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Comparative studies on constitutive models for cohesive interface cracks of quasi-brittle materials

International Nuclear Information System (INIS)

Shen Xinpu; Shen Guoxiao; Zhou Lin

2005-01-01

In this paper, Concerning on the modelling of quasi-brittle fracture process zone at interface crack of quasi-brittle materials and structures, typical constitutive models of interface cracks were compared. Numerical calculations of the constitutive behaviours of selected models were carried out at local level. Aiming at the simulation of quasi-brittle fracture of concrete-like materials and structures, the emphases of the qualitative comparisons of selected cohesive models are focused on: (1) the fundamental mode I and mode II behaviours of selected models; (2) dilatancy properties of the selected models under mixed mode fracture loading conditions. (authors)
Subcritical crack growth law and its consequences for lifetime statistics and size effect of quasibrittle structures

International Nuclear Information System (INIS)

Le, Jia-Liang; Bazant, Zdenek P; Bazant, Martin Z

2009-01-01

For brittle failures, the probability distribution of structural strength and lifetime are known to be Weibullian, in which case the knowledge of the mean and standard deviation suffices to determine the loading or time corresponding to a tolerable failure probability such as 10 -6 . Unfortunately, this is not so for quasibrittle structures, characterized by material inhomogeneities that are not negligible compared with the structure size (as is typical, e.g. for concrete, fibre composites, tough ceramics, rocks and sea ice). For such structures, the distribution of structural strength was shown to vary from almost Gaussian to Weibullian as a function of structure size (and also shape). Here we predict the size dependence of the distribution type for the lifetime of quasibrittle structures. To derive the lifetime statistics from the strength statistics, the subcritical crack growth law is requisite. This empirical law is shown to be justified by fracture mechanics of random crack jumps in the atomic lattice and the condition of equality of the energy dissipation rates calculated on the nano-scale and the macro-scale. The size effect on the lifetime is found to be much stronger than that on the structural strength. The theory is shown to match the experimentally observed systematic deviations of lifetime histograms from the Weibull distribution.
Formulation and computational aspects of plasticity and damage models with application to quasi-brittle materials

Energy Technology Data Exchange (ETDEWEB)

Chen, Z.; Schreyer, H.L. [New Mexico Engineering Research Institute, Albuquerque, NM (United States)

1995-09-01

The response of underground structures and transportation facilities under various external loadings and environments is critical for human safety as well as environmental protection. Since quasi-brittle materials such as concrete and rock are commonly used for underground construction, the constitutive modeling of these engineering materials, including post-limit behaviors, is one of the most important aspects in safety assessment. From experimental, theoretical, and computational points of view, this report considers the constitutive modeling of quasi-brittle materials in general and concentrates on concrete in particular. Based on the internal variable theory of thermodynamics, the general formulations of plasticity and damage models are given to simulate two distinct modes of microstructural changes, inelastic flow and degradation of material strength and stiffness, that identify the phenomenological nonlinear behaviors of quasi-brittle materials. The computational aspects of plasticity and damage models are explored with respect to their effects on structural analyses. Specific constitutive models are then developed in a systematic manner according to the degree of completeness. A comprehensive literature survey is made to provide the up-to-date information on prediction of structural failures, which can serve as a reference for future research.
Scaling strength distributions in quasi-brittle materials from micro-to macro-scales: A computational approach to modeling Nature-inspired structural ceramics

International Nuclear Information System (INIS)

Genet, Martin; Couegnat, Guillaume; Tomsia, Antoni P.; Ritchie, Robert O.

2014-01-01

This paper presents an approach to predict the strength distribution of quasi-brittle materials across multiple length-scales, with emphasis on Nature-inspired ceramic structures. It permits the computation of the failure probability of any structure under any mechanical load, solely based on considerations of the microstructure and its failure properties by naturally incorporating the statistical and size-dependent aspects of failure. We overcome the intrinsic limitations of single periodic unit-based approaches by computing the successive failures of the material components and associated stress redistributions on arbitrary numbers of periodic units. For large size samples, the microscopic cells are replaced by a homogenized continuum with equivalent stochastic and damaged constitutive behavior. After establishing the predictive capabilities of the method, and illustrating its potential relevance to several engineering problems, we employ it in the study of the shape and scaling of strength distributions across differing length-scales for a particular quasi-brittle system. We find that the strength distributions display a Weibull form for samples of size approaching the periodic unit; however, these distributions become closer to normal with further increase in sample size before finally reverting to a Weibull form for macroscopic sized samples. In terms of scaling, we find that the weakest link scaling applies only to microscopic, and not macroscopic scale, samples. These findings are discussed in relation to failure patterns computed at different size-scales. (authors)
Unified nano-mechanics based probabilistic theory of quasibrittle and brittle structures: I. Strength, static crack growth, lifetime and scaling

Science.gov (United States)

Le, Jia-Liang; Bažant, Zdeněk P.; Bazant, Martin Z.

2011-07-01

Engineering structures must be designed for an extremely low failure probability such as 10 -6, which is beyond the means of direct verification by histogram testing. This is not a problem for brittle or ductile materials because the type of probability distribution of structural strength is fixed and known, making it possible to predict the tail probabilities from the mean and variance. It is a problem, though, for quasibrittle materials for which the type of strength distribution transitions from Gaussian to Weibullian as the structure size increases. These are heterogeneous materials with brittle constituents, characterized by material inhomogeneities that are not negligible compared to the structure size. Examples include concrete, fiber composites, coarse-grained or toughened ceramics, rocks, sea ice, rigid foams and bone, as well as many materials used in nano- and microscale devices. This study presents a unified theory of strength and lifetime for such materials, based on activation energy controlled random jumps of the nano-crack front, and on the nano-macro multiscale transition of tail probabilities. Part I of this study deals with the case of monotonic and sustained (or creep) loading, and Part II with fatigue (or cyclic) loading. On the scale of the representative volume element of material, the probability distribution of strength has a Gaussian core onto which a remote Weibull tail is grafted at failure probability of the order of 10 -3. With increasing structure size, the Weibull tail penetrates into the Gaussian core. The probability distribution of static (creep) lifetime is related to the strength distribution by the power law for the static crack growth rate, for which a physical justification is given. The present theory yields a simple relation between the exponent of this law and the Weibull moduli for strength and lifetime. The benefit is that the lifetime distribution can be predicted from short-time tests of the mean size effect on
Experimental and Modelling Investigations of the Coupled Elastoplastic Damage of a Quasi-brittle Rock

Science.gov (United States)

Zhang, Jiu-Chang

2018-02-01

Triaxial compression tests are conducted on a quasi-brittle rock, limestone. The analyses show that elastoplastic deformation is coupled with damage. Based on the experimental investigation, a coupled elastoplastic damage model is developed within the framework of irreversible thermodynamics. The coupling effects between the plastic and damage dissipations are described by introducing an isotropic damage variable into the elastic stiffness and yield criterion. The novelty of the model is in the description of the thermodynamic force associated with damage, which is formulated as a state function of both elastic and plastic strain energies. The latter gives a full consideration on the comprehensive effects of plastic strain and stress changing processes in rock material on the development of damage. The damage criterion and potential are constructed to determine the onset and evolution of damage variable. The return mapping algorithms of the coupled model are deduced for three different inelastic corrections. Comparisons between test data and numerical simulations show that the coupled elastoplastic damage model is capable of describing the main mechanical behaviours of the quasi-brittle rock.
Quasi-brittle damage modeling based on incremental energy relaxation combined with a viscous-type regularization

Science.gov (United States)

Langenfeld, K.; Junker, P.; Mosler, J.

2018-05-01

This paper deals with a constitutive model suitable for the analysis of quasi-brittle damage in structures. The model is based on incremental energy relaxation combined with a viscous-type regularization. A similar approach—which also represents the inspiration for the improved model presented in this paper—was recently proposed in Junker et al. (Contin Mech Thermodyn 29(1):291-310, 2017). Within this work, the model introduced in Junker et al. (2017) is critically analyzed first. This analysis leads to an improved model which shows the same features as that in Junker et al. (2017), but which (i) eliminates unnecessary model parameters, (ii) can be better interpreted from a physics point of view, (iii) can capture a fully softened state (zero stresses), and (iv) is characterized by a very simple evolution equation. In contrast to the cited work, this evolution equation is (v) integrated fully implicitly and (vi) the resulting time-discrete evolution equation can be solved analytically providing a numerically efficient closed-form solution. It is shown that the final model is indeed well-posed (i.e., its tangent is positive definite). Explicit conditions guaranteeing this well-posedness are derived. Furthermore, by additively decomposing the stress rate into deformation- and purely time-dependent terms, the functionality of the model is explained. Illustrative numerical examples confirm the theoretical findings.
Quasi-brittle material behavior under cyclic loading: from virtual testing to structural computation

International Nuclear Information System (INIS)

Vassaux, Maxime

2015-01-01

Macroscopic constitutive laws are developed not only because they allow for large-scale computations but also because refine dissipative mechanisms observed at lower scales. Within the framework of this study, the development of such models is carried out in the context of seismic loading, that is to say reverse cyclic loading, applied to the quasi-brittle materials and more precisely, concrete-like materials. Nowadays, robust and predictive macroscopic constitutive laws are still rare because of the complexity of cracking related phenomena. Among the challenges to face, the material parameters identification is far from being the easiest due to the lack of experimental data. Indeed, the difficulties to carry out cyclic tests on concrete-like materials are numerous. To overcome these difficulties, a virtual testing approach based on a refine model is proposed in this study in order to feed continuum models with the missing material parameters. Adopting a microscopic point of view, a representative volume element is seen as a structure. The microscopic model has been developed with the aim to require a minimal number of material parameters which only need basic mechanical tests to be identified. From an existing lattice model developed to deal with monotonic loading, several enhancements have been realized in order to extend its range of applicability, making it capable of dealing with complex multi-axial cyclic loadings. The microscopic model has been validated as a virtual testing machine that is able to help the identification procedure of continuous constitutive laws. This identification approach has been applied on a new constitutive law developed within the framework of isotropic continuum damage mechanics accounting for cyclic related effects. In particular, the concept of regularized unilateral effect has been introduced to describe the progressive crack closure. The macroscopic model has been calibrated with the help from the aforementioned virtual testing
A fiber bundle-plastic chain model for quasi-brittle materials under uniaxial loading

International Nuclear Information System (INIS)

Shan, Zhi; Yu, Zhiwu

2015-01-01

A fiber bundle-plastic chain model for quasi-brittle materials under both uniaxial compression and tension conditions is developed. By introducing a plastic chain model into the fiber bundle model, a bundle-chain model for quasi-brittle materials is proposed with physical considerations. The model achieves a novel and convenient approach to describe the stochastic effective stress-driven plasticity. It is found that the numerical solutions obtained with this model agree with experimental results when subjected to both monotonic and cyclic uniaxial loading. The model generates a numerical solution with higher accuracy than the present models, when compared with the experimental results on certain problems. An example is shown which utilizes this model to describe the stochastic properties of a constitutive model given as standard. Furthermore, the difference between the existing plastic fiber bundle models in the literature and this model is also obtained in this work. (paper)
Three-Dimensional Network Model for Coupling of Fracture and Mass Transport in Quasi-Brittle Geomaterials

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Peter Grassl

2016-09-01

Full Text Available Dual three-dimensional networks of structural and transport elements were combined to model the effect of fracture on mass transport in quasi-brittle geomaterials. Element connectivity of the structural network, representing elasticity and fracture, was defined by the Delaunay tessellation of a random set of points. The connectivity of transport elements within the transport network was defined by the Voronoi tessellation of the same set of points. A new discretisation strategy for domain boundaries was developed to apply boundary conditions for the coupled analyses. The properties of transport elements were chosen to evolve with the crack opening values of neighbouring structural elements. Through benchmark comparisons involving non-stationary transport and fracture, the proposed dual network approach was shown to be objective with respect to element size and orientation.
Deterministic and stochastic analysis of size effects and damage evolution in quasi-brittle materials

NARCIS (Netherlands)

Gutiérrez, M.A.; Borst, R. de

1999-01-01

This study presents some recent results on damage evolution in quasi-brittle materials including stochastic imperfections. The material strength is described as a random field and coupled to the response. The most probable configurations of imperfections leading to failure are sought by means of an
Generalized Continuum: from Voigt to the Modeling of Quasi-Brittle Materials

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Jamile Salim Fuina

2010-12-01

Full Text Available This article discusses the use of the generalized continuum theories to incorporate the effects of the microstructure in the nonlinear finite element analysis of quasi-brittle materials and, thus, to solve mesh dependency problems. A description of the problem called numerically induced strain localization, often found in Finite Element Method material non-linear analysis, is presented. A brief historic about the Generalized Continuum Mechanics based models is presented, since the initial work of Voigt (1887 until the more recent studies. By analyzing these models, it is observed that the Cosserat and microstretch approaches are particular cases of a general formulation that describes the micromorphic continuum. After reporting attempts to incorporate the material microstructure in Classical Continuum Mechanics based models, the article shows the recent tendency of doing it according to assumptions of the Generalized Continuum Mechanics. Finally, it presents numerical results which enable to characterize this tendency as a promising way to solve the problem.
Micromechanical modelling of quasi-brittle materials behavior

International Nuclear Information System (INIS)

Li, V.C.

1992-01-01

This special issues on Micromechanical modelling of quasi-brittle materials behavior represents an outgrowth of presentations given at a symposium of the same title held at the 1991 ASME Applied Mechanics and Biomechanics Summer Conference at the Ohio State University. The symposium was organized to promote communication between researchers in three materials groups: rock, cementitious materials, ceramics and related composites. The enthusiastic response of both speakers and attendants at the ASME symposium convinced the organizer that it would be useful to put together a coherent volume which can reach a larger audience. It was decided that the papers individually and as a volume ought to provide a broader view, so that as much as possible, the work contained in each paper would be accessible to readers working in any of the three materials groups. Applied Mechanics Reviews presents an appropriate platform for achieving these objectives
Failure processes in soft and quasi-brittle materials with nonhomogeneous microstructures

Science.gov (United States)

Spring, Daniel W.

Material failure pervades the fields of materials science and engineering; it occurs at various scales and in various contexts. Understanding the mechanisms by which a material fails can lead to advancements in the way we design and build the world around us. For example, in structural engineering, understanding the fracture of concrete and steel can lead to improved structural systems and safer designs; in geological engineering, understanding the fracture of rock can lead to increased efficiency in oil and gas extraction; and in biological engineering, understanding the fracture of bone can lead to improvements in the design of bio-composites and medical implants. In this thesis, we numerically investigate a wide spectrum of failure behavior; in soft and quasi-brittle materials with nonhomogeneous microstructures considering a statistical distribution of material properties. The first topic we investigate considers the influence of interfacial interactions on the macroscopic constitutive response of particle reinforced elastomers. When a particle is embedded into an elastomer, the polymer chains in the elastomer tend to adsorb (or anchor) onto the surface of the particle; creating a region in the vicinity of each particle (often referred to as an interphase) with distinct properties from those in the bulk elastomer. This interphasial region has been known to exist for many decades, but is primarily omitted in computational investigations of such composites. In this thesis, we present an investigation into the influence of interphases on the macroscopic constitutive response of particle filled elastomers undergoing large deformations. In addition, at large deformations, a localized region of failure tends to accumulate around inclusions. To capture this localized region of failure (often referred to as interfacial debonding), we use cohesive zone elements which follow the Park-Paulino-Roesler traction-separation relation. To account for friction, we present a new
Towards understanding the influence of porosity on mechanical and fracture behaviour of quasi-brittle materials : Experiments and modelling

NARCIS (Netherlands)

Liu, D; Savija, B.; Smith, G.E.; Flewitt, P.E.J.; Lowe, T.; Schlangen, H.E.J.G.

2017-01-01

In this work, porosity-property relationships of quasi-brittle materials are explored through a combined experimental and numerical approach. In the experimental part, hemihyrate gypsum plaster powder (CaSO 4 ⋅1/2H 2 O CaSO4⋅1/2H2O) and expanded spherical polystyrene beads (1.5–2.0 mm dia.) have
Structural and Material Instability

DEFF Research Database (Denmark)

Cifuentes, Gustavo Cifuentes

This work is a small contribution to the general problem of structural and material instability. In this work, the main subject is the analysis of cracking and failure of structural elements made from quasi-brittle materials like concrete. The analysis is made using the finite element method. Three...
Mesoscale analysis of failure in quasi-brittle materials: comparison between lattice model and acoustic emission data.

Science.gov (United States)

Grégoire, David; Verdon, Laura; Lefort, Vincent; Grassl, Peter; Saliba, Jacqueline; Regoin, Jean-Pierre; Loukili, Ahmed; Pijaudier-Cabot, Gilles

2015-10-25

The purpose of this paper is to analyse the development and the evolution of the fracture process zone during fracture and damage in quasi-brittle materials. A model taking into account the material details at the mesoscale is used to describe the failure process at the scale of the heterogeneities. This model is used to compute histograms of the relative distances between damaged points. These numerical results are compared with experimental data, where the damage evolution is monitored using acoustic emissions. Histograms of the relative distances between damage events in the numerical calculations and acoustic events in the experiments exhibit good agreement. It is shown that the mesoscale model provides relevant information from the point of view of both global responses and the local failure process. © 2015 The Authors. International Journal for Numerical and Analytical Methods in Geomechanics published by John Wiley & Sons Ltd.
Fracture in quasi-brittle materials: experimental and numerical approach for the determination of an incremental model with generalized variables

International Nuclear Information System (INIS)

Morice, Erwan

2014-01-01

Fracture in quasi-brittle materials, such as ceramics or concrete, can be represented schematically by series of events of nucleation and coalescence of micro-cracks. Modeling this process is an important challenge for the reliability and life prediction of concrete structures, in particular the prediction of the permeability of damaged structures. A multi-scale approach is proposed. The global behavior is modeled within the fracture mechanics framework and the local behavior is modeled by the discrete element method. An approach was developed to condense the non linear behavior of the mortar. A model reduction technic is used to extract the relevant information from the discrete elements method. To do so, the velocity field is partitioned into mode I, II, linear and non-linear components, each component being characterized by an intensity factor and a fixed spatial distribution. The response of the material is hence condensed in the evolution of the intensity factors, used as non-local variables. A model was also proposed to predict the behavior of the crack for proportional and non-proportional mixed mode I+II loadings. An experimental campaign was finally conducted to characterize the fatigue and fracture behavior of mortar. The results show that fatigue crack growth can be of significant importance. The experimental velocity field determined, in the crack tip region, by DIC, were analyzed using the same technic as that used for analyzing the fields obtained by the discrete element method showing consistent results. (author)
Scaling of structural failure

Energy Technology Data Exchange (ETDEWEB)

Bazant, Z.P. [Northwestern Univ., Evanston, IL (United States); Chen, Er-Ping [Sandia National Lab., Albuquerque, NM (United States)

1997-01-01

This article attempts to review the progress achieved in the understanding of scaling and size effect in the failure of structures. Particular emphasis is placed on quasibrittle materials for which the size effect is complicated. Attention is focused on three main types of size effects, namely the statistical size effect due to randomness of strength, the energy release size effect, and the possible size effect due to fractality of fracture or microcracks. Definitive conclusions on the applicability of these theories are drawn. Subsequently, the article discusses the application of the known size effect law for the measurement of material fracture properties, and the modeling of the size effect by the cohesive crack model, nonlocal finite element models and discrete element models. Extensions to compression failure and to the rate-dependent material behavior are also outlined. The damage constitutive law needed for describing a microcracked material in the fracture process zone is discussed. Various applications to quasibrittle materials, including concrete, sea ice, fiber composites, rocks and ceramics are presented.
Fracture of niobium-base silicide coated alloy

International Nuclear Information System (INIS)

Davydova, A.D.; Zotov, Yu.P.; Ivashchenko, O.V.; Kushnareva, N.P.; Yarosh, I.P.

1990-01-01

Mechanical properties and character of fracture of Nb-W-Mo-Zr-C alloy composition with complex by composition and structure silicide coating under different states of stage-by-stage coating are studied. Structural features, character of fracture from ductile to quasibrittle transcrystalline one and, respectively, the composition plasticity level are defined by interrelation of fracture processes in coating, matrix plastic flow and possibility and way of stress relaxation on their boundary

Nonlinear analysis of reinforced concrete structures using software package abaqus

OpenAIRE

Marković Nemanja; Stojić Dragoslav; Cvetković Radovan

2014-01-01

Reinforced concrete (AB) is characterized by huge inhomogeneity resulting from the material characteristics of the concrete, then, quasi-brittle behavior during failure. These and other phenomena require the introduction of material nonlinearity in the modeling of reinforced concrete structures. This paper presents the modeling reinforced concrete in the software package ABAQUS. A brief theoretical overview is presented of methods such as: Concrete Damage Plasticity (CDP), Smeared Concrete Cr...
Coupled hydro-thermo-mechanical modeling of hydraulic fracturing in quasi-brittle rocks using BPM-DEM

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Ingrid Tomac

2017-02-01

Full Text Available This paper presents an improved understanding of coupled hydro-thermo-mechanical (HTM hydraulic fracturing of quasi-brittle rock using the bonded particle model (BPM within the discrete element method (DEM. BPM has been recently extended by the authors to account for coupled convective–conductive heat flow and transport, and to enable full hydro-thermal fluid–solid coupled modeling. The application of the work is on enhanced geothermal systems (EGSs, and hydraulic fracturing of hot dry rock (HDR is studied in terms of the impact of temperature difference between rock and a flowing fracturing fluid. Micro-mechanical investigation of temperature and fracturing fluid effects on hydraulic fracturing damage in rocks is presented. It was found that fracture is shorter with pronounced secondary microcracking along the main fracture for the case when the convective–conductive thermal heat exchange is considered. First, the convection heat exchange during low-viscosity fluid infiltration in permeable rock around the wellbore causes significant rock cooling, where a finger-like fluid infiltration was observed. Second, fluid infiltration inhibits pressure rise during pumping and delays fracture initiation and propagation. Additionally, thermal damage occurs in the whole area around the wellbore due to rock cooling and cold fluid infiltration. The size of a damaged area around the wellbore increases with decreasing fluid dynamic viscosity. Fluid and rock compressibility ratio was found to have significant effect on the fracture propagation velocity.
3D cellular automata finite element (CAFE) modelling and experimental observation of damage in quasi-brittle nuclear materials: Indentation of a SiC-SiC-fibre ceramic matrix composite

International Nuclear Information System (INIS)

Saucedo Mora, Luis; Mostafavi, Mahmoud; Marrow, T. James; Khoshkhou, Danial; Connolly, Brian; Reinhard, Christina; Atwood, Robert; Zhao, Shuang

2015-01-01

Cellular automata integrated with finite elements (CAFE) have been used to develop a method to account for the effect of microstructure on quasi-brittle damage development. The microstructure is simulated explicitly by subdividing a finite element into smaller cells. A heterogeneous structure is created from key cells (seeds) using defined characteristics; the influence of the initial finite element mesh is effectively removed during the development of the microstructure. Graded microstructures, textures, particle anisotropy and multiple phases can be readily simulated, such as those in composites and porous materials. A mesh-free framework has been developed to compute the damage development through the microstructure, using cellular automata. With this method, we can study the development of discontinuous cracking and damage coalescence, and its sensitivity to microstructure. Experiments have been carried out to observe the three-dimensional development of damage, using high-resolution synchrotron X-ray computed tomography and digital volume correlation to observe Hertzian indentation of a SiC-SiC fibre composite, quantifying damage by measurement of the displacement fields within the material. The results demonstrate the applicability of the modelling strategy to damage development, and show how model input data may be obtained from small specimen tests, which could be performed at elevated temperatures with irradiated materials. (authors)
Contribution to the structural vulnerability quantification: from the representative volume element to the member scale

International Nuclear Information System (INIS)

Richard, Benjamin

2016-01-01

This work is the synthesis of research activities I have conducted over the past decade aiming at improving the numerical description of some dissipative mechanisms at the material scale and quantifying the vulnerability of reinforced concrete structures. The main objectives of the research presented in this dissertation are: (i) to improve both the predictive capabilities and the numerical robustness of the time integration strategies of the continuous constitutive model when dealing with the cyclic behavior of quasi-brittle materials subjected to either long-term or short-term loadings, (ii) to improve numerical techniques capable of describing the discontinuous nature of cracking and related local dissipative phenomena, and (iii) to contribute to the definition of large-scale experimental campaigns and to organize international workshops aiming to better understand the complex behavior of reinforced concrete structures when subjected to extreme loadings, such as earthquakes. In the first part, we focus on the development and validation of a continuous constitutive model to describe the mechanical behavior of quasi-brittle materials subjected to cyclic loadings. Simplified strategies are also derived from full three-dimensional approaches to serve probabilistic techniques aiming at taking into account uncertainties and updating mechanical models. In the second part, some light is shed on some developments aiming at better quantifying the cracking features. Then, the results of experiments designed to assess the dynamic response of strongly asymmetric reinforced concrete structures are presented. The experimental data have led to numerical studies shared with the international scientific community. The lessons learned from this research is then employed to design research projects we plan to work on over the next few years. (author) [fr
Nonlinear analysis of reinforced concrete structures using software package abaqus

Directory of Open Access Journals (Sweden)

Marković Nemanja

2014-01-01

Full Text Available Reinforced concrete (AB is characterized by huge inhomogeneity resulting from the material characteristics of the concrete, then, quasi-brittle behavior during failure. These and other phenomena require the introduction of material nonlinearity in the modeling of reinforced concrete structures. This paper presents the modeling reinforced concrete in the software package ABAQUS. A brief theoretical overview is presented of methods such as: Concrete Damage Plasticity (CDP, Smeared Concrete Cracking (CSC, Cap Plasticity (CP and Drucker-Prager model (DPM. We performed a nonlinear analysis of two-storey reinforced concrete frame by applying CDP method for modeling material nonlinearity of concrete. We have analyzed damage zones, crack propagation and loading-deflection ratio.
Elastoplastic cup model for cement-based materials

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Yan Zhang

2010-03-01

Full Text Available Based on experimental data obtained from triaxial tests and a hydrostatic test, a cup model was formulated. Two plastic mechanisms, respectively a deviatoric shearing and a pore collapse, are taken into account. This model also considers the influence of confining pressure. In this paper, the calibration of the model is detailed and numerical simulations of the main mechanical behavior of cement paste over a large range of stress are described, showing good agreement with experimental results. The case study shows that this cup model has extensive applicability for cement-based materials and other quasi-brittle and high-porosity materials in a complex stress state.
Multiscale analysis of damage using dual and primal domain decomposition techniques

NARCIS (Netherlands)

Lloberas-Valls, O.; Everdij, F.P.X.; Rixen, D.J.; Simone, A.; Sluys, L.J.

2014-01-01

In this contribution, dual and primal domain decomposition techniques are studied for the multiscale analysis of failure in quasi-brittle materials. The multiscale strategy essentially consists in decomposing the structure into a number of nonoverlapping domains and considering a refined spatial
Some future directions in computational failure mechanics

NARCIS (Netherlands)

Borst, de R.; Carmeliet, J.; Pamin, J.; Sluys, L.J.; Kusters, G.M.A.; Hendriks, M.A.N.

1994-01-01

Continuum approaches are reviewed which can properly model localised deformations that act as a precursor to final fracture in quasi-brittle materials. Next, one such higher-order damaging continuum model is combined with a stochastic approach to describe the heterogeneity in quasi-brittle
Sadhana | Indian Academy of Sciences

Indian Academy of Sciences (India)

Home; Journals; Sadhana. Zdeněk P Bažant. Articles written in Sadhana. Volume 37 Issue 1 February 2012 pp 17-31. Size effect on strength and lifetime probability distributions of quasibrittle structures · Zdeněk P Bažant Jia-Liang Le · More Details Abstract Fulltext PDF. Engineering structures such as aircraft, bridges, ...
Development and deployment of constitutive softening routines in Eulerian hydrocodes.

Energy Technology Data Exchange (ETDEWEB)

Fuller, Timothy Jesse; Dewers, Thomas A.; Swan, Matthew Scot

2013-03-01

The state of the art in failure modeling enables assessment of crack nucleation, propagation, and progression to fragmentation due to high velocity impact. Vulnerability assessments suggest a need to track material behavior through failure, to the point of fragmentation and beyond. This eld of research is particularly challenging for structures made of porous quasi-brittle materials, such as ceramics used in modern armor systems, due to the complex material response when loading exceeds the quasi-brittle material's elastic limit. Further complications arise when incorporating the quasi-brittle material response in multi-material Eulerian hydrocode simulations. In this report, recent e orts in coupling a ceramic materials response in the post-failure regime with an Eulerian hydro code are described. Material behavior is modeled by the Kayenta material model [2] and Alegra as the host nite element code [14]. Kayenta, a three invariant phenomenological plasticity model originally developed for modeling the stress response of geologic materials, has in recent years been used with some success in the modeling of ceramic and other quasi-brittle materials to high velocity impact. Due to the granular nature of ceramic materials, Kayenta allows for signi cant pressures to develop due to dilatant plastic ow, even in shear dominated loading where traditional equations of state predict little or no pressure response. When a material's ability to carry further load is compromised, Kayenta allows the material's strength and sti ness to progressively degrade through the evolution of damage to the point of material failure. As material dilatation and damage progress, accommodations are made within Alegra to treat in a consistent manner the evolving state.
3-D cohesive finite element model for application in structural analysis of heavy duty composite pavements

DEFF Research Database (Denmark)

Skar, Asmus; Poulsen, Peter Noe

2015-01-01

The problem of stiffness degradation in composite pavement systems from localised fracture damage in the quasibrittle cement bound granular mixture are today taken into account only by empirical formulas. These formulas deals with a limited number of materials in a restricted range of design...... this paper presents a numerical analysis of the fracture behaviour of cement bound granular mixtures in composite concrete block pavement systems applying a cohesive model. The functionality of the proposed model is compared to experimental investigations of beam bending tests. The pavement is modelled......, it can be shown that adequately good prediction of the structural response of composite pavements is obtained for monotonic loading without significant computational cost, making the model applicable for engineering design purpose. It is envisaged that the methodology implemented in this study can...
Wedge-Splitting Test – Determination of Minimal Starting Notch Length for Various Cement Based Composites. Part I: Cohesive Crack Modelling

Czech Academy of Sciences Publication Activity Database

Veselý, V.; Řoutil, L.; Seitl, Stanislav

2011-01-01

Roč. 452-453, - (2011), s. 77-80 ISSN 1013-9826 R&D Projects: GA AV ČR KJB200410901 Institutional research plan: CEZ:AV0Z20410507 Keywords : wedge-splitting test * cementitious composites * quasi-brittle fracture * brittleness Subject RIV: JL - Materials Fatigue, Friction Mechanics
Wedge-Splitting Test – Determination of Minimal Starting Notch Length for Various Cement Based Composites

Czech Academy of Sciences Publication Activity Database

Seitl, Stanislav; Klusák, Jan; Veselý, V.; Řoutil, L.

452-453, - (2011), s. 81-84 ISSN 1013-9826 R&D Projects: GA AV ČR KJB200410901; GA ČR GA103/08/0963 Institutional research plan: CEZ:AV0Z20410507 Keywords : wedge-splitting test, cementitious composites, quasi-brittle fracture, brittle fracture Subject RIV: JL - Materials Fatigue, Friction Mechanics www.scientific.net
anisotropic crack modelling of reinforced concrete structures with an enhanced kinematics: application to bidimensional elements under cyclic loading

International Nuclear Information System (INIS)

Kishta, Ejona

2016-01-01

Civil engineering buildings, massive and unique, are mostly made of reinforced or prestressed concrete. Sustainability, tightness and safety are the major pillars of a building's performance. Cracking is a major phenomenon which impacts the buildings' behaviour under different loadings in terms of sustainability and structural capacity. Development of numerical models which describe accurately the response of quasi-brittle materials under complex loading remains an important research topic for the scientific community. The objective of this work is the development of a numerical model which represents explicitly cracking of reinforced concrete structures. Concrete and reinforced concrete degradation process, characterised by the appearance of several anisotropic crack families, is described by means of an anisotropic damage model accounting for oriented crack families. The kinematics of this model is enriched with a displacement jump in order to reproduce the development of cracks in the material during loading. This displacement jump is identified as the crack opening. The developed model is validated on simulations of plain concrete structures exhibiting model as well as mixed-mode failure. The performances of the enriched model are shown by the simulation of reinforced concrete structures such as a shear wall submitted to cyclic loading. (author) [fr
Investigation of the Quasi-Brittle Failure of Alashan Granite Viewed from Laboratory Experiments and Grain-Based Discrete Element Modeling.

Science.gov (United States)

Zhou, Jian; Zhang, Luqing; Yang, Duoxing; Braun, Anika; Han, Zhenhua

2017-07-21

Granite is a typical crystalline material, often used as a building material, but also a candidate host rock for the repository of high-level radioactive waste. The petrographic texture-including mineral constituents, grain shape, size, and distribution-controls the fracture initiation, propagation, and coalescence within granitic rocks. In this paper, experimental laboratory tests and numerical simulations of a grain-based approach in two-dimensional Particle Flow Code (PFC2D) were conducted on the mechanical strength and failure behavior of Alashan granite, in which the grain-like structure of granitic rock was considered. The microparameters for simulating Alashan granite were calibrated based on real laboratory strength values and strain-stress curves. The unconfined uniaxial compressive test and Brazilian indirect tensile test were performed using a grain-based approach to examine and discuss the influence of mineral grain size and distribution on the strength and patterns of microcracks in granitic rocks. The results show it is possible to reproduce the uniaxial compressive strength (UCS) and uniaxial tensile strength (UTS) of Alashan granite using the grain-based approach in PFC2D, and the average mineral size has a positive relationship with the UCS and UTS. During the modeling, most of the generated microcracks were tensile cracks. Moreover, the ratio of the different types of generated microcracks is related to the average grain size. When the average grain size in numerical models is increased, the ratio of the number of intragrain tensile cracks to the number of intergrain tensile cracks increases, and the UCS of rock samples also increases with this ratio. However, the variation in grain size distribution does not have a significant influence on the likelihood of generated microcracks.
Sadhana | Indian Academy of Sciences

Indian Academy of Sciences (India)

The paper presents a model, based on nonlinear fracture mechanics, for analysing crack propagation in quasi-brittle materials, such as concrete. The work is limited to two-dimensions, and therefore, the fracture modes of interest are mode I (pure tension) and mode II (pure shear). The constitutive model has been ...
A Comprehensive Study of the Polypropylene Fiber Reinforced Fly Ash Based Geopolymer

DEFF Research Database (Denmark)

Ranjbar, Navid; Mehrali, Mehdi; Behnia, Arash

2016-01-01

and long term impacts of different volume percentages of polypropylene fiber (PPF) reinforcement on fly ash based geopolymer composites. Different characteristics of the composite were compared at fresh state by flow measurement and hardened state by variation of shrinkage over time to assess the response...... of composites under flexural and compressive load conditions. The fiber-matrix interface, fiber surface and toughening mechanisms were assessed using field emission scan electron microscopy (FESEM) and atomic force microscopy (AFM). The results show that incorporation of PPF up to 3 wt % into the geopolymer......As a cementitious material, geopolymers show a high quasi-brittle behavior and a relatively low fracture energy. To overcome such a weakness, incorporation of fibers to a brittle matrix is a well-known technique to enhance the flexural properties. This study comprehensively evaluates the short...
Investigation of Quasi-Static Indentation Response of Inkjet Printed Sandwich Structures under Various Indenter Geometries

Science.gov (United States)

Dikshit, Vishwesh; Nagalingam, Arun Prasanth; Yap, Yee Ling; Sing, Swee Leong; Yeong, Wai Yee; Wei, Jun

2017-01-01

The objective of this investigation was to determine the quasi-static indentation response and failure mode in three-dimensional (3D) printed trapezoidal core structures, and to characterize the energy absorbed by the structures. In this work, the trapezoidal sandwich structure was designed in the following two ways. Firstly, the trapezoidal core along with its facesheet was 3D printed as a single element comprising a single material for both core and facesheet (type A); Secondly, the trapezoidal core along with facesheet was 3D printed, but with variation in facesheet materials (type B). Quasi-static indentation was carried out using three different indenters, namely standard hemispherical, conical, and flat indenters. Acoustic emission (AE) technique was used to capture brittle cracking in the specimens during indentation. The major failure modes were found to be brittle failure and quasi-brittle fractures. The measured indentation energy was at a maximum when using a conical indenter at 9.40 J and 9.66 J and was at a minimum when using a hemispherical indenter at 6.87 J and 8.82 J for type A and type B series specimens respectively. The observed maximum indenter displacements at failure were the effect of material variations and composite configurations in the facesheet. PMID:28772649
Fracture Mechanisms of Zirconium Diboride Ultra-High Temperature Ceramics under Pulse Loading

Science.gov (United States)

Skripnyak, Vladimir V.; Bragov, Anatolii M.; Skripnyak, Vladimir A.; Lomunov, Andrei K.; Skripnyak, Evgeniya G.; Vaganova, Irina K.

2015-06-01

Mechanisms of failure in ultra-high temperature ceramics (UHTC) based on zirconium diboride under pulse loading were studied experimentally by the method of SHPB and theoretically using the multiscale simulation method. The obtained experimental and numerical data are evidence of the quasi-brittle fracture character of nanostructured zirconium diboride ceramics under compression and tension at high strain rates and the room temperatures. Damage of nanostructured porous zirconium diboride -based UHTC can be formed under stress pulse amplitude below the Hugoniot elastic limit. Fracture of nanostructured ultra-high temperature ceramics under pulse and shock-wave loadings is provided by fast processes of intercrystalline brittle fracture and relatively slow processes of quasi-brittle failure via growth and coalescence of microcracks. A decrease of the shear strength can be caused by nano-voids clusters in vicinity of triple junctions between ceramic matrix grains and ultrafine-grained ceramics. This research was supported by grants from ``The Tomsk State University Academic D.I. Mendeleev Fund Program'' and also N. I. Lobachevski State University of Nizhny Novgorod (Grant of post graduate mobility).
Vibration-based structural health monitoring of harbor caisson structure

Science.gov (United States)

Lee, So-Young; Lee, So-Ra; Kim, Jeong-Tae

2011-04-01

This study presents vibration-based structural health monitoring method in foundation-structure interface of harbor caisson structure. In order to achieve the objective, the following approaches are implemented. Firstly, vibration-based response analysis method is selected and structural health monitoring (SHM) technique is designed for harbor caisson structure. Secondly, the performance of designed SHM technique for harbor structure is examined by FE analysis. Finally, the applicability of designed SHM technique for harbor structure is evaluated by dynamic tests on a lab-scaled caisson structure.

High tensile strength fly ash based geopolymer composite using copper coated micro steel fiber

DEFF Research Database (Denmark)

Ranjbar, Navid; Mehrali, Mehdi; Mehrali, Mohammad

2016-01-01

-matrix interaction. In this present study, effects of micro steel fibers (MSF) incorporation on mechanical properties of fly ash based geopolymer was investigated at different volume ratio of matrix. Various properties of the composite were compared in terms of fresh state by flow measurement and hardened state......As a ceramic-like material, geopolymers show a high quasi-brittle behavior and relatively low fracture energy. To overcome this, the addition of fibers to a brittle matrix is a well-known method to improve the flexural strength. Moreover, the success of the reinforcements is dependent on the fiber...... by variation of shrinkage over time to assess performance of the composites subjected to flexural and compressive load. The fiber-matrix interface, fiber surface and toughening mechanisms were assessed using field emission scan electron microscopy (FESEM) and atomic force microscopy (AFM) through a period...
A Comprehensive Study of the Polypropylene Fiber Reinforced Fly Ash Based Geopolymer.

Directory of Open Access Journals (Sweden)

Navid Ranjbar

Full Text Available As a cementitious material, geopolymers show a high quasi-brittle behavior and a relatively low fracture energy. To overcome such a weakness, incorporation of fibers to a brittle matrix is a well-known technique to enhance the flexural properties. This study comprehensively evaluates the short and long term impacts of different volume percentages of polypropylene fiber (PPF reinforcement on fly ash based geopolymer composites. Different characteristics of the composite were compared at fresh state by flow measurement and hardened state by variation of shrinkage over time to assess the response of composites under flexural and compressive load conditions. The fiber-matrix interface, fiber surface and toughening mechanisms were assessed using field emission scan electron microscopy (FESEM and atomic force microscopy (AFM. The results show that incorporation of PPF up to 3 wt % into the geopolymer paste reduces the shrinkage and enhances the energy absorption of the composites. While, it might reduce the ultimate flexural and compressive strength of the material depending on fiber content.
Shallow seismicity in volcanic system: what role does the edifice play?

Science.gov (United States)

Bean, Chris; Lokmer, Ivan

2017-04-01

Seismicity in the upper two kilometres in volcanic systems is complex and very diverse in nature. The origins lie in the multi-physics nature of source processes and in the often extreme heterogeneity in near surface structure, which introduces strong seismic wave propagation path effects that often 'hide' the source itself. Other complicating factors are that we are often in the seismic near-field so waveforms can be intrinsically more complex than in far-field earthquake seismology. The traditional focus for an explanation of the diverse nature of shallow seismic signals is to call on the direct action of fluids in the system. Fits to model data are then used to elucidate properties of the plumbing system. Here we show that solutions based on these conceptual models are not unique and that models based on a diverse range of quasi-brittle failure of low stiffness near surface structures are equally valid from a data fit perspective. These earthquake-like sources also explain aspects of edifice deformation that are as yet poorly quantified.
Reliability-based optimization of engineering structures

DEFF Research Database (Denmark)

Sørensen, John Dalsgaard

2008-01-01

The theoretical basis for reliability-based structural optimization within the framework of Bayesian statistical decision theory is briefly described. Reliability-based cost benefit problems are formulated and exemplitied with structural optimization. The basic reliability-based optimization...... problems are generalized to the following extensions: interactive optimization, inspection and repair costs, systematic reconstruction, re-assessment of existing structures. Illustrative examples are presented including a simple introductory example, a decision problem related to bridge re...
Mapping population-based structural connectomes.

Science.gov (United States)

Zhang, Zhengwu; Descoteaux, Maxime; Zhang, Jingwen; Girard, Gabriel; Chamberland, Maxime; Dunson, David; Srivastava, Anuj; Zhu, Hongtu

2018-05-15

Advances in understanding the structural connectomes of human brain require improved approaches for the construction, comparison and integration of high-dimensional whole-brain tractography data from a large number of individuals. This article develops a population-based structural connectome (PSC) mapping framework to address these challenges. PSC simultaneously characterizes a large number of white matter bundles within and across different subjects by registering different subjects' brains based on coarse cortical parcellations, compressing the bundles of each connection, and extracting novel connection weights. A robust tractography algorithm and streamline post-processing techniques, including dilation of gray matter regions, streamline cutting, and outlier streamline removal are applied to improve the robustness of the extracted structural connectomes. The developed PSC framework can be used to reproducibly extract binary networks, weighted networks and streamline-based brain connectomes. We apply the PSC to Human Connectome Project data to illustrate its application in characterizing normal variations and heritability of structural connectomes in healthy subjects. Copyright © 2018 Elsevier Inc. All rights reserved.
Biaxial testing for nuclear grade graphite by ball on three balls assessment

International Nuclear Information System (INIS)

Mohd Reusmaazran Yusof; Yusof Abdullah

2012-01-01

Nuclear grade (high-purity) graphite for fuel element and moderator material in Advanced Gas Cooling Reactors (AGR) displays large scatter in strength and a non-linear stress-strain response from the damage accumulation. These responses can be characterized as quasi-brittle behaviour. Current assessments of fracture in core graphite components are based on the linear elastic approximation and thus represent a major assumption. The quasi-brittle behaviour gives challenge to assess the real nuclear graphite component. The selected test method would help to bridge the gap between microscale to macro-scale in real reactor component. The small scale tests presented here can contribute some statistical data to manifests the failure in real component. The evaluation and choice of different solution design of biaxial test will be discussed in this paper. The ball on-three ball test method was used for assessment test follows by numerous of analytical method. The results shown that biaxial strength of the EY9 grade graphite depends on the method used for evaluation. Some of the analytical methods use to calculate biaxial strength were found not to be valid and therefore should not be used to assess the mechanical properties of nuclear graphite. (author)
Investigation on dynamic performance of concrete column crumb rubber steel and fiber concrete

Science.gov (United States)

Siti Nurul Nureda, M. Z.; Mariyana, A. K.; Khiyon, M. Iqbal; Rahman, M. S. Abdul; Nurizaty, Z.

2017-11-01

In general the Normal Concrete (NC) are by quasi-brittle failure, where, the nearly complete loss of loading capacity, once failure is initiated especially under dynamic loadings. The significance of this study is to improve the damping properties of concrete structure by utilization of the recycled materials from waste tires to be used in concrete as structural materials that improve seismic performance. In this study, the concrete containing 10% of fine crumb rubber and 1 % volume fraction of steel fiber from waste tires is use to investigate the dynamic performance (natural frequency and damping ratio).A small scale column were fabricated from Treated Crumb Rubber and Steel Fiber Concrete (TCRSFC) and NC were cast and cured for 28 days to investigate the dynamic performance. Based on analysis, dynamic modulus, damping ratio and natural frequency of TCRSFC has improved considerably by 5.18%, 109% and 10.94% when compared with NC. The TCRSFC producing concrete with the desired properties as well as to introduce the huge potential as dynamic resistance structure from severe damage especially prevention on catastrophic failure.
Reliability-Based Optimization in Structural Engineering

DEFF Research Database (Denmark)

Enevoldsen, I.; Sørensen, John Dalsgaard

1994-01-01

In this paper reliability-based optimization problems in structural engineering are formulated on the basis of the classical decision theory. Several formulations are presented: Reliability-based optimal design of structural systems with component or systems reliability constraints, reliability...
Structure based alignment and clustering of proteins (STRALCP)

Science.gov (United States)

Zemla, Adam T.; Zhou, Carol E.; Smith, Jason R.; Lam, Marisa W.

2013-06-18

Disclosed are computational methods of clustering a set of protein structures based on local and pair-wise global similarity values. Pair-wise local and global similarity values are generated based on pair-wise structural alignments for each protein in the set of protein structures. Initially, the protein structures are clustered based on pair-wise local similarity values. The protein structures are then clustered based on pair-wise global similarity values. For each given cluster both a representative structure and spans of conserved residues are identified. The representative protein structure is used to assign newly-solved protein structures to a group. The spans are used to characterize conservation and assign a "structural footprint" to the cluster.
Texture, microstructure, and fractal features of the low-cycle fatigue failure of the metal in pipeline welded joints

Science.gov (United States)

Usov, V. V.; Gopkalo, E. E.; Shkatulyak, N. M.; Gopkalo, A. P.; Cherneva, T. S.

2015-09-01

Crystallographic texture and fracture features are studied after low-cycle fatigue tests of laboratory specimens cut from the base metal and the characteristic zones of a welded joint in a pipeline after its longterm operation. The fractal dimensions of fracture surfaces are determined. The fractal dimension is shown to increase during the transition from ductile to quasi-brittle fracture, and a relation between the fractal dimension of a fracture surface and the fatigue life of the specimen is found.
Performance-based shape optimization of continuum structures

International Nuclear Information System (INIS)

Liang Qingquan

2010-01-01

This paper presents a performance-based optimization (PBO) method for optimal shape design of continuum structures with stiffness constraints. Performance-based design concepts are incorporated in the shape optimization theory to achieve optimal designs. In the PBO method, the traditional shape optimization problem of minimizing the weight of a continuum structure with displacement or mean compliance constraints is transformed to the problem of maximizing the performance of the structure. The optimal shape of a continuum structure is obtained by gradually eliminating inefficient finite elements from the structure until its performance is maximized. Performance indices are employed to monitor the performance of optimized shapes in an optimization process. Performance-based optimality criteria are incorporated in the PBO method to identify the optimum from the optimization process. The PBO method is used to produce optimal shapes of plane stress continuum structures and plates in bending. Benchmark numerical results are provided to demonstrate the effectiveness of the PBO method for generating the maximum stiffness shape design of continuum structures. It is shown that the PBO method developed overcomes the limitations of traditional shape optimization methods in optimal design of continuum structures. Performance-based optimality criteria presented can be incorporated in any shape and topology optimization methods to obtain optimal designs of continuum structures.
Plasma-based accelerator structures

International Nuclear Information System (INIS)

Schroeder, Carl B.

1999-01-01

Plasma-based accelerators have the ability to sustain extremely large accelerating gradients, with possible high-energy physics applications. This dissertation further develops the theory of plasma-based accelerators by addressing three topics: the performance of a hollow plasma channel as an accelerating structure, the generation of ultrashort electron bunches, and the propagation of laser pulses is underdense plasmas
Structure-based classification and ontology in chemistry

Directory of Open Access Journals (Sweden)

Hastings Janna

2012-04-01

Full Text Available Abstract Background Recent years have seen an explosion in the availability of data in the chemistry domain. With this information explosion, however, retrieving relevant results from the available information, and organising those results, become even harder problems. Computational processing is essential to filter and organise the available resources so as to better facilitate the work of scientists. Ontologies encode expert domain knowledge in a hierarchically organised machine-processable format. One such ontology for the chemical domain is ChEBI. ChEBI provides a classification of chemicals based on their structural features and a role or activity-based classification. An example of a structure-based class is 'pentacyclic compound' (compounds containing five-ring structures, while an example of a role-based class is 'analgesic', since many different chemicals can act as analgesics without sharing structural features. Structure-based classification in chemistry exploits elegant regularities and symmetries in the underlying chemical domain. As yet, there has been neither a systematic analysis of the types of structural classification in use in chemistry nor a comparison to the capabilities of available technologies. Results We analyze the different categories of structural classes in chemistry, presenting a list of patterns for features found in class definitions. We compare these patterns of class definition to tools which allow for automation of hierarchy construction within cheminformatics and within logic-based ontology technology, going into detail in the latter case with respect to the expressive capabilities of the Web Ontology Language and recent extensions for modelling structured objects. Finally we discuss the relationships and interactions between cheminformatics approaches and logic-based approaches. Conclusion Systems that perform intelligent reasoning tasks on chemistry data require a diverse set of underlying computational
A data base for aging of structural materials

International Nuclear Information System (INIS)

Oland, C.B.; Naus, D.J.; Jerath, S.

1993-01-01

USNRC initiated a Structural Aging (SAG) Program ORNL. The objective of the program is to provide assistance in identifying potential structural safety issues and to establish acceptance criteria for use in nuclear power plant evaluations for continued service. One main part focuses on the development of a Structural Materials Information Center where long-term and environment-dependent material properties are being collected and assembled into a data base. This data base is presented in two complementary formats. The Structural Materials Handbook is an expandable, hard-copy reference document that contains the complete data base for each material. The Structural Materials Electronic Data Base is accessible using an IBM-compatible personal computer. This paper presents an overview of the Structural Materials Information Center and briefly describes the features of the handbook and the electronic data base. In addition, a proposed method for using the data base to establish current property values for materials in existing concrete structures and to estimate the future performance of these materials is also presented
Ensemble-based prediction of RNA secondary structures.

Science.gov (United States)

Aghaeepour, Nima; Hoos, Holger H

2013-04-24

Accurate structure prediction methods play an important role for the understanding of RNA function. Energy-based, pseudoknot-free secondary structure prediction is one of the most widely used and versatile approaches, and improved methods for this task have received much attention over the past five years. Despite the impressive progress that as been achieved in this area, existing evaluations of the prediction accuracy achieved by various algorithms do not provide a comprehensive, statistically sound assessment. Furthermore, while there is increasing evidence that no prediction algorithm consistently outperforms all others, no work has been done to exploit the complementary strengths of multiple approaches. In this work, we present two contributions to the area of RNA secondary structure prediction. Firstly, we use state-of-the-art, resampling-based statistical methods together with a previously published and increasingly widely used dataset of high-quality RNA structures to conduct a comprehensive evaluation of existing RNA secondary structure prediction procedures. The results from this evaluation clarify the performance relationship between ten well-known existing energy-based pseudoknot-free RNA secondary structure prediction methods and clearly demonstrate the progress that has been achieved in recent years. Secondly, we introduce AveRNA, a generic and powerful method for combining a set of existing secondary structure prediction procedures into an ensemble-based method that achieves significantly higher prediction accuracies than obtained from any of its component procedures. Our new, ensemble-based method, AveRNA, improves the state of the art for energy-based, pseudoknot-free RNA secondary structure prediction by exploiting the complementary strengths of multiple existing prediction procedures, as demonstrated using a state-of-the-art statistical resampling approach. In addition, AveRNA allows an intuitive and effective control of the trade-off between
A data base for aging of structural materials

International Nuclear Information System (INIS)

Oland, C.B.; Naus, D.J.; Jerath, S.

1993-01-01

The U.S. Nuclear Regulatory Commission (USNRC) initiated a Structural Aging (SAG) Program at the Oak Ridge National Laboratory (ORNL). The objective of the program is to provide assistance in identifying potential structural safety issues and to establish acceptance criteria for use in nuclear power plant evaluations for continued service. One of the main parts of the program focuses on the development of a Structural Materials Information Center where long-term and environment-dependent material properties are being collected and assembled into a data base. This data base is presented in two complementary formats. The Structural Materials Handbook is an expandable, hard-copy reference document that contains the complete data base for each material. The Structural Materials Electronic Data Base is accessible using an IBM-compatible personal computer. This paper presents an overview of the Structural Materials Information Center and briefly describes the features of the handbook and the electronic data base. In addition, a proposed method for using the data base to establish current property values for materials in existing concrete structures and to estimate the future performance of these materials is also presented. (author)
Structure-Based Turbulence Model

National Research Council Canada - National Science Library

Reynolds, W

2000-01-01

.... Maire carried out this work as part of his Phi) research. During the award period we began to explore ways to simplify the structure-based modeling so that it could be used in repetitive engineering calculations...
IPE data base structure and insights

International Nuclear Information System (INIS)

Lehner, J.; Youngblood, R.

1993-01-01

A data base (the ''IPE Insights Data Base''), has been developed that stores data obtained from the Individual Plant Examinations (IPEs) which licensees of nuclear power plants are conducting in response to the Nuclear Regulatory Commission's (NRC) Generic Letter GL88-20. The data base, which is a collection of linked dbase files, stores information about individual plant designs, core damage frequency, and containment performance in a uniform, structured way. This data base can be queried and used as a computational tool to derive insights regarding the plants for which data is stored. This paper sets out the objectives of the IPE Insights Data Base, describes its structure and contents, illustrates sample queries, and discusses possible future uses
Stability in a fiber bundle model: Existence of strong links and the effect of disorder

Science.gov (United States)

Roy, Subhadeep

2018-05-01

The present paper deals with a fiber bundle model which consists of a fraction α of infinitely strong fibers. The inclusion of such an unbreakable fraction has been proven to affect the failure process in early studies, especially around a critical value αc. The present work has a twofold purpose: (i) a study of failure abruptness, mainly the brittle to quasibrittle transition point with varying α and (ii) variation of αc as we change the strength of disorder introduced in the model. The brittle to quasibrittle transition is confirmed from the failure abruptness. On the other hand, the αc is obtained from the knowledge of failure abruptness as well as the statistics of avalanches. It is observed that the brittle to quasibrittle transition point scales to lower values, suggesting more quasi-brittle-like continuous failure when α is increased. At the same time, the bundle becomes stronger as there are larger numbers of strong links to support the external stress. High α in a highly disordered bundle leads to an ideal situation where the bundle strength, as well as the predictability in failure process is very high. Also, the critical fraction αc, required to make the model deviate from the conventional results, increases with decreasing strength of disorder. The analytical expression for αc shows good agreement with the numerical results. Finally, the findings in the paper are compared with previous results and real-life applications of composite materials.
Economic structure and performance of forest-based industries

International Nuclear Information System (INIS)

O'Laughlin, J.

1989-01-01

This paper reports on the economic structure, conduct, and performance of industries dependent on the nation's forests that are topics of special importance for research. A major challenge to research involving industrial organization of forest-based industries is to link descriptions of structure, conduct, and industrial performance in ways that facilitate public and private policy making. Not to be overlooked is the need to continue efforts to monitor changes in structure and conduct dimensions at the national level and to conduct baseline studies of industry structure-conduct-performance at regional, state, and local levels. Specifically needed is research that will improve understanding of restructuring within the wood-based industry; definitions of the wood-based industry and segments thereof; linkages between structure and regional economic development; timberland as a managerial and economic variable; structural consequences of technological innovations; corporate strategies as related to performance; structural dimensions in an international setting; and structure and performance of nonwood-based forest industries. Economics research focused in such directions will go far toward improving the manner in which the nation's many forest industries organize and conduct their activities

IPE data base structure and insights

International Nuclear Information System (INIS)

Lehner, J.; Youngblood, R.

