Amplitude interpretation and visualization of three-dimensional reflection data

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

Enachescu, M.E.

1994-07-01

Digital recording and processing of modern three-dimensional surveys allow for relative good preservation and correct spatial positioning of seismic reflection amplitude. A four-dimensional seismic reflection field matrix R (x,y,t,A), which can be computer visualized (i.e., real-time interactively rendered, edited, and animated), is now available to the interpreter. The amplitude contains encoded geological information indirectly related to lithologies and reservoir properties. The magnitude of the amplitude depends not only on the acoustic impedance contrast across a boundary, but is also strongly affected by the shape of the reflective boundary. This allows the interpreter to image subtle tectonic and structural elements notmore » obvious on time-structure maps. The use of modern workstations allows for appropriate color coding of the total available amplitude range, routine on-screen time/amplitude extraction, and late display of horizon amplitude maps (horizon slices) or complex amplitude-structure spatial visualization. Stratigraphic, structural, tectonic, fluid distribution, and paleogeographic information are commonly obtained by displaying the amplitude variation A = A(x,y,t) associated with a particular reflective surface or seismic interval. As illustrated with several case histories, traditional structural and stratigraphic interpretation combined with a detailed amplitude study generally greatly enhance extraction of subsurface geological information from a reflection data volume. In the context of three-dimensional seismic surveys, the horizon amplitude map (horizon slice), amplitude attachment to structure and [open quotes]bright clouds[close quotes] displays are very powerful tools available to the interpreter.« less

Depth-tunable three-dimensional display with interactive light field control

NASA Astrophysics Data System (ADS)

Xie, Songlin; Wang, Peng; Sang, Xinzhu; Li, Chenyu; Dou, Wenhua; Xiao, Liquan

2016-07-01

A software-defined depth-tunable three-dimensional (3D) display with interactive 3D depth control is presented. With the proposed post-processing system, the disparity of the multi-view media can be freely adjusted. Benefiting from a wealth of information inherently contains in dense multi-view images captured with parallel arrangement camera array, the 3D light field is built and the light field structure is controlled to adjust the disparity without additional acquired depth information since the light field structure itself contains depth information. A statistical analysis based on the least square is carried out to extract the depth information inherently exists in the light field structure and the accurate depth information can be used to re-parameterize light fields for the autostereoscopic display, and a smooth motion parallax can be guaranteed. Experimental results show that the system is convenient and effective to adjust the 3D scene performance in the 3D display.

Phase space interrogation of the empirical response modes for seismically excited structures

NASA Astrophysics Data System (ADS)

Paul, Bibhas; George, Riya C.; Mishra, Sudib K.

2017-07-01

Conventional Phase Space Interrogation (PSI) for structural damage assessment relies on exciting the structure with low dimensional chaotic waveform, thereby, significantly limiting their applicability to large structures. The PSI technique is presently extended for structure subjected to seismic excitations. The high dimensionality of the phase space for seismic response(s) are overcome by the Empirical Mode Decomposition (EMD), decomposing the responses to a number of intrinsic low dimensional oscillatory modes, referred as Intrinsic Mode Functions (IMFs). Along with their low dimensionality, a few IMFs, retain sufficient information of the system dynamics to reflect the damage induced changes. The mutually conflicting nature of low-dimensionality and the sufficiency of dynamic information are taken care by the optimal choice of the IMF(s), which is shown to be the third/fourth IMFs. The optimal IMF(s) are employed for the reconstruction of the Phase space attractor following Taken's embedding theorem. The widely referred Changes in Phase Space Topology (CPST) feature is then employed on these Phase portrait(s) to derive the damage sensitive feature, referred as the CPST of the IMFs (CPST-IMF). The legitimacy of the CPST-IMF is established as a damage sensitive feature by assessing its variation with a number of damage scenarios benchmarked in the IASC-ASCE building. The damage localization capability, remarkable tolerance to noise contamination and the robustness under different seismic excitations of the feature are demonstrated.

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

Kim, Sang Beom; Dsilva, Carmeline J.; Debenedetti, Pablo G., E-mail: pdebene@princeton.edu

Understanding the mechanisms by which proteins fold from disordered amino-acid chains to spatially ordered structures remains an area of active inquiry. Molecular simulations can provide atomistic details of the folding dynamics which complement experimental findings. Conventional order parameters, such as root-mean-square deviation and radius of gyration, provide structural information but fail to capture the underlying dynamics of the protein folding process. It is therefore advantageous to adopt a method that can systematically analyze simulation data to extract relevant structural as well as dynamical information. The nonlinear dimensionality reduction technique known as diffusion maps automatically embeds the high-dimensional folding trajectories inmore » a lower-dimensional space from which one can more easily visualize folding pathways, assuming the data lie approximately on a lower-dimensional manifold. The eigenvectors that parametrize the low-dimensional space, furthermore, are determined systematically, rather than chosen heuristically, as is done with phenomenological order parameters. We demonstrate that diffusion maps can effectively characterize the folding process of a Trp-cage miniprotein. By embedding molecular dynamics simulation trajectories of Trp-cage folding in diffusion maps space, we identify two folding pathways and intermediate structures that are consistent with the previous studies, demonstrating that this technique can be employed as an effective way of analyzing and constructing protein folding pathways from molecular simulations.« less

Two-dimensional wind tunnel

NASA Technical Reports Server (NTRS)

1982-01-01

Information on the Japanese National Aerospace Laboratory two dimensional transonic wind tunnel, completed at the end of 1979 is presented. Its construction is discussed in detail, and the wind tunnel structure, operation, test results, and future plans are presented.

What did Erwin mean? The physics of information from the materials genomics of aperiodic crystals and water to molecular information catalysts and life.

PubMed

Varn, D P; Crutchfield, J P

2016-03-13

Erwin Schrödinger famously and presciently ascribed the vehicle transmitting the hereditary information underlying life to an 'aperiodic crystal'. We compare and contrast this, only later discovered to be stored in the linear biomolecule DNA, with the information-bearing, layered quasi-one-dimensional materials investigated by the emerging field of chaotic crystallography. Despite differences in functionality, the same information measures capture structure and novelty in both, suggesting an intimate coherence between the information character of biotic and abiotic matter-a broadly applicable physics of information. We review layered solids and consider three examples of how information- and computation-theoretic techniques are being applied to understand their structure. In particular, (i) we review recent efforts to apply new kinds of information measures to quantify disordered crystals; (ii) we discuss the structure of ice I in information-theoretic terms; and (iii) we recount recent investigations into the structure of tris(bicyclo[2.1.1]hexeno)benzene, showing how an information-theoretic analysis yields additional insight into its structure. We then illustrate a new Second Law of Thermodynamics that describes information processing in active low-dimensional materials, reviewing Maxwell's Demon and a new class of molecular devices that act as information catalysts. Lastly, we conclude by speculating on how these ideas from informational materials science may impact biology. © 2016 The Author(s).

Three-dimensional electron diffraction as a complementary technique to powder X-ray diffraction for phase identification and structure solution of powders.

PubMed

Yun, Yifeng; Zou, Xiaodong; Hovmöller, Sven; Wan, Wei

2015-03-01

Phase identification and structure determination are important and widely used techniques in chemistry, physics and materials science. Recently, two methods for automated three-dimensional electron diffraction (ED) data collection, namely automated diffraction tomography (ADT) and rotation electron diffraction (RED), have been developed. Compared with X-ray diffraction (XRD) and two-dimensional zonal ED, three-dimensional ED methods have many advantages in identifying phases and determining unknown structures. Almost complete three-dimensional ED data can be collected using the ADT and RED methods. Since each ED pattern is usually measured off the zone axes by three-dimensional ED methods, dynamic effects are much reduced compared with zonal ED patterns. Data collection is easy and fast, and can start at any arbitrary orientation of the crystal, which facilitates automation. Three-dimensional ED is a powerful technique for structure identification and structure solution from individual nano- or micron-sized particles, while powder X-ray diffraction (PXRD) provides information from all phases present in a sample. ED suffers from dynamic scattering, while PXRD data are kinematic. Three-dimensional ED methods and PXRD are complementary and their combinations are promising for studying multiphase samples and complicated crystal structures. Here, two three-dimensional ED methods, ADT and RED, are described. Examples are given of combinations of three-dimensional ED methods and PXRD for phase identification and structure determination over a large number of different materials, from Ni-Se-O-Cl crystals, zeolites, germanates, metal-organic frameworks and organic compounds to intermetallics with modulated structures. It is shown that three-dimensional ED is now as feasible as X-ray diffraction for phase identification and structure solution, but still needs further development in order to be as accurate as X-ray diffraction. It is expected that three-dimensional ED methods will become crucially important in the near future.

Three-dimensional periodic dielectric structures having photonic Dirac points

DOEpatents

Bravo-Abad, Jorge; Joannopoulos, John D.; Soljacic, Marin

2015-06-02

The dielectric, three-dimensional photonic materials disclosed herein feature Dirac-like dispersion in quasi-two-dimensional systems. Embodiments include a face-centered cubic (fcc) structure formed by alternating layers of dielectric rods and dielectric slabs patterned with holes on respective triangular lattices. This fcc structure also includes a defect layer, which may comprise either dielectric rods or a dielectric slab with patterned with holes. This defect layer introduces Dirac cone dispersion into the fcc structure's photonic band structure. Examples of these fcc structures enable enhancement of the spontaneous emission coupling efficiency (the .beta.-factor) over large areas, contrary to the conventional wisdom that the .beta.-factor degrades as the system's size increases. These results enable large-area, low-threshold lasers; single-photon sources; quantum information processing devices; and energy harvesting systems.

Compound Structure-Independent Activity Prediction in High-Dimensional Target Space.

PubMed

Balfer, Jenny; Hu, Ye; Bajorath, Jürgen

2014-08-01

Profiling of compound libraries against arrays of targets has become an important approach in pharmaceutical research. The prediction of multi-target compound activities also represents an attractive task for machine learning with potential for drug discovery applications. Herein, we have explored activity prediction in high-dimensional target space. Different types of models were derived to predict multi-target activities. The models included naïve Bayesian (NB) and support vector machine (SVM) classifiers based upon compound structure information and NB models derived on the basis of activity profiles, without considering compound structure. Because the latter approach can be applied to incomplete training data and principally depends on the feature independence assumption, SVM modeling was not applicable in this case. Furthermore, iterative hybrid NB models making use of both activity profiles and compound structure information were built. In high-dimensional target space, NB models utilizing activity profile data were found to yield more accurate activity predictions than structure-based NB and SVM models or hybrid models. An in-depth analysis of activity profile-based models revealed the presence of correlation effects across different targets and rationalized prediction accuracy. Taken together, the results indicate that activity profile information can be effectively used to predict the activity of test compounds against novel targets. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tomography and Purification of the Temporal-Mode Structure of Quantum Light

NASA Astrophysics Data System (ADS)

Ansari, Vahid; Donohue, John M.; Allgaier, Markus; Sansoni, Linda; Brecht, Benjamin; Roslund, Jonathan; Treps, Nicolas; Harder, Georg; Silberhorn, Christine

2018-05-01

High-dimensional quantum information processing promises capabilities beyond the current state of the art, but addressing individual information-carrying modes presents a significant experimental challenge. Here we demonstrate effective high-dimensional operations in the time-frequency domain of nonclassical light. We generate heralded photons with tailored temporal-mode structures through the pulse shaping of a broadband parametric down-conversion pump. We then implement a quantum pulse gate, enabled by dispersion-engineered sum-frequency generation, to project onto programmable temporal modes, reconstructing the quantum state in seven dimensions. We also manipulate the time-frequency structure by selectively removing temporal modes, explicitly demonstrating the effectiveness of engineered nonlinear processes for the mode-selective manipulation of quantum states.

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.

PubMed

Afanasyev, Pavel; Seer-Linnemayr, Charlotte; Ravelli, Raimond B G; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V; Pannu, Navraj S; Schatz, Michael; van Heel, Marin

2017-09-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.

Interpretable dimensionality reduction of single cell transcriptome data with deep generative models.

PubMed

Ding, Jiarui; Condon, Anne; Shah, Sohrab P

2018-05-21

Single-cell RNA-sequencing has great potential to discover cell types, identify cell states, trace development lineages, and reconstruct the spatial organization of cells. However, dimension reduction to interpret structure in single-cell sequencing data remains a challenge. Existing algorithms are either not able to uncover the clustering structures in the data or lose global information such as groups of clusters that are close to each other. We present a robust statistical model, scvis, to capture and visualize the low-dimensional structures in single-cell gene expression data. Simulation results demonstrate that low-dimensional representations learned by scvis preserve both the local and global neighbor structures in the data. In addition, scvis is robust to the number of data points and learns a probabilistic parametric mapping function to add new data points to an existing embedding. We then use scvis to analyze four single-cell RNA-sequencing datasets, exemplifying interpretable two-dimensional representations of the high-dimensional single-cell RNA-sequencing data.

Geometrical structure of Neural Networks: Geodesics, Jeffrey's Prior and Hyper-ribbons

NASA Astrophysics Data System (ADS)

Hayden, Lorien; Alemi, Alex; Sethna, James

2014-03-01

Neural networks are learning algorithms which are employed in a host of Machine Learning problems including speech recognition, object classification and data mining. In practice, neural networks learn a low dimensional representation of high dimensional data and define a model manifold which is an embedding of this low dimensional structure in the higher dimensional space. In this work, we explore the geometrical structure of a neural network model manifold. A Stacked Denoising Autoencoder and a Deep Belief Network are trained on handwritten digits from the MNIST database. Construction of geodesics along the surface and of slices taken from the high dimensional manifolds reveal a hierarchy of widths corresponding to a hyper-ribbon structure. This property indicates that neural networks fall into the class of sloppy models, in which certain parameter combinations dominate the behavior. Employing this information could prove valuable in designing both neural network architectures and training algorithms. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No . DGE-1144153.

Coherent diffraction imaging: consistency of the assembled three-dimensional distribution.

PubMed

Tegze, Miklós; Bortel, Gábor

2016-07-01

The short pulses of X-ray free-electron lasers can produce diffraction patterns with structural information before radiation damage destroys the particle. From the recorded diffraction patterns the structure of particles or molecules can be determined on the nano- or even atomic scale. In a coherent diffraction imaging experiment thousands of diffraction patterns of identical particles are recorded and assembled into a three-dimensional distribution which is subsequently used to solve the structure of the particle. It is essential to know, but not always obvious, that the assembled three-dimensional reciprocal-space intensity distribution is really consistent with the measured diffraction patterns. This paper shows that, with the use of correlation maps and a single parameter calculated from them, the consistency of the three-dimensional distribution can be reliably validated.

Modeling and numerical simulations of growth and morphologies of three dimensional aggregated silver films

NASA Astrophysics Data System (ADS)

Davis, L. J.; Boggess, M.; Kodpuak, E.; Deutsch, M.

2012-11-01

We report on a model for the deposition of three dimensional, aggregated nanocrystalline silver films, and an efficient numerical simulation method developed for visualizing such structures. We compare our results to a model system comprising chemically deposited silver films with morphologies ranging from dilute, uniform distributions of nanoparticles to highly porous aggregated networks. Disordered silver films grown in solution on silica substrates are characterized using digital image analysis of high resolution scanning electron micrographs. While the latter technique provides little volume information, plane-projected (two dimensional) island structure and surface coverage may be reliably determined. Three parameters governing film growth are evaluated using these data and used as inputs for the deposition model, greatly reducing computing requirements while still providing direct access to the complete (bulk) structure of the films throughout the growth process. We also show how valuable three dimensional characteristics of the deposited materials can be extracted using the simulated structures.

Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

ERIC Educational Resources Information Center

Rzepa, Henry S.

2016-01-01

Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

Resource for structure related information on transmembrane proteins

NASA Astrophysics Data System (ADS)

Tusnády, Gábor E.; Simon, István

Transmembrane proteins are involved in a wide variety of vital biological processes including transport of water-soluble molecules, flow of information and energy production. Despite significant efforts to determine the structures of these proteins, only a few thousand solved structures are known so far. Here, we review the various resources for structure-related information on these types of proteins ranging from the 3D structure to the topology and from the up-to-date databases to the various Internet sites and servers dealing with structure prediction and structure analysis. Abbreviations: 3D, three dimensional; PDB, Protein Data Bank; TMP, transmembrane protein.

Entangled singularity patterns of photons in Ince-Gauss modes

NASA Astrophysics Data System (ADS)

Krenn, Mario; Fickler, Robert; Huber, Marcus; Lapkiewicz, Radek; Plick, William; Ramelow, Sven; Zeilinger, Anton

2013-01-01

Photons with complex spatial mode structures open up possibilities for new fundamental high-dimensional quantum experiments and for novel quantum information tasks. Here we show entanglement of photons with complex vortex and singularity patterns called Ince-Gauss modes. In these modes, the position and number of singularities vary depending on the mode parameters. We verify two-dimensional and three-dimensional entanglement of Ince-Gauss modes. By measuring one photon and thereby defining its singularity pattern, we nonlocally steer the singularity structure of its entangled partner, while the initial singularity structure of the photons is undefined. In addition we measure an Ince-Gauss specific quantum-correlation function with possible use in future quantum communication protocols.

Six dimensional X-ray Tensor Tomography with a compact laboratory setup

NASA Astrophysics Data System (ADS)

Sharma, Y.; Wieczorek, M.; Schaff, F.; Seyyedi, S.; Prade, F.; Pfeiffer, F.; Lasser, T.

2016-09-01

Attenuation based X-ray micro computed tomography (XCT) provides three-dimensional images with micrometer resolution. However, there is a trade-off between the smallest size of the structures that can be resolved and the measurable sample size. In this letter, we present an imaging method using a compact laboratory setup that reveals information about micrometer-sized structures within samples that are several orders of magnitudes larger. We combine the anisotropic dark-field signal obtained in a grating interferometer and advanced tomographic reconstruction methods to reconstruct a six dimensional scattering tensor at every spatial location in three dimensions. The scattering tensor, thus obtained, encodes information about the orientation of micron-sized structures such as fibres in composite materials or dentinal tubules in human teeth. The sparse acquisition schemes presented in this letter enable the measurement of the full scattering tensor at every spatial location and can be easily incorporated in a practical, commercially feasible laboratory setup using conventional X-ray tubes, thus allowing for widespread industrial applications.

Close-range laser scanning in forests: towards physically based semantics across scales.

PubMed

Morsdorf, F; Kükenbrink, D; Schneider, F D; Abegg, M; Schaepman, M E

2018-04-06

Laser scanning with its unique measurement concept holds the potential to revolutionize the way we assess and quantify three-dimensional vegetation structure. Modern laser systems used at close range, be it on terrestrial, mobile or unmanned aerial platforms, provide dense and accurate three-dimensional data whose information just waits to be harvested. However, the transformation of such data to information is not as straightforward as for airborne and space-borne approaches, where typically empirical models are built using ground truth of target variables. Simpler variables, such as diameter at breast height, can be readily derived and validated. More complex variables, e.g. leaf area index, need a thorough understanding and consideration of the physical particularities of the measurement process and semantic labelling of the point cloud. Quantified structural models provide a framework for such labelling by deriving stem and branch architecture, a basis for many of the more complex structural variables. The physical information of the laser scanning process is still underused and we show how it could play a vital role in conjunction with three-dimensional radiative transfer models to shape the information retrieval methods of the future. Using such a combined forward and physically based approach will make methods robust and transferable. In addition, it avoids replacing observer bias from field inventories with instrument bias from different laser instruments. Still, an intensive dialogue with the users of the derived information is mandatory to potentially re-design structural concepts and variables so that they profit most of the rich data that close-range laser scanning provides.

Two-Dimensional Spectroscopy Is Being Used to Address Core Scientific Questions in Biology and Materials Science.

PubMed

Petti, Megan K; Lomont, Justin P; Maj, Michał; Zanni, Martin T

2018-02-15

Two-dimensional spectroscopy is a powerful tool for extracting structural and dynamic information from a wide range of chemical systems. We provide a brief overview of the ways in which two-dimensional visible and infrared spectroscopies are being applied to elucidate fundamental details of important processes in biological and materials science. The topics covered include amyloid proteins, photosynthetic complexes, ion channels, photovoltaics, batteries, as well as a variety of promising new methods in two-dimensional spectroscopy.

Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research.

PubMed

Ercius, Peter; Alaidi, Osama; Rames, Matthew J; Ren, Gang

2015-10-14

Three-dimensional (3D) structural analysis is essential to understand the relationship between the structure and function of an object. Many analytical techniques, such as X-ray diffraction, neutron spectroscopy, and electron microscopy imaging, are used to provide structural information. Transmission electron microscopy (TEM), one of the most popular analytic tools, has been widely used for structural analysis in both physical and biological sciences for many decades, in which 3D objects are projected into two-dimensional (2D) images. In many cases, 2D-projection images are insufficient to understand the relationship between the 3D structure and the function of nanoscale objects. Electron tomography (ET) is a technique that retrieves 3D structural information from a tilt series of 2D projections, and is gradually becoming a mature technology with sub-nanometer resolution. Distinct methods to overcome sample-based limitations have been separately developed in both physical and biological science, although they share some basic concepts of ET. This review discusses the common basis for 3D characterization, and specifies difficulties and solutions regarding both hard and soft materials research. It is hoped that novel solutions based on current state-of-the-art techniques for advanced applications in hybrid matter systems can be motivated. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research

PubMed Central

Alaidi, Osama; Rames, Matthew J.

2016-01-01

Three-dimensional (3D) structural analysis is essential to understand the relationship between the structure and function of an object. Many analytical techniques, such as X-ray diffraction, neutron spectroscopy, and electron microscopy imaging, are used to provide structural information. Transmission electron microscopy (TEM), one of the most popular analytic tools, has been widely used for structural analysis in both physical and biological sciences for many decades, in which 3D objects are projected into two-dimensional (2D) images. In many cases, 2D-projection images are insufficient to understand the relationship between the 3D structure and the function of nanoscale objects. Electron tomography (ET) is a technique that retrieves 3D structural information from a tilt series of 2D projections, and is gradually becoming a mature technology with sub-nanometer resolution. Distinct methods to overcome sample-based limitations have been separately developed in both physical and biological science, although they share some basic concepts of ET. This review discusses the common basis for 3D characterization, and specifies difficulties and solutions regarding both hard and soft materials research. It is hoped that novel solutions based on current state-of-the-art techniques for advanced applications in hybrid matter systems can be motivated. PMID:26087941

Three-Dimensional Extension of a Digital Library Service System

ERIC Educational Resources Information Center

Xiao, Long

2010-01-01

Purpose: The paper aims to provide an overall methodology and case study for the innovation and extension of a digital library, especially the service system. Design/methodology/approach: Based on the three-dimensional structure theory of the information service industry, this paper combines a comprehensive analysis with the practical experiences…

Development and Validation of the Implicit Information from Lewis Structures Instrument(IILSI): Do Students Connect Structures with Properties?

ERIC Educational Resources Information Center

Cooper, Melanie M.; Underwood, Sonia M.; Hilley, Caleb Z.

2012-01-01

Lewis structures are a simplified two dimensional "cartoon" of molecular structure that allow a knowledgeable user to predict the types of properties a particular substance may exhibit. However, prior research shows that many students fail to recognize these structure-property connections and are unable to decode the information…

A discrete search algorithm for finding the structure of protein backbones and side chains.

PubMed

Sallaume, Silas; Martins, Simone de Lima; Ochi, Luiz Satoru; Da Silva, Warley Gramacho; Lavor, Carlile; Liberti, Leo

2013-01-01

Some information about protein structure can be obtained by using Nuclear Magnetic Resonance (NMR) techniques, but they provide only a sparse set of distances between atoms in a protein. The Molecular Distance Geometry Problem (MDGP) consists in determining the three-dimensional structure of a molecule using a set of known distances between some atoms. Recently, a Branch and Prune (BP) algorithm was proposed to calculate the backbone of a protein, based on a discrete formulation for the MDGP. We present an extension of the BP algorithm that can calculate not only the protein backbone, but the whole three-dimensional structure of proteins.

SINGER: A Computer Code for General Analysis of Two-Dimensional Reinforced Concrete Structures. Volume 1. Solution Process

DTIC Science & Technology

1975-05-01

Conference on Earthquake Engineering, Santiago de Chile, 13-18 January 1969, Vol. I , Session B2, Chilean Association oil Seismology and Earth- quake...Nuclear Agency May 1975 DISTRIBUTED BY: KJ National Technical Information Service U. S. DEPARTMENT OF COMMERCE ^804J AFWL-TR-74-228, Vol. I ...CM o / i ’•fu.r ) V V AFWL-TR- 74-228 Vol. I SINGER: A COMPUTER CODE FOR GENERAL ANALYSIS OF TWO-DIMENSIONAL CONCRETE STRUCTURES Volum« I

Evaluation of Deep Learning Representations of Spatial Storm Data

NASA Astrophysics Data System (ADS)

Gagne, D. J., II; Haupt, S. E.; Nychka, D. W.

2017-12-01

The spatial structure of a severe thunderstorm and its surrounding environment provide useful information about the potential for severe weather hazards, including tornadoes, hail, and high winds. Statistics computed over the area of a storm or from the pre-storm environment can provide descriptive information but fail to capture structural information. Because the storm environment is a complex, high-dimensional space, identifying methods to encode important spatial storm information in a low-dimensional form should aid analysis and prediction of storms by statistical and machine learning models. Principal component analysis (PCA), a more traditional approach, transforms high-dimensional data into a set of linearly uncorrelated, orthogonal components ordered by the amount of variance explained by each component. The burgeoning field of deep learning offers two potential approaches to this problem. Convolutional Neural Networks are a supervised learning method for transforming spatial data into a hierarchical set of feature maps that correspond with relevant combinations of spatial structures in the data. Generative Adversarial Networks (GANs) are an unsupervised deep learning model that uses two neural networks trained against each other to produce encoded representations of spatial data. These different spatial encoding methods were evaluated on the prediction of severe hail for a large set of storm patches extracted from the NCAR convection-allowing ensemble. Each storm patch contains information about storm structure and the near-storm environment. Logistic regression and random forest models were trained using the PCA and GAN encodings of the storm data and were compared against the predictions from a convolutional neural network. All methods showed skill over climatology at predicting the probability of severe hail. However, the verification scores among the methods were very similar and the predictions were highly correlated. Further evaluations are being performed to determine how the choice of input variables affects the results.

SPECIAL ISSUE DEVOTED TO THE 80TH BIRTHDAY OF S.A. AKHMANOV: Excitation of coherent polaritons in a two-dimensional atomic lattice

NASA Astrophysics Data System (ADS)

Barinov, I. O.; Alodzhants, A. P.; Arakelyan, Sergei M.

2009-07-01

We describe a new type of spatially periodic structure (lattice models): a polaritonic crystal formed by a two-dimensional lattice of trapped two-level atoms interacting with the electromagnetic field in a cavity (or in a one-dimensional array of tunnelling-coupled microcavities), which allows polaritons to be fully localised. Using a one-dimensional polaritonic crystal as an example, we analyse conditions for quantum degeneracy of a lower-polariton gas and those for quantum optical information recording and storage.

Structure of turbulence in three-dimensional boundary layers

NASA Technical Reports Server (NTRS)

Subramanian, Chelakara S.

1993-01-01

This report provides an overview of the three dimensional turbulent boundary layer concepts and of the currently available experimental information for their turbulence modeling. It is found that more reliable turbulence data, especially of the Reynolds stress transport terms, is needed to improve the existing modeling capabilities. An experiment is proposed to study the three dimensional boundary layer formed by a 'sink flow' in a fully developed two dimensional turbulent boundary layer. Also, the mean and turbulence field measurement procedure using a three component laser Doppler velocimeter is described.

Tensor of effective susceptibility in random magnetic composites: Application to two-dimensional and three-dimensional cases

NASA Astrophysics Data System (ADS)

Posnansky, Oleg P.

2018-05-01

The measuring of dynamic magnetic susceptibility by nuclear magnetic resonance is used for revealing information about the internal structure of various magnetoactive composites. The response of such material on the applied external static and time-varying magnetic fields encodes intrinsic dynamic correlations and depends on links between macroscopic effective susceptibility and structure on the microscopic scale. In the current work we carried out computational analysis of the frequency dependent dynamic magnetic susceptibility and demonstrated its dependence on the microscopic architectural elements while also considering Euclidean dimensionality. The proposed numerical method is efficient in the simulation of nuclear magnetic resonance experiments in two- and three-dimensional random magnetic media by choosing and modeling the influence of the concentration of components and internal hierarchical characteristics of physical parameters.

Structure solution of network materials by solid-state NMR without knowledge of the crystallographic space group.

PubMed

Brouwer, Darren H

2013-01-01

An algorithm is presented for solving the structures of silicate network materials such as zeolites or layered silicates from solid-state (29)Si double-quantum NMR data for situations in which the crystallographic space group is not known. The algorithm is explained and illustrated in detail using a hypothetical two-dimensional network structure as a working example. The algorithm involves an atom-by-atom structure building process in which candidate partial structures are evaluated according to their agreement with Si-O-Si connectivity information, symmetry restraints, and fits to (29)Si double quantum NMR curves followed by minimization of a cost function that incorporates connectivity, symmetry, and quality of fit to the double quantum curves. The two-dimensional network material is successfully reconstructed from hypothetical NMR data that can be reasonably expected to be obtained for real samples. This advance in "NMR crystallography" is expected to be important for structure determination of partially ordered silicate materials for which diffraction provides very limited structural information. Copyright © 2013 Elsevier Inc. All rights reserved.

The three-dimensional genome organization of Drosophila melanogaster through data integration.

PubMed

Li, Qingjiao; Tjong, Harianto; Li, Xiao; Gong, Ke; Zhou, Xianghong Jasmine; Chiolo, Irene; Alber, Frank

2017-07-31

Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome's organization. It remains a major challenge to integrate such data from various complementary experimental methods. Here, we present an approach for data integration to determine a population of complete three-dimensional genome structures that are statistically consistent with data from both genome-wide chromosome conformation capture (Hi-C) and lamina-DamID experiments. Our structures resolve the genome at the resolution of topological domains, and reproduce simultaneously both sets of experimental data. Importantly, this data deconvolution framework allows for structural heterogeneity between cells, and hence accounts for the expected plasticity of genome structures. As a case study we choose Drosophila melanogaster embryonic cells, for which both data types are available. Our three-dimensional genome structures have strong predictive power for structural features not directly visible in the initial data sets, and reproduce experimental hallmarks of the D. melanogaster genome organization from independent and our own imaging experiments. Also they reveal a number of new insights about genome organization and its functional relevance, including the preferred locations of heterochromatic satellites of different chromosomes, and observations about homologous pairing that cannot be directly observed in the original Hi-C or lamina-DamID data. Our approach allows systematic integration of Hi-C and lamina-DamID data for complete three-dimensional genome structure calculation, while also explicitly considering genome structural variability.

1-Dimensional AgVO3 nanowires hybrid with 2-dimensional graphene nanosheets to create 3-dimensional composite aerogels and their improved electrochemical properties

NASA Astrophysics Data System (ADS)

Liang, Liying; Xu, Yimeng; Lei, Yong; Liu, Haimei

2014-03-01

Three-dimensional (3D) porous composite aerogels have been synthesized via an innovative in situ hydrothermal method assisted by a freeze-drying process. In this hybrid structure, one-dimensional (1D) AgVO3 nanowires are uniformly dispersed on two-dimensional (2D) graphene nanosheet surfaces and/or are penetrated through the graphene sheets, forming 3D porous composite aerogels. As cathode materials for lithium-ion batteries, the composite aerogels exhibit high discharge capacity, excellent rate capability, and good cycling stability.Three-dimensional (3D) porous composite aerogels have been synthesized via an innovative in situ hydrothermal method assisted by a freeze-drying process. In this hybrid structure, one-dimensional (1D) AgVO3 nanowires are uniformly dispersed on two-dimensional (2D) graphene nanosheet surfaces and/or are penetrated through the graphene sheets, forming 3D porous composite aerogels. As cathode materials for lithium-ion batteries, the composite aerogels exhibit high discharge capacity, excellent rate capability, and good cycling stability. Electronic supplementary information (ESI) available: Preparation, characterization, SEM images, XRD patterns, and XPS of AgVO3/GAs. See DOI: 10.1039/c3nr06899d

Dipeptide Structural Analysis Using Two-Dimensional NMR for the Undergraduate Advanced Laboratory

ERIC Educational Resources Information Center

Gonzalez, Elizabeth; Dolino, Drew; Schwartzenburg, Danielle; Steiger, Michelle A.

2015-01-01

A laboratory experiment was developed to introduce students in either an organic chemistry or biochemistry lab course to two-dimensional nuclear magnetic resonance (2D NMR) spectroscopy using simple biomolecules. The goal of this experiment is for students to understand and interpret the information provided by a 2D NMR spectrum. Students are…

3D Imaging with Structured Illumination for Advanced Security Applications

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

Birch, Gabriel Carisle; Dagel, Amber Lynn; Kast, Brian A.

2015-09-01

Three-dimensional (3D) information in a physical security system is a highly useful dis- criminator. The two-dimensional data from an imaging systems fails to provide target dis- tance and three-dimensional motion vector, which can be used to reduce nuisance alarm rates and increase system effectiveness. However, 3D imaging devices designed primarily for use in physical security systems are uncommon. This report discusses an architecture favorable to physical security systems; an inexpensive snapshot 3D imaging system utilizing a simple illumination system. The method of acquiring 3D data, tests to understand illumination de- sign, and software modifications possible to maximize information gathering capabilitymore » are discussed.« less

Selective separation of fluorinated compounds from complex organic mixtures by pyrolysis-comprehensive two-dimensional gas chromatography coupled to high-resolution time-of-flight mass spectrometry.

PubMed

Nakajima, Yoji; Arinami, Yuko; Yamamoto, Kiyoshi

2014-12-29

The usefulness of comprehensive two-dimensional gas chromatography (GC×GC) was demonstrated for the selective separation of fluorinated compounds from organic mixtures, such as kerosene/perfluorokerosene mixtures, pyrolysis products derived from polyethylene/ethylene-tetrafluoroethylene alternating copolymer mixture and poly[2-(perfluorohexyl)ethyl acrylate]. Perfluorocarbons were completely separated from hydrocarbons in the two-dimensional chromatogram. Fluorohydrocarbons in the pyrolysis products of polyethylene/ethylene-tetrafluoroethylene alternating copolymer mixture were selectively isolated from their hydrocarbon counterparts and regularly arranged according to their chain length and fluorine content in the two-dimensional chromatogram. A reliable structural analysis of the fluorohydrocarbons was achieved by combining effective GC×GC positional information with accurate mass spectral data obtained by high-resolution time-of-flight mass spectrometry (HRTOF-MS). 2-(Perfluorohexyl)ethyl acrylate monomer, dimer, and trimer as well as 2-(perfluorohexyl)ethyl alcohol in poly[2-(perfluorohexyl)ethyl acrylate] pyrolysis products were detected in the bottommost part of the two-dimensional chromatogram with separation from hydrocarbons possessing terminal structure information about the polymer, such as α-methylstyrene. Pyrolysis-GC×GC/HRTOF-MS appeared particularly suitable for the characterization of fluorinated polymer microstructures, such as monomer sequences and terminal groups. Copyright © 2014 Elsevier B.V. All rights reserved.

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin

PubMed Central

Seer-Linnemayr, Charlotte; Ravelli, Raimond B. G.; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V.; Pannu, Navraj S.; Schatz, Michael; van Heel, Marin

2017-01-01

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the ‘Einstein from random noise’ problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous (‘four-dimensional’) cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, ‘random-startup’ three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external ‘starting models’. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive ‘ABC-4D’ pipeline is based on the two-dimensional reference-free ‘alignment by classification’ (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure. PMID:28989723

Label-free imaging of the dynamics of cell-to-cell string-like structure bridging in the free-space by low-coherent quantitative phase microscopy

NASA Astrophysics Data System (ADS)

Yamauchi, Toyohiko; Iwai, Hidenao; Yamashita, Yutaka

2013-03-01

We succeeded in utilizing our low-coherent quantitative phase microscopy (LC-QPM) to achieve label-free and three-dimensional imaging of string-like structures bridging the free-space between live cells. In past studies, three dimensional morphology of the string-like structures between cells had been investigated by electron microscopies and fluorescence microscopies and these structures were called "membrane nanotubes" or "tunneling nanotubes." However, use of electron microscopy inevitably kills these cells and fluorescence microscopy is itself a potentially invasive method. To achieve noninvasive imaging of live cells, we applied our LC-QPM which is a reflection-type, phase resolved and full-field interference microscope employing a low-coherent light source. LC-QPM is able to visualize the three-dimensional morphology of live cells without labeling by means of low-coherence interferometry. The lateral (diffraction limit) and longitudinal (coherence-length) spatial resolution of LC-QPM were respectively 0.49 and 0.93 micrometers and the repeatability of the phase measurement was 0.02 radians (1.0 nm). We successfully obtained three-dimensional morphology of live cultured epithelial cells (cell type: HeLa, derived from cervix cancer) and were able to clearly observe the individual string-like structures interconnecting the cells. When we performed volumetric imaging, a 80 micrometer by 60 micrometer by 6.5 micrometer volume was scanned every 5.67 seconds and 70 frames of a three-dimensional movie were recorded for a duration of 397 seconds. Moreover, the optical phase images gave us detailed information about the three-dimensional morphology of the string-like structure at sub-wavelength resolution. We believe that our LC-QPM will be a useful tool for the study of three-dimensional morphology of live cells.

High-dimensional Controlled-phase Gate Between a 2 N -dimensional Photon and N Three-level Artificial Atoms

NASA Astrophysics Data System (ADS)

Ma, Yun-Ming; Wang, Tie-Jun

2017-10-01

Higher-dimensional quantum system is of great interest owing to the outstanding features exhibited in the implementation of novel fundamental tests of nature and application in various quantum information tasks. High-dimensional quantum logic gate is a key element in scalable quantum computation and quantum communication. In this paper, we propose a scheme to implement a controlled-phase gate between a 2 N -dimensional photon and N three-level artificial atoms. This high-dimensional controlled-phase gate can serve as crucial components of the high-capacity, long-distance quantum communication. We use the high-dimensional Bell state analysis as an example to show the application of this device. Estimates on the system requirements indicate that our protocol is realizable with existing or near-further technologies. This scheme is ideally suited to solid-state integrated optical approaches to quantum information processing, and it can be applied to various system, such as superconducting qubits coupled to a resonator or nitrogen-vacancy centers coupled to a photonic-band-gap structures.

Nanoscale insights on one- and two-dimensional material structures

NASA Astrophysics Data System (ADS)

Floresca, Herman Carlo

The race for smaller, faster and more efficient devices has led researchers to explore the possibilities of utilizing nanostructures for scaling. These one-dimensional and two-dimensional materials have properties that are attractive for this purpose but are still not well controlled. Control comes with a complete understanding of the materials' electrical, thermal, optical and structural characteristics but is difficult to obtain due to their small scale. This work is intended to help researchers overcome the difficulty in studying nanostructures by providing techniques for analysis and insights of nanostructures that have not been previously available. Two nanostructures were studied: silicon nanowires and graphene. The nanowires were prepared for cross-section transmission electron microscopy (TEM) to discover the effects that controlled oxidation has on the dimensions and shape of the nanowires. Since cross-section TEM is not able to provide information about surface structure, a method for manipulating the wires with orientation control was developed. With this ability, all three orthogonal views of the nanowire were compiled for a comprehensive study on its structure in terms of shape and surface roughness. Graphene was used for a two-dimensional analytical technique that took advantage of customized computer programs for data acquisition, measurement and display. With the information provided, distinctions between grain boundary types in polycrystalline graphene were made and supported by statistical information from the software's output. It was also applied to a growth series of graphene samples in conjunction with scanning electron microscopy (SEM) images and electron backscatter diffraction (EBSD) maps. The results help point to origins of graphene's polycrystalline nature. This dissertation concludes with a thought towards the future by highlighting a method that can help analyze nanostructures, which may become incorporated into the structures of large devices. The fold-out method is a TEM sample preparation technique utilizing a focused ion beam (FIB) for site specific thinning across a large sample area. Its process is demonstrated along with advantages over conventional methods.

CH5M3D: an HTML5 program for creating 3D molecular structures.

PubMed

Earley, Clarke W

2013-11-18

While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user's computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/.

CH5M3D: an HTML5 program for creating 3D molecular structures

PubMed Central

2013-01-01

Background While a number of programs and web-based applications are available for the interactive display of 3-dimensional molecular structures, few of these provide the ability to edit these structures. For this reason, we have developed a library written in JavaScript to allow for the simple creation of web-based applications that should run on any browser capable of rendering HTML5 web pages. While our primary interest in developing this application was for educational use, it may also prove useful to researchers who want a light-weight application for viewing and editing small molecular structures. Results Molecular compounds are drawn on the HTML5 Canvas element, with the JavaScript code making use of standard techniques to allow display of three-dimensional structures on a two-dimensional canvas. Information about the structure (bond lengths, bond angles, and dihedral angles) can be obtained using a mouse or other pointing device. Both atoms and bonds can be added or deleted, and rotation about bonds is allowed. Routines are provided to read structures either from the web server or from the user’s computer, and creation of galleries of structures can be accomplished with only a few lines of code. Documentation and examples are provided to demonstrate how users can access all of the molecular information for creation of web pages with more advanced features. Conclusions A light-weight (≈ 75 kb) JavaScript library has been made available that allows for the simple creation of web pages containing interactive 3-dimensional molecular structures. Although this library is designed to create web pages, a web server is not required. Installation on a web server is straightforward and does not require any server-side modules or special permissions. The ch5m3d.js library has been released under the GNU GPL version 3 open-source license and is available from http://sourceforge.net/projects/ch5m3d/. PMID:24246004

Comparison of Cellulose Supramolecular Structures Between Nanocrystals of Different Origins

Treesearch

Umesh P. Agarwal; Richard S. Reiner; Christopher G. Hunt; Jeffery Catchmark; E. Johan Foster; Akira Isogai

2015-01-01

In this study, morphologies and supramolecular structures of CNCs from wood-pulp, cotton, bacteria, tunicate, and cladophora were investigated. TEM was used to study the morphological aspects of the nanocrystals whereas Raman spectroscopy provided information on the cellulose molecular structure and its organization within a CNC. Dimensional differences between the...

One-Dimensional Perovskite Manganite Oxide Nanostructures: Recent Developments in Synthesis, Characterization, Transport Properties, and Applications

NASA Astrophysics Data System (ADS)

Li, Lei; Liang, Lizhi; Wu, Heng; Zhu, Xinhua

2016-03-01

One-dimensional nanostructures, including nanowires, nanorods, nanotubes, nanofibers, and nanobelts, have promising applications in mesoscopic physics and nanoscale devices. In contrast to other nanostructures, one-dimensional nanostructures can provide unique advantages in investigating the size and dimensionality dependence of the materials' physical properties, such as electrical, thermal, and mechanical performances, and in constructing nanoscale electronic and optoelectronic devices. Among the one-dimensional nanostructures, one-dimensional perovskite manganite nanostructures have been received much attention due to their unusual electron transport and magnetic properties, which are indispensable for the applications in microelectronic, magnetic, and spintronic devices. In the past two decades, much effort has been made to synthesize and characterize one-dimensional perovskite manganite nanostructures in the forms of nanorods, nanowires, nanotubes, and nanobelts. Various physical and chemical deposition techniques and growth mechanisms are explored and developed to control the morphology, identical shape, uniform size, crystalline structure, defects, and homogenous stoichiometry of the one-dimensional perovskite manganite nanostructures. This article provides a comprehensive review of the state-of-the-art research activities that focus on the rational synthesis, structural characterization, fundamental properties, and unique applications of one-dimensional perovskite manganite nanostructures in nanotechnology. It begins with the rational synthesis of one-dimensional perovskite manganite nanostructures and then summarizes their structural characterizations. Fundamental physical properties of one-dimensional perovskite manganite nanostructures are also highlighted, and a range of unique applications in information storages, field-effect transistors, and spintronic devices are discussed. Finally, we conclude this review with some perspectives/outlook and future researches in these fields.

One-Dimensional Perovskite Manganite Oxide Nanostructures: Recent Developments in Synthesis, Characterization, Transport Properties, and Applications.

PubMed

Li, Lei; Liang, Lizhi; Wu, Heng; Zhu, Xinhua

2016-12-01

One-dimensional nanostructures, including nanowires, nanorods, nanotubes, nanofibers, and nanobelts, have promising applications in mesoscopic physics and nanoscale devices. In contrast to other nanostructures, one-dimensional nanostructures can provide unique advantages in investigating the size and dimensionality dependence of the materials' physical properties, such as electrical, thermal, and mechanical performances, and in constructing nanoscale electronic and optoelectronic devices. Among the one-dimensional nanostructures, one-dimensional perovskite manganite nanostructures have been received much attention due to their unusual electron transport and magnetic properties, which are indispensable for the applications in microelectronic, magnetic, and spintronic devices. In the past two decades, much effort has been made to synthesize and characterize one-dimensional perovskite manganite nanostructures in the forms of nanorods, nanowires, nanotubes, and nanobelts. Various physical and chemical deposition techniques and growth mechanisms are explored and developed to control the morphology, identical shape, uniform size, crystalline structure, defects, and homogenous stoichiometry of the one-dimensional perovskite manganite nanostructures. This article provides a comprehensive review of the state-of-the-art research activities that focus on the rational synthesis, structural characterization, fundamental properties, and unique applications of one-dimensional perovskite manganite nanostructures in nanotechnology. It begins with the rational synthesis of one-dimensional perovskite manganite nanostructures and then summarizes their structural characterizations. Fundamental physical properties of one-dimensional perovskite manganite nanostructures are also highlighted, and a range of unique applications in information storages, field-effect transistors, and spintronic devices are discussed. Finally, we conclude this review with some perspectives/outlook and future researches in these fields.

High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography

NASA Astrophysics Data System (ADS)

Kim, Kyoohyun; Yoon, HyeOk; Diez-Silva, Monica; Dao, Ming; Dasari, Ramachandra R.; Park, YongKeun

2014-01-01

We present high-resolution optical tomographic images of human red blood cells (RBC) parasitized by malaria-inducing Plasmodium falciparum (Pf)-RBCs. Three-dimensional (3-D) refractive index (RI) tomograms are reconstructed by recourse to a diffraction algorithm from multiple two-dimensional holograms with various angles of illumination. These 3-D RI tomograms of Pf-RBCs show cellular and subcellular structures of host RBCs and invaded parasites in fine detail. Full asexual intraerythrocytic stages of parasite maturation (ring to trophozoite to schizont stages) are then systematically investigated using optical diffraction tomography algorithms. These analyses provide quantitative information on the structural and chemical characteristics of individual host Pf-RBCs, parasitophorous vacuole, and cytoplasm. The in situ structural evolution and chemical characteristics of subcellular hemozoin crystals are also elucidated.

High-resolution three-dimensional imaging of red blood cells parasitized by Plasmodium falciparum and in situ hemozoin crystals using optical diffraction tomography

PubMed Central

Kim, Kyoohyun; Yoon, HyeOk; Diez-Silva, Monica; Dao, Ming; Dasari, Ramachandra R.

2013-01-01

Abstract. We present high-resolution optical tomographic images of human red blood cells (RBC) parasitized by malaria-inducing Plasmodium falciparum (Pf)-RBCs. Three-dimensional (3-D) refractive index (RI) tomograms are reconstructed by recourse to a diffraction algorithm from multiple two-dimensional holograms with various angles of illumination. These 3-D RI tomograms of Pf-RBCs show cellular and subcellular structures of host RBCs and invaded parasites in fine detail. Full asexual intraerythrocytic stages of parasite maturation (ring to trophozoite to schizont stages) are then systematically investigated using optical diffraction tomography algorithms. These analyses provide quantitative information on the structural and chemical characteristics of individual host Pf-RBCs, parasitophorous vacuole, and cytoplasm. The in situ structural evolution and chemical characteristics of subcellular hemozoin crystals are also elucidated. PMID:23797986

Touching proteins with virtual bare hands - Visualizing protein-drug complexes and their dynamics in self-made virtual reality using gaming hardware

NASA Astrophysics Data System (ADS)

Ratamero, Erick Martins; Bellini, Dom; Dowson, Christopher G.; Römer, Rudolf A.

2018-06-01

The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal chemists while attempting the above to access the information contained in three-dimensional structures by using two-dimensional projections, which can preclude disclosure of useful features. A more accessible and intuitive visualization of the three-dimensional configuration of the atomic geometry in the models can be achieved through the implementation of immersive virtual reality (VR). While bespoke commercial VR suites are available, in this work, we present a freely available software pipeline for visualising protein structures through VR. New consumer hardware, such as the uc(HTC Vive) and the uc(Oculus Rift) utilized in this study, are available at reasonable prices. As an instructive example, we have combined VR visualization with fast algorithms for simulating intramolecular motions of protein flexibility, in an effort to further improve structure-led drug design by exposing molecular interactions that might be hidden in the less informative static models. This is a paradigmatic test case scenario for many similar applications in computer-aided molecular studies and design.

Touching proteins with virtual bare hands : Visualizing protein-drug complexes and their dynamics in self-made virtual reality using gaming hardware.

PubMed

Ratamero, Erick Martins; Bellini, Dom; Dowson, Christopher G; Römer, Rudolf A

2018-06-07

The ability to precisely visualize the atomic geometry of the interactions between a drug and its protein target in structural models is critical in predicting the correct modifications in previously identified inhibitors to create more effective next generation drugs. It is currently common practice among medicinal chemists while attempting the above to access the information contained in three-dimensional structures by using two-dimensional projections, which can preclude disclosure of useful features. A more accessible and intuitive visualization of the three-dimensional configuration of the atomic geometry in the models can be achieved through the implementation of immersive virtual reality (VR). While bespoke commercial VR suites are available, in this work, we present a freely available software pipeline for visualising protein structures through VR. New consumer hardware, such as the HTC VIVE and the OCULUS RIFT utilized in this study, are available at reasonable prices. As an instructive example, we have combined VR visualization with fast algorithms for simulating intramolecular motions of protein flexibility, in an effort to further improve structure-led drug design by exposing molecular interactions that might be hidden in the less informative static models. This is a paradigmatic test case scenario for many similar applications in computer-aided molecular studies and design.

Recent advances in electron tomography: TEM and HAADF-STEM tomography for materials science and semiconductor applications.

PubMed

Kübel, Christian; Voigt, Andreas; Schoenmakers, Remco; Otten, Max; Su, David; Lee, Tan-Chen; Carlsson, Anna; Bradley, John

2005-10-01

Electron tomography is a well-established technique for three-dimensional structure determination of (almost) amorphous specimens in life sciences applications. With the recent advances in nanotechnology and the semiconductor industry, there is also an increasing need for high-resolution three-dimensional (3D) structural information in physical sciences. In this article, we evaluate the capabilities and limitations of transmission electron microscopy (TEM) and high-angle-annular-dark-field scanning transmission electron microscopy (HAADF-STEM) tomography for the 3D structural characterization of partially crystalline to highly crystalline materials. Our analysis of catalysts, a hydrogen storage material, and different semiconductor devices shows that features with a diameter as small as 1-2 nm can be resolved in three dimensions by electron tomography. For partially crystalline materials with small single crystalline domains, bright-field TEM tomography provides reliable 3D structural information. HAADF-STEM tomography is more versatile and can also be used for high-resolution 3D imaging of highly crystalline materials such as semiconductor devices.

Self-assembled three-dimensional chiral colloidal architecture

NASA Astrophysics Data System (ADS)

Ben Zion, Matan Yah; He, Xiaojin; Maass, Corinna C.; Sha, Ruojie; Seeman, Nadrian C.; Chaikin, Paul M.

2017-11-01

Although stereochemistry has been a central focus of the molecular sciences since Pasteur, its province has previously been restricted to the nanometric scale. We have programmed the self-assembly of micron-sized colloidal clusters with structural information stemming from a nanometric arrangement. This was done by combining DNA nanotechnology with colloidal science. Using the functional flexibility of DNA origami in conjunction with the structural rigidity of colloidal particles, we demonstrate the parallel self-assembly of three-dimensional microconstructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality.

Two-Dimensional Sectioned Images and Three-Dimensional Surface Models for Learning the Anatomy of the Female Pelvis

ERIC Educational Resources Information Center

Shin, Dong Sun; Jang, Hae Gwon; Hwang, Sung Bae; Har, Dong-Hwan; Moon, Young Lae; Chung, Min Suk

2013-01-01

In the Visible Korean project, serially sectioned images of the pelvis were made from a female cadaver. Outlines of significant structures in the sectioned images were drawn and stacked to build surface models. To improve the accessibility and informational content of these data, a five-step process was designed and implemented. First, 154 pelvic…

Confocal Imaging of porous media

NASA Astrophysics Data System (ADS)

Shah, S.; Crawshaw, D.; Boek, D.

2012-12-01

Carbonate rocks, which hold approximately 50% of the world's oil and gas reserves, have a very complicated and heterogeneous structure in comparison with sandstone reservoir rock. We present advances with different techniques to image, reconstruct, and characterize statistically the micro-geometry of carbonate pores. The main goal here is to develop a technique to obtain two dimensional and three dimensional images using Confocal Laser Scanning Microscopy. CLSM is used in epi-fluorescent imaging mode, allowing for the very high optical resolution of features well below 1μm size. Images of pore structures were captured using CLSM imaging where spaces in the carbonate samples were impregnated with a fluorescent, dyed epoxy-resin, and scanned in the x-y plane by a laser probe. We discuss the sample preparation in detail for Confocal Imaging to obtain sub-micron resolution images of heterogeneous carbonate rocks. We also discuss the technical and practical aspects of this imaging technique, including its advantages and limitation. We present several examples of this application, including studying pore geometry in carbonates, characterizing sub-resolution porosity in two dimensional images. We then describe approaches to extract statistical information about porosity using image processing and spatial correlation function. We have managed to obtain very low depth information in z -axis (~ 50μm) to develop three dimensional images of carbonate rocks with the current capabilities and limitation of CLSM technique. Hence, we have planned a novel technique to obtain higher depth information to obtain high three dimensional images with sub-micron resolution possible in the lateral and axial planes.

An unsupervised two-stage clustering approach for forest structure classification based on X-band InSAR data - A case study in complex temperate forest stands

NASA Astrophysics Data System (ADS)

Abdullahi, Sahra; Schardt, Mathias; Pretzsch, Hans

2017-05-01

Forest structure at stand level plays a key role for sustainable forest management, since the biodiversity, productivity, growth and stability of the forest can be positively influenced by managing its structural diversity. In contrast to field-based measurements, remote sensing techniques offer a cost-efficient opportunity to collect area-wide information about forest stand structure with high spatial and temporal resolution. Especially Interferometric Synthetic Aperture Radar (InSAR), which facilitates worldwide acquisition of 3d information independent from weather conditions and illumination, is convenient to capture forest stand structure. This study purposes an unsupervised two-stage clustering approach for forest structure classification based on height information derived from interferometric X-band SAR data which was performed in complex temperate forest stands of Traunstein forest (South Germany). In particular, a four dimensional input data set composed of first-order height statistics was non-linearly projected on a two-dimensional Self-Organizing Map, spatially ordered according to similarity (based on the Euclidean distance) in the first stage and classified using the k-means algorithm in the second stage. The study demonstrated that X-band InSAR data exhibits considerable capabilities for forest structure classification. Moreover, the unsupervised classification approach achieved meaningful and reasonable results by means of comparison to aerial imagery and LiDAR data.

Eros in Stereo

NASA Image and Video Library

2000-05-07

Stereo imaging, an important tool on NASA NEAR Shoemaker for geologic analysis of Eros, provides three-dimensional information on the asteroid landforms and structures. 3D glasses are necessary to view this image.

PolySac3DB: an annotated data base of 3 dimensional structures of polysaccharides.

PubMed

Sarkar, Anita; Pérez, Serge

2012-11-14

Polysaccharides are ubiquitously present in the living world. Their structural versatility makes them important and interesting components in numerous biological and technological processes ranging from structural stabilization to a variety of immunologically important molecular recognition events. The knowledge of polysaccharide three-dimensional (3D) structure is important in studying carbohydrate-mediated host-pathogen interactions, interactions with other bio-macromolecules, drug design and vaccine development as well as material science applications or production of bio-ethanol. PolySac3DB is an annotated database that contains the 3D structural information of 157 polysaccharide entries that have been collected from an extensive screening of scientific literature. They have been systematically organized using standard names in the field of carbohydrate research into 18 categories representing polysaccharide families. Structure-related information includes the saccharides making up the repeat unit(s) and their glycosidic linkages, the expanded 3D representation of the repeat unit, unit cell dimensions and space group, helix type, diffraction diagram(s) (when applicable), experimental and/or simulation methods used for structure description, link to the abstract of the publication, reference and the atomic coordinate files for visualization and download. The database is accompanied by a user-friendly graphical user interface (GUI). It features interactive displays of polysaccharide structures and customized search options for beginners and experts, respectively. The site also serves as an information portal for polysaccharide structure determination techniques. The web-interface also references external links where other carbohydrate-related resources are available. PolySac3DB is established to maintain information on the detailed 3D structures of polysaccharides. All the data and features are available via the web-interface utilizing the search engine and can be accessed at http://polysac3db.cermav.cnrs.fr.

A one-dimensional diffusion analogy model for estimation of tide heights in selected tidal marshes in Connecticut

USGS Publications Warehouse

Bjerklie, David M.; O’Brien, Kevin; Rozsa, Ron

2013-01-01

A one-dimensional diffusion analogy model for estimating tide heights in coastal marshes was developed and calibrated by using data from previous tidal-marsh studies. The method is simpler to use than other one- and two-dimensional hydrodynamic models because it does not require marsh depth and tidal prism information; however, the one-dimensional diffusion analogy model cannot be used to estimate tide heights, flow velocities, and tide arrival times for tide conditions other than the highest tide for which it is calibrated. Limited validation of the method indicates that it has an accuracy within 0.3 feet. The method can be applied with limited calibration information that is based entirely on remote sensing or geographic information system data layers. The method can be used to estimate high-tide heights in tidal wetlands drained by tide gates where tide levels cannot be observed directly by opening the gates without risk of flooding properties and structures. A geographic information system application of the method is demonstrated for Sybil Creek marsh in Branford, Connecticut. The tidal flux into this marsh is controlled by two tide gates that prevent full tidal inundation of the marsh. The method application shows reasonable tide heights for the gates-closed condition (the normal condition) and the one-gate-open condition on the basis of comparison with observed heights. The condition with all tide gates open (two gates) was simulated with the model; results indicate where several structures would be flooded if the gates were removed as part of restoration efforts or if the tide gates were to fail.

Computational methods for constructing protein structure models from 3D electron microscopy maps.

PubMed

Esquivel-Rodríguez, Juan; Kihara, Daisuke

2013-10-01

Protein structure determination by cryo-electron microscopy (EM) has made significant progress in the past decades. Resolutions of EM maps have been improving as evidenced by recently reported structures that are solved at high resolutions close to 3Å. Computational methods play a key role in interpreting EM data. Among many computational procedures applied to an EM map to obtain protein structure information, in this article we focus on reviewing computational methods that model protein three-dimensional (3D) structures from a 3D EM density map that is constructed from two-dimensional (2D) maps. The computational methods we discuss range from de novo methods, which identify structural elements in an EM map, to structure fitting methods, where known high resolution structures are fit into a low-resolution EM map. A list of available computational tools is also provided. Copyright © 2013 Elsevier Inc. All rights reserved.

Monoterpene Unknowns Identified Using IR, [to the first power]H-NMR, [to the thirteenth power]C-NMR, DEPT, COSY, and HETCOR

ERIC Educational Resources Information Center

Alty, Lisa T.

2005-01-01

A study identifies a compound from a set of monoterpenes using infrared (IR) and one-dimensional (1D) nuclear magnetic resonance (NMR) techniques. After identifying the unknown, each carbon and proton signal can be interpreted and assigned to the structure using the information in the two-dimensional (2D) NMR spectra, correlation spectroscopy…

Six-dimensional real and reciprocal space small-angle X-ray scattering tomography

NASA Astrophysics Data System (ADS)

Schaff, Florian; Bech, Martin; Zaslansky, Paul; Jud, Christoph; Liebi, Marianne; Guizar-Sicairos, Manuel; Pfeiffer, Franz

2015-11-01

When used in combination with raster scanning, small-angle X-ray scattering (SAXS) has proven to be a valuable imaging technique of the nanoscale, for example of bone, teeth and brain matter. Although two-dimensional projection imaging has been used to characterize various materials successfully, its three-dimensional extension, SAXS computed tomography, poses substantial challenges, which have yet to be overcome. Previous work using SAXS computed tomography was unable to preserve oriented SAXS signals during reconstruction. Here we present a solution to this problem and obtain a complete SAXS computed tomography, which preserves oriented scattering information. By introducing virtual tomography axes, we take advantage of the two-dimensional SAXS information recorded on an area detector and use it to reconstruct the full three-dimensional scattering distribution in reciprocal space for each voxel of the three-dimensional object in real space. The presented method could be of interest for a combined six-dimensional real and reciprocal space characterization of mesoscopic materials with hierarchically structured features with length scales ranging from a few nanometres to a few millimetres—for example, biomaterials such as bone or teeth, or functional materials such as fuel-cell or battery components.

Six-dimensional real and reciprocal space small-angle X-ray scattering tomography.

PubMed

Schaff, Florian; Bech, Martin; Zaslansky, Paul; Jud, Christoph; Liebi, Marianne; Guizar-Sicairos, Manuel; Pfeiffer, Franz

2015-11-19

When used in combination with raster scanning, small-angle X-ray scattering (SAXS) has proven to be a valuable imaging technique of the nanoscale, for example of bone, teeth and brain matter. Although two-dimensional projection imaging has been used to characterize various materials successfully, its three-dimensional extension, SAXS computed tomography, poses substantial challenges, which have yet to be overcome. Previous work using SAXS computed tomography was unable to preserve oriented SAXS signals during reconstruction. Here we present a solution to this problem and obtain a complete SAXS computed tomography, which preserves oriented scattering information. By introducing virtual tomography axes, we take advantage of the two-dimensional SAXS information recorded on an area detector and use it to reconstruct the full three-dimensional scattering distribution in reciprocal space for each voxel of the three-dimensional object in real space. The presented method could be of interest for a combined six-dimensional real and reciprocal space characterization of mesoscopic materials with hierarchically structured features with length scales ranging from a few nanometres to a few millimetres--for example, biomaterials such as bone or teeth, or functional materials such as fuel-cell or battery components.

X-ray scattering data and structural genomics

NASA Astrophysics Data System (ADS)

Doniach, Sebastian

2003-03-01

High throughput structural genomics has the ambitious goal of determining the structure of all, or a very large number of protein folds using the high-resolution techniques of protein crystallography and NMR. However, the program is facing significant bottlenecks in reaching this goal, which include problems of protein expression and crystallization. In this talk, some preliminary results on how the low-resolution technique of small-angle X-ray solution scattering (SAXS) can help ameliorate some of these bottlenecks will be presented. One of the most significant bottlenecks arises from the difficulty of crystallizing integral membrane proteins, where only a handful of structures are available compared to thousands of structures for soluble proteins. By 3-dimensional reconstruction from SAXS data, the size and shape of detergent-solubilized integral membrane proteins can be characterized. This information can then be used to classify membrane proteins which constitute some 25% of all genomes. SAXS may also be used to study the dependence of interparticle interference scattering on solvent conditions so that regions of the protein solution phase diagram which favor crystallization can be elucidated. As a further application, SAXS may be used to provide physical constraints on computational methods for protein structure prediction based on primary sequence information. This in turn can help in identifying structural homologs of a given protein, which can then give clues to its function. D. Walther, F. Cohen and S. Doniach. "Reconstruction of low resolution three-dimensional density maps from one-dimensional small angle x-ray scattering data for biomolecules." J. Appl. Cryst. 33(2):350-363 (2000). Protein structure prediction constrained by solution X-ray scattering data and structural homology identification Zheng WJ, Doniach S JOURNAL OF MOLECULAR BIOLOGY , v. 316(#1) pp. 173-187 FEB 8, 2002

Three-dimensional geologic model of the southeastern Espanola Basin, Santa Fe County, New Mexico

USGS Publications Warehouse

Pantea, Michael P.; Hudson, Mark R.; Grauch, V.J.S.; Minor, Scott A.

2011-01-01

This multimedia model and report show and describe digital three-dimensional faulted surfaces and volumes of lithologic units that confine and constrain the basin-fill aquifers within the Espanola Basin of north-central New Mexico. These aquifers are the primary groundwater resource for the cities of Santa Fe and Espanola, six Pueblo nations, and the surrounding areas. The model presented in this report is a synthesis of geologic information that includes (1) aeromagnetic and gravity data and seismic cross sections; (2) lithologic descriptions, interpretations, and geophysical logs from selected drill holes; (3) geologic maps, geologic cross sections, and interpretations; and (4) mapped faults and interpreted faults from geophysical data. Modeled faults individually or collectively affect the continuity of the rocks that contain the basin aquifers; they also help define the form of this rift basin. Structure, trend, and dip data not previously published were added; these structures are derived from interpretations of geophysical information and recent field observations. Where possible, data were compared and validated and reflect the complex relations of structures in this part of the Rio Grande rift. This interactive geologic framework model can be used as a tool to visually explore and study geologic structures within the Espanola Basin, to show the connectivity of geologic units of high and low permeability between and across faults, and to show approximate dips of the lithologic units. The viewing software can be used to display other data and information, such as drill-hole data, within this geologic framework model in three-dimensional space.

