Energetic Lanthanide Complexes: Coordination Chemistry and Explosives Applications

NASA Astrophysics Data System (ADS)

Manner, Virginia; Barker, Beau; Sanders, Eric; Laintz, Kenneth; Scott, Brian; Preston, Daniel; Sandstrom, Mary; Reardon, Bettina

2013-06-01

Metals are generally added to organic molecular explosives in a heterogeneous composite to improve overall heat and energy release. In order to avoid creating a mixture that can vary in homogeneity, energetic organic molecules can be directly bonded to high molecular weight metals, forming a single metal complex with Angstrom-scale separation between the metal and the explosive. To probe the relationship between the structural properties of metal complexes and explosive performance, a new series of energetic lanthanide complexes has been prepared using energetic ligands such as NTO (5-nitro-2,4-dihydro-1,2,4-triazole-3-one). These are the first examples of lanthanide NTO complexes where no water is coordinated to the metal, demonstrating novel control of the coordination environment. The complexes have been characterized by X-ray crystallography, NMR and IR spectroscopies, photoluminescence, and sensitivity testing. The structural and energetic properties are discussed in the context of enhanced blast effects and detection. Cheetah calculations have been performed to fine-tune physical properties, creating a systematic method for producing explosives with ``tailor made'' characteristics. These new complexes will be benchmarks for further study in the field of metalized high explosives.

Energy minimization for self-organized structure formation and actuation

NASA Astrophysics Data System (ADS)

Kofod, Guggi; Wirges, Werner; Paajanen, Mika; Bauer, Siegfried

2007-02-01

An approach for creating complex structures with embedded actuation in planar manufacturing steps is presented. Self-organization and energy minimization are central to this approach, illustrated with a model based on minimization of the hyperelastic free energy strain function of a stretched elastomer and the bending elastic energy of a plastic frame. A tulip-shaped gripper structure illustrates the technological potential of the approach. Advantages are simplicity of manufacture, complexity of final structures, and the ease with which any electroactive material can be exploited as means of actuation.

Creating 3D Physical Models to Probe Student Understanding of Macromolecular Structure

ERIC Educational Resources Information Center

Cooper, A. Kat; Oliver-Hoyo, M. T.

2017-01-01

The high degree of complexity of macromolecular structure is extremely difficult for students to process. Students struggle to translate the simplified two-dimensional representations commonly used in biochemistry instruction to three-dimensional aspects crucial in understanding structure-property relationships. We designed four different physical…

The structure, distribution, and biomass of the world's forests

Treesearch

Yude Pan; Richard A. Birdsey; Oliver L. Phillips; Robert B. Jackson

2013-01-01

Forests are the dominant terrestrial ecosystem on Earth. We review the environmental factors controlling their structure and global distribution and evaluate their current and future trajectory. Adaptations of trees to climate and resource gradients, coupled with disturbances and forest dynamics, create complex geographical patterns in forest assemblages and structures...

Care maps for children with medical complexity.

PubMed

Adams, Sherri; Nicholas, David; Mahant, Sanjay; Weiser, Natalie; Kanani, Ronik; Boydell, Katherine; Cohen, Eyal

2017-12-01

Children with medical complexity require multiple providers and services to keep them well and at home. A care map is a patient/family-created diagram that pictorially maps out this complex web of services. This study explored what care maps mean for families and healthcare providers to inform potential for clinical use. Parents (n=15) created care maps (hand drawn n=10 and computer-generated n=5) and participated in semi-structured interviews about the process of developing care maps and their perceived impact. Healthcare providers (n=30) reviewed the parent-created care maps and participated in semi-structured interviews. Data were analysed for themes and emerging theory using a grounded theory analytical approach. Data analysis revealed 13 overarching themes that were further categorized into three domains: features (characteristics of care maps), functions (what care maps do), and emerging outcomes (benefits of care map use). These domains further informed a definition and a theoretical model of how care maps work. Our findings suggest that care maps may be a way of supporting patient- and family-centred care by graphically identifying and integrating experiences of the family as well as priorities for moving forward. Care maps were endorsed as a useful tool by families and providers. They help healthcare providers better understand parental priorities for care. Parents can create care maps to demonstrate the complex burden of care. They are a unique visual way to incorporate narrative medicine into practice. © 2017 Mac Keith Press.

NCI Scientists Get Deep Look at CRISPR Complex Through Deep Freeze | Poster

Cancer.gov

To get a closer look at one CRISPR complex, researchers from NCI’s Center for Cancer Research and their collaborators recently put it “on ice” with cryo-electron microscopy, creating highly detailed images that show its biological structures in multiple states at a molecular level.

Complexities in Subsetting Satellite Level 2 Data

NASA Astrophysics Data System (ADS)

Huwe, P.; Wei, J.; Albayrak, A.; Silberstein, D. S.; Alfred, J.; Savtchenko, A. K.; Johnson, J. E.; Hearty, T.; Meyer, D. J.

2017-12-01

Satellite Level 2 data presents unique challenges for tools and services. From nonlinear spatial geometry to inhomogeneous file data structure to inconsistent temporal variables to complex data variable dimensionality to multiple file formats, there are many difficulties in creating general tools for Level 2 data support. At NASA Goddard Earth Sciences Data and Information Services Center (GES DISC), we are implementing a general Level 2 Subsetting service for Level 2 data. In this presentation, we will unravel some of the challenges faced in creating this service and the strategies we used to surmount them.

RiboSketch: Versatile Visualization of Multi-stranded RNA and DNA Secondary Structure.

PubMed

Lu, Jacob S; Bindewald, Eckart; Kasprzak, Wojciech; Shapiro, Bruce A

2018-06-15

Creating clear, visually pleasing 2D depictions of RNA and DNA strands and their interactions is important to facilitate and communicate insights related to nucleic acid structure. Here we present RiboSketch, a secondary structure image production application that enables the visualization of multistranded structures via layout algorithms, comprehensive editing capabilities, and a multitude of simulation modes. These interactive features allow RiboSketch to create publication quality diagrams for structures with a wide range of composition, size, and complexity. The program may be run in any web browser without the need for installation, or as a standalone Java application. https://binkley2.ncifcrf.gov/users/bindewae/ribosketch_web.

Lattice-cell orientation disorder in complex spinel oxides

DOE PAGES

Chen, Yan; Cheng, Yongqiang; Li, Juchuan; ...

2016-11-07

Transition metal (TM) substitution has been widely applied to change complex oxides crystal structures to create high energy density electrodes materials in high performance rechargeable lithium-ion batteries. The complex local structure in the oxides imparted by the TM arrangement often impacts their electrochemical behaviors by influencing the diffusion and intercalation of lithium. Here, a major discrepancy is demonstrated between the global and local structures of the promising high energy density and high voltage LiNi 0.5Mn 1.5O 4 spinel cathode material that contradicts the existing structural models. A new single-phase lattice-cell orientation disorder model is proposed as the mechanism for themore » local ordering that explains how the inhomogeneous local distortions and the coherent connection give rise to the global structure in the complex oxide. As a result, the single-phase model is consistent with the electrochemical behavior observation of the materials.« less

Origami by frontal photopolymerization.

PubMed

Zhao, Zeang; Wu, Jiangtao; Mu, Xiaoming; Chen, Haosen; Qi, H Jerry; Fang, Daining

2017-04-01

Origami structures are of great interest in microelectronics, soft actuators, mechanical metamaterials, and biomedical devices. Current methods of fabricating origami structures still have several limitations, such as complex material systems or tedious processing steps. We present a simple approach for creating three-dimensional (3D) origami structures by the frontal photopolymerization method, which can be easily implemented by using a commercial projector. The concept of our method is based on the volume shrinkage during photopolymerization. By adding photoabsorbers into the polymer resin, an attenuated light field is created and leads to a nonuniform curing along the thickness direction. The layer directly exposed to light cures faster than the next layer; this nonuniform curing degree leads to nonuniform curing-induced volume shrinkage. This further introduces a nonuniform stress field, which drives the film to bend toward the newly formed side. The degree of bending can be controlled by adjusting the gray scale and the irradiation time, an easy approach for creating origami structures. The behavior is examined both experimentally and theoretically. Two methods are also proposed to create different types of 3D origami structures.

Molnets: An Artificial Chemistry Based on Neural Networks

NASA Technical Reports Server (NTRS)

Colombano, Silvano; Luk, Johnny; Segovia-Juarez, Jose L.; Lohn, Jason; Clancy, Daniel (Technical Monitor)

2002-01-01

The fundamental problem in the evolution of matter is to understand how structure-function relationships are formed and increase in complexity from the molecular level all the way to a genetic system. We have created a system where structure-function relationships arise naturally and without the need of ad hoc function assignments to given structures. The idea was inspired by neural networks, where the structure of the net embodies specific computational properties. In this system networks interact with other networks to create connections between the inputs of one net and the outputs of another. The newly created net then recomputes its own synaptic weights, based on anti-hebbian rules. As a result some connections may be cut, and multiple nets can emerge as products of a 'reaction'. The idea is to study emergent reaction behaviors, based on simple rules that constitute a pseudophysics of the system. These simple rules are parameterized to produce behaviors that emulate chemical reactions. We find that these simple rules show a gradual increase in the size and complexity of molecules. We have been building a virtual artificial chemistry laboratory for discovering interesting reactions and for testing further ideas on the evolution of primitive molecules. Some of these ideas include the potential effect of membranes and selective diffusion according to molecular size.

The relationship between the understory shrub component of coastal forests and the conservation of forest carnivores

Treesearch

Keith M. Slauson; William J. Zielinski

2007-01-01

The physical structure of vegetation is an important predictor of habitat for wildlife species. The coastal forests of the Redwood region are highly productive, supporting structurally-diverse forest habitats. The major elements of structural diversity in these forests include trees, shrubs, and herbaceous plants, which together create three-dimensional complexity. In...

Using Modules in Teaching Complex Analysis

ERIC Educational Resources Information Center

Kinney, William M.

2017-01-01

Educational modules can play an important part in revitalizing the teaching and learning of complex analysis. At the Westmont College workshop on the subject in June 2014, time was spent generating ideas and creating structures for module proposals. Sharing some of those ideas and giving a few example modules is the main purpose of this paper. The…

The use of a digital computer for calculation of acoustic fields of complex vibrating structures by the reciprocity principle

NASA Technical Reports Server (NTRS)

Rimskiy-Korsakov, A. V.; Belousov, Y. I.

1973-01-01

A program was compiled for calculating acoustical pressure levels, which might be created by vibrations of complex structures (an assembly of shells and rods), under the influence of a given force, for cases when these fields cannot be measured directly. The acoustical field is determined according to transition frequency and pulse characteristics of the structure in the projection mode. Projection characteristics are equal to the reception characteristics, for vibrating systems in which the reciprocity principle holds true. Characteristics in the receiving mode are calculated on the basis of experimental data on a point pulse space velocity source (input signal) and vibration response of the structure (output signal). The space velocity of a pulse source, set at a point in space r, where it is necessary to calculate the sound field of the structure p(r,t), is determined by measurements of acoustic pressure, created by a point source at a distance R. The vibration response is measured at the point where the forces F and f exciting the system should act.

Tree growth visualization

Treesearch

L. Linsen; B.J. Karis; E.G. McPherson; B. Hamann

2005-01-01

In computer graphics, models describing the fractal branching structure of trees typically exploit the modularity of tree structures. The models are based on local production rules, which are applied iteratively and simultaneously to create a complex branching system. The objective is to generate three-dimensional scenes of often many realistic- looking and non-...

Exploring the Complexities of Children's Inquiries in Science: Knowledge Production Through Participatory Practices

NASA Astrophysics Data System (ADS)

Siry, Christina

2013-12-01

Beginning with the assumption that young children are capable of producing unprecedented knowledges about science phenomena, this paper explores the complexities of children's inquiries within open-ended investigations. I ask two central questions: (1) how can we (teachers, researchers, and children themselves) use and build upon children's explorations in science in practice? and (2) what pedagogical approaches can position children as experts on their experiences to facilitate children's sense of ownership in the process of learning science? Six vignettes from a Kindergarten classroom are analyzed to elaborate the central claim of this work, which is that when children are engaged in collaborative open-ended activities, science emerges from their interactions. Open-ended structures allowed for teachers and children to facilitate further investigations collaboratively, and participatory structures mediated children's representations and explanations of their investigations. Evidence of children's interactions is used to illustrate the complexities of children's explorations, and pedagogical approaches that create the spaces for children to create knowledge are highlighted.

Complexities in Subsetting Level 2 Data

NASA Technical Reports Server (NTRS)

Huwe, Paul; Wei, Jennifer; Meyer, David; Silberstein, David S.; Alfred, Jerome; Savtchenko, Andrey K.; Johnson, James E.; Albayrak, Arif; Hearty, Thomas

2017-01-01

Satellite Level 2 data presents unique challenges for tools and services. From nonlinear spatial geometry to inhomogeneous file data structure to inconsistent temporal variables to complex data variable dimensionality to multiple file formats, there are many difficulties in creating general tools for Level 2 data support. At NASA Goddard Earth Sciences Data and Information Services Center (GES DISC), we are implementing a general Level 2 Subsetting service for Level 2 data to a user-specified spatio-temporal region of interest (ROI). In this presentation, we will unravel some of the challenges faced in creating this service and the strategies we used to surmount them.

Breast Imaging in the Era of Big Data: Structured Reporting and Data Mining.

PubMed

Margolies, Laurie R; Pandey, Gaurav; Horowitz, Eliot R; Mendelson, David S

2016-02-01

The purpose of this article is to describe structured reporting and the development of large databases for use in data mining in breast imaging. The results of millions of breast imaging examinations are reported with structured tools based on the BI-RADS lexicon. Much of these data are stored in accessible media. Robust computing power creates great opportunity for data scientists and breast imagers to collaborate to improve breast cancer detection and optimize screening algorithms. Data mining can create knowledge, but the questions asked and their complexity require extremely powerful and agile databases. New data technologies can facilitate outcomes research and precision medicine.

Active materials by four-dimension printing

NASA Astrophysics Data System (ADS)

Ge, Qi; Qi, H. Jerry; Dunn, Martin L.

2013-09-01

We advance a paradigm of printed active composite materials realized by directly printing glassy shape memory polymer fibers in an elastomeric matrix. We imbue the active composites with intelligence via a programmed lamina and laminate architecture and a subsequent thermomechanical training process. The initial configuration is created by three-dimension (3D) printing, and then the programmed action of the shape memory fibers creates time dependence of the configuration—the four-dimension (4D) aspect. We design and print laminates in thin plate form that can be thermomechanically programmed to assume complex three-dimensional configurations including bent, coiled, and twisted strips, folded shapes, and complex contoured shapes with nonuniform, spatially varying curvature. The original flat plate shape can be recovered by heating the material again. We also show how the printed active composites can be directly integrated with other printed functionalities to create devices; here we demonstrate this by creating a structure that can assemble itself.

Age-related patterns of forest complexity and carbon storage in pine and aspen-birch ecosystems of northern Minnesota, USA

Treesearch

John B. Bradford; Douglas N. Kastendick

2010-01-01

Forest managers are seeking strategies to create stands that can adapt to new climatic conditions and simultaneously help mitigate increases in atmospheric CO2. Adaptation strategies often focus on enhancing resilience by maximizing forest complexity in terms of species composition and size structure, while mitigation involves sustaining carbon...

Opinion: The use of natural hazard modeling for decision making under uncertainty

Treesearch

David E. Calkin; Mike Mentis

2015-01-01

Decision making to mitigate the effects of natural hazards is a complex undertaking fraught with uncertainty. Models to describe risks associated with natural hazards have proliferated in recent years. Concurrently, there is a growing body of work focused on developing best practices for natural hazard modeling and to create structured evaluation criteria for complex...

Structure-property relationships of a biological mesocrystal in the adult sea urchin spine

PubMed Central

Seto, Jong; Ma, Yurong; Davis, Sean A.; Meldrum, Fiona; Gourrier, Aurelien; Kim, Yi-Yeoun; Schilde, Uwe; Sztucki, Michael; Burghammer, Manfred; Maltsev, Sergey; Jäger, Christian; Cölfen, Helmut

2012-01-01

Structuring over many length scales is a design strategy widely used in Nature to create materials with unique functional properties. We here present a comprehensive analysis of an adult sea urchin spine, and in revealing a complex, hierarchical structure, show how Nature fabricates a material which diffracts as a single crystal of calcite and yet fractures as a glassy material. Each spine comprises a highly oriented array of Mg-calcite nanocrystals in which amorphous regions and macromolecules are embedded. It is postulated that this mesocrystalline structure forms via the crystallization of a dense array of amorphous calcium carbonate (ACC) precursor particles. A residual surface layer of ACC and/or macromolecules remains around the nanoparticle units which creates the mesocrystal structure and contributes to the conchoidal fracture behavior. Nature’s demonstration of how crystallization of an amorphous precursor phase can create a crystalline material with remarkable properties therefore provides inspiration for a novel approach to the design and synthesis of synthetic composite materials. PMID:22343283

Structure-property relationships of a biological mesocrystal in the adult sea urchin spine.

PubMed

Seto, Jong; Ma, Yurong; Davis, Sean A; Meldrum, Fiona; Gourrier, Aurelien; Kim, Yi-Yeoun; Schilde, Uwe; Sztucki, Michael; Burghammer, Manfred; Maltsev, Sergey; Jäger, Christian; Cölfen, Helmut

2012-03-06

Structuring over many length scales is a design strategy widely used in Nature to create materials with unique functional properties. We here present a comprehensive analysis of an adult sea urchin spine, and in revealing a complex, hierarchical structure, show how Nature fabricates a material which diffracts as a single crystal of calcite and yet fractures as a glassy material. Each spine comprises a highly oriented array of Mg-calcite nanocrystals in which amorphous regions and macromolecules are embedded. It is postulated that this mesocrystalline structure forms via the crystallization of a dense array of amorphous calcium carbonate (ACC) precursor particles. A residual surface layer of ACC and/or macromolecules remains around the nanoparticle units which creates the mesocrystal structure and contributes to the conchoidal fracture behavior. Nature's demonstration of how crystallization of an amorphous precursor phase can create a crystalline material with remarkable properties therefore provides inspiration for a novel approach to the design and synthesis of synthetic composite materials.

A sophisticated cad tool for the creation of complex models for electromagnetic interaction analysis

NASA Astrophysics Data System (ADS)

Dion, Marc; Kashyap, Satish; Louie, Aloisius

1991-06-01

This report describes the essential features of the MS-DOS version of DIDEC-DREO, an interactive program for creating wire grid, surface patch, and cell models of complex structures for electromagnetic interaction analysis. It uses the device-independent graphics library DIGRAF and the graphics kernel system HALO, and can be executed on systems with various graphics devices. Complicated structures can be created by direct alphanumeric keyboard entry, digitization of blueprints, conversion form existing geometric structure files, and merging of simple geometric shapes. A completed DIDEC geometric file may then be converted to the format required for input to a variety of time domain and frequency domain electromagnetic interaction codes. This report gives a detailed description of the program DIDEC-DREO, its installation, and its theoretical background. Each available interactive command is described. The associated program HEDRON which generates simple geometric shapes, and other programs that extract the current amplitude data from electromagnetic interaction code outputs, are also discussed.

Cryo-EM Structure of the TOM Core Complex from Neurospora crassa.

PubMed

Bausewein, Thomas; Mills, Deryck J; Langer, Julian D; Nitschke, Beate; Nussberger, Stephan; Kühlbrandt, Werner

2017-08-10

The TOM complex is the main entry gate for protein precursors from the cytosol into mitochondria. We have determined the structure of the TOM core complex by cryoelectron microscopy (cryo-EM). The complex is a 148 kDa symmetrical dimer of ten membrane protein subunits that create a shallow funnel on the cytoplasmic membrane surface. In the core of the dimer, the β-barrels of the Tom40 pore form two identical preprotein conduits. Each Tom40 pore is surrounded by the transmembrane segments of the α-helical subunits Tom5, Tom6, and Tom7. Tom22, the central preprotein receptor, connects the two Tom40 pores at the dimer interface. Our structure offers detailed insights into the molecular architecture of the mitochondrial preprotein import machinery. Copyright © 2017 Elsevier Inc. All rights reserved.

The structure of human tripeptidyl peptidase II as determined by a hybrid approach.

PubMed

Schönegge, Anne-Marie; Villa, Elizabeth; Förster, Friedrich; Hegerl, Reiner; Peters, Jürgen; Baumeister, Wolfgang; Rockel, Beate

2012-04-04

Tripeptidyl-peptidase II (TPPII) is a high molecular mass (∼5 MDa) serine protease, which is thought to act downstream of the 26S proteasome, cleaving peptides released by the latter. Here, the structure of human TPPII (HsTPPII) has been determined to subnanometer resolution by cryoelectron microscopy and single-particle analysis. The complex is built from two strands forming a quasihelical structure harboring a complex system of inner cavities. HsTPPII particles exhibit some polymorphism resulting in complexes consisting of nine or of eight dimers per strand. To obtain deeper insights into the architecture and function of HsTPPII, we have created a pseudoatomic structure of the HsTPPII spindle using a comparative model of HsTPPII dimers and molecular dynamics flexible fitting. Analyses of the resulting hybrid structure of the HsTPPII holocomplex provide new insights into the mechanism of maturation and activation. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

Chen, Yan; Cheng, Yongqiang; Li, Juchuan

Transition metal (TM) substitution has been widely applied to change complex oxides crystal structures to create high energy density electrodes materials in high performance rechargeable lithium-ion batteries. The complex local structure in the oxides imparted by the TM arrangement often impacts their electrochemical behaviors by influencing the diffusion and intercalation of lithium. Here, a major discrepancy is demonstrated between the global and local structures of the promising high energy density and high voltage LiNi 0.5Mn 1.5O 4 spinel cathode material that contradicts the existing structural models. A new single-phase lattice-cell orientation disorder model is proposed as the mechanism for themore » local ordering that explains how the inhomogeneous local distortions and the coherent connection give rise to the global structure in the complex oxide. As a result, the single-phase model is consistent with the electrochemical behavior observation of the materials.« less

Controlled evaporative self-assembly of confined microfluids: A route to complex ordered structures

NASA Astrophysics Data System (ADS)

Byun, Myunghwan

The evaporative self-assembly of nonvolatile solutes such as polymers, nanocrystals, and carbon nanotubes has been widely recognized as a non-lithographic means of producing a diverse range of intriguing complex structures. Due to the spatial variation of evaporative flux and possible convection, however, these non-equilibrium dissipative structures (e.g., fingering patterns and polygonal network structures) are often irregularly and stochastically organized. Yet for many applications in microelectronics, data storage devices, and biotechnology, it is highly desirable to achieve surface patterns having a well-controlled spatial arrangement. To date, only a few elegant studies have centered on precise control over the evaporation process to produce ordered structures. In a remarked comparison with conventional lithography techniques, surface patterning by controlled solvent evaporation is simple and cost-effective, offering a lithography- and external field-free means to organize nonvolatile materials into ordered microscopic structures over large surface areas. The ability to engineer an evaporative self-assembly process that yields a wide range of complex, self-organizing structures over large areas offers tremendous potential for applications in electronics, optoelectronics, and bio- or chemical sensors. We developed a facile, robust tool for evaporating polymer, nanoparticle, or DNA solutions in curve-on-flat geometries to create versatile, highly regular microstructures, including hierarchically structured polymer blend rings, conjugated polymer "snake-skins", block copolymer stripes, and punch-hole-like meshes, biomolecular microring arrays, etc. The mechanism of structure formation was elucidated both experimentally and theoretically. Our method further enhances current fabrication approaches to creating highly ordered structures in a simple and cost-effective manner, envisioning the potential to be tailored for use in photonics, optoelectronics, microfluidic devices, nanotechnology and biotechnology, etc.

A Complexity Theory Approach to Sustainability: A Longitudinal Study in Two London NHS Hospitals

ERIC Educational Resources Information Center

Mitleton-Kelly, Eve

2011-01-01

Purpose: The purpose of this paper is to demonstrate that organisational sustainability is not a continuation of the status quo but, seen from a complexity theory perspective, is a continuous dynamic process of co-evolution with a changing environment. It is underpinned by learning, and it creates new structures and ways of working to adjust and…

Stereotypic and complex phrase types provide structural evidence for a multi-message display in humpback whales (Megaptera novaeangliae).

PubMed

Murray, Anita; Dunlop, Rebecca A; Noad, Michael J; Goldizen, Anne W

2018-02-01

Male humpback whales produce a mating display called "song." Behavioral studies indicate song has inter- and/or intra-sexual functionality, suggesting song may be a multi-message display. Multi-message displays often include stereotypic components that convey group membership for mate attraction and/or male-male interactions, and complex components that convey individual quality for courtship. Humpback whale song contains sounds ("units") arranged into sequences ("phrases"). Repetitions of a specific phrase create a "theme." Within a theme, imperfect phrase repetitions ("phrase variants") create variability among phrases of the same type ("phrase type"). The hypothesis that song contains stereotypic and complex phrase types, structural characteristics consistent with a multi-message display, is investigated using recordings of 17 east Australian males (8:2004, 9:2011). Phrase types are categorized as stereotypic or complex using number of unit types, number of phrase variants, and the proportion of phrases that is unique to an individual versus shared amongst males. Unit types are determined using self-organizing maps. Phrase variants are determined by Levenshtein distances between phrases. Stereotypic phrase types have smaller numbers of unit types and shared phrase variants. Complex phrase types have larger numbers of unit types and unique phrase variants. This study supports the hypothesis that song could be a multi-message display.

Correlations between Community Structure and Link Formation in Complex Networks

PubMed Central

Liu, Zhen; He, Jia-Lin; Kapoor, Komal; Srivastava, Jaideep

2013-01-01

Background Links in complex networks commonly represent specific ties between pairs of nodes, such as protein-protein interactions in biological networks or friendships in social networks. However, understanding the mechanism of link formation in complex networks is a long standing challenge for network analysis and data mining. Methodology/Principal Findings Links in complex networks have a tendency to cluster locally and form so-called communities. This widely existed phenomenon reflects some underlying mechanism of link formation. To study the correlations between community structure and link formation, we present a general computational framework including a theory for network partitioning and link probability estimation. Our approach enables us to accurately identify missing links in partially observed networks in an efficient way. The links having high connection likelihoods in the communities reveal that links are formed preferentially to create cliques and accordingly promote the clustering level of the communities. The experimental results verify that such a mechanism can be well captured by our approach. Conclusions/Significance Our findings provide a new insight into understanding how links are created in the communities. The computational framework opens a wide range of possibilities to develop new approaches and applications, such as community detection and missing link prediction. PMID:24039818

Chemically Patterned Inverse Opal Created by a Selective Photolysis Modification Process.

PubMed

Tian, Tian; Gao, Ning; Gu, Chen; Li, Jian; Wang, Hui; Lan, Yue; Yin, Xianpeng; Li, Guangtao

2015-09-02

Anisotropic photonic crystal materials have long been pursued for their broad applications. A novel method for creating chemically patterned inverse opals is proposed here. The patterning technique is based on selective photolysis of a photolabile polymer together with postmodification on released amine groups. The patterning method allows regioselective modification within an inverse opal structure, taking advantage of selective chemical reaction. Moreover, combined with the unique signal self-reporting feature of the photonic crystal, the fabricated structure is capable of various applications, including gradient photonic bandgap and dynamic chemical patterns. The proposed method provides the ability to extend the structural and chemical complexity of the photonic crystal, as well as its potential applications.

Tailored optical vector fields for ultrashort-pulse laser induced complex surface plasmon structuring.

PubMed

Ouyang, J; Perrie, W; Allegre, O J; Heil, T; Jin, Y; Fearon, E; Eckford, D; Edwardson, S P; Dearden, G

2015-05-18

Precise tailoring of optical vector beams is demonstrated, shaping their focal electric fields and used to create complex laser micro-patterning on a metal surface. A Spatial Light Modulator (SLM) and a micro-structured S-waveplate were integrated with a picosecond laser system and employed to structure the vector fields into radial and azimuthal polarizations with and without a vortex phase wavefront as well as superposition states. Imprinting Laser Induced Periodic Surface Structures (LIPSS) elucidates the detailed vector fields around the focal region. In addition to clear azimuthal and radial plasmon surface structures, unique, variable logarithmic spiral micro-structures with a pitch Λ ∼1μm, not observed previously, were imprinted on the surface, confirming unambiguously the complex 2D focal electric fields. We show clearly also how the Orbital Angular Momentum(OAM) associated with a helical wavefront induces rotation of vector fields along the optic axis of a focusing lens and confirmed by the observed surface micro-structures.

Crystal structural analysis of protein–protein interactions drastically destabilized by a single mutation

PubMed Central

Urakubo, Yoshiaki; Ikura, Teikichi; Ito, Nobutoshi

2008-01-01

The complex of barnase (bn) and barstar (bs), which has been widely studied as a model for quantitative analysis of protein–protein interactions, is significantly destabilized by a single mutation, namely, bs Asp39 → Ala, which corresponds to a change of 7.7 kcal·mol−1 in the free energy of binding. However, there has been no structural information available to explain such a drastic destabilization. In the present study, we determined the structure of the mutant complex at 1.58 Å resolution by X-ray crystallography. The complex was similar to the wild-type complex in terms of overall and interface structures; however, the hydrogen bond network mediated by water molecules at the interface was significantly different. Several water molecules filled the cavity created by the mutation and consequently caused rearrangement of the hydrated water molecules at the interface. The water molecules were redistributed into a channel-like structure that penetrated into the complex. Furthermore, molecular dynamics simulations showed that the mutation increased the mobility of water molecules at the interface. Since such a drastic change in hydration was not observed in other mutant complexes of bn and bs, the significant destabilization of the interaction may be due to this channel-like structure of hydrated water molecules. PMID:18441234

Nekton assemblage structure in natural and created marsh-edge habitats of the Guadalupe Estuary, Texas, USA

NASA Astrophysics Data System (ADS)

Zeug, Steven C.; Shervette, Virginia R.; Hoeinghaus, David J.; Davis, Stephen E., III

2007-02-01

Natural and created Spartina brackish marsh habitats in the Guadalupe Estuary, adjacent to the Aransas National Wildlife Refuge, Texas, USA were surveyed during spring, summer, and fall 2004 to evaluate the equivalence of nekton assemblages in an old (>30 years) created marsh. During each season, six replicate samples were collected in each marsh type using a 1-m 2 drop sampler. Multivariate analysis revealed significant differences in nekton assemblage structure among marsh type, both within and across seasons. Species richness was significantly higher in the natural marsh in spring and summer but not in fall. Several species that were dominant in the natural marsh but rare or absent in the created marsh had strong correlations with the presence of oyster substrate that was only encountered in natural marsh samples. Although cumulative richness was greater in the natural marsh, eight species were collected only from the created marsh. Shrimp and fish biomass was significantly higher in natural marsh. Analysis of the density, biomass and size structure of three commercially important crustaceans indicated that the created marsh supported similar biomass of some species (white shrimp, blue crab); however, the size structure of some populations was variable among marshes (blue crab, brown shrimp). We conclude that lower substrate complexity (specifically oyster) and soil organic content in the created marsh reduced measures of nekton similarity and recommend that these features be addressed in future restoration efforts.

Conserved tetramer junction in the kinetochore Ndc80 complex

PubMed Central

Valverde, Roberto; Ingram, Jessica; Harrison, Stephen C.

2016-01-01

Summary The heterotetrameric Ndc80 complex establishes connectivity along the principal longitudinal axis of a kinetochore. Its two heterodimeric subcomplexes, each with a globular end and a coiled-coil shaft, connect end-to-end to create a ∼600 Å long rod spanning the gap from centromere-proximal structures to spindle microtubules. Neither subcomplex has a known function on its own, but the heterotetrameric organization and the characteristics of the junction are conserved from yeast to man. We have determined crystal structures of two shortened (“dwarf”) Ndc80 complexes that contain the full tetramer junction and both globular ends. The junction connects two α-helical coiled coils through regions of four-chain and three-chain overlap. The complexity of its structure depends on interactions among conserved amino-acid residues, suggesting a binding site for additional cellular factor(s) not yet identified. PMID:27851957

Calcifying tissue regeneration via biomimetic materials chemistry

PubMed Central

Green, David W.; Goto, Tazuko K.; Kim, Kye-Seong; Jung, Han-Sung

2014-01-01

Materials chemistry is making a fundamental impact in regenerative sciences providing many platforms for tissue development. However, there is a surprising paucity of replacements that accurately mimic the structure and function of the structural fabric of tissues or promote faithful tissue reconstruction. Methodologies in biomimetic materials chemistry have shown promise in replicating morphologies, architectures and functional building blocks of acellular mineralized tissues dentine, enamel and bone or that can be used to fully regenerate them with integrated cell populations. Biomimetic materials chemistry encompasses the two processes of crystal formation and mineralization of crystals into inorganic formations on organic templates. This review will revisit the successes of biomimetics materials chemistry in regenerative medicine, including coccolithophore simulants able to promote in vivo bone formation. In-depth knowledge of biomineralization throughout evolution informs the biomimetic materials chemist of the most effective techniques for regenerative framework construction exemplified via exploitation of liquid crystals (LCs) and complex self-organizing media. Therefore, a new innovative direction would be to create chemical environments that perform reaction–diffusion exchanges as the basis for building complex biomimetic inorganic structures. This has evolved widely in biology, as have LCs, serving as self-organizing templates in pattern formation of structural biomaterials. For instance, a study is highlighted in which artificially fabricated chiral LCs, made from bacteriophages are transformed into a faithful copy of enamel. While chemical-based strategies are highly promising at creating new biomimetic structures there are limits to the degree of complexity that can be generated. Thus, there may be good reason to implement living or artificial cells in ‘morphosynthesis’ of complex inorganic constructs. In the future, cellular construction is probably key to instruct building of ultimate biomimetic hierarchies with a totality of functions. PMID:25320063

Three-dimensional printing of complex biological structures by freeform reversible embedding of suspended hydrogels

PubMed Central

Hinton, Thomas J.; Jallerat, Quentin; Palchesko, Rachelle N.; Park, Joon Hyung; Grodzicki, Martin S.; Shue, Hao-Jan; Ramadan, Mohamed H.; Hudson, Andrew R.; Feinberg, Adam W.

2015-01-01

We demonstrate the additive manufacturing of complex three-dimensional (3D) biological structures using soft protein and polysaccharide hydrogels that are challenging or impossible to create using traditional fabrication approaches. These structures are built by embedding the printed hydrogel within a secondary hydrogel that serves as a temporary, thermoreversible, and biocompatible support. This process, termed freeform reversible embedding of suspended hydrogels, enables 3D printing of hydrated materials with an elastic modulus <500 kPa including alginate, collagen, and fibrin. Computer-aided design models of 3D optical, computed tomography, and magnetic resonance imaging data were 3D printed at a resolution of ~200 μm and at low cost by leveraging open-source hardware and software tools. Proof-of-concept structures based on femurs, branched coronary arteries, trabeculated embryonic hearts, and human brains were mechanically robust and recreated complex 3D internal and external anatomical architectures. PMID:26601312

Interpreting three-dimensional structures from two-dimensional images: a web-based interactive 3D teaching model of surgical liver anatomy

PubMed Central

Crossingham, Jodi L; Jenkinson, Jodie; Woolridge, Nick; Gallinger, Steven; Tait, Gordon A; Moulton, Carol-Anne E

2009-01-01

Background: Given the increasing number of indications for liver surgery and the growing complexity of operations, many trainees in surgical, imaging and related subspecialties require a good working knowledge of the complex intrahepatic anatomy. Computed tomography (CT), the most commonly used liver imaging modality, enhances our understanding of liver anatomy, but comprises a two-dimensional (2D) representation of a complex 3D organ. It is challenging for trainees to acquire the necessary skills for converting these 2D images into 3D mental reconstructions because learning opportunities are limited and internal hepatic anatomy is complicated, asymmetrical and variable. We have created a website that uses interactive 3D models of the liver to assist trainees in understanding the complex spatial anatomy of the liver and to help them create a 3D mental interpretation of this anatomy when viewing CT scans. Methods: Computed tomography scans were imported into DICOM imaging software (OsiriX™) to obtain 3D surface renderings of the liver and its internal structures. Using these 3D renderings as a reference, 3D models of the liver surface and the intrahepatic structures, portal veins, hepatic veins, hepatic arteries and the biliary system were created using 3D modelling software (Cinema 4D™). Results: Using current best practices for creating multimedia tools, a unique, freely available, online learning resource has been developed, entitled Visual Interactive Resource for Teaching, Understanding And Learning Liver Anatomy (VIRTUAL Liver) (http://pie.med.utoronto.ca/VLiver). This website uses interactive 3D models to provide trainees with a constructive resource for learning common liver anatomy and liver segmentation, and facilitates the development of the skills required to mentally reconstruct a 3D version of this anatomy from 2D CT scans. Discussion: Although the intended audience for VIRTUAL Liver consists of residents in various medical and surgical specialties, the website will also be useful for other health care professionals (i.e. radiologists, nurses, hepatologists, radiation oncologists, family doctors) and educators because it provides a comprehensive resource for teaching liver anatomy. PMID:19816618

The structure of the yeast NADH dehydrogenase (Ndi1) reveals overlapping binding sites for water- and lipid-soluble substrates.

PubMed

Iwata, Momi; Lee, Yang; Yamashita, Tetsuo; Yagi, Takao; Iwata, So; Cameron, Alexander D; Maher, Megan J

2012-09-18

Bioenergy is efficiently produced in the mitochondria by the respiratory system consisting of complexes I-V. In various organisms, complex I can be replaced by the alternative NADH-quinone oxidoreductase (NDH-2), which catalyzes the transfer of an electron from NADH via FAD to quinone, without proton pumping. The Ndi1 protein from Saccharomyces cerevisiae is a monotopic membrane protein, directed to the matrix. A number of studies have investigated the potential use of Ndi1 as a therapeutic agent against complex I disorders, and the NDH-2 enzymes have emerged as potential therapeutic targets for treatments against the causative agents of malaria and tuberculosis. Here we present the crystal structures of Ndi1 in its substrate-free, NAD(+)- and ubiquinone- (UQ2) complexed states. The structures reveal that Ndi1 is a peripheral membrane protein forming an intimate dimer, in which packing of the monomeric units within the dimer creates an amphiphilic membrane-anchor domain structure. Crucially, the structures of the Ndi1-NAD(+) and Ndi1-UQ2 complexes show overlapping binding sites for the NAD(+) and quinone substrates.

