structure, but also conformational changes at each step. Each reference structure in the G protein cycle was modeled as an elastic network model and subjected to normal mode analysis. Our simulation data suggests that activated receptors trigger conformational changes of the Gα subunit that are thermodynamically favorable for opening of the nucleotide-binding pocket and GDP release. Furthermore, the effects of GTP binding and hydrolysis on mobility changes of the C and N termini and switch regions are elucidated. In summary, our simulation results enabled us to provide detailed descriptions of the structural and dynamic features of the G protein cycle. PMID:27483005

Aeroelastic modeling of rotor blades with spanwise variable elastic axis offset: Classic issues revisited and new formulations

NASA Technical Reports Server (NTRS)

Bielawa, Richard L.

1988-01-01

In response to a systematic methodology assessment program directed to the aeroelastic stability of hingeless helicopter rotor blades, improved basic aeroelastic reformulations and new formulations relating to structural sweep were achieved. Correlational results are presented showing the substantially improved performance of the G400 aeroelastic analysis incorporating these new formulations. The formulations pertain partly to sundry solutions to classic problem areas, relating to dynamic inflow with vortex-ring state operation and basic blade kinematics, but mostly to improved physical modeling of elastic axis offset (structural sweep) in the presence of nonlinear structural twist. Specific issues addressed are an alternate modeling of the delta EI torsional excitation due to compound bending using a force integration approach, and the detailed kinematic representation of an elastically deflected point mass of a beam with both structural sweep and nonlinear twist.

A modified Finite Element-Transfer Matrix for control design of space structures

NASA Technical Reports Server (NTRS)

Tan, T.-M.; Yousuff, A.; Bahar, L. Y.; Konstandinidis, M.

1990-01-01

The Finite Element-Transfer Matrix (FETM) method was developed for reducing the computational efforts involved in structural analysis. While being widely used by structural analysts, this method does, however, have certain limitations, particularly when used for the control design of large flexible structures. In this paper, a new formulation based on the FETM method is presented. The new method effectively overcomes the limitations in the original FETM method, and also allows an easy construction of reduced models that are tailored for the control design. Other advantages of this new method include the ability to extract open loop frequencies and mode shapes with less computation, and simplification of the design procedures for output feedback, constrained compensation, and decentralized control. The development of this new method and the procedures for generating reduced models using this method are described in detail and the role of the reduced models in control design is discussed through an illustrative example.

Diffusion paths formation for Cu{sup +} ions in superionic Cu{sub 6}PS{sub 5}I single crystals studied in terms of structural phase transition

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

Gagor, A.; Pietraszko, A.; Kaynts, D.

2005-11-15

In order to understand the structural transformations leading to high ionic conductivity of Cu{sup +} ions in Cu{sub 6}PS{sub 5}I argyrodite compound, the detailed structure analysis based on single-crystal X-ray diffraction has been performed. Below the phase transition at T{sub c}=(144-169)K Cu{sub 6}PS{sub 5}I belongs to monoclinic, ferroelastic phase (space group Cc) with ordered copper sublattice. Above T{sub c} delocalization of copper ions begins and crystal changes the symmetry to cubic superstructure with space group F-43c (a{sup '}=19.528A, z=32). Finally, above T{sub 1}=274K increasing disordering of the Cu{sup +} ions heightens the symmetry to F-43m (a=9.794A, z=4). In this work,more » the final structural model of two cubic phases is presented including the detailed temperature evolution of positions and site occupation factors of copper ions (R{sub 1}=0.0397 for F-43c phase, and 0.0245 for F-43m phase). Possible diffusion paths for the copper ions are represented by means of the atomic displacement factors and split model. The structural results coincide well with the previously reported non-Arrhenius behavior of conductivity and indicate significant change in conduction mechanism.« less

Structure, Intent and Conformance Monitoring in ATC

NASA Technical Reports Server (NTRS)

Reynolds, Tom G.; Histon, Jonathan M.; Davison, Hayley J.; Hansman, R. John

2004-01-01

Infield studies of current Air Traffic Control operations it is found that controllers rely on underlying airspace structure to reduce the complexity of the planning and conformance monitoring tasks. The structure appears to influence the controller's working mental model through abstractions that reduce the apparent cognitive complexity. These structure-based abstractions are useful for the controller's key tasks of planning, implementing, monitoring, and evaluating tactical situations. In addition, the structure-based abstractions appear to be important in the maintenance of Situation Awareness. The process of conformance monitoring is analyzed in more detail and an approach to conformance monitoring which utilizes both the structure-based abstractions and intent is presented.

Making ecological models adequate

USGS Publications Warehouse

Getz, Wayne M.; Marshall, Charles R.; Carlson, Colin J.; Giuggioli, Luca; Ryan, Sadie J.; Romañach, Stephanie; Boettiger, Carl; Chamberlain, Samuel D.; Larsen, Laurel; D'Odorico, Paolo; O'Sullivan, David

2018-01-01

Critical evaluation of the adequacy of ecological models is urgently needed to enhance their utility in developing theory and enabling environmental managers and policymakers to make informed decisions. Poorly supported management can have detrimental, costly or irreversible impacts on the environment and society. Here, we examine common issues in ecological modelling and suggest criteria for improving modelling frameworks. An appropriate level of process description is crucial to constructing the best possible model, given the available data and understanding of ecological structures. Model details unsupported by data typically lead to over parameterisation and poor model performance. Conversely, a lack of mechanistic details may limit a model's ability to predict ecological systems’ responses to management. Ecological studies that employ models should follow a set of model adequacy assessment protocols that include: asking a series of critical questions regarding state and control variable selection, the determinacy of data, and the sensitivity and validity of analyses. We also need to improve model elaboration, refinement and coarse graining procedures to better understand the relevancy and adequacy of our models and the role they play in advancing theory, improving hind and forecasting, and enabling problem solving and management.

The development of advanced manufacturing systems

NASA Astrophysics Data System (ADS)

Doumeingts, Guy; Vallespir, Bruno; Darricau, Didier; Roboam, Michel

Various methods for the design of advanced manufacturing systems (AMSs) are reviewed. The specifications for AMSs and problems inherent in their development are first discussed. Three models, the Computer Aided Manufacturing-International model, the National Bureau of Standards model, and the GRAI model, are considered in detail. Hierarchical modeling tools such as structured analysis and design techniques, Petri nets, and the Icam definition method are used in the development of integrated manufacturing models. Finally, the GRAI method is demonstrated in the design of specifications for the production management system of the Snecma AMS.

Refinement of protein termini in template-based modeling using conformational space annealing.

PubMed

Park, Hahnbeom; Ko, Junsu; Joo, Keehyoung; Lee, Julian; Seok, Chaok; Lee, Jooyoung

2011-09-01

The rapid increase in the number of experimentally determined protein structures in recent years enables us to obtain more reliable protein tertiary structure models than ever by template-based modeling. However, refinement of template-based models beyond the limit available from the best templates is still needed for understanding protein function in atomic detail. In this work, we develop a new method for protein terminus modeling that can be applied to refinement of models with unreliable terminus structures. The energy function for terminus modeling consists of both physics-based and knowledge-based potential terms with carefully optimized relative weights. Effective sampling of both the framework and terminus is performed using the conformational space annealing technique. This method has been tested on a set of termini derived from a nonredundant structure database and two sets of termini from the CASP8 targets. The performance of the terminus modeling method is significantly improved over our previous method that does not employ terminus refinement. It is also comparable or superior to the best server methods tested in CASP8. The success of the current approach suggests that similar strategy may be applied to other types of refinement problems such as loop modeling or secondary structure rearrangement. Copyright © 2011 Wiley-Liss, Inc.

Wave propagation in equivalent continuums representing truss lattice materials

DOE PAGES

Messner, Mark C.; Barham, Matthew I.; Kumar, Mukul; ...

2015-07-29

Stiffness scales linearly with density in stretch-dominated lattice meta-materials offering the possibility of very light yet very stiff structures. Current additive manufacturing techniques can assemble structures from lattice materials, but the design of such structures will require accurate, efficient simulation methods. Equivalent continuum models have several advantages over discrete truss models of stretch dominated lattices, including computational efficiency and ease of model construction. However, the development an equivalent model suitable for representing the dynamic response of a periodic truss in the small deformation regime is complicated by microinertial effects. This study derives a dynamic equivalent continuum model for periodic trussmore » structures suitable for representing long-wavelength wave propagation and verifies it against the full Bloch wave theory and detailed finite element simulations. The model must incorporate microinertial effects to accurately reproduce long wavelength characteristics of the response such as anisotropic elastic soundspeeds. Finally, the formulation presented here also improves upon previous work by preserving equilibrium at truss joints for simple lattices and by improving numerical stability by eliminating vertices in the effective yield surface.« less

Segments.

ERIC Educational Resources Information Center

Zemsky, Robert; Shaman, Susan; Shapiro, Daniel B.

2001-01-01

Presents a market taxonomy for higher education, including what it reveals about the structure of the market, the model's technical attributes, and its capacity to explain pricing behavior. Details the identification of the principle seams separating one market segment from another and how student aspirations help to organize the market, making…

Sentential Negation in English

ERIC Educational Resources Information Center

Mowarin, Macaulay

2009-01-01

This paper undertakes a detailed analysis of sentential negation in the English language with Chomsky's Government-Binding theory of Transformational Grammar as theoretical model. It distinguishes between constituent and sentential negation in English. The essay identifies the exact position of Negation phrase in an English clause structure. It…

ToxRefDB: Classifying ToxCast™ Phase I Chemicals Utilizing Structured Toxicity Information

EPA Science Inventory

There is an essential need for highly detailed chemicals classifications within the ToxCast™ research program. In order to develop predictive models and biological signatures utilizing high-throughput screening (HTS) and in vitro genomic data, relevant endpoints and toxicities m...