Utility of three-dimensional and multiplanar reformatted computed tomography for evaluation of pediatric congenital spine abnormalities.

PubMed

Newton, Peter O; Hahn, Gregory W; Fricka, Kevin B; Wenger, Dennis R

2002-04-15

A retrospective radiographic review of 31 patients with congenital spine abnormalities who underwent conventional radiography and advanced imaging studies was conducted. To analyze the utility of three-dimensional computed tomography with multiplanar reformatted images for congenital spine anomalies, as compared with plain radiographs and axial two-dimensional computed tomography imaging. Conventional radiographic imaging for congenital spine disorders often are difficult to interpret because of the patient's small size, the complexity of the disorder, a deformity not in the plane of the radiographs, superimposed structures, and difficulty in forming a mental three-dimensional image. Multiplanar reformatted and three-dimensional computed tomographic imaging offers many potential advantages for defining congenital spine anomalies including visualization of the deformity in any plane, from any angle, with the overlying structures subtracted. The imaging studies of patients who had undergone a three-dimensional computed tomography for congenital deformities of the spine between 1992 and 1998 were reviewed (31 cases). All plain radiographs and axial two-dimensional computed tomography images performed before the three-dimensional computed tomography were reviewed and the findings documented. This was repeated for the three-dimensional reconstructions and, when available, the multiplanar reformatted images (15 cases). In each case, the utility of the advanced imaging was graded as one of the following: Grade A (substantial new information obtained), Grade B (confirmatory with improved visualization and understanding of the deformity), and Grade C (no added useful information obtained). In 17 of 31 cases, the multiplanar reformatted and three-dimensional images allowed identification of unrecognized malformations. In nine additional cases, the advanced imaging was helpful in better visualizing and understanding previously identified deformities. In five cases, no new information was gained. The standard and curved multiplanar reformatted images were best for defining the occiput-C1-C2 anatomy and the extent of segmentation defects. The curved multiplanar reformatted images were especially helpful in keeping the spine from "coming in" and "going out" of the plane of the image when there was significant spine deformity in the sagittal or coronal plane. The three-dimensional reconstructions proved valuable in defining failures of formation. Advanced computed tomography imaging (three-dimensional computed tomography and curved/standard multiplanar reformatted images) allows better definition of congenital spine anomalies. More than 50% of the cases showed additional abnormalities not appreciated on plain radiographs or axial two-dimensional computed tomography images. Curved multiplanar reformatted images allowed imaging in the coronal and sagittal planes of the entire deformity.

Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.

PubMed

Kato, Koichi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Oda, Akifumi

2017-10-12

Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.

In Situ Three-Dimensional Reciprocal-Space Mapping of Diffuse Scattering Intensity Distribution and Data Analysis for Precursor Phenomenon in Shape-Memory Alloy

NASA Astrophysics Data System (ADS)

Cheng, Tian-Le; Ma, Fengde D.; Zhou, Jie E.; Jennings, Guy; Ren, Yang; Jin, Yongmei M.; Wang, Yu U.

2012-01-01

Diffuse scattering contains rich information on various structural disorders, thus providing a useful means to study the nanoscale structural deviations from the average crystal structures determined by Bragg peak analysis. Extraction of maximal information from diffuse scattering requires concerted efforts in high-quality three-dimensional (3D) data measurement, quantitative data analysis and visualization, theoretical interpretation, and computer simulations. Such an endeavor is undertaken to study the correlated dynamic atomic position fluctuations caused by thermal vibrations (phonons) in precursor state of shape-memory alloys. High-quality 3D diffuse scattering intensity data around representative Bragg peaks are collected by using in situ high-energy synchrotron x-ray diffraction and two-dimensional digital x-ray detector (image plate). Computational algorithms and codes are developed to construct the 3D reciprocal-space map of diffuse scattering intensity distribution from the measured data, which are further visualized and quantitatively analyzed to reveal in situ physical behaviors. Diffuse scattering intensity distribution is explicitly formulated in terms of atomic position fluctuations to interpret the experimental observations and identify the most relevant physical mechanisms, which help set up reduced structural models with minimal parameters to be efficiently determined by computer simulations. Such combined procedures are demonstrated by a study of phonon softening phenomenon in precursor state and premartensitic transformation of Ni-Mn-Ga shape-memory alloy.

Hierarchical brain mapping via a generalized Dirichlet solution for mapping brain manifolds

NASA Astrophysics Data System (ADS)

Joshi, Sarang C.; Miller, Michael I.; Christensen, Gary E.; Banerjee, Ayan; Coogan, Tom; Grenander, Ulf

1995-08-01

In this paper we present a coarse-to-fine approach for the transformation of digital anatomical textbooks from the ideal to the individual that unifies the work on landmark deformations and volume based transformation. The Hierarchical approach is linked to the Biological problem itself, coming out of the various kinds of information which is provided by the anatomists. This information is in the form of points, lines, surfaces and sub-volumes corresponding to 0, 1, 2, and 3 dimensional sub-manifolds respectively. The algorithm is driven by these sub- manifolds. We follow the approach that the highest dimensional transformation is a result from the solution of a sequence of lower dimensional problems driven by successive refinements or partitions of the images into various Biologically meaningful sub-structures.

A sedimentological approach to hydrologic characterization: A detailed three-dimensional study of an outcrop of the Sierra Ladrones Formation, Albuquerque basin

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

Lohmann, R.C.

1992-01-01

Three-dimensional geologic outcrop studies which quantitatively describe the geologic architecture of deposits of a specific depositional environment are a necessary requirement for characterization of the permeability structure of an aquifer. The objective of this study is to address this need for quantitative, three-dimensional outcrop studies. For this study, a 10,000 m{sup 2} by 25 m high outcrop of Pliocene-Pleistocene Sierra Ladrones Formation located near Belen, New Mexico was mapped in detail, and the geologic architecture was quantified using geostatistical variogram analysis. In general, the information contained in this study should be useful for hydrologists working on the characterization of aquifersmore » from similar depositional environments such as this one. However, for the permeability correlation study to be truly useful, the within-element correlation structure needs to be superimposed on the elements themselves instead of using mean log (k) values, as was done for this study. Such information is derived from outcrop permeability sampling such as the work of Davis (1990) and Goggin et al. (1988).« less

Single-photon-level quantum image memory based on cold atomic ensembles

PubMed Central

Ding, Dong-Sheng; Zhou, Zhi-Yuan; Shi, Bao-Sen; Guo, Guang-Can

2013-01-01

A quantum memory is a key component for quantum networks, which will enable the distribution of quantum information. Its successful development requires storage of single-photon light. Encoding photons with spatial shape through higher-dimensional states significantly increases their information-carrying capability and network capacity. However, constructing such quantum memories is challenging. Here we report the first experimental realization of a true single-photon-carrying orbital angular momentum stored via electromagnetically induced transparency in a cold atomic ensemble. Our experiments show that the non-classical pair correlation between trigger photon and retrieved photon is retained, and the spatial structure of input and retrieved photons exhibits strong similarity. More importantly, we demonstrate that single-photon coherence is preserved during storage. The ability to store spatial structure at the single-photon level opens the possibility for high-dimensional quantum memories. PMID:24084711

A comparison of VRML and animation of rotation for teaching 3-dimensional crystal lattice structures

NASA Astrophysics Data System (ADS)

Sauls, Barbara Lynn

Chemistry students often have difficulty visualizing abstract concepts of molecules and atoms, which may lead to misconceptions. The three-dimensionality of these structures presents a challenge to educators. Typical methods of teaching include text with two-dimensional graphics and structural models. Improved methods to allow visualization of 3D structures may improve learning of these concepts. This research compared the use of Virtual Reality Modeling Language (VRML) and animation of rotation for teaching three-dimensional structures. VRML allows full control of objects by altering angle, size, rotation, and provides the ability to zoom into and through objects. Animations may only be stopped, restarted and replayed. A web-based lesson teaching basic concepts of crystals, which requires comprehension of their three-dimensional structure was given to 100 freshmen chemistry students. Students were stratified by gender then randomly to one of two lessons, which were identical except for the multimedia method used to show the lattices and unit cells. One method required exploration of the structures using VRML, the other provided animations of the same structures rotating. The students worked through an examination as the lesson progressed. A Welch t' test was used to compare differences between groups. No significant difference in mean achievement was found between the two methods, between genders, or within gender. There was no significant difference in mean total SAT in the animation and VRML group. Total time on task had no significant difference nor did enjoyment of the lesson. Students, however, spent 14% less time maneuvering VRML structures than viewing the animations of rotation. Neither method proved superior for presenting three-dimensional information. The students spent less time maneuvering the VRML structures with no difference in mean score so the use of VRML may be more efficient. The investigator noted some manipulation difficulties using VRML to rotate structures. Some students had difficulty obtaining the correct angle required to properly interpret spatial relationships. This led to frustration and caused some students to quit trying before they could answer questions fully. Even though there were some difficulties, outcomes were not affected. Higher scores, however, may have been achieved had the students been proficient in VRML maneuvering.

Revealing the planar chemistry of two-dimensional heterostructures at the atomic level.

PubMed

Chou, Harry; Ismach, Ariel; Ghosh, Rudresh; Ruoff, Rodney S; Dolocan, Andrei

2015-06-23

Two-dimensional (2D) atomic crystals and their heterostructures are an intense area of study owing to their unique properties that result from structural planar confinement. Intrinsically, the performance of a planar vertical device is linked to the quality of its 2D components and their interfaces, therefore requiring characterization tools that can reveal both its planar chemistry and morphology. Here, we propose a characterization methodology combining (micro-) Raman spectroscopy, atomic force microscopy and time-of-flight secondary ion mass spectrometry to provide structural information, morphology and planar chemical composition at virtually the atomic level, aimed specifically at studying 2D vertical heterostructures. As an example system, a graphene-on-h-BN heterostructure is analysed to reveal, with an unprecedented level of detail, the subtle chemistry and interactions within its layer structure that can be assigned to specific fabrication steps. Such detailed chemical information is of crucial importance for the complete integration of 2D heterostructures into functional devices.

Topological Landscapes: A Terrain Metaphor for ScientificData

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

Weber, Gunther H.; Bremer, Peer-Timo; Pascucci, Valerio

2007-08-01

Scientific visualization and illustration tools are designed to help people understand the structure and complexity of scientific data with images that are as informative and intuitive as possible. In this context, the use of metaphors plays an important role, since they make complex information easily accessible by using commonly known concepts. In this paper we propose a new metaphor, called 'Topological Landscapes', which facilitates understanding the topological structure of scalar functions. The basic idea is to construct a terrain with the same topology as a given dataset and to display the terrain as an easily understood representation of the actualmore » input data. In this projection from an n-dimensional scalar function to a two-dimensional (2D) model we preserve function values of critical points, the persistence (function span) of topological features, and one possible additional metric property (in our examples volume). By displaying this topologically equivalent landscape together with the original data we harness the natural human proficiency in understanding terrain topography and make complex topological information easily accessible.« less

Structural dynamics of tropical moist forest gaps

Treesearch

Maria O. Hunter; Michael Keller; Douglas Morton; Bruce Cook; Michael Lefsky; Mark Ducey; Scott Saleska; Raimundo Cosme de Oliveira; Juliana Schietti

2015-01-01

Gap phase dynamics are the dominant mode of forest turnover in tropical forests. However, gap processes are infrequently studied at the landscape scale. Airborne lidar data offer detailed information on three-dimensional forest structure, providing a means to characterize fine-scale (1 m) processes in tropical forests over large areas. Lidar-based estimates of forest...

Dimensionality of the 9-item Utrecht Work Engagement Scale revisited: A Bayesian structural equation modeling approach.

PubMed

Fong, Ted C T; Ho, Rainbow T H

2015-01-01

The aim of this study was to reexamine the dimensionality of the widely used 9-item Utrecht Work Engagement Scale using the maximum likelihood (ML) approach and Bayesian structural equation modeling (BSEM) approach. Three measurement models (1-factor, 3-factor, and bi-factor models) were evaluated in two split samples of 1,112 health-care workers using confirmatory factor analysis and BSEM, which specified small-variance informative priors for cross-loadings and residual covariances. Model fit and comparisons were evaluated by posterior predictive p-value (PPP), deviance information criterion, and Bayesian information criterion (BIC). None of the three ML-based models showed an adequate fit to the data. The use of informative priors for cross-loadings did not improve the PPP for the models. The 1-factor BSEM model with approximately zero residual covariances displayed a good fit (PPP>0.10) to both samples and a substantially lower BIC than its 3-factor and bi-factor counterparts. The BSEM results demonstrate empirical support for the 1-factor model as a parsimonious and reasonable representation of work engagement.

Constraining Mass Anomalies Using Trans-dimensional Gravity Inversions

NASA Astrophysics Data System (ADS)

Izquierdo, K.; Montesi, L.; Lekic, V.

2016-12-01

The density structure of planetary interiors constitutes a key constraint on their composition, temperature, and dynamics. This has motivated the development of non-invasive methods to infer 3D distribution of density anomalies within a planet's interior using gravity observations made from the surface or orbit. On Earth, this information can be supplemented by seismic and electromagnetic observations, but such data are generally not available on other planets and inferences must be made from gravity observations alone. Unfortunately, inferences of density anomalies from gravity are non-unique and even the dimensionality of the problem - i.e., the number of density anomalies detectable in the planetary interior - is unknown. In this project, we use the Reversible Jump Markov chain Monte Carlo (RJMCMC) algorithm to approach gravity inversions in a trans-dimensional way, that is, considering the magnitude of the mass, the latitude, longitude, depth and number of anomalies itself as unknowns to be constrained by the observed gravity field at the surface of a planet. Our approach builds upon previous work using trans-dimensional gravity inversions in which the density contrast between the anomaly and the surrounding material is known. We validate the algorithm by analyzing a synthetic gravity field produced by a known density structure and comparing the retrieved and input density structures. We find excellent agreement between the input and retrieved structure when working in 1D and 2D domains. However, in 3D domains, comprehensive exploration of the much larger space of possible models makes search efficiency a key ingredient in successful gravity inversion. We find that upon a sufficiently long RJMCMC run, it is possible to use statistical information to recover a predicted model that matches the real model. We argue that even more complex problems, such as those involving real gravity acceleration data of a planet as the constraint, our trans-dimensional gravity inversion algorithm provides a good option to overcome the problem of non-uniqueness while achieving parsimony in gravity inversions.

SSEP: secondary structural elements of proteins

PubMed Central

Shanthi, V.; Selvarani, P.; Kiran Kumar, Ch.; Mohire, C. S.; Sekar, K.

2003-01-01

SSEP is a comprehensive resource for accessing information related to the secondary structural elements present in the 25 and 90% non-redundant protein chains. The database contains 1771 protein chains from 1670 protein structures and 6182 protein chains from 5425 protein structures in 25 and 90% non-redundant protein chains, respectively. The current version provides information about the α-helical segments and β-strand fragments of varying lengths. In addition, it also contains the information about 310-helix, β- and ν-turns and hairpin loops. The free graphics program RASMOL has been interfaced with the search engine to visualize the three-dimensional structures of the user queried secondary structural fragment. The database is updated regularly and is available through Bioinformatics web server at http://cluster.physics.iisc.ernet.in/ssep/ or http://144.16.71.148/ssep/. PMID:12824336

Accurate prediction of interfacial residues in two-domain proteins using evolutionary information: implications for three-dimensional modeling.

PubMed

Bhaskara, Ramachandra M; Padhi, Amrita; Srinivasan, Narayanaswamy

2014-07-01

With the preponderance of multidomain proteins in eukaryotic genomes, it is essential to recognize the constituent domains and their functions. Often function involves communications across the domain interfaces, and the knowledge of the interacting sites is essential to our understanding of the structure-function relationship. Using evolutionary information extracted from homologous domains in at least two diverse domain architectures (single and multidomain), we predict the interface residues corresponding to domains from the two-domain proteins. We also use information from the three-dimensional structures of individual domains of two-domain proteins to train naïve Bayes classifier model to predict the interfacial residues. Our predictions are highly accurate (∼85%) and specific (∼95%) to the domain-domain interfaces. This method is specific to multidomain proteins which contain domains in at least more than one protein architectural context. Using predicted residues to constrain domain-domain interaction, rigid-body docking was able to provide us with accurate full-length protein structures with correct orientation of domains. We believe that these results can be of considerable interest toward rational protein and interaction design, apart from providing us with valuable information on the nature of interactions. © 2013 Wiley Periodicals, Inc.

Describing polyhedral tilings and higher dimensional polytopes by sequence of their two-dimensional components

PubMed Central

Nishio, Kengo; Miyazaki, Takehide

2017-01-01

Polyhedral tilings are often used to represent structures such as atoms in materials, grains in crystals, foams, galaxies in the universe, etc. In the previous paper, we have developed a theory to convert a way of how polyhedra are arranged to form a polyhedral tiling into a codeword (series of numbers) from which the original structure can be recovered. The previous theory is based on the idea of forming a polyhedral tiling by gluing together polyhedra face to face. In this paper, we show that the codeword contains redundant digits not needed for recovering the original structure, and develop a theory to reduce the redundancy. For this purpose, instead of polyhedra, we regard two-dimensional regions shared by faces of adjacent polyhedra as building blocks of a polyhedral tiling. Using the present method, the same information is represented by a shorter codeword whose length is reduced by up to the half of the original one. Shorter codewords are easier to handle for both humans and computers, and thus more useful to describe polyhedral tilings. By generalizing the idea of assembling two-dimensional components to higher dimensional polytopes, we develop a unified theory to represent polyhedral tilings and polytopes of different dimensions in the same light. PMID:28094254

Investigations of photosynthetic light harvesting by two-dimensional electronic spectroscopy

NASA Astrophysics Data System (ADS)

Read, Elizabeth Louise

Photosynthesis begins with the harvesting of sunlight by antenna pigments, organized in a network of pigment-protein complexes that rapidly funnel energy to photochemical reaction centers. The intricate design of these systems---the widely varying structural motifs of pigment organization within proteins and protein organization within a larger, cooperative network---underlies the remarkable speed and efficiency of light harvesting. Advances in femtosecond laser spectroscopy have enabled researchers to follow light energy on its course through the energetic levels of photosynthetic systems. Now, newly-developed femtosecond two-dimensional electronic spectroscopy reveals deeper insight into the fundamental molecular interactions and dynamics that emerge in these structures. The following chapters present investigations of a number of natural light-harvesting complexes using two-dimensional electronic spectroscopy. These studies demonstrate the various types of information contained in experimental two-dimensional spectra, and they show that the technique makes it possible to probe pigment-protein complexes on the length- and time-scales relevant to their functioning. New methods are described that further extend the capabilities of two-dimensional electronic spectroscopy, for example, by independently controlling the excitation laser pulse polarizations. The experiments, coupled with theoretical simulation, elucidate spatial pathways of energy flow, unravel molecular and electronic structures, and point to potential new quantum mechanical mechanisms of light harvesting.

Three-dimensional cardiac architecture determined by two-photon microtomy

NASA Astrophysics Data System (ADS)

Huang, Hayden; MacGillivray, Catherine; Kwon, Hyuk-Sang; Lammerding, Jan; Robbins, Jeffrey; Lee, Richard T.; So, Peter

2009-07-01

Cardiac architecture is inherently three-dimensional, yet most characterizations rely on two-dimensional histological slices or dissociated cells, which remove the native geometry of the heart. We previously developed a method for labeling intact heart sections without dissociation and imaging large volumes while preserving their three-dimensional structure. We further refine this method to permit quantitative analysis of imaged sections. After data acquisition, these sections are assembled using image-processing tools, and qualitative and quantitative information is extracted. By examining the reconstructed cardiac blocks, one can observe end-to-end adjacent cardiac myocytes (cardiac strands) changing cross-sectional geometries, merging and separating from other strands. Quantitatively, representative cross-sectional areas typically used for determining hypertrophy omit the three-dimensional component; we show that taking orientation into account can significantly alter the analysis. Using fast-Fourier transform analysis, we analyze the gross organization of cardiac strands in three dimensions. By characterizing cardiac structure in three dimensions, we are able to determine that the α crystallin mutation leads to hypertrophy with cross-sectional area increases, but not necessarily via changes in fiber orientation distribution.

C-ME: A 3D Community-Based, Real-Time Collaboration Tool for Scientific Research and Training

PubMed Central

Kolatkar, Anand; Kennedy, Kevin; Halabuk, Dan; Kunken, Josh; Marrinucci, Dena; Bethel, Kelly; Guzman, Rodney; Huckaby, Tim; Kuhn, Peter

2008-01-01

The need for effective collaboration tools is growing as multidisciplinary proteome-wide projects and distributed research teams become more common. The resulting data is often quite disparate, stored in separate locations, and not contextually related. Collaborative Molecular Modeling Environment (C-ME) is an interactive community-based collaboration system that allows researchers to organize information, visualize data on a two-dimensional (2-D) or three-dimensional (3-D) basis, and share and manage that information with collaborators in real time. C-ME stores the information in industry-standard databases that are immediately accessible by appropriate permission within the computer network directory service or anonymously across the internet through the C-ME application or through a web browser. The system addresses two important aspects of collaboration: context and information management. C-ME allows a researcher to use a 3-D atomic structure model or a 2-D image as a contextual basis on which to attach and share annotations to specific atoms or molecules or to specific regions of a 2-D image. These annotations provide additional information about the atomic structure or image data that can then be evaluated, amended or added to by other project members. PMID:18286178

Image restoration and superresolution as probes of small scale far-IR structure in star forming regions

NASA Technical Reports Server (NTRS)

Lester, D. F.; Harvey, P. M.; Joy, M.; Ellis, H. B., Jr.

1986-01-01

Far-infrared continuum studies from the Kuiper Airborne Observatory are described that are designed to fully exploit the small-scale spatial information that this facility can provide. This work gives the clearest picture to data on the structure of galactic and extragalactic star forming regions in the far infrared. Work is presently being done with slit scans taken simultaneously at 50 and 100 microns, yielding one-dimensional data. Scans of sources in different directions have been used to get certain information on two dimensional structure. Planned work with linear arrays will allow us to generalize our techniques to two dimensional image restoration. For faint sources, spatial information at the diffraction limit of the telescope is obtained, while for brighter sources, nonlinear deconvolution techniques have allowed us to improve over the diffraction limit by as much as a factor of four. Information on the details of the color temperature distribution is derived as well. This is made possible by the accuracy with which the instrumental point-source profile (PSP) is determined at both wavelengths. While these two PSPs are different, data at different wavelengths can be compared by proper spatial filtering. Considerable effort has been devoted to implementing deconvolution algorithms. Nonlinear deconvolution methods offer the potential of superresolution -- that is, inference of power at spatial frequencies that exceed D lambda. This potential is made possible by the implicit assumption by the algorithm of positivity of the deconvolved data, a universally justifiable constraint for photon processes. We have tested two nonlinear deconvolution algorithms on our data; the Richardson-Lucy (R-L) method and the Maximum Entropy Method (MEM). The limits of image deconvolution techniques for achieving spatial resolution are addressed.

Structure Size Enhanced Histogram

NASA Astrophysics Data System (ADS)

Wesarg, Stefan; Kirschner, Matthias

Direct volume visualization requires the definition of transfer functions (TFs) for the assignment of opacity and color. Multi-dimensional TFs are based on at least two image properties, and are specified by means of 2D histograms. In this work we propose a new type of a 2D histogram which combines gray value with information about the size of the structures. This structure size enhanced (SSE) histogram is an intuitive approach for representing anatomical features. Clinicians — the users we are focusing on — are much more familiar with selecting features by their size than by their gradient magnitude value. As a proof of concept, we employ the SSE histogram for the definition of two-dimensional TFs for the visualization of 3D MRI and CT image data.

PDB to AMPL Conversion

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

Anna Johnston, SNL 9215

2002-09-01

PDB to AMPL Conversion was written to convert protein data base files to AMPL files. The protein data bases on the internet contain a wealth of information about the structue and makeup of proteins. Each file contains information derived by one or more experiments and contains information on how the experiment waw performed, the amino acid building blocks of each chain, and often the three-dimensional structure of the protein extracted from the experiments. The way a protein folds determines much about its function. Thus, studying the three-dimensional structure of the protein is of great interest. Analysing the contact maps ismore » one way to examine the structure. A contact map is a graph which has a linear back bone of amino acids for nodes (i.e., adjacent amino acids are always connected) and vertices between non-adjacent nodes if they are close enough to be considered in contact. If the graphs are similar then the folds of the protein and their function should also be similar. This software extracts the contact maps from a protein data base file and puts in into AMPL data format. This format is designed for use in AMPL, a programming language for simplifying linear programming formulations.« less

CLICK: The new USGS center for LIDAR information coordination and knowledge

USGS Publications Warehouse

Stoker, Jason M.; Greenlee, Susan K.; Gesch, Dean B.; Menig, Jordan C.

2006-01-01

Elevation data is rapidly becoming an important tool for the visualization and analysis of geographic information. The creation and display of three-dimensional models representing bare earth, vegetation, and structures have become major requirements for geographic research in the past few years. Light Detection and Ranging (lidar) has been increasingly accepted as an effective and accurate technology for acquiring high-resolution elevation data for bare earth, vegetation, and structures. Lidar is an active remote sensing system that records the distance, or range, of a laser fi red from an airborne or space borne platform such as an airplane, helicopter or satellite to objects or features on the Earth’s surface. By converting lidar data into bare ground topography and vegetation or structural morphologic information, extremely accurate, high-resolution elevation models can be derived to visualize and quantitatively represent scenes in three dimensions. In addition to high-resolution digital elevation models (Evans et al., 2001), other lidar-derived products include quantitative estimates of vegetative features such as canopy height, canopy closure, and biomass (Lefsky et al., 2002), and models of urban areas such as building footprints and three-dimensional city models (Maas, 2001).

Data Warehouse Design from HL7 Clinical Document Architecture Schema.

PubMed

Pecoraro, Fabrizio; Luzi, Daniela; Ricci, Fabrizio L

2015-01-01

This paper proposes a semi-automatic approach to extract clinical information structured in a HL7 Clinical Document Architecture (CDA) and transform it in a data warehouse dimensional model schema. It is based on a conceptual framework published in a previous work that maps the dimensional model primitives with CDA elements. Its feasibility is demonstrated providing a case study based on the analysis of vital signs gathered during laboratory tests.

Leak detection utilizing analog binaural (VLSI) techniques

NASA Technical Reports Server (NTRS)

Hartley, Frank T. (Inventor)

1995-01-01

A detection method and system utilizing silicon models of the traveling wave structure of the human cochlea to spatially and temporally locate a specific sound source in the presence of high noise pandemonium. The detection system combines two-dimensional stereausis representations, which are output by at least three VLSI binaural hearing chips, to generate a three-dimensional stereausis representation including both binaural and spectral information which is then used to locate the sound source.

Structural and congenital heart disease interventions: the role of three-dimensional printing.

PubMed

Meier, L M; Meineri, M; Qua Hiansen, J; Horlick, E M

2017-02-01

Advances in catheter-based interventions in structural and congenital heart disease have mandated an increased demand for three-dimensional (3D) visualisation of complex cardiac anatomy. Despite progress in 3D imaging modalities, the pre- and periprocedural visualisation of spatial anatomy is relegated to two-dimensional flat screen representations. 3D printing is an evolving technology based on the concept of additive manufacturing, where computerised digital surface renders are converted into physical models. Printed models replicate complex structures in tangible forms that cardiovascular physicians and surgeons can use for education, preprocedural planning and device testing. In this review we discuss the different steps of the 3D printing process, which include image acquisition, segmentation, printing methods and materials. We also examine the expanded applications of 3D printing in the catheter-based treatment of adult patients with structural and congenital heart disease while highlighting the current limitations of this technology in terms of segmentation, model accuracy and dynamic capabilities. Furthermore, we provide information on the resources needed to establish a hospital-based 3D printing laboratory.

Full equations utilities (FEQUTL) model for the approximation of hydraulic characteristics of open channels and control structures during unsteady flow

USGS Publications Warehouse

Franz, Delbert D.; Melching, Charles S.

1997-01-01

The Full EQuations UTiLities (FEQUTL) model is a computer program for computation of tables that list the hydraulic characteristics of open channels and control structures as a function of upstream and downstream depths; these tables facilitate the simulation of unsteady flow in a stream system with the Full Equations (FEQ) model. Simulation of unsteady flow requires many iterations for each time period computed. Thus, computation of hydraulic characteristics during the simulations is impractical, and preparation of function tables and application of table look-up procedures facilitates simulation of unsteady flow. Three general types of function tables are computed: one-dimensional tables that relate hydraulic characteristics to upstream flow depth, two-dimensional tables that relate flow through control structures to upstream and downstream flow depth, and three-dimensional tables that relate flow through gated structures to upstream and downstream flow depth and gate setting. For open-channel reaches, six types of one-dimensional function tables contain different combinations of the top width of flow, area, first moment of area with respect to the water surface, conveyance, flux coefficients, and correction coefficients for channel curvilinearity. For hydraulic control structures, one type of one-dimensional function table contains relations between flow and upstream depth, and two types of two-dimensional function tables contain relations among flow and upstream and downstream flow depths. For hydraulic control structures with gates, a three-dimensional function table lists the system of two-dimensional tables that contain the relations among flow and upstream and downstream flow depths that correspond to different gate openings. Hydraulic control structures for which function tables containing flow relations are prepared in FEQUTL include expansions, contractions, bridges, culverts, embankments, weirs, closed conduits (circular, rectangular, and pipe-arch shapes), dam failures, floodways, and underflow gates (sluice and tainter gates). The theory for computation of the hydraulic characteristics is presented for open channels and for each hydraulic control structure. For the hydraulic control structures, the theory is developed from the results of experimental tests of flow through the structure for different upstream and downstream flow depths. These tests were done to describe flow hydraulics for a single, steady-flow design condition and, thus, do not provide complete information on flow transitions (for example, between free- and submerged-weir flow) that may result in simulation of unsteady flow. Therefore, new procedures are developed to approximate the hydraulics of flow transitions for culverts, embankments, weirs, and underflow gates.

Dimensionality of organizational justice in a call center context.

PubMed

Flint, Douglas; Haley, Lynn M; McNally, Jeffrey J

2012-04-01

Summary.-Employees in three call centers were surveyed about their perceptions of organizational justice. Four factors were measured: distributive justice, procedural justice, interpersonal justice, and informational justice. Structural equation modeling was employed to test whether a two-, three-, or four-factor model best fit the call center data. A three-factor model of distributive, procedural, and informational justice provided the best fit to these data. The three-factor model that showed the best fit does not conform to any of the more traditional models identified in the organizational justice literature. This implies that the context in which organizational justice is measured may play a role in identifying which justice factors are relevant to employees. Findings add to the empirical evidence on the dimensionality of organizational justice and imply that dimensionality of organizational justice is more context-dependent than previously thought.

Engineering Three-Dimensional Collagen-IKVAV Matrix to Mimic Neural Microenvironment

PubMed Central

2013-01-01

Engineering the cellular microenvironment has great potential to create a platform technology toward engineering of tissue and organs. This study aims to engineer a neural microenvironment through fabrication of three-dimensional (3D) engineered collagen matrixes mimicking in-vivo-like conditions. Collagen was chemically modified with a pentapeptide epitope consisting of isoleucine-lysine-valine-alanine-valine (IKVAV) to mimic laminin structure supports of the neural extracellular matrix (ECM). Three-dimensional collagen matrixes with and without IKVAV peptide modification were fabricated by freeze-drying technology and chemical cross-linking with glutaraldehyde. Structural information of 3D collagen matrixes indicated interconnected pores structure with an average pore size of 180 μm. Our results indicated that culture of dorsal root ganglion (DRG) cells in 3D collagen matrix was greatly influenced by 3D culture method and significantly enhanced with engineered collagen matrix conjugated with IKVAV peptide. It may be concluded that an appropriate 3D culture of neurons enables DRG to positively improve the cellular fate toward further acceleration in tissue regeneration. PMID:23705903

Self-organization of a self-assembled supramolecular rectangle, square, and three-dimensional cage on Au111 surfaces.

PubMed

Yuan, Qun-Hui; Wan, Li-Jun; Jude, Hershel; Stang, Peter J

2005-11-23

The structure and conformation of three self-assembled supramolecular species, a rectangle, a square, and a three-dimensional cage, on Au111 surfaces were investigated by scanning tunneling microscopy. These supramolecular assemblies adsorb on Au111 surfaces and self-organize to form highly ordered adlayers with distinct conformations that are consistent with their chemical structures. The faces of the supramolecular rectangle and square lie flat on the surface, preserving their rectangle and square conformations, respectively. The three-dimensional cage also forms well-ordered adlayers on the gold surface, forming regular molecular rows of assemblies. When the rectangle and cage were mixed together, the assemblies separated into individual domains, and no mixed adlayers were observed. These results provide direct evidence of the noncrystalline solid-state structures of these assemblies and information about how they self-organize on Au111 surfaces, which is of importance in the potential manufacturing of functional nanostructures and devices.

A Bayesian trans-dimensional approach for the fusion of multiple geophysical datasets

NASA Astrophysics Data System (ADS)

JafarGandomi, Arash; Binley, Andrew

2013-09-01

We propose a Bayesian fusion approach to integrate multiple geophysical datasets with different coverage and sensitivity. The fusion strategy is based on the capability of various geophysical methods to provide enough resolution to identify either subsurface material parameters or subsurface structure, or both. We focus on electrical resistivity as the target material parameter and electrical resistivity tomography (ERT), electromagnetic induction (EMI), and ground penetrating radar (GPR) as the set of geophysical methods. However, extending the approach to different sets of geophysical parameters and methods is straightforward. Different geophysical datasets are entered into a trans-dimensional Markov chain Monte Carlo (McMC) search-based joint inversion algorithm. The trans-dimensional property of the McMC algorithm allows dynamic parameterisation of the model space, which in turn helps to avoid bias of the post-inversion results towards a particular model. Given that we are attempting to develop an approach that has practical potential, we discretize the subsurface into an array of one-dimensional earth-models. Accordingly, the ERT data that are collected by using two-dimensional acquisition geometry are re-casted to a set of equivalent vertical electric soundings. Different data are inverted either individually or jointly to estimate one-dimensional subsurface models at discrete locations. We use Shannon's information measure to quantify the information obtained from the inversion of different combinations of geophysical datasets. Information from multiple methods is brought together via introducing joint likelihood function and/or constraining the prior information. A Bayesian maximum entropy approach is used for spatial fusion of spatially dispersed estimated one-dimensional models and mapping of the target parameter. We illustrate the approach with a synthetic dataset and then apply it to a field dataset. We show that the proposed fusion strategy is successful not only in enhancing the subsurface information but also as a survey design tool to identify the appropriate combination of the geophysical tools and show whether application of an individual method for further investigation of a specific site is beneficial.

Estimating forest structure parameters within Fort Lewis Military Reservation using airborne laser scanner (LIDAR) data.

Treesearch

Hans-Erik Andersen; Jeffrey R. Foster; Stephen E. Reutebuch

2003-01-01

Three-dimensional (3-D) forest structure information is critical to support a variety of ecosystem management objectives on the Fort Lewis Military Reservation, including habitat assessment, ecological restoration, fire management, and commercial timber harvest. In particular, the Forestry Program at Fort Lewis requires measurements of shrub, understory, and overstory...

A preliminary investigation of the nocturnal temperature structure above the city of Edmonton, Alberta

Treesearch

D. Yap

1977-01-01

Information about the nocturnal temperature structure over Edmonton, Alberta. Observations of the temperature fields, including two- and three-dimensional forms of the nocturnal heat island, were obtained from minisonde ascents, an instrumented helicopter, and towers during a 3-week urban air-pollution field study. Results show that urban-induced temperature...

Structure Learning in Bayesian Sensorimotor Integration

PubMed Central

Genewein, Tim; Hez, Eduard; Razzaghpanah, Zeynab; Braun, Daniel A.

2015-01-01

Previous studies have shown that sensorimotor processing can often be described by Bayesian learning, in particular the integration of prior and feedback information depending on its degree of reliability. Here we test the hypothesis that the integration process itself can be tuned to the statistical structure of the environment. We exposed human participants to a reaching task in a three-dimensional virtual reality environment where we could displace the visual feedback of their hand position in a two dimensional plane. When introducing statistical structure between the two dimensions of the displacement, we found that over the course of several days participants adapted their feedback integration process in order to exploit this structure for performance improvement. In control experiments we found that this adaptation process critically depended on performance feedback and could not be induced by verbal instructions. Our results suggest that structural learning is an important meta-learning component of Bayesian sensorimotor integration. PMID:26305797

Author Correction: Atomic-resolution three-dimensional hydration structures on a heterogeneously charged surface.

PubMed

Umeda, Kenichi; Zivanovic, Lidija; Kobayashi, Kei; Ritala, Juha; Kominami, Hiroaki; Spijker, Peter; Foster, Adam S; Yamada, Hirofumi

2018-05-23

The original version of the Supplementary Information associated with this Article contained an error in Supplementary Figure 9e,f in which the y-axes were incorrectly labelled from '-40' to '40', rather than the correct '-400' to '400'. The HTML has been updated to include a corrected version of the Supplementary Information.

OOMM--Object-Oriented Matrix Modelling: an instrument for the integration of the Brasilia Regional Health Information System.

PubMed

Cammarota, M; Huppes, V; Gaia, S; Degoulet, P

1998-01-01

The development of Health Information Systems is widely determined by the establishment of the underlying information models. An Object-Oriented Matrix Model (OOMM) is described which target is to facilitate the integration of the overall health system. The model is based on information modules named micro-databases that are structured in a three-dimensional network: planning, health structures and information systems. The modelling tool has been developed as a layer on top of a relational database system. A visual browser facilitates the development and maintenance of the information model. The modelling approach has been applied to the Brasilia University Hospital since 1991. The extension of the modelling approach to the Brasilia regional health system is considered.

Observation of the magnetic flux and three-dimensional structure of skyrmion lattices by electron holography.

PubMed

Park, Hyun Soon; Yu, Xiuzhen; Aizawa, Shinji; Tanigaki, Toshiaki; Akashi, Tetsuya; Takahashi, Yoshio; Matsuda, Tsuyoshi; Kanazawa, Naoya; Onose, Yoshinori; Shindo, Daisuke; Tonomura, Akira; Tokura, Yoshinori

2014-05-01

Skyrmions are nanoscale spin textures that are viewed as promising candidates as information carriers in future spintronic devices. Skyrmions have been observed using neutron scattering and microscopy techniques. Real-space imaging using electrons is a straightforward way to interpret spin configurations by detecting the phase shifts due to electromagnetic fields. Here, we report the first observation by electron holography of the magnetic flux and the three-dimensional spin configuration of a skyrmion lattice in Fe(0.5)Co(0.5)Si thin samples. The magnetic flux inside and outside a skyrmion was directly visualized and the handedness of the magnetic flux flow was found to be dependent on the direction of the applied magnetic field. The electron phase shifts φ in the helical and skyrmion phases were determined using samples with a stepped thickness t (from 55 nm to 510 nm), revealing a linear relationship (φ = 0.00173 t). The phase measurements were used to estimate the three-dimensional structures of both the helical and skyrmion phases, demonstrating that electron holography is a useful tool for studying complex magnetic structures and for three-dimensional, real-space mapping of magnetic fields.

Microgravity

NASA Image and Video Library

2000-04-19

Dr. Marc Pusey (seated) and Dr. Craig Kundrot use computers to analyze x-ray maps and generate three-dimensional models of protein structures. With this information, scientists at Marshall Space Flight Center can learn how proteins are made and how they work. The computer screen depicts a proten structure as a ball-and-stick model. Other models depict the actual volume occupied by the atoms, or the ribbon-like structures that are crucial to a protein's function.

Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research

DOE PAGES

Ercius, Peter; Alaidi, Osama; Rames, Matthew J.; ...

2015-06-18

Three-dimensional (3D) structural analysis is essential to understand the relationship between the structure and function of an object. Many analytical techniques, such as X-ray diffraction, neutron spectroscopy, and electron microscopy imaging, are used to provide structural information. Transmission electron microscopy (TEM), one of the most popular analytic tools, has been widely used for structural analysis in both physical and biological sciences for many decades, in which 3D objects are projected into two-dimensional (2D) images. In many cases, 2D-projection images are insufficient to understand the relationship between the 3D structure and the function of nanoscale objects. Electron tomography (ET) is amore » technique that retrieves 3D structural information from a tilt series of 2D projections, and is gradually becoming a mature technology with sub-nanometer resolution. Distinct methods to overcome sample-based limitations have been separately developed in both physical and biological science, although they share some basic concepts of ET. Here, this review discusses the common basis for 3D characterization, and specifies difficulties and solutions regarding both hard and soft materials research. It is hoped that novel solutions based on current state-of-the-art techniques for advanced applications in hybrid matter systems can be motivated. Electron tomography produces quantitative 3D reconstructions for biological and physical sciences from sets of 2D projections acquired at different tilting angles in a transmission electron microscope. Finally, state-of-the-art techniques capable of producing 3D representations such as Pt-Pd core-shell nanoparticles and IgG1 antibody molecules are reviewed.« less

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

Steiner, J.L.; Lime, J.F.; Elson, J.S.

One dimensional TRAC transient calculations of the process inherent ultimate safety (PIUS) advanced reactor design were performed for a pump-trip SCRAM. The TRAC calculations showed that the reactor power response and shutdown were in qualitative agreement with the one-dimensional analyses presented in the PIUS Preliminary Safety Information Document (PSID) submitted by Asea Brown Boveri (ABB) to the US Nuclear Regulatory Commission for preapplication safety review. The PSID analyses were performed with the ABB-developed RIGEL code. The TRAC-calculated phenomena and trends were also similar to those calculated with another one-dimensional PIUS model, the Brookhaven National Laboratory developed PIPA code. A TRACmore » pump-trip SCRAM transient has also been calculated with a TRAC model containing a multi-dimensional representation of the PIUS intemal flow structures and core region. The results obtained using the TRAC fully one-dimensional PIUS model are compared to the RIGEL, PIPA, and TRAC multi-dimensional results.« less

Forest Attributes from Radar Interferometric Structure and its Fusion with Optical Remote Sensing

NASA Technical Reports Server (NTRS)

Treuhaft, Robert N.; Law, Beverly E.; Asner, Gregory P.

2004-01-01

The possibility of global, three-dimensional remote sensing of forest structure with interferometric synthetic aperture radar (InSAR) bears on important forest ecological processes, particularly the carbon cycle. InSAR supplements two-dimensional remote sensing with information in the vertical dimension. Its strengths in potential for global coverage complement those of lidar (light detecting and ranging), which has the potential for high-accuracy vertical profiles over small areas. InSAR derives its sensitivity to forest vertical structure from the differences in signals received by two, spatially separate radar receivers. Estimation of parameters describing vertical structure requires multiple-polarization, multiple-frequency, or multiple-baseline InSAR. Combining InSAR with complementary remote sensing techniques, such as hyperspectral optical imaging and lidar, can enhance vertical-structure estimates and consequent biophysical quantities of importance to ecologists, such as biomass. Future InSAR experiments will supplement recent airborne and spaceborne demonstrations, and together with inputs from ecologists regarding structure, they will suggest designs for future spaceborne strategies for measuring global vegetation structure.

A holistic approach to determine tree structural complexity based on laser scanning data and fractal analysis.

PubMed

Seidel, Dominik

2018-01-01

The three-dimensional forest structure affects many ecosystem functions and services provided by forests. As forests are made of trees it seems reasonable to approach their structure by investigating individual tree structure. Based on three-dimensional point clouds from laser scanning, a newly developed holistic approach is presented that enables to calculate the box dimension as a measure of structural complexity of individual trees using fractal analysis. It was found that the box dimension of trees was significantly different among the tested species, among trees belonging to the same species but exposed to different growing conditions (at gap vs. forest interior) or to different kinds of competition (intraspecific vs. interspecific). Furthermore, it was shown that the box dimension is positively related to the trees' growth rate. The box dimension was identified as an easy to calculate measure that integrates the effect of several external drivers of tree structure, such as competition strength and type, while simultaneously providing information on structure-related properties, like tree growth.

[Three-dimensional finite element study on the change of glossopharyngeum in patient with obstructive sleep apnea hypopnea syndrome during titrated mandible advancement].

PubMed

Yang, Suixing; Feng, Jing; Zhang, Zuo; Qu, Aili; Gong, Miao; Tang, Jie; Fan, Junheng; Li, Songqing; Zhao, Yanling

2013-04-01

To construct a three-dimensional finite element model of the upper airway and adjacent structure of an obstructive sleep apnea hypopnea syndrome (OSAHS) patient for biomechanical analysis. And to study the influence of glossopharyngeum of an OSAHS patient with three-dimensional finite element model during titrated mandible advancement. DICOM format image information of an OSAHS patient's upper airway was obtained by thin-section CT scanning and digital image processing were utilized to construct a three-dimensional finite element model by Mimics 10.0, Imageware 10.0 and Ansys software. The changes and the law of glossopharyngeum were observed by biomechanics and morphology after loading with titrated mandible advancement. A three-dimensional finite element model of the adjacent upper airway structure of OSAHS was established successfully. After loading, the transverse diameter of epiglottis tip of glossopharyngeum increased significantly, although the sagittal diameter decreased correspondingly. The principal stress was mainly distributed in anterior wall of the upper airway. The location of principal stress concentration did not change significantly with the increasing of distance. The stress of glossopharyngeum increased during titrated mandible advancement. A more precise three-dimensional finite model of upper airway and adjacent structure of an OSAHS patient is established and improved efficiency by Mimics, Imageware and Ansys software. The glossopharyngeum of finite element model of OSAHS is analyzed by titrated mandible advancement and can effectively show the relationship between mandible advancement and the glossopharyngeum.

Private algebras in quantum information and infinite-dimensional complementarity

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

Crann, Jason, E-mail: jason-crann@carleton.ca; Laboratoire de Mathématiques Paul Painlevé–UMR CNRS 8524, UFR de Mathématiques, Université Lille 1–Sciences et Technologies, 59655 Villeneuve d’Ascq Cédex; Kribs, David W., E-mail: dkribs@uoguelph.ca

We introduce a generalized framework for private quantum codes using von Neumann algebras and the structure of commutants. This leads naturally to a more general notion of complementary channel, which we use to establish a generalized complementarity theorem between private and correctable subalgebras that applies to both the finite and infinite-dimensional settings. Linear bosonic channels are considered and specific examples of Gaussian quantum channels are given to illustrate the new framework together with the complementarity theorem.

NALDB: nucleic acid ligand database for small molecules targeting nucleic acid

PubMed Central

Kumar Mishra, Subodh; Kumar, Amit

2016-01-01

Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php PMID:26896846

A Novel Method Using Abstract Convex Underestimation in Ab-Initio Protein Structure Prediction for Guiding Search in Conformational Feature Space.

PubMed

Hao, Xiao-Hu; Zhang, Gui-Jun; Zhou, Xiao-Gen; Yu, Xu-Feng

2016-01-01

To address the searching problem of protein conformational space in ab-initio protein structure prediction, a novel method using abstract convex underestimation (ACUE) based on the framework of evolutionary algorithm was proposed. Computing such conformations, essential to associate structural and functional information with gene sequences, is challenging due to the high-dimensionality and rugged energy surface of the protein conformational space. As a consequence, the dimension of protein conformational space should be reduced to a proper level. In this paper, the high-dimensionality original conformational space was converted into feature space whose dimension is considerably reduced by feature extraction technique. And, the underestimate space could be constructed according to abstract convex theory. Thus, the entropy effect caused by searching in the high-dimensionality conformational space could be avoided through such conversion. The tight lower bound estimate information was obtained to guide the searching direction, and the invalid searching area in which the global optimal solution is not located could be eliminated in advance. Moreover, instead of expensively calculating the energy of conformations in the original conformational space, the estimate value is employed to judge if the conformation is worth exploring to reduce the evaluation time, thereby making computational cost lower and the searching process more efficient. Additionally, fragment assembly and the Monte Carlo method are combined to generate a series of metastable conformations by sampling in the conformational space. The proposed method provides a novel technique to solve the searching problem of protein conformational space. Twenty small-to-medium structurally diverse proteins were tested, and the proposed ACUE method was compared with It Fix, HEA, Rosetta and the developed method LEDE without underestimate information. Test results show that the ACUE method can more rapidly and more efficiently obtain the near-native protein structure.

Three-Dimensional Geologic Model of Complex Fault Structures in the Upper Seco Creek Area, Medina and Uvalde Counties, South-Central Texas

USGS Publications Warehouse

Pantea, Michael P.; Cole, James C.; Smith, Bruce D.; Faith, Jason R.; Blome, Charles D.; Smith, David V.

2008-01-01

This multimedia report shows and describes digital three-dimensional faulted geologic surfaces and volumes of the lithologic units of the Edwards aquifer in the upper Seco Creek area of Medina and Uvalde Counties in south-central Texas. This geologic framework model was produced using (1) geologic maps and interpretations of depositional environments and paleogeography; (2) lithologic descriptions, interpretations, and geophysical logs from 31 drill holes; (3) rock core and detailed lithologic descriptions from one drill hole; (4) helicopter electromagnetic geophysical data; and (5) known major and minor faults in the study area. These faults were used because of their individual and collective effects on the continuity of the aquifer-forming units in the Edwards Group. Data and information were compared and validated with each other and reflect the complex relationships of structures in the Seco Creek area of the Balcones fault zone. This geologic framework model can be used as a tool to visually explore and study geologic structures within the Seco Creek area of the Balcones fault zone and to show the connectivity of hydrologic units of high and low permeability between and across faults. The software can be used to display other data and information, such as drill-hole data, on this geologic framework model in three-dimensional space.

How Community Has Shaped the Protein Data Bank

PubMed Central

Berman, Helen M.; Kleywegt, Gerard J.; Nakamura, Haruki; Markley, John L.

2015-01-01

Following several years of community discussion, the Protein Data Bank (PDB) was established in 1971 as a public repository for the coordinates of three-dimensional models of biological macromolecules. Since then, the number, size, and complexity of structural models have continued to grow, reflecting the productivity of structural biology. Managed by the Worldwide PDB organization, the PDB has been able to meet increasing demands for the quantity of structural information and of quality. In addition to providing unrestricted access to structural information, the PDB also works to promote data standards and to raise the profile of structural biology with broader audiences. In this perspective, we describe the history of PDB and the many ways in which the community continues to shape the archive. PMID:24010707

A Structure and Scheme for the Evaluation of Innovative Programs. The EPIC Brief, Issue No. 2.

ERIC Educational Resources Information Center

Objective evaluation of school programs is a process in which a school staff collects information used to provide feedback as to whether or not a given set of objectives has been met. The Evaluative Programs for Innovativ e Curriculums (EPIC) four-step scheme of objective evaluation is based on a three-dimensional structure of variables…

Entanglement entropy for (3+1)-dimensional topological order with excitations

NASA Astrophysics Data System (ADS)

Wen, Xueda; He, Huan; Tiwari, Apoorv; Zheng, Yunqin; Ye, Peng

2018-02-01

Excitations in (3+1)-dimensional [(3+1)D] topologically ordered phases have very rich structures. (3+1)D topological phases support both pointlike and stringlike excitations, and in particular the loop (closed string) excitations may admit knotted and linked structures. In this work, we ask the following question: How do different types of topological excitations contribute to the entanglement entropy or, alternatively, can we use the entanglement entropy to detect the structure of excitations, and further obtain the information of the underlying topological order? We are mainly interested in (3+1)D topological order that can be realized in Dijkgraaf-Witten (DW) gauge theories, which are labeled by a finite group G and its group 4-cocycle ω ∈H4[G ;U(1 ) ] up to group automorphisms. We find that each topological excitation contributes a universal constant lndi to the entanglement entropy, where di is the quantum dimension that depends on both the structure of the excitation and the data (G ,ω ) . The entanglement entropy of the excitations of the linked/unlinked topology can capture different information of the DW theory (G ,ω ) . In particular, the entanglement entropy introduced by Hopf-link loop excitations can distinguish certain group 4-cocycles ω from the others.

A Four-Dimensional Probabilistic Atlas of the Human Brain

PubMed Central

Mazziotta, John; Toga, Arthur; Evans, Alan; Fox, Peter; Lancaster, Jack; Zilles, Karl; Woods, Roger; Paus, Tomas; Simpson, Gregory; Pike, Bruce; Holmes, Colin; Collins, Louis; Thompson, Paul; MacDonald, David; Iacoboni, Marco; Schormann, Thorsten; Amunts, Katrin; Palomero-Gallagher, Nicola; Geyer, Stefan; Parsons, Larry; Narr, Katherine; Kabani, Noor; Le Goualher, Georges; Feidler, Jordan; Smith, Kenneth; Boomsma, Dorret; Pol, Hilleke Hulshoff; Cannon, Tyrone; Kawashima, Ryuta; Mazoyer, Bernard

2001-01-01

The authors describe the development of a four-dimensional atlas and reference system that includes both macroscopic and microscopic information on structure and function of the human brain in persons between the ages of 18 and 90 years. Given the presumed large but previously unquantified degree of structural and functional variance among normal persons in the human population, the basis for this atlas and reference system is probabilistic. Through the efforts of the International Consortium for Brain Mapping (ICBM), 7,000 subjects will be included in the initial phase of database and atlas development. For each subject, detailed demographic, clinical, behavioral, and imaging information is being collected. In addition, 5,800 subjects will contribute DNA for the purpose of determining genotype– phenotype–behavioral correlations. The process of developing the strategies, algorithms, data collection methods, validation approaches, database structures, and distribution of results is described in this report. Examples of applications of the approach are described for the normal brain in both adults and children as well as in patients with schizophrenia. This project should provide new insights into the relationship between microscopic and macroscopic structure and function in the human brain and should have important implications in basic neuroscience, clinical diagnostics, and cerebral disorders. PMID:11522763

Characterization and classification of vegetation canopy structure and distribution within the Great Smoky Mountains National Park using LiDAR

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

Kumar, Jitendra; HargroveJr., William Walter; Norman, Steven P

Vegetation canopy structure is a critically important habit characteristic for many threatened and endangered birds and other animal species, and it is key information needed by forest and wildlife managers for monitoring and managing forest resources, conservation planning and fostering biodiversity. Advances in Light Detection and Ranging (LiDAR) technologies have enabled remote sensing-based studies of vegetation canopies by capturing three-dimensional structures, yielding information not available in two-dimensional images of the landscape pro- vided by traditional multi-spectral remote sensing platforms. However, the large volume data sets produced by airborne LiDAR instruments pose a significant computational challenge, requiring algorithms to identify andmore » analyze patterns of interest buried within LiDAR point clouds in a computationally efficient manner, utilizing state-of-art computing infrastructure. We developed and applied a computationally efficient approach to analyze a large volume of LiDAR data and to characterize and map the vegetation canopy structures for 139,859 hectares (540 sq. miles) in the Great Smoky Mountains National Park. This study helps improve our understanding of the distribution of vegetation and animal habitats in this extremely diverse ecosystem.« less

Geo3DML: A standard-based exchange format for 3D geological models

NASA Astrophysics Data System (ADS)

Wang, Zhangang; Qu, Honggang; Wu, Zixing; Wang, Xianghong

2018-01-01

A geological model (geomodel) in three-dimensional (3D) space is a digital representation of the Earth's subsurface, recognized by geologists and stored in resultant geological data (geodata). The increasing demand for data management and interoperable applications of geomodelscan be addressed by developing standard-based exchange formats for the representation of not only a single geological object, but also holistic geomodels. However, current standards such as GeoSciML cannot incorporate all the geomodel-related information. This paper presents Geo3DML for the exchange of 3D geomodels based on the existing Open Geospatial Consortium (OGC) standards. Geo3DML is based on a unified and formal representation of structural models, attribute models and hierarchical structures of interpreted resultant geodata in different dimensional views, including drills, cross-sections/geomaps and 3D models, which is compatible with the conceptual model of GeoSciML. Geo3DML aims to encode all geomodel-related information integrally in one framework, including the semantic and geometric information of geoobjects and their relationships, as well as visual information. At present, Geo3DML and some supporting tools have been released as a data-exchange standard by the China Geological Survey (CGS).

Incorporating biological information in sparse principal component analysis with application to genomic data.

PubMed

Li, Ziyi; Safo, Sandra E; Long, Qi

2017-07-11

Sparse principal component analysis (PCA) is a popular tool for dimensionality reduction, pattern recognition, and visualization of high dimensional data. It has been recognized that complex biological mechanisms occur through concerted relationships of multiple genes working in networks that are often represented by graphs. Recent work has shown that incorporating such biological information improves feature selection and prediction performance in regression analysis, but there has been limited work on extending this approach to PCA. In this article, we propose two new sparse PCA methods called Fused and Grouped sparse PCA that enable incorporation of prior biological information in variable selection. Our simulation studies suggest that, compared to existing sparse PCA methods, the proposed methods achieve higher sensitivity and specificity when the graph structure is correctly specified, and are fairly robust to misspecified graph structures. Application to a glioblastoma gene expression dataset identified pathways that are suggested in the literature to be related with glioblastoma. The proposed sparse PCA methods Fused and Grouped sparse PCA can effectively incorporate prior biological information in variable selection, leading to improved feature selection and more interpretable principal component loadings and potentially providing insights on molecular underpinnings of complex diseases.

Bioinformatics approaches for structural and functional analysis of proteins in secondary metabolism in Withania somnifera.

PubMed

Sanchita; Singh, Swati; Sharma, Ashok

2014-11-01

Withania somnifera (Ashwagandha) is an affluent storehouse of large number of pharmacologically active secondary metabolites known as withanolides. These secondary metabolites are produced by withanolide biosynthetic pathway. Very less information is available on structural and functional aspects of enzymes involved in withanolides biosynthetic pathways of Withiana somnifera. We therefore performed a bioinformatics analysis to look at functional and structural properties of these important enzymes. The pathway enzymes taken for this study were 3-Hydroxy-3-methylglutaryl coenzyme A reductase, 1-Deoxy-D-xylulose-5-phosphate synthase, 1-Deoxy-D-xylulose-5-phosphate reductase, farnesyl pyrophosphate synthase, squalene synthase, squalene epoxidase, and cycloartenol synthase. The prediction of secondary structure was performed for basic structural information. Three-dimensional structures for these enzymes were predicted. The physico-chemical properties such as pI, AI, GRAVY and instability index were also studied. The current information will provide a platform to know the structural attributes responsible for the function of these protein until experimental structures become available.

Computer Models of Proteins

NASA Technical Reports Server (NTRS)

2000-01-01

Dr. Marc Pusey (seated) and Dr. Craig Kundrot use computers to analyze x-ray maps and generate three-dimensional models of protein structures. With this information, scientists at Marshall Space Flight Center can learn how proteins are made and how they work. The computer screen depicts a proten structure as a ball-and-stick model. Other models depict the actual volume occupied by the atoms, or the ribbon-like structures that are crucial to a protein's function.

Three-Dimensional RNA Structure of the Major HIV-1 Packaging Signal Region

PubMed Central

Stephenson, James D.; Li, Haitao; Kenyon, Julia C.; Symmons, Martyn; Klenerman, Dave; Lever, Andrew M.L.

2013-01-01

Summary HIV-1 genomic RNA has a noncoding 5′ region containing sequential conserved structural motifs that control many parts of the life cycle. Very limited data exist on their three-dimensional (3D) conformation and, hence, how they work structurally. To assemble a working model, we experimentally reassessed secondary structure elements of a 240-nt region and used single-molecule distances, derived from fluorescence resonance energy transfer, between defined locations in these elements as restraints to drive folding of the secondary structure into a 3D model with an estimated resolution below 10 Å. The folded 3D model satisfying the data is consensual with short nuclear-magnetic-resonance-solved regions and reveals previously unpredicted motifs, offering insight into earlier functional assays. It is a 3D representation of this entire region, with implications for RNA dimerization and protein binding during regulatory steps. The structural information of this highly conserved region of the virus has the potential to reveal promising therapeutic targets. PMID:23685210

CARTAM. The Cartesian Access Method for Data Structures with n-dimensional Keys.

DTIC Science & Technology

1979-01-01

become apparent later, I have chosen to store structural information in an explicit binary tree , with modifications. instead of the left and right links of...the usual binary tree , I use the child and twin pointers of a ring structure or circular list. This ring structure as illustrated in figure 3-1* also...Since the file is being stored as an explicit binary tree , note that additional records are being generated, and the concept of an Ni-thm record for

NIAS-Server: Neighbors Influence of Amino acids and Secondary Structures in Proteins.

PubMed

Borguesan, Bruno; Inostroza-Ponta, Mario; Dorn, Márcio

2017-03-01

The exponential growth in the number of experimentally determined three-dimensional protein structures provide a new and relevant knowledge about the conformation of amino acids in proteins. Only a few of probability densities of amino acids are publicly available for use in structure validation and prediction methods. NIAS (Neighbors Influence of Amino acids and Secondary structures) is a web-based tool used to extract information about conformational preferences of amino acid residues and secondary structures in experimental-determined protein templates. This information is useful, for example, to characterize folds and local motifs in proteins, molecular folding, and can help the solution of complex problems such as protein structure prediction, protein design, among others. The NIAS-Server and supplementary data are available at http://sbcb.inf.ufrgs.br/nias .

Pollen structure visualization using high-resolution laboratory-based hard X-ray tomography.

PubMed

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.

Multiscale modeling of three-dimensional genome

NASA Astrophysics Data System (ADS)

Zhang, Bin; Wolynes, Peter

The genome, the blueprint of life, contains nearly all the information needed to build and maintain an entire organism. A comprehensive understanding of the genome is of paramount interest to human health and will advance progress in many areas, including life sciences, medicine, and biotechnology. The overarching goal of my research is to understand the structure-dynamics-function relationships of the human genome. In this talk, I will be presenting our efforts in moving towards that goal, with a particular emphasis on studying the three-dimensional organization, the structure of the genome with multi-scale approaches. Specifically, I will discuss the reconstruction of genome structures at both interphase and metaphase by making use of data from chromosome conformation capture experiments. Computationally modeling of chromatin fiber at atomistic level from first principles will also be presented as our effort for studying the genome structure from bottom up.

Electron crystallography of PhoE porin, an outer membrane, channel- forming protein from E. coli

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

Walian, P.J.

1989-11-01

One approach to studying the structure of membrane proteins is the use of electron crystallography. Dr. Bing Jap has crystallized PhoE pore-forming protein (porin) from the outer membrane of escherichia coli (E. coli) into monolayer crystals. The findings of this research and those of Jap (1988, 1989) have determined these crystals to be highly ordered, yielding structural information to a resolution of better than 2.8 angstroms. The task of this thesis has been to collect and process the electron diffraction patterns necessary to generate a complete three-dimensional set of high resolution structure factor amplitudes of PhoE porin. Fourier processing ofmore » these amplitudes when combined with the corresponding phase data is expected to yield the three-dimensional structure of PhoE porin at better than 3.5 angstroms resolution. 92 refs., 33 figs., 3 tabs. (CBS)« less

Westward tilt of low-latitude plasma blobs as observed by the Swarm constellation

NASA Astrophysics Data System (ADS)

Park, Jaeheung; Lühr, Hermann; Michaelis, Ingo; Stolle, Claudia; Rauberg, Jan; Buchert, Stephan; Gill, Reine; Merayo, Jose M. G.; Brauer, Peter

2015-04-01

In this study we investigate the three-dimensional structure of low-latitude plasma blobs using multi-instrument and multisatellite observations of the Swarm constellation. During the early commissioning phase the Swarm satellites were flying at the same altitude with zonal separation of about 0.5∘ in geographic longitude. Electron density data from the three satellites constrain the blob morphology projected onto the horizontal plane. Magnetic field deflections around blobs, which originate from field-aligned currents near the irregularity boundaries, constrain the blob structure projected onto the plane perpendicular to the ambient magnetic field. As the two constraints are given for two noncoplanar surfaces, we can get information on the three-dimensional structure of blobs. Combined observation results suggest that blobs are contained within tilted shells of geomagnetic flux tubes, which are similar to the shell structure of equatorial plasma bubbles suggested by previous studies.

Time dependent deformation and stress in the lithosphere. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Yang, M.

1980-01-01

Efficient computer programs incorporating frontal solution and time stepping procedure were developed for the modelling of geodynamic problems. This scheme allows for investigating the quasi static phenomena including the effects of the rheological structure of a tectonically active region. From three dimensional models of strike slip earthquakes, it was found that lateral variation of viscosity affects the characteristics of surface deformations. The vertical deformation is especially informative about the viscosity structure in a strike slip fault zone. A three dimensional viscoelastic model of a thrust earthquake indicated that the transient disturbance on plate velocity due to a great plate boundary earthquake is significant at intermediate distances, but becomes barely measurable 1000 km away from the source.