A measuring tool for tree-rings analysis

NASA Astrophysics Data System (ADS)

Shumilov, Oleg; Kanatjev, Alexander; Kasatkina, Elena

2013-04-01

A special tool has been created for the annual tree-ring widths measurement and analysis. It consists of professional scanner, computer system and software. This created complex in many aspects does not yield the similar systems (LINTAB, WinDENDRO), but in comparison to manual measurement systems, it offers a number of advantages: productivity gain, possibility of archiving the results of the measurements at any stage of the processing, operator comfort. It has been developed a new software, allowing processing of samples of different types (cores, saw cuts), including those which is difficult to process, having got a complex wood structure (inhomogeneity of growing in different directions, missed, light and false rings etc.). This software can analyze pictures made with optical scanners, analog or digital cameras. The complex software program was created on programming language C++, being compatible with modern operating systems like Windows X. Annual ring widths are measured along paths traced interactively. These paths can have any orientation and can be created so that ring widths are measured perpendicular to ring boundaries. A graphic of ring-widths in function of the year is displayed on a screen during the analysis and it can be used for visual and numerical cross-dating and comparison with other series or master-chronologies. Ring widths are saved to the text files in a special format, and those files are converted to the format accepted for data conservation in the International Tree-Ring Data Bank. The created complex is universal in application that will allow its use for decision of the different problems in biology and ecology. With help of this complex it has been reconstructed a long-term juniper (1328-2004) and pine (1445-2005) tree-ring chronologies on the base of samples collected at Kola Peninsula (northwestern Russia).

Contributions of gopher mound and casting disturbances to plant community structure in a Cascade Range meadow complex

Treesearch

M. Case; C.B. Halpern; S.A. Levin

2013-01-01

Pocket gophers (Geomyidae) are major agents of disturbance in North American grasslands. Gopher mounds bury existing plants and influence community structure through various mechanisms. However, in mountain meadows that experience winter snowpack, gophers also create winter castings, smaller tube-shaped deposits, previously ignored in studies of plant–gopher...

Build your own soil: exploring microfluidics to create microbial habitat structures

PubMed Central

Aleklett, Kristin; Kiers, E Toby; Ohlsson, Pelle; Shimizu, Thomas S; Caldas, Victor EA; Hammer, Edith C

2018-01-01

Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats. PMID:29135971

Dihydroquinazolines as a novel class of Trypanosoma brucei trypanothione reductase inhibitors: discovery, synthesis, and characterization of their binding mode by protein crystallography.

PubMed

Patterson, Stephen; Alphey, Magnus S; Jones, Deuan C; Shanks, Emma J; Street, Ian P; Frearson, Julie A; Wyatt, Paul G; Gilbert, Ian H; Fairlamb, Alan H

2011-10-13

Trypanothione reductase (TryR) is a genetically validated drug target in the parasite Trypanosoma brucei , the causative agent of human African trypanosomiasis. Here we report the discovery, synthesis, and development of a novel series of TryR inhibitors based on a 3,4-dihydroquinazoline scaffold. In addition, a high resolution crystal structure of TryR, alone and in complex with substrates and inhibitors from this series, is presented. This represents the first report of a high resolution complex between a noncovalent ligand and this enzyme. Structural studies revealed that upon ligand binding the enzyme undergoes a conformational change to create a new subpocket which is occupied by an aryl group on the ligand. Therefore, the inhibitor, in effect, creates its own small binding pocket within the otherwise large, solvent exposed active site. The TryR-ligand structure was subsequently used to guide the synthesis of inhibitors, including analogues that challenged the induced subpocket. This resulted in the development of inhibitors with improved potency against both TryR and T. brucei parasites in a whole cell assay.

Stem cell bioprinting for applications in regenerative medicine.

PubMed

Tricomi, Brad J; Dias, Andrew D; Corr, David T

2016-11-01

Many regenerative medicine applications seek to harness the biologic power of stem cells in architecturally complex scaffolds or microenvironments. Traditional tissue engineering methods cannot create such intricate structures, nor can they precisely control cellular position or spatial distribution. These limitations have spurred advances in the field of bioprinting, aimed to satisfy these structural and compositional demands. Bioprinting can be defined as the programmed deposition of cells or other biologics, often with accompanying biomaterials. In this concise review, we focus on recent advances in stem cell bioprinting, including performance, utility, and applications in regenerative medicine. More specifically, this review explores the capability of bioprinting to direct stem cell fate, engineer tissue(s), and create functional vascular networks. Furthermore, the unique challenges and concerns related to bioprinting living stem cells, such as viability and maintaining multi- or pluripotency, are discussed. The regenerative capacity of stem cells, when combined with the structural/compositional control afforded by bioprinting, provides a unique and powerful tool to address the complex demands of tissue engineering and regenerative medicine applications. © 2016 New York Academy of Sciences.

The Formation of Shell Galaxies Similar to NGC 7600 in the Cold Dark Matter Cosmogony

NASA Astrophysics Data System (ADS)

Cooper, Andrew P.; Martínez-Delgado, David; Helly, John; Frenk, Carlos; Cole, Shaun; Crawford, Ken; Zibetti, Stefano; Carballo-Bello, Julio A.; GaBany, R. Jay

2011-12-01

We present new deep observations of "shell" structures in the halo of the nearby elliptical galaxy NGC 7600, alongside a movie of galaxy formation in a cold dark matter (CDM) universe. The movie, based on an ab initio cosmological simulation, shows how continuous accretion of clumps of dark matter and stars creates a swath of diffuse circumgalactic structures. The disruption of a massive clump on a near-radial orbit creates a complex system of transient concentric shells which bare a striking resemblance to those of NGC 7600. With the aid of the simulation we interpret NGC 7600 in the context of the CDM model.

The Control of Anisotropic Transport in Manganites by Stripy Domains

NASA Astrophysics Data System (ADS)

Ju, Changcheng; Lu, Xiaomei; Chu, Yinghao

2014-03-01

Epitaxial thin film acts as a significant tool to investigate novel phenomena of complex oxide systems. Extrinsic constraint1 of uniform or certain designed buffer layer strain could be easily implanted to these materials. However, the strain distribution might be quite complicated by involving micro- or nano-lattice distortions which could partially relax the strain and determine the complex phase diagrams of thin film, meanwhile introducing structural and physical inhomogeneities. In this work , we report 71° striped ferroelectric domains created in BFO can also epitaxially lock the perovskite manganites leading to the emerge of ordered structural domain. LSMO/BFO hetero-epitaxial samples are deposited by PLD. The 71° periodic striped domains and coherent growth are demonstrated by PFM and X-ray analysis. Plan-view TEM and X-ray RSM have been used to confirm the epitaxial relationships of the functional layers and IP lattice constant. Both the simulation and structural analysis demonstrate we can create a periodic ordered stripe structural domain in LSMO. And this will leave an anisotropic distribution of structural domain walls which makes it possible to capture the anisotropic tunneling for strong electron-lattice coupling in manganites. Temperature-dependent resistivity measurements reveal a substantial anisotropic resistivities and a remarkable shift of the MI transition between the perpendicular and parallel to the stripe domain directions.

PDBToSDF: Create ligand structure files from PDB file.

PubMed

Muppalaneni, Naresh Babu; Rao, Allam Appa

2011-01-01

Protein Data Bank (PDB) file contains atomic data for protein and ligand in protein-ligand complexes. Structure data file (SDF) contains data for atoms, bonds, connectivity and coordinates of molecule for ligands. We describe PDBToSDF as a tool to separate the ligand data from pdb file for the calculation of ligand properties like molecular weight, number of hydrogen bond acceptors, hydrogen bond receptors easily.

Cavitation, Flow Structure and Turbulence in the Tip Region of a Rotor Blade

NASA Technical Reports Server (NTRS)

Wu, H.; Miorini, R.; Soranna, F.; Katz, J.; Michael, T.; Jessup, S.

2010-01-01

Objectives: Measure the flow structure and turbulence within a Naval, axial waterjet pump. Create a database for benchmarking and validation of parallel computational efforts. Address flow and turbulence modeling issues that are unique to this complex environment. Measure and model flow phenomena affecting cavitation within the pump and its effect on pump performance. This presentation focuses on cavitation phenomena and associated flow structure in the tip region of a rotor blade.

A novel scene management technology for complex virtual battlefield environment

NASA Astrophysics Data System (ADS)

Sheng, Changchong; Jiang, Libing; Tang, Bo; Tang, Xiaoan

2018-04-01

The efficient scene management of virtual environment is an important research content of computer real-time visualization, which has a decisive influence on the efficiency of drawing. However, Traditional scene management methods do not suitable for complex virtual battlefield environments, this paper combines the advantages of traditional scene graph technology and spatial data structure method, using the idea of management and rendering separation, a loose object-oriented scene graph structure is established to manage the entity model data in the scene, and the performance-based quad-tree structure is created for traversing and rendering. In addition, the collaborative update relationship between the above two structural trees is designed to achieve efficient scene management. Compared with the previous scene management method, this method is more efficient and meets the needs of real-time visualization.

Automatic high-throughput screening of colloidal crystals using machine learning

NASA Astrophysics Data System (ADS)

Spellings, Matthew; Glotzer, Sharon C.

Recent improvements in hardware and software have united to pose an interesting problem for computational scientists studying self-assembly of particles into crystal structures: while studies covering large swathes of parameter space can be dispatched at once using modern supercomputers and parallel architectures, identifying the different regions of a phase diagram is often a serial task completed by hand. While analytic methods exist to distinguish some simple structures, they can be difficult to apply, and automatic identification of more complex structures is still lacking. In this talk we describe one method to create numerical ``fingerprints'' of local order and use them to analyze a study of complex ordered structures. We can use these methods as first steps toward automatic exploration of parameter space and, more broadly, the strategic design of new materials.

Physical properties of mixed dairy food proteins

USDA-ARS?s Scientific Manuscript database

Mixed food protein gels are complex systems, which changes functional behaviors such as gelling properties and viscosity depending on the miscibility of the proteins. We have noted that differences in co-solubility of mixed proteins created unique network structures and gel properties. The effects o...

Some aspects of radical cascade and relay reactions

PubMed Central

Quiclet-Sire, Béatrice; Zard, Samir Z.

2017-01-01

The ability to create carbon–carbon bonds is at the heart of organic synthesis. Radical processes are particularly apt at creating such bonds, especially in cascade or relay sequences where more than one bond is formed, allowing for a rapid assembly of complex structures. In the present brief overview, examples taken from the authors' laboratory will serve to illustrate the strategic impact of radical-based approaches on synthetic planning. Transformations involving nitrogen-centred radicals, electron transfer from metallic nickel and the reversible degenerative exchange of xanthates will be presented and discussed. The last method has proved to be a particularly powerful tool for the intermolecular creation of carbon–carbon bonds by radical additions even to unactivated alkenes. Various functional groups can be brought into the same molecule in a convergent manner and made to react together in order to further increase the structural complexity. One important benefit of this chemistry is the so-called RAFT/MADIX technology for the manufacture of block copolymers of almost any desired architecture. PMID:28484329

Control superstructure of rigid polyelectrolytes in oppositely charged hydrogels via programmed internal stress

NASA Astrophysics Data System (ADS)

Takahashi, Riku; Wu, Zi Liang; Arifuzzaman, Md; Nonoyama, Takayuki; Nakajima, Tasuku; Kurokawa, Takayuki; Gong, Jian Ping

2014-08-01

Biomacromolecules usually form complex superstructures in natural biotissues, such as different alignments of collagen fibres in articular cartilages, for multifunctionalities. Inspired by nature, there are efforts towards developing multiscale ordered structures in hydrogels (recognized as one of the best candidates of soft biotissues). However, creating complex superstructures in gels are hardly realized because of the absence of effective approaches to control the localized molecular orientation. Here we introduce a method to create various superstructures of rigid polyanions in polycationic hydrogels. The control of localized orientation of rigid molecules, which are sensitive to the internal stress field of the gel, is achieved by tuning the swelling mismatch between masked and unmasked regions of the photolithographic patterned gel. Furthermore, we develop a double network structure to toughen the hydrogels with programmed superstructures, which deform reversibly under large strain. This work presents a promising pathway to develop superstructures in hydrogels and should shed light on designing biomimetic materials with intricate molecular alignments.

Automating gene library synthesis by structure-based combinatorial protein engineering: examples from plant sesquiterpene synthases.

PubMed

Dokarry, Melissa; Laurendon, Caroline; O'Maille, Paul E

2012-01-01

Structure-based combinatorial protein engineering (SCOPE) is a homology-independent recombination method to create multiple crossover gene libraries by assembling defined combinations of structural elements ranging from single mutations to domains of protein structure. SCOPE was originally inspired by DNA shuffling, which mimics recombination during meiosis, where mutations from parental genes are "shuffled" to create novel combinations in the resulting progeny. DNA shuffling utilizes sequence identity between parental genes to mediate template-switching events (the annealing and extension of one parental gene fragment on another) in PCR reassembly reactions to generate crossovers and hence recombination between parental genes. In light of the conservation of protein structure and degeneracy of sequence, SCOPE was developed to enable the "shuffling" of distantly related genes with no requirement for sequence identity. The central principle involves the use of oligonucleotides to encode for crossover regions to choreograph template-switching events during PCR assembly of gene fragments to create chimeric genes. This approach was initially developed to create libraries of hybrid DNA polymerases from distantly related parents, and later developed to create a combinatorial mutant library of sesquiterpene synthases to explore the catalytic landscapes underlying the functional divergence of related enzymes. This chapter presents a simplified protocol of SCOPE that can be integrated with different mutagenesis techniques and is suitable for automation by liquid-handling robots. Two examples are presented to illustrate the application of SCOPE to create gene libraries using plant sesquiterpene synthases as the model system. In the first example, we outline how to create an active-site library as a series of complex mixtures of diverse mutants. In the second example, we outline how to create a focused library as an array of individual clones to distil minimal combinations of functionally important mutations. Through these examples, the principles of the technique are illustrated and the suitability of automating various aspects of the procedure for given applications are discussed. Copyright © 2012 Elsevier Inc. All rights reserved.

New materials with microgels

NASA Astrophysics Data System (ADS)

Kim, Jin-Woong

2009-03-01

This talk introduces a flexible and straightforward method for generating responsive microgel materials with new structures by using a microfluidic technique. We demonstrate that this approach enables tight control over the size and monodispersity of droplets as well as the interfacial structures, which is essential for determining release and transport kinetics of encapsulated components. We also show that responsiveness of microgel materials is controllable by tuning their structure, thereby allowing us to overcome the limitation of length scales, since the diffusion of water molecules through the structured gel phase is much faster than through a bulk gel phase of similar dimensions. We have generated a variety of novel gel structures: microgels with complex structures, microgel shells, 3D gel network with a truly fast response, and responsive colloidosomes. The robustness and versatility of this approach are expected to generate more complex systems and create new possibilities to develop novel materials in practical applications, including drug delivery, foods, and cosmetics.

Synthesis of triazole-based and imidazole-based zinc catalysts

DOEpatents

Valdez, Carlos A.; Satcher, Jr., Joe H.; Aines, Roger D.; Baker, Sarah E.

2013-03-12

Various methods and structures of complexes and molecules are described herein related to a zinc-centered catalyst for removing carbon dioxide from atmospheric or aqueous environments. According to one embodiment, a method for creating a tris(triazolyl)pentaerythritol molecule includes contacting a pentaerythritol molecule with a propargyl halide molecule to create a trialkyne molecule, and contacting the trialkyne molecule with an azide molecule to create the tris(triazolyl)pentaerythritol molecule. In another embodiment, a method for creating a tris(imidazolyl)pentaerythritol molecule includes alkylating an imidazole 2-carbaldehyde molecule to create a monoalkylated aldehyde molecule, reducing the monoalkylated aldehyde molecule to create an alcohol molecule, converting the alcohol molecule to create an alkyl halide molecule using thionyl halide, and reacting the alkyl halide molecule with a pentaerythritol molecule to create a tris(imidazolyl)pentaerythritol molecule. In another embodiment, zinc is bound to the tris(triazolyl)pentaerythritol molecule to create a zinc-centered tris(triazolyl)pentaerythritol catalyst for removing carbon dioxide from atmospheric or aqueous environments.

Integrating structure-from-motion photogrammetry with geospatial software as a novel technique for quantifying 3D ecological characteristics of coral reefs

PubMed Central

Delparte, D; Gates, RD; Takabayashi, M

2015-01-01

The structural complexity of coral reefs plays a major role in the biodiversity, productivity, and overall functionality of reef ecosystems. Conventional metrics with 2-dimensional properties are inadequate for characterization of reef structural complexity. A 3-dimensional (3D) approach can better quantify topography, rugosity and other structural characteristics that play an important role in the ecology of coral reef communities. Structure-from-Motion (SfM) is an emerging low-cost photogrammetric method for high-resolution 3D topographic reconstruction. This study utilized SfM 3D reconstruction software tools to create textured mesh models of a reef at French Frigate Shoals, an atoll in the Northwestern Hawaiian Islands. The reconstructed orthophoto and digital elevation model were then integrated with geospatial software in order to quantify metrics pertaining to 3D complexity. The resulting data provided high-resolution physical properties of coral colonies that were then combined with live cover to accurately characterize the reef as a living structure. The 3D reconstruction of reef structure and complexity can be integrated with other physiological and ecological parameters in future research to develop reliable ecosystem models and improve capacity to monitor changes in the health and function of coral reef ecosystems. PMID:26207190

Synthesis, crystal structure and study of magnetocaloric effect and single molecular magnetic behaviour in discrete lanthanide complexes.

PubMed

Adhikary, Amit; Sheikh, Javeed Ahmad; Biswas, Soumava; Konar, Sanjit

2014-06-28

The synthesis, crystal structure and magnetic properties of four polynuclear lanthanide coordination complexes having molecular formulae, [Gd3(2)(1)L(H2O)8(Cl)](Cl)4·10H2O (1), [Dy3L(2)(1)(H2O)9](Cl)5·6H2O (2) [Gd6L(2)(2)(HCO2)4(μ3-OH)4(DMF)6(H2O)2](Cl)2·4H2O (3) and [Dy6L(2)(2)(HCO2)4(μ3-OH)4(DMF)6(H2O)2](Cl)2·4H2O (4) (where H2L(1) = bis[(2-pyridyl)methylene]pyridine-2,6-dicarbohydrazide and H4L(2) = bis[2-hydroxy-benzylidene]pyridine-2,6-dicarbohydrazide) are reported. Structural investigation by X-ray crystallography reveals similar structural features for complexes 1 and 2 and they exhibit butterfly like shapes of the molecules. Non-covalent interactions between the molecules create double helical arrangements for both molecules. Complexes 3 and 4 are isostructural and the core structures feature four distorted hemi-cubanes connected by vertex sharing. Magnetic studies unveil significant magnetic entropy changes for complexes 1, 3 and slow relaxation of magnetization for both dysprosium analogues 2 and 4.

Necessity of creating digital tools to ensure efficiency of technical means

NASA Astrophysics Data System (ADS)

Rakov, V. I.; Zakharova, O. V.

2018-05-01

The authors estimated the problems of functioning of technical objects. The article notes that the increasing complexity of automation systems may lead to an increase of the redundant resource in proportion to the number of components and relationships in the system, and to the need of the redundant resource constant change that can make implementation of traditional structures with redundancy unnecessarily costly (Standby System, Fault Tolerance, High Availability). It proposes the idea of creating digital tools to ensure efficiency of technical facilities.

Atomic model for the dimeric FO region of mitochondrial ATP synthase.

PubMed

Guo, Hui; Bueler, Stephanie A; Rubinstein, John L

2017-11-17

Mitochondrial adenosine triphosphate (ATP) synthase produces the majority of ATP in eukaryotic cells, and its dimerization is necessary to create the inner membrane folds, or cristae, characteristic of mitochondria. Proton translocation through the membrane-embedded F O region turns the rotor that drives ATP synthesis in the soluble F 1 region. Although crystal structures of the F 1 region have illustrated how this rotation leads to ATP synthesis, understanding how proton translocation produces the rotation has been impeded by the lack of an experimental atomic model for the F O region. Using cryo-electron microscopy, we determined the structure of the dimeric F O complex from Saccharomyces cerevisiae at a resolution of 3.6 angstroms. The structure clarifies how the protons travel through the complex, how the complex dimerizes, and how the dimers bend the membrane to produce cristae. Copyright © 2017, American Association for the Advancement of Science.

A distal point mutation in the streptavidin-biotin complex preserves structure but diminishes binding affinity: experimental evidence of electronic polarization effects?

PubMed

Baugh, Loren; Le Trong, Isolde; Cerutti, David S; Gülich, Susanne; Stayton, Patrick S; Stenkamp, Ronald E; Lybrand, Terry P

2010-06-08

We have identified a distal point mutation in streptavidin that causes a 1000-fold reduction in biotin binding affinity without disrupting the equilibrium complex structure. The F130L mutation creates a small cavity occupied by a water molecule; however, all neighboring side chain positions are preserved, and protein-biotin hydrogen bonds are unperturbed. Molecular dynamics simulations reveal a reduced mobility of biotin binding residues but no observable destabilization of protein-ligand interactions. Our combined structural and computational studies suggest that the additional water molecule may affect binding affinity through an electronic polarization effect that impacts the highly cooperative hydrogen bonding network in the biotin binding pocket.

Candide in St. Louis

ERIC Educational Resources Information Center

Yee, Roger

1974-01-01

A young, St. Louis, Missouri, architectural firm, seeking a personal style of practice, has succeeded in creating structures that reveal client input, and which are sensitive, articulate, and at ease with complexity. Describes an elementary school, a condominium, a shopping mall, a high school, and a "community mall." Illustrated with photographs…

Resolving complex chromosome structures during meiosis: versatile deployment of Smc5/6.

PubMed

Verver, Dideke E; Hwang, Grace H; Jordan, Philip W; Hamer, Geert

2016-03-01

The Smc5/6 complex, along with cohesin and condensin, is a member of the structural maintenance of chromosome (SMC) family, large ring-like protein complexes that are essential for chromatin structure and function. Thanks to numerous studies of the mitotic cell cycle, Smc5/6 has been implicated to have roles in homologous recombination, restart of stalled replication forks, maintenance of ribosomal DNA (rDNA) and heterochromatin, telomerase-independent telomere elongation, and regulation of chromosome topology. The nature of these functions implies that the Smc5/6 complex also contributes to the profound chromatin changes, including meiotic recombination, that characterize meiosis. Only recently, studies in diverse model organisms have focused on the potential meiotic roles of the Smc5/6 complex. Indeed, Smc5/6 appears to be essential for meiotic recombination. However, due to both the complexity of the process of meiosis and the versatility of the Smc5/6 complex, many additional meiotic functions have been described. In this review, we provide a clear overview of the multiple functions found so far for the Smc5/6 complex in meiosis. Additionally, we compare these meiotic functions with the known mitotic functions in an attempt to find a common denominator and thereby create clarity in the field of Smc5/6 research.

Computational design of a self-assembling symmetrical β-propeller protein.

PubMed

Voet, Arnout R D; Noguchi, Hiroki; Addy, Christine; Simoncini, David; Terada, Daiki; Unzai, Satoru; Park, Sam-Yong; Zhang, Kam Y J; Tame, Jeremy R H

2014-10-21

The modular structure of many protein families, such as β-propeller proteins, strongly implies that duplication played an important role in their evolution, leading to highly symmetrical intermediate forms. Previous attempts to create perfectly symmetrical propeller proteins have failed, however. We have therefore developed a new and rapid computational approach to design such proteins. As a test case, we have created a sixfold symmetrical β-propeller protein and experimentally validated the structure using X-ray crystallography. Each blade consists of 42 residues. Proteins carrying 2-10 identical blades were also expressed and purified. Two or three tandem blades assemble to recreate the highly stable sixfold symmetrical architecture, consistent with the duplication and fusion theory. The other proteins produce different monodisperse complexes, up to 42 blades (180 kDa) in size, which self-assemble according to simple symmetry rules. Our procedure is suitable for creating nano-building blocks from different protein templates of desired symmetry.

Bim Automation: Advanced Modeling Generative Process for Complex Structures

NASA Astrophysics Data System (ADS)

Banfi, F.; Fai, S.; Brumana, R.

2017-08-01

The new paradigm of the complexity of modern and historic structures, which are characterised by complex forms, morphological and typological variables, is one of the greatest challenges for building information modelling (BIM). Generation of complex parametric models needs new scientific knowledge concerning new digital technologies. These elements are helpful to store a vast quantity of information during the life cycle of buildings (LCB). The latest developments of parametric applications do not provide advanced tools, resulting in time-consuming work for the generation of models. This paper presents a method capable of processing and creating complex parametric Building Information Models (BIM) with Non-Uniform to NURBS) with multiple levels of details (Mixed and ReverseLoD) based on accurate 3D photogrammetric and laser scanning surveys. Complex 3D elements are converted into parametric BIM software and finite element applications (BIM to FEA) using specific exchange formats and new modelling tools. The proposed approach has been applied to different case studies: the BIM of modern structure for the courtyard of West Block on Parliament Hill in Ottawa (Ontario) and the BIM of Masegra Castel in Sondrio (Italy), encouraging the dissemination and interaction of scientific results without losing information during the generative process.

PriC-mediated DNA replication restart requires PriC complex formation with the single-stranded DNA-binding protein.

PubMed

Wessel, Sarah R; Marceau, Aimee H; Massoni, Shawn C; Zhou, Ruobo; Ha, Taekjip; Sandler, Steven J; Keck, James L

2013-06-14

Frequent collisions between cellular DNA replication complexes (replisomes) and obstacles such as damaged DNA or frozen protein complexes make DNA replication fork progression surprisingly sporadic. These collisions can lead to the ejection of replisomes prior to completion of replication, which, if left unrepaired, results in bacterial cell death. As such, bacteria have evolved DNA replication restart mechanisms that function to reload replisomes onto abandoned DNA replication forks. Here, we define a direct interaction between PriC, a key Escherichia coli DNA replication restart protein, and the single-stranded DNA-binding protein (SSB), a protein that is ubiquitously associated with DNA replication forks. PriC/SSB complex formation requires evolutionarily conserved residues from both proteins, including a pair of Arg residues from PriC and the C terminus of SSB. In vitro, disruption of the PriC/SSB interface by sequence changes in either protein blocks the first step of DNA replication restart, reloading of the replicative DnaB helicase onto an abandoned replication fork. Consistent with the critical role of PriC/SSB complex formation in DNA replication restart, PriC variants that cannot bind SSB are non-functional in vivo. Single-molecule experiments demonstrate that PriC binding to SSB alters SSB/DNA complexes, exposing single-stranded DNA and creating a platform for other proteins to bind. These data lead to a model in which PriC interaction with SSB remodels SSB/DNA structures at abandoned DNA replication forks to create a DNA structure that is competent for DnaB loading.

Strategies to Reduce Hospitalizations of Children With Medical Complexity Through Complex Care: Expert Perspectives.

PubMed

Coller, Ryan J; Nelson, Bergen B; Klitzner, Thomas S; Saenz, Adrianna A; Shekelle, Paul G; Lerner, Carlos F; Chung, Paul J

Interventions to reduce disproportionate hospital use among children with medical complexity (CMC) are needed. We conducted a rigorous, structured process to develop intervention strategies aiming to reduce hospitalizations within a complex care program population. A complex care medical home program used 1) semistructured interviews of caregivers of CMC experiencing acute, unscheduled hospitalizations and 2) literature review on preventing hospitalizations among CMC to develop key drivers for lowering hospital utilization and link them with intervention strategies. Using an adapted version of the RAND/UCLA Appropriateness Method, an expert panel rated each model for effectiveness at impacting each key driver and ultimately reducing hospitalizations. The complex care program applied these findings to select a final set of feasible intervention strategies for implementation. Intervention strategies focused on expanding access to familiar providers, enhancing general or technical caregiver knowledge and skill, creating specific and proactive crisis or contingency plans, and improving transitions between hospital and home. Activities aimed to facilitate family-centered, flexible implementation and consideration of all of the child's environments, including school and while traveling. Tailored activities and special attention to the highest utilizing subset of CMC were also critical for these interventions. A set of intervention strategies to reduce hospitalizations among CMC, informed by key drivers, can be created through a structured, reproducible process. Both this process and the results may be relevant to clinical programs and researchers aiming to reduce hospital utilization through the medical home for CMC. Copyright © 2017 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

Fluid-Structure Interaction Modeling of the Reefed Stages of the Orion Spacecraft Main Parachutes

NASA Astrophysics Data System (ADS)

Boswell, Cody W.

Spacecraft parachutes are typically used in multiple stages, starting with a "reefed" stage where a cable along the parachute skirt constrains the diameter to be less than the diameter in the subsequent stage. After a certain period of time during the descent, the cable is cut and the parachute "disreefs" (i.e. expands) to the next stage. Computing the parachute shape at the reefed stage and fluid-structure interaction (FSI) modeling during the disreefing involve computational challenges beyond those we have in FSI modeling of fully-open spacecraft parachutes. These additional challenges are created by the increased geometric complexities and by the rapid changes in the parachute geometry. The computational challenges are further increased because of the added geometric porosity of the latest design, where the "windows" created by the removal of panels and the wider gaps created by the removal of sails compound the geometric and flow complexity. Orion spacecraft main parachutes will have three stages, with computation of the Stage 1 shape and FSI modeling of disreefing from Stage 1 to Stage 2 being the most challenging. We present the special modeling techniques we devised to address the computational challenges and the results from the computations carried out. We also present the methods we devised to calculate for a parachute gore the radius of curvature in the circumferential direction. The curvature values are intended for quick and simple engineering analysis in estimating the structural stresses.

Neuroarchitecture and neuroanatomy of the Drosophila central complex: A GAL4-based dissection of protocerebral bridge neurons and circuits.

PubMed

Wolff, Tanya; Iyer, Nirmala A; Rubin, Gerald M

2015-05-01

Insects exhibit an elaborate repertoire of behaviors in response to environmental stimuli. The central complex plays a key role in combining various modalities of sensory information with an insect's internal state and past experience to select appropriate responses. Progress has been made in understanding the broad spectrum of outputs from the central complex neuropils and circuits involved in numerous behaviors. Many resident neurons have also been identified. However, the specific roles of these intricate structures and the functional connections between them remain largely obscure. Significant gains rely on obtaining a comprehensive catalog of the neurons and associated GAL4 lines that arborize within these brain regions, and on mapping neuronal pathways connecting these structures. To this end, small populations of neurons in the Drosophila melanogaster central complex were stochastically labeled using the multicolor flip-out technique and a catalog was created of the neurons, their morphologies, trajectories, relative arrangements, and corresponding GAL4 lines. This report focuses on one structure of the central complex, the protocerebral bridge, and identifies just 17 morphologically distinct cell types that arborize in this structure. This work also provides new insights into the anatomical structure of the four components of the central complex and its accessory neuropils. Most strikingly, we found that the protocerebral bridge contains 18 glomeruli, not 16, as previously believed. Revised wiring diagrams that take into account this updated architectural design are presented. This updated map of the Drosophila central complex will facilitate a deeper behavioral and physiological dissection of this sophisticated set of structures. © 2014 Wiley Periodicals, Inc.

Conformation-Directed Formation of Self-Healing Diblock Copolypeptide Hydrogels via Polyion Complexation.

PubMed

Sun, Yintao; Wollenberg, Alexander L; O'Shea, Timothy Mark; Cui, Yanxiang; Zhou, Z Hong; Sofroniew, Michael V; Deming, Timothy J

2017-10-25

Synthetic diblock copolypeptides were designed to incorporate oppositely charged ionic segments that form β-sheet-structured hydrogel assemblies via polyion complexation when mixed in aqueous media. The observed chain conformation directed assembly was found to be required for efficient hydrogel formation and provided distinct and useful properties to these hydrogels, including self-healing after deformation, microporous architecture, and stability against dilution in aqueous media. While many promising self-assembled materials have been prepared using disordered or liquid coacervate polyion complex (PIC) assemblies, the use of ordered chain conformations in PIC assemblies to direct formation of new supramolecular morphologies is unprecedented. The promising attributes and unique features of the β-sheet-structured PIC hydrogels described here highlight the potential of harnessing conformational order derived from PIC assembly to create new supramolecular materials.

Non-covalent synthesis of supermicelles with complex architectures using spatially confined hydrogen-bonding interactions

PubMed Central

Li, Xiaoyu; Gao, Yang; Boott, Charlotte E.; Winnik, Mitchell A.; Manners, Ian

2015-01-01

Nature uses orthogonal interactions over different length scales to construct structures with hierarchical levels of order and provides an important source of inspiration for the creation of synthetic functional materials. Here, we report the programmed assembly of monodisperse cylindrical block comicelle building blocks with crystalline cores to create supermicelles using spatially confined hydrogen-bonding interactions. We also demonstrate that it is possible to further program the self-assembly of these synthetic building blocks into structures of increased complexity by combining hydrogen-bonding interactions with segment solvophobicity. The overall approach offers an efficient, non-covalent synthesis method for the solution-phase fabrication of a range of complex and potentially functional supermicelle architectures in which the crystallization, hydrogen-bonding and solvophobic interactions are combined in an orthogonal manner. PMID:26337527

Variable-retention harvesting as a silvicultural option for lodgepole pine

Treesearch

Christopher R. Keyes; Thomas E. Perry; Elaine K. Sutherland; David K. Wright; Joel M. Egan

2014-01-01

Bark beetle-induced mortality in forested landscapes of structurally uniform, even-aged lodgepole pine stands has inspired a growing interest in the potential of silvicultural treatments to enhance resilience by increasing spatial and vertical complexity. Silvicultural treatments can simulate mixed-severity disturbances that create multiaged lodgepole pine stands,...

Design and Implementation of the Game-Design and Learning Program

ERIC Educational Resources Information Center

Akcaoglu, Mete

2016-01-01

Design involves solving complex, ill-structured problems. Design tasks are consequently, appropriate contexts for children to exercise higher-order thinking and problem-solving skills. Although creating engaging and authentic design contexts for young children is difficult within the confines of traditional schooling, recently, game-design has…

Identifying Configurations of Higher Education: Reflections on Concepts That Compare Complex Cultural Settings

ERIC Educational Resources Information Center

Alheit, Peter

2013-01-01

This paper examines the idea of qualitative comparing in order to create a "heuristic concept" that will enable relational structures to be examined, drawing on the sociological tradition founded by Norbert Elias. Subsequently, an empirical research example -- the comparison of three "mentality spaces" in post-socialist…

Effects of Fault Segmentation, Mechanical Interaction, and Structural Complexity on Earthquake-Generated Deformation

ERIC Educational Resources Information Center

Haddad, David Elias

2014-01-01

Earth's topographic surface forms an interface across which the geodynamic and geomorphic engines interact. This interaction is best observed along crustal margins where topography is created by active faulting and sculpted by geomorphic processes. Crustal deformation manifests as earthquakes at centennial to millennial timescales. Given that…

Teacher Expectations and Student Literacy Engagement and Achievement

ERIC Educational Resources Information Center

Pantaleo, Sylvia

2016-01-01

Notwithstanding the complex and dynamic nature of teaching and learning in schools, over four decades of research findings have consistently revealed a correlation between teacher expectations and student achievement. Focusing on teacher expectations for the narrative structures created by young children, this article features a discussion of data…

Assessing Quality in Home Visiting Programs

ERIC Educational Resources Information Center

Korfmacher, Jon; Laszewski, Audrey; Sparr, Mariel; Hammel, Jennifer

2013-01-01

Defining quality and designing a quality assessment measure for home visitation programs is a complex and multifaceted undertaking. This article summarizes the process used to create the Home Visitation Program Quality Rating Tool (HVPQRT) and identifies next steps for its development. The HVPQRT measures both structural and dynamic features of…

Engaging with Molecular Form to Understand Function

ERIC Educational Resources Information Center

Barber, Nicola C.; Stark, Louisa A.

2014-01-01

Cells are bustling factories with diverse and prolific arrays of molecular machinery. Remarkably, this machinery self-organizes to carry out the complex biochemical activities characteristic of life. When Watson and Crick published the structure of DNA, they noted that DNA base pairing creates a double-stranded form that provides a means of…

Research on energy stock market associated network structure based on financial indicators

NASA Astrophysics Data System (ADS)

Xi, Xian; An, Haizhong

2018-01-01

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

Crew Launch Vehicle Mobile Launcher Solid Rocket Motor Plume Induced Environment

NASA Technical Reports Server (NTRS)

Vu, Bruce T.; Sulyma, Peter

2008-01-01

The plume-induced environment created by the Ares 1 first stage, five-segment reusable solid rocket motor (RSRMV) will impose high heating rates and impact pressures on Launch Complex 39. The extremes of these environments pose a potential threat to weaken or even cause structural components to fail if insufficiently designed. Therefore the ability to accurately predict these environments is critical to assist in specifying structural design requirements to insure overall structural integrity and flight safety. This paper presents the predicted thermal and pressure environments induced by the launch of the Crew Launch Vehicle (CLV) from Launch Complex (LC) 39. Once the environments are predicted, a follow-on thermal analysis is required to determine the surface temperature response and the degradation rate of the materials. An example of structures responding to the plume-induced environment will be provided.

Hierarchical Micro/Nano Structures by Combined Self-Organized Dewetting and Photopatterning of Photoresist Thin Films.

PubMed

Sachan, Priyanka; Kulkarni, Manish; Sharma, Ashutosh

2015-11-17

Photoresists are the materials of choice for micro/nanopatterning and device fabrication but are rarely used as a self-assembly material. We report for the first time a novel interplay of self-assembly and photolithography for fabrication of hierarchical and ordered micro/nano structures. We create self-organized structures by the intensified dewetting of unstable thin (∼10 nm to 1 μm) photoresist films by annealing them in an optimal solvent and nonsolvent liquid mixture that allows spontaneous dewetting to form micro/nano smooth dome-like structures. The density, size (∼100 nm to millimeters), and curvature/contact angle of the dome/droplet structures are controlled by the film thickness, composition of the dewetting liquid, and time of annealing. Ordered dewetted structures are obtained simply by creating spatial variation of viscosity by ultraviolet exposure or by photopatterning before dewetting. Further, the structures thus fabricated are readily photopatterned again on the finer length scales after dewetting. We illustrate the approach by fabricating several three-dimensional structures of varying complexity with secondary and tertiary features.