1994-01-01

A data base (the open-quotes IPE Insights Data Baseclose quotes), has been developed that stores data obtained from the Individual Plant Examinations (IPEs) which licensees of nuclear power plants are conducting in response to the Nuclear Regulatory Commission's (NRC) Generic Letter GL88-20. The data base, which is a collection of linked dBase files, stores information about individual plant designs, core damage frequency, and containment performance in a uniform, structured way. This data base can be queried and used as a computational tool to derive insights regarding the plants for which data is stored. This paper sets out the objectives of the IPE Insights Data Base, describes its structure and contents, illustrates sample queries, and discusses possible future uses
Molecular dynamics simulations of quasi-brittle crack development in iron

Energy Technology Data Exchange (ETDEWEB)

Borodin, V.A., E-mail: borodin@dni.polin.kiae.su [Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe (Germany); NRC Kurchatov Institute, Kurchatov Sq. 1, 123182 Moscow (Russian Federation); Vladimirov, P.V., E-mail: Pavel.Vladimirov@kit.edu [Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe (Germany)

2011-08-31

The paper presents the results of molecular dynamics (MD) simulations of three-dimensional kinetics of micro-crack propagation in alpha-iron and the accompanying lattice transformations at the crack tips. We show that crack initiation on {l_brace}0 0 1{r_brace} planes in iron is preceded with the emission of compact slip bands from the pre-crack tips, in agreement with the predictions of the earlier quasi-two-dimensional simulations. The application of Voronoi decomposition technique for atomic short-range order processing has allowed us to clarify the kinetics of structural transformations at the tips of nucleating and propagating cracks for three most common systems of crack propagation in iron. It is demonstrated that the compact slip bands emanating from the crack tips not only accompany crack nucleation, but remain an essential feature of the crack propagation on {l_brace}0 0 1{r_brace} planes. Due to the strong coupling between the crack tip and slip band propagation, the crack propagation can be limited by slip band interaction with microstructural obstacles, abundantly created in ferritic-martensitic steels in radiation environment of nuclear facilities.
Design of Composite Structures Using Knowledge-Based and Case Based Reasoning

Science.gov (United States)

Lambright, Jonathan Paul

1996-01-01

A method of using knowledge based and case based reasoning to assist designers during conceptual design tasks of composite structures was proposed. The cooperative use of heuristics, procedural knowledge, and previous similar design cases suggests a potential reduction in design cycle time and ultimately product lead time. The hypothesis of this work is that the design process of composite structures can be improved by using Case-Based Reasoning (CBR) and Knowledge-Based (KB) reasoning in the early design stages. The technique of using knowledge-based and case-based reasoning facilitates the gathering of disparate information into one location that is easily and readily available. The method suggests that the inclusion of downstream life-cycle issues into the conceptual design phase reduces potential of defective, and sub-optimal composite structures. Three industry experts were interviewed extensively. The experts provided design rules, previous design cases, and test problems. A Knowledge Based Reasoning system was developed using the CLIPS (C Language Interpretive Procedural System) environment and a Case Based Reasoning System was developed using the Design Memory Utility For Sharing Experiences (MUSE) xviii environment. A Design Characteristic State (DCS) was used to document the design specifications, constraints, and problem areas using attribute-value pair relationships. The DCS provided consistent design information between the knowledge base and case base. Results indicated that the use of knowledge based and case based reasoning provided a robust design environment for composite structures. The knowledge base provided design guidance from well defined rules and procedural knowledge. The case base provided suggestions on design and manufacturing techniques based on previous similar designs and warnings of potential problems and pitfalls. The case base complemented the knowledge base and extended the problem solving capability beyond the existence of
Structural Health Monitoring Based on Combined Structural Global and Local Frequencies

Directory of Open Access Journals (Sweden)

Jilin Hou

2014-01-01

Full Text Available This paper presents a parameter estimation method for Structural Health Monitoring based on the combined measured structural global frequencies and structural local frequencies. First, the global test is experimented to obtain the low order modes which can reflect the global information of the structure. Secondly, the mass is added on the member of structure to increase the local dynamic characteristic and to make the member have local primary frequency, which belongs to structural local frequency and is sensitive to local parameters. Then the parameters of the structure can be optimized accurately using the combined structural global frequencies and structural local frequencies. The effectiveness and accuracy of the proposed method are verified by the experiment of a space truss.
Reliability Based Ship Structural Design

DEFF Research Database (Denmark)

Dogliani, M.; Østergaard, C.; Parmentier, G.

1996-01-01

This paper deals with the development of different methods that allow the reliability-based design of ship structures to be transferred from the area of research to the systematic application in current design. It summarises the achievements of a three-year collaborative research project dealing...... with developments of models of load effects and of structural collapse adopted in reliability formulations which aim at calibrating partial safety factors for ship structural design. New probabilistic models of still-water load effects are developed both for tankers and for containerships. New results are presented...... structure of several tankers and containerships. The results of the reliability analysis were the basis for the definition of a target safety level which was used to asses the partial safety factors suitable for in a new design rules format to be adopted in modern ship structural design. Finally...
Proposed Doctrine Based Structure of the Armored Reconnaissance Squadron

Science.gov (United States)

2017-06-09

squadron. A new structure was proposed based on the deduced required capabilities, utilizing organizational theory and current army practices. This...squadron, which now puts greater emphasis on this analysis to link structure to doctrinally based task. Organizational Theory Since earliest...expect to find capability based discourse; there is a lack of proposed structure based on capability, task or equipment . The Armour Bulletin serves
Density-based and transport-based core-periphery structures in networks.

Science.gov (United States)

Lee, Sang Hoon; Cucuringu, Mihai; Porter, Mason A

2014-03-01

Networks often possess mesoscale structures, and studying them can yield insights into both structure and function. It is most common to study community structure, but numerous other types of mesoscale structures also exist. In this paper, we examine core-periphery structures based on both density and transport. In such structures, core network components are well-connected both among themselves and to peripheral components, which are not well-connected to anything. We examine core-periphery structures in a wide range of examples of transportation, social, and financial networks-including road networks in large urban areas, a rabbit warren, a dolphin social network, a European interbank network, and a migration network between counties in the United States. We illustrate that a recently developed transport-based notion of node coreness is very useful for characterizing transportation networks. We also generalize this notion to examine core versus peripheral edges, and we show that the resulting diagnostic is also useful for transportation networks. To examine the properties of transportation networks further, we develop a family of generative models of roadlike networks. We illustrate the effect of the dimensionality of the embedding space on transportation networks, and we demonstrate that the correlations between different measures of coreness can be very different for different types of networks.
Organizational structure in process-based organizations

NARCIS (Netherlands)

Vanhaverbeke, W.P.M.; Torremans, H.P.M.

1999-01-01

This paper investigates the role of the organization structure in process-based organizations. We argue that companies cannot be designed upon organizational processes only or that process management can be simply imposed as an additional structural dimension on top of the existing functional or
A plane stress softening plasticity model for orthotropic materials

NARCIS (Netherlands)

Lourenço, P.B.; Borst, R. de; Rots, J.G.

1997-01-01

A plane stress model has been developed for quasi-brittle orthotropic materials. The theory of plasticity, which is adopted to describe the inelastic behaviour, utilizes modern algorithmic concepts, including an implicit Euler backward return mapping scheme, a local Newton-Raphson method and a
Magnetophoresis of flexible DNA-based dumbbell structures

Science.gov (United States)

Babić, B.; Ghai, R.; Dimitrov, K.

2008-02-01

Controlled movement and manipulation of magnetic micro- and nanostructures using magnetic forces can give rise to important applications in biomedecine, diagnostics, and immunology. We report controlled magnetophoresis and stretching, in aqueous solution, of a DNA-based dumbbell structure containing magnetic and diamagnetic microspheres. The velocity and stretching of the dumbbell were experimentally measured and correlated with a theoretical model based on the forces acting on individual magnetic beads or the entire dumbbell structures. The results show that precise and predictable manipulation of dumbbell structures is achievable and can potentially be applied to immunomagnetic cell separators.
Semiconductor wire array structures, and solar cells and photodetectors based on such structures

Science.gov (United States)

Kelzenberg, Michael D.; Atwater, Harry A.; Briggs, Ryan M.; Boettcher, Shannon W.; Lewis, Nathan S.; Petykiewicz, Jan A.

2014-08-19

A structure comprising an array of semiconductor structures, an infill material between the semiconductor materials, and one or more light-trapping elements is described. Photoconverters and photoelectrochemical devices based on such structure also described.
Substrate structures for InP-based devices

International Nuclear Information System (INIS)

Wanlass, M.W.; Sheldon, P.

1990-01-01

A substrate structure for an InP-based semiconductor device having an InP based film is described. The substrate structure includes a substrate region having a lightweight bulk substrate and an upper GaAs layer. An interconnecting region is disposed between the substrate region and the InP-based device. The interconnecting region includes a compositionally graded intermediate layer substantially lattice-matched at the opposite end to the InP=based film. The interconnecting region further includes a dislocation mechanism disposed between the GaAs layer and the InP-based film in cooperation with the graded intermediate layer, the buffer mechanism blocking and inhibiting propagation of threading dislocations between the substrate region, and the InP-based device
Structure-based barcoding of proteins.

Science.gov (United States)

Metri, Rahul; Jerath, Gaurav; Kailas, Govind; Gacche, Nitin; Pal, Adityabarna; Ramakrishnan, Vibin

2014-01-01

A reduced representation in the format of a barcode has been developed to provide an overview of the topological nature of a given protein structure from 3D coordinate file. The molecular structure of a protein coordinate file from Protein Data Bank is first expressed in terms of an alpha-numero code and further converted to a barcode image. The barcode representation can be used to compare and contrast different proteins based on their structure. The utility of this method has been exemplified by comparing structural barcodes of proteins that belong to same fold family, and across different folds. In addition to this, we have attempted to provide an illustration to (i) the structural changes often seen in a given protein molecule upon interaction with ligands and (ii) Modifications in overall topology of a given protein during evolution. The program is fully downloadable from the website http://www.iitg.ac.in/probar/. © 2013 The Protein Society.
Fundamental issues in finite element analyses of localization of deformation

NARCIS (Netherlands)

Borst, de R.; Sluys, L.J.; Mühlhaus, H.-B.; Pamin, J.

1993-01-01

Classical continuum models, i.e. continuum models that do not incorporate an internal length scale, suffer from excessive mesh dependence when strain-softening models are used in numerical analyses and cannot reproduce the size effect commonly observed in quasi-brittle failure. In this contribution
Diode rectifier bridge-based structure for DFIG-based wind turbine

DEFF Research Database (Denmark)

Zhu, Rongwu; Chen, Zhe; Wu, Xiaojie

2015-01-01

This paper proposes a new structure for the doubly-fed induction generator (DFIG)-based wind turbine. The proposed structure consists of a DFIG controlled by a partial rated power converter in the rotor side, a three-phase diode rectifier bridge (DRB) connected to the stator, and a DC/AC full rated...
Quality assessment of protein model-structures based on structural and functional similarities.

Science.gov (United States)

Konopka, Bogumil M; Nebel, Jean-Christophe; Kotulska, Malgorzata

2012-09-21

Experimental determination of protein 3D structures is expensive, time consuming and sometimes impossible. A gap between number of protein structures deposited in the World Wide Protein Data Bank and the number of sequenced proteins constantly broadens. Computational modeling is deemed to be one of the ways to deal with the problem. Although protein 3D structure prediction is a difficult task, many tools are available. These tools can model it from a sequence or partial structural information, e.g. contact maps. Consequently, biologists have the ability to generate automatically a putative 3D structure model of any protein. However, the main issue becomes evaluation of the model quality, which is one of the most important challenges of structural biology. GOBA--Gene Ontology-Based Assessment is a novel Protein Model Quality Assessment Program. It estimates the compatibility between a model-structure and its expected function. GOBA is based on the assumption that a high quality model is expected to be structurally similar to proteins functionally similar to the prediction target. Whereas DALI is used to measure structure similarity, protein functional similarity is quantified using standardized and hierarchical description of proteins provided by Gene Ontology combined with Wang's algorithm for calculating semantic similarity. Two approaches are proposed to express the quality of protein model-structures. One is a single model quality assessment method, the other is its modification, which provides a relative measure of model quality. Exhaustive evaluation is performed on data sets of model-structures submitted to the CASP8 and CASP9 contests. The validation shows that the method is able to discriminate between good and bad model-structures. The best of tested GOBA scores achieved 0.74 and 0.8 as a mean Pearson correlation to the observed quality of models in our CASP8 and CASP9-based validation sets. GOBA also obtained the best result for two targets of CASP8, and
A rate-dependent multi-scale crack model for concrete

NARCIS (Netherlands)

Karamnejad, A.; Nguyen, V.P.; Sluys, L.J.

2013-01-01

A multi-scale numerical approach for modeling cracking in heterogeneous quasi-brittle materials under dynamic loading is presented. In the model, a discontinuous crack model is used at macro-scale to simulate fracture and a gradient-enhanced damage model has been used at meso-scale to simulate
Integrated Reliability-Based Optimal Design of Structures

DEFF Research Database (Denmark)

Sørensen, John Dalsgaard; Thoft-Christensen, Palle

1987-01-01

In conventional optimal design of structural systems the weight or the initial cost of the structure is usually used as objective function. Further, the constraints require that the stresses and/or strains at some critical points have to be less than some given values. Finally, all variables......-based optimal design is discussed. Next, an optimal inspection and repair strategy for existing structural systems is presented. An optimization problem is formulated , where the objective is to minimize the expected total future cost of inspection and repair subject to the constraint that the reliability...... value. The reliability can be measured from an element and/or a systems point of view. A number of methods to solve reliability-based optimization problems has been suggested, see e.g. Frangopol [I]. Murotsu et al. (2], Thoft-Christensen & Sørensen (3] and Sørensen (4). For structures where...
Symmetric metamaterials based on flower-shaped structure

International Nuclear Information System (INIS)

Tuong, P.V.; Park, J.W.; Rhee, J.Y.; Kim, K.W.; Cheong, H.; Jang, W.H.; Lee, Y.P.

2013-01-01

We proposed new models of metamaterials (MMs) based on a flower-shaped structure (FSS), whose “meta-atoms” consist of two flower-shaped metallic parts separated by a dielectric layer. Like the non-symmetric MMs based on cut-wire-pairs or electric ring resonators, the symmetrical FSS demonstrates the negative permeability at GHz frequencies. Employing the results, we designed a symmetric negative-refractive-index MM [a symmetric combined structure (SCS)], which is composed of FSSs and cross continuous wires. The MM properties of the FSS and the SCS are presented numerically and experimentally. - Highlights: • A new designed of sub-wavelength metamaterial, flower-shaped structure was proposed. • Flower-shaped meta-atom illustrated effective negative permeability. • Based on the meta-atom, negative refractive index was conventionally gained. • Negative refractive index was demonstrated with symmetric properties for electromagnetic wave. • Dimensional parameters were studied under normal electromagnetic wave
Smartphone based hemispherical photography for canopy structure measurement

Science.gov (United States)

Wan, Xuefen; Cui, Jian; Jiang, Xueqin; Zhang, Jingwen; Yang, Yi; Zheng, Tao

2018-01-01

The canopy is the most direct and active interface layer of the interaction between plant and environment, and has important influence on energy exchange, biodiversity, ecosystem matter and climate change. The measurement about canopy structure of plant is an important foundation to analyze the pattern, process and operation mechanism of forest ecosystem. Through the study of canopy structure of plant, solar radiation, ambient wind speed, air temperature and humidity, soil evaporation, soil temperature and other forest environmental climate characteristics can be evaluated. Because of its accuracy and effectiveness, canopy structure measurement based on hemispherical photography has been widely studied. However, the traditional method of canopy structure hemispherical photogrammetry based on SLR camera and fisheye lens. This method is expensive and difficult to be used in some low-cost occasions. In recent years, smartphone technology has been developing rapidly. The smartphone not only has excellent image acquisition ability, but also has the considerable computational processing ability. In addition, the gyroscope and positioning function on the smartphone will also help to measure the structure of the canopy. In this paper, we present a smartphone based hemispherical photography system. The system consists of smart phones, low-cost fisheye lenses and PMMA adapters. We designed an Android based App to obtain the canopy hemisphere images through low-cost fisheye lenses and provide horizontal collimation information. In addition, the App will add the acquisition location tag obtained by GPS and auxiliary positioning method in hemisphere image information after the canopy structure hemisphere image acquisition. The system was tested in the urban forest after it was completed. The test results show that the smartphone based hemispherical photography system can effectively collect the high-resolution canopy structure image of the plant.

Dissimilarity-based classification of anatomical tree structures

DEFF Research Database (Denmark)

Sørensen, Lauge; Lo, Pechin Chien Pau; Dirksen, Asger

2011-01-01

A novel method for classification of abnormality in anatomical tree structures is presented. A tree is classified based on direct comparisons with other trees in a dissimilarity-based classification scheme. The pair-wise dissimilarity measure between two trees is based on a linear assignment betw...
Dissimilarity-based classification of anatomical tree structures

DEFF Research Database (Denmark)

Sørensen, Lauge Emil Borch Laurs; Lo, Pechin Chien Pau; Dirksen, Asger

2011-01-01

A novel method for classification of abnormality in anatomical tree structures is presented. A tree is classified based on direct comparisons with other trees in a dissimilarity-based classification scheme. The pair-wise dissimilarity measure between two trees is based on a linear assignment...
Equipment response spectra for base-isolated shear beam structures

International Nuclear Information System (INIS)

Ahmadi, G.; Su, L.

1992-01-01

Equipment response spectra in base-isolated structure under seismic ground excitations are studied. The equipment is treated as a single-degree-of-freedom system attached to a nonuniform elastic beam structural model. Several leading base isolation systems, including the laminated rubber bearing, the resilient-friction base isolator with and without a sliding upper plate, and the EDF system are considered. Deflection and acceleration response spectra for the equipment and the shear beam structure subject to a sinusoidal and the accelerogram of the N00W component of El Centro 1940 earthquake are evaluated. Primary-secondary interaction effects are included in the analysis. Several numerical parametric studies are carried out and the effectiveness of different base isolation systems in protecting the nonstructural components is studied. It is shown that use of properly designed base isolation systems provides considerable protection for secondary systems, as well as, the structure against severe seismic loadings. (orig.)
Design bases - Concrete structures

International Nuclear Information System (INIS)

Diaz-Llanos Ros, M.

1993-01-01

The most suitable title for Section 2 is 'Design Bases', which covers not only calculation but also the following areas: - Structural design concepts. - Project criteria. - Material specifications. These concepts are developed in more detail in the following sections. The numbering in this document is neither complete nor hierarchical since, for easier cross referencing, it corresponds to the paragraphs of Eurocode 2 Part 1 (hereinafter 'EUR-2') which are commented on. (author)
Strengthening of Concrete Structures with cement based bonded composites

DEFF Research Database (Denmark)

Täljsten, Björn; Blanksvärd, Thomas

2008-01-01

Polymers). The method is very efficient and has achieved world wide attention. However, there are some drawbacks with the use of epoxy, e.g. working environment, compatibility and permeability. Substituting the epoxy adherent with a cement based bonding agent will render a strengthening system...... with improved working environment and better compatibility to the base concrete structure. This study gives an overview of different cement based systems, all with very promising results for structural upgrading. Studied parameters are structural retrofit for bending, shear and confinement. It is concluded...
Reliability based Design of Coastal Structures

DEFF Research Database (Denmark)

Burcharth, H. F.

2003-01-01

Conventional design practice for coastal structures is deterministic in nature and is based on the concept of a design load which should not exceed the resistance (carrying capacity) of the structure. The design load is usually defined on a probabilistic basis as a characteristic value of the load......, for example the expectation (mean) value of the 100-year return period event. However, this selection is often made without consideration of the involved uncertainties. In most cases the resistance is defined in terms of the load that causes a certain design impact or damage to the structure...
A homogenization method for ductile-brittle composite laminates at large deformations

DEFF Research Database (Denmark)

Poulios, Konstantinos; Niordson, Christian Frithiof

2018-01-01

-elastic behavior in the reinforcement as well as for the bending stiffness of the reinforcement layers. Additionally to previously proposed models, the present method includes Lemaitre type damage for the reinforcement, making it applicable to a wider range of engineering applications. The capability...... of the proposed method in representing the combined effect of plasticity, damage and buckling at microlevel within a homogenized setting is demonstrated by means of direct comparisons to a reference discrete model.......This paper presents a high fidelity homogenization method for periodically layered composite structures that accounts for plasticity in the matrix material and quasi-brittle damage in the reinforcing layers, combined with strong geometrical nonlinearities. A set of deliberately chosen internal...
Event-based model diagnosis of rainfall-runoff model structures

International Nuclear Information System (INIS)

Stanzel, P.

2012-01-01

The objective of this research is a comparative evaluation of different rainfall-runoff model structures. Comparative model diagnostics facilitate the assessment of strengths and weaknesses of each model. The application of multiple models allows an analysis of simulation uncertainties arising from the selection of model structure, as compared with effects of uncertain parameters and precipitation input. Four different model structures, including conceptual and physically based approaches, are compared. In addition to runoff simulations, results for soil moisture and the runoff components of overland flow, interflow and base flow are analysed. Catchment runoff is simulated satisfactorily by all four model structures and shows only minor differences. Systematic deviations from runoff observations provide insight into model structural deficiencies. While physically based model structures capture some single runoff events better, they do not generally outperform conceptual model structures. Contributions to uncertainty in runoff simulations stemming from the choice of model structure show similar dimensions to those arising from parameter selection and the representation of precipitation input. Variations in precipitation mainly affect the general level and peaks of runoff, while different model structures lead to different simulated runoff dynamics. Large differences between the four analysed models are detected for simulations of soil moisture and, even more pronounced, runoff components. Soil moisture changes are more dynamical in the physically based model structures, which is in better agreement with observations. Streamflow contributions of overland flow are considerably lower in these models than in the more conceptual approaches. Observations of runoff components are rarely made and are not available in this study, but are shown to have high potential for an effective selection of appropriate model structures (author) [de
Plant-based food and feed protein structure changes induced by gene-transformation, heating and bio-ethanol processing: a synchrotron-based molecular structure and nutrition research program.

Science.gov (United States)

Yu, Peiqiang

2010-11-01

Unlike traditional "wet" analytical methods which during processing for analysis often result in destruction or alteration of the intrinsic protein structures, advanced synchrotron radiation-based Fourier transform infrared microspectroscopy has been developed as a rapid and nondestructive and bioanalytical technique. This cutting-edge synchrotron-based bioanalytical technology, taking advantages of synchrotron light brightness (million times brighter than sun), is capable of exploring the molecular chemistry or structure of a biological tissue without destruction inherent structures at ultra-spatial resolutions. In this article, a novel approach is introduced to show the potential of the advanced synchrotron-based analytical technology, which can be used to study plant-based food or feed protein molecular structure in relation to nutrient utilization and availability. Recent progress was reported on using synchrotron-based bioanalytical technique synchrotron radiation-based Fourier transform infrared microspectroscopy and diffused reflectance infrared Fourier transform spectroscopy to detect the effects of gene-transformation (Application 1), autoclaving (Application 2), and bio-ethanol processing (Application 3) on plant-based food and feed protein structure changes on a molecular basis. The synchrotron-based technology provides a new approach for plant-based protein structure research at ultra-spatial resolutions at cellular and molecular levels.
A protein relational database and protein family knowledge bases to facilitate structure-based design analyses.

Science.gov (United States)

Mobilio, Dominick; Walker, Gary; Brooijmans, Natasja; Nilakantan, Ramaswamy; Denny, R Aldrin; Dejoannis, Jason; Feyfant, Eric; Kowticwar, Rupesh K; Mankala, Jyoti; Palli, Satish; Punyamantula, Sairam; Tatipally, Maneesh; John, Reji K; Humblet, Christine

2010-08-01

The Protein Data Bank is the most comprehensive source of experimental macromolecular structures. It can, however, be difficult at times to locate relevant structures with the Protein Data Bank search interface. This is particularly true when searching for complexes containing specific interactions between protein and ligand atoms. Moreover, searching within a family of proteins can be tedious. For example, one cannot search for some conserved residue as residue numbers vary across structures. We describe herein three databases, Protein Relational Database, Kinase Knowledge Base, and Matrix Metalloproteinase Knowledge Base, containing protein structures from the Protein Data Bank. In Protein Relational Database, atom-atom distances between protein and ligand have been precalculated allowing for millisecond retrieval based on atom identity and distance constraints. Ring centroids, centroid-centroid and centroid-atom distances and angles have also been included permitting queries for pi-stacking interactions and other structural motifs involving rings. Other geometric features can be searched through the inclusion of residue pair and triplet distances. In Kinase Knowledge Base and Matrix Metalloproteinase Knowledge Base, the catalytic domains have been aligned into common residue numbering schemes. Thus, by searching across Protein Relational Database and Kinase Knowledge Base, one can easily retrieve structures wherein, for example, a ligand of interest is making contact with the gatekeeper residue.
Tamper indicating and sensing optical-based smart structures

International Nuclear Information System (INIS)

Sliva, P.; Anheier, N.C.; Gordon, N.R.; Simmons, K.L.; Stahl, K.A.; Undem, H.A.

1995-05-01

This paper has presented an overview of the type of optical-based structures that can be designed and constructed. These smart structures are capable of responding to their environment. The examples given represent a modest sampling of the complexity that can be achieved in both design and practice. Tamper-indicating containers and smart, sensing windows demonstrate just a few of the applications. We have shown that optical-based smart structures can be made multifunctional with the sensing built in. The next generation smart structure will combine the sensing functionality of these optical-based smart structures with other sensors such as piezoelectrics and electro-rheological fluids to not only be able to respond to the environment, but to adapt to it as well. An example of functionality in this regime would be a piezosensor that senses pressure changes (e.g., shock waves), which then causes an electro-rheological fluid to change viscosity. A fiber sensor located in or near the electro-rheological fluid senses the stiffness change and sends a signal through a feedback loop back to the piezosensor for additional adjustments to the electro-rheological fluid
Generalized structured component analysis a component-based approach to structural equation modeling

CERN Document Server

Hwang, Heungsun

2014-01-01

Winner of the 2015 Sugiyama Meiko Award (Publication Award) of the Behaviormetric Society of Japan Developed by the authors, generalized structured component analysis is an alternative to two longstanding approaches to structural equation modeling: covariance structure analysis and partial least squares path modeling. Generalized structured component analysis allows researchers to evaluate the adequacy of a model as a whole, compare a model to alternative specifications, and conduct complex analyses in a straightforward manner. Generalized Structured Component Analysis: A Component-Based Approach to Structural Equation Modeling provides a detailed account of this novel statistical methodology and its various extensions. The authors present the theoretical underpinnings of generalized structured component analysis and demonstrate how it can be applied to various empirical examples. The book enables quantitative methodologists, applied researchers, and practitioners to grasp the basic concepts behind this new a...
Neighboring Structure Visualization on a Grid-based Layout.

Science.gov (United States)

Marcou, G; Horvath, D; Varnek, A

2017-10-01

Here, we describe an algorithm to visualize chemical structures on a grid-based layout in such a way that similar structures are neighboring. It is based on structure reordering with the help of the Hilbert Schmidt Independence Criterion, representing an empirical estimate of the Hilbert-Schmidt norm of the cross-covariance operator. The method can be applied to any layout of bi- or three-dimensional shape. The approach is demonstrated on a set of dopamine D5 ligands visualized on squared, disk and spherical layouts. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Analysis of a Frame-Shear Wall Concrete Structure by Using Base Isolation and Evaluation of Structure-Soil Interaction

Directory of Open Access Journals (Sweden)

H. I. Polat

2017-12-01

Full Text Available A base isolation system is a type of earthquake-resistant structure design approach based on the principle of reducing a structure’s earthquake response rather than increasing the structure’s earthquake resistance capacity. Seismic base isolated structures have the ability to make large displacements relative to the level of insulation elements. This means that a large structure performs very small displacements between floors during an earthquake and exhibits a rigid body behavior. At this point, the earthquake forces acting on the structure decrease along with the floors. In this article a school building composed of frame-shear wall is resolved primarily with the traditional fixed base structure system, mode shapes are found and periods are obtained. For earthquake response analysis, earthquake loads are distributed to the floors using the equivalent seismic load method and structural elements experiencing capacity problems are found. Then, using the earthquake record, larger failure of cross sections and capacity problems are obtained compared to the first method. In the second stage, the same structure is dissolved again by placing the lead core rubber base isolators between the base and the vertical structural members. The periods of structures under earthquake load have increased significantly by utilizing base isolation, as a result of that spectral accelerations decreased. Thus, large decreases in the shear forces acting to the structure are determined and failures of cross sections are removed.
Gradient-based optimization in nonlinear structural dynamics

DEFF Research Database (Denmark)

Dou, Suguang

The intrinsic nonlinearity of mechanical structures can give rise to rich nonlinear dynamics. Recently, nonlinear dynamics of micro-mechanical structures have contributed to developing new Micro-Electro-Mechanical Systems (MEMS), for example, atomic force microscope, passive frequency divider......, frequency stabilization, and disk resonator gyroscope. For advanced design of these structures, it is of considerable value to extend current optimization in linear structural dynamics into nonlinear structural dynamics. In this thesis, we present a framework for modelling, analysis, characterization......, and optimization of nonlinear structural dynamics. In the modelling, nonlinear finite elements are used. In the analysis, nonlinear frequency response and nonlinear normal modes are calculated based on a harmonic balance method with higher-order harmonics. In the characterization, nonlinear modal coupling...
Peak-Broadening of Floor Response Spectra for Base Isolated Nuclear Structures

International Nuclear Information System (INIS)

Ju, Heekun; Choun, Young-Sun; Kim, Min-Kyu

2015-01-01

In this paper, uncertainties in developing FRS are explained first. Then FDRS of a fixed structure is computed using a conventional method as an example. Lastly FRS of a base-isolated structure is computed and suitability of current peak-broadening method is examined. Uncertainties in the material property of structure influence FRS of fixed structures significantly, but their effect on FRS of base-isolated structures is negligible. Nuclear structures should be designed to ensure the safety of equipment and components mounted on their floors. However, coupled analysis of a structure and components is complex, so equipment is separately analyzed using floor response spectra (FRS). FRS calculated from dynamic analysis of structural model should be modified to create floor design response spectra (FDRS), the input for seismic design of equipment. For nuclear structures, smoothing and broadening peaks of FRS is required to account for uncertainties owing to material properties of structures, soil, modeling techniques, and others. The peak broadening method proposed for fixed based structures may not be appropriate for base-isolated structures because of additional uncertainties in the property of isolation bearings. For base-isolated structures, mechanical property of isolator plays a dominant role on the change of FRS. As base-isolated nuclear plants should meet the ASCE provisions, uncertainty in the isolation system would be around 10%. For the base isolated 3-storied beam model with 2.5-sec isolation period, 6.9% of broadening ratio was enough for development of FDRS at the required variation condition. Also for the models with various isolation periods, less than 10% of broadening ratio was sufficient
Graph-based linear scaling electronic structure theory

Energy Technology Data Exchange (ETDEWEB)

Niklasson, Anders M. N., E-mail: amn@lanl.gov; Negre, Christian F. A.; Cawkwell, Marc J.; Swart, Pieter J.; Germann, Timothy C.; Bock, Nicolas [Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Mniszewski, Susan M.; Mohd-Yusof, Jamal; Wall, Michael E.; Djidjev, Hristo [Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Rubensson, Emanuel H. [Division of Scientific Computing, Department of Information Technology, Uppsala University, Box 337, SE-751 05 Uppsala (Sweden)

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.
Structural Acoustic Physics Based Modeling of Curved Composite Shells

Science.gov (United States)

2017-09-19

NUWC-NPT Technical Report 12,236 19 September 2017 Structural Acoustic Physics -Based Modeling of Curved Composite Shells Rachel E. Hesse...SUBTITLE Structural Acoustic Physics -Based Modeling of Curved Composite Shells 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT...study was to use physics -based modeling (PBM) to investigate wave propagations through curved shells that are subjected to acoustic excitation. An
Data base on structural materials aging properties

International Nuclear Information System (INIS)

Oland, C.B.

1992-01-01

The US Nuclear Regulatory Commission has initiated a Structural Aging Program at the Oak Ridge National Laboratory to identify potential structural safety issues related to continued service of nuclear power plants and to establish criteria for evaluating and resolving these issues. One of the tasks in this program focuses on the establishment of a Structural Materials Information Center where long-term and environment-dependent properties of concretes and other structural materials are being collected and assembled into a data base. These properties will be used to evaluate the current condition of critical structural components in nuclear power plants and to estimate the future performance of these materials during the continued service period
Structural design systems using knowledge-based techniques

International Nuclear Information System (INIS)

Orsborn, K.

1993-01-01

Engineering information management and the corresponding information systems are of a strategic importance for industrial enterprises. This thesis treats the interdisciplinary field of designing computing systems for structural design and analysis using knowledge-based techniques. Specific conceptual models have been designed for representing the structure and the process of objects and activities in a structural design and analysis domain. In this thesis, it is shown how domain knowledge can be structured along several classification principles in order to reduce complexity and increase flexibility. By increasing the conceptual level of the problem description and representation of the domain knowledge in a declarative form, it is possible to enhance the development, maintenance and use of software for mechanical engineering. This will result in a corresponding increase of the efficiency of the mechanical engineering design process. These ideas together with the rule-based control point out the leverage of declarative knowledge representation within this domain. Used appropriately, a declarative knowledge representation preserves information better, is more problem-oriented and change-tolerant than procedural representations. 74 refs

Search-based model identification of smart-structure damage

Science.gov (United States)

Glass, B. J.; Macalou, A.

1991-01-01

This paper describes the use of a combined model and parameter identification approach, based on modal analysis and artificial intelligence (AI) techniques, for identifying damage or flaws in a rotating truss structure incorporating embedded piezoceramic sensors. This smart structure example is representative of a class of structures commonly found in aerospace systems and next generation space structures. Artificial intelligence techniques of classification, heuristic search, and an object-oriented knowledge base are used in an AI-based model identification approach. A finite model space is classified into a search tree, over which a variant of best-first search is used to identify the model whose stored response most closely matches that of the input. Newly-encountered models can be incorporated into the model space. This adaptativeness demonstrates the potential for learning control. Following this output-error model identification, numerical parameter identification is used to further refine the identified model. Given the rotating truss example in this paper, noisy data corresponding to various damage configurations are input to both this approach and a conventional parameter identification method. The combination of the AI-based model identification with parameter identification is shown to lead to smaller parameter corrections than required by the use of parameter identification alone.
Discrete fracture in quasi-brittle materials under compressive and tensile stress states

CSIR Research Space (South Africa)

Klerck, PA

2004-01-01

Full Text Available A method for modelling discrete fracture in geomaterials under tensile and compressive stress fields has been developed based on a Mohr-Coulomb failure surface in compression and three independent anisotropic rotating crack models in tension...
Hard and soft acids and bases: structure and process.

Science.gov (United States)

Reed, James L

2012-07-05

Under investigation is the structure and process that gives rise to hard-soft behavior in simple anionic atomic bases. That for simple atomic bases the chemical hardness is expected to be the only extrinsic component of acid-base strength, has been substantiated in the current study. A thermochemically based operational scale of chemical hardness was used to identify the structure within anionic atomic bases that is responsible for chemical hardness. The base's responding electrons have been identified as the structure, and the relaxation that occurs during charge transfer has been identified as the process giving rise to hard-soft behavior. This is in contrast the commonly accepted explanations that attribute hard-soft behavior to varying degrees of electrostatic and covalent contributions to the acid-base interaction. The ability of the atomic ion's responding electrons to cause hard-soft behavior has been assessed by examining the correlation of the estimated relaxation energies of the responding electrons with the operational chemical hardness. It has been demonstrated that the responding electrons are able to give rise to hard-soft behavior in simple anionic bases.
Benefits of Risk Based Inspection Planning for Offshore Structures

DEFF Research Database (Denmark)

Straub, D.M.; Goyet, J.; Sørensen, John Dalsgaard

2006-01-01

The economical benefits of applying risk-based inspection planning (RBI) for offshore structures subject to fatigue are evaluated based on experiences from past industrial projects. To this end, the factors influencing the cost of inspection, repair and failure of structures are discussed......, the financial benefit of RBI is assessed....
A structural informatics approach to mine kinase knowledge bases.

Science.gov (United States)

Brooijmans, Natasja; Mobilio, Dominick; Walker, Gary; Nilakantan, Ramaswamy; Denny, Rajiah A; Feyfant, Eric; Diller, David; Bikker, Jack; Humblet, Christine

2010-03-01

In this paper, we describe a combination of structural informatics approaches developed to mine data extracted from existing structure knowledge bases (Protein Data Bank and the GVK database) with a focus on kinase ATP-binding site data. In contrast to existing systems that retrieve and analyze protein structures, our techniques are centered on a database of ligand-bound geometries in relation to residues lining the binding site and transparent access to ligand-based SAR data. We illustrate the systems in the context of the Abelson kinase and related inhibitor structures. 2009 Elsevier Ltd. All rights reserved.
A component-based open hypermedia approach to integreting structure services

DEFF Research Database (Denmark)

Grønbæk, Kaj; Nürnberg, Peter J.; Bucka-Lassen, Dirk

1999-01-01

In this paper, we consider the issue of integrating different structure services within a component-based open hypermedia system. We do so by considering the task of collaborative editing, which calls for a variety of different structures traditionally supplied by different structure services. We...... discuss the nature of collaborative editing and how it can be supported by a combination of spatial and navigational hypermedia services. We then present a component-based open hypermedia system architecture and describe various methods of integrating different structure services provided within...... such an architecture. We show the advantages of integration within a component-based framework over other means of integration, highlighting some of the main advantages of the component-based approach to open hypermedia system design and implementation....
Oxidation resistance coating for niobium base structural composites

International Nuclear Information System (INIS)

Tabaru, T.; Shobu, K.; Kim, J.H.; Hirai, H.; Hanada, S.

2003-01-01

Oxidation behavior of Al-rich Mo(Si,Al) 2 base alloys, which is a candidate material for the oxidation resistance coating on Nb base structural composites, were investigated by thermogravimetry. The Mo(Si,Al) 2 base alloys containing Mo 5 (Si,Al) 3 up to about 10 vol% exhibits excellent oxidation resistance at temperatures ranging from 780 to 1580 K, particularly at 1580 K due to continuous Al 2 O 3 layer development. To evaluate the applicability of the Mo(Si,Al) 2 base coating, plasma spraying on Nb base composites were undertaken. However, interface reaction layer was found to form during the following heat treatment. Preparation of Mo(Si,Al) 2 /Al 2 O 3 /Nb layered structures via powder metallurgical process was attempted to preclude diffusion reaction between coating and substrate. (orig.)
URS DataBase: universe of RNA structures and their motifs.

Science.gov (United States)

Baulin, Eugene; Yacovlev, Victor; Khachko, Denis; Spirin, Sergei; Roytberg, Mikhail

2016-01-01

The Universe of RNA Structures DataBase (URSDB) stores information obtained from all RNA-containing PDB entries (2935 entries in October 2015). The content of the database is updated regularly. The database consists of 51 tables containing indexed data on various elements of the RNA structures. The database provides a web interface allowing user to select a subset of structures with desired features and to obtain various statistical data for a selected subset of structures or for all structures. In particular, one can easily obtain statistics on geometric parameters of base pairs, on structural motifs (stems, loops, etc.) or on different types of pseudoknots. The user can also view and get information on an individual structure or its selected parts, e.g. RNA-protein hydrogen bonds. URSDB employs a new original definition of loops in RNA structures. That definition fits both pseudoknot-free and pseudoknotted secondary structures and coincides with the classical definition in case of pseudoknot-free structures. To our knowledge, URSDB is the first database supporting searches based on topological classification of pseudoknots and on extended loop classification.Database URL: http://server3.lpm.org.ru/urs/. © The Author(s) 2016. Published by Oxford University Press.
NMR in structure-based drug design.

Science.gov (United States)

Carneiro, Marta G; Ab, Eiso; Theisgen, Stephan; Siegal, Gregg

2017-11-08

NMR spectroscopy is a powerful technique that can provide valuable structural information for drug discovery endeavors. Here, we discuss the strengths (and limitations) of NMR applications to structure-based drug discovery, highlighting the different levels of resolution and throughput obtainable. Additionally, the emerging field of paramagnetic NMR in drug discovery and recent developments in approaches to speed up and automate protein-observed NMR data collection and analysis are discussed. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.
Intelligent-based Structural Damage Detection Model

International Nuclear Information System (INIS)

Lee, Eric Wai Ming; Yu, K.F.

2010-01-01

This paper presents the application of a novel Artificial Neural Network (ANN) model for the diagnosis of structural damage. The ANN model, denoted as the GRNNFA, is a hybrid model combining the General Regression Neural Network Model (GRNN) and the Fuzzy ART (FA) model. It not only retains the important features of the GRNN and FA models (i.e. fast and stable network training and incremental growth of network structure) but also facilitates the removal of the noise embedded in the training samples. Structural damage alters the stiffness distribution of the structure and so as to change the natural frequencies and mode shapes of the system. The measured modal parameter changes due to a particular damage are treated as patterns for that damage. The proposed GRNNFA model was trained to learn those patterns in order to detect the possible damage location of the structure. Simulated data is employed to verify and illustrate the procedures of the proposed ANN-based damage diagnosis methodology. The results of this study have demonstrated the feasibility of applying the GRNNFA model to structural damage diagnosis even when the training samples were noise contaminated.
Intelligent-based Structural Damage Detection Model

Science.gov (United States)

Lee, Eric Wai Ming; Yu, Kin Fung

2010-05-01

This paper presents the application of a novel Artificial Neural Network (ANN) model for the diagnosis of structural damage. The ANN model, denoted as the GRNNFA, is a hybrid model combining the General Regression Neural Network Model (GRNN) and the Fuzzy ART (FA) model. It not only retains the important features of the GRNN and FA models (i.e. fast and stable network training and incremental growth of network structure) but also facilitates the removal of the noise embedded in the training samples. Structural damage alters the stiffness distribution of the structure and so as to change the natural frequencies and mode shapes of the system. The measured modal parameter changes due to a particular damage are treated as patterns for that damage. The proposed GRNNFA model was trained to learn those patterns in order to detect the possible damage location of the structure. Simulated data is employed to verify and illustrate the procedures of the proposed ANN-based damage diagnosis methodology. The results of this study have demonstrated the feasibility of applying the GRNNFA model to structural damage diagnosis even when the training samples were noise contaminated.
Knowledge base and neural network approach for protein secondary structure prediction.

Science.gov (United States)

Patel, Maulika S; Mazumdar, Himanshu S

2014-11-21

Protein structure prediction is of great relevance given the abundant genomic and proteomic data generated by the genome sequencing projects. Protein secondary structure prediction is addressed as a sub task in determining the protein tertiary structure and function. In this paper, a novel algorithm, KB-PROSSP-NN, which is a combination of knowledge base and modeling of the exceptions in the knowledge base using neural networks for protein secondary structure prediction (PSSP), is proposed. The knowledge base is derived from a proteomic sequence-structure database and consists of the statistics of association between the 5-residue words and corresponding secondary structure. The predicted results obtained using knowledge base are refined with a Backpropogation neural network algorithm. Neural net models the exceptions of the knowledge base. The Q3 accuracy of 90% and 82% is achieved on the RS126 and CB396 test sets respectively which suggest improvement over existing state of art methods. Copyright © 2014 Elsevier Ltd. All rights reserved.
Pre-Stressing Timber-Based Plate Tensegrity Structures

DEFF Research Database (Denmark)

Falk, Andreas; Kirkegaard, Poul Henning

2012-01-01

Tensile structures occur in numerous varieties utilising combinations of tension and compression. Introducing structural plates in the basic tensegrity unit and tensegric assemblies varies the range of feasible topologies and provides the structural system with an integrated surface. The present...... paper considers the concept of plate tensegrity based on CLT plates (cross-laminated timber). It combines the principles of tensegrity with the principles of plate shells and is characterised by a plate shell stabilised by struts and cables. The paper deals with material aspects and robustness of timber...
Reliability based Robustness of Timber Structures through NDT Data Updating

DEFF Research Database (Denmark)

Sousa, Hélder S.; Sørensen, John Dalsgaard; Kirkegaard, Poul Henning

2011-01-01

This work presents a framework for reliability-based assessment of timber structures / members using data gathered from non-destructive test results. These results are used for modeling an update of the mechanical characteristics of timber, using Bayesian methods. Results gathered from ultrasound...... of the structure, thus, being possible to evaluate reliability based in time dependent factors, as well to categorize that structure in terms of robustness. For exemplification of the underlined concepts, three different types of structures are studied....
Reliability-Based Structural Optimization of Wave Energy Converters

Directory of Open Access Journals (Sweden)

Simon Ambühl

2014-12-01

Full Text Available More and more wave energy converter (WEC concepts are reaching prototypelevel. Once the prototype level is reached, the next step in order to further decrease thelevelized cost of energy (LCOE is optimizing the overall system with a focus on structuraland maintenance (inspection costs, as well as on the harvested power from the waves.The target of a fully-developed WEC technology is not maximizing its power output,but minimizing the resulting LCOE. This paper presents a methodology to optimize thestructural design of WECs based on a reliability-based optimization problem and the intentto maximize the investor’s benefits by maximizing the difference between income (e.g., fromselling electricity and the expected expenses (e.g., structural building costs or failure costs.Furthermore, different development levels, like prototype or commercial devices, may havedifferent main objectives and will be located at different locations, as well as receive varioussubsidies. These points should be accounted for when performing structural optimizationsof WECs. An illustrative example on the gravity-based foundation of the Wavestar deviceis performed showing how structural design can be optimized taking target reliability levelsand different structural failure modes due to extreme loads into account.
Microstructure and structural phase transitions in iron-based superconductors

International Nuclear Information System (INIS)

Wang Zhen; Cai Yao; Yang Huai-Xin; Tian Huan-Fang; Wang Zhi-Wei; Ma Chao; Chen Zhen; Li Jian-Qi

2013-01-01

Crystal structures and microstructural features, such as structural phase transitions, defect structures, and chemical and structural inhomogeneities, are known to have profound effects on the physical properties of superconducting materials. Recently, many studies on the structural properties of Fe-based high-T c superconductors have been published. This review article will mainly focus on the typical microstructural features in samples that have been well characterized by physical measurements. (i) Certain common structural features are discussed, in particular, the crystal structural features for different superconducting families, the local structural distortions in the Fe 2 Pn 2 (Pn = P As, Sb) or Fe 2 Ch 2 (Ch = S, Se, Te) blocks, and the structural transformations in the 122 system. (ii) In FeTe(Se) (11 family), the superconductivity, chemical and structural inhomogeneities are investigated and discussed in correlation with superconductivity. (iii) In the K 0.8 Fe 1.6+x Se 2 system, we focus on the typical compounds with emphasis on the Fe-vacancy order and phase separations. The microstructural features in other superconducting materials are also briefly discussed. (topical review - iron-based high temperature superconductors)
Value of information-based inspection planning for offshore structures

DEFF Research Database (Denmark)

Irman, Arifian Agusta; Thöns, Sebastian; Leira, Bernt J.

2017-01-01

with each inspection strategy. A simplified and generic risk-based inspection planning utilizing pre- posterior Bayesian decision analysis had been proposed by Faber et al. [1] and Straub [2]. This paper provides considerations on the theoretical background and a Value of Information analysis......-based inspection planning. The paper will start out with a review of the state-of-art RBI planning procedure based on Bayesian decision theory and its application in offshore structure integrity management. An example of the Value of Information approach is illustrated and it is pointed to further research......Asset integrity and management is an important part of the oil and gas industry especially for existing offshore structures. With declining oil price, the production rate is an important factor to be maintained that makes integrity of the structures one of the main concerns. Reliability based...
Radiographic observation and semi-analytical reconstruction of fracture process zone silicate composite specimen

Czech Academy of Sciences Publication Activity Database

Vavřík, Daniel; Jandejsek, Ivan; Fíla, Tomáš; Veselý, V.

2013-01-01

Roč. 58, č. 3 (2013), s. 315-326 ISSN 0001-7043 R&D Projects: GA ČR(CZ) GAP105/11/1551 Institutional support: RVO:68378297 Keywords : cementitious composite * quasi-brittle fracture * fracture process zone * digital radiography Subject RIV: JL - Materials Fatigue, Friction Mechanics http://journal.it.cas.cz/index.php?stranka=contents
Structure of 2,4-Diaminopyrimidine - Theobromine Alternate Base Pairs

Science.gov (United States)

Gengeliczki, Zsolt; Callahan, Michael P.; Kabelac, Martin; Rijs, Anouk M.; deVries, Mattanjah S.

2011-01-01

We report the structure of clusters of 2,4-diaminopyrimidine with 3,7-dimethylxanthine (theobromine) in the gas phase determined by IR-UV double resonance spectroscopy in both the near-IR and mid-IR regions in combination with ab initio computations. These clusters represent potential alternate nucleobase pairs, geometrically equivalent to guanine-cytosine. We have found the four lowest energy structures, which include the Watson-Crick base pairing motif. This Watson-Crick structure has not been observed by resonant two-photon ionization (R2PI) in the gas phase for the canonical DNA base pairs.
Electronic structure of Fe-based superconductors

Indian Academy of Sciences (India)

Abstract. Fe-based superconductors have drawn much attention during the last decade due to the presence of superconductivity in materials containing the magnetic element, Fe, and the coexistence of superconductivity and magnetism. Extensive study of the electronic structure of these systems suggested the dominant ...

Discrete Discriminant analysis based on tree-structured graphical models

DEFF Research Database (Denmark)

Perez de la Cruz, Gonzalo; Eslava, Guillermina

The purpose of this paper is to illustrate the potential use of discriminant analysis based on tree{structured graphical models for discrete variables. This is done by comparing its empirical performance using estimated error rates for real and simulated data. The results show that discriminant a...... analysis based on tree{structured graphical models is a simple nonlinear method competitive with, and sometimes superior to, other well{known linear methods like those assuming mutual independence between variables and linear logistic regression.......The purpose of this paper is to illustrate the potential use of discriminant analysis based on tree{structured graphical models for discrete variables. This is done by comparing its empirical performance using estimated error rates for real and simulated data. The results show that discriminant...
A Tensor-Based Structural Damage Identification and Severity Assessment

Science.gov (United States)

Anaissi, Ali; Makki Alamdari, Mehrisadat; Rakotoarivelo, Thierry; Khoa, Nguyen Lu Dang

2018-01-01

Early damage detection is critical for a large set of global ageing infrastructure. Structural Health Monitoring systems provide a sensor-based quantitative and objective approach to continuously monitor these structures, as opposed to traditional engineering visual inspection. Analysing these sensed data is one of the major Structural Health Monitoring (SHM) challenges. This paper presents a novel algorithm to detect and assess damage in structures such as bridges. This method applies tensor analysis for data fusion and feature extraction, and further uses one-class support vector machine on this feature to detect anomalies, i.e., structural damage. To evaluate this approach, we collected acceleration data from a sensor-based SHM system, which we deployed on a real bridge and on a laboratory specimen. The results show that our tensor method outperforms a state-of-the-art approach using the wavelet energy spectrum of the measured data. In the specimen case, our approach succeeded in detecting 92.5% of induced damage cases, as opposed to 61.1% for the wavelet-based approach. While our method was applied to bridges, its algorithm and computation can be used on other structures or sensor-data analysis problems, which involve large series of correlated data from multiple sensors. PMID:29301314
Synthesis/literature review for determining structural layer coefficients (SLC) of bases.

Science.gov (United States)

2014-12-01

FDOTs current method of determining a base material structural layer coefficient (SLC) is detailed in the : Materials Manual, Chapter 2.1, Structural Layer Coefficients for Flexible Pavement Base Materials. : Currently, any new base material not a...
Fragment approaches in structure-based drug discovery

International Nuclear Information System (INIS)

Hubbard, Roderick E.

2008-01-01

Fragment-based methods are successfully generating novel and selective drug-like inhibitors of protein targets, with a number of groups reporting compounds entering clinical trials. This paper summarizes the key features of the approach as one of the tools in structure-guided drug discovery. There has been considerable interest recently in what is known as 'fragment-based lead discovery'. The novel feature of the approach is to begin with small low-affinity compounds. The main advantage is that a larger potential chemical diversity can be sampled with fewer compounds, which is particularly important for new target classes. The approach relies on careful design of the fragment library, a method that can detect binding of the fragment to the protein target, determination of the structure of the fragment bound to the target, and the conventional use of structural information to guide compound optimization. In this article the methods are reviewed, and experiences in fragment-based discovery of lead series of compounds against kinases such as PDK1 and ATPases such as Hsp90 are discussed. The examples illustrate some of the key benefits and issues of the approach and also provide anecdotal examples of the patterns seen in selectivity and the binding mode of fragments across different protein targets
The Latent Structure of Secure Base Script Knowledge

Science.gov (United States)

Waters, Theodore E. A.; Fraley, R. Chris; Groh, Ashley M.; Steele, Ryan D.; Vaughn, Brian E.; Bost, Kelly K.; Veríssimo, Manuela; Coppola, Gabrielle; Roisman, Glenn I.

2015-01-01

There is increasing evidence that attachment representations abstracted from childhood experiences with primary caregivers are organized as a cognitive script describing secure base use and support (i.e., the "secure base script"). To date, however, the latent structure of secure base script knowledge has gone unexamined--this despite…
Reliability Based Optimization of Structural Systems

DEFF Research Database (Denmark)

Sørensen, John Dalsgaard

1987-01-01

The optimization problem to design structural systems such that the reliability is satisfactory during the whole lifetime of the structure is considered in this paper. Some of the quantities modelling the loads and the strength of the structure are modelled as random variables. The reliability...... is estimated using first. order reliability methods ( FORM ). The design problem is formulated as the optimization problem to minimize a given cost function such that the reliability of the single elements satisfies given requirements or such that the systems reliability satisfies a given requirement....... For these optimization problems it is described how a sensitivity analysis can be performed. Next, new optimization procedures to solve the optimization problems are presented. Two of these procedures solve the system reliability based optimization problem sequentially using quasi-analytical derivatives. Finally...
Interactive physically-based structural modeling of hydrocarbon systems

International Nuclear Information System (INIS)

Bosson, Mael; Grudinin, Sergei; Bouju, Xavier; Redon, Stephane

2012-01-01

Hydrocarbon systems have been intensively studied via numerical methods, including electronic structure computations, molecular dynamics and Monte Carlo simulations. Typically, these methods require an initial structural model (atomic positions and types, topology, etc.) that may be produced using scripts and/or modeling tools. For many systems, however, these building methods may be ineffective, as the user may have to specify the positions of numerous atoms while maintaining structural plausibility. In this paper, we present an interactive physically-based modeling tool to construct structural models of hydrocarbon systems. As the user edits the geometry of the system, atomic positions are also influenced by the Brenner potential, a well-known bond-order reactive potential. In order to be able to interactively edit systems containing numerous atoms, we introduce a new adaptive simulation algorithm, as well as a novel algorithm to incrementally update the forces and the total potential energy based on the list of updated relative atomic positions. The computational cost of the adaptive simulation algorithm depends on user-defined error thresholds, and our potential update algorithm depends linearly with the number of updated bonds. This allows us to enable efficient physically-based editing, since the computational cost is decoupled from the number of atoms in the system. We show that our approach may be used to effectively build realistic models of hydrocarbon structures that would be difficult or impossible to produce using other tools.
Electronic structure of Fe-based superconductors

Indian Academy of Sciences (India)

2015-05-29

May 29, 2015 ... Fe-based superconductors have drawn much attention during the last decade due to the presence of superconductivity in materials containing the magnetic element, Fe, and the coexistence of superconductivity and magnetism. Extensive study of the electronic structure of these systems suggested the ...
Reliability-Based Structural Optimization of Wave Energy Converters

DEFF Research Database (Denmark)

Ambühl, Simon; Kramer, Morten; Sørensen, John Dalsgaard

2014-01-01

More and more wave energy converter (WEC) concepts are reaching prototype level. Once the prototype level is reached, the next step in order to further decrease the levelized cost of energy (LCOE) is optimizing the overall system with a focus on structural and maintenance (inspection) costs......, as well as on the harvested power from the waves. The target of a fully-developed WEC technology is not maximizing its power output, but minimizing the resulting LCOE. This paper presents a methodology to optimize the structural design of WECs based on a reliability-based optimization problem...
Reliability analysis of offshore structures using OMA based fatigue stresses

DEFF Research Database (Denmark)

Silva Nabuco, Bruna; Aissani, Amina; Glindtvad Tarpø, Marius

2017-01-01

focus is on the uncertainty observed on the different stresses used to predict the damage. This uncertainty can be reduced by Modal Based Fatigue Monitoring which is a technique based on continuously measuring of the accelerations in few points of the structure with the use of accelerometers known...... points of the structure, the stress history can be calculated in any arbitrary point of the structure. The accuracy of the estimated actual stress is analyzed by experimental tests on a scale model where the obtained stresses are compared to strain gauges measurements. After evaluating the fatigue...... stresses directly from the operational response of the structure, a reliability analysis is performed in order to estimate the reliability of using Modal Based Fatigue Monitoring for long term fatigue studies....
Data base on avian mortality on man-made structures

Energy Technology Data Exchange (ETDEWEB)

Dailey, N. S.