Self-assembled three-dimensional chiral colloidal architecture.

PubMed

Ben Zion, Matan Yah; He, Xiaojin; Maass, Corinna C; Sha, Ruojie; Seeman, Nadrian C; Chaikin, Paul M

2017-11-03

Although stereochemistry has been a central focus of the molecular sciences since Pasteur, its province has previously been restricted to the nanometric scale. We have programmed the self-assembly of micron-sized colloidal clusters with structural information stemming from a nanometric arrangement. This was done by combining DNA nanotechnology with colloidal science. Using the functional flexibility of DNA origami in conjunction with the structural rigidity of colloidal particles, we demonstrate the parallel self-assembly of three-dimensional microconstructs, evincing highly specific geometry that includes control over position, dihedral angles, and cluster chirality. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Simulation of radiation effects on three-dimensional computer optical memories

NASA Technical Reports Server (NTRS)

Moscovitch, M.; Emfietzoglou, D.

1997-01-01

A model was developed to simulate the effects of heavy charged-particle (HCP) radiation on the information stored in three-dimensional computer optical memories. The model is based on (i) the HCP track radial dose distribution, (ii) the spatial and temporal distribution of temperature in the track, (iii) the matrix-specific radiation-induced changes that will affect the response, and (iv) the kinetics of transition of photochromic molecules from the colored to the colorless isomeric form (bit flip). It is shown that information stored in a volume of several nanometers radius around the particle's track axis may be lost. The magnitude of the effect is dependent on the particle's track structure.

Three-dimensional Analysis of Nanomaterials by Scanning Probe Nanotomography

NASA Astrophysics Data System (ADS)

Efimov, Anton E.; Agapova, Olga I.; Mochalov, Konstantin E.; Agapov, Igor I.

Micro and nanostructure of scaffolds made from fibroin of Bombyx mori silkworm by salt leaching technique was studied by scanning probe nanotomography. Nanopores with dimensions in range from 30 to 180 nm are observed in the scaffold volume. Three - dimensional analysis of obtained data shows that degree of scaffold nanoporosity is 0.5% and nanopores are not interconnected with each other. Usage of scanning probe nanotomography technique enables to obtain unique nanoscale information of 3D structure of biopolymer nanomaterials.

ONR Far East Scientific Information Bulletin. Volume 13. Number 3, July to September 1988

DTIC Science & Technology

1988-09-01

dimensional circulate in the film plane much as in the films as the temperature is reduced. The bulk, and H is not greatly affected . But cause of...T) is not affecte ’ X by dimensional change (Ref 32). On the 20 - x other hand, at lower temperatures, when cc PM. is sm aller than d c, but exceeds d...implications for parameters affect composition and back- heterojunction-based device structures. ground acceptor concentration); low T is Misfit

Method of fabricating free-form, high-aspect ratio components for high-current, high-speed microelectrics

DOEpatents

Maxwell, James L; Rose, Chris R; Black, Marcie R; Springer, Robert W

2014-03-11

Microelectronic structures and devices, and method of fabricating a three-dimensional microelectronic structure is provided, comprising passing a first precursor material for a selected three-dimensional microelectronic structure into a reaction chamber at temperatures sufficient to maintain said precursor material in a predominantly gaseous state; maintaining said reaction chamber under sufficient pressures to enhance formation of a first portion of said three-dimensional microelectronic structure; applying an electric field between an electrode and said microelectronic structure at a desired point under conditions whereat said first portion of a selected three-dimensional microelectronic structure is formed from said first precursor material; positionally adjusting either said formed three-dimensional microelectronic structure or said electrode whereby further controlled growth of said three-dimensional microelectronic structure occurs; passing a second precursor material for a selected three-dimensional microelectronic structure into a reaction chamber at temperatures sufficient to maintain said precursor material in a predominantly gaseous state; maintaining said reaction chamber under sufficient pressures whereby a second portion of said three-dimensional microelectronic structure formation is enhanced; applying an electric field between an electrode and said microelectronic structure at a desired point under conditions whereat said second portion of a selected three-dimensional microelectronic structure is formed from said second precursor material; and, positionally adjusting either said formed three-dimensional microelectronic structure or said electrode whereby further controlled growth of said three-dimensional microelectronic structure occurs.

From Principal Component to Direct Coupling Analysis of Coevolution in Proteins: Low-Eigenvalue Modes are Needed for Structure Prediction

PubMed Central

Cocco, Simona; Monasson, Remi; Weigt, Martin

2013-01-01

Various approaches have explored the covariation of residues in multiple-sequence alignments of homologous proteins to extract functional and structural information. Among those are principal component analysis (PCA), which identifies the most correlated groups of residues, and direct coupling analysis (DCA), a global inference method based on the maximum entropy principle, which aims at predicting residue-residue contacts. In this paper, inspired by the statistical physics of disordered systems, we introduce the Hopfield-Potts model to naturally interpolate between these two approaches. The Hopfield-Potts model allows us to identify relevant ‘patterns’ of residues from the knowledge of the eigenmodes and eigenvalues of the residue-residue correlation matrix. We show how the computation of such statistical patterns makes it possible to accurately predict residue-residue contacts with a much smaller number of parameters than DCA. This dimensional reduction allows us to avoid overfitting and to extract contact information from multiple-sequence alignments of reduced size. In addition, we show that low-eigenvalue correlation modes, discarded by PCA, are important to recover structural information: the corresponding patterns are highly localized, that is, they are concentrated in few sites, which we find to be in close contact in the three-dimensional protein fold. PMID:23990764

Gaussian processes with built-in dimensionality reduction: Applications to high-dimensional uncertainty propagation

NASA Astrophysics Data System (ADS)

Tripathy, Rohit; Bilionis, Ilias; Gonzalez, Marcial

2016-09-01

Uncertainty quantification (UQ) tasks, such as model calibration, uncertainty propagation, and optimization under uncertainty, typically require several thousand evaluations of the underlying computer codes. To cope with the cost of simulations, one replaces the real response surface with a cheap surrogate based, e.g., on polynomial chaos expansions, neural networks, support vector machines, or Gaussian processes (GP). However, the number of simulations required to learn a generic multivariate response grows exponentially as the input dimension increases. This curse of dimensionality can only be addressed, if the response exhibits some special structure that can be discovered and exploited. A wide range of physical responses exhibit a special structure known as an active subspace (AS). An AS is a linear manifold of the stochastic space characterized by maximal response variation. The idea is that one should first identify this low dimensional manifold, project the high-dimensional input onto it, and then link the projection to the output. If the dimensionality of the AS is low enough, then learning the link function is a much easier problem than the original problem of learning a high-dimensional function. The classic approach to discovering the AS requires gradient information, a fact that severely limits its applicability. Furthermore, and partly because of its reliance to gradients, it is not able to handle noisy observations. The latter is an essential trait if one wants to be able to propagate uncertainty through stochastic simulators, e.g., through molecular dynamics codes. In this work, we develop a probabilistic version of AS which is gradient-free and robust to observational noise. Our approach relies on a novel Gaussian process regression with built-in dimensionality reduction. In particular, the AS is represented as an orthogonal projection matrix that serves as yet another covariance function hyper-parameter to be estimated from the data. To train the model, we design a two-step maximum likelihood optimization procedure that ensures the orthogonality of the projection matrix by exploiting recent results on the Stiefel manifold, i.e., the manifold of matrices with orthogonal columns. The additional benefit of our probabilistic formulation, is that it allows us to select the dimensionality of the AS via the Bayesian information criterion. We validate our approach by showing that it can discover the right AS in synthetic examples without gradient information using both noiseless and noisy observations. We demonstrate that our method is able to discover the same AS as the classical approach in a challenging one-hundred-dimensional problem involving an elliptic stochastic partial differential equation with random conductivity. Finally, we use our approach to study the effect of geometric and material uncertainties in the propagation of solitary waves in a one dimensional granular system.

Gaussian processes with built-in dimensionality reduction: Applications to high-dimensional uncertainty propagation

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

Tripathy, Rohit, E-mail: rtripath@purdue.edu; Bilionis, Ilias, E-mail: ibilion@purdue.edu; Gonzalez, Marcial, E-mail: marcial-gonzalez@purdue.edu

2016-09-15

Uncertainty quantification (UQ) tasks, such as model calibration, uncertainty propagation, and optimization under uncertainty, typically require several thousand evaluations of the underlying computer codes. To cope with the cost of simulations, one replaces the real response surface with a cheap surrogate based, e.g., on polynomial chaos expansions, neural networks, support vector machines, or Gaussian processes (GP). However, the number of simulations required to learn a generic multivariate response grows exponentially as the input dimension increases. This curse of dimensionality can only be addressed, if the response exhibits some special structure that can be discovered and exploited. A wide range ofmore » physical responses exhibit a special structure known as an active subspace (AS). An AS is a linear manifold of the stochastic space characterized by maximal response variation. The idea is that one should first identify this low dimensional manifold, project the high-dimensional input onto it, and then link the projection to the output. If the dimensionality of the AS is low enough, then learning the link function is a much easier problem than the original problem of learning a high-dimensional function. The classic approach to discovering the AS requires gradient information, a fact that severely limits its applicability. Furthermore, and partly because of its reliance to gradients, it is not able to handle noisy observations. The latter is an essential trait if one wants to be able to propagate uncertainty through stochastic simulators, e.g., through molecular dynamics codes. In this work, we develop a probabilistic version of AS which is gradient-free and robust to observational noise. Our approach relies on a novel Gaussian process regression with built-in dimensionality reduction. In particular, the AS is represented as an orthogonal projection matrix that serves as yet another covariance function hyper-parameter to be estimated from the data. To train the model, we design a two-step maximum likelihood optimization procedure that ensures the orthogonality of the projection matrix by exploiting recent results on the Stiefel manifold, i.e., the manifold of matrices with orthogonal columns. The additional benefit of our probabilistic formulation, is that it allows us to select the dimensionality of the AS via the Bayesian information criterion. We validate our approach by showing that it can discover the right AS in synthetic examples without gradient information using both noiseless and noisy observations. We demonstrate that our method is able to discover the same AS as the classical approach in a challenging one-hundred-dimensional problem involving an elliptic stochastic partial differential equation with random conductivity. Finally, we use our approach to study the effect of geometric and material uncertainties in the propagation of solitary waves in a one dimensional granular system.« less

Robust hashing with local models for approximate similarity search.

PubMed

Song, Jingkuan; Yang, Yi; Li, Xuelong; Huang, Zi; Yang, Yang

2014-07-01

Similarity search plays an important role in many applications involving high-dimensional data. Due to the known dimensionality curse, the performance of most existing indexing structures degrades quickly as the feature dimensionality increases. Hashing methods, such as locality sensitive hashing (LSH) and its variants, have been widely used to achieve fast approximate similarity search by trading search quality for efficiency. However, most existing hashing methods make use of randomized algorithms to generate hash codes without considering the specific structural information in the data. In this paper, we propose a novel hashing method, namely, robust hashing with local models (RHLM), which learns a set of robust hash functions to map the high-dimensional data points into binary hash codes by effectively utilizing local structural information. In RHLM, for each individual data point in the training dataset, a local hashing model is learned and used to predict the hash codes of its neighboring data points. The local models from all the data points are globally aligned so that an optimal hash code can be assigned to each data point. After obtaining the hash codes of all the training data points, we design a robust method by employing l2,1 -norm minimization on the loss function to learn effective hash functions, which are then used to map each database point into its hash code. Given a query data point, the search process first maps it into the query hash code by the hash functions and then explores the buckets, which have similar hash codes to the query hash code. Extensive experimental results conducted on real-life datasets show that the proposed RHLM outperforms the state-of-the-art methods in terms of search quality and efficiency.

Cross-Linking/Mass Spectrometry for Studying Protein Structures and Protein-Protein Interactions: Where Are We Now and Where Should We Go from Here?

PubMed

Sinz, Andrea

2018-05-28

Structural mass spectrometry (MS) is gaining increasing importance for deriving valuable three-dimensional structural information on proteins and protein complexes, and it complements existing techniques, such as NMR spectroscopy and X-ray crystallography. Structural MS unites different MS-based techniques, such as hydrogen/deuterium exchange, native MS, ion-mobility MS, protein footprinting, and chemical cross-linking/MS, and it allows fundamental questions in structural biology to be addressed. In this Minireview, I will focus on the cross-linking/MS strategy. This method not only delivers tertiary structural information on proteins, but is also increasingly being used to decipher protein interaction networks, both in vitro and in vivo. Cross-linking/MS is currently one of the most promising MS-based approaches to derive structural information on very large and transient protein assemblies and intrinsically disordered proteins. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

In situ synchrotron X-ray diffraction study on epitaxial-growth dynamics of III–V semiconductors

NASA Astrophysics Data System (ADS)

Takahasi, Masamitu

2018-05-01

The application of in situ synchrotron X-ray diffraction (XRD) to the molecular-beam epitaxial (MBE) growth of III–V semiconductors is overviewed along with backgrounds of the diffraction theory and instrumentation. X-rays are sensitive not only to the surface of growing films but also to buried interfacial structures because of their large penetration depth. Moreover, a spatial coherence length up to µm order makes X-rays widely applicable to the characterization of low-dimensional structures, such as quantum dots and wires. In situ XRD studies during growth were performed using an X-ray diffractometer, which was combined with an MBE chamber. X-ray reciprocal space mapping at a speed matching a typical growth rate was achieved using intense X-rays available from a synchrotron light source and an area detector. The importance of measuring the three-dimensional distribution of XRD intensity in a reciprocal space map is demonstrated for the MBE growth of two-, one-, and zero-dimensional structures. A large amount of information about the growth process of two-dimensional InGaAs/GaAs(001) epitaxial films has been provided by three-dimensional X-ray reciprocal mappings, including the anisotropic strain relaxation, the compositional inhomogeneity, and the evolution of surface and interfacial roughness. For one-dimensional GaAs nanowires grown in a Au-catalyzed vapor-liquid–solid mode, the relationship between the diameter of the nanowires and the formation of polytypes has been suggested on the basis of in situ XRD measurements. In situ three-dimensional X-ray reciprocal space mapping is also shown to be useful for determining the lateral and vertical sizes of self-assembled InAs/GaAs(001) quantum dots as well as their internal strain distributions during growth.

32 CFR 701.18 - Agency record.

Code of Federal Regulations, 2013 CFR

2013-07-01

... are stored as various kinds of media, such as: (a) Products of data compilation (all books, maps... following categories: (1) Objects or articles, such as structures, furniture, paintings, three-dimensional... Register, the National Technical Information Service, or the Internet, normally need not be processed under...

32 CFR 701.18 - Agency record.

Code of Federal Regulations, 2014 CFR

2014-07-01

... are stored as various kinds of media, such as: (a) Products of data compilation (all books, maps... following categories: (1) Objects or articles, such as structures, furniture, paintings, three-dimensional... Register, the National Technical Information Service, or the Internet, normally need not be processed under...

32 CFR 701.18 - Agency record.

Code of Federal Regulations, 2012 CFR

2012-07-01

... are stored as various kinds of media, such as: (a) Products of data compilation (all books, maps... following categories: (1) Objects or articles, such as structures, furniture, paintings, three-dimensional... Register, the National Technical Information Service, or the Internet, normally need not be processed under...

32 CFR 701.18 - Agency record.

Code of Federal Regulations, 2011 CFR

2011-07-01

... are stored as various kinds of media, such as: (a) Products of data compilation (all books, maps... following categories: (1) Objects or articles, such as structures, furniture, paintings, three-dimensional... Register, the National Technical Information Service, or the Internet, normally need not be processed under...

EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB).

PubMed

Beaver, John E; Bourne, Philip E; Ponomarenko, Julia V

2007-02-21

Structural information about epitopes, particularly the three-dimensional (3D) structures of antigens in complex with immune receptors, presents a valuable source of data for immunology. This information is available in the Protein Data Bank (PDB) and provided in curated form by the Immune Epitope Database and Analysis Resource (IEDB). With continued growth in these data and the importance in understanding molecular level interactions of immunological interest there is a need for new specialized molecular visualization and analysis tools. The EpitopeViewer is a platform-independent Java application for the visualization of the three-dimensional structure and sequence of epitopes and analyses of their interactions with antigen-specific receptors of the immune system (antibodies, T cell receptors and MHC molecules). The viewer renders both 3D views and two-dimensional plots of intermolecular interactions between the antigen and receptor(s) by reading curated data from the IEDB and/or calculated on-the-fly from atom coordinates from the PDB. The 3D views and associated interactions can be saved for future use and publication. The EpitopeViewer can be accessed from the IEDB Web site http://www.immuneepitope.org through the quick link 'Browse Records by 3D Structure.' The EpitopeViewer is designed and been tested for use by immunologists with little or no training in molecular graphics. The EpitopeViewer can be launched from most popular Web browsers without user intervention. A Java Runtime Environment (RJE) 1.4.2 or higher is required.

Zooming in on vibronic structure by lowest-value projection reconstructed 4D coherent spectroscopy

NASA Astrophysics Data System (ADS)

Harel, Elad

2018-05-01

A fundamental goal of chemical physics is an understanding of microscopic interactions in liquids at and away from equilibrium. In principle, this microscopic information is accessible by high-order and high-dimensionality nonlinear optical measurements. Unfortunately, the time required to execute such experiments increases exponentially with the dimensionality, while the signal decreases exponentially with the order of the nonlinearity. Recently, we demonstrated a non-uniform acquisition method based on radial sampling of the time-domain signal [W. O. Hutson et al., J. Phys. Chem. Lett. 9, 1034 (2018)]. The four-dimensional spectrum was then reconstructed by filtered back-projection using an inverse Radon transform. Here, we demonstrate an alternative reconstruction method based on the statistical analysis of different back-projected spectra which results in a dramatic increase in sensitivity and at least a 100-fold increase in dynamic range compared to conventional uniform sampling and Fourier reconstruction. These results demonstrate that alternative sampling and reconstruction methods enable applications of increasingly high-order and high-dimensionality methods toward deeper insights into the vibronic structure of liquids.

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

PubMed

Hall, L H; Hall, L M

2005-01-01

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

ASTROP2 Users Manual: A Program for Aeroelastic Stability Analysis of Propfans

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Lucero, John M.

1996-01-01

This manual describes the input data required for using the second version of the ASTROP2 (Aeroelastic STability and Response Of Propulsion systems - 2 dimensional analysis) computer code. In ASTROP2, version 2.0, the program is divided into two modules: 2DSTRIP, which calculates the structural dynamic information; and 2DASTROP, which calculates the unsteady aerodynamic force coefficients from which the aeroelastic stability can be determined. In the original version of ASTROP2, these two aspects were performed in a single program. The improvements to version 2.0 include an option to account for counter rotation, improved numerical integration, accommodation for non-uniform inflow distribution, and an iterative scheme to flutter frequency convergence. ASTROP2 can be used for flutter analysis of multi-bladed structures such as those found in compressors, turbines, counter rotating propellers or propfans. The analysis combines a two-dimensional, unsteady cascade aerodynamics model and a three dimensional, normal mode structural model using strip theory. The flutter analysis is formulated in the frequency domain resulting in an eigenvalue determinant. The flutter frequency and damping can be inferred from the eigenvalues.

New modes of electron microscopy for materials science enabled by fast direct electron detectors

NASA Astrophysics Data System (ADS)

Minor, Andrew

There is an ongoing revolution in the development of electron detector technology that has enabled modes of electron microscopy imaging that had only before been theorized. The age of electron microscopy as a tool for imaging is quickly giving way to a new frontier of multidimensional datasets to be mined. These improvements in electron detection have enabled cryo-electron microscopy to resolve the three-dimensional structures of non-crystalized proteins, revolutionizing structural biology. In the physical sciences direct electron detectors has enabled four-dimensional reciprocal space maps of materials at atomic resolution, providing all the structural information about nanoscale materials in one experiment. This talk will highlight the impact of direct electron detectors for materials science, including a new method of scanning nanobeam diffraction. With faster detectors we can take a series of 2D diffraction patterns at each position in a 2D STEM raster scan resulting in a four-dimensional data set. For thin film analysis, direct electron detectors hold the potential to enable strain, polarization, composition and electrical field mapping over relatively large fields of view, all from a single experiment.

Probing quasi-one-dimensional band structures by plasmon spectroscopy

NASA Astrophysics Data System (ADS)

Lichtenstein, T.; Mamiyev, Z.; Braun, C.; Sanna, S.; Schmidt, W. G.; Tegenkamp, C.; Pfnür, H.

2018-04-01

The plasmon dispersion is inherently related to the continuum of electron-hole pair excitations. Therefore, the comparison of this continuum, as derived from band structure calculations, with experimental data of plasmon dispersion, can yield direct information about the form of the occupied as well as the unoccupied band structure in the vicinity of the Fermi level. The relevance of this statement is illustrated by a detailed analysis of plasmon dispersions in quasi-one-dimensional systems combining experimental electron energy loss spectroscopy with quantitative density-functional theory (DFT) calculations. Si(557)-Au and Si(335)-Au with single atomic chains per terrace are compared with the Si(775)-Au system, which has a double Au chain on each terrace. We demonstrate that both hybridization between Si surface states and the Au chains as well as electronic correlations lead to increasing deviations from the nearly free electron picture that is suggested by a too simple interpretation of data of angular resolved photoemission (ARPES) of these systems, particularly for the double chain system. These deviations are consistently predicted by the DFT calculations. Thus also dimensional crossover can be explained.

Trans-dimensional and hierarchical Bayesian approaches toward rigorous estimation of seismic sources and structures in the Northeast Asia

NASA Astrophysics Data System (ADS)

Kim, Seongryong; Tkalčić, Hrvoje; Mustać, Marija; Rhie, Junkee; Ford, Sean

2016-04-01

A framework is presented within which we provide rigorous estimations for seismic sources and structures in the Northeast Asia. We use Bayesian inversion methods, which enable statistical estimations of models and their uncertainties based on data information. Ambiguities in error statistics and model parameterizations are addressed by hierarchical and trans-dimensional (trans-D) techniques, which can be inherently implemented in the Bayesian inversions. Hence reliable estimation of model parameters and their uncertainties is possible, thus avoiding arbitrary regularizations and parameterizations. Hierarchical and trans-D inversions are performed to develop a three-dimensional velocity model using ambient noise data. To further improve the model, we perform joint inversions with receiver function data using a newly developed Bayesian method. For the source estimation, a novel moment tensor inversion method is presented and applied to regional waveform data of the North Korean nuclear explosion tests. By the combination of new Bayesian techniques and the structural model, coupled with meaningful uncertainties related to each of the processes, more quantitative monitoring and discrimination of seismic events is possible.

Information Extraction of Tourist Geological Resources Based on 3d Visualization Remote Sensing Image

NASA Astrophysics Data System (ADS)

Wang, X.

2018-04-01

Tourism geological resources are of high value in admiration, scientific research and universal education, which need to be protected and rationally utilized. In the past, most of the remote sensing investigations of tourism geological resources used two-dimensional remote sensing interpretation method, which made it difficult for some geological heritages to be interpreted and led to the omission of some information. This aim of this paper is to assess the value of a method using the three-dimensional visual remote sensing image to extract information of geological heritages. skyline software system is applied to fuse the 0.36 m aerial images and 5m interval DEM to establish the digital earth model. Based on the three-dimensional shape, color tone, shadow, texture and other image features, the distribution of tourism geological resources in Shandong Province and the location of geological heritage sites were obtained, such as geological structure, DaiGu landform, granite landform, Volcanic landform, sandy landform, Waterscapes, etc. The results show that using this method for remote sensing interpretation is highly recognizable, making the interpretation more accurate and comprehensive.

Studies on Manfred Eigen's model for the self-organization of information processing.

PubMed

Ebeling, W; Feistel, R

2018-05-01

In 1971, Manfred Eigen extended the principles of Darwinian evolution to chemical processes, from catalytic networks to the emergence of information processing at the molecular level, leading to the emergence of life. In this paper, we investigate some very general characteristics of this scenario, such as the valuation process of phenotypic traits in a high-dimensional fitness landscape, the effect of spatial compartmentation on the valuation, and the self-organized transition from structural to symbolic genetic information of replicating chain molecules. In the first part, we perform an analysis of typical dynamical properties of continuous dynamical models of evolutionary processes. In particular, we study the mapping of genotype to continuous phenotype spaces following the ideas of Wright and Conrad. We investigate typical features of a Schrödinger-like dynamics, the consequences of the high dimensionality, the leading role of saddle points, and Conrad's extra-dimensional bypass. In the last part, we discuss in brief the valuation of compartment models and the self-organized emergence of molecular symbols at the beginning of life.

Four-dimensional optical coherence tomography imaging of total liquid ventilated rats

NASA Astrophysics Data System (ADS)

Kirsten, Lars; Schnabel, Christian; Gaertner, Maria; Koch, Edmund

2013-06-01

Optical coherence tomography (OCT) can be utilized for the spatially and temporally resolved visualization of alveolar tissue and its dynamics in rodent models, which allows the investigation of lung dynamics on the microscopic scale of single alveoli. The findings could provide experimental input data for numerical simulations of lung tissue mechanics and could support the development of protective ventilation strategies. Real four-dimensional OCT imaging permits the acquisition of several OCT stacks within one single ventilation cycle. Thus, the entire four-dimensional information is directly obtained. Compared to conventional virtual four-dimensional OCT imaging, where the image acquisition is extended over many ventilation cycles and is triggered on pressure levels, real four-dimensional OCT is less vulnerable against motion artifacts and non-reproducible movement of the lung tissue over subsequent ventilation cycles, which widely reduces image artifacts. However, OCT imaging of alveolar tissue is affected by refraction and total internal reflection at air-tissue interfaces. Thus, only the first alveolar layer beneath the pleura is visible. To circumvent this effect, total liquid ventilation can be carried out to match the refractive indices of lung tissue and the breathing medium, which improves the visibility of the alveolar structure, the image quality and the penetration depth and provides the real structure of the alveolar tissue. In this study, a combination of four-dimensional OCT imaging with total liquid ventilation allowed the visualization of the alveolar structure in rat lung tissue benefiting from the improved depth range beneath the pleura and from the high spatial and temporal resolution.

On-chip photonic-phononic emitter-receiver apparatus

DOEpatents

Cox, Jonathan Albert; Jarecki, Jr., Robert L.; Rakich, Peter Thomas; Wang, Zheng; Shin, Heedeuk; Siddiqui, Aleem; Starbuck, Andrew Lea

2017-07-04

A radio-frequency photonic devices employs photon-phonon coupling for information transfer. The device includes a membrane in which a two-dimensionally periodic phononic crystal (PnC) structure is patterned. The device also includes at least a first optical waveguide embedded in the membrane. At least a first line-defect region interrupts the PnC structure. The first optical waveguide is embedded within the line-defect region.

Fabrication and characterization of graphene hydrogel via hydrothermal approach as a scaffold for preliminary study of cell growth

PubMed Central

Lim, HN; Huang, NM; Lim, SS; Harrison, I; Chia, CH

2011-01-01

Background Three-dimensional assembly of graphene hydrogel is rapidly attracting the interest of researchers because of its wide range of applications in energy storage, electronics, electrochemistry, and waste water treatment. Information on the use of graphene hydrogel for biological purposes is lacking, so we conducted a preliminary study to determine the suitability of graphene hydrogel as a substrate for cell growth, which could potentially be used as building blocks for biomolecules and tissue engineering applications. Methods A three-dimensional structure of graphene hydrogel was prepared via a simple hydrothermal method using two-dimensional large-area graphene oxide nanosheets as a precursor. Results The concentration and lateral size of the graphene oxide nanosheets influenced the structure of the hydrogel. With larger-area graphene oxide nanosheets, the graphene hydrogel could be formed at a lower concentration. X-ray diffraction patterns revealed that the oxide functional groups on the graphene oxide nanosheets were reduced after hydrothermal treatment. The three-dimensional graphene hydrogel matrix was used as a scaffold for proliferation of a MG63 cell line. Conclusion Guided filopodia protrusions of MG63 on the hydrogel were observed on the third day of cell culture, demonstrating compatibility of the graphene hydrogel structure for bioapplications. PMID:21931479

A matrix dependent/algebraic multigrid approach for extruded meshes with applications to ice sheet modeling

DOE PAGES

Tuminaro, Raymond S.; Perego, Mauro; Tezaur, Irina Kalashnikova; ...

2016-10-06

A multigrid method is proposed that combines ideas from matrix dependent multigrid for structured grids and algebraic multigrid for unstructured grids. It targets problems where a three-dimensional mesh can be viewed as an extrusion of a two-dimensional, unstructured mesh in a third dimension. Our motivation comes from the modeling of thin structures via finite elements and, more specifically, the modeling of ice sheets. Extruded meshes are relatively common for thin structures and often give rise to anisotropic problems when the thin direction mesh spacing is much smaller than the broad direction mesh spacing. Within our approach, the first few multigridmore » hierarchy levels are obtained by applying matrix dependent multigrid to semicoarsen in a structured thin direction fashion. After sufficient structured coarsening, the resulting mesh contains only a single layer corresponding to a two-dimensional, unstructured mesh. Algebraic multigrid can then be employed in a standard manner to create further coarse levels, as the anisotropic phenomena is no longer present in the single layer problem. The overall approach remains fully algebraic, with the minor exception that some additional information is needed to determine the extruded direction. Furthermore, this facilitates integration of the solver with a variety of different extruded mesh applications.« less

Annual-ring-type quasi-phase-matching crystal for generation of narrowband high-dimensional entanglement

NASA Astrophysics Data System (ADS)

Hua, Yi-Lin; Zhou, Zong-Quan; Liu, Xiao; Yang, Tian-Shu; Li, Zong-Feng; Li, Pei-Yun; Chen, Geng; Xu, Xiao-Ye; Tang, Jian-Shun; Xu, Jin-Shi; Li, Chuan-Feng; Guo, Guang-Can

2018-01-01

A photon pair can be entangled in many degrees of freedom such as polarization, time bins, and orbital angular momentum (OAM). Among them, the OAM of photons can be entangled in an infinite-dimensional Hilbert space which enhances the channel capacity of sharing information in a network. Twisted photons generated by spontaneous parametric down-conversion offer an opportunity to create this high-dimensional entanglement, but a photon pair generated by this process is typically wideband, which makes it difficult to interface with the quantum memories in a network. Here we propose an annual-ring-type quasi-phase-matching (QPM) crystal for generation of the narrowband high-dimensional entanglement. The structure of the QPM crystal is designed by tracking the geometric divergences of the OAM modes that comprise the entangled state. The dimensionality and the quality of the entanglement can be greatly enhanced with the annual-ring-type QPM crystal.

Non-classical photon correlation in a two-dimensional photonic lattice.

PubMed

Gao, Jun; Qiao, Lu-Feng; Lin, Xiao-Feng; Jiao, Zhi-Qiang; Feng, Zhen; Zhou, Zheng; Gao, Zhen-Wei; Xu, Xiao-Yun; Chen, Yuan; Tang, Hao; Jin, Xian-Min

2016-06-13

Quantum interference and quantum correlation, as two main features of quantum optics, play an essential role in quantum information applications, such as multi-particle quantum walk and boson sampling. While many experimental demonstrations have been done in one-dimensional waveguide arrays, it remains unexplored in higher dimensions due to tight requirement of manipulating and detecting photons in large-scale. Here, we experimentally observe non-classical correlation of two identical photons in a fully coupled two-dimensional structure, i.e. photonic lattice manufactured by three-dimensional femtosecond laser writing. Photon interference consists of 36 Hong-Ou-Mandel interference and 9 bunching. The overlap between measured and simulated distribution is up to 0.890 ± 0.001. Clear photon correlation is observed in the two-dimensional photonic lattice. Combining with controllably engineered disorder, our results open new perspectives towards large-scale implementation of quantum simulation on integrated photonic chips.

Registering 2D and 3D imaging data of bone during healing.

PubMed

Hoerth, Rebecca M; Baum, Daniel; Knötel, David; Prohaska, Steffen; Willie, Bettina M; Duda, Georg N; Hege, Hans-Christian; Fratzl, Peter; Wagermaier, Wolfgang

2015-04-01

PURPOSE/AIMS OF THE STUDY: Bone's hierarchical structure can be visualized using a variety of methods. Many techniques, such as light and electron microscopy generate two-dimensional (2D) images, while micro-computed tomography (µCT) allows a direct representation of the three-dimensional (3D) structure. In addition, different methods provide complementary structural information, such as the arrangement of organic or inorganic compounds. The overall aim of the present study is to answer bone research questions by linking information of different 2D and 3D imaging techniques. A great challenge in combining different methods arises from the fact that they usually reflect different characteristics of the real structure. We investigated bone during healing by means of µCT and a couple of 2D methods. Backscattered electron images were used to qualitatively evaluate the tissue's calcium content and served as a position map for other experimental data. Nanoindentation and X-ray scattering experiments were performed to visualize mechanical and structural properties. We present an approach for the registration of 2D data in a 3D µCT reference frame, where scanning electron microscopies serve as a methodic link. Backscattered electron images are perfectly suited for registration into µCT reference frames, since both show structures based on the same physical principles. We introduce specific registration tools that have been developed to perform the registration process in a semi-automatic way. By applying this routine, we were able to exactly locate structural information (e.g. mineral particle properties) in the 3D bone volume. In bone healing studies this will help to better understand basic formation, remodeling and mineralization processes.

Design and application of BIM based digital sand table for construction management

NASA Astrophysics Data System (ADS)

Fuquan, JI; Jianqiang, LI; Weijia, LIU

2018-05-01

This paper explores the design and application of BIM based digital sand table for construction management. Aiming at the demands and features of construction management plan for bridge and tunnel engineering, the key functional features of digital sand table should include three-dimensional GIS, model navigation, virtual simulation, information layers, and data exchange, etc. That involving the technology of 3D visualization and 4D virtual simulation of BIM, breakdown structure of BIM model and project data, multi-dimensional information layers, and multi-source data acquisition and interaction. Totally, the digital sand table is a visual and virtual engineering information integrated terminal, under the unified data standard system. Also, the applications shall contain visual constructing scheme, virtual constructing schedule, and monitoring of construction, etc. Finally, the applicability of several basic software to the digital sand table is analyzed.

Supervised Machine-Learning-Based Determination of Three-Dimensional Structure of Metallic Nanoparticles

DOE PAGES

Timoshenko, Janis; Lu, Deyu; Lin, Yuewei; ...

2017-09-29

Tracking the structure of heterogeneous catalysts under operando conditions remains a challenge due to the paucity of experimental techniques that can provide atomic-level information for catalytic metal species. Here we report on the use of X-ray absorption near edge structure (XANES) spectroscopy and supervised machine learning (SML) for refining the three-dimensional geometry of metal catalysts. SML is used to unravel the hidden relationship between the XANES features and catalyst geometry. To train our SML method, we rely on ab-initio XANES simulations. Our approach allows one to solve the structure of a metal catalyst from its experimental XANES, as demonstrated heremore » by reconstructing the average size, shape and morphology of well-defined platinum nanoparticles. This method is applicable to the determination of the nanoparticle structure in operando studies and can be generalized to other nanoscale systems. In conclusion, it also allows on-the-fly XANES analysis, and is a promising approach for high-throughput and time-dependent studies.« less

Determination of the three-dimensional structure of oligosaccharides in the solid state from experimental 13C NMR data and ab initio chemical shift surfaces.

PubMed

Sergeyev, Ivan; Moyna, Guillermo

2005-05-02

A novel method for the determination of the three-dimensional (3D) structure of oligosaccharides in the solid state using experimental 13C NMR data is presented. The approach employs this information, combined with 13C chemical shift surfaces (CSSs) for the glycosidic bond carbons in the generation of NMR pseudopotential energy functions suitable for use as constraints in molecular modeling simulations. Application of the method to trehalose, cellobiose, and cellotetraose produces 3D models that agree remarkably well with the reported X-ray structures, with phi and psi dihedral angles that are within 10 degrees from the ones observed in the crystals. The usefulness of the approach is further demonstrated in the determination of the 3D structure of the cellohexaose, an hexasaccharide for which no X-ray data has been reported, as well as in the generation of accurate structural models for cellulose II and amylose V6.

Applications of the Cambridge Structural Database in chemical education1

PubMed Central

Battle, Gary M.; Ferrence, Gregory M.; Allen, Frank H.

2010-01-01

The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal–organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout. PMID:20877495

Supervised Machine-Learning-Based Determination of Three-Dimensional Structure of Metallic Nanoparticles

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

Timoshenko, Janis; Lu, Deyu; Lin, Yuewei

Tracking the structure of heterogeneous catalysts under operando conditions remains a challenge due to the paucity of experimental techniques that can provide atomic-level information for catalytic metal species. Here we report on the use of X-ray absorption near edge structure (XANES) spectroscopy and supervised machine learning (SML) for refining the three-dimensional geometry of metal catalysts. SML is used to unravel the hidden relationship between the XANES features and catalyst geometry. To train our SML method, we rely on ab-initio XANES simulations. Our approach allows one to solve the structure of a metal catalyst from its experimental XANES, as demonstrated heremore » by reconstructing the average size, shape and morphology of well-defined platinum nanoparticles. This method is applicable to the determination of the nanoparticle structure in operando studies and can be generalized to other nanoscale systems. In conclusion, it also allows on-the-fly XANES analysis, and is a promising approach for high-throughput and time-dependent studies.« less

Applications of the Cambridge Structural Database in chemical education.

PubMed

Battle, Gary M; Ferrence, Gregory M; Allen, Frank H

2010-10-01

The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout.

Tail dependence and information flow: Evidence from international equity markets

NASA Astrophysics Data System (ADS)

Al Rahahleh, Naseem; Bhatti, M. Ishaq; Adeinat, Iman

2017-05-01

Bhatti and Nguyen (2012) used the copula approach to measure the tail dependence between a number of international markets. They observed that some country pairs exhibit only left-tail dependence whereas others show only right-tail. However, the flow of information from uni-dimensional (one-tail) to bi-dimensional (two-tails) between various markets was not accounted for. In this study, we address the flow of information of this nature by using the dynamic conditional correlation (DCC-GARCH) model. More specifically, we use various versions of the DCC models to explain the nexus between the information flow of international equity and to explain the stochastic forward vs. backward dynamics of financial markets based on data for a 15-year period comprising 3,782 observations. We observed that the information flow between the US and Hong Kong markets and between the US and Australian markets are bi-directional. We also observed that the DCC model captures a wider co-movement structure and inter-connectedness compared to the symmetric Joe-Clayton copula.

How community has shaped the Protein Data Bank.

PubMed

Berman, Helen M; Kleywegt, Gerard J; Nakamura, Haruki; Markley, John L

2013-09-03

Following several years of community discussion, the Protein Data Bank (PDB) was established in 1971 as a public repository for the coordinates of three-dimensional models of biological macromolecules. Since then, the number, size, and complexity of structural models have continued to grow, reflecting the productivity of structural biology. Managed by the Worldwide PDB organization, the PDB has been able to meet increasing demands for the quantity of structural information and of quality. In addition to providing unrestricted access to structural information, the PDB also works to promote data standards and to raise the profile of structural biology with broader audiences. In this perspective, we describe the history of PDB and the many ways in which the community continues to shape the archive. Copyright © 2013 Elsevier Ltd. All rights reserved.

The use of experimental structures to model protein dynamics.

PubMed

Katebi, Ataur R; Sankar, Kannan; Jia, Kejue; Jernigan, Robert L

2015-01-01

The number of solved protein structures submitted in the Protein Data Bank (PDB) has increased dramatically in recent years. For some specific proteins, this number is very high-for example, there are over 550 solved structures for HIV-1 protease, one protein that is essential for the life cycle of human immunodeficiency virus (HIV) which causes acquired immunodeficiency syndrome (AIDS) in humans. The large number of structures for the same protein and its variants include a sample of different conformational states of the protein. A rich set of structures solved experimentally for the same protein has information buried within the dataset that can explain the functional dynamics and structural mechanism of the protein. To extract the dynamics information and functional mechanism from the experimental structures, this chapter focuses on two methods-Principal Component Analysis (PCA) and Elastic Network Models (ENM). PCA is a widely used statistical dimensionality reduction technique to classify and visualize high-dimensional data. On the other hand, ENMs are well-established simple biophysical method for modeling the functionally important global motions of proteins. This chapter covers the basics of these two. Moreover, an improved ENM version that utilizes the variations found within a given set of structures for a protein is described. As a practical example, we have extracted the functional dynamics and mechanism of HIV-1 protease dimeric structure by using a set of 329 PDB structures of this protein. We have described, step by step, how to select a set of protein structures, how to extract the needed information from the PDB files for PCA, how to extract the dynamics information using PCA, how to calculate ENM modes, how to measure the congruency between the dynamics computed from the principal components (PCs) and the ENM modes, and how to compute entropies using the PCs. We provide the computer programs or references to software tools to accomplish each step and show how to use these programs and tools. We also include computer programs to generate movies based on PCs and ENM modes and describe how to visualize them.

The Use of Experimental Structures to Model Protein Dynamics

PubMed Central

Katebi, Ataur R.; Sankar, Kannan; Jia, Kejue; Jernigan, Robert L.

2014-01-01

Summary The number of solved protein structures submitted in the Protein Data Bank (PDB) has increased dramatically in recent years. For some specific proteins, this number is very high – for example, there are over 550 solved structures for HIV-1 protease, one protein that is essential for the life cycle of human immunodeficiency virus (HIV) which causes acquired immunodeficiency syndrome (AIDS) in humans. The large number of structures for the same protein and its variants include a sample of different conformational states of the protein. A rich set of structures solved experimentally for the same protein has information buried within the dataset that can explain the functional dynamics and structural mechanism of the protein. To extract the dynamics information and functional mechanism from the experimental structures, this chapter focuses on two methods – Principal Component Analysis (PCA) and Elastic Network Models (ENM). PCA is a widely used statistical dimensionality reduction technique to classify and visualize high-dimensional data. On the other hand, ENMs are well-established simple biophysical method for modeling the functionally important global motions of proteins. This chapter covers the basics of these two. Moreover, an improved ENM version that utilizes the variations found within a given set of structures for a protein is described. As a practical example, we have extracted the functional dynamics and mechanism of HIV-1 protease dimeric structure by using a set of 329 PDB structures of this protein. We have described, step by step, how to select a set of protein structures, how to extract the needed information from the PDB files for PCA, how to extract the dynamics information using PCA, how to calculate ENM modes, how to measure the congruency between the dynamics computed from the principal components (PCs) and the ENM modes, and how to compute entropies using the PCs. We provide the computer programs or references to software tools to accomplish each step and show how to use these programs and tools. We also include computer programs to generate movies based on PCs and ENM modes and describe how to visualize them. PMID:25330965

Can Semi-Supervised Learning Explain Incorrect Beliefs about Categories?

ERIC Educational Resources Information Center

Kalish, Charles W.; Rogers, Timothy T.; Lang, Jonathan; Zhu, Xiaojin

2011-01-01

Three experiments with 88 college-aged participants explored how unlabeled experiences--learning episodes in which people encounter objects without information about their category membership--influence beliefs about category structure. Participants performed a simple one-dimensional categorization task in a brief supervised learning phase, then…

Dynamic Imaging of Mouse Embryos and Cardiodynamics in Static Culture.

PubMed

Lopez, Andrew L; Larina, Irina V

2018-01-01

The heart is a dynamic organ that quickly undergoes morphological and mechanical changes through early embryonic development. Characterizing these early moments is important for our understanding of proper embryonic development and the treatment of heart disease. Traditionally, tomographic imaging modalities and fluorescence-based microscopy are excellent approaches to visualize structural features and gene expression patterns, respectively, and connect aberrant gene programs to pathological phenotypes. However, these approaches usually require static samples or fluorescent markers, which can limit how much information we can derive from the dynamic and mechanical changes that regulate heart development. Optical coherence tomography (OCT) is unique in this circumstance because it allows for the acquisition of three-dimensional structural and four-dimensional (3D + time) functional images of living mouse embryos without fixation or contrast reagents. In this chapter, we focus on how OCT can visualize heart morphology at different stages of development and provide cardiodynamic information to reveal mechanical properties of the developing heart.

Two-dimensional fourier transform spectrometer

DOEpatents

DeFlores, Lauren; Tokmakoff, Andrei

2016-10-25

The present invention relates to a system and methods for acquiring two-dimensional Fourier transform (2D FT) spectra. Overlap of a collinear pulse pair and probe induce a molecular response which is collected by spectral dispersion of the signal modulated probe beam. Simultaneous collection of the molecular response, pulse timing and characteristics permit real time phasing and rapid acquisition of spectra. Full spectra are acquired as a function of pulse pair timings and numerically transformed to achieve the full frequency-frequency spectrum. This method demonstrates the ability to acquire information on molecular dynamics, couplings and structure in a simple apparatus. Multi-dimensional methods can be used for diagnostic and analytical measurements in the biological, biomedical, and chemical fields.

Two-dimensional fourier transform spectrometer

DOEpatents

DeFlores, Lauren; Tokmakoff, Andrei

2013-09-03

The present invention relates to a system and methods for acquiring two-dimensional Fourier transform (2D FT) spectra. Overlap of a collinear pulse pair and probe induce a molecular response which is collected by spectral dispersion of the signal modulated probe beam. Simultaneous collection of the molecular response, pulse timing and characteristics permit real time phasing and rapid acquisition of spectra. Full spectra are acquired as a function of pulse pair timings and numerically transformed to achieve the full frequency-frequency spectrum. This method demonstrates the ability to acquire information on molecular dynamics, couplings and structure in a simple apparatus. Multi-dimensional methods can be used for diagnostic and analytical measurements in the biological, biomedical, and chemical fields.

Boundary acquisition for setup of numerical simulation

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

Diegert, C.

1997-12-31

The author presents a work flow diagram that includes a path that begins with taking experimental measurements, and ends with obtaining insight from results produced by numerical simulation. Two examples illustrate this path: (1) Three-dimensional imaging measurement at micron scale, using X-ray tomography, provides information on the boundaries of irregularly-shaped alumina oxide particles held in an epoxy matrix. A subsequent numerical simulation predicts the electrical field concentrations that would occur in the observed particle configurations. (2) Three-dimensional imaging measurement at meter scale, again using X-ray tomography, provides information on the boundaries fossilized bone fragments in a Parasaurolophus crest recently discoveredmore » in New Mexico. A subsequent numerical simulation predicts acoustic response of the elaborate internal structure of nasal passageways defined by the fossil record. The author must both add value, and must change the format of the three-dimensional imaging measurements before the define the geometric boundary initial conditions for the automatic mesh generation, and subsequent numerical simulation. The author applies a variety of filters and statistical classification algorithms to estimate the extents of the structures relevant to the subsequent numerical simulation, and capture these extents as faceted geometries. The author will describe the particular combination of manual and automatic methods used in the above two examples.« less

A review of some problems in global-local stress analysis

NASA Technical Reports Server (NTRS)

Nelson, Richard B.

1989-01-01

The various types of local-global finite-element problems point out the need to develop a new generation of software. First, this new software needs to have a complete analysis capability, encompassing linear and nonlinear analysis of 1-, 2-, and 3-dimensional finite-element models, as well as mixed dimensional models. The software must be capable of treating static and dynamic (vibration and transient response) problems, including the stability effects of initial stress, and the software should be able to treat both elastic and elasto-plastic materials. The software should carry a set of optional diagnostics to assist the program user during model generation in order to help avoid obvious structural modeling errors. In addition, the program software should be well documented so the user has a complete technical reference for each type of element contained in the program library, including information on such topics as the type of numerical integration, use of underintegration, and inclusion of incompatible modes, etc. Some packaged information should also be available to assist the user in building mixed-dimensional models. An important advancement in finite-element software should be in the development of program modularity, so that the user can select from a menu various basic operations in matrix structural analysis.

Three-dimensional distribution of polymorphs and magnesium in a calcified underwater attachment system by diffraction tomography

PubMed Central

Leemreize, Hanna; Almer, Jonathan D.; Stock, Stuart R.; Birkedal, Henrik

2013-01-01

Biological materials display complicated three-dimensional hierarchical structures. Determining these structures is essential in understanding the link between material design and properties. Herein, we show how diffraction tomography can be used to determine the relative placement of the calcium carbonate polymorphs calcite and aragonite in the highly mineralized holdfast system of the bivalve Anomia simplex. In addition to high fidelity and non-destructive mapping of polymorphs, we use detailed analysis of X-ray diffraction peak positions in reconstructed powder diffraction data to determine the local degree of Mg substitution in the calcite phase. These data show how diffraction tomography can provide detailed multi-length scale information on complex materials in general and of biomineralized tissues in particular. PMID:23804437

Side information in coded aperture compressive spectral imaging

NASA Astrophysics Data System (ADS)

Galvis, Laura; Arguello, Henry; Lau, Daniel; Arce, Gonzalo R.

2017-02-01

Coded aperture compressive spectral imagers sense a three-dimensional cube by using two-dimensional projections of the coded and spectrally dispersed source. These imagers systems often rely on FPA detectors, SLMs, micromirror devices (DMDs), and dispersive elements. The use of the DMDs to implement the coded apertures facilitates the capture of multiple projections, each admitting a different coded aperture pattern. The DMD allows not only to collect the sufficient number of measurements for spectrally rich scenes or very detailed spatial scenes but to design the spatial structure of the coded apertures to maximize the information content on the compressive measurements. Although sparsity is the only signal characteristic usually assumed for reconstruction in compressing sensing, other forms of prior information such as side information have been included as a way to improve the quality of the reconstructions. This paper presents the coded aperture design in a compressive spectral imager with side information in the form of RGB images of the scene. The use of RGB images as side information of the compressive sensing architecture has two main advantages: the RGB is not only used to improve the reconstruction quality but to optimally design the coded apertures for the sensing process. The coded aperture design is based on the RGB scene and thus the coded aperture structure exploits key features such as scene edges. Real reconstructions of noisy compressed measurements demonstrate the benefit of the designed coded apertures in addition to the improvement in the reconstruction quality obtained by the use of side information.

A three-dimensional polyhedral unit model for grain boundary structure in fcc metals

NASA Astrophysics Data System (ADS)

Banadaki, Arash Dehghan; Patala, Srikanth

2017-03-01

One of the biggest challenges in developing truly bottom-up models for the performance of polycrystalline materials is the lack of robust quantitative structure-property relationships for interfaces. As a first step in analyzing such relationships, we present a polyhedral unit model to classify the geometrical nature of atomic packing along grain boundaries. While the atomic structure in disordered systems has been a topic of interest for many decades, geometrical analyses of grain boundaries has proven to be particularly challenging because of the wide range of structures that are possible depending on the underlying macroscopic crystallographic character. In this article, we propose an algorithm that can partition the atomic structure into a connected array of three-dimensional polyhedra, and thus, present a three-dimensional polyhedral unit model for grain boundaries. A point-pattern matching algorithm is also provided for quantifying the distortions of the observed grain boundary polyhedral units. The polyhedral unit model is robust enough to capture the structure of high-Σ, mixed character interfaces and, hence, provides a geometric tool for comparing grain boundary structures across the five-parameter crystallographic phase-space. Since the obtained polyhedral units circumscribe the voids present in the structure, such a description provides valuable information concerning segregation sites within the grain boundary. We anticipate that this technique will serve as a powerful tool in the analysis of grain boundary structure. The polyhedral unit model is also applicable to a wide array of material systems as the proposed algorithm is not limited by the underlying lattice structure.

Laser-induced fluorescence imaging of subsurface tissue structures with a volume holographic spatial-spectral imaging system.

PubMed

Luo, Yuan; Gelsinger-Austin, Paul J; Watson, Jonathan M; Barbastathis, George; Barton, Jennifer K; Kostuk, Raymond K

2008-09-15

A three-dimensional imaging system incorporating multiplexed holographic gratings to visualize fluorescence tissue structures is presented. Holographic gratings formed in volume recording materials such as a phenanthrenquinone poly(methyl methacrylate) photopolymer have narrowband angular and spectral transmittance filtering properties that enable obtaining spatial-spectral information within an object. We demonstrate this imaging system's ability to obtain multiple depth-resolved fluorescence images simultaneously.

EDCs DataBank: 3D-Structure database of endocrine disrupting chemicals.

PubMed

Montes-Grajales, Diana; Olivero-Verbel, Jesus

2015-01-02

Endocrine disrupting chemicals (EDCs) are a group of compounds that affect the endocrine system, frequently found in everyday products and epidemiologically associated with several diseases. The purpose of this work was to develop EDCs DataBank, the only database of EDCs with three-dimensional structures. This database was built on MySQL using the EU list of potential endocrine disruptors and TEDX list. It contains the three-dimensional structures available on PubChem, as well as a wide variety of information from different databases and text mining tools, useful for almost any kind of research regarding EDCs. The web platform was developed employing HTML, CSS and PHP languages, with dynamic contents in a graphic environment, facilitating information analysis. Currently EDCs DataBank has 615 molecules, including pesticides, natural and industrial products, cosmetics, drugs and food additives, among other low molecular weight xenobiotics. Therefore, this database can be used to study the toxicological effects of these molecules, or to develop pharmaceuticals targeting hormone receptors, through docking studies, high-throughput virtual screening and ligand-protein interaction analysis. EDCs DataBank is totally user-friendly and the 3D-structures of the molecules can be downloaded in several formats. This database is freely available at http://edcs.unicartagena.edu.co. Copyright © 2014. Published by Elsevier Ireland Ltd.

NASTRAN computer system level 12.1

NASA Technical Reports Server (NTRS)

Butler, T. G.

1971-01-01

Program uses finite element displacement method for solving linear response of large, three-dimensional structures subject to static, dynamic, thermal, and random loadings. Program adapts to computers of different manufacture, permits up-dating and extention, allows interchange of output and input information between users, and is extensively documented.

THE THREE DIMENSIONAL STRUCTURE OF ASPERGILLUS NIGER PECTIN LYASE AT 1.7-A RESOLUTION. (U915444)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

A Glimpse in the Third Dimension for Electrical Resistivity Profiles

NASA Astrophysics Data System (ADS)

Robbins, A. R.; Plattner, A.

2017-12-01

We present an electrode layout strategy designed to enhance the popular two-dimensional electrical resistivity profile. Offsetting electrodes from the traditional linear layout and using 3-D inversion software allows for mapping the three-dimensional electrical resistivity close to the profile plane. We established a series of synthetic tests using simulated data generated from chosen resistivity distributions with a three-dimensional target feature. All inversions and simulations were conducted using freely-available ERT software, BERT and E4D. Synthetic results demonstrate the effectiveness of the offset electrode approach, whereas the linear layout failed to resolve the three-dimensional character of our subsurface feature. A field survey using trench backfill as a known resistivity contrast confirmed our synthetic tests. As we show, 3-D inversions of linear layouts for starting models without previously known structure are futile ventures because they generate symmetric resistivity solutions with respect to the profile plane. This is a consequence of the layout's inherent symmetrical sensitivity patterns. An offset electrode layout is not subject to the same limitation, as the collective measurements do not share a common sensitivity symmetry. For practitioners, this approach presents a low-cost improvement of a traditional geophysical method which is simple to use yet may provide critical information about the three dimensional structure of the subsurface close to the profile.

SequenceCEROSENE: a computational method and web server to visualize spatial residue neighborhoods at the sequence level.

PubMed

Heinke, Florian; Bittrich, Sebastian; Kaiser, Florian; Labudde, Dirk

2016-01-01

To understand the molecular function of biopolymers, studying their structural characteristics is of central importance. Graphics programs are often utilized to conceive these properties, but with the increasing number of available structures in databases or structure models produced by automated modeling frameworks this process requires assistance from tools that allow automated structure visualization. In this paper a web server and its underlying method for generating graphical sequence representations of molecular structures is presented. The method, called SequenceCEROSENE (color encoding of residues obtained by spatial neighborhood embedding), retrieves the sequence of each amino acid or nucleotide chain in a given structure and produces a color coding for each residue based on three-dimensional structure information. From this, color-highlighted sequences are obtained, where residue coloring represent three-dimensional residue locations in the structure. This color encoding thus provides a one-dimensional representation, from which spatial interactions, proximity and relations between residues or entire chains can be deduced quickly and solely from color similarity. Furthermore, additional heteroatoms and chemical compounds bound to the structure, like ligands or coenzymes, are processed and reported as well. To provide free access to SequenceCEROSENE, a web server has been implemented that allows generating color codings for structures deposited in the Protein Data Bank or structure models uploaded by the user. Besides retrieving visualizations in popular graphic formats, underlying raw data can be downloaded as well. In addition, the server provides user interactivity with generated visualizations and the three-dimensional structure in question. Color encoded sequences generated by SequenceCEROSENE can aid to quickly perceive the general characteristics of a structure of interest (or entire sets of complexes), thus supporting the researcher in the initial phase of structure-based studies. In this respect, the web server can be a valuable tool, as users are allowed to process multiple structures, quickly switch between results, and interact with generated visualizations in an intuitive manner. The SequenceCEROSENE web server is available at https://biosciences.hs-mittweida.de/seqcerosene.

Effective Mass Calculations for Two-dimensional Gas of Dipolar Fermions

NASA Astrophysics Data System (ADS)

Seydi, I.; Abedinpour, S. H.; Tanatar, B.

2017-06-01

We consider a two-dimensional system of ultracold dipolar fermions with dipole moments aligned in the perpendicular direction. We use the static structure factor information from Fermi-Hypernetted-Chain calculations to obtain the effective many-body dipole-dipole interaction and calculate the many-body effective mass of the system within the G0W approximation to the self-energy. A large cancellation between different contributions to the self-energy results in a weak dependence of the effective mass on the interaction strength over a large range of coupling constants.

Three-dimensional video imaging of drainage and imbibition processes in model porous medium

NASA Astrophysics Data System (ADS)

Sharma, Prerna; Aswathi, P.; Sane, Anit; Ghosh, Shankar; Bhattacharya, Sabyasachi

2011-03-01

We report experimental results where we have performed three dimensional video imaging of the displacement of an oil phase by an aqueous phase and vice versa in a model porous medium. The stability of the oil water interface was studied as a function of their viscosity ratios, the wettability of the porous medium and the variation in the pore size distribution. Our experiments captures the pore scale information of the displacement process and its role in determining the long time structure of the interface.

Chemical composition and surfactant characteristics of marine foams investigated by means of UV-vis, FTIR and FTNIR spectroscopy.

PubMed

Mecozzi, Mauro; Pietroletti, Marco

2016-11-01

In this study, we collected the ultraviolet-visible (UV-vis), Fourier transform infrared (FTIR) and Fourier transform near-infrared (FTNIR) spectra of marine foams from different sites and foams produced by marine living organisms (i.e. algae and molluscs) to retrieve information about their molecular and structural composition. UV-vis spectra gave information concerning the lipid and pigment contents of foams. FTIR spectroscopy gave a more detailed qualitative information regarding carbohydrates, lipids and proteins in addition with information about the mineral contents of foams. FTNIR spectra confirmed the presence of carbohydrates, lipids and proteins in foams. Then, due to the higher content of structural information of FTIR spectroscopy with respect to FTNIR and UV-vis, we join the FTIR spectra of marine foams to those of humic substance from marine sediments and to the spectra of foams obtained by living organisms. We submitted this resulting FTIR spectral dataset to statistical multivariate methods to investigate specific aspects of foams such as structural similarity among foams and in addition, contributions from the organic matter of living organisms. Cluster analysis (CA) evidenced several cases (i.e. clusters) of marine foams having high structural similarity with foams from vegetal and animal samples and with humic substance extracted from sediments. These results suggested that all the living organisms of the marine environment can give contributions to the chemical composition of foams. Moreover, as CA also evidenced cases of structural differences within foam samples, we applied two-dimensional correlation analysis (2DCORR) to the FTIR spectra of marine foams to investigate the molecular characteristics which caused these structural differences. Asynchronous spectra of two-dimensional correlation analysis showed that the structural heterogeneity among foam samples depended reasonably on the presence and on the qualitative difference of electrostatic (hydrogen bonds) and nonpolar (van der Waals and π-π) interactions involving carbohydrate proteins and lipids present. The presence and relevance of these interactions agree with the supramolecular and surfactant characteristics of marine organic matter described in the scientific literature.

Neural Schematics as a unified formal graphical representation of large-scale Neural Network Structures.

PubMed

Ehrlich, Matthias; Schüffny, René

2013-01-01

One of the major outcomes of neuroscientific research are models of Neural Network Structures (NNSs). Descriptions of these models usually consist of a non-standardized mixture of text, figures, and other means of visual information communication in print media. However, as neuroscience is an interdisciplinary domain by nature, a standardized way of consistently representing models of NNSs is required. While generic descriptions of such models in textual form have recently been developed, a formalized way of schematically expressing them does not exist to date. Hence, in this paper we present Neural Schematics as a concept inspired by similar approaches from other disciplines for a generic two dimensional representation of said structures. After introducing NNSs in general, a set of current visualizations of models of NNSs is reviewed and analyzed for what information they convey and how their elements are rendered. This analysis then allows for the definition of general items and symbols to consistently represent these models as Neural Schematics on a two dimensional plane. We will illustrate the possibilities an agreed upon standard can yield on sampled diagrams transformed into Neural Schematics and an example application for the design and modeling of large-scale NNSs.

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

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

Lewis, Nicholas H. C.; Dong, Hui; Oliver, Thomas A. A.

2015-09-28

Two dimensional electronic spectroscopy has proven to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derivemore » response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.« less

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy

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

Lewis, Nicholas H. C.; Dong, Hui; Oliver, Thomas A. A.

2015-09-28

Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derivemore » response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.« less

A method for the direct measurement of electronic site populations in a molecular aggregate using two-dimensional electronic-vibrational spectroscopy.

PubMed

Lewis, Nicholas H C; Dong, Hui; Oliver, Thomas A A; Fleming, Graham R

2015-09-28

Two dimensional electronic spectroscopy has proved to be a valuable experimental technique to reveal electronic excitation dynamics in photosynthetic pigment-protein complexes, nanoscale semiconductors, organic photovoltaic materials, and many other types of systems. It does not, however, provide direct information concerning the spatial structure and dynamics of excitons. 2D infrared spectroscopy has become a widely used tool for studying structural dynamics but is incapable of directly providing information concerning electronic excited states. 2D electronic-vibrational (2DEV) spectroscopy provides a link between these domains, directly connecting the electronic excitation with the vibrational structure of the system under study. In this work, we derive response functions for the 2DEV spectrum of a molecular dimer and propose a method by which 2DEV spectra could be used to directly measure the electronic site populations as a function of time following the initial electronic excitation. We present results from the response function simulations which show that our proposed approach is substantially valid. This method provides, to our knowledge, the first direct experimental method for measuring the electronic excited state dynamics in the spatial domain, on the molecular scale.

Posterior Parietal Cortex Drives Inferotemporal Activations During Three-Dimensional Object Vision.

PubMed

Van Dromme, Ilse C; Premereur, Elsie; Verhoef, Bram-Ernst; Vanduffel, Wim; Janssen, Peter

2016-04-01

The primate visual system consists of a ventral stream, specialized for object recognition, and a dorsal visual stream, which is crucial for spatial vision and actions. However, little is known about the interactions and information flow between these two streams. We investigated these interactions within the network processing three-dimensional (3D) object information, comprising both the dorsal and ventral stream. Reversible inactivation of the macaque caudal intraparietal area (CIP) during functional magnetic resonance imaging (fMRI) reduced fMRI activations in posterior parietal cortex in the dorsal stream and, surprisingly, also in the inferotemporal cortex (ITC) in the ventral visual stream. Moreover, CIP inactivation caused a perceptual deficit in a depth-structure categorization task. CIP-microstimulation during fMRI further suggests that CIP projects via posterior parietal areas to the ITC in the ventral stream. To our knowledge, these results provide the first causal evidence for the flow of visual 3D information from the dorsal stream to the ventral stream, and identify CIP as a key area for depth-structure processing. Thus, combining reversible inactivation and electrical microstimulation during fMRI provides a detailed view of the functional interactions between the two visual processing streams.

Posterior Parietal Cortex Drives Inferotemporal Activations During Three-Dimensional Object Vision

PubMed Central

Van Dromme, Ilse C.; Premereur, Elsie; Verhoef, Bram-Ernst; Vanduffel, Wim; Janssen, Peter

2016-01-01

The primate visual system consists of a ventral stream, specialized for object recognition, and a dorsal visual stream, which is crucial for spatial vision and actions. However, little is known about the interactions and information flow between these two streams. We investigated these interactions within the network processing three-dimensional (3D) object information, comprising both the dorsal and ventral stream. Reversible inactivation of the macaque caudal intraparietal area (CIP) during functional magnetic resonance imaging (fMRI) reduced fMRI activations in posterior parietal cortex in the dorsal stream and, surprisingly, also in the inferotemporal cortex (ITC) in the ventral visual stream. Moreover, CIP inactivation caused a perceptual deficit in a depth-structure categorization task. CIP-microstimulation during fMRI further suggests that CIP projects via posterior parietal areas to the ITC in the ventral stream. To our knowledge, these results provide the first causal evidence for the flow of visual 3D information from the dorsal stream to the ventral stream, and identify CIP as a key area for depth-structure processing. Thus, combining reversible inactivation and electrical microstimulation during fMRI provides a detailed view of the functional interactions between the two visual processing streams. PMID:27082854

Network-constrained group lasso for high-dimensional multinomial classification with application to cancer subtype prediction.