A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more.

PubMed

Rivas, Elena; Lang, Raymond; Eddy, Sean R

2012-02-01

The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using complex nearest-neighbor models, including CONTRAfold, Simfold, and ContextFold. Little work has been reported on generative probabilistic models (stochastic context-free grammars [SCFGs]) of comparable complexity, although probabilistic models are generally easier to train and to use. To explore a range of probabilistic models of increasing complexity, and to directly compare probabilistic, thermodynamic, and discriminative approaches, we created TORNADO, a computational tool that can parse a wide spectrum of RNA grammar architectures (including the standard nearest-neighbor model and more) using a generalized super-grammar that can be parameterized with probabilities, energies, or arbitrary scores. By using TORNADO, we find that probabilistic nearest-neighbor models perform comparably to (but not significantly better than) discriminative methods. We find that complex statistical models are prone to overfitting RNA structure and that evaluations should use structurally nonhomologous training and test data sets. Overfitting has affected at least one published method (ContextFold). The most important barrier to improving statistical approaches for RNA secondary structure prediction is the lack of diversity of well-curated single-sequence RNA secondary structures in current RNA databases.

A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more

PubMed Central

Rivas, Elena; Lang, Raymond; Eddy, Sean R.

2012-01-01

The standard approach for single-sequence RNA secondary structure prediction uses a nearest-neighbor thermodynamic model with several thousand experimentally determined energy parameters. An attractive alternative is to use statistical approaches with parameters estimated from growing databases of structural RNAs. Good results have been reported for discriminative statistical methods using complex nearest-neighbor models, including CONTRAfold, Simfold, and ContextFold. Little work has been reported on generative probabilistic models (stochastic context-free grammars [SCFGs]) of comparable complexity, although probabilistic models are generally easier to train and to use. To explore a range of probabilistic models of increasing complexity, and to directly compare probabilistic, thermodynamic, and discriminative approaches, we created TORNADO, a computational tool that can parse a wide spectrum of RNA grammar architectures (including the standard nearest-neighbor model and more) using a generalized super-grammar that can be parameterized with probabilities, energies, or arbitrary scores. By using TORNADO, we find that probabilistic nearest-neighbor models perform comparably to (but not significantly better than) discriminative methods. We find that complex statistical models are prone to overfitting RNA structure and that evaluations should use structurally nonhomologous training and test data sets. Overfitting has affected at least one published method (ContextFold). The most important barrier to improving statistical approaches for RNA secondary structure prediction is the lack of diversity of well-curated single-sequence RNA secondary structures in current RNA databases. PMID:22194308

Comparison of Commercial Structure-From Photogrammety Software Used for Underwater Three-Dimensional Modeling of Coral Reef Environments

NASA Astrophysics Data System (ADS)

Burns, J. H. R.; Delparte, D.

2017-02-01

Structural complexity in ecosystems creates an assortment of microhabitat types and has been shown to support greater diversity and abundance of associated organisms. The 3D structure of an environment also directly affects important ecological parameters such as habitat provisioning and light availability and can therefore strongly influence ecosystem function. Coral reefs are architecturally complex 3D habitats, whose structure is intrinsically linked to the ecosystem biodiversity, productivity, and function. The field of coral ecology has, however, been primarily limited to using 2-dimensional (2D) planar survey techniques for studying the physical structure of reefs. This conventional approach fails to capture or quantify the intricate structural complexity of corals that influences habitat facilitation and biodiversity. A 3-dimensional (3D) approach can obtain accurate measurements of architectural complexity, topography, rugosity, volume, and other structural characteristics that affect biodiversity and abundance of reef organisms. Structurefrom- Motion (SfM) photogrammetry is an emerging computer vision technology that provides a simple and cost-effective method for 3D reconstruction of natural environments. SfM has been used in several studies to investigate the relationship between habitat complexity and ecological processes in coral reef ecosystems. This study compared two commercial SfM software packages, Agisoft Photoscan Pro and Pix4Dmapper Pro 3.1, in order to assess the cpaability and spatial accuracy of these programs for conducting 3D modeling of coral reef habitats at three spatial scales.

How Analysts Cognitively “Connect the Dots”

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

Bradel, Lauren; Self, Jessica S.; Endert, Alexander

2013-06-04

As analysts attempt to make sense of a collection of documents, such as intelligence analysis reports, they may wish to “connect the dots” between pieces of information that may initially seem unrelated. This process of synthesizing information between information requires users to make connections between pairs of documents, creating a conceptual story. We conducted a user study to analyze the process by which users connect pairs of documents and how they spatially arrange information. Users created conceptual stories that connected the dots using organizational strategies that ranged in complexity. We propose taxonomies for cognitive connections and physical structures used whenmore » trying to “connect the dots” between two documents. We compared the user-created stories with a data-mining algorithm that constructs chains of documents using co-occurrence metrics. Using the insight gained into the storytelling process, we offer design considerations for the existing data mining algorithm and corresponding tools to combine the power of data mining and the complex cognitive processing of analysts.« less

Apparatus for electrohydrodynamically assembling patterned colloidal structures

NASA Technical Reports Server (NTRS)

Trau, Mathias (Inventor); Aksay, Ilhan A. (Inventor); Saville, Dudley A. (Inventor)

2000-01-01

A method apparatus is provided for electrophoretically depositing particles onto an electrode, and electrohydrodynamically assembling the particles into crystalline structures. Specifically, the present method and apparatus creates a current flowing through a solution to cause identically charged electrophoretically deposited colloidal particles to attract each other over very large distances (<5 particle diameters) on the surface of electrodes to form two-dimensional colloidal crystals. The attractive force can be created with both DC and AC fields and can modulated by adjusting either the field strength or frequency of the current. Modulating this lateral attraction between the particles causes the reversible formation of two-dimensional fluid and crystalline colloidal states on the electrode surface. Further manipulation allows for the formation of two or three-dimensional colloidal crystals, as well as more complex designed structures. Once the required structures are formed, these three-dimension colloidal crystals can be permanently frozen or glued by controlled coagulation induced by to the applied field to form a stable crystalline structure.

Micrometer-scale fabrication of complex three dimensional lattice + basis structures in silicon

DOE PAGES

Burckel, D. Bruce; Resnick, Paul J.; Finnegan, Patrick S.; ...

2015-01-01

A complementary metal oxide semiconductor (CMOS) compatible version of membrane projection lithography (MPL) for fabrication of micrometer-scale three-dimensional structures is presented. The approach uses all inorganic materials and standard CMOS processing equipment. In a single layer, MPL is capable of creating all 5 2D-Bravais lattices. Furthermore, standard semiconductor processing steps can be used in a layer-by-layer approach to create fully three dimensional structures with any of the 14 3D-Bravais lattices. The unit cell basis is determined by the projection of the membrane pattern, with many degrees of freedom for defining functional inclusions. Here we demonstrate several unique structural motifs, andmore » characterize 2D arrays of unit cells with split ring resonators in a silicon matrix. The structures exhibit strong polarization dependent resonances and, for properly oriented split ring resonators (SRRs), coupling to the magnetic field of a normally incident transverse electromagnetic wave, a response unique to 3D inclusions.« less

Method for electrohydrodynamically assembling patterned colloidal structures

NASA Technical Reports Server (NTRS)

Trau, Mathias (Inventor); Aksay, Ilhan A. (Inventor); Saville, Dudley A. (Inventor)

1999-01-01

A method apparatus is provided for electrophoretically depositing particles onto an electrode, and electrohydrodynamically assembling the particles into crystalline structures. Specifically, the present method and apparatus creates a current flowing through a solution to cause identically charged electrophoretically deposited colloidal particles to attract each other over very large distances (<5 particle diameters) on the surface of electrodes to form two-dimensional colloidal crystals. The attractive force can be created with both DC and AC fields and can modulated by adjusting either the field strength or frequency of the current. Modulating this lateral attraction between the particles causes the reversible formation of two-dimensional fluid and crystalline colloidal states on the electrode surface. Further manipulation allows for the formation of two or three-dimensional colloidal crystals, as well as more complex designed structures. Once the required structures are formed, these three-dimension colloidal crystals can be permanently frozen or glued by controlled coagulation induced by to the applied field to form a stable crystalline structure.

3D Bioprinting of Artificial Tissues: Construction of Biomimetic Microstructures.

PubMed

Luo, Yongxiang; Lin, Xin; Huang, Peng

2018-04-24

It is promising that artificial tissues/organs for clinical application can be produced via 3D bioprinting of living cells and biomaterials. The construction of microstructures biomimicking native tissues is crucially important to create artificial tissues with biological functions. For instance, the fabrication of vessel-like networks to supply cells with initial nutrient and oxygen, and the arrangement of multiple types of cells for creating lamellar/complex tissues through 3D bioprinting are widely reported. The current advances in 3D bioprinting of artificial tissues from the view of construction of biomimetic microstructures, especially the fabrication of lamellar, vascular, and complex structures are summarized. In the end, the conclusion and perspective of 3D bioprinting for clinical applications are elaborated. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Silver(I) complexes with hydantoins and allantoin: synthesis, crystal and molecular structure, cytotoxicity and pharmacokinetics.

PubMed

Puszyńska-Tuszkanow, Mariola; Grabowski, Tomasz; Daszkiewicz, Marek; Wietrzyk, Joanna; Filip, Beata; Maciejewska, Gabriela; Cieślak-Golonka, Maria

2011-01-01

Coordination polymers [Ag(L(1,3))](n) (L(1)=hydantoin, L(3)=5,5-dimethylhydantoin), {[Ag(L(2))](.)0.5H(2)O}(n) (L(2)=1-methylhydantoin) and [Ag(NH(3))(L(4))](n) (L(4)=allantoin) were prepared and characterized by elemental analysis, spectroscopic (IR, FTIR and NMR), thermal and mass spectrometry methods. The crystal structure of {[Ag(1-methylhydantoin)]·0,5H(2)O}(n) was determined and analyzed. Three 1-methylhydantoinate ligands create a T-shape (CN=3) coordination sphere around the Ag(+) ion. Additionally, a short Ag⋯Ag distance of 2.997Å was found in the structure resulting in the expanded [3+2] environment of a distorted square shape. The [Ag(L(2))] entities are bound to each other by the bridging organic ligands. Thus a two-dimensional coordination polymer is created with water molecules located between the layers. In contrast to hydantoins, the allantoin complex contains an additional ammonia molecule in the coordination sphere. Moreover, in the Ag-alla complex the M-organic ligand binding site is shifted to the N-atom of the ureid chain. Free ligands are cytotoxically inactive against human MCF-7 and A549 cancer cell lines and mouse fibroblasts Balb/3T3. The silver hydantoin complexes exhibit a very strong activity against these lines. (The introduction of the methyl groups to the ring slightly increases resistance only against the A549 cell line.) In contrast, the silver complex of allantoin shows only a weak activity which may be related to the presence of the cytotoxic ammonia group in the composition of the compound and/or the different binding site of the ligand. Calculated in silico physiochemical parameters are promising for the future application of the complexes as drugs. Copyright © 2010 Elsevier Inc. All rights reserved.

Complexity VIII. Ontology of closure in complex systems: The C* hypothesis and the O° notation

NASA Astrophysics Data System (ADS)

Chandler, Jerry LR

1999-03-01

Closure is a common characteristic of mathematical, natural and socio-cultural systems. Whether one is describing a graph, a molecule, a cell, a human, or a nation state, closure is implicitly understood. An objective of this paper is to continue a construction of a systematic framework for closure which is sufficient for future quantitative transdisciplinary investigations. A further objective is to extend the Birkhoff-von Neumann criterion for quantum systems to complex natural objects. The C* hypothesis is being constructed to be consistent with algebraic category theory (Ehresmann and Vanbremeersch, 1987, 1997, Chandler, 1990, 1991, Chandler, Ehresmann and Vanbremeersch, 1996). Five aspects of closure will be used to construct a framework for categories of complex systems: 1. Truth functions in mathematics and the natural sciences 2. Systematic descriptions in the mks and O° notations 3. Organizational structures in hierarchical scientific languages 4. Transitive organizational pathways in the causal structures of complex behaviors 5. Composing additive, multiplicative and exponential operations in complex systems Truth functions can be formal or objective or subjective, depending on the complexity of the system and on our capability to represent the fine structure of the system symbolically, observationally or descriptively. "Complete" material representations of the fine structure of a system may allow truth functions to be created over sets of one to one correspondences. Less complete descriptions can support less stringent truth functions based on coherence or subjective judgments. The role of human values in creating and perpetuating truth functions can be placed in context of the degree of fine structure in the system's description. The organization of complex systems are hypothesized to be categorizable into degrees relative to one another, thereby creating an ordering relationship. This ordering relationship is denoted by the symbols: O°1, O°2,O°3... For example, for material systems, an ordering relation such as particles, atoms, molecules, cells, tissues, organs, individuals and social groups might be assigned to classify observations for medical purposes. The C* hypothesis asserts that any complex system can be described in terms of four enumerable concepts: closure, conformation, concatenation and cyclicity. Mappings between objects are constructed within a notation for organization. Causality is organized within C* as pathways of relationships in time. The notation of organizational degrees is used to distinguish a directionality for causality: 1. bottom-up (energy flows) 2. top-down (control processes or dominating variables), 3. outside — inward (ecoment on organism) and 4. inside — outward (organism on ecoment). Closures are asserted to emerge from evolutionary cooperation. It is asserted that truth functions emerged from the necessity of an organism to identify ecoments where life can prosper. For example, basic truth functions of mathematics (operations of addition, multiplication and exponentiation) are made operationally consistent within the biochemical operations of sustaining exponential cellular growth. These fundamental mathematical functions can provide a logical basis (in conjunction with conservation rules) for a construction of complex material categories at higher degrees of organization. It is remarked that these simple functions suggests a biochemical origin for the intuitionistic philosophy of mathematics. The emergence and success of mathematics is conjectured to result from the need to acquire a consistent basis for communication among individuals seeking to cooperate socially. This suggests a cultural closure over a collection of individual closures.

Continuous Optical 3D Printing of Green Aliphatic Polyurethanes.

PubMed

Pyo, Sang-Hyun; Wang, Pengrui; Hwang, Henry H; Zhu, Wei; Warner, John; Chen, Shaochen

2017-01-11

Photosensitive diurethanes were prepared from a green chemistry synthesis pathway based on methacrylate-functionalized six-membered cyclic carbonate and biogenic amines. A continuous optical 3D printing method for the diurethanes was developed to create user-defined gradient stiffness and smooth complex surface microstructures in seconds. The green chemistry-derived polyurethane (gPU) showed high optical transparency, and we demonstrate the ability to tune the material stiffness of the printed structure along a gradient by controlling the exposure time and selecting various amine compounds. High-resolution 3D biomimetic structures with smooth curves and complex contours were printed using our gPU. High cell viability (over 95%) was demonstrated during cytocompatibility testing using C3H 10T1/2 cells seeded directly on the printed structures.

New possibilities using additive manufacturing with materials that are difficult to process and with complex structures

NASA Astrophysics Data System (ADS)

Olsson, Anders; Hellsing, Maja S.; Rennie, Adrian R.

2017-05-01

Additive manufacturing (or 3D printing) opens the possibility of creating new designs and manufacturing objects with new materials rapidly and economically. Particularly for use with polymers and polymer composites, simple printers can make high quality products, and these can be produced easily in offices, schools and in workshops and laboratories. This technology has opened a route for many to test ideas or to make custom devices. It is possible to easily manufacture complex geometries that would be difficult or even impossible to create with traditional methods. Naturally this technology has attracted attention in many fields that include the production of medical devices and prostheses, mechanical engineering as well as basic sciences. Materials that are highly problematic to machine can be used. We illustrate process developments with an account of the production of printer parts to cope with polymer fillers that are hard and abrasive; new nozzles with ruby inserts designed for such materials are durable and can be used to print boron carbide composites. As with other materials, complex parts can be printed using boron carbide composites with fine structures, such as screw threads and labels to identify materials. General ideas about design for this new era of manufacturing customised parts are presented.

Split green fluorescent protein as a modular binding partner for protein crystallization

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

Nguyen, Hau B.; Hung, Li-Wei; Yeates, Todd O.

2013-12-01

A strategy using a new split green fluorescent protein (GFP) as a modular binding partner to form stable protein complexes with a target protein is presented. The modular split GFP may open the way to rapidly creating crystallization variants. A modular strategy for protein crystallization using split green fluorescent protein (GFP) as a crystallization partner is demonstrated. Insertion of a hairpin containing GFP β-strands 10 and 11 into a surface loop of a target protein provides two chain crossings between the target and the reconstituted GFP compared with the single connection afforded by terminal GFP fusions. This strategy was testedmore » by inserting this hairpin into a loop of another fluorescent protein, sfCherry. The crystal structure of the sfCherry-GFP(10–11) hairpin in complex with GFP(1–9) was determined at a resolution of 2.6 Å. Analysis of the complex shows that the reconstituted GFP is attached to the target protein (sfCherry) in a structurally ordered way. This work opens the way to rapidly creating crystallization variants by reconstituting a target protein bearing the GFP(10–11) hairpin with a variety of GFP(1–9) mutants engineered for favorable crystallization.« less

Cyclization strategies of meditopes: affinity and diffraction studies of meditope–Fab complexes

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

Bzymek, Krzysztof P.; Ma, Yuelong; Avery, Kendra A.

An overview of cyclization strategies of a Fab-binding peptide to maximize affinity. Recently, a unique binding site for a cyclic 12-residue peptide was discovered within a cavity formed by the light and heavy chains of the cetuximab Fab domain. In order to better understand the interactions that drive this unique complex, a number of variants including the residues within the meditope peptide and the antibody, as well as the cyclization region of the meditope peptide, were created. Here, multiple crystal structures of meditope peptides incorporating different cyclization strategies bound to the central cavity of the cetuximab Fab domain are presented.more » The affinity of each cyclic derivative for the Fab was determined by surface plasmon resonance and correlated to structural differences. Overall, it was observed that the disulfide bond used to cyclize the peptide favorably packs against a hydrophobic ‘pocket’ and that amidation and acetylation of the original disulfide meditope increased the overall affinity ∼2.3-fold. Conversely, replacing the terminal cysteines with serines and thus creating a linear peptide reduced the affinity over 50-fold, with much of this difference being reflected in a decrease in the on-rate. Other cyclization methods, including the formation of a lactam, reduced the affinity but not to the extent of the linear peptide. Collectively, the structural and kinetic data presented here indicate that small perturbations introduced by different cyclization strategies can significantly affect the affinity of the meditope–Fab complex.« less

Microbial bebop: creating music from complex dynamics in microbial ecology.

PubMed

Larsen, Peter; Gilbert, Jack

2013-01-01

In order for society to make effective policy decisions on complex and far-reaching subjects, such as appropriate responses to global climate change, scientists must effectively communicate complex results to the non-scientifically specialized public. However, there are few ways however to transform highly complicated scientific data into formats that are engaging to the general community. Taking inspiration from patterns observed in nature and from some of the principles of jazz bebop improvisation, we have generated Microbial Bebop, a method by which microbial environmental data are transformed into music. Microbial Bebop uses meter, pitch, duration, and harmony to highlight the relationships between multiple data types in complex biological datasets. We use a comprehensive microbial ecology, time course dataset collected at the L4 marine monitoring station in the Western English Channel as an example of microbial ecological data that can be transformed into music. Four compositions were generated (www.bio.anl.gov/MicrobialBebop.htm.) from L4 Station data using Microbial Bebop. Each composition, though deriving from the same dataset, is created to highlight different relationships between environmental conditions and microbial community structure. The approach presented here can be applied to a wide variety of complex biological datasets.

Crystal structure of norcoclaurine-6-O-methyltransferase, a key rate-limiting step in the synthesis of benzylisoquinoline alkaloids.

PubMed

Robin, Adeline Y; Giustini, Cécile; Graindorge, Matthieu; Matringe, Michel; Dumas, Renaud

2016-09-01

Growing pharmaceutical interest in benzylisoquinoline alkaloids (BIA) coupled with their chemical complexity make metabolic engineering of microbes to create alternative platforms of production an increasingly attractive proposition. However, precise knowledge of rate-limiting enzymes and negative feedback inhibition by end-products of BIA metabolism is of paramount importance for this emerging field of synthetic biology. In this work we report the structural characterization of (S)-norcoclaurine-6-O-methyltransferase (6OMT), a key rate-limiting step enzyme involved in the synthesis of reticuline, the final intermediate to be shared between the different end-products of BIA metabolism, such as morphine, papaverine, berberine and sanguinarine. Four different crystal structures of the enzyme from Thalictrum flavum (Tf 6OMT) were solved: the apoenzyme, the complex with S-adenosyl-l-homocysteine (SAH), the complexe with SAH and the substrate and the complex with SAH and a feedback inhibitor, sanguinarine. The Tf 6OMT structural study provides a molecular understanding of its substrate specificity, active site structure and reaction mechanism. This study also clarifies the inhibition of Tf 6OMT by previously suggested feedback inhibitors. It reveals its high and time-dependent sensitivity toward sanguinarine. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Creating Spaces for International and Multi(inter)cultural Perspectives in Undergraduate Public Relations Education.

ERIC Educational Resources Information Center

Bardhan, Nilanjana

2003-01-01

Considers students' views on the need to bridge the gap between current undergraduate curricular content and the international and multi(inter)cultural complexities of today's industry. Indicates that students are far from apathetic about multicultural and international learning. Cites certain curricular and structural impediments to expanding…

Use of Problem-Based Learning in the Teaching and Learning of Horticultural Production

ERIC Educational Resources Information Center

Abbey, Lord; Dowsett, Eric; Sullivan, Jan

2017-01-01

Purpose: Problem-based learning (PBL), a relatively novel teaching and learning process in horticulture, was investigated. Proper application of PBL can potentially create a learning context that enhances student learning. Design/Methodology/Approach: Students worked on two complex ill-structured problems: (1) to produce fresh baby greens for a…

Making Meaning: Individual and Group Response within a Book Club Structure

ERIC Educational Resources Information Center

Barone, Diane

2013-01-01

This article positions a view of student responses with relation to current literacy expectations. Student responses to a single book, "The Egypt Game," are explored. The responses are analysed from a group and individual student perspectives. The responses demonstrate the complex understandings that young students created about this book.…

Nasal Anatomy and Function.

PubMed

Patel, Ruchin G

2017-02-01

The nose is a complex structure important in facial aesthetics and in respiratory physiology. Nasal defects can pose a challenge to reconstructive surgeons who must re-create nasal symmetry while maintaining nasal function. A basic understanding of the underlying nasal anatomy is thus necessary for successful nasal reconstruction. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

The Multiple Roles that Youth Development Program Leaders Adopt with Youth

ERIC Educational Resources Information Center

Walker, Kathrin C.

2011-01-01

The roles that program leaders establish in their relationships with youth structure how leaders are able to foster youth development. This article examines the complex roles program leaders create in youth programs and investigates how they balanced multiple roles to most effectively respond to the youth they serve. Analyses of qualitative data…

Two dimensional finite element heat transfer models for softwood

Treesearch

Hongmei Gu; John F. Hunt

2004-01-01

The anisotropy of wood creates a complex problem for solving heat and mass transfer problems that require analyses be based on fundamental material properties of the wood structure. Most heat transfer models use average thermal properties across either the radial or tangential directions and have not differentiated the effects of cellular alignment, earlywood/latewood...

Novice and Experienced Instructional Software Developers: Effects on Materials Created with Instructional Software Templates

ERIC Educational Resources Information Center

Boot, Eddy W.; van Merrienboer, Jeroen J. G.; Veerman, Arja L.

2007-01-01

The development of instructional software is a complex process, posing high demands to the technical and didactical expertise of developers. Domain specialists rather than professional developers are often responsible for it, but authoring tools with pre-structured templates claim to compensate for this limited experience. This study compares…

Sensor-Topology Based Simplicial Complex Reconstruction from Mobile Laser Scanning

NASA Astrophysics Data System (ADS)

Guinard, S.; Vallet, B.

2018-05-01

We propose a new method for the reconstruction of simplicial complexes (combining points, edges and triangles) from 3D point clouds from Mobile Laser Scanning (MLS). Our main goal is to produce a reconstruction of a scene that is adapted to the local geometry of objects. Our method uses the inherent topology of the MLS sensor to define a spatial adjacency relationship between points. We then investigate each possible connexion between adjacent points and filter them by searching collinear structures in the scene, or structures perpendicular to the laser beams. Next, we create triangles for each triplet of self-connected edges. Last, we improve this method with a regularization based on the co-planarity of triangles and collinearity of remaining edges. We compare our results to a naive simplicial complexes reconstruction based on edge length.

Neuroarchitecture and neuroanatomy of the Drosophila central complex: A GAL4-based dissection of protocerebral bridge neurons and circuits

PubMed Central

Wolff, Tanya; Iyer, Nirmala A; Rubin, Gerald M

2015-01-01

Insects exhibit an elaborate repertoire of behaviors in response to environmental stimuli. The central complex plays a key role in combining various modalities of sensory information with an insect's internal state and past experience to select appropriate responses. Progress has been made in understanding the broad spectrum of outputs from the central complex neuropils and circuits involved in numerous behaviors. Many resident neurons have also been identified. However, the specific roles of these intricate structures and the functional connections between them remain largely obscure. Significant gains rely on obtaining a comprehensive catalog of the neurons and associated GAL4 lines that arborize within these brain regions, and on mapping neuronal pathways connecting these structures. To this end, small populations of neurons in the Drosophila melanogaster central complex were stochastically labeled using the multicolor flip-out technique and a catalog was created of the neurons, their morphologies, trajectories, relative arrangements, and corresponding GAL4 lines. This report focuses on one structure of the central complex, the protocerebral bridge, and identifies just 17 morphologically distinct cell types that arborize in this structure. This work also provides new insights into the anatomical structure of the four components of the central complex and its accessory neuropils. Most strikingly, we found that the protocerebral bridge contains 18 glomeruli, not 16, as previously believed. Revised wiring diagrams that take into account this updated architectural design are presented. This updated map of the Drosophila central complex will facilitate a deeper behavioral and physiological dissection of this sophisticated set of structures. J. Comp. Neurol. 523:997–1037, 2015. © 2014 Wiley Periodicals, Inc. PMID:25380328

The Case for Adopting the "Species Complex" Nomenclature for the Etiologic Agents of Cryptococcosis.

PubMed

Kwon-Chung, Kyung J; Bennett, John E; Wickes, Brian L; Meyer, Wieland; Cuomo, Christina A; Wollenburg, Kurt R; Bicanic, Tihana A; Castañeda, Elizabeth; Chang, Yun C; Chen, Jianghan; Cogliati, Massimo; Dromer, Françoise; Ellis, David; Filler, Scott G; Fisher, Matthew C; Harrison, Thomas S; Holland, Steven M; Kohno, Shigeru; Kronstad, James W; Lazera, Marcia; Levitz, Stuart M; Lionakis, Michail S; May, Robin C; Ngamskulrongroj, Popchai; Pappas, Peter G; Perfect, John R; Rickerts, Volker; Sorrell, Tania C; Walsh, Thomas J; Williamson, Peter R; Xu, Jianping; Zelazny, Adrian M; Casadevall, Arturo

2017-01-01

Cryptococcosis is a potentially lethal disease of humans/animals caused by Cryptococcus neoformans and Cryptococcus gattii . Distinction between the two species is based on phenotypic and genotypic characteristics. Recently, it was proposed that C. neoformans be divided into two species and C. gattii into five species based on a phylogenetic analysis of 115 isolates. While this proposal adds to the knowledge about the genetic diversity and population structure of cryptococcosis agents, the published genotypes of 2,606 strains have already revealed more genetic diversity than is encompassed by seven species. Naming every clade as a separate species at this juncture will lead to continuing nomenclatural instability. In the absence of biological differences between clades and no consensus about how DNA sequence alone can delineate a species, we recommend using " Cryptococcus neoformans species complex" and " C. gattii species complex" as a practical intermediate step, rather than creating more species. This strategy recognizes genetic diversity without creating confusion.

3D printing the pterygopalatine fossa: a negative space model of a complex structure.

PubMed

Bannon, Ross; Parihar, Shivani; Skarparis, Yiannis; Varsou, Ourania; Cezayirli, Enis

2018-02-01

The pterygopalatine fossa is one of the most complex anatomical regions to understand. It is poorly visualized in cadaveric dissection and most textbooks rely on schematic depictions. We describe our approach to creating a low-cost, 3D model of the pterygopalatine fossa, including its associated canals and foramina, using an affordable "desktop" 3D printer. We used open source software to create a volume render of the pterygopalatine fossa from axial slices of a head computerised tomography scan. These data were then exported to a 3D printer to produce an anatomically accurate model. The resulting 'negative space' model of the pterygopalatine fossa provides a useful and innovative aid for understanding the complex anatomical relationships of the pterygopalatine fossa. This model was designed primarily for medical students; however, it will also be of interest to postgraduates in ENT, ophthalmology, neurosurgery, and radiology. The technical process described may be replicated by other departments wishing to develop their own anatomical models whilst incurring minimal costs.

Zeolite-like liquid crystals

NASA Astrophysics Data System (ADS)

Poppe, Silvio; Lehmann, Anne; Scholte, Alexander; Prehm, Marko; Zeng, Xiangbing; Ungar, Goran; Tschierske, Carsten

2015-10-01

Zeolites represent inorganic solid-state materials with porous structures of fascinating complexity. Recently, significant progress was made by reticular synthesis of related organic solid-state materials, such as metal-organic or covalent organic frameworks. Herein we go a step further and report the first example of a fluid honeycomb mimicking a zeolitic framework. In this unique self-assembled liquid crystalline structure, transverse-lying π-conjugated rod-like molecules form pentagonal channels, encircling larger octagonal channels, a structural motif also found in some zeolites. Additional bundles of coaxial molecules penetrate the centres of the larger channels, unreachable by chains attached to the honeycomb framework. This creates a unique fluid hybrid structure combining positive and negative anisotropies, providing the potential for tuning the directionality of anisotropic optical, electrical and magnetic properties. This work also demonstrates a new approach to complex soft-matter self-assembly, by using frustration between space filling and the entropic penalty of chain extension.

Volumetric data analysis using Morse-Smale complexes

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

Natarajan, V; Pascucci, V

2005-10-13

The 3D Morse-Smale complex is a fundamental topological construct that partitions the domain of a real-valued function into regions having uniform gradient flow behavior. In this paper, we consider the construction and selective presentation of cells of the Morse-Smale complex and their use in the analysis and visualization of scientific datasets. We take advantage of the fact that cells of different dimension often characterize different types of features present in the data. For example, critical points pinpoint changes in topology by showing where components of the level sets are created, destroyed or modified in genus. Edges of the Morse-Smale complexmore » extract filament-like features that are not explicitly modeled in the original data. Interactive selection and rendering of portions of the Morse-Smale complex introduces fundamental data management challenges due to the unstructured nature of the complex even for structured inputs. We describe a data structure that stores the Morse-Smale complex and allows efficient selective traversal of regions of interest. Finally, we illustrate the practical use of this approach by applying it to cryo-electron microscopy data of protein molecules.« less

Free energy surface of the Michaelis complex of lactate dehydrogenase: a network analysis of microsecond simulations.

PubMed

Pan, Xiaoliang; Schwartz, Steven D

2015-04-30

It has long been recognized that the structure of a protein creates a hierarchy of conformations interconverting on multiple time scales. The conformational heterogeneity of the Michaelis complex is of particular interest in the context of enzymatic catalysis in which the reactant is usually represented by a single conformation of the enzyme/substrate complex. Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of two forms of the cofactor nicotinamide adenine dinucleotide (NADH and NAD(+)). Recent experimental results suggest that multiple substates exist within the Michaelis complex of LDH, and they show a strong variance in their propensity toward the on-enzyme chemical step. In this study, microsecond-scale all-atom molecular dynamics simulations were performed on LDH to explore the free energy landscape of the Michaelis complex, and network analysis was used to characterize the distribution of the conformations. Our results provide a detailed view of the kinetic network of the Michaelis complex and the structures of the substates at atomistic scales. They also shed light on the complete picture of the catalytic mechanism of LDH.

Photonics walking up a human hair

NASA Astrophysics Data System (ADS)

Zeng, Hao; Parmeggiani, Camilla; Martella, Daniele; Wasylczyk, Piotr; Burresi, Matteo; Wiersma, Diederik S.

2016-03-01

While animals have access to sugars as energy source, this option is generally not available to artificial machines and robots. Energy delivery is thus the bottleneck for creating independent robots and machines, especially on micro- and nano- meter length scales. We have found a way to produce polymeric nano-structures with local control over the molecular alignment, which allowed us to solve the above issue. By using a combination of polymers, of which part is optically sensitive, we can create complex functional structures with nanometer accuracy, responsive to light. In particular, this allowed us to realize a structure that can move autonomously over surfaces (it can "walk") using the environmental light as its energy source. The robot is only 60 μm in total length, thereby smaller than any known terrestrial walking species, and it is capable of random, directional walking and rotating on different dry surfaces.

Programming curvature using origami tessellations

NASA Astrophysics Data System (ADS)

Dudte, Levi H.; Vouga, Etienne; Tachi, Tomohiro; Mahadevan, L.

2016-05-01

Origami describes rules for creating folded structures from patterns on a flat sheet, but does not prescribe how patterns can be designed to fit target shapes. Here, starting from the simplest periodic origami pattern that yields one-degree-of-freedom collapsible structures--we show that scale-independent elementary geometric constructions and constrained optimization algorithms can be used to determine spatially modulated patterns that yield approximations to given surfaces of constant or varying curvature. Paper models confirm the feasibility of our calculations. We also assess the difficulty of realizing these geometric structures by quantifying the energetic barrier that separates the metastable flat and folded states. Moreover, we characterize the trade-off between the accuracy to which the pattern conforms to the target surface, and the effort associated with creating finer folds. Our approach enables the tailoring of origami patterns to drape complex surfaces independent of absolute scale, as well as the quantification of the energetic and material cost of doing so.

Magnetic Microhelix Coil Structures

NASA Astrophysics Data System (ADS)

Smith, Elliot J.; Makarov, Denys; Sanchez, Samuel; Fomin, Vladimir M.; Schmidt, Oliver G.

2011-08-01

Together with the well-known ferro- and antiferromagnetic ordering, nature has created a variety of complex helical magnetic configurations. Here, we design and investigate three-dimensional microhelix coil structures that are radial-, corkscrew-, and hollow-bar-magnetized. The magnetization configurations of the differently magnetized coils are experimentally revealed by probing their specific dynamic response to an external magnetic field. Helix coils offer an opportunity to realize microscale geometries of the magnetic toroidal moment, observed so far only in bulk multiferroic materials.

Practical Implementation of Semi-Automated As-Built Bim Creation for Complex Indoor Environments

NASA Astrophysics Data System (ADS)

Yoon, S.; Jung, J.; Heo, J.

2015-05-01

In recent days, for efficient management and operation of existing buildings, the importance of as-built BIM is emphasized in AEC/FM domain. However, fully automated as-built BIM creation is a tough issue since newly-constructed buildings are becoming more complex. To manage this problem, our research group has developed a semi-automated approach, focusing on productive 3D as-built BIM creation for complex indoor environments. In order to test its feasibility for a variety of complex indoor environments, we applied the developed approach to model the `Charlotte stairs' in Lotte World Mall, Korea. The approach includes 4 main phases: data acquisition, data pre-processing, geometric drawing, and as-built BIM creation. In the data acquisition phase, due to its complex structure, we moved the scanner location several times to obtain the entire point clouds of the test site. After which, data pre-processing phase entailing point-cloud registration, noise removal, and coordinate transformation was followed. The 3D geometric drawing was created using the RANSAC-based plane detection and boundary tracing methods. Finally, in order to create a semantically-rich BIM, the geometric drawing was imported into the commercial BIM software. The final as-built BIM confirmed that the feasibility of the proposed approach in the complex indoor environment.

Photonics and application of dipyrrinates in the optical devices

NASA Astrophysics Data System (ADS)

Aksenova, Iu; Bashkirtsev, D.; Prokopenko, A.; Kuznetsova, R.; Dudina, N.; Berezin, M.

2016-08-01

In this paper spectral-luminescent, lasing, photochemical, and sensory characteristics of a number of Zn(II) and B(III) coordination complexes with dipyrrinates with different structures are presented. We have discussed relations of the structure of investigated compounds and formed solvates with their optical characteristics. The results showed that alkyl substituted dipyrrinates derivatives have excellent luminescent characteristics and demonstrated effective lasing upon excitation of Nd:YAG-laser. They can be used as active media for liquid tunable lasers. Zinc and boron fluoride complexes of dipyrrinates with heavy atoms in structure don't have fluorescence but have long-lived emission due to increased nonradiative intersystem processes in the excited state by the mechanism of a heavy atom. For solid samples based on halogenated complexes was found dependency of the long-lived emission intensity of the oxygen concentration in gas flow. The presence of line segment indicates the possibility of the use of these complexes as a basis for creation of optical sensors for oxygen. Moreover, results of a study of halogen-substituted aza-complexes under irradiation are presented. Such complexes are promising for the creating media for generation of singlet oxygen (1O2), which is important for photodynamic therapy in medicine and photocatalytic reactions in the industry.

Composing Music with Complex Networks

NASA Astrophysics Data System (ADS)

Liu, Xiaofan; Tse, Chi K.; Small, Michael

In this paper we study the network structure in music and attempt to compose music artificially. Networks are constructed with nodes and edges corresponding to musical notes and their co-occurrences. We analyze sample compositions from Bach, Mozart, Chopin, as well as other types of music including Chinese pop music. We observe remarkably similar properties in all networks constructed from the selected compositions. Power-law exponents of degree distributions, mean degrees, clustering coefficients, mean geodesic distances, etc. are reported. With the network constructed, music can be created by using a biased random walk algorithm, which begins with a randomly chosen note and selects the subsequent notes according to a simple set of rules that compares the weights of the edges, weights of the nodes, and/or the degrees of nodes. The newly created music from complex networks will be played in the presentation.

[Tissue printing; the potential application of 3D printing in medicine].