1978-01-01

A computerized data base concerning avian mortality on man-made structures is available for searching at the Ecological Sciences Information Center of the Information Center Complex, Information Division, Oak Ridge National Laboratory. This data base, which contains entries from the available literature, provides information on avian mortality from either collision into or electrocution on man-made structures. Primary emphasis has been placed on avian collision with obstacles such as television and radio towers, airport ceilometers, transmission lines, and cooling towers. Other structures included in the studies are fences, glass walls and windows, lighthouses, telegraph and telephone wires, buildings, monuments, smokestacks, and water towers.
Cognitive diagnostic assessment based on knowledge structure

Directory of Open Access Journals (Sweden)

Huang Sue-Fen

2018-01-01

Full Text Available The purpose of this study is to provide an integrated method of fuzzy theory basis for individualized concept structure analysis. In order to insight the misconception of learning basic mathematics and progress teaching. This method integrates Fuzzy Logic Model of Perception (FLMP and Interpretive Structural Modelling (ISM. The combined algorithm could analyze individualized concepts structure based on the comparisons with concept structure of expert. In this paper, some well-known knowledge structure assessment methods will be discussed. For item connection, Bart et al ordering theory and Takeya’s item relational structure provided ordering coefficient to construct item relationships and hierarchies. For concepts or skills connection, Warfield’s ISM and Lin et al Concept Advanced Interpretive Structural Modelling (CAISM provided to construct graphic relationship among elements and display the individualized concept hierarchy structure by numeric and picture. Samples contain 427 which come from Min-Hwei Junior College. Subjects were analyzed by CAISM. It shows the traditional assessment is not the only criteria; it must be combined with other assessment tools. The result shows that CAISM gives meaningful learning and lacks of learners.
Betavoltaic Battery Conversion Efficiency Improvement Based on Interlayer Structures

International Nuclear Information System (INIS)

Li Da-Rang; Jiang Lan; Yin Jian-Hua; Lin Nai; Tan Yuan-Yuan

2012-01-01

Significant differences among the doping densities of PN junctions in semiconductors cause lattice mismatch and lattice defects that increase the recombination current of betavoltaic batteries. This extensively decreases the open circuit voltage and the short current, which results in low conversion efficiency. This study proposes P + PINN + -structure based betavoltaic batteries by adding an interlayer to typical PIN structures to improve conversion efficiency. Numerical simulations are conducted for the energy deposition of beta particles along the thickness direction in semiconductors. Based on this, 63 Ni-radiation GaAs batteries with PIN and P + PINN + structures are designed and fabricated to experimentally verify the proposed design. It turns out that the conversion efficiency of the betavoltaic battery with the proposed P + PINN + structure is about 1.45 times higher than that with the traditional PIN structure. (cross-disciplinary physics and related areas of science and technology)
Towards Computerized Adaptive Assessment Based on Structured Tasks

NARCIS (Netherlands)

Tvarožek, Jozef; Kravcik, Milos; Bieliková, Mária

2008-01-01

Tvarožek, J., Kravčík, M., & Bieliková, M. (2008). Towards Computerized Adaptive Assessment Based on Structured Tasks. In W. Nejdl et al. (Eds.), Adaptive Hypermedia and Adaptive Web-Based Systems (pp. 224-234). Springer Berlin / Heidelberg.
Design and manufacturing of bio-based sandwich structures

CSIR Research Space (South Africa)

John, Maya J

2017-03-01

Full Text Available The aim of this chapter is to discuss the design and manufacturing of bio-based sandwich structures. As the economic advantages of weight reduction have become mandatory for many advanced industries, bio-based sandwich panels have emerged...
Vibrational Based Inspection of Civil Engineering Structures

DEFF Research Database (Denmark)

Rytter, Anders

at the University of Aalborg from 1988 to 1991. Secondly, a research project, In-Field Vibration Based Inspection of Civil Engineering Structures, which has been performed as a pilot project by the Consulting Engineers Rambøll, Hannemann and Højlund in cooperation with the department of Building Technology......The thesis has been written in relation to two different research projects. Firstly, an offshore test programme, Integrated Experimental/Numerical Analysis of the Dynamic behavior of offshore structures, which was performed at the department of Building Technology and Structural Engineering...... and Structural Engineering at the University of Aalborg since the beginning of 1992. Both projects have been supported by the Danish Technical Research Council. Further, the first mentioned project was supported by the Danish Energy Agency. Their financial support is gratefully acknowledged....
Image-based corrosion recognition for ship steel structures

Science.gov (United States)

Ma, Yucong; Yang, Yang; Yao, Yuan; Li, Shengyuan; Zhao, Xuefeng

2018-03-01

Ship structures are subjected to corrosion inevitably in service. Existed image-based methods are influenced by the noises in images because they recognize corrosion by extracting features. In this paper, a novel method of image-based corrosion recognition for ship steel structures is proposed. The method utilizes convolutional neural networks (CNN) and will not be affected by noises in images. A CNN used to recognize corrosion was designed through fine-turning an existing CNN architecture and trained by datasets built using lots of images. Combining the trained CNN classifier with a sliding window technique, the corrosion zone in an image can be recognized.
Structure-Based Search for New Inhibitors of Cholinesterases

Directory of Open Access Journals (Sweden)

Barbara Malawska

2013-03-01

Full Text Available Cholinesterases are important biological targets responsible for regulation of cholinergic transmission, and their inhibitors are used for the treatment of Alzheimer’s disease. To design new cholinesterase inhibitors, of different structure-based design strategies was followed, including the modification of compounds from a previously developed library and a fragment-based design approach. This led to the selection of heterodimeric structures as potential inhibitors. Synthesis and biological evaluation of selected candidates confirmed that the designed compounds were acetylcholinesterase inhibitors with IC50 values in the mid-nanomolar to low micromolar range, and some of them were also butyrylcholinesterase inhibitors.
A novel knowledge-based potential for RNA 3D structure evaluation

Science.gov (United States)

Yang, Yi; Gu, Qi; Zhang, Ben-Gong; Shi, Ya-Zhou; Shao, Zhi-Gang

2018-03-01

Ribonucleic acids (RNAs) play a vital role in biology, and knowledge of their three-dimensional (3D) structure is required to understand their biological functions. Recently structural prediction methods have been developed to address this issue, but a series of RNA 3D structures are generally predicted by most existing methods. Therefore, the evaluation of the predicted structures is generally indispensable. Although several methods have been proposed to assess RNA 3D structures, the existing methods are not precise enough. In this work, a new all-atom knowledge-based potential is developed for more accurately evaluating RNA 3D structures. The potential not only includes local and nonlocal interactions but also fully considers the specificity of each RNA by introducing a retraining mechanism. Based on extensive test sets generated from independent methods, the proposed potential correctly distinguished the native state and ranked near-native conformations to effectively select the best. Furthermore, the proposed potential precisely captured RNA structural features such as base-stacking and base-pairing. Comparisons with existing potential methods show that the proposed potential is very reliable and accurate in RNA 3D structure evaluation. Project supported by the National Science Foundation of China (Grants Nos. 11605125, 11105054, 11274124, and 11401448).
Distance matrix-based approach to protein structure prediction.

Science.gov (United States)

Kloczkowski, Andrzej; Jernigan, Robert L; Wu, Zhijun; Song, Guang; Yang, Lei; Kolinski, Andrzej; Pokarowski, Piotr

2009-03-01

Much structural information is encoded in the internal distances; a distance matrix-based approach can be used to predict protein structure and dynamics, and for structural refinement. Our approach is based on the square distance matrix D = [r(ij)(2)] containing all square distances between residues in proteins. This distance matrix contains more information than the contact matrix C, that has elements of either 0 or 1 depending on whether the distance r (ij) is greater or less than a cutoff value r (cutoff). We have performed spectral decomposition of the distance matrices D = sigma lambda(k)V(k)V(kT), in terms of eigenvalues lambda kappa and the corresponding eigenvectors v kappa and found that it contains at most five nonzero terms. A dominant eigenvector is proportional to r (2)--the square distance of points from the center of mass, with the next three being the principal components of the system of points. By predicting r (2) from the sequence we can approximate a distance matrix of a protein with an expected RMSD value of about 7.3 A, and by combining it with the prediction of the first principal component we can improve this approximation to 4.0 A. We can also explain the role of hydrophobic interactions for the protein structure, because r is highly correlated with the hydrophobic profile of the sequence. Moreover, r is highly correlated with several sequence profiles which are useful in protein structure prediction, such as contact number, the residue-wise contact order (RWCO) or mean square fluctuations (i.e. crystallographic temperature factors). We have also shown that the next three components are related to spatial directionality of the secondary structure elements, and they may be also predicted from the sequence, improving overall structure prediction. We have also shown that the large number of available HIV-1 protease structures provides a remarkable sampling of conformations, which can be viewed as direct structural information about the

SA-Search: a web tool for protein structure mining based on a Structural Alphabet

OpenAIRE

Guyon, Frédéric; Camproux, Anne-Claude; Hochez, Joëlle; Tufféry, Pierre

2004-01-01

SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of f...
Study on geology and geological structure based on literature studies

International Nuclear Information System (INIS)

Funaki, Hironori; Ishii, Eiichi; Yasue, Ken-ichi; Takahashi, Kazuharu

2005-03-01

Japan Nuclear Cycle Development Institute (JNC) is proceeding with underground research laboratory (URL) project for the sedimentary rock in Horonobe, Hokkaido. This project is an investigation project which is planned over 20 years. Surface-based investigations (Phase 1) have been conducted for the present. The purposes of the Phase 1 are to construct the geological environment model (geological-structural, hydrogeological, and hydrochemical models) and to confirm the applicability of investigation technologies for the geological environment. The geological-structural model comprises the base for the hydrogeological and hydrochemical models. We constructed the geological-structural model by mainly using data obtained from literature studies. Particulars regarding which data the model is based on and who has performed the interpretation are also saved for traceability. As a result, we explain the understanding of degree and the need of information on stratigraphy and discontinuous structure. (author)
Structure-based inference of molecular functions of proteins of unknown function from Berkeley Structural Genomics Center

Energy Technology Data Exchange (ETDEWEB)

Kim, Sung-Hou; Shin, Dong Hae; Hou, Jingtong; Chandonia, John-Marc; Das, Debanu; Choi, In-Geol; Kim, Rosalind; Kim, Sung-Hou

2007-09-02

Advances in sequence genomics have resulted in an accumulation of a huge number of protein sequences derived from genome sequences. However, the functions of a large portion of them cannot be inferred based on the current methods of sequence homology detection to proteins of known functions. Three-dimensional structure can have an important impact in providing inference of molecular function (physical and chemical function) of a protein of unknown function. Structural genomics centers worldwide have been determining many 3-D structures of the proteins of unknown functions, and possible molecular functions of them have been inferred based on their structures. Combined with bioinformatics and enzymatic assay tools, the successful acceleration of the process of protein structure determination through high throughput pipelines enables the rapid functional annotation of a large fraction of hypothetical proteins. We present a brief summary of the process we used at the Berkeley Structural Genomics Center to infer molecular functions of proteins of unknown function.
Protein structure refinement using a quantum mechanics-based chemical shielding predictor.

Science.gov (United States)

Bratholm, Lars A; Jensen, Jan H

2017-03-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ , 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1-0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural
Single-Walled Carbon-Nanotubes-Based Organic Memory Structures

Directory of Open Access Journals (Sweden)

Sundes Fakher

2016-09-01

Full Text Available The electrical behaviour of organic memory structures, based on single-walled carbon-nanotubes (SWCNTs, metal–insulator–semiconductor (MIS and thin film transistor (TFT structures, using poly(methyl methacrylate (PMMA as the gate dielectric, are reported. The drain and source electrodes were fabricated by evaporating 50 nm gold, and the gate electrode was made from 50 nm-evaporated aluminium on a clean glass substrate. Thin films of SWCNTs, embedded within the insulating layer, were used as the floating gate. SWCNTs-based memory devices exhibited clear hysteresis in their electrical characteristics (capacitance–voltage (C–V for MIS structures, as well as output and transfer characteristics for transistors. Both structures were shown to produce reliable and large memory windows by virtue of high capacity and reduced charge leakage. The hysteresis in the output and transfer characteristics, the shifts in the threshold voltage of the transfer characteristics, and the flat-band voltage shift in the MIS structures were attributed to the charging and discharging of the SWCNTs floating gate. Under an appropriate gate bias (1 s pulses, the floating gate is charged and discharged, resulting in significant threshold voltage shifts. Pulses as low as 1 V resulted in clear write and erase states.
Simulation tools for guided wave based structural health monitoring

Science.gov (United States)

Mesnil, Olivier; Imperiale, Alexandre; Demaldent, Edouard; Baronian, Vahan; Chapuis, Bastien

2018-04-01

Structural Health Monitoring (SHM) is a thematic derived from Non Destructive Evaluation (NDE) based on the integration of sensors onto or into a structure in order to monitor its health without disturbing its regular operating cycle. Guided wave based SHM relies on the propagation of guided waves in plate-like or extruded structures. Using piezoelectric transducers to generate and receive guided waves is one of the most widely accepted paradigms due to the low cost and low weight of those sensors. A wide range of techniques for flaw detection based on the aforementioned setup is available in the literature but very few of these techniques have found industrial applications yet. A major difficulty comes from the sensitivity of guided waves to a substantial number of parameters such as the temperature or geometrical singularities, making guided wave measurement difficult to analyze. In order to apply guided wave based SHM techniques to a wider spectrum of applications and to transfer those techniques to the industry, the CEA LIST develops novel numerical methods. These methods facilitate the evaluation of the robustness of SHM techniques for multiple applicative cases and ease the analysis of the influence of various parameters, such as sensors positioning or environmental conditions. The first numerical tool is the guided wave module integrated to the commercial software CIVA, relying on a hybrid modal-finite element formulation to compute the guided wave response of perturbations (cavities, flaws…) in extruded structures of arbitrary cross section such as rails or pipes. The second numerical tool is based on the spectral element method [2] and simulates guided waves in both isotropic (metals) and orthotropic (composites) plate like-structures. This tool is designed to match the widely accepted sparse piezoelectric transducer array SHM configuration in which each embedded sensor acts as both emitter and receiver of guided waves. This tool is under development and
Integrated Teaching of Structure-Based Drug Design and Biopharmaceutics: A Computer-Based Approach

Science.gov (United States)

Sutch, Brian T.; Romero, Rebecca M.; Neamati, Nouri; Haworth, Ian S.

2012-01-01

Rational drug design requires expertise in structural biology, medicinal chemistry, physiology, and related fields. In teaching structure-based drug design, it is important to develop an understanding of the need for early recognition of molecules with "drug-like" properties as a key component. That is, it is not merely sufficient to teach…
Response of base isolated structure during strong ground motions beyond design earthquakes

International Nuclear Information System (INIS)

Yabana, Shuichi; Ishida, Katsuhiko; Shiojiri, Hiroo

1991-01-01

In Japan, some base isolated structures for fast breeder reactors (FBR) are tried to design. When a base isolated structure are designed, the relative displacement of isolators are generally limited so sa to be remain in linear state of those during design earthquakes. But to estimate safety margin of a base isolated structure, the response of that until the failure must be obtained experimentally to analytically during strong ground motions of beyond design earthquake. The aim of this paper is to investigate the response of a base isolated structure when the stiffness of the isolators hardens and to simulate the response during strong ground motions of beyond design earthquakes. The optimum characteristics of isolators, with which the margin of the structure are increased, are discussed. (author)
Capturing alternative secondary structures of RNA by decomposition of base-pairing probabilities.

Science.gov (United States)

Hagio, Taichi; Sakuraba, Shun; Iwakiri, Junichi; Mori, Ryota; Asai, Kiyoshi

2018-02-19

It is known that functional RNAs often switch their functions by forming different secondary structures. Popular tools for RNA secondary structures prediction, however, predict the single 'best' structures, and do not produce alternative structures. There are bioinformatics tools to predict suboptimal structures, but it is difficult to detect which alternative secondary structures are essential. We proposed a new computational method to detect essential alternative secondary structures from RNA sequences by decomposing the base-pairing probability matrix. The decomposition is calculated by a newly implemented software tool, RintW, which efficiently computes the base-pairing probability distributions over the Hamming distance from arbitrary reference secondary structures. The proposed approach has been demonstrated on ROSE element RNA thermometer sequence and Lysine RNA ribo-switch, showing that the proposed approach captures conformational changes in secondary structures. We have shown that alternative secondary structures are captured by decomposing base-paring probabilities over Hamming distance. Source code is available from http://www.ncRNA.org/RintW .
Structured Performance Analysis for Component Based Systems

OpenAIRE

Salmi , N.; Moreaux , Patrice; Ioualalen , M.

2012-01-01

International audience; The Component Based System (CBS) paradigm is now largely used to design software systems. In addition, performance and behavioural analysis remains a required step for the design and the construction of efficient systems. This is especially the case of CBS, which involve interconnected components running concurrent processes. % This paper proposes a compositional method for modeling and structured performance analysis of CBS. Modeling is based on Stochastic Well-formed...
FRF-based structural damage detection of controlled buildings with podium structures: Experimental investigation

Science.gov (United States)

Xu, Y. L.; Huang, Q.; Zhan, S.; Su, Z. Q.; Liu, H. J.

2014-06-01

How to use control devices to enhance system identification and damage detection in relation to a structure that requires both vibration control and structural health monitoring is an interesting yet practical topic. In this study, the possibility of using the added stiffness provided by control devices and frequency response functions (FRFs) to detect damage in a building complex was explored experimentally. Scale models of a 12-storey main building and a 3-storey podium structure were built to represent a building complex. Given that the connection between the main building and the podium structure is most susceptible to damage, damage to the building complex was experimentally simulated by changing the connection stiffness. To simulate the added stiffness provided by a semi-active friction damper, a steel circular ring was designed and used to add the related stiffness to the building complex. By varying the connection stiffness using an eccentric wheel excitation system and by adding or not adding the circular ring, eight cases were investigated and eight sets of FRFs were measured. The experimental results were used to detect damage (changes in connection stiffness) using a recently proposed FRF-based damage detection method. The experimental results showed that the FRF-based damage detection method could satisfactorily locate and quantify damage.
A Method for Vibration-Based Structural Interrogation and Health Monitoring Based on Signal Cross-Correlation

International Nuclear Information System (INIS)

Trendafilova, I

2011-01-01

Vibration-based structural interrogation and health monitoring is a field which is concerned with the estimation of the current state of a structure or a component from its vibration response with regards to its ability to perform its intended function appropriately. One way to approach this problem is through damage features extracted from the measured structural vibration response. This paper suggests to use a new concept for the purposes of vibration-based health monitoring. The correlation between two signals, an input and an output, measured on the structure is used to develop a damage indicator. The paper investigates the applicability of the signal cross-correlation and a nonlinear alternative, the average mutual information between the two signals, for the purposes of structural health monitoring and damage assessment. The suggested methodology is applied and demonstrated for delamination detection in a composite beam.
Electronic and chemical properties of graphene-based structures:

DEFF Research Database (Denmark)

Vanin, Marco

In the present thesis several aspects of graphene-based structures have been investigated using density functional theory calculations to solve the electronic structure problem. A review of the implementation of a localized basis-set within the projector augmented wave method - the way of describ...... are attractive candidates although issues regarding the poisoning of the active site remain to be addressed....
Nonlocal continuum-based modeling of mechanical characteristics of nanoscopic structures

Energy Technology Data Exchange (ETDEWEB)

Rafii-Tabar, Hashem, E-mail: rafii-tabar@nano.ipm.ac.ir [Department of Medical Physics and Biomedical Engineering, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran (Iran, Islamic Republic of); Ghavanloo, Esmaeal, E-mail: ghavanloo@shirazu.ac.ir [School of Mechanical Engineering, Shiraz University, Shiraz 71963-16548 (Iran, Islamic Republic of); Fazelzadeh, S. Ahmad [School of Mechanical Engineering, Shiraz University, Shiraz 71963-16548 (Iran, Islamic Republic of)

2016-06-06

Insight into the mechanical characteristics of nanoscopic structures is of fundamental interest and indeed poses a great challenge to the research communities around the world. These structures are ultra fine in size and consequently performing standard experiments to measure their various properties is an extremely difficult and expensive endeavor. Hence, to predict the mechanical characteristics of the nanoscopic structures, different theoretical models, numerical modeling techniques, and computer-based simulation methods have been developed. Among several proposed approaches, the nonlocal continuum-based modeling is of particular significance because the results obtained from this modeling for different nanoscopic structures are in very good agreement with the data obtained from both experimental and atomistic-based studies. A review of the essentials of this model together with its applications is presented here. Our paper is a self contained presentation of the nonlocal elasticity theory and contains the analysis of the recent works employing this model within the field of nanoscopic structures. In this review, the concepts from both the classical (local) and the nonlocal elasticity theories are presented and their applications to static and dynamic behavior of nanoscopic structures with various morphologies are discussed. We first introduce the various nanoscopic structures, both carbon-based and non carbon-based types, and then after a brief review of the definitions and concepts from classical elasticity theory, and the basic assumptions underlying size-dependent continuum theories, the mathematical details of the nonlocal elasticity theory are presented. A comprehensive discussion on the nonlocal version of the beam, the plate and the shell theories that are employed in modeling of the mechanical properties and behavior of nanoscopic structures is then provided. Next, an overview of the current literature discussing the application of the nonlocal models
Nonlocal continuum-based modeling of mechanical characteristics of nanoscopic structures

International Nuclear Information System (INIS)

Rafii-Tabar, Hashem; Ghavanloo, Esmaeal; Fazelzadeh, S. Ahmad

2016-01-01

Insight into the mechanical characteristics of nanoscopic structures is of fundamental interest and indeed poses a great challenge to the research communities around the world. These structures are ultra fine in size and consequently performing standard experiments to measure their various properties is an extremely difficult and expensive endeavor. Hence, to predict the mechanical characteristics of the nanoscopic structures, different theoretical models, numerical modeling techniques, and computer-based simulation methods have been developed. Among several proposed approaches, the nonlocal continuum-based modeling is of particular significance because the results obtained from this modeling for different nanoscopic structures are in very good agreement with the data obtained from both experimental and atomistic-based studies. A review of the essentials of this model together with its applications is presented here. Our paper is a self contained presentation of the nonlocal elasticity theory and contains the analysis of the recent works employing this model within the field of nanoscopic structures. In this review, the concepts from both the classical (local) and the nonlocal elasticity theories are presented and their applications to static and dynamic behavior of nanoscopic structures with various morphologies are discussed. We first introduce the various nanoscopic structures, both carbon-based and non carbon-based types, and then after a brief review of the definitions and concepts from classical elasticity theory, and the basic assumptions underlying size-dependent continuum theories, the mathematical details of the nonlocal elasticity theory are presented. A comprehensive discussion on the nonlocal version of the beam, the plate and the shell theories that are employed in modeling of the mechanical properties and behavior of nanoscopic structures is then provided. Next, an overview of the current literature discussing the application of the nonlocal models
Multi-parameter crack tip stress state description for evaluation of nonlinear zone width in silicate composite specimens in component splitting/bending test geometry

Czech Academy of Sciences Publication Activity Database

Veselý, V.; Frantík, P.; Sopek, J.; Malíková, L.; Seitl, Stanislav

2015-01-01

Roč. 38, č. 2 (2015), s. 200-214 ISSN 8756-758X R&D Projects: GA ČR(CZ) GAP104/11/0833 Institutional support: RVO:68081723 Keywords : near-crack tip fields * Williams series * higher-order terms * stress field * failure criterion * nonlinear zone * quasi-brittle fracture * splitting-bending geometry Subject RIV: JL - Materials Fatigue, Friction Mechanics Impact factor: 1.838, year: 2015
Blind Test of Physics-Based Prediction of Protein Structures

Science.gov (United States)

Shell, M. Scott; Ozkan, S. Banu; Voelz, Vincent; Wu, Guohong Albert; Dill, Ken A.

2009-01-01

We report here a multiprotein blind test of a computer method to predict native protein structures based solely on an all-atom physics-based force field. We use the AMBER 96 potential function with an implicit (GB/SA) model of solvation, combined with replica-exchange molecular-dynamics simulations. Coarse conformational sampling is performed using the zipping and assembly method (ZAM), an approach that is designed to mimic the putative physical routes of protein folding. ZAM was applied to the folding of six proteins, from 76 to 112 monomers in length, in CASP7, a community-wide blind test of protein structure prediction. Because these predictions have about the same level of accuracy as typical bioinformatics methods, and do not utilize information from databases of known native structures, this work opens up the possibility of predicting the structures of membrane proteins, synthetic peptides, or other foldable polymers, for which there is little prior knowledge of native structures. This approach may also be useful for predicting physical protein folding routes, non-native conformations, and other physical properties from amino acid sequences. PMID:19186130
Fishnet statistics for probabilistic strength and scaling of nacreous imbricated lamellar materials

Science.gov (United States)

Luo, Wen; Bažant, Zdeněk P.

2017-12-01

Similar to nacre (or brick masonry), imbricated (or staggered) lamellar structures are widely found in nature and man-made materials, and are of interest for biomimetics. They can achieve high defect insensitivity and fracture toughness, as demonstrated in previous studies. But the probability distribution with a realistic far-left tail is apparently unknown. Here, strictly for statistical purposes, the microstructure of nacre is approximated by a diagonally pulled fishnet with quasibrittle links representing the shear bonds between parallel lamellae (or platelets). The probability distribution of fishnet strength is calculated as a sum of a rapidly convergent series of the failure probabilities after the rupture of one, two, three, etc., links. Each of them represents a combination of joint probabilities and of additive probabilities of disjoint events, modified near the zone of failed links by the stress redistributions caused by previously failed links. Based on previous nano- and multi-scale studies at Northwestern, the strength distribution of each link, characterizing the interlamellar shear bond, is assumed to be a Gauss-Weibull graft, but with a deeper Weibull tail than in Type 1 failure of non-imbricated quasibrittle materials. The autocorrelation length is considered equal to the link length. The size of the zone of failed links at maximum load increases with the coefficient of variation (CoV) of link strength, and also with fishnet size. With an increasing width-to-length aspect ratio, a rectangular fishnet gradually transits from the weakest-link chain to the fiber bundle, as the limit cases. The fishnet strength at failure probability 10-6 grows with the width-to-length ratio. For a square fishnet boundary, the strength at 10-6 failure probability is about 11% higher, while at fixed load the failure probability is about 25-times higher than it is for the non-imbricated case. This is a major safety advantage of the fishnet architecture over particulate
Inelastic Structural Control Based on MBC and FAM

Directory of Open Access Journals (Sweden)

Li Gang

2011-01-01

Full Text Available A complex structure has the characters of many degrees of freedom and intricate shape, especially inelastic behavior under strong external loadings. It is hard to apply the structural control technology to it. In this paper, a new method that combines the Market-Based Control (MBC strategy and Force Analogy Method (FAM is presented to analyze the inelastic behavior of structure with magnetorheological dampers. The MBC is used to reduce the structural vibration response, and FAM is proposed to perform the inelastic analysis. A numerical example is used to compare the control effect of the new method and LQR algorithm, which show the accuracy and efficiency of the proposed computational method.
Reliability-Based Calibration of Load Duration Factors for Timber Structures

DEFF Research Database (Denmark)

Sørensen, John Dalsgaard; Svensson, Staffan; Stang, Birgitte Friis Dela

2005-01-01

John Dalsgaard Sørensen, Staffan Svensson, Birgitte Dela Stang : Reliability-Based Calibration of Load Duration Factors for Timber Structures Abstract : The load bearing capacity of timber structures decrease with time depending on the type of load and timber. Based on representative limit...... states and stochastic models for timber structures, load duration factors are calibrated using probabilistic methods. Load duration e.ects are estimated on basis of simulation of realizations of wind, snow and imposed loads in accordance with the load models in the Danish structural codes. Three damage...... accumulation models are considered, namely Gerhards model, Barrett and Foschi _ s model and Foschi and Yao _ s model. The parameters in these models are .tted by the Maximum Likelihood Method using data relevant for Danish structural timber and the statistical uncertainty is quanti .ed. The reliability...

Nanoscale structure and atomic disorder in the iron-based chalcogenides

Directory of Open Access Journals (Sweden)

Naurang Lal Saini

2013-01-01

Full Text Available The multiband iron-based superconductors have layered structure with a phase diagram characterized by a complex interplay of charge, spin and lattice excitations, with nanoscale atomic structure playing a key role in their fundamental electronic properties. In this paper, we briefly review nanoscale structure and atomic disorder in iron-based chalcogenide superconductors. We focus on the Fe(Se,S1−xTex (11-type and K0.8Fe1.6Se2 (122-type systems, discussing their local structure obtained by extended x-ray absorption fine structure. Local structure studies on the Fe(Se,S1−xTex system reveal clear nanoscale phase separation characterized by coexisting components of different atomic configurations, similar to the case of random alloys. In fact, the Fe–Se/S and Fe–Te distances in the ternary Fe(Se,S1−xTex are found to be closer to the respective distances in the binary FeSe/FeS and FeTe systems, showing significant divergence of the local structure from the average one. The observed features are characteristic of ternary random alloys, indicating breaking of the local symmetry in these materials. On the other hand, K0.8Fe1.6Se2 is known for phase separation in an iron-vacancy ordered phase and an in-plane compressed lattice phase. The local structure of these 122-type chalcogenides shows that this system is characterized by a large local disorder. Indeed, the experiments suggest a nanoscale glassy phase in K0.8Fe1.6Se2, with the superconductivity being similar to the granular materials. While the 11-type structure has no spacer layer, the 122-type structure contains intercalated atoms unlike the 1111-type REFeAsO (RE = rare earth oxypnictides, having well-defined REO spacer layers. It is clear that the interlayer atomic correlations in these iron-based superconducting structures play an important role in structural stability as well as superconductivity and magnetism.
Modern earthquake engineering offshore and land-based structures

CERN Document Server

Jia, Junbo

2017-01-01

This book addresses applications of earthquake engineering for both offshore and land-based structures. It is self-contained as a reference work and covers a wide range of topics, including topics related to engineering seismology, geotechnical earthquake engineering, structural engineering, as well as special contents dedicated to design philosophy, determination of ground motions, shock waves, tsunamis, earthquake damage, seismic response of offshore and arctic structures, spatial varied ground motions, simplified and advanced seismic analysis methods, sudden subsidence of offshore platforms, tank liquid impacts during earthquakes, seismic resistance of non-structural elements, and various types of mitigation measures, etc. The target readership includes professionals in offshore and civil engineering, officials and regulators, as well as researchers and students in this field.
Structural protein descriptors in 1-dimension and their sequence-based predictions.

Science.gov (United States)

Kurgan, Lukasz; Disfani, Fatemeh Miri

2011-09-01

The last few decades observed an increasing interest in development and application of 1-dimensional (1D) descriptors of protein structure. These descriptors project 3D structural features onto 1D strings of residue-wise structural assignments. They cover a wide-range of structural aspects including conformation of the backbone, burying depth/solvent exposure and flexibility of residues, and inter-chain residue-residue contacts. We perform first-of-its-kind comprehensive comparative review of the existing 1D structural descriptors. We define, review and categorize ten structural descriptors and we also describe, summarize and contrast over eighty computational models that are used to predict these descriptors from the protein sequences. We show that the majority of the recent sequence-based predictors utilize machine learning models, with the most popular being neural networks, support vector machines, hidden Markov models, and support vector and linear regressions. These methods provide high-throughput predictions and most of them are accessible to a non-expert user via web servers and/or stand-alone software packages. We empirically evaluate several recent sequence-based predictors of secondary structure, disorder, and solvent accessibility descriptors using a benchmark set based on CASP8 targets. Our analysis shows that the secondary structure can be predicted with over 80% accuracy and segment overlap (SOV), disorder with over 0.9 AUC, 0.6 Matthews Correlation Coefficient (MCC), and 75% SOV, and relative solvent accessibility with PCC of 0.7 and MCC of 0.6 (0.86 when homology is used). We demonstrate that the secondary structure predicted from sequence without the use of homology modeling is as good as the structure extracted from the 3D folds predicted by top-performing template-based methods.
Spatial structure of an individual-based plant–pollinator network

DEFF Research Database (Denmark)

Dupont, Yoko Luise; Nielsen, Kristian Trøjelsgaard; Hagen, Melanie

2014-01-01

The influence of space on the structure (e.g. modularity) of complex ecological networks remains largely unknown. Here, we sampled an individual-based plant–pollinator network by following the movements and flower visits of marked bumblebee individuals within a population of thistle plants...... for which the identities and spatial locations of stems were mapped in a 50  50 m study plot. The plant–pollinator network was dominated by parasitic male bumblebees and had a significantly modular structure, with four identified modules being clearly separated in space. This indicated that individual....... This demonstrated that individual-based plant–pollinator networks are influenced by both the spatial structure of plant populations and individual-specific plant traits. Additionally, bumblebee individuals with long observation times were important for both the connectivity between and within modules. The latter...
Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field.

Science.gov (United States)

Xu, Dong; Zhang, Yang

2012-07-01

Ab initio protein folding is one of the major unsolved problems in computational biology owing to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1-20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 nonhomologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in one-third cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction experiment, QUARK server outperformed the second and third best servers by 18 and 47% based on the cumulative Z-score of global distance test-total scores in the FM category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress toward the solution of the most important problem in the field. Copyright © 2012 Wiley Periodicals, Inc.
Multilayered photonic integration on SOI platform using waveguide-based bridge structure

Science.gov (United States)

Majumder, Saikat; Chakraborty, Rajib

2018-06-01

A waveguide based structure on silicon on insulator platform is proposed for vertical integration in photonic integrated circuits. The structure consists of two multimode interference couplers connected by a single mode (SM) section which can act as a bridge over any other underlying device. Two more SM sections acts as input and output of the first and second multimode couplers respectively. Potential application of this structure is in multilayered photonic links. It is shown that the efficiency of the structure can be improved by making some design modifications. The entire simulation is done using effective-index based matrix method. The feature size chosen are comparable to waveguides fabricated previously so as to fabricate the proposed structure easily.
Team Scaffolds: How Minimal Team Structures Enable Role-based Coordination

OpenAIRE

Valentine, Melissa A

2013-01-01

In this dissertation, I integrate research on role-based coordination with concepts adapted from the team effectiveness literature to theorize how minimal team structures support effective coordination when people do not work together regularly. I argue that role-based coordination among relative strangers can be interpersonally challenging and propose that team scaffolds (minimal team structures that bound groups of roles rather than groups of individuals) may provide occupants with a tempor...
Coordination Analysis Using Global Structural Constraints and Alignment-based Local Features

Science.gov (United States)

Hara, Kazuo; Shimbo, Masashi; Matsumoto, Yuji

We propose a hybrid approach to coordinate structure analysis that combines a simple grammar to ensure consistent global structure of coordinations in a sentence, and features based on sequence alignment to capture local symmetry of conjuncts. The weight of the alignment-based features, which in turn determines the score of coordinate structures, is optimized by perceptron training on a given corpus. A bottom-up chart parsing algorithm efficiently finds the best scoring structure, taking both nested or non-overlapping flat coordinations into account. We demonstrate that our approach outperforms existing parsers in coordination scope detection on the Genia corpus.
Pollen structure visualization using high-resolution laboratory-based hard X-ray tomography.

Science.gov (United States)

Li, Qiong; Gluch, Jürgen; Krüger, Peter; Gall, Martin; Neinhuis, Christoph; Zschech, Ehrenfried

2016-10-14

A laboratory-based X-ray microscope is used to investigate the 3D structure of unstained whole pollen grains. For the first time, high-resolution laboratory-based hard X-ray microscopy is applied to study pollen grains. Based on the efficient acquisition of statistically relevant information-rich images using Zernike phase contrast, both surface- and internal structures of pine pollen - including exine, intine and cellular structures - are clearly visualized. The specific volumes of these structures are calculated from the tomographic data. The systematic three-dimensional study of pollen grains provides morphological and structural information about taxonomic characters that are essential in palynology. Such studies have a direct impact on disciplines such as forestry, agriculture, horticulture, plant breeding and biodiversity. Copyright © 2016 Elsevier Inc. All rights reserved.
General enumeration of RNA secondary structures based on new ...

African Journals Online (AJOL)

Crick base pairs between AU and GC. Based on the new representation, this paper also computes the number of various types of constrained secondary structures taking the minimum stack length 1 and minimum size m for each bonding loop as ...
Designing Structure-Dependent MPC-Based AGC Schemes Considering Network Topology

Directory of Open Access Journals (Sweden)

Young-Sik Jang

2015-04-01

Full Text Available This paper presents the important features of structure-dependent model predictive control (MPC-based approaches for automatic generation control (AGC considering network topology. Since power systems have various generators under different topologies, it is necessary to reflect the characteristics of generators in power networks and the control system structures in order to improve the dynamic performance of AGC. Specifically, considering control system structures is very important because not only can the topological problems be reduced, but also a computing system for AGC in a bulk-power system can be realized. Based on these considerations, we propose new schemes in the proposed controller for minimizing inadvertent line flows and computational burden, which strengthen the advantages of MPC-based approach for AGC. Analysis and simulation results in the IEEE 39-bus model system show different dynamic behaviors among structure-dependent control schemes and possible improvements in computational burden via the proposed control scheme while system operators in each balancing area consider physical load reference ramp constraints among generators.
Non-Watson Crick base pairs might stabilize RNA structural motifs in ...

Indian Academy of Sciences (India)

Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural ...
Estimating material parameters of a structurally based constitutive relation for skin mechanics

KAUST Repository

Jor, Jessica W. Y.; Nash, Martyn P.; Nielsen, Poul M. F.; Hunter, Peter J.

2010-01-01

This paper presents a structurally based modeling framework to characterize the structure-function relation in skin tissues, based upon biaxial tensile experiments performed in vitro on porcine skin. Equi-axial deformations were imposed
Particle swarm optimization of the stable structure of tetrahexahedral Pt-based bimetallic nanoparticles

Energy Technology Data Exchange (ETDEWEB)

Liu, Tun-Dong; Fan, Tian-E [Center for Cloud Computing and Big Data, Department of Automation, Xiamen University, Xiamen 361005 (China); Shao, Gui-Fang, E-mail: gfshao@xmu.edu.cn [Center for Cloud Computing and Big Data, Department of Automation, Xiamen University, Xiamen 361005 (China); Zheng, Ji-Wen [Center for Cloud Computing and Big Data, Department of Automation, Xiamen University, Xiamen 361005 (China); Wen, Yu-Hua [Institute of Theoretical Physics and Astrophysics, Department of Physics, Xiamen University, Xiamen 361005 (China)

2014-08-14

Bimetallic nanoparticles, enclosed by high-index facets, have great catalytic activity and selectivity owing to the synergy effects of high-index facets and the electronic structures of alloy. In this paper, a discrete particle swarm optimization algorithm was employed to systematically investigate the structural stability and features of tetrahexahedral Pt-based bimetallic nanoparticles with high-index facets. Different Pt/Ag, Pt/Cu, Pt/Pd atom ratios and particle sizes were considered in this work. The simulation results reveal that these alloy nanoparticles exhibit considerably different structural characteristics. Pt–Ag nanoparticles tend to form Pt–Ag core–shell structure. Pt–Cu nanoparticles are preferred to take multi-shell structure with Cu on the outer surface while Pt–Pd nanoparticles present a mixing structure in the interior and Pd-dominated surface. Atomic distribution and bonding characteristics were applied to further characterize the structural features of Pt-based nanoparticles. This study provides an important insight into the structural stability and features of Pt-based nanoparticles with different alloys. - Highlights: • We explore the structural stability of Pt-based alloy NPs by a discrete PSO. • Our study discovers the different structural characteristics for Pt-based NPs. • Alloy composition and size have important effects on the surface segregation. • Our work shows strong phase separation for Pt–Ag NPs while weak for Pt–Pd NPs.
Particle swarm optimization of the stable structure of tetrahexahedral Pt-based bimetallic nanoparticles

International Nuclear Information System (INIS)

Liu, Tun-Dong; Fan, Tian-E; Shao, Gui-Fang; Zheng, Ji-Wen; Wen, Yu-Hua

2014-01-01

Bimetallic nanoparticles, enclosed by high-index facets, have great catalytic activity and selectivity owing to the synergy effects of high-index facets and the electronic structures of alloy. In this paper, a discrete particle swarm optimization algorithm was employed to systematically investigate the structural stability and features of tetrahexahedral Pt-based bimetallic nanoparticles with high-index facets. Different Pt/Ag, Pt/Cu, Pt/Pd atom ratios and particle sizes were considered in this work. The simulation results reveal that these alloy nanoparticles exhibit considerably different structural characteristics. Pt–Ag nanoparticles tend to form Pt–Ag core–shell structure. Pt–Cu nanoparticles are preferred to take multi-shell structure with Cu on the outer surface while Pt–Pd nanoparticles present a mixing structure in the interior and Pd-dominated surface. Atomic distribution and bonding characteristics were applied to further characterize the structural features of Pt-based nanoparticles. This study provides an important insight into the structural stability and features of Pt-based nanoparticles with different alloys. - Highlights: • We explore the structural stability of Pt-based alloy NPs by a discrete PSO. • Our study discovers the different structural characteristics for Pt-based NPs. • Alloy composition and size have important effects on the surface segregation. • Our work shows strong phase separation for Pt–Ag NPs while weak for Pt–Pd NPs
MEMS-Based Fuel Reformer with Suspended Membrane Structure

Science.gov (United States)

Chang, Kuei-Sung; Tanaka, Shuji; Esashi, Masayoshi

We report a MEMS-based fuel reformer for supplying hydrogen to micro-fuel cells for portable applications. A combustor and a reforming chamber are fabricated at either side of a suspended membrane structure. This design is used to improve the overall thermal efficiency, which is a critical issue to realize a micro-fuel reformer. The suspended membrane structure design provided good thermal isolation. The micro-heaters consumed 0.97W to maintain the reaction zone of the MEMS-based fuel reformer at 200°C, but further power saving is necessary by improving design and fabrication. The conversion rate of methanol to hydrogen was about 19% at 180°C by using evaporated copper as a reforming catalyst. The catalytic combustion of hydrogen started without any assistance of micro-heaters. By feeding the fuel mixture of an equivalence ratio of 0.35, the temperature of the suspended membrane structure was maintained stable at 100°C with a combustion efficiency of 30%. In future works, we will test a micro-fuel reformer by using a micro-combustor to supply heat.
From crystal to compound: structure-based antimalarial drug discovery.

Science.gov (United States)

Drinkwater, Nyssa; McGowan, Sheena

2014-08-01

Despite a century of control and eradication campaigns, malaria remains one of the world's most devastating diseases. Our once-powerful therapeutic weapons are losing the war against the Plasmodium parasite, whose ability to rapidly develop and spread drug resistance hamper past and present malaria-control efforts. Finding new and effective treatments for malaria is now a top global health priority, fuelling an increase in funding and promoting open-source collaborations between researchers and pharmaceutical consortia around the world. The result of this is rapid advances in drug discovery approaches and technologies, with three major methods for antimalarial drug development emerging: (i) chemistry-based, (ii) target-based, and (iii) cell-based. Common to all three of these approaches is the unique ability of structural biology to inform and accelerate drug development. Where possible, SBDD (structure-based drug discovery) is a foundation for antimalarial drug development programmes, and has been invaluable to the development of a number of current pre-clinical and clinical candidates. However, as we expand our understanding of the malarial life cycle and mechanisms of resistance development, SBDD as a field must continue to evolve in order to develop compounds that adhere to the ideal characteristics for novel antimalarial therapeutics and to avoid high attrition rates pre- and post-clinic. In the present review, we aim to examine the contribution that SBDD has made to current antimalarial drug development efforts, covering hit discovery to lead optimization and prevention of parasite resistance. Finally, the potential for structural biology, particularly high-throughput structural genomics programmes, to identify future targets for drug discovery are discussed.
Knowledge-Based Systems for the Assessment and Management of Bridge Structures

DEFF Research Database (Denmark)

Miyamoto, A.; Thoft-Christensen, Palle; Yan, B.

2004-01-01

. The aim of this paper is to summarize the finding of up-to-date research articles concerning the application of knowledge-based systems to assessment and management of structures and to illustrate the potential of such systems in the structural engineering. Two modern bridge management systems (BMS......It is becoming an important social problem to make maintenance and rehabilitation of existing infrastructures such as bridges, buildings, etc. The kernel of such structure management is to develop a method of safety assessment on items which include remaining life and load carrying capacity......'s) are presented in the paper. The first is a BMS to assess the performance and derive optimal strategies for inspection and maintenance of concrete structures using reliability based and knowledge based systems. The second is the concrete bridge rating expert system (BREX) to evaluate the performance of existing...
An efficicient data structure for three-dimensional vertex based finite volume method

Science.gov (United States)

Akkurt, Semih; Sahin, Mehmet

2017-11-01

A vertex based three-dimensional finite volume algorithm has been developed using an edge based data structure.The mesh data structure of the given algorithm is similar to ones that exist in the literature. However, the data structures are redesigned and simplied in order to fit requirements of the vertex based finite volume method. In order to increase the cache efficiency, the data access patterns for the vertex based finite volume method are investigated and these datas are packed/allocated in a way that they are close to each other in the memory. The present data structure is not limited with tetrahedrons, arbitrary polyhedrons are also supported in the mesh without putting any additional effort. Furthermore, the present data structure also supports adaptive refinement and coarsening. For the implicit and parallel implementation of the FVM algorithm, PETSc and MPI libraries are employed. The performance and accuracy of the present algorithm are tested for the classical benchmark problems by comparing the CPU time for the open source algorithms.
Optical-based smart structures for tamper-indicating applications

International Nuclear Information System (INIS)

Sliva, P.; Anheier, N.C.; Simmons, K.L.; Undem, H.A.

1996-11-01

This report is a compilation of several related projects performed from 1991 through 1996 concerning the design, construction, and application of optical-based smart structure to tamper-indicating and sensing secure containers. Due to several influences, the projects were carried through to varying degrees of completion. Cancellation of the overall project at the client level motivated the authors to gather all of the technology and ideas about smart structures developed during these several projects, whether completed or just conceptualized, into one document. Although each section individually discusses a specific project, the overall document is written chronologically with each successive section showing how increased smart structure complexity was integrated into the container

Deployable structures for a human lunar base

Science.gov (United States)

Gruber, Petra; Häuplik, Sandra; Imhof, Barbara; Özdemir, Kürsad; Waclavicek, Rene; Perino, Maria Antoinetta

2007-06-01

The study Lunar exploration architecture—deployable structures for a lunar base was performed within the Alcatel Alenia Space “Lunar Exploration Architecture” study for the European Space Agency. The purpose of the study was to investigate bionic concepts applicable to deployable structures and to interpret the findings for possible implementation concepts. The study aimed at finding innovative solutions for deployment possibilities. Translating folding/unfolding principles from nature, candidate geometries were developed and researched using models, drawings and visualisations. The use of materials, joints between structural elements and construction details were investigated for these conceptual approaches. Reference scenarios were used to identify the technical and environmental conditions, which served as design drivers. Mechanical issues and the investigation of deployment processes narrowed the selection down to six chosen concepts. Their applicability was evaluated at a conceptual stage in relation to the timescale of the mission.
Coupled vertical-rocking response of base-isolated structures

International Nuclear Information System (INIS)

Pan, T.C.; Kelly, J.M.

1984-01-01

A base-isolated building can have a small horizontal eccentricity between the center of mass of the superstructure and the center of rigidity of the supporting bearings. The structure can be modeled as a rigid block with tributary masses supported on massless rubber bearings placed at a constant elevation below the center of mass. Perturbation methods are implemented to find the dynamic characteristics for both the detuned and the perfectly tuned cases. The Green's functions for the displacement response of the system are derived for the undamped and the damped conditions. The response spectrum modal superposition method is used in estimating the maximum acceleration. A simple method, accounting for the effect of closely spaced modes, is proposed for combining modal maxima and results in an approximate single-degree-of-freedom solution. This approximate solution may be used for thepreliminary design of a base-isolated structure. Numerical results for a base-isolated building subjected to the vertical component of the El Centro earthquake of 1940 were carried out for comparison with analytical results. It is shown that the effect of rocking coupling on the vertical seismic response of baseisolated structures can generally be neglected because of the combined effects of the time lag between the maximum translational and rotational responses and the influence of damping in the isolation system
A probabilistic fragment-based protein structure prediction algorithm.

Directory of Open Access Journals (Sweden)

David Simoncini

Full Text Available Conformational sampling is one of the bottlenecks in fragment-based protein structure prediction approaches. They generally start with a coarse-grained optimization where mainchain atoms and centroids of side chains are considered, followed by a fine-grained optimization with an all-atom representation of proteins. It is during this coarse-grained phase that fragment-based methods sample intensely the conformational space. If the native-like region is sampled more, the accuracy of the final all-atom predictions may be improved accordingly. In this work we present EdaFold, a new method for fragment-based protein structure prediction based on an Estimation of Distribution Algorithm. Fragment-based approaches build protein models by assembling short fragments from known protein structures. Whereas the probability mass functions over the fragment libraries are uniform in the usual case, we propose an algorithm that learns from previously generated decoys and steers the search toward native-like regions. A comparison with Rosetta AbInitio protocol shows that EdaFold is able to generate models with lower energies and to enhance the percentage of near-native coarse-grained decoys on a benchmark of [Formula: see text] proteins. The best coarse-grained models produced by both methods were refined into all-atom models and used in molecular replacement. All atom decoys produced out of EdaFold's decoy set reach high enough accuracy to solve the crystallographic phase problem by molecular replacement for some test proteins. EdaFold showed a higher success rate in molecular replacement when compared to Rosetta. Our study suggests that improving low resolution coarse-grained decoys allows computational methods to avoid subsequent sampling issues during all-atom refinement and to produce better all-atom models. EdaFold can be downloaded from http://www.riken.jp/zhangiru/software.html [corrected].
Predictive Methods for Dense Polymer Networks: Combating Bias with Bio-Based Structures

Science.gov (United States)

2016-03-16

Combating bias with bio - based structures 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Andrew J. Guenthner...unlimited. PA Clearance 16152 Integrity  Service  Excellence Predictive methods for dense polymer networks: Combating bias with bio -based...Architectural Bias • Comparison of Petroleum-Based and Bio -Based Chemical Architectures • Continuing Research on Structure-Property Relationships using
Morphing Wing Structural Optimization Using Opposite-Based Population-Based Incremental Learning and Multigrid Ground Elements

Directory of Open Access Journals (Sweden)

S. Sleesongsom

2015-01-01

Full Text Available This paper has twin aims. Firstly, a multigrid design approach for optimization of an unconventional morphing wing is proposed. The structural design problem is assigned to optimize wing mass, lift effectiveness, and buckling factor subject to structural safety requirements. Design variables consist of partial topology, nodal positions, and component sizes of a wing internal structure. Such a design process can be accomplished by using multiple resolutions of ground elements, which is called a multigrid approach. Secondly, an opposite-based multiobjective population-based incremental learning (OMPBIL is proposed for comparison with the original multiobjective population-based incremental learning (MPBIL. Multiobjective design problems with single-grid and multigrid design variables are then posed and tackled by OMPBIL and MPBIL. The results show that using OMPBIL in combination with a multigrid design approach is the best design strategy. OMPBIL is superior to MPBIL since the former provides better population diversity. Aeroelastic trim for an elastic morphing wing is also presented.
Structure-based, rational design of T cell receptors

Directory of Open Access Journals (Sweden)

Vincent eZoete

2013-09-01

Full Text Available Adoptive cell transfer using engineered T cells is emerging as a promising treatment for metastatic melanoma. Such an approach allows one to introduce TCR modifications that, while maintaining the specificity for the targeted antigen, can enhance the binding and kinetic parameters for the interaction pMHC. Using the well-characterized 2C TCR/SIYR/H-2K(b structure as a model system, we demonstrated that a binding free energy decomposition based on the MM-GBSA approach provides a detailed and reliable description of the TCR/pMHC interactions at the structural and thermodynamic levels. Starting from this result, we developed a new structure-based approach, to rationally design new TCR sequences, and applied it to the BC1 TCR targeting the HLA-A2 restricted NY-ESO-1157-165 cancer-testis epitope. 54% of the designed sequence replacements exhibited improved pMHC-binding as compared to the native TCR, with up to 150 fold increase in affinity, while preserving specificity. Genetically-engineered CD8+ T cells expressing these modified TCRs showed an improved functional activity compared to those expressing BC1 TCR. We measured maximum levels of activities for TCRs within the upper limit of natural affinity. Beyond the affinity threshold at KD < 1 μM we observed an attenuation in cellular function. We have also developed a homology modeling-based approach, TCRep 3D, to obtain accurate structural models of any TCR-pMHC complexes. We have complemented the approach with a simplified rigid method to predict the TCR orientation over pMHC. These methods potentially extend the use of our TCR engineering method to entire TCR repertoires for which no X-ray structure is available. We have also performed a steered molecular dynamics study of the unbinding of the TCR-pMHC complex to get a better understanding of how TCRs interact with pMHCs. This entire rational TCR design pipeline is now being used to produce rationally optimized TCRs for adoptive cell therapies of
Probabilistic structural damage identification based on vibration data

International Nuclear Information System (INIS)

Hao, H.; Xia, Y.

2001-01-01

Vibration-based methods are being rapidly developed and applied to detect structural damage in civil, mechanical and aerospace engineering communities in the last two decades. But uncertainties existing in the structural model and measured vibration data might lead to unreliable results. This paper will present some recent research results to tackle the above mentioned uncertainty problems. By assuming each of the FE model parameters and measured vibration data as a normally distributed random variable, a probabilistic damage detection procedure is developed based on perturbation method and validated by Monte Carlo simulation technique. With this technique, the damage probability of each structural element can be determined. The method developed has been verified by applying it to identify the damages of laboratory tested structures. It was proven that, as compared to the deterministic damage identification method, the present method can not only reduce the possibility of false identification, but also give the identification results in terms of probability. which is deemed more realistic and practical in detecting possible damages in a structure. It has also been found that the modal data included in damage identification analysis have a great influence on the identification results. With a sensitivity study, an optimal measurement set for damage detection is determined. This set includes the optimal measurement locations and the most appropriate modes that should be used in the damage identification analysis. Numerical results indicated that if the optimal set determined in a pre-analysis is used in the damage detection better results will be achieved. (author)
Seismic Response Analysis and Design of Structure with Base Isolation

International Nuclear Information System (INIS)

Rosko, Peter

2010-01-01

The paper reports the study on seismic response and energy distribution of a multi-story civil structure. The nonlinear analysis used the 2003 Bam earthquake acceleration record as the excitation input to the structural model. The displacement response was analyzed in time domain and in frequency domain. The displacement and its derivatives result energy components. The energy distribution in each story provides useful information for the structural upgrade with help of added devices. The objective is the structural displacement response minimization. The application of the structural seismic response research is presented in base-isolation example.
Structure based design of 11β-HSD1 inhibitors.

Science.gov (United States)

Singh, Suresh; Tice, Colin

2010-11-01

Controlling elevated tissue-specific levels of cortisol may provide a novel therapeutic approach for treating metabolic syndrome. This concept has spurred large scale medicinal chemistry efforts in the pharmaceutical industry for the design of 11β-HSD1 inhibitors. High resolution X-ray crystal structures of inhibitors in complex with the enzyme have facilitated the structure-based design of diverse classes of molecules. A summary of binding modes, trends in structure-activity relationships, and the pharmacodynamic data of inhibitors from each class is presented.
Adaptive Functional-Based Neuro-Fuzzy-PID Incremental Controller Structure

Directory of Open Access Journals (Sweden)

Ashraf Ahmed Fahmy

2014-03-01

Full Text Available This paper presents an adaptive functional-based Neuro-fuzzy-PID incremental (NFPID controller structure that can be tuned either offline or online according to required controller performance. First, differential membership functions are used to represent the fuzzy membership functions of the input-output space of the three term controller. Second, controller rules are generated based on the discrete proportional, derivative, and integral function for the fuzzy space. Finally, a fully differentiable fuzzy neural network is constructed to represent the developed controller for either offline or online controller parameter adaptation. Two different adaptation methods are used for controller tuning, offline method based on controller transient performance cost function optimization using Bees Algorithm, and online method based on tracking error minimization using back-propagation with momentum algorithm. The proposed control system was tested to show the validity of the controller structure over a fixed PID controller gains to control SCARA type robot arm.
Investigation of RNA Structure by High-Throughput SHAPE-Based Probing Methods

DEFF Research Database (Denmark)

Poulsen, Line Dahl

of highthroughput SHAPE-based approaches to investigate RNA structure based on novel SHAPE reagents that permit selection of full-length cDNAs. The SHAPE Selection (SHAPES) method is applied to the foot-and-mouth disease virus (FMDV) plus strand RNA genome, and the data is used to construct a genome-wide structural...... that they are functional. The SHAPES method is further applied to the hepatitis C virus (HCV), where the data is used to refine known and predicted structures. Over the past years, the interest of studying RNA structure in their native environment has been increased, and to allow studying RNA structure inside living cells...... using the SHAPE Selection approach, I introduce a biotinylated probing reagent. This chemical can cross cell membranes and reacts with RNA inside the cells, allowing the structural conformations to be studied in the context of physiological relevant conditions in living cells. The methods and results...
Data Extraction Based on Page Structure Analysis

Directory of Open Access Journals (Sweden)

Ren Yichao

2017-01-01

Full Text Available The information we need has some confusing problems such as dispersion and different organizational structure. In addition, because of the existence of unstructured data like natural language and images, extracting local content pages is extremely difficult. In the light of of the problems above, this article will apply a method combined with page structure analysis algorithm and page data extraction algorithm to accomplish the gathering of network data. In this way, the problem that traditional complex extraction model behave poorly when dealing with large-scale data is perfectly solved and the page data extraction efficiency is also boosted to a new level. In the meantime, the article will also make a comparison about pages and content of different types between the methods of DOM structure based on the page and HTML regularities of distribution. After all of those, we may find a more efficient extract method.
Tungsten - Yttrium Based Nuclear Structural Materials

Science.gov (United States)

Ramana, Chintalapalle; Chessa, Jack; Martinenz, Gustavo

2013-04-01

The challenging problem currently facing the nuclear science community in this 21st century is design and development of novel structural materials, which will have an impact on the next-generation nuclear reactors. The materials available at present include reduced activation ferritic/martensitic steels, dispersion strengthened reduced activation ferritic steels, and vanadium- or tungsten-based alloys. These materials exhibit one or more specific problems, which are either intrinsic or caused by reactors. This work is focussed towards tungsten-yttrium (W-Y) based alloys and oxide ceramics, which can be utilized in nuclear applications. The goal is to derive a fundamental scientific understanding of W-Y-based materials. In collaboration with University of Califonia -- Davis, the project is designated to demonstrate the W-Y based alloys, ceramics and composites with enhanced physical, mechanical, thermo-chemical properties and higher radiation resistance. Efforts are focussed on understanding the microstructure, manipulating materials behavior under charged-particle and neutron irradiation, and create a knowledge database of defects, elemental diffusion/segregation, and defect trapping along grain boundaries and interfaces. Preliminary results will be discussed.
Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings

International Nuclear Information System (INIS)

Montalvao, Rinaldo W.; De Simone, Alfonso; Vendruscolo, Michele

2012-01-01

Residual dipolar couplings (RDCs) have the potential of providing detailed information about the conformational fluctuations of proteins. It is very challenging, however, to extract such information because of the complex relationship between RDCs and protein structures. A promising approach to decode this relationship involves structure-based calculations of the alignment tensors of protein conformations. By implementing this strategy to generate structural restraints in molecular dynamics simulations we show that it is possible to extract effectively the information provided by RDCs about the conformational fluctuations in the native states of proteins. The approach that we present can be used in a wide range of alignment media, including Pf1, charged bicelles and gels. The accuracy of the method is demonstrated by the analysis of the Q factors for RDCs not used as restraints in the calculations, which are significantly lower than those corresponding to existing high-resolution structures and structural ensembles, hence showing that we capture effectively the contributions to RDCs from conformational fluctuations.
Reliability-based inspection of prestressed concrete containment structures

International Nuclear Information System (INIS)

Pandey, M.D.