PubMed

Tian, Xinyu; Wang, Xuefeng; Chen, Jun

2014-01-01

Classic multinomial logit model, commonly used in multiclass regression problem, is restricted to few predictors and does not take into account the relationship among variables. It has limited use for genomic data, where the number of genomic features far exceeds the sample size. Genomic features such as gene expressions are usually related by an underlying biological network. Efficient use of the network information is important to improve classification performance as well as the biological interpretability. We proposed a multinomial logit model that is capable of addressing both the high dimensionality of predictors and the underlying network information. Group lasso was used to induce model sparsity, and a network-constraint was imposed to induce the smoothness of the coefficients with respect to the underlying network structure. To deal with the non-smoothness of the objective function in optimization, we developed a proximal gradient algorithm for efficient computation. The proposed model was compared to models with no prior structure information in both simulations and a problem of cancer subtype prediction with real TCGA (the cancer genome atlas) gene expression data. The network-constrained mode outperformed the traditional ones in both cases.

Local structure-based image decomposition for feature extraction with applications to face recognition.

PubMed

Qian, Jianjun; Yang, Jian; Xu, Yong

2013-09-01

This paper presents a robust but simple image feature extraction method, called image decomposition based on local structure (IDLS). It is assumed that in the local window of an image, the macro-pixel (patch) of the central pixel, and those of its neighbors, are locally linear. IDLS captures the local structural information by describing the relationship between the central macro-pixel and its neighbors. This relationship is represented with the linear representation coefficients determined using ridge regression. One image is actually decomposed into a series of sub-images (also called structure images) according to a local structure feature vector. All the structure images, after being down-sampled for dimensionality reduction, are concatenated into one super-vector. Fisher linear discriminant analysis is then used to provide a low-dimensional, compact, and discriminative representation for each super-vector. The proposed method is applied to face recognition and examined using our real-world face image database, NUST-RWFR, and five popular, publicly available, benchmark face image databases (AR, Extended Yale B, PIE, FERET, and LFW). Experimental results show the performance advantages of IDLS over state-of-the-art algorithms.

Mom's shadow: structure-from-motion in newly hatched chicks as revealed by an imprinting procedure.

PubMed

Mascalzoni, Elena; Regolin, Lucia; Vallortigara, Giorgio

2009-03-01

The ability to recognize three-dimensional objects from two-dimensional (2-D) displays was investigated in domestic chicks, focusing on the role of the object's motion. In Experiment 1 newly hatched chicks, imprinted on a three-dimensional (3-D) object, were allowed to choose between the shadows of the familiar object and of an object never seen before. In Experiments 2 and 3 random-dot displays were used to produce the perception of a solid shape only when set in motion. Overall, the results showed that domestic chicks were able to recognize familiar shapes from 2-D motion stimuli. It is likely that similar general mechanisms underlying the perception of structure-from-motion and the extraction of 3-D information are shared by humans and animals. The present data shows that they occur similarly in birds as known for mammals, two separate vertebrate classes; this possibly indicates a common phylogenetic origin of these processes.

Spontaneous formation of three-dimensionally ordered Bi-rich nanostructures within GaAs1-x Bi x /GaAs quantum wells

NASA Astrophysics Data System (ADS)

Luna, E.; Wu, M.; Hanke, M.; Puustinen, J.; Guina, M.; Trampert, A.

2016-08-01

In this work, we report on the spontaneous formation of ordered arrays of nanometer-sized Bi-rich structures due to lateral composition modulations in Ga(As,Bi)/GaAs quantum wells grown by molecular beam epitaxy. The overall microstructure and chemical distribution is investigated using transmission electron microscopy. The information is complemented by synchrotron x-ray grazing incidence diffraction, which provides insight into the in-plane arrangement. Due to the vertical inheritance of the lateral modulation, the Bi-rich nanostructures eventually shape into a three-dimensional assembly. Whereas the Bi-rich nanostructures are created via two-dimensional phase separation at the growing surface, our results suggest that the process is assisted by Bi segregation which is demonstrated to be strong and more complex than expected, implying both lateral and vertical (surface segregation) mass transport. As demonstrated here, the inherent thermodynamic miscibility gap of Ga(As,Bi) alloys can be exploited to create highly uniform Bi-rich units embedded in a quantum confinement structure.

Framework for SEM contour analysis

NASA Astrophysics Data System (ADS)

Schneider, L.; Farys, V.; Serret, E.; Fenouillet-Beranger, C.

2017-03-01

SEM images provide valuable information about patterning capability. Geometrical properties such as Critical Dimension (CD) can be extracted from them and are used to calibrate OPC models, thus making OPC more robust and reliable. However, there is currently a shortage of appropriate metrology tools to inspect complex two-dimensional patterns in the same way as one would work with simple one-dimensional patterns. In this article we present a full framework for the analysis of SEM images. It has been proven to be fast, reliable and robust for every type of structure, and particularly for two-dimensional structures. To achieve this result, several innovative solutions have been developed and will be presented in the following pages. Firstly, we will present a new noise filter which is used to reduce noise on SEM images, followed by an efficient topography identifier, and finally we will describe the use of a topological skeleton as a measurement tool that can extend CD measurements on all kinds of patterns.

Mapping of photoreceptor dysfunction using high resolution three-dimensional spectral optical coherence tomography

NASA Astrophysics Data System (ADS)

Sikorski, B. L.; Szkulmowski, M.; Kałużny, J. J.; Bajraszewski, T.; Kowalczyk, A.; Wojtkowski, M.

2008-02-01

The ability to obtain reliable information on functional status of photoreceptor layer is essential for assessing vision impairment in patients with macular diseases. The reconstruction of three-dimensional retinal structure in vivo using Spectral Optical Coherence Tomography (Spectral OCT) became possible with a recent progress of the OCT field. Three-dimensional data collected by Spectral OCT devices comprise information on light intensity back-reflected from the junction between photoreceptor outer and inner segments (IS/OS) and thus can be used for evaluating photoreceptors impairment. In this paper, we introduced so called Spectral OCT reflectivity maps - a new method of selecting and displaying the spatial distribution of reflectivity of individual retinal layers. We analyzed the reflectivity of the IS/OS layer in various macular diseases. We have measured eyes of 49 patients with photoreceptor dysfunction in course of age-related macular degeneration, macular holes, central serous chorioretinopathy, acute zonal occult outer retinopathy, multiple evanescent white dot syndrome, acute posterior multifocal placoid pigment epitheliopathy, drug-induced retinopathy and congenital disorders.

Three-dimensional super-resolved live cell imaging through polarized multi-angle TIRF.

PubMed

Zheng, Cheng; Zhao, Guangyuan; Liu, Wenjie; Chen, Youhua; Zhang, Zhimin; Jin, Luhong; Xu, Yingke; Kuang, Cuifang; Liu, Xu

2018-04-01

Measuring three-dimensional nanoscale cellular structures is challenging, especially when the structure is dynamic. Owing to the informative total internal reflection fluorescence (TIRF) imaging under varied illumination angles, multi-angle (MA) TIRF has been examined to offer a nanoscale axial and a subsecond temporal resolution. However, conventional MA-TIRF still performs badly in lateral resolution and fails to characterize the depth image in densely distributed regions. Here, we emphasize the lateral super-resolution in the MA-TIRF, exampled by simply introducing polarization modulation into the illumination procedure. Equipped with a sparsity and accelerated proximal algorithm, we examine a more precise 3D sample structure compared with previous methods, enabling live cell imaging with a temporal resolution of 2 s and recovering high-resolution mitochondria fission and fusion processes. We also shared the recovery program, which is the first open-source recovery code for MA-TIRF, to the best of our knowledge.

Three-Dimensional Integrated Survey for Building Investigations.

PubMed

Costantino, Domenica; Angelini, Maria Giuseppa

2015-11-01

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

NALDB: nucleic acid ligand database for small molecules targeting nucleic acid.

PubMed

Kumar Mishra, Subodh; Kumar, Amit

2016-01-01

Nucleic acid ligand database (NALDB) is a unique database that provides detailed information about the experimental data of small molecules that were reported to target several types of nucleic acid structures. NALDB is the first ligand database that contains ligand information for all type of nucleic acid. NALDB contains more than 3500 ligand entries with detailed pharmacokinetic and pharmacodynamic information such as target name, target sequence, ligand 2D/3D structure, SMILES, molecular formula, molecular weight, net-formal charge, AlogP, number of rings, number of hydrogen bond donor and acceptor, potential energy along with their Ki, Kd, IC50 values. All these details at single platform would be helpful for the development and betterment of novel ligands targeting nucleic acids that could serve as a potential target in different diseases including cancers and neurological disorders. With maximum 255 conformers for each ligand entry, our database is a multi-conformer database and can facilitate the virtual screening process. NALDB provides powerful web-based search tools that make database searching efficient and simplified using option for text as well as for structure query. NALDB also provides multi-dimensional advanced search tool which can screen the database molecules on the basis of molecular properties of ligand provided by database users. A 3D structure visualization tool has also been included for 3D structure representation of ligands. NALDB offers an inclusive pharmacological information and the structurally flexible set of small molecules with their three-dimensional conformers that can accelerate the virtual screening and other modeling processes and eventually complement the nucleic acid-based drug discovery research. NALDB can be routinely updated and freely available on bsbe.iiti.ac.in/bsbe/naldb/HOME.php. Database URL: http://bsbe.iiti.ac.in/bsbe/naldb/HOME.php. © The Author(s) 2016. Published by Oxford University Press.

PACSY, a relational database management system for protein structure and chemical shift analysis.

PubMed

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

2012-10-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

What Can Interfacial Water Molecules Tell Us About Solute Structure?

NASA Astrophysics Data System (ADS)

Willard, Adam

The molecular structure of bulk liquid water reflects a molecular tendency to engage in tetrahedrally coordinated hydrogen bonding. At a solute interface waters preferred three-dimensional hydrogen bonding network must conform to a locally anisotropy interfacial environment. Interfacial water molecules adopt configurations that balance water-solute and water-water interactions. The arrangements of interfacial water molecules, therefore encode information about the effective solute-water interactions. This solute-specific information is difficult to extract, however, because interfacial structure also reflects waters collective response to an anisotropic hydrogen bonding environment. Here I present a methodology for characterizing the molecular-level structure of liquid water interface from simulation data. This method can be used to explore waters static and/or dynamic response to a wide range of chemically and topologically heterogeneous solutes such as proteins.

Why environmental scientists are becoming Bayesians

Treesearch

James S. Clark

2005-01-01

Advances in computational statistics provide a general framework for the high dimensional models typically needed for ecological inference and prediction. Hierarchical Bayes (HB) represents a modelling structure with capacity to exploit diverse sources of information, to accommodate influences that are unknown (or unknowable), and to draw inference on large numbers of...

Modeling Spatial Relationships within a Fuzzy Framework.

ERIC Educational Resources Information Center

Petry, Frederick E.; Cobb, Maria A.

1998-01-01

Presents a model for representing and storing binary topological and directional relationships between 2-dimensional objects that is used to provide a basis for fuzzy querying capabilities. A data structure called an abstract spatial graph (ASG) is defined for the binary relationships that maintains all necessary information regarding topology and…

Classification of trabeculae into three-dimensional rodlike and platelike structures via local inertial anisotropy.

PubMed

Vasilić, Branimir; Rajapakse, Chamith S; Wehrli, Felix W

2009-07-01

Trabecular bone microarchitecture is a significant determinant of the bone's mechanical properties and is thus of major clinical relevance in predicting fracture risk. The three-dimensional nature of trabecular bone is characterized by parameters describing scale, topology, and orientation of structural elements. However, none of the current methods calculates all three types of parameters simultaneously and in three dimensions. Here the authors present a method that produces a continuous classification of voxels as belonging to platelike or rodlike structures that determines their orientation and estimates their thickness. The method, dubbed local inertial anisotropy (LIA), treats the image as a distribution of mass density and the orientation of trabeculae is determined from a locally calculated tensor of inertia at each voxel. The orientation entropies of rods and plates are introduced, which can provide new information about microarchitecture not captured by existing parameters. The robustness of the method to noise corruption, resolution reduction, and image rotation is demonstrated. Further, the method is compared with established three-dimensional parameters including the structure-model index and topological surface-to-curve ratio. Finally, the method is applied to data acquired in a previous translational pilot study showing that the trabecular bone of untreated hypogonadal men is less platelike than that of their eugonadal peers.

Vibrational and mechanical properties of single layer MXene structures: a first-principles investigation

NASA Astrophysics Data System (ADS)

Yorulmaz, Uğur; Özden, Ayberk; Perkgöz, Nihan K.; Ay, Feridun; Sevik, Cem

2016-08-01

MXenes, carbides, nitrides and carbonitrides of early transition metals are the new members of two dimensional materials family given with a formula of {{{M}}}n+1 X n . Recent advances in chemical exfoliation and CVD growth of these crystals together with their promising performance in electrochemical energy storage systems have triggered the interest in these two dimensional structures. In this work, we employ first principles calculations for n = 1 structures of Sc, Ti, Zr, Mo and Hf pristine MXenes and their fully surface terminated forms with F and O. We systematically investigated the dynamical and mechanical stability of both pristine and fully terminated MXene structures to determine the possible MXene candidates for experimental realization. In conjunction with an extensive stability analysis, we report Raman and infrared active mode frequencies for the first time, providing indispensable information for the experimental elaboration of MXene field. After determining dynamically stable MXenes, we provide their phonon dispersion relations, electronic and mechanical properties.

Vibrational and mechanical properties of single layer MXene structures: a first-principles investigation.

PubMed

Yorulmaz, Uğur; Özden, Ayberk; Perkgöz, Nihan K; Ay, Feridun; Sevik, Cem

2016-08-19

MXenes, carbides, nitrides and carbonitrides of early transition metals are the new members of two dimensional materials family given with a formula of [Formula: see text] X n . Recent advances in chemical exfoliation and CVD growth of these crystals together with their promising performance in electrochemical energy storage systems have triggered the interest in these two dimensional structures. In this work, we employ first principles calculations for n = 1 structures of Sc, Ti, Zr, Mo and Hf pristine MXenes and their fully surface terminated forms with F and O. We systematically investigated the dynamical and mechanical stability of both pristine and fully terminated MXene structures to determine the possible MXene candidates for experimental realization. In conjunction with an extensive stability analysis, we report Raman and infrared active mode frequencies for the first time, providing indispensable information for the experimental elaboration of MXene field. After determining dynamically stable MXenes, we provide their phonon dispersion relations, electronic and mechanical properties.

Study of the correlation parameters of the surface structure of disordered semiconductors by the two-dimensional DFA and average mutual information methods

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

Alpatov, A. V.; Vikhrov, S. P.; Rybina, N. V., E-mail: pgnv@mail.ru

The processes of self-organization of the surface structure of hydrogenated amorphous silicon are studied by the methods of fluctuation analysis and average mutual information on the basis of atomic-force-microscopy images of the surface. It is found that all of the structures can be characterized by a correlation vector and represented as a superposition of harmonic components and noise. It is shown that, under variations in the technological parameters of the production of a-Si:H films, the correlation properties of their structure vary as well. As the substrate temperature is increased, the formation of structural irregularities becomes less efficient; in this case,more » the length of the correlation vector and the degree of structural ordering increase. It is shown that the procedure based on the method of fluctuation analysis in combination with the method of average mutual information provides a means for studying the self-organization processes in any structures on different length scales.« less

On the Locality of Transient Electromagnetic Soundings with a Single-Loop Configuration

NASA Astrophysics Data System (ADS)

Barsukov, P. O.; Fainberg, E. B.

2018-03-01

The possibilities of reconstructing two-dimensional (2D) cross sections based on the data of the profile soundings by the transient electromagnetic method (TEM) with a single ungrounded loop are illustrated on three-dimensional (3D) models. The process of reconstruction includes three main steps: transformation of the responses in the depth dependence of resistivity ρ(h) measured along the profile, with their subsequent stitching into the 2D pseudo section; point-by-point one-dimensional (1D) inversion of the responses with the starting model constructed based on the transformations; and correction of the 2D cross section with the use of 2.5-dimensional (2.5D) block inversion. It is shown that single-loop TEM soundings allow studying the geological media within a local domain the lateral dimensions of which are commensurate with the depth of the investigation. The structure of the medium beyond this domain insignificantly affects the sounding results. This locality enables the TEM to reconstruct the geoelectrical structure of the medium from the 2D cross sections with the minimal distortions caused by the lack of information beyond the profile of the transient response measurements.

A one-dimensional model of solid-earth electrical resistivity beneath Florida

USGS Publications Warehouse

Blum, Cletus; Love, Jeffrey J.; Pedrie, Kolby; Bedrosian, Paul A.; Rigler, E. Joshua

2015-11-19

An estimated one-dimensional layered model of electrical resistivity beneath Florida was developed from published geological and geophysical information. The resistivity of each layer is represented by plausible upper and lower bounds as well as a geometric mean resistivity. Corresponding impedance transfer functions, Schmucker-Weidelt transfer functions, apparent resistivity, and phase responses are calculated for inducing geomagnetic frequencies ranging from 10−5 to 100 hertz. The resulting one-dimensional model and response functions can be used to make general estimates of time-varying electric fields associated with geomagnetic storms such as might represent induction hazards for electric-power grid operation. The plausible upper- and lower-bound resistivity structures show the uncertainty, giving a wide range of plausible time-varying electric fields.

Profiling analysis of low molecular weight heparins by multiple heart-cutting two dimensional chromatography with quadruple time-of-flight mass spectrometry.

PubMed

Ouyang, Yilan; Zeng, Yangyang; Rong, Yinxiu; Song, Yue; Shi, Lv; Chen, Bo; Yang, Xinlei; Xu, Naiyu; Linhardt, Robert J; Zhang, Zhenqing

2015-09-01

Low molecular weight heparins (LMWHs) are polydisperse and microheterogenous mixtures of polysaccharides used as anticoagulant drugs. Profiling analysis is important for obtaining deeper insights into the structure of LMWHs. Previous oligosaccharide mapping methods are relatively low resolution and are unable to show an entire picture of the structural complexity of LMWHs. In the current study a profiling method was developed relying on multiple heart-cutting, two-dimensional, ultrahigh performance liquid chromatography with quadruple time-of-flight mass spectrometry. This represents an efficient, automated, and robust approach for profiling LMWHs. Using size-exclusion chromatography and ion-pairing reversed-phase chromatography in a two-dimensional separation, LMW components of different sizes and LMW components of the same size but with different charges and polarities can be resolved, providing a more complete picture of a LMWH. Structural information on each component was then obtained with quadrupole time-of-flight mass spectrometry. More than 80 and 120 oligosaccharides were observed and unambiguously assigned from the LMWHs, nadroparin and enoxaparin, respectively. This method might be useful for quality control of LMWHs and as a powerful tool for heparin-related glycomics.

Unveiling One-Dimensional Supramolecular Structures Formed through π-π Stacking of Phenothiazines by Differential Pulse Voltammetry.

PubMed

Carvalho, Fernando R; Zampieri, Eduardo H; Caetano, Wilker; Silva, Rafael

2017-05-19

Organic-based nanomaterials can be self-assembled by strong and directional intermolecular forces such as π-π interactions. Experimental information about the stability, size, and geometry of the formed structures is very limited for species that easily aggregate, even at very low concentrations. Differential pulse voltammetry (DPV) can unveil the formation, growth, and also the stability window of ordered, one-dimensional, lamellar self-aggregates formed by supramolecular π stacking of phenothiazines at micromolar (10 -6  mol L -1 ) concentrations. The self-diffusion features of the species at different concentrations are determined by DPV and used to probe the π staking process through the concept of the frictional resistance. It is observed that toluidine blue and methylene blue start to self-aggregate around 9 μmol L -1 , and that the self-aggregation process occurs by one-dimensional growth as the concentration of the phenothiazines is increased up to around 170 μmol L -1 for toluidine blue and 200 μmol L -1 for methylene blue. At higher concentrations, the aggregation process leads to structures with lower anisometry. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genetic algorithm-based multi-objective optimal absorber system for three-dimensional seismic structures

NASA Astrophysics Data System (ADS)

Ren, Wenjie; Li, Hongnan; Song, Gangbing; Huo, Linsheng

2009-03-01

The problem of optimizing an absorber system for three-dimensional seismic structures is addressed. The objective is to determine the number and position of absorbers to minimize the coupling effects of translation-torsion of structures at minimum cost. A procedure for a multi-objective optimization problem is developed by integrating a dominance-based selection operator and a dominance-based penalty function method. Based on the two-branch tournament genetic algorithm, the selection operator is constructed by evaluating individuals according to their dominance in one run. The technique guarantees the better performing individual winning its competition, provides a slight selection pressure toward individuals and maintains diversity in the population. Moreover, due to the evaluation for individuals in each generation being finished in one run, less computational effort is taken. Penalty function methods are generally used to transform a constrained optimization problem into an unconstrained one. The dominance-based penalty function contains necessary information on non-dominated character and infeasible position of an individual, essential for success in seeking a Pareto optimal set. The proposed approach is used to obtain a set of non-dominated designs for a six-storey three-dimensional building with shape memory alloy dampers subjected to earthquake.

Self-aligning and compressed autosophy video databases

NASA Astrophysics Data System (ADS)

Holtz, Klaus E.

1993-04-01

Autosophy, an emerging new science, explains `self-assembling structures,' such as crystals or living trees, in mathematical terms. This research provides a new mathematical theory of `learning' and a new `information theory' which permits the growing of self-assembling data network in a computer memory similar to the growing of `data crystals' or `data trees' without data processing or programming. Autosophy databases are educated very much like a human child to organize their own internal data storage. Input patterns, such as written questions or images, are converted to points in a mathematical omni dimensional hyperspace. The input patterns are then associated with output patterns, such as written answers or images. Omni dimensional information storage will result in enormous data compression because each pattern fragment is only stored once. Pattern recognition in the text or image files is greatly simplified by the peculiar omni dimensional storage method. Video databases will absorb input images from a TV camera and associate them with textual information. The `black box' operations are totally self-aligning where the input data will determine their own hyperspace storage locations. Self-aligning autosophy databases may lead to a new generation of brain-like devices.

Molecular design of anticancer drug leads based on three-dimensional quantitative structure-activity relationship.

PubMed

Huang, Xiao Yan; Shan, Zhi Jie; Zhai, Hong Lin; Li, Li Na; Zhang, Xiao Yun

2011-08-22

Heat shock protein 90 (Hsp90) takes part in the developments of several cancers. Novobiocin, a typically C-terminal inhibitor for Hsp90, will probably used as an important anticancer drug in the future. In this work, we explored the valuable information and designed new novobiocin derivatives based on a three-dimensional quantitative structure-activity relationship (3D QSAR). The comparative molecular field analysis and comparative molecular similarity indices analysis models with high predictive capability were established, and their reliabilities are supported by the statistical parameters. Based on the several important influence factors obtained from these models, six new novobiocin derivatives with higher inhibitory activities were designed and confirmed by the molecular simulation with our models, which provide the potential anticancer drug leads for further research.

Collisionless Dynamics and the Cosmic Web

NASA Astrophysics Data System (ADS)

Hahn, Oliver

2016-10-01

I review the nature of three-dimensional collapse in the Zeldovich approximation, how it relates to the underlying nature of the three-dimensional Lagrangian manifold and naturally gives rise to a hierarchical structure formation scenario that progresses through collapse from voids to pancakes, filaments and then halos. I then discuss how variations of the Zeldovich approximation (based on the gravitational or the velocity potential) have been used to define classifications of the cosmic large-scale structure into dynamically distinct parts. Finally, I turn to recent efforts to devise new approaches relying on tessellations of the Lagrangian manifold to follow the fine-grained dynamics of the dark matter fluid into the highly non-linear regime and both extract the maximum amount of information from existing simulations as well as devise new simulation techniques for cold collisionless dynamics.

A topological multilayer model of the human body.

PubMed

Barbeito, Antonio; Painho, Marco; Cabral, Pedro; O'Neill, João

2015-11-04

Geographical information systems deal with spatial databases in which topological models are described with alphanumeric information. Its graphical interfaces implement the multilayer concept and provide powerful interaction tools. In this study, we apply these concepts to the human body creating a representation that would allow an interactive, precise, and detailed anatomical study. A vector surface component of the human body is built using a three-dimensional (3-D) reconstruction methodology. This multilayer concept is implemented by associating raster components with the corresponding vector surfaces, which include neighbourhood topology enabling spatial analysis. A root mean square error of 0.18 mm validated the three-dimensional reconstruction technique of internal anatomical structures. The expansion of the identification and the development of a neighbourhood analysis function are the new tools provided in this model.

Generating Neuron Geometries for Detailed Three-Dimensional Simulations Using AnaMorph.

PubMed

Mörschel, Konstantin; Breit, Markus; Queisser, Gillian

2017-07-01

Generating realistic and complex computational domains for numerical simulations is often a challenging task. In neuroscientific research, more and more one-dimensional morphology data is becoming publicly available through databases. This data, however, only contains point and diameter information not suitable for detailed three-dimensional simulations. In this paper, we present a novel framework, AnaMorph, that automatically generates water-tight surface meshes from one-dimensional point-diameter files. These surface triangulations can be used to simulate the electrical and biochemical behavior of the underlying cell. In addition to morphology generation, AnaMorph also performs quality control of the semi-automatically reconstructed cells coming from anatomical reconstructions. This toolset allows an extension from the classical dimension-reduced modeling and simulation of cellular processes to a full three-dimensional and morphology-including method, leading to novel structure-function interplay studies in the medical field. The developed numerical methods can further be employed in other areas where complex geometries are an essential component of numerical simulations.

Three-dimensional model of the hydrostratigraphy and structure of the area in and around the U.S. Army-Camp Stanley Storage Activity Area, northern Bexar County, Texas

USGS Publications Warehouse

Pantea, Michael P.; Blome, Charles D.; Clark, Allan K.

2014-01-01

A three-dimensional model of the Camp Stanley Storage Activity area defines and illustrates the surface and subsurface hydrostratigraphic architecture of the military base and adjacent areas to the south and west using EarthVision software. The Camp Stanley model contains 11 hydrostratigraphic units in descending order: 1 model layer representing the Edwards aquifer; 1 model layer representing the upper Trinity aquifer; 6 model layers representing the informal hydrostratigraphic units that make up the upper part of the middle Trinity aquifer; and 3 model layers representing each, the Bexar, Cow Creek, and the top of the Hammett of the lower part of the middle Trinity aquifer. The Camp Stanley three-dimensional model includes 14 fault structures that generally trend northeast/southwest. The top of Hammett hydrostratigraphic unit was used to propagate and validate all fault structures and to confirm most of the drill-hole data. Differences between modeled and previously mapped surface geology reflect interpretation of fault relations at depth, fault relations to hydrostratigraphic contacts, and surface digital elevation model simplification to fit the scale of the model. In addition, changes based on recently obtained drill-hole data and field reconnaissance done during the construction of the model. The three-dimensional modeling process revealed previously undetected horst and graben structures in the northeastern and southern parts of the study area. This is atypical, as most faults in the area are en echelon that step down southeasterly to the Gulf Coast. The graben structures may increase the potential for controlling or altering local groundwater flow.

Development of an unstructured solution adaptive method for the quasi-three-dimensional Euler and Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Jiang, Yi-Tsann

1993-01-01

A general solution adaptive scheme-based on a remeshing technique is developed for solving the two-dimensional and quasi-three-dimensional Euler and Favre-averaged Navier-Stokes equations. The numerical scheme is formulated on an unstructured triangular mesh utilizing an edge-based pointer system which defines the edge connectivity of the mesh structure. Jameson's four-stage hybrid Runge-Kutta scheme is used to march the solution in time. The convergence rate is enhanced through the use of local time stepping and implicit residual averaging. As the solution evolves, the mesh is regenerated adaptively using flow field information. Mesh adaptation parameters are evaluated such that an estimated local numerical error is equally distributed over the whole domain. For inviscid flows, the present approach generates a complete unstructured triangular mesh using the advancing front method. For turbulent flows, the approach combines a local highly stretched structured triangular mesh in the boundary layer region with an unstructured mesh in the remaining regions to efficiently resolve the important flow features. One-equation and two-equation turbulence models are incorporated into the present unstructured approach. Results are presented for a wide range of flow problems including two-dimensional multi-element airfoils, two-dimensional cascades, and quasi-three-dimensional cascades. This approach is shown to gain flow resolution in the refined regions while achieving a great reduction in the computational effort and storage requirements since solution points are not wasted in regions where they are not required.

Development of an unstructured solution adaptive method for the quasi-three-dimensional Euler and Navier-Stokes equations

NASA Technical Reports Server (NTRS)

Jiang, Yi-Tsann; Usab, William J., Jr.

1993-01-01

A general solution adaptive scheme based on a remeshing technique is developed for solving the two-dimensional and quasi-three-dimensional Euler and Favre-averaged Navier-Stokes equations. The numerical scheme is formulated on an unstructured triangular mesh utilizing an edge-based pointer system which defines the edge connectivity of the mesh structure. Jameson's four-stage hybrid Runge-Kutta scheme is used to march the solution in time. The convergence rate is enhanced through the use of local time stepping and implicit residual averaging. As the solution evolves, the mesh is regenerated adaptively using flow field information. Mesh adaptation parameters are evaluated such that an estimated local numerical error is equally distributed over the whole domain. For inviscid flows, the present approach generates a complete unstructured triangular mesh using the advancing front method. For turbulent flows, the approach combines a local highly stretched structured triangular mesh in the boundary layer region with an unstructured mesh in the remaining regions to efficiently resolve the important flow features. One-equation and two-equation turbulence models are incorporated into the present unstructured approach. Results are presented for a wide range of flow problems including two-dimensional multi-element airfoils, two-dimensional cascades, and quasi-three-dimensional cascades. This approach is shown to gain flow resolution in the refined regions while achieving a great reduction in the computational effort and storage requirements since solution points are not wasted in regions where they are not required.

Abiological origin of described stromatolites older than 3.2 Ga

NASA Technical Reports Server (NTRS)

Lowe, D. R.

1994-01-01

The three well-documented occurrences of three-dimensional stromatolites older than 3.2 Ga meet most criteria for biogenicity except the presence of fossil bacteria. However, they also show features more consistent with nonbiological origins. Small conical structures in the Strelley Pool chert in the upper part of the Warrawoona Group (3.5-3.2 Ga), Western Australia, lack the structure typical of stromatolites and probably formed mainly through evaporitc precipitation. A domal structure from the North Pole chert, Warrawoona Group, formed by soft-sediment deformation or originally flat layers. Laminated chert containing domal and pseudocolumnar structures in the Onverwacht Group (3.5-3.3 Ga), Barberton Greenstone Belt, South Africa, extends downward into veins and cavities, where it formed through inorganic precipitation. Although bacterial communities were widespread on Earth prior to 3.2 Ga, these particular three-dimensional structures are probably abiotic in origin and do not provide information on the paleobiology or paleoecology of early organisms. The paucity of Archean stromatolites older than 3.2 Ga probably reflects the paucity of known and possibly extant carbonate deposits of this age.

Rational redesign of inhibitors of furin/kexin processing proteases by electrostatic mutations.

PubMed

Cai, Xiao-hui; Zhang, Qing; Ding, Da-fu

2004-12-01

To model the three-dimensional structure and investigate the interaction mechanism of the proprotein convertase furin/kexin and their inhibitors (eglin c mutants). The three-dimensional complex structures of furin/kexin with its inhibitors, eglin c mutants, were generated by modeller program using the newly published X-ray crystallographical structures of mouse furin and yeast kexin as templates. The electrostatic interaction energy of each complex was calculated and the results were compared with the experimentally determined inhibition constants to find the correlation between them. High quality models of furin/kexin-eglin c mutants were obtained and used for calculation of the electrostatic interaction energies between the proteases and their inhibitors. The calculated electrostatic energies of interaction showed a linear correlation to the experimental inhibition constants. The modeled structures give good explanations of the specificity of eglin c mutants to furin/kexin. The electrostatic interactions play important roles in inhibitory activity of eglin c mutants to furin/kexin. The results presented here provided quantitative structural and functional information concerning the role of the charge-charge interactions in the binding of furin/kexin and their inhibitors.

Experimental Retrieval of Target Structure Information from Laser-Induced Rescattered Photoelectron Momentum Distributions

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

Okunishi, M.; Pruemper, G.; Shimada, K.

We have measured two-dimensional photoelectron momentum spectra of Ne, Ar, and Xe generated by 800-nm, 100-fs laser pulses and succeeded in identifying the spectral ridge region (back-rescattered ridges) which marks the location of the returning electrons that have been backscattered at their maximum kinetic energies. We demonstrate that the structural information, in particular the differential elastic scattering cross sections of the target ion by free electrons, can be accurately extracted from the intensity distributions of photoelectrons on the ridges, thus effecting a first step toward laser-induced self-imaging of the target, with unprecedented spatial and temporal resolutions.

Quantification of Soil Pore Structure Based on Minkowski-Functions

NASA Astrophysics Data System (ADS)

Vogel, H.; Weller, U.; Schlüter, S.

2009-05-01

The porous structure in soils and other geologic media is typically a complex 3-dimensional object. Most of the physical material properties including mechanical and hydraulic characteristics are immediately linked to this structure which can be directly observed using non-invasive techniques as e.g. X-ray tomography. It is an old dream and still a formidable challenge to related structural features of porous media to their physical properties. In this contribution we present a scale-invariant concept to quantify pore structure based on a limited set of meaningful morphological functions. They are based on d+1 Minkowski functionals as defined for d-dimensional bodies. These basic quantities are determined as a function of pore size obtained by filter procedures using mathematical morphology. The resulting Minkowski functions provide valuable information on pore size, pore surface area and pore topology having the potential to be linked to physical properties. The theoretical background and the related algorithms are presented and the approach is demonstrated for the structure of an arable topsoil obtained by X-ray micro tomography. We also discuss the fundamental problem of limited resolution which is critical for any attempt to quantify structural features at any scale.

Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Villanueva, Josep; Villegas, Virtudes; Querol, Enrique; Avilés, Francesc X; Serrano, Luis

2002-09-01

In the post-genomic era, several projects focused on the massive experimental resolution of the three-dimensional structures of all the proteins of different organisms have been initiated. Simultaneously, significant progress has been made in the ab initio prediction of protein three-dimensional structure. One of the keys to the success of such a prediction is the use of local information (i.e. secondary structure). Here we describe a new limited proteolysis methodology, based on the use of unspecific exoproteases coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), to map quickly secondary structure elements of a protein from both ends, the N- and C-termini. We show that the proteolytic patterns (mass spectra series) obtained can be interpreted in the light of the conformation and local stability of the analyzed proteins, a direct correlation being observed between the predicted and the experimentally derived protein secondary structure. Further, this methodology can be easily applied to check rapidly the folding state of a protein and characterize mutational effects on protein conformation and stability. Moreover, given global stability information, this methodology allows one to locate the protein regions of increased or decreased conformational stability. All of this can be done with a small fraction of the amount of protein required by most of the other methods for conformational analysis. Thus limited exoproteolysis, together with MALDI-TOF MS, can be a useful tool to achieve quickly the elucidation of protein structure and stability. Copyright 2002 John Wiley & Sons, Ltd.

Simulations of Living Cell Origins Using a Cellular Automata Model

NASA Astrophysics Data System (ADS)

Ishida, Takeshi

2014-04-01

Understanding the generalized mechanisms of cell self-assembly is fundamental for applications in various fields, such as mass producing molecular machines in nanotechnology. Thus, the details of real cellular reaction networks and the necessary conditions for self-organized cells must be elucidated. We constructed a 2-dimensional cellular automata model to investigate the emergence of biological cell formation, which incorporated a looped membrane and a membrane-bound information system (akin to a genetic code and gene expression system). In particular, with an artificial reaction system coupled with a thermal system, the simultaneous formation of a looped membrane and an inner reaction process resulted in a more stable structure. These double structures inspired the primitive biological cell formation process from chemical evolution stage. With a model to simulate cellular self-organization in a 2-dimensional cellular automata model, 3 phenomena could be realized: (1) an inner reaction system developed as an information carrier precursor (akin to DNA); (2) a cell border emerged (akin to a cell membrane); and (3) these cell structures could divide into 2. This double-structured cell was considered to be a primary biological cell. The outer loop evolved toward a lipid bilayer membrane, and inner polymeric particles evolved toward precursor information carriers (evolved toward DNA). This model did not completely clarify all the necessary and sufficient conditions for biological cell self-organization. Further, our virtual cells remained unstable and fragile. However, the "garbage bag model" of Dyson proposed that the first living cells were deficient; thus, it would be reasonable that the earliest cells were more unstable and fragile than the simplest current unicellular organisms.

Simulations of living cell origins using a cellular automata model.

PubMed

Ishida, Takeshi

2014-04-01

Understanding the generalized mechanisms of cell self-assembly is fundamental for applications in various fields, such as mass producing molecular machines in nanotechnology. Thus, the details of real cellular reaction networks and the necessary conditions for self-organized cells must be elucidated. We constructed a 2-dimensional cellular automata model to investigate the emergence of biological cell formation, which incorporated a looped membrane and a membrane-bound information system (akin to a genetic code and gene expression system). In particular, with an artificial reaction system coupled with a thermal system, the simultaneous formation of a looped membrane and an inner reaction process resulted in a more stable structure. These double structures inspired the primitive biological cell formation process from chemical evolution stage. With a model to simulate cellular self-organization in a 2-dimensional cellular automata model, 3 phenomena could be realized: (1) an inner reaction system developed as an information carrier precursor (akin to DNA); (2) a cell border emerged (akin to a cell membrane); and (3) these cell structures could divide into 2. This double-structured cell was considered to be a primary biological cell. The outer loop evolved toward a lipid bilayer membrane, and inner polymeric particles evolved toward precursor information carriers (evolved toward DNA). This model did not completely clarify all the necessary and sufficient conditions for biological cell self-organization. Further, our virtual cells remained unstable and fragile. However, the "garbage bag model" of Dyson proposed that the first living cells were deficient; thus, it would be reasonable that the earliest cells were more unstable and fragile than the simplest current unicellular organisms.

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

PubMed

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

2017-12-01

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

NMR in structural genomics to increase structural coverage of the protein universe: Delivered by Prof. Kurt Wüthrich on 7 July 2013 at the 38th FEBS Congress in St. Petersburg, Russia.

PubMed

Serrano, Pedro; Dutta, Samit K; Proudfoot, Andrew; Mohanty, Biswaranjan; Susac, Lukas; Martin, Bryan; Geralt, Michael; Jaroszewski, Lukasz; Godzik, Adam; Elsliger, Marc; Wilson, Ian A; Wüthrich, Kurt

2016-11-01

For more than a decade, the Joint Center for Structural Genomics (JCSG; www.jcsg.org) worked toward increased three-dimensional structure coverage of the protein universe. This coordinated quest was one of the main goals of the four high-throughput (HT) structure determination centers of the Protein Structure Initiative (PSI; www.nigms.nih.gov/Research/specificareas/PSI). To achieve the goals of the PSI, the JCSG made use of the complementarity of structure determination by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy to increase and diversify the range of targets entering the HT structure determination pipeline. The overall strategy, for both techniques, was to determine atomic resolution structures for representatives of large protein families, as defined by the Pfam database, which had no structural coverage and could make significant contributions to biological and biomedical research. Furthermore, the experimental structures could be leveraged by homology modeling to further expand the structural coverage of the protein universe and increase biological insights. Here, we describe what could be achieved by this structural genomics approach, using as an illustration the contributions from 20 NMR structure determinations out of a total of 98 JCSG NMR structures, which were selected because they are the first three-dimensional structure representations of the respective Pfam protein families. The information from this small sample is representative for the overall results from crystal and NMR structure determination in the JCSG. There are five new folds, which were classified as domains of unknown functions (DUF), three of the proteins could be functionally annotated based on three-dimensional structure similarity with previously characterized proteins, and 12 proteins showed only limited similarity with previous deposits in the Protein Data Bank (PDB) and were classified as DUFs. © 2016 Federation of European Biochemical Societies.

SAIL--stereo-array isotope labeling.

PubMed

Kainosho, Masatsune; Güntert, Peter

2009-11-01

Optimal stereospecific and regiospecific labeling of proteins with stable isotopes enhances the nuclear magnetic resonance (NMR) method for the determination of the three-dimensional protein structures in solution. Stereo-array isotope labeling (SAIL) offers sharpened lines, spectral simplification without loss of information and the ability to rapidly collect and automatically evaluate the structural restraints required to solve a high-quality solution structure for proteins up to twice as large as before. This review gives an overview of stable isotope labeling methods for NMR spectroscopy with proteins and provides an in-depth treatment of the SAIL technology.

Automated method for structural segmentation of nasal airways based on cone beam computed tomography

NASA Astrophysics Data System (ADS)

Tymkovych, Maksym Yu.; Avrunin, Oleg G.; Paliy, Victor G.; Filzow, Maksim; Gryshkov, Oleksandr; Glasmacher, Birgit; Omiotek, Zbigniew; DzierŻak, RóŻa; Smailova, Saule; Kozbekova, Ainur

2017-08-01

The work is dedicated to the segmentation problem of human nasal airways using Cone Beam Computed Tomography. During research, we propose a specialized approach of structured segmentation of nasal airways. That approach use spatial information, symmetrisation of the structures. The proposed stages can be used for construction a virtual three dimensional model of nasal airways and for production full-scale personalized atlases. During research we build the virtual model of nasal airways, which can be used for construction specialized medical atlases and aerodynamics researches.

X-ray coherent scattering tomography of textured material (Conference Presentation)

NASA Astrophysics Data System (ADS)

Zhu, Zheyuan; Pang, Shuo

2017-05-01

Small-angle X-ray scattering (SAXS) measures the signature of angular-dependent coherently scattered X-rays, which contains richer information in material composition and structure compared to conventional absorption-based computed tomography. SAXS image reconstruction method of a 2 or 3 dimensional object based on computed tomography, termed as coherent scattering computed tomography (CSCT), enables the detection of spatially-resolved, material-specific isotropic scattering signature inside an extended object, and provides improved contrast for medical diagnosis, security screening, and material characterization applications. However, traditional CSCT methods assumes materials are fine powders or amorphous, and possess isotropic scattering profiles, which is not generally true for all materials. Anisotropic scatters cannot be captured using conventional CSCT method and result in reconstruction errors. To obtain correct information from the sample, we designed new imaging strategy which incorporates extra degree of detector motion into X-ray scattering tomography for the detection of anisotropic scattered photons from a series of two-dimensional intensity measurements. Using a table-top, narrow-band X-ray source and a panel detector, we demonstrate the anisotropic scattering profile captured from an extended object and the reconstruction of a three-dimensional object. For materials possessing a well-organized crystalline structure with certain symmetry, the scatter texture is more predictable. We will also discuss the compressive schemes and implementation of data acquisition to improve the collection efficiency and accelerate the imaging process.

From protein sequence to dynamics and disorder with DynaMine.

PubMed

Cilia, Elisa; Pancsa, Rita; Tompa, Peter; Lenaerts, Tom; Vranken, Wim F

2013-01-01

Protein function and dynamics are closely related; however, accurate dynamics information is difficult to obtain. Here based on a carefully assembled data set derived from experimental data for proteins in solution, we quantify backbone dynamics properties on the amino-acid level and develop DynaMine--a fast, high-quality predictor of protein backbone dynamics. DynaMine uses only protein sequence information as input and shows great potential in distinguishing regions of different structural organization, such as folded domains, disordered linkers, molten globules and pre-structured binding motifs of different sizes. It also identifies disordered regions within proteins with an accuracy comparable to the most sophisticated existing predictors, without depending on prior disorder knowledge or three-dimensional structural information. DynaMine provides molecular biologists with an important new method that grasps the dynamical characteristics of any protein of interest, as we show here for human p53 and E1A from human adenovirus 5.

PACSY, a relational database management system for protein structure and chemical shift analysis

PubMed Central

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

2012-01-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

For operation of the Computer Software Management and Information Center (COSMIC)

NASA Technical Reports Server (NTRS)

Carmon, J. L.

1983-01-01

Computer programs for large systems of normal equations, an interactive digital signal process, structural analysis of cylindrical thrust chambers, swirling turbulent axisymmetric recirculating flows in practical isothermal combustor geometrics, computation of three dimensional combustor performance, a thermal radiation analysis system, transient response analysis, and a software design analysis are summarized.

THREE-DIMENSIONAL QUANTITATIVE STRUCTURE-PROPERTY RELATIONSHIP (3D-QSPR) MODELS FOR PREDICTION OF THERMODYNAMIC PROPERTIES OF POLYCHLORINATED BIPHENYLS (PCBS): ENTHALPY OF VAPORIZATION. (R826133)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Can genetics help psychometrics? Improving dimensionality assessment through genetic factor modeling.

PubMed

Franić, Sanja; Dolan, Conor V; Borsboom, Denny; Hudziak, James J; van Beijsterveldt, Catherina E M; Boomsma, Dorret I

2013-09-01

In the present article, we discuss the role that quantitative genetic methodology may play in assessing and understanding the dimensionality of psychological (psychometric) instruments. Specifically, we study the relationship between the observed covariance structures, on the one hand, and the underlying genetic and environmental influences giving rise to such structures, on the other. We note that this relationship may be such that it hampers obtaining a clear estimate of dimensionality using standard tools for dimensionality assessment alone. One situation in which dimensionality assessment may be impeded is that in which genetic and environmental influences, of which the observed covariance structure is a function, differ from each other in structure and dimensionality. We demonstrate that in such situations settling dimensionality issues may be problematic, and propose using quantitative genetic modeling to uncover the (possibly different) dimensionalities of the underlying genetic and environmental structures. We illustrate using simulations and an empirical example on childhood internalizing problems.

Big Data Analytics for Scanning Transmission Electron Microscopy Ptychography

NASA Astrophysics Data System (ADS)

Jesse, S.; Chi, M.; Belianinov, A.; Beekman, C.; Kalinin, S. V.; Borisevich, A. Y.; Lupini, A. R.

2016-05-01

Electron microscopy is undergoing a transition; from the model of producing only a few micrographs, through the current state where many images and spectra can be digitally recorded, to a new mode where very large volumes of data (movies, ptychographic and multi-dimensional series) can be rapidly obtained. Here, we discuss the application of so-called “big-data” methods to high dimensional microscopy data, using unsupervised multivariate statistical techniques, in order to explore salient image features in a specific example of BiFeO3 domains. Remarkably, k-means clustering reveals domain differentiation despite the fact that the algorithm is purely statistical in nature and does not require any prior information regarding the material, any coexisting phases, or any differentiating structures. While this is a somewhat trivial case, this example signifies the extraction of useful physical and structural information without any prior bias regarding the sample or the instrumental modality. Further interpretation of these types of results may still require human intervention. However, the open nature of this algorithm and its wide availability, enable broad collaborations and exploratory work necessary to enable efficient data analysis in electron microscopy.

3D Printing of Biomolecular Models for Research and Pedagogy

PubMed Central

Da Veiga Beltrame, Eduardo; Tyrwhitt-Drake, James; Roy, Ian; Shalaby, Raed; Suckale, Jakob; Pomeranz Krummel, Daniel

2017-01-01

The construction of physical three-dimensional (3D) models of biomolecules can uniquely contribute to the study of the structure-function relationship. 3D structures are most often perceived using the two-dimensional and exclusively visual medium of the computer screen. Converting digital 3D molecular data into real objects enables information to be perceived through an expanded range of human senses, including direct stereoscopic vision, touch, and interaction. Such tangible models facilitate new insights, enable hypothesis testing, and serve as psychological or sensory anchors for conceptual information about the functions of biomolecules. Recent advances in consumer 3D printing technology enable, for the first time, the cost-effective fabrication of high-quality and scientifically accurate models of biomolecules in a variety of molecular representations. However, the optimization of the virtual model and its printing parameters is difficult and time consuming without detailed guidance. Here, we provide a guide on the digital design and physical fabrication of biomolecule models for research and pedagogy using open source or low-cost software and low-cost 3D printers that use fused filament fabrication technology. PMID:28362403

Three-Dimensional Model for Preservation and Restoration of Architectural Heritage

NASA Technical Reports Server (NTRS)

Marchis, Elena

2011-01-01

Thc aim of the research will be to create a model, three-dimensional mathematical. implementation. consultation and assistance to "large" restoration projects that will assist the structural analysis, allowing easier display of dynamic strain. analysis and lighting noise. It could also be a valuable tool for decision support. therefore. may simulate several possible scenarios for intervention, This model appears therefore an excellent support for recovering. ordering and monitoring information about materials and data (stage of restoration. photographs. sampling points. results of diagnostic tests, etc.) collected dynamically during the "life" of the cultural heritage. allowing to document its complete history

Micromachined integrated quantum circuit containing a superconducting qubit

NASA Astrophysics Data System (ADS)

Brecht, Teresa; Chu, Yiwen; Axline, Christopher; Pfaff, Wolfgang; Blumoff, Jacob; Chou, Kevin; Krayzman, Lev; Frunzio, Luigi; Schoelkopf, Robert

We demonstrate a functional multilayer microwave integrated quantum circuit (MMIQC). This novel hardware architecture combines the high coherence and isolation of three-dimensional structures with the advantages of integrated circuits made with lithographic techniques. We present fabrication and measurement of a two-cavity/one-qubit prototype, including a transmon coupled to a three-dimensional microwave cavity micromachined in a silicon wafer. It comprises a simple MMIQC with competitive lifetimes and the ability to perform circuit QED operations in the strong dispersive regime. Furthermore, the design and fabrication techniques that we have developed are extensible to more complex quantum information processing devices.

Wave field restoration using three-dimensional Fourier filtering method.

PubMed

Kawasaki, T; Takai, Y; Ikuta, T; Shimizu, R

2001-11-01

A wave field restoration method in transmission electron microscopy (TEM) was mathematically derived based on a three-dimensional (3D) image formation theory. Wave field restoration using this method together with spherical aberration correction was experimentally confirmed in through-focus images of amorphous tungsten thin film, and the resolution of the reconstructed phase image was successfully improved from the Scherzer resolution limit to the information limit. In an application of this method to a crystalline sample, the surface structure of Au(110) was observed in a profile-imaging mode. The processed phase image showed quantitatively the atomic relaxation of the topmost layer.

Volumetric three-dimensional intravascular ultrasound visualization using shape-based nonlinear interpolation

PubMed Central

2013-01-01

Background Intravascular ultrasound (IVUS) is a standard imaging modality for identification of plaque formation in the coronary and peripheral arteries. Volumetric three-dimensional (3D) IVUS visualization provides a powerful tool to overcome the limited comprehensive information of 2D IVUS in terms of complex spatial distribution of arterial morphology and acoustic backscatter information. Conventional 3D IVUS techniques provide sub-optimal visualization of arterial morphology or lack acoustic information concerning arterial structure due in part to low quality of image data and the use of pixel-based IVUS image reconstruction algorithms. In the present study, we describe a novel volumetric 3D IVUS reconstruction algorithm to utilize IVUS signal data and a shape-based nonlinear interpolation. Methods We developed an algorithm to convert a series of IVUS signal data into a fully volumetric 3D visualization. Intermediary slices between original 2D IVUS slices were generated utilizing the natural cubic spline interpolation to consider the nonlinearity of both vascular structure geometry and acoustic backscatter in the arterial wall. We evaluated differences in image quality between the conventional pixel-based interpolation and the shape-based nonlinear interpolation methods using both virtual vascular phantom data and in vivo IVUS data of a porcine femoral artery. Volumetric 3D IVUS images of the arterial segment reconstructed using the two interpolation methods were compared. Results In vitro validation and in vivo comparative studies with the conventional pixel-based interpolation method demonstrated more robustness of the shape-based nonlinear interpolation algorithm in determining intermediary 2D IVUS slices. Our shape-based nonlinear interpolation demonstrated improved volumetric 3D visualization of the in vivo arterial structure and more realistic acoustic backscatter distribution compared to the conventional pixel-based interpolation method. Conclusions This novel 3D IVUS visualization strategy has the potential to improve ultrasound imaging of vascular structure information, particularly atheroma determination. Improved volumetric 3D visualization with accurate acoustic backscatter information can help with ultrasound molecular imaging of atheroma component distribution. PMID:23651569

Three-Dimensional Motion Estimation Using Shading Information in Multiple Frames

DTIC Science & Technology

1989-09-01

j. Threle-D.imensionai GO Motion Estimation U sing, Shadin g Ilnformation in Multiple Frames- IJean-Pierre Schotf MIT Artifi -cial intelligence...vision 3-D structure 3-D vision- shape from shading multiple frames 20. ABSTRACT (Cofrn11,00 an reysrf* OWd Of Rssss00n7 Ad 4111111& F~ block f)nseq See...motion and shading have been treated as two disjoint problems. On the one hand, researchers studying motion or structure from motion often assume

RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA.

PubMed

Martinez, Hugo M; Maizel, Jacob V; Shapiro, Bruce A

2008-06-01

Using primary and secondary structure information of an RNA molecule, the program RNA2D3D automatically and rapidly produces a first-order approximation of a 3-dimensional conformation consistent with this information. Applicable to structures of arbitrary branching complexity and pseudoknot content, it features efficient interactive graphical editing for the removal of any overlaps introduced by the initial generating procedure and for making conformational changes favorable to targeted features and subsequent refinement. With emphasis on fast exploration of alternative 3D conformations, one may interactively add or delete base-pairs, adjacent stems can be coaxially stacked or unstacked, single strands can be shaped to accommodate special constraints, and arbitrary subsets can be defined and manipulated as rigid bodies. Compaction, whereby base stacking within stems is optimally extended into connecting single strands, is also available as a means of strategically making the structures more compact and revealing folding motifs. Subsequent refinement of the first-order approximation, of modifications, and for the imposing of tertiary constraints is assisted with standard energy refinement techniques. Previously determined coordinates for any part of the molecule are readily incorporated, and any part of the modeled structure can be output as a PDB or XYZ file. Illustrative applications in the areas of ribozymes, viral kissing loops, viral internal ribosome entry sites, and nanobiology are presented.

Ullmann-type coupling of brominated tetrathienoanthracene on copper and silver

NASA Astrophysics Data System (ADS)

Gutzler, Rico; Cardenas, Luis; Lipton-Duffin, Josh; El Garah, Mohamed; Dinca, Laurentiu E.; Szakacs, Csaba E.; Fu, Chaoying; Gallagher, Mark; Vondráček, Martin; Rybachuk, Maksym; Perepichka, Dmitrii F.; Rosei, Federico

2014-02-01

We report the synthesis of extended two-dimensional organic networks on Cu(111), Ag(111), Cu(110), and Ag(110) from thiophene-based molecules. A combination of scanning tunnelling microscopy and X-ray photoemission spectroscopy yields insight into the reaction pathways from single molecules towards the formation of two-dimensional organometallic and polymeric structures via Ullmann reaction dehalogenation and C-C coupling. The thermal stability of the molecular networks is probed by annealing at elevated temperatures of up to 500 °C. On Cu(111) only organometallic structures are formed, while on Ag(111) both organometallic and covalent polymeric networks were found to coexist. The ratio between organometallic and covalent bonds could be controlled by means of the annealing temperature. The thiophene moieties start degrading at 200 °C on the copper surface, whereas on silver the degradation process becomes significant only at 400 °C. Our work reveals how the interplay of a specific surface type and temperature steers the formation of organometallic and polymeric networks and describes how these factors influence the structural integrity of two-dimensional organic networks.We report the synthesis of extended two-dimensional organic networks on Cu(111), Ag(111), Cu(110), and Ag(110) from thiophene-based molecules. A combination of scanning tunnelling microscopy and X-ray photoemission spectroscopy yields insight into the reaction pathways from single molecules towards the formation of two-dimensional organometallic and polymeric structures via Ullmann reaction dehalogenation and C-C coupling. The thermal stability of the molecular networks is probed by annealing at elevated temperatures of up to 500 °C. On Cu(111) only organometallic structures are formed, while on Ag(111) both organometallic and covalent polymeric networks were found to coexist. The ratio between organometallic and covalent bonds could be controlled by means of the annealing temperature. The thiophene moieties start degrading at 200 °C on the copper surface, whereas on silver the degradation process becomes significant only at 400 °C. Our work reveals how the interplay of a specific surface type and temperature steers the formation of organometallic and polymeric networks and describes how these factors influence the structural integrity of two-dimensional organic networks. Electronic supplementary information (ESI) available: Additional STM data and DFT results. See DOI: 10.1039/c3nr05710k

Joint spatial-spectral hyperspectral image clustering using block-diagonal amplified affinity matrix

NASA Astrophysics Data System (ADS)

Fan, Lei; Messinger, David W.

2018-03-01

The large number of spectral channels in a hyperspectral image (HSI) produces a fine spectral resolution to differentiate between materials in a scene. However, difficult classes that have similar spectral signatures are often confused while merely exploiting information in the spectral domain. Therefore, in addition to spectral characteristics, the spatial relationships inherent in HSIs should also be considered for incorporation into classifiers. The growing availability of high spectral and spatial resolution of remote sensors provides rich information for image clustering. Besides the discriminating power in the rich spectrum, contextual information can be extracted from the spatial domain, such as the size and the shape of the structure to which one pixel belongs. In recent years, spectral clustering has gained popularity compared to other clustering methods due to the difficulty of accurate statistical modeling of data in high dimensional space. The joint spatial-spectral information could be effectively incorporated into the proximity graph for spectral clustering approach, which provides a better data representation by discovering the inherent lower dimensionality from the input space. We embedded both spectral and spatial information into our proposed local density adaptive affinity matrix, which is able to handle multiscale data by automatically selecting the scale of analysis for every pixel according to its neighborhood of the correlated pixels. Furthermore, we explored the "conductivity method," which aims at amplifying the block diagonal structure of the affinity matrix to further improve the performance of spectral clustering on HSI datasets.

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

PubMed

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

2014-01-01

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

Creating Physical 3D Stereolithograph Models of Brain and Skull

PubMed Central

Kelley, Daniel J.; Farhoud, Mohammed; Meyerand, M. Elizabeth; Nelson, David L.; Ramirez, Lincoln F.; Dempsey, Robert J.; Wolf, Alan J.; Alexander, Andrew L.; Davidson, Richard J.

2007-01-01

The human brain and skull are three dimensional (3D) anatomical structures with complex surfaces. However, medical images are often two dimensional (2D) and provide incomplete visualization of structural morphology. To overcome this loss in dimension, we developed and validated a freely available, semi-automated pathway to build 3D virtual reality (VR) and hand-held, stereolithograph models. To evaluate whether surface visualization in 3D was more informative than in 2D, undergraduate students (n = 50) used the Gillespie scale to rate 3D VR and physical models of both a living patient-volunteer's brain and the skull of Phineas Gage, a historically famous railroad worker whose misfortune with a projectile tamping iron provided the first evidence of a structure-function relationship in brain. Using our processing pathway, we successfully fabricated human brain and skull replicas and validated that the stereolithograph model preserved the scale of the VR model. Based on the Gillespie ratings, students indicated that the biological utility and quality of visual information at the surface of VR and stereolithograph models were greater than the 2D images from which they were derived. The method we developed is useful to create VR and stereolithograph 3D models from medical images and can be used to model hard or soft tissue in living or preserved specimens. Compared to 2D images, VR and stereolithograph models provide an extra dimension that enhances both the quality of visual information and utility of surface visualization in neuroscience and medicine. PMID:17971879

A quadratically regularized functional canonical correlation analysis for identifying the global structure of pleiotropy with NGS data

PubMed Central

Zhu, Yun; Fan, Ruzong; Xiong, Momiao

2017-01-01

Investigating the pleiotropic effects of genetic variants can increase statistical power, provide important information to achieve deep understanding of the complex genetic structures of disease, and offer powerful tools for designing effective treatments with fewer side effects. However, the current multiple phenotype association analysis paradigm lacks breadth (number of phenotypes and genetic variants jointly analyzed at the same time) and depth (hierarchical structure of phenotype and genotypes). A key issue for high dimensional pleiotropic analysis is to effectively extract informative internal representation and features from high dimensional genotype and phenotype data. To explore correlation information of genetic variants, effectively reduce data dimensions, and overcome critical barriers in advancing the development of novel statistical methods and computational algorithms for genetic pleiotropic analysis, we proposed a new statistic method referred to as a quadratically regularized functional CCA (QRFCCA) for association analysis which combines three approaches: (1) quadratically regularized matrix factorization, (2) functional data analysis and (3) canonical correlation analysis (CCA). Large-scale simulations show that the QRFCCA has a much higher power than that of the ten competing statistics while retaining the appropriate type 1 errors. To further evaluate performance, the QRFCCA and ten other statistics are applied to the whole genome sequencing dataset from the TwinsUK study. We identify a total of 79 genes with rare variants and 67 genes with common variants significantly associated with the 46 traits using QRFCCA. The results show that the QRFCCA substantially outperforms the ten other statistics. PMID:29040274

Concept mapping as an approach for expert-guided model building: The example of health literacy.

PubMed

Soellner, Renate; Lenartz, Norbert; Rudinger, Georg

2017-02-01

Concept mapping served as the starting point for the aim of capturing the comprehensive structure of the construct of 'health literacy.' Ideas about health literacy were generated by 99 experts and resulted in 105 statements that were subsequently organized by 27 experts in an unstructured card sorting. Multidimensional scaling was applied to the sorting data and a two and three-dimensional solution was computed. The three dimensional solution was used in subsequent cluster analysis and resulted in a concept map of nine "clusters": (1) self-regulation, (2) self-perception, (3) proactive approach to health, (4) basic literacy and numeracy skills, (5) information appraisal, (6) information search, (7) health care system knowledge and acting, (8) communication and cooperation, and (9) beneficial personality traits. Subsequently, this concept map served as a starting point for developing a "qualitative" structural model of health literacy and a questionnaire for the measurement of health literacy. On the basis of questionnaire data, a "quantitative" structural model was created by first applying exploratory factor analyses (EFA) and then cross-validating the model with confirmatory factor analyses (CFA). Concept mapping proved to be a highly valuable tool for the process of model building up to translational research in the "real world". Copyright © 2016 Elsevier Ltd. All rights reserved.

A discrete Fourier-encoded, diagonal-free experiment to simplify homonuclear 2D NMR correlations.

PubMed

Huang, Zebin; Guan, Quanshuai; Chen, Zhong; Frydman, Lucio; Lin, Yulan

2017-07-21

Nuclear magnetic resonance (NMR) spectroscopy has long served as an irreplaceable, versatile tool in physics, chemistry, biology, and materials sciences, owing to its ability to study molecular structure and dynamics in detail. In particular, the connectivity of chemical sites within molecules, and thereby molecular structure, becomes visible by multi-dimensional NMR. Homonuclear correlation experiments are a powerful tool for identifying coupled spins. Generally, diagonal peaks in these correlation spectra display the strongest intensities and do not offer any new information beyond the standard one-dimensional spectrum, whereas weaker, symmetrically placed cross peaks contain most of the coupling information. The cross peaks near the diagonal are often affected by the tails of strong diagonal peaks or even obscured entirely by the diagonal. In this paper, we demonstrate a homonuclear encoding approach based on imparting a discrete phase modulation of the targeted cross peaks and combine it with a site-selective sculpting scheme, capable of simplifying the patterns arising in these 2D correlation spectra. The theoretical principles of the new methods are laid out, and experimental observations are rationalized on the basis of theoretical analyses. The ensuing techniques provide a new way to retrieve 2D coupling information within homonuclear spin systems, with enhanced sensitivity, speed, and clarity.

A discrete Fourier-encoded, diagonal-free experiment to simplify homonuclear 2D NMR correlations

NASA Astrophysics Data System (ADS)

Huang, Zebin; Guan, Quanshuai; Chen, Zhong; Frydman, Lucio; Lin, Yulan

2017-07-01

Nuclear magnetic resonance (NMR) spectroscopy has long served as an irreplaceable, versatile tool in physics, chemistry, biology, and materials sciences, owing to its ability to study molecular structure and dynamics in detail. In particular, the connectivity of chemical sites within molecules, and thereby molecular structure, becomes visible by multi-dimensional NMR. Homonuclear correlation experiments are a powerful tool for identifying coupled spins. Generally, diagonal peaks in these correlation spectra display the strongest intensities and do not offer any new information beyond the standard one-dimensional spectrum, whereas weaker, symmetrically placed cross peaks contain most of the coupling information. The cross peaks near the diagonal are often affected by the tails of strong diagonal peaks or even obscured entirely by the diagonal. In this paper, we demonstrate a homonuclear encoding approach based on imparting a discrete phase modulation of the targeted cross peaks and combine it with a site-selective sculpting scheme, capable of simplifying the patterns arising in these 2D correlation spectra. The theoretical principles of the new methods are laid out, and experimental observations are rationalized on the basis of theoretical analyses. The ensuing techniques provide a new way to retrieve 2D coupling information within homonuclear spin systems, with enhanced sensitivity, speed, and clarity.