PubMed

Visser, Jetze; Melchels, Ferry P W; Dhert, Wouter J A; Malda, Jos

2013-01-01

Complex structures based on a digital blueprint can be created using a 3D printer. As this blueprint can be created using patient imaging data, there are many potential patient-specific applications of 3D printing in medicine. Individually printed metal implants and synthetic devices are currently being used on a limited scale in clinical practice. Researchers in the field of regenerative medicine are now going a step further by printing a combination of cells, growth factors and biomaterials. This process is known as 'bioprinting'. It can be used to copy the complex organization of natural tissue required to repair or replace damaged tissues or organs. The technique needs to be optimized, however, and more knowledge is required regarding the development of printed living constructs into functional tissues before 'tissue from the printer' can be clinically applied.

NDE standards for high temperature materials

NASA Technical Reports Server (NTRS)

Vary, Alex

1991-01-01

High temperature materials include monolithic ceramics for automotive gas turbine engines and also metallic/intermetallic and ceramic matrix composites for a range of aerospace applications. These are materials that can withstand extreme operating temperatures that will prevail in advanced high-efficiency gas turbine engines. High temperature engine components are very likely to consist of complex composite structures with three-dimensionality interwoven and various intermixed ceramic fibers. The thermomechanical properties of components made of these materials are actually created in-place during processing and fabrication stages. The complex nature of these new materials creates strong incentives for exact standards for unambiguous evaluations of defects and microstructural characteristics. NDE techniques and standards that will ultimately be applicable to production and quality control of high temperature materials and structures are still emerging. The needs range from flaw detection to below 100 micron levels in monolithic ceramics to global imaging of fiber architecture and matrix densification anomalies in composites. The needs are different depending on the processing stage, fabrication method, and nature of the finished product. The standards are discussed that must be developed in concert with advances in NDE technology, materials processing research, and fabrication development. High temperature materials and structures that fail to meet stringent specifications and standards are unlikely to compete successfully either technologically or in international markets.

Learning predictive statistics from temporal sequences: Dynamics and strategies

PubMed Central

Wang, Rui; Shen, Yuan; Tino, Peter; Welchman, Andrew E.; Kourtzi, Zoe

2017-01-01

Human behavior is guided by our expectations about the future. Often, we make predictions by monitoring how event sequences unfold, even though such sequences may appear incomprehensible. Event structures in the natural environment typically vary in complexity, from simple repetition to complex probabilistic combinations. How do we learn these structures? Here we investigate the dynamics of structure learning by tracking human responses to temporal sequences that change in structure unbeknownst to the participants. Participants were asked to predict the upcoming item following a probabilistic sequence of symbols. Using a Markov process, we created a family of sequences, from simple frequency statistics (e.g., some symbols are more probable than others) to context-based statistics (e.g., symbol probability is contingent on preceding symbols). We demonstrate the dynamics with which individuals adapt to changes in the environment's statistics—that is, they extract the behaviorally relevant structures to make predictions about upcoming events. Further, we show that this structure learning relates to individual decision strategy; faster learning of complex structures relates to selection of the most probable outcome in a given context (maximizing) rather than matching of the exact sequence statistics. Our findings provide evidence for alternate routes to learning of behaviorally relevant statistics that facilitate our ability to predict future events in variable environments. PMID:28973111

Learning predictive statistics from temporal sequences: Dynamics and strategies.

PubMed

Wang, Rui; Shen, Yuan; Tino, Peter; Welchman, Andrew E; Kourtzi, Zoe

2017-10-01

Human behavior is guided by our expectations about the future. Often, we make predictions by monitoring how event sequences unfold, even though such sequences may appear incomprehensible. Event structures in the natural environment typically vary in complexity, from simple repetition to complex probabilistic combinations. How do we learn these structures? Here we investigate the dynamics of structure learning by tracking human responses to temporal sequences that change in structure unbeknownst to the participants. Participants were asked to predict the upcoming item following a probabilistic sequence of symbols. Using a Markov process, we created a family of sequences, from simple frequency statistics (e.g., some symbols are more probable than others) to context-based statistics (e.g., symbol probability is contingent on preceding symbols). We demonstrate the dynamics with which individuals adapt to changes in the environment's statistics-that is, they extract the behaviorally relevant structures to make predictions about upcoming events. Further, we show that this structure learning relates to individual decision strategy; faster learning of complex structures relates to selection of the most probable outcome in a given context (maximizing) rather than matching of the exact sequence statistics. Our findings provide evidence for alternate routes to learning of behaviorally relevant statistics that facilitate our ability to predict future events in variable environments.

Light activated nitric oxide releasing materials

NASA Astrophysics Data System (ADS)

Muizzi Casanas, Dayana Andreina

The ability to control the location and dosage of biologically active molecules inside the human body can be critical to maximizing effective treatment of cardiovascular diseases like angina. The current standard of treatment relies on the metabolism of organonitrate drugs into nitric oxide (NO), which are not specific, and also show problems with densitization with long-term use. There is a need then to create a treatment method that gives targeted release of NO. Metal-nitrosyl (M-NO) complexes can be used for delivery of NO since the release of NO can be controlled with light. However, the NO-releasing drug must be activated with red light to ensure maximum penetration of light through tissue. However, the release of NO from M-NO complexes with red-light activation is a significant challenge since the energy required to break the metal-NO bond is usually larger than the energy provided by red light. The goal of this project was to create red- sensitive, NO-releasing materials based on Ru-salen-nitrosyl compounds. Our approach was to first modify Ru salen complexes to sensitize the photochemistry for release of NO after red light irradiation. Next, we pursued polymerization of the Ru-salen complexes. We report the synthesis and quantitative photochemical characterization of a series of ruthenium salen nitrosyl complexes. These complexes were modified by incorporating electron donating groups in the salen ligand structure at key locations to increase electron density on the Ru. Complexes with either an --OH or --OCH3 substituent showed an improvement in the quantum yield of release of NO upon blue light irradiation compared to the unmodified salen. These --OH and --OCH3 complexes were also sensitized for NO release after red light activation, however the red-sensitive complexes were unstable and showed ligand substitution on the order of minutes. The substituted complexes remained sensitive for NO release, but only after blue light irradiation. The Ru-nitrosyl complexes could be regenerated by treatment of the complex with solutions of nitrite. Treatment of the exhaustively irradiated solutions with excess NO2- led to generation of a Ru-NO complex that was sensitive to blue light. Preliminary work on creating metallopolymers of Ru-salen-NO is also discussed.

Reaction-diffusion controlled growth of complex structures

NASA Astrophysics Data System (ADS)

Noorduin, Willem; Mahadevan, L.; Aizenberg, Joanna

2013-03-01

Understanding how the emergence of complex forms and shapes in biominerals came about is both of fundamental and practical interest. Although biomineralization processes and organization strategies to give higher order architectures have been studied extensively, synthetic approaches to mimic these self-assembled structures are highly complex and have been difficult to emulate, let alone replicate. The emergence of solution patterns has been found in reaction-diffusion systems such as Turing patterns and the BZ reaction. Intrigued by this spontaneous formation of complexity we explored if similar processes can lead to patterns in the solid state. We here identify a reaction-diffusion system in which the shape of the solidified products is a direct readout of the environmental conditions. Based on insights in the underlying mechanism, we developed a toolbox of engineering strategies to deterministically sculpt patterns and shapes, and combine different morphologies to create a landscape of hierarchical multi scale-complex tectonic architectures with unprecedented levels of complexity. These findings may hold profound implications for understanding, mimicking and ultimately expanding upon nature's morphogenesis strategies, allowing the synthesis of advanced highly complex microscale materials and devices. WLN acknowledges the Netherlands Organization for Scientific Research for financial support

Crystal structure of plant light-harvesting complex shows the active, energy-transmitting state

PubMed Central

Barros, Tiago; Royant, Antoine; Standfuss, Jörg; Dreuw, Andreas; Kühlbrandt, Werner

2009-01-01

Plants dissipate excess excitation energy as heat by non-photochemical quenching (NPQ). NPQ has been thought to resemble in vitro aggregation quenching of the major antenna complex, light harvesting complex of photosystem II (LHC-II). Both processes are widely believed to involve a conformational change that creates a quenching centre of two neighbouring pigments within the complex. Using recombinant LHC-II lacking the pigments implicated in quenching, we show that they have no particular role. Single crystals of LHC-II emit strong, orientation-dependent fluorescence with an emission maximum at 680 nm. The average lifetime of the main 680 nm crystal emission at 100 K is 1.31 ns, but only 0.39 ns for LHC-II aggregates under identical conditions. The strong emission and comparatively long fluorescence lifetimes of single LHC-II crystals indicate that the complex is unquenched, and that therefore the crystal structure shows the active, energy-transmitting state of LHC-II. We conclude that quenching of excitation energy in the light-harvesting antenna is due to the molecular interaction with external pigments in vitro or other pigment–protein complexes such as PsbS in vivo, and does not require a conformational change within the complex. PMID:19131972

The Challenges of Globalization: Changes in Education Policy and Practice in the Greek Context

ERIC Educational Resources Information Center

Vidali, Eva L.; Adams, Leah D.

2006-01-01

Globalization has been associated with rapid and significant changes in national and international politics and a growing complexity in economic and sociocultural realms. Inevitably, the new realities create pressures in social and economic structures that, in turn, shape changes at national levels. The field of education is drawn into these…

The fuelbed: a key element of the Fuel Characteristic Classification System.

Treesearch

Cynthia L. Riccardi; Roger D. Ottmar; David V. Sandberg; Anne Andreu; Ella Elman; Karen Kopper; Jennifer Long

2007-01-01

Wildland fuelbed characteristics are temporally and spatially complex and can vary widely across regions. To capture this variability, we designed the Fuel Characteristic Classification System (FCCS), a national system to create fuelbeds and classify those fuelbeds for their capacity to support fire and consume fuels. This paper describes the structure of the fuelbeds...

A Brief History of an Ethnographic Database: The HRAF Collection of Ethnography

ERIC Educational Resources Information Center

Roe, Sandra K.

2007-01-01

Since 1950, the Human Relations Area Files, Inc. has produced what is currently known as the eHRAF Collection of Ethnography. This article explores the reasons why it was created and describes the structure of this complex collection of ethnographic works. Over time, this resource has been produced in four different formats: paper slips,…

Teachers' Perceptions of the Learning Environment and Their Knowledge Base in a Training Program for Novice University Teachers

ERIC Educational Resources Information Center

Johannes, Christine; Fendler, Jan; Seidel, Tina

2013-01-01

Despite the complexity of teaching, learning to teach in universities is often "learning by doing". To provide novice university teachers with pedagogic teaching knowledge and to help them develop specific teaching objectives, we created a structured, video-based, one-year training program. In focusing on the core features of…

Theoretical thermal conductivity equation for uniform density wood cells

Treesearch

John F. Hunt; Hongmei Gu; Patricia Lebow

2008-01-01

The anisotropy of wood creates a complex problem requiring that analyses be based on fundamental material properties and characteristics of the wood structure to solve heat transfer problems. A two-dimensional finite element model that evaluates the effective thermal conductivity of a wood cell over the full range of moisture contents and porosities was previously...

Modeling a Neural Network as a Teaching Tool for the Learning of the Structure-Function Relationship

ERIC Educational Resources Information Center

Salinas, Dino G.; Acevedo, Cristian; Gomez, Christian R.

2010-01-01

The authors describe an activity they have created in which students can visualize a theoretical neural network whose states evolve according to a well-known simple law. This activity provided an uncomplicated approach to a paradigm commonly represented through complex mathematical formulation. From their observations, students learned many basic…

A Head in Virtual Reality: Development of A Dynamic Head and Neck Model

ERIC Educational Resources Information Center

Nguyen, Ngan; Wilson, Timothy D.

2009-01-01

Advances in computer and interface technologies have made it possible to create three-dimensional (3D) computerized models of anatomical structures for visualization, manipulation, and interaction in a virtual 3D environment. In the past few decades, a multitude of digital models have been developed to facilitate complex spatial learning of the…

Learning to see, seeing to learn: visual aspects of sensemaking

NASA Astrophysics Data System (ADS)

Russell, Daniel M.

2003-06-01

When one says "I see," what is usually meant is "I understand." But what does it mean to create a sense of understanding a large, complex, problem, one with many interlocking pieces, sometimes ill-fitting data and the occasional bit of contradictory information? The traditional computer science perspective on helping people towards understanding is to provide an armamentarium of tools and techniques - databases, query tools and a variety of graphing methods. As a field, we have an overly simple perspective on what it means to grapple with real information. In practice, people who try to make sense of some thing (say, the life sciences, the Middle East, the large scale structure of the universe, their taxes) are faced with a complex collection of information, some in easy-to-digest structured forms, but with many relevant parts scattered hither and yon, in forms and shapes too difficult to manage. To create an understanding, we find that people create representations of complex information. Yet using representations relies on fairly sophisticated perceptual practices. These practices are in no way preordained, but subject to the kinds of perceptual and cognitive phenomena we see in every day life. In order to understand our information environments, we need to learn to perceive these perceptual elements, and understand when they do, and do not, work to our advantage. A more powerful approach to the problem of supporting realistic sensemaking practice is to design information environments that accommodate both the world"s information realities and people"s cognitive characteristics. This paper argues that visual aspects of representation use often dominate sensemaking behavior, and illustrates this by showing three sensemaking tools we have built that take advantage of this property.

A topological hierarchy for functions on triangulated surfaces.

PubMed

Bremer, Peer-Timo; Edelsbrunner, Herbert; Hamann, Bernd; Pascucci, Valerio

2004-01-01

We combine topological and geometric methods to construct a multiresolution representation for a function over a two-dimensional domain. In a preprocessing stage, we create the Morse-Smale complex of the function and progressively simplify its topology by cancelling pairs of critical points. Based on a simple notion of dependency among these cancellations, we construct a hierarchical data structure supporting traversal and reconstruction operations similarly to traditional geometry-based representations. We use this data structure to extract topologically valid approximations that satisfy error bounds provided at runtime.

Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community

PubMed Central

Cormier, Catherine Y.; Mohr, Stephanie E.; Zuo, Dongmei; Hu, Yanhui; Rolfs, Andreas; Kramer, Jason; Taycher, Elena; Kelley, Fontina; Fiacco, Michael; Turnbull, Greggory; LaBaer, Joshua

2010-01-01

The Protein Structure Initiative Material Repository (PSI-MR; http://psimr.asu.edu) provides centralized storage and distribution for the protein expression plasmids created by PSI researchers. These plasmids are a resource that allows the research community to dissect the biological function of proteins whose structures have been identified by the PSI. The plasmid annotation, which includes the full length sequence, vector information and associated publications, is stored in a freely available, searchable database called DNASU (http://dnasu.asu.edu). Each PSI plasmid is also linked to a variety of additional resources, which facilitates cross-referencing of a particular plasmid to protein annotations and experimental data. Plasmid samples can be requested directly through the website. We have also developed a novel strategy to avoid the most common concern encountered when distributing plasmids namely, the complexity of material transfer agreement (MTA) processing and the resulting delays this causes. The Expedited Process MTA, in which we created a network of institutions that agree to the terms of transfer in advance of a material request, eliminates these delays. Our hope is that by creating a repository of expression-ready plasmids and expediting the process for receiving these plasmids, we will help accelerate the accessibility and pace of scientific discovery. PMID:19906724

a Chiral Tag Study of the Absolute Configuration of Camphor

NASA Astrophysics Data System (ADS)

Pratt, David; Evangelisti, Luca; Smart, Taylor; Holdren, Martin S.; Mayer, Kevin J.; West, Channing; Pate, Brooks

2017-06-01

The chiral tagging method for rotational spectroscopy uses an established approach in chiral analysis of creating a complex with an enantiopure tag so that enantiomers of the molecule of interest are converted to diastereomer complexes. Since the diastereomers have distinct structure, they give distinguishable rotational spectra. Camphor was chosen as an example for the chiral tag method because it has spectral properties that could pose challenges to the use of three wave mixing rotational spectroscopy to establish absolute configuration. Specifically, one of the dipole moment components of camphor is small making three wave mixing measurements challenging and placing high accuracy requirements on computational chemistry for calculating the dipole moment direction in the principal axis system. The chiral tag measurements of camphor used the hydrogen bond donor 3-butyn-2-ol. Quantum chemistry calculations using the B3LYP-D3BJ method and the def2TZVP basis set identified 7 low energy isomers of the chiral complex. The two lowest energy complexes of the homochiral and heterochiral complexes are observed in a measurement using racemic tag. Absolute configuration is confirmed by the use of an enantiopure tag sample. Spectra with ^{13}C-sensitivity were acquired so that the carbon substitution structure of the complex could be obtained to provide a structure of camphor with correct stereochemistry. The chiral tag complex spectra can also be used to estimate the enantiomeric excess of the sample and analysis of the broadband spectrum indicates that the sample enantiopurity is higher than 99.5%. The structure of the complex is analyzed to determine the extent of geometry modification that occurs upon formation of the complex. These results show that initial isomer searches with fixed geometries will be accurate. The reduction in computation time from fixed geometry assumptions will be discussed.

Programs for transferring data between a relational data base and a finite element structural analysis program

NASA Technical Reports Server (NTRS)

Johnson, S. C.

1982-01-01

An interface system for passing data between a relational information management (RIM) data base complex and engineering analysis language (EAL), a finite element structural analysis program is documented. The interface system, implemented on a CDC Cyber computer, is composed of two FORTRAN programs called RIM2EAL and EAL2RIM. The RIM2EAL reads model definition data from RIM and creates a file of EAL commands to define the model. The EAL2RIM reads model definition and EAL generated analysis data from EAL's data library and stores these data dirctly in a RIM data base. These two interface programs and the format for the RIM data complex are described.

Towards a standard licensing scheme for the access and use of satellite earth observation data for disaster management

NASA Astrophysics Data System (ADS)

Clark, Nathan E.

2017-10-01

This paper explores from the view of the data recipient and user the complexities of creating a common licensing scheme for the access and use of satellite earth observation (EO) data in international disaster management (DM) activities. EO data contributions in major disaster events often involve numerous data providers with separate licensing mechanisms for controlling the access, uses, and distribution of data by the end users. A lack of standardization among the terminology, wording, and conditions within these licenses creates a complex legal environment for users, and often prevents them from using, sharing and combining datasets in an effective and timely manner. It also creates uncertainty among data providers as to the types of licensing controls that should be applied in disaster scenarios. This paper builds from an ongoing comparative analysis of the common and conflicting conditions among data licenses that must be addressed in order to facilitate easier access and use of EO data within the DM sector and offers recommendations towards the alignment of the structural and technical aspects of licenses among data providers.

Dynamics of plasma−dust structures formed in a trap created in the narrowing of a current channel in a magnetic field

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

Dzlieva, E. S., E-mail: plasmadust@yandex.ru; Karasev, V. Yu., E-mail: v.karasev@spbu.ru; Pavlov, S. I.

The geometry and dynamics of plasma−dust structures in a longitudinal magnetic field is studied experimentally. The structures are formed in a glow-discharge trap created in the double electric layer produced as a result of discharge narrowing by means of a dielectric insert introduced in the discharge tube. Studies of structures formed in the new type of glow-discharge trap are of interest from the standpoint of future experiments with complex plasmas in superstrong magnetic fields in which the dust component is magnetized. Different types of dielectric inserts were used: conical and plane ones with symmetric and asymmetric apertures. Conditions for themore » existence of stable dust structures are determined for dust grains of different density and different dispersity. According to the experimental results, the angular velocity of dust rotation is ≥10 s{sup –1}, which is the fastest type of dust motion for all types of discharges in a magnetic field. The rotation is interpreted by analyzing the dynamics of individual dust grains.« less

Change in Cardiopulmonary Arrest Response in an Anesthesiology Residency: A practice-based learning initiative.

PubMed

Takla, Amgad; Dorotta, Ihab; Staszak, John; Tetzlaff, John E

2007-01-01

Because of increases in the acuity in our patient population, increasing complexity of the care provided and the structure of our residency, we decided to systematically alter our participation in the hospital-wide cardiac arrest system. The need to provide optimum service in an increasingly complex clinical care system was the motivation for change. With substantive input from trainees and practitioners, we created a multi-tier-system of response along with predefined criteria for the anesthesiology response. We report the result of our practice based learning initiative.

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

PubMed Central

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

2016-01-01

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

Engineering complex tissues.

PubMed

Atala, Anthony; Kasper, F Kurtis; Mikos, Antonios G

2012-11-14

Tissue engineering has emerged at the intersection of numerous disciplines to meet a global clinical need for technologies to promote the regeneration of functional living tissues and organs. The complexity of many tissues and organs, coupled with confounding factors that may be associated with the injury or disease underlying the need for repair, is a challenge to traditional engineering approaches. Biomaterials, cells, and other factors are needed to design these constructs, but not all tissues are created equal. Flat tissues (skin); tubular structures (urethra); hollow, nontubular, viscus organs (vagina); and complex solid organs (liver) all present unique challenges in tissue engineering. This review highlights advances in tissue engineering technologies to enable regeneration of complex tissues and organs and to discuss how such innovative, engineered tissues can affect the clinic.

Gigadalton-scale shape-programmable DNA assemblies

NASA Astrophysics Data System (ADS)

Wagenbauer, Klaus F.; Sigl, Christian; Dietz, Hendrik

2017-12-01

Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging. Here we show that natural assembly principles can be combined with the methods of DNA origami to produce gigadalton-scale structures with controlled sizes. DNA sequence information is used to encode the shapes of individual DNA origami building blocks, and the geometry and details of the interactions between these building blocks then control their copy numbers, positions and orientations within higher-order assemblies. We illustrate this strategy by creating planar rings of up to 350 nanometres in diameter and with atomic masses of up to 330 megadaltons, micrometre-long, thick tubes commensurate in size to some bacilli, and three-dimensional polyhedral assemblies with sizes of up to 1.2 gigadaltons and 450 nanometres in diameter. We achieve efficient assembly, with yields of up to 90 per cent, by using building blocks with validated structure and sufficient rigidity, and an accurate design with interaction motifs that ensure that hierarchical assembly is self-limiting and able to proceed in equilibrium to allow for error correction. We expect that our method, which enables the self-assembly of structures with sizes approaching that of viruses and cellular organelles, can readily be used to create a range of other complex structures with well defined sizes, by exploiting the modularity and high degree of addressability of the DNA origami building blocks used.

Gigadalton-scale shape-programmable DNA assemblies.

PubMed

Wagenbauer, Klaus F; Sigl, Christian; Dietz, Hendrik

2017-12-06

Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging. Here we show that natural assembly principles can be combined with the methods of DNA origami to produce gigadalton-scale structures with controlled sizes. DNA sequence information is used to encode the shapes of individual DNA origami building blocks, and the geometry and details of the interactions between these building blocks then control their copy numbers, positions and orientations within higher-order assemblies. We illustrate this strategy by creating planar rings of up to 350 nanometres in diameter and with atomic masses of up to 330 megadaltons, micrometre-long, thick tubes commensurate in size to some bacilli, and three-dimensional polyhedral assemblies with sizes of up to 1.2 gigadaltons and 450 nanometres in diameter. We achieve efficient assembly, with yields of up to 90 per cent, by using building blocks with validated structure and sufficient rigidity, and an accurate design with interaction motifs that ensure that hierarchical assembly is self-limiting and able to proceed in equilibrium to allow for error correction. We expect that our method, which enables the self-assembly of structures with sizes approaching that of viruses and cellular organelles, can readily be used to create a range of other complex structures with well defined sizes, by exploiting the modularity and high degree of addressability of the DNA origami building blocks used.

STEM-EELS analysis of multipole surface plasmon modes in symmetry-broken AuAg nanowire dimers

NASA Astrophysics Data System (ADS)

Schubert, Ina; Sigle, Wilfried; van Aken, Peter A.; Trautmann, Christina; Toimil-Molares, Maria Eugenia

2015-03-01

Surface plasmon coupling in nanowires separated by small gaps generates high field enhancements at the position of the gap and is thus of great interest for sensing applications. It is known that the nanowire dimensions and in particular the symmetry of the structures has strong influence on the plasmonic properties of the dimer structure. Here, we report on multipole surface plasmon coupling in symmetry-broken AuAg nanowire dimers. Our dimers, consisting of two nanowires with different lengths and separated by gaps of only 10 to 30 nm, were synthesized by pulsed electrochemical deposition in ion track-etched polymer templates. Electron energy-loss spectroscopy in scanning transmission electron microscopy allows us to resolve up to nine multipole order surface plasmon modes of these dimers spectrally separated from each other. The spectra evidence plasmon coupling between resonances of different multipole order, resulting in the generation of additional plasmonic modes. Since such complex structures require elaborated synthesis techniques, dimer structures with complex composition, morphology and shape are created. We demonstrate that finite element simulations on pure Au dimers can predict the generated resonances in the fabricated structures. The excellent agreement of our experiment on AuAg dimers with finite integration simulations using CST microwave studio manifests great potential to design complex structures for sensing applications.

Mapping healthcare systems: a policy relevant analytic tool

PubMed Central

Sekhri Feachem, Neelam; Afshar, Ariana; Pruett, Cristina; Avanceña, Anton L.V.

2017-01-01

Abstract Background In the past decade, an international consensus on the value of well-functioning systems has driven considerable health systems research. This research falls into two broad categories. The first provides conceptual frameworks that take complex healthcare systems and create simplified constructs of interactions and functions. The second focuses on granular inputs and outputs. This paper presents a novel translational mapping tool – the University of California, San Francisco mapping tool (the Tool) - which bridges the gap between these two areas of research, creating a platform for multi-country comparative analysis. Methods Using the Murray-Frenk framework, we create a macro-level representation of a country's structure, focusing on how it finances and delivers healthcare. The map visually depicts the fundamental policy questions in healthcare system design: funding sources and amount spent through each source, purchasers, populations covered, provider categories; and the relationship between these entities. Results We use the Tool to provide a macro-level comparative analysis of the structure of India's and Thailand's healthcare systems. Conclusions As part of the systems strengthening arsenal, the Tool can stimulate debate about the merits and consequences of different healthcare systems structural designs, using a common framework that fosters multi-country comparative analyses. PMID:28541518

Hierarchically nested river landform sequences

NASA Astrophysics Data System (ADS)

Pasternack, G. B.; Weber, M. D.; Brown, R. A.; Baig, D.

2017-12-01

River corridors exhibit landforms nested within landforms repeatedly down spatial scales. In this study we developed, tested, and implemented a new way to create river classifications by mapping domains of fluvial processes with respect to the hierarchical organization of topographic complexity that drives fluvial dynamism. We tested this approach on flow convergence routing, a morphodynamic mechanism with different states depending on the structure of nondimensional topographic variability. Five nondimensional landform types with unique functionality (nozzle, wide bar, normal channel, constricted pool, and oversized) represent this process at any flow. When this typology is nested at base flow, bankfull, and floodprone scales it creates a system with up to 125 functional types. This shows how a single mechanism produces complex dynamism via nesting. Given the classification, we answered nine specific scientific questions to investigate the abundance, sequencing, and hierarchical nesting of these new landform types using a 35-km gravel/cobble river segment of the Yuba River in California. The nested structure of flow convergence routing landforms found in this study revealed that bankfull landforms are nested within specific floodprone valley landform types, and these types control bankfull morphodynamics during moderate to large floods. As a result, this study calls into question the prevailing theory that the bankfull channel of a gravel/cobble river is controlled by in-channel, bankfull, and/or small flood flows. Such flows are too small to initiate widespread sediment transport in a gravel/cobble river with topographic complexity.

Hybrid experimental/analytical models of structural dynamics - Creation and use for predictions

NASA Technical Reports Server (NTRS)

Balmes, Etienne

1993-01-01

An original complete methodology for the construction of predictive models of damped structural vibrations is introduced. A consistent definition of normal and complex modes is given which leads to an original method to accurately identify non-proportionally damped normal mode models. A new method to create predictive hybrid experimental/analytical models of damped structures is introduced, and the ability of hybrid models to predict the response to system configuration changes is discussed. Finally a critical review of the overall methodology is made by application to the case of the MIT/SERC interferometer testbed.

Neural networks for structural design - An integrated system implementation

NASA Technical Reports Server (NTRS)

Berke, Laszlo; Hafez, Wassim; Pao, Yoh-Han

1992-01-01

The development of powerful automated procedures to aid the creative designer is becoming increasingly critical for complex design tasks. In the work described here Artificial Neural Nets are applied to acquire structural analysis and optimization domain expertise. Based on initial instructions from the user an automated procedure generates random instances of structural analysis and/or optimization 'experiences' that cover a desired domain. It extracts training patterns from the created instances, constructs and trains an appropriate network architecture and checks the accuracy of net predictions. The final product is a trained neural net that can estimate analysis and/or optimization results instantaneously.

Structural characterization of O- and C-glycosylating variants of the landomycin glycosyltransferase LanGT2.

PubMed

Tam, Heng Keat; Härle, Johannes; Gerhardt, Stefan; Rohr, Jürgen; Wang, Guojun; Thorson, Jon S; Bigot, Aurélien; Lutterbeck, Monika; Seiche, Wolfgang; Breit, Bernhard; Bechthold, Andreas; Einsle, Oliver

2015-02-23

The structures of the O-glycosyltransferase LanGT2 and the engineered, C-C bond-forming variant LanGT2S8Ac show how the replacement of a single loop can change the functionality of the enzyme. Crystal structures of the enzymes in complex with a nonhydrolyzable nucleotide-sugar analogue revealed that there is a conformational transition to create the binding sites for the aglycon substrate. This induced-fit transition was explored by molecular docking experiments with various aglycon substrates. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stoichiometry control of complex oxides by sequential pulsed-laser deposition from binary-oxide targets

DOE PAGES

Herklotz, A.; Dörr, Kathrin; Ward, T. Z.; ...

2015-04-03

In this paper, to have precise atomic layer control over interfaces, we examine the growth of complex oxides through the sequential deposition from binary targets by pulsed laser deposition. In situ reflection high-energy electron diffraction (RHEED) is used to control the growth and achieve films with excellent structural quality. The growth from binary oxide targets is fundamentally different from single target growth modes and shows more similarities to shuttered growth by molecular beam epitaxy. The RHEED intensity oscillations of non-stoichiometric growth are consistent with a model of island growth and accumulation of excess material on the surface that can bemore » utilized to determine the correct stoichiometry for growth. Correct monolayer doses can be determined through an envelope frequency in the RHEED intensity oscillations. In order to demonstrate the ability of this growth technique to create complex heterostructures, the artificial n = 2 and 3 Sr n +1Ti n O 3 n +1 Ruddlesden-Popper phases are grown with good long-range order. Finally, this method enables the precise unit-cell level control over the structure of perovskite-type oxides, and thus the growth of complex materials with improved structural quality and electronic functionality.« less

Stoichiometry control of complex oxides by sequential pulsed-laser deposition from binary-oxide targets

DOE PAGES

Herklotz, Andreas; Dorr, Kathrin; Ward, Thomas Zac; ...

2015-04-03

To have precise atomic layer control over interfaces, we examine the growth of complex oxides through the sequential deposition from binary targets by pulsed laser deposition. In situ reflection high-energy electron diffraction (RHEED) is used to control the growth and achieve films with excellent structural quality. The growth from binary oxide targets is fundamentally different from single target growth modes and shows more similarities to shuttered growth by molecular beam epitaxy. The RHEED intensity oscillations of non-stoichiometric growth are consistent with a model of island growth and accumulation of excess material on the surface that can be utilized to determinemore » the correct stoichiometry for growth. Correct monolayer doses can be determined through an envelope frequency in the RHEED intensity oscillations. In order to demonstrate the ability of this growth technique to create complex heterostructures, the artificial n = 2 and 3 Sr n+1Ti nO 3 n+1 Ruddlesden-Popper phases are grown with good long-range order. Furthermore, this method enables the precise unit-cell level control over the structure of perovskite-type oxides, and thus the growth of complex materials with improved structural quality and electronic functionality.« less

Electron microscopy and in vitro deneddylation reveal similar architectures and biochemistry of isolated human and Flag-mouse COP9 signalosome complexes

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

Rockel, Beate; Schmaler, Tilo; Huang, Xiaohua

2014-07-25

Highlights: • Deneddylation rates of human erythrocyte and mouse fibroblast CSN are very similar. • 3D models of native human and mouse CSN reveal common architectures. • The cryo-structure of native mammalian CSN shows a horseshoe subunit arrangement. - Abstract: The COP9 signalosome (CSN) is a regulator of the ubiquitin (Ub) proteasome system (UPS). In the UPS, proteins are Ub-labeled for degradation by Ub ligases conferring substrate specificity. The CSN controls a large family of Ub ligases called cullin-RING ligases (CRLs), which ubiquitinate cell cycle regulators, transcription factors and DNA damage response proteins. The CSN possesses structural similarities with themore » 26S proteasome Lid complex and the translation initiation complex 3 (eIF3) indicating similar ancestry and function. Initial structures were obtained 14 years ago by 2D electron microscopy (EM). Recently, first 3D molecular models of the CSN were created on the basis of negative-stain EM and single-particle analysis, mostly with recombinant complexes. Here, we compare deneddylating activity and structural features of CSN complexes purified in an elaborate procedure from human erythrocytes and efficiently pulled down from mouse Flag-CSN2 B8 fibroblasts. In an in vitro deneddylation assay both the human and the mouse CSN complexes deneddylated Nedd8-Cul1 with comparable rates. 3D structural models of the erythrocyte CSN as well as of the mouse Flag-CSN were generated by negative stain EM and by cryo-EM. Both complexes show a central U-shaped segment from which several arms emanate. This structure, called the horseshoe, is formed by the PCI domain subunits. CSN5 and CSN6 point away from the horseshoe. Compared to 3D models of negatively stained CSN complexes, densities assigned to CSN2 and CSN4 are better defined in the cryo-map. Because biochemical and structural results obtained with CSN complexes isolated from human erythrocytes and purified by Flag-CSN pulldown from mouse B8 fibroblasts are very similar, Flag-CSN pulldowns are a proper alternative to CSN preparation from erythrocytes.« less

Knowledge Discovery in Spectral Data by Means of Complex Networks

PubMed Central

Zanin, Massimiliano; Papo, David; Solís, José Luis González; Espinosa, Juan Carlos Martínez; Frausto-Reyes, Claudio; Anda, Pascual Palomares; Sevilla-Escoboza, Ricardo; Boccaletti, Stefano; Menasalvas, Ernestina; Sousa, Pedro

2013-01-01

In the last decade, complex networks have widely been applied to the study of many natural and man-made systems, and to the extraction of meaningful information from the interaction structures created by genes and proteins. Nevertheless, less attention has been devoted to metabonomics, due to the lack of a natural network representation of spectral data. Here we define a technique for reconstructing networks from spectral data sets, where nodes represent spectral bins, and pairs of them are connected when their intensities follow a pattern associated with a disease. The structural analysis of the resulting network can then be used to feed standard data-mining algorithms, for instance for the classification of new (unlabeled) subjects. Furthermore, we show how the structure of the network is resilient to the presence of external additive noise, and how it can be used to extract relevant knowledge about the development of the disease. PMID:24957895

Knowledge discovery in spectral data by means of complex networks.

PubMed

Zanin, Massimiliano; Papo, David; Solís, José Luis González; Espinosa, Juan Carlos Martínez; Frausto-Reyes, Claudio; Anda, Pascual Palomares; Sevilla-Escoboza, Ricardo; Jaimes-Reategui, Rider; Boccaletti, Stefano; Menasalvas, Ernestina; Sousa, Pedro

2013-03-11

In the last decade, complex networks have widely been applied to the study of many natural and man-made systems, and to the extraction of meaningful information from the interaction structures created by genes and proteins. Nevertheless, less attention has been devoted to metabonomics, due to the lack of a natural network representation of spectral data. Here we define a technique for reconstructing networks from spectral data sets, where nodes represent spectral bins, and pairs of them are connected when their intensities follow a pattern associated with a disease. The structural analysis of the resulting network can then be used to feed standard data-mining algorithms, for instance for the classification of new (unlabeled) subjects. Furthermore, we show how the structure of the network is resilient to the presence of external additive noise, and how it can be used to extract relevant knowledge about the development of the disease.

Active vibration suppression of helicopter horizontal stabilizers

NASA Astrophysics Data System (ADS)

Cinquemani, Simone; Cazzulani, Gabriele; Resta, Ferruccio

2017-04-01

Helicopters are among the most complex machines ever made. While ensuring high performance from the aeronautical point of view, they are not very comfortable due to vibration mainly created by the main rotor and by the interaction with the surrounding air. One of the most solicited structural elements of the vehicle are the horizontal stabilizers. These elements are particularly stressed because of their composite structure which, while guaranteeing lightness and strength, is characterized by a low damping. This work makes a preliminary analysis on the dynamics of the structure and proposes different solutions to actively suppress vibrations. Among them, the best in terms of the relationship between performance and weight / complexity of the system is that based on inertial actuators mounted on the inside of the horizontal stabilizers. The work addresses the issue of the design of the device and its use in the stabilizer from both the numerical and the experimental points of view.

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system.

PubMed

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database in which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. This database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.

Developmental Evaluation Framework for Innovation and Learning Networks: Integration of the Structure, Process and Outcomes

ERIC Educational Resources Information Center

Ramstad, Elise

2009-01-01

Purpose: During the past decade new types of broader networks that aim to achieve widespread effects in the working life have emerged. These are typically based on an interactive innovation approach, where knowledge is created jointly together with diverse players. At the moment, the challenge is how to evaluate these complex networks and learning…

Finite element analyses of two dimensional, anisotropic heat transfer in wood

Treesearch

John F. Hunt; Hongmei Gu

2004-01-01

The anisotropy of wood creates a complex problem for solving heat and mass transfer problems that require analyses be based on fundamental material properties of the wood structure. Inputting basic orthogonal properties of the wood material alone are not sufficient for accurate modeling because wood is a combination of porous fiber cells that are aligned and mis-...

Living Tomorrow... An Inquiry into the Preparation of Young People for Working Life in Europe. 3rd Edition.

ERIC Educational Resources Information Center

Deforge, Ives

Technological advances have created changes in working life. Automation displaces more workers than the service industry can absorb. The jobs that are left are often downgraded from the complexity they have formerly enjoyed. As society becomes more and more automated, unemployment becomes structural. How do we prepare young people for the jobs of…

Metal-directed design of supramolecular protein assemblies

PubMed Central

Bailey, Jake B.; Subramanian, Rohit H.; Churchfield, Lewis A.