1996-03-01

A study was undertaken to develop a reliability-based approach to the planning of inspection programs for prestressed concrete containment structures. The main function of the prestressing system is to ensure the leak integrity of the containment by maintaining a compressive state of stress under the tensile forces which arise in a hypothesized loss of coolant accident. Prestressing force losses (due to creep and shrinkage, stress relaxation or tendon corrosion) can lead to tensile stresses under accident pressure, resulting in loss of containment leak integrity due to concrete cracking and tensile yielding of the non-prestressed reinforcement. Therefore, the evaluation of prestressing inspection programs was based on their effectiveness in maintaining an acceptable reliability level with respect to a limit state representing yeilding of non-prestressed reinforcement. An annual target reliability of 10 -4 was used for this limit state. As specified in CSA-N287.7, the evaluation of prestressing systems for containment structures is based on the results of lift-off tests to determine the prestressing force. For unbonded systems the tests are carried out on a randomly selected sample from each tendon group in the structure. For bonded systems, the test is carried out on an unbonded test beam that matches the section geometry and material properties of the containment structure. It was found that flexural testing is useful in updating the probability of concrete cracking under accident pressure. For unbonded systems, the analysis indicated that the sample size recommended by the CSA Standard (4% of the tendon population) is adequate. The CSA recommendation for a five year inspection interval is conservative unless severe degradation of the prestressing system, characterized by a high prestressing loss rate (>3%) and a large coefficient of variation of the measured prestressing force (>15%), is observed
Structure-sequence based analysis for identification of conserved regions in proteins

Science.gov (United States)

Zemla, Adam T; Zhou, Carol E; Lam, Marisa W; Smith, Jason R; Pardes, Elizabeth

2013-05-28

Disclosed are computational methods, and associated hardware and software products for scoring conservation in a protein structure based on a computationally identified family or cluster of protein structures. A method of computationally identifying a family or cluster of protein structures in also disclosed herein.
Protein structure refinement using a quantum mechanics-based chemical shielding predictor

DEFF Research Database (Denmark)

Bratholm, Lars Andersen; Jensen, Jan Halborg

2017-01-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor...... of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic...
Form Exploration of Folded Plate Timber Structures based on Performance Criteria

DEFF Research Database (Denmark)

Falk, Andreas; Buelow, Peter Von

2011-01-01

This paper presents an explorative study on applications of cross-laminated timber (CLT) elements in shell structures. Previous studies of plate tensegrity, folded plate roofs interacting with stabilising steel-based systems and studies inspired by origami show a widening range of possibilities...... to develop timber-based shells. Steadily rising interest in rationality during pre-fabrication, transport and on-site construction in contemporary industrialised production increases the competitiveness of CLT-based elements and systems and the architectural applications are getting more common and more...... experimental. Folded plate structures which are the focus of this paper present several issues of structural importance – potential mechanisms, subdivision of surfaces etc. – and the hereby presented study aims at exploring developed typologies, using computer tools for developed optimisation procedures...
Structural analysis of paintings based on brush strokes

Science.gov (United States)

Sablatnig, Robert; Kammerer, Paul; Zolda, Ernestine

1998-05-01

The origin of works of art can often not be attributed to a certain artist. Likewise it is difficult to say whether paintings or drawings are originals or forgeries. In various fields of art new technical methods are used to examine the age, the state of preservation and the origin of the materials used. For the examination of paintings, radiological methods like X-ray and infra-red diagnosis, digital radiography, computer-tomography, etc. and color analyzes are employed to authenticate art. But all these methods do not relate certain characteristics in art work to a specific artist -- the artist's personal style. In order to study this personal style of a painter, experts in art history and image processing try to examine the 'structural signature' based on brush strokes within paintings, in particular in portrait miniatures. A computer-aided classification and recognition system for portrait miniatures is developed, which enables a semi- automatic classification and forgery detection based on content, color, and brush strokes. A hierarchically structured classification scheme is introduced which separates the classification into three different levels of information: color, shape of region, and structure of brush strokes.
Analysis of energy-based algorithms for RNA secondary structure prediction

Directory of Open Access Journals (Sweden)

Hajiaghayi Monir

2012-02-01

Full Text Available Abstract Background RNA molecules play critical roles in the cells of organisms, including roles in gene regulation, catalysis, and synthesis of proteins. Since RNA function depends in large part on its folded structures, much effort has been invested in developing accurate methods for prediction of RNA secondary structure from the base sequence. Minimum free energy (MFE predictions are widely used, based on nearest neighbor thermodynamic parameters of Mathews, Turner et al. or those of Andronescu et al. Some recently proposed alternatives that leverage partition function calculations find the structure with maximum expected accuracy (MEA or pseudo-expected accuracy (pseudo-MEA methods. Advances in prediction methods are typically benchmarked using sensitivity, positive predictive value and their harmonic mean, namely F-measure, on datasets of known reference structures. Since such benchmarks document progress in improving accuracy of computational prediction methods, it is important to understand how measures of accuracy vary as a function of the reference datasets and whether advances in algorithms or thermodynamic parameters yield statistically significant improvements. Our work advances such understanding for the MFE and (pseudo-MEA-based methods, with respect to the latest datasets and energy parameters. Results We present three main findings. First, using the bootstrap percentile method, we show that the average F-measure accuracy of the MFE and (pseudo-MEA-based algorithms, as measured on our largest datasets with over 2000 RNAs from diverse families, is a reliable estimate (within a 2% range with high confidence of the accuracy of a population of RNA molecules represented by this set. However, average accuracy on smaller classes of RNAs such as a class of 89 Group I introns used previously in benchmarking algorithm accuracy is not reliable enough to draw meaningful conclusions about the relative merits of the MFE and MEA-based algorithms

Radiation defect formation in two-barrier structures based on silicon

International Nuclear Information System (INIS)

Madatov, R.S.; Abbasov, F.P.; Mustafayev, Yu.M.

2013-01-01

It was developed a silicon-based photodetector with high integral sensitivity in low-wave spectrum. It was investigated the effect of gamma radiation on the mechanism of current transport in the structure of Schottky barrier type and in transitions. It is shown that the double-barrier structures can improve the photovoltaic parameters of conventional detectors. For the first time it was obtained and studied the characteristics of two-barrier structures created on the same plane. The advantages over conventional structures are shown. The annealing point is changing the structure of radiation defects and leads to their disappearance
A primer on polymer nomenclature: Structure-based, sourced-based and trade names

Science.gov (United States)

Polymer nomenclature is important because it is part of the language of polymer science and is needed for polymer identification, reference, and documentation. A primer on polymer nomenclature is provided herein for people new to the field or for instructional use. Both structure-based and source-...
A key heterogeneous structure of fractal networks based on inverse renormalization scheme

Science.gov (United States)

Bai, Yanan; Huang, Ning; Sun, Lina

2018-06-01

Self-similarity property of complex networks was found by the application of renormalization group theory. Based on this theory, network topologies can be classified into universality classes in the space of configurations. In return, through inverse renormalization scheme, a given primitive structure can grow into a pure fractal network, then adding different types of shortcuts, it exhibits different characteristics of complex networks. However, the effect of primitive structure on networks structural property has received less attention. In this paper, we introduce a degree variance index to measure the dispersion of nodes degree in the primitive structure, and investigate the effect of the primitive structure on network structural property quantified by network efficiency. Numerical simulations and theoretical analysis show a primitive structure is a key heterogeneous structure of generated networks based on inverse renormalization scheme, whether or not adding shortcuts, and the network efficiency is positively correlated with degree variance of the primitive structure.
Assessment of soil-structure interaction effects based on simple modes

International Nuclear Information System (INIS)

Philippacopoulos, A.J.; Miller, C.A.

1983-01-01

Soil-structure interaction effects are investigated using a simple mathematical model which employs three degrees-of-freedom. The foundation is approximated by a homogeneous, isotropic, elastic half-space. Harmonic functions and a recorded earthquake are used to represent the free-field input motion. Variations of the response characteristics due to structural and interaction parameters are demonstrated. Response spectra are presented that display the magnitude of the maximum structural response for a range of fixed-base structural frequencies, interaction frequencies and damping. Conclusions are obtained regarding the behavior of the response of the soil-structure system. The findings reported herein can be used for the interpretation of the results of soil-structure interaction analyses of nuclear plant structures that are performed with available computer codes
Structure and properties of polymer-silicate nanocomposites based on polytetrafluoroethylene

Energy Technology Data Exchange (ETDEWEB)

Sleptsova, Sardana A.; Okhlopkova, Aitalina A. [North-Eastern Federal University, Yakutsk (Russian Federation)

2011-07-01

The results of physicomechanical, tribological , and structural investigation of polytetrafluoroethylene based polymers and natural layered silicates are reported. It is shown that the tribological behaviour of the composites can be significantly improved by introducing a small amount of activated silicates. The results of structural examination of the composite friction surfaces by scanning-probe microscopy and IR spectroscopy are discussed. Key words: polytetrafluoroethylene, layered silicates, wear resistance, friction coefficient, structure, IR-spectrum.
Structural system identification based on variational mode decomposition

Science.gov (United States)

Bagheri, Abdollah; Ozbulut, Osman E.; Harris, Devin K.

2018-03-01

In this paper, a new structural identification method is proposed to identify the modal properties of engineering structures based on dynamic response decomposition using the variational mode decomposition (VMD). The VMD approach is a decomposition algorithm that has been developed as a means to overcome some of the drawbacks and limitations of the empirical mode decomposition method. The VMD-based modal identification algorithm decomposes the acceleration signal into a series of distinct modal responses and their respective center frequencies, such that when combined their cumulative modal responses reproduce the original acceleration response. The decaying amplitude of the extracted modal responses is then used to identify the modal damping ratios using a linear fitting function on modal response data. Finally, after extracting modal responses from available sensors, the mode shape vector for each of the decomposed modes in the system is identified from all obtained modal response data. To demonstrate the efficiency of the algorithm, a series of numerical, laboratory, and field case studies were evaluated. The laboratory case study utilized the vibration response of a three-story shear frame, whereas the field study leveraged the ambient vibration response of a pedestrian bridge to characterize the modal properties of the structure. The modal properties of the shear frame were computed using analytical approach for a comparison with the experimental modal frequencies. Results from these case studies demonstrated that the proposed method is efficient and accurate in identifying modal data of the structures.
Experimental demonstration of dielectric structure based two beam acceleration

International Nuclear Information System (INIS)

Gai, W.; Conde, M. E.; Konecny, R.; Power, J. G.; Schoessow, P.; Sun, X.; Zou, P.

2000-01-01

We report on the experimental results of the dielectric based two beam accelerator (step-up transformer). By using a single high charge beam, we have generated and extracted a high power RF pulse from a 7.8 GHz primary dielectric structure and then subsequently transferred to a second accelerating structure with higher dielectric constant and smaller transverse dimensions. We have measured the energy change of a second (witness) beam passing through the acceleration stage. The measured gradient is >4 times the deceleration gradient. The detailed experiment of set-up and results of the measurements are dimmed. Future plans for the development of a 100 MeV demonstration accelerator based on this technique is presented
Experimental demonstration of dielectric structure based two beam acceleration.

Energy Technology Data Exchange (ETDEWEB)

Gai, W.; Conde, M. E.; Konecny, R.; Power, J. G.; Schoessow, P.; Sun, X.; Zou, P.

2000-11-28

We report on the experimental results of the dielectric based two beam accelerator (step-up transformer). By using a single high charge beam, we have generated and extracted a high power RF pulse from a 7.8 GHz primary dielectric structure and then subsequently transferred to a second accelerating structure with higher dielectric constant and smaller transverse dimensions. We have measured the energy change of a second (witness) beam passing through the acceleration stage. The measured gradient is >4 times the deceleration gradient. The detailed experiment of set-up and results of the measurements are dimmed. Future plans for the development of a 100 MeV demonstration accelerator based on this technique is presented.
The influence of affective and cognitive arguments on message judgement and attitude change: The moderating effects of meta-bases and structural bases.

Science.gov (United States)

Keer, Mario; van den Putte, Bas; Neijens, Peter; de Wit, John

2013-01-01

This study investigated whether the efficacy of affective vs. cognitive persuasive messages was moderated by (1) individuals' subjective assessments of whether their attitudes were based on affect or cognition (i.e. meta-bases) and (2) the degree individuals' attitudes were correlated with affect and cognition (i.e. structural bases). Participants (N = 97) were randomly exposed to a message containing either affective or cognitive arguments discouraging binge drinking. The results demonstrated that meta-bases and not structural bases moderated the influence of argument type on message judgement. Affective (cognitive) messages were judged more positively when individuals' meta-bases were more affective (cognitive). In contrast, structural bases and not meta-bases moderated the influence of argument type on attitude and intention change following exposure to the message. Surprisingly, change was greater among individuals who read a message that mismatched their structural attitude base. Affective messages were more effective as attitudes were more cognition-based, and vice versa. Thus, although individuals prefer messages that match their meta-base, attitude and intention change regarding binge drinking are best established by mismatching their structural base.
PCANet-Based Structural Representation for Nonrigid Multimodal Medical Image Registration

Directory of Open Access Journals (Sweden)

Xingxing Zhu

2018-05-01

Full Text Available Nonrigid multimodal image registration remains a challenging task in medical image processing and analysis. The structural representation (SR-based registration methods have attracted much attention recently. However, the existing SR methods cannot provide satisfactory registration accuracy due to the utilization of hand-designed features for structural representation. To address this problem, the structural representation method based on the improved version of the simple deep learning network named PCANet is proposed for medical image registration. In the proposed method, PCANet is firstly trained on numerous medical images to learn convolution kernels for this network. Then, a pair of input medical images to be registered is processed by the learned PCANet. The features extracted by various layers in the PCANet are fused to produce multilevel features. The structural representation images are constructed for two input images based on nonlinear transformation of these multilevel features. The Euclidean distance between structural representation images is calculated and used as the similarity metrics. The objective function defined by the similarity metrics is optimized by L-BFGS method to obtain parameters of the free-form deformation (FFD model. Extensive experiments on simulated and real multimodal image datasets show that compared with the state-of-the-art registration methods, such as modality-independent neighborhood descriptor (MIND, normalized mutual information (NMI, Weber local descriptor (WLD, and the sum of squared differences on entropy images (ESSD, the proposed method provides better registration performance in terms of target registration error (TRE and subjective human vision.
Structural Phenomenon of Cement-Based Composite Elements in Ultimate Limit State

Directory of Open Access Journals (Sweden)

I. Iskhakov

2016-01-01

Full Text Available Cement-based composite materials have minimum of two components, one of which has higher strength compared to the other. Such materials include concrete, reinforced concrete (RC, and ferrocement, applied in single- or two-layer RC elements. This paper discusses experimental and theoretical results, obtained by the authors in the recent three decades. The authors have payed attention to a structural phenomenon that many design features (parameters, properties, etc. at ultimate limit state (ULS of a structure are twice higher (or lower than at initial loading state. This phenomenon is evident at material properties, structures (or their elements, and static and/or dynamic structural response. The phenomenon is based on two ideas that were developed by first author: quasi-isotropic state of a structure at ULS and minimax principle. This phenomenon is supported by experimental and theoretical results, obtained for various structures, like beams, frames, spatial structures, and structural joints under static or/and dynamic loadings. This study provides valuable indicators for experiments’ planning and estimation of structural state. The phenomenon provides additional equation(s for calculating parameters that are usually obtained experimentally and can lead to developing design concepts and RC theory, in which the number of empirical design coefficients will be minimal.
Barrier potential design criteria in multiple-quantum-well-based solar-cell structures

Science.gov (United States)

Mohaidat, Jihad M.; Shum, Kai; Wang, W. B.; Alfano, R. R.

1994-01-01

The barrier potential design criteria in multiple-quantum-well (MQW)-based solar-cell structures is reported for the purpose of achieving maximum efficiency. The time-dependent short-circuit current density at the collector side of various MQW solar-cell structures under resonant condition was numerically calculated using the time-dependent Schroedinger equation. The energy efficiency of solar cells based on the InAs/Ga(y)In(1-y)As and GaAs/Al(x)Ga(1-x)As MQW structues were compared when carriers are excited at a particular solar-energy band. Using InAs/Ga(y)In(1-y)As MQW structures it is found that a maximum energy efficiency can be achieved if the structure is designed with barrier potential of about 450 meV. The efficiency is found to decline linearly as the barrier potential increases for GaAs/Al(x)Ga(1-x)As MQW-structure-based solar cells.
Valence band electronic structure of Pd based ternary chalcogenide superconductors

Energy Technology Data Exchange (ETDEWEB)

Lohani, H. [Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005 (India); Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085 (India); Mishra, P. [Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005 (India); Goyal, R.; Awana, V.P.S. [National Physical Laboratory(CSIR), Dr. K. S. Krishnan Road, New Delhi 110012 (India); Sekhar, B.R., E-mail: sekhar@iopb.res.in [Institute of Physics, Sachivalaya Marg, Bhubaneswar 751005 (India); Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085 (India)

2016-12-15

Highlights: • VB Photoemission study and DFT calculations on Pd based ternary superconductors are presented. • Nb{sub 2}Pd{sub 0.95}S{sub 5} shows a temperature dependent pseudogap. • VB spectral features of ternary superconductors are correlated to their structural geometry. - Abstract: We present a comparative study of the valence band electronic structure of Pd based ternary chalcogenide superconductors Nb{sub 2}Pd{sub 0.95}S{sub 5}, Ta{sub 2}Pd{sub 0.97}S{sub 6} and Ta{sub 2}Pd{sub 0.97}Te{sub 6} using experimental photoemission spectroscopy and density functional based theoretical calculations. We observe a qualitatively similarity between valence band (VB) spectra of Nb{sub 2}Pd{sub 0.95}S{sub 5} and Ta{sub 2}Pd{sub 0.97}S{sub 6}. Further, we find a pseudogap feature in Nb{sub 2}Pd{sub 0.95}S{sub 5} at low temperature, unlike other two compounds. We have correlated the structural geometry with the differences in VB spectra of these compounds. The different atomic packing in these compounds could vary the strength of inter-orbital hybridization among various atoms which leads to difference in their electronic structure as clearly observed in our DOS calculations.
Quantitative structure-activity relationship (QSAR) models for polycyclic aromatic hydrocarbons (PAHs) dissipation in rhizosphere based on molecular structure and effect size

International Nuclear Information System (INIS)

Ma Bin; Chen Huaihai; Xu Minmin; Hayat, Tahir; He Yan; Xu Jianming

2010-01-01

Rhizoremediation is a significant form of bioremediation for polycyclic aromatic hydrocarbons (PAHs). This study examined the role of molecular structure in determining the rhizosphere effect on PAHs dissipation. Effect size in meta-analysis was employed as activity dataset for building quantitative structure-activity relationship (QSAR) models and accumulative effect sizes of 16 PAHs were used for validation of these models. Based on the genetic algorithm combined with partial least square regression, models for comprehensive dataset, Poaceae dataset, and Fabaceae dataset were built. The results showed that information indices, calculated as information content of molecules based on the calculation of equivalence classes from the molecular graph, were the most important molecular structural indices for QSAR models of rhizosphere effect on PAHs dissipation. The QSAR model, based on the molecular structure indices and effect size, has potential to be used in studying and predicting the rhizosphere effect of PAHs dissipation. - Effect size based on meta-analysis was used for building PAHs dissipation quantitative structure-activity relationship (QSAR) models.
Quantitative structure-activity relationship (QSAR) models for polycyclic aromatic hydrocarbons (PAHs) dissipation in rhizosphere based on molecular structure and effect size

Energy Technology Data Exchange (ETDEWEB)

Ma Bin; Chen Huaihai; Xu Minmin; Hayat, Tahir [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China); He Yan, E-mail: yhe2006@zju.edu.c [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China); Xu Jianming, E-mail: jmxu@zju.edu.c [Zhejiang Provincial Key Laboratory of Subtropical Soil and Plant Nutrition, College of Environmental and Natural Resource Sciences, Zhejiang University, Hangzhou 310029 (China)

2010-08-15

Rhizoremediation is a significant form of bioremediation for polycyclic aromatic hydrocarbons (PAHs). This study examined the role of molecular structure in determining the rhizosphere effect on PAHs dissipation. Effect size in meta-analysis was employed as activity dataset for building quantitative structure-activity relationship (QSAR) models and accumulative effect sizes of 16 PAHs were used for validation of these models. Based on the genetic algorithm combined with partial least square regression, models for comprehensive dataset, Poaceae dataset, and Fabaceae dataset were built. The results showed that information indices, calculated as information content of molecules based on the calculation of equivalence classes from the molecular graph, were the most important molecular structural indices for QSAR models of rhizosphere effect on PAHs dissipation. The QSAR model, based on the molecular structure indices and effect size, has potential to be used in studying and predicting the rhizosphere effect of PAHs dissipation. - Effect size based on meta-analysis was used for building PAHs dissipation quantitative structure-activity relationship (QSAR) models.
Structure-based Markov random field model for representing evolutionary constraints on functional sites.

Science.gov (United States)

Jeong, Chan-Seok; Kim, Dongsup

2016-02-24

Elucidating the cooperative mechanism of interconnected residues is an important component toward understanding the biological function of a protein. Coevolution analysis has been developed to model the coevolutionary information reflecting structural and functional constraints. Recently, several methods have been developed based on a probabilistic graphical model called the Markov random field (MRF), which have led to significant improvements for coevolution analysis; however, thus far, the performance of these models has mainly been assessed by focusing on the aspect of protein structure. In this study, we built an MRF model whose graphical topology is determined by the residue proximity in the protein structure, and derived a novel positional coevolution estimate utilizing the node weight of the MRF model. This structure-based MRF method was evaluated for three data sets, each of which annotates catalytic site, allosteric site, and comprehensively determined functional site information. We demonstrate that the structure-based MRF architecture can encode the evolutionary information associated with biological function. Furthermore, we show that the node weight can more accurately represent positional coevolution information compared to the edge weight. Lastly, we demonstrate that the structure-based MRF model can be reliably built with only a few aligned sequences in linear time. The results show that adoption of a structure-based architecture could be an acceptable approximation for coevolution modeling with efficient computation complexity.
SA-Search: a web tool for protein structure mining based on a Structural Alphabet.

Science.gov (United States)

Guyon, Frédéric; Camproux, Anne-Claude; Hochez, Joëlle; Tufféry, Pierre

2004-07-01

SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search.
SMOG@ctbp: simplified deployment of structure-based models in GROMACS.

Science.gov (United States)

Noel, Jeffrey K; Whitford, Paul C; Sanbonmatsu, Karissa Y; Onuchic, José N

2010-07-01

Molecular dynamics simulations with coarse-grained and/or simplified Hamiltonians are an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Structure-based Hamiltonians, simplified models developed from the energy landscape theory of protein folding, have become a standard tool for investigating biomolecular dynamics. SMOG@ctbp is an effort to simplify the use of structure-based models. The purpose of the web server is two fold. First, the web tool simplifies the process of implementing a well-characterized structure-based model on a state-of-the-art, open source, molecular dynamics package, GROMACS. Second, the tutorial-like format helps speed the learning curve of those unfamiliar with molecular dynamics. A web tool user is able to upload any multi-chain biomolecular system consisting of standard RNA, DNA and amino acids in PDB format and receive as output all files necessary to implement the model in GROMACS. Both C(alpha) and all-atom versions of the model are available. SMOG@ctbp resides at http://smog.ucsd.edu.
Quantifying vegetation distribution and structure using high resolution drone-based structure-from-motion photogrammetry

Science.gov (United States)

Zhang, J.; Okin, G.

2017-12-01

Vegetation is one of the most important driving factors of different ecosystem processes in drylands. The structure of vegetation controls the spatial distribution of moisture and heat in the canopy and the surrounding area. Also, the structure of vegetation influences both airflow and boundary layer resistance above the land surface. Multispectral satellite remote sensing has been widely used to monitor vegetation coverage and its change; however, it can only capture 2D images, which do not contain the vertical information of vegetation. In situ observation uses different methods to measure the structure of vegetation, and their results are accurate; however, these methods are laborious and time-consuming, and susceptible to undersampling in spatial heterogeneity. Drylands are sparsely covered by short plants, which allows the drone fly at a relatively low height to obtain ultra-high resolution images. Structure-from-motion (SfM) is a photogrammetric method that was proved to produce 3D model based on 2D images. Drone-based remote sensing can obtain the multiangle images for one object, which can be used to constructed 3D models of vegetation in drylands. Using these images detected by the drone, the orthomosaics and digital surface model (DSM) can be built. In this study, the drone-based remote sensing was conducted in Jornada Basin, New Mexico, in the spring of 2016 and 2017, and three derived vegetation parameters (i.e., canopy size, bare soil gap size, and plant height) were compared with those obtained with field measurement. The correlation coefficient of canopy size, bare soil gap size, and plant height between drone images and field data are 0.91, 0.96, and 0.84, respectively. The two-year averaged root-mean-square error (RMSE) of canopy size, bare soil gap size, and plant height between drone images and field data are 0.61 m, 1.21 m, and 0.25 cm, respectively. The two-year averaged measure error (ME) of canopy size, bare soil gap size, and plant height
Weighted voting-based consensus clustering for chemical structure databases

Science.gov (United States)

Saeed, Faisal; Ahmed, Ali; Shamsir, Mohd Shahir; Salim, Naomie

2014-06-01

The cluster-based compound selection is used in the lead identification process of drug discovery and design. Many clustering methods have been used for chemical databases, but there is no clustering method that can obtain the best results under all circumstances. However, little attention has been focused on the use of combination methods for chemical structure clustering, which is known as consensus clustering. Recently, consensus clustering has been used in many areas including bioinformatics, machine learning and information theory. This process can improve the robustness, stability, consistency and novelty of clustering. For chemical databases, different consensus clustering methods have been used including the co-association matrix-based, graph-based, hypergraph-based and voting-based methods. In this paper, a weighted cumulative voting-based aggregation algorithm (W-CVAA) was developed. The MDL Drug Data Report (MDDR) benchmark chemical dataset was used in the experiments and represented by the AlogP and ECPF_4 descriptors. The results from the clustering methods were evaluated by the ability of the clustering to separate biologically active molecules in each cluster from inactive ones using different criteria, and the effectiveness of the consensus clustering was compared to that of Ward's method, which is the current standard clustering method in chemoinformatics. This study indicated that weighted voting-based consensus clustering can overcome the limitations of the existing voting-based methods and improve the effectiveness of combining multiple clusterings of chemical structures.

All carbon coaxial supercapacitors based on hollow carbon nanotube sleeve structure

International Nuclear Information System (INIS)

Zang, Xiaobei; Xu, Ruiqiao; Zhang, Yangyang; Zhang, Li; Wei, Jinquan; Wang, Kunlin; Zhu, Hongwei; Li, Xinming

2015-01-01

All carbon coaxial supercapacitors based on hollow carbon nanotube (CNT) sleeve structure are assembled and tested. The key advantage of the structure is that the inner core electrode is variable from CNT sleeve sponges, to CNT fibers, reduced graphene oxide fibers, and graphene woven fabrics. By changing core electrodes from sleeve sponges to CNT fibers, the electrochemical performance has been significantly enhanced. The capacitance based on sleeve sponge + CNT fiber double the capacitances of double-sleeve sponge supercapacitors thanks to reduction of the series and internal resistances. Besides, the coaxial sleeve structure possesses many other features, including high rate capacitance, long cycle life, and good flexibility. (paper)
Discovering new PI3Kα inhibitors with a strategy of combining ligand-based and structure-based virtual screening.

Science.gov (United States)

Yu, Miao; Gu, Qiong; Xu, Jun

2018-02-01

PI3Kα is a promising drug target for cancer chemotherapy. In this paper, we report a strategy of combing ligand-based and structure-based virtual screening to identify new PI3Kα inhibitors. First, naïve Bayesian (NB) learning models and a 3D-QSAR pharmacophore model were built based upon known PI3Kα inhibitors. Then, the SPECS library was screened by the best NB model. This resulted in virtual hits, which were validated by matching the structures against the pharmacophore models. The pharmacophore matched hits were then docked into PI3Kα crystal structures to form ligand-receptor complexes, which are further validated by the Glide-XP program to result in structural validated hits. The structural validated hits were examined by PI3Kα inhibitory assay. With this screening protocol, ten PI3Kα inhibitors with new scaffolds were discovered with IC 50 values ranging 0.44-31.25 μM. The binding affinities for the most active compounds 33 and 74 were estimated through molecular dynamics simulations and MM-PBSA analyses.
Discovering new PI3Kα inhibitors with a strategy of combining ligand-based and structure-based virtual screening

Science.gov (United States)

Yu, Miao; Gu, Qiong; Xu, Jun

2018-02-01

PI3Kα is a promising drug target for cancer chemotherapy. In this paper, we report a strategy of combing ligand-based and structure-based virtual screening to identify new PI3Kα inhibitors. First, naïve Bayesian (NB) learning models and a 3D-QSAR pharmacophore model were built based upon known PI3Kα inhibitors. Then, the SPECS library was screened by the best NB model. This resulted in virtual hits, which were validated by matching the structures against the pharmacophore models. The pharmacophore matched hits were then docked into PI3Kα crystal structures to form ligand-receptor complexes, which are further validated by the Glide-XP program to result in structural validated hits. The structural validated hits were examined by PI3Kα inhibitory assay. With this screening protocol, ten PI3Kα inhibitors with new scaffolds were discovered with IC50 values ranging 0.44-31.25 μM. The binding affinities for the most active compounds 33 and 74 were estimated through molecular dynamics simulations and MM-PBSA analyses.
Vibration-based health monitoring and model refinement of civil engineering structures

Energy Technology Data Exchange (ETDEWEB)

Farrar, C.R.; Doebling, S.W.

1997-10-01

Damage or fault detection, as determined by changes in the dynamic properties of structures, is a subject that has received considerable attention in the technical literature beginning approximately 30 years ago. The basic idea is that changes in the structure`s properties, primarily stiffness, will alter the dynamic properties of the structure such as resonant frequencies and mode shapes, and properties derived from these quantities such as modal-based flexibility. Recently, this technology has been investigated for applications to health monitoring of large civil engineering structures. This presentation will discuss such a study undertaken by engineers from New Mexico Sate University, Sandia National Laboratory and Los Alamos National Laboratory. Experimental modal analyses were performed in an undamaged interstate highway bridge and immediately after four successively more severe damage cases were inflicted in the main girder of the structure. Results of these tests provide insight into the abilities of modal-based damage ID methods to identify damage and the current limitations of this technology. Closely related topics that will be discussed are the use of modal properties to validate computer models of the structure, the use of these computer models in the damage detection process, and the general lack of experimental investigation of large civil engineering structures.
Yellow fluorescent protein phiYFPv (Phialidium): structure and structure-based mutagenesis

Energy Technology Data Exchange (ETDEWEB)

Pletneva, Nadya V.; Pletnev, Vladimir Z., E-mail: vzpletnev@gmail.com; Souslova, Ekaterina; Chudakov, Dmitry M. [Russian Academy of Sciences, Moscow (Russian Federation); Lukyanov, Sergey [Russian Academy of Sciences, Moscow (Russian Federation); Nizhny Novgorod State Medical Academy, Nizhny Novgorod (Russian Federation); Martynov, Vladimir I.; Arhipova, Svetlena; Artemyev, Igor [Russian Academy of Sciences, Moscow (Russian Federation); Wlodawer, Alexander [National Cancer Institute, Frederick, MD 21702 (United States); Dauter, Zbigniew [National Cancer Institute, Argonne, IL 60439 (United States); Pletnev, Sergei [National Cancer Institute, Argonne, IL 60439 (United States); SAIC-Frederick, 9700 South Cass Avenue, Argonne, IL 60439 (United States); Russian Academy of Sciences, Moscow (Russian Federation)

2013-06-01

The yellow fluorescent protein phiYFPv with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium. The yellow fluorescent protein phiYFPv (λ{sub em}{sup max} ≃ 537 nm) with improved folding has been developed from the spectrally identical wild-type phiYFP found in the marine jellyfish Phialidium. The latter fluorescent protein is one of only two known cases of naturally occurring proteins that exhibit emission spectra in the yellow–orange range (535–555 nm). Here, the crystal structure of phiYFPv has been determined at 2.05 Å resolution. The ‘yellow’ chromophore formed from the sequence triad Thr65-Tyr66-Gly67 adopts the bicyclic structure typical of fluorophores emitting in the green spectral range. It was demonstrated that perfect antiparallel π-stacking of chromophore Tyr66 and the proximal Tyr203, as well as Val205, facing the chromophore phenolic ring are chiefly responsible for the observed yellow emission of phiYFPv at 537 nm. Structure-based site-directed mutagenesis has been used to identify the key functional residues in the chromophore environment. The obtained results have been utilized to improve the properties of phiYFPv and its homologous monomeric biomarker tagYFP.
A Bayesian Network Based Adaptability Design of Product Structures for Function Evolution

Directory of Open Access Journals (Sweden)

Shaobo Li

2018-03-01

Full Text Available Structure adaptability design is critical for function evolution in product families, in which many structural and functional design factors are intertwined together with manufacturing cost, customer satisfaction, and final market sales. How to achieve a delicate balance among all of these factors to maximize the market performance of the product is too complicated to address based on traditional domain experts’ knowledge or some ad hoc heuristics. Here, we propose a quantitative product evolution design model that is based on Bayesian networks to model the dynamic relationship between customer needs and product structure design. In our model, all of the structural or functional features along with customer satisfaction, manufacturing cost, sale price, market sales, and indirect factors are modeled as random variables denoted as nodes in the Bayesian networks. The structure of the Bayesian model is then determined based on the historical data, which captures the dynamic sophisticated relationship of customer demands of a product, structural design, and market performance. Application of our approach to an electric toothbrush product family evolution design problem shows that our model allows for designers to interrogate with the model and obtain theoretical and decision support for dynamic product feature design process.
Rotational stellar structures based on the Lagrangian variational principle

International Nuclear Information System (INIS)

Yasutake, Nobutoshi; Fujisawa, Kotaro; Yamada, Shoichi

2017-01-01

A new method for multi-dimensional stellar structures is proposed in this study. As for stellar evolution calculations, the Heney method is the defacto standard now, but basically assumed to be spherical symmetric. It is one of the difficulties for deformed stellar-evolution calculations to trace the potentially complex movements of each fluid element. On the other hand, our new method is very suitable to follow such movements, since it is based on the Lagrange coordinate. This scheme is also based on the variational principle, which is adopted to the studies for the pasta structures inside of neutron stars. Our scheme could be a major break through for evolution calculations of any types of deformed stars: proto-planets, proto-stars, and proto-neutron stars, etc. (paper)
Rotational stellar structures based on the Lagrangian variational principle

Science.gov (United States)

Yasutake, Nobutoshi; Fujisawa, Kotaro; Yamada, Shoichi

2017-06-01

A new method for multi-dimensional stellar structures is proposed in this study. As for stellar evolution calculations, the Heney method is the defacto standard now, but basically assumed to be spherical symmetric. It is one of the difficulties for deformed stellar-evolution calculations to trace the potentially complex movements of each fluid element. On the other hand, our new method is very suitable to follow such movements, since it is based on the Lagrange coordinate. This scheme is also based on the variational principle, which is adopted to the studies for the pasta structures inside of neutron stars. Our scheme could be a major break through for evolution calculations of any types of deformed stars: proto-planets, proto-stars, and proto-neutron stars, etc.
Structure-Based Virtual Screening of Commercially Available Compound Libraries.

Science.gov (United States)

Kireev, Dmitri

2016-01-01

Virtual screening (VS) is an efficient hit-finding tool. Its distinctive strength is that it allows one to screen compound libraries that are not available in the lab. Moreover, structure-based (SB) VS also enables an understanding of how the hit compounds bind the protein target, thus laying ground work for the rational hit-to-lead progression. SBVS requires a very limited experimental effort and is particularly well suited for academic labs and small biotech companies that, unlike pharmaceutical companies, do not have physical access to quality small-molecule libraries. Here, we describe SBVS of commercial compound libraries for Mer kinase inhibitors. The screening protocol relies on the docking algorithm Glide complemented by a post-docking filter based on structural protein-ligand interaction fingerprints (SPLIF).
Tuneable complementary metamaterial structures based on graphene for single and multiple transparency windows.

Science.gov (United States)

Ding, Jun; Arigong, Bayaner; Ren, Han; Zhou, Mi; Shao, Jin; Lu, Meng; Chai, Yang; Lin, Yuankun; Zhang, Hualiang

2014-08-22

Novel graphene-based tunable plasmonic metamaterials featuring single and multiple transparency windows are numerically studied in this paper. The designed structures consist of a graphene layer perforated with quadrupole slot structures and dolmen-like slot structures printed on a substrate. Specifically, the graphene-based quadrupole slot structure can realize a single transparency window, which is achieved without breaking the structure symmetry. Further investigations have shown that the single transparency window in the proposed quadrupole slot structure is more likely originated from the quantum effect of Autler-Townes splitting. Then, by introducing a dipole slot to the quadrupole slot structure to form the dolmen-like slot structure, an additional transmission dip could occur in the transmission spectrum, thus, a multiple-transparency-window system can be achieved (for the first time for graphene-based devices). More importantly, the transparency windows for both the quadrupole slot and the dolmen-like slot structures can be dynamically controlled over a broad frequency range by varying the Fermi energy levels of the graphene layer (through electrostatic gating). The proposed slot metamaterial structures with tunable single and multiple transparency windows could find potential applications in many areas such as multiple-wavelength slow-light devices, active plasmonic switching, and optical sensing.
Structural reliability analysis based on the cokriging technique

International Nuclear Information System (INIS)

Zhao Wei; Wang Wei; Dai Hongzhe; Xue Guofeng

2010-01-01

Approximation methods are widely used in structural reliability analysis because they are simple to create and provide explicit functional relationships between the responses and variables in stead of the implicit limit state function. Recently, the kriging method which is a semi-parameter interpolation technique that can be used for deterministic optimization and structural reliability has gained popularity. However, to fully exploit the kriging method, especially in high-dimensional problems, a large number of sample points should be generated to fill the design space and this can be very expensive and even impractical in practical engineering analysis. Therefore, in this paper, a new method-the cokriging method, which is an extension of kriging, is proposed to calculate the structural reliability. cokriging approximation incorporates secondary information such as the values of the gradients of the function being approximated. This paper explores the use of the cokriging method for structural reliability problems by comparing it with the Kriging method based on some numerical examples. The results indicate that the cokriging procedure described in this work can generate approximation models to improve on the accuracy and efficiency for structural reliability problems and is a viable alternative to the kriging.
A Modified Fatigue Damage Model for High-Cycle Fatigue Life Prediction

Directory of Open Access Journals (Sweden)

Meng Wang

2016-01-01

Full Text Available Based on the assumption of quasibrittle failure under high-cycle fatigue for the metal material, the damage constitutive equation and the modified damage evolution equation are obtained with continuum damage mechanics. Then, finite element method (FEM is used to describe the failure process of metal material. The increment of specimen’s life and damage state can be researched using damage mechanics-FEM. Finally, the lifetime of the specimen is got at the given stress level. The damage mechanics-FEM is inserted into ABAQUS with subroutine USDFLD and the Python language is used to simulate the fatigue process of titanium alloy specimens. The simulation results have a good agreement with the testing results under constant amplitude loading, which proves the accuracy of the method.
Efficient identification of critical residues based only on protein structure by network analysis.

Directory of Open Access Journals (Sweden)

Michael P Cusack

2007-05-01

Full Text Available Despite the increasing number of published protein structures, and the fact that each protein's function relies on its three-dimensional structure, there is limited access to automatic programs used for the identification of critical residues from the protein structure, compared with those based on protein sequence. Here we present a new algorithm based on network analysis applied exclusively on protein structures to identify critical residues. Our results show that this method identifies critical residues for protein function with high reliability and improves automatic sequence-based approaches and previous network-based approaches. The reliability of the method depends on the conformational diversity screened for the protein of interest. We have designed a web site to give access to this software at http://bis.ifc.unam.mx/jamming/. In summary, a new method is presented that relates critical residues for protein function with the most traversed residues in networks derived from protein structures. A unique feature of the method is the inclusion of the conformational diversity of proteins in the prediction, thus reproducing a basic feature of the structure/function relationship of proteins.
Alcohol sensor based on u-bent hetero-structured fiber optic

Science.gov (United States)

Patrialova, Sefi N.; Hatta, Agus M.; Sekartedjo, Sekartedjo

2016-11-01

A sensor based on a fiber optic hetero-structure to determine the concentration of alcohol has been proposed. The structure of the sensing probe in this research is a singlemode-multimode-singlemode (SMS) which bent into Ushaped and soon called as SMS u-bent. The SMS structure was chosen to get a higher sensitivity. This research utilizes the principle of multimode interference and evanescent field by modifying the cladding with various alcohol concentration. Testing of the sensor's performance has been done by measuring the sensor's power output response to the length of the SMS fiber optic, bending diameter, and alcohol concentration. Based on the experiment result, the ubent SMS fiber optic with 50 mm bending diameter and 63 mm MMF lenght has the highest sensitivity, 3.87 dB/% and the minimum resolution, 0.26 x 10-3 %.
Optimal design of base isolation and energy dissipation system for nuclear power plant structures

International Nuclear Information System (INIS)

Zhou Fulin

1991-01-01

This paper suggests the method of optimal design of base isolation and energy dissipation system for earthquake resistant nuclear power plant structures. This method is based on dynamic analysis, shaking table tests for a 1/4 scale model, and a great number of low cycle fatigue failure tests for energy dissipating elements. A set of calculation formulas for optimal design of structures with base isolation and energy dissipation system were introduced, which are able to be used in engineering design for earthquake resistant nuclear power plant structures or other kinds of structures. (author)
Understanding of Android-Based Robotic and Game Structure

Science.gov (United States)

Phongtraychack, A.; Syryamkin, V.

2018-05-01

The development of an android with impressive lifelike appearance and behavior has been a long-standing goal in robotics and a new and exciting approach of smartphone-based robotics for research and education. Recent years have been progressive for many technologies, which allowed creating such androids. There are different examples including the autonomous Erica android system capable of conversational interaction and speech synthesis technologies. The behavior of Android-based robot could be running on the phone as the robot performed a task outdoors. In this paper, we present an overview and understanding of the platform of Android-based robotic and game structure for research and education.
Fragment-based quantitative structure-activity relationship (FB-QSAR) for fragment-based drug design.

Science.gov (United States)

Du, Qi-Shi; Huang, Ri-Bo; Wei, Yu-Tuo; Pang, Zong-Wen; Du, Li-Qin; Chou, Kuo-Chen

2009-01-30

In cooperation with the fragment-based design a new drug design method, the so-called "fragment-based quantitative structure-activity relationship" (FB-QSAR) is proposed. The essence of the new method is that the molecular framework in a family of drug candidates are divided into several fragments according to their substitutes being investigated. The bioactivities of molecules are correlated with the physicochemical properties of the molecular fragments through two sets of coefficients in the linear free energy equations. One coefficient set is for the physicochemical properties and the other for the weight factors of the molecular fragments. Meanwhile, an iterative double least square (IDLS) technique is developed to solve the two sets of coefficients in a training data set alternately and iteratively. The IDLS technique is a feedback procedure with machine learning ability. The standard Two-dimensional quantitative structure-activity relationship (2D-QSAR) is a special case, in the FB-QSAR, when the whole molecule is treated as one entity. The FB-QSAR approach can remarkably enhance the predictive power and provide more structural insights into rational drug design. As an example, the FB-QSAR is applied to build a predictive model of neuraminidase inhibitors for drug development against H5N1 influenza virus. (c) 2008 Wiley Periodicals, Inc.
CRBRP structural and thermal margin beyond the design base

International Nuclear Information System (INIS)

Strawbridge, L.E.

1979-01-01

Prudent margins beyond the design base have been included in the design of Clinch River Breeder Reactor Plant to further reduce the risk to the public from highly improbable occurrences. These margins include Structural Margin Beyond the Design Base to address the energetics aspects and Thermal Margin Beyond the Design Base to address the longer term thermal and radiological consequences. The assessments that led to the specification of these margins are described, along with the experimental support for those assessments. 8 refs
Structured Light-Based 3D Reconstruction System for Plants

OpenAIRE

Nguyen, Thuy Tuong; Slaughter, David C.; Max, Nelson; Maloof, Julin N.; Sinha, Neelima

2015-01-01

Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants. This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud regi...
Qrator: A web-based curation tool for glycan structures

Science.gov (United States)

Eavenson, Matthew; Kochut, Krys J; Miller, John A; Ranzinger, René; Tiemeyer, Michael; Aoki, Kazuhiro; York, William S

2015-01-01

Most currently available glycan structure databases use their own proprietary structure representation schema and contain numerous annotation errors. These cause problems when glycan databases are used for the annotation or mining of data generated in the laboratory. Due to the complexity of glycan structures, curating these databases is often a tedious and labor-intensive process. However, rigorously validating glycan structures can be made easier with a curation workflow that incorporates a structure-matching algorithm that compares candidate glycans to a canonical tree that embodies structural features consistent with established mechanisms for the biosynthesis of a particular class of glycans. To this end, we have implemented Qrator, a web-based application that uses a combination of external literature and database references, user annotations and canonical trees to assist and guide researchers in making informed decisions while curating glycans. Using this application, we have started the curation of large numbers of N-glycans, O-glycans and glycosphingolipids. Our curation workflow allows creating and extending canonical trees for these classes of glycans, which have subsequently been used to improve the curation workflow. PMID:25165068

Parametric and Non-Parametric Vibration-Based Structural Identification Under Earthquake Excitation

Science.gov (United States)

Pentaris, Fragkiskos P.; Fouskitakis, George N.

2014-05-01

The problem of modal identification in civil structures is of crucial importance, and thus has been receiving increasing attention in recent years. Vibration-based methods are quite promising as they are capable of identifying the structure's global characteristics, they are relatively easy to implement and they tend to be time effective and less expensive than most alternatives [1]. This paper focuses on the off-line structural/modal identification of civil (concrete) structures subjected to low-level earthquake excitations, under which, they remain within their linear operating regime. Earthquakes and their details are recorded and provided by the seismological network of Crete [2], which 'monitors' the broad region of south Hellenic arc, an active seismic region which functions as a natural laboratory for earthquake engineering of this kind. A sufficient number of seismic events are analyzed in order to reveal the modal characteristics of the structures under study, that consist of the two concrete buildings of the School of Applied Sciences, Technological Education Institute of Crete, located in Chania, Crete, Hellas. Both buildings are equipped with high-sensitivity and accuracy seismographs - providing acceleration measurements - established at the basement (structure's foundation) presently considered as the ground's acceleration (excitation) and at all levels (ground floor, 1st floor, 2nd floor and terrace). Further details regarding the instrumentation setup and data acquisition may be found in [3]. The present study invokes stochastic, both non-parametric (frequency-based) and parametric methods for structural/modal identification (natural frequencies and/or damping ratios). Non-parametric methods include Welch-based spectrum and Frequency response Function (FrF) estimation, while parametric methods, include AutoRegressive (AR), AutoRegressive with eXogeneous input (ARX) and Autoregressive Moving-Average with eXogeneous input (ARMAX) models[4, 5
Interactive Reliability-Based Optimization of Structural Systems

DEFF Research Database (Denmark)

Pedersen, Claus

In order to introduce the basic concepts within the field of reliability-based structural optimization problems, this chapter is devoted to a brief outline of the basic theories. Therefore, this chapter is of a more formal nature and used as a basis for the remaining parts of the thesis. In section...... 2.2 a general non-linear optimization problem and corresponding terminology are presented whereupon optimality conditions and the standard form of an iterative optimization algorithm are outlined. Subsequently, the special properties and characteristics concerning structural optimization problems...... are treated in section 2.3. With respect to the reliability evalutation, the basic theory behind a reliability analysis and estimation of probability of failure by the First-Order Reliability Method (FORM) and the iterative Rackwitz-Fiessler (RF) algorithm are considered in section 2.5 in which...
Reliability-Based Optimal Design for Very Large Floating Structure

Institute of Scientific and Technical Information of China (English)

ZHANG Shu-hua(张淑华); FUJIKUBO Masahiko

2003-01-01

Costs and losses induced by possible future extreme environmental conditions and difficulties in repairing post-yielding damage strongly suggest the need for proper consideration in design rather than just life loss prevention. This can be addressed through the development of design methodology that balances the initial cost of the very large floating structure (VLFS) against the expected potential losses resulting from future extreme wave-induced structural damage. Here, the development of a methodology for determining optimal, cost-effective design will be presented and applied to a VLFS located in the Tokyo bay. Optimal design criteria are determined based on the total expected life-cycle cost and acceptable damage probability and curvature of the structure, and a set of sizes of the structure are obtained. The methodology and applications require expressions of the initial cost and the expected life-cycle damage cost as functions of the optimal design variables. This study includes the methodology, total life-cycle cost function, structural damage modeling, and reliability analysis.
Simulations for irradiation of silicon-based structures

International Nuclear Information System (INIS)

Sagatova, A.; Pavlovic, M.; Sedlackova, K.; Necas, V.; Hybler, P.; Zatko, B.

2013-01-01

The software ModePEB for modelling of electron beam processing in multilayer flat objects was shown to be a very useful tool for optimization of the irradiation of silicon based structures. Except its significant help in setting-up the accelerator parameters corresponding to a desired dose, its proven reliability and consistency with the measured data makes the ModePEB an inevitable instrument for design and optimization of electron irradiation experiments. (authors)
Probability based high temperature engineering creep and structural fire resistance

CERN Document Server

Razdolsky, Leo

2017-01-01

This volume on structural fire resistance is for aerospace, structural, and fire prevention engineers; architects, and educators. It bridges the gap between prescriptive- and performance-based methods and simplifies very complex and comprehensive computer analyses to the point that the structural fire resistance and high temperature creep deformations will have a simple, approximate analytical expression that can be used in structural analysis and design. The book emphasizes methods of the theory of engineering creep (stress-strain diagrams) and mathematical operations quite distinct from those of solid mechanics absent high-temperature creep deformations, in particular the classical theory of elasticity and structural engineering. Dr. Razdolsky’s previous books focused on methods of computing the ultimate structural design load to the different fire scenarios. The current work is devoted to the computing of the estimated ultimate resistance of the structure taking into account the effect of high temperatur...
Structural and photoluminescence properties of Si-based nanosheet bundles rooted on Si substrates

Science.gov (United States)

Yuan, Peiling; Tamaki, Ryo; Kusazaki, Shinya; Atsumi, Nanae; Saito, Yuya; Kumazawa, Yuki; Ahsan, Nazmul; Okada, Yoshitaka; Ishida, Akihiro; Tatsuoka, Hirokazu

2018-04-01

Si-based nanosheet bundles were synthesized by the extraction of Ca atoms from CaSi2 microwalls grown on Si substrates by inositol hexakisphosphate solution or thermal treatment in FeCl2 vapor. The structural and photoluminescence properties of the Si-based nanosheet bundles were examined. The photoluminescence emissions in the visible region were clearly observed, and the temperature and excitation intensity dependences of the emissions were characterized. The observed Si-based nanosheets consist of thin Si layers, and a superlattice-like layered structural model is proposed to describe the Si-based nanosheet bundle structures and their photoluminescence property. The photoluminescence property of the nanosheets significantly depends on their treatment process. The luminescence mechanism of the nanosheets was discussed.
An atlas-based multimodal registration method for 2D images with discrepancy structures.

Science.gov (United States)

Lv, Wenchao; Chen, Houjin; Peng, Yahui; Li, Yanfeng; Li, Jupeng

2018-06-04

An atlas-based multimodal registration method for 2-dimension images with discrepancy structures was proposed in this paper. Atlas was utilized for complementing the discrepancy structure information in multimodal medical images. The scheme includes three steps: floating image to atlas registration, atlas to reference image registration, and field-based deformation. To evaluate the performance, a frame model, a brain model, and clinical images were employed in registration experiments. We measured the registration performance by the squared sum of intensity differences. Results indicate that this method is robust and performs better than the direct registration for multimodal images with discrepancy structures. We conclude that the proposed method is suitable for multimodal images with discrepancy structures. Graphical Abstract An Atlas-based multimodal registration method schematic diagram.
Automated Glioblastoma Segmentation Based on a Multiparametric Structured Unsupervised Classification

Science.gov (United States)

Juan-Albarracín, Javier; Fuster-Garcia, Elies; Manjón, José V.; Robles, Montserrat; Aparici, F.; Martí-Bonmatí, L.; García-Gómez, Juan M.

2015-01-01

Automatic brain tumour segmentation has become a key component for the future of brain tumour treatment. Currently, most of brain tumour segmentation approaches arise from the supervised learning standpoint, which requires a labelled training dataset from which to infer the models of the classes. The performance of these models is directly determined by the size and quality of the training corpus, whose retrieval becomes a tedious and time-consuming task. On the other hand, unsupervised approaches avoid these limitations but often do not reach comparable results than the supervised methods. In this sense, we propose an automated unsupervised method for brain tumour segmentation based on anatomical Magnetic Resonance (MR) images. Four unsupervised classification algorithms, grouped by their structured or non-structured condition, were evaluated within our pipeline. Considering the non-structured algorithms, we evaluated K-means, Fuzzy K-means and Gaussian Mixture Model (GMM), whereas as structured classification algorithms we evaluated Gaussian Hidden Markov Random Field (GHMRF). An automated postprocess based on a statistical approach supported by tissue probability maps is proposed to automatically identify the tumour classes after the segmentations. We evaluated our brain tumour segmentation method with the public BRAin Tumor Segmentation (BRATS) 2013 Test and Leaderboard datasets. Our approach based on the GMM model improves the results obtained by most of the supervised methods evaluated with the Leaderboard set and reaches the second position in the ranking. Our variant based on the GHMRF achieves the first position in the Test ranking of the unsupervised approaches and the seventh position in the general Test ranking, which confirms the method as a viable alternative for brain tumour segmentation. PMID:25978453
Structural health monitoring methodology for aircraft condition-based maintenance

Science.gov (United States)

Saniger, Jordi; Reithler, Livier; Guedra-Degeorges, Didier; Takeda, Nobuo; Dupuis, Jean Pierre

2001-06-01

Reducing maintenance costs while keeping a constant level of safety is a major issue for Air Forces and airlines. The long term perspective is to implement condition based maintenance to guarantee a constant safety level while decreasing maintenance costs. On this purpose, the development of a generalized Structural Health Monitoring System (SHMS) is needed. The objective of such a system is to localize the damages and to assess their severity, with enough accuracy to allow low cost corrective actions. The present paper describes a SHMS based on acoustic emission technology. This choice was driven by its reliability and wide use in the aerospace industry. The described SHMS uses a new learning methodology which relies on the generation of artificial acoustic emission events on the structure and an acoustic emission sensor network. The calibrated acoustic emission events picked up by the sensors constitute the knowledge set that the system relies on. With this methodology, the anisotropy of composite structures is taken into account, thus avoiding the major cause of errors of classical localization methods. Moreover, it is adaptive to different structures as it does not rely on any particular model but on measured data. The acquired data is processed and the event's location and corrected amplitude are computed. The methodology has been demonstrated and experimental tests on elementary samples presented a degree of accuracy of 1cm.
Electric field responsive origami structures using electrostriction-based active materials

Science.gov (United States)

Ahmed, Saad; Arrojado, Erika; Sigamani, Nirmal; Ounaies, Zoubeida

2015-04-01

The objective of origami engineering is to combine origami principles with advanced materials to yield active origami shapes, which fold and unfold in response to external stimuli. We are investigating the use of P(VDF-TrFE-CTFE), a relaxor ferroelectric terpolymer, to realize origami-inspired folding and unfolding of structures and to actuate so-called action origami structures. To accomplish these two objectives, we have explored different approaches to the P(VDF-TrFECTFE) polymer actuator construction, ranging from unimorph to multilayered stacks. Electromechanical characterization of the terpolymer-based actuators is conducted with a focus on free strain, force-displacement and blocked force. Moreover dynamic thickness strains of P(VDF-TrFE-CTFE) terpolymer at different frequencies ranging from 0.1Hz to 10Hz is also measured. Quantifying the performance of terpolymer-based actuators is important to the design of action origami structures. Following these studies, action origami prototypes based on catapult, flapping butterfly wings and barking fox are actuated and characterization of these prototypes are conducted by studying impact of various parameters such as electric field magnitude and frequency, number of active layers, and actuator dimensions.
Task-oriented structural design of manipulators based on operability evaluation

International Nuclear Information System (INIS)

Kotosaka, Shin-ya; Asama, Hajime; Takata, Shozo; Hiraoka, Hiroyuki; Kohda, Takehisa; Matsumoto, Akihiro; Endo, Isao.

1995-01-01

In this paper, a new method for designing the structure of manipulators based on evaluation of their adaptability to tasks is proposed. In the method, task directions are classified into three kinds of direction; operational direction, constrained direction and free direction. On each direction, condition of constraints by task environment is represented. The tasks are represented by a set of direction and condition of constraints. A new criterion, operability, is defined to quantify adaptability of manipulator to tasks, taking account of mobility in operational directions and immobility in constrained directions. The mobility and immobility is calculated based on the Jacobian matrix of manipulator. The operability evaluation method is implemented, and applied to structural design of manipulators, in which link parameters are optimized by the genetic algorithm. This system can derive suitable structure of manipulator to various tasks. The effectiveness of the system is shown concerning examples of welding tasks. (author)
Metamorphoses of electronic structure of FeSe-based superconductors (Review Article)

International Nuclear Information System (INIS)

Pustovit, Yu.V.; Kordyuk, A.A.

2016-01-01

The electronic structure of FeSe, the simplest iron-based superconductor (Fe-SC), conceals a potential of dramatic increase of Tc that realizes under pressure or in a single layer film. This is also the system where nematicity, the phenomenon of a keen current interest, is most easy to study since it is not accompanied by the antiferromagnetic transition like in all other Fe-SC. Here we overview recent experimental data on electronic structure of FeSe-based superconductors: isovalently doped crystals, intercalates, and single layer films, trying to clarify its topology and possible relation of this topology to superconductivity. We argue that the marked differences between the experimental and calculated band structures for all FeSe compounds can be described by a hoping selective renormalization model for a spin/orbital correlated state that may naturally ex-plain both the evolution of the band structure with temperature and nematicity.
Protein structure based prediction of catalytic residues.

Science.gov (United States)

Fajardo, J Eduardo; Fiser, Andras

2013-02-22

Worldwide structural genomics projects continue to release new protein structures at an unprecedented pace, so far nearly 6000, but only about 60% of these proteins have any sort of functional annotation. We explored a range of features that can be used for the prediction of functional residues given a known three-dimensional structure. These features include various centrality measures of nodes in graphs of interacting residues: closeness, betweenness and page-rank centrality. We also analyzed the distance of functional amino acids to the general center of mass (GCM) of the structure, relative solvent accessibility (RSA), and the use of relative entropy as a measure of sequence conservation. From the selected features, neural networks were trained to identify catalytic residues. We found that using distance to the GCM together with amino acid type provide a good discriminant function, when combined independently with sequence conservation. Using an independent test set of 29 annotated protein structures, the method returned 411 of the initial 9262 residues as the most likely to be involved in function. The output 411 residues contain 70 of the annotated 111 catalytic residues. This represents an approximately 14-fold enrichment of catalytic residues on the entire input set (corresponding to a sensitivity of 63% and a precision of 17%), a performance competitive with that of other state-of-the-art methods. We found that several of the graph based measures utilize the same underlying feature of protein structures, which can be simply and more effectively captured with the distance to GCM definition. This also has the added the advantage of simplicity and easy implementation. Meanwhile sequence conservation remains by far the most influential feature in identifying functional residues. We also found that due the rapid changes in size and composition of sequence databases, conservation calculations must be recalibrated for specific reference databases.
Hierarchical structure for audio-video based semantic classification of sports video sequences

Science.gov (United States)

Kolekar, M. H.; Sengupta, S.