A biomechanical modeling guided simultaneous motion estimation and image reconstruction technique (SMEIR-Bio) for 4D-CBCT reconstruction

NASA Astrophysics Data System (ADS)

Huang, Xiaokun; Zhang, You; Wang, Jing

2017-03-01

Four-dimensional (4D) cone-beam computed tomography (CBCT) enables motion tracking of anatomical structures and removes artifacts introduced by motion. However, the imaging time/dose of 4D-CBCT is substantially longer/higher than traditional 3D-CBCT. We previously developed a simultaneous motion estimation and image reconstruction (SMEIR) algorithm, to reconstruct high-quality 4D-CBCT from limited number of projections to reduce the imaging time/dose. However, the accuracy of SMEIR is limited in reconstructing low-contrast regions with fine structure details. In this study, we incorporate biomechanical modeling into the SMEIR algorithm (SMEIR-Bio), to improve the reconstruction accuracy at low-contrast regions with fine details. The efficacy of SMEIR-Bio is evaluated using 11 lung patient cases and compared to that of the original SMEIR algorithm. Qualitative and quantitative comparisons showed that SMEIR-Bio greatly enhances the accuracy of reconstructed 4D-CBCT volume in low-contrast regions, which can potentially benefit multiple clinical applications including the treatment outcome analysis.

Distributed parameter modeling of repeated truss structures

NASA Technical Reports Server (NTRS)

Wang, Han-Ching

1994-01-01

A new approach to find homogeneous models for beam-like repeated flexible structures is proposed which conceptually involves two steps. The first step involves the approximation of 3-D non-homogeneous model by a 1-D periodic beam model. The structure is modeled as a 3-D non-homogeneous continuum. The displacement field is approximated by Taylor series expansion. Then, the cross sectional mass and stiffness matrices are obtained by energy equivalence using their additive properties. Due to the repeated nature of the flexible bodies, the mass, and stiffness matrices are also periodic. This procedure is systematic and requires less dynamics detail. The first step involves the homogenization from a 1-D periodic beam model to a 1-D homogeneous beam model. The periodic beam model is homogenized into an equivalent homogeneous beam model using the additive property of compliance along the generic axis. The major departure from previous approaches in literature is using compliance instead of stiffness in homogenization. An obvious justification is that the stiffness is additive at each cross section but not along the generic axis. The homogenized model preserves many properties of the original periodic model.

Electronic structure description of the cis-MoOS unit in models for molybdenum hydroxylases.

PubMed

Doonan, Christian J; Rubie, Nick D; Peariso, Katrina; Harris, Hugh H; Knottenbelt, Sushilla Z; George, Graham N; Young, Charles G; Kirk, Martin L

2008-01-09

The molybdenum hydroxylases catalyze the oxidation of numerous aromatic heterocycles and simple organics and, unlike other hydroxylases, utilize water as the source of oxygen incorporated into the product. The electronic structures of the cis-MoOS units in CoCp2[TpiPrMoVOS(OPh)] and TpiPrMoVIOS(OPh) (TpiPr = hydrotris(3-isopropylpyrazol-1-yl)borate), new models for molybdenum hydroxylases, have been studied in detail using S K-edge X-ray absorption spectroscopy, vibrational spectroscopy, and detailed bonding calculations. The results show a highly delocalized Mo=S pi* LUMO redox orbital that is formally Mo(dxy) with approximately 35% sulfido ligand character. Vibrational spectroscopy has been used to quantitate Mo-Ssulfido bond order changes in the cis-MoOS units as a function of redox state. Results support a redox active molecular orbital that has a profound influence on MoOS bonding through changes to the relative electro/nucleophilicity of the terminal sulfido ligand accompanying oxidation state changes. The bonding description for these model cis-MoOS systems supports enzyme mechanisms that are under orbital control and dominantly influenced by the unique electronic structure of the cis-MoOS site. The electronic structure of the oxidized enzyme site is postulated to play a role in polarizing a substrate carbon center for nucleophilic attack by metal activated water and acting as an electron sink in the two-electron oxidation of substrates.

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.

Cellulose synthases: new insights from crystallography and modeling.

PubMed

Slabaugh, Erin; Davis, Jonathan K; Haigler, Candace H; Yingling, Yaroslava G; Zimmer, Jochen

2014-02-01

Detailed information about the structure and biochemical mechanisms of cellulose synthase (CelS) proteins remained elusive until a complex containing the catalytic subunit (BcsA) of CelS from Rhodobacter sphaeroides was crystalized. Additionally, a 3D structure of most of the cytosolic domain of a plant CelS (GhCESA1 from cotton, Gossypium hirsutum) was produced by computational modeling. This predicted structure contributes to our understanding of how plant CelS proteins may be similar and different as compared with BcsA. In this review, we highlight how these structures impact our understanding of the synthesis of cellulose and other extracellular polysaccharides. We show how the structures can be used to generate hypotheses for experiments testing mechanisms of glucan synthesis and translocation in plant CelS. Copyright © 2013 Elsevier Ltd. All rights reserved.

Accurate 3d Scanning of Damaged Ancient Greek Inscriptions for Revealing Weathered Letters

NASA Astrophysics Data System (ADS)

Papadaki, A. I.; Agrafiotis, P.; Georgopoulos, A.; Prignitz, S.

2015-02-01

In this paper two non-invasive non-destructive alternative techniques to the traditional and invasive technique of squeezes are presented alongside with specialized developed processing methods, aiming to help the epigraphists to reveal and analyse weathered letters in ancient Greek inscriptions carved in masonry or marble. The resulting 3D model would serve as a detailed basis for the epigraphists to try to decipher the inscription. The data were collected by using a Structured Light scanner. The creation of the final accurate three dimensional model is a complicated procedure requiring large computation cost and human effort. It includes the collection of geometric data in limited space and time, the creation of the surface, the noise filtering and the merging of individual surfaces. The use of structured light scanners is time consuming and requires costly hardware and software. Therefore an alternative methodology for collecting 3D data of the inscriptions was also implemented for reasons of comparison. Hence, image sequences from varying distances were collected using a calibrated DSLR camera aiming to reconstruct the 3D scene through SfM techniques in order to evaluate the efficiency and the level of precision and detail of the obtained reconstructed inscriptions. Problems in the acquisition processes as well as difficulties in the alignment step and mesh optimization are also encountered. A meta-processing framework is proposed and analysed. Finally, the results of processing and analysis and the different 3D models are critically inspected and then evaluated by a specialist in terms of accuracy, quality and detail of the model and the capability of revealing damaged and "hidden" letters.

Coupled Monte Carlo neutronics and thermal hydraulics for power reactors

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

Bernnat, W.; Buck, M.; Mattes, M.

The availability of high performance computing resources enables more and more the use of detailed Monte Carlo models even for full core power reactors. The detailed structure of the core can be described by lattices, modeled by so-called repeated structures e.g. in Monte Carlo codes such as MCNP5 or MCNPX. For cores with mainly uniform material compositions, fuel and moderator temperatures, there is no problem in constructing core models. However, when the material composition and the temperatures vary strongly a huge number of different material cells must be described which complicate the input and in many cases exceed code ormore » memory limits. The second problem arises with the preparation of corresponding temperature dependent cross sections and thermal scattering laws. Only if these problems can be solved, a realistic coupling of Monte Carlo neutronics with an appropriate thermal-hydraulics model is possible. In this paper a method for the treatment of detailed material and temperature distributions in MCNP5 is described based on user-specified internal functions which assign distinct elements of the core cells to material specifications (e.g. water density) and temperatures from a thermal-hydraulics code. The core grid itself can be described with a uniform material specification. The temperature dependency of cross sections and thermal neutron scattering laws is taken into account by interpolation, requiring only a limited number of data sets generated for different temperatures. Applications will be shown for the stationary part of the Purdue PWR benchmark using ATHLET for thermal- hydraulics and for a generic Modular High Temperature reactor using THERMIX for thermal- hydraulics. (authors)« less

Propulsive performance of pitching foils with variable chordwise flexibility

NASA Astrophysics Data System (ADS)

Zeyghami, Samane; Moored, Keith; Lehigh University Team

2017-11-01

Many swimming and flying animals propel themselves efficiently through water by oscillating flexible fins. These fins are not homogeneously flexible, but instead their flexural stiffness varies along their chord and span. Here we seek to evaluate the effect stiffness profile on the propulsive performance of pitching foils. Stiffness profile characterizes the variation in the local fin stiffness along the chord. To this aim, we developed a low order model of a functionally-graded material where the chordwise flexibility is modeled by two torsional springs along the chordline and the stiffness and location of the springs can be varied arbitrarily. The torsional spring structural model is then strongly coupled to a boundary element fluid model to simulate the fluid-structure interactions. Keeping the leading edge kinematics unchanged, we alter the stiffness profile of the foil and allow it to swim freely in response to the resulting hydrodynamic forces. We then detail the dependency of the hydrodynamic performance and the wake structure to the variations in the local structural properties of the foil.

Space Generic Open Avionics Architecture (SGOAA) standard specification

NASA Technical Reports Server (NTRS)

Wray, Richard B.; Stovall, John R.

1994-01-01

This standard establishes the Space Generic Open Avionics Architecture (SGOAA). The SGOAA includes a generic functional model, processing structural model, and an architecture interface model. This standard defines the requirements for applying these models to the development of spacecraft core avionics systems. The purpose of this standard is to provide an umbrella set of requirements for applying the generic architecture models to the design of a specific avionics hardware/software processing system. This standard defines a generic set of system interface points to facilitate identification of critical services and interfaces. It establishes the requirement for applying appropriate low level detailed implementation standards to those interfaces points. The generic core avionics functions and processing structural models provided herein are robustly tailorable to specific system applications and provide a platform upon which the interface model is to be applied.

The Sylview graphical interface to the SYLVAN STAND STRUCTURE model with examples from southern bottomland hardwood forests

Treesearch

David R. Larsen; Ian Scott

2010-01-01

In the field of forestry, the output of forest growth models provide a wealth of detailed information that can often be difficult to analyze and perceive due to presentation either as plain text summary tables or static stand visualizations. This paper describes the design and implementation of a cross-platform computer application for dynamic and interactive forest...

Observed and simulated ground motions in the San Bernardino basin region for the Hector Mine, California, earthquake

USGS Publications Warehouse

Graves, R.W.; Wald, D.J.