2016-01-01

Owing to their central roles in cellular signaling, construction, and biochemistry, protein-protein interactions (PPIs) and protein self-assembly have become a major focus of molecular design and synthetic biology. In order to circumvent the complexity of constructing extensive non-covalent interfaces, which are typically involved in natural PPIs and protein self-assembly, we have developed two design strategies, Metal-Directed Protein Self-Assembly (MDPSA) and Metal-Templated Interface Redesign (MeTIR). These strategies, inspired by both the proposed evolutionary roles of metals and their prevalence in natural PPIs, take advantage of the favorable properties of metal coordination (bonding strength, directionality, and reversibility) to guide protein self-assembly with minimal design and engineering. Using a small, monomeric protein (cytochrome cb562) as a model building block, we employed MDPSA and MeTIR to create a diverse array of functional supramolecular architectures which range from structurally tunable oligomers to metalloprotein complexes that can properly self-assemble in living cells into novel metalloenzymes. The design principles and strategies outlined herein should be readily applicable to other protein systems with the goal of creating new PPIs and protein assemblies with structures and functions not yet produced by natural evolution. PMID:27586336

Three-dimensional printed ultrasound and photoacoustic training phantoms for vasculature access (Conference Presentation)

NASA Astrophysics Data System (ADS)

Nikitichev, Daniil I.; Xia, Wenfeng; West, Simeon J.; Desjardins, Adrien E.; Ourselin, Sebastien; Vercauteren, Tom

2017-03-01

Ultrasound (US) imaging is widely used to guide vascular access procedures such as arterial and venous cannulation. As needle visualisation with US imaging can be very challenging, it is easy to misplace the needle in the patient and it can be life threating. Photoacoustic (PA) imaging is well suited to image medical needles and catheters that are commonly used for vascular access. To improve the success rate, a certain level of proficiency is required that can be gained through extensive practice on phantoms. Unfortunately, commercial training phantoms are expensive and custom-made phantoms usually do not replicate the anatomy very well. Thus, there is a great demand for more realistic and affordable ultrasound and photoacoustic imaging phantoms for vasculature access procedures training. Three-dimensional (3D) printing can help create models that replicate complex anatomical geometries. However, the available 3D printed materials do not possess realistic tissue properties. Alternatively, tissue-mimicking materials can be employed using casting and 3D printed moulds but this approach is limited to the creation of realistic outer shapes with no replication of complex internal structures. In this study, we developed a realistic vasculature access phantom using a combination of mineral oil based materials as background tissue and a non-toxic, water dissolvable filament material to create complex vascular structure using 3D printing. US and PA images of the phantoms comprising the complex vasculature network were acquired. The results show that 3D printing can facilitate the fabrication of anatomically realistic training phantoms, with designs that can be customized and shared electronically.

Ordered patterns and structures via interfacial self-assembly: superlattices, honeycomb structures and coffee rings.

PubMed

Ma, Hongmin; Hao, Jingcheng

2011-11-01

Self-assembly is now being intensively studied in chemistry, physics, biology, and materials engineering and has become an important "bottom-up" approach to create intriguing structures for different applications. Self-assembly is not only a practical approach for creating a variety of nanostructures, but also shows great superiority in building hierarchical structures with orders on different length scales. The early work in self-assembly focused on molecular self-assembly in bulk solution, including the resultant dye aggregates, liposomes, vesicles, liquid crystals, gels and so on. Interfacial self-assembly has been a great concern over the last two decades, largely because of the unique and ingenious roles of this method for constructing materials at interfaces, such as self-assembled monolayers, Langmuir-Blodgett films, and capsules. Nanocrystal superlattices, honeycomb films and coffee rings are intriguing structural materials with more complex features and can be prepared by interfacial self-assembly on different length scales. In this critical review, we outline the recent development in the preparation and application of colloidal nanocrystal superlattices, honeycomb-patterned macroporous structures by the breath figure method, and coffee-ring-like patterns (247 references). This journal is © The Royal Society of Chemistry 2011

Programmable DNA tile self-assembly using a hierarchical sub-tile strategy.

PubMed

Shi, Xiaolong; Lu, Wei; Wang, Zhiyu; Pan, Linqiang; Cui, Guangzhao; Xu, Jin; LaBean, Thomas H

2014-02-21

DNA tile based self-assembly provides a bottom-up approach to construct desired nanostructures. DNA tiles have been directly constructed from ssDNA and readily self-assembled into 2D lattices and 3D superstructures. However, for more complex lattice designs including algorithmic assemblies requiring larger tile sets, a more modular approach could prove useful. This paper reports a new DNA 'sub-tile' strategy to easily create whole families of programmable tiles. Here, we demonstrate the stability and flexibility of our sub-tile structures by constructing 3-, 4- and 6-arm DNA tiles that are subsequently assembled into 2D lattices and 3D nanotubes according to a hierarchical design. Assembly of sub-tiles, tiles, and superstructures was analyzed using polyacrylamide gel electrophoresis and atomic force microscopy. DNA tile self-assembly methods provide a bottom-up approach to create desired nanostructures; the sub-tile strategy adds a useful new layer to this technique. Complex units can be made from simple parts. The sub-tile approach enables the rapid redesign and prototyping of complex DNA tile sets and tiles with asymmetric designs.

Can misfolded proteins be beneficial? The HAMLET case.

PubMed

Pettersson-Kastberg, Jenny; Aits, Sonja; Gustafsson, Lotta; Mossberg, Anki; Storm, Petter; Trulsson, Maria; Persson, Filip; Mok, K Hun; Svanborg, Catharina

2009-01-01

By changing the three-dimensional structure, a protein can attain new functions, distinct from those of the native protein. Amyloid-forming proteins are one example, in which conformational change may lead to fibril formation and, in many cases, neurodegenerative disease. We have proposed that partial unfolding provides a mechanism to generate new and useful functional variants from a given polypeptide chain. Here we present HAMLET (Human Alpha-lactalbumin Made LEthal to Tumor cells) as an example where partial unfolding and the incorporation of cofactor create a complex with new, beneficial properties. Native alpha-lactalbumin functions as a substrate specifier in lactose synthesis, but when partially unfolded the protein binds oleic acid and forms the tumoricidal HAMLET complex. When the properties of HAMLET were first described they were surprising, as protein folding intermediates and especially amyloid-forming protein intermediates had been regarded as toxic conformations, but since then structural studies have supported functional diversity arising from a change in fold. The properties of HAMLET suggest a mechanism of structure-function variation, which might help the limited number of human protein genes to generate sufficient structural diversity to meet the diverse functional demands of complex organisms.

Natural Product Screening Reveals Naphthoquinone Complex I Bypass Factors

PubMed Central

Mevers, Emily; Higgins, Kathleen W.; Fomina, Yevgenia; Zhang, Jianming; Mandinova, Anna; Newman, David; Shaw, Stanley Y.; Clardy, Jon; Mootha, Vamsi K.

2016-01-01

Deficiency of mitochondrial complex I is encountered in both rare and common diseases, but we have limited therapeutic options to treat this lesion to the oxidative phosphorylation system (OXPHOS). Idebenone and menadione are redox-active molecules capable of rescuing OXPHOS activity by engaging complex I-independent pathways of entry, often referred to as “complex I bypass.” In the present study, we created a cellular model of complex I deficiency by using CRISPR genome editing to knock out Ndufa9 in mouse myoblasts, and utilized this cell line to develop a high-throughput screening platform for novel complex I bypass factors. We screened a library of ~40,000 natural product extracts and performed bioassay-guided fractionation on a subset of the top scoring hits. We isolated four plant-derived 1,4-naphthoquinone complex I bypass factors with structural similarity to menadione: chimaphilin and 3-chloro-chimaphilin from Chimaphila umbellata and dehydro-α-lapachone and dehydroiso-α-lapachone from Stereospermum euphoroides. We also tested a small number of structurally related naphthoquinones from commercial sources and identified two additional compounds with complex I bypass activity: 2-methoxy-1,4-naphthoquinone and 2-methoxy-3-methyl-1,4,-naphthoquinone. The six novel complex I bypass factors reported here expand this class of molecules and will be useful as tool compounds for investigating complex I disease biology. PMID:27622560

Combining Amine-Reactive Cross-Linkers and Photo-Reactive Amino Acids for 3D-Structure Analysis of Proteins and Protein Complexes.

PubMed

Lössl, Philip; Sinz, Andrea

2016-01-01

During the last 15 years, the combination of chemical cross-linking and high-resolution mass spectrometry (MS) has matured into an alternative approach for analyzing 3D-structures of proteins and protein complexes. Using the distance constraints imposed by the cross-links, models of the protein or protein complex under investigation can be created. The majority of cross-linking studies are currently conducted with homobifunctional amine-reactive cross-linkers. We extend this "traditional" cross-linking/MS strategy by adding complementary photo-cross-linking data. For this, the diazirine-containing unnatural amino acids photo-leucine and photo-methionine are incorporated into the proteins and cross-link formation is induced by UV-A irradiation. The advantage of the photo-cross-linking strategy is that it is not restricted to lysine residues and that hydrophobic regions in proteins can be targeted, which is advantageous for investigating membrane proteins. We consider the strategy of combining cross-linkers with orthogonal reactivities and distances to be ideally suited for maximizing the amount of structural information that can be gained from a cross-linking experiment.

Emulsion Inks for 3D Printing of High Porosity Materials.

PubMed

Sears, Nicholas A; Dhavalikar, Prachi S; Cosgriff-Hernandez, Elizabeth M

2016-08-01

Photocurable emulsion inks for use with solid freeform fabrication (SFF) to generate constructs with hierarchical porosity are presented. A high internal phase emulsion (HIPE) templating technique was utilized to prepare water-in-oil emulsions from a hydrophobic photopolymer, surfactant, and water. These HIPEs displayed strong shear thinning behavior that permitted layer-by-layer deposition into complex shapes and adequately high viscosity at low shear for shape retention after extrusion. Each layer was actively polymerized with an ultraviolet cure-on-dispense (CoD) technique and compositions with sufficient viscosity were able to produce tall, complex scaffolds with an internal lattice structure and microscale porosity. Evaluation of the rheological and cure properties indicated that the viscosity and cure rate both played an important role in print fidelity. These 3D printed polyHIPE constructs benefit from the tunable pore structure of emulsion templated material and the designed architecture of 3D printing. As such, these emulsion inks can be used to create ultra high porosity constructs with complex geometries and internal lattice structures not possible with traditional manufacturing techniques. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Yang, Xi; Wang, Shanshan; Ghiviriga, Ion

A novel synthetic method to create gold based metallo–oligomers/polymers via the combination of inorganic click (iClick) with intermolecular aurophilic interactions is demonstrated. Complexes [PEt 3Au] 4(μ-N 3C 2C 6H 5) (1) and [PPhMe 2Au] 43C 2C 6H 5) (2) and {[PEt 3Au] 4[(μ-N 3C 2) 2-9,9-dihexyl-9H-fluorene]} n (8) have been synthesized via iClick. The tetranuclear structures of 1 and 2, induced by aurophilic bonding, are confirmed in the solid state through single crystal X-ray diffraction experiments and in solution via variable temperature NMR spectroscopy. The extended 1D structure of 8 is constructed by aurophilic induced self-assembly. 1H DOSY NMR analysismore » reveals that the aurophilic bonds in 1, 2, and 8 are retained in the solution phase. The degree of polymerization within complex 8 is temperature and concentration dependent, as determined by 1H DOSY NMR. The complex 8 is a rare example of a solution stable higher ordered structure linked by aurophilic interactions.« less

Integration of motor proteins - towards an ATP fueled soft actuator.

PubMed

Kakugo, Akira; Shikinaka, Kazuhiro; Gong, Jian Ping

2008-09-01

We present a soft bio-machine constructed from biological motors (actin/myosin). We have found that chemically cross-linked polymer-actin complex gel filaments can move on myosin coated surfaces with a velocity as high as that of native F-actin, by coupling to ATP hydrolysis. Additionally, it is shown that the velocity of polymer-actin complex gel depends on the species of polycations binding to the F-actins. Since the design of functional actuators of well-defined size and morphology is important, the structural behavior of polymer-actin complexes has been investigated. Our results show that the morphology and growth size of polymer-actin complex can be controlled by changes in the electrostatic interactions between F-actins and polycations. Our results indicate that bio actuators with desired shapes can be created by using a polymer-actin complex.

Scalable nanohelices for predictive studies and enhanced 3D visualization.

PubMed

Meagher, Kwyn A; Doblack, Benjamin N; Ramirez, Mercedes; Davila, Lilian P

2014-11-12

Spring-like materials are ubiquitous in nature and of interest in nanotechnology for energy harvesting, hydrogen storage, and biological sensing applications. For predictive simulations, it has become increasingly important to be able to model the structure of nanohelices accurately. To study the effect of local structure on the properties of these complex geometries one must develop realistic models. To date, software packages are rather limited in creating atomistic helical models. This work focuses on producing atomistic models of silica glass (SiO₂) nanoribbons and nanosprings for molecular dynamics (MD) simulations. Using an MD model of "bulk" silica glass, two computational procedures to precisely create the shape of nanoribbons and nanosprings are presented. The first method employs the AWK programming language and open-source software to effectively carve various shapes of silica nanoribbons from the initial bulk model, using desired dimensions and parametric equations to define a helix. With this method, accurate atomistic silica nanoribbons can be generated for a range of pitch values and dimensions. The second method involves a more robust code which allows flexibility in modeling nanohelical structures. This approach utilizes a C++ code particularly written to implement pre-screening methods as well as the mathematical equations for a helix, resulting in greater precision and efficiency when creating nanospring models. Using these codes, well-defined and scalable nanoribbons and nanosprings suited for atomistic simulations can be effectively created. An added value in both open-source codes is that they can be adapted to reproduce different helical structures, independent of material. In addition, a MATLAB graphical user interface (GUI) is used to enhance learning through visualization and interaction for a general user with the atomistic helical structures. One application of these methods is the recent study of nanohelices via MD simulations for mechanical energy harvesting purposes.

Influence maximization based on partial network structure information: A comparative analysis on seed selection heuristics

NASA Astrophysics Data System (ADS)

Erkol, Şirag; Yücel, Gönenç

In this study, the problem of seed selection is investigated. This problem is mainly treated as an optimization problem, which is proved to be NP-hard. There are several heuristic approaches in the literature which mostly use algorithmic heuristics. These approaches mainly focus on the trade-off between computational complexity and accuracy. Although the accuracy of algorithmic heuristics are high, they also have high computational complexity. Furthermore, in the literature, it is generally assumed that complete information on the structure and features of a network is available, which is not the case in most of the times. For the study, a simulation model is constructed, which is capable of creating networks, performing seed selection heuristics, and simulating diffusion models. Novel metric-based seed selection heuristics that rely only on partial information are proposed and tested using the simulation model. These heuristics use local information available from nodes in the synthetically created networks. The performances of heuristics are comparatively analyzed on three different network types. The results clearly show that the performance of a heuristic depends on the structure of a network. A heuristic to be used should be selected after investigating the properties of the network at hand. More importantly, the approach of partial information provided promising results. In certain cases, selection heuristics that rely only on partial network information perform very close to similar heuristics that require complete network data.

Harmonic Structure Predicts the Enjoyment of Uplifting Trance Music.

PubMed

Agres, Kat; Herremans, Dorien; Bigo, Louis; Conklin, Darrell

2016-01-01

An empirical investigation of how local harmonic structures (e.g., chord progressions) contribute to the experience and enjoyment of uplifting trance (UT) music is presented. The connection between rhythmic and percussive elements and resulting trance-like states has been highlighted by musicologists, but no research, to our knowledge, has explored whether repeated harmonic elements influence affective responses in listeners of trance music. Two alternative hypotheses are discussed, the first highlighting the direct relationship between repetition/complexity and enjoyment, and the second based on the theoretical inverted-U relationship described by the Wundt curve. We investigate the connection between harmonic structure and subjective enjoyment through interdisciplinary behavioral and computational methods: First we discuss an experiment in which listeners provided enjoyment ratings for computer-generated UT anthems with varying levels of harmonic repetition and complexity. The anthems were generated using a statistical model trained on a corpus of 100 uplifting trance anthems created for this purpose, and harmonic structure was constrained by imposing particular repetition structures (semiotic patterns defining the order of chords in the sequence) on a professional UT music production template. Second, the relationship between harmonic structure and enjoyment is further explored using two computational approaches, one based on average Information Content, and another that measures average tonal tension between chords. The results of the listening experiment indicate that harmonic repetition does in fact contribute to the enjoyment of uplifting trance music. More compelling evidence was found for the second hypothesis discussed above, however some maximally repetitive structures were also preferred. Both computational models provide evidence for a Wundt-type relationship between complexity and enjoyment. By systematically manipulating the structure of chord progressions, we have discovered specific harmonic contexts in which repetitive or complex structure contribute to the enjoyment of uplifting trance music.

Harmonic Structure Predicts the Enjoyment of Uplifting Trance Music

PubMed Central

Agres, Kat; Herremans, Dorien; Bigo, Louis; Conklin, Darrell

2017-01-01

An empirical investigation of how local harmonic structures (e.g., chord progressions) contribute to the experience and enjoyment of uplifting trance (UT) music is presented. The connection between rhythmic and percussive elements and resulting trance-like states has been highlighted by musicologists, but no research, to our knowledge, has explored whether repeated harmonic elements influence affective responses in listeners of trance music. Two alternative hypotheses are discussed, the first highlighting the direct relationship between repetition/complexity and enjoyment, and the second based on the theoretical inverted-U relationship described by the Wundt curve. We investigate the connection between harmonic structure and subjective enjoyment through interdisciplinary behavioral and computational methods: First we discuss an experiment in which listeners provided enjoyment ratings for computer-generated UT anthems with varying levels of harmonic repetition and complexity. The anthems were generated using a statistical model trained on a corpus of 100 uplifting trance anthems created for this purpose, and harmonic structure was constrained by imposing particular repetition structures (semiotic patterns defining the order of chords in the sequence) on a professional UT music production template. Second, the relationship between harmonic structure and enjoyment is further explored using two computational approaches, one based on average Information Content, and another that measures average tonal tension between chords. The results of the listening experiment indicate that harmonic repetition does in fact contribute to the enjoyment of uplifting trance music. More compelling evidence was found for the second hypothesis discussed above, however some maximally repetitive structures were also preferred. Both computational models provide evidence for a Wundt-type relationship between complexity and enjoyment. By systematically manipulating the structure of chord progressions, we have discovered specific harmonic contexts in which repetitive or complex structure contribute to the enjoyment of uplifting trance music. PMID:28119641

Self-folding with shape memory composites at the millimeter scale

NASA Astrophysics Data System (ADS)

Felton, S. M.; Becker, K. P.; Aukes, D. M.; Wood, R. J.

2015-08-01

Self-folding is an effective method for creating 3D shapes from flat sheets. In particular, shape memory composites—laminates containing shape memory polymers—have been used to self-fold complex structures and machines. To date, however, these composites have been limited to feature sizes larger than one centimeter. We present a new shape memory composite capable of folding millimeter-scale features. This technique can be activated by a global heat source for simultaneous folding, or by resistive heaters for sequential folding. It is capable of feature sizes ranging from 0.5 to 40 mm, and is compatible with multiple laminate compositions. We demonstrate the ability to produce complex structures and mechanisms by building two self-folding pieces: a model ship and a model bumblebee.

Complex Patterns of Local Adaptation in Teosinte

PubMed Central

Pyhäjärvi, Tanja; Hufford, Matthew B.; Mezmouk, Sofiane; Ross-Ibarra, Jeffrey

2013-01-01

Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation. PMID:23902747

Effects of Pre-Existing Target Structure on the Formation of Large Craters

NASA Technical Reports Server (NTRS)

Barnouin-Jha, O. S.; Cintala, M. J.; Crawford, D. A.

2003-01-01

The shapes of large-scale craters and the mechanics responsible for melt generation are influenced by broad and small-scale structures present in a target prior to impact. For example, well-developed systems of fractures often create craters that appear square in outline, good examples being Meteor Crater, AZ and the square craters of 433 Eros. Pre-broken target material also affects melt generation. Kieffer has shown how the shock wave generated in Coconino sandstone at Meteor crater created reverberations which, in combination with the natural target heterogeneity present, created peaks and troughs in pressure and compressed density as individual grains collided to produce a range of shock mineralogies and melts within neighboring samples. In this study, we further explore how pre-existing target structure influences various aspects of the cratering process. We combine experimental and numerical techniques to explore the connection between the scales of the impact generated shock wave and the pre-existing target structure. We focus on the propagation of shock waves in coarse, granular media, emphasizing its consequences on excavation, crater growth, ejecta production, cratering efficiency, melt generation, and crater shape. As a baseline, we present a first series of results for idealized targets where the particles are all identical in size and possess the same shock impedance. We will also present a few results, whereby we increase the complexities of the target properties by varying the grain size, strength, impedance and frictional properties. In addition, we investigate the origin and implications of reverberations that are created by the presence of physical and chemical heterogeneity in a target.

DNA-based construction at the nanoscale: emerging trends and applications

NASA Astrophysics Data System (ADS)

Lourdu Xavier, P.; Chandrasekaran, Arun Richard

2018-02-01

The field of structural DNA nanotechnology has evolved remarkably—from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes—in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.

DNA-based construction at the nanoscale: emerging trends and applications.

PubMed

Xavier, P Lourdu; Chandrasekaran, Arun Richard

2018-02-09

The field of structural DNA nanotechnology has evolved remarkably-from the creation of artificial immobile junctions to the recent DNA-protein hybrid nanoscale shapes-in a span of about 35 years. It is now possible to create complex DNA-based nanoscale shapes and large hierarchical assemblies with greater stability and predictability, thanks to the development of computational tools and advances in experimental techniques. Although it started with the original goal of DNA-assisted structure determination of difficult-to-crystallize molecules, DNA nanotechnology has found its applications in a myriad of fields. In this review, we cover some of the basic and emerging assembly principles: hybridization, base stacking/shape complementarity, and protein-mediated formation of nanoscale structures. We also review various applications of DNA nanostructures, with special emphasis on some of the biophysical applications that have been reported in recent years. In the outlook, we discuss further improvements in the assembly of such structures, and explore possible future applications involving super-resolved fluorescence, single-particle cryo-electron (cryo-EM) and x-ray free electron laser (XFEL) nanoscopic imaging techniques, and in creating new synergistic designer materials.

Six uranyl-organic frameworks with naphthalene-dicarboxylic acid and bipyridyl-based spacers: syntheses, structures, and properties.

PubMed

Xu, Wei; Ren, Ya-Nan; Xie, Miao; Zhou, Lin-Xia; Zheng, Yue-Qing

2018-03-28

A new series of uranium coordination polymers have been hydrothermally synthesized by using 1,4-naphthalene dicarboxylic acid (H 2 NDC), namely, (H 3 O) 2 [(UO 2 ) 2 (NDC) 3 ]·H 2 O (1), (H 2 -bpp)[(UO 2 ) 2 (NDC) 3 ]·EtOH·5H 2 O (2), (H 2 -bpe) 2/2 [(UO 2 ) 2 (NDC) 3 ]·EtOH (3), (H 2 -bpp)[(UO 2 ) 2 (NDC) 3 ]·5H 2 O (4), (H 2 -bpp)[(UO 2 )(HNDC)(NDC)] 2 ·2H 2 O (5), and (H 2 -bpy)[(UO 2 )(NDC) 2 ] (6) [bpp = 1,3-di(4-pyridyl) propane, bpe = 4,4'-vinylenedipyridine, bpy = 4,4'-bipyridine]. Single-crystal X-ray diffraction demonstrates that complex 1 represents the uranyl-organic polycatenated framework derived from a simple two-dimensional honeycomb grid network structure via a H 2 NDC linker. Complexes 2-4 contain the dinuclear motifs of the two UO 7 pentagonal and one UO 8 hexagonal bipyramids which are linked by NDC 2- anions creating a (UO 2 ) 4 (NDC) 2 unit, and further extend to a 2D layer through NDC 2- anions. Complex 5 displays a 1D zigzag double chain structure, in which the carboxylate groups of the NDC 2- anions adopt a chelate mode and further extends to a 2D framework via hydrogen bonds. The 1D structure of complex 6 is similar to the zigzag chain of complex 5. In addition, powder X-ray diffraction, elemental analysis, IR, thermal stability and luminescence properties of all complexes have also been investigated in this paper. The photocatalytic properties of the six complexes for the degradation of tetracycline hydrochloride (TC) under UV irradiation have been examined. Moreover, density functional theory (DFT) calculations were carried out to explore the electronic structural and bonding properties of the uranyl complexes 1-6.

Epidemic spreading on complex networks with community structures

PubMed Central

Stegehuis, Clara; van der Hofstad, Remco; van Leeuwaarden, Johan S. H.

2016-01-01

Many real-world networks display a community structure. We study two random graph models that create a network with similar community structure as a given network. One model preserves the exact community structure of the original network, while the other model only preserves the set of communities and the vertex degrees. These models show that community structure is an important determinant of the behavior of percolation processes on networks, such as information diffusion or virus spreading: the community structure can both enforce as well as inhibit diffusion processes. Our models further show that it is the mesoscopic set of communities that matters. The exact internal structures of communities barely influence the behavior of percolation processes across networks. This insensitivity is likely due to the relative denseness of the communities. PMID:27440176

UHPC and NSFRC in Severe Environmental Conditions

NASA Astrophysics Data System (ADS)

Rehacek, S.; Citek, D.; Kolisko, J.

2017-10-01

Structure and properties of cement composite are time-varying characteristics, depending among others on environmental conditions. The key idea is a struggle for complex research of joint effect of physical, chemical and dynamic loads on the internal structure of cement composite and understanding the correlation between changes in microstructure and macro-scale properties. During the experimental program, specimens will be exposed to combined influence of freeze-thaw cycles, aggressive chemical agents and dynamic loading. The aim is to create a theoretical basis for design of effective cement composites meant to be used in severe environmental conditions.

Hyperfine-Structure-Induced Depolarization of Impulsively Aligned I2 Molecules

NASA Astrophysics Data System (ADS)

Thomas, Esben F.; Søndergaard, Anders A.; Shepperson, Benjamin; Henriksen, Niels E.; Stapelfeldt, Henrik

2018-04-01

A moderately intense 450 fs laser pulse is used to create rotational wave packets in gas phase I2 molecules. The ensuing time-dependent alignment, measured by Coulomb explosion imaging with a delayed probe pulse, exhibits the characteristic revival structures expected for rotational wave packets but also a complex nonperiodic substructure and decreasing mean alignment not observed before. A quantum mechanical model attributes the phenomena to coupling between the rotational angular momenta and the nuclear spins through the electric quadrupole interaction. The calculated alignment trace agrees very well with the experimental results.

A Virtual Aluminum Reduction Cell

NASA Astrophysics Data System (ADS)

Zhang, Hongliang; Zhou, Chenn Q.; Wu, Bing; Li, Jie

2013-11-01

The most important component in the aluminum industry is the aluminum reduction cell; it has received considerable interests and resources to conduct research to improve its productivity and energy efficiency. The current study focused on the integration of numerical simulation data and virtual reality technology to create a scientifically and practically realistic virtual aluminum reduction cell by presenting complex cell structures and physical-chemical phenomena. The multiphysical field simulation models were first built and solved in ANSYS software (ANSYS Inc., Canonsburg, PA, USA). Then, the methodology of combining the simulation results with virtual reality was introduced, and a virtual aluminum reduction cell was created. The demonstration showed that a computer-based world could be created in which people who are not analysis experts can see the detailed cell structure in a context that they can understand easily. With the application of the virtual aluminum reduction cell, even people who are familiar with aluminum reduction cell operations can gain insights that make it possible to understand the root causes of observed problems and plan design changes in much less time.

Research Update: Focused ion beam direct writing of magnetic patterns with controlled structural and magnetic properties

NASA Astrophysics Data System (ADS)

Urbánek, Michal; Flajšman, Lukáš; Křižáková, Viola; Gloss, Jonáš; Horký, Michal; Schmid, Michael; Varga, Peter

2018-06-01

Focused ion beam irradiation of metastable Fe78Ni22 thin films grown on Cu(100) substrates is used to create ferromagnetic, body-centered cubic patterns embedded into paramagnetic, face-centered-cubic surrounding. The structural and magnetic phase transformation can be controlled by varying parameters of the transforming gallium ion beam. The focused ion beam parameters such as the ion dose, number of scans, and scanning direction can be used not only to control a degree of transformation but also to change the otherwise four-fold in-plane magnetic anisotropy into the uniaxial anisotropy along a specific crystallographic direction. This change is associated with a preferred growth of specific crystallographic domains. The possibility to create magnetic patterns with continuous magnetization transitions and at the same time to create patterns with periodical changes in magnetic anisotropy makes this system an ideal candidate for rapid prototyping of a large variety of nanostructured samples. Namely, spin-wave waveguides and magnonic crystals can be easily combined into complex devices in a single fabrication step.

Fused filament 3D printing of ionic polymer-metal composites for soft robotics

NASA Astrophysics Data System (ADS)

Carrico, James D.; Leang, Kam K.

2017-04-01

Additive manufacturing techniques are used to create three-dimensional structures with complex shapes and features from polymer and/or metal materials. For example, fused filament three-dimensional (3D) printing utilizes non-electroactive polymers, such as acrylonitrile butadiene styrene (ABS) and polylactic acid (PLA), to build structures and components in a layer-by-layer fashion for a wide variety of applications. Presented here is a summary of recent work on a fused filament 3D-printing technique to create 3D ionic polymer-metal composite (IPMC) structures for applications in soft robotics. The 3D printing technique overcomes some of the limitations of existing manufacturing processes for creating IPMCs, such as limited shapes and sizes and time-consuming manufacturing steps. In the process described, first a precursor material (non-acid Nafion precursor resin) is extruded into a thermoplastic filament for 3D printing. Then, a custom-designed 3D printer is described that utilizes the precursor filament to manufacture custom-shaped structures. Finally, the 3D-printed samples are functionalized by hydrolyzing them in an aqueous solution of potassium hydroxide and dimethyl sulfoxide, followed by application of platinum electrodes. Presented are example 3D-printed single and multi-degree-of-freedom IPMC actuators and characterization results, as well as example soft-robotic devices to demonstrate the potential of this process.

A probabilistic framework for identifying biosignatures using Pathway Complexity

NASA Astrophysics Data System (ADS)

Marshall, Stuart M.; Murray, Alastair R. G.; Cronin, Leroy

2017-11-01

One thing that discriminates living things from inanimate matter is their ability to generate similarly complex or non-random structures in a large abundance. From DNA sequences to folded protein structures, living cells, microbial communities and multicellular structures, the material configurations in biology can easily be distinguished from non-living material assemblies. Many complex artefacts, from ordinary bioproducts to human tools, though they are not living things, are ultimately produced by biological processes-whether those processes occur at the scale of cells or societies, they are the consequences of living systems. While these objects are not living, they cannot randomly form, as they are the product of a biological organism and hence are either technological or cultural biosignatures. A generalized approach that aims to evaluate complex objects as possible biosignatures could be useful to explore the cosmos for new life forms. However, it is not obvious how it might be possible to create such a self-contained approach. This would require us to prove rigorously that a given artefact is too complex to have formed by chance. In this paper, we present a new type of complexity measure, which we call `Pathway Complexity', that allows us not only to threshold the abiotic-biotic divide, but also to demonstrate a probabilistic approach based on object abundance and complexity which can be used to unambiguously assign complex objects as biosignatures. We hope that this approach will not only open up the search for biosignatures beyond the Earth, but also allow us to explore the Earth for new types of biology, and to determine when a complex chemical system discovered in the laboratory could be considered alive. This article is part of the themed issue 'Reconceptualizing the origins of life'.

3D Chemical Patterning of Micromaterials for Encoded Functionality.

PubMed

Ceylan, Hakan; Yasa, Immihan Ceren; Sitti, Metin

2017-03-01

Programming local chemical properties of microscale soft materials with 3D complex shapes is indispensable for creating sophisticated functionalities, which has not yet been possible with existing methods. Precise spatiotemporal control of two-photon crosslinking is employed as an enabling tool for 3D patterning of microprinted structures for encoding versatile chemical moieties. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Two-dimensional finite element heat transfer model of softwood. Part III, Effect of moisture content on thermal conductivity

Treesearch

Hongmei Gu; John F. Hunt

2007-01-01

The anisotropy of wood creates a complex problem for solving heat and mass transfer problems that require analyses be based on fundamental material properties of the wood structure. Most heat transfer models for softwood use average thermal properties across either the radial or tangential direction and do not differentiate the effects of cellular alignment or...

Development of input data layers for the FARSITE fire growth model for the Selway-Bitterroot Wilderness Complex, USA

Treesearch

Robert E. Keane; Janice L. Garner; Kirsten M. Schmidt; Donald G. Long; James P. Menakis; Mark A. Finney

1998-01-01

Fuel and vegetation spatial data layers required by the spatially explicit fire growth model FARSITE were developed for all lands in and around the Selway-Bitterroot Wilderness Area in Idaho and Montana. Satellite imagery and terrain modeling were used to create the three base vegetation spatial data layers of potential vegetation, cover type, and structural stage....

Reduced complexity structural modeling for automated airframe synthesis

NASA Technical Reports Server (NTRS)

Hajela, Prabhat

1987-01-01

A procedure is developed for the optimum sizing of wing structures based on representing the built-up finite element assembly of the structure by equivalent beam models. The reduced-order beam models are computationally less demanding in an optimum design environment which dictates repetitive analysis of several trial designs. The design procedure is implemented in a computer program requiring geometry and loading information to create the wing finite element model and its equivalent beam model, and providing a rapid estimate of the optimum weight obtained from a fully stressed design approach applied to the beam. The synthesis procedure is demonstrated for representative conventional-cantilever and joined wing configurations.

Numerical-experimental investigation of resonance characteristics of a sounding board

NASA Astrophysics Data System (ADS)

Shlychkov, S. V.

2007-05-01

The paper presents results of numerical and experimental investigations into the vibrations of thin-walled structures, considering such their features as the complexity of geometry, the laminated structure of walls, the anisotropy of materials, the presence of stiffeners, and the initial stresses. The object of the study is the sounding board of an acoustic guitar, the main structural material of which is a three-layer birch veneer. Based on the finite-element method, a corresponding calculation model is created, and the steady-state regimes of forced vibrations of the sounding board are investigated. A good correspondence between calculation results and experimental data is found to exist.

Structure of GlnK1 with bound effectors indicates regulatory mechanism for ammonia uptake.

PubMed

Yildiz, Ozkan; Kalthoff, Christoph; Raunser, Stefan; Kühlbrandt, Werner

2007-01-24

A binary complex of the ammonia channel Amt1 from Methanococcus jannaschii and its cognate P(II) signalling protein GlnK1 has been produced and characterized. Complex formation is prevented specifically by the effector molecules Mg-ATP and 2-ketoglutarate. Single-particle electron microscopy of the complex shows that GlnK1 binds on the cytoplasmic side of Amt1. Three high-resolution X-ray structures of GlnK1 indicate that the functionally important T-loop has an extended, flexible conformation in the absence of Mg-ATP, but assumes a compact, tightly folded conformation upon Mg-ATP binding, which in turn creates a 2-ketoglutarate-binding site. We propose a regulatory mechanism by which nitrogen uptake is controlled by the binding of both effector molecules to GlnK1. At normal effector levels, a 2-ketoglutarate molecule binding at the apex of the compact T-loop would prevent complex formation, ensuring uninhibited ammonia uptake. At low levels of Mg-ATP, the extended loops would seal the ammonia channels in the complex. Binding of both effector molecules to P(II) signalling proteins may thus represent an effective feedback mechanism for regulating ammonium uptake through the membrane.

Novel polyelectrolyte complex based carbon nanotube composite architectures

NASA Astrophysics Data System (ADS)

Razdan, Sandeep

This study focuses on creating novel architectures of carbon nanotubes using polyelectrolytes. Polyelectrolytes are unique polymers possessing resident charges on the macromolecular chains. This property, along with their biocompatibility (true for most polymers used in this study) makes them ideal candidates for a variety of applications such as membranes, drug delivery systems, scaffold materials etc. Carbon nanotubes are also unique one-dimensional nanoscale materials that possess excellent electrical, mechanical and thermal properties owing to their small size, high aspect ratio, graphitic structure and strength arising from purely covalent bonds in the molecular structure. The present study tries to investigate the synthesis processes and material properties of carbon nanotube composites comprising of polyelectrolyte complexes. Carbon nanotubes are dispersed in a polyelectrolyte and are induced into taking part in a complexation process with two oppositely charged polyelectrolytes. The resulting stoichiometric precipitate is then drawn into fiber form and dried as such. The material properties of the carbon nanotube fibers were characterized and related to synthesis parameters and material interactions. Also, an effort was made to understand and predict fiber morphology resulting from the complexation and drawing process. The study helps to delineate the synthesis and properties of the said polyelectrolyte complex-carbon nanotube architectures and highlights useful properties, such as electrical conductivity and mechanical strength, which could make these structures promising candidates for a variety of applications.

Differential effects of habitat complexity, predators and competitors on abundance of juvenile and adult coral reef fishes.

PubMed

Almany, Glenn R

2004-09-01

Greater structural complexity is often associated with greater abundance and diversity, perhaps because high complexity habitats reduce predation and competition. Using 16 spatially isolated live-coral reefs in the Bahamas, I examined how abundance of juvenile (recruit) and adult (non-recruit) fishes was affected by two factors: (1) structural habitat complexity and (2) the presence of predators and interference competitors. Manipulating the abundance of low and high complexity corals created two levels of habitat complexity, which was cross-factored with the presence or absence of resident predators (sea basses and moray eels) plus interference competitors (territorial damselfishes). Over 60 days, predators and competitors greatly reduced recruit abundance regardless of habitat complexity, but did not affect adult abundance. In contrast, increased habitat complexity had a strong positive effect on adult abundance and a weak positive effect on recruit abundance. Differential responses of recruits and adults may be related to the differential effects of habitat complexity on their primary predators. Sedentary recruits are likely most preyed upon by small resident predators that ambush prey, while larger adult fishes that forage widely and use reefs primarily for shelter are likely most preyed upon by large transient predators that chase prey. Increased habitat complexity may have inhibited foraging by transient predators but not resident predators. Results demonstrate the importance of habitat complexity to community dynamics, which is of concern given the accelerated degradation of habitats worldwide.