2005-07-01

A hierarchical structure for sports event classification based on audio and video content analysis is proposed in this paper. Compared to the event classifications in other games, those of cricket are very challenging and yet unexplored. We have successfully solved cricket video classification problem using a six level hierarchical structure. The first level performs event detection based on audio energy and Zero Crossing Rate (ZCR) of short-time audio signal. In the subsequent levels, we classify the events based on video features using a Hidden Markov Model implemented through Dynamic Programming (HMM-DP) using color or motion as a likelihood function. For some of the game-specific decisions, a rule-based classification is also performed. Our proposed hierarchical structure can easily be applied to any other sports. Our results are very promising and we have moved a step forward towards addressing semantic classification problems in general.
Cyclic fatigue of a high-strength corrosion-resistant sheet TRIP steel

Science.gov (United States)

Terent'ev, V. F.; Alekseeva, L. E.; Korableva, S. A.; Prosvirnin, D. V.; Pankova, M. N.; Filippov, G. A.

2014-04-01

The mechanical properties of 0.3- and 0.8-mm-thick high-strength corrosion-resistant TRIP steel having various levels of strength properties are studied during static and cyclic loading in the high-cycle fatigue range. The fatigue fracture surface is analyzed by fractography, and the obtained results demonstrate ductile and quasi-brittle fracture mechanisms of this steel depending on the strength properties of the steel and the content of deformation martensite in it.
Pipeline Structural Damage Detection Using Self-Sensing Technology and PNN-Based Pattern Recognition

International Nuclear Information System (INIS)

Lee, Chang Gil; Park, Woong Ki; Park, Seung Hee

2011-01-01

In a structure, damage can occur at several scales from micro-cracking to corrosion or loose bolts. This makes the identification of damage difficult with one mode of sensing. Hence, a multi-mode actuated sensing system is proposed based on a self-sensing circuit using a piezoelectric sensor. In the self sensing-based multi-mode actuated sensing, one mode provides a wide frequency-band structural response from the self-sensed impedance measurement and the other mode provides a specific frequency-induced structural wavelet response from the self-sensed guided wave measurement. In this study, an experimental study on the pipeline system is carried out to verify the effectiveness and the robustness of the proposed structural health monitoring approach. Different types of structural damage are artificially inflicted on the pipeline system. To classify the multiple types of structural damage, a supervised learning-based statistical pattern recognition is implemented by composing a two-dimensional space using the damage indices extracted from the impedance and guided wave features. For more systematic damage classification, several control parameters to determine an optimal decision boundary for the supervised learning-based pattern recognition are optimized. Finally, further research issues will be discussed for real-world implementation of the proposed approach
In Pursuit of Natural Logics for Ontology-Structured Knowledge Bases

DEFF Research Database (Denmark)

Nilsson, Jørgen Fischer

2015-01-01

We argue for adopting a form of natural logic for ontology-structured knowledge bases with complex sentences. This serves to ease reading of knowledge base for domain experts and to make reasoning and querying and path-finding more comprehensible. We explain natural logic as a development from tr...
At technique for visualizing electrostatic fields based on their topological structures

International Nuclear Information System (INIS)

Handa, Susumu

2004-01-01

In molecular science, visualization techniques based on computer graphics are now well established as a tool to interpret simulation results, since molecules are complicated in the structures and mutual interactions. As a probe to study such molecular interactions, electrostatic fields are considered to be useful. However, since they are given as 3D vector fields having complicated distributions, conventional drawing techniques are inadequate. In this article, a new approach based on topological structures in vector fields is presented to visualize the electrostatic fields of molecules. The scheme is to select regions of interest only from the topological structures of the fields. An example in applications to chemical reactions of an amino acid complex is presented to show how the scheme is used. (author)
Structure formation in fibrous materials based on poly-3-hydroxybutyrate for traumatology

Science.gov (United States)

Olkhov, A. A.; Sklyanchuk, E. D.; Staroverova, O. V.; Abbasov, T. A.; Guryev, V. V.; Akatov, V. S.; Fadeyeva, I. S.; Fesenko, N. I.; Filatov, Yu. N.; Iordanskii, A. L.

2015-10-01

The paper reviews the structure formation of fibrous materials based on poly-3-hydroxybutyrate depending on parameters of electrospinning and characteristics of polymer solution. Fiber structure was studied by DSC, ESR and SEM. The molecular weight affects the diameter and uniformity of the fiber. An electromechanical impact leads to an orientation of crystalline structure in the fiber. The design of an artificial bioresorbable implant based on nano- and microfibers of poly-3-hydroxybutyrate is created. Dynamics of growth of mesenchymal stem cells on poly-3-hydroxybutyrate scaffolds is studied. Successful field tests of implants of the Achilles tendon in Wistar rats are conducted.
Structure modulates similarity-based interference in sluicing: An eye tracking study.

Directory of Open Access Journals (Sweden)

Jesse A. Harris

2015-12-01

Full Text Available In cue-based content-addressable approaches to memory, a target and its competitors are retrieved in parallel from memory via a fast, associative cue-matching procedure under a severely limited focus of attention. Such a parallel matching procedure could in principle ignore the serial order or hierarchical structure characteristic of linguistic relations. I present an eye tracking while reading experiment that investigates whether the sentential position of a potential antecedent modulates the strength of similarity-based interference, a well-studied effect in which increased similarity in features between a target and its competitors results in slower and less accurate retrieval overall. The manipulation trades on an independently established Locality bias in sluiced structures to associate a wh-remnant (which ones in clausal ellipsis with the most local correlate (some wines, as in The tourists enjoyed some wines, but I don’t know which ones. The findings generally support cue-based parsing models of sentence processing that are subject to similarity-based interference in retrieval, and provide additional support to the growing body of evidence that retrieval is sensitive to both the structural position of a target antecedent and its competitors, and the specificity of retrieval cues.

Structural and spectral comparisons between isomeric benzisothiazole and benzothiazole based aromatic heterocyclic dyes

Science.gov (United States)

Wang, Yin-Ge; Wang, Yue-Hua; Tao, Tao; Qian, Hui-Fen; Huang, Wei

2015-09-01

A pair of isomeric heterocyclic compounds, namely 3-amino-5-nitro-[2,1]-benzisothiazole and 2-amino-6-nitrobenzothiazole, are used as the diazonium components to couple with two N-substituted 4-aminobenzene derivatives. As a result, two pairs of isomeric aromatic heterocyclic azo dyes have been produced and they are structurally and spectrally characterized and compared including single-crystal structures, electronic spectra, solvatochromism and reversible acid-base discoloration, thermal stability and theoretically calculations. It is concluded that both benzisothiazole and benzothiazole based dyes show planar molecular structures and offset π-π stacking interactions, solvatochromism and reversible acid-base discoloration. Furthermore, benzisothiazole based aromatic heterocyclic dyes exhibit higher thermal stability, larger solvatochromic effects and maximum absorption wavelengths than corresponding benzothiazole based ones, which can be explained successfully by the differences of their calculated isomerization energy, dipole moment and molecular band gaps.
A Study on the Data Compression Technology-Based Intelligent Data Acquisition (IDAQ System for Structural Health Monitoring of Civil Structures

Directory of Open Access Journals (Sweden)

Gwanghee Heo

2017-07-01

Full Text Available In this paper, a data compression technology-based intelligent data acquisition (IDAQ system was developed for structural health monitoring of civil structures, and its validity was tested using random signals (El-Centro seismic waveform. The IDAQ system was structured to include a high-performance CPU with large dynamic memory for multi-input and output in a radio frequency (RF manner. In addition, the embedded software technology (EST has been applied to it to implement diverse logics needed in the process of acquiring, processing and transmitting data. In order to utilize IDAQ system for the structural health monitoring of civil structures, this study developed an artificial filter bank by which structural dynamic responses (acceleration were efficiently acquired, and also optimized it on the random El-Centro seismic waveform. All techniques developed in this study have been embedded to our system. The data compression technology-based IDAQ system was proven valid in acquiring valid signals in a compressed size.
Frequency Response Function Based Damage Identification for Aerospace Structures

Science.gov (United States)

Oliver, Joseph Acton

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

Science.gov (United States)

Korovin, M. S.; Fomenko, A. N.

2017-12-01

Nowadays, the use of hierarchically built structures in biology and medicine arouses much interest. The aim of this work is to review and summarize the available literature data about hierarchically organized structures in biomedical application. Nanoparticles can serve as an example of such structures. Medicine holds a special place among various application methods of similar systems. Special attention is paid to inorganic nanoparticles based on different metal oxides and hydroxides, such as iron, zinc, copper, and aluminum. Our investigations show that low-dimensional nanostructures based on aluminum oxides and hydroxides have an inhibitory effect on tumor cells and possess an antimicrobial activity. At the same time, it is obvious that the large-scale use of nanoparticles by humans needs to thoroughly study their properties. Special attention should be paid to the study of nanoparticle interaction with living biological objects. The numerous data show that there is no clear understanding of interaction mechanisms between nanoparticles and various cell types.
Nanodiamond-Based Composite Structures for Biomedical Imaging and Drug Delivery.

Science.gov (United States)

Rosenholm, Jessica M; Vlasov, Igor I; Burikov, Sergey A; Dolenko, Tatiana A; Shenderova, Olga A

2015-02-01

Nanodiamond particles are widely recognized candidates for biomedical applications due to their excellent biocompatibility, bright photoluminescence based on color centers and outstanding photostability. Recently, more complex architectures with a nanodiamond core and an external shell or nanostructure which provides synergistic benefits have been developed, and their feasibility for biomedical applications has been demonstrated. This review is aimed at summarizing recent achievements in the fabrication and functional demonstrations of nanodiamond-based composite structures, along with critical considerations that should be taken into account in the design of such structures from a biomedical point of view. A particular focus of the review is core/shell structures of nanodiamond surrounded by porous silica shells, which demonstrate a remarkable increase in drug loading efficiency; as well as nanodiamonds decorated with carbon dots, which have excellent potential as bioimaging probes. Other combinations are also considered, relying on the discussed inherent properties of the inorganic materials being integrated in a way to advance inorganic nanomedicine in the quest for better health-related nanotechnology.
Control of noise and structural vibration a MATLAB-based approach

CERN Document Server

Mao, Qibo

2013-01-01

Control of Noise and Structural Vibration presents a MATLAB®-based approach to solving the problems of undesirable noise generation and transmission by structures and of undesirable vibration within structures in response to environmental or operational forces. The fundamentals of acoustics, vibration and coupling between vibrating structures and the sound fields they generate are introduced including a discussion of the finite element method for vibration analysis. Following this, the treatment of sound and vibration control begins, illustrated by example systems such as beams, plates and double plate structures. Sensor and actuator placement is explained as is the idea of modal sensor–actuators. The design of appropriate feedback systems includes consideration of basic stability criteria and robust active structural acoustic control. Single and multi-mode positive position feedback (PPF) control systems are also described in the context of loudspeaker–duct model with non-collocated loudspeaker–microp...
Mechanical Properties Of 3D-Structure Composites Based On Warp-Knitted Spacer Fabrics

Directory of Open Access Journals (Sweden)

Chen Si

2015-06-01

Full Text Available In this paper, the mechanical properties (compression and impact behaviours of three-dimension structure (3D-structure composites based on warp-knitted spacer fabrics have been thoroughly investigated. In order to discuss the effect of fabric structural parameters on the mechanical performance of composites, six different types of warp-knitted spacer fabrics having different structural parameters (such as outer layer structure, diameter of spacer yarn, spacer yarn inclination angle and thickness were involved for comparison study. The 3D-structure composites were fabricated based on a flexible polyurethane foam. The produced composites were characterised for compression and impact properties. The findings obtained indicate that the fabric structural parameters have strong influence on the compression and impact responses of 3D-structure composites. Additionally, the impact test carried out on the 3D-structure composites shows that the impact loads do not affect the integrity of composite structure. All the results reveal that the product exhibits promising mechanical performance and its service life can be sustained.
Structure of transformer oil-based magnetic fluids studied using acoustic spectroscopy

International Nuclear Information System (INIS)

Kúdelčík, Jozef; Bury, Peter; Drga, Jozef; Kopčanský, Peter; Závišová, Vlasta; Timko, Milan

2013-01-01

The structural changes in transformer oil-based magnetic fluids upon the effect of an external magnetic field and temperature were studied by acoustic spectroscopy. The attenuation of acoustic wave was measured as a function of the magnetic field in the range of 0–300 mT and in the temperature range of 15–35 °C for various magnetic nanoparticles concentrations. The effect of anisotropy of the acoustic attenuation was determined, too. The both strong influence of the magnetic field on the acoustic attenuation and its hysteresis were observed. When a magnetic field is increased, the interaction between the external magnetic field and the magnetic moments of the nanoparticles occurs, leading to the aggregation of magnetic nanoparticles and following clusters formation. However, the temperature of magnetic fluids also has very important influence on the structural changes because of the mechanism of thermal motion that acts against the cluster creation. The observed influences of both magnetic field and temperature on the investigated magnetic fluid structure are discussed. - Highlights: ► Structural changes in transformer oil-based magnetic fluids were investigated. ► The acoustic spectroscopy as the method of investigation was used. ► The influence of magnetic field on the structural was studied. ► The influence of temperatures on the structures was investigated, too. ► The influence of external conditions on the structure of MF is interpreted.
Protein Function Prediction Based on Sequence and Structure Information

KAUST Repository

Smaili, Fatima Z.

2016-01-01

operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching
Assessment of Peer-Based and Structural Strategies for Increasing ...

African Journals Online (AJOL)

Assessment of Peer-Based and Structural Strategies for Increasing Male Participation in an Antenatal Setting in Lilongwe, Malawi. SM Mphonda, NE Rosenberg, E Kamanga, I Mofolo, G Mwale, E Boa, M Mwale, F Martinson, I Hoffman, MC Hosseinipour ...
Optimization design of LED heat dissipation structure based on strip fins

Science.gov (United States)

Xue, Lingyun; Wan, Wenbin; Chen, Qingguang; Rao, Huanle; Xu, Ping

2018-03-01

To solve the heat dissipation problem of LED, a radiator structure based on strip fins is designed and the method to optimize the structure parameters of strip fins is proposed in this paper. The combination of RBF neural networks and particle swarm optimization (PSO) algorithm is used for modeling and optimization respectively. During the experiment, the 150 datasets of LED junction temperature when structure parameters of number of strip fins, length, width and height of the fins have different values are obtained by ANSYS software. Then RBF neural network is applied to build the non-linear regression model and the parameters optimization of structure based on particle swarm optimization algorithm is performed with this model. The experimental results show that the lowest LED junction temperature reaches 43.88 degrees when the number of hidden layer nodes in RBF neural network is 10, the two learning factors in particle swarm optimization algorithm are 0.5, 0.5 respectively, the inertia factor is 1 and the maximum number of iterations is 100, and now the number of fins is 64, the distribution structure is 8*8, and the length, width and height of fins are 4.3mm, 4.48mm and 55.3mm respectively. To compare the modeling and optimization results, LED junction temperature at the optimized structure parameters was simulated and the result is 43.592°C which approximately equals to the optimal result. Compared with the ordinary plate-fin-type radiator structure whose temperature is 56.38°C, the structure greatly enhances heat dissipation performance of the structure.
Structured-Light Based 3d Laser Scanning of Semi-Submerged Structures

Science.gov (United States)

van der Lucht, J.; Bleier, M.; Leutert, F.; Schilling, K.; Nüchter, A.

2018-05-01

In this work we look at 3D acquisition of semi-submerged structures with a triangulation based underwater laser scanning system. The motivation is that we want to simultaneously capture data above and below water to create a consistent model without any gaps. The employed structured light scanner consist of a machine vision camera and a green line laser. In order to reconstruct precise surface models of the object it is necessary to model and correct for the refraction of the laser line and camera rays at the water-air boundary. We derive a geometric model for the refraction at the air-water interface and propose a method for correcting the scans. Furthermore, we show how the water surface is directly estimated from sensor data. The approach is verified using scans captured with an industrial manipulator to achieve reproducible scanner trajectories with different incident angles. We show that the proposed method is effective for refractive correction and that it can be applied directly to the raw sensor data without requiring any external markers or targets.
STRUCTURED-LIGHT BASED 3D LASER SCANNING OF SEMI-SUBMERGED STRUCTURES

Directory of Open Access Journals (Sweden)

J. van der Lucht

2018-05-01

Full Text Available In this work we look at 3D acquisition of semi-submerged structures with a triangulation based underwater laser scanning system. The motivation is that we want to simultaneously capture data above and below water to create a consistent model without any gaps. The employed structured light scanner consist of a machine vision camera and a green line laser. In order to reconstruct precise surface models of the object it is necessary to model and correct for the refraction of the laser line and camera rays at the water-air boundary. We derive a geometric model for the refraction at the air-water interface and propose a method for correcting the scans. Furthermore, we show how the water surface is directly estimated from sensor data. The approach is verified using scans captured with an industrial manipulator to achieve reproducible scanner trajectories with different incident angles. We show that the proposed method is effective for refractive correction and that it can be applied directly to the raw sensor data without requiring any external markers or targets.
Dependence of credit spread and macro-conditions based on an alterable structure model

Science.gov (United States)

2018-01-01

The fat-tail financial data and cyclical financial market makes it difficult for the fixed structure model based on Gaussian distribution to characterize the dynamics of corporate bonds spreads. Using a flexible structure model based on generalized error distribution, this paper focuses on the impact of macro-level factors on the spreads of corporate bonds in China. It is found that in China's corporate bonds market, macroeconomic conditions have obvious structural transformational effects on bonds spreads, and their structural features remain stable with the downgrade of bonds ratings. The impact of macroeconomic conditions on spreads is significant for different structures, and the differences between the structures increase as ratings decline. For different structures, the persistent characteristics of bonds spreads are obviously stronger than those of recursive ones, which suggest an obvious speculation in bonds market. It is also found that the structure switching of bonds with different ratings is not synchronous, which indicates the shift of investment between different grades of bonds. PMID:29723295
Dependence of credit spread and macro-conditions based on an alterable structure model.

Science.gov (United States)

Xie, Yun; Tian, Yixiang; Xiao, Zhuang; Zhou, Xiangyun

2018-01-01

The fat-tail financial data and cyclical financial market makes it difficult for the fixed structure model based on Gaussian distribution to characterize the dynamics of corporate bonds spreads. Using a flexible structure model based on generalized error distribution, this paper focuses on the impact of macro-level factors on the spreads of corporate bonds in China. It is found that in China's corporate bonds market, macroeconomic conditions have obvious structural transformational effects on bonds spreads, and their structural features remain stable with the downgrade of bonds ratings. The impact of macroeconomic conditions on spreads is significant for different structures, and the differences between the structures increase as ratings decline. For different structures, the persistent characteristics of bonds spreads are obviously stronger than those of recursive ones, which suggest an obvious speculation in bonds market. It is also found that the structure switching of bonds with different ratings is not synchronous, which indicates the shift of investment between different grades of bonds.
Coach simplified structure modeling and optimization study based on the PBM method

Science.gov (United States)

Zhang, Miaoli; Ren, Jindong; Yin, Ying; Du, Jian

2016-09-01

For the coach industry, rapid modeling and efficient optimization methods are desirable for structure modeling and optimization based on simplified structures, especially for use early in the concept phase and with capabilities of accurately expressing the mechanical properties of structure and with flexible section forms. However, the present dimension-based methods cannot easily meet these requirements. To achieve these goals, the property-based modeling (PBM) beam modeling method is studied based on the PBM theory and in conjunction with the characteristics of coach structure of taking beam as the main component. For a beam component of concrete length, its mechanical characteristics are primarily affected by the section properties. Four section parameters are adopted to describe the mechanical properties of a beam, including the section area, the principal moments of inertia about the two principal axles, and the torsion constant of the section. Based on the equivalent stiffness strategy, expressions for the above section parameters are derived, and the PBM beam element is implemented in HyperMesh software. A case is realized using this method, in which the structure of a passenger coach is simplified. The model precision is validated by comparing the basic performance of the total structure with that of the original structure, including the bending and torsion stiffness and the first-order bending and torsional modal frequencies. Sensitivity analysis is conducted to choose design variables. The optimal Latin hypercube experiment design is adopted to sample the test points, and polynomial response surfaces are used to fit these points. To improve the bending and torsion stiffness and the first-order torsional frequency and taking the allowable maximum stresses of the braking and left turning conditions as constraints, the multi-objective optimization of the structure is conducted using the NSGA-II genetic algorithm on the ISIGHT platform. The result of the
Road Network Selection Based on Road Hierarchical Structure Control

Directory of Open Access Journals (Sweden)

HE Haiwei

2015-04-01

Full Text Available A new road network selection method based on hierarchical structure is studied. Firstly, road network is built as strokes which are then classified into hierarchical collections according to the criteria of betweenness centrality value (BC value. Secondly, the hierarchical structure of the strokes is enhanced using structural characteristic identification technique. Thirdly, the importance calculation model was established according to the relationships among the hierarchical structure of the strokes. Finally, the importance values of strokes are got supported with the model's hierarchical calculation, and with which the road network is selected. Tests are done to verify the advantage of this method by comparing it with other common stroke-oriented methods using three kinds of typical road network data. Comparision of the results show that this method had few need to semantic data, and could eliminate the negative influence of edge strokes caused by the criteria of BC value well. So, it is better to maintain the global hierarchical structure of road network, and suitable to meet with the selection of various kinds of road network at the same time.
Density-functional band-structure calculations for La-, Y-, and Sc-filled CoP3-based skutterudite structures

International Nuclear Information System (INIS)

Loevvik, O.M.; Prytz, O.

2004-01-01

The crystal structure, thermodynamic stability, and electronic structure of La-, Y-, and Sc-filled CoP 3 are predicted from density-functional band-structure calculations. The size of the cubic voids in the skutterudite structure is changed much less than the difference in size between the different filling atoms, and we expect that the larger rattling amplitude of the smaller Sc and Y atoms may decrease the lattice thermal conductivity of Sc- and Y-filled structures significantly compared to La-filled structures. The solubility of La, Y, and Sc in CoP 3 is calculated to be around 5, 3-6 %, and below 1% at 0 K, respectively. Based on similar systems, this is expected to increase considerably if Fe is substituted for Co. Fe substitution is also expected to compensate the increased charge carrier concentration of the filled structures that is seen in the calculated electron density of states. In conclusion, Sc- or Y-filled (FeCo)P 3 skutterudite structures are promising materials for thermoelectric applications
Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures

Directory of Open Access Journals (Sweden)

Carugo Oliviero

2011-10-01

Full Text Available Abstract Background Hydration is crucial for RNA structure and function. X-ray crystallography is the most commonly used method to determine RNA structures and hydration and, therefore, statistical surveys are based on crystallographic results, the number of which is quickly increasing. Results A statistical analysis of the water molecule distribution in high-resolution X-ray structures of unpaired RNA nucleotides showed that: different bases have the same penchant to be surrounded by water molecules; clusters of water molecules indicate possible hydration sites, which, in some cases, match those of the major and minor grooves of RNA and DNA double helices; complex hydrogen bond networks characterize the solvation of the nucleotides, resulting in a significant rigidity of the base and its surrounding water molecules. Interestingly, the hydration sites around unpaired RNA bases do not match, in general, the positions that are occupied by the second nucleotide when the base-pair is formed. Conclusions The hydration sites around unpaired RNA bases were found. They do not replicate the atom positions of complementary bases in the Watson-Crick pairs.
Diffusion under water-saturated conditions in PFA/OPC-based structural concrete

International Nuclear Information System (INIS)

Harris, A.W.; Nickerson, A.K.

1990-05-01

A substantial proportion of the volume of the UK radioactive waste repository is likely to be composed of materials based on hydraulic cements. This includes the structural components, which are likely to be manufactured from concrete. The mass transport characteristics of dissolved species for a typical structural concrete, based on a mixture of pulverised fuel ash and ordinary Portland cement, have been measured in a water-saturated condition. Both the water permeability and the diffusion parameters (for caesium, strontium and iodide ion and tritiated water diffusion) are low compared to values obtained for other structural concretes. The intrinsic diffusion coefficients for iodide and caesium ions are in the range 2-5x10 -14 m 2 s -1 . There is no evidence of significant sorption of any of the diffusants studied. (author)

Web-based three-dimensional Virtual Body Structures: W3D-VBS.

Science.gov (United States)

Temkin, Bharti; Acosta, Eric; Hatfield, Paul; Onal, Erhan; Tong, Alex

2002-01-01

Major efforts are being made to improve the teaching of human anatomy to foster cognition of visuospatial relationships. The Visible Human Project of the National Library of Medicine makes it possible to create virtual reality-based applications for teaching anatomy. Integration of traditional cadaver and illustration-based methods with Internet-based simulations brings us closer to this goal. Web-based three-dimensional Virtual Body Structures (W3D-VBS) is a next-generation immersive anatomical training system for teaching human anatomy over the Internet. It uses Visible Human data to dynamically explore, select, extract, visualize, manipulate, and stereoscopically palpate realistic virtual body structures with a haptic device. Tracking user's progress through evaluation tools helps customize lesson plans. A self-guided "virtual tour" of the whole body allows investigation of labeled virtual dissections repetitively, at any time and place a user requires it.
Bending-active reciprocal structures based on equilateral polyhedral geometries

DEFF Research Database (Denmark)

Popovic Larsen, Olga; BRANCART, Stijn; DE TEMMERMAN, Niels

2017-01-01

As mutually supported beam structures, reciprocal frames limit the number of components that are joined at each connection to two. However, this system of intermediate connections introduces undesirable bending moments in the beam elements. By utilising elastic deformation to create curved...... of parts of reciprocal bending-active components based on a selection of polyhedral dome types. To simplify the assembly of the structures and avoid the manual bending of the components on site, we introduce the concept of a double-layered, pre-bent component. Finally, this paper presents the development...
Nanoscale characterization of martensite structures in copper based shape memory alloys

Energy Technology Data Exchange (ETDEWEB)

Adiguzel, O, E-mail: oadiguzel@firat.edu.t [Firat University Department of Physics, 23169 Elazig (Turkey)

2010-11-01

Martensitic transformations are first order displacive transitions and occur in the materials on cooling from high temperature. Shape memory effect is an unusual property exhibited by certain alloy systems, and leads to martensitic transition. Copper-based alloys exhibit this property in beta phase field which possess simple bcc- structures, austenite structure at high-temperatures. As temperature is lowered the austenite undergoes martensitic transition following two ordering reactions, and structural changes in nanoscale govern this transition. Atomic movements are also confined to interatomic lengths in sub-{mu}m or angstrom scale in martensitic transformation. The formation of the layered structures in copper based alloys consists of shears and shear mechanism. Martensitic transformations occur in a few steps with the cooperative movement of atoms less than interatomic distances by means of lattice invariant shears on a {l_brace}110{r_brace} - type plane of austenite matrix which is basal plane or stacking plane of martensite. The lattice invariant shears occurs, in two opposite directions, <110> -type directions on the {l_brace}110{r_brace}-type plane. These shears gives rise to the formation of layered structure.
Module-based structure design of wheeled mobile robot

Directory of Open Access Journals (Sweden)

Z. Luo

2018-02-01

Full Text Available This paper proposes an innovative and systematic approach for synthesizing mechanical structures of wheeled mobile robots. The principle and terminologies used for the proposed synthesis method are presented by adopting the concept of modular design, isomorphic and non-isomorphic, and set theory with its associated combinatorial mathematics. The modular-based innovative synthesis and design of wheeled robots were conducted at two levels. Firstly at the module level, by creative design and analysing the structures of classic wheeled robots, a wheel module set containing four types of wheel mechanisms, a suspension module set consisting of five types of suspension frames and a chassis module set composed of five types of rigid or articulated chassis were designed and generalized. Secondly at the synthesis level, two kinds of structure synthesis modes, namely the isomorphic-combination mode and the non-isomorphic combination mode were proposed to synthesize mechanical structures of wheeled robots; which led to 241 structures for wheeled mobile robots including 236 novel ones. Further, mathematical models and a software platform were developed to provide appropriate and intuitive tools for simulating and evaluating performance of the wheeled robots that were proposed in this paper. Eventually, physical prototypes of sample wheeled robots/rovers were developed and tested so as to prove and validate the principle and methodology presented in this paper.
Effects of Piezoelectric (PZT) Sensor Bonding and the Characteristics of the Host Structure on Impedance Based Structural Health Monitoring

Science.gov (United States)

Jalloh, Abdul

2005-01-01

This study was conducted to investigate the effects of certain factors on the impedance signal in structural health monitoring. These factors were: the quality of the bond between the sensor and the host structure, and the characteristics of the host structure, such as geometry, mass, and material properties. This work was carried out to answer a set of questions, related to these factors, that were developed by the project team. The project team was comprised of Dr. Doug Ramers and Dr. Abdul Jalloh of the Summer Faculty Fellowship Program, Mr. Arnaldo Colon- Perez, a student intern from the University of Puerto Rico of Turabo, and Mr. John Lassiter and Mr. Bob Engberg of the Structural and Dynamics Test Group at NASA Marshall Space Flight Center (MSFC). This study was based on a review of the literature on structural health monitoring to investigate the factors referred to above because there was not enough time to plan and conduct the appropriate tests at MSFC during the tenure of the Summer Faculty Fellowship Program project members. The surveyed literature documents works on structural health monitoring that were based on laboratory tests that were conducted using bolted trusses and other civil engineering type structures for the most part. These are not the typical types of structures used in designing and building NASA s space vehicles and systems. It was therefore recommended that tests be conducted using NASA type structures, such as pressure vessels, to validate the observations made in this report.
A Task-Based Approach to Organization: Knowledge, Communication and Structure

OpenAIRE

Luis Garicano; Yanhui Wu

2010-01-01

We bridge a gap between organizational economics and strategy research by developing a task-based approach to analyze organizational knowledge, process and structure, and deriving testable implications for the relation between production and organizational structure. We argue that organization emerges to integrate disperse knowledge and to coordinate talent in production and is designed to complement the limitations of human ability. The complexity of the tasks undertaken determines the optim...
Structure-based assessment of disease-related mutations in human voltage-gated sodium channels

Directory of Open Access Journals (Sweden)

Weiyun Huang

2017-02-01

Full Text Available ABSTRACT Voltage-gated sodium (Nav channels are essential for the rapid upstroke of action potentials and the propagation of electrical signals in nerves and muscles. Defects of Nav channels are associated with a variety of channelopathies. More than 1000 disease-related mutations have been identified in Nav channels, with Nav1.1 and Nav1.5 each harboring more than 400 mutations. Nav channels represent major targets for a wide array of neurotoxins and drugs. Atomic structures of Nav channels are required to understand their function and disease mechanisms. The recently determined atomic structure of the rabbit voltage-gated calcium (Cav channel Cav1.1 provides a template for homology-based structural modeling of the evolutionarily related Nav channels. In this Resource article, we summarized all the reported disease-related mutations in human Nav channels, generated a homologous model of human Nav1.7, and structurally mapped disease-associated mutations. Before the determination of structures of human Nav channels, the analysis presented here serves as the base framework for mechanistic investigation of Nav channelopathies and for potential structure-based drug discovery.
Structure-based assessment of disease-related mutations in human voltage-gated sodium channels.

Science.gov (United States)

Huang, Weiyun; Liu, Minhao; Yan, S Frank; Yan, Nieng

2017-06-01

Voltage-gated sodium (Na v ) channels are essential for the rapid upstroke of action potentials and the propagation of electrical signals in nerves and muscles. Defects of Na v channels are associated with a variety of channelopathies. More than 1000 disease-related mutations have been identified in Na v channels, with Na v 1.1 and Na v 1.5 each harboring more than 400 mutations. Na v channels represent major targets for a wide array of neurotoxins and drugs. Atomic structures of Na v channels are required to understand their function and disease mechanisms. The recently determined atomic structure of the rabbit voltage-gated calcium (Ca v ) channel Ca v 1.1 provides a template for homology-based structural modeling of the evolutionarily related Na v channels. In this Resource article, we summarized all the reported disease-related mutations in human Na v channels, generated a homologous model of human Na v 1.7, and structurally mapped disease-associated mutations. Before the determination of structures of human Na v channels, the analysis presented here serves as the base framework for mechanistic investigation of Na v channelopathies and for potential structure-based drug discovery.
Tree decomposition based fast search of RNA structures including pseudoknots in genomes.

Science.gov (United States)

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

2005-01-01

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

Directory of Open Access Journals (Sweden)

Chen Chun

2008-03-01

Full Text Available Abstract Background With the rapid emergence of RNA databases and newly identified non-coding RNAs, an efficient compression algorithm for RNA sequence and structural information is needed for the storage and analysis of such data. Although several algorithms for compressing DNA sequences have been proposed, none of them are suitable for the compression of RNA sequences with their secondary structures simultaneously. This kind of compression not only facilitates the maintenance of RNA data, but also supplies a novel way to measure the informational complexity of RNA structural data, raising the possibility of studying the relationship between the functional activities of RNA structures and their complexities, as well as various structural properties of RNA based on compression. Results RNACompress employs an efficient grammar-based model to compress RNA sequences and their secondary structures. The main goals of this algorithm are two fold: (1 present a robust and effective way for RNA structural data compression; (2 design a suitable model to represent RNA secondary structure as well as derive the informational complexity of the structural data based on compression. Our extensive tests have shown that RNACompress achieves a universally better compression ratio compared with other sequence-specific or common text-specific compression algorithms, such as Gencompress, winrar and gzip. Moreover, a test of the activities of distinct GTP-binding RNAs (aptamers compared with their structural complexity shows that our defined informational complexity can be used to describe how complexity varies with activity. These results lead to an objective means of comparing the functional properties of heteropolymers from the information perspective. Conclusion A universal algorithm for the compression of RNA secondary structure as well as the evaluation of its informational complexity is discussed in this paper. We have developed RNACompress, as a useful tool
Structure-Based Low-Rank Model With Graph Nuclear Norm Regularization for Noise Removal.

Science.gov (United States)

Ge, Qi; Jing, Xiao-Yuan; Wu, Fei; Wei, Zhi-Hui; Xiao, Liang; Shao, Wen-Ze; Yue, Dong; Li, Hai-Bo

2017-07-01

Nonlocal image representation methods, including group-based sparse coding and block-matching 3-D filtering, have shown their great performance in application to low-level tasks. The nonlocal prior is extracted from each group consisting of patches with similar intensities. Grouping patches based on intensity similarity, however, gives rise to disturbance and inaccuracy in estimation of the true images. To address this problem, we propose a structure-based low-rank model with graph nuclear norm regularization. We exploit the local manifold structure inside a patch and group the patches by the distance metric of manifold structure. With the manifold structure information, a graph nuclear norm regularization is established and incorporated into a low-rank approximation model. We then prove that the graph-based regularization is equivalent to a weighted nuclear norm and the proposed model can be solved by a weighted singular-value thresholding algorithm. Extensive experiments on additive white Gaussian noise removal and mixed noise removal demonstrate that the proposed method achieves a better performance than several state-of-the-art algorithms.
BLAST-based structural annotation of protein residues using Protein Data Bank.

Science.gov (United States)

Singh, Harinder; Raghava, Gajendra P S

2016-01-25

In the era of next-generation sequencing where thousands of genomes have been already sequenced; size of protein databases is growing with exponential rate. Structural annotation of these proteins is one of the biggest challenges for the computational biologist. Although, it is easy to perform BLAST search against Protein Data Bank (PDB) but it is difficult for a biologist to annotate protein residues from BLAST search. A web-server StarPDB has been developed for structural annotation of a protein based on its similarity with known protein structures. It uses standard BLAST software for performing similarity search of a query protein against protein structures in PDB. This server integrates wide range modules for assigning different types of annotation that includes, Secondary-structure, Accessible surface area, Tight-turns, DNA-RNA and Ligand modules. Secondary structure module allows users to predict regular secondary structure states to each residue in a protein. Accessible surface area predict the exposed or buried residues in a protein. Tight-turns module is designed to predict tight turns like beta-turns in a protein. DNA-RNA module developed for predicting DNA and RNA interacting residues in a protein. Similarly, Ligand module of server allows one to predicted ligands, metal and nucleotides ligand interacting residues in a protein. In summary, this manuscript presents a web server for comprehensive annotation of a protein based on similarity search. It integrates number of visualization tools that facilitate users to understand structure and function of protein residues. This web server is available freely for scientific community from URL http://crdd.osdd.net/raghava/starpdb .
Simulation of chloride transport based description soil structure

International Nuclear Information System (INIS)

Mahmood-ul-Hassan, M.; Akhtar, M.S.; Gill, S.M.; Nabi, G.

2003-01-01

There is a need of environmental implications of rapid appearance of surface by applying chemical at depths below the vadose zone (tile line or shallow groundwater) for developing better insight into solute flow mechanism through the arable lands. Transport of chloride, a representative non-adsorbing solute, through a moderately structured silty clay loam soil (Gujranwala series, Typic Ustochrepts) and an un-structured sandy loam soil (Nabipur series, Typic Camborthid) was characterized and two existing models viz. convection dispersion equation (CDE) and preferential flow models were tested. The flux average of solute concentration in the outflow as a function of cumulative drainage was fitted to the models. The CDE fitted, relatively, better in the non-structured soil than in the moderately structured soil. Dispersivity value determined by CDE was very high for the structured soil which is physically not possible. The preferential flow model fitted well in the Gujranwala soil, but not in the Nabipur soil. The breakthrough characteristics i.e. drainage to peak concentration (Dp), symmetry coefficient (SC), skewness, and kurtosis were compared. Chloride breakthrough was earlier than expected based on piston flow. It indicated preferential flow in both the soils, yet, immediate appearance of the tracer in the Gujranwala soil demonstrated even larger magnitude of the preferential flow. Breakthrough curves' parameters indicated a large amount of the solute movement through the preferred pathways by passing the soil matrix in the Gujranwala soil. The study suggests that some soil structure parameters (size/shape and degree of aggregation) should be incorporated in the solute transport models.(author)
Base isolation strategies for structures and components

International Nuclear Information System (INIS)

Varma, Veto; Reddy, G.R.; Vaze, K.K.; Kushwaha, H.S.

2003-08-01

In the present report the effect of laminated rubber bearing (LRB) system on the dynamic response of the structure was studied. A LRB system was designed and tested in the laboratory for its dynamic characteristics. Finite element analysis was also performed and based on this analysis, isolator for PHWR nuclear power plant was designed. Analysis of the building was performed with and without isolator. Comparison of responses was made in terms of frequencies, accelerations and displacements and floor response spectra. (author)
Structure of transformer oil-based magnetic fluids studied using acoustic spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Kudelcik, Jozef, E-mail: kudelcik@fyzika.uniza.sk [Department of Physics, University of Zilina, Univerzitna 1, 010 01 Zilina (Slovakia); Bury, Peter; Drga, Jozef [Department of Physics, University of Zilina, Univerzitna 1, 010 01 Zilina (Slovakia); Kopcansky, Peter; Zavisova, Vlasta; Timko, Milan [Department of Magnetism, IEP SAS, Watsonova 47, 040 01 Kosice (Slovakia)

2013-01-15

The structural changes in transformer oil-based magnetic fluids upon the effect of an external magnetic field and temperature were studied by acoustic spectroscopy. The attenuation of acoustic wave was measured as a function of the magnetic field in the range of 0-300 mT and in the temperature range of 15-35 Degree-Sign C for various magnetic nanoparticles concentrations. The effect of anisotropy of the acoustic attenuation was determined, too. The both strong influence of the magnetic field on the acoustic attenuation and its hysteresis were observed. When a magnetic field is increased, the interaction between the external magnetic field and the magnetic moments of the nanoparticles occurs, leading to the aggregation of magnetic nanoparticles and following clusters formation. However, the temperature of magnetic fluids also has very important influence on the structural changes because of the mechanism of thermal motion that acts against the cluster creation. The observed influences of both magnetic field and temperature on the investigated magnetic fluid structure are discussed. - Highlights: Black-Right-Pointing-Pointer Structural changes in transformer oil-based magnetic fluids were investigated. Black-Right-Pointing-Pointer The acoustic spectroscopy as the method of investigation was used. Black-Right-Pointing-Pointer The influence of magnetic field on the structural was studied. Black-Right-Pointing-Pointer The influence of temperatures on the structures was investigated, too. Black-Right-Pointing-Pointer The influence of external conditions on the structure of MF is interpreted.
Bioinspired twisted composites based on Bouligand structures

Science.gov (United States)

Pinto, F.; Iervolino, O.; Scarselli, G.; Ginzburg, D.; Meo, M.

2016-04-01

The coupling between structural support and protection makes biological systems an important source of inspiration for the development of advanced smart composite structures. In particular, some particular material configurations can be implemented into traditional composites in order to improve their impact resistance and the out-of-plane properties, which represents one of the major weakness of commercial carbon fibres reinforced polymers (CFRP) structures. Based on this premise, a three-dimensional twisted arrangement shown in a vast multitude of biological systems (such as the armoured cuticles of Scarabei, the scales of Arapaima Gigas and the smashing club of Odontodactylus Scyllarus) has been replicated to develop an improved structural material characterised by a high level of in-plane isotropy and a higher interfacial strength generated by the smooth stiffness transition between each layer of fibrils. Indeed, due to their intrinsic layered nature, interlaminar stresses are one of the major causes of failure of traditional CFRP and are generated by the mismatch of the elastic properties between plies in a traditional laminate. Since the energy required to open a crack or a delamination between two adjacent plies is due to the difference between their orientations, the gradual angle variation obtained by mimicking the Bouligand Structures could improve energy absorption and the residual properties of carbon laminates when they are subjected to low velocity impact event. Two different bioinspired laminates were manufactured following a double helicoidal approach and a rotational one and were subjected to a complete test campaign including low velocity impact loading and compared to a traditional quasi-isotropic panel. Fractography analysis via X-Ray tomography was used to understand the mechanical behaviour of the different laminates and the residual properties were evaluated via Compression After Impact (CAI) tests. Results confirmed that the biological
Continuous Record Laplace-based Inference about the Break Date in Structural Change Models

OpenAIRE

Casini, Alessandro; Perron, Pierre

2018-01-01

Building upon the continuous record asymptotic framework recently introduced by Casini and Perron (2017a) for inference in structural change models, we propose a Laplace-based (Quasi-Bayes) procedure for the construction of the estimate and confidence set for the date of a structural change. The procedure relies on a Laplace-type estimator defined by an integration-based rather than an optimization-based method. A transformation of the leastsquares criterion function is evaluated in order to ...
Global stability-based design optimization of truss structures using ...

Indian Academy of Sciences (India)

Furthermore, a pure pareto-ranking based multi-objective optimization model is employed for the design optimization of the truss structure with multiple objectives. The computational performance of the optimization model is increased by implementing an island model into its evolutionary search mechanism. The proposed ...
RNAHelix: computational modeling of nucleic acid structures with Watson-Crick and non-canonical base pairs.

Science.gov (United States)

Bhattacharyya, Dhananjay; Halder, Sukanya; Basu, Sankar; Mukherjee, Debasish; Kumar, Prasun; Bansal, Manju

2017-02-01

Comprehensive analyses of structural features of non-canonical base pairs within a nucleic acid double helix are limited by the availability of a small number of three dimensional structures. Therefore, a procedure for model building of double helices containing any given nucleotide sequence and base pairing information, either canonical or non-canonical, is seriously needed. Here we describe a program RNAHelix, which is an updated version of our widely used software, NUCGEN. The program can regenerate duplexes using the dinucleotide step and base pair orientation parameters for a given double helical DNA or RNA sequence with defined Watson-Crick or non-Watson-Crick base pairs. The original structure and the corresponding regenerated structure of double helices were found to be very close, as indicated by the small RMSD values between positions of the corresponding atoms. Structures of several usual and unusual double helices have been regenerated and compared with their original structures in terms of base pair RMSD, torsion angles and electrostatic potentials and very high agreements have been noted. RNAHelix can also be used to generate a structure with a sequence completely different from an experimentally determined one or to introduce single to multiple mutation, but with the same set of parameters and hence can also be an important tool in homology modeling and study of mutation induced structural changes.
Particle filtering based structural assessment with acoustic emission sensing

Science.gov (United States)

Yan, Wuzhao; Abdelrahman, Marwa; Zhang, Bin; Ziehl, Paul

2017-02-01

Nuclear structures are designed to withstand severe loading events under various stresses. Over time, aging of structural systems constructed with concrete and steel will occur. This deterioration may reduce service life of nuclear facilities and/or lead to unnecessary or untimely repairs. Therefore, online monitoring of structures in nuclear power plants and waste storage has drawn significant attention in recent years. Of many existing non-destructive evaluation and structural monitoring approaches, acoustic emission is promising for assessment of structural damage because it is non-intrusive and is sensitive to corrosion and crack growth in reinforced concrete elements. To provide a rapid, actionable, and graphical means for interpretation Intensity Analysis plots have been developed. This approach provides a means for classification of damage. Since the acoustic emission measurement is only an indirect indicator of structural damage, potentially corrupted by non-genuine data, it is more suitable to estimate the states of corrosion and cracking in a Bayesian estimation framework. In this paper, we will utilize the accelerated corrosion data from a specimen at the University of South Carolina to develop a particle filtering-based diagnosis and prognosis algorithm. Promising features of the proposed algorithm are described in terms of corrosion state estimation and prediction of degradation over time to a predefined threshold.

A vorticity based approach to handle the fluid-structure interaction problems

Energy Technology Data Exchange (ETDEWEB)

Farahbakhsh, Iman; Ghassemi, Hassan [Department of Ocean Engineering, Amirkabir University of Technology, Tehran (Iran, Islamic Republic of); Sabetghadam, Fereidoun, E-mail: i.farahbakhsh@aut.ac.ir [Mechanical and Aerospace Engineering Department, Science and Research Branch, Islamic Azad University (IAU), Tehran (Iran, Islamic Republic of)

2016-02-15

A vorticity based approach for the numerical solution of the fluid-structure interaction problems is introduced in which the fluid and structure(s) can be viewed as a continuum. Retrieving the vorticity field and recalculating a solenoidal velocity field, specially at the fluid-structure interface, are the kernel of the proposed algorithm. In the suggested method, a variety of constitutive equations as a function of left Cauchy–Green deformation tensor can be applied for modeling the structure domain. A nonlinear Mooney–Rivlin and Saint Venant–Kirchhoff model are expressed in terms of the left Cauchy–Green deformation tensor and the presented method is able to model the behavior of a visco-hyperelastic structure in the incompressible flow. Some numerical experiments, with considering the neo-Hookean model for structure domain, are executed and the results are validated via the available results from literature. (paper)
Structure-based drug design for G protein-coupled receptors.

Science.gov (United States)

Congreve, Miles; Dias, João M; Marshall, Fiona H

2014-01-01

Our understanding of the structural biology of G protein-coupled receptors has undergone a transformation over the past 5 years. New protein-ligand complexes are described almost monthly in high profile journals. Appreciation of how small molecules and natural ligands bind to their receptors has the potential to impact enormously how medicinal chemists approach this major class of receptor targets. An outline of the key topics in this field and some recent examples of structure- and fragment-based drug design are described. A table is presented with example views of each G protein-coupled receptor for which there is a published X-ray structure, including interactions with small molecule antagonists, partial and full agonists. The possible implications of these new data for drug design are discussed. © 2014 Elsevier B.V. All rights reserved.
Comportement et fragmentation dynamique des matériaux quasi-fragiles

OpenAIRE

Rouabhi , Ahmed

2004-01-01

This thesis seeks to find a computational methodology to simulate both the behaviour and the fragmentation of quasi-brittle materials, such as rocks and concrete, under dynamic loading. Such a methodology will help to a better understanding of the explosive rock breakage mechanisms and, as consequence, will contribute in the optimization of blasting performances. In this study, we consider that the fragmentation process is a natural extension of the fracture process. In order to describe the ...
A user exposure based approach for non-structural road network vulnerability analysis.

Directory of Open Access Journals (Sweden)

Lei Jin

Full Text Available Aiming at the dense urban road network vulnerability without structural negative consequences, this paper proposes a novel non-structural road network vulnerability analysis framework. Three aspects of the framework are mainly described: (i the rationality of non-structural road network vulnerability, (ii the metrics for negative consequences accounting for variant road conditions, and (iii the introduction of a new vulnerability index based on user exposure. Based on the proposed methodology, a case study in the Sioux Falls network which was usually threatened by regular heavy snow during wintertime is detailedly discussed. The vulnerability ranking of links of Sioux Falls network with respect to heavy snow scenario is identified. As a result of non-structural consequences accompanied by conceivable degeneration of network, there are significant increases in generalized travel time costs which are measurements for "emotionally hurt" of topological road network.
Structural Mass Spectrometry of Proteins Using Hydroxyl Radical Based Protein Footprinting

OpenAIRE

Wang, Liwen; Chance, Mark R.

2011-01-01

Structural MS is a rapidly growing field with many applications in basic research and pharmaceutical drug development. In this feature article the overall technology is described and several examples of how hydroxyl radical based footprinting MS can be used to map interfaces, evaluate protein structure, and identify ligand dependent conformational changes in proteins are described.
Cohesive stresses and size effect in quasi-brittle materials

Indian Academy of Sciences (India)

Author Affiliations. V E Saouma1 D Natekar2. Department of Civil, Environmental and Architectural Engineering, University of Colorado, Boulder, CO 803090427, USA; Department of Mechanical Engineering, University of Colorado, Boulder, CO 803090427, USA ...
Structure based classification for bile salt export pump (BSEP) inhibitors using comparative structural modeling of human BSEP

Science.gov (United States)

Jain, Sankalp; Grandits, Melanie; Richter, Lars; Ecker, Gerhard F.

2017-06-01

The bile salt export pump (BSEP) actively transports conjugated monovalent bile acids from the hepatocytes into the bile. This facilitates the formation of micelles and promotes digestion and absorption of dietary fat. Inhibition of BSEP leads to decreased bile flow and accumulation of cytotoxic bile salts in the liver. A number of compounds have been identified to interact with BSEP, which results in drug-induced cholestasis or liver injury. Therefore, in silico approaches for flagging compounds as potential BSEP inhibitors would be of high value in the early stage of the drug discovery pipeline. Up to now, due to the lack of a high-resolution X-ray structure of BSEP, in silico based identification of BSEP inhibitors focused on ligand-based approaches. In this study, we provide a homology model for BSEP, developed using the corrected mouse P-glycoprotein structure (PDB ID: 4M1M). Subsequently, the model was used for docking-based classification of a set of 1212 compounds (405 BSEP inhibitors, 807 non-inhibitors). Using the scoring function ChemScore, a prediction accuracy of 81% on the training set and 73% on two external test sets could be obtained. In addition, the applicability domain of the models was assessed based on Euclidean distance. Further, analysis of the protein-ligand interaction fingerprints revealed certain functional group-amino acid residue interactions that could play a key role for ligand binding. Though ligand-based models, due to their high speed and accuracy, remain the method of choice for classification of BSEP inhibitors, structure-assisted docking models demonstrate reasonably good prediction accuracies while additionally providing information about putative protein-ligand interactions.
Precision Hopping/Rolling Robotic Surface Probe Based on Tensegrity Structures

Data.gov (United States)

National Aeronautics and Space Administration — We propose to overcome the limitations of wheeled surface rovers by combining recent advances in ball-shaped soft-robots based on tensegrity structures (a tension...
Probability based load combinations for design of category I structures

International Nuclear Information System (INIS)

Reich, M.; Hwang, H.

1985-01-01

This paper discusses a reliability analysis method and a procedure for developing the load combination design criteria for category I structures. For safety evaluation of category I concrete structures under various static and dynamic loads, a probability-based reliability analysis method has been developed. This reliability analysis method is also used as a tool for determining the load factors for design of category I structures. In this paper, the load combinations for design of concrete containments, corresponding to a target limit state probability of 1.0 x 10 -6 in 4 years, are described. A comparison of containments designed using the ASME code and the proposed design criteria is also presented
Protein Function Prediction Based on Sequence and Structure Information

KAUST Repository

Smaili, Fatima Z.

2016-05-25

The number of available protein sequences in public databases is increasing exponentially. However, a significant fraction of these sequences lack functional annotation which is essential to our understanding of how biological systems and processes operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching these predicted models, using global and local similarities, through three independent enzyme commission (EC) and gene ontology (GO) function libraries. The method was tested on 250 “hard” proteins, which lack homologous templates in both structure and function libraries. The results show that this method outperforms the conventional prediction methods based on sequence similarity or threading. Additionally, our method could be improved even further by incorporating protein-protein interaction information. Overall, the method we use provides an efficient approach for automated functional annotation of non-homologous proteins, starting from their sequence.
International Workshop on Advanced Dynamics and Model Based Control of Structures and Machines

CERN Document Server

Belyaev, Alexander; Krommer, Michael

2017-01-01

The papers in this volume present and discuss the frontiers in the mechanics of controlled machines and structures. They are based on papers presented at the International Workshop on Advanced Dynamics and Model Based Control of Structures and Machines held in Vienna in September 2015. The workshop continues a series of international workshops held in Linz (2008) and St. Petersburg (2010).
LIFE-CYCLE COST MODEL AND DESIGN OPTIMIZATION OF BASE ISOLATED BUILDING STRUCTURES

Directory of Open Access Journals (Sweden)

Chara C. Mitropoulou

2016-11-01

Full Text Available Design of economic structures adequately resistant to withstand during their service life, without catastrophic failures, all possible loading conditions and to absorb the induced seismic energy in a controlled fashion, has been the subject of intensive research so far. Modern buildings usually contain extremely sensitive and costly equipment that are vital in business, commerce, education and/or health care. The building contents frequently are more valuable than the buildings them-selves. Furthermore, hospitals, communication and emergency centres, police and fire stations must be operational when needed most: immediately after an earthquake. Conventional con-struction can cause very high floor accelerations in stiff buildings and large interstorey drifts in flexible structures. These two factors cause difficulties in insuring the safety of both building and its contents. For this reason base-isolated structures are considered as an efficient alternative design practice to the conventional fixed-base one. In this study a systematic assessment of op-timized fixed and base-isolated reinforced concrete buildings is presented in terms of their initial and total cost taking into account the life-cycle cost of the structures.
Estimating material parameters of a structurally based constitutive relation for skin mechanics

KAUST Repository

Jor, Jessica W. Y.

2010-11-25

This paper presents a structurally based modeling framework to characterize the structure-function relation in skin tissues, based upon biaxial tensile experiments performed in vitro on porcine skin. Equi-axial deformations were imposed by stretching circular skin specimens uniformly along twelve directions, and the resultant loads at the membrane attachment points were measured. Displacement fields at each deformation step were tracked using an image 2D cross-correlation technique. A modeling framework was developed to simulate the experiments, whereby measured forces were applied to finite element models that were created to represent the geometry and structure of the tissue samples. Parameters of a structurally based constitutive relation were then identified using nonlinear optimization. Results showed that the ground matrix stiffness ranged from 5 to 32 kPa, fiber orientation mean from 2 to 13. from the torso midline, fiber undulation mean from 1.04 to 1.34 and collagen fiber stiffness from 48 to 366 MPa. It was concluded that the objective function was highly sensitive to the mean orientation and that a priori information about fiber orientation mean was important for the reliable identification of constitutive parameters. © Springer-Verlag 2010.
Structure and sensitivity analysis of individual-based predator–prey models

International Nuclear Information System (INIS)

Imron, Muhammad Ali; Gergs, Andre; Berger, Uta

2012-01-01

The expensive computational cost of sensitivity analyses has hampered the use of these techniques for analysing individual-based models in ecology. A relatively cheap computational cost, referred to as the Morris method, was chosen to assess the relative effects of all parameters on the model’s outputs and to gain insights into predator–prey systems. Structure and results of the sensitivity analysis of the Sumatran tiger model – the Panthera Population Persistence (PPP) and the Notonecta foraging model (NFM) – were compared. Both models are based on a general predation cycle and designed to understand the mechanisms behind the predator–prey interaction being considered. However, the models differ significantly in their complexity and the details of the processes involved. In the sensitivity analysis, parameters that directly contribute to the number of prey items killed were found to be most influential. These were the growth rate of prey and the hunting radius of tigers in the PPP model as well as attack rate parameters and encounter distance of backswimmers in the NFM model. Analysis of distances in both of the models revealed further similarities in the sensitivity of the two individual-based models. The findings highlight the applicability and importance of sensitivity analyses in general, and screening design methods in particular, during early development of ecological individual-based models. Comparison of model structures and sensitivity analyses provides a first step for the derivation of general rules in the design of predator–prey models for both practical conservation and conceptual understanding. - Highlights: ► Structure of predation processes is similar in tiger and backswimmer model. ► The two individual-based models (IBM) differ in space formulations. ► In both models foraging distance is among the sensitive parameters. ► Morris method is applicable for the sensitivity analysis even of complex IBMs.
Structurally stable graphene oxide-based nanofiltration membranes with bioadhesive polydopamine coating

Science.gov (United States)

Wang, Chongbin; Li, Zhiyuan; Chen, Jianxin; Yin, Yongheng; Wu, Hong

2018-01-01

Graphene oxide (GO)-based membranes possess promising potential in liquid separation for its high flux. The state-of-art GO-based membranes need to be supported by a substrate to ensure that the ultra-thin GO layer can withstand transmembrane pressure in practical applications. The interfacial compatibility of this kind of composite membrane remains a great challenge due to the intrinsic difference in chemical/physical properties between the GO sheets and the substrate. In this paper, a structurally stable GO-based composite nanofiltration membrane was fabricated by coupling the mussel-inspired adhesive platform and filtration-assisted assembly of GO laminates. The water flux for the prepared GO-based nanofiltration membrane reached up to 85 L m-2 h-1 bar-1 with a high retention above 95% and 100% for Orange G and Congo Red, respectively. The membrane exhibited highly stable structure owing to the covalent and noncovalent interactions between GO separation layer and dopamine adhesive platform.
Physics-Based Hazard Assessment for Critical Structures Near Large Earthquake Sources

Science.gov (United States)

Hutchings, L.; Mert, A.; Fahjan, Y.; Novikova, T.; Golara, A.; Miah, M.; Fergany, E.; Foxall, W.