Assessment of Schrodinger Eigenmaps for target detection

NASA Astrophysics Data System (ADS)

Dorado Munoz, Leidy P.; Messinger, David W.; Czaja, Wojtek

2014-06-01

Non-linear dimensionality reduction methods have been widely applied to hyperspectral imagery due to its structure as the information can be represented in a lower dimension without losing information, and because the non-linear methods preserve the local geometry of the data while the dimension is reduced. One of these methods is Laplacian Eigenmaps (LE), which assumes that the data lies on a low dimensional manifold embedded in a high dimensional space. LE builds a nearest neighbor graph, computes its Laplacian and performs the eigendecomposition of the Laplacian. These eigenfunctions constitute a basis for the lower dimensional space in which the geometry of the manifold is preserved. In addition to the reduction problem, LE has been widely used in tasks such as segmentation, clustering, and classification. In this regard, a new Schrodinger Eigenmaps (SE) method was developed and presented as a semi-supervised classification scheme in order to improve the classification performance and take advantage of the labeled data. SE is an algorithm built upon LE, where the former Laplacian operator is replaced by the Schrodinger operator. The Schrodinger operator includes a potential term V, that, taking advantage of the additional information such as labeled data, allows clustering of similar points. In this paper, we explore the idea of using SE in target detection. In this way, we present a framework where the potential term V is defined as a barrier potential: a diagonal matrix encoding the spatial position of the target, and the detection performance is evaluated by using different targets and different hyperspectral scenes.

Replace-approximation method for ambiguous solutions in factor analysis of ultrasonic hepatic perfusion

NASA Astrophysics Data System (ADS)

Zhang, Ji; Ding, Mingyue; Yuchi, Ming; Hou, Wenguang; Ye, Huashan; Qiu, Wu

2010-03-01

Factor analysis is an efficient technique to the analysis of dynamic structures in medical image sequences and recently has been used in contrast-enhanced ultrasound (CEUS) of hepatic perfusion. Time-intensity curves (TICs) extracted by factor analysis can provide much more diagnostic information for radiologists and improve the diagnostic rate of focal liver lesions (FLLs). However, one of the major drawbacks of factor analysis of dynamic structures (FADS) is nonuniqueness of the result when only the non-negativity criterion is used. In this paper, we propose a new method of replace-approximation based on apex-seeking for ambiguous FADS solutions. Due to a partial overlap of different structures, factor curves are assumed to be approximately replaced by the curves existing in medical image sequences. Therefore, how to find optimal curves is the key point of the technique. No matter how many structures are assumed, our method always starts to seek apexes from one-dimensional space where the original high-dimensional data is mapped. By finding two stable apexes from one dimensional space, the method can ascertain the third one. The process can be continued until all structures are found. This technique were tested on two phantoms of blood perfusion and compared to the two variants of apex-seeking method. The results showed that the technique outperformed two variants in comparison of region of interest measurements from phantom data. It can be applied to the estimation of TICs derived from CEUS images and separation of different physiological regions in hepatic perfusion.

Sampling and Visualizing Creases with Scale-Space Particles

PubMed Central

Kindlmann, Gordon L.; Estépar, Raúl San José; Smith, Stephen M.; Westin, Carl-Fredrik

2010-01-01

Particle systems have gained importance as a methodology for sampling implicit surfaces and segmented objects to improve mesh generation and shape analysis. We propose that particle systems have a significantly more general role in sampling structure from unsegmented data. We describe a particle system that computes samplings of crease features (i.e. ridges and valleys, as lines or surfaces) that effectively represent many anatomical structures in scanned medical data. Because structure naturally exists at a range of sizes relative to the image resolution, computer vision has developed the theory of scale-space, which considers an n-D image as an (n + 1)-D stack of images at different blurring levels. Our scale-space particles move through continuous four-dimensional scale-space according to spatial constraints imposed by the crease features, a particle-image energy that draws particles towards scales of maximal feature strength, and an inter-particle energy that controls sampling density in space and scale. To make scale-space practical for large three-dimensional data, we present a spline-based interpolation across scale from a small number of pre-computed blurrings at optimally selected scales. The configuration of the particle system is visualized with tensor glyphs that display information about the local Hessian of the image, and the scale of the particle. We use scale-space particles to sample the complex three-dimensional branching structure of airways in lung CT, and the major white matter structures in brain DTI. PMID:19834216

Protein Engineering Approaches in the Post-Genomic Era.

PubMed

Singh, Raushan K; Lee, Jung-Kul; Selvaraj, Chandrabose; Singh, Ranjitha; Li, Jinglin; Kim, Sang-Yong; Kalia, Vipin C

2018-01-01

Proteins are one of the most multifaceted macromolecules in living systems. Proteins have evolved to function under physiological conditions and, therefore, are not usually tolerant of harsh experimental and environmental conditions. The growing use of proteins in industrial processes as a greener alternative to chemical catalysts often demands constant innovation to improve their performance. Protein engineering aims to design new proteins or modify the sequence of a protein to create proteins with new or desirable functions. With the emergence of structural and functional genomics, protein engineering has been invigorated in the post-genomic era. The three-dimensional structures of proteins with known functions facilitate protein engineering approaches to design variants with desired properties. There are three major approaches of protein engineering research, namely, directed evolution, rational design, and de novo design. Rational design is an effective method of protein engineering when the threedimensional structure and mechanism of the protein is well known. In contrast, directed evolution does not require extensive information and a three-dimensional structure of the protein of interest. Instead, it involves random mutagenesis and selection to screen enzymes with desired properties. De novo design uses computational protein design algorithms to tailor synthetic proteins by using the three-dimensional structures of natural proteins and their folding rules. The present review highlights and summarizes recent protein engineering approaches, and their challenges and limitations in the post-genomic era. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Rational Protein Engineering Guided by Deep Mutational Scanning

PubMed Central

Shin, HyeonSeok; Cho, Byung-Kwan

2015-01-01

Sequence–function relationship in a protein is commonly determined by the three-dimensional protein structure followed by various biochemical experiments. However, with the explosive increase in the number of genome sequences, facilitated by recent advances in sequencing technology, the gap between protein sequences available and three-dimensional structures is rapidly widening. A recently developed method termed deep mutational scanning explores the functional phenotype of thousands of mutants via massive sequencing. Coupled with a highly efficient screening system, this approach assesses the phenotypic changes made by the substitution of each amino acid sequence that constitutes a protein. Such an informational resource provides the functional role of each amino acid sequence, thereby providing sufficient rationale for selecting target residues for protein engineering. Here, we discuss the current applications of deep mutational scanning and consider experimental design. PMID:26404267

A coarse-grained Monte Carlo approach to diffusion processes in metallic nanoparticles

NASA Astrophysics Data System (ADS)

Hauser, Andreas W.; Schnedlitz, Martin; Ernst, Wolfgang E.

2017-06-01

A kinetic Monte Carlo approach on a coarse-grained lattice is developed for the simulation of surface diffusion processes of Ni, Pd and Au structures with diameters in the range of a few nanometers. Intensity information obtained via standard two-dimensional transmission electron microscopy imaging techniques is used to create three-dimensional structure models as input for a cellular automaton. A series of update rules based on reaction kinetics is defined to allow for a stepwise evolution in time with the aim to simulate surface diffusion phenomena such as Rayleigh breakup and surface wetting. The material flow, in our case represented by the hopping of discrete portions of metal on a given grid, is driven by the attempt to minimize the surface energy, which can be achieved by maximizing the number of filled neighbor cells.

Practical application of stereological methods in experimental kidney animal models.

PubMed

Fernández García, María Teresa; Núñez Martínez, Paula; García de la Fuente, Vanessa; Sánchez Pitiot, Marta; Muñiz Salgueiro, María Del Carmen; Perillán Méndez, Carmen; Argüelles Luis, Juan; Astudillo González, Aurora

The kidneys are vital organs responsible for excretion, fluid and electrolyte balance and hormone production. The nephrons are the kidney's functional and structural units. The number, size and distribution of the nephron components contain relevant information on renal function. Stereology is a branch of morphometry that applies mathematical principles to obtain three-dimensional information from serial, parallel and equidistant two-dimensional microscopic sections. Because of the complexity of stereological studies and the lack of scientific literature on the subject, the aim of this paper is to clearly explain, through animal models, the basic concepts of stereology and how to calculate the main kidney stereological parameters that can be applied in future experimental studies. Copyright © 2016 Sociedad Española de Nefrología. Published by Elsevier España, S.L.U. All rights reserved.

Target recognition and scene interpretation in image/video understanding systems based on network-symbolic models

NASA Astrophysics Data System (ADS)

Kuvich, Gary

2004-08-01

Vision is only a part of a system that converts visual information into knowledge structures. These structures drive the vision process, resolving ambiguity and uncertainty via feedback, and provide image understanding, which is an interpretation of visual information in terms of these knowledge models. These mechanisms provide a reliable recognition if the object is occluded or cannot be recognized as a whole. It is hard to split the entire system apart, and reliable solutions to the target recognition problems are possible only within the solution of a more generic Image Understanding Problem. Brain reduces informational and computational complexities, using implicit symbolic coding of features, hierarchical compression, and selective processing of visual information. Biologically inspired Network-Symbolic representation, where both systematic structural/logical methods and neural/statistical methods are parts of a single mechanism, is the most feasible for such models. It converts visual information into relational Network-Symbolic structures, avoiding artificial precise computations of 3-dimensional models. Network-Symbolic Transformations derive abstract structures, which allows for invariant recognition of an object as exemplar of a class. Active vision helps creating consistent models. Attention, separation of figure from ground and perceptual grouping are special kinds of network-symbolic transformations. Such Image/Video Understanding Systems will be reliably recognizing targets.

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures

PubMed Central

2010-01-01

Background Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. Description RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl. Conclusions RNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field. PMID:20459631

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures.

PubMed

Popenda, Mariusz; Szachniuk, Marta; Blazewicz, Marek; Wasik, Szymon; Burke, Edmund K; Blazewicz, Jacek; Adamiak, Ryszard W

2010-05-06

Recent discoveries concerning novel functions of RNA, such as RNA interference, have contributed towards the growing importance of the field. In this respect, a deeper knowledge of complex three-dimensional RNA structures is essential to understand their new biological functions. A number of bioinformatic tools have been proposed to explore two major structural databases (PDB, NDB) in order to analyze various aspects of RNA tertiary structures. One of these tools is RNA FRABASE 1.0, the first web-accessible database with an engine for automatic search of 3D fragments within PDB-derived RNA structures. This search is based upon the user-defined RNA secondary structure pattern. In this paper, we present and discuss RNA FRABASE 2.0. This second version of the system represents a major extension of this tool in terms of providing new data and a wide spectrum of novel functionalities. An intuitionally operated web server platform enables very fast user-tailored search of three-dimensional RNA fragments, their multi-parameter conformational analysis and visualization. RNA FRABASE 2.0 has stored information on 1565 PDB-deposited RNA structures, including all NMR models. The RNA FRABASE 2.0 search engine algorithms operate on the database of the RNA sequences and the new library of RNA secondary structures, coded in the dot-bracket format extended to hold multi-stranded structures and to cover residues whose coordinates are missing in the PDB files. The library of RNA secondary structures (and their graphics) is made available. A high level of efficiency of the 3D search has been achieved by introducing novel tools to formulate advanced searching patterns and to screen highly populated tertiary structure elements. RNA FRABASE 2.0 also stores data and conformational parameters in order to provide "on the spot" structural filters to explore the three-dimensional RNA structures. An instant visualization of the 3D RNA structures is provided. RNA FRABASE 2.0 is freely available at http://rnafrabase.cs.put.poznan.pl. RNA FRABASE 2.0 provides a novel database and powerful search engine which is equipped with new data and functionalities that are unavailable elsewhere. Our intention is that this advanced version of the RNA FRABASE will be of interest to all researchers working in the RNA field.

High-resolution three-dimensional structural microscopy by single-angle Bragg ptychography

DOE PAGES

Hruszkewycz, S. O.; Allain, M.; Holt, M. V.; ...

2016-11-21

Coherent X-ray microscopy by phase retrieval of Bragg diffraction intensities enables lattice distortions within a crystal to be imaged at nanometre-scale spatial resolutions in three dimensions. While this capability can be used to resolve structure–property relationships at the nanoscale under working conditions, strict data measurement requirements can limit the application of current approaches. Here, in this work, we introduce an efficient method of imaging three-dimensional (3D) nanoscale lattice behaviour and strain fields in crystalline materials with a methodology that we call 3D Bragg projection ptychography (3DBPP). This method enables 3D image reconstruction of a crystal volume from a series ofmore » two-dimensional X-ray Bragg coherent intensity diffraction patterns measured at a single incident beam angle. Structural information about the sample is encoded along two reciprocal-space directions normal to the Bragg diffracted exit beam, and along the third dimension in real space by the scanning beam. Finally, we present our approach with an analytical derivation, a numerical demonstration, and an experimental reconstruction of lattice distortions in a component of a nanoelectronic prototype device.« less

Three-dimensional HDlive imaging of an umbilical cord cyst.

PubMed

Inubashiri, Eisuke; Nishiyama, Naomi; Tatedo, Sayuri; Minami, Hiina; Saitou, Atushi; Watanabe, Yukio; Sugawara, Masaki

2018-04-01

Umbilical cord cysts (UCC) are a rare congenital malformation. Previous reports have suggested that the second- and third-trimester UCC may be associated with other structural anomalies or chromosomal abnormalities. Therefore, high-quality imaging is clinically important for the antenatal diagnosis of UCC and to conduct a precise anatomical survey of intrauterine abnormalities. There have been few reports of antenatal diagnosis of UCC with the conventional two- and three-dimensional ultrasonography. In this report, we demonstrate the novel visual depiction of UCC in utero with three-dimensional HDlive imaging, which helps substantially with prenatal diagnosis. A case with an abnormal placental mass at 16 weeks and 5 days of gestation was observed in detail using HDlive. HDlive revealed very realistic images of the intrauterine abnormality: the oval lesion was smooth with regular contours and a homogenous wall at the site of cord insertion on the placenta. In addition, we confirmed the absent of umbilical cord, placental, and fetal structural anomalies. Here, we report a case wherein HDlive may have provided clinically valuable information for prenatal diagnosis of UCC and offered a potential advantage relative to the conventional US.

A metallo-DNA nanowire with uninterrupted one-dimensional silver array

NASA Astrophysics Data System (ADS)

Kondo, Jiro; Tada, Yoshinari; Dairaku, Takenori; Hattori, Yoshikazu; Saneyoshi, Hisao; Ono, Akira; Tanaka, Yoshiyuki

2017-10-01

The double-helix structure of DNA, in which complementary strands reversibly hybridize to each other, not only explains how genetic information is stored and replicated, but also has proved very attractive for the development of nanomaterials. The discovery of metal-mediated base pairs has prompted the generation of short metal-DNA hybrid duplexes by a bottom-up approach. Here we describe a metallo-DNA nanowire—whose structure was solved by high-resolution X-ray crystallography—that consists of dodecamer duplexes held together by four different metal-mediated base pairs (the previously observed C-Ag-C, as well as G-Ag-G, G-Ag-C and T-Ag-T) and linked to each other through G overhangs involved in interduplex G-Ag-G. The resulting hybrid nanowires are 2 nm wide with a length of the order of micrometres to millimetres, and hold the silver ions in uninterrupted one-dimensional arrays along the DNA helical axis. The hybrid nanowires are further assembled into three-dimensional lattices by interactions between adenine residues, fully bulged out of the double helix.

Beyond comorbidity: Toward a dimensional and hierarchal approach to understanding psychopathology across the lifespan

PubMed Central

Forbes, Miriam K.; Tackett, Jennifer L.; Markon, Kristian E.; Krueger, Robert F.

2016-01-01

In this review, we propose a novel developmentally informed framework to push research beyond a focus on comorbidity between discrete diagnostic categories, and to move towards research based on the well-validated dimensional and hierarchical structure of psychopathology. For example, a large body of research speaks to the validity and utility of the Internalizing and Externalizing (IE) spectra as organizing constructs for research on common forms of psychopathology. The IE spectra act as powerful explanatory variables that channel the psychopathological effects of genetic and environmental risk factors, predict adaptive functioning, and account for the likelihood of disorder-level manifestations of psychopathology. As such, our proposed theoretical framework uses the IE spectra as central constructs to guide future psychopathology research across the lifespan. The framework is particularly flexible, as any of the facets or factors from the dimensional and hierarchical structure of psychopathology can form the focus of research. We describe the utility and strengths of this framework for developmental psychopathology in particular, and explore avenues for future research. PMID:27739384

Analysis of human plasma lipids by using comprehensive two-dimensional gas chromatography with dual detection and with the support of high-resolution time-of-flight mass spectrometry for structural elucidation.

PubMed

Salivo, Simona; Beccaria, Marco; Sullini, Giuseppe; Tranchida, Peter Q; Dugo, Paola; Mondello, Luigi

2015-01-01

The main focus of the present research is the analysis of the unsaponifiable lipid fraction of human plasma by using data derived from comprehensive two-dimensional gas chromatography with dual quadrupole mass spectrometry and flame ionization detection. This approach enabled us to attain both mass spectral information and analyte percentage data. Furthermore, gas chromatography coupled with high-resolution time-of-flight mass spectrometry was used to increase the reliability of identification of several unsaponifiable lipid constituents. The synergism between both the high-resolution gas chromatography and mass spectrometry processes enabled us to attain a more in-depth knowledge of the unsaponifiable fraction of human plasma. Additionally, information was attained on the fatty acid and triacylglycerol composition of the plasma samples, subjected to investigation by using comprehensive two-dimensional gas chromatography with dual quadrupole mass spectrometry and flame ionization detection and high-performance liquid chromatography with atmospheric pressure chemical ionization quadrupole mass spectrometry, respectively. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Silicon/Carbon Anodes with One-Dimensional Pore Structure for Lithium-Ion Batteries

DTIC Science & Technology

2012-02-28

REPORT Silicon/Carbon Anodes with One-Dimensional Pore Structure for Lithium - Ion Batteries 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: A series of...Dimensional Pore Structure for Lithium - Ion Batteries Report Title ABSTRACT A series of composite electrode materials have been synthesized and...1 Silicon/Carbon Anodes with One-Dimensional Pore Structure for Lithium - Ion Batteries Grant # W911NF1110231 Annual Progress report June

Procedural validity of the AUDADIS-5 depression, anxiety and post-traumatic stress disorder modules: substance abusers and others in the general population*

PubMed Central

Hasin, Deborah S.; Shmulewitz, Dvora; Stohl, Malka; Greenstein, Eliana; Aivadyan, Christina; Morita, Kara; Saha, Tulshi; Aharonovich, Efrat; Jung, Jeesun; Zhang, Haitao; Nunes, Edward V.; Grant, Bridget F.

2016-01-01

Background Little is known about the procedural validity of lay-administered, fully-structured assessments of depressive, anxiety and post-traumatic stress (PTSD) disorders in the general population as determined by comparison to clinical re-appraisal, and whether this differs between current regular substance abusers and others. We evaluated the procedural validity of the Alcohol Use Disorder and Associated Disabilities Interview Schedule, DSM-5 Version (AUDADIS-5) assessment of these disorders through clinician re-interviews. Methods Test-retest design among respondents from the National Epidemiologic Survey on Alcohol and Related Conditions-III (NESARC-III): (264 current regular substance abusers, 447 others). Clinicians blinded to AUDADIS-5 results administered the semi-structured Psychiatric Research Interview for Substance and Mental Disorders, DSM-5 version (PRISM-5). AUDADIS-5/PRISM-5 concordance was indicated by kappa (κ) for diagnoses and intraclass correlation coefficients (ICC) for dimensional measures (DSM-5 symptom or criterion counts). Results were compared between current regular substance abusers and others. Results AUDADIS-5 and PRISM-5 concordance for DSM-5 depressive disorders, anxiety disorders and PTSD was generally fair to moderate (κ =0.24–0.59), with concordance on dimensional scales much better (ICC=0.53–0.81). Concordance differed little between regular substance abusers and others. Conclusions AUDADIS-5/PRISM-5 concordance indicated procedural validity for the AUDADIS-5 among substance abusers and others, suggesting that AUDADIS-5 diagnoses of DSM-5 depressive, anxiety and PTSD diagnoses are informative measures in both groups in epidemiologic studies. The stronger concordance on dimensional measures supports the current movement towards dimensional psychopathology measures, suggesting that such measures provide important information for research in the NESARC-III and other datasets, and possibly for clinical purposes as well. PMID:25939727

Softly-confined water cluster between freestanding graphene sheets

NASA Astrophysics Data System (ADS)

Agustian, Rifan; Akaishi, Akira; Nakamura, Jun

2018-01-01

Confined water could adopt new forms not seen in the open air, such as a two-dimensional (2D) square ice trapped between two graphene sheets [Algara-Siller et al., Nature 519, 443-445 (2015)]. In this study, in order to investigate how the flexibility of graphene affects the confined structure of water molecules, we employed classical molecular dynamics simulations with Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential to produce a soft-confining property of graphene. We discovered various solid-like structures of water molecules ranging from two-dimensional to three-dimensional structure encapsulated between two freestanding graphene sheets even at room temperature (300K). A small amount of water encapsulation leads to a layered two-dimensional form with triangular structure. On the other hand, large amounts of water molecules take a three-dimensional flying-saucer-like form with the square ice intra-layer structure. There is also a metastable state where both two-dimensional and three-dimensional structures coexist.

Fractal geometry in an expanding, one-dimensional, Newtonian universe.

PubMed

Miller, Bruce N; Rouet, Jean-Louis; Le Guirriec, Emmanuel

2007-09-01

Observations of galaxies over large distances reveal the possibility of a fractal distribution of their positions. The source of fractal behavior is the lack of a length scale in the two body gravitational interaction. However, even with new, larger, sample sizes from recent surveys, it is difficult to extract information concerning fractal properties with confidence. Similarly, three-dimensional N-body simulations with a billion particles only provide a thousand particles per dimension, far too small for accurate conclusions. With one-dimensional models these limitations can be overcome by carrying out simulations with on the order of a quarter of a million particles without compromising the computation of the gravitational force. Here the multifractal properties of two of these models that incorporate different features of the dynamical equations governing the evolution of a matter dominated universe are compared. For each model at least two scaling regions are identified. By employing criteria from dynamical systems theory it is shown that only one of them can be geometrically significant. The results share important similarities with galaxy observations, such as hierarchical clustering and apparent bifractal geometry. They also provide insights concerning possible constraints on length and time scales for fractal structure. They clearly demonstrate that fractal geometry evolves in the mu (position, velocity) space. The observed patterns are simply a shadow (projection) of higher-dimensional structure.

Preventing Data Ambiguity in Infectious Diseases with Four-Dimensional and Personalized Evaluations

PubMed Central

Iandiorio, Michelle J.; Fair, Jeanne M.; Chatzipanagiotou, Stylianos; Ioannidis, Anastasios; Trikka-Graphakos, Eleftheria; Charalampaki, Nikoletta; Sereti, Christina; Tegos, George P.; Hoogesteijn, Almira L.; Rivas, Ariel L.

2016-01-01

Background Diagnostic errors can occur, in infectious diseases, when anti-microbial immune responses involve several temporal scales. When responses span from nanosecond to week and larger temporal scales, any pre-selected temporal scale is likely to miss some (faster or slower) responses. Hoping to prevent diagnostic errors, a pilot study was conducted to evaluate a four-dimensional (4D) method that captures the complexity and dynamics of infectious diseases. Methods Leukocyte-microbial-temporal data were explored in canine and human (bacterial and/or viral) infections, with: (i) a non-structured approach, which measures leukocytes or microbes in isolation; and (ii) a structured method that assesses numerous combinations of interacting variables. Four alternatives of the structured method were tested: (i) a noise-reduction oriented version, which generates a single (one data point-wide) line of observations; (ii) a version that measures complex, three-dimensional (3D) data interactions; (iii) a non-numerical version that displays temporal data directionality (arrows that connect pairs of consecutive observations); and (iv) a full 4D (single line-, complexity-, directionality-based) version. Results In all studies, the non-structured approach revealed non-interpretable (ambiguous) data: observations numerically similar expressed different biological conditions, such as recovery and lack of recovery from infections. Ambiguity was also found when the data were structured as single lines. In contrast, two or more data subsets were distinguished and ambiguity was avoided when the data were structured as complex, 3D, single lines and, in addition, temporal data directionality was determined. The 4D method detected, even within one day, changes in immune profiles that occurred after antibiotics were prescribed. Conclusions Infectious disease data may be ambiguous. Four-dimensional methods may prevent ambiguity, providing earlier, in vivo, dynamic, complex, and personalized information that facilitates both diagnostics and selection or evaluation of anti-microbial therapies. PMID:27411058

Optimizing Coverage of Three-Dimensional Wireless Sensor Networks by Means of Photon Mapping

DTIC Science & Technology

2013-12-01

information if it does not display a currently valid OMB control number. 1. REPORT DATE DEC 2013 2. REPORT TYPE 3. DATES COVERED 00-00-2013 to 00-00...information about the monitored space is sensed?” Solving this formulation of the AGP relies upon the creation of a model describing how a set of...simulated photons will propagate in a 3D virtual environment. Furthermore, the photon model requires an efficient data structure with small memory

Two-dimensional infrared spectroscopy reveals the complex behaviour of an amyloid fibril inhibitor

NASA Astrophysics Data System (ADS)

Middleton, Chris T.; Marek, Peter; Cao, Ping; Chiu, Chi-Cheng; Singh, Sadanand; Woys, Ann Marie; de Pablo, Juan J.; Raleigh, Daniel P.; Zanni, Martin T.

2012-05-01

Amyloid formation has been implicated in the pathology of over 20 human diseases, but the rational design of amyloid inhibitors is hampered by a lack of structural information about amyloid-inhibitor complexes. We use isotope labelling and two-dimensional infrared spectroscopy to obtain a residue-specific structure for the complex of human amylin (the peptide responsible for islet amyloid formation in type 2 diabetes) with a known inhibitor (rat amylin). Based on its sequence, rat amylin should block formation of the C-terminal β-sheet, but at 8 h after mixing, rat amylin blocks the N-terminal β-sheet instead. At 24 h after mixing, rat amylin blocks neither β-sheet and forms its own β-sheet, most probably on the outside of the human fibrils. This is striking, because rat amylin is natively disordered and not previously known to form amyloid β-sheets. The results show that even seemingly intuitive inhibitors may function by unforeseen and complex structural processes.

The magnetotelluric phase tensor analysis of the Sembalun-Propok area, West Nusa Tenggara, Indonesia

NASA Astrophysics Data System (ADS)

Febriani, F.; Widarto, D. S.; Gaffar, E.; Nasution, A.; Grandis, H.

2017-04-01

The subsurface structure of the Sembalun-Propok area, NTB, Indonesia, has been investigated using magnetotelluric method (MT). To obtain the information of the dimensionality of the regional structure and determine the regional strike of the study area, the phase tensor analysis has been performed in this study. The results show that most of the skew angle values (β) are distributed within ± 5°. It indicates that the regional structure of the study area can be assumed as two dimensional. In addition, to determine the regional strike of the study area, we also calculated the major axes of the phase tensor. The result presents that the regional strike of the study area is about N330°E. According to the results of the phase tensor analysis, we rotated the impedance tensor to N330°E and performed 2-D inversion modeling. The result presents that the substructure model suits with the geological background of the study area.

Autism Spectrum Disorders as a Qualitatively Distinct Category from Typical Behavior in a Large, Clinically Ascertained Sample

ERIC Educational Resources Information Center

Frazier, Thomas W.; Youngstrom, Eric A.; Sinclair, Leslie; Kubu, Cynthia S.; Law, Paul; Rezai, Ali; Constantino, John N.; Eng, Charis

2010-01-01

The present study evaluated the hypothesis that autism spectrum disorders (ASDs) are best represented as a discrete category distinct from typical behavior within autism-affected families. The latent structure, categorical versus dimensional, of ASDs informs future diagnostic revisions, clinical assessment, and the design of future research. Data…

Into the third dimension: Benefits of incorporating LiDAR data in wildlife habitat models

Treesearch

Melissa J. Merrick; John L. Koprowski; Craig Wilcox

2013-01-01

LiDAR (Light detection and ranging) is a tool with potential for characterizing wildlife habitat by providing detailed, three-dimensional landscape information not available from other remote sensing applications. The ability to accurately map structural components such as canopy height, canopy cover, woody debris, tree density, and ground surface has potential to...

Geometric MCMC for infinite-dimensional inverse problems

NASA Astrophysics Data System (ADS)

Beskos, Alexandros; Girolami, Mark; Lan, Shiwei; Farrell, Patrick E.; Stuart, Andrew M.

2017-04-01

Bayesian inverse problems often involve sampling posterior distributions on infinite-dimensional function spaces. Traditional Markov chain Monte Carlo (MCMC) algorithms are characterized by deteriorating mixing times upon mesh-refinement, when the finite-dimensional approximations become more accurate. Such methods are typically forced to reduce step-sizes as the discretization gets finer, and thus are expensive as a function of dimension. Recently, a new class of MCMC methods with mesh-independent convergence times has emerged. However, few of them take into account the geometry of the posterior informed by the data. At the same time, recently developed geometric MCMC algorithms have been found to be powerful in exploring complicated distributions that deviate significantly from elliptic Gaussian laws, but are in general computationally intractable for models defined in infinite dimensions. In this work, we combine geometric methods on a finite-dimensional subspace with mesh-independent infinite-dimensional approaches. Our objective is to speed up MCMC mixing times, without significantly increasing the computational cost per step (for instance, in comparison with the vanilla preconditioned Crank-Nicolson (pCN) method). This is achieved by using ideas from geometric MCMC to probe the complex structure of an intrinsic finite-dimensional subspace where most data information concentrates, while retaining robust mixing times as the dimension grows by using pCN-like methods in the complementary subspace. The resulting algorithms are demonstrated in the context of three challenging inverse problems arising in subsurface flow, heat conduction and incompressible flow control. The algorithms exhibit up to two orders of magnitude improvement in sampling efficiency when compared with the pCN method.

Joint Model and Parameter Dimension Reduction for Bayesian Inversion Applied to an Ice Sheet Flow Problem

NASA Astrophysics Data System (ADS)

Ghattas, O.; Petra, N.; Cui, T.; Marzouk, Y.; Benjamin, P.; Willcox, K.

2016-12-01

Model-based projections of the dynamics of the polar ice sheets play a central role in anticipating future sea level rise. However, a number of mathematical and computational challenges place significant barriers on improving predictability of these models. One such challenge is caused by the unknown model parameters (e.g., in the basal boundary conditions) that must be inferred from heterogeneous observational data, leading to an ill-posed inverse problem and the need to quantify uncertainties in its solution. In this talk we discuss the problem of estimating the uncertainty in the solution of (large-scale) ice sheet inverse problems within the framework of Bayesian inference. Computing the general solution of the inverse problem--i.e., the posterior probability density--is intractable with current methods on today's computers, due to the expense of solving the forward model (3D full Stokes flow with nonlinear rheology) and the high dimensionality of the uncertain parameters (which are discretizations of the basal sliding coefficient field). To overcome these twin computational challenges, it is essential to exploit problem structure (e.g., sensitivity of the data to parameters, the smoothing property of the forward model, and correlations in the prior). To this end, we present a data-informed approach that identifies low-dimensional structure in both parameter space and the forward model state space. This approach exploits the fact that the observations inform only a low-dimensional parameter space and allows us to construct a parameter-reduced posterior. Sampling this parameter-reduced posterior still requires multiple evaluations of the forward problem, therefore we also aim to identify a low dimensional state space to reduce the computational cost. To this end, we apply a proper orthogonal decomposition (POD) approach to approximate the state using a low-dimensional manifold constructed using ``snapshots'' from the parameter reduced posterior, and the discrete empirical interpolation method (DEIM) to approximate the nonlinearity in the forward problem. We show that using only a limited number of forward solves, the resulting subspaces lead to an efficient method to explore the high-dimensional posterior.

A fully 3D approach for metal artifact reduction in computed tomography.

PubMed

Kratz, Barbel; Weyers, Imke; Buzug, Thorsten M

2012-11-01

In computed tomography imaging metal objects in the region of interest introduce inconsistencies during data acquisition. Reconstructing these data leads to an image in spatial domain including star-shaped or stripe-like artifacts. In order to enhance the quality of the resulting image the influence of the metal objects can be reduced. Here, a metal artifact reduction (MAR) approach is proposed that is based on a recomputation of the inconsistent projection data using a fully three-dimensional Fourier-based interpolation. The success of the projection space restoration depends sensitively on a sensible continuation of neighboring structures into the recomputed area. Fortunately, structural information of the entire data is inherently included in the Fourier space of the data. This can be used for a reasonable recomputation of the inconsistent projection data. The key step of the proposed MAR strategy is the recomputation of the inconsistent projection data based on an interpolation using nonequispaced fast Fourier transforms (NFFT). The NFFT interpolation can be applied in arbitrary dimension. The approach overcomes the problem of adequate neighborhood definitions on irregular grids, since this is inherently given through the usage of higher dimensional Fourier transforms. Here, applications up to the third interpolation dimension are presented and validated. Furthermore, prior knowledge may be included by an appropriate damping of the transform during the interpolation step. This MAR method is applicable on each angular view of a detector row, on two-dimensional projection data as well as on three-dimensional projection data, e.g., a set of sequential acquisitions at different spatial positions, projection data of a spiral acquisition, or cone-beam projection data. Results of the novel MAR scheme based on one-, two-, and three-dimensional NFFT interpolations are presented. All results are compared in projection data space and spatial domain with the well-known one-dimensional linear interpolation strategy. In conclusion, it is recommended to include as much spatial information into the recomputation step as possible. This is realized by increasing the dimension of the NFFT. The resulting image quality can be enhanced considerably.

Hydrological model parameter dimensionality is a weak measure of prediction uncertainty

NASA Astrophysics Data System (ADS)

Pande, S.; Arkesteijn, L.; Savenije, H.; Bastidas, L. A.

2015-04-01

This paper shows that instability of hydrological system representation in response to different pieces of information and associated prediction uncertainty is a function of model complexity. After demonstrating the connection between unstable model representation and model complexity, complexity is analyzed in a step by step manner. This is done measuring differences between simulations of a model under different realizations of input forcings. Algorithms are then suggested to estimate model complexity. Model complexities of the two model structures, SAC-SMA (Sacramento Soil Moisture Accounting) and its simplified version SIXPAR (Six Parameter Model), are computed on resampled input data sets from basins that span across the continental US. The model complexities for SIXPAR are estimated for various parameter ranges. It is shown that complexity of SIXPAR increases with lower storage capacity and/or higher recession coefficients. Thus it is argued that a conceptually simple model structure, such as SIXPAR, can be more complex than an intuitively more complex model structure, such as SAC-SMA for certain parameter ranges. We therefore contend that magnitudes of feasible model parameters influence the complexity of the model selection problem just as parameter dimensionality (number of parameters) does and that parameter dimensionality is an incomplete indicator of stability of hydrological model selection and prediction problems.

Learning structure-property relationship in crystalline materials: A study of lanthanide-transition metal alloys

NASA Astrophysics Data System (ADS)

Pham, Tien-Lam; Nguyen, Nguyen-Duong; Nguyen, Van-Doan; Kino, Hiori; Miyake, Takashi; Dam, Hieu-Chi

2018-05-01

We have developed a descriptor named Orbital Field Matrix (OFM) for representing material structures in datasets of multi-element materials. The descriptor is based on the information regarding atomic valence shell electrons and their coordination. In this work, we develop an extension of OFM called OFM1. We have shown that these descriptors are highly applicable in predicting the physical properties of materials and in providing insights on the materials space by mapping into a low embedded dimensional space. Our experiments with transition metal/lanthanide metal alloys show that the local magnetic moments and formation energies can be accurately reproduced using simple nearest-neighbor regression, thus confirming the relevance of our descriptors. Using kernel ridge regressions, we could accurately reproduce formation energies and local magnetic moments calculated based on first-principles, with mean absolute errors of 0.03 μB and 0.10 eV/atom, respectively. We show that meaningful low-dimensional representations can be extracted from the original descriptor using descriptive learning algorithms. Intuitive prehension on the materials space, qualitative evaluation on the similarities in local structures or crystalline materials, and inference in the designing of new materials by element substitution can be performed effectively based on these low-dimensional representations.

Free-space propagation of high-dimensional structured optical fields in an urban environment

PubMed Central

Lavery, Martin P. J.; Peuntinger, Christian; Günthner, Kevin; Banzer, Peter; Elser, Dominique; Boyd, Robert W.; Padgett, Miles J.; Marquardt, Christoph; Leuchs, Gerd

2017-01-01

Spatially structured optical fields have been used to enhance the functionality of a wide variety of systems that use light for sensing or information transfer. As higher-dimensional modes become a solution of choice in optical systems, it is important to develop channel models that suitably predict the effect of atmospheric turbulence on these modes. We investigate the propagation of a set of orthogonal spatial modes across a free-space channel between two buildings separated by 1.6 km. Given the circular geometry of a common optical lens, the orthogonal mode set we choose to implement is that described by the Laguerre-Gaussian (LG) field equations. Our study focuses on the preservation of phase purity, which is vital for spatial multiplexing and any system requiring full quantum-state tomography. We present experimental data for the modal degradation in a real urban environment and draw a comparison to recognized theoretical predictions of the link. Our findings indicate that adaptations to channel models are required to simulate the effects of atmospheric turbulence placed on high-dimensional structured modes that propagate over a long distance. Our study indicates that with mitigation of vortex splitting, potentially through precorrection techniques, one could overcome the challenges in a real point-to-point free-space channel in an urban environment. PMID:29075663

Free-space propagation of high-dimensional structured optical fields in an urban environment.

PubMed

Lavery, Martin P J; Peuntinger, Christian; Günthner, Kevin; Banzer, Peter; Elser, Dominique; Boyd, Robert W; Padgett, Miles J; Marquardt, Christoph; Leuchs, Gerd

2017-10-01

Spatially structured optical fields have been used to enhance the functionality of a wide variety of systems that use light for sensing or information transfer. As higher-dimensional modes become a solution of choice in optical systems, it is important to develop channel models that suitably predict the effect of atmospheric turbulence on these modes. We investigate the propagation of a set of orthogonal spatial modes across a free-space channel between two buildings separated by 1.6 km. Given the circular geometry of a common optical lens, the orthogonal mode set we choose to implement is that described by the Laguerre-Gaussian (LG) field equations. Our study focuses on the preservation of phase purity, which is vital for spatial multiplexing and any system requiring full quantum-state tomography. We present experimental data for the modal degradation in a real urban environment and draw a comparison to recognized theoretical predictions of the link. Our findings indicate that adaptations to channel models are required to simulate the effects of atmospheric turbulence placed on high-dimensional structured modes that propagate over a long distance. Our study indicates that with mitigation of vortex splitting, potentially through precorrection techniques, one could overcome the challenges in a real point-to-point free-space channel in an urban environment.

Development of multi-dimensional action checklist for promoting new approaches in participatory occupational safety and health in small and medium-sized enterprises.

PubMed

Nishikido, Noriko; Yuasa, Akiko; Motoki, Chiharu; Tanaka, Mika; Arai, Sumiko; Matsuda, Kazumi; Ikeda, Tomoko; Iijima, Miyoko; Hirata, Mamoru; Hojoh, Minoru; Tsutaki, Miho; Ito, Akiyoshi; Maeda, Kazutoshi; Miyoshi, Yukari; Mitsuhashi, Hiroyuki; Fukuda, Eiko; Kawakami, Yuko

2006-01-01

To meet diversified health needs in workplaces, especially in developed countries, occupational safety and health (OSH) activities should be extended. The objective of this study is to develop a new multi-dimensional action checklist that can support employers and workers in understanding a wide range of OSH activities and to promote participation in OSH in small and medium-sized enterprises (SMEs). The general structure of and specific items in the new action checklist were discussed in a focus group meeting with OSH specialists based upon the results of a literature review and our previous interviews with company employers and workers. To assure practicality and validity, several sessions were held to elicit the opinions of company members and, as a result, modifications were made. The new multi-dimensional action checklist was finally formulated consisting of 6 core areas, 9 technical areas, and 61 essential items. Each item was linked to a suitable section in the information guidebook that we developed concomitantly with the action checklist. Combined usage of the action checklist with the information guidebook would provide easily comprehended information and practical support. Intervention studies using this newly developed action checklist will clarify the effectiveness of the new approach to OSH in SMEs.

On some structure-turbulence interaction problems

NASA Technical Reports Server (NTRS)

Maekawa, S.; Lin, Y. K.

1976-01-01

The interactions between a turbulent flow structure; responding to its excitation were studied. The turbulence was typical of those associated with a boundary layer, having a cross-spectral density indicative of convection and statistical decay. A number of structural models were considered. Among the one-dimensional models were an unsupported infinite beam and a periodically supported infinite beam. The fuselage construction of an aircraft was then considered. For the two-dimensional case a simple membrane was used to illustrate the type of formulation applicable to most two-dimensional structures. Both the one-dimensional and two-dimensional structures studied were backed by a cavity filled with an initially quiescent fluid to simulate the acoustic environment when the structure forms one side of a cabin of a sea vessel or aircraft.

Robust membrane detection based on tensor voting for electron tomography.

PubMed

Martinez-Sanchez, Antonio; Garcia, Inmaculada; Asano, Shoh; Lucic, Vladan; Fernandez, Jose-Jesus

2014-04-01

Electron tomography enables three-dimensional (3D) visualization and analysis of the subcellular architecture at a resolution of a few nanometers. Segmentation of structural components present in 3D images (tomograms) is often necessary for their interpretation. However, it is severely hampered by a number of factors that are inherent to electron tomography (e.g. noise, low contrast, distortion). Thus, there is a need for new and improved computational methods to facilitate this challenging task. In this work, we present a new method for membrane segmentation that is based on anisotropic propagation of the local structural information using the tensor voting algorithm. The local structure at each voxel is then refined according to the information received from other voxels. Because voxels belonging to the same membrane have coherent structural information, the underlying global structure is strengthened. In this way, local information is easily integrated at a global scale to yield segmented structures. This method performs well under low signal-to-noise ratio typically found in tomograms of vitrified samples under cryo-tomography conditions and can bridge gaps present on membranes. The performance of the method is demonstrated by applications to tomograms of different biological samples and by quantitative comparison with standard template matching procedure. Copyright © 2014 Elsevier Inc. All rights reserved.

Integrative analysis of transcriptomic and metabolomic data via sparse canonical correlation analysis with incorporation of biological information.

PubMed

Safo, Sandra E; Li, Shuzhao; Long, Qi

2018-03-01

Integrative analysis of high dimensional omics data is becoming increasingly popular. At the same time, incorporating known functional relationships among variables in analysis of omics data has been shown to help elucidate underlying mechanisms for complex diseases. In this article, our goal is to assess association between transcriptomic and metabolomic data from a Predictive Health Institute (PHI) study that includes healthy adults at a high risk of developing cardiovascular diseases. Adopting a strategy that is both data-driven and knowledge-based, we develop statistical methods for sparse canonical correlation analysis (CCA) with incorporation of known biological information. Our proposed methods use prior network structural information among genes and among metabolites to guide selection of relevant genes and metabolites in sparse CCA, providing insight on the molecular underpinning of cardiovascular disease. Our simulations demonstrate that the structured sparse CCA methods outperform several existing sparse CCA methods in selecting relevant genes and metabolites when structural information is informative and are robust to mis-specified structural information. Our analysis of the PHI study reveals that a number of gene and metabolic pathways including some known to be associated with cardiovascular diseases are enriched in the set of genes and metabolites selected by our proposed approach. © 2017, The International Biometric Society.

Constructing financial network based on PMFG and threshold method

NASA Astrophysics Data System (ADS)

Nie, Chun-Xiao; Song, Fu-Tie

2018-04-01

Based on planar maximally filtered graph (PMFG) and threshold method, we introduced a correlation-based network named PMFG-based threshold network (PTN). We studied the community structure of PTN and applied ISOMAP algorithm to represent PTN in low-dimensional Euclidean space. The results show that the community corresponds well to the cluster in the Euclidean space. Further, we studied the dynamics of the community structure and constructed the normalized mutual information (NMI) matrix. Based on the real data in the market, we found that the volatility of the market can lead to dramatic changes in the community structure, and the structure is more stable during the financial crisis.

Method for making a bio-compatible scaffold

DOEpatents

Cesarano, III, Joseph; Stuecker, John N [Albuquerque, NM; Dellinger, Jennifer G [Champaigne, IL; Jamison, Russell D [Urbana, IL

2006-01-31

A method for forming a three-dimensional, biocompatible, porous scaffold structure using a solid freeform fabrication technique (referred to herein as robocasting) that can be used as a medical implant into a living organism, such as a human or other mammal. Imaging technology and analysis is first used to determine the three-dimensional design required for the medical implant, such as a bone implant or graft, fashioned as a three-dimensional, biocompatible scaffold structure. The robocasting technique is used to either directly produce the three-dimensional, porous scaffold structure or to produce an over-sized three-dimensional, porous scaffold lattice which can be machined to produce the designed three-dimensional, porous scaffold structure for implantation.

Structural Analysis Methods for Structural Health Management of Future Aerospace Vehicles

NASA Technical Reports Server (NTRS)

Tessler, Alexander

2007-01-01

Two finite element based computational methods, Smoothing Element Analysis (SEA) and the inverse Finite Element Method (iFEM), are reviewed, and examples of their use for structural health monitoring are discussed. Due to their versatility, robustness, and computational efficiency, the methods are well suited for real-time structural health monitoring of future space vehicles, large space structures, and habitats. The methods may be effectively employed to enable real-time processing of sensing information, specifically for identifying three-dimensional deformed structural shapes as well as the internal loads. In addition, they may be used in conjunction with evolutionary algorithms to design optimally distributed sensors. These computational tools have demonstrated substantial promise for utilization in future Structural Health Management (SHM) systems.

Optimal contact definition for reconstruction of contact maps.

PubMed

Duarte, Jose M; Sathyapriya, Rajagopal; Stehr, Henning; Filippis, Ioannis; Lappe, Michael

2010-05-27

Contact maps have been extensively used as a simplified representation of protein structures. They capture most important features of a protein's fold, being preferred by a number of researchers for the description and study of protein structures. Inspired by the model's simplicity many groups have dedicated a considerable amount of effort towards contact prediction as a proxy for protein structure prediction. However a contact map's biological interest is subject to the availability of reliable methods for the 3-dimensional reconstruction of the structure. We use an implementation of the well-known distance geometry protocol to build realistic protein 3-dimensional models from contact maps, performing an extensive exploration of many of the parameters involved in the reconstruction process. We try to address the questions: a) to what accuracy does a contact map represent its corresponding 3D structure, b) what is the best contact map representation with regard to reconstructability and c) what is the effect of partial or inaccurate contact information on the 3D structure recovery. Our results suggest that contact maps derived from the application of a distance cutoff of 9 to 11A around the Cbeta atoms constitute the most accurate representation of the 3D structure. The reconstruction process does not provide a single solution to the problem but rather an ensemble of conformations that are within 2A RMSD of the crystal structure and with lower values for the pairwise average ensemble RMSD. Interestingly it is still possible to recover a structure with partial contact information, although wrong contacts can lead to dramatic loss in reconstruction fidelity. Thus contact maps represent a valid approximation to the structures with an accuracy comparable to that of experimental methods. The optimal contact definitions constitute key guidelines for methods based on contact maps such as structure prediction through contacts and structural alignments based on maximum contact map overlap.

Optimal contact definition for reconstruction of Contact Maps

PubMed Central

2010-01-01

Background Contact maps have been extensively used as a simplified representation of protein structures. They capture most important features of a protein's fold, being preferred by a number of researchers for the description and study of protein structures. Inspired by the model's simplicity many groups have dedicated a considerable amount of effort towards contact prediction as a proxy for protein structure prediction. However a contact map's biological interest is subject to the availability of reliable methods for the 3-dimensional reconstruction of the structure. Results We use an implementation of the well-known distance geometry protocol to build realistic protein 3-dimensional models from contact maps, performing an extensive exploration of many of the parameters involved in the reconstruction process. We try to address the questions: a) to what accuracy does a contact map represent its corresponding 3D structure, b) what is the best contact map representation with regard to reconstructability and c) what is the effect of partial or inaccurate contact information on the 3D structure recovery. Our results suggest that contact maps derived from the application of a distance cutoff of 9 to 11Å around the Cβ atoms constitute the most accurate representation of the 3D structure. The reconstruction process does not provide a single solution to the problem but rather an ensemble of conformations that are within 2Å RMSD of the crystal structure and with lower values for the pairwise average ensemble RMSD. Interestingly it is still possible to recover a structure with partial contact information, although wrong contacts can lead to dramatic loss in reconstruction fidelity. Conclusions Thus contact maps represent a valid approximation to the structures with an accuracy comparable to that of experimental methods. The optimal contact definitions constitute key guidelines for methods based on contact maps such as structure prediction through contacts and structural alignments based on maximum contact map overlap. PMID:20507547

An improved stochastic fractal search algorithm for 3D protein structure prediction.

PubMed

Zhou, Changjun; Sun, Chuan; Wang, Bin; Wang, Xiaojun

2018-05-03

Protein structure prediction (PSP) is a significant area for biological information research, disease treatment, and drug development and so on. In this paper, three-dimensional structures of proteins are predicted based on the known amino acid sequences, and the structure prediction problem is transformed into a typical NP problem by an AB off-lattice model. This work applies a novel improved Stochastic Fractal Search algorithm (ISFS) to solve the problem. The Stochastic Fractal Search algorithm (SFS) is an effective evolutionary algorithm that performs well in exploring the search space but falls into local minimums sometimes. In order to avoid the weakness, Lvy flight and internal feedback information are introduced in ISFS. In the experimental process, simulations are conducted by ISFS algorithm on Fibonacci sequences and real peptide sequences. Experimental results prove that the ISFS performs more efficiently and robust in terms of finding the global minimum and avoiding getting stuck in local minimums.

Applied and implied semantics in crystallographic publishing

PubMed Central

2012-01-01

Background Crystallography is a data-rich, software-intensive scientific discipline with a community that has undertaken direct responsibility for publishing its own scientific journals. That community has worked actively to develop information exchange standards allowing readers of structure reports to access directly, and interact with, the scientific content of the articles. Results Structure reports submitted to some journals of the International Union of Crystallography (IUCr) can be automatically validated and published through an efficient and cost-effective workflow. Readers can view and interact with the structures in three-dimensional visualization applications, and can access the experimental data should they wish to perform their own independent structure solution and refinement. The journals also layer on top of this facility a number of automated annotations and interpretations to add further scientific value. Conclusions The benefits of semantically rich information exchange standards have revolutionised the scholarly publishing process for crystallography, and establish a model relevant to many other physical science disciplines. PMID:22932420

Three-Dimensional Reconstruction and Solar Energy Potential Estimation of Buildings

NASA Astrophysics Data System (ADS)

Chen, Y.; Li, M.; Cheng, L.; Xu, H.; Li, S.; Liu, X.

2017-12-01

In the context of the construction of low-carbon cities, green cities and eco-cities, the ability of the airborne and mobile LiDAR should be explored in urban renewable energy research. As the main landscape in urban environment, buildings have large regular envelopes could receive a huge amount of solar radiation. In this study, a relatively complete calculation scheme about building roof and façade solar utilization potential is proposed, using building three-dimensional geometric feature information. For measuring the city-level building solar irradiance, the precise three-dimensional building roof and façade models should be first reconstructed from the airborne and mobile LiDAR, respectively. In order to obtaining the precise geometric structure of building facades from the mobile LiDAR data, a new method for structure detection and the three-dimensional reconstruction of building façades from mobile LiDAR data is proposed. The method consists of three steps: the preprocessing of façade points, the detection of façade structure, the restoration and reconstruction of building façade. As a result, the reconstruction method can effectively deal with missing areas caused by occlusion, viewpoint limitation, and uneven point density, as well as realizing the highly complete 3D reconstruction of a building façade. Furthermore, the window areas can be excluded for more accurate estimation of solar utilization potential. After then, the solar energy utilization potential of global building roofs and facades is estimate by using the solar irradiance model, which combine the analysis of the building shade and sky diffuse, based on the analysis of the geometrical structure of buildings.

Atomically-thick two-dimensional crystals: electronic structure regulation and energy device construction.

PubMed

Sun, Yongfu; Gao, Shan; Xie, Yi

2014-01-21

Atomically-thick two-dimensional crystals can provide promising opportunities to satisfy people's requirement of next-generation flexible and transparent nanodevices. However, the characterization of these low-dimensional structures and the understanding of their clear structure-property relationship encounter many great difficulties, owing to the lack of long-range order in the third dimensionality. In this review, we survey the recent progress in fine structure characterization by X-ray absorption fine structure spectroscopy and also overview electronic structure modulation by density-functional calculations in the ultrathin two-dimensional crystals. In addition, we highlight their structure-property relationship, transparent and flexible device construction as well as wide applications in photoelectrochemical water splitting, photodetectors, thermoelectric conversion, touchless moisture sensing, supercapacitors and lithium ion batteries. Finally, we outline the major challenges and opportunities that face the atomically-thick two-dimensional crystals. It is anticipated that the present review will deepen people's understanding of this field and hence contribute to guide the future design of high-efficiency energy-related devices.

A Stochastic Evolutionary Model for Protein Structure Alignment and Phylogeny

PubMed Central

Challis, Christopher J.; Schmidler, Scott C.

2012-01-01

We present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model, and mutations follow a standard substitution matrix, whereas backbone atoms diffuse in three-dimensional space according to an Ornstein–Uhlenbeck process. The model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully accounting for uncertainty. The inclusion of structural information enables phylogenetic inference on time scales not previously attainable with sequence evolution models. The model also provides a tool for testing evolutionary hypotheses and improving our understanding of protein structural evolution. PMID:22723302

Two- and Three-Dimensional Probes of Parity in Primordial Gravity Waves.

PubMed

Masui, Kiyoshi Wesley; Pen, Ue-Li; Turok, Neil

2017-06-02

We show that three-dimensional information is critical to discerning the effects of parity violation in the primordial gravity-wave background. If present, helical gravity waves induce parity-violating correlations in the cosmic microwave background (CMB) between parity-odd polarization B modes and parity-even temperature anisotropies (T) or polarization E modes. Unfortunately, EB correlations are much weaker than would be naively expected, which we show is due to an approximate symmetry resulting from the two-dimensional nature of the CMB. The detectability of parity-violating correlations is exacerbated by the fact that the handedness of individual modes cannot be discerned in the two-dimensional CMB, leading to a noise contribution from scalar matter perturbations. In contrast, the tidal imprints of primordial gravity waves fossilized into the large-scale structure of the Universe are a three-dimensional probe of parity violation. Using such fossils the handedness of gravity waves may be determined on a mode-by-mode basis, permitting future surveys to probe helicity at the percent level if the amplitude of primordial gravity waves is near current observational upper limits.

[Localization of perforators in the lower leg by digital antomy imaging methods].

PubMed

Wei, Peng; Ma, Liang-Liang; Fang, Ye-Dong; Xia, Wei-Zhi; Ding, Mao-Chao; Mei, Jin

2012-03-01

To offer both the accurate three-dimensional anatomical information and algorithmic morphology of perforators in the lower leg for perforator flaps design. The cadaver was injected with a modified lead oxide-gelatin mixture. Radiography was first performed and the images were analyzed using the software Photoshop and Scion Image. Then spiral CT scan was also performed and 3-dimensional images were reconstructed with MIMICS 10.01 software. There are (27 +/- 4) perforators whose outer diameter > or = 0.5 mm ( average, 0.8 +/- 0.2 mm). The average pedicle length within the superficial fascia is (37.3 +/- 18.6) mm. The average supplied area of each perforator is (49.5 +/- 25.5) cm2. The three-dimensional model displayed accurate morphology structure and three-dimensional distribution of the perforator-to- perforator and perforator-to-source artery. The 3D reconstruction model can clearly show the geometric, local details and three-dimensional distribution. It is a considerable method for the study of morphological characteristics of the individual perforators in human calf and preoperative planning of the perforator flap.

Aspects of the dimensional changes of jersey structures after knitting process

NASA Astrophysics Data System (ADS)

Szabo, M.; Barbu, I.; Jiaru, L.

2017-08-01

The study proposes a statistical analysis by applying a mathematical model for the study of the dimensional changes of jersey structures made of 100% cotton yarn, with 58/1 metric count of yarn. The Structures are presented as tubular knitted metrage and are designed for underwear and/or outer garments. By analysing the jersey structures, from dimensional stability point of view, there can be observed that values in the limits are within the ±2% interval, values which are considered appropriate. Following the experimental researches, there are proposed solutions for the reduction of dimensional changes on both directions of the knit, on the stich course direction and also on the stich courses in vertical direction, being analyzed the behaviour of the knitted fabrics during relaxation after knitting process. The problem of the dimensional stability of the knitted fabrics is extensive researched. The knitted structures are elastic structures, this being a reason for which dimensional stability will always be a topical theme. The jersey structures, due to the distribution of the platinum loop in the knit plane, due to the relative small number of yarn-yarn contact points that causes the threads to slide into the structure, due to the spiral of the tubular metrage structure, are among those whose dimensional stability is difficult to control. The technical characteristics of the yarns, the technical characteristics of the knitting machines and the technological parameters of the knitting machine are the elements which will be correlated in order to obtain structures with minimum dimensional changes. In order to obtain knitted structures with adequate dimensional stability, this means within ±2%, it is necessary that the dimensional changes during the relaxation periods after knitting and chemical finishing being minimum. For this, all the processes to be applied will be conducted with appropriate and uniform tensions throughout the technological flow. The relaxation periods of 72 hours should be strictly respected, folded and under standard atmospheric conditions, both after knitting and after chemical finishing. The jersey structures are plane structured made on knitting machines equiped with font. There will be analyzed the dimensional changes of the jersey structures made of 100% cotton yarn, Nm 58/1, after the relaxation after knitting process througout the corelation between the technical characteristics of the yarns, of the technological parameter of the knitting operation and of some technical characteristici of the knitting machine.

Hierarchical Discriminant Analysis.

PubMed

Lu, Di; Ding, Chuntao; Xu, Jinliang; Wang, Shangguang

2018-01-18

The Internet of Things (IoT) generates lots of high-dimensional sensor intelligent data. The processing of high-dimensional data (e.g., data visualization and data classification) is very difficult, so it requires excellent subspace learning algorithms to learn a latent subspace to preserve the intrinsic structure of the high-dimensional data, and abandon the least useful information in the subsequent processing. In this context, many subspace learning algorithms have been presented. However, in the process of transforming the high-dimensional data into the low-dimensional space, the huge difference between the sum of inter-class distance and the sum of intra-class distance for distinct data may cause a bias problem. That means that the impact of intra-class distance is overwhelmed. To address this problem, we propose a novel algorithm called Hierarchical Discriminant Analysis (HDA). It minimizes the sum of intra-class distance first, and then maximizes the sum of inter-class distance. This proposed method balances the bias from the inter-class and that from the intra-class to achieve better performance. Extensive experiments are conducted on several benchmark face datasets. The results reveal that HDA obtains better performance than other dimensionality reduction algorithms.

Modeling drying of three-dimensional pulp molded structures. Part I, Experimental program

Treesearch

Heike Nyist; John F. Hunt; Margit Tamasy-Bano

1998-01-01

Researchers at the USDA Forest Products Laboratory have developed a new three-dimensional structural panel, called FPL Spaceboard. This panel is formed using a U.S. patented three-dimensional mold capable of using a variety of fibrous materials with either the wet- or dry-forming process. Structurally, the panel departs from the traditional two-dimensional panel by...

Experimental Investigation of Relative Permeability Upscaling from the Micro-Scale to the Macro-Scale

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

Pyrak-Nolte, Laura J.; Cheng, JiangTao; Yu, Ping

2003-01-29

During this reporting period, shown experimentally that the optical coherence imaging system can acquire information on grain interfaces and void shape for a maximum depth of half a millimeter into sandstone. The measurement of interfacial area per volume (IAV), capillary pressure and saturation in two dimensional micro-models structures has shown the existence of a unique relationship among these hydraulic parameters for different pore geometry. The measurement of interfacial area per volume on a three-dimensional natural sample, i.e., sandstone, has shown the homogeneity of IAV with depth in a sample when the fluids are in equilibrium.

Combining 1D and 2D linear discriminant analysis for palmprint recognition

NASA Astrophysics Data System (ADS)

Zhang, Jian; Ji, Hongbing; Wang, Lei; Lin, Lin

2011-11-01

In this paper, a novel feature extraction method for palmprint recognition termed as Two-dimensional Combined Discriminant Analysis (2DCDA) is proposed. By connecting the adjacent rows of a image sequentially, the obtained new covariance matrices contain the useful information among local geometry structures in the image, which is eliminated by 2DLDA. In this way, 2DCDA combines LDA and 2DLDA for a promising recognition accuracy, but the number of coefficients of its projection matrix is lower than that of other two-dimensional methods. Experimental results on the CASIA palmprint database demonstrate the effectiveness of the proposed method.

Potential applications of MMC and aluminum-lithium alloys in cameras for CRAF spacecraft. [Comet Rendezvous Asteroid Flyby Mission

NASA Technical Reports Server (NTRS)

Lane, Marc; Hsieh, Cheng; Adams, Lloyd

1989-01-01

In undertaking the design of a 2000-mm focal length camera for the Mariner Mark II series of spacecraft, JPL sought novel materials with the requisite dimensional and thermal stability, outgassing and corrosion resistance, low mass, high stiffness, and moderate cost. Metal-matrix composites and Al-Li alloys have, in addition to excellent mechanical properties and low density, a suitably low coefficient of thermal expansion, high specific stiffness, and good electrical conductivity. The greatest single obstacle to application of these materials to camera structure design is noted to have been the lack of information regarding long-term dimensional stability.

Polymorphism in 'L' shaped lipids: structure of N-, O-diacylethanolamines with mixed acyl chains.

PubMed

Tarafdar, Pradip K; Swamy, Musti J

2009-11-01

Although solid state polymorphism in lipids has been established by spectroscopic and calorimetric studies long ago, only in a few cases crystal structures of different polymorphs of the same compound have been reported, possibly due to difficulties in obtaining high quality single crystals of individual polymorphs. Recent studies show that N-, O-diacylethanolamines (DAEs) can be derived by the O-acylation of the stress-related lipids, the N-acylethanolamines under physiological conditions. In this study, two DAEs with mixed acyl chains, namely N-palmitoyl, O-octanoylethanolamine and N-palmitoyl, O-decanoylethanolamine have been synthesized and their three-dimensional structures were determined. Both the compounds were found to adopt 'L' shaped structures and exist in two polymorphic forms, alpha and beta. In the alpha form a mixed-type chain packing has been observed whereas in the beta form the chain packing is symmetric. Similar polymorphic forms are likely to exist in other 'L' shaped lipids such as 1,3-diacylglycerols and ceramides, where polymorphism has been detected earlier, but three-dimensional structures - which can give precise information about the packing at atomic resolution - have not been reported.

Detection and extraction of orientation-and-scale-dependent information from two-dimensional GPR data with tuneable directional wavelet filters

NASA Astrophysics Data System (ADS)

Tzanis, Andreas

2013-02-01

The Ground Probing Radar (GPR) is a valuable tool for near surface geological, geotechnical, engineering, environmental, archaeological and other work. GPR images of the subsurface frequently contain geometric information (constant or variable-dip reflections) from various structures such as bedding, cracks, fractures, etc. Such features are frequently the target of the survey; however, they are usually not good reflectors and they are highly localized in time and in space. Their scale is therefore a factor significantly affecting their detectability. At the same time, the GPR method is very sensitive to broadband noise from buried small objects, electromagnetic anthropogenic activity and systemic factors, which frequently blurs the reflections from such targets. This paper introduces a method to de-noise GPR data and extract geometric information from scale-and-dip dependent structural features, based on one-dimensional B-Spline Wavelets, two-dimensional directional B-Spline Wavelet (BSW) Filters and two-dimensional Gabor Filters. A directional BSW Filter is built by sidewise arranging s identical one-dimensional wavelets of length L, tapering the s-parallel direction (span) with a suitable window function and rotating the resulting matrix to the desired orientation. The length L of the wavelet defines the temporal and spatial scale to be isolated and the span determines the length over which to smooth (spatial resolution). The Gabor Filter is generated by multiplying an elliptical Gaussian by a complex plane wave; at any orientation the temporal or spatial scale(s) to be isolated are determined by the wavelength. λ of the plane wave and the spatial resolution by the spatial aspect ratio γ, which specifies the ellipticity of the support of the Gabor function. At any orientation, both types of filter may be tuned at any frequency or spatial wavenumber by varying the length or the wavelength respectively. The filters can be applied directly to two-dimensional radargrams, in which case they abstract information about given scales at given orientations. Alternatively, they can be rotated to different orientations under adaptive control, so that they remain tuned at a given frequency or wavenumber and the resulting images can be stacked in the LS sense, so as to obtain a complete representation of the input data at a given temporal or spatial scale. In addition to isolating geometrical information for further scrutiny, the proposed filtering methods can be used to enhance the S/N ratio in a manner particularly suitable for GPR data, because the frequency response of the filters mimics the frequency characteristics of the source wavelet. Finally, signal attenuation and temporal localization are closely associated: low attenuation interfaces tend to produce reflections rich in high frequencies and fine-scale localization as a function of time. Conversely, high attenuation interfaces will produce reflections rich in low frequencies and broad localization. Accordingly, the temporal localization characteristics of the filters may be exploited to investigate the characteristics of signal propagation (hence material properties). The method is shown to be very effective in extracting fine to coarse scale information from noisy data and is demonstrated with applications to noisy GPR data from archaeometric and geotechnical surveys.