Directional selection can drive the evolution of modularity in complex traits

PubMed Central

Melo, Diogo; Marroig, Gabriel

2015-01-01

Modularity is a central concept in modern biology, providing a powerful framework for the study of living organisms on many organizational levels. Two central and related questions can be posed in regard to modularity: How does modularity appear in the first place, and what forces are responsible for keeping and/or changing modular patterns? We approached these questions using a quantitative genetics simulation framework, building on previous results obtained with bivariate systems and extending them to multivariate systems. We developed an individual-based model capable of simulating many traits controlled by many loci with variable pleiotropic relations between them, expressed in populations subject to mutation, recombination, drift, and selection. We used this model to study the problem of the emergence of modularity, and hereby show that drift and stabilizing selection are inefficient at creating modular variational structures. We also demonstrate that directional selection can have marked effects on the modular structure between traits, actively promoting a restructuring of genetic variation in the selected population and potentially facilitating the response to selection. Furthermore, we give examples of complex covariation created by simple regimes of combined directional and stabilizing selection and show that stabilizing selection is important in the maintenance of established covariation patterns. Our results are in full agreement with previous results for two-trait systems and further extend them to include scenarios of greater complexity. Finally, we discuss the evolutionary consequences of modular patterns being molded by directional selection. PMID:25548154

Directional selection can drive the evolution of modularity in complex traits.

PubMed

Melo, Diogo; Marroig, Gabriel

2015-01-13

Modularity is a central concept in modern biology, providing a powerful framework for the study of living organisms on many organizational levels. Two central and related questions can be posed in regard to modularity: How does modularity appear in the first place, and what forces are responsible for keeping and/or changing modular patterns? We approached these questions using a quantitative genetics simulation framework, building on previous results obtained with bivariate systems and extending them to multivariate systems. We developed an individual-based model capable of simulating many traits controlled by many loci with variable pleiotropic relations between them, expressed in populations subject to mutation, recombination, drift, and selection. We used this model to study the problem of the emergence of modularity, and hereby show that drift and stabilizing selection are inefficient at creating modular variational structures. We also demonstrate that directional selection can have marked effects on the modular structure between traits, actively promoting a restructuring of genetic variation in the selected population and potentially facilitating the response to selection. Furthermore, we give examples of complex covariation created by simple regimes of combined directional and stabilizing selection and show that stabilizing selection is important in the maintenance of established covariation patterns. Our results are in full agreement with previous results for two-trait systems and further extend them to include scenarios of greater complexity. Finally, we discuss the evolutionary consequences of modular patterns being molded by directional selection.

Pathways towards instability in financial networks

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

Pathways towards instability in financial networks

PubMed Central

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

2017-01-01

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

Musical Creativity “Revealed” in Brain Structure: Interplay between Motor, Default Mode, and Limbic Networks

PubMed Central

Bashwiner, David M.; Wertz, Christopher J.; Flores, Ranee A.; Jung, Rex E.

2016-01-01

Creative behaviors are among the most complex that humans engage in, involving not only highly intricate, domain-specific knowledge and skill, but also domain-general processing styles and the affective drive to create. This study presents structural imaging data indicating that musically creative people (as indicated by self-report) have greater cortical surface area or volume in a) regions associated with domain-specific higher-cognitive motor activity and sound processing (dorsal premotor cortex, supplementary and pre-supplementary motor areas, and planum temporale), b) domain-general creative-ideation regions associated with the default mode network (dorsomedial prefrontal cortex, middle temporal gyrus, and temporal pole), and c) emotion-related regions (orbitofrontal cortex, temporal pole, and amygdala). These findings suggest that domain-specific musical expertise, default-mode cognitive processing style, and intensity of emotional experience might all coordinate to motivate and facilitate the drive to create music. PMID:26888383

Pathways towards instability in financial networks.

PubMed

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

2017-02-21

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

Fibrillar films obtained from sodium soap fibers and polyelectrolyte multilayers.

PubMed

Zawko, Scott A; Schmidt, Christine E

2011-08-01

An objective of tissue engineering is to create synthetic polymer scaffolds with a fibrillar microstructure similar to the extracellular matrix. Here, we present a novel method for creating polymer fibers using the layer-by-layer method and sacrificial templates composed of sodium soap fibers. Soap fibers were prepared from neutralized fatty acids using a sodium chloride crystal dissolution method. Polyelectrolyte multilayers (PEMs) of polystyrene sulfonate and polyallylamine hydrochloride were deposited onto the soap fibers, crosslinked with glutaraldehyde, and then the soap fibers were leached with warm water and ethanol. The morphology of the resulting PEM structures was a dense network of fibers surrounded by a nonfibrillar matrix. Microscopy revealed that the PEM fibers were solid structures, presumably composed of polyelectrolytes complexed with residual fatty acids. These fibrillar PEM films were found to support the attachment of human dermal fibroblasts. Copyright © 2011 Wiley Periodicals, Inc.

Multi-agent electricity market modeling with EMCAS.

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

North, M.; Macal, C.; Conzelmann, G.

2002-09-05

Electricity systems are a central component of modern economies. Many electricity markets are transitioning from centrally regulated systems to decentralized markets. Furthermore, several electricity markets that have recently undergone this transition have exhibited extremely unsatisfactory results, most notably in California. These high stakes transformations require the introduction of largely untested regulatory structures. Suitable tools that can be used to test these regulatory structures before they are applied to real systems are required. Multi-agent models can provide such tools. To better understand the requirements such as tool, a live electricity market simulation was created. This experience helped to shape the developmentmore » of the multi-agent Electricity Market Complex Adaptive Systems (EMCAS) model. To explore EMCAS' potential, several variations of the live simulation were created. These variations probed the possible effects of changing power plant outages and price setting rules on electricity market prices.« less

Distributed rewiring model for complex networking: The effect of local rewiring rules on final structural properties.

PubMed

López Chavira, Magali Alexander; Marcelín-Jiménez, Ricardo

2017-01-01

The study of complex networks has become an important subject over the last decades. It has been shown that these structures have special features, such as their diameter, or their average path length, which in turn are the explanation of some functional properties in a system such as its fault tolerance, its fragility before attacks, or the ability to support routing procedures. In the present work, we study some of the forces that help a network to evolve to the point where structural properties are settled. Although our work is mainly focused on the possibility of applying our ideas to Information and Communication Technologies systems, we consider that our results may contribute to understanding different scenarios where complex networks have become an important modeling tool. Using a discrete event simulator, we get each node to discover the shortcuts that may connect it with regions away from its local environment. Based on this partial knowledge, each node can rewire some of its links, which allows modifying the topology of the entire underlying graph to achieve new structural properties. We proposed a distributed rewiring model that creates networks with features similar to those found in complex networks. Although each node acts in a distributed way and seeking to reduce only the trajectories of its packets, we observed a decrease of diameter and an increase in clustering coefficient in the global structure compared to the initial graph. Furthermore, we can find different final structures depending on slight changes in the local rewiring rules.

Mapping healthcare systems: a policy relevant analytic tool.

PubMed

Sekhri Feachem, Neelam; Afshar, Ariana; Pruett, Cristina; Avanceña, Anton L V

2017-07-01

In the past decade, an international consensus on the value of well-functioning systems has driven considerable health systems research. This research falls into two broad categories. The first provides conceptual frameworks that take complex healthcare systems and create simplified constructs of interactions and functions. The second focuses on granular inputs and outputs. This paper presents a novel translational mapping tool - the University of California, San Francisco mapping tool (the Tool) - which bridges the gap between these two areas of research, creating a platform for multi-country comparative analysis. Using the Murray-Frenk framework, we create a macro-level representation of a country's structure, focusing on how it finances and delivers healthcare. The map visually depicts the fundamental policy questions in healthcare system design: funding sources and amount spent through each source, purchasers, populations covered, provider categories; and the relationship between these entities. We use the Tool to provide a macro-level comparative analysis of the structure of India's and Thailand's healthcare systems. As part of the systems strengthening arsenal, the Tool can stimulate debate about the merits and consequences of different healthcare systems structural designs, using a common framework that fosters multi-country comparative analyses. © The Author 2017. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene.

Fluid-structure interaction modeling of clusters of spacecraft parachutes with modified geometric porosity

NASA Astrophysics Data System (ADS)

Takizawa, Kenji; Tezduyar, Tayfun E.; Boben, Joseph; Kostov, Nikolay; Boswell, Cody; Buscher, Austin

2013-12-01

To increase aerodynamic performance, the geometric porosity of a ringsail spacecraft parachute canopy is sometimes increased, beyond the "rings" and "sails" with hundreds of "ring gaps" and "sail slits." This creates extra computational challenges for fluid-structure interaction (FSI) modeling of clusters of such parachutes, beyond those created by the lightness of the canopy structure, geometric complexities of hundreds of gaps and slits, and the contact between the parachutes of the cluster. In FSI computation of parachutes with such "modified geometric porosity," the flow through the "windows" created by the removal of the panels and the wider gaps created by the removal of the sails cannot be accurately modeled with the Homogenized Modeling of Geometric Porosity (HMGP), which was introduced to deal with the hundreds of gaps and slits. The flow needs to be actually resolved. All these computational challenges need to be addressed simultaneously in FSI modeling of clusters of spacecraft parachutes with modified geometric porosity. The core numerical technology is the Stabilized Space-Time FSI (SSTFSI) technique, and the contact between the parachutes is handled with the Surface-Edge-Node Contact Tracking (SENCT) technique. In the computations reported here, in addition to the SSTFSI and SENCT techniques and HMGP, we use the special techniques we have developed for removing the numerical spinning component of the parachute motion and for restoring the mesh integrity without a remesh. We present results for 2- and 3-parachute clusters with two different payload models.

Grayscale lithography-automated mask generation for complex three-dimensional topography

NASA Astrophysics Data System (ADS)

Loomis, James; Ratnayake, Dilan; McKenna, Curtis; Walsh, Kevin M.

2016-01-01

Grayscale lithography is a relatively underutilized technique that enables fabrication of three-dimensional (3-D) microstructures in photosensitive polymers (photoresists). By spatially modulating ultraviolet (UV) dosage during the writing process, one can vary the depth at which photoresist is developed. This means complex structures and bioinspired designs can readily be produced that would otherwise be cost prohibitive or too time intensive to fabricate. The main barrier to widespread grayscale implementation, however, stems from the laborious generation of mask files required to create complex surface topography. We present a process and associated software utility for automatically generating grayscale mask files from 3-D models created within industry-standard computer-aided design (CAD) suites. By shifting the microelectromechanical systems (MEMS) design onus to commonly used CAD programs ideal for complex surfacing, engineering professionals already familiar with traditional 3-D CAD software can readily utilize their pre-existing skills to make valuable contributions to the MEMS community. Our conversion process is demonstrated by prototyping several samples on a laser pattern generator-capital equipment already in use in many foundries. Finally, an empirical calibration technique is shown that compensates for nonlinear relationships between UV exposure intensity and photoresist development depth as well as a thermal reflow technique to help smooth microstructure surfaces.

Physical characteristics of lanthanide complexes that act as magnetization transfer (MT) contrast agents

NASA Astrophysics Data System (ADS)

Zhang, Shanrong; Sherry, A. Dean

2003-02-01

Rapid water exchange is normally considered a prerequisite for efficient Gd3+-based MRI contrast agents. Yet recent measures of exchange rates in some Gd3+ complexes have shown that water exchange can become limiting when such complexes are attached to larger macromolecular structures. A new class of lanthanide complexes that display unusually slow water exchange (bound water lifetimes (τM298) > 10 μs) has recently been reported. This apparent disadvantage may be taken advantage of by switching the metal ion from gadolinium(III) to a lanthanide that shifts the bound water resonance substantially away from bulk water. Given appropriate water exchange kinetics, one can then alter the intensity of the bulk water signal by selective presaturation of this highly shifted, Ln3+-bound water resonance. This provides the basis of a new method to alter MR image contrast in tissue. We have synthesized a variety of DOTA-tetra(amide) ligands to evaluate as potential magnetization transfer (MT) contrast agents and found that the bound water lifetimes in these complexes are sensitive to both ligand structure (a series of Eu3+ complexes have τM298 values that range from 1 to 1300 μs) and the identity of the paramagnetic Ln3+ cation (from 3 to 800 μs for a single ligand). This demonstrates that it may be possible either to fine-tune the ligand structure or to select proper lanthanide cation to create an optimal MT agent for any clinical imaging field.

Huygens' optical vector wave field synthesis via in-plane electric dipole metasurface.

PubMed

Park, Hyeonsoo; Yun, Hansik; Choi, Chulsoo; Hong, Jongwoo; Kim, Hwi; Lee, Byoungho

2018-04-16

We investigate Huygens' optical vector wave field synthesis scheme for electric dipole metasurfaces with the capability of modulating in-plane polarization and complex amplitude and discuss the practical issues involved in realizing multi-modulation metasurfaces. The proposed Huygens' vector wave field synthesis scheme identifies the vector Airy disk as a synthetic unit element and creates a designed vector optical field by integrating polarization-controlled and complex-modulated Airy disks. The metasurface structure for the proposed vector field synthesis is analyzed in terms of the signal-to-noise ratio of the synthesized field distribution. The design of practical metasurface structures with true vector modulation capability is possible through the analysis of the light field modulation characteristics of various complex modulated geometric phase metasurfaces. It is shown that the regularization of meta-atoms is a key factor that needs to be considered in field synthesis, given that it is essential for a wide range of optical field synthetic applications, including holographic displays, microscopy, and optical lithography.

Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks

NASA Astrophysics Data System (ADS)

Singleton, Martin R.; Dillingham, Mark S.; Gaudier, Martin; Kowalczykowski, Stephen C.; Wigley, Dale B.

2004-11-01

RecBCD is a multi-functional enzyme complex that processes DNA ends resulting from a double-strand break. RecBCD is a bipolar helicase that splits the duplex into its component strands and digests them until encountering a recombinational hotspot (Chi site). The nuclease activity is then attenuated and RecBCD loads RecA onto the 3' tail of the DNA. Here we present the crystal structure of RecBCD bound to a DNA substrate. In this initiation complex, the DNA duplex has been split across the RecC subunit to create a fork with the separated strands each heading towards different helicase motor subunits. The strands pass along tunnels within the complex, both emerging adjacent to the nuclease domain of RecB. Passage of the 3' tail through one of these tunnels provides a mechanism for the recognition of a Chi sequence by RecC within the context of double-stranded DNA. Gating of this tunnel suggests how nuclease activity might be regulated.

Coherent wavepackets in the Fenna-Matthews-Olson complex are robust to excitonic-structure perturbations caused by mutagenesis

NASA Astrophysics Data System (ADS)

Maiuri, Margherita; Ostroumov, Evgeny E.; Saer, Rafael G.; Blankenship, Robert E.; Scholes, Gregory D.

2018-02-01

Femtosecond pulsed excitation of light-harvesting complexes creates oscillatory features in their response. This phenomenon has inspired a large body of work aimed at uncovering the origin of the coherent beatings and possible implications for function. Here we exploit site-directed mutagenesis to change the excitonic level structure in Fenna-Matthews-Olson (FMO) complexes and compare the coherences using broadband pump-probe spectroscopy. Our experiments detect two oscillation frequencies with dephasing on a picosecond timescale—both at 77 K and at room temperature. By studying these coherences with selective excitation pump-probe experiments, where pump excitation is in resonance only with the lowest excitonic state, we show that the key contributions to these oscillations stem from ground-state vibrational wavepackets. These experiments explicitly show that the coherences—although in the ground electronic state—can be probed at the absorption resonances of other bacteriochlorophyll molecules because of delocalization of the electronic excitation over several chromophores.

Synthesis and crystal structure of an oxovanadium(IV) complex with a pyrazolone ligand and its use as a heterogeneous catalyst for the oxidation of styrene under mild conditions.

PubMed

Parihar, Sanjay; Pathan, Soyeb; Jadeja, R N; Patel, Anjali; Gupta, Vivek K

2012-01-16

1-Phenyl-3-methyl-4-touloyl-5-pyrazolone (ligand) was synthesized and used to prepare an oxovanadium(IV) complex. The complex was characterized by single-crystal X-ray analysis and various spectroscopic techniques. The single-crystal X-ray analysis of the complex shows that the ligands are coordinated in a syn configuration to each other and create a distorted octahedral environment around the metal ion. A heterogeneous catalyst comprising an oxovanadium(IV) complex and hydrous zirconia was synthesized, characterized by various physicochemical techniques, and successfully used for the solvent-free oxidation of styrene. The influence of the reaction parameters (percent loading, molar ratio of the substrate to H(2)O(2), amount of catalyst, and reaction time) was studied. The catalyst was reused three times without any significant loss in the catalytic activity.

Low complexity 1D IDCT for 16-bit parallel architectures

NASA Astrophysics Data System (ADS)

Bivolarski, Lazar

2007-09-01

This paper shows that using the Loeffler, Ligtenberg, and Moschytz factorization of 8-point IDCT [2] one-dimensional (1-D) algorithm as a fast approximation of the Discrete Cosine Transform (DCT) and using only 16 bit numbers, it is possible to create in an IEEE 1180-1990 compliant and multiplierless algorithm with low computational complexity. This algorithm as characterized by its structure is efficiently implemented on parallel high performance architectures as well as due to its low complexity is sufficient for wide range of other architectures. Additional constraint on this work was the requirement of compliance with the existing MPEG standards. The hardware implementation complexity and low resources where also part of the design criteria for this algorithm. This implementation is also compliant with the precision requirements described in MPEG IDCT precision specification ISO/IEC 23002-1. Complexity analysis is performed as an extension to the simple measure of shifts and adds for the multiplierless algorithm as additional operations are included in the complexity measure to better describe the actual transform implementation complexity.

Engineering yeast consortia for surface-display of complex cellulosome structures

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

Chen, Wilfred

As our society marches toward a more technologically advanced future, energy and environmental sustainability are some of the most challenging problems we face today. Biomass is one of the most abundant renewable-feedstock for sustainable production of biofuels. However, the main technological obstacle to more widespread uses of this resource is the lack of low-cost technologies to overcome the recalcitrant nature of the cellulosic structure, especially the hydrolysis step on highly ordered celluloses. In this proposal, we successfully engineered several efficient and inexpensive whole-cell biocatalysts in an effort to produce economically compatible and sustainable biofuels, namely cellulosic ethanol. Our approach wasmore » to display of a highly efficient cellulolytic enzyme complex, named cellulosome, on the surface of a historical ethanol producer Saccharomyces cerevisiae for the simultaneous and synergistic saccharification and fermentation of cellulose to ethanol. We first demonstrated the feasibility of assembling a mini-cellulosome by incubating E. coli lysates expressing three different cellulases. Resting cells displaying mini-cellulosomes produced 4-fold more ethanol from phosphoric acid-swollen cellulose (PASC) than cultures with only added enzymes. The flexibility to assemble the mini-cellulosome structure was further demonstrated using a synthetic yeast consortium through intracellular complementation. Direct ethanol production from PASC was demonstrated with resting cell cultures. To create a microorganism suitable for a more cost-effective process, called consolidated bioprocessing (CBP), a synthetic consortium capable of displaying mini-cellulosomes on the cell surface via intercellular complementation was created. To further improve the efficiency, a new adaptive strategy of employing anchoring and adaptor scaffoldins to amplify the number of enzymatic subunits was developed, resulting in the creation of an artificial tetravalent cellulosome on the yeast surface and a significant improvement in cellulosic ethanol production. Although this adaptive strategy is ideal for assembling more complex cellulosome for large-scale production of cellulosic ethanol, a substantially larger number of enzymes (up to 10 to 12) is needed to better mimic the natural cellulosome structures for practical usage of the technology.« less

KDM2B Recruitment of the Polycomb Group Complex, PRC1.1, Requires Cooperation between PCGF1 and BCORL1.

PubMed

Wong, Sarah J; Gearhart, Micah D; Taylor, Alexander B; Nanyes, David R; Ha, Daniel J; Robinson, Angela K; Artigas, Jason A; Lee, Oliver J; Demeler, Borries; Hart, P John; Bardwell, Vivian J; Kim, Chongwoo A

2016-10-04

KDM2B recruits H2A-ubiquitinating activity of a non-canonical Polycomb Repression Complex 1 (PRC1.1) to CpG islands, facilitating gene repression. We investigated the molecular basis of recruitment using in vitro assembly assays to identify minimal components, subcomplexes, and domains required for recruitment. A minimal four-component PRC1.1 complex can be assembled by combining two separately isolated subcomplexes: the DNA-binding KDM2B/SKP1 heterodimer and the heterodimer of BCORL1 and PCGF1, a core component of PRC1.1. The crystal structure of the KDM2B/SKP1/BCORL1/PCGF1 complex illustrates the crucial role played by the PCGF1/BCORL1 heterodimer. The BCORL1 PUFD domain positions residues preceding the RAWUL domain of PCGF1 to create an extended interface for interaction with KDM2B, which is unique to the PCGF1-containing PRC1.1 complex. The structure also suggests how KDM2B might simultaneously function in PRC1.1 and an SCF ubiquitin ligase complex and the possible molecular consequences of BCOR PUFD internal tandem duplications found in pediatric kidney and brain tumors. Copyright © 2016 Elsevier Ltd. All rights reserved.

PDB-wide collection of binding data: current status of the PDBbind database.

PubMed

Liu, Zhihai; Li, Yan; Han, Li; Li, Jie; Liu, Jie; Zhao, Zhixiong; Nie, Wei; Liu, Yuchen; Wang, Renxiao

2015-02-01

Molecular recognition between biological macromolecules and organic small molecules plays an important role in various life processes. Both structural information and binding data of biomolecular complexes are indispensable for depicting the underlying mechanism in such an event. The PDBbind database was created to collect experimentally measured binding data for the biomolecular complexes throughout the Protein Data Bank (PDB). It thus provides the linkage between structural information and energetic properties of biomolecular complexes, which is especially desirable for computational studies or statistical analyses. Since its first public release in 2004, the PDBbind database has been updated on an annual basis. The latest release (version 2013) provides experimental binding affinity data for 10,776 biomolecular complexes in PDB, including 8302 protein-ligand complexes and 2474 other types of complexes. In this article, we will describe the current methods used for compiling PDBbind and the updated status of this database. We will also review some typical applications of PDBbind published in the scientific literature. All contents of this database are freely accessible at the PDBbind-CN Web server at http://www.pdbbind-cn.org/. wangrx@mail.sioc.ac.cn. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Changes in spectrochemical and catalytic properties of biopolymer anchored Cu(II) and Ni(II) catalysts by electron beam irradiation.

PubMed

Antony, R; Suja Pon Mini, P S; Theodore David Manickam, S; Sanjeev, Ganesh; Mitu, Liviu; Balakumar, S

2015-01-01

Chitosan (a biopolymer) anchored Cu(II) and Ni(II) Schiff base complexes, [M(OIAC)Cl2] (M: Cu/Ni and OIAC: ([2-oxo-1H-indol-3-ylidene]amino)chitosan) were electron beam irradiated by different doses (100 Gy, 1 kGy and 10 kGy). The electron beam has shown potential impact on biopolymer's support, in detail chain linking and chain scissoring, as evidenced by viscosity studies, FT-IR and X-ray diffraction spectroscopic techniques. Due to these structural changes, thermal properties of the complexes were found to be changed. The surface of these heterogeneous complexes was also effectually altered by electron beam. As a consequence, pores and holes were created as probed by SEM technique. The catalytic activity of both non-irradiated and irradiated complexes was investigated in the aerobic oxidation of cyclohexane using hydrogen peroxide oxidant. The catalytic ability of the complexes was enhanced significantly after irradiation as the result of surface changes. The reusability of the complexes was also greatly affected because of the structural variations in polymeric support. In terms of both better catalytic activity along with the reusability, 1 kGy is suggested as the best dose to attain adequate increase in catalytic activity and good reusability. Copyright © 2015 Elsevier B.V. All rights reserved.

Electrostatic redesign of the [myoglobin, cytochrome b5] interface to create a well-defined docked complex with rapid interprotein electron transfer.

PubMed

Xiong, Peng; Nocek, Judith M; Griffin, Amanda K K; Wang, Jingyun; Hoffman, Brian M

2009-05-27

Cyt b(5) is the electron-carrier "repair" protein that reduces met-Mb and met-Hb to their O(2)-carrying ferroheme forms. Studies of electron transfer (ET) between Mb and cyt b(5) revealed that they react on a "Dynamic Docking" (DD) energy landscape on which binding and reactivity are uncoupled: binding is weak and involves an ensemble of nearly isoenergetic configurations, only a few of which are reactive; those few contribute negligibly to binding. We set the task of redesigning the surface of Mb so that its reaction with cyt b(5) instead would occur on a conventional "simple docking" (SD) energy landscape, on which a complex exhibits a well-defined (set of) reactive binding configuration(s), with binding and reactivity thus no longer being decoupled. We prepared a myoglobin (Mb) triple mutant (D44K/D60K/E85K; Mb(+6)) substituted with Zn-deuteroporphyrin and monitored cytochrome b(5) (cyt b(5)) binding and electron transfer (ET) quenching of the (3)ZnMb(+6) triplet state. In contrast, to Mb(WT), the three charge reversals around the "front-face" heme edge of Mb(+6) have directed cyt b(5) to a surface area of Mb adjacent to its heme, created a well-defined, most-stable structure that supports good ET pathways, and apparently coupled binding and ET: both K(a) and k(et) are increased by the same factor of approximately 2 x 10(2), creating a complex that exhibits a large ET rate constant, k(et) = 10(6 1) s(-1), and is in slow exchange (k(off) < k(et)). In short, these mutations indeed appear to have created the sought-for conversion from DD to simple docking (SD) energy landscapes.

Accountability in the UK Healthcare System: An Overview

PubMed Central

Peckham, Stephen

2014-01-01

Recent changes in the English National Health Service (NHS) have introduced new complexities into the accountability arrangements for healthcare services. This commentary describes how the new organizational structures have challenged the traditional centralized accountability structures by creating a more dispersed system of governance for local health-care commissioners. It sets the context of discussions about accountability in the UK NHS and then describes the key changes in England following the implementation of the NHS reforms in April 2013. The commentary concludes that while there is increased complexity of accountability within a more decentralized and fragmented healthcare system, the government's goal of achieving increased local autonomy and greater control by general practitioners (GPs) will probably not be realized. In particular, the system will continue to have strongly centralized aspects, with increased regulation and central political responsibility. PMID:25305399

Anion-induced reconstitution of a self-assembling system to express a chloride-binding Co10L15 pentagonal prism.

PubMed

Riddell, Imogen A; Smulders, Maarten M J; Clegg, Jack K; Hristova, Yana R; Breiner, Boris; Thoburn, John D; Nitschke, Jonathan R

2012-09-01

Biochemical systems are adaptable, capable of reconstitution at all levels to achieve the functions associated with life. Synthetic chemical systems are more limited in their ability to reorganize to achieve new functions; they can reconfigure to bind an added substrate (template effect) or one binding event may modulate a receptor's affinity for a second substrate (allosteric effect). Here we describe a synthetic chemical system that is capable of structural reconstitution on receipt of one anionic signal (perchlorate) to create a tight binding pocket for another anion (chloride). The complex, barrel-like structure of the chloride receptor is templated by five perchlorate anions. This second-order templation phenomenon allows chemical networks to be envisaged that express more complex responses to chemical signals than is currently feasible.

Complexity and compositionality in fluid intelligence.

PubMed

Duncan, John; Chylinski, Daphne; Mitchell, Daniel J; Bhandari, Apoorva

2017-05-16

Compositionality, or the ability to build complex cognitive structures from simple parts, is fundamental to the power of the human mind. Here we relate this principle to the psychometric concept of fluid intelligence, traditionally measured with tests of complex reasoning. Following the principle of compositionality, we propose that the critical function in fluid intelligence is splitting a complex whole into simple, separately attended parts. To test this proposal, we modify traditional matrix reasoning problems to minimize requirements on information integration, working memory, and processing speed, creating problems that are trivial once effectively divided into parts. Performance remains poor in participants with low fluid intelligence, but is radically improved by problem layout that aids cognitive segmentation. In line with the principle of compositionality, we suggest that effective cognitive segmentation is important in all organized behavior, explaining the broad role of fluid intelligence in successful cognition.

Steric hindrances create a discrete linear Dy4 complex exhibiting SMM behaviour.

PubMed

Lin, Shuang-Yan; Zhao, Lang; Ke, Hongshan; Guo, Yun-Nan; Tang, Jinkui; Guo, Yang; Dou, Jianmin

2012-03-21

Two linear tetranuclear lanthanide complexes of general formula [Ln(4)(L)(2)(C(6)H(5)COO)(12)(MeOH)(4)], where HL = 2,6-bis((furan-2-ylmethylimino)methyl)-4-methylphenol, () and Ln(III) = Dy(III) (1) and Gd(III) (2), have been synthesized and characterized. The crystal structural analysis demonstrates that two Schiff-base ligands inhibit the growth of benzoate bridged 1D chains, leading to the isolation of discrete tetranuclear complexes due to their steric hindrances. Every Ln(III) ion is coordinated by eight donor atoms in a distorted bicapped trigonal-prismatic arrangement. Alternating current (ac) susceptibility measurements of complex 1 reveal a frequency- and temperature-dependent out-of-phase signal under zero dc field, typical of single-molecule magnet (SMM) behaviour with an anisotropic barrier Δ(eff) = 17.2 K.

Mimicking the colourful wing scale structure of the Papilio blumei butterfly.

PubMed

Kolle, Mathias; Salgard-Cunha, Pedro M; Scherer, Maik R J; Huang, Fumin; Vukusic, Pete; Mahajan, Sumeet; Baumberg, Jeremy J; Steiner, Ullrich

2010-07-01

The brightest and most vivid colours in nature arise from the interaction of light with surfaces that exhibit periodic structure on the micro- and nanoscale. In the wings of butterflies, for example, a combination of multilayer interference, optical gratings, photonic crystals and other optical structures gives rise to complex colour mixing. Although the physics of structural colours is well understood, it remains a challenge to create artificial replicas of natural photonic structures. Here we use a combination of layer deposition techniques, including colloidal self-assembly, sputtering and atomic layer deposition, to fabricate photonic structures that mimic the colour mixing effect found on the wings of the Indonesian butterfly Papilio blumei. We also show that a conceptual variation to the natural structure leads to enhanced optical properties. Our approach offers improved efficiency, versatility and scalability compared with previous approaches.

Binding in alkali and alkaline-earth tetrahydroborates: Special position of magnesium tetrahydroborate

NASA Astrophysics Data System (ADS)

Łodziana, Zbigniew; van Setten, Michiel J.

2010-01-01

Compounds of light elements and hydrogen are currently extensively studied due to their potential application in the field of hydrogen or energy storage. A number of new interesting tetrahydroborates that are especially promising due to their very high gravimetric hydrogen content were recently reported. However, the determination and understanding of their complex crystalline structures has created considerable debate. Metal tetrahydroborates, in general, form a large variety of structures ranging from simple for NaBH4 to very complex for Mg(BH4)2 . Despite the extensive discussion in the literature no clear explanation has been offered for this variety so far. In this paper we analyze the structural and electronic properties of a broad range of metal tetrahydroborates and reveal the factors that determine their structure: ionic bonding, the orientation of the BH4 groups, and the coordination number of the metal cation. We show, in a simple way, that the charge transfer in the metal tetrahydroborates rationally explains the structural diversity of these compounds. Being ionic systems, the metal tetrahydroborates fall into the classification of Linus Pauling. By using the ionic radius for the BH4 group as determined in this paper, this allows for structural predictions for new and mixed compounds.

A stochastic multiple imputation algorithm for missing covariate data in tree-structured survival analysis.

PubMed

Wallace, Meredith L; Anderson, Stewart J; Mazumdar, Sati

2010-12-20

Missing covariate data present a challenge to tree-structured methodology due to the fact that a single tree model, as opposed to an estimated parameter value, may be desired for use in a clinical setting. To address this problem, we suggest a multiple imputation algorithm that adds draws of stochastic error to a tree-based single imputation method presented by Conversano and Siciliano (Technical Report, University of Naples, 2003). Unlike previously proposed techniques for accommodating missing covariate data in tree-structured analyses, our methodology allows the modeling of complex and nonlinear covariate structures while still resulting in a single tree model. We perform a simulation study to evaluate our stochastic multiple imputation algorithm when covariate data are missing at random and compare it to other currently used methods. Our algorithm is advantageous for identifying the true underlying covariate structure when complex data and larger percentages of missing covariate observations are present. It is competitive with other current methods with respect to prediction accuracy. To illustrate our algorithm, we create a tree-structured survival model for predicting time to treatment response in older, depressed adults. Copyright © 2010 John Wiley & Sons, Ltd.

Three-Dimensional Printing of Complex Structures by Freeform Reversible Embedding of Suspended Hydrogels (FRESH)

NASA Astrophysics Data System (ADS)

Feinberg, Adam

We demonstrate the additive manufacturing of complex three-dimensional (3D) structures using soft protein and polysaccharide hydrogels that are challenging or impossible to create using traditional fabrication approaches. These structures are built by embedding the printed hydrogel within a secondary hydrogel that serves as a temporary, thermoreversible, and biocompatible support. This process, termed freeform reversible embedding of suspended hydrogels (FRESH), enables 3D printing of hydrated materials with an elastic modulus less than 500 kPa including alginate, collagen, hyaluronic acid and fibrin. A range of crosslinking mechanisms can be used depending on the polymer being printed, including ionic, enzymatic, pH, thermal and light based approaches. CAD models of 3D optical, computed tomography, and magnetic resonance imaging data can be 3D printed at a resolution of 100 μm and at low cost by leveraging open-source hardware and software tools. Proof-of-concept structures based on femurs, branched coronary arteries, trabeculated embryonic hearts, and human brains are mechanically robust and recreate complex 3D internal and external anatomical architectures. Recent advances have improved the resolution and broadened the range of materials that can be FRESH 3D printed. This work was supported in part by the NIH Director's New Innovator Award (DP2HL117750) and the NSF CAREER Award (1454248).

Structural basis for the recognition of Asef by adenomatous polyposis coli

PubMed Central

Zhang, Zhenyi; Chen, Leyi; Gao, Lei; Lin, Kui; Zhu, Liang; Lu, Yang; Shi, Xiaoshan; Gao, Yuan; Zhou, Jing; Xu, Ping; Zhang, Jian; Wu, Geng

2012-01-01

Adenomatous polyposis coli (APC) regulates cell-cell adhesion and cell migration through activating the APC-stimulated guanine nucleotide-exchange factor (GEF; Asef), which is usually autoinhibited through the binding between its Src homology 3 (SH3) and Dbl homology (DH) domains. The APC-activated Asef stimulates the small GTPase Cdc42, which leads to decreased cell-cell adherence and enhanced cell migration. In colorectal cancers, truncated APC constitutively activates Asef and promotes cancer cell migration and angiogenesis. Here, we report crystal structures of the human APC/Asef complex. We find that the armadillo repeat domain of APC uses a highly conserved surface groove to recognize the APC-binding region (ABR) of Asef, conformation of which changes dramatically upon binding to APC. Key residues on APC and Asef for the complex formation were mutated and their importance was demonstrated by binding and activity assays. Structural superimposition of the APC/Asef complex with autoinhibited Asef suggests that the binding between APC and Asef might create a steric clash between Asef-DH domain and APC, which possibly leads to a conformational change in Asef that stimulates its GEF activity. Our structures thus elucidate the molecular mechanism of Asef recognition by APC, as well as provide a potential target for pharmaceutical intervention against cancers. PMID:21788986

a Chiral Tagging Strategy for Determining Absolute Configuration and Enantiomeric Excess by Molecular Rotational Spectroscopy

NASA Astrophysics Data System (ADS)

Evangelisti, Luca; Caminati, Walther; Patterson, David; Thomas, Javix; Xu, Yunjie; West, Channing; Pate, Brooks

2017-06-01

The introduction of three wave mixing rotational spectroscopy by Patterson, Schnell, and Doyle [1,2] has expanded applications of molecular rotational spectroscopy into the field of chiral analysis. Chiral analysis of a molecule is the quantitative measurement of the relative abundances of all stereoisomers of the molecule and these include both diastereomers (with distinct molecular rotational spectra) and enantiomers (with equivalent molecular rotational spectra). This work adapts a common strategy in chiral analysis of enantiomers to molecular rotational spectroscopy. A "chiral tag" is attached to the molecule of interest by making a weakly bound complex in a pulsed jet expansion. When this tag molecule is enantiopure, it will create diastereomeric complexes with the two enantiomers of the molecule being analyzed and these can be differentiated by molecule rotational spectroscopy. Identifying the structure of this complex, with knowledge of the absolute configuration of the tag, establishes the absolute configuration of the molecule of interest. Furthermore, the diastereomer complex spectra can be used to determine the enantiomeric excess of the sample. The ability to perform chiral analysis will be illustrated by a study of solketal using propylene oxide as the tag. The possibility of using current methods of quantum chemistry to assign a specific structure to the chiral tag complex will be discussed. Finally, chiral tag rotational spectroscopy offers a "gold standard" method for determining the absolute configuration of the molecule through determination of the substitution structure of the complex. When this measurement is possible, rotational spectroscopy can deliver a quantitative three dimensional structure of the molecule with correct stereochemistry as the analysis output. [1] David Patterson, Melanie Schnell, John M. Doyle, Nature 497, 475 (2013). [2] David Patterson, John M. Doyle, Phys. Rev. Lett. 111, 023008 (2013).

Architectures for Cognitive Systems

DTIC Science & Technology

2010-02-01

highly modular many- node chip was designed which addressed power efficiency to the maximum extent possible. Each node contains an Asynchronous Field...optimization to perform complex cognitive computing operations. This project focused on the design of the core and integration across a four node chip . A...follow on project will focus on creating a 3 dimensional stack of chips that is enabled by the low power usage. The chip incorporates structures to

Study of Varying Boundary Layer Height on Turret Flow Structures

DTIC Science & Technology

2011-06-01

fluid dynamics. The difficulties of the problem arise in modeling several complex flow features including separation, reattachment, three-dimensional...impossible. In this case, the approach is to create a model to calculate the properties of interest. The main issue with resolving turbulent flows...operation and their effect is modeled through subgrid scale models . As a result, the the most important turbulent scales are resolved and the

Magnetic tape user guide

NASA Technical Reports Server (NTRS)

Evans, A. B.; Lee, L. L.

1985-01-01

This User Guide provides a general introduction to the structure, use, and handling of magnetic tapes at Langley Research Center (LaRC). The topics covered are tape terminology, physical characteristics, error prevention and detection, and creating, using, and maintaining tapes. Supplementary documentation is referenced where it might be helpful. The documentation is included for the tape utility programs, BLOCK, UNBLOCK, and TAPEDMP, which are available at the Central Scientific Computing Complex at LaRC.