2004-01-01

During the MW 7.1 Hector Mine earthquake, peak ground velocities recorded at sites in the central San Bernardino basin region were up to 2 times larger and had significantly longer durations of strong shaking than sites just outside the basin. To better understand the effects of 3D structure on the long-period ground-motion response in this region, we have performed finite-difference simulations for this earthquake. The simulations are numerically accurate for periods of 2 sec and longer and incorporate the detailed spatial and temporal heterogeneity of source rupture, as well as complex 3D basin structure. Here, we analyze three models of the San Bernardino basin: model A (with structural constraints from gravity and seismic reflection data), model F (water well and seismic refraction data), and the Southern California Earthquake Center version 3 model (hydrologic and seismic refraction data). Models A and F are characterized by a gradual increase in sediment thickness toward the south with an abrupt step-up in the basement surface across the San Jacinto fault. The basin structure in the SCEC version 3 model has a nearly uniform sediment thickness of 1 km with little basement topography along the San Jacinto fault. In models A and F, we impose a layered velocity structure within the sediments based on the seismic refraction data and an assumed depth-dependent Vp/Vs ratio. Sediment velocities within the SCEC version 3 model are given by a smoothly varying rule-based function that is calibrated to the seismic refraction measurements. Due to computational limitations, the minimum shear-wave velocity is fixed at 600 m/sec in all of the models. Ground-motion simulations for both models A and F provide a reasonably good match to the amplitude and waveform characteristics of the recorded motions. In these models, surface waves are generated as energy enters the basin through the gradually sloping northern margin. Due to the basement step along the San Jacinto fault, the surface wave energy is confined to the region north of this structure, consistent with the observations. The SCEC version 3 model, lacking the basin geometry complexity present in the other two models, fails to provide a satisfactory match to the characteristics of the observed motions. Our study demonstrates the importance of using detailed and accurate basin geometry for predicting ground motions and also highlights the utility of integrating geological, geophysical, and seismological observations in the development and validation of 3D velocity models.

A Novel Shape Parameterization Approach

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

1999-01-01

This paper presents a novel parameterization approach for complex shapes suitable for a multidisciplinary design optimization application. The approach consists of two basic concepts: (1) parameterizing the shape perturbations rather than the geometry itself and (2) performing the shape deformation by means of the soft objects animation algorithms used in computer graphics. Because the formulation presented in this paper is independent of grid topology, we can treat computational fluid dynamics and finite element grids in a similar manner. The proposed approach is simple, compact, and efficient. Also, the analytical sensitivity derivatives are easily computed for use in a gradient-based optimization. This algorithm is suitable for low-fidelity (e.g., linear aerodynamics and equivalent laminated plate structures) and high-fidelity analysis tools (e.g., nonlinear computational fluid dynamics and detailed finite element modeling). This paper contains the implementation details of parameterizing for planform, twist, dihedral, thickness, and camber. The results are presented for a multidisciplinary design optimization application consisting of nonlinear computational fluid dynamics, detailed computational structural mechanics, performance, and a simple propulsion module.

Model of Ni-63 battery with realistic PIN structure

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

Munson, Charles E.; Voss, Paul L.; Ougazzaden, Abdallah, E-mail: aougazza@georgiatech-metz.fr

2015-09-14

GaN, with its wide bandgap of 3.4 eV, has emerged as an efficient material for designing high-efficiency betavoltaic batteries. An important part of designing efficient betavoltaic batteries involves a good understanding of the full process, from the behavior of the nuclear material and the creation of electron-hole pairs all the way through the collection of photo-generated carriers. This paper presents a detailed model based on Monte Carlo and Silvaco for a GaN-based betavoltaic battery device, modeled after Ni-63 as an energy source. The accuracy of the model is verified by comparing it with experimental values obtained for a GaN-based p-i-nmore » structure under scanning electron microscope illumination.« less

NASA Langley developments in response calculations needed for failure and life prediction

NASA Technical Reports Server (NTRS)

Housner, Jerrold M.

1993-01-01

NASA Langley developments in response calculations needed for failure and life predictions are discussed. Topics covered include: structural failure analysis in concurrent engineering; accuracy of independent regional modeling demonstrated on classical example; functional interface method accurately joins incompatible finite element models; interface method for insertion of local detail modeling extended to curve pressurized fuselage window panel; interface concept for joining structural regions; motivation for coupled 2D-3D analysis; compression panel with discontinuous stiffener coupled 2D-3D model and axial surface strains at the middle of the hat stiffener; use of adaptive refinement with multiple methods; adaptive mesh refinement; and studies on quantity effect of bow-type initial imperfections on reliability of stiffened panels.

TLS from fundamentals to practice

PubMed Central

Urzhumtsev, Alexandre; Afonine, Pavel V.; Adams, Paul D.

2014-01-01

The Translation-Libration-Screw-rotation (TLS) model of rigid-body harmonic displacements introduced in crystallography by Schomaker & Trueblood (1968) is now a routine tool in macromolecular studies and is a feature of most modern crystallographic structure refinement packages. In this review we consider a number of simple examples that illustrate important features of the TLS model. Based on these examples simplified formulae are given for several special cases that may occur in structure modeling and refinement. The derivation of general TLS formulae from basic principles is also provided. This manuscript describes the principles of TLS modeling, as well as some select algorithmic details for practical application. An extensive list of applications references as examples of TLS in macromolecular crystallography refinement is provided. PMID:25249713

Model of Ni-63 battery with realistic PIN structure

NASA Astrophysics Data System (ADS)

Munson, Charles E.; Arif, Muhammad; Streque, Jeremy; Belahsene, Sofiane; Martinez, Anthony; Ramdane, Abderrahim; El Gmili, Youssef; Salvestrini, Jean-Paul; Voss, Paul L.; Ougazzaden, Abdallah

2015-09-01

GaN, with its wide bandgap of 3.4 eV, has emerged as an efficient material for designing high-efficiency betavoltaic batteries. An important part of designing efficient betavoltaic batteries involves a good understanding of the full process, from the behavior of the nuclear material and the creation of electron-hole pairs all the way through the collection of photo-generated carriers. This paper presents a detailed model based on Monte Carlo and Silvaco for a GaN-based betavoltaic battery device, modeled after Ni-63 as an energy source. The accuracy of the model is verified by comparing it with experimental values obtained for a GaN-based p-i-n structure under scanning electron microscope illumination.

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.;

Coarse-grained description of cosmic structure from Szekeres models

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

Sussman, Roberto A.; Gaspar, I. Delgado; Hidalgo, Juan Carlos, E-mail: sussman@nucleares.unam.mx, E-mail: ismael.delgadog@uaem.edu.mx, E-mail: hidalgo@fis.unam.mx

2016-03-01

We show that the full dynamical freedom of the well known Szekeres models allows for the description of elaborated 3-dimensional networks of cold dark matter structures (over-densities and/or density voids) undergoing ''pancake'' collapse. By reducing Einstein's field equations to a set of evolution equations, which themselves reduce in the linear limit to evolution equations for linear perturbations, we determine the dynamics of such structures, with the spatial comoving location of each structure uniquely specified by standard early Universe initial conditions. By means of a representative example we examine in detail the density contrast, the Hubble flow and peculiar velocities ofmore » structures that evolved, from linear initial data at the last scattering surface, to fully non-linear 10–20 Mpc scale configurations today. To motivate further research, we provide a qualitative discussion on the connection of Szekeres models with linear perturbations and the pancake collapse of the Zeldovich approximation. This type of structure modelling provides a coarse grained—but fully relativistic non-linear and non-perturbative —description of evolving large scale cosmic structures before their virialisation, and as such it has an enormous potential for applications in cosmological research.« less

Discovering relevance knowledge in data: a growing cell structures approach.

PubMed

Azuaje, F; Dubitzky, W; Black, N; Adamson, K

2000-01-01

Both information retrieval and case-based reasoning systems rely on effective and efficient selection of relevant data. Typically, relevance in such systems is approximated by similarity or indexing models. However, the definition of what makes data items similar or how they should be indexed is often nontrivial and time-consuming. Based on growing cell structure artificial neural networks, this paper presents a method that automatically constructs a case retrieval model from existing data. Within the case-based reasoning (CBR) framework, the method is evaluated for two medical prognosis tasks, namely, colorectal cancer survival and coronary heart disease risk prognosis. The results of the experiments suggest that the proposed method is effective and robust. To gain a deeper insight and understanding of the underlying mechanisms of the proposed model, a detailed empirical analysis of the models structural and behavioral properties is also provided.

Coarse-grained mechanics of viral shells

NASA Astrophysics Data System (ADS)

Klug, William S.; Gibbons, Melissa M.

2008-03-01

We present an approach for creating three-dimensional finite element models of viral capsids from atomic-level structural data (X-ray or cryo-EM). The models capture heterogeneous geometric features and are used in conjunction with three-dimensional nonlinear continuum elasticity to simulate nanoindentation experiments as performed using atomic force microscopy. The method is extremely flexible; able to capture varying levels of detail in the three-dimensional structure. Nanoindentation simulations are presented for several viruses: Hepatitis B, CCMV, HK97, and φ29. In addition to purely continuum elastic models a multiscale technique is developed that combines finite-element kinematics with MD energetics such that large-scale deformations are facilitated by a reduction in degrees of freedom. Simulations of these capsid deformation experiments provide a testing ground for the techniques, as well as insight into the strength-determining mechanisms of capsid deformation. These methods can be extended as a framework for modeling other proteins and macromolecular structures in cell biology.

Compressive Loading and Modeling of Stitched Composite Stiffeners

NASA Technical Reports Server (NTRS)

Leone, Frank A., Jr.; Jegley, Dawn C.; Linton, Kim A.

2016-01-01

A series of single-frame and single-stringer compression tests were conducted at NASA Langley Research Center on specimens harvested from a large panel built using the Pultruded Rod Stitched Efficient Unitized Structure (PRSEUS) concept. Different frame and stringer designs were used in fabrication of the PRSEUS panel. In this paper, the details of the experimental testing of single-frame and single-stringer compression specimens are presented, as well as discussions on the performance of the various structural configurations included in the panel. Nonlinear finite element models were developed to further understand the failure processes observed during the experimental campaign.