Insights into the dissolution and the three-dimensional structure of insensitive munitions formulations.

PubMed

Taylor, Susan; Ringelberg, David B; Dontsova, Katerina; Daghlian, Charles P; Walsh, Marianne E; Walsh, Michael R

2013-11-01

Two compounds, 2,4-dinitroanisole (DNAN) and 3-nitro-1,2,4-triazol-5-one (NTO) are the main ingredients in a suite of explosive formulations that are being, or soon will be, fielded at military training ranges. We aim to understand the dissolution characteristics of DNAN and NTO and three insensitive muntions (IM) formulations that contain them. This information is needed to accurately predict the environmental fate of IM constituents, some of which may be toxic to people and the environment. We used Raman spectroscopy to identify the different constituents in the IM formulations and micro computed tomography to image their three-dimensional structure. These are the first three-dimensional images of detonated explosive particles. For multi-component explosives the solubility of the individual constituents and the fraction of each constituent wetted by water controls the dissolution. We found that the order of magnitude differences in solubility amongst the constituents of these IM formulations quickly produced hole-riddled particles when these were exposed to water. Micro-computed tomography showed that particles resulting from field detonations were fractured, producing conduits by which water could access the interior of the particle. We think that micro-computed tomography can also be used to determine the initial composition of IM particles and to track how their compositions change as the particles dissolve. This information is critical to quantifying dissolution and developing physically based dissolution models. Published by Elsevier Ltd.

Enhanced ICBM Diffusion Tensor Template of the Human Brain

PubMed Central

Zhang, Shengwei; Peng, Huiling; Dawe, Robert J.; Arfanakis, Konstantinos

2010-01-01

Development of a diffusion tensor (DT) template that is representative of the micro-architecture of the human brain is crucial for comparisons of neuronal structural integrity and brain connectivity across populations, as well as for the generation of a detailed white matter atlas. Furthermore, a DT template in ICBM space may simplify consolidation of information from DT, anatomical and functional MRI studies. The previously developed “IIT DT brain template” was produced in ICBM-152 space, based on a large number of subjects from a limited age-range, using data with minimal image artifacts, and non-linear registration. That template was characterized by higher image sharpness, provided the ability to distinguish smaller white matter fiber structures, and contained fewer image artifacts, than several previously published DT templates. However, low-dimensional registration was used in the development of that template, which led to a mismatch of DT information across subjects, eventually manifested as loss of local diffusion information and errors in the final tensors. Also, low-dimensional registration led to a mismatch of the anatomy in the IIT and ICBM-152 templates. In this work, a significantly improved DT brain template in ICBM-152 space was developed, using high-dimensional non-linear registration and the raw data collected for the purposes of the IIT template. The accuracy of inter-subject DT matching was significantly increased compared to that achieved for the development of the IIT template. Consequently, the new template contained DT information that was more representative of single-subject human brain data, and was characterized by higher image sharpness than the IIT template. Furthermore, a bootstrap approach demonstrated that the variance of tensor characteristics was lower in the new template. Additionally, compared to the IIT template, brain anatomy in the new template more accurately matched ICBM-152 space. Finally, spatial normalization of a number of DT datasets through registration to the new and existing IIT templates was improved when using the new template. PMID:20851772

High-Dimensional Quantum Information Processing with Linear Optics

NASA Astrophysics Data System (ADS)

Fitzpatrick, Casey A.

Quantum information processing (QIP) is an interdisciplinary field concerned with the development of computers and information processing systems that utilize quantum mechanical properties of nature to carry out their function. QIP systems have become vastly more practical since the turn of the century. Today, QIP applications span imaging, cryptographic security, computation, and simulation (quantum systems that mimic other quantum systems). Many important strategies improve quantum versions of classical information system hardware, such as single photon detectors and quantum repeaters. Another more abstract strategy engineers high-dimensional quantum state spaces, so that each successful event carries more information than traditional two-level systems allow. Photonic states in particular bring the added advantages of weak environmental coupling and data transmission near the speed of light, allowing for simpler control and lower system design complexity. In this dissertation, numerous novel, scalable designs for practical high-dimensional linear-optical QIP systems are presented. First, a correlated photon imaging scheme using orbital angular momentum (OAM) states to detect rotational symmetries in objects using measurements, as well as building images out of those interactions is reported. Then, a statistical detection method using chains of OAM superpositions distributed according to the Fibonacci sequence is established and expanded upon. It is shown that the approach gives rise to schemes for sorting, detecting, and generating the recursively defined high-dimensional states on which some quantum cryptographic protocols depend. Finally, an ongoing study based on a generalization of the standard optical multiport for applications in quantum computation and simulation is reported upon. The architecture allows photons to reverse momentum inside the device. This in turn enables realistic implementation of controllable linear-optical scattering vertices for carrying out quantum walks on arbitrary graph structures, a powerful tool for any quantum computer. It is shown that the novel architecture provides new, efficient capabilities for the optical quantum simulation of Hamiltonians and topologically protected states. Further, these simulations use exponentially fewer resources than feedforward techniques, scale linearly to higher-dimensional systems, and use only linear optics, thus offering a concrete experimentally achievable implementation of graphical models of discrete-time quantum systems.

Mapping High Dimensional Sparse Customer Requirements into Product Configurations

NASA Astrophysics Data System (ADS)

Jiao, Yao; Yang, Yu; Zhang, Hongshan

2017-10-01

Mapping customer requirements into product configurations is a crucial step for product design, while, customers express their needs ambiguously and locally due to the lack of domain knowledge. Thus the data mining process of customer requirements might result in fragmental information with high dimensional sparsity, leading the mapping procedure risk uncertainty and complexity. The Expert Judgment is widely applied against that background since there is no formal requirements for systematic or structural data. However, there are concerns on the repeatability and bias for Expert Judgment. In this study, an integrated method by adjusted Local Linear Embedding (LLE) and Naïve Bayes (NB) classifier is proposed to map high dimensional sparse customer requirements to product configurations. The integrated method adjusts classical LLE to preprocess high dimensional sparse dataset to satisfy the prerequisite of NB for classifying different customer requirements to corresponding product configurations. Compared with Expert Judgment, the adjusted LLE with NB performs much better in a real-world Tablet PC design case both in accuracy and robustness.

Modalities for Visualization of Cortical Bone Remodeling: The Past, Present, and Future

PubMed Central

Harrison, Kimberly D.; Cooper, David M. L.

2015-01-01

Bone’s ability to respond to load-related phenomena and repair microdamage is achieved through the remodeling process, which renews bone by activating groups of cells known as basic multicellular units (BMUs). The products of BMUs, secondary osteons, have been extensively studied via classic two-dimensional techniques, which have provided a wealth of information on how histomorphology relates to skeletal structure and function. Remodeling is critical in maintaining healthy bone tissue; however, in osteoporotic bone, imbalanced resorption results in increased bone fragility and fracture. With increasing life expectancy, such degenerative bone diseases are a growing concern. The three-dimensional (3D) morphology of BMUs and their correlation to function, however, are not well-characterized and little is known about the specific mechanisms that initiate and regulate their activity within cortical bone. We believe a key limitation has been the lack of 3D information about BMU morphology and activity. Thus, this paper reviews methodologies for 3D investigation of cortical bone remodeling and, specifically, structures associated with BMU activity (resorption spaces) and the structures they create (secondary osteons), spanning from histology to modern ex vivo imaging modalities, culminating with the growing potential of in vivo imaging. This collection of papers focuses on the theme of “putting the ‘why’ back into bone architecture.” Remodeling is one of two mechanisms “how” bone structure is dynamically modified and thus an improved 3D understanding of this fundamental process is crucial to ultimately understanding the “why.” PMID:26322017

[Studies on the structure-activity relationship of retinoids--Hansch analysis and 3D-OSAR studies on specific ligands of retinoid x receptor].

PubMed

Huang, N; Chu, F; Guo, Z

1998-06-01

Retinoids (Vitamin A, its metabolites and synthetic analogues) play important roles in a variety of biological processes, including cellular differentiation, proliferation and apoptosis. The many diverse actions of retinoids attribute to the ability of regulating transcription of different target genes through activation of multiple retinoid nuclear receptors (RAR of RXR). So, retinoids with selective binding ability to specific receptor may not only have improved therapeutic indices, but may also be invaluable for elucidating the molecular mechanism of retinoidal transcriptional activation. Based on the two dimensional and three dimensional quantitative structure-activity relationships of specific ligands of RXR, we carried out mimesis of environment of ligands interacting with their receptor and, to some extent, mapping the topological and physico-chemical characteristics of receptor. The knowledge of the QSAR study will offer detailed molecular information for design, synthesis and biological evaluation in drug research and development.

Spectral implementation of some quantum algorithms by one- and two-dimensional nuclear magnetic resonance

NASA Astrophysics Data System (ADS)

Das, Ranabir; Kumar, Anil

2004-10-01

Quantum information processing has been effectively demonstrated on a small number of qubits by nuclear magnetic resonance. An important subroutine in any computing is the readout of the output. "Spectral implementation" originally suggested by Z. L. Madi, R. Bruschweiler, and R. R. Ernst [J. Chem. Phys. 109, 10603 (1999)], provides an elegant method of readout with the use of an extra "observer" qubit. At the end of computation, detection of the observer qubit provides the output via the multiplet structure of its spectrum. In spectral implementation by two-dimensional experiment the observer qubit retains the memory of input state during computation, thereby providing correlated information on input and output, in the same spectrum. Spectral implementation of Grover's search algorithm, approximate quantum counting, a modified version of Berstein-Vazirani problem, and Hogg's algorithm are demonstrated here in three- and four-qubit systems.

Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping

NASA Astrophysics Data System (ADS)

Bongiovanni, Marie N.; Godet, Julien; Horrocks, Mathew H.; Tosatto, Laura; Carr, Alexander R.; Wirthensohn, David C.; Ranasinghe, Rohan T.; Lee, Ji-Eun; Ponjavic, Aleks; Fritz, Joelle V.; Dobson, Christopher M.; Klenerman, David; Lee, Steven F.

2016-12-01

Super-resolution microscopy allows biological systems to be studied at the nanoscale, but has been restricted to providing only positional information. Here, we show that it is possible to perform multi-dimensional super-resolution imaging to determine both the position and the environmental properties of single-molecule fluorescent emitters. The method presented here exploits the solvatochromic and fluorogenic properties of nile red to extract both the emission spectrum and the position of each dye molecule simultaneously enabling mapping of the hydrophobicity of biological structures. We validated this by studying synthetic lipid vesicles of known composition. We then applied both to super-resolve the hydrophobicity of amyloid aggregates implicated in neurodegenerative diseases, and the hydrophobic changes in mammalian cell membranes. Our technique is easily implemented by inserting a transmission diffraction grating into the optical path of a localization-based super-resolution microscope, enabling all the information to be extracted simultaneously from a single image plane.

Multi-dimensional super-resolution imaging enables surface hydrophobicity mapping

PubMed Central

Bongiovanni, Marie N.; Godet, Julien; Horrocks, Mathew H.; Tosatto, Laura; Carr, Alexander R.; Wirthensohn, David C.; Ranasinghe, Rohan T.; Lee, Ji-Eun; Ponjavic, Aleks; Fritz, Joelle V.; Dobson, Christopher M.; Klenerman, David; Lee, Steven F.

2016-01-01

Super-resolution microscopy allows biological systems to be studied at the nanoscale, but has been restricted to providing only positional information. Here, we show that it is possible to perform multi-dimensional super-resolution imaging to determine both the position and the environmental properties of single-molecule fluorescent emitters. The method presented here exploits the solvatochromic and fluorogenic properties of nile red to extract both the emission spectrum and the position of each dye molecule simultaneously enabling mapping of the hydrophobicity of biological structures. We validated this by studying synthetic lipid vesicles of known composition. We then applied both to super-resolve the hydrophobicity of amyloid aggregates implicated in neurodegenerative diseases, and the hydrophobic changes in mammalian cell membranes. Our technique is easily implemented by inserting a transmission diffraction grating into the optical path of a localization-based super-resolution microscope, enabling all the information to be extracted simultaneously from a single image plane. PMID:27929085

Using the small alignment index chaos indicator to characterize the vibrational dynamics of a molecular system: LiNC-LiCN.

PubMed

Benitez, P; Losada, J C; Benito, R M; Borondo, F

2015-10-01

A study of the dynamical characteristics of the phase space corresponding to the vibrations of the LiNC-LiCN molecule using an analysis based on the small alignment index (SALI) is presented. SALI is a good indicator of chaos that can easily determine whether a given trajectory is regular or chaotic regardless of the dimensionality of the system, and can also provide a wealth of dynamical information when conveniently implemented. In two-dimensional (2D) systems SALI maps are computed as 2D phase space representations, where the SALI asymptotic values are represented in color scale. We show here how these maps provide full information on the dynamical phase space structure of the LiNC-LiCN system, even quantifying numerically the volume of the different zones of chaos and regularity as a function of the molecule excitation energy.

Three-dimensional geostatistical inversion of flowmeter and pumping test data.

PubMed

Li, Wei; Englert, Andreas; Cirpka, Olaf A; Vereecken, Harry

2008-01-01

We jointly invert field data of flowmeter and multiple pumping tests in fully screened wells to estimate hydraulic conductivity using a geostatistical method. We use the steady-state drawdowns of pumping tests and the discharge profiles of flowmeter tests as our data in the inference. The discharge profiles need not be converted to absolute hydraulic conductivities. Consequently, we do not need measurements of depth-averaged hydraulic conductivity at well locations. The flowmeter profiles contain information about relative vertical distributions of hydraulic conductivity, while drawdown measurements of pumping tests provide information about horizontal fluctuation of the depth-averaged hydraulic conductivity. We apply the method to data obtained at the Krauthausen test site of the Forschungszentrum Jülich, Germany. The resulting estimate of our joint three-dimensional (3D) geostatistical inversion shows an improved 3D structure in comparison to the inversion of pumping test data only.

Estimating the functional dimensionality of neural representations.

PubMed

Ahlheim, Christiane; Love, Bradley C

2018-06-07

Recent advances in multivariate fMRI analysis stress the importance of information inherent to voxel patterns. Key to interpreting these patterns is estimating the underlying dimensionality of neural representations. Dimensions may correspond to psychological dimensions, such as length and orientation, or involve other coding schemes. Unfortunately, the noise structure of fMRI data inflates dimensionality estimates and thus makes it difficult to assess the true underlying dimensionality of a pattern. To address this challenge, we developed a novel approach to identify brain regions that carry reliable task-modulated signal and to derive an estimate of the signal's functional dimensionality. We combined singular value decomposition with cross-validation to find the best low-dimensional projection of a pattern of voxel-responses at a single-subject level. Goodness of the low-dimensional reconstruction is measured as Pearson correlation with a test set, which allows to test for significance of the low-dimensional reconstruction across participants. Using hierarchical Bayesian modeling, we derive the best estimate and associated uncertainty of underlying dimensionality across participants. We validated our method on simulated data of varying underlying dimensionality, showing that recovered dimensionalities match closely true dimensionalities. We then applied our method to three published fMRI data sets all involving processing of visual stimuli. The results highlight three possible applications of estimating the functional dimensionality of neural data. Firstly, it can aid evaluation of model-based analyses by revealing which areas express reliable, task-modulated signal that could be missed by specific models. Secondly, it can reveal functional differences across brain regions. Thirdly, knowing the functional dimensionality allows assessing task-related differences in the complexity of neural patterns. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

3D imaging of a rice pollen grain using transmission X-ray microscopy.

PubMed

Wang, Shengxiang; Wang, Dajiang; Wu, Qiao; Gao, Kun; Wang, Zhili; Wu, Ziyu

2015-07-01

For the first time, the three-dimensional (3D) ultrastructure of an intact rice pollen cell has been obtained using a full-field transmission hard X-ray microscope operated in Zernike phase contrast mode. After reconstruction and segmentation from a series of projection images, complete 3D structural information of a 35 µm rice pollen grain is presented at a resolution of ∼100 nm. The reconstruction allows a clear differentiation of various subcellular structures within the rice pollen grain, including aperture, lipid body, mitochondrion, nucleus and vacuole. Furthermore, quantitative information was obtained about the distribution of cytoplasmic organelles and the volume percentage of each kind of organelle. These results demonstrate that transmission X-ray microscopy can be quite powerful for non-destructive investigation of 3D structures of whole eukaryotic cells.

NMR-based diffusion lattice imaging

NASA Astrophysics Data System (ADS)

Laun, Frederik Bernd; Müller, Lars; Kuder, Tristan Anselm

2016-03-01

Nuclear magnetic resonance (NMR) diffusion experiments are widely employed as they yield information about structures hindering the diffusion process, e.g., about cell membranes. While it has been shown in recent articles that these experiments can be used to determine the shape of closed pores averaged over a volume of interest, it is still an open question how much information can be gained in open well-connected systems. In this theoretical work, it is shown that the full structure information of connected periodic systems is accessible. To this end, the so-called "SEquential Rephasing by Pulsed field-gradient Encoding N Time intervals" (SERPENT) sequence is used, which employs several diffusion encoding gradient pulses with different amplitudes. Two two-dimensional solid matrices that are surrounded by an NMR-visible medium are considered: a hexagonal lattice of cylinders and a rectangular lattice of isosceles triangles.

Graphene-enhanced infrared near-field microscopy.

PubMed

Li, Peining; Wang, Tao; Böckmann, Hannes; Taubner, Thomas

2014-08-13

Graphene is a promising two-dimensional platform for widespread nanophotonic applications. Recent theories have predicted that graphene can also enhance evanescent fields for subdiffraction-limited imaging. Here, for the first time we experimentally demonstrate that monolayer graphene offers a 7-fold enhancement of evanescent information, improving conventional infrared near-field microscopy to resolve buried structures at a 500 nm depth with λ/11-resolution.

A comparison of forest canopy models derived from LIDAR and INSAR data in a Pacific Northwest conifer forest.

Treesearch

Hans-Erik Andersen; Robert J. McGaughey; Ward W. Carson; Stephen E. Reutebuch; Bryan Mercer; Jeremy Allan

2004-01-01

Active remote sensing technologies, including interferometric radar (InSAR) and airborne laser scanning (LIDAR) have the potential to provide accurate information relating to three-dimensional forest canopy structure over extensive areas of the landscape. In order to assess the capabilities of these alternative systems for characterizing the forest canopy dimensions,...

Probing Phonon Dynamics in Individual Single-Walled Carbon Nanotubes.

PubMed

Jiang, Tao; Hong, Hao; Liu, Can; Liu, Wei-Tao; Liu, Kaihui; Wu, Shiwei

2018-04-11

Interactions between elementary excitations, such as carriers, phonons, and plasmons, are critical for understanding the optical and electronic properties of materials. The significance of these interactions is more prominent in low-dimensional materials and can dominate their physical properties due to the enhanced interactions between these excitations. One-dimensional single-walled carbon nanotubes provide an ideal system for studying such interactions due to their perfect physical structures and rich electronic properties. Here we investigated G-mode phonon dynamics in individual suspended chirality-resolved single-walled carbon nanotubes by time-resolved anti-Stokes Raman spectroscopy. The improved technique allowed us to probe the intrinsic phonon information on a single-tube level and exclude the influences of tube-tube and tube-substrate interactions. We found that the G-mode phonon lifetime ranges from 0.75-2.25 ps and critically depends on whether the tube is metallic or semiconducting. In comparison with the phonon lifetimes in graphene and graphite, we revealed structure-dependent carrier-phonon and phonon-phonon interactions in nanotubes. Our results provide new information for optimizing the design of nanotube electronic/optoelectronic devices by better understanding and utilizing their phonon decay channels.

A Multivariate Granger Causality Concept towards Full Brain Functional Connectivity.

PubMed

Schmidt, Christoph; Pester, Britta; Schmid-Hertel, Nicole; Witte, Herbert; Wismüller, Axel; Leistritz, Lutz

2016-01-01

Detecting changes of spatially high-resolution functional connectivity patterns in the brain is crucial for improving the fundamental understanding of brain function in both health and disease, yet still poses one of the biggest challenges in computational neuroscience. Currently, classical multivariate Granger Causality analyses of directed interactions between single process components in coupled systems are commonly restricted to spatially low- dimensional data, which requires a pre-selection or aggregation of time series as a preprocessing step. In this paper we propose a new fully multivariate Granger Causality approach with embedded dimension reduction that makes it possible to obtain a representation of functional connectivity for spatially high-dimensional data. The resulting functional connectivity networks may consist of several thousand vertices and thus contain more detailed information compared to connectivity networks obtained from approaches based on particular regions of interest. Our large scale Granger Causality approach is applied to synthetic and resting state fMRI data with a focus on how well network community structure, which represents a functional segmentation of the network, is preserved. It is demonstrated that a number of different community detection algorithms, which utilize a variety of algorithmic strategies and exploit topological features differently, reveal meaningful information on the underlying network module structure.

Lysine N[superscript zeta]-Decarboxylation Switch and Activation of the [beta]-Lactam Sensor Domain of BlaR1 Protein of Methicillin-resistant Staphylococcus aureus

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

Borbulevych, Oleg; Kumarasiri, Malika; Wilson, Brian

The integral membrane protein BlaR1 of methicillin-resistant Staphylococcus aureus senses the presence of {beta}-lactam antibiotics in the milieu and transduces the information to the cytoplasm, where the biochemical events that unleash induction of antibiotic resistance mechanisms take place. We report herein by two-dimensional and three-dimensional NMR experiments of the sensor domain of BlaR1 in solution and by determination of an x-ray structure for the apo protein that Lys-392 of the antibiotic-binding site is posttranslationally modified by N{sup {zeta}}-carboxylation. Additional crystallographic and NMR data reveal that on acylation of Ser-389 by antibiotics, Lys-392 experiences N{sup {zeta}}-decarboxylation. This unique process, termed themore » lysine N{sup {zeta}}-decarboxylation switch, arrests the sensor domain in the activated ('on') state, necessary for signal transduction and all the subsequent biochemical processes. We present structural information on how this receptor activation process takes place, imparting longevity to the antibiotic-receptor complex that is needed for the induction of the antibiotic-resistant phenotype in methicillin-resistant S. aureus.« less

Big Data Analytics for Scanning Transmission Electron Microscopy Ptychography

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

Jesse, S.; Chi, M.; Belianinov, A.

Electron microscopy is undergoing a transition; from the model of producing only a few micrographs, through the current state where many images and spectra can be digitally recorded, to a new mode where very large volumes of data (movies, ptychographic and multi-dimensional series) can be rapidly obtained. In this paper, we discuss the application of so-called “big-data” methods to high dimensional microscopy data, using unsupervised multivariate statistical techniques, in order to explore salient image features in a specific example of BiFeO 3 domains. Remarkably, k-means clustering reveals domain differentiation despite the fact that the algorithm is purely statistical in naturemore » and does not require any prior information regarding the material, any coexisting phases, or any differentiating structures. While this is a somewhat trivial case, this example signifies the extraction of useful physical and structural information without any prior bias regarding the sample or the instrumental modality. Further interpretation of these types of results may still require human intervention. Finally, however, the open nature of this algorithm and its wide availability, enable broad collaborations and exploratory work necessary to enable efficient data analysis in electron microscopy.« less

Big Data Analytics for Scanning Transmission Electron Microscopy Ptychography

DOE PAGES

Jesse, S.; Chi, M.; Belianinov, A.; ...

2016-05-23

Electron microscopy is undergoing a transition; from the model of producing only a few micrographs, through the current state where many images and spectra can be digitally recorded, to a new mode where very large volumes of data (movies, ptychographic and multi-dimensional series) can be rapidly obtained. In this paper, we discuss the application of so-called “big-data” methods to high dimensional microscopy data, using unsupervised multivariate statistical techniques, in order to explore salient image features in a specific example of BiFeO 3 domains. Remarkably, k-means clustering reveals domain differentiation despite the fact that the algorithm is purely statistical in naturemore » and does not require any prior information regarding the material, any coexisting phases, or any differentiating structures. While this is a somewhat trivial case, this example signifies the extraction of useful physical and structural information without any prior bias regarding the sample or the instrumental modality. Further interpretation of these types of results may still require human intervention. Finally, however, the open nature of this algorithm and its wide availability, enable broad collaborations and exploratory work necessary to enable efficient data analysis in electron microscopy.« less

Big Data Analytics for Scanning Transmission Electron Microscopy Ptychography

PubMed Central

Jesse, S.; Chi, M.; Belianinov, A.; Beekman, C.; Kalinin, S. V.; Borisevich, A. Y.; Lupini, A. R.

2016-01-01

Electron microscopy is undergoing a transition; from the model of producing only a few micrographs, through the current state where many images and spectra can be digitally recorded, to a new mode where very large volumes of data (movies, ptychographic and multi-dimensional series) can be rapidly obtained. Here, we discuss the application of so-called “big-data” methods to high dimensional microscopy data, using unsupervised multivariate statistical techniques, in order to explore salient image features in a specific example of BiFeO3 domains. Remarkably, k-means clustering reveals domain differentiation despite the fact that the algorithm is purely statistical in nature and does not require any prior information regarding the material, any coexisting phases, or any differentiating structures. While this is a somewhat trivial case, this example signifies the extraction of useful physical and structural information without any prior bias regarding the sample or the instrumental modality. Further interpretation of these types of results may still require human intervention. However, the open nature of this algorithm and its wide availability, enable broad collaborations and exploratory work necessary to enable efficient data analysis in electron microscopy. PMID:27211523

Three dimensional macroporous architectures and aerogels built of carbon nanotubes and/or graphene: synthesis and applications.

PubMed

Nardecchia, Stefania; Carriazo, Daniel; Ferrer, M Luisa; Gutiérrez, María C; del Monte, Francisco

2013-01-21

Carbon nanotubes and graphene are some of the most intensively explored carbon allotropes in materials science. This interest mainly resides in their unique properties with electrical conductivities as high as 10(4) S cm(-1), thermal conductivities as high as 5000 W m(-1) K and superior mechanical properties with elastic moduli on the order of 1 TPa for both of them. The possibility to translate the individual properties of these monodimensional (e.g. carbon nanotubes) and bidimensional (e.g. graphene) building units into two-dimensional free-standing thick and thin films has paved the way for using these allotropes in a number of applications (including photocatalysis, electrochemistry, electronics and optoelectronics, among others) as well as for the preparation of biological and chemical sensors. More recently and while recognizing the tremendous interest of these two-dimensional structures, researchers are noticing that the performance of certain devices can experience a significant enhancement by the use of three-dimensional architectures and/or aerogels because of the increase of active material per projected area. This is obviously the case as long as the nanometre-sized building units remain accessible so that the concept of hierarchical three-dimensional organization is critical to guarantee the mass transport and, as consequence, performance enhancement. Thus, this review aims to describe the different synthetic processes used for preparation of these three-dimensional architectures and/or aerogels containing either any or both allotropes, and the different fields of application in which the particular structure of these materials provided a significant enhancement in the efficacy as compared to their two-dimensional analogues or even opened the path to novel applications. The unprecedented compilation of information from both CNT- and graphene-based three-dimensional architectures and/or aerogels in a single revision is also of interest because it allows a straightforward comparison between the particular features provided by each allotrope.

Manifold learning in machine vision and robotics

NASA Astrophysics Data System (ADS)

Bernstein, Alexander

2017-02-01

Smart algorithms are used in Machine vision and Robotics to organize or extract high-level information from the available data. Nowadays, Machine learning is an essential and ubiquitous tool to automate extraction patterns or regularities from data (images in Machine vision; camera, laser, and sonar sensors data in Robotics) in order to solve various subject-oriented tasks such as understanding and classification of images content, navigation of mobile autonomous robot in uncertain environments, robot manipulation in medical robotics and computer-assisted surgery, and other. Usually such data have high dimensionality, however, due to various dependencies between their components and constraints caused by physical reasons, all "feasible and usable data" occupy only a very small part in high dimensional "observation space" with smaller intrinsic dimensionality. Generally accepted model of such data is manifold model in accordance with which the data lie on or near an unknown manifold (surface) of lower dimensionality embedded in an ambient high dimensional observation space; real-world high-dimensional data obtained from "natural" sources meet, as a rule, this model. The use of Manifold learning technique in Machine vision and Robotics, which discovers a low-dimensional structure of high dimensional data and results in effective algorithms for solving of a large number of various subject-oriented tasks, is the content of the conference plenary speech some topics of which are in the paper.

Worldwide Protein Data Bank validation information: usage and trends.

PubMed

Smart, Oliver S; Horský, Vladimír; Gore, Swanand; Svobodová Vařeková, Radka; Bendová, Veronika; Kleywegt, Gerard J; Velankar, Sameer

2018-03-01

Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to obtain advice on the methods and standards to be used to validate structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and three-dimensional electron cryo-microscopy. The resulting wwPDB validation pipeline is an integral part of the wwPDB OneDep deposition, biocuration and validation system. The wwPDB Validation Service webserver (https://validate.wwpdb.org) can be used to perform checks prior to deposition. Here, it is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. The ValTrends DB database provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics.

Worldwide Protein Data Bank validation information: usage and trends

PubMed Central

Horský, Vladimír; Gore, Swanand; Svobodová Vařeková, Radka; Bendová, Veronika

2018-01-01

Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to obtain advice on the methods and standards to be used to validate structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and three-dimensional electron cryo-microscopy. The resulting wwPDB validation pipeline is an integral part of the wwPDB OneDep deposition, biocuration and validation system. The wwPDB Validation Service webserver (https://validate.wwpdb.org) can be used to perform checks prior to deposition. Here, it is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. The ValTrendsDB database provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics. PMID:29533231

Practical Methods for Including Torsional Anharmonicity in Thermochemical Calculations on Complex Molecules: The Internal-Coordinate Multi-Structural Approximation

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

Zheng, J.; Yu, T.; Papajak, E.

2011-01-01

Many methods for correcting harmonic partition functions for the presence of torsional motions employ some form of one-dimensional torsional treatment to replace the harmonic contribution of a specific normal mode. However, torsions are often strongly coupled to other degrees of freedom, especially other torsions and low-frequency bending motions, and this coupling can make assigning torsions to specific normal modes problematic. Here, we present a new class of methods, called multi-structural (MS) methods, that circumvents the need for such assignments by instead adjusting the harmonic results by torsional correction factors that are determined using internal coordinates. We present three versions ofmore » the MS method: (i) MS-AS based on including all structures (AS), i.e., all conformers generated by internal rotations; (ii) MS-ASCB based on all structures augmented with explicit conformational barrier (CB) information, i.e., including explicit calculations of all barrier heights for internal-rotation barriers between the conformers; and (iii) MS-RS based on including all conformers generated from a reference structure (RS) by independent torsions. In the MS-AS scheme, one has two options for obtaining the local periodicity parameters, one based on consideration of the nearly separable limit and one based on strongly coupled torsions. The latter involves assigning the local periodicities on the basis of Voronoi volumes. The methods are illustrated with calculations for ethanol, 1-butanol, and 1-pentyl radical as well as two one-dimensional torsional potentials. The MS-AS method is particularly interesting because it does not require any information about conformational barriers or about the paths that connect the various structures.« less

Practical methods for including torsional anharmonicity in thermochemical calculations on complex molecules: the internal-coordinate multi-structural approximation.

PubMed

Zheng, Jingjing; Yu, Tao; Papajak, Ewa; Alecu, I M; Mielke, Steven L; Truhlar, Donald G

2011-06-21

Many methods for correcting harmonic partition functions for the presence of torsional motions employ some form of one-dimensional torsional treatment to replace the harmonic contribution of a specific normal mode. However, torsions are often strongly coupled to other degrees of freedom, especially other torsions and low-frequency bending motions, and this coupling can make assigning torsions to specific normal modes problematic. Here, we present a new class of methods, called multi-structural (MS) methods, that circumvents the need for such assignments by instead adjusting the harmonic results by torsional correction factors that are determined using internal coordinates. We present three versions of the MS method: (i) MS-AS based on including all structures (AS), i.e., all conformers generated by internal rotations; (ii) MS-ASCB based on all structures augmented with explicit conformational barrier (CB) information, i.e., including explicit calculations of all barrier heights for internal-rotation barriers between the conformers; and (iii) MS-RS based on including all conformers generated from a reference structure (RS) by independent torsions. In the MS-AS scheme, one has two options for obtaining the local periodicity parameters, one based on consideration of the nearly separable limit and one based on strongly coupled torsions. The latter involves assigning the local periodicities on the basis of Voronoi volumes. The methods are illustrated with calculations for ethanol, 1-butanol, and 1-pentyl radical as well as two one-dimensional torsional potentials. The MS-AS method is particularly interesting because it does not require any information about conformational barriers or about the paths that connect the various structures.

Guiding Conformation Space Search with an All-Atom Energy Potential

PubMed Central

Brunette, TJ; Brock, Oliver

2009-01-01

The most significant impediment for protein structure prediction is the inadequacy of conformation space search. Conformation space is too large and the energy landscape too rugged for existing search methods to consistently find near-optimal minima. To alleviate this problem, we present model-based search, a novel conformation space search method. Model-based search uses highly accurate information obtained during search to build an approximate, partial model of the energy landscape. Model-based search aggregates information in the model as it progresses, and in turn uses this information to guide exploration towards regions most likely to contain a near-optimal minimum. We validate our method by predicting the structure of 32 proteins, ranging in length from 49 to 213 amino acids. Our results demonstrate that model-based search is more effective at finding low-energy conformations in high-dimensional conformation spaces than existing search methods. The reduction in energy translates into structure predictions of increased accuracy. PMID:18536015

Electron-hole liquid in semiconductors and low-dimensional structures

NASA Astrophysics Data System (ADS)

Sibeldin, N. N.

2017-11-01

The condensation of excitons into an electron-hole liquid (EHL) and the main EHL properties in bulk semiconductors and low-dimensional structures are considered. The EHL properties in bulk materials are discussed primarily in qualitative terms based on the experimental results obtained for germanium and silicon. Some of the experiments in which the main EHL thermodynamic parameters (density and binding energy) have been obtained are described and the basic factors that determine these parameters are considered. Topics covered include the effect of external perturbations (uniaxial strain and magnetic field) on EHL stability; phase diagrams for a nonequilibrium exciton-gas-EHL system; information on the size and concentration of electron-hole drops (EHDs) under various experimental conditions; the kinetics of exciton condensation and of recombination in the exciton-gas-EHD system; dynamic EHD properties and the motion of EHDs under the action of external forces; the properties of giant EHDs that form in potential wells produced by applying an inhomogeneous strain to the crystal; and effects associated with the drag of EHDs by nonequilibrium phonons (phonon wind), including the dynamics and formation of an anisotropic spatial structure of the EHD cloud. In discussing EHLs in low-dimensional structures, a number of studies are reviewed on the observation and experimental investigation of phenomena such as spatially indirect (dipolar) electron-hole and exciton (dielectric) liquids in GaAs/AlGaAs structures with double quantum wells (QWs), EHDs containing only a few electron-hole pairs (dropletons), EHLs in type-I silicon QWs, and spatially direct and dipolar EHLs in type-II silicon-germanium heterostructures.

Information Gain Based Dimensionality Selection for Classifying Text Documents

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

Dumidu Wijayasekara; Milos Manic; Miles McQueen

2013-06-01

Selecting the optimal dimensions for various knowledge extraction applications is an essential component of data mining. Dimensionality selection techniques are utilized in classification applications to increase the classification accuracy and reduce the computational complexity. In text classification, where the dimensionality of the dataset is extremely high, dimensionality selection is even more important. This paper presents a novel, genetic algorithm based methodology, for dimensionality selection in text mining applications that utilizes information gain. The presented methodology uses information gain of each dimension to change the mutation probability of chromosomes dynamically. Since the information gain is calculated a priori, the computational complexitymore » is not affected. The presented method was tested on a specific text classification problem and compared with conventional genetic algorithm based dimensionality selection. The results show an improvement of 3% in the true positives and 1.6% in the true negatives over conventional dimensionality selection methods.« less

Coherent structures and flow topology of transitional separated-reattached flow over two and three dimensional geometrical shapes

NASA Astrophysics Data System (ADS)

Diabil, Hayder Azeez; Li, Xin Kai; Abdalla, Ibrahim Elrayah

2017-09-01

Large-scale organized motions (commonly referred to coherent structures) and flow topology of a transitional separated-reattached flow have been visualised and investigated using flow visualisation techniques. Two geometrical shapes including two-dimensional flat plate with rectangular leading edge and three-dimensional square cylinder are chosen to shed a light on the flow topology and present coherent structures of the flow over these shapes. For both geometries and in the early stage of the transition, two-dimensional Kelvin-Helmholtz rolls are formed downstream of the leading edge. They are observed to be twisting around the square cylinder while they stay flat in the case of the two-dimensional flat plate. For both geometrical shapes, the two-dimensional Kelvin-Helmholtz rolls move downstream of the leading edge and they are subjected to distortion to form three-dimensional hairpin structures. The flow topology in the flat plate is different from that in the square cylinder. For the flat plate, there is a merging process by a pairing of the Kelvin-Helmholtz rolls to form a large structure that breaks down directly into many hairpin structures. For the squire cylinder case, the Kelvin-Helmholtz roll evolves topologically to form a hairpin structure. In the squire cylinder case, the reattachment length is much shorter and a forming of the three-dimensional structures is closer to the leading edge than that in the flat plate case.

Study of the Chemical Space of Selected Bacteriostatic Sulfonamides from an Information Theory Point of View.

PubMed

López-Rosa, Sheila; Molina-Espíritu, Moyocoyani; Esquivel, Rodolfo O; Soriano-Correa, Catalina; Dehesa, Jésus S

2016-12-05

The relative structural location of a selected group of 27 sulfonamide-like molecules in a chemical space defined by three information theory quantities (Shannon entropy, Fisher information, and disequilibrium) is discussed. This group is composed of 15 active bacteriostatic molecules, 11 theoretically designed ones, and para-aminobenzoic acid. This endeavor allows molecules that share common chemical properties through the molecular backbone, but with significant differences in the identity of the chemical substituents, which might result in bacteriostatic activity, to be structurally classified and characterized. This is performed by quantifying the structural changes on the electron density distribution due to different functional groups and number of electrons. The macroscopic molecular features are described by means of the entropy-like notions of spatial electronic delocalization, order, and uniformity. Hence, an information theory three-dimensional space (IT-3D) emerges that allows molecules with common properties to be gathered. This space witnesses the biological activity of the sulfonamides. Some structural aspects and information theory properties can be associated, as a result of the IT-3D chemical space, with the bacteriostatic activity of these molecules. Most interesting is that the active bacteriostatic molecules are more similar to para-aminobenzoic acid than to the theoretically designed analogues. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Volume rendering based on magnetic resonance imaging: advances in understanding the three-dimensional anatomy of the human knee

PubMed Central

Anastasi, Giuseppe; Bramanti, Placido; Di Bella, Paolo; Favaloro, Angelo; Trimarchi, Fabio; Magaudda, Ludovico; Gaeta, Michele; Scribano, Emanuele; Bruschetta, Daniele; Milardi, Demetrio

2007-01-01

The choice of medical imaging techniques, for the purpose of the present work aimed at studying the anatomy of the knee, derives from the increasing use of images in diagnostics, research and teaching, and the subsequent importance that these methods are gaining within the scientific community. Medical systems using virtual reality techniques also offer a good alternative to traditional methods, and are considered among the most important tools in the areas of research and teaching. In our work we have shown some possible uses of three-dimensional imaging for the study of the morphology of the normal human knee, and its clinical applications. We used the direct volume rendering technique, and created a data set of images and animations to allow us to visualize the single structures of the human knee in three dimensions. Direct volume rendering makes use of specific algorithms to transform conventional two-dimensional magnetic resonance imaging sets of slices into see-through volume data set images. It is a technique which does not require the construction of intermediate geometric representations, and has the advantage of allowing the visualization of a single image of the full data set, using semi-transparent mapping. Digital images of human structures, and in particular of the knee, offer important information about anatomical structures and their relationships, and are of great value in the planning of surgical procedures. On this basis we studied seven volunteers with an average age of 25 years, who underwent magnetic resonance imaging. After elaboration of the data through post-processing, we analysed the structure of the knee in detail. The aim of our investigation was the three-dimensional image, in order to comprehend better the interactions between anatomical structures. We believe that these results, applied to living subjects, widen the frontiers in the areas of teaching, diagnostics, therapy and scientific research. PMID:17645453

Multiple brain atlas database and atlas-based neuroimaging system.

PubMed

Nowinski, W L; Fang, A; Nguyen, B T; Raphel, J K; Jagannathan, L; Raghavan, R; Bryan, R N; Miller, G A

1997-01-01

For the purpose of developing multiple, complementary, fully labeled electronic brain atlases and an atlas-based neuroimaging system for analysis, quantification, and real-time manipulation of cerebral structures in two and three dimensions, we have digitized, enhanced, segmented, and labeled the following print brain atlases: Co-Planar Stereotaxic Atlas of the Human Brain by Talairach and Tournoux, Atlas for Stereotaxy of the Human Brain by Schaltenbrand and Wahren, Referentially Oriented Cerebral MRI Anatomy by Talairach and Tournoux, and Atlas of the Cerebral Sulci by Ono, Kubik, and Abernathey. Three-dimensional extensions of these atlases have been developed as well. All two- and three-dimensional atlases are mutually preregistered and may be interactively registered with an actual patient's data. An atlas-based neuroimaging system has been developed that provides support for reformatting, registration, visualization, navigation, image processing, and quantification of clinical data. The anatomical index contains about 1,000 structures and over 400 sulcal patterns. Several new applications of the brain atlas database also have been developed, supported by various technologies such as virtual reality, the Internet, and electronic publishing. Fusion of information from multiple atlases assists the user in comprehensively understanding brain structures and identifying and quantifying anatomical regions in clinical data. The multiple brain atlas database and atlas-based neuroimaging system have substantial potential impact in stereotactic neurosurgery and radiotherapy by assisting in visualization and real-time manipulation in three dimensions of anatomical structures, in quantitative neuroradiology by allowing interactive analysis of clinical data, in three-dimensional neuroeducation, and in brain function studies.

Statistical Machine Learning for Structured and High Dimensional Data

DTIC Science & Technology

2014-09-17

AFRL-OSR-VA-TR-2014-0234 STATISTICAL MACHINE LEARNING FOR STRUCTURED AND HIGH DIMENSIONAL DATA Larry Wasserman CARNEGIE MELLON UNIVERSITY Final...Re . 8-98) v Prescribed by ANSI Std. Z39.18 14-06-2014 Final Dec 2009 - Aug 2014 Statistical Machine Learning for Structured and High Dimensional...area of resource-constrained statistical estimation. machine learning , high-dimensional statistics U U U UU John Lafferty 773-702-3813 > Research under

Structural formation of huntingtin-like aggregates probed by small-angle neutron scattering

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

Stanley, Christopher B; Perevozchikova, Tatiana; Berthelier-Jung, Valerie M

2011-01-01

In several neurodegenerative disorders, including Huntington s disease (HD), aspects concerning the earliest of protein structures that form along the aggregation pathway have increasingly gained attention since these particular species are likely to be neurotoxic. We used time-resolved small-angle neutron scattering (SANS) to probe in solution these transient structures formed by peptides having the N-terminal sequence context of mutant huntingtin (Htt) exon 1. We obtained snapshots of the formed aggregates as the kinetic reaction ensued to yield quantitative information on their size and mass. At the early stage, small precursor species with an initial radius of gyration (Rg) of 16.1more » 5.9 and average mass of a dimer to trimer were monitored. Structural growth was treated as two modes with a transition from three-dimensional early aggregate formation to two-dimensional fibril growth and association. Our SANS results on the internal structure of the mature fibrils demonstrate loose packing with about 1 peptide per 4.75 -sheet repeat distance, which is shown to be quantitatively consistent with a -helix model. This research provides new insights into the structures forming along the pathway of Htt exon 1 aggregation and should assist in determining the role that precursors play in neuronal toxicity.« less

Helical structures in vertically aligned dust particle chains in a complex plasma

NASA Astrophysics Data System (ADS)

Hyde, Truell W.; Kong, Jie; Matthews, Lorin S.

2013-05-01

Self-assembly of structures from vertically aligned, charged dust particle bundles within a glass box placed on the lower, powered electrode of a Gaseous Electronics Conference rf reference cell were produced and examined experimentally. Self-organized formation of one-dimensional vertical chains, two-dimensional zigzag structures, and three-dimensional helical structures of triangular, quadrangular, pentagonal, hexagonal, and heptagonal symmetries are shown to occur. System evolution is shown to progress from a one-dimensional chain structure, through a zigzag transition to a two-dimensional, spindlelike structure, and then to various three-dimensional, helical structures exhibiting multiple symmetries. Stable configurations are found to be dependent upon the system confinement, γ2=ω0h/ω0v2 (where ω0h,v are the horizontal and vertical dust resonance frequencies), the total number of particles within a bundle, and the rf power. For clusters having fixed numbers of particles, the rf power at which structural phase transitions occur is repeatable and exhibits no observable hysteresis. The critical conditions for these structural phase transitions as well as the basic symmetry exhibited by the one-, two-, and three-dimensional structures that subsequently develop are in good agreement with the theoretically predicted configurations of minimum energy determined employing molecular dynamics simulations for charged dust particles confined in a prolate, spheroidal potential as presented theoretically by Kamimura and Ishihara [Kamimura and Ishihara, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.85.016406 85, 016406 (2012)].

Assessing Dimensionality of Noncompensatory Multidimensional Item Response Theory with Complex Structures

ERIC Educational Resources Information Center

Svetina, Dubravka

2013-01-01

The purpose of this study was to investigate the effect of complex structure on dimensionality assessment in noncompensatory multidimensional item response models using dimensionality assessment procedures based on DETECT (dimensionality evaluation to enumerate contributing traits) and NOHARM (normal ogive harmonic analysis robust method). Five…

3D annotation and manipulation of medical anatomical structures

NASA Astrophysics Data System (ADS)

Vitanovski, Dime; Schaller, Christian; Hahn, Dieter; Daum, Volker; Hornegger, Joachim

2009-02-01

Although the medical scanners are rapidly moving towards a three-dimensional paradigm, the manipulation and annotation/labeling of the acquired data is still performed in a standard 2D environment. Editing and annotation of three-dimensional medical structures is currently a complex task and rather time-consuming, as it is carried out in 2D projections of the original object. A major problem in 2D annotation is the depth ambiguity, which requires 3D landmarks to be identified and localized in at least two of the cutting planes. Operating directly in a three-dimensional space enables the implicit consideration of the full 3D local context, which significantly increases accuracy and speed. A three-dimensional environment is as well more natural optimizing the user's comfort and acceptance. The 3D annotation environment requires the three-dimensional manipulation device and display. By means of two novel and advanced technologies, Wii Nintendo Controller and Philips 3D WoWvx display, we define an appropriate 3D annotation tool and a suitable 3D visualization monitor. We define non-coplanar setting of four Infrared LEDs with a known and exact position, which are tracked by the Wii and from which we compute the pose of the device by applying a standard pose estimation algorithm. The novel 3D renderer developed by Philips uses either the Z-value of a 3D volume, or it computes the depth information out of a 2D image, to provide a real 3D experience without having some special glasses. Within this paper we present a new framework for manipulation and annotation of medical landmarks directly in three-dimensional volume.

a Probabilistic Embedding Clustering Method for Urban Structure Detection

NASA Astrophysics Data System (ADS)

Lin, X.; Li, H.; Zhang, Y.; Gao, L.; Zhao, L.; Deng, M.

2017-09-01

Urban structure detection is a basic task in urban geography. Clustering is a core technology to detect the patterns of urban spatial structure, urban functional region, and so on. In big data era, diverse urban sensing datasets recording information like human behaviour and human social activity, suffer from complexity in high dimension and high noise. And unfortunately, the state-of-the-art clustering methods does not handle the problem with high dimension and high noise issues concurrently. In this paper, a probabilistic embedding clustering method is proposed. Firstly, we come up with a Probabilistic Embedding Model (PEM) to find latent features from high dimensional urban sensing data by "learning" via probabilistic model. By latent features, we could catch essential features hidden in high dimensional data known as patterns; with the probabilistic model, we can also reduce uncertainty caused by high noise. Secondly, through tuning the parameters, our model could discover two kinds of urban structure, the homophily and structural equivalence, which means communities with intensive interaction or in the same roles in urban structure. We evaluated the performance of our model by conducting experiments on real-world data and experiments with real data in Shanghai (China) proved that our method could discover two kinds of urban structure, the homophily and structural equivalence, which means clustering community with intensive interaction or under the same roles in urban space.

Ultra-wideband three-dimensional optoacoustic tomography.

PubMed

Gateau, Jérôme; Chekkoury, Andrei; Ntziachristos, Vasilis

2013-11-15

Broadband optoacoustic waves generated by biological tissues excited with nanosecond laser pulses carry information corresponding to a wide range of geometrical scales. Typically, the frequency content present in the signals generated during optoacoustic imaging is much larger compared to the frequency band captured by common ultrasonic detectors, the latter typically acting as bandpass filters. To image optical absorption within structures ranging from entire organs to microvasculature in three dimensions, we implemented optoacoustic tomography with two ultrasound linear arrays featuring a center frequency of 6 and 24 MHz, respectively. In the present work, we show that complementary information on anatomical features could be retrieved and provide a better understanding on the localization of structures in the general anatomy by analyzing multi-bandwidth datasets acquired on a freshly excised kidney.

Confinement and Structural Changes in Vertically Aligned Dust Structures

NASA Astrophysics Data System (ADS)

Hyde, Truell

2013-10-01

In physics, confinement is known to influence collective system behavior. Examples include coulomb crystal variants such as those formed from ions or dust particles (classical), electrons in quantum dots (quantum) and the structural changes observed in vertically aligned dust particle systems formed within a glass box placed on the lower electrode of a Gaseous Electronics Conference (GEC) rf reference cell. Recent experimental studies have expanded the above to include the biological domain by showing that the stability and dynamics of proteins confined through encapsulation and enzyme molecules placed in inorganic cavities such as those found in biosensors are also directly influenced by their confinement. In this paper, the self-assembly and subsequent collective behavior of structures formed from n, charged dust particles interacting with one another and located within a glass box placed on the lower, powered electrode of a GEC rf reference cell is discussed. Self-organized formation of vertically aligned one-dimensional chains, two-dimensional zigzag structures, and three-dimensional helical structures of triangular, quadrangular, pentagonal, hexagonal, and heptagonal symmetries are shown to occur. System evolution is shown to progress from one-dimensional chain structures, through a zigzag transition to a two-dimensional, spindle like structures, and then to various three-dimensional, helical structures exhibiting various symmetries. Stable configurations are shown to be strongly dependent upon system confinement. The critical conditions for structural transitions as well as the basic symmetry exhibited by the one-, two-, and three-dimensional structures that subsequently develop will be shown to be in good agreement with molecular dynamics simulations.

[3D visualization and analysis of vocal fold dynamics].

PubMed

Bohr, C; Döllinger, M; Kniesburges, S; Traxdorf, M

2016-04-01

Visual investigation methods of the larynx mainly allow for the two-dimensional presentation of the three-dimensional structures of the vocal fold dynamics. The vertical component of the vocal fold dynamics is often neglected, yielding a loss of information. The latest studies show that the vertical dynamic components are in the range of the medio-lateral dynamics and play a significant role within the phonation process. This work presents a method for future 3D reconstruction and visualization of endoscopically recorded vocal fold dynamics. The setup contains a high-speed camera (HSC) and a laser projection system (LPS). The LPS projects a regular grid on the vocal fold surfaces and in combination with the HSC allows a three-dimensional reconstruction of the vocal fold surface. Hence, quantitative information on displacements and velocities can be provided. The applicability of the method is presented for one ex-vivo human larynx, one ex-vivo porcine larynx and one synthetic silicone larynx. The setup introduced allows the reconstruction of the entire visible vocal fold surfaces for each oscillation status. This enables a detailed analysis of the three dimensional dynamics (i. e. displacements, velocities, accelerations) of the vocal folds. The next goal is the miniaturization of the LPS to allow clinical in-vivo analysis in humans. We anticipate new insight on dependencies between 3D dynamic behavior and the quality of the acoustic outcome for healthy and disordered phonation.

PHOTONICS AND NANOTECHNOLOGY Laser generation of nanostructures on the surface and in the bulk of solids

NASA Astrophysics Data System (ADS)

Bityurin, N. M.

2010-12-01

This paper considers nanostructuring of solid surfaces by nano-optical techniques, primarily by laser particle nanolithography. Threshold processes are examined that can be used for laser structuring of solid surfaces, with particular attention to laser swelling of materials. Fundamental spatial resolution issues in three-dimensional (3D) laser nanostructuring are analysed with application to laser nanopolymerisation and 3D optical information recording. The formation of nanostructures in the bulk of solids due to their structural instability under irradiation is exemplified by photoinduced formation of nanocomposites.

Three Dimensional Immobilization of Beta-Galactosidase on a Silicon Surface (Preprint)

DTIC Science & Technology

2006-12-01

initial activity after 10 days at 24°C. The ability to generate three- dimensional structures with enhanced loading capacity for biosensing molecules...dimensional structures for biosensors (Charles et al. 2004). Silicon samples that had been washed but not activated with APTS did not retain any enzyme...preparation. The use of silica particles to build a 3-dimensional structure not only provides an increased capacity for the immobilization of β

From Two‐ to Three‐Dimensional Structures of a Supertetrahedral Boran Using Density Functional Calculations

PubMed Central

Getmanskii, Iliya V.; Steglenko, Dmitrii V.; Koval, Vitaliy V.; Zaitsev, Stanislav A.

2017-01-01

Abstract With help of the DFT calculations and imposing of periodic boundary conditions the geometrical and electronic structures were investigated of two‐ and three‐dimensional boron systems designed on the basis of graphane and diamond lattices in which carbons were replaced with boron tetrahedrons. The consequent studies of two‐ and three‐layer systems resulted in the construction of a three‐dimensional supertetrahedral borane crystal structure. The two‐dimensional supertetrahedral borane structures with less than seven layers are dynamically unstable. At the same time the three‐dimensional superborane systems were found to be dynamically stable. Lack of the forbidden electronic zone for the studied boron systems testifies that these structures can behave as good conductors. The low density of the supertetrahedral borane crystal structures (0.9 g cm−3) is close to that of water, which offers the perspective for their application as aerospace and cosmic materials. PMID:28402596

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.

PubMed

Boniecki, Michal J; Lach, Grzegorz; Dawson, Wayne K; Tomala, Konrad; Lukasz, Pawel; Soltysinski, Tomasz; Rother, Kristian M; Bujnicki, Janusz M

2016-04-20

RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Characterization of Homopolymer and Polymer Blend Films by Phase Sensitive Acoustic Microscopy

NASA Astrophysics Data System (ADS)

Ngwa, Wilfred; Wannemacher, Reinhold; Grill, Wolfgang

2003-03-01

CHARACTERIZATION OF HOMOPOLYMER AND POLYMER BLEND FILMS BY PHASE SENSITIVE ACOUSTIC MICROSCOPY W Ngwa, R Wannemacher, W Grill Institute of Experimental Physics II, University of Leipzig, 04103 Leipzig, Germany Abstract We have used phase sensitive acoustic microscopy (PSAM) to study homopolymer thin films of polystyrene (PS) and poly (methyl methacrylate) (PMMA), as well as PS/PMMA blend films. We show from our results that PSAM can be used as a complementary and highly valuable technique for elucidating the three-dimensional (3D) morphology and micromechanical properties of thin films. Three-dimensional image acquisition with vector contrast provides the basis for: complex V(z) analysis (per image pixel), 3D image processing, height profiling, and subsurface image analysis of the polymer films. Results show good agreement with previous studies. In addition, important new information on the three dimensional structure and properties of polymer films is obtained. Homopolymer film structure analysis reveals (pseudo-) dewetting by retraction of droplets, resulting in a morphology that can serve as a starting point for the analysis of polymer blend thin films. The outcome of confocal laser scanning microscopy studies, performed on the same samples are correlated with the obtained results. Advantages and limitations of PSAM are discussed.

Visualization of Sources in the Universe

NASA Astrophysics Data System (ADS)

Kafatos, M.; Cebral, J. R.

1993-12-01

We have begun to develop a series of visualization tools of importance to the display of astronomical data and have applied these to the visualization of cosmological sources in the recently formed Institute for Computational Sciences and Informatics at GMU. One can use a three-dimensional perspective plot of the density surface for three dimensional data and in this case the iso-level contours are three- dimensional surfaces. Sophisticated rendering algorithms combined with multiple source lighting allow us to look carefully at such density contours and to see fine structure on the surface of the density contours. Stereoscopic and transparent rendering can give an even more sophisticated approach with multi-layered surfaces providing information at different levels. We have applied these methods to looking at density surfaces of 3-D data such as 100 clusters of galaxies and 2500 galaxies in the CfA redshift survey. Our plots presented are based on three variables, right ascension, declination and redshift. We have also obtained density structures in 2-D for the distribution of gamma-ray bursts (where distances are unknown) and the distribution of a variety of sources such as clusters of galaxies. Our techniques allow for correlations to be done visually.

Constrained Low-Rank Learning Using Least Squares-Based Regularization.

PubMed

Li, Ping; Yu, Jun; Wang, Meng; Zhang, Luming; Cai, Deng; Li, Xuelong

2017-12-01

Low-rank learning has attracted much attention recently due to its efficacy in a rich variety of real-world tasks, e.g., subspace segmentation and image categorization. Most low-rank methods are incapable of capturing low-dimensional subspace for supervised learning tasks, e.g., classification and regression. This paper aims to learn both the discriminant low-rank representation (LRR) and the robust projecting subspace in a supervised manner. To achieve this goal, we cast the problem into a constrained rank minimization framework by adopting the least squares regularization. Naturally, the data label structure tends to resemble that of the corresponding low-dimensional representation, which is derived from the robust subspace projection of clean data by low-rank learning. Moreover, the low-dimensional representation of original data can be paired with some informative structure by imposing an appropriate constraint, e.g., Laplacian regularizer. Therefore, we propose a novel constrained LRR method. The objective function is formulated as a constrained nuclear norm minimization problem, which can be solved by the inexact augmented Lagrange multiplier algorithm. Extensive experiments on image classification, human pose estimation, and robust face recovery have confirmed the superiority of our method.

Three-dimensional dynamic thermal imaging of structural flaws by dual-band infrared computed tomography

NASA Astrophysics Data System (ADS)

DelGrande, Nancy; Dolan, Kenneth W.; Durbin, Philip F.; Gorvad, Michael R.; Kornblum, B. T.; Perkins, Dwight E.; Schneberk, Daniel J.; Shapiro, Arthur B.

1993-11-01

We discuss three-dimensional dynamic thermal imaging of structural flaws using dual-band infrared (DBIR) computed tomography. Conventional (single-band) thermal imaging is difficult to interpret. It yields imprecise or qualitative information (e.g., when subsurface flaws produce weak heat flow anomalies masked by surface clutter). We use the DBIR imaging technique to clarify interpretation. We capture the time history of surface temperature difference patterns at the epoxy-glue disbond site of a flash-heated lap joint. This type of flawed structure played a significant role in causing damage to the Aloha Aircraft fuselage on the aged Boeing 737 jetliner. The magnitude of surface-temperature differences versus time for 0.1 mm air layer compared to 0.1 mm glue layer, varies from 0.2 to 1.6 degree(s)C, for simultaneously scanned front and back surfaces. The scans are taken every 42 ms from 0 to 8 s after the heat flash. By ratioing 3 - 5 micrometers and 8 - 12 micrometers DBIR images, we located surface temperature patterns from weak heat flow anomalies at the disbond site and remove the emissivity mask from surface paint of roughness variations. Measurements compare well with calculations based on TOPAX3D, a three-dimensional, finite element computer model. We combine infrared, ultrasound and x-ray imaging methods to study heat transfer, bond quality and material differences associated with the lap joint disbond site.

Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers

NASA Astrophysics Data System (ADS)

Ploetz, Evelyn; Lerner, Eitan; Husada, Florence; Roelfs, Martin; Chung, Sangyoon; Hohlbein, Johannes; Weiss, Shimon; Cordes, Thorben

2016-09-01

Advanced microscopy methods allow obtaining information on (dynamic) conformational changes in biomolecules via measuring a single molecular distance in the structure. It is, however, extremely challenging to capture the full depth of a three-dimensional biochemical state, binding-related structural changes or conformational cross-talk in multi-protein complexes using one-dimensional assays. In this paper we address this fundamental problem by extending the standard molecular ruler based on Förster resonance energy transfer (FRET) into a two-dimensional assay via its combination with protein-induced fluorescence enhancement (PIFE). We show that donor brightness (via PIFE) and energy transfer efficiency (via FRET) can simultaneously report on e.g., the conformational state of double stranded DNA (dsDNA) following its interaction with unlabelled proteins (BamHI, EcoRV, and T7 DNA polymerase gp5/trx). The PIFE-FRET assay uses established labelling protocols and single molecule fluorescence detection schemes (alternating-laser excitation, ALEX). Besides quantitative studies of PIFE and FRET ruler characteristics, we outline possible applications of ALEX-based PIFE-FRET for single-molecule studies with diffusing and immobilized molecules. Finally, we study transcription initiation and scrunching of E. coli RNA-polymerase with PIFE-FRET and provide direct evidence for the physical presence and vicinity of the polymerase that causes structural changes and scrunching of the transcriptional DNA bubble.

Generation of a three-dimensional ultrastructural model of human respiratory cilia.

PubMed

Burgoyne, Thomas; Dixon, Mellisa; Luther, Pradeep; Hogg, Claire; Shoemark, Amelia

2012-12-01

The ultrastructures of cilia and flagella are highly similar and well conserved through evolution. Consequently, Chlamydomonas is commonly used as a model organism for the study of human respiratory cilia. Since detailed models of Chlamydomonas axonemes were generated using cryoelectron tomography, disparities among some of the ultrastructural features have become apparent when compared with human cilia. Extrapolating information on human disease from the Chlamydomonas model may lead to discrepancies in translational research. This study aimed to establish the first three-dimensional ultrastructural model of human cilia. Tomograms of transverse sections (n = 6) and longitudinal sections (n = 9) of human nasal respiratory cilia were generated from three healthy volunteers. Key features of the cilium were resolved using subatomic averaging, and were measured. For validation of the method, a model of the well characterized structure of Chlamydomonas reinhardtii was simultaneously generated. Data were combined to create a fully quantified three-dimensional reconstruction of human nasal respiratory cilia. We highlight key differences in the axonemal sheath, microtubular doublets, radial spokes, and dynein arms between the two structures. We show a decreased axial periodicity of the radial spokes, inner dynein arms, and central pair protrusions in the human model. We propose that this first human model will provide a basis for research into the function and structure of human respiratory cilia in health and in disease.

Application Perspective of 2D+SCALE Dimension

NASA Astrophysics Data System (ADS)

Karim, H.; Rahman, A. Abdul

2016-09-01

Different applications or users need different abstraction of spatial models, dimensionalities and specification of their datasets due to variations of required analysis and output. Various approaches, data models and data structures are now available to support most current application models in Geographic Information System (GIS). One of the focuses trend in GIS multi-dimensional research community is the implementation of scale dimension with spatial datasets to suit various scale application needs. In this paper, 2D spatial datasets that been scaled up as the third dimension are addressed as 2D+scale (or 3D-scale) dimension. Nowadays, various data structures, data models, approaches, schemas, and formats have been proposed as the best approaches to support variety of applications and dimensionality in 3D topology. However, only a few of them considers the element of scale as their targeted dimension. As the scale dimension is concerned, the implementation approach can be either multi-scale or vario-scale (with any available data structures and formats) depending on application requirements (topology, semantic and function). This paper attempts to discuss on the current and new potential applications which positively could be integrated upon 3D-scale dimension approach. The previous and current works on scale dimension as well as the requirements to be preserved for any given applications, implementation issues and future potential applications forms the major discussion of this paper.

Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers

PubMed Central

Ploetz, Evelyn; Lerner, Eitan; Husada, Florence; Roelfs, Martin; Chung, SangYoon; Hohlbein, Johannes; Weiss, Shimon; Cordes, Thorben

2016-01-01

Advanced microscopy methods allow obtaining information on (dynamic) conformational changes in biomolecules via measuring a single molecular distance in the structure. It is, however, extremely challenging to capture the full depth of a three-dimensional biochemical state, binding-related structural changes or conformational cross-talk in multi-protein complexes using one-dimensional assays. In this paper we address this fundamental problem by extending the standard molecular ruler based on Förster resonance energy transfer (FRET) into a two-dimensional assay via its combination with protein-induced fluorescence enhancement (PIFE). We show that donor brightness (via PIFE) and energy transfer efficiency (via FRET) can simultaneously report on e.g., the conformational state of double stranded DNA (dsDNA) following its interaction with unlabelled proteins (BamHI, EcoRV, and T7 DNA polymerase gp5/trx). The PIFE-FRET assay uses established labelling protocols and single molecule fluorescence detection schemes (alternating-laser excitation, ALEX). Besides quantitative studies of PIFE and FRET ruler characteristics, we outline possible applications of ALEX-based PIFE-FRET for single-molecule studies with diffusing and immobilized molecules. Finally, we study transcription initiation and scrunching of E. coli RNA-polymerase with PIFE-FRET and provide direct evidence for the physical presence and vicinity of the polymerase that causes structural changes and scrunching of the transcriptional DNA bubble. PMID:27641327

Sequence diagrams and the presentation of structural and evolutionary relationships among proteins.

PubMed

Thomas, B R

1975-01-01

Protein sequences mapped on two-dimensional diagrams show characteristic patterns that should be of value in visualising sequence information and in distinguishing simpler structures. A convenient map form for comparative purposes is the alpha-helix diagram with aminoacid distribution analogous to the surface of an alpha-helix oriented so that an alpha-helix structure corresponds on the diagram to a vertical band 3.6 residues wide. The sequence diagram for an alpha-keratin, high-sulphur protein suggests a new form of polypeptide helix based on a repeating unit of five which may be an important component of alpha-keratin fibres.

An approximation method for configuration optimization of trusses

NASA Technical Reports Server (NTRS)

Hansen, Scott R.; Vanderplaats, Garret N.

1988-01-01

Two- and three-dimensional elastic trusses are designed for minimum weight by varying the areas of the members and the location of the joints. Constraints on member stresses and Euler buckling are imposed and multiple static loading conditions are considered. The method presented here utilizes an approximate structural analysis based on first order Taylor series expansions of the member forces. A numerical optimizer minimizes the weight of the truss using information from the approximate structural analysis. Comparisons with results from other methods are made. It is shown that the method of forming an approximate structural analysis based on linearized member forces leads to a highly efficient method of truss configuration optimization.

A Multitaper, Causal Decomposition for Stochastic, Multivariate Time Series: Application to High-Frequency Calcium Imaging Data.

PubMed

Sornborger, Andrew T; Lauderdale, James D

2016-11-01

Neural data analysis has increasingly incorporated causal information to study circuit connectivity. Dimensional reduction forms the basis of most analyses of large multivariate time series. Here, we present a new, multitaper-based decomposition for stochastic, multivariate time series that acts on the covariance of the time series at all lags, C ( τ ), as opposed to standard methods that decompose the time series, X ( t ), using only information at zero-lag. In both simulated and neural imaging examples, we demonstrate that methods that neglect the full causal structure may be discarding important dynamical information in a time series.

Differentiating Fragmentation Pathways of Cholesterol by Two-Dimensional Fourier Transform Ion Cyclotron Resonance Mass Spectrometry.

PubMed

van Agthoven, Maria A; Barrow, Mark P; Chiron, Lionel; Coutouly, Marie-Aude; Kilgour, David; Wootton, Christopher A; Wei, Juan; Soulby, Andrew; Delsuc, Marc-André; Rolando, Christian; O'Connor, Peter B

2015-12-01

Two-dimensional Fourier transform ion cyclotron resonance mass spectrometry is a data-independent analytical method that records the fragmentation patterns of all the compounds in a sample. This study shows the implementation of atmospheric pressure photoionization with two-dimensional (2D) Fourier transform ion cyclotron resonance mass spectrometry. In the resulting 2D mass spectrum, the fragmentation patterns of the radical and protonated species from cholesterol are differentiated. This study shows the use of fragment ion lines, precursor ion lines, and neutral loss lines in the 2D mass spectrum to determine fragmentation mechanisms of known compounds and to gain information on unknown ion species in the spectrum. In concert with high resolution mass spectrometry, 2D Fourier transform ion cyclotron resonance mass spectrometry can be a useful tool for the structural analysis of small molecules. Graphical Abstract ᅟ.

Three-dimensional photogrammetric measurement of magnetic field lines in the WEGA stellarator

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

Drewelow, Peter; Braeuer, Torsten; Otte, Matthias

2009-12-15

The magnetic confinement of plasmas in fusion experiments can significantly degrade due to perturbations of the magnetic field. A precise analysis of the magnetic field in a stellarator-type experiment utilizes electrons as test particles following the magnetic field line. The usual fluorescent detector for this electron beam limits the provided information to two-dimensional cut views at certain toroidal positions. However, the technique described in this article allows measuring the three-dimensional structure of the magnetic field by means of close-range photogrammetry. After testing and optimizing the main diagnostic components, measurements of the magnetic field lines were accomplished with a spatial resolutionmore » of 5 mm. The results agree with numeric calculations, qualifying this technique as an additional tool to investigate magnetic field configurations in a stellarator. For a possible future application, ways are indicated on how to reduce experimental error sources.« less

Quality Inspection and Analysis of Three-Dimensional Geographic Information Model Based on Oblique Photogrammetry

NASA Astrophysics Data System (ADS)

Dong, S.; Yan, Q.; Xu, Y.; Bai, J.

2018-04-01

In order to promote the construction of digital geo-spatial framework in China and accelerate the construction of informatization mapping system, three-dimensional geographic information model emerged. The three-dimensional geographic information model based on oblique photogrammetry technology has higher accuracy, shorter period and lower cost than traditional methods, and can more directly reflect the elevation, position and appearance of the features. At this stage, the technology of producing three-dimensional geographic information models based on oblique photogrammetry technology is rapidly developing. The market demand and model results have been emerged in a large amount, and the related quality inspection needs are also getting larger and larger. Through the study of relevant literature, it is found that there are a lot of researches on the basic principles and technical characteristics of this technology, and relatively few studies on quality inspection and analysis. On the basis of summarizing the basic principle and technical characteristics of oblique photogrammetry technology, this paper introduces the inspection contents and inspection methods of three-dimensional geographic information model based on oblique photogrammetry technology. Combined with the actual inspection work, this paper summarizes the quality problems of three-dimensional geographic information model based on oblique photogrammetry technology, analyzes the causes of the problems and puts forward the quality control measures. It provides technical guidance for the quality inspection of three-dimensional geographic information model data products based on oblique photogrammetry technology in China and provides technical support for the vigorous development of three-dimensional geographic information model based on oblique photogrammetry technology.

New Systems for the Management of Data. The Case Study of the Chapter House of Santa Maria Novella in Florence

NASA Astrophysics Data System (ADS)

Battini, C.

2013-02-01

The technological solutions, made available today, offer opportunities of great interest for the detection in the field of cultural heritage; instrumentation for the survey and advanced multimedia representations for objects of archaeological, artistic, architectural. Since we changed the type of information, not more interpretation consists of a single piece of data, but from a set of data, must be changed, consequently, also the systems for their management or better, if until now the only situation of interest was that of having to deal with the data representing only the text, data are now made up of sounds, images, video and three-dimensional models. For these reasons and others, we can discuss in continuation, systems and storage structures classics are still not sufficient to manage these new realities. An architectural structure is a set of three-dimensional components that define spatially a form and a project idea; so that the representation of the architecture may not avail itself simply means two-dimensional graphs to describe it and describe it in all its parts, but need, and it is now possible, systems that provide for the possibility to analyze from multiple points of view the forms that compose it. The communication media can play a very important role to get directions on the actions of restoration and enhancement of the cultural and environmental heritage. Help can be provided by information and its simulation systems of virtual reality with which, in addition to conveying information, you can view models to better describe the development that the well has had in history. This research starts from the need to develop new systems of representation and data management. Objective of the project is to increase and share knowledge of architecture and the environment. Dynamic representations, relational databases, devices use data, are the main tools of this research. The study addressed led to the creation of a system that allows the transmission and analysis of data collected and, at the same time, also creates the possibility of access to users not experts in the field of 3D graphics; this has been made possible through the development the project "3DWS" (3D | WEB | SURVEY). The project involved the creation of a container structured as a web site, in which were placed the materials collected and processed including sketches, photographs, vector data, three-dimensional models and analysis issues. Within this system, three-dimensional models developed were then used as a communication tool with immediate visual link to sub-pages with a greater degree of definition. It is a simple and intuitive tree structure that allows both the visitor to the specialist scholar to focus on portions too small and detail of the product, without losing sight of the general configuration of departure. To make feasible a further degree of usability of information, the system has been implemented with image viewers metrics in high definition. The images produced are a fundamental basis, strictly from the point of view of science and technology, for the conservation, management and enhancement of the historical and artistic heritage. The case study investigated is the Chapter House of Santa Maria Novella in Florence.

Multi-Dimensional Damage Detection for Surfaces and Structures

NASA Technical Reports Server (NTRS)

Williams, Martha; Lewis, Mark; Roberson, Luke; Medelius, Pedro; Gibson, Tracy; Parks, Steen; Snyder, Sarah

2013-01-01

Current designs for inflatable or semi-rigidized structures for habitats and space applications use a multiple-layer construction, alternating thin layers with thicker, stronger layers, which produces a layered composite structure that is much better at resisting damage. Even though such composite structures or layered systems are robust, they can still be susceptible to penetration damage. The ability to detect damage to surfaces of inflatable or semi-rigid habitat structures is of great interest to NASA. Damage caused by impacts of foreign objects such as micrometeorites can rupture the shell of these structures, causing loss of critical hardware and/or the life of the crew. While not all impacts will have a catastrophic result, it will be very important to identify and locate areas of the exterior shell that have been damaged by impacts so that repairs (or other provisions) can be made to reduce the probability of shell wall rupture. This disclosure describes a system that will provide real-time data regarding the health of the inflatable shell or rigidized structures, and information related to the location and depth of impact damage. The innovation described here is a method of determining the size, location, and direction of damage in a multilayered structure. In the multi-dimensional damage detection system, layers of two-dimensional thin film detection layers are used to form a layered composite, with non-detection layers separating the detection layers. The non-detection layers may be either thicker or thinner than the detection layers. The thin-film damage detection layers are thin films of materials with a conductive grid or striped pattern. The conductive pattern may be applied by several methods, including printing, plating, sputtering, photolithography, and etching, and can include as many detection layers that are necessary for the structure construction or to afford the detection detail level required. The damage is detected using a detector or sensory system, which may include a time domain reflectometer, resistivity monitoring hardware, or other resistance-based systems. To begin, a layered composite consisting of thin-film damage detection layers separated by non-damage detection layers is fabricated. The damage detection layers are attached to a detector that provides details regarding the physical health of each detection layer individually. If damage occurs to any of the detection layers, a change in the electrical properties of the detection layers damaged occurs, and a response is generated. Real-time analysis of these responses will provide details regarding the depth, location, and size estimation of the damage. Multiple damages can be detected, and the extent (depth) of the damage can be used to generate prognostic information related to the expected lifetime of the layered composite system. The detection system can be fabricated very easily using off-the-shelf equipment, and the detection algorithms can be written and updated (as needed) to provide the level of detail needed based on the system being monitored. Connecting to the thin film detection layers is very easy as well. The truly unique feature of the system is its flexibility; the system can be designed to gather as much (or as little) information as the end user feels necessary. Individual detection layers can be turned on or off as necessary, and algorithms can be used to optimize performance. The system can be used to generate both diagnostic and prognostic information related to the health of layer composite structures, which will be essential if such systems are utilized for space exploration. The technology is also applicable to other in-situ health monitoring systems for structure integrity.

Label-free three-dimensional imaging of cell nucleus using third-harmonic generation microscopy

NASA Astrophysics Data System (ADS)

Lin, Jian; Zheng, Wei; Wang, Zi; Huang, Zhiwei

2014-09-01

We report the implementation of the combined third-harmonic generation (THG) and two-photon excited fluorescence (TPEF) microscopy for label-free three-dimensional (3-D) imaging of cell nucleus morphological changes in liver tissue. THG imaging shows regular spherical shapes of normal hepatocytes nuclei with inner chromatin structures while revealing the condensation of chromatins and nuclear fragmentations in hepatocytes of diseased liver tissue. Colocalized THG and TPEF imaging provides complementary information of cell nuclei and cytoplasm in tissue. This work suggests that 3-D THG microscopy has the potential for quantitative analysis of nuclear morphology in cells at a submicron-resolution without the need for DNA staining.

Plenoptic Imaging of a Three Dimensional Cold Atom Cloud

NASA Astrophysics Data System (ADS)

Lott, Gordon

2017-04-01

A plenoptic imaging system is capable of sampling the rays of light in a volume, both spatially and angularly, providing information about the three dimensional (3D) volume being imaged. The extraction of the 3D structure of a cold atom cloud is demonstrated, using a single plenoptic camera and a single image. The reconstruction is tested against a reference image and the results discussed along with the capabilities and limitations of the imaging system. This capability is useful when the 3D distribution of the atoms is desired, such as determining the shape of an atom trap, particularly when there is limited optical access. Gratefully acknowledge support from AFRL.

Label-free three-dimensional imaging of cell nucleus using third-harmonic generation microscopy

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

Lin, Jian; Zheng, Wei; Wang, Zi

2014-09-08

We report the implementation of the combined third-harmonic generation (THG) and two-photon excited fluorescence (TPEF) microscopy for label-free three-dimensional (3-D) imaging of cell nucleus morphological changes in liver tissue. THG imaging shows regular spherical shapes of normal hepatocytes nuclei with inner chromatin structures while revealing the condensation of chromatins and nuclear fragmentations in hepatocytes of diseased liver tissue. Colocalized THG and TPEF imaging provides complementary information of cell nuclei and cytoplasm in tissue. This work suggests that 3-D THG microscopy has the potential for quantitative analysis of nuclear morphology in cells at a submicron-resolution without the need for DNA staining.

Simulation of femtosecond two-dimensional electronic spectra of conical intersections

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

Krčmář, Jindřich; Gelin, Maxim F.; Domcke, Wolfgang

2015-08-21

We have simulated femtosecond two-dimensional (2D) electronic spectra for an excited-state conical intersection using the wave-function version of the equation-of-motion phase-matching approach. We show that 2D spectra at fixed values of the waiting time provide information on the structure of the vibronic eigenstates of the conical intersection, while the evolution of the spectra with the waiting time reveals predominantly ground-state wave-packet dynamics. The results show that 2D spectra of conical intersection systems differ significantly from those obtained for chromophores with well separated excited-state potential-energy surfaces. The spectral signatures which can be attributed to conical intersections are discussed.

Structural Analysis of MoS2 and other 2D layered materials using LEEM/LEED-I(V) and STM

NASA Astrophysics Data System (ADS)

Grady, Maxwell; Dai, Zhongwei; Jin, Wencan; Dadap, Jerry; Osgood, Richard; Sadowski, Jerzy; Pohl, Karsten

Layered two-dimensional materials, such as molybdenum disulfide, MoS2, are of interest for the development of many types of novel electronic devices. To fully understand the interfaces between these new materials, the atomic reconstructions at their surfaces must be understood. Low Energy Electron Microscopy and Diffraction, LEEM/ μLEED, present a unique method for rapid material characterization in real space and reciprocal space with high resolution. Here we present a study of the surface structure of 2H-MoS2 using μLEED intensity-voltage analysis. To aid this analysis, software is under development to automate the procedure of extracting I(V) curves from LEEM and LEED data. When matched with computational modeling, this data provides information with angstrom level resolution concerning the three dimensional atomic positions. We demonstrate that the surface structure of bulk MoS2 is distinct from the bulk crystal structure and exhibits a smaller surface relaxation at 320K compared to previous results at 95K. Furthermore, suspended monolayer samples exhibit large interlayer relaxations compared to the bulk surface termination. Further techniques for refining layer thickness determination are under development.

Microstructure of β-Sitosterol:γ-Oryzanol Edible Organogels.

PubMed

Matheson, Andrew B; Koutsos, Vasileios; Dalkas, Georgios; Euston, Stephen; Clegg, Paul

2017-05-09

Rheology and atomic force microscopy (AFM) were employed to examine the microstructure of β-sitosterol:γ-oryzanol organogels in sunflower oil. Using time-resolved rheology, we followed gel formation, paying specific attention to the fibril aggregation process, which had not been studied in detail previously for this system. Using AFM, we observed gel structures directly and obtained detailed information on the gel structure, far exceeding previous studies. Our analysis suggests that though gels are formed by the self-assembly and aggregation of one-dimensional fibrils, the manner in which these fibrils aggregate into ribbons results in complex structures of higher dimensionality. We emphasize that it is a surprise to find ribbons and not twisted strands. Comparing AFM images of 10% w/w and 20% w/w gelator systems, we observed differences in the degree of branching which are consistent with the rheology. We also observed the individual self-assembled fibrils which make up these gels with much greater clarity than in previous microscopy studies, and the fibril diameters of ∼9.8 nm we measured agree excellently with those obtained from existing small-angle neutron scattering data. These results provide new insight into the structure and formation kinetics of this important organogel system.

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal.

PubMed

Clabbers, M T B; van Genderen, E; Wan, W; Wiegers, E L; Gruene, T; Abrahams, J P

2017-09-01

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm 3 , i.e. no more than 6 × 10 5 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures.

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal

PubMed Central

Clabbers, M. T. B.; van Genderen, E.; Wiegers, E. L.; Gruene, T.; Abrahams, J. P.

2017-01-01

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm3, i.e. no more than 6 × 105 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures. PMID:28876237

Computing algebraic transfer entropy and coupling directions via transcripts

NASA Astrophysics Data System (ADS)

Amigó, José M.; Monetti, Roberto; Graff, Beata; Graff, Grzegorz

2016-11-01

Most random processes studied in nonlinear time series analysis take values on sets endowed with a group structure, e.g., the real and rational numbers, and the integers. This fact allows to associate with each pair of group elements a third element, called their transcript, which is defined as the product of the second element in the pair times the first one. The transfer entropy of two such processes is called algebraic transfer entropy. It measures the information transferred between two coupled processes whose values belong to a group. In this paper, we show that, subject to one constraint, the algebraic transfer entropy matches the (in general, conditional) mutual information of certain transcripts with one variable less. This property has interesting practical applications, especially to the analysis of short time series. We also derive weak conditions for the 3-dimensional algebraic transfer entropy to yield the same coupling direction as the corresponding mutual information of transcripts. A related issue concerns the use of mutual information of transcripts to determine coupling directions in cases where the conditions just mentioned are not fulfilled. We checked the latter possibility in the lowest dimensional case with numerical simulations and cardiovascular data, and obtained positive results.

Biomimetic peptoid polymers

DOEpatents

Zuckermann, Ronald N.; Chu, Tammy K.; Nam, Ki Tae

2015-07-07

The present invention provides for novel peptoid oligomers that are capable of self-assembling into two-dimensional sheet structures. The peptoid oligomers can have alternately hydrophilic or polar side-chains and hydrophobic or apolar side-chains. The peptoid oligomers, and the two-dimensional sheet structures, can be applied to biological applications where the peptoid plays a role as a biological scaffold or building block. Also, the two-dimensional sheet structures of the present invention can be used as two-dimensional nanostructures in device applications.

Parsimony and goodness-of-fit in multi-dimensional NMR inversion

NASA Astrophysics Data System (ADS)

Babak, Petro; Kryuchkov, Sergey; Kantzas, Apostolos

2017-01-01

Multi-dimensional nuclear magnetic resonance (NMR) experiments are often used for study of molecular structure and dynamics of matter in core analysis and reservoir evaluation. Industrial applications of multi-dimensional NMR involve a high-dimensional measurement dataset with complicated correlation structure and require rapid and stable inversion algorithms from the time domain to the relaxation rate and/or diffusion domains. In practice, applying existing inverse algorithms with a large number of parameter values leads to an infinite number of solutions with a reasonable fit to the NMR data. The interpretation of such variability of multiple solutions and selection of the most appropriate solution could be a very complex problem. In most cases the characteristics of materials have sparse signatures, and investigators would like to distinguish the most significant relaxation and diffusion values of the materials. To produce an easy to interpret and unique NMR distribution with the finite number of the principal parameter values, we introduce a new method for NMR inversion. The method is constructed based on the trade-off between the conventional goodness-of-fit approach to multivariate data and the principle of parsimony guaranteeing inversion with the least number of parameter values. We suggest performing the inversion of NMR data using the forward stepwise regression selection algorithm. To account for the trade-off between goodness-of-fit and parsimony, the objective function is selected based on Akaike Information Criterion (AIC). The performance of the developed multi-dimensional NMR inversion method and its comparison with conventional methods are illustrated using real data for samples with bitumen, water and clay.

Electronic structure of boron based single and multi-layer two dimensional materials

NASA Astrophysics Data System (ADS)

Miyazato, Itsuki; Takahashi, Keisuke

2017-09-01

Two dimensional nanosheets based on boron and Group VA elements are designed and characterized using first principles calculations. B-N, B-P, B-As, B-Sb, and B-Bi are found to possess honeycomb structures where formation energies indicate exothermic reactions. Contrary to B-N, the cases of B-P, B-As, B-Sb, and B-Bi nanosheets are calculated to possess narrow band gaps. In addition, calculations reveal that the electronegativity difference between B and Group VA elements in the designed materials is a good indicator to predict the charge transfer and band gap of the two dimensional materials. Hydrogen adsorption over defect-free B-Sb and B-Bi results in exothermic reactions, while defect-free B-N, B-P, and B-As result in endothermic reactions. The layerability of the designed two dimensional materials is also investigated where the electronic structure of two-layered two dimensional materials is strongly coupled with how the two dimensional materials are layered. Thus, one can consider that the properties of two dimensional materials can be controlled by the composition of two dimensional materials and the structure of layers.

Theoretical modeling of the electronic structure and exchange interactions in a Cu(II)Pc one-dimensional chain

NASA Astrophysics Data System (ADS)

Wu, Wei; Fisher, A. J.; Harrison, N. M.

2011-07-01

We calculate the electronic structure and exchange interactions in a copper(II)phthalocyanine [Cu(II)Pc] crystal as a one-dimensional molecular chain using hybrid exchange density functional theory (DFT). In addition, the intermolecular exchange interactions are also calculated in a molecular dimer using Green’s function perturbation theory (GFPT) to illustrate the underlying physics. We find that the exchange interactions depend strongly on the stacking angle, but weakly on the sliding angle (defined in the text). The hybrid DFT calculations also provide an insight into the electronic structure of the Cu(II)Pc molecular chain and demonstrate that on-site electron correlations have a significant effect on the nature of the ground state, the band gap, and magnetic excitations. The exchange interactions predicted by our DFT calculations and GFPT calculations agree qualitatively with the recent experimental results on newly found η-Cu(II)Pc and the previous results for the α and β phases. This work provides a reliable theoretical basis for the further application of Cu(II)Pc to molecular spintronics and organic-based quantum information processing.

Invasive plants transform the three-dimensional structure of rain forests

PubMed Central

Asner, Gregory P.; Hughes, R. Flint; Vitousek, Peter M.; Knapp, David E.; Kennedy-Bowdoin, Ty; Boardman, Joseph; Martin, Roberta E.; Eastwood, Michael; Green, Robert O.

2008-01-01

Biological invasions contribute to global environmental change, but the dynamics and consequences of most invasions are difficult to assess at regional scales. We deployed an airborne remote sensing system that mapped the location and impacts of five highly invasive plant species across 221,875 ha of Hawaiian ecosystems, identifying four distinct ways that these species transform the three-dimensional (3D) structure of native rain forests. In lowland to montane forests, three invasive tree species replace native midcanopy and understory plants, whereas one understory invader excludes native species at the ground level. A fifth invasive nitrogen-fixing tree, in combination with a midcanopy alien tree, replaces native plants at all canopy levels in lowland forests. We conclude that this diverse array of alien plant species, each representing a different growth form or functional type, is changing the fundamental 3D structure of native Hawaiian rain forests. Our work also demonstrates how an airborne mapping strategy can identify and track the spread of certain invasive plant species, determine ecological consequences of their proliferation, and provide detailed geographic information to conservation and management efforts. PMID:18316720

Distributed digital signal processors for multi-body flexible structures

NASA Technical Reports Server (NTRS)

Lee, Gordon K. F.

1992-01-01

Multi-body flexible structures, such as those currently under investigation in spacecraft design, are large scale (high-order) dimensional systems. Controlling and filtering such structures is a computationally complex problem. This is particularly important when many sensors and actuators are located along the structure and need to be processed in real time. This report summarizes research activity focused on solving the signal processing (that is, information processing) issues of multi-body structures. A distributed architecture is developed in which single loop processors are employed for local filtering and control. By implementing such a philosophy with an embedded controller configuration, a supervising controller may be used to process global data and make global decisions as the local devices are processing local information. A hardware testbed, a position controller system for a servo motor, is employed to illustrate the capabilities of the embedded controller structure. Several filtering and control structures which can be modeled as rational functions can be implemented on the system developed in this research effort. Thus the results of the study provide a support tool for many Control/Structure Interaction (CSI) NASA testbeds such as the Evolutionary model and the nine-bay truss structure.

Quantitative Analysis Of Three-dimensional Branching Systems From X-ray Computed Microtomography Data

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

McKinney, Adriana L.; Varga, Tamas

Branching structures such as lungs, blood vessels and plant roots play a critical role in life. Growth, structure, and function of these branching structures have an immense effect on our lives. Therefore, quantitative size information on such structures in their native environment is invaluable for studying their growth and the effect of the environment on them. X-ray computed tomography (XCT) has been an effective tool for in situ imaging and analysis of branching structures. We developed a costless tool that approximates the surface and volume of branching structures. Our methodology of noninvasive imaging, segmentation and extraction of quantitative information ismore » demonstrated through the analysis of a plant root in its soil medium from 3D tomography data. XCT data collected on a grass specimen was used to visualize its root structure. A suite of open-source software was employed to segment the root from the soil and determine its isosurface, which was used to calculate its volume and surface. This methodology of processing 3D data is applicable to other branching structures even when the structure of interest is of similar x-ray attenuation to its environment and difficulties arise with sample segmentation.« less

Exploring the atomic structure and conformational flexibility of a 320 Å long engineered viral fiber using X-ray crystallography.

PubMed

Bhardwaj, Anshul; Casjens, Sherwood R; Cingolani, Gino

2014-02-01

Protein fibers are widespread in nature, but only a limited number of high-resolution structures have been determined experimentally. Unlike globular proteins, fibers are usually recalcitrant to form three-dimensional crystals, preventing single-crystal X-ray diffraction analysis. In the absence of three-dimensional crystals, X-ray fiber diffraction is a powerful tool to determine the internal symmetry of a fiber, but it rarely yields atomic resolution structural information on complex protein fibers. An 85-residue-long minimal coiled-coil repeat unit (MiCRU) was previously identified in the trimeric helical core of tail needle gp26, a fibrous protein emanating from the tail apparatus of the bacteriophage P22 virion. Here, evidence is provided that an MiCRU can be inserted in frame inside the gp26 helical core to generate a rationally extended fiber (gp26-2M) which, like gp26, retains a trimeric quaternary structure in solution. The 2.7 Å resolution crystal structure of this engineered fiber, which measures ∼320 Å in length and is only 20-35 Å wide, was determined. This structure, the longest for a trimeric protein fiber to be determined to such a high resolution, reveals the architecture of 22 consecutive trimerization heptads and provides a framework to decipher the structural determinants for protein fiber assembly, stability and flexibility.

Structure and function of seed storage proteins in faba bean (Vicia faba L.).

PubMed

Liu, Yujiao; Wu, Xuexia; Hou, Wanwei; Li, Ping; Sha, Weichao; Tian, Yingying

2017-05-01

The protein subunit is the most important basic unit of protein, and its study can unravel the structure and function of seed storage proteins in faba bean. In this study, we identified six specific protein subunits in Faba bean (cv. Qinghai 13) combining liquid chromatography (LC), liquid chromatography-electronic spray ionization mass (LC-ESI-MS/MS) and bio-information technology. The results suggested a diversity of seed storage proteins in faba bean, and a total of 16 proteins (four GroEL molecular chaperones and 12 plant-specific proteins) were identified from 97-, 96-, 64-, 47-, 42-, and 38-kD-specific protein subunits in faba bean based on the peptide sequence. We also analyzed the composition and abundance of the amino acids, the physicochemical characteristics, secondary structure, three-dimensional structure, transmembrane domain, and possible subcellular localization of these identified proteins in faba bean seed, and finally predicted function and structure. The three-dimensional structures were generated based on homologous modeling, and the protein function was analyzed based on the annotation from the non-redundant protein database (NR database, NCBI) and function analysis of optimal modeling. The objective of this study was to identify the seed storage proteins in faba bean and confirm the structure and function of these proteins. Our results can be useful for the study of protein nutrition and achieve breeding goals for optimal protein quality in faba bean.

The prediction of crystal structure by merging knowledge methods with first principles quantum mechanics

NASA Astrophysics Data System (ADS)

Ceder, Gerbrand

2007-03-01

The prediction of structure is a key problem in computational materials science that forms the platform on which rational materials design can be performed. Finding structure by traditional optimization methods on quantum mechanical energy models is not possible due to the complexity and high dimensionality of the coordinate space. An unusual, but efficient solution to this problem can be obtained by merging ideas from heuristic and ab initio methods: In the same way that scientist build empirical rules by observation of experimental trends, we have developed machine learning approaches that extract knowledge from a large set of experimental information and a database of over 15,000 first principles computations, and used these to rapidly direct accurate quantum mechanical techniques to the lowest energy crystal structure of a material. Knowledge is captured in a Bayesian probability network that relates the probability to find a particular crystal structure at a given composition to structure and energy information at other compositions. We show that this approach is highly efficient in finding the ground states of binary metallic alloys and can be easily generalized to more complex systems.

Three dimensional electron microscopy and in silico tools for macromolecular structure determination

PubMed Central

Borkotoky, Subhomoi; Meena, Chetan Kumar; Khan, Mohammad Wahab; Murali, Ayaluru

2013-01-01

Recently, structural biology witnessed a major tool - electron microscopy - in solving the structures of macromolecules in addition to the conventional techniques, X-ray crystallography and nuclear magnetic resonance (NMR). Three dimensional transmission electron microscopy (3DTEM) is one of the most sophisticated techniques for structure determination of molecular machines. Known to give the 3-dimensional structures in its native form with literally no upper limit on size of the macromolecule, this tool does not need the crystallization of the protein. Combining the 3DTEM data with in silico tools, one can have better refined structure of a desired complex. In this review we are discussing about the recent advancements in three dimensional electron microscopy and tools associated with it. PMID:27092033

General solution for quantitative dark-field contrast imaging with grating interferometers

NASA Astrophysics Data System (ADS)

Strobl, M.

2014-11-01

Grating interferometer based imaging with X-rays and neutrons has proven to hold huge potential for applications in key research fields conveying biology and medicine as well as engineering and magnetism, respectively. The thereby amenable dark-field imaging modality implied the promise to access structural information beyond reach of direct spatial resolution. However, only here a yet missing approach is reported that finally allows exploiting this outstanding potential for non-destructive materials characterizations. It enables to obtain quantitative structural small angle scattering information combined with up to 3-dimensional spatial image resolution even at lab based x-ray or at neutron sources. The implied two orders of magnitude efficiency gain as compared to currently available techniques in this regime paves the way for unprecedented structural investigations of complex sample systems of interest for material science in a vast range of fields.

Investigation of signal models and methods for evaluating structures of processing telecommunication information exchange systems under acoustic noise conditions

NASA Astrophysics Data System (ADS)

Kropotov, Y. A.; Belov, A. A.; Proskuryakov, A. Y.; Kolpakov, A. A.

2018-05-01

The paper considers models and methods for estimating signals during the transmission of information messages in telecommunication systems of audio exchange. One-dimensional probability distribution functions that can be used to isolate useful signals, and acoustic noise interference are presented. An approach to the estimation of the correlation and spectral functions of the parameters of acoustic signals is proposed, based on the parametric representation of acoustic signals and the components of the noise components. The paper suggests an approach to improving the efficiency of interference cancellation and highlighting the necessary information when processing signals from telecommunications systems. In this case, the suppression of acoustic noise is based on the methods of adaptive filtering and adaptive compensation. The work also describes the models of echo signals and the structure of subscriber devices in operational command telecommunications systems.

Augmented Reality in Scientific Publications-Taking the Visualization of 3D Structures to the Next Level.

PubMed

Wolle, Patrik; Müller, Matthias P; Rauh, Daniel

2018-03-16

The examination of three-dimensional structural models in scientific publications allows the reader to validate or invalidate conclusions drawn by the authors. However, either due to a (temporary) lack of access to proper visualization software or a lack of proficiency, this information is not necessarily available to every reader. As the digital revolution is quickly progressing, technologies have become widely available that overcome the limitations and offer to all the opportunity to appreciate models not only in 2D, but also in 3D. Additionally, mobile devices such as smartphones and tablets allow access to this information almost anywhere, at any time. Since access to such information has only recently become standard practice, we want to outline straightforward ways to incorporate 3D models in augmented reality into scientific publications, books, posters, and presentations and suggest that this should become general practice.

7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source

PubMed Central

Pedrini, Bill; Tsai, Ching-Ju; Capitani, Guido; Padeste, Celestino; Hunter, Mark S.; Zatsepin, Nadia A.; Barty, Anton; Benner, W. Henry; Boutet, Sébastien; Feld, Geoffrey K.; Hau-Riege, Stefan P.; Kirian, Richard A.; Kupitz, Christopher; Messerschmitt, Marc; Ogren, John I.; Pardini, Tommaso; Segelke, Brent; Williams, Garth J.; Spence, John C. H.; Abela, Rafael; Coleman, Matthew; Evans, James E.; Schertler, Gebhard F. X.; Frank, Matthias; Li, Xiao-Dan

2014-01-01

Membrane proteins arranged as two-dimensional crystals in the lipid environment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. Previously, X-ray diffraction from individual two-dimensional crystals did not represent a suitable investigational tool because of radiation damage. The recent availability of ultrashort pulses from X-ray free-electron lasers (XFELs) has now provided a means to outrun the damage. Here, we report on measurements performed at the Linac Coherent Light Source XFEL on bacteriorhodopsin two-dimensional crystals mounted on a solid support and kept at room temperature. By merging data from about a dozen single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 Å, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase in the resolution. The presented results pave the way for further XFEL studies on two-dimensional crystals, which may include pump–probe experiments at subpicosecond time resolution. PMID:24914166

The Structure Lacuna

PubMed Central

Boeyens, Jan C.A.; Levendis, Demetrius C.

2012-01-01

Molecular symmetry is intimately connected with the classical concept of three-dimensional molecular structure. In a non-classical theory of wave-like interaction in four-dimensional space-time, both of these concepts and traditional quantum mechanics lose their operational meaning, unless suitably modified. A required reformulation should emphasize the importance of four-dimensional effects like spin and the symmetry effects of space-time curvature that could lead to a fundamentally different understanding of molecular symmetry and structure in terms of elementary number theory. Isolated single molecules have no characteristic shape and macro-biomolecules only develop robust three-dimensional structure in hydrophobic response to aqueous cellular media. PMID:22942753

A Structure-Based Distance Metric for High-Dimensional Space Exploration with Multi-Dimensional Scaling

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

Lee, Hyun Jung; McDonnell, Kevin T.; Zelenyuk, Alla

2014-03-01

Although the Euclidean distance does well in measuring data distances within high-dimensional clusters, it does poorly when it comes to gauging inter-cluster distances. This significantly impacts the quality of global, low-dimensional space embedding procedures such as the popular multi-dimensional scaling (MDS) where one can often observe non-intuitive layouts. We were inspired by the perceptual processes evoked in the method of parallel coordinates which enables users to visually aggregate the data by the patterns the polylines exhibit across the dimension axes. We call the path of such a polyline its structure and suggest a metric that captures this structure directly inmore » high-dimensional space. This allows us to better gauge the distances of spatially distant data constellations and so achieve data aggregations in MDS plots that are more cognizant of existing high-dimensional structure similarities. Our MDS plots also exhibit similar visual relationships as the method of parallel coordinates which is often used alongside to visualize the high-dimensional data in raw form. We then cast our metric into a bi-scale framework which distinguishes far-distances from near-distances. The coarser scale uses the structural similarity metric to separate data aggregates obtained by prior classification or clustering, while the finer scale employs the appropriate Euclidean distance.« less

Early differential sensitivity of evoked-potentials to local and global shape during the perception of three-dimensional objects.

PubMed

Leek, E Charles; Roberts, Mark; Oliver, Zoe J; Cristino, Filipe; Pegna, Alan J

2016-08-01

Here we investigated the time course underlying differential processing of local and global shape information during the perception of complex three-dimensional (3D) objects. Observers made shape matching judgments about pairs of sequentially presented multi-part novel objects. Event-related potentials (ERPs) were used to measure perceptual sensitivity to 3D shape differences in terms of local part structure and global shape configuration - based on predictions derived from hierarchical structural description models of object recognition. There were three types of different object trials in which stimulus pairs (1) shared local parts but differed in global shape configuration; (2) contained different local parts but shared global configuration or (3) shared neither local parts nor global configuration. Analyses of the ERP data showed differential amplitude modulation as a function of shape similarity as early as the N1 component between 146-215ms post-stimulus onset. These negative amplitude deflections were more similar between objects sharing global shape configuration than local part structure. Differentiation among all stimulus types was reflected in N2 amplitude modulations between 276-330ms. sLORETA inverse solutions showed stronger involvement of left occipitotemporal areas during the N1 for object discrimination weighted towards local part structure. The results suggest that the perception of 3D object shape involves parallel processing of information at local and global scales. This processing is characterised by relatively slow derivation of 'fine-grained' local shape structure, and fast derivation of 'coarse-grained' global shape configuration. We propose that the rapid early derivation of global shape attributes underlies the observed patterns of N1 amplitude modulations. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Flow Structure and Force Variation with Aspect Ratio for a Two-Degree-of-Freedom Flapping Wing

NASA Astrophysics Data System (ADS)

Burge, Matthew; Favale, James; Ringuette, Matthew

2014-11-01

We investigate experimentally the effect of aspect ratio (AR) on the flow structure and forces of a two-degree-of-freedom flapping wing. Flapping wings are known to produce complex and unsteady vortex loop structures, and the objective is to characterize their variation with AR and how this influences the lift force. Previous results on rotating wings demonstrated that changes in AR significantly affect the three-dimensional flow structure and lift coefficient. This is primarily due to the relatively greater influence of the tip vortex for lower AR. At Reynolds number of order O(103) we test wings of AR = 2-4, values typically found in nature, with simplified planform shapes. The lift force is measured using a submersible transducer at the base of the wing in a glycerin-water mixture. The qualitative, three-dimensional vortex loop structure for different ARs is obtained using multi-color dye flow visualization. Guided by this, quantitative three-component flow information, namely vorticity, the Q-criterion, and circulation, is acquired from stereoscopic particle image velocimetry in key planes. Of interest is how these parameters and the vortex loop topology vary with AR, and their connection to features in the unsteady force signal. This work is supported by the National Science Foundation, Award Number 1336548, supervised by Dr. Dimitrios Papavassiliou.

A hybrid molecular dynamics study on the non-Newtonian rheological behaviors of shear thickening fluid.

PubMed

Chen, Kaihui; Wang, Yu; Xuan, Shouhu; Gong, Xinglong

2017-07-01

To investigate the microstructural evolution dependency on the apparent viscosity in shear-thickening fluids (STFs), a hybrid mesoscale model combined with stochastic rotation dynamics (SRD) and molecular dynamics (MD) is used. Muller-Plathe reverse perturbation method is adopted to analyze the viscosities of STFs in a two-dimensional model. The characteristic of microstructural evolution of the colloidal suspensions under different shear rate is studied. The effect of diameter of colloidal particles and the phase volume fraction on the shear thickening behavior is investigated. Under low shear rate, the two-atom structure is formed, because of the strong particle attractions in adjacent layers. At higher shear rate, the synergetic pair structure extends to layered structure along flow direction because of the increasing hydrodynamics action. As the shear rate rises continuously, the layered structure rotates and collides with other particles, then turned to be individual particles under extension or curve string structure under compression. Finally, at the highest shear rate, the strings curve more severely and get into two-dimensional cluster. The apparent viscosity of the system changes from shear-thinning behavior to the shear-thickening behavior. This work presents valuable information for further understanding the shear thickening mechanism. Copyright © 2017 Elsevier Inc. All rights reserved.

Automated NMR structure determination of stereo-array isotope labeled ubiquitin from minimal sets of spectra using the SAIL-FLYA system.

PubMed

Ikeya, Teppei; Takeda, Mitsuhiro; Yoshida, Hitoshi; Terauchi, Tsutomu; Jee, Jun-Goo; Kainosho, Masatsune; Güntert, Peter

2009-08-01

Stereo-array isotope labeling (SAIL) has been combined with the fully automated NMR structure determination algorithm FLYA to determine the three-dimensional structure of the protein ubiquitin from different sets of input NMR spectra. SAIL provides a complete stereo- and regio-specific pattern of stable isotopes that results in sharper resonance lines and reduced signal overlap, without information loss. Here we show that as a result of the superior quality of the SAIL NMR spectra, reliable, fully automated analyses of the NMR spectra and structure calculations are possible using fewer input spectra than with conventional uniformly 13C/15N-labeled proteins. FLYA calculations with SAIL ubiquitin, using a single three-dimensional "through-bond" spectrum (and 2D HSQC spectra) in addition to the 13C-edited and 15N-edited NOESY spectra for conformational restraints, yielded structures with an accuracy of 0.83-1.15 A for the backbone RMSD to the conventionally determined solution structure of SAIL ubiquitin. NMR structures can thus be determined almost exclusively from the NOESY spectra that yield the conformational restraints, without the need to record many spectra only for determining intermediate, auxiliary data of the chemical shift assignments. The FLYA calculations for this report resulted in 252 ubiquitin structure bundles, obtained with different input data but identical structure calculation and refinement methods. These structures cover the entire range from highly accurate structures to seriously, but not trivially, wrong structures, and thus constitute a valuable database for the substantiation of structure validation methods.

Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain.

PubMed

Ali, Anjum A; Dale, Anders M; Badea, Alexandra; Johnson, G Allan

2005-08-15

We present the automated segmentation of magnetic resonance microscopy (MRM) images of the C57BL/6J mouse brain into 21 neuroanatomical structures, including the ventricular system, corpus callosum, hippocampus, caudate putamen, inferior colliculus, internal capsule, globus pallidus, and substantia nigra. The segmentation algorithm operates on multispectral, three-dimensional (3D) MR data acquired at 90-microm isotropic resolution. Probabilistic information used in the segmentation is extracted from training datasets of T2-weighted, proton density-weighted, and diffusion-weighted acquisitions. Spatial information is employed in the form of prior probabilities of occurrence of a structure at a location (location priors) and the pairwise probabilities between structures (contextual priors). Validation using standard morphometry indices shows good consistency between automatically segmented and manually traced data. Results achieved in the mouse brain are comparable with those achieved in human brain studies using similar techniques. The segmentation algorithm shows excellent potential for routine morphological phenotyping of mouse models.

Wavelet analysis methods for radiography of multidimensional growth of planar mixing layers

DOE PAGES

Merritt, Elizabeth Catherine; Doss, Forrest William

2016-07-06

The counter-propagating shear campaign is examining instability growth and its transition to turbulence in the high-energy-density physics regime using a laser-driven counter-propagating flow platform. In these experiments, we observe consistent complex break-up of and structure growth in a tracer layer placed at the shear flow interface during the instability growth phase. We present a wavelet-transform based analysis technique capable of characterizing the scale- and directionality-resolved average intensity perturbations in static radiographs of the experiment. This technique uses the complete spatial information available in each radiograph to describe the structure evolution. We designed this analysis technique to generate a two-dimensional powermore » spectrum for each radiograph from which we can recover information about structure widths, amplitudes, and orientations. Lastly, the evolution of the distribution of power in the spectra for an experimental series is a potential metric for quantifying the structure size evolution as well as a system’s evolution towards isotropy.« less

Wavelet analysis methods for radiography of multidimensional growth of planar mixing layers

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

Merritt, E. C., E-mail: emerritt@lanl.gov; Doss, F. W.

2016-07-15

The counter-propagating shear campaign is examining instability growth and its transition to turbulence in the high-energy-density physics regime using a laser-driven counter-propagating flow platform. In these experiments, we observe consistent complex break-up of and structure growth in a tracer layer placed at the shear flow interface during the instability growth phase. We present a wavelet-transform based analysis technique capable of characterizing the scale- and directionality-resolved average intensity perturbations in static radiographs of the experiment. This technique uses the complete spatial information available in each radiograph to describe the structure evolution. We designed this analysis technique to generate a two-dimensional powermore » spectrum for each radiograph from which we can recover information about structure widths, amplitudes, and orientations. The evolution of the distribution of power in the spectra for an experimental series is a potential metric for quantifying the structure size evolution as well as a system’s evolution towards isotropy.« less

DDRprot: a database of DNA damage response-related proteins.

PubMed

Andrés-León, Eduardo; Cases, Ildefonso; Arcas, Aida; Rojas, Ana M

2016-01-01

The DNA Damage Response (DDR) signalling network is an essential system that protects the genome's integrity. The DDRprot database presented here is a resource that integrates manually curated information on the human DDR network and its sub-pathways. For each particular DDR protein, we present detailed information about its function. If involved in post-translational modifications (PTMs) with each other, we depict the position of the modified residue/s in the three-dimensional structures, when resolved structures are available for the proteins. All this information is linked to the original publication from where it was obtained. Phylogenetic information is also shown, including time of emergence and conservation across 47 selected species, family trees and sequence alignments of homologues. The DDRprot database can be queried by different criteria: pathways, species, evolutionary age or involvement in (PTM). Sequence searches using hidden Markov models can be also used.Database URL: http://ddr.cbbio.es. © The Author(s) 2016. Published by Oxford University Press.

Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins.

PubMed

Hsing, Michael; Cherkasov, Artem

2008-06-25

Insertions and deletions (indels) represent a common type of sequence variations, which are less studied and pose many important biological questions. Recent research has shown that the presence of sizable indels in protein sequences may be indicative of protein essentiality and their role in protein interaction networks. Examples of utilization of indels for structure-based drug design have also been recently demonstrated. Nonetheless many structural and functional characteristics of indels remain less researched or unknown. We have created a web-based resource, Indel PDB, representing a structural database of insertions/deletions identified from the sequence alignments of highly similar proteins found in the Protein Data Bank (PDB). Indel PDB utilized large amounts of available structural information to characterize 1-, 2- and 3-dimensional features of indel sites. Indel PDB contains 117,266 non-redundant indel sites extracted from 11,294 indel-containing proteins. Unlike loop databases, Indel PDB features more indel sequences with secondary structures including alpha-helices and beta-sheets in addition to loops. The insertion fragments have been characterized by their sequences, lengths, locations, secondary structure composition, solvent accessibility, protein domain association and three dimensional structures. By utilizing the data available in Indel PDB, we have studied and presented here several sequence and structural features of indels. We anticipate that Indel PDB will not only enable future functional studies of indels, but will also assist protein modeling efforts and identification of indel-directed drug binding sites.

Quantification of soil structure based on Minkowski functions

NASA Astrophysics Data System (ADS)

Vogel, H.-J.; Weller, U.; Schlüter, S.

2010-10-01

The structure of soils and other geologic media is a complex three-dimensional object. Most of the physical material properties including mechanical and hydraulic characteristics are immediately linked to the structure given by the pore space and its spatial distribution. It is an old dream and still a formidable challenge to relate structural features of porous media to their functional properties. Using tomographic techniques, soil structure can be directly observed at a range of spatial scales. In this paper we present a scale-invariant concept to quantify complex structures based on a limited set of meaningful morphological functions. They are based on d+1 Minkowski functionals as defined for d-dimensional bodies. These basic quantities are determined as a function of pore size or aggregate size obtained by filter procedures using mathematical morphology. The resulting Minkowski functions provide valuable information on the size of pores and aggregates, the pore surface area and the pore topology having the potential to be linked to physical properties. The theoretical background and the related algorithms are presented and the approach is demonstrated for the pore structure of an arable soil and the pore structure of a sand both obtained by X-ray micro-tomography. We also analyze the fundamental problem of limited resolution which is critical for any attempt to quantify structural features at any scale using samples of different size recorded at different resolutions. The results demonstrate that objects smaller than 5 voxels are critical for quantitative analysis.

Preliminary Groundwater Simulations To Compare Different Reconstruction Methods of 3-d Alluvial Heterogeneity

NASA Astrophysics Data System (ADS)

Teles, V.; de Marsily, G.; Delay, F.; Perrier, E.

Alluvial floodplains are extremely heterogeneous aquifers, whose three-dimensional structures are quite difficult to model. In general, when representing such structures, the medium heterogeneity is modeled with classical geostatistical or Boolean meth- ods. Another approach, still in its infancy, is called the genetic method because it simulates the generation of the medium by reproducing sedimentary processes. We developed a new genetic model to obtain a realistic three-dimensional image of allu- vial media. It does not simulate the hydrodynamics of sedimentation but uses semi- empirical and statistical rules to roughly reproduce fluvial deposition and erosion. The main processes, either at the stream scale or at the plain scale, are modeled by simple rules applied to "sediment" entities or to conceptual "erosion" entities. The model was applied to a several kilometer long portion of the Aube River floodplain (France) and reproduced the deposition and erosion cycles that occurred during the inferred climate periods (15 000 BP to present). A three-dimensional image of the aquifer was gener- ated, by extrapolating the two-dimensional information collected on a cross-section of the floodplain. Unlike geostatistical methods, this extrapolation does not use a statis- tical spatial analysis of the data, but a genetic analysis, which leads to a more realistic structure. Groundwater flow and transport simulations in the alluvium were carried out with a three-dimensional flow code or simulator (MODFLOW), using different rep- resentations of the alluvial reservoir of the Aube River floodplain: first an equivalent homogeneous medium, and then different heterogeneous media built either with the traditional geostatistical approach simulating the permeability distribution, or with the new genetic model presented here simulating sediment facies. In the latter case, each deposited entity of a given lithology was assigned a constant hydraulic conductivity value. Results of these models have been compared to assess the value of the genetic approach and will be presented.

Towards realistic flow modelling. Creation and evaluation of two-dimensional simulated porous media: An image analysis approach

NASA Astrophysics Data System (ADS)

Anguy, Yannick; Bernard, Dominique; Ehrlich, Robert

1996-05-01

This work is part of an attempt to quantify the relationship between the permeability tensor ( K) and the micro-structure of natural porous media. A brief account is first provided of popular theories used to relate the micro-structure to K. Reasons for the lack of predictive power and restricted generality of current models are discussed. An alternative is an empirically based implicit model wherein K is expressed as a consequence of a few “pore-types” arising from the dynamics of depositional processes. The analytical form of that implicit model arises from evidence of universal association between pore-type and throat size in sandstones and carbonates. An explicit model, relying on the local change of scale technique is then addressed. That explicit model allows, from knowledge of the three-dimensional micro-geometry to calculate K explicitly without having recourse to any constitutive assumptions. The predictive and general character of the explicit model is underlined. The relevance of the change of scale technique is recalled to be contingent on the availability of rock-like three-dimensional synthetic media. A random stationary ergodic process is developed, that allows us to generate three-dimensional synthetic media from a two-dimensional autocorrelation function r(λ x ,λ y ) and associated probability density function ∈ β measured on a single binary image. The focus of this work is to ensure the rock-like character of those synthetic media. This is done first through a direct approach: n two-dimensional synthetic media, derived from single set ( ∈ β , r(λ x ,λ y )) yield n permeability tensors K {/i-1,n i} (calculated by the local change of scale) of the same order. This is a necessary condition to ensure that r(λ x ,λ y ) and ∈ β carry all structural information relevant to K. The limits of this direct approach, in terms of required Central Process Unit time and Memory is underlined, raising the need for an alternative. This is done by comparing the pore-type content of a sandstone sample and n synthetic media derived from r(λ x ,λ y ) and ∈ β measured on that sandstone-sample. Achievement of a good match ensures that the synthetic media comprise the fundamental structural level of all natural sandstones, that is a domainal structure of well-packed clusters of grains bounded by loose-packed pores.

Integrated Aeromechanics with Three-Dimensional Solid-Multibody Structures

NASA Technical Reports Server (NTRS)

Datta, Anubhav; Johnson, Wayne

2014-01-01

A full three-dimensional finite element-multibody structural dynamic solver is coupled to a three-dimensional Reynolds-averaged Navier-Stokes solver for the prediction of integrated aeromechanical stresses and strains on a rotor blade in forward flight. The objective is to lay the foundations of all major pieces of an integrated three-dimensional rotor dynamic analysis - from model construction to aeromechanical solution to stress/strain calculation. The primary focus is on the aeromechanical solution. Two types of three-dimensional CFD/CSD interfaces are constructed for this purpose with an emphasis on resolving errors from geometry mis-match so that initial-stage approximate structural geometries can also be effectively analyzed. A three-dimensional structural model is constructed as an approximation to a UH-60A-like fully articulated rotor. The aerodynamic model is identical to the UH-60A rotor. For preliminary validation measurements from a UH-60A high speed flight is used where CFD coupling is essential to capture the advancing side tip transonic effects. The key conclusion is that an integrated aeromechanical analysis is indeed possible with three-dimensional structural dynamics but requires a careful description of its geometry and discretization of its parts.

Simulation of Water-Surface Elevations and Velocity Distributions at the U.S. Highway 13 Bridge over the Tar River at Greenville, North Carolina, Using One- and Two-Dimensional Steady-State Hydraulic Models

USGS Publications Warehouse

Wagner, Chad R.

2007-01-01

The use of one-dimensional hydraulic models currently is the standard method for estimating velocity fields through a bridge opening for scour computations and habitat assessment. Flood-flow contraction through bridge openings, however, is hydrodynamically two dimensional and often three dimensional. Although there is awareness of the utility of two-dimensional models to predict the complex hydraulic conditions at bridge structures, little guidance is available to indicate whether a one- or two-dimensional model will accurately estimate the hydraulic conditions at a bridge site. The U.S. Geological Survey, in cooperation with the North Carolina Department of Transportation, initiated a study in 2004 to compare one- and two-dimensional model results with field measurements at complex riverine and tidal bridges in North Carolina to evaluate the ability of each model to represent field conditions. The field data consisted of discharge and depth-averaged velocity profiles measured with an acoustic Doppler current profiler and surveyed water-surface profiles for two high-flow conditions. For the initial study site (U.S. Highway 13 over the Tar River at Greenville, North Carolina), the water-surface elevations and velocity distributions simulated by the one- and two-dimensional models showed appreciable disparity in the highly sinuous reach upstream from the U.S. Highway 13 bridge. Based on the available data from U.S. Geological Survey streamgaging stations and acoustic Doppler current profiler velocity data, the two-dimensional model more accurately simulated the water-surface elevations and the velocity distributions in the study reach, and contracted-flow magnitudes and direction through the bridge opening. To further compare the results of the one- and two-dimensional models, estimated hydraulic parameters (flow depths, velocities, attack angles, blocked flow width) for measured high-flow conditions were used to predict scour depths at the U.S. Highway 13 bridge by using established methods. Comparisons of pier-scour estimates from both models indicated that the scour estimates from the two-dimensional model were as much as twice the depth of the estimates from the one-dimensional model. These results can be attributed to higher approach velocities and the appreciable flow angles at the piers simulated by the two-dimensional model and verified in the field. Computed flood-frequency estimates of the 10-, 50-, 100-, and 500-year return-period floods on the Tar River at Greenville were also simulated with both the one- and two-dimensional models. The simulated water-surface profiles and velocity fields of the various return-period floods were used to compare the modeling approaches and provide information on what return-period discharges would result in road over-topping and(or) pressure flow. This information is essential in the design of new and replacement structures. The ability to accurately simulate water-surface elevations and velocity magnitudes and distributions at bridge crossings is essential in assuring that bridge plans balance public safety with the most cost-effective design. By compiling pertinent bridge-site characteristics and relating them to the results of several model-comparison studies, the framework for developing guidelines for selecting the most appropriate model for a given bridge site can be accomplished.

Binocular stereo matching method based on structure tensor

NASA Astrophysics Data System (ADS)

Song, Xiaowei; Yang, Manyi; Fan, Yubo; Yang, Lei

2016-10-01

In a binocular visual system, to recover the three-dimensional information of the object, the most important step is to acquire matching points. Structure tensor is the vector representation of each point in its local neighborhood. Therefore, structure tensor performs well in region detection of local structure, and it is very suitable for detecting specific graphics such as pedestrians, cars and road signs in the image. In this paper, the structure tensor is combined with the luminance information to form the extended structure tensor. The directional derivatives of luminance in x and y directions are calculated, so that the local structure of the image is more prominent. Meanwhile, the Euclidean distance between the eigenvectors of key points is used as the similarity determination metric of key points in the two images. By matching, the coordinates of the matching points in the detected target are precisely acquired. In this paper, experiments were performed on the captured left and right images. After the binocular calibration, image matching was done to acquire the matching points, and then the target depth was calculated according to these matching points. By comparison, it is proved that the structure tensor can accurately acquire the matching points in binocular stereo matching.

Motivated Proteins: A web application for studying small three-dimensional protein motifs

PubMed Central

Leader, David P; Milner-White, E James

2009-01-01

Background Small loop-shaped motifs are common constituents of the three-dimensional structure of proteins. Typically they comprise between three and seven amino acid residues, and are defined by a combination of dihedral angles and hydrogen bonding partners. The most abundant of these are αβ-motifs, asx-motifs, asx-turns, β-bulges, β-bulge loops, β-turns, nests, niches, Schellmann loops, ST-motifs, ST-staples and ST-turns. We have constructed a database of such motifs from a range of high-quality protein structures and built a web application as a visual interface to this. Description The web application, Motivated Proteins, provides access to these 12 motifs (with 48 sub-categories) in a database of over 400 representative proteins. Queries can be made for specific categories or sub-categories of motif, motifs in the vicinity of ligands, motifs which include part of an enzyme active site, overlapping motifs, or motifs which include a particular amino acid sequence. Individual proteins can be specified, or, where appropriate, motifs for all proteins listed. The results of queries are presented in textual form as an (X)HTML table, and may be saved as parsable plain text or XML. Motifs can be viewed and manipulated either individually or in the context of the protein in the Jmol applet structural viewer. Cartoons of the motifs imposed on a linear representation of protein secondary structure are also provided. Summary information for the motifs is available, as are histograms of amino acid distribution, and graphs of dihedral angles at individual positions in the motifs. Conclusion Motivated Proteins is a publicly and freely accessible web application that enables protein scientists to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schema. PMID:19210785

Rigorous Approach in Investigation of Seismic Structure and Source Characteristicsin Northeast Asia: Hierarchical and Trans-dimensional Bayesian Inversion

NASA Astrophysics Data System (ADS)

Mustac, M.; Kim, S.; Tkalcic, H.; Rhie, J.; Chen, Y.; Ford, S. R.; Sebastian, N.

2015-12-01

Conventional approaches to inverse problems suffer from non-linearity and non-uniqueness in estimations of seismic structures and source properties. Estimated results and associated uncertainties are often biased by applied regularizations and additional constraints, which are commonly introduced to solve such problems. Bayesian methods, however, provide statistically meaningful estimations of models and their uncertainties constrained by data information. In addition, hierarchical and trans-dimensional (trans-D) techniques are inherently implemented in the Bayesian framework to account for involved error statistics and model parameterizations, and, in turn, allow more rigorous estimations of the same. Here, we apply Bayesian methods throughout the entire inference process to estimate seismic structures and source properties in Northeast Asia including east China, the Korean peninsula, and the Japanese islands. Ambient noise analysis is first performed to obtain a base three-dimensional (3-D) heterogeneity model using continuous broadband waveforms from more than 300 stations. As for the tomography of surface wave group and phase velocities in the 5-70 s band, we adopt a hierarchical and trans-D Bayesian inversion method using Voronoi partition. The 3-D heterogeneity model is further improved by joint inversions of teleseismic receiver functions and dispersion data using a newly developed high-efficiency Bayesian technique. The obtained model is subsequently used to prepare 3-D structural Green's functions for the source characterization. A hierarchical Bayesian method for point source inversion using regional complete waveform data is applied to selected events from the region. The seismic structure and source characteristics with rigorously estimated uncertainties from the novel Bayesian methods provide enhanced monitoring and discrimination of seismic events in northeast Asia.

From Two- to Three-Dimensional Structures of a Supertetrahedral Boran Using Density Functional Calculations.

PubMed

Getmanskii, Iliya V; Minyaev, Ruslan M; Steglenko, Dmitrii V; Koval, Vitaliy V; Zaitsev, Stanislav A; Minkin, Vladimir I

2017-08-14

With help of the DFT calculations and imposing of periodic boundary conditions the geometrical and electronic structures were investigated of two- and three-dimensional boron systems designed on the basis of graphane and diamond lattices in which carbons were replaced with boron tetrahedrons. The consequent studies of two- and three-layer systems resulted in the construction of a three-dimensional supertetrahedral borane crystal structure. The two-dimensional supertetrahedral borane structures with less than seven layers are dynamically unstable. At the same time the three-dimensional superborane systems were found to be dynamically stable. Lack of the forbidden electronic zone for the studied boron systems testifies that these structures can behave as good conductors. The low density of the supertetrahedral borane crystal structures (0.9 g cm -3 ) is close to that of water, which offers the perspective for their application as aerospace and cosmic materials. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Bayesian depth estimation from monocular natural images.

PubMed

Su, Che-Chun; Cormack, Lawrence K; Bovik, Alan C

2017-05-01

Estimating an accurate and naturalistic dense depth map from a single monocular photographic image is a difficult problem. Nevertheless, human observers have little difficulty understanding the depth structure implied by photographs. Two-dimensional (2D) images of the real-world environment contain significant statistical information regarding the three-dimensional (3D) structure of the world that the vision system likely exploits to compute perceived depth, monocularly as well as binocularly. Toward understanding how this might be accomplished, we propose a Bayesian model of monocular depth computation that recovers detailed 3D scene structures by extracting reliable, robust, depth-sensitive statistical features from single natural images. These features are derived using well-accepted univariate natural scene statistics (NSS) models and recent bivariate/correlation NSS models that describe the relationships between 2D photographic images and their associated depth maps. This is accomplished by building a dictionary of canonical local depth patterns from which NSS features are extracted as prior information. The dictionary is used to create a multivariate Gaussian mixture (MGM) likelihood model that associates local image features with depth patterns. A simple Bayesian predictor is then used to form spatial depth estimates. The depth results produced by the model, despite its simplicity, correlate well with ground-truth depths measured by a current-generation terrestrial light detection and ranging (LIDAR) scanner. Such a strong form of statistical depth information could be used by the visual system when creating overall estimated depth maps incorporating stereopsis, accommodation, and other conditions. Indeed, even in isolation, the Bayesian predictor delivers depth estimates that are competitive with state-of-the-art "computer vision" methods that utilize highly engineered image features and sophisticated machine learning algorithms.

Automated determination of fibrillar structures by simultaneous model building and fiber diffraction refinement.

PubMed

Potrzebowski, Wojciech; André, Ingemar

2015-07-01

For highly oriented fibrillar molecules, three-dimensional structures can often be determined from X-ray fiber diffraction data. However, because of limited information content, structure determination and validation can be challenging. We demonstrate that automated structure determination of protein fibers can be achieved by guiding the building of macromolecular models with fiber diffraction data. We illustrate the power of our approach by determining the structures of six bacteriophage viruses de novo using fiber diffraction data alone and together with solid-state NMR data. Furthermore, we demonstrate the feasibility of molecular replacement from monomeric and fibrillar templates by solving the structure of a plant virus using homology modeling and protein-protein docking. The generated models explain the experimental data to the same degree as deposited reference structures but with improved structural quality. We also developed a cross-validation method for model selection. The results highlight the power of fiber diffraction data as structural constraints.