2017-09-01

We argue that for critical structures near large earthquake sources: (1) the ergodic assumption, recent history, and simplified descriptions of the hazard are not appropriate to rely on for earthquake ground motion prediction and can lead to a mis-estimation of the hazard and risk to structures; (2) a physics-based approach can address these issues; (3) a physics-based source model must be provided to generate realistic phasing effects from finite rupture and model near-source ground motion correctly; (4) wave propagations and site response should be site specific; (5) a much wider search of possible sources of ground motion can be achieved computationally with a physics-based approach; (6) unless one utilizes a physics-based approach, the hazard and risk to structures has unknown uncertainties; (7) uncertainties can be reduced with a physics-based approach, but not with an ergodic approach; (8) computational power and computer codes have advanced to the point that risk to structures can be calculated directly from source and site-specific ground motions. Spanning the variability of potential ground motion in a predictive situation is especially difficult for near-source areas, but that is the distance at which the hazard is the greatest. The basis of a "physical-based" approach is ground-motion syntheses derived from physics and an understanding of the earthquake process. This is an overview paper and results from previous studies are used to make the case for these conclusions. Our premise is that 50 years of strong motion records is insufficient to capture all possible ranges of site and propagation path conditions, rupture processes, and spatial geometric relationships between source and site. Predicting future earthquake scenarios is necessary; models that have little or no physical basis but have been tested and adjusted to fit available observations can only "predict" what happened in the past, which should be considered description as opposed to prediction
Methods for simulation-based analysis of fluid-structure interaction.

Energy Technology Data Exchange (ETDEWEB)

Barone, Matthew Franklin; Payne, Jeffrey L.

2005-10-01

Methods for analysis of fluid-structure interaction using high fidelity simulations are critically reviewed. First, a literature review of modern numerical techniques for simulation of aeroelastic phenomena is presented. The review focuses on methods contained within the arbitrary Lagrangian-Eulerian (ALE) framework for coupling computational fluid dynamics codes to computational structural mechanics codes. The review treats mesh movement algorithms, the role of the geometric conservation law, time advancement schemes, wetted surface interface strategies, and some representative applications. The complexity and computational expense of coupled Navier-Stokes/structural dynamics simulations points to the need for reduced order modeling to facilitate parametric analysis. The proper orthogonal decomposition (POD)/Galerkin projection approach for building a reduced order model (ROM) is presented, along with ideas for extension of the methodology to allow construction of ROMs based on data generated from ALE simulations.
Lightweight carbon nanotube-based structural-energy storage devices for micro unmanned systems

Science.gov (United States)

Rivera, Monica; Cole, Daniel P.; Hahm, Myung Gwan; Reddy, Arava L. M.; Vajtai, Robert; Ajayan, Pulickel M.; Karna, Shashi P.; Bundy, Mark L.

2012-06-01

There is a strong need for small, lightweight energy storage devices that can satisfy the ever increasing power and energy demands of micro unmanned systems. Currently, most commercial and developmental micro unmanned systems utilize commercial-off-the-shelf (COTS) lithium polymer batteries for their energy storage needs. While COTS lithium polymer batteries are the industry norm, the weight of these batteries can account for up to 60% of the overall system mass and the capacity of these batteries can limit mission durations to the order of only a few minutes. One method to increase vehicle endurance without adding mass or sacrificing payload capabilities is to incorporate multiple system functions into a single material or structure. For example, the body or chassis of a micro vehicle could be replaced with a multifunctional material that would serve as both the vehicle structure and the on-board energy storage device. In this paper we present recent progress towards the development of carbon nanotube (CNT)-based structural-energy storage devices for micro unmanned systems. Randomly oriented and vertically aligned CNT-polymer composite electrodes with varying degrees of flexibility are used as the primary building blocks for lightweight structural-supercapacitors. For the purpose of this study, the mechanical properties of the CNT-based electrodes and the charge-discharge behavior of the supercapacitor devices are examined. Because incorporating multifunctionality into a single component often degrades the properties or performance of individual structures, the performance and property tradeoffs of the CNT-based structural-energy storage devices will also be discussed.
Investigations of Structural Requirements for BRD4 Inhibitors through Ligand- and Structure-Based 3D QSAR Approaches

Directory of Open Access Journals (Sweden)

Adeena Tahir

2018-06-01

Full Text Available The bromodomain containing protein 4 (BRD4 recognizes acetylated histone proteins and plays numerous roles in the progression of a wide range of cancers, due to which it is under intense investigation as a novel anti-cancer drug target. In the present study, we performed three-dimensional quantitative structure activity relationship (3D-QSAR molecular modeling on a series of 60 inhibitors of BRD4 protein using ligand- and structure-based alignment and different partial charges assignment methods by employing comparative molecular field analysis (CoMFA and comparative molecular similarity indices analysis (CoMSIA approaches. The developed models were validated using various statistical methods, including non-cross validated correlation coefficient (r2, leave-one-out (LOO cross validated correlation coefficient (q2, bootstrapping, and Fisher’s randomization test. The highly reliable and predictive CoMFA (q2 = 0.569, r2 = 0.979 and CoMSIA (q2 = 0.500, r2 = 0.982 models were obtained from a structure-based 3D-QSAR approach using Merck molecular force field (MMFF94. The best models demonstrate that electrostatic and steric fields play an important role in the biological activities of these compounds. Hence, based on the contour maps information, new compounds were designed, and their binding modes were elucidated in BRD4 protein’s active site. Further, the activities and physicochemical properties of the designed molecules were also predicted using the best 3D-QSAR models. We believe that predicted models will help us to understand the structural requirements of BRD4 protein inhibitors that belong to quinolinone and quinazolinone classes for the designing of better active compounds.
Structural covariance in the hallucinating brain: a voxel-based morphometry study

Science.gov (United States)

Modinos, Gemma; Vercammen, Ans; Mechelli, Andrea; Knegtering, Henderikus; McGuire, Philip K.; Aleman, André

2009-01-01

Background Neuroimaging studies have indicated that a number of cortical regions express altered patterns of structural covariance in schizophrenia. The relation between these alterations and specific psychotic symptoms is yet to be investigated. We used voxel-based morphometry to examine regional grey matter volumes and structural covariance associated with severity of auditory verbal hallucinations. Methods We applied optimized voxel-based morphometry to volumetric magnetic resonance imaging data from 26 patients with medication-resistant auditory verbal hallucinations (AVHs); statistical inferences were made at p < 0.05 after correction for multiple comparisons. Results Grey matter volume in the left inferior frontal gyrus was positively correlated with severity of AVHs. Hallucination severity influenced the pattern of structural covariance between this region and the left superior/middle temporal gyri, the right inferior frontal gyrus and hippocampus, and the insula bilaterally. Limitations The results are based on self-reported severity of auditory hallucinations. Complementing with a clinician-based instrument could have made the findings more compelling. Future studies would benefit from including a measure to control for other symptoms that may covary with AVHs and for the effects of antipsychotic medication. Conclusion The results revealed that overall severity of AVHs modulated cortical intercorrelations between frontotemporal regions involved in language production and verbal monitoring, supporting the critical role of this network in the pathophysiology of hallucinations. PMID:19949723

Structures of human cytosolic and mitochondrial nucleotidases: implications for structure-based design of selective inhibitors

Czech Academy of Sciences Publication Activity Database

Pachl, Petr; Fábry, Milan; Rosenberg, Ivan; Šimák, Ondřej; Řezáčová, Pavlína; Brynda, Jiří

2014-01-01

Roč. 70, February (2014), s. 461-470 ISSN 0907-4449 R&D Projects: GA ČR GA203/09/0820 Institutional support: RVO:68378050 ; RVO:61388963 Keywords : 5′(3′)-deoxyribonucleotidases * enzyme inhibition * hydrolases * structure-based drug design Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 7.232, year: 2013
From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library.

Science.gov (United States)

Bietz, Stefan; Inhester, Therese; Lauck, Florian; Sommer, Kai; von Behren, Mathias M; Fährrolfes, Rainer; Flachsenberg, Florian; Meyder, Agnes; Nittinger, Eva; Otto, Thomas; Hilbig, Matthias; Schomburg, Karen T; Volkamer, Andrea; Rarey, Matthias

2017-11-10

Nowadays, computational approaches are an integral part of life science research. Problems related to interpretation of experimental results, data analysis, or visualization tasks highly benefit from the achievements of the digital era. Simulation methods facilitate predictions of physicochemical properties and can assist in understanding macromolecular phenomena. Here, we will give an overview of the methods developed in our group that aim at supporting researchers from all life science areas. Based on state-of-the-art approaches from structural bioinformatics and cheminformatics, we provide software covering a wide range of research questions. Our all-in-one web service platform ProteinsPlus (http://proteins.plus) offers solutions for pocket and druggability prediction, hydrogen placement, structure quality assessment, ensemble generation, protein-protein interaction classification, and 2D-interaction visualization. Additionally, we provide a software package that contains tools targeting cheminformatics problems like file format conversion, molecule data set processing, SMARTS editing, fragment space enumeration, and ligand-based virtual screening. Furthermore, it also includes structural bioinformatics solutions for inverse screening, binding site alignment, and searching interaction patterns across structure libraries. The software package is available at http://software.zbh.uni-hamburg.de. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.
A Novel SMA-based Concept for Airfoil Structural Morphing

Science.gov (United States)

Barbarino, S.; Pecora, R.; Lecce, L.; Concilio, A.; Ameduri, S.; Calvi, E.

2009-08-01

The adaptive structures concept is of great interest in the aerospace field because of the several benefits which can be accomplished in the fields including noise reduction, load alleviation, weight reduction, etc., at a level in which they can be considered as compulsory in the design of future aircraft. Improvements in terms of the aerodynamic efficiency, aeroelastic behavior, stability, and manoeuvrability performance have already been proved through many international studies in the past. In the family of the Smart Materials, Shape Memory Alloys (SMA) seem to be a suitable solution for many static applications. Their high structural integrability in conjunction with actuation capabilities and a favorable performance per weight ratio, allows the development of original architectures. In this study, a morphing wing trailing edge concept is presented; morphing ability was introduced with the aim of replacing a conventional flap device. A compliant rib structure was designed, based on SMA actuators exhibiting structural potential (bearing external aerodynamic loads). Numerical results, achieved through a FE approach, are presented in terms of trailing edge induced displacement and morphed shape.
Model based fault diagnosis in a centrifugal pump application using structural analysis

DEFF Research Database (Denmark)

Kallesøe, C. S.; Izadi-Zamanabadi, Roozbeh; Rasmussen, Henrik

2004-01-01

A model based approach for fault detection and isolation in a centrifugal pump is proposed in this paper. The fault detection algorithm is derived using a combination of structural analysis, Analytical Redundant Relations (ARR) and observer designs. Structural considerations on the system are used...
Model Based Fault Diagnosis in a Centrifugal Pump Application using Structural Analysis

DEFF Research Database (Denmark)

Kallesøe, C. S.; Izadi-Zamanabadi, Roozbeh; Rasmussen, Henrik

2004-01-01

A model based approach for fault detection and isolation in a centrifugal pump is proposed in this paper. The fault detection algorithm is derived using a combination of structural analysis, Analytical Redundant Relations (ARR) and observer designs. Structural considerations on the system are used...
Structural modeling and fuzzy-logic based diagnosis of a ship propulsion benchmark

DEFF Research Database (Denmark)

Izadi-Zamanabadi, Roozbeh; Blanke, M.; Katebi, S.D.

2000-01-01

An analysis of structural model of a ship propulsion benchmark leads to identifying the subsystems with inherent redundant information. For a nonlinear part of the system, a Fuzzy logic based FD algorithm with adaptive threshold is employed. The results illustrate the applicability of structural...
Reliability-Based Inspection Planning for Structural Systems

DEFF Research Database (Denmark)

Sørensen, John Dalsgaard

1993-01-01

A general model for reliability-based optimal inspection and repair strategies for structural systems is described. The total expected costs in the design lifetime is minimized with the number of inspections, the inspection times and efforts as decision variables. The equivalence of this model...... with a preposterior analysis from statistical decision theory is discussed. It is described how information obtained by an inspection can be used in a repair decision. Stochastic models for inspection, measurement and repair actions are presented. The general model is applied for inspection and repair planning...
An improved AODV routing protocol based on tower structure

Directory of Open Access Journals (Sweden)

Li Yong Qiang

2016-01-01

Full Text Available The paper proposed a new routing protocol(IAODV based on tower structure in the Ad Hoc network for the problem which Location Routing Protocol need hardware and Complex algorithm. By the simulation, The complexity of the new routing protocol is reduced without reducing the performance of the network.
Voting-based consensus clustering for combining multiple clusterings of chemical structures

Directory of Open Access Journals (Sweden)

Saeed Faisal

2012-12-01

Full Text Available Abstract Background Although many consensus clustering methods have been successfully used for combining multiple classifiers in many areas such as machine learning, applied statistics, pattern recognition and bioinformatics, few consensus clustering methods have been applied for combining multiple clusterings of chemical structures. It is known that any individual clustering method will not always give the best results for all types of applications. So, in this paper, three voting and graph-based consensus clusterings were used for combining multiple clusterings of chemical structures to enhance the ability of separating biologically active molecules from inactive ones in each cluster. Results The cumulative voting-based aggregation algorithm (CVAA, cluster-based similarity partitioning algorithm (CSPA and hyper-graph partitioning algorithm (HGPA were examined. The F-measure and Quality Partition Index method (QPI were used to evaluate the clusterings and the results were compared to the Ward’s clustering method. The MDL Drug Data Report (MDDR dataset was used for experiments and was represented by two 2D fingerprints, ALOGP and ECFP_4. The performance of voting-based consensus clustering method outperformed the Ward’s method using F-measure and QPI method for both ALOGP and ECFP_4 fingerprints, while the graph-based consensus clustering methods outperformed the Ward’s method only for ALOGP using QPI. The Jaccard and Euclidean distance measures were the methods of choice to generate the ensembles, which give the highest values for both criteria. Conclusions The results of the experiments show that consensus clustering methods can improve the effectiveness of chemical structures clusterings. The cumulative voting-based aggregation algorithm (CVAA was the method of choice among consensus clustering methods.
Frequency response function (FRF) based updating of a laser spot welded structure

Science.gov (United States)

Zin, M. S. Mohd; Rani, M. N. Abdul; Yunus, M. A.; Sani, M. S. M.; Wan Iskandar Mirza, W. I. I.; Mat Isa, A. A.

2018-04-01

The objective of this paper is to present frequency response function (FRF) based updating as a method for matching the finite element (FE) model of a laser spot welded structure with a physical test structure. The FE model of the welded structure was developed using CQUAD4 and CWELD element connectors, and NASTRAN was used to calculate the natural frequencies, mode shapes and FRF. Minimization of the discrepancies between the finite element and experimental FRFs was carried out using the exceptional numerical capability of NASTRAN Sol 200. The experimental work was performed under free-free boundary conditions using LMS SCADAS. Avast improvement in the finite element FRF was achieved using the frequency response function (FRF) based updating with two different objective functions proposed.
A Review of the Piezoelectric Electromechanical Impedance Based Structural Health Monitoring Technique for Engineering Structures

Directory of Open Access Journals (Sweden)

Wongi S. Na

2018-04-01

Full Text Available The birth of smart materials such as piezoelectric (PZT transducers has aided in revolutionizing the field of structural health monitoring (SHM based on non-destructive testing (NDT methods. While a relatively new NDT method known as the electromechanical (EMI technique has been investigated for more than two decades, there are still various problems that must be solved before it is applied to real structures. The technique, which has a significant potential to contribute to the creation of one of the most effective SHM systems, involves the use of a single PZT for exciting and sensing of the host structure. In this paper, studies applied for the past decade related to the EMI technique have been reviewed to understand its trend. In addition, new concepts and ideas proposed by various authors are also surveyed, and the paper concludes with a discussion of the potential directions for future works.
Multifunctional Polymer-Based Graphene Foams with Buckled Structure and Negative Poisson’s Ratio

Science.gov (United States)

Dai, Zhaohe; Weng, Chuanxin; Liu, Luqi; Hou, Yuan; Zhao, Xuanliang; Kuang, Jun; Shi, Jidong; Wei, Yueguang; Lou, Jun; Zhang, Zhong

2016-01-01

In this study, we report the polymer-based graphene foams through combination of bottom-up assembly and simple triaxially buckled structure design. The resulting polymer-based graphene foams not only effectively transfer the functional properties of graphene, but also exhibit novel negative Poisson’s ratio (NPR) behaviors due to the presence of buckled structure. Our results show that after the introduction of buckled structure, improvement in stretchability, toughness, flexibility, energy absorbing ability, hydrophobicity, conductivity, piezoresistive sensitivity and crack resistance could be achieved simultaneously. The combination of mechanical properties, multifunctional performance and unusual deformation behavior would lead to the use of our polymer-based graphene foams for a variety of novel applications in future such as stretchable capacitors or conductors, sensors and oil/water separators and so on. PMID:27608928
Kinetics of radiation-induced structural alterations in electron-irradiated polymer-based composites

International Nuclear Information System (INIS)

Zaikin, Yu.A.; Potanin, A.S.; Koztaeva, U.P.

2002-01-01

Complete text of publication follows. In our previous studies measurements of internal friction temperature dependence were used for characterization of thermally activated and radiation-induced structural evolution in different types of polymer-based composites. This paper supplements these measurements with kinetic studies of internal friction (IF) parameters and EPR signals in a glass-cloth epoxy-filled laminate ST-ETF after electron irradiation up to doses of 1-10 MGy. Experiment have shown that the lifetime of free radicals in this composite considerably exceeds the characteristic time of molecular structural rearrangement due to scission and cross-linking after irradiation, as determined from IF measurements. This result is explained by slow proceeding of sterically hindered disproportionation reactions that stabilize the end groups of the macro-chain disrupt during irradiation and finally fix the act of scission. A mathematical model is formulated for description of structural evolution and alterations of IF parameters in polymer-based composites during and after electron irradiation. The description is based on the track model of radiation damage in polymers and phenomenological theory of radiation-induced structural transformations. General description does not give details of radiation-chemical conversion in different structural components of composites but indicates the direction of their structural evolution. In the model considered a composite material was divided into three parts (binder, filler, and a boundary layer). It was supposed that after primary distribution of radiation energy radiation-chemical conversion proceeds independently in each of these regions. It was also suggested that all the radical reactions were of the second order. On the example of glass-cloth laminate ST-ETF it is shown that this model allows to describe alterations in composite structural characteristics during irradiation and in the course of their self-organization after
Photonic crystals based on opals and inverse opals: synthesis and structural features

International Nuclear Information System (INIS)

Klimonsky, S O; Abramova, Vera V; Sinitskii, Alexander S; Tretyakov, Yuri D

2011-01-01

Methods of synthesis of photonic crystals based on opals and inverse opals are considered. Their structural features are discussed. Data on different types of structural defects and their influence on the optical properties of opaline materials are systematized. The possibilities of investigation of structural defects by optical spectroscopy, electron microscopy, microradian X-ray diffraction, laser diffraction and using an analysis of Kossel ring patterns are described. The bibliography includes 253 references.
Correlation based method for comparing and reconstructing quasi-identical two-dimensional structures

International Nuclear Information System (INIS)

Mejia-Barbosa, Y.

2000-03-01

We show a method for comparing and reconstructing two similar amplitude-only structures, which are composed by the same number of identical apertures. The structures are two-dimensional and differ only in the location of one of the apertures. The method is based on a subtraction algorithm, which involves the auto-correlations and cross-correlation functions of the compared structures. Experimental results illustrate the feasibility of the method. (author)
Investigating energy-based pool structure selection in the structure ensemble modeling with experimental distance constraints: The example from a multidomain protein Pub1.

Science.gov (United States)

Zhu, Guanhua; Liu, Wei; Bao, Chenglong; Tong, Dudu; Ji, Hui; Shen, Zuowei; Yang, Daiwen; Lu, Lanyuan

2018-05-01

The structural variations of multidomain proteins with flexible parts mediate many biological processes, and a structure ensemble can be determined by selecting a weighted combination of representative structures from a simulated structure pool, producing the best fit to experimental constraints such as interatomic distance. In this study, a hybrid structure-based and physics-based atomistic force field with an efficient sampling strategy is adopted to simulate a model di-domain protein against experimental paramagnetic relaxation enhancement (PRE) data that correspond to distance constraints. The molecular dynamics simulations produce a wide range of conformations depicted on a protein energy landscape. Subsequently, a conformational ensemble recovered with low-energy structures and the minimum-size restraint is identified in good agreement with experimental PRE rates, and the result is also supported by chemical shift perturbations and small-angle X-ray scattering data. It is illustrated that the regularizations of energy and ensemble-size prevent an arbitrary interpretation of protein conformations. Moreover, energy is found to serve as a critical control to refine the structure pool and prevent data overfitting, because the absence of energy regularization exposes ensemble construction to the noise from high-energy structures and causes a more ambiguous representation of protein conformations. Finally, we perform structure-ensemble optimizations with a topology-based structure pool, to enhance the understanding on the ensemble results from different sources of pool candidates. © 2018 Wiley Periodicals, Inc.
Large-Scale, Exhaustive Lattice-Based Structural Auditing of SNOMED CT

Science.gov (United States)

Zhang, Guo-Qiang

One criterion for the well-formedness of ontologies is that their hierarchical structure form a lattice. Formal Concept Analysis (FCA) has been used as a technique for assessing the quality of ontologies, but is not scalable to large ontologies such as SNOMED CT. We developed a methodology called Lattice-based Structural Auditing (LaSA), for auditing biomedical ontologies, implemented through automated SPARQL queries, in order to exhaustively identify all non-lattice pairs in SNOMED CT. The percentage of non-lattice pairs ranges from 0 to 1.66 among the 19 SNOMED CT hierarchies. Preliminary manual inspection of a limited portion of the 518K non-lattice pairs, among over 34 million candidate pairs, revealed inconsistent use of precoordination in SNOMED CT, but also a number of false positives. Our results are consistent with those based on FCA, with the advantage that the LaSA computational pipeline is scalable and applicable to ontological systems consisting mostly of taxonomic links. This work is based on collaboration with Olivier Bodenreider from the National Library of Medicine, Bethesda, USA.
Structure and magnetism in novel group IV element-based magnetic materials

Energy Technology Data Exchange (ETDEWEB)

Tsui, Frank [Univ. of North Carolina, Chapel Hill, NC (United States)

2013-08-14

The project is to investigate structure, magnetism and spin dependent states of novel group IV element-based magnetic thin films and heterostructures as a function of composition and epitaxial constraints. The materials systems of interest are Si-compatible epitaxial films and heterostructures of Si/Ge-based magnetic ternary alloys grown by non-equilibrium molecular beam epitaxy (MBE) techniques, specifically doped magnetic semiconductors (DMS) and half-metallic Heusler alloys. Systematic structural, chemical, magnetic, and electrical measurements are carried out, using x-ray microbeam techniques, magnetotunneling spectroscopy and microscopy, and magnetotransport. The work is aimed at elucidating the nature and interplay between structure, chemical order, magnetism, and spin-dependent states in these novel materials, at developing materials and techniques to realize and control fully spin polarized states, and at exploring fundamental processes that stabilize the epitaxial magnetic nanostructures and control the electronic and magnetic states in these complex materials. Combinatorial approach provides the means for the systematic studies, and the complex nature of the work necessitates this approach.
SMOG 2: A Versatile Software Package for Generating Structure-Based Models.

Science.gov (United States)

Noel, Jeffrey K; Levi, Mariana; Raghunathan, Mohit; Lammert, Heiko; Hayes, Ryan L; Onuchic, José N; Whitford, Paul C

2016-03-01

Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.
SMOG 2: A Versatile Software Package for Generating Structure-Based Models.

Directory of Open Access Journals (Sweden)

Jeffrey K Noel

2016-03-01

Full Text Available Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.

Development of uncertainty-based work injury model using Bayesian structural equation modelling.

Science.gov (United States)

Chatterjee, Snehamoy

2014-01-01

This paper proposed a Bayesian method-based structural equation model (SEM) of miners' work injury for an underground coal mine in India. The environmental and behavioural variables for work injury were identified and causal relationships were developed. For Bayesian modelling, prior distributions of SEM parameters are necessary to develop the model. In this paper, two approaches were adopted to obtain prior distribution for factor loading parameters and structural parameters of SEM. In the first approach, the prior distributions were considered as a fixed distribution function with specific parameter values, whereas, in the second approach, prior distributions of the parameters were generated from experts' opinions. The posterior distributions of these parameters were obtained by applying Bayesian rule. The Markov Chain Monte Carlo sampling in the form Gibbs sampling was applied for sampling from the posterior distribution. The results revealed that all coefficients of structural and measurement model parameters are statistically significant in experts' opinion-based priors, whereas, two coefficients are not statistically significant when fixed prior-based distributions are applied. The error statistics reveals that Bayesian structural model provides reasonably good fit of work injury with high coefficient of determination (0.91) and less mean squared error as compared to traditional SEM.
Band structure calculation of GaSe-based nanostructures using empirical pseudopotential method

International Nuclear Information System (INIS)

Osadchy, A V; Obraztsova, E D; Volotovskiy, S G; Golovashkin, D L; Savin, V V

2016-01-01

In this paper we present the results of band structure computer simulation of GaSe- based nanostructures using the empirical pseudopotential method. Calculations were performed using a specially developed software that allows performing simulations using cluster computing. Application of this method significantly reduces the demands on computing resources compared to traditional approaches based on ab-initio techniques and provides receiving the adequate comparable results. The use of cluster computing allows to obtain information for structures that require an explicit account of a significant number of atoms, such as quantum dots and quantum pillars. (paper)
Stability and electronic structure of Zr-based ternary metallic glasses and relevant compounds

International Nuclear Information System (INIS)

Hasegawa, M.; Soda, K.; Sato, H.; Suzuki, T.; Taketomi, T.; Takeuchi, T.; Kato, H.; Mizutani, U.

2007-01-01

The electronic structure of the Zr-based metallic glasses has been investigated by theoretical and experimental approaches. One approach is band calculations of the Zr 2 Ni (Zr 66.7 Ni 33.3 ) compound to investigate the electronic structure of the Zr 66.7 Ni 33.3 metallic glass (ΔT x = 0 K) of which the local atomic structure is similar to that of the Zr 2 Ni compound. The other is photoemission spectroscopy of the Zr 50 Cu 35 Al 15 bulk metallic glass (BMG) (ΔT x = 69 K). Here ΔT x = T x - T g where T x and T g are crystallization and glass transition temperature, respectively. Both results and previous ones on the Zr 55 Cu 30 Ni 5 Al 10 BMG indicate that there is a pseudogap at the Fermi level in the electronic structure of these Zr-based metallic glasses, independent of the value of the ΔT x . This implies that the pseudogap at the Fermi level is one of the factors that stabilize the glass phase of Zr-based metallic glasses
A pairwise residue contact area-based mean force potential for discrimination of native protein structure

Directory of Open Access Journals (Sweden)

Pezeshk Hamid

2010-01-01

Full Text Available Abstract Background Considering energy function to detect a correct protein fold from incorrect ones is very important for protein structure prediction and protein folding. Knowledge-based mean force potentials are certainly the most popular type of interaction function for protein threading. They are derived from statistical analyses of interacting groups in experimentally determined protein structures. These potentials are developed at the atom or the amino acid level. Based on orientation dependent contact area, a new type of knowledge-based mean force potential has been developed. Results We developed a new approach to calculate a knowledge-based potential of mean-force, using pairwise residue contact area. To test the performance of our approach, we performed it on several decoy sets to measure its ability to discriminate native structure from decoys. This potential has been able to distinguish native structures from the decoys in the most cases. Further, the calculated Z-scores were quite high for all protein datasets. Conclusions This knowledge-based potential of mean force can be used in protein structure prediction, fold recognition, comparative modelling and molecular recognition. The program is available at http://www.bioinf.cs.ipm.ac.ir/softwares/surfield
MOVPE and characterization of GaN-based structures on alternative substrates

Energy Technology Data Exchange (ETDEWEB)

Dikme, Y.

2006-06-20

This study involves growth experiments of GaN-based layer structures on silicon (Si), lithium aluminate (LiAlO{sub 2}) and the composite substrate SiCOI. Substrate specific preparation and growth procedures were developed. Because of the different lattice constants and thermal expansion coefficients between GaN and the substrate materials and because of the high depositions temperatures (>1000 C) complex interlayers are required to create a crossover from the substrate to the GaN layer and to prevent substrate/layer bowing and cracks developing in the epitaxial layers. Crystallographic, thermal and electronic properties of these materials were investigated and the developed layers were used as buffer layers for electronic and opto electronic devices. On Si AlN/GaN distributed Bragg reflectors (DBR), InGaN/GaN multiple quantum well (MQW) and AlGaN/GaN HEMT (high electron mobility transistor) were demonstrated. The transistor structures showed high power densities, which were comparable to industrially fabricated devices. As well as the reflection of a certain wavelength region, the DBR layers additionally showed positive influence on succeeding GaN top layer optical properties. For the first time laser emission of an optically pumped InGaN/GaN MQW on Si was demonstrated with low excitation density and a high operating temperature. GaN-based structures were deposited on LiAlO2 in the m-plane crystal orientation; that do not exhibit polarization mechanisms in growth direction. For the deposition of coalesced GaN films a seal-coating of the LiAlO{sub 2} surface was developed and finally LED structures were grown on these substrates. For the first time electroluminescence of LED structures on LiAlO{sub 2} was achieved. The growth on the composite substrate SiCOI was initiated with an HT AlN layer and it was demonstrated that SiCOI is comparable to a bulk SiC substrate for the GaN-based epitaxy. The developed and investigated layer structure served as buffer for the
Fast protein tertiary structure retrieval based on global surface shape similarity.

Science.gov (United States)

Sael, Lee; Li, Bin; La, David; Fang, Yi; Ramani, Karthik; Rustamov, Raif; Kihara, Daisuke

2008-09-01

Characterization and identification of similar tertiary structure of proteins provides rich information for investigating function and evolution. The importance of structure similarity searches is increasing as structure databases continue to expand, partly due to the structural genomics projects. A crucial drawback of conventional protein structure comparison methods, which compare structures by their main-chain orientation or the spatial arrangement of secondary structure, is that a database search is too slow to be done in real-time. Here we introduce a global surface shape representation by three-dimensional (3D) Zernike descriptors, which represent a protein structure compactly as a series expansion of 3D functions. With this simplified representation, the search speed against a few thousand structures takes less than a minute. To investigate the agreement between surface representation defined by 3D Zernike descriptor and conventional main-chain based representation, a benchmark was performed against a protein classification generated by the combinatorial extension algorithm. Despite the different representation, 3D Zernike descriptor retrieved proteins of the same conformation defined by combinatorial extension in 89.6% of the cases within the top five closest structures. The real-time protein structure search by 3D Zernike descriptor will open up new possibility of large-scale global and local protein surface shape comparison. 2008 Wiley-Liss, Inc.
Visualizing RNA Secondary Structure Base Pair Binding Probabilities using Nested Concave Hulls

OpenAIRE

Sansen , Joris; Bourqui , Romain; Thebault , Patricia; Allali , Julien; Auber , David

2015-01-01

International audience; The challenge 1 of the BIOVIS 2015 design contest consists in designing an intuitive visual depiction of base pairs binding probabilities for secondary structure of ncRNA. Our representation depicts the potential nucleotide pairs binding using nested concave hulls over the computed MFE ncRNA secondary structure. Thus, it allows to identify regions with a high level of uncertainty in the MFE computation and the structures which seem to match to reality.
Fluid, solid and fluid-structure interaction simulations on patient-based abdominal aortic aneurysm models.

Science.gov (United States)

Kelly, Sinead; O'Rourke, Malachy

2012-04-01

This article describes the use of fluid, solid and fluid-structure interaction simulations on three patient-based abdominal aortic aneurysm geometries. All simulations were carried out using OpenFOAM, which uses the finite volume method to solve both fluid and solid equations. Initially a fluid-only simulation was carried out on a single patient-based geometry and results from this simulation were compared with experimental results. There was good qualitative and quantitative agreement between the experimental and numerical results, suggesting that OpenFOAM is capable of predicting the main features of unsteady flow through a complex patient-based abdominal aortic aneurysm geometry. The intraluminal thrombus and arterial wall were then included, and solid stress and fluid-structure interaction simulations were performed on this, and two other patient-based abdominal aortic aneurysm geometries. It was found that the solid stress simulations resulted in an under-estimation of the maximum stress by up to 5.9% when compared with the fluid-structure interaction simulations. In the fluid-structure interaction simulations, flow induced pressure within the aneurysm was found to be up to 4.8% higher than the value of peak systolic pressure imposed in the solid stress simulations, which is likely to be the cause of the variation in the stress results. In comparing the results from the initial fluid-only simulation with results from the fluid-structure interaction simulation on the same patient, it was found that wall shear stress values varied by up to 35% between the two simulation methods. It was concluded that solid stress simulations are adequate to predict the maximum stress in an aneurysm wall, while fluid-structure interaction simulations should be performed if accurate prediction of the fluid wall shear stress is necessary. Therefore, the decision to perform fluid-structure interaction simulations should be based on the particular variables of interest in a given
Vision based condition assessment of structures

International Nuclear Information System (INIS)

Uhl, Tadeusz; Kohut, Piotr; Holak, Krzysztof; Krupinski, Krzysztof

2011-01-01

In this paper, a vision-based method for measuring a civil engineering construction's in-plane deflection curves is presented. The displacement field of the analyzed object which results from loads was computed by means of a digital image correlation coefficient. Image registration techniques were introduced to increase the flexibility of the method. The application of homography mapping enabled the deflection field to be computed from two images of the structure, acquired from two different points in space. An automatic shape filter and a corner detector were implemented to calculate the homography mapping between the two views. The developed methodology, created architecture and the capabilities of software tools, as well as experimental results obtained from tests made on a lab set-up and civil engineering constructions, are discussed.
A scheme of hidden-structure attribute-based encryption with multiple authorities

Science.gov (United States)

Ling, J.; Weng, A. X.

2018-05-01

In the most of the CP-ABE schemes with hidden access structure, both all the user attributes and the key generation are managed by only one authority. The key generation efficiency will decrease as the number of user increases, and the data will encounter security issues as the only authority is attacked. We proposed a scheme of hidden-structure attribute-based encryption with multiple authorities, which introduces multiple semi-trusted attribute authorities, avoiding the threat even though one or more authorities are attacked. We also realized user revocation by managing a revocation list. Based on DBDH assumption, we proved that our scheme is of IND-CMA security. The analysis shows that our scheme improves the key generation efficiency.
Towards risk-based structural integrity methods for PWRs

International Nuclear Information System (INIS)

Chapman, O.J.V.; Lloyd, R.B.

1992-01-01

This paper describes the development of risk-based structural integrity assurance methods and their application to Pressurized Water Reactor (PWR) plant. In-service inspection is introduced as a way of reducing the failure probability of high risk sites and the latter are identified using reliability analysis; the extent and interval of inspection can also be optimized. The methodology is illustrated by reference to the aspect of reliability of weldments in PWR systems. (author)
Feedback structure based entropy approach for multiple-model estimation

Institute of Scientific and Technical Information of China (English)

Shen-tu Han; Xue Anke; Guo Yunfei

2013-01-01

The variable-structure multiple-model (VSMM) approach, one of the multiple-model (MM) methods, is a popular and effective approach in handling problems with mode uncertainties. The model sequence set adaptation (MSA) is the key to design a better VSMM. However, MSA methods in the literature have big room to improve both theoretically and practically. To this end, we propose a feedback structure based entropy approach that could find the model sequence sets with the smallest size under certain conditions. The filtered data are fed back in real time and can be used by the minimum entropy (ME) based VSMM algorithms, i.e., MEVSMM. Firstly, the full Markov chains are used to achieve optimal solutions. Secondly, the myopic method together with particle filter (PF) and the challenge match algorithm are also used to achieve sub-optimal solutions, a trade-off between practicability and optimality. The numerical results show that the proposed algorithm provides not only refined model sets but also a good robustness margin and very high accuracy.
Fibre-reinforced composite structures based on thermoplastic matrices with embedded piezoceramic modules

International Nuclear Information System (INIS)

Hufenbach, Werner A; Modler, Niels; Winkler, Anja; Ilg, Juergen; Rupitsch, Stefan J

2014-01-01

The paper presents recent developments for the integration of piezoceramic modules into fibre-reinforced composite structures based on thermoplastic matrices. An adapted hot pressing technology is conceptualized that allows for material homogeneous integration of the active modules. The main focus of this contribution is on the development of a robust and continuous manufacturing process of such novel active composites as well as on the operational testing of the produced samples. Therefore, selected specimens are manufactured as bending beams and investigated by means of electrical impedance measurements, modal analysis and structural excitation tests. In particular, the functionality of representative specimens is characterized based on frequency as well as spatially resolved deflection measurements. Moreover, the mentioned samples are compared to non-integrated piezoceramic modules and to equivalent passive reinforced composite structures. (paper)
eSBMTools 1.0: enhanced native structure-based modeling tools.

Science.gov (United States)

Lutz, Benjamin; Sinner, Claude; Heuermann, Geertje; Verma, Abhinav; Schug, Alexander

2013-11-01

Molecular dynamics simulations provide detailed insights into the structure and function of biomolecular systems. Thus, they complement experimental measurements by giving access to experimentally inaccessible regimes. Among the different molecular dynamics techniques, native structure-based models (SBMs) are based on energy landscape theory and the principle of minimal frustration. Typically used in protein and RNA folding simulations, they coarse-grain the biomolecular system and/or simplify the Hamiltonian resulting in modest computational requirements while achieving high agreement with experimental data. eSBMTools streamlines running and evaluating SBM in a comprehensive package and offers high flexibility in adding experimental- or bioinformatics-derived restraints. We present a software package that allows setting up, modifying and evaluating SBM for both RNA and proteins. The implemented workflows include predicting protein complexes based on bioinformatics-derived inter-protein contact information, a standardized setup of protein folding simulations based on the common PDB format, calculating reaction coordinates and evaluating the simulation by free-energy calculations with weighted histogram analysis method or by phi-values. The modules interface with the molecular dynamics simulation program GROMACS. The package is open source and written in architecture-independent Python2. http://sourceforge.net/projects/esbmtools/. alexander.schug@kit.edu. Supplementary data are available at Bioinformatics online.
Rehabilitation reliability of the road pavement structure with recycled base course with foamed bitumen

Science.gov (United States)

Buczyński, P.

2018-05-01

This article presents a new approach to reliability assessment of the road structure in which the base layer will be constructed in the process of cold deep recycling with foamed bitumen. In order to properly assess the reliability of the structure with the recycled base, it is necessary to determine the distribution of stress and strain in typical pavement layer systems. The true stress and strain values were established for particular structural layers using the complex modulus (E*) determined based on the master curves. The complex modulus was determined by the direct tension-compression test on cylindrical specimens (DTC-CY) at five temperatures (-7°C, 5°C, 13°C, 25°C, 40°C) and six loading times (0.1 Hz, 0.3 Hz, 1 Hz, 3 Hz, 10 Hz, 20 Hz) in accordance with EN 12697-26 in the linear viscoelasticity (LVE) range for small strains ranging from 25 to 50 με. The master curves of the complex modulus were constructed using the Richards model for the mixtures typically incorporated in structural layers, i.e., SMA11, AC16W, AC22P and MCAS. The values of the modulus characterizing particular layers were determined with temperature distribution in the structure taken into account, when the surface temperature was 40°C. The stress distribution was established for those calculation models. The stress values were used to evaluate the fatigue life under controlled stress conditions (IT-FT). This evaluation, with the controlled stress corresponding to that in the structure, facilitated the quality assessment of the rehabilitated recycled base course. Results showed that the recycled base mixtures having the indirect tensile strength (ITSDRY) similar to the stress in the structure under analysis needed an additional fatigue life evaluation in the indirect tensile test ITT. This approach to the recycled base quality assessment will allow eliminating the damage induced by overloading.
Lagrangian based methods for coherent structure detection

Energy Technology Data Exchange (ETDEWEB)

Allshouse, Michael R., E-mail: mallshouse@chaos.utexas.edu [Center for Nonlinear Dynamics and Department of Physics, University of Texas at Austin, Austin, Texas 78712 (United States); Peacock, Thomas, E-mail: tomp@mit.edu [Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)

2015-09-15

There has been a proliferation in the development of Lagrangian analytical methods for detecting coherent structures in fluid flow transport, yielding a variety of qualitatively different approaches. We present a review of four approaches and demonstrate the utility of these methods via their application to the same sample analytic model, the canonical double-gyre flow, highlighting the pros and cons of each approach. Two of the methods, the geometric and probabilistic approaches, are well established and require velocity field data over the time interval of interest to identify particularly important material lines and surfaces, and influential regions, respectively. The other two approaches, implementing tools from cluster and braid theory, seek coherent structures based on limited trajectory data, attempting to partition the flow transport into distinct regions. All four of these approaches share the common trait that they are objective methods, meaning that their results do not depend on the frame of reference used. For each method, we also present a number of example applications ranging from blood flow and chemical reactions to ocean and atmospheric flows.
Analysis, Design, and Construction of a Base-Isolated Multiple Building Structure

Directory of Open Access Journals (Sweden)

Stefano Sorace

2014-01-01

Full Text Available The analysis and design of a multiple residential building, seismically protected by a base isolation system incorporating double friction pendulum sliders as protective devices, are presented in the paper. The building, situated in the suburban area of Florence, is composed of four independent reinforced concrete framed structures, mutually separated by three thermal expansion joints. The plan is L-shaped, with dimensions of about 75 m in the longitudinal direction and about 30 m along the longest side of the transversal direction. These characteristics identify the structure as the largest example of a base-isolated “artificial ground” ever built in Italy. The base isolation solution guarantees lower costs, a much greater performance, and a finer architectural look, as compared to a conventional fixed-base antiseismic design. The characteristics of the building and the isolators, the mechanical properties and the experimental characterization campaign and preliminary sizing carried out on the latter, and the nonlinear time-history design and performance assessment analyses developed on the base isolated building are reported in this paper, along with details about the installation of the isolators and the plants and highlights of the construction works.
Structure of nanoparticles in transformer oil-based magnetic fluids, anisotropy of acoustic attenuation

International Nuclear Information System (INIS)

Kúdelčík, Jozef; Bury, Peter; Kopčanský, Peter; Timko, Milan

2015-01-01

The anisotropy of acoustic attenuation in transformer oil-based magnetic fluids upon the external magnetic field was studied to discover the structure of nanoparticles. When a magnetic field is increased, the interaction between the external magnetic field and the magnetic moments of the nanoparticles leads to the aggregation of magnetic nanoparticles and following clusters formation. However, the temperature of magnetic fluids and the concentration of nanoparticles also have very important influence on the structural changes. The measurement of the dependence of the acoustic attenuation on the angle between the magnetic field direction and acoustic wave vector (anisotropy) can give the useful information about the structure of magnetic nanoparticles formations. In the present, the results of anisotropy measurements of the transformer oil-based magnetic fluids are described and using appropriate theory the basic parameters of clusters are calculated. On the basis of the performed calculations, the proportion of the acoustic wave energy used for excitation of the translational and rotational degrees of freedom was also established. - Highlights: • Nanoparticles formation in transformer oil-based magnetic fluids was investigated. • The anisotropy acoustic spectroscopy as the method of investigation was used. • The external conditions on the structure of magnetic fluids were studied. • The structure parameters using suitable theoretical model were determined
Structure of nanoparticles in transformer oil-based magnetic fluids, anisotropy of acoustic attenuation

Energy Technology Data Exchange (ETDEWEB)

Kúdelčík, Jozef, E-mail: kudelcik@fyzika.uniza.sk [Department of Physics, University of Žilina, Univerzitná 1, 010 01 Žilina (Slovakia); Bury, Peter [Department of Physics, University of Žilina, Univerzitná 1, 010 01 Žilina (Slovakia); Kopčanský, Peter; Timko, Milan [Department of Magnetism, IEP SAS, Watsonova 47, 040 01 Košice (Slovakia)

2015-08-15

The anisotropy of acoustic attenuation in transformer oil-based magnetic fluids upon the external magnetic field was studied to discover the structure of nanoparticles. When a magnetic field is increased, the interaction between the external magnetic field and the magnetic moments of the nanoparticles leads to the aggregation of magnetic nanoparticles and following clusters formation. However, the temperature of magnetic fluids and the concentration of nanoparticles also have very important influence on the structural changes. The measurement of the dependence of the acoustic attenuation on the angle between the magnetic field direction and acoustic wave vector (anisotropy) can give the useful information about the structure of magnetic nanoparticles formations. In the present, the results of anisotropy measurements of the transformer oil-based magnetic fluids are described and using appropriate theory the basic parameters of clusters are calculated. On the basis of the performed calculations, the proportion of the acoustic wave energy used for excitation of the translational and rotational degrees of freedom was also established. - Highlights: • Nanoparticles formation in transformer oil-based magnetic fluids was investigated. • The anisotropy acoustic spectroscopy as the method of investigation was used. • The external conditions on the structure of magnetic fluids were studied. • The structure parameters using suitable theoretical model were determined.
Scenario based approach to structural damage detection and its value in a risk and reliability perspective

DEFF Research Database (Denmark)

Hovgaard, Mads Knude; Hansen, Jannick Balleby; Brincker, Rune

2013-01-01

A scenario- and vibration based structural damage detection method is demonstrated though simulation. The method is Finite Element (FE) based. The value of the monitoring is calculated using structural reliability theory. A high cycle fatigue crack propagation model is assumed as the damage mecha......- and without monitoring. Monte Carlo Sampling (MCS) is used to estimate the probabilities and the tower of an onshore NREL 5MW wind turbine is given as a calculation case......A scenario- and vibration based structural damage detection method is demonstrated though simulation. The method is Finite Element (FE) based. The value of the monitoring is calculated using structural reliability theory. A high cycle fatigue crack propagation model is assumed as the damage...

Multi-atlas pancreas segmentation: Atlas selection based on vessel structure.

Science.gov (United States)

Karasawa, Ken'ichi; Oda, Masahiro; Kitasaka, Takayuki; Misawa, Kazunari; Fujiwara, Michitaka; Chu, Chengwen; Zheng, Guoyan; Rueckert, Daniel; Mori, Kensaku

2017-07-01

Automated organ segmentation from medical images is an indispensable component for clinical applications such as computer-aided diagnosis (CAD) and computer-assisted surgery (CAS). We utilize a multi-atlas segmentation scheme, which has recently been used in different approaches in the literature to achieve more accurate and robust segmentation of anatomical structures in computed tomography (CT) volume data. Among abdominal organs, the pancreas has large inter-patient variability in its position, size and shape. Moreover, the CT intensity of the pancreas closely resembles adjacent tissues, rendering its segmentation a challenging task. Due to this, conventional intensity-based atlas selection for pancreas segmentation often fails to select atlases that are similar in pancreas position and shape to those of the unlabeled target volume. In this paper, we propose a new atlas selection strategy based on vessel structure around the pancreatic tissue and demonstrate its application to a multi-atlas pancreas segmentation. Our method utilizes vessel structure around the pancreas to select atlases with high pancreatic resemblance to the unlabeled volume. Also, we investigate two types of applications of the vessel structure information to the atlas selection. Our segmentations were evaluated on 150 abdominal contrast-enhanced CT volumes. The experimental results showed that our approach can segment the pancreas with an average Jaccard index of 66.3% and an average Dice overlap coefficient of 78.5%. Copyright © 2017 Elsevier B.V. All rights reserved.
Photovoltaic X-ray detectors based on epitaxial GaAs structures

Energy Technology Data Exchange (ETDEWEB)

Achmadullin, R.A. [Institute of Radio Engineering and Electronics, Russian Academy of Sciences, 1 Ac. Vvedenski square, Fryazino 141190, Moscow region (Russian Federation); Artemov, V.V. [Shubnikov Institute of Crystallography, Russian Academy of Sciences, 59 Leninski pr., Moscow B-333, 117333 (Russian Federation); Dvoryankin, V.F. [Institute of Radio Engineering and Electronics, Russian Academy of Sciences, 1 Ac. Vvedenski square, Fryazino 141190, Moscow region (Russian Federation)]. E-mail: vfd217@ire216.msk.su; Dvoryankina, G.G. [Institute of Radio Engineering and Electronics, Russian Academy of Sciences, 1 Ac. Vvedenski square, Fryazino 141190, Moscow region (Russian Federation); Dikaev, Yu.M. [Institute of Radio Engineering and Electronics, Russian Academy of Sciences, 1 Ac. Vvedenski square, Fryazino 141190, Moscow region (Russian Federation); Ermakov, M.G. [Institute of Radio Engineering and Electronics, Russian Academy of Sciences, 1 Ac. Vvedenski square, Fryazino 141190, Moscow region (Russian Federation); Ermakova, O.N. [Institute of Radio Engineering and Electronics, Russian Academy of Sciences, 1 Ac. Vvedenski square, Fryazino 141190, Moscow region (Russian Federation); Chmil, V.B. [Scientific State Center, High Energy Physics Institute, Protvino, Moscow region (Russian Federation); Holodenko, A.G. [Scientific State Center, High Energy Physics Institute, Protvino, Moscow region (Russian Federation); Kudryashov, A.A.; Krikunov, A.I.; Petrov, A.G.; Telegin, A.A. [Institute of Radio Engineering and Electronics, Russian Academy of Sciences, 1 Ac. Vvedenski square, Fryazino 141190, Moscow region (Russian Federation); Vorobiev, A.P. [Scientific State Center, High Energy Physics Institute, Protvino, Moscow region (Russian Federation)

2005-12-01

A new type of the photovoltaic X-ray detector based on epitaxial p{sup +}-n-n'-n{sup +} GaAs structures which provides a high efficiency of charge collection in the non-bias operation mode at room temperature is proposed. The GaAs epitaxial structures were grown by vapor-phase epitaxy on heavily doped n{sup +}-GaAs(1 0 0) substrates. The absorption efficiency of GaAs X-ray detector is discussed. I-V and C-V characteristics of the photovoltaic X-ray detectors are analyzed. The built-in electric field profiles in the depletion region of epitaxial structures are measured by the EBIC method. Charge collection efficiency to {alpha}-particles and {gamma}-radiation are measured. The application of X-ray detectors is discussed.
Structure and manual of radioisotope-production data base, ISOP

International Nuclear Information System (INIS)

Hata, Kentaro; Terunuma, Kusuo

1994-02-01

We planned on collecting the information of radioisotope production which was obtained from research works and tasks at the Department of Radioisotopes in JAERI, and constructed a proto-type data base ISOP after discussion of the kinds and properties of the information available for radioisotope production. In this report the structure and the manual of ISOP are described. (author)
A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs.

Science.gov (United States)

Kumbhar, Sadhana; Johannsen, Silke; Sigel, Roland K O; Waller, Mark P; Müller, Jens

2013-10-01

A series of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations was performed on models of a DNA duplex with artificial silver(I)-mediated imidazole base pairs. The optimized structures were compared to the original experimental NMR structure (Nat. Chem. 2 (2010) 229-234). The metal⋯metal distances are significantly shorter (~0.5Å) in the QM/MM model than in the original NMR structure. As a result, argentophilic interactions are feasible between the silver(I) ions of neighboring metal-mediated base pairs. Using the computationally determined metal⋯metal distances, a re-refined NMR solution structure of the DNA duplex was obtained. In this new NMR structure, all experimental constraints remain fulfilled. The new NMR structure shows less deviation from the regular B-type conformation than the original one. This investigation shows that the application of QM/MM models to generate additional constraints to be used during NMR structural refinements represents an elegant approach to obtaining high-resolution NMR structures. Copyright © 2013 Elsevier Inc. All rights reserved.
Homogenization-based topology optimization for high-resolution manufacturable micro-structures

DEFF Research Database (Denmark)

Groen, Jeroen Peter; Sigmund, Ole

2018-01-01

This paper presents a projection method to obtain high-resolution, manufacturable structures from efficient and coarse-scale, homogenization-based topology optimization results. The presented approach bridges coarse and fine scale, such that the complex periodic micro-structures can be represented...... by a smooth and continuous lattice on the fine mesh. A heuristic methodology allows control of the projected topology, such that a minimum length-scale on both solid and void features is ensured in the final result. Numerical examples show excellent behavior of the method, where performances of the projected...
Optimization of morphing flaps based on fluid structure interaction modeling

DEFF Research Database (Denmark)

Barlas, Athanasios; Akay, Busra

2018-01-01

This article describes the design optimization of morphing trailing edge flaps for wind turbines with ‘smart blades’. A high fidelity Fluid Structure Interaction (FSI) simulation framework is utilized, comprised of 2D Finite Element Analysis (FEA) and Computational Fluid Dynamics (CFD) models....... A coupled aero-structural simulation of a 10% chordwise length morphing trailing edge flap for a 4 MW wind turbine rotor is carried out and response surfaces are produced with respect to the flap internal geometry design parameters for the design conditions. Surrogate model based optimization is applied...
The optimal design of the bed structure of bedstand based on ABAQUS

Science.gov (United States)

Yang, Xudong; Dong, Yu; Ge, Qingkuan; Wang, Song

2017-12-01

Hydraulic transmission bedstand is one kind of the most commonly used in engineering machinery companies, and the bed structure is the most important part. Based on the original hydraulic transmission bedstand bed structure and the CAE technology, the original bed structure is improved. The optimized bed greatly saves the material of the production bed and improves the seismic performance of the bed. In the end, the performance of the optimized bed was compared with the original bed.
Socio-political structure of Tokat at the bases of the local elections

OpenAIRE

D. Ali Arslan; Mehmet Karataş; Sadettin Baştürk; Gülten Arslan

2013-01-01

The major ofjective of this study was to examine and discuss the political structure of Tokat and its place in the general political structure of Turkish society by using methods and techniques of political sociology. Structural-functionalist approach was used as the theoretical base. In the other words the formation of political power in Tokat and the overall operation and changing regularities were investigated. Both the province of Tokat and Tokat city center selected as the sampling group...
GNSS-based multi-sensor system for structural monitoring applications

Science.gov (United States)

Bogusz, Janusz; Figurski, Mariusz; Nykiel, Grzegorz; Szolucha, Marcin; Wrona, Maciej

2012-03-01

In 2007 the Centre of Applied Geomatics of the Military University of Technology started measurements aimed at the monitoring of the dynamic state of the engineering structures using GNSS. The complexity of the problem forced us to apply an integrated system architecture. This concept is based on simultaneous measuring some selected elements of the structure using various types of sensors. Measurement information from numerous instruments is numerically integrated for determining the investigated parameter, e.g., the displacement vector. The CAG team performed the tests using such a system on the two permanent 500-meters long bridges, the temporary bridge crossing for military purposes and the 300-meters high chimney of the CHP station. The information about displacement vector together with the characteristic frequencies of the structure were determined using different techniques for increasing of its reliability. This paper presents the results of such tests, gives description of the integrated system designed in the CAG and brings forward with the plans for the future.
Optimization of power plants management structure based on the generalized criteria of the efficiency

Directory of Open Access Journals (Sweden)

Salov Aleksey

2017-01-01

Full Text Available In the article, the analysis of the operation of power plants in the conditions of economic restructuring to ensure successful entry into the market is carried out. The analysis of the five management structures, including current, typical structure and re-designed by the authors is presented. There are developed the partial efficiency criteria of the management structures that characterize the most important properties - the balance, integrity, controllability and stability. Local criteria of the analyzed structures do not allow to make a definite conclusion about the effectiveness of one of the structures analyzed, formulated global efficiency criterion. There is developed the global criterion of the comparative effectiveness of the management systems based on the DEA method (Data envelopment analysis, taking into account the complex of the proposed local criteria. The considered management structures are ranked based on the generalized criterion of efficiency.
Fracture Characteristics of C/SiC Composites for Rocket Nozzle at Elevated Temperature

Energy Technology Data Exchange (ETDEWEB)

Yoon, Dong Hyun; Lee, Jeong Won; Kim, Jae Hoon [Chungnam Nat’l Univ., Daejeon (Korea, Republic of); Sihn, Ihn Cheol; Lim, Byung Joo [Dai-Yang Industries Co., Daejeon (Korea, Republic of)

2016-11-15

In a solid propulsion system, the rocket nozzle is exposed to high temperature combustion gas. Hence, choosing an appropriate material that could demonstrate adequate performance at high temperature is important. As advanced materials, carbon/silicon carbide composites (C/SiC) have been studied with the aim of using them for the rocket nozzle throat. However, when compared with typical structural materials, C/SiC composites are relatively weak in terms of both strength and toughness, owing to their quasi-brittle behavior and oxidation at high temperatures. Therefore, it is important to evaluate the thermal and mechanical properties of this material before using it in this application. This study presents an experimental method to investigate the fracture behavior of C/SiC composite material manufactured using liquid silicon infiltration (LSI) method at elevated temperatures. In particular, the effects of major parameters, such as temperature, loading, oxidation conditions, and fiber direction on strength and fracture characteristics were investigated. Fractography analysis of the fractured specimens was performed using an SEM.
Structure-based characterization of multiprotein complexes.

Science.gov (United States)

Wiederstein, Markus; Gruber, Markus; Frank, Karl; Melo, Francisco; Sippl, Manfred J

2014-07-08

Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.
UAV-based urban structural damage assessment using object-based image analysis and semantic reasoning

Science.gov (United States)

Fernandez Galarreta, J.; Kerle, N.; Gerke, M.

2015-06-01

Structural damage assessment is critical after disasters but remains a challenge. Many studies have explored the potential of remote sensing data, but limitations of vertical data persist. Oblique imagery has been identified as more useful, though the multi-angle imagery also adds a new dimension of complexity. This paper addresses damage assessment based on multi-perspective, overlapping, very high resolution oblique images obtained with unmanned aerial vehicles (UAVs). 3-D point-cloud assessment for the entire building is combined with detailed object-based image analysis (OBIA) of façades and roofs. This research focuses not on automatic damage assessment, but on creating a methodology that supports the often ambiguous classification of intermediate damage levels, aiming at producing comprehensive per-building damage scores. We identify completely damaged structures in the 3-D point cloud, and for all other cases provide the OBIA-based damage indicators to be used as auxiliary information by damage analysts. The results demonstrate the usability of the 3-D point-cloud data to identify major damage features. Also the UAV-derived and OBIA-processed oblique images are shown to be a suitable basis for the identification of detailed damage features on façades and roofs. Finally, we also demonstrate the possibility of aggregating the multi-perspective damage information at building level.
A resource-based theory of market structure and organizational form

NARCIS (Netherlands)

van Witteloostuijn, A.; Boone, C.A.J.J.