Analysis of Yb3+/Er3+-codoped microring resonator cross-grid matrices

NASA Astrophysics Data System (ADS)

Vallés, Juan A.; Gǎlǎtuş, Ramona

2014-09-01

An analytic model of the scattering response of a highly Yb3+/Er3+-codoped phosphate glass microring resonator matrix is considered to obtain the transfer functions of an M x N cross-grid microring resonator structure. Then a detailed model is used to calculate the pump and signal propagation, including a microscopic statistical formalism to describe the high-concentration induced energy-transfer mechanisms and passive and active features are combined to realistically simulate the performance as a wavelength-selective amplifier or laser. This analysis allows the optimization of these structures for telecom or sensing applications.

Probing the free energy landscape of the FBP28WW domain using multiple techniques.

PubMed

Periole, Xavier; Allen, Lucy R; Tamiola, Kamil; Mark, Alan E; Paci, Emanuele

2009-05-01

The free-energy landscape of a small protein, the FBP 28 WW domain, has been explored using molecular dynamics (MD) simulations with alternative descriptions of the molecule. The molecular models used range from coarse-grained to all-atom with either an implicit or explicit treatment of the solvent. Sampling of conformation space was performed using both conventional and temperature-replica exchange MD simulations. Experimental chemical shifts and NOEs were used to validate the simulations, and experimental phi values both for validation and as restraints. This combination of different approaches has provided insight into the free energy landscape and barriers encountered by the protein during folding and enabled the characterization of native, denatured and transition states which are compatible with the available experimental data. All the molecular models used stabilize well defined native and denatured basins; however, the degree of agreement with the available experimental data varies. While the most detailed, explicit solvent model predicts the data reasonably accurately, it does not fold despite a simulation time 10 times that of the experimental folding time. The less detailed models performed poorly relative to the explicit solvent model: an implicit solvent model stabilizes a ground state which differs from the experimental native state, and a structure-based model underestimates the size of the barrier between the two states. The use of experimental phi values both as restraints, and to extract structures from unfolding simulations, result in conformations which, although not necessarily true transition states, appear to share the geometrical characteristics of transition state structures. In addition to characterizing the native, transition and denatured states of this particular system in this work, the advantages and limitations of using varying levels of representation are discussed. 2008 Wiley Periodicals, Inc.

LYRA, a webserver for lymphocyte receptor structural modeling.

PubMed

Klausen, Michael Schantz; Anderson, Mads Valdemar; Jespersen, Martin Closter; Nielsen, Morten; Marcatili, Paolo

2015-07-01

The accurate structural modeling of B- and T-cell receptors is fundamental to gain a detailed insight in the mechanisms underlying immunity and in developing new drugs and therapies. The LYRA (LYmphocyte Receptor Automated modeling) web server (http://www.cbs.dtu.dk/services/LYRA/) implements a complete and automated method for building of B- and T-cell receptor structural models starting from their amino acid sequence alone. The webserver is freely available and easy to use for non-specialists. Upon submission, LYRA automatically generates alignments using ad hoc profiles, predicts the structural class of each hypervariable loop, selects the best templates in an automatic fashion, and provides within minutes a complete 3D model that can be downloaded or inspected online. Experienced users can manually select or exclude template structures according to case specific information. LYRA is based on the canonical structure method, that in the last 30 years has been successfully used to generate antibody models of high accuracy, and in our benchmarks this approach proves to achieve similarly good results on TCR modeling, with a benchmarked average RMSD accuracy of 1.29 and 1.48 Å for B- and T-cell receptors, respectively. To the best of our knowledge, LYRA is the first automated server for the prediction of TCR structure. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Orphan Basin crustal structure from a dense wide-angle seismic profile - Tomographic inversion

NASA Astrophysics Data System (ADS)

Watremez, Louise; Lau, K. W. Helen; Nedimović, Mladen R.; Louden, Keith E.; Karner, Garry D.

2014-05-01

Orphan Basin is located on the eastern margin of Canada, offshore of Newfoundland and East of Flemish Cap. It is an aborted continental rift formed by multiple episodes of rifting. The crustal structure across the basin has been determined by an earlier refraction study using 15 instruments on a 550 km long line. It shows that the continental crust was extended over an unusually wide region but did not break apart. The crustal structure of the basin thus documents stages in the formation of a magma-poor rifted margin up to crustal breakup. The OBWAVE (Orphan Basin Wide-Angle Velocity Experiment) survey was carried out to image crustal structures across the basin and better understand the processes of formation of this margin. The spacing of the 89 recording stations varies from 3 to 5 km along this 500-km-long line, which was acquired along a pre-existing reflection line. The highest resolution section corresponds to the part of the profile where the crust was expected to be the thinnest. We present the results from a joint tomography inversion of first and Moho reflected arrival times. The high data density allows us to define crustal structures with greater detail than for typical studies and to improve the understanding of the processes leading to the extreme stretching of continental crust. The final model was computed following a detailed parametric study to determine the optimal parameters controlling the ray-tracing and the inversion processes. The final model shows very good resolution. In particular, Monte Carlo standard deviations of crustal velocities and Moho depths are generally < 50 m/s and within 1 km, respectively. In comparison to the velocity models of typical seismic refraction profiles, results from the OBWAVE study show a notable improvement in the resolution of the velocity model and in the level of detail observed using the least a priori information possible. The final model allows us to determine the crustal thinning and variable structures across the basin. In particular, we observe (1) a zone of extreme thinning, where the crust is thinner than 7 km; (2) basement highs and lows highlighting the blocks that accommodate the crustal thinning; (3) a central block that is thicker compared to the rest of the basin; (4) lower crustal thinning that is highly variable, which suggests a ductile deformation in the lower crust and an extensional discrepancy between the upper and lower crust (DDS); and (5) no evidence for upper-mantle serpentinization under the ultra-thinned crust. Furthermore, we show the importance of structural inheritance in rifting of the Avalon crust. Thus, we suggest that Orphan Basin is the result of rifting of a non-homogeneous Avalon terrane where the lower crust is primarily ductile.

Adaptive unified continuum FEM modeling of a 3D FSI benchmark problem.

PubMed

Jansson, Johan; Degirmenci, Niyazi Cem; Hoffman, Johan

2017-09-01

In this paper, we address a 3D fluid-structure interaction benchmark problem that represents important characteristics of biomedical modeling. We present a goal-oriented adaptive finite element methodology for incompressible fluid-structure interaction based on a streamline diffusion-type stabilization of the balance equations for mass and momentum for the entire continuum in the domain, which is implemented in the Unicorn/FEniCS software framework. A phase marker function and its corresponding transport equation are introduced to select the constitutive law, where the mesh tracks the discontinuous fluid-structure interface. This results in a unified simulation method for fluids and structures. We present detailed results for the benchmark problem compared with experiments, together with a mesh convergence study. Copyright © 2016 John Wiley & Sons, Ltd.

Application of the PM6 method to modeling the solid state

PubMed Central

2008-01-01

The applicability of the recently developed PM6 method for modeling various properties of a wide range of organic and inorganic crystalline solids has been investigated. Although the geometries of most systems examined were reproduced with good accuracy, severe errors were found in the predicted structures of a small number of solids. The origin of these errors was investigated, and a strategy for improving the method proposed. Figure Detail of Structure of Dihydrogen Phosphate in KH2PO4 (upper pair) and in (CH3)4NH2PO4. (Footnote): X-ray structures on left, PM6 structure on right. Electronic supplementary material The online version of this article (doi:10.1007/s00894-008-0299-7) contains supplementary material, which is available to authorized users. PMID:18449579

Electron tomography study of isolated human centrioles.

PubMed

Ibrahim, Rana; Messaoudi, Cédric; Chichon, Francisco Javier; Celati, Claude; Marco, Sergio

2009-01-01

Centrioles are components of the centrosome, which is present in most eukaryotic cells (from protozoa to mammals). They organize the microtubule skeleton during interphase and the mitotic spindle during cell division. In ciliate cells, centrioles form basal bodies that are involved in cellular motility. Despite their important roles in biology, the detailed structure of centrioles remains obscure. This work contributes to a more complete model of centriole structure. The authors used electron tomography of isolated centrosomes from the human lymphoblast KE37 to explore the details of subdistal appendages and centriole lumen organization in mother centrioles. Their results reveal that each of the nine subdistal appendages is composed of two halves (20 nm diameter each) fused in a 40 nm tip that extends 100 nm from where it anchors to microtubules. The centriole lumen is filled at the distal domain by a 45 nm periodic stack of rings. Each ring has a 30 nm diameter, is 15 nm thick, and appears to be tilted at 53 degrees perpendicular to the centriole axis. The rings are anchored to microtubules by arms. Based on their results, the authors propose a model of the mother centriole distal structure. Copyright 2008 Wiley-Liss, Inc.

Weighing trees with lasers: advances, challenges and opportunities

PubMed Central

Boni Vicari, M.; Burt, A.; Calders, K.; Lewis, S. L.; Raumonen, P.; Wilkes, P.

2018-01-01

Terrestrial laser scanning (TLS) is providing exciting new ways to quantify tree and forest structure, particularly above-ground biomass (AGB). We show how TLS can address some of the key uncertainties and limitations of current approaches to estimating AGB based on empirical allometric scaling equations (ASEs) that underpin all large-scale estimates of AGB. TLS provides extremely detailed non-destructive measurements of tree form independent of tree size and shape. We show examples of three-dimensional (3D) TLS measurements from various tropical and temperate forests and describe how the resulting TLS point clouds can be used to produce quantitative 3D models of branch and trunk size, shape and distribution. These models can drastically improve estimates of AGB, provide new, improved large-scale ASEs, and deliver insights into a range of fundamental tree properties related to structure. Large quantities of detailed measurements of individual 3D tree structure also have the potential to open new and exciting avenues of research in areas where difficulties of measurement have until now prevented statistical approaches to detecting and understanding underlying patterns of scaling, form and function. We discuss these opportunities and some of the challenges that remain to be overcome to enable wider adoption of TLS methods. PMID:29503726

Fine resolution mapping of population age-structures for health and development applications.