Specialty Task Force: A Strategic Component to Electronic Health Record (EHR) Optimization.

PubMed

Romero, Mary Rachel; Staub, Allison

2016-01-01

Post-implementation stage comes after an electronic health record (EHR) deployment. Analyst and end users deal with the reality that some of the concepts and designs initially planned and created may not be complementary to the workflow; creating anxiety, dissatisfaction, and failure with early adoption of system. Problems encountered during deployment are numerous and can vary from simple to complex. Redundant ticket submission creates backlog for Information Technology personnel resulting in delays in resolving concerns with EHR system. The process of optimization allows for evaluation of system and reassessment of users' needs. A solid and well executed optimization infrastructure can help minimize unexpected end-user disruptions and help tailor the system to meet regulatory agency goals and practice standards. A well device plan to resolve problems during post implementation is necessary for cost containment and to streamline communication efforts. Creating a specialty specific collaborative task force is efficacious and expedites resolution of users' concerns through a more structured process.

Combinatorics and synchronization in natural semiotics

NASA Astrophysics Data System (ADS)

Orsucci, Franco; Giuliani, Alessandro; Webber, Charles; Zbilut, Joseph; Fonagy, Peter; Mazza, Marianna

2006-03-01

In this study the derivation of an objective metrics to appreciate the degree of structuring of written and spoken texts is presented. The proposed metrics is based on the scoring of recurrences inside a text by means of the application of recurrence quantification analysis (RQA), a nonlinear technique widely used in other fields of sciences. The adopted approach allowed us to create a ranking of different poems strictly related to their prosodic structure and, more importantly, the possibility to recognize the same structure across different languages, to define a level of structuring typical of spoken texts and identifying the progressive synchronization of a dyadic relation between two speakers in terms of relative complexity of their speeches. These results suggest the possibility of introducing objective measurement methods into humanities studies.

Bio-Organic Nanotechnology: Using Proteins and Synthetic Polymers for Nanoscale Devices

NASA Technical Reports Server (NTRS)

Molnar, Linda K.; Xu, Ting; Trent, Jonathan D.; Russell, Thomas P.

2003-01-01

While the ability of proteins to self-assemble makes them powerful tools in nanotechnology, in biological systems protein-based structures ultimately depend on the context in which they form. We combine the self-assembling properties of synthetic diblock copolymers and proteins to construct intricately ordered, three-dimensional polymer protein structures with the ultimate goal of forming nano-scale devices. This hybrid approach takes advantage of the capabilities of organic polymer chemistry to build ordered structures and the capabilities of genetic engineering to create proteins that are selective for inorganic or organic substrates. Here, microphase-separated block copolymers coupled with genetically engineered heat shock proteins are used to produce nano-scale patterning that maximizes the potential for both increased structural complexity and integrity.

Ice matrix in reconfigurable microfluidic systems

NASA Astrophysics Data System (ADS)

Bossi, A. M.; Vareijka, M.; Piletska, E. V.; Turner, A. P. F.; Meglinski, I.; Piletsky, S. A.

2013-07-01

Microfluidic devices find many applications in biotechnologies. Here, we introduce a flexible and biocompatible microfluidic ice-based platform with tunable parameters and configuration of microfluidic patterns that can be changed multiple times during experiments. Freezing and melting of cavities, channels and complex relief structures created and maintained in the bulk of ice by continuous scanning of an infrared laser beam are used as a valve action in microfluidic systems. We demonstrate that pre-concentration of samples and transport of ions and dyes through the open channels created can be achieved in ice microfluidic patterns by IR laser-assisted zone melting. The proposed approach can be useful for performing separation and sensing processes in flexible reconfigurable microfluidic devices.

Hierarchical Ada robot programming system (HARPS)- A complete and working telerobot control system based on the NASREM model

NASA Technical Reports Server (NTRS)

Leake, Stephen; Green, Tom; Cofer, Sue; Sauerwein, Tim

1989-01-01

HARPS is a telerobot control system that can perform some simple but useful tasks. This capability is demonstrated by performing the ORU exchange demonstration. HARPS is based on NASREM (NASA Standard Reference Model). All software is developed in Ada, and the project incorporates a number of different CASE (computer-aided software engineering) tools. NASREM was found to be a valid and useful model for building a telerobot control system. Its hierarchical and distributed structure creates a natural and logical flow for implementing large complex robust control systems. The ability of Ada to create and enforce abstraction enhanced the implementation of such control systems.

Engineering fluid flow using sequenced microstructures

NASA Astrophysics Data System (ADS)

Amini, Hamed; Sollier, Elodie; Masaeli, Mahdokht; Xie, Yu; Ganapathysubramanian, Baskar; Stone, Howard A.; di Carlo, Dino

2013-05-01

Controlling the shape of fluid streams is important across scales: from industrial processing to control of biomolecular interactions. Previous approaches to control fluid streams have focused mainly on creating chaotic flows to enhance mixing. Here we develop an approach to apply order using sequences of fluid transformations rather than enhancing chaos. We investigate the inertial flow deformations around a library of single cylindrical pillars within a microfluidic channel and assemble these net fluid transformations to engineer fluid streams. As these transformations provide a deterministic mapping of fluid elements from upstream to downstream of a pillar, we can sequentially arrange pillars to apply the associated nested maps and, therefore, create complex fluid structures without additional numerical simulation. To show the range of capabilities, we present sequences that sculpt the cross-sectional shape of a stream into complex geometries, move and split a fluid stream, perform solution exchange and achieve particle separation. A general strategy to engineer fluid streams into a broad class of defined configurations in which the complexity of the nonlinear equations of fluid motion are abstracted from the user is a first step to programming streams of any desired shape, which would be useful for biological, chemical and materials automation.

RMS Titanic and the emergence of new concepts on consortial nature of microbial events.

PubMed

Cullimore, D Roy; Pellegrino, Charles; Johnston, Lori

2002-01-01

The RMS Titanic sank in 1912 and created a historical event that still ripples through time. Stories were told and lessons learned but the science has only just begun. Today the fading remains of the ship resemble the hanging gardens of Babylon except that it is not plants that drape the walls but complex microbial growths called rusticles. These organisms have been found to be not a species, like plants and animals, but to be structures created by complex communities of bacterial species. Like the discovery of tube worms in the mid-oceanic vents, the nature of these rusticles presents another biological discovery of a fundamental nature. Essentially these microbial consortia on the RMS Titanic have generated structures of a mass that would rival whales and elephants while gradually extracting the iron from the steel. Rusticle-like consortia appear to play many roles within the environment, and it is perhaps the RMS Titanic that is showing that there is a new way to understand the form, function, and nature of microorganisms. This understanding would develop by considering the bacteria not as individual species functioning independently but as consortia of species functioning in community structures within a common habitat. This concept, if adopted, would change dramatically the manner in which a microbial ecologist and any scientist or engineer would view the occurrence of a slime, encrustation, biocolloid, rust flake, iron pan, salt deposit, and perhaps even some of the diseases that remain unexplained as a disease of unknown cause.

Organogold oligomers: Exploiting iClick and aurophilic cluster formation to prepare solution stable Au 4 repeating units

DOE PAGES

Yang, Xi; Wang, Shanshan; Ghiviriga, Ion; ...

2015-05-19

A novel synthetic method to create gold based metallo–oligomers/polymers via the combination of inorganic click (iClick) with intermolecular aurophilic interactions is demonstrated. Complexes [PEt 3Au] 4(μ-N 3C 2C 6H 5) (1) and [PPhMe 2Au] 43C 2C 6H 5) (2) and {[PEt 3Au] 4[(μ-N 3C 2) 2-9,9-dihexyl-9H-fluorene]} n (8) have been synthesized via iClick. The tetranuclear structures of 1 and 2, induced by aurophilic bonding, are confirmed in the solid state through single crystal X-ray diffraction experiments and in solution via variable temperature NMR spectroscopy. The extended 1D structure of 8 is constructed by aurophilic induced self-assembly. 1H DOSY NMR analysismore » reveals that the aurophilic bonds in 1, 2, and 8 are retained in the solution phase. The degree of polymerization within complex 8 is temperature and concentration dependent, as determined by 1H DOSY NMR. The complex 8 is a rare example of a solution stable higher ordered structure linked by aurophilic interactions.« less

Vacancy-impurity centers in diamond: prospects for synthesis and applications

NASA Astrophysics Data System (ADS)

Ekimov, E. A.; Kondrin, M. V.

2017-06-01

The bright luminescence of impurity-vacancy complexes, combined with high chemical and radiation resistance, makes diamond an attractive platform for the production of single-photon emitters and luminescent biomarkers for applications in nanoelectronics and medicine. Two representatives of this kind of defects in diamond, silicon-vacancy (SiV) and germanium-vacancy (GeV) centers, are discussed in this review; their similarities and differences are demonstrated in terms of the more thoroughly studied nitrogen-vacancy (NV) complexes. The recent discovery of GeV luminescent centers opens a unique opportunity for the controlled synthesis of single-photon emitters in nanodiamonds. We demonstrate prospects for the high-pressure high-temperature (HPHT) technique to create single-photon emitters, not only as an auxiliary to chemical vapor deposition (CVD) and ion-implantation methods but also as a primary synthesis tool for producing color centers in nanodiamonds. Besides practical applications, comparative studies of these two complexes, which belong to the same structural class of defects, have a fundamental importance for deeper understanding of shelving levels, the electronic structure, and optical properties of these centers. In conclusion, we discuss several open problems regarding the structure, charge state, and practical application of these centers, which still require a solution.

Memory for product sounds: the effect of sound and label type.

PubMed

Ozcan, Elif; van Egmond, René

2007-11-01

The (mnemonic) interactions between auditory, visual, and the semantic systems have been investigated using structurally complex auditory stimuli (i.e., product sounds). Six types of product sounds (air, alarm, cyclic, impact, liquid, mechanical) that vary in spectral-temporal structure were presented in four label type conditions: self-generated text, text, image, and pictogram. A memory paradigm that incorporated free recall, recognition, and matching tasks was employed. The results for the sound type suggest that the amount of spectral-temporal structure in a sound can be indicative for memory performance. Findings related to label type suggest that 'self' creates a strong bias for the retrieval and the recognition of sounds that were self-labeled; the density and the complexity of the visual information (i.e., pictograms) hinders the memory performance ('visual' overshadowing effect); and image labeling has an additive effect on the recall and matching tasks (dual coding). Thus, the findings suggest that the memory performances for product sounds are task-dependent.

Structural Basis for Selective Inhibition of Mycobacterium tuberculosis Protein Tyrosine Phosphatase PtpB

PubMed Central

Grundner, Christoph; Perrin, Dominique; van Huijsduijnen, Rob Hooft; Swinnen, Dominique; Gonzalez, Jérome; Gee, Christine L.; Wells, Timothy N.; Alber, Tom

2007-01-01

Tyrosine kinases and phosphatases establish the crucial balance of tyrosine phosphorylation in cellular signaling, but creating specific inhibitors of protein Tyr phosphatases (PTPs) remains a challenge. Here we report the development of a potent, selective inhibitor of Mycobacterium tuberculosis PtpB, a bacterial PTP that is secreted into host cells where it disrupts unidentified signaling pathways. The inhibitor, (oxalylamino-methylene)-thiophene sulfonamide (OMTS), showed an IC50 of 440 +/− 50 nM and >60-fold specificity for PtpB over six human PTPs. The 2-Å resolution crystal structure of PtpB in complex with OMTS revealed a large rearrangement of the enzyme, with some residues shifting >27 Å relative to the PtpB:PO4 complex. Extensive contacts with the catalytic loop provide a potential basis for inhibitor selectivity. Two OMTS molecules bound adjacent to each other, raising the possibility of a second substrate phosphotyrosine binding site in PtpB. The PtpB:OMTS structure provides an unanticipated framework to guide inhibitor improvement. PMID:17437721

Adding Hierarchical Objects to Relational Database General-Purpose XML-Based Information Managements

NASA Technical Reports Server (NTRS)

Lin, Shu-Chun; Knight, Chris; La, Tracy; Maluf, David; Bell, David; Tran, Khai Peter; Gawdiak, Yuri

2006-01-01

NETMARK is a flexible, high-throughput software system for managing, storing, and rapid searching of unstructured and semi-structured documents. NETMARK transforms such documents from their original highly complex, constantly changing, heterogeneous data formats into well-structured, common data formats in using Hypertext Markup Language (HTML) and/or Extensible Markup Language (XML). The software implements an object-relational database system that combines the best practices of the relational model utilizing Structured Query Language (SQL) with those of the object-oriented, semantic database model for creating complex data. In particular, NETMARK takes advantage of the Oracle 8i object-relational database model using physical-address data types for very efficient keyword searches of records across both context and content. NETMARK also supports multiple international standards such as WEBDAV for drag-and-drop file management and SOAP for integrated information management using Web services. The document-organization and -searching capabilities afforded by NETMARK are likely to make this software attractive for use in disciplines as diverse as science, auditing, and law enforcement.

Semiconductor nanowires: A platform for nanoscience and nanotechnology

PubMed Central

Lieber, Charles M.

2012-01-01

Advances in nanoscience and nanotechnology critically depend on the development of nanostructures whose properties are controlled during synthesis. We focus on this critical concept using semiconductor nanowires, which provide the capability through design and rational synthesis to realize unprecedented structural and functional complexity in building blocks as a platform material. First, a brief review of the synthesis of complex modulated nanowires in which rational design and synthesis can be used to precisely control composition, structure, and, most recently, structural topology is discussed. Second, the unique functional characteristics emerging from our exquisite control of nanowire materials are illustrated using several selected examples from nanoelectronics and nano-enabled energy. Finally, the remarkable power of nanowire building blocks is further highlighted through their capability to create unprecedented, active electronic interfaces with biological systems. Recent work pushing the limits of both multiplexed extracellular recording at the single-cell level and the first examples of intracellular recording is described, as well as the prospects for truly blurring the distinction between nonliving nanoelectronic and living biological systems. PMID:22707850

Effects of reactive Mn(III)-oxalate complexes on structurally intact plant cell walls

NASA Astrophysics Data System (ADS)

Summering, J. A.; Keiluweit, M.; Goni, M. A.; Nico, P. S.; Kleber, M.

2011-12-01

Lignin components in the in plant litter are commonly assumed to have longer residence times in soil than many other compounds, which are supposedly, more easily degradable. The supposed resistance of lignin compounds to decomposition is generally attributed to the complex chain of biochemical steps required to create footholds in the non-porous structure of ligno-cellulose in cell walls. Interestingly, Mn(III) complexes have shown the ability to degrade ligno-cellulose. Mn(III) chelated by ligands such as oxalate are soluble oxidizers with a high affinity for lignin structures. Here we determined (i) the formation and decay kinetics of the Mn(III)-oxalate complexes in aqueous solution and (ii) the effects that these complexes have on intact ligno-cellulose. UV/vis spectroscopy and iodometric titrations confirmed the transient nature of Mn(III)-oxalate complexes with decay rates being in the order of hours. Zinnia elegans tracheary elements - a model ligno-cellulose substrate - were treated with Mn(III)-oxalate complexes in a newly developed flow-through reactor. Soluble decomposition products released during the treatment were analyzed by GC/MS and the degree of cell integrity was measured by cell counts, pre- and post-treatment counts indicate a decrease in intact Zinnia elegans as a result of Mn(III)-treatment. GC/MS results showed the release of a multitude of solubilized lignin breakdown products from plant cell walls. We conclude that Mn(III)-oxalate complexes have the ability to lyse intact plant cells and solubilize lignin. Lignin decomposition may thus be seen as resource dependent, with Mn(III) a powerful resource that should be abundant in terrestrial characterized by frequent redox fluctuations.

NCAR's Research Data Archive: OPeNDAP Access for Complex Datasets

NASA Astrophysics Data System (ADS)

Dattore, R.; Worley, S. J.

2014-12-01

Many datasets have complex structures including hundreds of parameters and numerous vertical levels, grid resolutions, and temporal products. Making these data accessible is a challenge for a data provider. OPeNDAP is powerful protocol for delivering in real-time multi-file datasets that can be ingested by many analysis and visualization tools, but for these datasets there are too many choices about how to aggregate. Simple aggregation schemes can fail to support, or at least make it very challenging, for many potential studies based on complex datasets. We address this issue by using a rich file content metadata collection to create a real-time customized OPeNDAP service to match the full suite of access possibilities for complex datasets. The Climate Forecast System Reanalysis (CFSR) and it's extension, the Climate Forecast System Version 2 (CFSv2) datasets produced by the National Centers for Environmental Prediction (NCEP) and hosted by the Research Data Archive (RDA) at the Computational and Information Systems Laboratory (CISL) at NCAR are examples of complex datasets that are difficult to aggregate with existing data server software. CFSR and CFSv2 contain 141 distinct parameters on 152 vertical levels, six grid resolutions and 36 products (analyses, n-hour forecasts, multi-hour averages, etc.) where not all parameter/level combinations are available at all grid resolution/product combinations. These data are archived in the RDA with the data structure provided by the producer; no additional re-organization or aggregation have been applied. Since 2011, users have been able to request customized subsets (e.g. - temporal, parameter, spatial) from the CFSR/CFSv2, which are processed in delayed-mode and then downloaded to a user's system. Until now, the complexity has made it difficult to provide real-time OPeNDAP access to the data. We have developed a service that leverages the already-existing subsetting interface and allows users to create a virtual dataset with its own structure (das, dds). The user receives a URL to the customized dataset that can be used by existing tools to ingest, analyze, and visualize the data. This presentation will detail the metadata system and OPeNDAP server that enable user-customized real-time access and show an example of how a visualization tool can access the data.

Programmable self-assembly of three-dimensional nanostructures from 104 unique components

PubMed Central

Ong, Luvena L.; Hanikel, Nikita; Yaghi, Omar K.; Grun, Casey; Strauss, Maximilian T.; Bron, Patrick; Lai-Kee-Him, Josephine; Schueder, Florian; Wang, Bei; Wang, Pengfei; Kishi, Jocelyn Y.; Myhrvold, Cameron A.; Zhu, Allen; Jungmann, Ralf

2017-01-01

Nucleic acids (DNA and RNA) are widely used to construct nanoscale structures with ever increasing complexity1–14 for possible applications in fields as diverse as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early examples typically containing on the order of 10 unique DNA strands. The introduction of DNA origami4, which uses many staple strands to fold one long scaffold strand into a desired structure, gave access to kilo- to mega-dalton nanostructures containing about 102 unique DNA strands6,7,10,13 . Aiming for even larger DNA origami structures is in principle possible15,16, but faces the challenge of having to manufacture and route an increasingly long scaffold strand. An alternative and in principle more readily scalable approach uses DNA brick assembly8,9, which doesn’t need a scaffold and instead uses hundreds of short DNA brick strands that self-assemble according to specific inter-brick interactions. First-generation bricks used to create 3D structures are 32-nt long with four 8-nt binding domains that directed 102 distinct bricks into well-formed assemblies, but attempts to create larger structures encountered practical challenges and had limited success.9 Here we show that a new generation of DNA bricks with longer binding domains makes it possible to self-assemble 0.1 – 1 giga-dalton three-dimensional nanostructures from 104 unique components, including a 0.5 giga-dalton cuboid containing 30,000 unique bricks and a 1 giga-dalton rotationally symmetric tetramer. We also assemble a cuboid containing 10,000 bricks and 20,000 uniquely addressable ‘nano-voxels’ that serves as a molecular canvas for three-dimensional sculpting, with introduction of sophisticated user-prescribed 3D cavities yielding structures such as letters, a complex helicoid and a teddy bear. We anticipate that, with further optimization, even larger assemblies might be accessible and prove useful as scaffolds or for positioning functional components. PMID:29219968

Synthesis, X-ray structure and cytotoxic effect of nickel(II) complexes with pyrazole ligands.

PubMed

Sobiesiak, Marta; Lorenz, Ingo-Peter; Mayer, Peter; Woźniczka, Magdalena; Kufelnicki, Aleksander; Krajewska, Urszula; Rozalski, Marek; Budzisz, Elzbieta

2011-12-01

Here we present the synthesis of the new Ni(II) complexes with chelating ligands 1-benzothiazol-2-yl-3,5-dimethyl-1H-pyrazole (a), 5-(2-hydroxyphenyl)-3-methyl-1-(2-pyridylo)-1H-pyrazole-4-carboxylic acid methyl ester (b) and 1-benzothiazol-2-yl-5-(2-hydroxyphenyl)-3-methyl-1H-pyrazole-4-carboxylic acid methyl ester (c). These ligands a-c create solid complexes with Ni(II). The crystal and molecular structures of two complexes were determined by X-ray diffraction method. Thermal stability of two complexes with ligand c by TG/DTG and DSC methods were also shown. Cytotoxic activity of all the complexes against three tumour cell lines and to normal endothelial cells (HUVEC) was also estimated. Complexes with ligand c exhibited relatively high cytotoxic activity towards HL-60 and NALM-6 leukaemia cells and WM-115 melanoma cells. Cytotoxic effectiveness of one of these complexes against melanoma WM-115 cells was two times higher than that of cisplatin. The protonation constant log K=9.63 of ligand b corresponding to the phenol 2-hydroxy group has been determined in 10% (v/v) DMSO/water solution (25°C). The coordination modes (formation of two monomeric species: NiL and NiL(2)) in the complexes with Ni(II) are discussed for b on the basis of the potentiometric and UV/Vis data. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

Ab-initio calculation for cation vacancy formation energy in anti-fluorite structure

NASA Astrophysics Data System (ADS)

Saleel, V. P. Saleel Ahammad; Chitra, D.; Veluraja, K.; Eithiraj, R. D.

2018-04-01

Lithium oxide (Li2O) has been suggested as a suitable breeder blanket material for fusion reactors. Li+ vacancies are created by neutron irradiation, forming bulk defect complex whose extra character is experimentally unclear. We present a theoretical study of Li2O using density functional theory (DFT) with a plane-wave basis set. The generalized gradient approximation (GGA) and local-density approximation (LDA) were used for exchange and correlation. Here we address the total energy for defect free, cation defect, cation vacancy and vacancy formation energy in Li2O crystal in anti-fluorite structure.

Structure and Engineering of Francisella novicida Cas9

PubMed Central

Hirano, Hisato; Gootenberg, Jonathan S.; Horii, Takuro; Abudayyeh, Omar O.; Kimura, Mika; Hsu, Patrick D.; Nakane, Takanori; Ishitani, Ryuichiro; Hatada, Izuho; Zhang, Feng; Nishimasu, Hiroshi; Nureki, Osamu

2016-01-01

Summary The RNA-guided endonuclease Cas9 cleaves double-stranded DNA targets complementary to the guide RNA, and has been applied to programmable genome editing. Cas9-mediated cleavage requires a protospacer adjacent motif (PAM) juxtaposed with the DNA target sequence, thus constricting the range of targetable sites. Here, we report the 1.7 Å resolution crystal structures of Cas9 from Francisella novicida (FnCas9), one of the largest Cas9 orthologs, in complex with a guide RNA and its PAM-containing DNA targets. A structural comparison of FnCas9 with other Cas9 orthologs revealed striking conserved and divergent features among distantly related CRISPR-Cas9 systems. We found that FnCas9 recognizes the 5′-NGG-3′ PAM, and used the structural information to create a variant that can recognize the more relaxed 5′-YG-3′ PAM. Furthermore, we demonstrated that pre-assembled FnCas9 ribonucleoprotein complexes can be microinjected into mouse zygotes to edit endogenous sites with the 5′-YG-3′ PAMs, thus expanding the target space of the CRISPR-Cas9 toolbox. PMID:26875867

Structure transition in lipids and nucleic acids of tumor cells under anticancer drugs applications

NASA Astrophysics Data System (ADS)

Dovbeshko, G. I.; Repnytska, O. P.; Tryndiak, V. P.; Todor, I. N.

2003-12-01

Interaction of DNA and phospholipids from Carcinoma Guerina resistant and sensitive cells of Wistar line rats with anti-cancer drugs - cis-platin and doxorubicin (DOX) have been studied in vivo and in vitro experiments. Surface enhanced infrared absorption (SEIRA) spectroscopy was applied for registration of conformational changes in DNA and lipids induced by anti-cancer drugs. It has been shown in vivo experiment that doxorubicin influences less structural disordering of the membrane than cis-platin. Cis-platin creates irreversible complex with memebrane phospholipids, strongly interacting with phosophates and carbohydrate chains. Doxorubicin influences the ordering of carbohydrate chains and does not strongly influence phosphate heads. This change seems to be partially reversible. In contrast, in vivo experiment the doxorubicin strongly influences the DNA structure, leading to DNA stabilization and formation of new H-bonds in DNA-doxorubicin complex. We have not registered the interaction of DNA with cis-platin in vivo experiment. Experiment in vitro for cis-platin incubation with phospholipids from cancer cells during 0.5 hour at 37°C has not shown those drastic structural peculiarities that it was observed in vivo experiments.

Probing Protein Structure in Vivo with FRET

PubMed Central

Davis, Trisha; Muller, Eric

2012-01-01

Fluorescence resonance energy transfer (FRET) is widely used to construct probes for cellular activities and to complement two-hybrid results that predict protein-protein interactions. The Yeast Resource Center promotes an underutilized potential of FRET as an in vivo tool to position proteins within low resolution structures derived from electron microscopy. The success of this approach using widefield microscopy depends upon the choice of filter sets, standardized image acquisition, a robust metric and controls matched to the structure under investigation. A comparison of various CFP and YFP filter combinations from Chroma and Semrock demonstrated the strength of the Chroma filters when coupled with our FRET metric, termed FretR. Coupling CFP and YFP to a selection of proteins of known structure allowed us to create a standard curve of FretR versus distance. How well other FRET metrics conform was also evaluated. Finally FretR was linked to an approximation of the efficiency of energy transfer. Together this feature set has allowed us to contribute to our understanding of the organization of the yeast spindle pole body, cohesin complex and gamma-tubulin complex.

SM-TF: A structural database of small molecule-transcription factor complexes.

PubMed

Xu, Xianjin; Ma, Zhiwei; Sun, Hongmin; Zou, Xiaoqin

2016-06-30

Transcription factors (TFs) are the proteins involved in the transcription process, ensuring the correct expression of specific genes. Numerous diseases arise from the dysfunction of specific TFs. In fact, over 30 TFs have been identified as therapeutic targets of about 9% of the approved drugs. In this study, we created a structural database of small molecule-transcription factor (SM-TF) complexes, available online at http://zoulab.dalton.missouri.edu/SM-TF. The 3D structures of the co-bound small molecule and the corresponding binding sites on TFs are provided in the database, serving as a valuable resource to assist structure-based drug design related to TFs. Currently, the SM-TF database contains 934 entries covering 176 TFs from a variety of species. The database is further classified into several subsets by species and organisms. The entries in the SM-TF database are linked to the UniProt database and other sequence-based TF databases. Furthermore, the druggable TFs from human and the corresponding approved drugs are linked to the DrugBank. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Structure and Engineering of Francisella novicida Cas9.

PubMed

Hirano, Hisato; Gootenberg, Jonathan S; Horii, Takuro; Abudayyeh, Omar O; Kimura, Mika; Hsu, Patrick D; Nakane, Takanori; Ishitani, Ryuichiro; Hatada, Izuho; Zhang, Feng; Nishimasu, Hiroshi; Nureki, Osamu

2016-02-25

The RNA-guided endonuclease Cas9 cleaves double-stranded DNA targets complementary to the guide RNA and has been applied to programmable genome editing. Cas9-mediated cleavage requires a protospacer adjacent motif (PAM) juxtaposed with the DNA target sequence, thus constricting the range of targetable sites. Here, we report the 1.7 Å resolution crystal structures of Cas9 from Francisella novicida (FnCas9), one of the largest Cas9 orthologs, in complex with a guide RNA and its PAM-containing DNA targets. A structural comparison of FnCas9 with other Cas9 orthologs revealed striking conserved and divergent features among distantly related CRISPR-Cas9 systems. We found that FnCas9 recognizes the 5'-NGG-3' PAM, and used the structural information to create a variant that can recognize the more relaxed 5'-YG-3' PAM. Furthermore, we demonstrated that the FnCas9-ribonucleoprotein complex can be microinjected into mouse zygotes to edit endogenous sites with the 5'-YG-3' PAM, thus expanding the target space of the CRISPR-Cas9 toolbox. Copyright © 2016 Elsevier Inc. All rights reserved.

[3,3]-Sigmatropic rearrangements: recent applications in the total synthesis of natural products†

PubMed Central

Ilardi, Elizabeth A.; Stivala, Craig E.

2014-01-01

Among the fundamental chemical transformations in organic synthesis, the [3,3]-sigmatropic rearrangement occupies a unique position as a powerful, reliable, and well-defined method for the stereoselective construction of carbon–carbon or carbon–heteroatom bonds. While many other reactions can unite two subunits and create a new bond, the strengths of sigmatropic rearrangements derive from their ability to enable structural reorganization with unmatched build-up of complexity. Recent applications that illustrate [3,3]-sigmatropic processes as a key concept in the synthesis of complex natural products are described in this tutorial review, covering literature from about 2001 through early 2009. PMID:19847347

Molecular engineering of polymersome surface topology

PubMed Central

Ruiz-Pérez, Lorena; Messager, Lea; Gaitzsch, Jens; Joseph, Adrian; Sutto, Ludovico; Gervasio, Francesco Luigi; Battaglia, Giuseppe

2016-01-01

Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from the molecular to mesoscopic level. We report an example of using fully synthetic systems that mimic two levels of self-assembly. We show the formation of vesicles using amphiphilic copolymers whose chemical nature is chosen to control both membrane formation and membrane-confined interactions. We report polymersomes with patterns that emerge by engineering interfacial tension within the polymersome surface. This allows the formation of domains whose topology is tailored by chemical synthesis, paving the avenue to complex supramolecular designs functionally similar to those found in viruses and trafficking vesicles. PMID:27152331

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

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

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

An affinity-structure database of helix-turn-helix: DNA complexes with a universal coordinate system

DOE PAGES

AlQuraishi, Mohammed; Tang, Shengdong; Xia, Xide

2015-11-19

Molecular interactions between proteins and DNA molecules underlie many cellular processes, including transcriptional regulation, chromosome replication, and nucleosome positioning. Computational analyses of protein-DNA interactions rely on experimental data characterizing known protein-DNA interactions structurally and biochemically. While many databases exist that contain either structural or biochemical data, few integrate these two data sources in a unified fashion. Such integration is becoming increasingly critical with the rapid growth of structural and biochemical data, and the emergence of algorithms that rely on the synthesis of multiple data types to derive computational models of molecular interactions. We have developed an integrated affinity-structure database inmore » which the experimental and quantitative DNA binding affinities of helix-turn-helix proteins are mapped onto the crystal structures of the corresponding protein-DNA complexes. This database provides access to: (i) protein-DNA structures, (ii) quantitative summaries of protein-DNA binding affinities using position weight matrices, and (iii) raw experimental data of protein-DNA binding instances. Critically, this database establishes a correspondence between experimental structural data and quantitative binding affinity data at the single basepair level. Furthermore, we present a novel alignment algorithm that structurally aligns the protein-DNA complexes in the database and creates a unified residue-level coordinate system for comparing the physico-chemical environments at the interface between complexes. Using this unified coordinate system, we compute the statistics of atomic interactions at the protein-DNA interface of helix-turn-helix proteins. We provide an interactive website for visualization, querying, and analyzing this database, and a downloadable version to facilitate programmatic analysis. Lastly, this database will facilitate the analysis of protein-DNA interactions and the development of programmatic computational methods that capitalize on integration of structural and biochemical datasets. The database can be accessed at http://ProteinDNA.hms.harvard.edu.« less

Synthesis of dynamic phase profile by the correlation technique for spatial control of optical beams in multiplexing and switching

NASA Astrophysics Data System (ADS)

Bugaychuk, Svitlana A.; Gnatovskyy, Vladimir O.; Sidorenko, Andrey V.; Pryadko, Igor I.; Negriyko, Anatoliy M.

2015-11-01

New approach for the correlation technique, which is based on multiple periodic structures to create a controllable angular spectrum, is proposed and investigated both theoretically and experimentally. The transformation of an initial laser beam occurs due to the actions of consecutive phase periodic structures, which may differ by their parameters. Then, after the Fourier transformation of a complex diffraction field, the output diffraction orders will be changed both by their intensities and by their spatial position. The controllable change of output angular spectrum is carried out by a simple control of the parameters of the periodic structures. We investigate several simple examples of such management.

Workshop on Molecular Animation

PubMed Central

Bromberg, Sarina; Chiu, Wah; Ferrin, Thomas E.

2011-01-01

Summary February 25–26, 2010, in San Francisco, the Resource for Biocomputing, Visualization and Informatics (RBVI) and the National Center for Macromolecular Imaging (NCMI) hosted a molecular animation workshop for 21 structural biologists, molecular animators, and creators of molecular visualization software. Molecular animation aims to visualize scientific understanding of biomolecular processes and structures. The primary goal of the workshop was to identify the necessary tools for: producing high quality molecular animations, understanding complex molecular and cellular structures, creating publication supplementary materials and conference presentations, and teaching science to students and the public. Another use of molecular animation emerged in the workshop: helping to focus scientific inquiry about the motions of molecules and enhancing informal communication within and between laboratories. PMID:20947014

Generation of continuously rotating polarization by combining cross-polarizations and its application in surface structuring.

PubMed

Lam, Billy; Zhang, Jihua; Guo, Chunlei

2017-08-01

In this study, we develop a simple but highly effective technique that generates a continuously varying polarization within a laser beam. This is achieved by having orthogonal linear polarizations on each side of the beam. By simply focusing such a laser beam, we can attain a gradually and continuously changing polarization within the entire Rayleigh range due to diffraction. To demonstrate this polarization distribution, we apply this laser beam onto a metal surface and create a continuously rotating laser induced periodic surface structure pattern. This technique provides a very effective way to produce complex surface structures that may potentially find applications, such as polarization modulators and metasurfaces.

Cytoskeletal motor-driven active self-assembly in in vitro systems

DOE PAGES

Lam, A. T.; VanDelinder, V.; Kabir, A. M. R.; ...

2015-11-11

Molecular motor-driven self-assembly has been an active area of soft matter research for the past decade. Because molecular motors transform chemical energy into mechanical work, systems which employ molecular motors to drive self-assembly processes are able to overcome kinetic and thermodynamic limits on assembly time, size, complexity, and structure. Here, we review the progress in elucidating and demonstrating the rules and capabilities of motor-driven active self-assembly. Lastly, we focus on the types of structures created and the degree of control realized over these structures, and discuss the next steps necessary to achieve the full potential of this assembly mode whichmore » complements robotic manipulation and passive self-assembly.« less

Oyster reef restoration in the Northern Gulf of Mexico: effect of artificial substrate and sge on nekton and benthic macroinvertebrate assemblage use

USGS Publications Warehouse

Brown, Laura A.; Furlong, Jessica N.; Brown, Kenneth M.; LaPeyre, Megan K.

2013-01-01

In the northern Gulf of Mexico (GOM), reefs built by eastern oysters, Crassostrea virginica, provide critical habitat within shallow estuaries, and recent efforts have focused on restoring reefs to benefit nekton and benthic macroinvertebrates. We compared nekton and benthic macroinvertebrate assemblages at historic, newly created (<5years) and old (>6years) shell and rock substrate reefs. Using crab traps, gill-nets, otter trawls, cast nets, and benthic macroinvertebrate collectors, 20 shallow reefs (<5m) in the northern GOM were sampled throughout the summer of 2011. We compared nekton and benthic assemblage abundance, diversity and composition across reef types. Except for benthic macroinvertebrate abundance, which was significantly higher on old rock reefs as compared to historic reefs, all reefs were similar to historic reefs, suggesting created reefs provide similar support of nekton and benthic assemblages as historic reefs. To determine refuge value of oyster structure for benthic macroinvertebrates compared to bare bottom, we tested preferences of juvenile crabs across depth and refuge complexity in the presence and absence of adult blue crabs (Callinectes sapidus). Juveniles were more likely to use deep water with predators present only when provided oyster structure. Provision of structural material to support and sustain development of benthic and mobile reef communities may be the most important factor in determining reef value to these assemblages, with biophysical characteristics related to reef location influencing assemblage patterns in areas with structure; if so, appropriately locating created reefs is critical.

Complex multidisciplinary system composition for aerospace vehicle conceptual design

NASA Astrophysics Data System (ADS)

Gonzalez, Lex

Although, there exists a vast amount of work concerning the analysis, design, integration of aerospace vehicle systems, there is no standard for how this data and knowledge should be combined in order to create a synthesis system. Each institution creating a synthesis system has in house vehicle and hardware components they are attempting to model and proprietary methods with which to model them. This leads to the fact that synthesis systems begin as one-off creations meant to answer a specific problem. As the scope of the synthesis system grows to encompass more and more problems, so does its size and complexity; in order for a single synthesis system to answer multiple questions the number of methods and method interface must increase. As a means to curtail the requirement that the increase of an aircraft synthesis systems capability leads to an increase in its size and complexity, this research effort focuses on the idea that each problem in aerospace requires its own analysis framework. By focusing on the creation of a methodology which centers on the matching of an analysis framework towards the problem being solved, the complexity of the analysis framework is decoupled from the complexity of the system that creates it. The derived methodology allows for the composition of complex multi-disciplinary systems (CMDS) through the automatic creation and implementation of system and disciplinary method interfaces. The CMDS Composition process follows a four step methodology meant to take a problem definition and progress towards the creation of an analysis framework meant to answer said problem. The unique implementation of the CMDS Composition process take user selected disciplinary analysis methods and automatically integrates them, together in order to create a syntactically composable analysis framework. As a means of assessing the validity of the CMDS Composition process a prototype system (AVDDBMS) has been developed. AVD DBMS has been used to model the Generic Hypersonic Vehicle (GHV), an open source family of hypersonic vehicles originating from the Air Force Research Laboratory. AVDDBMS has been applied in three different ways in order to assess its validity: Verification using GHV disciplinary data, Validation using selected disciplinary analysis methods, and Application of the CMDS Composition Process to assess the design solution space for the GHV hardware. The research demonstrates the holistic effect that selection of individual disciplinary analysis methods has on the structure and integration of the analysis framework.