We argue that combining the insights from both the industrial organization and organizational ecology perspectives is likely to produce value added. We develop a resource-based theory of market structure, where resources pertain to the environmental assets (together forming the resource space)
A new entropy based method for computing software structural complexity

CERN Document Server

Roca, J L

2002-01-01

In this paper a new methodology for the evaluation of software structural complexity is described. It is based on the entropy evaluation of the random uniform response function associated with the so called software characteristic function SCF. The behavior of the SCF with the different software structures and their relationship with the number of inherent errors is investigated. It is also investigated how the entropy concept can be used to evaluate the complexity of a software structure considering the SCF as a canonical representation of the graph associated with the control flow diagram. The functions, parameters and algorithms that allow to carry out this evaluation are also introduced. After this analytic phase follows the experimental phase, verifying the consistency of the proposed metric and their boundary conditions. The conclusion is that the degree of software structural complexity can be measured as the entropy of the random uniform response function of the SCF. That entropy is in direct relation...
Tunable elastic parity-time symmetric structure based on the shunted piezoelectric materials

Science.gov (United States)

Hou, Zhilin; Assouar, Badreddine

2018-02-01

We theoretically and numerically report on the tunable elastic Parity-Time (PT) symmetric structure based on shunted piezoelectric units. We show that the elastic loss and gain can be archived in piezoelectric materials when they are shunted by external circuits containing positive and negative resistances. We present and discuss, as an example, the strongly dependent relationship between the exceptional points of a three-layered system and the impedance of their external shunted circuit. The achieved results evidence that the PT symmetric structures based on this proposed concept can actively be tuned without any change of their geometric configurations.
An optimum organizational structure for a large earth-orbiting multidisciplinary Space Base

Science.gov (United States)

Ragusa, J. M.

1973-01-01

The purpose of this exploratory study was to identify an optimum hypothetical organizational structure for a large earth-orbiting multidisciplinary research and applications (R&A) Space Base manned by a mixed crew of technologists. Since such a facility does not presently exist, in situ empirical testing was not possible. Study activity was, therefore, concerned with the identification of a desired organizational structural model rather than the empirical testing of it. The essential finding of this research was that a four-level project type 'total matrix' model will optimize the efficiency and effectiveness of Space Base technologists.
Bridge Structure Deformation Prediction Based on GNSS Data Using Kalman-ARIMA-GARCH Model.

Science.gov (United States)

Xin, Jingzhou; Zhou, Jianting; Yang, Simon X; Li, Xiaoqing; Wang, Yu

2018-01-19

Bridges are an essential part of the ground transportation system. Health monitoring is fundamentally important for the safety and service life of bridges. A large amount of structural information is obtained from various sensors using sensing technology, and the data processing has become a challenging issue. To improve the prediction accuracy of bridge structure deformation based on data mining and to accurately evaluate the time-varying characteristics of bridge structure performance evolution, this paper proposes a new method for bridge structure deformation prediction, which integrates the Kalman filter, autoregressive integrated moving average model (ARIMA), and generalized autoregressive conditional heteroskedasticity (GARCH). Firstly, the raw deformation data is directly pre-processed using the Kalman filter to reduce the noise. After that, the linear recursive ARIMA model is established to analyze and predict the structure deformation. Finally, the nonlinear recursive GARCH model is introduced to further improve the accuracy of the prediction. Simulation results based on measured sensor data from the Global Navigation Satellite System (GNSS) deformation monitoring system demonstrated that: (1) the Kalman filter is capable of denoising the bridge deformation monitoring data; (2) the prediction accuracy of the proposed Kalman-ARIMA-GARCH model is satisfactory, where the mean absolute error increases only from 3.402 mm to 5.847 mm with the increment of the prediction step; and (3) in comparision to the Kalman-ARIMA model, the Kalman-ARIMA-GARCH model results in superior prediction accuracy as it includes partial nonlinear characteristics (heteroscedasticity); the mean absolute error of five-step prediction using the proposed model is improved by 10.12%. This paper provides a new way for structural behavior prediction based on data processing, which can lay a foundation for the early warning of bridge health monitoring system based on sensor data using sensing
Bridge Structure Deformation Prediction Based on GNSS Data Using Kalman-ARIMA-GARCH Model

Directory of Open Access Journals (Sweden)

Jingzhou Xin

2018-01-01

Full Text Available Bridges are an essential part of the ground transportation system. Health monitoring is fundamentally important for the safety and service life of bridges. A large amount of structural information is obtained from various sensors using sensing technology, and the data processing has become a challenging issue. To improve the prediction accuracy of bridge structure deformation based on data mining and to accurately evaluate the time-varying characteristics of bridge structure performance evolution, this paper proposes a new method for bridge structure deformation prediction, which integrates the Kalman filter, autoregressive integrated moving average model (ARIMA, and generalized autoregressive conditional heteroskedasticity (GARCH. Firstly, the raw deformation data is directly pre-processed using the Kalman filter to reduce the noise. After that, the linear recursive ARIMA model is established to analyze and predict the structure deformation. Finally, the nonlinear recursive GARCH model is introduced to further improve the accuracy of the prediction. Simulation results based on measured sensor data from the Global Navigation Satellite System (GNSS deformation monitoring system demonstrated that: (1 the Kalman filter is capable of denoising the bridge deformation monitoring data; (2 the prediction accuracy of the proposed Kalman-ARIMA-GARCH model is satisfactory, where the mean absolute error increases only from 3.402 mm to 5.847 mm with the increment of the prediction step; and (3 in comparision to the Kalman-ARIMA model, the Kalman-ARIMA-GARCH model results in superior prediction accuracy as it includes partial nonlinear characteristics (heteroscedasticity; the mean absolute error of five-step prediction using the proposed model is improved by 10.12%. This paper provides a new way for structural behavior prediction based on data processing, which can lay a foundation for the early warning of bridge health monitoring system based on sensor data
Base Isolation for Seismic Retrofitting of a Multiple Building Structure: Design, Construction, and Assessment

Directory of Open Access Journals (Sweden)

Massimiliano Ferraioli

2017-01-01

Full Text Available The paper deals with the seismic retrofit of a multiple building structure belonging to the Hospital Centre of Avellino (Italy. At first, the paper presents the preliminary investigations, the in situ measurements and laboratory tests, and the seismic assessment of the existing fixed-base structures. Having studied different strategies, base isolation proved to be the more appropriate, also for the possibility offered by the geometry of the building to easily create an isolation interface at the ground level. The paper presents the design project, the construction process, and the details of the isolation intervention. Some specific issues of base isolation for seismic retrofitting of multiple building structures were lightened. Finally, the seismic assessment of the base-isolated building was carried out. The seismic response was evaluated through nonlinear time-history analysis, using the well-known Bouc-Wen model as the constitutive law of the isolation bearings. For reliable dynamic analyses, a suite of natural accelerograms compatible with acceleration spectra of Italian Code was first selected and then applied along both horizontal directions. The results were finally used to address some of the critical issues of the seismic response of the base-isolated multiple building structure: accidental torsional effects and potential poundings during strong earthquakes.

Targeting Dengue Virus NS-3 Helicase by Ligand based Pharmacophore Modeling and Structure based Virtual Screening

Science.gov (United States)

Halim, Sobia A.; Khan, Shanza; Khan, Ajmal; Wadood, Abdul; Mabood, Fazal; Hussain, Javid; Al-Harrasi, Ahmed

2017-10-01

Dengue fever is an emerging public health concern, with several million viral infections occur annually, for which no effective therapy currently exist. Non-structural protein 3 (NS-3) Helicase encoded by the dengue virus (DENV) is considered as a potential drug target to design new and effective drugs against dengue. Helicase is involved in unwinding of dengue RNA. This study was conducted to design new NS-3 Helicase inhibitor by in silico ligand- and structure based approaches. Initially ligand-based pharmacophore model was generated that was used to screen a set of 1201474 compounds collected from ZINC Database. The compounds matched with the pharmacophore model were docked into the active site of NS-3 helicase. Based on docking scores and binding interactions, twenty five compounds are suggested to be potential inhibitors of NS3 Helicase. The pharmacokinetic properties of these hits were predicted. The selected hits revealed acceptable ADMET properties. This study identified potential inhibitors of NS-3 Helicase in silico, and can be helpful in the treatment of Dengue.
The Seismic Reliability of Offshore Structures Based on Nonlinear Time History Analyses

International Nuclear Information System (INIS)

Hosseini, Mahmood; Karimiyani, Somayyeh; Ghafooripour, Amin; Jabbarzadeh, Mohammad Javad

2008-01-01

Regarding the past earthquakes damages to offshore structures, as vital structures in the oil and gas industries, it is important that their seismic design is performed by very high reliability. Accepting the Nonlinear Time History Analyses (NLTHA) as the most reliable seismic analysis method, in this paper an offshore platform of jacket type with the height of 304 feet, having a deck of 96 feet by 94 feet, and weighing 290 million pounds has been studied. At first, some Push-Over Analyses (POA) have been preformed to recognize the more critical members of the jacket, based on the range of their plastic deformations. Then NLTHA have been performed by using the 3-components accelerograms of 100 earthquakes, covering a wide range of frequency content, and normalized to three Peak Ground Acceleration (PGA) levels of 0.3 g, 0.65 g, and 1.0 g. By using the results of NLTHA the damage and rupture probabilities of critical member have been studied to assess the reliability of the jacket structure. Regarding that different structural members of the jacket have different effects on the stability of the platform, an ''importance factor'' has been considered for each critical member based on its location and orientation in the structure, and then the reliability of the whole structure has been obtained by combining the reliability of the critical members, each having its specific importance factor
Grid-based electronic structure calculations: The tensor decomposition approach

Energy Technology Data Exchange (ETDEWEB)

Rakhuba, M.V., E-mail: rakhuba.m@gmail.com [Skolkovo Institute of Science and Technology, Novaya St. 100, 143025 Skolkovo, Moscow Region (Russian Federation); Oseledets, I.V., E-mail: i.oseledets@skoltech.ru [Skolkovo Institute of Science and Technology, Novaya St. 100, 143025 Skolkovo, Moscow Region (Russian Federation); Institute of Numerical Mathematics, Russian Academy of Sciences, Gubkina St. 8, 119333 Moscow (Russian Federation)

2016-05-01

We present a fully grid-based approach for solving Hartree–Fock and all-electron Kohn–Sham equations based on low-rank approximation of three-dimensional electron orbitals. Due to the low-rank structure the total complexity of the algorithm depends linearly with respect to the one-dimensional grid size. Linear complexity allows for the usage of fine grids, e.g. 8192{sup 3} and, thus, cheap extrapolation procedure. We test the proposed approach on closed-shell atoms up to the argon, several molecules and clusters of hydrogen atoms. All tests show systematical convergence with the required accuracy.
Acoustic investigation of structure of magnetic fluids based on transformer oil mogul

International Nuclear Information System (INIS)

Kudelcik, J.; Bury, P.; Kopcansky, P.; Timko, M.

2013-01-01

In this paper the authors study the influence of temperature on the changes of the acoustic attenuation in magnetic fluids based on transformer oil MOGUL caused by an external magnetic field measured. The influences of both magnetic field and temperature on the structures of investigated magnetic fluids based on the transformer oil MOGUL were observed using acoustic spectroscopy. The effect of external magnetic field on the creation of clusters of nanoparticles in magnetic fluids was confirmed and their influence on the development of attenuation was described. In this type of magnetic fluid complicated structures of clusters at magnetic field over 100 mT are created. These structures are than at higher magnetic field almost stable. This state of equilibrium is not function of time. Measurements also confirmed that the lifetime of these structures or clusters is very short. The further investigation of the time and temperature dependences of the acoustic attenuation on the magnetic field at different concentrations of magnetic nanoparticles and various direction of magnetic field are necessary to understand all processes in this magnetic fluid. (authors)
Research on energy stock market associated network structure based on financial indicators

Science.gov (United States)

Xi, Xian; An, Haizhong

2018-01-01

A financial market is a complex system consisting of many interacting units. In general, due to the various types of information exchange within the industry, there is a relationship between the stocks that can reveal their clear structural characteristics. Complex network methods are powerful tools for studying the internal structure and function of the stock market, which allows us to better understand the stock market. Applying complex network methodology, a stock associated network model based on financial indicators is created. Accordingly, we set threshold value and use modularity to detect the community network, and we analyze the network structure and community cluster characteristics of different threshold situations. The study finds that the threshold value of 0.7 is the abrupt change point of the network. At the same time, as the threshold value increases, the independence of the community strengthens. This study provides a method of researching stock market based on the financial indicators, exploring the structural similarity of financial indicators of stocks. Also, it provides guidance for investment and corporate financial management.
Fiber Temperature Sensor Based on Micro-mechanical Membranes and Optical Interference Structure

International Nuclear Information System (INIS)

Liu Yueming; Tian Weijian; Hua Jing

2011-01-01

A novel fiber temperature sensor is presented theoretically and experimentally in this paper. Its working principle is based on Optical Fabry-Perot interference structure that is formed between a polished optical fiber end and micro-mechanical Bi-layered membranes. When ambient temperature is varying, Bi-layered membranes will be deflected and the length of Fabry-Perot cavity will be changed correspondingly. By detecting the reflecting optical intensity from the Fabry-Perot cavity, the ambient temperature can be measured. Using finite element software ANSYS, the sensor structure was optimized based on optical Interference theory and Bi-layered membranes thermal expansion theory, and theoretical characteristics was simulated by computer software. In the end, using optical fiber 2x2 coupler and photo-electrical detector, the fabricated sample sensor was tested successfully by experiment that demonstrating above theoretical analysis and simulation results. This sensor has some favorable features, such as: micro size owing to its micro-mechanical structure, high sensitivity owing to its working Fabry-Perot interference cavity structure, and optical integration character by using optical fiber techniques.
System data structures for on-line distributed data base management system

International Nuclear Information System (INIS)

Wade, J.A.

1981-01-01

Described herein are the data structures used in implementing a distributed data base management system (DBMS) for the Mirror Fusion Test Facility (MFTF), a part of the Mirror Fusion Energy Program at the Lawrence Livermore National Laboratory. The hardware and software frameworks within which the DBMS have been developed are first described, followed by a brief look at the motivation and fundamental design goals of the system. The structures are given in detail
Structural health monitoring system of soccer arena based on optical sensors

Science.gov (United States)

Shishkin, Victor V.; Churin, Alexey E.; Kharenko, Denis S.; Zheleznova, Maria A.; Shelemba, Ivan S.

2014-05-01

A structural health monitoring system based on optical sensors has been developed and installed on the indoor soccer arena "Zarya" in Novosibirsk. The system integrates 119 fiber optic sensors: 85 strain, 32 temperature and 2 displacement sensors. In addition, total station is used for measuring displacement in 45 control points. All of the constituents of the supporting structure are subjects for monitoring: long-span frames with under floor ties, connections, purlins and foundation.
System data structures for on-line distributed data base management system

Energy Technology Data Exchange (ETDEWEB)

Wade, J.A.

1981-01-28

Described herein are the data structures used in implementing a distributed data base management system (DBMS) for the Mirror Fusion Test Facility (MFTF), a part of the Mirror Fusion Energy Program at the Lawrence Livermore National Laboratory. The hardware and software frameworks within which the DBMS have been developed are first described, followed by a brief look at the motivation and fundamental design goals of the system. The structures are given in detail.
Vision based condition assessment of structures

Energy Technology Data Exchange (ETDEWEB)

Uhl, Tadeusz; Kohut, Piotr; Holak, Krzysztof; Krupinski, Krzysztof, E-mail: tuhl@agh.edu.pl, E-mail: pko@agh.edu.pl, E-mail: holak@agh.edu.pl, E-mail: krzysiek.krupinski@wp.pl [Department of Robotics and Mechatronics, AGH-University of Science and Technology, Al.Mickiewicza 30, 30-059 Cracow (Poland)

2011-07-19

In this paper, a vision-based method for measuring a civil engineering construction's in-plane deflection curves is presented. The displacement field of the analyzed object which results from loads was computed by means of a digital image correlation coefficient. Image registration techniques were introduced to increase the flexibility of the method. The application of homography mapping enabled the deflection field to be computed from two images of the structure, acquired from two different points in space. An automatic shape filter and a corner detector were implemented to calculate the homography mapping between the two views. The developed methodology, created architecture and the capabilities of software tools, as well as experimental results obtained from tests made on a lab set-up and civil engineering constructions, are discussed.
Ultrafast protein structure-based virtual screening with Panther

Science.gov (United States)

Niinivehmas, Sanna P.; Salokas, Kari; Lätti, Sakari; Raunio, Hannu; Pentikäinen, Olli T.

2015-10-01

Molecular docking is by far the most common method used in protein structure-based virtual screening. This paper presents Panther, a novel ultrafast multipurpose docking tool. In Panther, a simple shape-electrostatic model of the ligand-binding area of the protein is created by utilizing the protein crystal structure. The features of the possible ligands are then compared to the model by using a similarity search algorithm. On average, one ligand can be processed in a few minutes by using classical docking methods, whereas using Panther processing takes Panther protocol can be used in several applications, such as speeding up the early phases of drug discovery projects, reducing the number of failures in the clinical phase of the drug development process, and estimating the environmental toxicity of chemicals. Panther-code is available in our web pages (http://www.jyu.fi/panther) free of charge after registration.
Thermodynamic heuristics with case-based reasoning: combined insights for RNA pseudoknot secondary structure.

Science.gov (United States)

Al-Khatib, Ra'ed M; Rashid, Nur'Aini Abdul; Abdullah, Rosni

2011-08-01

The secondary structure of RNA pseudoknots has been extensively inferred and scrutinized by computational approaches. Experimental methods for determining RNA structure are time consuming and tedious; therefore, predictive computational approaches are required. Predicting the most accurate and energy-stable pseudoknot RNA secondary structure has been proven to be an NP-hard problem. In this paper, a new RNA folding approach, termed MSeeker, is presented; it includes KnotSeeker (a heuristic method) and Mfold (a thermodynamic algorithm). The global optimization of this thermodynamic heuristic approach was further enhanced by using a case-based reasoning technique as a local optimization method. MSeeker is a proposed algorithm for predicting RNA pseudoknot structure from individual sequences, especially long ones. This research demonstrates that MSeeker improves the sensitivity and specificity of existing RNA pseudoknot structure predictions. The performance and structural results from this proposed method were evaluated against seven other state-of-the-art pseudoknot prediction methods. The MSeeker method had better sensitivity than the DotKnot, FlexStem, HotKnots, pknotsRG, ILM, NUPACK and pknotsRE methods, with 79% of the predicted pseudoknot base-pairs being correct.
Three-dimensional glue detection and evaluation based on linear structured light

Science.gov (United States)

Xiao, Zhitao; Yang, Ruipeng; Geng, Lei; Liu, Yanbei

2018-01-01

During the online glue detection of body in white (BIW), the purpose of traditional glue detection based on machine vision is the localization and segmentation of glue, which is dissatisfactory for estimating the uniformity of glue with complex shape. A three-dimensional glue detection method based on the linear structured light and the movement parameters of robot is proposed. Firstly, the linear structured light and epipolar constraint algorithm are used for sign matching of binocular vision. Then, hand-eye relationship between robot and binocular camera is utilized to unified coordinate system. Finally, a structured light stripe extraction method is proposed to extract the sub-pixel coordinates of the light strip center. Experiments results demonstrate that the propose method can estimate the shape of glue accurately. For three kinds of glue with complex shape and uneven illumination, our method can detect the positions of blemishes. The absolute error of measurement is less than 1.04mm and the relative error is less than 10% respectively, which is suitable for online glue detection in BIW.
Pumped shot noise in adiabatically modulated graphene-based double-barrier structures.

Science.gov (United States)

Zhu, Rui; Lai, Maoli

2011-11-16

Quantum pumping processes are accompanied by considerable quantum noise. Based on the scattering approach, we investigated the pumped shot noise properties in adiabatically modulated graphene-based double-barrier structures. It is found that compared with the Poisson processes, the pumped shot noise is dramatically enhanced where the dc pumped current changes flow direction, which demonstrates the effect of the Klein paradox.
Pumped shot noise in adiabatically modulated graphene-based double-barrier structures

Science.gov (United States)

Zhu, Rui; Lai, Maoli

2011-11-01

Quantum pumping processes are accompanied by considerable quantum noise. Based on the scattering approach, we investigated the pumped shot noise properties in adiabatically modulated graphene-based double-barrier structures. It is found that compared with the Poisson processes, the pumped shot noise is dramatically enhanced where the dc pumped current changes flow direction, which demonstrates the effect of the Klein paradox.
Design and practice for a picture archiving and communication system based structured report module

International Nuclear Information System (INIS)

Tian Junzhang; Jiang Guihua; Zheng Liyin; Ou Jingchai; Wu Pingyang; Hong Wensong; Jin Lin; Huang Dajiang; Zhang Xuelin

2004-01-01

Objective: To design and explore structured report module based on PACS, and to make diagnostic reports with pictures and words in application of computer implementing synchronous transmission of reports and pictures. Methods: 1000 Mb trunk net was adopted in PACS and 100 Mb was exchanged on tabletop. Structured report was designed with six function modules including basic item area, image sign area, diagnostic impression area, advice area, signature area, and picture area by application of programming language such as Delphi 6.0 and VC ++ 6.0. DICOM. Medical images or waveform were inserted directly in the diagnosis report through citing DICOM composite object. Basic function library was designed and constructed in whole system environment. Results: The structured report module based on PACS could structure image diagnosis report in inerrability structure in term of compute. The time and period of reports were shortened and utilization of report original datum were improved. Conclusion: The structured report module was in favor of promotion to combine with clinic teaching and scientific research. The quality and efficiency of image diagnosis work were raised by structured report module
Capturing hammerhead ribozyme structures in action by modulating general base catalysis.

Directory of Open Access Journals (Sweden)

Young-In Chi

2008-09-01

Full Text Available We have obtained precatalytic (enzyme-substrate complex and postcatalytic (enzyme-product complex crystal structures of an active full-length hammerhead RNA that cleaves in the crystal. Using the natural satellite tobacco ringspot virus hammerhead RNA sequence, the self-cleavage reaction was modulated by substituting the general base of the ribozyme, G12, with A12, a purine variant with a much lower pKa that does not significantly perturb the ribozyme's atomic structure. The active, but slowly cleaving, ribozyme thus permitted isolation of enzyme-substrate and enzyme-product complexes without modifying the nucleophile or leaving group of the cleavage reaction, nor any other aspect of the substrate. The predissociation enzyme-product complex structure reveals RNA and metal ion interactions potentially relevant to transition-state stabilization that are absent in precatalytic structures.
Synthesis and structural characterization of some trisulfide analoges of thiouracil-based antithyroid drugs

Science.gov (United States)

Bhabak, Krishna P.; Bhowmick, Debasish

2012-08-01

Thiourea-based antithyroid drugs are effectively used for the treatment of hyperthyroidism. In this paper, we describe the synthesis of new trisulfides (11-12) from the commonly used thiourea-based antithyroid drugs such as 6-n-propyl-2-thiouracil (PTU) and 6-methyl-2-thiouracil (MTU) in the reaction with I2/KI system. Structural analysis by single crystal X-ray diffraction studies revealed the stabilization of trisulfides by a lactam-lactim tautomerism facilitating effective intramolecular as well as intermolecular non-covalent interactions. Although the structures of both trisulfides were found to be quite similar, a notable difference in the intermolecular interactions was observed between compounds 11 and 12 leading to different structural patterns. Structural stabilization of these trisulfides by tautomerism followed by intramolecular as well as intermolecular H-bonds makes these molecules as perfect examples in molecular recognition with self-complementary donor and acceptor units within a single molecule.
Crack width monitoring of concrete structures based on smart film

International Nuclear Information System (INIS)

Zhang, Benniu; Wang, Shuliang; Li, Xingxing; Zhang, Xu; Yang, Guang; Qiu, Minfeng

2014-01-01

Due to its direct link to structural security, crack width is thought to be one of the most important parameters reflecting damage conditions of concrete structures. However, the width problem is difficult to solve with the existing structural health monitoring methods. In this paper, crack width monitoring by means of adhering enameled copper wires with different ultimate strains on the surface of structures is proposed, based on smart film crack monitoring put forward by the present authors. The basic idea of the proposed method is related to a proportional relationship between the crack width and ultimate strain of the broken wire. Namely, when a certain width of crack passes through the wire, some low ultimate strain wires will be broken and higher ultimate strain wires may stay non-broken until the crack extends to a larger scale. Detection of the copper wire condition as broken or non-broken may indicate the width of the structural crack. Thereafter, a multi-layered stress transfer model and specimen experiment are performed to quantify the relationship. A practical smart film is then redesigned with this idea and applied to Chongqing Jiangjin Yangtze River Bridge. (paper)
Crack width monitoring of concrete structures based on smart film

Science.gov (United States)

Zhang, Benniu; Wang, Shuliang; Li, Xingxing; Zhang, Xu; Yang, Guang; Qiu, Minfeng

2014-04-01

Due to its direct link to structural security, crack width is thought to be one of the most important parameters reflecting damage conditions of concrete structures. However, the width problem is difficult to solve with the existing structural health monitoring methods. In this paper, crack width monitoring by means of adhering enameled copper wires with different ultimate strains on the surface of structures is proposed, based on smart film crack monitoring put forward by the present authors. The basic idea of the proposed method is related to a proportional relationship between the crack width and ultimate strain of the broken wire. Namely, when a certain width of crack passes through the wire, some low ultimate strain wires will be broken and higher ultimate strain wires may stay non-broken until the crack extends to a larger scale. Detection of the copper wire condition as broken or non-broken may indicate the width of the structural crack. Thereafter, a multi-layered stress transfer model and specimen experiment are performed to quantify the relationship. A practical smart film is then redesigned with this idea and applied to Chongqing Jiangjin Yangtze River Bridge.

Structure and properties of compositions based on petroleum sulfonic acids

Energy Technology Data Exchange (ETDEWEB)

Tutorskii, I.A.; Sultanova, A.S.; Belkina, E.V.; Fomin, A.G. [Lomonosov Academy of Fine Chemical Technology, Moscow (Russian Federation)

1995-03-01

Colloidal characteristics of compositions based on petroleum sulfonic acids were studied. Neutralized heavy oil residue exhibits surface-active properties and contains an ultradisperse filler. Analysis of the compositions by size-exclusion-chromatography shows deep structural changes in the heavy acid residue upon neutralization with calcium carbonate.
Support system of a structure on a support base

International Nuclear Information System (INIS)

Arene, G.; Renaux, C.; Minguet, J.L.; Chantot, H.

1984-01-01

Two series of strips are fixed to the structure to be supported and to the base to define each one a closed convex envelope; the strips are flexible in the radial direction with regard to the envelope. The two series of strips are connected by a treillis of rigid bars set to form juxtaposed V or X. A good transversal rigidity and a certain radial flexibility are obtained. The invention can be applied to a fast neutron nuclear reactor, the reactor comprising a vertical axis vessel filled with liquid metal; the vessel rests on a support foundation by means of the support system proposed by the invention. The support system allows the supported structure to resist the effects of an eventual earthquake and brutal temperature variations [fr
PAN-based carbon fiber negative electrodes for structural lithium-ion batteries

OpenAIRE

Hellqvist Kjell, Maria; Jacques, Eric; Zenkert, Dan; Behm, Mårten; Lindbergh, Göran

2011-01-01

Several grades of commercially-available polyacrylonitrile (PAN)-based carbon fibers have been studied for structural lithium-ion batteries to understand how the sizing, different lithiation rates and number of fibers per tow affect the available reversible capacity, when used as both current collector and electrode, for use in structural batteries. The study shows that at moderate lithiation rates, 100 mA g-1, most of the carbon fibers display a reversible capacity close to or above 100 mAh ...
Structure Based Sequence Dependent Stiffness Scale for Trinucleotides: A Direct Method

OpenAIRE

Gromiha, M. Michael

2000-01-01

A new set of stiffness parameters for all the 32trinucleotide units has been set up directly from thethree dimensional structures of DNA molecules. It wasobserved that GAC/GTC is the stiffest trinucleotideand ACC/GGT is the most flexible one. The averagestiffness values computed for a set of operatorsequences using the new parameters correlate very wellwith the protein-DNA binding specificity and bindingfree energy change of 434 repressor and Cro repressor,respectively. The new structure base...
Scenario-Based Analysis on the Structural Change of Land Uses in China

Directory of Open Access Journals (Sweden)

Qian Xu

2013-01-01

Full Text Available Land Use/Land Cover change (LUCC is a key aspect of global environmental change, which has a significant impact on climate change. In the background of increasing global warming resulting from greenhouse effect, to understand the impact of land use change on climate change is necessary and meaningful. In this study, we choose China as the study area and explore the possible land use change trends based on the AgLU module and ERB module of global change assessment model (GCAM model and Global Change Assessment Model. We design three scenarios based on socioeconomic development and simulated the corresponding structure change of land use according to the three scenarios with different parameters. Then we simulate the different emission of CO2 under different scenarios based on the simulation results of structure change of land use. At last, we choose the most suitable scenario that could control the emission of CO2 best and obtain the relatively better land use structure change for adaption of climate change. Through this research we can provide a theoretical basis for the future land use planning to adapt to climate change.
Properties and Structure of In Situ Transformed PAN-Based Carbon Fibers

Directory of Open Access Journals (Sweden)

Jingjing Cao

2018-06-01

Full Text Available Carbon fibers in situ prepared during the hot-pressed sintering in a vacuum is termed in situ transformed polyacrylonitrile-based (PAN-based carbon fibers, and the fibrous precursors are the pre-oxidized PAN fibers. The properties and structure of in situ transformed PAN-based carbon fibers are investigated by Nano indenter, SEM, TEM, XRD, and Raman. The results showed that the microstructure of the fiber surface layer was compact, while the core was loose, with evenly-appearing microvoids. The elastic modulus and nanohardness of the fiber surface layer (303.87 GPa and 14.82 GPa were much higher than that of the core (16.57 GPa and 1.54 GPa, and its interlayer spacing d002 and crystallinity were about 0.347 nm and 0.97 respectively. It was found that the preferred orientation of the surface carbon layers with ordered carbon atomic arrangement tended to be parallel to the fiber axis, whereas the fiber core in the amorphous region exhibited a random texture and the carbon atomic arrangement was in a disordered state. It indicates that the in situ transformed PAN-based carbon fibers possess significantly turbostratic structure and anisotropy.
Structurally Based Therapeutic Evaluation: A Therapeutic and Practical Approach to Teaching Medicinal Chemistry.

Science.gov (United States)

Alsharif, Naser Z.; And Others

1997-01-01

Explains structurally based therapeutic evaluation of drugs, which uses seven therapeutic criteria in translating chemical and structural knowledge into therapeutic decision making in pharmaceutical care. In a Creighton University (Nebraska) medicinal chemistry course, students apply the approach to solve patient-related therapeutic problems in…
An embedded crack in a constant strain triangle utilizing extended finite element concepts

DEFF Research Database (Denmark)

Olesen, J.F.; Poulsen, P.N.

2013-01-01

This paper revisits the formulation of the CST element with an embedded discrete crack taking advantage of the direct formulations developed within the framework of the extended finite element method, XFEM. The result is a simple element for modeling cohesive fracture processes in quasi-brittle m......This paper revisits the formulation of the CST element with an embedded discrete crack taking advantage of the direct formulations developed within the framework of the extended finite element method, XFEM. The result is a simple element for modeling cohesive fracture processes in quasi......-element discontinuity of displacements. The formulation is based on a variational principle of virtual work involving only the interpolation of displacements. The good performance of the element is demonstrated through the comparison with three benchmark tests in which a single crack is propagated: The center cracked...
Electronic structures and band gaps of chains and sheets based on phenylacetylene units

International Nuclear Information System (INIS)

Kondo, Masakazu; Nozaki, Daijiro; Tachibana, Masamitsu; Yumura, Takashi; Yoshizawa, Kazunari

2005-01-01

We investigate the electronic structures of polymers composed of π-conjugated phenylacetylene (PA) units, m-PA-based and p-PA-based wires, at the extended Hueckel level of theory. It is demonstrated that these conjugated systems should have a variety of electric conductance. All of the one-dimensional (1D) chains and the two-dimensional (2D) sheet based on the m-PA unit are insulators with large band gaps of 2.56 eV because there is no effective orbital interaction with neighboring chains. On the other hand, p-PA-based 1D chains have relatively small band gaps that decrease with an increase in chain width (1.17-1.74 eV) and are semiconductive. The p-PA-based sheet called 'graphyne', a 2D-limit of the p-PA-based 1D chains, shows a small band gap of 0.89 eV. The variety of band electronic structures is discussed in terms of frontier crystal orbitals
Sparse data structure design for wavelet-based methods

Directory of Open Access Journals (Sweden)

Latu Guillaume

2011-12-01

Full Text Available This course gives an introduction to the design of efficient datatypes for adaptive wavelet-based applications. It presents some code fragments and benchmark technics useful to learn about the design of sparse data structures and adaptive algorithms. Material and practical examples are given, and they provide good introduction for anyone involved in the development of adaptive applications. An answer will be given to the question: how to implement and efficiently use the discrete wavelet transform in computer applications? A focus will be made on time-evolution problems, and use of wavelet-based scheme for adaptively solving partial differential equations (PDE. One crucial issue is that the benefits of the adaptive method in term of algorithmic cost reduction can not be wasted by overheads associated to sparse data management.
Analysis of structures based on a characteristic-strain model of creep

Energy Technology Data Exchange (ETDEWEB)

Bolton, J. [Alstom Power, Newbold Road, Rugby CV21 2NH (United Kingdom)], E-mail: janjohn.bolton@virgin.net

2008-01-15

A companion paper [Bolton J. In: A characteristic-strain model for creep, ECCC/I.Mech.E. conference on creep and fracture in high-temperature components, London, September 2005] describes a creep model based on a constant 'characteristic strain' at any temperature. The present paper discusses the application of such a model, first to simple structures and then to engineering components of general form under steady loading. A basis is proposed for identifying the stress within a structure, or within the critical part of a structure, which can be considered to govern both its overall and local deformations. The concept is similar to skeletal-point stress but is more readily applied to components of any shape. The implementation of the concept of 'structural stress' is discussed in the context of finite-element creep calculations. Consideration is given to the analysis of cracked structures, where very high strains at the crack tip must be accommodated.
Analysis of structures based on a characteristic-strain model of creep

Energy Technology Data Exchange (ETDEWEB)

Bolton, J. [Alstom Power, Newbold Road, Rugby CV21 2NH (United Kingdom)], E-mail: janjohn.bolton@virgin.net

2008-01-15

A companion paper [Bolton J. In: A characteristic-strain model for creep, ECCC/I.Mech.E. conference on creep and fracture in high-temperature components, London, September 2005] describes a creep model based on a constant 'characteristic strain' at any temperature. The present paper discusses the application of such a model, first to simple structures and then to engineering components of general form under steady loading. A basis is proposed for identifying the stress within a structure, or within the critical part of a structure, which can be considered to govern both its overall and local deformations. The concept is similar to skeletal-point stress but is more readily applied to components of any shape. The implementation of the concept of 'structural stress' is discussed in the context of finite-element creep calculations. Consideration is given to the analysis of cracked structures, where very high strains at the crack tip must be accommodated.
Analysis of structures based on a characteristic-strain model of creep

International Nuclear Information System (INIS)

Bolton, J.

2008-01-01

A companion paper [Bolton J. In: A characteristic-strain model for creep, ECCC/I.Mech.E. conference on creep and fracture in high-temperature components, London, September 2005] describes a creep model based on a constant 'characteristic strain' at any temperature. The present paper discusses the application of such a model, first to simple structures and then to engineering components of general form under steady loading. A basis is proposed for identifying the stress within a structure, or within the critical part of a structure, which can be considered to govern both its overall and local deformations. The concept is similar to skeletal-point stress but is more readily applied to components of any shape. The implementation of the concept of 'structural stress' is discussed in the context of finite-element creep calculations. Consideration is given to the analysis of cracked structures, where very high strains at the crack tip must be accommodated
A comparative study on stress and compliance based structural topology optimization

Science.gov (United States)

Hailu Shimels, G.; Dereje Engida, W.; Fakhruldin Mohd, H.

2017-10-01

Most of structural topology optimization problems have been formulated and solved to either minimize compliance or weight of a structure under volume or stress constraints, respectively. Even if, a lot of researches are conducted on these two formulation techniques separately, there is no clear comparative study between the two approaches. This paper intends to compare these formulation techniques, so that an end user or designer can choose the best one based on the problems they have. Benchmark problems under the same boundary and loading conditions are defined, solved and results are compared based on these formulations. Simulation results shows that the two formulation techniques are dependent on the type of loading and boundary conditions defined. Maximum stress induced in the design domain is higher when the design domains are formulated using compliance based formulations. Optimal layouts from compliance minimization formulation has complex layout than stress based ones which may lead the manufacturing of the optimal layouts to be challenging. Optimal layouts from compliance based formulations are dependent on the material to be distributed. On the other hand, optimal layouts from stress based formulation are dependent on the type of material used to define the design domain. High computational time for stress based topology optimization is still a challenge because of the definition of stress constraints at element level. Results also shows that adjustment of convergence criterions can be an alternative solution to minimize the maximum stress developed in optimal layouts. Therefore, a designer or end user should choose a method of formulation based on the design domain defined and boundary conditions considered.
Structure-Based Algorithms for Microvessel Classification

KAUST Repository

Smith, Amy F.

2015-02-01

© 2014 The Authors. Microcirculation published by John Wiley & Sons Ltd. Objective: Recent developments in high-resolution imaging techniques have enabled digital reconstruction of three-dimensional sections of microvascular networks down to the capillary scale. To better interpret these large data sets, our goal is to distinguish branching trees of arterioles and venules from capillaries. Methods: Two novel algorithms are presented for classifying vessels in microvascular anatomical data sets without requiring flow information. The algorithms are compared with a classification based on observed flow directions (considered the gold standard), and with an existing resistance-based method that relies only on structural data. Results: The first algorithm, developed for networks with one arteriolar and one venular tree, performs well in identifying arterioles and venules and is robust to parameter changes, but incorrectly labels a significant number of capillaries as arterioles or venules. The second algorithm, developed for networks with multiple inlets and outlets, correctly identifies more arterioles and venules, but is more sensitive to parameter changes. Conclusions: The algorithms presented here can be used to classify microvessels in large microvascular data sets lacking flow information. This provides a basis for analyzing the distinct geometrical properties and modelling the functional behavior of arterioles, capillaries, and venules.
Grating-based X-ray tomography of 3D food structures

DEFF Research Database (Denmark)

Miklos, Rikke; Nielsen, Mikkel Schou; Einarsdottir, Hildur

2016-01-01

A novel grating based X-ray phase-contrast tomographic method has been used to study how partly substitution of meat proteins with two different types of soy proteins affect the structure of the formed protein gel in meat emulsions. The measurements were performed at the Swiss synchrotron radiati...
High renewable content sandwich structures based on flax-basalt hybrids and biobased epoxy polymers

Science.gov (United States)

Colomina, S.; Boronat, T.; Fenollar, O.; Sánchez-Nacher, L.; Balart, R.

2014-05-01

In the last years, a growing interest in the development of high environmental efficiency materials has been detected and this situation is more accentuated in the field of polymers and polymer composites. In this work, green composite sandwich structures with high renewable content have been developed with core cork materials. The base resin for composites was a biobased epoxy resin derived from epoxidized vegetable oils. Hybrid basalt-flax fabrics have been used as reinforcements for composites and the influence of the stacking sequence has been evaluated in order to optimize the appropriate laminate structure for the sandwich bases. Core cork materials with different thickness have been used to evaluate performance of sandwich structures thus leading to high renewable content composite sandwich structures. Results show that position of basalt fabrics plays a key role in flexural fracture of sandwich structures due to differences in stiffness between flax and basalt fibers.
Higher order structural effects stabilizing the reverse watson-crick guanine-cytosine base pair in functional RNAs

KAUST Repository

Chawla, Mohit

2013-10-10

The G:C reverse Watson-Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. 2013 The Author(s).
TLP Structural Health Monitoring Based on Vibration Signal of Energy Harvesting System

Directory of Open Access Journals (Sweden)

Vahid Jahangiri

Full Text Available Abstract Structural Health Monitoring (SHM of Tension Leg Platform (TLP is very crucial for preventing catastrophic and sudden collapse of the structures. One of the methods of monitoring these structures is implementing SHM sensors. Supplying energy for these sensors for a long period is a challenging problem. So, one of the new methods of supplying energy for SHM, is usage of mechanical energy. In this method, the piezoelectric material is employed to convert the mechanical energy which is resulted from vibration of structure, to electrical energy. The advantage of this method is based on not implementing the battery charging system. Therefore, in this paper, after modeling TLP structure, energy supplying of these sensors with piezoelectric converters is studied. Furthermore, fault diagnosis of these structures in the presence of different uncertainties is proposed by the features of voltage signal, produced from piezoelectric patches and fuzzy classification method. Results show that this method can diagnose faults of the structure with an acceptable success rate.
Observer based on sliding mode variable structure for synchronization of chaotic systems

International Nuclear Information System (INIS)

Yin Xunhe; Shan Xiuming; Ren Yong

2003-01-01

In the paper an approach, based on the state observer of sliding mode variable structure, is used for synchronizing chaotic systems. It does not require either the computation of the Lyapunov exponents, or the initial conditions belonging to the same basin of attraction as the existed approaches based on the state observer for synchronizing chaotic systems. The approach is more robust against noise and parameter mismatch than the existed approaches based on the state observer for synchronizing chaotic systems, because the former uses variable structure control, which is strong robust with respect to noise and parameter mismatch in the error dynamics, the later uses an appropriate choice of the feedback gain. Two well-known chaotic systems, a chaotic Roessler system and a hyperchaotic Roessler system are considered as illustrative examples to demonstrate the effectiveness of the used approach by numerical simulations

Intermolecular G-quadruplex structure-based fluorescent DNA detection system.

Science.gov (United States)

Zhou, Hui; Wu, Zai-Sheng; Shen, Guo-Li; Yu, Ru-Qin

2013-03-15

Adopting multi-donors to pair with one acceptor could improve the performance of fluorogenic detection probes. However, common dyes (e.g., fluorescein) in close proximity to each other would self-quench the fluorescence, and the fluorescence is difficult to restore. In this contribution, we constructed a novel "multi-donors-to-one acceptor" fluorescent DNA detection system by means of the intermolecular G-quadruplex (IGQ) structure-based fluorescence signal enhancement combined with the hairpin oligonucleotide. The novel IGQ-hairpin system was characterized using the p53 gene as the model target DNA. The proposed system showed an improved assay performance due to the introduction of IGQ-structure into fluorescent signaling probes, which could inhibit the background fluorescence and increase fluorescence restoration amplitude of fluoresceins upon target DNA hybridization. The proof-of-concept scheme is expected to provide new insight into the potential of G-quadruplex structure and promote the application of fluorescent oligonucleotide probes in fundamental research, diagnosis, and treatment of genetic diseases. Copyright © 2012 Elsevier B.V. All rights reserved.
Scalable, ultra-resistant structural colors based on network metamaterials

KAUST Repository

Galinski, Henning

2017-05-05

Structural colors have drawn wide attention for their potential as a future printing technology for various applications, ranging from biomimetic tissues to adaptive camouflage materials. However, an efficient approach to realize robust colors with a scalable fabrication technique is still lacking, hampering the realization of practical applications with this platform. Here, we develop a new approach based on large-scale network metamaterials that combine dealloyed subwavelength structures at the nanoscale with lossless, ultra-thin dielectric coatings. By using theory and experiments, we show how subwavelength dielectric coatings control a mechanism of resonant light coupling with epsilon-near-zero regions generated in the metallic network, generating the formation of saturated structural colors that cover a wide portion of the spectrum. Ellipsometry measurements support the efficient observation of these colors, even at angles of 70°. The network-like architecture of these nanomaterials allows for high mechanical resistance, which is quantified in a series of nano-scratch tests. With such remarkable properties, these metastructures represent a robust design technology for real-world, large-scale commercial applications.
Model-based leakage localization in drinking water distribution networks using structured residuals

OpenAIRE

Puig Cayuela, Vicenç; Rosich, Albert

2013-01-01

In this paper, a new model based approach to leakage localization in drinking water networks is proposed based on generating a set of structured residuals. The residual evaluation is based on a numerical method based on an enhanced Newton-Raphson algorithm. The proposed method is suitable for water network systems because the non-linearities of the model make impossible to derive analytical residuals. Furthermore, the computed residuals are designed so that leaks are decoupled, which impro...
Structural invariance of multiple intelligences, based on the level of execution.

Science.gov (United States)

Almeida, Leandro S; Prieto, María Dolores; Ferreira, Arístides; Ferrando, Mercedes; Ferrandiz, Carmen; Bermejo, Rosario; Hernández, Daniel

2011-11-01

The independence of multiple intelligences (MI) of Gardner's theory has been debated since its conception. This article examines whether the one- factor structure of the MI theory tested in previous studies is invariant for low and high ability students. Two hundred ninety-four children (aged 5 to 7) participated in this study. A set of Gardner's Multiple Intelligence assessment tasks based on the Spectrum Project was used. To analyze the invariance of a general dimension of intelligence, the different models of behaviours were studied in samples of participants with different performance on the Spectrum Project tasks with Multi-Group Confirmatory Factor Analysis (MGCFA). Results suggest an absence of structural invariance in Gardner's tasks. Exploratory analyses suggest a three-factor structure for individuals with higher performance levels and a two-factor structure for individuals with lower performance levels.
System Reliability of Timber Trusses Based on Non-Linear Structural Modelling

DEFF Research Database (Denmark)

Hansson, Martin; Ellegaard, Peter

2006-01-01

. In this paper, Monte Carlo simulations of a timber W-truss with punched metal plate fasteners (nail plates) are performed. Structural timber displays a significant variability in strength and stiffness both within and between members and is described by a statistic model calibrated against data from Norway......Structural design is today concerned with single component performance where each limit state is related to a single mode of failure of a single component. Further, in limit state codes the strength variables are related to a deterministic value (usually the 5-percentile). However, in a structure...... with a number of elements, two different effects (called system effects) can be found: - The probabilistic system effect that is based on the reduced probability that weak sections coincide with the most stressed sections. - Structural load-sharing that is the ability to redistribute load between members...
Rock Failure Analysis Based on a Coupled Elastoplastic-Logarithmic Damage Model

Science.gov (United States)

Abdia, M.; Molladavoodi, H.; Salarirad, H.

2017-12-01

The rock materials surrounding the underground excavations typically demonstrate nonlinear mechanical response and irreversible behavior in particular under high in-situ stress states. The dominant causes of irreversible behavior are plastic flow and damage process. The plastic flow is controlled by the presence of local shear stresses which cause the frictional sliding. During this process, the net number of bonds remains unchanged practically. The overall macroscopic consequence of plastic flow is that the elastic properties (e.g. the stiffness of the material) are insensitive to this type of irreversible change. The main cause of irreversible changes in quasi-brittle materials such as rock is the damage process occurring within the material. From a microscopic viewpoint, damage initiates with the nucleation and growth of microcracks. When the microcracks length reaches a critical value, the coalescence of them occurs and finally, the localized meso-cracks appear. The macroscopic and phenomenological consequence of damage process is stiffness degradation, dilatation and softening response. In this paper, a coupled elastoplastic-logarithmic damage model was used to simulate the irreversible deformations and stiffness degradation of rock materials under loading. In this model, damage evolution & plastic flow rules were formulated in the framework of irreversible thermodynamics principles. To take into account the stiffness degradation and softening on post-peak region, logarithmic damage variable was implemented. Also, a plastic model with Drucker-Prager yield function was used to model plastic strains. Then, an algorithm was proposed to calculate the numerical steps based on the proposed coupled plastic and damage constitutive model. The developed model has been programmed in VC++ environment. Then, it was used as a separate and new constitutive model in DEM code (UDEC). Finally, the experimental Oolitic limestone rock behavior was simulated based on the developed
Alcohol sensor based on single-mode-multimode-single-mode fiber structure

Science.gov (United States)

Mefina Yulias, R.; Hatta, A. M.; Sekartedjo, Sekartedjo

2016-11-01

Alcohol sensor based on Single-mode -Multimode-Single-mode (SMS) fiber structure is being proposed to sense alcohol concentration in alcohol-water mixtures. This proposed sensor uses refractive index sensing as its sensing principle. Fabricated SMS fiber structure had 40 m of multimode length. With power input -6 dBm and wavelength 1550 nm, the proposed sensor showed good response with sensitivity 1,983 dB per % v/v with measurement range 05 % v/v and measurement span 0,5% v/v.
Structural damage detection based on stochastic subspace identification and statistical pattern recognition: I. Theory

Science.gov (United States)

Ren, W. X.; Lin, Y. Q.; Fang, S. E.

2011-11-01

One of the key issues in vibration-based structural health monitoring is to extract the damage-sensitive but environment-insensitive features from sampled dynamic response measurements and to carry out the statistical analysis of these features for structural damage detection. A new damage feature is proposed in this paper by using the system matrices of the forward innovation model based on the covariance-driven stochastic subspace identification of a vibrating system. To overcome the variations of the system matrices, a non-singularity transposition matrix is introduced so that the system matrices are normalized to their standard forms. For reducing the effects of modeling errors, noise and environmental variations on measured structural responses, a statistical pattern recognition paradigm is incorporated into the proposed method. The Mahalanobis and Euclidean distance decision functions of the damage feature vector are adopted by defining a statistics-based damage index. The proposed structural damage detection method is verified against one numerical signal and two numerical beams. It is demonstrated that the proposed statistics-based damage index is sensitive to damage and shows some robustness to the noise and false estimation of the system ranks. The method is capable of locating damage of the beam structures under different types of excitations. The robustness of the proposed damage detection method to the variations in environmental temperature is further validated in a companion paper by a reinforced concrete beam tested in the laboratory and a full-scale arch bridge tested in the field.
Applying Adaptive Swarm Intelligence Technology with Structuration in Web-Based Collaborative Learning

Science.gov (United States)

Huang, Yueh-Min; Liu, Chien-Hung

2009-01-01

One of the key challenges in the promotion of web-based learning is the development of effective collaborative learning environments. We posit that the structuration process strongly influences the effectiveness of technology used in web-based collaborative learning activities. In this paper, we propose an ant swarm collaborative learning (ASCL)…
Pose Self-Measurement of Noncooperative Spacecraft Based on Solar Panel Triangle Structure

Directory of Open Access Journals (Sweden)

Jingzhou Song

2015-01-01

Full Text Available Aiming at the recognition and location of noncooperative spacecraft, this paper presents a monocular vision pose measurement method based on solar triangle structure. First of all, an autonomous recognition algorithm of feature structure based on sliding window Hough transformation (SWHT and inscribed circle of a triangle is proposed, and the image coordinates of feature points on the triangle can be obtained relying on this algorithm, combined with the P4P algorithm and the structure of spacecraft, calculating the relative pose of target expressed by rotation and translation matrix. The whole algorithm can be loaded into the prewritten onboard program, which will get the autocomplete feature structure extraction and relative pose measurement without human intervention, and this method does not need to mount any markers on the target. Then compare the measured values with the accurate value of the laser tracker, so that a conclusion can be drawn that the maximum position error is lower than 5% and the rotation error is lower than 4%, which meets the requirements of noncooperative spacecraft’s pose measurement for observations, tracking, and docking in the final rendezvous phase.
Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies.

Science.gov (United States)

Ochs, Christopher; He, Zhe; Zheng, Ling; Geller, James; Perl, Yehoshua; Hripcsak, George; Musen, Mark A

2016-06-01

An Abstraction Network is a compact summary of an ontology's structure and content. In previous research, we showed that Abstraction Networks support quality assurance (QA) of biomedical ontologies. The development of an Abstraction Network and its associated QA methodologies, however, is a labor-intensive process that previously was applicable only to one ontology at a time. To improve the efficiency of the Abstraction-Network-based QA methodology, we introduced a QA framework that uses uniform Abstraction Network derivation techniques and QA methodologies that are applicable to whole families of structurally similar ontologies. For the family-based framework to be successful, it is necessary to develop a method for classifying ontologies into structurally similar families. We now describe a structural meta-ontology that classifies ontologies according to certain structural features that are commonly used in the modeling of ontologies (e.g., object properties) and that are important for Abstraction Network derivation. Each class of the structural meta-ontology represents a family of ontologies with identical structural features, indicating which types of Abstraction Networks and QA methodologies are potentially applicable to all of the ontologies in the family. We derive a collection of 81 families, corresponding to classes of the structural meta-ontology, that enable a flexible, streamlined family-based QA methodology, offering multiple choices for classifying an ontology. The structure of 373 ontologies from the NCBO BioPortal is analyzed and each ontology is classified into multiple families modeled by the structural meta-ontology. Copyright © 2016 Elsevier Inc. All rights reserved.
Characterization and crystal structures of new Schiff base macrocyclic compounds

Czech Academy of Sciences Publication Activity Database

Khalaji, A.D.; Ghoran, S.H.; Pojarová, Michaela; Dušek, Michal

2015-01-01

Roč. 56, č. 7 (2015), s. 1410-1414 ISSN 0022-4766 R&D Projects: GA ČR(CZ) GA14-03276S Institutional support: RVO:68378271 Keywords : synthesis * macrocyclic Schiff base * single crystal structure analysis * spectroscopy Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.536, year: 2015
An agent-based method for simulating porous fluid-saturated structures with indistinguishable components

Science.gov (United States)

Kashani, Jamal; Pettet, Graeme John; Gu, YuanTong; Zhang, Lihai; Oloyede, Adekunle

2017-10-01

Single-phase porous materials contain multiple components that intermingle up to the ultramicroscopic level. Although the structures of the porous materials have been simulated with agent-based methods, the results of the available methods continue to provide patterns of distinguishable solid and fluid agents which do not represent materials with indistinguishable phases. This paper introduces a new agent (hybrid agent) and category of rules (intra-agent rule) that can be used to create emergent structures that would more accurately represent single-phase structures and materials. The novel hybrid agent carries the characteristics of system's elements and it is capable of changing within itself, while also responding to its neighbours as they also change. As an example, the hybrid agent under one-dimensional cellular automata formalism in a two-dimensional domain is used to generate patterns that demonstrate the striking morphological and characteristic similarities with the porous saturated single-phase structures where each agent of the ;structure; carries semi-permeability property and consists of both fluid and solid in space and at all times. We conclude that the ability of the hybrid agent to change locally provides an enhanced protocol to simulate complex porous structures such as biological tissues which could facilitate models for agent-based techniques and numerical methods.
Real-time vibration-based structural damage detection using one-dimensional convolutional neural networks

Science.gov (United States)

Abdeljaber, Osama; Avci, Onur; Kiranyaz, Serkan; Gabbouj, Moncef; Inman, Daniel J.

2017-02-01

Structural health monitoring (SHM) and vibration-based structural damage detection have been a continuous interest for civil, mechanical and aerospace engineers over the decades. Early and meticulous damage detection has always been one of the principal objectives of SHM applications. The performance of a classical damage detection system predominantly depends on the choice of the features and the classifier. While the fixed and hand-crafted features may either be a sub-optimal choice for a particular structure or fail to achieve the same level of performance on another structure, they usually require a large computation power which may hinder their usage for real-time structural damage detection. This paper presents a novel, fast and accurate structural damage detection system using 1D Convolutional Neural Networks (CNNs) that has an inherent adaptive design to fuse both feature extraction and classification blocks into a single and compact learning body. The proposed method performs vibration-based damage detection and localization of the damage in real-time. The advantage of this approach is its ability to extract optimal damage-sensitive features automatically from the raw acceleration signals. Large-scale experiments conducted on a grandstand simulator revealed an outstanding performance and verified the computational efficiency of the proposed real-time damage detection method.
SDSL-ESR-based protein structure characterization.

Science.gov (United States)

Strancar, Janez; Kavalenka, Aleh; Urbancic, Iztok; Ljubetic, Ajasja; Hemminga, Marcus A

2010-03-01

As proteins are key molecules in living cells, knowledge about their structure can provide important insights and applications in science, biotechnology, and medicine. However, many protein structures are still a big challenge for existing high-resolution structure-determination methods, as can be seen in the number of protein structures published in the Protein Data Bank. This is especially the case for less-ordered, more hydrophobic and more flexible protein systems. The lack of efficient methods for structure determination calls for urgent development of a new class of biophysical techniques. This work attempts to address this problem with a novel combination of site-directed spin labelling electron spin resonance spectroscopy (SDSL-ESR) and protein structure modelling, which is coupled by restriction of the conformational spaces of the amino acid side chains. Comparison of the application to four different protein systems enables us to generalize the new method and to establish a general procedure for determination of protein structure.
Numerical Study on the Seismic Response of Structure with Consideration of the Behavior of Base Mat Uplift

Directory of Open Access Journals (Sweden)

Guo-Bo Wang

2017-01-01

Full Text Available The foundation might be separated from the supporting soil if the earthquake is big enough, which is known as base mat uplift. This paper proposed a simplified calculation model in which spring element is adopted to simulate the interaction between soil and structure. The load-deformation curve (F-D curve of the spring element can be designated to represent the base mat uplift, in which the pressure can be applied while tensile forces are not allowed. Key factors, such as seismic wave types, seismic wave excitation directions, seismic wave amplitudes, soil shear velocities, structure stiffness, and the ratio of structure height to width (H/B, were considered in the analysis. It is shown that (1 seismic wave type has significant influence on structure response due to different frequency components it contained; (2 the vertical input of seismic wave greatly affected structure response in vertical direction, while it has little impacts in horizontal direction; (3 base mat uplift is easier to take place in soil with higher shear velocity; (4 structure H/B value has complicated influence on base mat uplift. The outcome of this research is assumed to provide some references for the seismic design of the structure due to base mat uplift.
The Characterization of Surface Acoustic Wave Devices Based on AlN-Metal Structures

Directory of Open Access Journals (Sweden)

Lin Shu

2016-04-01

Full Text Available We report in this paper on the study of surface acoustic wave (SAW resonators based on an AlN/titanium alloy (TC4 structure. The AlN/TC4 structure with different thicknesses of AlN films was simulated, and the acoustic propagating modes were discussed. Based on the simulation results, interdigital transducers with a periodic length of 24 μm were patterned by lift-off photolithography techniques on the AlN films/TC4 structure, while the AlN film thickness was in the range 1.5–3.5 μm. The device performances in terms of quality factor (Q-factor and electromechanical coupling coefficient (k2 were determined from the measure S11 parameters. The Q-factor and k2 were strongly dependent not only on the normalized AlN film thickness but also on the full-width at half-maximum (FWHM of AlN (002 peak. The dispersion curve of the SAW phase velocity was analyzed, and the experimental results showed a good agreement with simulations. The temperature behaviors of the devices were also presented and discussed. The prepared SAW resonators based on AlN/TC4 structure have potential applications in integrated micromechanical sensing systems.
Scaling Mode Shapes in Output-Only Structure by a Mass-Change-Based Method

Directory of Open Access Journals (Sweden)

Liangliang Yu

2017-01-01

Full Text Available A mass-change-based method based on output-only data for the rescaling of mode shapes in operational modal analysis (OMA is introduced. The mass distribution matrix, which is defined as a diagonal matrix whose diagonal elements represent the ratios among the diagonal elements of the mass matrix, is calculated using the unscaled mode shapes. Based on the theory of null space, the mass distribution vector or mass distribution matrix is obtained. A small mass with calibrated weight is added to a certain location of the structure, and then the mass distribution vector of the modified structure is estimated. The mass matrix is identified according to the difference of the mass distribution vectors between the original and modified structures. Additionally, the universal set of modes is unnecessary when calculating the mass distribution matrix, indicating that modal truncation is allowed in the proposed method. The mass-scaled mode shapes estimated in OMA according to the proposed method are compared with those obtained by experimental modal analysis. A simulation is employed to validate the feasibility of the method. Finally, the method is tested on output-only data from an experiment on a five-storey structure, and the results confirm the effectiveness of the method.
A Corner-Point-Grid-Based Voxelization Method for Complex Geological Structure Model with Folds

Science.gov (United States)

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.
A New XOR Structure Based on Resonant-Tunneling High Electron Mobility Transistor

Directory of Open Access Journals (Sweden)

Mohammad Javad Sharifi

2009-01-01

Full Text Available A new structure for an exclusive-OR (XOR gate based on the resonant-tunneling high electron mobility transistor (RTHEMT is introduced which comprises only an RTHEMT and two FETs. Calculations are done by utilizing a new subcircuit model for simulating the RTHEMT in the SPICE simulator. Details of the design, input, and output values and margins, delay of each transition, maximum operating frequency, static and dynamic power dissipations of the new structure are discussed and calculated and the performance is compared with other XOR gates which confirm that the presented structure has a high performance. Furthermore, to the best of authors' knowledge, it has the least component count in comparison to the existing structures.