PubMed

Alegana, V A; Atkinson, P M; Pezzulo, C; Sorichetta, A; Weiss, D; Bird, T; Erbach-Schoenberg, E; Tatem, A J

2015-04-06

The age-group composition of populations varies considerably across the world, and obtaining accurate, spatially detailed estimates of numbers of children under 5 years is important in designing vaccination strategies, educational planning or maternal healthcare delivery. Traditionally, such estimates are derived from population censuses, but these can often be unreliable, outdated and of coarse resolution for resource-poor settings. Focusing on Nigeria, we use nationally representative household surveys and their cluster locations to predict the proportion of the under-five population in 1 × 1 km using a Bayesian hierarchical spatio-temporal model. Results showed that land cover, travel time to major settlements, night-time lights and vegetation index were good predictors and that accounting for fine-scale variation, rather than assuming a uniform proportion of under 5 year olds can result in significant differences in health metrics. The largest gaps in estimated bednet and vaccination coverage were in Kano, Katsina and Jigawa. Geolocated household surveys are a valuable resource for providing detailed, contemporary and regularly updated population age-structure data in the absence of recent census data. By combining these with covariate layers, age-structure maps of unprecedented detail can be produced to guide the targeting of interventions in resource-poor settings.

Millimeter wave radiative transfer studies for precipitation measurements

NASA Technical Reports Server (NTRS)

Vivekanandan, J.; Evans, Frank

1989-01-01

Scattering calculations using the discrete dipole approximation and vector radiative transfer calculations were performed to model multiparameter radar return and passive microwave emission for a simple model of a winter storm. The issue of dendrite riming was addressed by computing scattering properties of thin ice disks with varying bulk density. It was shown that C-band multiparameter radar contains information about particle density and the number concentration of the ice particles. The radiative transfer modeling indicated that polarized multifrequency passive microwave emission may be used to infer some properties of ice hydrometers. Detailed radar modeling and vector radiative transfer modeling is in progress to enhance the understanding of simultaneous radar and radiometer measurements, as in the case of the proposed TRMM field program. A one-dimensional cloud model will be used to simulate the storm structure in detail and study the microphysics, such as size and density. Multifrequency polarized radiometer measurements from the SSMI satellite instrument will be analyzed in relation to dual-frequency and dual-polarization radar measurements.

Probing the structural dynamics of the CRISPR-Cas9 RNA-guided DNA-cleavage system by coarse-grained modeling.

PubMed

Zheng, Wenjun

2017-02-01

In the adaptive immune systems of many bacteria and archaea, the Cas9 endonuclease forms a complex with specific guide/scaffold RNA to identify and cleave complementary target sequences in foreign DNA. This DNA targeting machinery has been exploited in numerous applications of genome editing and transcription control. However, the molecular mechanism of the Cas9 system is still obscure. Recently, high-resolution structures have been solved for Cas9 in different structural forms (e.g., unbound forms, RNA-bound binary complexes, and RNA-DNA-bound tertiary complexes, corresponding to an inactive state, a pre-target-bound state, and a cleavage-competent or product state), which offered key structural insights to the Cas9 mechanism. To further probe the structural dynamics of Cas9 interacting with RNA and DNA at the amino-acid level of details, we have performed systematic coarse-grained modeling using an elastic network model and related analyses. Our normal mode analysis predicted a few key modes of collective motions that capture the observed conformational changes featuring large domain motions triggered by binding of RNA and DNA. Our flexibility analysis identified specific regions with high or low flexibility that coincide with key functional sites (such as DNA/RNA-binding sites, nuclease cleavage sites, and key hinges). We also identified a small set of hotspot residues that control the energetics of functional motions, which overlap with known functional sites and offer promising targets for future mutagenesis efforts to improve the specificity of Cas9. Finally, we modeled the conformational transitions of Cas9 from the unbound form to the binary complex and then the tertiary complex, and predicted a distinct sequence of domain motions. In sum, our findings have offered rich structural and dynamic details relevant to the Cas9 machinery, and will guide future investigation and engineering of the Cas9 systems. Proteins 2017; 85:342-353. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Biosecurity and Open-Source Biology: The Promise and Peril of Distributed Synthetic Biological Technologies.

PubMed

Evans, Nicholas G; Selgelid, Michael J

2015-08-01

In this article, we raise ethical concerns about the potential misuse of open-source biology (OSB): biological research and development that progresses through an organisational model of radical openness, deskilling, and innovation. We compare this organisational structure to that of the open-source software model, and detail salient ethical implications of this model. We demonstrate that OSB, in virtue of its commitment to openness, may be resistant to governance attempts.

The Communication Audit as a Library Management Tool.

ERIC Educational Resources Information Center

Cortez, Edwin M.; Bunge, Charles A.

1987-01-01

Discusses the relationship between effective organizational communication and specific library contexts and reviews the historical development of communication audits as a means of studying communication effectiveness. The generic structure of such audits is described and two models are presented in detail, including techniques for gathering and…

Isogeometric analysis: a powerful numerical tool for the elastic analysis of historical masonry arches

NASA Astrophysics Data System (ADS)

Cazzani, Antonio; Malagù, Marcello; Turco, Emilio

2016-03-01

We illustrate a numerical tool for analyzing plane arches such as those frequently used in historical masonry heritage. It is based on a refined elastic mechanical model derived from the isogeometric approach. In particular, geometry and displacements are modeled by means of non-uniform rational B-splines. After a brief introduction, outlining the basic assumptions of this approach and the corresponding modeling choices, several numerical applications to arches, which are typical of masonry structures, show the performance of this novel technique. These are discussed in detail to emphasize the advantage and potential developments of isogeometric analysis in the field of structural analysis of historical masonry buildings with complex geometries.

Aeroelastic modeling for the FIT (Functional Integration Technology) team F/A-18 simulation

NASA Technical Reports Server (NTRS)

Zeiler, Thomas A.; Wieseman, Carol D.

1989-01-01

As part of Langley Research Center's commitment to developing multidisciplinary integration methods to improve aerospace systems, the Functional Integration Technology (FIT) team was established to perform dynamics integration research using an existing aircraft configuration, the F/A-18. An essential part of this effort has been the development of a comprehensive simulation modeling capability that includes structural, control, and propulsion dynamics as well as steady and unsteady aerodynamics. The structural and unsteady aerodynamics contributions come from an aeroelastic mode. Some details of the aeroelastic modeling done for the Functional Integration Technology (FIT) team research are presented. Particular attention is given to work done in the area of correction factors to unsteady aerodynamics data.

Integration of multi-objective structural optimization into cementless hip prosthesis design: Improved Austin-Moore model.

PubMed

Kharmanda, G

2016-11-01

A new strategy of multi-objective structural optimization is integrated into Austin-Moore prosthesis in order to improve its performance. The new resulting model is so-called Improved Austin-Moore. The topology optimization is considered as a conceptual design stage to sketch several kinds of hollow stems according to the daily loading cases. The shape optimization presents the detailed design stage considering several objectives. Here, A new multiplicative formulation is proposed as a performance scale in order to define the best compromise between several requirements. Numerical applications on 2D and 3D problems are carried out to show the advantages of the proposed model.

A Cloud Microphysics Model for the Gas Giant Planets

NASA Astrophysics Data System (ADS)

Palotai, Csaba J.; Le Beau, Raymond P.; Shankar, Ramanakumar; Flom, Abigail; Lashley, Jacob; McCabe, Tyler

2016-10-01

Recent studies have significantly increased the quality and the number of observed meteorological features on the jovian planets, revealing banded cloud structures and discrete features. Our current understanding of the formation and decay of those clouds also defines the conceptual modes about the underlying atmospheric dynamics. The full interpretation of the new observational data set and the related theories requires modeling these features in a general circulation model (GCM). Here, we present details of our bulk cloud microphysics model that was designed to simulate clouds in the Explicit Planetary Hybrid-Isentropic Coordinate (EPIC) GCM for the jovian planets. The cloud module includes hydrological cycles for each condensable species that consist of interactive vapor, cloud and precipitation phases and it also accounts for latent heating and cooling throughout the transfer processes (Palotai and Dowling, 2008. Icarus, 194, 303-326). Previously, the self-organizing clouds in our simulations successfully reproduced the vertical and horizontal ammonia cloud structure in the vicinity of Jupiter's Great Red Spot and Oval BA (Palotai et al. 2014, Icarus, 232, 141-156). In our recent work, we extended this model to include water clouds on Jupiter and Saturn, ammonia clouds on Saturn, and methane clouds on Uranus and Neptune. Details of our cloud parameterization scheme, our initial results and their comparison with observations will be shown. The latest version of EPIC model is available as open source software from NASA's PDS Atmospheres Node.

Functional connectivity dynamically evolves on multiple time-scales over a static structural connectome: Models and mechanisms.

PubMed

Cabral, Joana; Kringelbach, Morten L; Deco, Gustavo

2017-10-15

Over the last decade, we have observed a revolution in brain structural and functional Connectomics. On one hand, we have an ever-more detailed characterization of the brain's white matter structural connectome. On the other, we have a repertoire of consistent functional networks that form and dissipate over time during rest. Despite the evident spatial similarities between structural and functional connectivity, understanding how different time-evolving functional networks spontaneously emerge from a single structural network requires analyzing the problem from the perspective of complex network dynamics and dynamical system's theory. In that direction, bottom-up computational models are useful tools to test theoretical scenarios and depict the mechanisms at the genesis of resting-state activity. Here, we provide an overview of the different mechanistic scenarios proposed over the last decade via computational models. Importantly, we highlight the need of incorporating additional model constraints considering the properties observed at finer temporal scales with MEG and the dynamical properties of FC in order to refresh the list of candidate scenarios. Copyright © 2017 Elsevier Inc. All rights reserved.

Automated Reconstruction of Historic Roof Structures from Point Clouds - Development and Examples

NASA Astrophysics Data System (ADS)

Pöchtrager, M.; Styhler-Aydın, G.; Döring-Williams, M.; Pfeifer, N.