Two-dimensional interferometric characterization of laser-induced refractive index profiles in bulk Topas polymer

NASA Astrophysics Data System (ADS)

Hessler, Steffen; Rosenberger, Manuel; Schmauss, Bernhard; Hellmann, Ralf

2018-01-01

In this paper we precisely determine laser-induced refractive index profiles created in cyclic olefin copolymer Topas 6017 employing a sophisticated phase shifting Mach-Zehnder interferometry approach. Beyond the usual one-dimensional modification depth measurement we highlight that for straight waveguide structures also a two-dimensional refractive index distribution can be directly obtained providing full information of a waveguide's exact cross section and its gradient refractive index contrast. Deployed as direct data input in optical waveguide simulation, the evaluated 2D refractive index profiles permit a detailed calculation of the waveguides' actual mode profiles. Furthermore, conventional one-dimensional interferometric measurements for refractive index depth profiles with varying total imposed laser fluence of a 248 nm KrF excimer laser are included to investigate the effect on refractive index modification depth. Maximum surface refractive index increase turns out to attain up to 1.86 ·10-3 enabling laser-written optical waveguide channels. Additionally, a comprehensive optical material characterization in terms of dispersion, thermo-optic coefficient and absorption measurement of unmodified and UV-modified Topas 6017 is carried out.

3D Flow visualization in virtual reality

NASA Astrophysics Data System (ADS)

Pietraszewski, Noah; Dhillon, Ranbir; Green, Melissa

2017-11-01

By viewing fluid dynamic isosurfaces in virtual reality (VR), many of the issues associated with the rendering of three-dimensional objects on a two-dimensional screen can be addressed. In addition, viewing a variety of unsteady 3D data sets in VR opens up novel opportunities for education and community outreach. In this work, the vortex wake of a bio-inspired pitching panel was visualized using a three-dimensional structural model of Q-criterion isosurfaces rendered in virtual reality using the HTC Vive. Utilizing the Unity cross-platform gaming engine, a program was developed to allow the user to control and change this model's position and orientation in three-dimensional space. In addition to controlling the model's position and orientation, the user can ``scroll'' forward and backward in time to analyze the formation and shedding of vortices in the wake. Finally, the user can toggle between different quantities, while keeping the time step constant, to analyze flow parameter relationships at specific times during flow development. The information, data, or work presented herein was funded in part by an award from NYS Department of Economic Development (DED) through the Syracuse Center of Excellence.

3D visualization of molecular structures in the MOGADOC database

NASA Astrophysics Data System (ADS)

Vogt, Natalja; Popov, Evgeny; Rudert, Rainer; Kramer, Rüdiger; Vogt, Jürgen

2010-08-01

The MOGADOC database (Molecular Gas-Phase Documentation) is a powerful tool to retrieve information about compounds which have been studied in the gas-phase by electron diffraction, microwave spectroscopy and molecular radio astronomy. Presently the database contains over 34,500 bibliographic references (from the beginning of each method) for about 10,000 inorganic, organic and organometallic compounds and structural data (bond lengths, bond angles, dihedral angles, etc.) for about 7800 compounds. Most of the implemented molecular structures are given in a three-dimensional (3D) presentation. To create or edit and visualize the 3D images of molecules, new tools (special editor and Java-based 3D applet) were developed. Molecular structures in internal coordinates were converted to those in Cartesian coordinates.

New software for statistical analysis of Cambridge Structural Database data

PubMed Central

Sykes, Richard A.; McCabe, Patrick; Allen, Frank H.; Battle, Gary M.; Bruno, Ian J.; Wood, Peter A.

2011-01-01

A collection of new software tools is presented for the analysis of geometrical, chemical and crystallographic data from the Cambridge Structural Database (CSD). This software supersedes the program Vista. The new functionality is integrated into the program Mercury in order to provide statistical, charting and plotting options alongside three-dimensional structural visualization and analysis. The integration also permits immediate access to other information about specific CSD entries through the Mercury framework, a common requirement in CSD data analyses. In addition, the new software includes a range of more advanced features focused towards structural analysis such as principal components analysis, cone-angle correction in hydrogen-bond analyses and the ability to deal with topological symmetry that may be exhibited in molecular search fragments. PMID:22477784

3D topography of biologic tissue by multiview imaging and structured light illumination

NASA Astrophysics Data System (ADS)

Liu, Peng; Zhang, Shiwu; Xu, Ronald

2014-02-01

Obtaining three-dimensional (3D) information of biologic tissue is important in many medical applications. This paper presents two methods for reconstructing 3D topography of biologic tissue: multiview imaging and structured light illumination. For each method, the working principle is introduced, followed by experimental validation on a diabetic foot model. To compare the performance characteristics of these two imaging methods, a coordinate measuring machine (CMM) is used as a standard control. The wound surface topography of the diabetic foot model is measured by multiview imaging and structured light illumination methods respectively and compared with the CMM measurements. The comparison results show that the structured light illumination method is a promising technique for 3D topographic imaging of biologic tissue.

The Numerical Analysis of a Turbulent Compressible Jet. Degree awarded by Ohio State Univ., 2000

NASA Technical Reports Server (NTRS)

DeBonis, James R.

2001-01-01

A numerical method to simulate high Reynolds number jet flows was formulated and applied to gain a better understanding of the flow physics. Large-eddy simulation was chosen as the most promising approach to model the turbulent structures due to its compromise between accuracy and computational expense. The filtered Navier-Stokes equations were developed including a total energy form of the energy equation. Subgrid scale models for the momentum and energy equations were adapted from compressible forms of Smagorinsky's original model. The effect of using disparate temporal and spatial accuracy in a numerical scheme was discovered through one-dimensional model problems and a new uniformly fourth-order accurate numerical method was developed. Results from two- and three-dimensional validation exercises show that the code accurately reproduces both viscous and inviscid flows. Numerous axisymmetric jet simulations were performed to investigate the effect of grid resolution, numerical scheme, exit boundary conditions and subgrid scale modeling on the solution and the results were used to guide the three-dimensional calculations. Three-dimensional calculations of a Mach 1.4 jet showed that this LES simulation accurately captures the physics of the turbulent flow. The agreement with experimental data was relatively good and is much better than results in the current literature. Turbulent intensities indicate that the turbulent structures at this level of modeling are not isotropic and this information could lend itself to the development of improved subgrid scale models for LES and turbulence models for RANS simulations. A two point correlation technique was used to quantify the turbulent structures. Two point space correlations were used to obtain a measure of the integral length scale, which proved to be approximately 1/2 D(sub j). Two point space-time correlations were used to obtain the convection velocity for the turbulent structures. This velocity ranged from 0.57 to 0.71 U(sub j).

Reduced dimensionality (3,2)D NMR experiments and their automated analysis: implications to high-throughput structural studies on proteins.

PubMed

Reddy, Jithender G; Kumar, Dinesh; Hosur, Ramakrishna V

2015-02-01

Protein NMR spectroscopy has expanded dramatically over the last decade into a powerful tool for the study of their structure, dynamics, and interactions. The primary requirement for all such investigations is sequence-specific resonance assignment. The demand now is to obtain this information as rapidly as possible and in all types of protein systems, stable/unstable, soluble/insoluble, small/big, structured/unstructured, and so on. In this context, we introduce here two reduced dimensionality experiments – (3,2)D-hNCOcanH and (3,2)D-hNcoCAnH – which enhance the previously described 2D NMR-based assignment methods quite significantly. Both the experiments can be recorded in just about 2-3 h each and hence would be of immense value for high-throughput structural proteomics and drug discovery research. The applicability of the method has been demonstrated using alpha-helical bovine apo calbindin-D9k P43M mutant (75 aa) protein. Automated assignment of this data using AUTOBA has been presented, which enhances the utility of these experiments. The backbone resonance assignments so derived are utilized to estimate secondary structures and the backbone fold using Web-based algorithms. Taken together, we believe that the method and the protocol proposed here can be used for routine high-throughput structural studies of proteins. Copyright © 2014 John Wiley & Sons, Ltd.

Knotty structures of the evolving heliospheric magnetic fields.

NASA Astrophysics Data System (ADS)

Roth, Ilan

2013-04-01

The analogy between MHD and knot theory is utilized in an analysis of structure, stability and evolution of complex magnetic heliospheric flux tubes. Planar projection of a three-dimensional magnetic configuration depicts the structure as a two-dimensional diagram with crossings, to which one may assign mathematical operations leading to robust topological invariants. These invariants enrich the topological information of magnetic configurations beyond helicity. It is conjectured that the field which emerges from the solar photosphere is structured as one of simplest knot invariants - unknot or prime knot, and these flux ropes are then stretched while carried by the solar wind into the interplanetary medium. Preservation of invariants for small diffusivity and large cross section of the emerging magnetic flux makes them impervious to large scale reconnection, allowing us to predict the observed structures at 1AU as elongated prime knots. Similar structures may be observed in magnetic clouds which got disconnected from their foot-points and in ion drop-out configurations from a compact flare source in solar impulsive solar events. Observation of small scale magnetic features consistent with prime knot may indicate spatial intermittency and non-Gaussian statistics in the turbulent cascade process. For flux tubes with higher resistivity, magnetic energy decay rate should decrease with increased knot complexity as the invariants are then harder to be violated. Future measurements are suggested for distinctly oriented magnetic fields with directionally varying suprathermal particle fluxes.

One-dimensional, two-dimensional, and three-dimensional photonic crystals fabricated with interferometric techniques on ultrafine-grain silver halide emulsions

NASA Astrophysics Data System (ADS)

Ulibarrena, Manuel; Carretero, Luis; Acebal, Pablo; Madrigal, Roque; Blaya, Salvador; Fimia, Antonio

2004-09-01

Holographic techniques have been used for manufacturing multiple band one-dimensional, two-dimensional, and three-dimensional photonic crystals with different configurations, by multiplexing reflection and transmission setups on a single layer of holographic material. The recording material used for storage is an ultra fine grain silver halide emulsion, with an average grain size around 20 nm. The results are a set of photonic crystals with the one-dimensional, two-dimensional, and three-dimensional index modulation structure consisting of silver halide particles embedded in the gelatin layer of the emulsion. The characterisation of the fabricated photonic crystals by measuring their transmission band structures has been done and compared with theoretical calculations.

Soliton structures in the (1+1)-dimensional Ginzburg–Landau equation with a parity-time-symmetric potential in ultrafast optics

NASA Astrophysics Data System (ADS)

Li, Wenyi; Ma, Guoli; Yu, Weitian; Zhang, Yujia; Liu, Mengli; Yang, Chunyu; Liu, Wenjun

2018-03-01

Not Available Project supported by the National Natural Science Foundation of China (Grant No. 11674036), the Beijing Youth Top-notch Talent Support Program, China (Grant No. 2017000026833ZK08), and the Fund of State Key Laboratory of Information Photonics and Optical Communications (Beijing University of Posts and Telecommunications) (Grant Nos. IPOC2016ZT04 and IPOC2017ZZ05).

On Monotone Embedding in Information Geometry (Open Access)

DTIC Science & Technology

2015-06-25

the non-parametric ( infinite - dimensional ) setting, as well [4,6], with the α-connection structure cast in a more general way. Theorem 1 of [4] gives... the weighting function for taking the expectation of random variables in calculating the Riemannian metric (G = 1 reduces to F - geometry , with the ...is a trivial rewriting of the convex function f used by [2]. This paper will start in Section 1

SPECTRAL LINE DE-CONFUSION IN AN INTENSITY MAPPING SURVEY

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

Cheng, Yun-Ting; Bock, James; Bradford, C. Matt

2016-12-01

Spectral line intensity mapping (LIM) has been proposed as a promising tool to efficiently probe the cosmic reionization and the large-scale structure. Without detecting individual sources, LIM makes use of all available photons and measures the integrated light in the source confusion limit to efficiently map the three-dimensional matter distribution on large scales as traced by a given emission line. One particular challenge is the separation of desired signals from astrophysical continuum foregrounds and line interlopers. Here we present a technique to extract large-scale structure information traced by emission lines from different redshifts, embedded in a three-dimensional intensity mapping data cube.more » The line redshifts are distinguished by the anisotropic shape of the power spectra when projected onto a common coordinate frame. We consider the case where high-redshift [C ii] lines are confused with multiple low-redshift CO rotational lines. We present a semi-analytic model for [C ii] and CO line estimates based on the cosmic infrared background measurements, and show that with a modest instrumental noise level and survey geometry, the large-scale [C ii] and CO power spectrum amplitudes can be successfully extracted from a confusion-limited data set, without external information. We discuss the implications and limits of this technique for possible LIM experiments.« less

Development of flood routing simulation system of digital Qingjiang based on integrated spatial information technology

NASA Astrophysics Data System (ADS)

Yuan, Yanbin; Zhou, You; Zhu, Yaqiong; Yuan, Xiaohui; Sælthun, N. R.

2007-11-01

Based on digital technology, flood routing simulation system development is an important component of "digital catchment". Taking QingJiang catchment as a pilot case, in-depth analysis on informatization of Qingjiang catchment management being the basis, aiming at catchment data's multi-source, - dimension, -element, -subject, -layer and -class feature, the study brings the design thought and method of "subject-point-source database" (SPSD) to design system structure in order to realize the unified management of catchments data in great quantity. Using the thought of integrated spatial information technology for reference, integrating hierarchical structure development model of digital catchment is established. The model is general framework of the flood routing simulation system analysis, design and realization. In order to satisfy the demands of flood routing three-dimensional simulation system, the object-oriented spatial data model are designed. We can analyze space-time self-adapting relation between flood routing and catchments topography, express grid data of terrain by using non-directed graph, apply breadth first search arithmetic, set up search method for the purpose of dynamically searching stream channel on the basis of simulated three-dimensional terrain. The system prototype is therefore realized. Simulation results have demonstrated that the proposed approach is feasible and effective in the application.

3-D Imaging Systems for Agricultural Applications—A Review

PubMed Central

Vázquez-Arellano, Manuel; Griepentrog, Hans W.; Reiser, David; Paraforos, Dimitris S.

2016-01-01

Efficiency increase of resources through automation of agriculture requires more information about the production process, as well as process and machinery status. Sensors are necessary for monitoring the status and condition of production by recognizing the surrounding structures such as objects, field structures, natural or artificial markers, and obstacles. Currently, three dimensional (3-D) sensors are economically affordable and technologically advanced to a great extent, so a breakthrough is already possible if enough research projects are commercialized. The aim of this review paper is to investigate the state-of-the-art of 3-D vision systems in agriculture, and the role and value that only 3-D data can have to provide information about environmental structures based on the recent progress in optical 3-D sensors. The structure of this research consists of an overview of the different optical 3-D vision techniques, based on the basic principles. Afterwards, their application in agriculture are reviewed. The main focus lays on vehicle navigation, and crop and animal husbandry. The depth dimension brought by 3-D sensors provides key information that greatly facilitates the implementation of automation and robotics in agriculture. PMID:27136560

Multiscale morphological filtering for analysis of noisy and complex images

NASA Astrophysics Data System (ADS)

Kher, A.; Mitra, S.

Images acquired with passive sensing techniques suffer from illumination variations and poor local contrasts that create major difficulties in interpretation and identification tasks. On the other hand, images acquired with active sensing techniques based on monochromatic illumination are degraded with speckle noise. Mathematical morphology offers elegant techniques to handle a wide range of image degradation problems. Unlike linear filters, morphological filters do not blur the edges and hence maintain higher image resolution. Their rich mathematical framework facilitates the design and analysis of these filters as well as their hardware implementation. Morphological filters are easier to implement and are more cost effective and efficient than several conventional linear filters. Morphological filters to remove speckle noise while maintaining high resolution and preserving thin image regions that are particularly vulnerable to speckle noise were developed and applied to SAR imagery. These filters used combination of linear (one-dimensional) structuring elements in different (typically four) orientations. Although this approach preserves more details than the simple morphological filters using two-dimensional structuring elements, the limited orientations of one-dimensional elements approximate the fine details of the region boundaries. A more robust filter designed recently overcomes the limitation of the fixed orientations. This filter uses a combination of concave and convex structuring elements. Morphological operators are also useful in extracting features from visible and infrared imagery. A multiresolution image pyramid obtained with successive filtering and a subsampling process aids in the removal of the illumination variations and enhances local contrasts. A morphology-based interpolation scheme was also introduced to reduce intensity discontinuities created in any morphological filtering task. The generality of morphological filtering techniques in extracting information from a wide variety of images obtained with active and passive sensing techniques is discussed. Such techniques are particularly useful in obtaining more information from fusion of complex images by different sensors such as SAR, visible, and infrared.

Multiscale Morphological Filtering for Analysis of Noisy and Complex Images

NASA Technical Reports Server (NTRS)

Kher, A.; Mitra, S.

1993-01-01

Images acquired with passive sensing techniques suffer from illumination variations and poor local contrasts that create major difficulties in interpretation and identification tasks. On the other hand, images acquired with active sensing techniques based on monochromatic illumination are degraded with speckle noise. Mathematical morphology offers elegant techniques to handle a wide range of image degradation problems. Unlike linear filters, morphological filters do not blur the edges and hence maintain higher image resolution. Their rich mathematical framework facilitates the design and analysis of these filters as well as their hardware implementation. Morphological filters are easier to implement and are more cost effective and efficient than several conventional linear filters. Morphological filters to remove speckle noise while maintaining high resolution and preserving thin image regions that are particularly vulnerable to speckle noise were developed and applied to SAR imagery. These filters used combination of linear (one-dimensional) structuring elements in different (typically four) orientations. Although this approach preserves more details than the simple morphological filters using two-dimensional structuring elements, the limited orientations of one-dimensional elements approximate the fine details of the region boundaries. A more robust filter designed recently overcomes the limitation of the fixed orientations. This filter uses a combination of concave and convex structuring elements. Morphological operators are also useful in extracting features from visible and infrared imagery. A multiresolution image pyramid obtained with successive filtering and a subsampling process aids in the removal of the illumination variations and enhances local contrasts. A morphology-based interpolation scheme was also introduced to reduce intensity discontinuities created in any morphological filtering task. The generality of morphological filtering techniques in extracting information from a wide variety of images obtained with active and passive sensing techniques is discussed. Such techniques are particularly useful in obtaining more information from fusion of complex images by different sensors such as SAR, visible, and infrared.

Tomographic image via background subtraction using an x-ray projection image and a priori computed tomography

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

Zhang Jin; Yi Byongyong; Lasio, Giovanni

Kilovoltage x-ray projection images (kV images for brevity) are increasingly available in image guided radiotherapy (IGRT) for patient positioning. These images are two-dimensional (2D) projections of a three-dimensional (3D) object along the x-ray beam direction. Projecting a 3D object onto a plane may lead to ambiguities in the identification of anatomical structures and to poor contrast in kV images. Therefore, the use of kV images in IGRT is mainly limited to bony landmark alignments. This work proposes a novel subtraction technique that isolates a slice of interest (SOI) from a kV image with the assistance of a priori information frommore » a previous CT scan. The method separates structural information within a preselected SOI by suppressing contributions to the unprocessed projection from out-of-SOI-plane structures. Up to a five-fold increase in the contrast-to-noise ratios (CNRs) was observed in selected regions of the isolated SOI, when compared to the original unprocessed kV image. The tomographic image via background subtraction (TIBS) technique aims to provide a quick snapshot of the slice of interest with greatly enhanced image contrast over conventional kV x-ray projections for fast and accurate image guidance of radiation therapy. With further refinements, TIBS could, in principle, provide real-time tumor localization using gantry-mounted x-ray imaging systems without the need for implanted markers.« less

Treatment planning for internal emitter therapy: Methods, applications and clinical implications

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

Sgouros, G.

1999-01-01

Treatment planning involves three basic steps: (1) a procedure must be devised that will provide the most relevant information, (2) the procedure must be applied and (3) the resulting information must be translated into a definition of the optimum implementation. There are varying degrees of treatment planning that may be implemented in internal emitter therapy. As in chemotherapy, the information from a Phase 1 study may be used to treat patients based upon body surface area. If treatment planning is included on a patient-specific basis, a pretherapy, trace-labeled, administration of the radiopharmaceutical is generally required. The data collected following themore » tracer dose may range from time-activity curves of blood and whole-body for use in blood, marrow or total body absorbed dose estimation to patient imaging for three-dimensional internal emitter dosimetry. The most ambitious approach requires a three-dimensional set of images representing radionuclide distribution (SPECT or PET) and a corresponding set of images representing anatomy (CT or MRI). The absorbed dose (or dose-rate) distribution may be obtained by convolution of a point kernel with the radioactivity distribution or by direct Monte Carlo calculation. A critical requirement for both techniques is the development of an overall structure that makes it possible, in a routine manner, to input the images, to identify the structures of interest and to display the results of the dose calculations in a clinically relevant manner. 52 refs., 4 figs., 1 tab.« less

Continuum modeling of three-dimensional truss-like space structures

NASA Technical Reports Server (NTRS)

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

1978-01-01

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

Multiple-wavelength neutron holography with pulsed neutrons

PubMed Central

Hayashi, Kouichi; Ohoyama, Kenji; Happo, Naohisa; Matsushita, Tomohiro; Hosokawa, Shinya; Harada, Masahide; Inamura, Yasuhiro; Nitani, Hiroaki; Shishido, Toetsu; Yubuta, Kunio

2017-01-01

Local structures around impurities in solids provide important information for understanding the mechanisms of material functions, because most of them are controlled by dopants. For this purpose, the x-ray absorption fine structure method, which provides radial distribution functions around specific elements, is most widely used. However, a similar method using neutron techniques has not yet been developed. If one can establish a method of local structural analysis with neutrons, then a new frontier of materials science can be explored owing to the specific nature of neutron scattering—that is, its high sensitivity to light elements and magnetic moments. Multiple-wavelength neutron holography using the time-of-flight technique with pulsed neutrons has great potential to realize this. We demonstrated multiple-wavelength neutron holography using a Eu-doped CaF2 single crystal and obtained a clear three-dimensional atomic image around trivalent Eu substituted for divalent Ca, revealing an interesting feature of the local structure that allows it to maintain charge neutrality. The new holography technique is expected to provide new information on local structures using the neutron technique. PMID:28835917

Multiple-wavelength neutron holography with pulsed neutrons.

PubMed

Hayashi, Kouichi; Ohoyama, Kenji; Happo, Naohisa; Matsushita, Tomohiro; Hosokawa, Shinya; Harada, Masahide; Inamura, Yasuhiro; Nitani, Hiroaki; Shishido, Toetsu; Yubuta, Kunio

2017-08-01

Local structures around impurities in solids provide important information for understanding the mechanisms of material functions, because most of them are controlled by dopants. For this purpose, the x-ray absorption fine structure method, which provides radial distribution functions around specific elements, is most widely used. However, a similar method using neutron techniques has not yet been developed. If one can establish a method of local structural analysis with neutrons, then a new frontier of materials science can be explored owing to the specific nature of neutron scattering-that is, its high sensitivity to light elements and magnetic moments. Multiple-wavelength neutron holography using the time-of-flight technique with pulsed neutrons has great potential to realize this. We demonstrated multiple-wavelength neutron holography using a Eu-doped CaF 2 single crystal and obtained a clear three-dimensional atomic image around trivalent Eu substituted for divalent Ca, revealing an interesting feature of the local structure that allows it to maintain charge neutrality. The new holography technique is expected to provide new information on local structures using the neutron technique.

Mathematical modeling of transformation process of structurally unstable magnetic configurations into structurally stable ones in two-dimensional and three-dimensional geometry

NASA Astrophysics Data System (ADS)

Inovenkov, Igor; Echkina, Eugenia; Ponomarenko, Loubov

Magnetic reconnection is a fundamental process in astrophysical, space and laboratory plasma. In essence, it represents a change of topology of the magnetic field caused by readjustment of the structure of the magnetic field lines. This change leads to release of energy accumulated in the field. We consider transformation process of structurally unstable magnetic configurations into the structurally steady ones from the point of view of the Catastrophe theory. Special attention is paid to modeling of evolution of the structurally unstable three-dimensional magnetic fields.

Parallel computation of three-dimensional aeroelastic fluid-structure interaction

NASA Astrophysics Data System (ADS)

Sadeghi, Mani

This dissertation presents a numerical method for the parallel computation of aeroelasticity (ParCAE). A flow solver is coupled to a structural solver by use of a fluid-structure interface method. The integration of the three-dimensional unsteady Navier-Stokes equations is performed in the time domain, simultaneously to the integration of a modal three-dimensional structural model. The flow solution is accelerated by using a multigrid method and a parallel multiblock approach. Fluid-structure coupling is achieved by subiteration. A grid-deformation algorithm is developed to interpolate the deformation of the structural boundaries onto the flow grid. The code is formulated to allow application to general, three-dimensional, complex configurations with multiple independent structures. Computational results are presented for various configurations, such as turbomachinery blade rows and aircraft wings. Investigations are performed on vortex-induced vibrations, effects of cascade mistuning on flutter, and cases of nonlinear cascade and wing flutter.

Stability and electronic properties of low-dimensional nanostructures

NASA Astrophysics Data System (ADS)

Guan, Jie

As the devices used in daily life become smaller and more concentrated, traditional three-dimensional (3D) bulk materials have reached their limit in size. Low-dimensional nanomaterials have been attracting more attention in research and getting widely applied in many industrial fields because of their atomic-level size, unique advanced properties, and varied nanostructures. In this thesis, I have studied the stability and mechanical and electronic properties of zero-dimensional (0D) structures including carbon fullerenes, nanotori, metallofullerenes and phosphorus fullerenes, one-dimensional (1D) structures including carbon nanotubes and phosphorus nanotubes, as well as two-dimensional (2D) structures including layered transition metal dichalcogenides (TMDs), phosphorene and phosphorus carbide (PC). I first briefly introduce the scientific background and the motivation of all the work in this thesis. Then the computational techniques, mainly density functional theory (DFT), are reviewed in Chapter 2. In Chapter 3, I investigate the stability and electronic structure of endohedral rare-earth metallofullerene La C60 and the trifluoromethylized La C60(CF3)n with n ≤ 5. Odd n is preferred due to the closed-shell electronic configuration or large HOMO-LUMO gap, which is also meaningful for the separation of C 60-based metallofullerenes. Mechanical and electronic properties of layered materials including TMDs and black phosphorus are studied in Chapter 4 and 5. In Chapter 4, a metallic NbSe2/semiconducting WSe2 bilayer is investigated and besides a rigid band shift associated with charge transfer, the presence of NbSe2 does not modify the electronic structure of WSe2. Structural similarity and small lattice mismatch results in the heterojunction being capable of efficiently transferring charge acrossthe interface. In Chapter 5, I investigate the dependence of stability and electronic band structure on the in-layer strain in bulk black phosphorus. In Chapters 6, 7 and 8, novel 2D structures are predicted theoretically. In Chapter 6, I propose two new stable structural phases of layered phosphorus besides the layered alpha-P (black) and beta-P (blue) phosphorus allotropes. A metal-insulator transition caused by inlayer strain or changing the number of layers is found in the new gamma-P phase. An unforeseen benefit is the possibility to connect different structural phases at no energy cost, which further leads to a paradigm of constructing very stable, faceted phosphorus nanotube and fullerene structures by laterally joining nanoribbons or patches of different planar phosphorene phases, which is discussed in Chapter 7. In Chapter 8, I propose previously unknown allotropes of PC in the stable shape of an atomically thin layer. Different stable geometries, which result from the competition between sp2 bonding found in graphitic C and sp3 bonding found in black P, display different electronic properties including metallic, semi-metallic with an anisotropic Dirac cone, and direct-gap semiconductors with their gap tunable by in-layer strain. In Chapter 9, I propose a fast method to determine the local curvature in 2D systems with arbitrary shape. The curvature information, combined with elastic constants obtained for a planar system, provides an accurate estimate of the local stability in the framework of continuum elasticity theory. This approach can be applied to all 2D structures. Finally, I present general conclusions from the PhD Thesis work in Chapter 10.

Teleportation between distant qudits via scattering of mobile qubits

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

Ciccarello, Francesco; Zarcone, Michelangelo; Bose, Sougato

2010-04-15

We consider a one-dimensional structure where noninteracting spin-s scattering centers, such as quantum impurities or multilevel atoms, are embedded at given positions. We show that the injection into the structure of unpolarized flying qubits, such as electrons or photons, along with path detection suffice to accomplish spin-state teleportation between two centers via a third ancillary one. No action over the internal quantum state of both the spin-s particles and the flying qubits is required. The protocol enables the transfer of quantum information between well-separated static entities in nanostructures by exploiting a very low control mechanism, namely scattering.

Optical second harmonic images of 90 deg domain structure in BaTiO3 and periodically inverted antiparallel domains in LiTaO3

NASA Astrophysics Data System (ADS)

Uesu, Y.; Kurimura, S.; Yamamoto, Y.

1995-04-01

Applied is a microscope to observations of 90 deg ferroelectric domain structure in BaTiO3 and inverted periodically are ferroelectric domains in LiTaO3. It is founded that the second harmonic generation microscope gives information which cannot be obtained by ordinary optical microscopes. The developed nonlinear optical microscope builds two dimensional second harmonic image of a specimen with inhomogenous distribution of d(sub ijk) and applied the microscope to observations of inhomogeneity in some nonlinear-optical organic microcrystals.

X-ray Fluorescence Holography: Principles, Apparatus, and Applications

NASA Astrophysics Data System (ADS)

Hayashi, Kouichi; Korecki, Pawel

2018-06-01

X-ray fluorescence holography (XFH) is an atomic structure determination technique that combines the capabilities of X-ray diffraction and X-ray fluorescence spectroscopy. It provides a unique means of gaining fully three-dimensional information about the local atomic structure and lattice site positions of selected elements inside compound samples. In this work, we discuss experimental and theoretical aspects that are essential for the efficient recording and analysis of X-ray fluorescence holograms and review the most recent advances in XFH. We describe experiments performed with brilliant synchrotron radiation as well as with tabletop setups that employ conventional X-ray tubes.

Computer-Aided Drug Design Methods.

PubMed

Yu, Wenbo; MacKerell, Alexander D

2017-01-01

Computational approaches are useful tools to interpret and guide experiments to expedite the antibiotic drug design process. Structure-based drug design (SBDD) and ligand-based drug design (LBDD) are the two general types of computer-aided drug design (CADD) approaches in existence. SBDD methods analyze macromolecular target 3-dimensional structural information, typically of proteins or RNA, to identify key sites and interactions that are important for their respective biological functions. Such information can then be utilized to design antibiotic drugs that can compete with essential interactions involving the target and thus interrupt the biological pathways essential for survival of the microorganism(s). LBDD methods focus on known antibiotic ligands for a target to establish a relationship between their physiochemical properties and antibiotic activities, referred to as a structure-activity relationship (SAR), information that can be used for optimization of known drugs or guide the design of new drugs with improved activity. In this chapter, standard CADD protocols for both SBDD and LBDD will be presented with a special focus on methodologies and targets routinely studied in our laboratory for antibiotic drug discoveries.

Toward correlating structure and mechanics of platelets.

PubMed

Sorrentino, Simona; Studt, Jan-Dirk; Horev, Melanie Bokstad; Medalia, Ohad; Sapra, K Tanuj

2016-09-02

The primary physiological function of blood platelets is to seal vascular lesions after injury and form hemostatic thrombi in order to prevent blood loss. This task relies on the formation of strong cellular-extracellular matrix interactions in the subendothelial lesions. The cytoskeleton of a platelet is key to all of its functions: its ability to spread, adhere and contract. Despite the medical significance of platelets, there is still no high-resolution structural information of their cytoskeleton. Here, we discuss and present 3-dimensional (3D) structural analysis of intact platelets by using cryo-electron tomography (cryo-ET) and atomic force microscopy (AFM). Cryo-ET provides in situ structural analysis and AFM gives stiffness maps of the platelets. In the future, combining high-resolution structural and mechanical techniques will bring new understanding of how structural changes modulate platelet stiffness during activation and adhesion.

Three-dimensional hydrogeologic framework model of the Rio Grande transboundary region of New Mexico and Texas, USA, and northern Chihuahua, Mexico

USGS Publications Warehouse

Sweetkind, Donald S.

2017-09-08

As part of a U.S. Geological Survey study in cooperation with the Bureau of Reclamation, a digital three-dimensional hydrogeologic framework model was constructed for the Rio Grande transboundary region of New Mexico and Texas, USA, and northern Chihuahua, Mexico. This model was constructed to define the aquifer system geometry and subsurface lithologic characteristics and distribution for use in a regional numerical hydrologic model. The model includes five hydrostratigraphic units: river channel alluvium, three informal subdivisions of Santa Fe Group basin fill, and an undivided pre-Santa Fe Group bedrock unit. Model input data were compiled from published cross sections, well data, structure contour maps, selected geophysical data, and contiguous compilations of surficial geology and structural features in the study area. These data were used to construct faulted surfaces that represent the upper and lower subsurface hydrostratigraphic unit boundaries. The digital three-dimensional hydrogeologic framework model is constructed through combining faults, the elevation of the tops of each hydrostratigraphic unit, and boundary lines depicting the subsurface extent of each hydrostratigraphic unit. The framework also compiles a digital representation of the distribution of sedimentary facies within each hydrostratigraphic unit. The digital three-dimensional hydrogeologic model reproduces with reasonable accuracy the previously published subsurface hydrogeologic conceptualization of the aquifer system and represents the large-scale geometry of the subsurface aquifers. The model is at a scale and resolution appropriate for use as the foundation for a numerical hydrologic model of the study area.

THREE-DIMENSIONAL RANDOM ACCESS MULTIPHOTON MICROSCOPY FOR FAST FUNCTIONAL IMAGING OF NEURONAL ACTIVITY

PubMed Central

Reddy, Gaddum Duemani; Kelleher, Keith; Fink, Rudy; Saggau, Peter

2009-01-01

The dynamic ability of neuronal dendrites to shape and integrate synaptic responses is the hallmark of information processing in the brain. Effectively studying this phenomenon requires concurrent measurements at multiple sites on live neurons. Significant progress has been made by optical imaging systems which combine confocal and multiphoton microscopy with inertia-free laser scanning. However, all systems developed to date restrict fast imaging to two dimensions. This severely limits the extent to which neurons can be studied, since they represent complex three-dimensional (3D) structures. Here we present a novel imaging system that utilizes a unique arrangement of acousto-optic deflectors to steer a focused ultra-fast laser beam to arbitrary locations in 3D space without moving the objective lens. As we demonstrate, this highly versatile random-access multiphoton microscope supports functional imaging of complex 3D cellular structures such as neuronal dendrites or neural populations at acquisition rates on the order of tens of kilohertz. PMID:18432198

Ultrathin Two-Dimensional Covalent Organic Framework Nanosheets: Preparation and Application in Highly Sensitive and Selective DNA Detection.

PubMed

Peng, Yongwu; Huang, Ying; Zhu, Yihan; Chen, Bo; Wang, Liying; Lai, Zhuangchai; Zhang, Zhicheng; Zhao, Meiting; Tan, Chaoliang; Yang, Nailiang; Shao, Fangwei; Han, Yu; Zhang, Hua

2017-06-28

The ability to prepare ultrathin two-dimensional (2D) covalent organic framework (COF) nanosheets (NSs) in high yield is of great importance for the further exploration of their unique properties and potential applications. Herein, by elaborately designing and choosing two flexible molecules with C 3v molecular symmetry as building units, a novel imine-linked COF, namely, TPA-COF, with a hexagonal layered structure and sheet-like morphology, is synthesized. Since the flexible building units are integrated into the COF skeletons, the interlayer stacking becomes weak, resulting in the easy exfoliation of TPA-COF into ultrathin 2D NSs. Impressively, for the first time, the detailed structural information, i.e., the pore channels and individual building units in the NSs, is clearly visualized by using the recently developed low-dose imaging technique of transmission electron microscopy (TEM). As a proof-of-concept application, the obtained ultrathin COF NSs are used as a novel fluorescence sensing platform for the highly sensitive and selective detection of DNA.

A study of the comparative anatomy of the brain of domestic ruminants using magnetic resonance imaging.

PubMed

Schmidt, M J; Langen, N; Klumpp, S; Nasirimanesh, F; Shirvanchi, P; Ondreka, N; Kramer, M

2012-01-01

Although magnetic resonance imaging has been used to examine the brain of domestic ruminants, detailed information relating the precise anatomical features in these species is lacking. In this study the brain structures of calves (Bos taurus domesticus), sheep (Ovis aries), goats (Capra hircus) and a mesaticephalic dog (Canis lupis familiaris) were examined using T2-weighed Turbo Spin Echo sequences; three-dimensional models based on high-resolution gradient echo scans were used to identify brain sulci and gyri in two-dimensional images. The ruminant brains examined were similar in structure and organisation to those of other mammals but particular features included the deep depression of the insula and the pronounced gyri of the cortices, the dominant position of the visual (optic nerve, optic chiasm and rostral colliculus) and olfactory (olfactory bulb, olfactory tracts and piriform lobe) systems, and the relatively large size of the diencephalon. Copyright © 2010 Elsevier Ltd. All rights reserved.

Diagnostic ability of computed tomography using DentaScan software in endodontics: case reports.

PubMed

Siotia, Jaya; Gupta, Sunil K; Acharya, Shashi R; Saraswathi, Vidya

2011-01-01

Radiographic examination is essential in diagnosis and treatment planning in endodontics. Conventional radiographs depict structures in two dimensions only. The ability to assess the area of interest in three dimensions is advantageous. Computed tomography is an imaging technique which produces three-dimensional images of an object by taking a series of two-dimensional sectional X-ray images. DentaScan is a computed tomography software program that allows the mandible and maxilla to be imaged in three planes: axial, panoramic, and cross-sectional. As computed tomography is used in endodontics, DentaScan can play a wider role in endodontic diagnosis. It provides valuable information in the assessment of the morphology of the root canal, diagnosis of root fractures, internal and external resorptions, pre-operative assessment of anatomic structures etc. The aim of this article is to explore the clinical usefulness of computed tomography and DentaScan in endodontic diagnosis, through a series of four cases of different endodontic problems.

The Impact of The Fractal Paradigm on Geography

NASA Astrophysics Data System (ADS)

De Cola, L.

2001-12-01

Being itself somewhat fractal, Benoit Mandelbrot's magnum opus THE FRACTAL GEOMETRY OF NATURE may be deconstructed in many ways, including geometrically, systematically, and epistemologically. Viewed as a work of geography it may be used to organize the major topics of interest to scientists preoccupied with the understanding of real-world space in astronomy, geology, meteorology, hydrology, and biology. We shall use it to highlight such recent geographic accomplishments as automated feature detection, understanding urban growth, and modeling the spread of disease in space and time. However, several key challenges remain unsolved, among them: 1. It is still not possible to move continuously from one map scale to another so that objects change their dimension smoothly. I.e. as a viewer zooms in on a map the zero-dimensional location of a city should gradually become a 2-dimensional polygon, then a network of 1-dimensional streets, then 3-dimensional buildings, etc. 2. Spatial autocorrelation continues to be regarded more as an econometric challenge than as a problem of scaling. Similarities of values among closely-spaced observation is not so much a problem to be overcome as a source of information about spatial structure. 3. Although the fractal paradigm is a powerful model for data analysis, its ideas and techniques need to be brought to bear on the problems of understanding such hierarchies as ecosystems (the flow networks of energy and matter), taxonomies (biological classification), and knowledge (hierarchies of bureaucratic information, networks of linked data, etc).

Variations of the superficial middle cerebral vein: classification using three-dimensional CT angiography.

PubMed

Suzuki, Y; Matsumoto, K

2000-05-01

Classification of variations of the superficial middle cerebral vein (SMCV) remains ambiguous. We propose a new classification system based on embryologic development for preoperative examination. Three-dimensional CT angiography was used to evaluate 500 SMCVs (in 250 patients). The outflow vessels from the SMCV were classified into seven types on the basis of embryologic development. The 3D CT angiograms in axial stereoscopic and oblique views and multiple intensity projection images were evaluated by the same neurosurgeon on two occasions. Inconsistent interpretations were regarded as equivocal. Three-dimensional CT angiography clearly depicted the SMCV running along the lesser wing or the middle cranial fossa. However, the outflow vessel could not be confirmed as the sphenoparietal, cavernous, or emissary type in 39 (8%) of the sides. SMCVs running in the middle cranial fossa to join the transverse sinus or superior petrosal sinus were accurately identified. SMCVs were present in 456 sides: 62% entered the sphenoparietal sinus or the cavernous sinus and 12% joined the emissary vein. Nine vessels were the superior petrosal type, 10 the basal type, 12 the squamosal type, and 44 the undeveloped type. Three-dimensional CT angiography can depict the vessels and their anatomic relationship to the bone structure, allowing identification of the SMCV variant in individual patients. Preoperative planning for skull base surgery requires such information to reduce the invasiveness of the procedure. With the use of our classification system, 3D CT angiography can provide exact and practical information concerning the SMCV.

Two-dimensional simulation and modeling in scanning electron microscope imaging and metrology research.

PubMed

Postek, Michael T; Vladár, András E; Lowney, Jeremiah R; Keery, William J

2002-01-01

Traditional Monte Carlo modeling of the electron beam-specimen interactions in a scanning electron microscope (SEM) produces information about electron beam penetration and output signal generation at either a single beam-landing location, or multiple landing positions. If the multiple landings lie on a line, the results can be graphed in a line scan-like format. Monte Carlo results formatted as line scans have proven useful in providing one-dimensional information about the sample (e.g., linewidth). When used this way, this process is called forward line scan modeling. In the present work, the concept of image simulation (or the first step in the inverse modeling of images) is introduced where the forward-modeled line scan data are carried one step further to construct theoretical two-dimensional (2-D) micrographs (i.e., theoretical SEM images) for comparison with similar experimentally obtained micrographs. This provides an ability to mimic and closely match theory and experiment using SEM images. Calculated and/or measured libraries of simulated images can be developed with this technique. The library concept will prove to be very useful in the determination of dimensional and other properties of simple structures, such as integrated circuit parts, where the shape of the features is preferably measured from a single top-down image or a line scan. This paper presents one approach to the generation of 2-D simulated images and presents some suggestions as to their application to critical dimension metrology.

Magnetic resonance spectroscopy and imaging for the study of fossils.

PubMed

Giovannetti, Giulio; Guerrini, Andrea; Salvadori, Piero A

2016-07-01

Computed tomography (CT) has long been used for investigating palaeontological specimens, as it is a nondestructive technique which avoids the need to dissolve or ionize the fossil sample. However, magnetic resonance spectroscopy (MRS) and magnetic resonance imaging (MRI) have recently gained ground as analytical tools for examination of palaeontological samples, by nondestructively providing information about the structure and composition of fossils. While MRI techniques are able to reveal the three-dimensional geometry of the trace fossil, MRS can provide information on the chemical composition of the samples. The multidimensional nature of MR (magnetic resonance) signals has potential to provide rich three-dimensional data on the palaeontological specimens and also to help in elucidating paleopathological and paleoecological questions. In this work the verified applications and the emerging uses of MRI and MRS in paleontology are reviewed, with particular attention to fossil spores, fossil plants, ambers, fossil invertebrates, and fossil vertebrate studies. Copyright © 2016 Elsevier Inc. All rights reserved.

Multi-dimensional knowledge translation: enabling health informatics capacity audits using patient journey models.

PubMed

Catley, Christina; McGregor, Carolyn; Percival, Jennifer; Curry, Joanne; James, Andrew

2008-01-01

This paper presents a multi-dimensional approach to knowledge translation, enabling results obtained from a survey evaluating the uptake of Information Technology within Neonatal Intensive Care Units to be translated into knowledge, in the form of health informatics capacity audits. Survey data, having multiple roles, patient care scenarios, levels, and hospitals, is translated using a structured data modeling approach, into patient journey models. The data model is defined such that users can develop queries to generate patient journey models based on a pre-defined Patient Journey Model architecture (PaJMa). PaJMa models are then analyzed to build capacity audits. Capacity audits offer a sophisticated view of health informatics usage, providing not only details of what IT solutions a hospital utilizes, but also answering the questions: when, how and why, by determining when the IT solutions are integrated into the patient journey, how they support the patient information flow, and why they improve the patient journey.

Analysis of micro computed tomography images; a look inside historic enamelled metal objects

NASA Astrophysics Data System (ADS)

van der Linden, Veerle; van de Casteele, Elke; Thomas, Mienke Simon; de Vos, Annemie; Janssen, Elsje; Janssens, Koen

2010-02-01

In this study the usefulness of micro-Computed Tomography (µ-CT) for the in-depth analysis of enamelled metal objects was tested. Usually investigations of enamelled metal artefacts are restricted to non-destructive surface analysis or analysis of cross sections after destructive sampling. Radiography, a commonly used technique in the field of cultural heritage studies, is limited to providing two-dimensional information about a three-dimensional object (Lang and Middleton, Radiography of Cultural Material, pp. 60-61, Elsevier-Butterworth-Heinemann, Amsterdam-Stoneham-London, 2005). Obtaining virtual slices and information about the internal structure of these objects was made possible by CT analysis. With this technique the underlying metal work was studied without removing the decorative enamel layer. Moreover visible defects such as cracks were measured in both width and depth and as of yet invisible defects and weaker areas are visualised. All these features are of great interest to restorers and conservators as they allow a view inside these objects without so much as touching them.

Case study of 3D fingerprints applications

PubMed Central

Liu, Feng; Liang, Jinrong; Shen, Linlin; Yang, Meng; Zhang, David; Lai, Zhihui

2017-01-01

Human fingers are 3D objects. More information will be provided if three dimensional (3D) fingerprints are available compared with two dimensional (2D) fingerprints. Thus, this paper firstly collected 3D finger point cloud data by Structured-light Illumination method. Additional features from 3D fingerprint images are then studied and extracted. The applications of these features are finally discussed. A series of experiments are conducted to demonstrate the helpfulness of 3D information to fingerprint recognition. Results show that a quick alignment can be easily implemented under the guidance of 3D finger shape feature even though this feature does not work for fingerprint recognition directly. The newly defined distinctive 3D shape ridge feature can be used for personal authentication with Equal Error Rate (EER) of ~8.3%. Also, it is helpful to remove false core point. Furthermore, a promising of EER ~1.3% is realized by combining this feature with 2D features for fingerprint recognition which indicates the prospect of 3D fingerprint recognition. PMID:28399141

Case study of 3D fingerprints applications.

PubMed

Liu, Feng; Liang, Jinrong; Shen, Linlin; Yang, Meng; Zhang, David; Lai, Zhihui

2017-01-01

Human fingers are 3D objects. More information will be provided if three dimensional (3D) fingerprints are available compared with two dimensional (2D) fingerprints. Thus, this paper firstly collected 3D finger point cloud data by Structured-light Illumination method. Additional features from 3D fingerprint images are then studied and extracted. The applications of these features are finally discussed. A series of experiments are conducted to demonstrate the helpfulness of 3D information to fingerprint recognition. Results show that a quick alignment can be easily implemented under the guidance of 3D finger shape feature even though this feature does not work for fingerprint recognition directly. The newly defined distinctive 3D shape ridge feature can be used for personal authentication with Equal Error Rate (EER) of ~8.3%. Also, it is helpful to remove false core point. Furthermore, a promising of EER ~1.3% is realized by combining this feature with 2D features for fingerprint recognition which indicates the prospect of 3D fingerprint recognition.

Thermal perturbation correlation of calcium binding Human centrin 3 and its structural changes

NASA Astrophysics Data System (ADS)

Pastrana-Rios, Belinda

2014-07-01

Perturbation-correlation moving-window two-dimensional (PCMW2D) correlation spectroscopy was applied for the determination of the individual transition temperatures of different vibrational modes located within structural components of a calcium binding protein known as Human centrin 3. This crucial information served to understand the contribution individual calcium binding sites made towards the stability of the EF-hand and therefore the protein without the use of probes. We are convinced that the general application of PCMW2D correlation spectroscopy can be applied to the study of proteins in general to ascertain the differences in the stability of structural motifs within proteins and its relationship to the actual transition temperature of unfolding.

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

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

Generation and confirmation of a (100 x 100)-dimensional entangled quantum system.

PubMed

Krenn, Mario; Huber, Marcus; Fickler, Robert; Lapkiewicz, Radek; Ramelow, Sven; Zeilinger, Anton

2014-04-29

Entangled quantum systems have properties that have fundamentally overthrown the classical worldview. Increasing the complexity of entangled states by expanding their dimensionality allows the implementation of novel fundamental tests of nature, and moreover also enables genuinely new protocols for quantum information processing. Here we present the creation of a (100 × 100)-dimensional entangled quantum system, using spatial modes of photons. For its verification we develop a novel nonlinear criterion which infers entanglement dimensionality of a global state by using only information about its subspace correlations. This allows very practical experimental implementation as well as highly efficient extraction of entanglement dimensionality information. Applications in quantum cryptography and other protocols are very promising.

Generation and confirmation of a (100 × 100)-dimensional entangled quantum system

PubMed Central

Krenn, Mario; Huber, Marcus; Fickler, Robert; Lapkiewicz, Radek; Ramelow, Sven; Zeilinger, Anton

2014-01-01

Entangled quantum systems have properties that have fundamentally overthrown the classical worldview. Increasing the complexity of entangled states by expanding their dimensionality allows the implementation of novel fundamental tests of nature, and moreover also enables genuinely new protocols for quantum information processing. Here we present the creation of a (100 × 100)-dimensional entangled quantum system, using spatial modes of photons. For its verification we develop a novel nonlinear criterion which infers entanglement dimensionality of a global state by using only information about its subspace correlations. This allows very practical experimental implementation as well as highly efficient extraction of entanglement dimensionality information. Applications in quantum cryptography and other protocols are very promising. PMID:24706902

Framework to model neutral particle flux in convex high aspect ratio structures using one-dimensional radiosity

NASA Astrophysics Data System (ADS)

Manstetten, Paul; Filipovic, Lado; Hössinger, Andreas; Weinbub, Josef; Selberherr, Siegfried

2017-02-01

We present a computationally efficient framework to compute the neutral flux in high aspect ratio structures during three-dimensional plasma etching simulations. The framework is based on a one-dimensional radiosity approach and is applicable to simulations of convex rotationally symmetric holes and convex symmetric trenches with a constant cross-section. The framework is intended to replace the full three-dimensional simulation step required to calculate the neutral flux during plasma etching simulations. Especially for high aspect ratio structures, the computational effort, required to perform the full three-dimensional simulation of the neutral flux at the desired spatial resolution, conflicts with practical simulation time constraints. Our results are in agreement with those obtained by three-dimensional Monte Carlo based ray tracing simulations for various aspect ratios and convex geometries. With this framework we present a comprehensive analysis of the influence of the geometrical properties of high aspect ratio structures as well as of the particle sticking probability on the neutral particle flux.

Copula based flexible modeling of associations between clustered event times.

PubMed

Geerdens, Candida; Claeskens, Gerda; Janssen, Paul

2016-07-01

Multivariate survival data are characterized by the presence of correlation between event times within the same cluster. First, we build multi-dimensional copulas with flexible and possibly symmetric dependence structures for such data. In particular, clustered right-censored survival data are modeled using mixtures of max-infinitely divisible bivariate copulas. Second, these copulas are fit by a likelihood approach where the vast amount of copula derivatives present in the likelihood is approximated by finite differences. Third, we formulate conditions for clustered right-censored survival data under which an information criterion for model selection is either weakly consistent or consistent. Several of the familiar selection criteria are included. A set of four-dimensional data on time-to-mastitis is used to demonstrate the developed methodology.

Computationally Driven Two-Dimensional Materials Design: What Is Next?

DOE PAGES

Pan, Jie; Lany, Stephan; Qi, Yue

2017-07-17

Two-dimensional (2D) materials offer many key advantages to innovative applications, such as spintronics and quantum information processing. Theoretical computations have accelerated 2D materials design. In this issue of ACS Nano, Kumar et al. report that ferromagnetism can be achieved in functionalized nitride MXene based on first-principles calculations. Their computational results shed light on a potentially vast group of materials for the realization of 2D magnets. In this Perspective, we briefly summarize the promising properties of 2D materials and the role theory has played in predicting these properties. Additionally, we discuss challenges and opportunities to boost the power of computation formore » the prediction of the 'structure-property-process (synthesizability)' relationship of 2D materials.« less

Principle of two-dimensional characterization of copolymers.

PubMed

Weidner, Steffen; Falkenhagen, Jana; Krueger, Ralph-Peter; Just, Ulrich

2007-07-01

Two-dimensional polymer characterization is used for a simultaneous analysis of molar masses and chemical heterogeneities (e.g., end groups, copolymer composition, etc.). This principle is based on coupling of two different chromatographic modes. Liquid adsorption chromatography at critical conditions (LACCC) is applied for a separation according to the chemical heterogeneity, whereas in the second-dimension fractions are analyzed with regard to their molar mass distribution by means of size exclusion chromatography (SEC). Because appropriate standards for a calibration of the SEC are seldom available, matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) was used to substitute the SEC. The LACCC-MALDI MS coupling enables acquiring additional structural information on copolymer composition, which can considerably enhance the performance of this coupled method.

Three-dimensional reconstruction of glycosomes in trypanosomatids of the genus Phytomonas.

PubMed

Attias, M; de Souza, W

1995-02-01

Computer aided three dimensional (3-D) reconstruction of cells from two isolates of protozoa of the genus Phytomonas, trypanosomatids found in plants, were made from 0.3 microm thick sections, imaged on a Zeiss 902 electron microscope with a energy filter for in ellastically scattered electrons, in order to obtain information about glycosomal shape diversity. Direct counts of peroxisomes (glycosomes) from Phytomonas sp. from Chamaesyce thymifolia indicated that there were fewer glycosomes per cell than the simple count of ultrathin section profiles would suggest and that these organelles could be long and branched. On the other hand, the stacked glycosomes observed in the isolate from Euphorbia characias were small individual structures and no connection was seen between them.

A three-dimensional potential-flow program with a geometry package for input data generation

NASA Technical Reports Server (NTRS)

Halsey, N. D.

1978-01-01

Information needed to run a computer program for the calculation of the potential flow about arbitrary three dimensional lifting configurations is presented. The program contains a geometry package which greatly reduces the task of preparing the input data. Starting from a very sparse set of coordinate data, the program automatically augments and redistributes the coordinates, calculates curves of intersection between components, and redistributes coordinates in the regions adjacent to the intersection curves in a suitable manner for use in the potential flow calculations. A brief summary of the program capabilities and options is given, as well as detailed instructions for the data input, a suggested structure for the program overlay, and the output for two test cases.

Interface between path and orbital angular momentum entanglement for high-dimensional photonic quantum information.

PubMed

Fickler, Robert; Lapkiewicz, Radek; Huber, Marcus; Lavery, Martin P J; Padgett, Miles J; Zeilinger, Anton

2014-07-30

Photonics has become a mature field of quantum information science, where integrated optical circuits offer a way to scale the complexity of the set-up as well as the dimensionality of the quantum state. On photonic chips, paths are the natural way to encode information. To distribute those high-dimensional quantum states over large distances, transverse spatial modes, like orbital angular momentum possessing Laguerre Gauss modes, are favourable as flying information carriers. Here we demonstrate a quantum interface between these two vibrant photonic fields. We create three-dimensional path entanglement between two photons in a nonlinear crystal and use a mode sorter as the quantum interface to transfer the entanglement to the orbital angular momentum degree of freedom. Thus our results show a flexible way to create high-dimensional spatial mode entanglement. Moreover, they pave the way to implement broad complex quantum networks where high-dimensionally entangled states could be distributed over distant photonic chips.

Implication of Broadband Dispersion Measurements in Constraining Upper Mantle Velocity Structures

NASA Astrophysics Data System (ADS)

Kuponiyi, A.; Kao, H.; Cassidy, J. F.; Darbyshire, F. A.; Dosso, S. E.; Gosselin, J. M.; Spence, G.

2017-12-01

Dispersion measurements from earthquake (EQ) data are traditionally inverted to obtain 1-D shear-wave velocity models, which provide information on deep earth structures. However, in many cases, EQ-derived dispersion measurements lack short-period information, which theoretically should provide details of shallow structures. We show that in at least some cases short-period information, such as can be obtained from ambient seismic noise (ASN) processing, must be combined with EQ dispersion measurements to properly constrain deeper (e.g. upper-mantle) structures. To verify this, synthetic dispersion data are generated using hypothetical velocity models under four scenarios: EQ only (with and without deep low-velocity layers) and combined EQ and ASN data (with and without deep low-velocity layers). The now "broadband" dispersion data are inverted using a trans-dimensional Bayesian framework with the aim of recovering the initial velocity models and assessing uncertainties. Our results show that the deep low-velocity layer could only be recovered from the inversion of the combined ASN-EQ dispersion measurements. Given this result, we proceed to describe a method for obtaining reliable broadband dispersion measurements from both ASN and EQ and show examples for real data. The implication of this study in the characterization of lithospheric and upper mantle structures, such as the Lithosphere-Asthenosphere Boundary (LAB), is also discussed.

Direct Numerical Simulation of a Temporally Evolving Incompressible Plane Wake: Effect of Initial Conditions on Evolution and Topology

NASA Technical Reports Server (NTRS)

Sondergaard, R.; Cantwell, B.; Mansour, N.

1997-01-01

Direct numerical simulations have been used to examine the effect of the initial disturbance field on the development of three-dimensionality and the transition to turbulence in the incompressible plane wake. The simulations were performed using a new numerical method for solving the time-dependent, three-dimensional, incompressible Navier-Stokes equations in flows with one infinite and two periodic directions. The method uses standard Fast Fourier Transforms and is applicable to cases where the vorticity field is compact in the infinite direction. Initial disturbances fields examined were combinations of two-dimensional waves and symmetric pairs of 60 deg oblique waves at the fundamental, subharmonic, and sub-subharmonic wavelengths. The results of these simulations indicate that the presence of 60 deg disturbances at the subharmonic streamwise wavelength results in the development of strong coherent three-dimensional structures. The resulting strong three-dimensional rate-of-strain triggers the growth of intense fine scale motions. Wakes initiated with 60 deg disturbances at the fundamental streamwise wavelength develop weak coherent streamwise structures, and do not develop significant fine scale motions, even at high Reynolds numbers. The wakes which develop strong three-dimensional structures exhibit growth rates on par with experimentally observed turbulent plane wakes. Wakes which develop only weak three-dimensional structures exhibit significantly lower late time growth rates. Preliminary studies of wakes initiated with an oblique fundamental and a two-dimensional subharmonic, which develop asymmetric coherent oblique structures at the subharmonic wavelength, indicate that significant fine scale motions only develop if the resulting oblique structures are above an angle of approximately 45 deg.

Virtual temporal bone: an interactive 3-dimensional learning aid for cranial base surgery.

PubMed

Kockro, Ralf A; Hwang, Peter Y K

2009-05-01

We have developed an interactive virtual model of the temporal bone for the training and teaching of cranial base surgery. The virtual model was based on the tomographic data of the Visible Human Project. The male Visible Human's computed tomographic data were volumetrically reconstructed as virtual bone tissue, and the individual photographic slices provided the basis for segmentation of the middle and inner ear structures, cranial nerves, vessels, and brainstem. These structures were created by using outlining and tube editing tools, allowing structural modeling either directly on the basis of the photographic data or according to information from textbooks and cadaver dissections. For training and teaching, the virtual model was accessed in the previously described 3-dimensional workspaces of the Dextroscope or Dextrobeam (Volume Interactions Pte, Ltd., Singapore), whose interfaces enable volumetric exploration from any perspective and provide virtual tools for drilling and measuring. We have simulated several cranial base procedures including approaches via the floor of the middle fossa and the lateral petrous bone. The virtual model suitably illustrated the core facts of anatomic spatial relationships while simulating different stages of bone drilling along a variety of surgical corridors. The system was used for teaching during training courses to plan and discuss operative anatomy and strategies. The Virtual Temporal Bone and its surrounding 3-dimensional workspace provide an effective way to study the essential surgical anatomy of this complex region and to teach and train operative strategies, especially when used as an adjunct to cadaver dissections.

Preparation of a functional fluorescent human Fas ligand extracellular domain derivative using a three-dimensional structure guided site-specific fluorochrome conjugation.

PubMed

Muraki, Michiro

2016-01-01

Human Fas ligand extracellular domain has been investigated as an important target protein in the field of medical biotechnology. In a recent study, the author developed an effective method to produce biologically active human Fas ligand extracellular domain derivatives using site-specific chemical modifications. A human Fas ligand extracellular domain derivative containing a reactive cysteine residue within its N-terminal tag sequence, which locates not proximal to the binding interface between the ligand and the receptor in terms of the three-dimensional structure, was modified by Fluorescein-5-Maleimide without impairing the specific binding activity toward human Fas receptor extracellular domain. The purified protein sample free of low molecular-weight contaminants showed a characteristic fluorescence spectrum derived from the attached Fluorescein moieties, and formed a stable binding complex with human Fas receptor extracellular domain-human IgG1 Fc domain fusion protein in solution. The conjugation number of the fluorochrome was estimated to be 2.5 per a single human Fas ligand extracellular domain trimer from the ratio of the absorbance value at 280 nm to that at 495 nm. A functional fluorescent human Fas ligand extracellular domain derivative was prepared via a site-specific conjugation of fluorochrome, which was guided by the three-dimensional structure information on the ligand-receptor complex. Fluorescent derivatives created by this method may contribute to the development of an improved diagnosis system for the diseases related to Fas receptor.

Information entropy to measure the spatial and temporal complexity of solute transport in heterogeneous porous media

NASA Astrophysics Data System (ADS)

Li, Weiyao; Huang, Guanhua; Xiong, Yunwu

2016-04-01

The complexity of the spatial structure of porous media, randomness of groundwater recharge and discharge (rainfall, runoff, etc.) has led to groundwater movement complexity, physical and chemical interaction between groundwater and porous media cause solute transport in the medium more complicated. An appropriate method to describe the complexity of features is essential when study on solute transport and conversion in porous media. Information entropy could measure uncertainty and disorder, therefore we attempted to investigate complexity, explore the contact between the information entropy and complexity of solute transport in heterogeneous porous media using information entropy theory. Based on Markov theory, two-dimensional stochastic field of hydraulic conductivity (K) was generated by transition probability. Flow and solute transport model were established under four conditions (instantaneous point source, continuous point source, instantaneous line source and continuous line source). The spatial and temporal complexity of solute transport process was characterized and evaluated using spatial moment and information entropy. Results indicated that the entropy increased as the increase of complexity of solute transport process. For the point source, the one-dimensional entropy of solute concentration increased at first and then decreased along X and Y directions. As time increased, entropy peak value basically unchanged, peak position migrated along the flow direction (X direction) and approximately coincided with the centroid position. With the increase of time, spatial variability and complexity of solute concentration increase, which result in the increases of the second-order spatial moment and the two-dimensional entropy. Information entropy of line source was higher than point source. Solute entropy obtained from continuous input was higher than instantaneous input. Due to the increase of average length of lithoface, media continuity increased, flow and solute transport complexity weakened, and the corresponding information entropy also decreased. Longitudinal macro dispersivity declined slightly at early time then rose. Solute spatial and temporal distribution had significant impacts on the information entropy. Information entropy could reflect the change of solute distribution. Information entropy appears a tool to characterize the spatial and temporal complexity of solute migration and provides a reference for future research.

Illustration as a way to explain the complex structures of foraminifera. The scientific drawing of Lukas Hottinger. In memoriam (1933-2011)

NASA Astrophysics Data System (ADS)

Leria, M.; Ferrandez, C.; Ruiz-Ortega, M.

2012-12-01

Scientific illustration is a fundamental tool for transmitting scientific knowledge because it allows to define aspects that cannot be appreciated just by text description, or by means of photography. This study is based on the collection of illustrations created by the paleontologist Lukas Hottinger (1933-2011) during his extensive career. Hottinger studied, described and illustrated foraminifera for more than fifty years. The use of illustration is essential for studying, describing and clasifying these marine microfossils. Foraminifera are a constituent of marine sedimentary rocks; the study of their internal anatomy often is made from thin sections of rocks, a destructive technique which provides only two dimensional sections. The internal three-dimensional morphology of a species must be interpreted and reconstructed from numerous random two-dimensional sections. New technologies, such as SEM or more recently X-ray Microtomography provided progressively better images of the internal structure but this information, while useful, is still insufficient to explain with simplicity and efficacy what an illustration of a synthetic 3D model shows at a glance. This study is based on a review of 78 publications by Lukas Hottinger on foraminiferal inner structure. In addition, up to 150 illustrations by Hottinger were analyzed, as well as other works written by his colleagues during the same years (1956-2009). Hottinger's work includes several reference papers on the structure and systematics of different groups of larger foraminifera in which his three dimensional models play a fundamental role in synthesizing and making understandable the complexity of these shells. Illustrations of 3D models were particularly selected because of their conceptual complexity. They do not represent a view of the foraminiferal structure that can be observe directly, but a synthetic abstraction constructed from the observation and interpretation of many random two-dimensional sections of diverse individuals. We also analyzed the evolution of the method and techniques of representation through the different papers, coming to the conclusion that they changed according to the printing methods and the current technology (e.g. computer drawing software), but the basic concept of drawings has not been highly modified. The preliminary results demonstrate that illustrations are a necessary and fundamental element in the study of foraminiferal structure, and that it is beneficial for the scientist to have a good knowledge of the various skills involved in drawing and illustration, in order to better disseminate the results of his research with clarity and make complexity comprehensible.