Simulations of the structure and dynamics of nanoparticle-based ionic liquids

KAUST Repository

Hong, Bingbing; Chremos, Alexandros; Panagiotopoulos, Athanassios Z.

2012-01-01

We use molecular dynamics simulations over microsecond time scales to study the structure and dynamics of coarse-grained models for nanoparticle-based ionic liquids. The systems of interest consist of particles with charged surface groups and linear
Nonlinear soil-structure interaction due to base slab uplift on the seismic response of an HTGR plant

International Nuclear Information System (INIS)

Kennedy, R.P.; Short, S.A.; Wesley, D.A.; Lee, T.H.

1975-01-01

The importance of the nonlinear soil-structure interaction effects resulting from substantial base slab uplift occurring during a seismic excitation are evaluated. The structure considered consisted of the containment building and prestressed concrete reactor vessel for a typical HTGR plant. A simplified dynamic mathematical model was utilized consisting of a conventional lumped mass structure with soil-structure interaction accounted for by translational and rotational springs whose properties are determined by elastic half space theory. Three different site soil conditions (a rock site, a moderately stiff soil and a soft soil site) and two levels of horizontal ground motion (0.3g and 0.5g earthquakes) were considered. It may be concluded that linear analysis can be used to conservatively estimate the important behavior of the base slab, even under conditions of substantial base slab uplift. For all cases investigated, linear analysis resulted in higher base overturning moments, greater toe pressures, and greater heel uplift distances than nonlinear analyses. It may also be concluded that the nonlinear effect of uplift does not result in any significant lengthening of the fundamental period of the structure. Also, except in the short period region only negligible differences exist between instructure response spectra based on linear analysis and those based on nonlinear analysis. Finally, for sites in which soil-structure interaction is not significant, as for the rock site, the peak structural response at all locations above the base mat are not significantly influenced by the nonlinear effects of base slab uplift. However, for the two soil sites, the peak shears and moments are, in a few instances, significantly different between linear and nonlinear analyses
Feasibility evaluation of a neutron grating interferometer with an analyzer grating based on a structured scintillator

Science.gov (United States)

Kim, Youngju; Kim, Jongyul; Kim, Daeseung; Hussey, Daniel. S.; Lee, Seung Wook

2018-03-01

We introduce an analyzer grating based on a structured scintillator fabricated by a gadolinium oxysulfide powder filling method for a symmetric Talbot-Lau neutron grating interferometer. This is an alternative way to analyze the Talbot self-image of a grating interferometer without using an absorption grating to block neutrons. Since the structured scintillator analyzer grating itself generates the signal for neutron detection, we do not need an additional scintillator screen as an absorption analyzer grating. We have developed and tested an analyzer grating based on a structured scintillator in our symmetric Talbot-Lau neutron grating interferometer to produce high fidelity absorption, differential phase, and dark-field contrast images. The acquired images have been compared to results of a grating interferometer utilizing a typical absorption analyzer grating with two commercial scintillation screens. The analyzer grating based on the structured scintillator enhances interference fringe visibility and shows a great potential for economical fabrication, compact system design, and so on. We report the performance of the analyzer grating based on a structured scintillator and evaluate its feasibility for the neutron grating interferometer.
Utilizing knowledge base of amino acids structural neighborhoods to predict protein-protein interaction sites.

Science.gov (United States)

Jelínek, Jan; Škoda, Petr; Hoksza, David

2017-12-06

Protein-protein interactions (PPI) play a key role in an investigation of various biochemical processes, and their identification is thus of great importance. Although computational prediction of which amino acids take part in a PPI has been an active field of research for some time, the quality of in-silico methods is still far from perfect. We have developed a novel prediction method called INSPiRE which benefits from a knowledge base built from data available in Protein Data Bank. All proteins involved in PPIs were converted into labeled graphs with nodes corresponding to amino acids and edges to pairs of neighboring amino acids. A structural neighborhood of each node was then encoded into a bit string and stored in the knowledge base. When predicting PPIs, INSPiRE labels amino acids of unknown proteins as interface or non-interface based on how often their structural neighborhood appears as interface or non-interface in the knowledge base. We evaluated INSPiRE's behavior with respect to different types and sizes of the structural neighborhood. Furthermore, we examined the suitability of several different features for labeling the nodes. Our evaluations showed that INSPiRE clearly outperforms existing methods with respect to Matthews correlation coefficient. In this paper we introduce a new knowledge-based method for identification of protein-protein interaction sites called INSPiRE. Its knowledge base utilizes structural patterns of known interaction sites in the Protein Data Bank which are then used for PPI prediction. Extensive experiments on several well-established datasets show that INSPiRE significantly surpasses existing PPI approaches.
Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures.

Science.gov (United States)

Matsuoka, Masanari; Sugita, Masatake; Kikuchi, Takeshi

2014-09-18

Proteins that share a high sequence homology while exhibiting drastically different 3D structures are investigated in this study. Recently, artificial proteins related to the sequences of the GA and IgG binding GB domains of human serum albumin have been designed. These artificial proteins, referred to as GA and GB, share 98% amino acid sequence identity but exhibit different 3D structures, namely, a 3α bundle versus a 4β + α structure. Discriminating between their 3D structures based on their amino acid sequences is a very difficult problem. In the present work, in addition to using bioinformatics techniques, an analysis based on inter-residue average distance statistics is used to address this problem. It was hard to distinguish which structure a given sequence would take only with the results of ordinary analyses like BLAST and conservation analyses. However, in addition to these analyses, with the analysis based on the inter-residue average distance statistics and our sequence tendency analysis, we could infer which part would play an important role in its structural formation. The results suggest possible determinants of the different 3D structures for sequences with high sequence identity. The possibility of discriminating between the 3D structures based on the given sequences is also discussed.
Infrared Fibers for Use in Space-Based Smart Structures

Science.gov (United States)

Tucker, Dennis S.; Nettles, Alan T.; Brantley, Lott W. (Technical Monitor)

2001-01-01

Infrared optical fibers are finding a number of applications including laser surgery, remote sensing, and nuclear radiation resistant links. Utilizing these fibers in space-based structures is another application, which can be exploited. Acoustic and thermal sensing are two areas in which these fibers could be utilized. In particular, fibers could be embedded in IM7/8552 toughened epoxy and incorporated into space structures both external and internal. ZBLAN optical fibers are a candidate, which have been studied extensively over the past 20 years for terrestrial applications. For the past seven years the effects of gravity on the crystallization behavior of ZBLAN optical fiber has been studied. It has been found that ZBLAN crystallization is suppressed in microgravity. This lack of crystallization leads to a fiber with better transmission characteristics than its terrestrial counterpart.
SABATPG-A Structural Analysis Based Automatic Test Generation System

Institute of Scientific and Technical Information of China (English)

李忠诚; 潘榆奇; 闵应骅

1994-01-01

A TPG system, SABATPG, is given based on a generic structural model of large circuits. Three techniques of partial implication, aftereffect of identified undetectable faults and shared sensitization with new concepts of localization and aftereffect are employed in the system to improve FAN algorithm. Experiments for the 10 ISCAS benchmark circuits show that the computing time of SABATPG for test generation is 19.42% less than that of FAN algorithm.
A New Structure Based on Cascaded Multilevel Converter for Variable Speed Wind Turbine

DEFF Research Database (Denmark)

Deng, Fujin; Chen, Zhe

2010-01-01

An alternative structure for variable speed wind turbine, using multiple permanent magnet synchronous generators (PMSGs) drive-train configuration and cascaded multilevel converter is proposed in this paper. This study presents a power electronic solution for the wind turbine. A transformer......-less cascaded multilevel converter interface based on PMSGs is developed to synthesize a desired high ac sinusoidal output voltage. The benefits of high power and high ac voltage make this structure possible to be applied in the wind power generation. In addition, the bulky transformer could be omitted....... A simulation model of 10 MW variable speed wind turbine based on PMSGs developed in PSCAD/EMTDC is presented. The dynamic performance of grid-connected wind turbine is analyzed. Simulation results shows that the proposed structure may be attractive in wind power generation....
A Fundamental Approach to Developing Aluminium based Bulk Amorphous Alloys based on Stable Liquid Metal Structures and Electronic Equilibrium - 154041

Science.gov (United States)

2017-03-28

AFRL-AFOSR-JP-TR-2017-0027 A Fundamental Approach to Developing Aluminium -based Bulk Amorphous Alloys based on Stable Liquid-Metal Structures and...to 16 Dec 2016 4. TITLE AND SUBTITLE A Fundamental Approach to Developing Aluminium -based Bulk Amorphous Alloys based on Stable Liquid-Metal...Air Force Research Laboratory for accurately predicting compositions of new amorphous alloys specifically based on aluminium with properties superior
Ply-based Optimization of Laminated Composite Shell Structures under Manufacturing Constraints

DEFF Research Database (Denmark)

Sørensen, Rene; Lund, Erik

2012-01-01

This work concerns a new ply-based parameterization for performing simultaneous material selection and topology optimization of fiber reinforced laminated composite structures while ensuring that a series of different manufacturing constraints are fulfilled. The material selection can either...
A hierarchical model for structure learning based on the physiological characteristics of neurons

Institute of Scientific and Technical Information of China (English)

WEI Hui

2007-01-01

Almost all applications of Artificial Neural Networks (ANNs) depend mainly on their memory ability.The characteristics of typical ANN models are fixed connections,with evolved weights,globalized representations,and globalized optimizations,all based on a mathematical approach.This makes those models to be deficient in robustness,efficiency of learning,capacity,anti-jamming between training sets,and correlativity of samples,etc.In this paper,we attempt to address these problems by adopting the characteristics of biological neurons in morphology and signal processing.A hierarchical neural network was designed and realized to implement structure learning and representations based on connected structures.The basic characteristics of this model are localized and random connections,field limitations of neuron fan-in and fan-out,dynamic behavior of neurons,and samples represented through different sub-circuits of neurons specialized into different response patterns.At the end of this paper,some important aspects of error correction,capacity,learning efficiency,and soundness of structural representation are analyzed theoretically.This paper has demonstrated the feasibility and advantages of structure learning and representation.This model can serve as a fundamental element of cognitive systems such as perception and associative memory.Key-words structure learning,representation,associative memory,computational neuroscience
Advanced image based methods for structural integrity monitoring: Review and prospects

Science.gov (United States)

Farahani, Behzad V.; Sousa, Pedro José; Barros, Francisco; Tavares, Paulo J.; Moreira, Pedro M. G. P.

2018-02-01

There is a growing trend in engineering to develop methods for structural integrity monitoring and characterization of in-service mechanical behaviour of components. The fast growth in recent years of image processing techniques and image-based sensing for experimental mechanics, brought about a paradigm change in phenomena sensing. Hence, several widely applicable optical approaches are playing a significant role in support of experiment. The current review manuscript describes advanced image based methods for structural integrity monitoring, and focuses on methods such as Digital Image Correlation (DIC), Thermoelastic Stress Analysis (TSA), Electronic Speckle Pattern Interferometry (ESPI) and Speckle Pattern Shearing Interferometry (Shearography). These non-contact full-field techniques rely on intensive image processing methods to measure mechanical behaviour, and evolve even as reviews such as this are being written, which justifies a special effort to keep abreast of this progress.
Generation of structural topologies using efficient technique based on sorted compliances

Science.gov (United States)

Mazur, Monika; Tajs-Zielińska, Katarzyna; Bochenek, Bogdan

2018-01-01

Topology optimization, although well recognized is still widely developed. It has gained recently more attention since large computational ability become available for designers. This process is stimulated simultaneously by variety of emerging, innovative optimization methods. It is observed that traditional gradient-based mathematical programming algorithms, in many cases, are replaced by novel and e cient heuristic methods inspired by biological, chemical or physical phenomena. These methods become useful tools for structural optimization because of their versatility and easy numerical implementation. In this paper engineering implementation of a novel heuristic algorithm for minimum compliance topology optimization is discussed. The performance of the topology generator is based on implementation of a special function utilizing information of compliance distribution within the design space. With a view to cope with engineering problems the algorithm has been combined with structural analysis system Ansys.
Gallium arsenide p+–n–p+-structures with impoverished base area

Directory of Open Access Journals (Sweden)

Karimov A. V.

2009-06-01

Full Text Available It is displayed experimentally, that the current transport’s mechanism through p+GaAs–nGaAs–p+GaAs-structure is formed by injection-tunnel and generation-recombination mechanisms. Injection-tunnel current prevails at modulation of base’s part which contains defects, and generation-recombination currents are determinative at modulation of base’s part with lesser defectiveness. p+GaAs–nGaAs–p+GaAs-structures are of interest for creating voltage suppressors and electronic switches on their base.
Automated brain structure segmentation based on atlas registration and appearance models

DEFF Research Database (Denmark)

van der Lijn, Fedde; de Bruijne, Marleen; Klein, Stefan

2012-01-01

Accurate automated brain structure segmentation methods facilitate the analysis of large-scale neuroimaging studies. This work describes a novel method for brain structure segmentation in magnetic resonance images that combines information about a structure’s location and appearance. The spatial...... with different magnetic resonance sequences, in which the hippocampus and cerebellum were segmented by an expert. Furthermore, the method is compared to two other segmentation techniques that were applied to the same data. Results show that the atlas- and appearance-based method produces accurate results...
Toward Wearable Energy Storage Devices: Paper-Based Biofuel Cells based on a Screen-Printing Array Structure.

Science.gov (United States)

Shitanda, Isao; Momiyama, Misaki; Watanabe, Naoto; Tanaka, Tomohiro; Tsujimura, Seiya; Hoshi, Yoshinao; Itagaki, Masayuki

2017-10-01

A novel paper-based biofuel cell with a series/parallel array structure has been fabricated, in which the cell voltage and output power can easily be adjusted as required by printing. The output of the fabricated 4-series/4-parallel biofuel cell reached 0.97±0.02 mW at 1.4 V, which is the highest output power reported to date for a paper-based biofuel cell. This work contributes to the development of flexible, wearable energy storage device.
Resistive switching in ZrO2 based metal-oxide-metal structures

International Nuclear Information System (INIS)

Kaerkkaenen, Irina

2014-01-01

The goal of this work is a deeper understanding of the influence of the (i) metal-oxide-metal (MOM) layer stacks configuration, (ii) the oxide films microstructure, (iii) and their defect structure on the appearance of different switching modes, i.e. unipolar (UP) and bipolar (BP). The first part deals with the fabrication of ZrO 2 thin films by an industrial compatible atomic layer deposition (ALD) process, the chemical, structural and morphological characterization of the films, the growth of ZrO 2 /TiO 2 bilayers, the integration of the layers into metal-oxide-metal (MOM) devices and the electrical characterization with focus on the RS behavior. In the second part the effect of the device structure, in particular the thickness of the electrochemical active electrode (EAE) and the ZrO 2 film morphology, on the RS switching polarity of Pt/ZrO 2 /(EAE) cells is discussed. ZrO 2 films and ZrO 2 /TiO 2 bilayers were grown by ALD and were carefully structurally and electrically characterized. The ZrO 2 films grown from Zr[N(CH 3 )C 2 H 5 ] 4 (TEMA-Zr) at 240 C were polycrystalline with a mixture of cubic/tetragonal phases. ALD/H 2 O-ZrO 2 films exhibited a random oriented polycrystalline structure, whereas the ALD/O 3 -ZrO 2 films consisted of preferably oriented cubic shaped grains. Pt/ZrO 2 /Ti/Pt structures with a Ti top electrode (TE) thickness of 5 to 20 nm showed unipolar type RS behavior, while by increasing the Ti TE thickness a gradual change of switching polarity from unipolar to bipolar with a completely bipolar type RS behavior for a Ti TE thickness of 40 nm is found. The switching in Pt/ZrO 2 /TiO 2 /Ti/Pt devices was unipolar, comparable to Pt/ZrO 2 /Ti/Pt cells. In contrast, bilayers with the reverse structure, Pt/TiO 2 /ZrO 2 /Ti/Pt, showed non-switching behavior. The effect of the cells stack structure on the polarity of the RS behavior was studied in detail for 20 nm thick ZrO 2 films grown by an ozone based ALD process and integrated into Pt/ZrO 2
Use of knowledge based systems for rational reliability analysis based inspection and maintenance planning for offshore structures

International Nuclear Information System (INIS)

Tang, M.X.; Dharmavasan, S.; Peers, S.M.C.

1994-01-01

The structural integrity of fixed offshore platforms is ensured by periodic inspections. In the past, decisions made as to when, where and how to inspect have been made by engineers using rules-of-thumb and general planning heuristics. It is now hoped that more rational inspection and maintenance scheduling may be carried out by applying recently developed techniques based on structural reliability methods. However, one of the problems associated with a theoretical approach is that it is not always possible to incorporate all the constraints that are present in a practical situation. These constraints modify the decisions made for analysis data input and the interpretation of the analysis results. Knowledge based systems provide a mean of encapsulating several different forms of information and knowledge within a computer system and hence can overcome this problem. In this paper, a prototype system being developed for integrating reliability based analysis with other constraints for inspection scheduling will be described. In addition, the scheduling model and the algorithms to carry out the scheduling will be explained. Furthermore, implementation details are also given
Development and validation of a strain-based Structural Health Monitoring system

Science.gov (United States)

Katsikeros, Ch. E.; Labeas, G. N.

2009-02-01

An innovative Structural Health Monitoring (SHM) methodology, based on structural strain measurements, which are processed by a back-propagation feed-forward Artificial Neural Network (ANN), is proposed. The demonstration of the SHM methodology and the identification of its capabilities and drawbacks are performed by applying the method in the prediction of fatigue damage states of a typical aircraft cracked lap-joint structure. An ANN of suitable architecture is developed and trained by numerically generated strain data sets, which have been preprocessed by Fast Fourier Transformation (FFT) for the extraction of the Fourier Descriptors (FDs). The Finite Element (FE) substructuring technique is implemented in the stress and strain analysis of the lap-joint structure, due to its efficiency in the calculation of the numerous strain data, which are necessary for the ANN training. The trained network is successfully validated, as it is proven capable to accurately predict crack positions and lengths of a lap-joint structure, which is damaged by fatigue cracks of unknown location and extent. The proposed methodology is applicable to the identification of more complex types of damage or to other critical structural locations, as its basic concept is generic.
Modal analysis of graphene-based structures for large deformations, contact and material nonlinearities

Science.gov (United States)

Ghaffari, Reza; Sauer, Roger A.

2018-06-01

The nonlinear frequencies of pre-stressed graphene-based structures, such as flat graphene sheets and carbon nanotubes, are calculated. These structures are modeled with a nonlinear hyperelastic shell model. The model is calibrated with quantum mechanics data and is valid for high strains. Analytical solutions of the natural frequencies of various plates are obtained for the Canham bending model by assuming infinitesimal strains. These solutions are used for the verification of the numerical results. The performance of the model is illustrated by means of several examples. Modal analysis is performed for square plates under pure dilatation or uniaxial stretch, circular plates under pure dilatation or under the effects of an adhesive substrate, and carbon nanotubes under uniaxial compression or stretch. The adhesive substrate is modeled with van der Waals interaction (based on the Lennard-Jones potential) and a coarse grained contact model. It is shown that the analytical natural frequencies underestimate the real ones, and this should be considered in the design of devices based on graphene structures.

Automated Clustering Analysis of Immunoglobulin Sequences in Chronic Lymphocytic Leukemia Based on 3D Structural Descriptors

DEFF Research Database (Denmark)

Marcatili, Paolo; Mochament, Konstantinos; Agathangelidis, Andreas

2016-01-01

study, we used the structure prediction tools PIGS and I-TASSER for creating the 3D models and the TM-align algorithm to superpose them. The innovation of the current methodology resides in the usage of methods adapted from 3D content-based search methodologies to determine the local structural...... determine it are extremely laborious and demanding. Hence, the ability to gain insight into the structure of Igs at large relies on the availability of tools and algorithms for producing accurate Ig structural models based on their primary sequence alone. These models can then be used to determine...... to achieve an optimal solution to this task yet their results were hindered mainly due to the lack of efficient clustering methods based on the similarity of 3D structure descriptors. Here, we present a novel workflow for robust Ig 3D modeling and automated clustering. We validated our protocol in chronic...
A cross-coupled-structure-based temperature sensor with reduced process variation sensitivity

Energy Technology Data Exchange (ETDEWEB)

Tie Meng; Cheng Xu, E-mail: tiemeng@mprc.pku.edu.c [Microprocessor Research and Development Center, Peking University, Beijing 100871 (China)

2009-04-15

An innovative, thermally-insensitive phenomenon of cascaded cross-coupled structures is found. And a novel CMOS temperature sensor based on a cross-coupled structure is proposed. This sensor consists of two different ring oscillators. The first ring oscillator generates pulses that have a period, changing linearly with temperature. Instead of using the system clock like in traditional sensors, the second oscillator utilizes a cascaded cross-coupled structure to generate temperature independent pulses to capture the result from the first oscillator. Due to the compensation between the two ring oscillators, errors caused by supply voltage variations and systematic process variations are reduced. The layout design of the sensor is based on the TSMC13G process standard cell library. Only three inverters are modified for proper channel width tuning without any other custom design. This allows for an easy integration of the sensor into cell-based chips. Post-layout simulations results show that an error lower than +-1.1 deg. C can be achieved in the full temperature range from -40 to 120 deg. C. As shown by SPICE simulations, the thermal insensitivity of the cross-coupled inverters can be realized for various TSMC technologies: 0.25 mum, 0.18 mum, 0.13 mum, and 65 nm.
Origami-based mechanical metamaterials with tunable frequency band structures (Conference Presentation)

Science.gov (United States)

Yasuda, Hiromi; Pratt, Riley; Yang, Jinkyu

2017-04-01

We investigate wave dynamics in origami-based mechanical metamaterials composed of bellows-like origami structures, specifically the Tachi-Miura Polyhedron (TMP). One of the unique features of the TMP is that its structural deformations take place only along the crease lines, therefore the structure can be made of rigid plates and hinges. By utilizing this feature, we introduce linear torsional springs to model the crease lines and derive the force and displacement relationship of the TMP structure along the longitudinal direction. Our analysis shows strain softening/hardening behaviors in compression/tensile regions respectively, and the force-displacement curve can be manipulated by altering the initial configuration of the TMP (e.g., the initial folding angle). We also fabricate physical prototypes and measure the force-displacement behavior to verify our analytical model. Based on this static analysis on the TMP, we simplify the TMP structure into a linkage model, preserving the tunable strain softening/hardening behaviors. Dynamic analysis is also conducted numerically to analyze the frequency response of the simplified TMP unit cell under harmonic excitations. The simplified TMP exhibits a transition between linear and nonlinear behaviors, which depends on the amplitude of the excitation and the initial configuration. In addition, we design a 1D system composed of simplified TMP unit cells and analyze the relationship between frequency and wave number. If two different configurations of the unit cell (e.g., different initial folding angles) are connected in an alternating arrangement, the system develops frequency bandgaps. These unique static/dynamic behaviors can be exploited to design engineering devices which can handle vibrations and impact in an efficient manner.
Matlab/Simulink Implementation of Wave-based Models for Microstrip Structures utilizing Short-circuited and Opened Stubs

Directory of Open Access Journals (Sweden)

Biljana P. Stošić

2011-12-01

Full Text Available This paper describes modeling and analyzing procedures for microstrip filters based on use of one-dimensional wave digital approach. Different filter structures are observed. One filter is based on quarter-wave length short-circuited stubs and connecting transmission lines. The other one is based on cross-junction opened stubs. Frequency responses are obtained by direct analysis of the block-based networks formed in Simulink toolbox of MATLAB environment. This wave-based method allows an accurate and efficient analysis of different microwave structures.
Study on the contact ratio of base mat of reactor buildings considering nonlinear soil-structure interaction effects

International Nuclear Information System (INIS)

Aihara, S.; Atsumi, K.; Ujiie, K.; Emori, K.; Odajima, M.; Masuda, K.

1983-01-01

The objective of this paper is to evaluate the nonlinear soil-structure interaction effects resulting from base mat uplift for static lateral loads. Nonlinear soil-structure interaction effects are modeled through the use of equivalent soil-structure interaction frictional and axial springs, which properties are determined by results of experimental data. It is assumed that normal stresses in compression and corresponding shear stresses, and friction, can occur in the area of contact between the embedded structure and soil. The remaining parts of the structure and soil are based on elastic analysis. A two-dimensional finite element method with incremental loadings is applied. The substructuring technique is used to reduce computation time. The results of this method with respect to the contact ratio of the base mat are compared with the values obtained by static elastic calculation which is simply derived from an overturning moment and a vertical load of the structure. This analytical concept will be developed into dynamic problems, and then it will be possible to state whether or not this concept can represent a true alternative for the contact ratio of the base mat of a structure. (orig./HP)
SDSL-ESR-based protein structure characterization

NARCIS (Netherlands)

Strancar, J.; Kavalenka, A.A.; Urbancic, I.; Ljubetic, A.; Hemminga, M.A.

2010-01-01

As proteins are key molecules in living cells, knowledge about their structure can provide important insights and applications in science, biotechnology, and medicine. However, many protein structures are still a big challenge for existing high-resolution structure-determination methods, as can be
Structure-activity relationship study of oxindole-based inhibitors of cyclin-dependent kinases based on least-squares support vector machines

International Nuclear Information System (INIS)

Li Jiazhong; Liu Huanxiang; Yao Xiaojun; Liu Mancang; Hu Zhide; Fan Botao

2007-01-01

The least-squares support vector machines (LS-SVMs), as an effective modified algorithm of support vector machine, was used to build structure-activity relationship (SAR) models to classify the oxindole-based inhibitors of cyclin-dependent kinases (CDKs) based on their activity. Each compound was depicted by the structural descriptors that encode constitutional, topological, geometrical, electrostatic and quantum-chemical features. The forward-step-wise linear discriminate analysis method was used to search the descriptor space and select the structural descriptors responsible for activity. The linear discriminant analysis (LDA) and nonlinear LS-SVMs method were employed to build classification models, and the best results were obtained by the LS-SVMs method with prediction accuracy of 100% on the test set and 90.91% for CDK1 and CDK2, respectively, as well as that of LDA models 95.45% and 86.36%. This paper provides an effective method to screen CDKs inhibitors
Structural changes and out-of-sample prediction of realized range-based variance in the stock market

Science.gov (United States)

Gong, Xu; Lin, Boqiang

2018-03-01

This paper aims to examine the effects of structural changes on forecasting the realized range-based variance in the stock market. Considering structural changes in variance in the stock market, we develop the HAR-RRV-SC model on the basis of the HAR-RRV model. Subsequently, the HAR-RRV and HAR-RRV-SC models are used to forecast the realized range-based variance of S&P 500 Index. We find that there are many structural changes in variance in the U.S. stock market, and the period after the financial crisis contains more structural change points than the period before the financial crisis. The out-of-sample results show that the HAR-RRV-SC model significantly outperforms the HAR-BV model when they are employed to forecast the 1-day, 1-week, and 1-month realized range-based variances, which means that structural changes can improve out-of-sample prediction of realized range-based variance. The out-of-sample results remain robust across the alternative rolling fixed-window, the alternative threshold value in ICSS algorithm, and the alternative benchmark models. More importantly, we believe that considering structural changes can help improve the out-of-sample performances of most of other existing HAR-RRV-type models in addition to the models used in this paper.
A continuum-based structural modeling approach for cellulose nanocrystals (CNCs)

Science.gov (United States)

Mehdi Shishehbor; Fernando L. Dri; Robert J. Moon; Pablo D. Zavattieri

2018-01-01

We present a continuum-based structural model to study the mechanical behavior of cel- lulose nanocrystals (CNCs), and analyze the effect of bonded and non-bonded interactions on the mechanical properties under various loading conditions. In particular, this model assumes the uncoupling between the bonded and non-bonded interactions and their be- havior is obtained...
Reliability Analysis of Sealing Structure of Electromechanical System Based on Kriging Model

Science.gov (United States)

Zhang, F.; Wang, Y. M.; Chen, R. W.; Deng, W. W.; Gao, Y.

2018-05-01

The sealing performance of aircraft electromechanical system has a great influence on flight safety, and the reliability of its typical seal structure is analyzed by researcher. In this paper, we regard reciprocating seal structure as a research object to study structural reliability. Having been based on the finite element numerical simulation method, the contact stress between the rubber sealing ring and the cylinder wall is calculated, and the relationship between the contact stress and the pressure of the hydraulic medium is built, and the friction force on different working conditions are compared. Through the co-simulation, the adaptive Kriging model obtained by EFF learning mechanism is used to describe the failure probability of the seal ring, so as to evaluate the reliability of the sealing structure. This article proposes a new idea of numerical evaluation for the reliability analysis of sealing structure, and also provides a theoretical basis for the optimal design of sealing structure.
Chinese wine classification system based on micrograph using combination of shape and structure features

Science.gov (United States)

Wan, Yi

2011-06-01

Chinese wines can be classification or graded by the micrographs. Micrographs of Chinese wines show floccules, stick and granule of variant shape and size. Different wines have variant microstructure and micrographs, we study the classification of Chinese wines based on the micrographs. Shape and structure of wines' particles in microstructure is the most important feature for recognition and classification of wines. So we introduce a feature extraction method which can describe the structure and region shape of micrograph efficiently. First, the micrographs are enhanced using total variation denoising, and segmented using a modified Otsu's method based on the Rayleigh Distribution. Then features are extracted using proposed method in the paper based on area, perimeter and traditional shape feature. Eight kinds total 26 features are selected. Finally, Chinese wine classification system based on micrograph using combination of shape and structure features and BP neural network have been presented. We compare the recognition results for different choices of features (traditional shape features or proposed features). The experimental results show that the better classification rate have been achieved using the combinational features proposed in this paper.
Vibration based structural health monitoring in fibre reinforced composites employing the modal strain energy method

NARCIS (Netherlands)

Loendersloot, Richard; Ooijevaar, T.H.; Warnet, Laurent; Akkerman, Remko; de Boer, Andries; Meguid, S.A.; Gomes, J.F.S.

2009-01-01

The feasibility of a vibration based damage identification method is investigated. The Modal Strain Energy method is applied to a T–beam structure. The dynamic response of an intact structure and a damaged, delaminated structure is analysed employing a commercially available Finite Element package.
Insights into the fold organization of TIM barrel from interaction energy based structure networks.

Science.gov (United States)

Vijayabaskar, M S; Vishveshwara, Saraswathi

2012-01-01

There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or "sequence conservation" as the basis for their understanding. Recently "interaction energy" based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the "interaction conservation" viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.
Safety management of pipelines based on structural reliability: historical perspective and progress

Energy Technology Data Exchange (ETDEWEB)

Beck, Andre Teofilo; Bazan, Felipe Alexander Vargas [Universidade de Sao Paulo (USP), SP (Brazil); Mendes, Renato [Petroleo Brasileiro S.A. (PETROBRAS), Rio de Janeiro, RJ (Brazil); Donato, Guilherme [Petroleo Brasileiro S.A. (PETROBRAS/CENPES), Rio de Janeiro, RJ (Brazil). Centro de Pesquisas e Desenvolvimento; Gardiner, Michael [GL Noble Denton, Loughborough (United Kingdom)

2012-07-01

Since the early beginnings in the sixties and seventies, Structural Reliability theory has reached a mature stage encompassing solid theoretical developments and increasing practical applications. Structural reliability methods have permeated the engineering profession, finding applications in code calibration, structural optimization, life extension of existing structures, life-cycle management of infrastructure risks and costs, and so on. This review paper shows that the ground work for Reliability Based Design and Assessment (RBDA) of onshore pipeline systems is already developed. Hence, this allows the economic management of the risks involved in operation of pipeline systems. It is shown that RBDA is a rational tool to safely manage the operational life of pipeline systems, optimizing initial design and the expenditures in inspection and maintenance operations. (author)
Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment.

Science.gov (United States)

Day, Ryan; Joo, Hyun; Chavan, Archana C; Lennox, Kristin P; Chen, Y Ann; Dahl, David B; Vannucci, Marina; Tsai, Jerry W

2013-02-01

As an alternative to the common template based protein structure prediction methods based on main-chain position, a novel side-chain centric approach has been developed. Together with a Bayesian loop modeling procedure and a combination scoring function, the Stone Soup algorithm was applied to the CASP9 set of template based modeling targets. Although the method did not generate as large of perturbations to the template structures as necessary, the analysis of the results gives unique insights into the differences in packing between the target structures and their templates. Considerable variation in packing is found between target and template structures even when the structures are close, and this variation is found due to 2 and 3 body packing interactions. Outside the inherent restrictions in packing representation of the PDB, the first steps in correctly defining those regions of variable packing have been mapped primarily to local interactions, as the packing at the secondary and tertiary structure are largely conserved. Of the scoring functions used, a loop scoring function based on water structure exhibited some promise for discrimination. These results present a clear structural path for further development of a side-chain centered approach to template based modeling. Copyright © 2012 Elsevier Ltd. All rights reserved.
Representative volumes and multi-scale modelling of quasi-brittle materials

NARCIS (Netherlands)

Gitman, I.M.

2006-01-01

Several different approaches are available in order to describe material behaviour. Considering material on the higher (macro) level of observation constitutes the macroscopic approach. However, the key to understand a macro materials behaviour lies in its mesostructure. As such the mesoscopic
Study on comparison of special moment frame steel structure (SMF) and base isolation special moment frame steel structure (BI-SMF) in Indonesia

Science.gov (United States)

Setiawan, Jody; Nakazawa, Shoji

2017-10-01

This paper discusses about comparison of seismic response behaviors, seismic performance and seismic loss function of a conventional special moment frame steel structure (SMF) and a special moment frame steel structure with base isolation (BI-SMF). The validation of the proposed simplified estimation method of the maximum deformation of the base isolation system by using the equivalent linearization method and the validation of the design shear force of the superstructure are investigated from results of the nonlinear dynamic response analysis. In recent years, the constructions of steel office buildings with seismic isolation system are proceeding even in Indonesia where the risk of earthquakes is high. Although the design code for the seismic isolation structure has been proposed, there is no actual construction example for special moment frame steel structure with base isolation. Therefore, in this research, the SMF and BI-SMF buildings are designed by Indonesian Building Code which are assumed to be built at Padang City in Indonesia. The material of base isolation system is high damping rubber bearing. Dynamic eigenvalue analysis and nonlinear dynamic response analysis are carried out to show the dynamic characteristics and seismic performance. In addition, the seismic loss function is obtained from damage state probability and repair cost. For the response analysis, simulated ground accelerations, which have the phases of recorded seismic waves (El Centro NS, El Centro EW, Kobe NS and Kobe EW), adapted to the response spectrum prescribed by the Indonesian design code, that has, are used.
Structural transformations in thermal treatment of carbon material based on Slantsy coke

Energy Technology Data Exchange (ETDEWEB)

Tyumentsev, V.A.; Semenov, P.V.; Podkopaev, S.A.; Noneshneva, N.P.; Golovin, A.V. [Chelyabinsk State University, Chelyabinsk (Russian Federation)

2000-07-01

Structural transformations occurring in a carbon material based on high-sulfur Slantsy coke during isothermal treatment (1200-2400{degree}C) under normal pressure in a nitrogen atmosphere were studied.
Structural, electronic and magnetic properties of Pr-based filled skutterudites: A first principle study

Science.gov (United States)

Yadav, Priya; Nautiyal, Shashank; Verma, U. P.

2018-04-01

Ternary skutterudites materials exhibit good electronic properties due to the unpaired d- and f- electrons of the transition and rare-earth metals, respectively. In this communication, we have performed the structural optimization of Pr-based filled skutterudite (PrCo4P12) for the first time and obtained the electronic band structure, density of states and magnetic moments by using the full-potential linearized augmented plane wave (FP-LAPW) method based on density functional theory (DFT). Our obtained magnetic moment of PrCo4P12 is ˜ 1.8 µB in which main contribution is due to Pr atom. Behavior of this material is metallic and it is most stable in body centered cubic (BCC) structure.
Structural Modifications for Torsional Vibration Control of Shafting Systems Based on Torsional Receptances

Directory of Open Access Journals (Sweden)

Zihao Liu

2016-01-01

Full Text Available Torsional vibration of shafts is a very important problem in engineering, in particular in ship engines and aeroengines. Due to their high levels of integration and complexity, it is hard to get their accurate structural data or accurate modal data. This lack of data is unhelpful to vibration control in the form of structural modifications. Besides, many parts in shaft systems are not allowed to be modified such as rotary inertia of a pump or an engine, which is designed for achieving certain functions. This paper presents a strategy for torsional vibration control of shaft systems in the form of structural modifications based on receptances, which does not need analytical or modal models of the systems under investigation. It only needs the torsional receptances of the system, which can be obtained by testing simple auxiliary structure attached to relevant locations of the shaft system and using the finite element model (FEM of the simple structure. An optimization problem is constructed to determine the required structural modifications, based on the actual requirements of modal frequencies and mode shapes. A numerical experiment is set up and the influence of several system parameters is analysed. Several scenarios of constraints in practice are considered. The numerical simulation results demonstrate the effectiveness of this method and its feasibility in solving torsional vibration problems in practice.

Reliability-Based Optimization of Structural Elements

DEFF Research Database (Denmark)

Sørensen, John Dalsgaard

In this paper structural elements from an optimization point of view are considered, i.e. only the geometry of a structural element is optimized. Reliability modelling of the structural element is discussed both from an element point of view and from a system point of view. The optimization...
Application of reliability based design concepts to transmission line structure foundations. Part 2

International Nuclear Information System (INIS)

DiGioia, A.M. Jr.; Rojas-Gonzalez, L.F.

1991-01-01

The application of reliability based design (RBD) methods to transmission line structure foundations has developed somewhat more slowly than that for the other structural components in line systems. In a previous paper, a procedure was proposed for the design of transmission line structures foundations using a probability based load and resistance factor design (LRFD) format. This procedure involved the determination of a foundation strength factor, φ F , which was used as a multiplier of the calculated nominal design strength to estimate the five percent exclusion limit strength required in the calculated nominal design strength to estimate the five percent exclusion limit strength required in the LRFD equation. Statistical analyses of results from full-scale load tests were used to obtain φ F values applicable to various nominal design strength equations and for drilled shafts subjected to uplift loads. These results clearly illustrated the significant economic benefits of conducting more detailed subsurface investigations for the design of transmission line structure foundations. A design example was also presented. In this paper the proposed procedure is extended to laterally load drilled shafts
Modeling of Structure Effect for Ferroelectric Capacitor Based on Poly(vinylidene fluoride-trifluoroethylene Ultrathin Films

Directory of Open Access Journals (Sweden)

Long Li

2017-12-01

Full Text Available The characteristics of ferroelectric capacitors with poly(vinylidene fluoride-trifluoroethlene (P(VDF-TrFE films have been studied at different structures of cell electrodes. It is suggested that the effect of electrode structures could induce changes of performance. Remarkably, cells with line electrodes display a better polarization and fatigue resistance than those with flat electrodes. For P(VDF-TrFE ultrathin films with different electrode structures, the models of charge compensation mechanism for depolarization field and domain fatigue decomposition are used to explain the effect of electrode structure. Furthermore, the driving voltage based on normal speed-functionality is designed, and the testing results show that the line electrode structure could induce a robust switching, which is determined by the free charges concentration in active layer. These findings provide an effective route to design the optimum structure for a ferroelectric capacitor based on P(VDF-TrFE copolymer ultrathin film.
Microstructural characterization and formation mechanism of 21° top facets of ZnO-based nanowall structures

Energy Technology Data Exchange (ETDEWEB)

Lee, Ju Ho [Reliability Technology Research Institute, Korea Electronics Technology Institute (KETI), 68 Yatap-dong, Bundang-gu, Seongnam 463-816 (Korea, Republic of); Kim, Dong Chan [OLED Research Team 2, Samsung Mobile Display, San 24 Nonseo-dong, Giheung-gu, Yongin 446-711 (Korea, Republic of); Kim, Sang Yun [Department of Materials Science and Engineering, KAIST and Center for Nanomaterials and Chemical Reactions, IBS, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701 (Korea, Republic of); Choi, SungSoon [Reliability Technology Research Institute, Korea Electronics Technology Institute (KETI), 68 Yatap-dong, Bundang-gu, Seongnam 463-816 (Korea, Republic of); Lee, Kwan-Hun [Electronics and Communication Engineering, Kwangwoon University, 447-1 Wolgye-dong, Nowon-gu, Seoul 139-701 (Korea, Republic of); Lee, Jeong Yong, E-mail: j.y.lee@kaist.ac.kr [Department of Materials Science and Engineering, KAIST and Center for Nanomaterials and Chemical Reactions, IBS, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701 (Korea, Republic of); Koun Cho, Hyung, E-mail: chohk@skku.edu [School of Advanced Materials Science and Engineering, Sungkyunkwan University, 300 Cheoncheon-dong, Jangan-gu, Suwon, Gyeonggi-do 440-746 (Korea, Republic of)

2013-03-01

This study reports the microstructural characterization and formation mechanism of the 21° top facets of ZnO-based nanowall structures. The ZnO-based nanowall structures reported previously by many other research groups have {112"¯0} planes as major planes and top facets with a specific angle in common, irrespective of the growth techniques and growth conditions. These nanowalls were found to exist between two adjacent nanowires with a c-axis preferred orientation, and the atoms at the junction of the nanowalls and nanowires perfectly coincided with each other at an atomic level, without any defects. The top facets of the nanowalls showed periodically stepped surfaces and were identified as {011"¯5} planes, which were perpendicular to the {112"¯0} major planes. On the basis of the microstructural characterization of the synthesized ZnO-based nanowall structures, the formation mechanism and atomic structure model of the 21° top facets of the nanowall structures are proposed.
Electronic transport in graphene-based structures: An effective cross-section approach

DEFF Research Database (Denmark)

Uppstu, Andreas; Saloriutta, Karri; Harju, Ari

2012-01-01

We show that transport in low-dimensional carbon structures with finite concentrations of scatterers can be modeled by utilizing scaling theory and effective cross sections. Our results are based on large-scale numerical simulations of carbon nanotubes and graphene nanoribbons, using a tight...
Structure-based control of complex networks with nonlinear dynamics.

Science.gov (United States)

Zañudo, Jorge Gomez Tejeda; Yang, Gang; Albert, Réka

2017-07-11

What can we learn about controlling a system solely from its underlying network structure? Here we adapt a recently developed framework for control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This feedback-based framework provides realizable node overrides that steer a system toward any of its natural long-term dynamic behaviors, regardless of the specific functional forms and system parameters. We use this framework on several real networks, identify the topological characteristics that underlie the predicted node overrides, and compare its predictions to those of structural controllability in control theory. Finally, we demonstrate this framework's applicability in dynamic models of gene regulatory networks and identify nodes whose override is necessary for control in the general case but not in specific model instances.
Ultrafast Dynamic Pressure Sensors Based on Graphene Hybrid Structure.

Science.gov (United States)

Liu, Shanbiao; Wu, Xing; Zhang, Dongdong; Guo, Congwei; Wang, Peng; Hu, Weida; Li, Xinming; Zhou, Xiaofeng; Xu, Hejun; Luo, Chen; Zhang, Jian; Chu, Junhao

2017-07-19

Mechanical flexible electronic skin has been focused on sensing various physical parameters, such as pressure and temperature. The studies of material design and array-accessible devices are the building blocks of strain sensors for subtle pressure sensing. Here, we report a new and facile preparation of a graphene hybrid structure with an ultrafast dynamic pressure response. Graphene oxide nanosheets are used as a surfactant to prevent graphene restacking in aqueous solution. This graphene hybrid structure exhibits a frequency-independent pressure resistive sensing property. Exceeding natural skin, such pressure sensors, can provide transient responses from static up to 10 000 Hz dynamic frequencies. Integrated by the controlling system, the array-accessible sensors can manipulate a robot arm and self-rectify the temperature of a heating blanket. This may pave a path toward the future application of graphene-based wearable electronics.
Shear Creep Simulation of Structural Plane of Rock Mass Based on Discontinuous Deformation Analysis

Directory of Open Access Journals (Sweden)

Guoxin Zhang

2017-01-01

Full Text Available Numerical simulations of the creep characteristics of the structural plane of rock mass are very useful. However, most existing simulation methods are based on continuum mechanics and hence are unsuitable in the case of large displacements and deformations. The discontinuous deformation analysis method proposed by Genhua is a discrete one and has a significant advantage when simulating the contacting problem of blocks. In this study, we combined the viscoelastic rheological model of Burgers with the discontinuous deformation analysis (DDA method. We also derived the recurrence formula for the creep deformation increment with the time step during numerical simulations. Based on the minimum potential energy principle, the general equilibrium equation was derived, and the shear creep deformation in the structural plane was considered. A numerical program was also developed and its effectiveness was confirmed based on the curves obtained by the creep test of the structural plane of a rock mass under different stress levels. Finally, the program was used to analyze the mechanism responsible for the creep features of the structural plane in the case of the toppling deformation of the rock slope. The results showed that the extended DDA method is an effective one.
Community structure in real-world networks from a non-parametrical synchronization-based dynamical approach

International Nuclear Information System (INIS)

Moujahid, Abdelmalik; D’Anjou, Alicia; Cases, Blanca

2012-01-01

Highlights: ► A synchronization-based algorithm for community structure detection is proposed. ► We model a complex network based on coupled nonidentical chaotic Rössler oscillators. ► The interaction scheme contemplates an uniformly increasing coupling force. ► The frequencies of oscillators are adapted according to a parameterless mechanism. ► The adaptation mechanism reveals the community structure present in the network. - Abstract: This work analyzes the problem of community structure in real-world networks based on the synchronization of nonidentical coupled chaotic Rössler oscillators each one characterized by a defined natural frequency, and coupled according to a predefined network topology. The interaction scheme contemplates an uniformly increasing coupling force to simulate a society in which the association between the agents grows in time. To enhance the stability of the correlated states that could emerge from the synchronization process, we propose a parameterless mechanism that adapts the characteristic frequencies of coupled oscillators according to a dynamic connectivity matrix deduced from correlated data. We show that the characteristic frequency vector that results from the adaptation mechanism reveals the underlying community structure present in the network.
Non-Contact Smartphone-Based Monitoring of Thermally Stressed Structures

Science.gov (United States)

Ozturk, Turgut; Mas, David; Rizzo, Piervincenzo

2018-01-01

The in-situ measurement of thermal stress in beams or continuous welded rails may prevent structural anomalies such as buckling. This study proposed a non-contact monitoring/inspection approach based on the use of a smartphone and a computer vision algorithm to estimate the vibrating characteristics of beams subjected to thermal stress. It is hypothesized that the vibration of a beam can be captured using a smartphone operating at frame rates higher than conventional 30 Hz, and the first few natural frequencies of the beam can be extracted using a computer vision algorithm. In this study, the first mode of vibration was considered and compared to the information obtained with a conventional accelerometer attached to the two structures investigated, namely a thin beam and a thick beam. The results show excellent agreement between the conventional contact method and the non-contact sensing approach proposed here. In the future, these findings may be used to develop a monitoring/inspection smartphone application to assess the axial stress of slender structures, to predict the neutral temperature of continuous welded rails, or to prevent thermal buckling. PMID:29670034
Table of periodic properties of fullerenes based on structural parameters.

Science.gov (United States)

Torrens, Francisco

2004-01-01

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

Science.gov (United States)

Athanasopoulos, N.; Siakavellas, N. J.

2015-12-01

Programmable thermal emissivity structures based on the bioinspired self-shape anisotropic materials were developed at macro-scale, and further studied theoretically at smaller scale. We study a novel concept, incorporating materials that are capable of transforming their shape via microstructural rearrangements under temperature stimuli, while avoiding the use of exotic shape memory materials or complex micro-mechanisms. Thus, programmed thermal emissivity behaviour of a surface is achievable. The self-shape structure reacts according to the temperature of the surrounding environment or the radiative heat flux. A surface which incorporates self-shape structures can be designed to quickly absorb radiative heat energy at low temperature levels, but is simultaneously capable of passively controlling its maximum temperature in order to prevent overheating. It resembles a “game” of colours, where two or more materials coexist with different values of thermal emissivity/ absorptivity/ reflectivity. The transformation of the structure conceals or reveals one of the materials, creating a surface with programmable - and therefore, variable- effective thermal emissivity. Variable thermal emissivity surfaces may be developed with a total hemispherical emissivity ratio (ɛEff_H/ɛEff_L) equal to 28.
Computational Modelling of Fracture Propagation in Rocks Using a Coupled Elastic-Plasticity-Damage Model

Directory of Open Access Journals (Sweden)

Isa Kolo

2016-01-01

Full Text Available A coupled elastic-plasticity-damage constitutive model, AK Model, is applied to predict fracture propagation in rocks. The quasi-brittle material model captures anisotropic effects and the distinct behavior of rocks in tension and compression. Calibration of the constitutive model is realized using experimental data for Carrara marble. Through the Weibull distribution function, heterogeneity effect is captured by spatially varying the elastic properties of the rock. Favorable comparison between model predictions and experiments for single-flawed specimens reveal that the AK Model is reliable and accurate for modelling fracture propagation in rocks.
Anthracene-Based Lanthanide Metal-Organic Frameworks: Synthesis, Structure, Photoluminescence, and Radioluminescence Properties

Directory of Open Access Journals (Sweden)

Stephan R. Mathis

2018-01-01

Full Text Available Four anthracene-based lanthanide metal-organic framework structures (MOFs were synthesized from the combination of the lanthanide ions, Eu3+, Tb3+, Er3+, and Tm3+, with 9,10-anthracenedicarboxylic acid (H2ADC in dimethylformamide (DMF under hydrothermal conditions. The 3-D networks crystalize in the triclinic system with P-1 space group with the following compositions: (i {{[Ln2(ADC3(DMF4·DMF]}n, Ln = Eu (1 and Tb (2} and (ii {{[Ln2(ADC3(DMF2(OH22·2DMF·H2O]}n, Ln = Er (3 and Tm (4}. The metal centers exist in various coordination environments; nine coordinate in (i, while seven and eight coordinate in (ii. The deprotonated ligand, ADC, assumes multiple coordination modes, with its carboxylate functional groups severely twisted away from the plane of the anthracene moiety. The structures show ligand-based photoluminescence, which appears to be significantly quenched when compared with that of the parent H2ADC solid powder. Structure 2 is the least quenched and showed an average photoluminescence lifetime from bi-exponential decay of 0.3 ns. On exposure to ionizing radiation, the structures show radioluminescence spectral features that are consistent with the isolation of the ligand units in its 3-D network. The spectral features vary among the 3-D networks and appear to suggest that the latter undergo significant changes in their molecular and/or electronic structure in the presence of the ionizing radiation.
Kink structures induced in nickel-based single crystal superalloys by high-Z element migration

Energy Technology Data Exchange (ETDEWEB)

Sun, Fei; Zhang, Jianxin [Key Laboratory for Liquid Structure and Heredity of Materials, Ministry of Education, Shandong University, Jinan 250061 (China); Mao, Shengcheng [Institute of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124 (China); Jiang, Ying [Center of Electron Microscopy and State Key Laboratory of Silicon Materials, Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Feng, Qiang [National Center for Materials Service Safety, University of Science and Technology Beijing, Beijing 100083 (China); State Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083 (China); Shen, Zhenju; Li, Jixue; Zhang, Ze [Center of Electron Microscopy and State Key Laboratory of Silicon Materials, Department of Materials Science and Engineering, Zhejiang University, Hangzhou 310027 (China); Han, Xiaodong [Institute of Microstructure and Property of Advanced Materials, Beijing University of Technology, Beijing 100124 (China)

2015-01-05

Highlights: • Innovative kink structures generate at the γ/γ′ interfaces in the crept superalloy. • Clusters of heavy elements congregate at the apex of the kinks. • Dislocation core absorbs hexagonal structural high-Z elements. - Abstract: Here, we investigate a new type of kink structure that is found at γ/γ′ interfaces in nickel-based single crystal superalloys. We studied these structures at the atomic and elemental level using aberration corrected high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM). The core of the dislocation absorbs high-Z elements (i.e., Co and Re) that adopt hexagonal arrangements, and it extrudes elements (i.e., Ni and Al) that adopt face centered cubic (fcc) structures. High-Z elements (i.e., Ta and W) and Cr, which is a low-Z element, are stabilized in body centered cubic (bcc) arrangements; Cr tends to behave like Re. High-Z elements, which migrate and adopt a hexagonal structure, induce kink formation at γ/γ′ interfaces. This process must be analyzed to fully understand the kinetics and dynamics of creep in nickel-based single crystal superalloys.
Guided wave based structural health monitoring: A review

International Nuclear Information System (INIS)

Mitra, Mira; Gopalakrishnan, S

2016-01-01

The paper provides a state of the art review of guided wave based structural health monitoring (SHM). First, the fundamental concepts of guided wave propagation and its implementation for SHM is explained. Following sections present the different modeling schemes adopted, developments in the area of transducers for generation, and sensing of wave, signal processing and imaging technique, statistical and machine learning schemes for feature extraction. Next, a section is presented on the recent advancements in nonlinear guided wave for SHM. This is followed by section on Rayleigh and SH waves. Next is a section on real-life implementation of guided wave for industrial problems. The paper, though briefly talks about the early development for completeness, is primarily focussed on the recent progress made in the last decade. The paper ends by discussing and highlighting the future directions and open areas of research in guided wave based SHM. (topical review)
Performance characterization of structured light-based fingerprint scanner

Science.gov (United States)

Hassebrook, Laurence G.; Wang, Minghao; Daley, Raymond C.

2013-05-01

Our group believes that the evolution of fingerprint capture technology is in transition to include 3-D non-contact fingerprint capture. More specifically we believe that systems based on structured light illumination provide the highest level of depth measurement accuracy. However, for these new technologies to be fully accepted by the biometric community, they must be compliant with federal standards of performance. At present these standards do not exist for this new biometric technology. We propose and define a set of test procedures to be used to verify compliance with the Federal Bureau of Investigation's image quality specification for Personal Identity Verification single fingerprint capture devices. The proposed test procedures include: geometric accuracy, lateral resolution based on intensity or depth, gray level uniformity and flattened fingerprint image quality. Several 2-D contact analogies, performance tradeoffs and optimization dilemmas are evaluated and proposed solutions are presented.
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

Directory of Open Access Journals (Sweden)

Toh Hiroyuki

2008-04-01

Full Text Available Abstract Background Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs. Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized. Results We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1 pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2 a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage. Conclusion The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.
Magnesium and aluminium-base products. For use as structural materials; Magnesium, aluminium et alliages. Emploi comme materiaux de structure

Energy Technology Data Exchange (ETDEWEB)

Bernard, J; Boudouresques, B; Alfille, L; Klersy, R [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires

1958-07-01

This paper deals with the ability of some Mg and Al-base products to be used as structural materials in thermal reactors. The results presented here are relating to investigations carried out for completing the design of french reactors. (author)Fren. [French] Les auteurs traitent de l'aptitude de quelques materiaux legers et ultra-legers a l'utilisation comme elements de structure des reacteurs thermiques. Les resultats presentes sont relatifs aux etudes effectuees pour l'etablissement des projets de piles fran ises. (auteur)
Stress-based topology optimization of concrete structures with prestressing reinforcements

Science.gov (United States)

Luo, Yangjun; Wang, Michael Yu; Deng, Zichen

2013-11-01

Following the extended two-material density penalization scheme, a stress-based topology optimization method for the layout design of prestressed concrete structures is proposed. The Drucker-Prager yield criterion is used to predict the asymmetrical strength failure of concrete. The prestress is considered by making a reasonable assumption on the prestressing orientation in each element and adding an additional load vector to the structural equilibrium function. The proposed optimization model is thus formulated as to minimize the reinforcement material volume under Drucker-Prager yield constraints on elemental concrete local stresses. In order to give a reasonable definition of concrete local stress and prevent the stress singularity phenomenon, the local stress interpolation function and the ɛ -relaxation technique are adopted. The topology optimization problem is solved using the method of moving asymptotes combined with an active set strategy. Numerical examples are given to show the efficiency of the proposed optimization method in the layout design of prestressed concrete structures.

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