2017-08-01

The analysis of historic roof constructions is an important task for planning the adaptive reuse of buildings or for maintenance and restoration issues. Current approaches to modeling roof constructions consist of several consecutive operations that need to be done manually or using semi-automatic routines. To increase efficiency and allow the focus to be on analysis rather than on data processing, a set of methods was developed for the fully automated analysis of the roof constructions, including integration of architectural and structural modeling. Terrestrial laser scanning permits high-detail surveying of large-scale structures within a short time. Whereas 3-D laser scan data consist of millions of single points on the object surface, we need a geometric description of structural elements in order to obtain a structural model consisting of beam axis and connections. Preliminary results showed that the developed methods work well for beams in flawless condition with a quadratic cross section and no bending. Deformations or damages such as cracks and cuts on the wooden beams can lead to incomplete representations in the model. Overall, a high degree of automation was achieved.

The application of SSADM to modelling the logical structure of proteins.

PubMed

Saldanha, J; Eccles, J

1991-10-01

A logical design that describes the overall structure of proteins, together with a more detailed design describing secondary and some supersecondary structures, has been constructed using the computer-aided software engineering (CASE) tool, Auto-mate. Auto-mate embodies the philosophy of the Structured Systems Analysis and Design Method (SSADM) which enables the logical design of computer systems. Our design will facilitate the building of large information systems, such as databases and knowledgebases in the field of protein structure, by the derivation of system requirements from our logical model prior to producing the final physical system. In addition, the study has highlighted the ease of employing SSADM as a formalism in which to conduct the transferral of concepts from an expert into a design for a knowledge-based system that can be implemented on a computer (the knowledge-engineering exercise). It has been demonstrated how SSADM techniques may be extended for the purpose of modelling the constituent Prolog rules. This facilitates the integration of the logical system design model with the derived knowledge-based system.

Insights into channel dysfunction from modelling and molecular dynamics simulations.

PubMed

Musgaard, Maria; Paramo, Teresa; Domicevica, Laura; Andersen, Ole Juul; Biggin, Philip C

2018-04-01

Developments in structural biology mean that the number of different ion channel structures has increased significantly in recent years. Structures of ion channels enable us to rationalize how mutations may lead to channelopathies. However, determining the structures of ion channels is still not trivial, especially as they necessarily exist in many distinct functional states. Therefore, the use of computational modelling can provide complementary information that can refine working hypotheses of both wild type and mutant ion channels. The simplest but still powerful tool is homology modelling. Many structures are available now that can provide suitable templates for many different types of ion channels, allowing a full three-dimensional interpretation of mutational effects. These structural models, and indeed the structures themselves obtained by X-ray crystallography, and more recently cryo-electron microscopy, can be subjected to molecular dynamics simulations, either as a tool to help explore the conformational dynamics in detail or simply as a means to refine the models further. Here we review how these approaches have been used to improve our understanding of how diseases might be linked to specific mutations in ion channel proteins. This article is part of the Special Issue entitled 'Channelopathies.' Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Structural characterisation of medically relevant protein assemblies by integrating mass spectrometry with computational modelling.

PubMed

Politis, Argyris; Schmidt, Carla

2018-03-20

Structural mass spectrometry with its various techniques is a powerful tool for the structural elucidation of medically relevant protein assemblies. It delivers information on the composition, stoichiometries, interactions and topologies of these assemblies. Most importantly it can deal with heterogeneous mixtures and assemblies which makes it universal among the conventional structural techniques. In this review we summarise recent advances and challenges in structural mass spectrometric techniques. We describe how the combination of the different mass spectrometry-based methods with computational strategies enable structural models at molecular levels of resolution. These models hold significant potential for helping us in characterizing the function of protein assemblies related to human health and disease. In this review we summarise the techniques of structural mass spectrometry often applied when studying protein-ligand complexes. We exemplify these techniques through recent examples from literature that helped in the understanding of medically relevant protein assemblies. We further provide a detailed introduction into various computational approaches that can be integrated with these mass spectrometric techniques. Last but not least we discuss case studies that integrated mass spectrometry and computational modelling approaches and yielded models of medically important protein assembly states such as fibrils and amyloids. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

P. falciparum Infection Durations and Infectiousness Are Shaped by Antigenic Variation and Innate and Adaptive Host Immunity in a Mathematical Model

PubMed Central

Eckhoff, Philip

2012-01-01

Many questions remain about P. falciparum within-host dynamics, immunity, and transmission–issues that may affect public health campaign planning. These gaps in knowledge concern the distribution of durations of malaria infections, determination of peak parasitemia during acute infection, the relationships among gametocytes and immune responses and infectiousness to mosquitoes, and the effect of antigenic structure on reinfection outcomes. The present model of intra-host dynamics of P. falciparum implements detailed representations of parasite and immune dynamics, with structures based on minimal extrapolations from first-principles biology in its foundations. The model is designed to quickly and readily accommodate gains in mechanistic understanding and to evaluate effects of alternative biological hypothesis through in silico experiments. Simulations follow the parasite from the liver-stage through the detailed asexual cycle to clearance while tracking gametocyte populations. The modeled immune system includes innate inflammatory and specific antibody responses to a repertoire of antigens. The mechanistic focus provides clear explanations for the structure of the distribution of infection durations through the interaction of antigenic variation and innate and adaptive immunity. Infectiousness to mosquitoes appears to be determined not only by the density of gametocytes but also by the level of inflammatory cytokines, which harmonizes an extensive series of study results. Finally, pre-existing immunity can either decrease or increase the duration of infections upon reinfection, depending on the degree of overlap in antigenic repertoires and the strength of the pre-existing immunity. PMID:23028698

Hierarchical combinatorial deep learning architecture for pancreas segmentation of medical computed tomography cancer images.

PubMed

Fu, Min; Wu, Wenming; Hong, Xiafei; Liu, Qiuhua; Jiang, Jialin; Ou, Yaobin; Zhao, Yupei; Gong, Xinqi

2018-04-24

Efficient computational recognition and segmentation of target organ from medical images are foundational in diagnosis and treatment, especially about pancreas cancer. In practice, the diversity in appearance of pancreas and organs in abdomen, makes detailed texture information of objects important in segmentation algorithm. According to our observations, however, the structures of previous networks, such as the Richer Feature Convolutional Network (RCF), are too coarse to segment the object (pancreas) accurately, especially the edge. In this paper, we extend the RCF, proposed to the field of edge detection, for the challenging pancreas segmentation, and put forward a novel pancreas segmentation network. By employing multi-layer up-sampling structure replacing the simple up-sampling operation in all stages, the proposed network fully considers the multi-scale detailed contexture information of object (pancreas) to perform per-pixel segmentation. Additionally, using the CT scans, we supply and train our network, thus get an effective pipeline. Working with our pipeline with multi-layer up-sampling model, we achieve better performance than RCF in the task of single object (pancreas) segmentation. Besides, combining with multi scale input, we achieve the 76.36% DSC (Dice Similarity Coefficient) value in testing data. The results of our experiments show that our advanced model works better than previous networks in our dataset. On the other words, it has better ability in catching detailed contexture information. Therefore, our new single object segmentation model has practical meaning in computational automatic diagnosis.

Adaptive optical microscope for brain imaging in vivo

NASA Astrophysics Data System (ADS)

Wang, Kai

2017-04-01

The optical heterogeneity of biological tissue imposes a major limitation to acquire detailed structural and functional information deep in the biological specimens using conventional microscopes. To restore optimal imaging performance, we developed an adaptive optical microscope based on direct wavefront sensing technique. This microscope can reliably measure and correct biological samples induced aberration. We demonstrated its performance and application in structural and functional brain imaging in various animal models, including fruit fly, zebrafish and mouse.

A Corner-Point-Grid-Based Voxelization Method for Complex Geological Structure Model with Folds

NASA Astrophysics Data System (ADS)

Chen, Qiyu; Mariethoz, Gregoire; Liu, Gang

2017-04-01

3D voxelization is the foundation of geological property modeling, and is also an effective approach to realize the 3D visualization of the heterogeneous attributes in geological structures. The corner-point grid is a representative data model among all voxel models, and is a structured grid type that is widely applied at present. When carrying out subdivision for complex geological structure model with folds, we should fully consider its structural morphology and bedding features to make the generated voxels keep its original morphology. And on the basis of which, they can depict the detailed bedding features and the spatial heterogeneity of the internal attributes. In order to solve the shortage of the existing technologies, this work puts forward a corner-point-grid-based voxelization method for complex geological structure model with folds. We have realized the fast conversion from the 3D geological structure model to the fine voxel model according to the rule of isocline in Ramsay's fold classification. In addition, the voxel model conforms to the spatial features of folds, pinch-out and other complex geological structures, and the voxels of the laminas inside a fold accords with the result of geological sedimentation and tectonic movement. This will provide a carrier and model foundation for the subsequent attribute assignment as well as the quantitative analysis and evaluation based on the spatial voxels. Ultimately, we use examples and the contrastive analysis between the examples and the Ramsay's description of isoclines to discuss the effectiveness and advantages of the method proposed in this work when dealing with the voxelization of 3D geologic structural model with folds based on corner-point grids.

Development, Validation and Parametric study of a 3-Year-Old Child Head Finite Element Model

NASA Astrophysics Data System (ADS)

Cui, Shihai; Chen, Yue; Li, Haiyan; Ruan, ShiJie

2015-12-01

Traumatic brain injury caused by drop and traffic accidents is an important reason for children's death and disability. Recently, the computer finite element (FE) head model has been developed to investigate brain injury mechanism and biomechanical responses. Based on CT data of a healthy 3-year-old child head, the FE head model with detailed anatomical structure was developed. The deep brain structures such as white matter, gray matter, cerebral ventricle, hippocampus, were firstly created in this FE model. The FE model was validated by comparing the simulation results with that of cadaver experiments based on reconstructing the child and adult cadaver experiments. In addition, the effects of skull stiffness on the child head dynamic responses were further investigated. All the simulation results confirmed the good biofidelity of the FE model.

Design Through Manufacturing: The Solid Model-Finite Element Analysis Interface

NASA Technical Reports Server (NTRS)

Rubin, Carol

2002-01-01

State-of-the-art computer aided design (CAD) presently affords engineers the opportunity to create solid models of machine parts reflecting every detail of the finished product. Ideally, in the aerospace industry, these models should fulfill two very important functions: (1) provide numerical. control information for automated manufacturing of precision parts, and (2) enable analysts to easily evaluate the stress levels (using finite element analysis - FEA) for all structurally significant parts used in aircraft and space vehicles. Today's state-of-the-art CAD programs perform function (1) very well, providing an excellent model for precision manufacturing. But they do not provide a straightforward and simple means of automating the translation from CAD to FEA models, especially for aircraft-type structures. Presently, the process of preparing CAD models for FEA consumes a great deal of the analyst's time.

3D molecular models of whole HIV-1 virions generated with cellPACK

PubMed Central

Goodsell, David S.; Autin, Ludovic; Forli, Stefano; Sanner, Michel F.; Olson, Arthur J.

2014-01-01

As knowledge of individual biological processes grows, it becomes increasingly useful to frame new findings within their larger biological contexts in order to generate new systems-scale hypotheses. This report highlights two major iterations of a whole virus model of HIV-1, generated with the cellPACK software. cellPACK integrates structural and systems biology data with packing algorithms to assemble comprehensive 3D models of cell-scale structures in molecular detail. This report describes the biological data, modeling parameters and cellPACK methods used to specify and construct editable models for HIV-1. Anticipating that cellPACK interfaces under development will enable researchers from diverse backgrounds to critique and improve the biological models, we discuss how cellPACK can be used as a framework to unify different types of data across all scales of biology. PMID:25253262

L-shaped piezoelectric motor--part II: analytical modeling.

PubMed

Avirovik, Dragan; Karami, M Amin; Inman, Daniel; Priya, Shashank

2012-01-01

This paper develops an analytical model for an L-shaped piezoelectric motor. The motor structure has been described in detail in Part I of this study. The coupling of the bending vibration mode of the bimorphs results in an elliptical motion at the tip. The emphasis of this paper is on the development of a precise analytical model which can predict the dynamic behavior of the motor based on its geometry. The motor was first modeled mechanically to identify the natural frequencies and mode shapes of the structure. Next, an electromechanical model of the motor was developed to take into account the piezoelectric effect, and dynamics of L-shaped piezoelectric motor were obtained as a function of voltage and frequency. Finally, the analytical model was validated by comparing it to experiment results and the finite element method (FEM). © 2012 IEEE

Modeling of Damage Initiation and Progression in a SiC/SiC Woven Ceramic Matrix Composite

NASA Technical Reports Server (NTRS)

Mital, Subodh K.; Goldberg, Robert K.; Bonacuse, Peter J.

2012-01-01

The goal of an ongoing project at NASA Glenn is to investigate the effects of the complex microstructure of a woven ceramic matrix composite and its variability on the effective properties and the durability of the material. Detailed analysis of these complex microstructures may provide clues for the material scientists who `design the material? or to structural analysts and designers who `design with the material? regarding damage initiation and damage propagation. A model material system, specifically a five-harness satin weave architecture CVI SiC/SiC composite composed of Sylramic-iBN fibers and a SiC matrix, has been analyzed. Specimens of the material were serially sectioned and polished to capture the detailed images of fiber tows, matrix and porosity. Open source analysis tools were used to isolate various constituents and finite elements models were then generated from simplified models of those images. Detailed finite element analyses were performed that examine how the variability in the local microstructure affected the macroscopic behavior as well as the local damage initiation and progression. Results indicate that the locations where damage initiated and propagated is linked to specific microstructural features.

A Numerical and Experimental Study of Damage Growth in a Composite Laminate

NASA Technical Reports Server (NTRS)

McElroy, Mark; Ratcliffe, James; Czabaj, Michael; Wang, John; Yuan, Fuh-Gwo

2014-01-01

The present study has three goals: (1) perform an experiment where a simple laminate damage process can be characterized in high detail; (2) evaluate the performance of existing commercially available laminate damage simulation tools by modeling the experiment; (3) observe and understand the underlying physics of damage in a composite honeycomb sandwich structure subjected to low-velocity impact. A quasi-static indentation experiment has been devised to provide detailed information about a simple mixed-mode damage growth process. The test specimens consist of an aluminum honeycomb core with a cross-ply laminate facesheet supported on a stiff uniform surface. When the sample is subjected to an indentation load, the honeycomb core provides support to the facesheet resulting in a gradual and stable damage growth process in the skin. This enables real time observation as a matrix crack forms, propagates through a ply, and then causes a delamination. Finite element analyses were conducted in ABAQUS/Explicit(TradeMark) 6.13 that used continuum and cohesive modeling techniques to simulate facesheet damage and a geometric and material nonlinear model to simulate core crushing. The high fidelity of the experimental data allows a detailed investigation and discussion of the accuracy of each numerical modeling approach.

An overview of multiphase cartilage mechanical modelling and its role in understanding function and pathology.

PubMed

Klika, Václav; Gaffney, Eamonn A; Chen, Ying-Chun; Brown, Cameron P

2016-09-01

There is a long history of mathematical and computational modelling with the objective of understanding the mechanisms governing cartilage׳s remarkable mechanical performance. Nonetheless, despite sophisticated modelling development, simulations of cartilage have consistently lagged behind structural knowledge and thus the relationship between structure and function in cartilage is not fully understood. However, in the most recent generation of studies, there is an emerging confluence between our structural knowledge and the structure represented in cartilage modelling. This raises the prospect of further refinement in our understanding of cartilage function and also the initiation of an engineering-level understanding for how structural degradation and ageing relates to cartilage dysfunction and pathology, as well as informing the potential design of prospective interventions. Aimed at researchers entering the field of cartilage modelling, we thus review the basic principles of cartilage models, discussing the underlying physics and assumptions in relatively simple settings, whilst presenting the derivation of relatively parsimonious multiphase cartilage models consistent with our discussions. We proceed to consider modern developments that start aligning the structure captured in the models with observed complexities. This emphasises the challenges associated with constitutive relations, boundary conditions, parameter estimation and validation in cartilage modelling programmes. Consequently, we further detail how both experimental interrogations and modelling developments can be utilised to investigate and reduce such difficulties before summarising how cartilage modelling initiatives may improve our understanding of cartilage ageing, pathology and intervention. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Modeling and analysis of the DSS-14 antenna control system

NASA Technical Reports Server (NTRS)

Gawronski, W.; Bartos, R.

1996-01-01

An improvement of pointing precision of the DSS-14 antenna is planned for the near future. In order to analyze the improvement limits and to design new controllers, a precise model of the antenna and the servo is developed, including a finite element model of the antenna structure and detailed models of the hydraulic drives and electronic parts. The DSS-14 antenna control system has two modes of operation: computer mode and precision mode. The principal goal of this investigation is to develop the model of the computer mode and to evaluate its performance. The DSS-14 antenna computer model consists of the antenna structure and drives in azimuth and elevation. For this model, the position servo loop is derived, and simulations of the closed-loop antenna dynamics are presented. The model is significantly different from that for the 34-m beam-waveguide antennas.

Design and experiment of data-driven modeling and flutter control of a prototype wing

NASA Astrophysics Data System (ADS)

Lum, Kai-Yew; Xu, Cai-Lin; Lu, Zhenbo; Lai, Kwok-Leung; Cui, Yongdong

2017-06-01

This paper presents an approach for data-driven modeling of aeroelasticity and its application to flutter control design of a wind-tunnel wing model. Modeling is centered on system identification of unsteady aerodynamic loads using computational fluid dynamics data, and adopts a nonlinear multivariable extension of the Hammerstein-Wiener system. The formulation is in modal coordinates of the elastic structure, and yields a reduced-order model of the aeroelastic feedback loop that is parametrized by airspeed. Flutter suppression is thus cast as a robust stabilization problem over uncertain airspeed, for which a low-order H∞ controller is computed. The paper discusses in detail parameter sensitivity and observability of the model, the former to justify the chosen model structure, and the latter to provide a criterion for physical sensor placement. Wind tunnel experiments confirm the validity of the modeling approach and the effectiveness of the control design.

Traditional Payment Models in Radiology: Historical Context for Ongoing Reform.

PubMed

Silva, Ezequiel; McGinty, Geraldine B; Hughes, Danny R; Duszak, Richard

2016-10-01

The passage of the Medicare Access and CHIP Reauthorization Act (MACRA) replaces the sustainable growth rate with a payment system based on quality and alternative payment model participation. The general structure of payment under MACRA is included in the statute, but the rules and regulations defining its implementation are yet to be formalized. It is imperative that the radiology profession inform policymakers on their role in health care under MACRA. This will require a detailed understanding of prior legislative and nonlegislative actions that helped shape MACRA. To that end, the authors provide a detailed historical context for payment reform, focusing on the payment quality initiatives and alternative payment model demonstrations that helped provide the foundation of future MACRA-driven payment reform. Copyright © 2016 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Free vibrations of thin-walled semicircular graphite-epoxy composite frames

NASA Technical Reports Server (NTRS)

Carden, Huey D.; Noor, Ahmed K.; Peters, Jeanne M.

1990-01-01

A detailed study is made of the effects of variations in lamination and material parameters of thin walled composite frames on their vibrational characteristics. The structures considered are semicircular thin walled frames with I and J sections. The flanges and webs of the frames are modeled by using 2-D shell and plate finite elements. A mixed formulation is used with the fundamental unknowns consisting of both the generalized displacements and stress resultants in the frame. The frequencies and modes predicted by the 2-D finite element model are compared with those obtained from experiments, as well as with the predictions of a non-dimensional thin walled beam finite element model. A detailed study is made of the sensitivity of the vibrational response to variations in the fiber orientation, material properties of the individual layers, and boundary conditions.

Free vibrations of thin-walled semicircular graphite-epoxy composite frames

NASA Technical Reports Server (NTRS)

Noor, Ahmed K.; Carden, Huey D.; Peters, Jeanne M.

1990-01-01

A detailed study is made of the effects of variations in lamination and material parameters of thin walled composite frames on their vibrational characteristics. The structures considered are semicircular thin walled frames with I and J sections. The flanges and webs of the frames are modelled by using 2-D shell and plate finite elements. A mixed formulation is used with the fundamental unknowns consisting of both the generalized displacements and stress resultants in the frames. The frequencies and modes predicted by the 2-D finite element model are compared with those obtained from experiments, as well as with the predictions of a 1-D thin walled beam finite element model. A detailed study is made of the sensitivity of the vibrational response to variations in the fiber orientation, material properties of the individual layers, and boundary conditions.

Modelling dynamics in protein crystal structures by ensemble refinement

PubMed Central

Burnley, B Tom; Afonine, Pavel V; Adams, Paul D; Gros, Piet

2012-01-01

Single-structure models derived from X-ray data do not adequately account for the inherent, functionally important dynamics of protein molecules. We generated ensembles of structures by time-averaged refinement, where local molecular vibrations were sampled by molecular-dynamics (MD) simulation whilst global disorder was partitioned into an underlying overall translation–libration–screw (TLS) model. Modeling of 20 protein datasets at 1.1–3.1 Å resolution reduced cross-validated Rfree values by 0.3–4.9%, indicating that ensemble models fit the X-ray data better than single structures. The ensembles revealed that, while most proteins display a well-ordered core, some proteins exhibit a ‘molten core’ likely supporting functionally important dynamics in ligand binding, enzyme activity and protomer assembly. Order–disorder changes in HIV protease indicate a mechanism of entropy compensation for ordering the catalytic residues upon ligand binding by disordering specific core residues. Thus, ensemble refinement extracts dynamical details from the X-ray data that allow a more comprehensive understanding of structure–dynamics–function relationships. DOI: http://dx.doi.org/10.7554/eLife.00311.001 PMID:23251785

Calcium-manganese oxides as structural and functional models for active site in oxygen evolving complex in photosystem II: lessons from simple models.

PubMed

Najafpour, Mohammad Mahdi

2011-01-01

The oxygen evolving complex in photosystem II which induces the oxidation of water to dioxygen in plants, algae and certain bacteria contains a cluster of one calcium and four manganese ions. It serves as a model to split water by sunlight. Reports on the mechanism and structure of photosystem II provide a more detailed architecture of the oxygen evolving complex and the surrounding amino acids. One challenge in this field is the development of artificial model compounds to study oxygen evolution reaction outside the complicated environment of the enzyme. Calcium-manganese oxides as structural and functional models for the active site of photosystem II are explained and reviewed in this paper. Because of related structures of these calcium-manganese oxides and the catalytic centers of active site of the oxygen evolving complex of photosystem II, the study may help to understand more about mechanism of oxygen evolution by the oxygen evolving complex of photosystem II. Copyright © 2010 Elsevier B.V. All rights reserved.

Deep space network software cost estimation model

NASA Technical Reports Server (NTRS)

Tausworthe, R. C.

1981-01-01

A parametric software cost estimation model prepared for Deep Space Network (DSN) Data Systems implementation tasks is presented. The resource estimation model incorporates principles and data from a number of existing models. The model calibrates task magnitude and difficulty, development environment, and software technology effects through prompted responses to a set of approximately 50 questions. Parameters in the model are adjusted to fit DSN software life cycle statistics. The estimation model output scales a standard DSN Work Breakdown Structure skeleton, which is then input into a PERT/CPM system, producing a detailed schedule and resource budget for the project being planned.

Style grammars for interactive visualization of architecture.

PubMed

Aliaga, Daniel G; Rosen, Paul A; Bekins, Daniel R

2007-01-01

Interactive visualization of architecture provides a way to quickly visualize existing or novel buildings and structures. Such applications require both fast rendering and an effortless input regimen for creating and changing architecture using high-level editing operations that automatically fill in the necessary details. Procedural modeling and synthesis is a powerful paradigm that yields high data amplification and can be coupled with fast-rendering techniques to quickly generate plausible details of a scene without much or any user interaction. Previously, forward generating procedural methods have been proposed where a procedure is explicitly created to generate particular content. In this paper, we present our work in inverse procedural modeling of buildings and describe how to use an extracted repertoire of building grammars to facilitate the visualization and quick modification of architectural structures and buildings. We demonstrate an interactive application where the user draws simple building blocks and, using our system, can automatically complete the building "in the style of" other buildings using view-dependent texture mapping or nonphotorealistic rendering techniques. Our system supports an arbitrary number of building grammars created from user subdivided building models and captured photographs. Using only edit, copy, and paste metaphors, the entire building styles can be altered and transferred from one building to another in a few operations, enhancing the ability to modify an existing architectural structure or to visualize a novel building in the style of the others.

A Conceptual Aerospace Vehicle Structural System Modeling, Analysis and Design Process

NASA Technical Reports Server (NTRS)

Mukhopadhyay, Vivek

2007-01-01

A process for aerospace structural concept analysis and design is presented, with examples of a blended-wing-body fuselage, a multi-bubble fuselage concept, a notional crew exploration vehicle, and a high altitude long endurance aircraft. Aerospace vehicle structures must withstand all anticipated mission loads, yet must be designed to have optimal structural weight with the required safety margins. For a viable systems study of advanced concepts, these conflicting requirements must be imposed and analyzed early in the conceptual design cycle, preferably with a high degree of fidelity. In this design process, integrated multidisciplinary analysis tools are used in a collaborative engineering environment. First, parametric solid and surface models including the internal structural layout are developed for detailed finite element analyses. Multiple design scenarios are generated for analyzing several structural configurations and material alternatives. The structural stress, deflection, strain, and margins of safety distributions are visualized and the design is improved. Over several design cycles, the refined vehicle parts and assembly models are generated. The accumulated design data is used for the structural mass comparison and concept ranking. The present application focus on the blended-wing-body vehicle structure and advanced composite material are also discussed.

Lidar-Based Rock-Fall Hazard Characterization of Cliffs

USGS Publications Warehouse

Collins, Brian D.; Greg M.Stock,

2017-01-01

Rock falls from cliffs and other steep slopes present numerous challenges for detailed geological characterization. In steep terrain, rock-fall source areas are both dangerous and difficult to access, severely limiting the ability to make detailed structural and volumetric measurements necessary for hazard assessment. Airborne and terrestrial lidar survey methods can provide high-resolution data needed for volumetric, structural, and deformation analyses of rock falls, potentially making these analyses straightforward and routine. However, specific methods to collect, process, and analyze lidar data of steep cliffs are needed to maximize analytical accuracy and efficiency. This paper presents observations showing how lidar data sets should be collected, filtered, registered, and georeferenced to tailor their use in rock fall characterization. Additional observations concerning surface model construction, volumetric calculations, and deformation analysis are also provided.

Northern New Jersey Nursing Education Consortium: a partnership for graduate nursing education.

PubMed

Quinless, F W; Levin, R F

1998-01-01

The purpose of this article is to describe the evolution and implementation of the Northern New Jersey Nursing Education consortium--a consortium of seven member institutions established in 1992. Details regarding the specific functions of the consortium relative to cross-registration of students in graduate courses, financial disbursement of revenue, faculty development activities, student services, library privileges, and institutional research review board mechanisms are described. The authors also review the administrative organizational structure through which the work conducted by the consortium occurs. Both the advantages and disadvantages of such a graduate consortium are explored, and specific examples of recent potential and real conflicts are fully discussed. The authors detail governance and structure of the consortium as a potential model for replication in other environments.

Water Oxidation Catalysis via Size-Selected Iridium Clusters

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

Halder, Avik; Liu, Cong; LIU, ZHUN

The detailed mechanism and efficacy of four electron electrochemical water oxidation depend critically upon the detailed atomic structure of each catalytic site, which are numerous and diverse in most metal oxides anodes. In order to limit the diversity of sites, arrays of discrete iridium clusters with identical metal atom number (Ir-2, Ir-4, or Ir-8) were deposited in submonolayer coverage on conductive oxide supports, and the electrochemical properties and activity of each was evaluated. Exceptional electroactivity for the oxygen evolving reaction (OER) was observed for all cluster samples in acidic electrolyte. Reproducible cluster-size-dependent trends in redox behavior were also resolved. First-principlesmore » computational models of the individual discrete-size clusters allow correlation of catalytic-site structure and multiplicity with redox behavior.« less

Nanoscale inhomogeneity and photoacid generation dynamics in extreme ultraviolet resist materials

NASA Astrophysics Data System (ADS)

Wu, Ping-Jui; Wang, Yu-Fu; Chen, Wei-Chi; Wang, Chien-Wei; Cheng, Joy; Chang, Vencent; Chang, Ching-Yu; Lin, John; Cheng, Yuan-Chung

2018-03-01

The development of extreme ultraviolet (EUV) lithography towards the 22 nm node and beyond depends critically on the availability of resist materials that meet stringent control requirements in resolution, line edge roughness, and sensitivity. However, the molecular mechanisms that govern the structure-function relationships in current EUV resist systems are not well understood. In particular, the nanoscale structures of the polymer base and the distributions of photoacid generators (PAGs) should play a critical roles in the performance of a resist system, yet currently available models for photochemical reactions in EUV resist systems are exclusively based on homogeneous bulk models that ignore molecular-level details of solid resist films. In this work, we investigate how microscopic molecular organizations in EUV resist affect photoacid generations in a bottom-up approach that describes structure-dependent electron-transfer dynamics in a solid film model. To this end, molecular dynamics simulations and stimulated annealing are used to obtain structures of a large simulation box containing poly(4-hydroxystyrene) (PHS) base polymers and triphenylsulfonium based PAGs. Our calculations reveal that ion-pair interactions govern the microscopic distributions of the polymer base and PAG molecules, resulting in a highly inhomogeneous system with nonuniform nanoscale chemical domains. Furthermore, the theoretical structures were used in combination of quantum chemical calculations and the Marcus theory to evaluate electron transfer rates between molecular sites, and then kinetic Monte Carlo simulations were carried out to model electron transfer dynamics with molecular structure details taken into consideration. As a result, the portion of thermalized electrons that are absorbed by the PAGs and the nanoscale spatial distribution of generated acids can be estimated. Our data reveal that the nanoscale inhomogeneous distributions of base polymers and PAGs strongly affect the electron transfer and the performance of the resist system. The implications to the performances of EUV resists and key engineering requirements for improved resist systems will also be discussed in this work. Our results shed light on the fundamental structure dependence of photoacid generation and the control of the nanoscale structures as well as base polymer-PAG interactions in EVU resist systems, and we expect these knowledge will be useful for the future development of improved EUV resist systems.