Magnetic resonance imaging-three-dimensional printing technology fabricates customized scaffolds for brain tissue engineering

PubMed Central

Fu, Feng; Qin, Zhe; Xu, Chao; Chen, Xu-yi; Li, Rui-xin; Wang, Li-na; Peng, Ding-wei; Sun, Hong-tao; Tu, Yue; Chen, Chong; Zhang, Sai; Zhao, Ming-liang; Li, Xiao-hong

2017-01-01

Conventional fabrication methods lack the ability to control both macro- and micro-structures of generated scaffolds. Three-dimensional printing is a solid free-form fabrication method that provides novel ways to create customized scaffolds with high precision and accuracy. In this study, an electrically controlled cortical impactor was used to induce randomized brain tissue defects. The overall shape of scaffolds was designed using rat-specific anatomical data obtained from magnetic resonance imaging, and the internal structure was created by computer-aided design. As the result of limitations arising from insufficient resolution of the manufacturing process, we magnified the size of the cavity model prototype five-fold to successfully fabricate customized collagen-chitosan scaffolds using three-dimensional printing. Results demonstrated that scaffolds have three-dimensional porous structures, high porosity, highly specific surface areas, pore connectivity and good internal characteristics. Neural stem cells co-cultured with scaffolds showed good viability, indicating good biocompatibility and biodegradability. This technique may be a promising new strategy for regenerating complex damaged brain tissues, and helps pave the way toward personalized medicine. PMID:28553343

iPad: Semantic annotation and markup of radiological images.

PubMed

Rubin, Daniel L; Rodriguez, Cesar; Shah, Priyanka; Beaulieu, Chris

2008-11-06

Radiological images contain a wealth of information,such as anatomy and pathology, which is often not explicit and computationally accessible. Information schemes are being developed to describe the semantic content of images, but such schemes can be unwieldy to operationalize because there are few tools to enable users to capture structured information easily as part of the routine research workflow. We have created iPad, an open source tool enabling researchers and clinicians to create semantic annotations on radiological images. iPad hides the complexity of the underlying image annotation information model from users, permitting them to describe images and image regions using a graphical interface that maps their descriptions to structured ontologies semi-automatically. Image annotations are saved in a variety of formats,enabling interoperability among medical records systems, image archives in hospitals, and the Semantic Web. Tools such as iPad can help reduce the burden of collecting structured information from images, and it could ultimately enable researchers and physicians to exploit images on a very large scale and glean the biological and physiological significance of image content.

Particle Acceleration, Magnetic Field Generation, and Emission in Relativistic Pair Jets

NASA Technical Reports Server (NTRS)

Nishikawa, K. I.; Hardee, P.; Hededal, C. B.; Richardson, G.; Sol, H.; Preece, R.; Fishman, G. J.

2004-01-01

Shock acceleration is a ubiquitous phenomenon in astrophysical plasmas. Plasma waves and their associated instabilities (e.g., Buneman, Weibel and other two-stream instabilities) created in collisionless shocks are responsible for particle (electron, positron, and ion) acceleration. Using a 3-D relativistic electromagnetic particle (REMP) code, we have investigated particle acceleration associated with a relativistic jet front propagating into an ambient plasma. We find that the growth times depend on the Lorenz factors of jets. The jets with larger Lorenz factors grow slower. Simulations show that the Weibel instability created in the collisionless shock front accelerates jet and ambient particles both perpendicular and parallel to the jet propagation direction. The small scale magnetic field structure generated by the Weibel instability is appropriate to the generation of "jitter" radiation from deflected electrons (positrons) as opposed to synchrotron radiation. The jitter radiation resulting from small scale magnetic field structures may be important for understanding the complex time structure and spectral evolution observed in gamma-ray bursts or other astrophysical sources containing relativistic jets and relativistic collisionless shocks.

Shape Complementarity of Protein-Protein Complexes at Multiple Resolutions

PubMed Central

Zhang, Qing; Sanner, Michel; Olson, Arthur J.

2010-01-01

Biological complexes typically exhibit intermolecular interfaces of high shape complementarity. Many computational docking approaches use this surface complementarity as a guide in the search for predicting the structures of protein-protein complexes. Proteins often undergo conformational changes in order to create a highly complementary interface when associating. These conformational changes are a major cause of failure for automated docking procedures when predicting binding modes between proteins using their unbound conformations. Low resolution surfaces in which high frequency geometric details are omitted have been used to address this problem. These smoothed, or blurred, surfaces are expected to minimize the differences between free and bound structures, especially those that are due to side chain conformations or small backbone deviations. In spite of the fact that this approach has been used in many docking protocols, there has yet to be a systematic study of the effects of such surface smoothing on the shape complementarity of the resulting interfaces. Here we investigate this question by computing shape complementarity of a set of 66 protein-protein complexes represented by multi-resolution blurred surfaces. Complexed and unbound structures are available for these protein-protein complexes. They are a subset of complexes from a non-redundant docking benchmark selected for rigidity (i.e. the proteins undergo limited conformational changes between their bound and unbound states). In this work we construct the surfaces by isocontouring a density map obtained by accumulating the densities of Gaussian functions placed at all atom centers of the molecule. The smoothness or resolution is specified by a Gaussian fall-off coefficient, termed “blobbyness”. Shape complementarity is quantified using a histogram of the shortest distances between two proteins' surface mesh vertices for both the crystallographic complexes and the complexes built using the protein structures in their unbound conformation. The histograms calculated for the bound complex structures demonstrate that medium resolution smoothing (blobbyness=−0.9) can reproduce about 88% of the shape complementarity of atomic resolution surfaces. Complexes formed from the free component structures show a partial loss of shape complementarity (more overlaps and gaps) with the atomic resolution surfaces. For surfaces smoothed to low resolution (blobbyness=−0.3), we find more consistency of shape complementarity between the complexed and free cases. To further reduce bad contacts without significantly impacting the good contacts we introduce another blurred surface, in which the Gaussian densities of flexible atoms are reduced. From these results we discuss the use of shape complementarity in protein-protein docking. PMID:18837463

Constructing the matrix

NASA Astrophysics Data System (ADS)

Elliott, John

2012-09-01

As part of our 'toolkit' for analysing an extraterrestrial signal, the facility for calculating structural affinity to known phenomena must be part of our core capabilities. Without such a resource, we risk compromising our potential for detection and decipherment or at least causing significant delay in the process. To create such a repository for assessing structural affinity, all known systems (language parameters) need to be structurally analysed to 'place' their 'system' within a relational communication matrix. This will need to include all known variants of language structure, whether 'living' (in current use) or ancient; this must also include endeavours to incorporate yet undeciphered scripts and non-human communication, to provide as complete a picture as possible. In creating such a relational matrix, post-detection decipherment will be assisted by a structural 'map' that will have the potential for 'placing' an alien communication with its nearest known 'neighbour', to assist subsequent categorisation of basic parameters as a precursor to decipherment. 'Universal' attributes and behavioural characteristics of known communication structure will form a range of templates (Elliott, 2001 [1] and Elliott et al., 2002 [2]), to support and optimise our attempt at categorising and deciphering the content of an extraterrestrial signal. Detection of the hierarchical layers, which comprise intelligent, complex communication, will then form a matrix of calculations that will ultimately score affinity through a relational matrix of structural comparison. In this paper we develop the rationales and demonstrate functionality with initial test results.

Fluid{Structure Interaction Modeling of Modified-Porosity Parachutes and Parachute Clusters

NASA Astrophysics Data System (ADS)

Boben, Joseph J.

To increase aerodynamic performance, the geometric porosity of a ringsail spacecraft parachute canopy is sometimes increased, beyond the "rings" and "sails" with hundreds of "ring gaps" and "sail slits." This creates extra computational challenges for fluid-structure interaction (FSI) modeling of clusters of such parachutes, beyond those created by the lightness of the canopy structure, geometric complexities of hundreds of gaps and slits, and the contact between the parachutes of the cluster. In FSI computation of parachutes with such "modified geometric porosity," the ow through the "windows" created by the removal of the panels and the wider gaps created by the removal of the sails cannot be accurately modeled with the Homogenized Modeling of Geometric Porosity (HMGP), which was introduced to deal with the hundreds of gaps and slits. The ow needs to be actually resolved. All these computational challenges need to be addressed simultaneously in FSI modeling of clusters of spacecraft parachutes with modified geometric porosity. The core numerical technology is the Stabilized Space-Time FSI (SSTFSI) technique, and the contact between the parachutes is handled with the Surface-Edge-Node Contact Tracking (SENCT) technique. In the computations reported here, in addition to the SSTFSI and SENCT techniques and HMGP, we use the special techniques we have developed for removing the numerical spinning component of the parachute motion and for restoring the mesh integrity without a remesh. We present results for 2- and 3-parachute clusters with two different payload models. We also present the FSI computations we carried out for a single, subscale modified-porosity parachute.

Building a virtual simulation platform for quasistatic breast ultrasound elastography using open source software: A preliminary investigation.

PubMed

Wang, Yu; Helminen, Emily; Jiang, Jingfeng

2015-09-01

Quasistatic ultrasound elastography (QUE) is being used to augment in vivo characterization of breast lesions. Results from early clinical trials indicated that there was a lack of confidence in image interpretation. Such confidence can only be gained through rigorous imaging tests using complex, heterogeneous but known media. The objective of this study is to build a virtual breast QUE simulation platform in the public domain that can be used not only for innovative QUE research but also for rigorous imaging tests. The main thrust of this work is to streamline biomedical ultrasound simulations by leveraging existing open source software packages including Field II (ultrasound simulator), VTK (geometrical visualization and processing), FEBio [finite element (FE) analysis], and Tetgen (mesh generator). However, integration of these open source packages is nontrivial and requires interdisciplinary knowledge. In the first step, a virtual breast model containing complex anatomical geometries was created through a novel combination of image-based landmark structures and randomly distributed (small) structures. Image-based landmark structures were based on data from the NIH Visible Human Project. Subsequently, an unstructured FE-mesh was created by Tetgen. In the second step, randomly positioned point scatterers were placed within the meshed breast model through an octree-based algorithm to make a virtual breast ultrasound phantom. In the third step, an ultrasound simulator (Field II) was used to interrogate the virtual breast phantom to obtain simulated ultrasound echo data. Of note, tissue deformation generated using a FE-simulator (FEBio) was the basis of deforming the original virtual breast phantom in order to obtain the postdeformation breast phantom for subsequent ultrasound simulations. Using the procedures described above, a full cycle of QUE simulations involving complex and highly heterogeneous virtual breast phantoms can be accomplished for the first time. Representative examples were used to demonstrate capabilities of this virtual simulation platform. In the first set of three ultrasound simulation examples, three heterogeneous volumes of interest were selected from a virtual breast ultrasound phantom to perform sophisticated ultrasound simulations. These resultant B-mode images realistically represented the underlying complex but known media. In the second set of three QUE examples, advanced applications in QUE were simulated. The first QUE example was to show breast tumors with complex shapes and/or compositions. The resultant strain images showed complex patterns that were normally seen in freehand clinical ultrasound data. The second and third QUE examples demonstrated (deformation-dependent) nonlinear strain imaging and time-dependent strain imaging, respectively. The proposed virtual QUE platform was implemented and successfully tested in this study. Through show-case examples, the proposed work has demonstrated its capabilities of creating sophisticated QUE data in a way that cannot be done through the manufacture of physical tissue-mimicking phantoms and other software. This open software architecture will soon be made available in the public domain and can be readily adapted to meet specific needs of different research groups to drive innovations in QUE.

An IPMC-enabled bio-inspired bending/twisting fin for underwater applications

NASA Astrophysics Data System (ADS)

Palmre, Viljar; Hubbard, Joel J.; Fleming, Maxwell; Pugal, David; Kim, Sungjun; Kim, Kwang J.; Leang, Kam K.

2013-01-01

This paper discusses the design, fabrication, and characterization of an ionic polymer-metal composite (IPMC) actuator-based bio-inspired active fin capable of bending and twisting motion. It is pointed out that IPMC strip actuators are used in the simple cantilever configuration to create simple bending (flapping-like) motion for propulsion in underwater autonomous systems. However, the resulting motion is a simple 1D bending and performance is rather limited. To enable more complex deformation, such as the flapping (pitch and heaving) motion of real pectoral and caudal fish fins, a new approach which involves molding or integrating IPMC actuators into a soft boot material to create an active control surface (called a ‘fin’) is presented. The fin can be used to realize complex deformation depending on the orientation and placement of the actuators. In contrast to previously created IPMCs with patterned electrodes for the same purpose, the proposed design avoids (1) the more expensive process of electroless plating platinum all throughout the surface of the actuator and (2) the need for specially patterning the electrodes. Therefore, standard shaped IPMC actuators such as those with rectangular dimensions with varying thicknesses can be used. One unique advantage of the proposed structural design is that custom shaped fins and control surfaces can be easily created without special materials processing. The molding process is cost effective and does not require functionalizing or ‘activating’ the boot material similar to creating IPMCs. For a prototype fin (90 mm wide × 60 mm long × 1.5 mm thick), the measured maximum tip displacement was approximately 44 mm and the twist angle of the fin exceeded 10°. Lift and drag measurements in water where the prototype fin with an airfoil profile was dragged through water at a velocity of 21 cm s-1 showed that the lift and drag forces can be affected by controlling the IPMCs embedded into the fin structure. These results suggest that such IPMC-enabled fin designs can be used for developing active propeller blades or control surfaces on underwater vehicles.

Battlespace Awareness: Heterogeneous Sensor Maps of Large Scale, Complex Environments

DTIC Science & Technology

2017-06-13

reference frames enable a system designer to describe the position of any sensor or platform at any point of time. This section introduces the...analysis to evaluate the quality of reconstructions created by our algorithms. CloudCompare is an open-source tool designed for this purpose [65]. In...structure of the data. The data term seeks to keep the proposed solution (u) similar to the originally observed values ( f ). A systems designer must

Near-infrared branding efficiently correlates light and electron microscopy.

PubMed

Bishop, Derron; Nikić, Ivana; Brinkoetter, Mary; Knecht, Sharmon; Potz, Stephanie; Kerschensteiner, Martin; Misgeld, Thomas

2011-06-05

The correlation of light and electron microscopy of complex tissues remains a major challenge. Here we report near-infrared branding (NIRB), which facilitates such correlation by using a pulsed, near-infrared laser to create defined fiducial marks in three dimensions in fixed tissue. As these marks are fluorescent and can be photo-oxidized to generate electron contrast, they can guide re-identification of previously imaged structures as small as dendritic spines by electron microscopy.

Structural and parameteric uncertainty quantification in cloud microphysics parameterization schemes

NASA Astrophysics Data System (ADS)

van Lier-Walqui, M.; Morrison, H.; Kumjian, M. R.; Prat, O. P.; Martinkus, C.

2017-12-01

Atmospheric model parameterization schemes employ approximations to represent the effects of unresolved processes. These approximations are a source of error in forecasts, caused in part by considerable uncertainty about the optimal value of parameters within each scheme -- parameteric uncertainty. Furthermore, there is uncertainty regarding the best choice of the overarching structure of the parameterization scheme -- structrual uncertainty. Parameter estimation can constrain the first, but may struggle with the second because structural choices are typically discrete. We address this problem in the context of cloud microphysics parameterization schemes by creating a flexible framework wherein structural and parametric uncertainties can be simultaneously constrained. Our scheme makes no assuptions about drop size distribution shape or the functional form of parametrized process rate terms. Instead, these uncertainties are constrained by observations using a Markov Chain Monte Carlo sampler within a Bayesian inference framework. Our scheme, the Bayesian Observationally-constrained Statistical-physical Scheme (BOSS), has flexibility to predict various sets of prognostic drop size distribution moments as well as varying complexity of process rate formulations. We compare idealized probabilistic forecasts from versions of BOSS with varying levels of structural complexity. This work has applications in ensemble forecasts with model physics uncertainty, data assimilation, and cloud microphysics process studies.

Monolithic photonic crystals created by partial coalescence of core-shell particles.

PubMed

Lee, Joon-Seok; Lim, Che Ho; Yang, Seung-Man; Kim, Shin-Hyun

2014-03-11

Colloidal crystals and their derivatives have been intensively studied and developed during the past two decades due to their unique photonic band gap properties. However, complex fabrication procedures and low mechanical stability severely limit their practical uses. Here, we report stable photonic structures created by using colloidal building blocks composed of an inorganic core and an organic shell. The core-shell particles are convectively assembled into an opal structure, which is then subjected to thermal annealing. During the heat treatment, the inorganic cores, which are insensitive to heat, retain their regular arrangement in a face-centered cubic lattice, while the organic shells are partially fused with their neighbors; this forms a monolithic structure with high mechanical stability. The interparticle distance and therefore stop band position are precisely controlled by the annealing time; the distance decreases and the stop band blue shifts during the annealing. The composite films can be further treated to give a high contrast in the refractive index. The inorganic cores are selectively removed from the composite by wet etching, thereby providing an organic film containing regular arrays of air cavities. The high refractive index contrast of the porous structure gives rise to pronounced structural colors and high reflectivity at the stop band position.

Deuterium Labeling Strategies for Creating Contrast in Structure-Function Studies of Model Bacterial Outer Membranes Using Neutron Reflectometry.

PubMed

Le Brun, Anton P; Clifton, Luke A; Holt, Stephen A; Holden, Peter J; Lakey, Jeremy H

2016-01-01

Studying the outer membrane of Gram-negative bacteria is challenging due to the complex nature of its structure. Therefore, simplified models are required to undertake structure-function studies of processes that occur at the outer membrane/fluid interface. Model membranes can be created by immobilizing bilayers to solid supports such as gold or silicon surfaces, or as monolayers on a liquid support where the surface pressure and fluidity of the lipids can be controlled. Both model systems are amenable to having their structure probed by neutron reflectometry, a technique that provides a one-dimensional depth profile through a membrane detailing its thickness and composition. One of the strengths of neutron scattering is the ability to use contrast matching, allowing molecules containing hydrogen and those enriched with deuterium to be highlighted or matched out against the bulk isotopic composition of the solvent. Lipopolysaccharides, a major component of the outer membrane, can be isolated for incorporation into model membranes. Here, we describe the deuteration of lipopolysaccharides from rough strains of Escherichia coli for incorporation into model outer membranes, and how the use of deuterated materials enhances structural analysis of model membranes by neutron reflectometry. © 2016 Elsevier Inc. All rights reserved.

Regulatory challenges and approaches to characterize nanomedicines and their follow-on similars.

PubMed

Mühlebach, Stefan; Borchard, Gerrit; Yildiz, Selcan

2015-03-01

Nanomedicines are highly complex products and are the result of difficult to control manufacturing processes. Nonbiological complex drugs and their biological counterparts can comprise nanoparticles and therefore show nanomedicine characteristics. They consist of not fully known nonhomomolecular structures, and can therefore not be characterized by physicochemical means only. Also, intended copies of nanomedicines (follow-on similars) may have clinically meaningful differences, creating the regulatory challenge of how to grant a high degree of assurance for patients' benefit and safety. As an example, the current regulatory approach for marketing authorization of intended copies of nonbiological complex drugs appears inappropriate; also, a valid strategy incorporating the complexity of such systems is undefined. To demonstrate sufficient similarity and comparability, a stepwise quality, nonclinical and clinical approach is necessary to obtain market authorization for follow-on products as therapeutic alternatives, substitution and/or interchangeable products. To fill the regulatory gap, harmonized and science-based standards are needed.

Complexity and compositionality in fluid intelligence

PubMed Central

Duncan, John; Chylinski, Daphne

2017-01-01

Compositionality, or the ability to build complex cognitive structures from simple parts, is fundamental to the power of the human mind. Here we relate this principle to the psychometric concept of fluid intelligence, traditionally measured with tests of complex reasoning. Following the principle of compositionality, we propose that the critical function in fluid intelligence is splitting a complex whole into simple, separately attended parts. To test this proposal, we modify traditional matrix reasoning problems to minimize requirements on information integration, working memory, and processing speed, creating problems that are trivial once effectively divided into parts. Performance remains poor in participants with low fluid intelligence, but is radically improved by problem layout that aids cognitive segmentation. In line with the principle of compositionality, we suggest that effective cognitive segmentation is important in all organized behavior, explaining the broad role of fluid intelligence in successful cognition. PMID:28461462

Complex Engineered Systems: A New Paradigm

NASA Astrophysics Data System (ADS)

Mina, Ali A.; Braha, Dan; Bar-Yam, Yaneer

Human history is often seen as an inexorable march towards greater complexity — in ideas, artifacts, social, political and economic systems, technology, and in the structure of life itself. While we do not have detailed knowledge of ancient times, it is reasonable to conclude that the average resident of New York City today faces a world of much greater complexity than the average denizen of Carthage or Tikal. A careful consideration of this change, however, suggests that most of it has occurred recently, and has been driven primarily by the emergence of technology as a force in human life. In the 4000 years separating the Indus Valley Civilization from 18th century Europe, human transportation evolved from the bullock cart to the hansom, and the methods of communication used by George Washington did not differ significantly from those used by Alexander or Rameses. The world has moved radically towards greater complexity in the last two centuries. We have moved from buggies and letter couriers to airplanes and the Internet — an increase in capacity, and through its diversity also in complexity, orders of magnitude greater than that accumulated through the rest of human history. In addition to creating iconic artifacts — the airplane, the car, the computer, the television, etc. — this change has had a profound effect on the scope of experience by creating massive, connected and multiultra- level systems — traffic networks, power grids, markets, multinational corporations — that defy analytical understanding and seem to have a life of their own. This is where complexity truly enters our lives.

Providing structural modules with self-integrity monitoring

NASA Astrophysics Data System (ADS)

Walton, W. B.; Ibanez, P.; Yessaie, G.

1988-08-01

With the advent of complex space structures (i.e., U.S. Space Station), the need for methods for remotely detecting structural damage will become greater. Some of these structures will have hundreds of individual structural elements (i.e., strut members). Should some of them become damaged, it could be virtually impossible to detect it using visual or similar inspection techniques. The damage of only a few individual members may or may not be a serious problem. However, should a significant number of the members be damaged, a significant problem could be created. The implementation of an appropriate remote damage detection scheme would greatly reduce the likelihood of a serious problem related to structural damage ever occurring. This report presents the results of the research conducted on remote structural damage detection approaches and the related mathematical algorithms. The research was conducted for the Small Business Innovation and Research (SBIR) Phase 2 National Aeronautics and Space Administration (NASA) Contract NAS7-961.

Providing structural modules with self-integrity monitoring

NASA Technical Reports Server (NTRS)

Walton, W. B.; Ibanez, P.; Yessaie, G.

1988-01-01

With the advent of complex space structures (i.e., U.S. Space Station), the need for methods for remotely detecting structural damage will become greater. Some of these structures will have hundreds of individual structural elements (i.e., strut members). Should some of them become damaged, it could be virtually impossible to detect it using visual or similar inspection techniques. The damage of only a few individual members may or may not be a serious problem. However, should a significant number of the members be damaged, a significant problem could be created. The implementation of an appropriate remote damage detection scheme would greatly reduce the likelihood of a serious problem related to structural damage ever occurring. This report presents the results of the research conducted on remote structural damage detection approaches and the related mathematical algorithms. The research was conducted for the Small Business Innovation and Research (SBIR) Phase 2 National Aeronautics and Space Administration (NASA) Contract NAS7-961.

Artificial enzymes based on supramolecular scaffolds.

PubMed

Dong, Zeyuan; Luo, Quan; Liu, Junqiu

2012-12-07

Enzymes are nanometer-sized molecules with three-dimensional structures created by the folding and self-assembly of polymeric chain-like components through supramolecular interactions. They are capable of performing catalytic functions usually accompanied by a variety of conformational states. The conformational diversities and complexities of natural enzymes exerted in catalysis seriously restrict the detailed understanding of enzymatic mechanisms in molecular terms. A supramolecular viewpoint is undoubtedly helpful in understanding the principle of enzyme catalysis. The emergence of supramolecular artificial enzymes therefore provides an alternative way to approach the structural complexity and thus to unravel the mystery of enzyme catalysis. This critical review covers the recent development of artificial enzymes designed based on supramolecular scaffolds ranging from the synthetic macrocycles to self-assembled nanometer-sized objects. Such findings are anticipated to facilitate the design of supramolecular artificial enzymes as well as their potential uses in important fields, such as manufacturing and food industries, environmental biosensors, pharmaceutics and so on.

Diamond and diamond-like carbon MEMS

NASA Astrophysics Data System (ADS)

Luo, J. K.; Fu, Y. Q.; Le, H. R.; Williams, J. A.; Spearing, S. M.; Milne, W. I.

2007-07-01

To generate complex cartilage/bone tissues, scaffolds must possess several structural features that are difficult to create using conventional scaffold design/fabrication technologies. Successful cartilage/bone regeneration depends on the ability to assemble chondrocytes/osteoblasts into three-dimensional (3D) scaffolds. Therefore, we developed a 3D scaffold fabrication system that applies the axiomatic approach to our microstereolithography system. The new system offers a reduced machine size by minimizing the optical components, and shows that the design matrix is decoupled. This analysis identified the key factors affecting microstructure fabrication and an improved scaffold fabrication system was constructed. The results demonstrate that precise, predesigned 3D structures can be fabricated. Using this 3D scaffold, cell adhesion behavior was observed. The use of 3D scaffolds might help determine key factors in the study of cell behavior in complex environments and could eventually lead to the optimal design of scaffolds for the regeneration of various tissues, such as cartilage and bone.

Complex band structures of transition metal dichalcogenide monolayers with spin-orbit coupling effects

NASA Astrophysics Data System (ADS)

Szczęśniak, Dominik; Ennaoui, Ahmed; Ahzi, Saïd

2016-09-01

Recently, the transition metal dichalcogenides have attracted renewed attention due to the potential use of their low-dimensional forms in both nano- and opto-electronics. In such applications, the electronic and transport properties of monolayer transition metal dichalcogenides play a pivotal role. The present paper provides a new insight into these essential properties by studying the complex band structures of popular transition metal dichalcogenide monolayers (MX 2, where M  =  Mo, W; X  =  S, Se, Te) while including spin-orbit coupling effects. The conducted symmetry-based tight-binding calculations show that the analytical continuation from the real band structures to the complex momentum space leads to nonlinear generalized eigenvalue problems. Herein an efficient method for solving such a class of nonlinear problems is presented and yields a complete set of physically relevant eigenvalues. Solutions obtained by this method are characterized and classified into propagating and evanescent states, where the latter states manifest not only monotonic but also oscillatory decay character. It is observed that some of the oscillatory evanescent states create characteristic complex loops at the direct band gap of MX 2 monolayers, where electrons can directly tunnel between the band gap edges. To describe these tunneling currents, decay behavior of electronic states in the forbidden energy region is elucidated and their importance within the ballistic transport regime is briefly discussed.

Verification of the anatomy and newly discovered histology of the G-spot complex.

PubMed

Ostrzenski, A; Krajewski, P; Ganjei-Azar, P; Wasiutynski, A J; Scheinberg, M N; Tarka, S; Fudalej, M

2014-10-01

To expand the anatomical investigations of the G-spot and to assess the G-spot's characteristic histological and immunohistochemical features. An observational study. International multicentre. Eight consecutive fresh human female cadavers. Anterior vaginal wall dissections were executed and G-spot microdissections were performed. All specimens were stained with haematoxylin and eosin (H&E). The tissues of two women were selected at random for immunohistochemical staining. The primary outcome measure was to document the anatomy of the G-spot. The secondary outcome measures were to identify the histology of the G-spot and to determine whether histological samples stained with H&E are sufficient to identify the G-spot. The anatomical existence of the G-spot was identified in all women and was in a diagonal plane. In seven (87.5%) and one (12.5%) of the women the G-spot complex was found on the left or right side, respectively. The G-spot was intimately fused with vessels, creating a complex. A large tangled vein-like vascular structure resembled an arteriovenous malformation and there were a few smaller feeding arteries. A band-like structure protruded from the tail of the G-spot. The size of the G-spot varied. Histologically, the G-spot was determined as a neurovascular complex structure. The neural component contained abundant peripheral nerve bundles and a nerve ganglion. The vascular component comprised large vein-like vessels and smaller feeding arteries. Circular and longitudinal muscles covered the G-complex. The anatomy of the G-spot complex was confirmed. The histology of the G-spot presents as neurovascular tissues with a nerve ganglion. H&E staining is sufficient for the identification of the G-spot complex. © 2014 Royal College of Obstetricians and Gynaecologists.

Simulation modeling to understand how selective foraging by beaver can drive the structure and function of a willow community

USGS Publications Warehouse

Peinetti, H.R.; Baker, B.W.; Coughenour, M.B.

2009-01-01

Beaver-willow (Castor-Salix) communities are a unique and vital component of healthy wetlands throughout the Holarctic region. Beaver selectively forage willow to provide fresh food, stored winter food, and construction material. The effects of this complex foraging behavior on the structure and function of willow communities is poorly understood. Simulation modeling may help ecologists understand these complex interactions. In this study, a modified version of the SAVANNA ecosystem model was developed to better understand how beaver foraging affects the structure and function of a willow community in a simulated riparian ecosystem in Rocky Mountain National Park, Colorado (RMNP). The model represents willow in terms of plant and stem dynamics and beaver foraging in terms of the quantity and quality of stems cut to meet the energetic and life history requirements of beaver. Given a site where all stems were equally available, the model suggested a simulated beaver family of 2 adults, 2 yearlings, and 2 kits required a minimum of 4 ha of willow (containing about10 stems m-2) to persist in a steady-state condition. Beaver created a willow community where the annual net primary productivity (ANPP) was 2 times higher and plant architecture was more diverse than the willow community without beaver. Beaver foraging created a plant architecture dominated by medium size willow plants, which likely explains how beaver can increase ANPP. Long-term simulations suggested that woody biomass stabilized at similar values even though availability differed greatly at initial condition. Simulations also suggested that willow ANPP increased across a range of beaver densities until beaver became food limited. Thus, selective foraging by beaver increased productivity, decreased biomass, and increased structural heterogeneity in a simulated willow community.

Creating Supportive Environments and Thriving in a Volatile, Uncertain, Complex, and Ambiguous World.

PubMed

Pabico, Christine

2015-10-01

Nurse executives (NEs) are operating in a volatile, uncertain, complex, and ambiguous world. NEs must create supportive environments that promote staff empowerment, resilience, and alignment, to ensure organizational success. In addition, NEs need to be transparent and create a culture of partnership with their staff. The ability of NEs to create and sustain this environment is vital in supporting teams to successfully navigate in today's healthcare environment.

Building generic anatomical models using virtual model cutting and iterative registration.

PubMed

Xiao, Mei; Soh, Jung; Meruvia-Pastor, Oscar; Schmidt, Eric; Hallgrímsson, Benedikt; Sensen, Christoph W

2010-02-08

Using 3D generic models to statistically analyze trends in biological structure changes is an important tool in morphometrics research. Therefore, 3D generic models built for a range of populations are in high demand. However, due to the complexity of biological structures and the limited views of them that medical images can offer, it is still an exceptionally difficult task to quickly and accurately create 3D generic models (a model is a 3D graphical representation of a biological structure) based on medical image stacks (a stack is an ordered collection of 2D images). We show that the creation of a generic model that captures spatial information exploitable in statistical analyses is facilitated by coupling our generalized segmentation method to existing automatic image registration algorithms. The method of creating generic 3D models consists of the following processing steps: (i) scanning subjects to obtain image stacks; (ii) creating individual 3D models from the stacks; (iii) interactively extracting sub-volume by cutting each model to generate the sub-model of interest; (iv) creating image stacks that contain only the information pertaining to the sub-models; (v) iteratively registering the corresponding new 2D image stacks; (vi) averaging the newly created sub-models based on intensity to produce the generic model from all the individual sub-models. After several registration procedures are applied to the image stacks, we can create averaged image stacks with sharp boundaries. The averaged 3D model created from those image stacks is very close to the average representation of the population. The image registration time varies depending on the image size and the desired accuracy of the registration. Both volumetric data and surface model for the generic 3D model are created at the final step. Our method is very flexible and easy to use such that anyone can use image stacks to create models and retrieve a sub-region from it at their ease. Java-based implementation allows our method to be used on various visualization systems including personal computers, workstations, computers equipped with stereo displays, and even virtual reality rooms such as the CAVE Automated Virtual Environment. The technique allows biologists to build generic 3D models of their interest quickly and accurately.

Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components

NASA Astrophysics Data System (ADS)

Ong, Luvena L.; Hanikel, Nikita; Yaghi, Omar K.; Grun, Casey; Strauss, Maximilian T.; Bron, Patrick; Lai-Kee-Him, Josephine; Schueder, Florian; Wang, Bei; Wang, Pengfei; Kishi, Jocelyn Y.; Myhrvold, Cameron; Zhu, Allen; Jungmann, Ralf; Bellot, Gaetan; Ke, Yonggang; Yin, Peng

2017-12-01

Nucleic acids (DNA and RNA) are widely used to construct nanometre-scale structures with ever increasing complexity, with possible application in fields such as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early kilodalton-scale examples containing typically tens of unique DNA strands. The introduction of DNA origami, which uses many staple strands to fold one long scaffold strand into a desired structure, has provided access to megadalton-scale nanostructures that contain hundreds of unique DNA strands. Even larger DNA origami structures are possible, but manufacturing and manipulating an increasingly long scaffold strand remains a challenge. An alternative and more readily scalable approach involves the assembly of DNA bricks, which each consist of four short binding domains arranged so that the bricks can interlock. This approach does not require a scaffold; instead, the short DNA brick strands self-assemble according to specific inter-brick interactions. First-generation bricks used to create three-dimensional structures are 32 nucleotides long, consisting of four eight-nucleotide binding domains. Protocols have been designed to direct the assembly of hundreds of distinct bricks into well formed structures, but attempts to create larger structures have encountered practical challenges and had limited success. Here we show that DNA bricks with longer, 13-nucleotide binding domains make it possible to self-assemble 0.1-1-gigadalton, three-dimensional nanostructures from tens of thousands of unique components, including a 0.5-gigadalton cuboid containing about 30,000 unique bricks and a 1-gigadalton rotationally symmetric tetramer. We also assembled a cuboid that contains around 10,000 bricks and about 20,000 uniquely addressable, 13-base-pair ‘voxels’ that serves as a molecular canvas for three-dimensional sculpting. Complex, user-prescribed, three-dimensional cavities can be produced within this molecular canvas, enabling the creation of shapes such as letters, a helicoid and a teddy bear. We anticipate that with further optimization of structure design, strand synthesis and assembly procedure even larger structures could be accessible, which could be useful for applications such as positioning functional components.

How to describe disordered structures

PubMed Central

Nishio, Kengo; Miyazaki, Takehide

2016-01-01

Disordered structures such as liquids and glasses, grains and foams, galaxies, etc. are often represented as polyhedral tilings. Characterizing the associated polyhedral tiling is a promising strategy to understand the disordered structure. However, since a variety of polyhedra are arranged in complex ways, it is challenging to describe what polyhedra are tiled in what way. Here, to solve this problem, we create the theory of how the polyhedra are tiled. We first formulate an algorithm to convert a polyhedron into a codeword that instructs how to construct the polyhedron from its building-block polygons. By generalizing the method to polyhedral tilings, we describe the arrangements of polyhedra. Our theory allows us to characterize polyhedral tilings, and thereby paves the way to study from short- to long-range order of disordered structures in a systematic way. PMID:27064833

How to describe disordered structures

NASA Astrophysics Data System (ADS)

Nishio, Kengo; Miyazaki, Takehide

2016-04-01

Disordered structures such as liquids and glasses, grains and foams, galaxies, etc. are often represented as polyhedral tilings. Characterizing the associated polyhedral tiling is a promising strategy to understand the disordered structure. However, since a variety of polyhedra are arranged in complex ways, it is challenging to describe what polyhedra are tiled in what way. Here, to solve this problem, we create the theory of how the polyhedra are tiled. We first formulate an algorithm to convert a polyhedron into a codeword that instructs how to construct the polyhedron from its building-block polygons. By generalizing the method to polyhedral tilings, we describe the arrangements of polyhedra. Our theory allows us to characterize polyhedral tilings, and thereby paves the way to study from short- to long-range order of disordered structures in a systematic way.

Predicting the structure of screw dislocations in nanoporous materials

NASA Astrophysics Data System (ADS)

Walker, Andrew M.; Slater, Ben; Gale, Julian D.; Wright, Kate

2004-10-01

Extended microscale crystal defects, including dislocations and stacking faults, can radically alter the properties of technologically important materials. Determining the atomic structure and the influence of defects on properties remains a major experimental and computational challenge. Using a newly developed simulation technique, the structure of the 1/2a <100> screw dislocation in nanoporous zeolite A has been modelled. The predicted channel structure has a spiral form that resembles a nanoscale corkscrew. Our findings suggest that the dislocation will enhance the transport of molecules from the surface to the interior of the crystal while retarding transport parallel to the surface. Crucially, the dislocation creates an activated, locally chiral environment that may have enantioselective applications. These predictions highlight the influence that microscale defects have on the properties of structurally complex materials, in addition to their pivotal role in crystal growth.

Photoswitching a Molecular Catalyst to Regulate CO 2 Hydrogenation

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

Priyadarshani, Nilusha; Ginovska-Pangovska, Bojana; Bays, J. Timothy

2015-07-24

Inspired by nature’s ability to regulate catalysis using physiological stimuli, azobenzene was incorporated into Rh(bis)diphosphine CO 2 hydrogenation catalysts to photoinitiate structural changes to modulate the resulting catalytic activity. The rhodium bound diphosphine ligands (P(Ph 2)-CH 2-N(R) CH 2-P(Ph2)) contain the terminal amine of a non-natural amino acid, either β-alanine (β-Ala) or γ-aminobutyric acid (GABA). For both β-ala and GABA containing complexes, the carboxylic acids of the amino acids were coupled to the amines of diaminoazobenzene, creating a rhodium bound trans-spanning tetraphosphine complex. The photo-induced cis-trans isomerization of the azobenzene-containing complexes imposes structural changes on these complexes, as evidenced bymore » 1H NMR. We found that the CO 2 hydrogenation activity for the β-ala bound Rh complex is 40% faster with azobenzene in the cis configuration (16 s -1) than in the trans conformation (11 s -1), while the γ-aminobutyric acid containing Rh complex has the same rate (~17 s -1) in either the cis or the trans configuration at 27 °C. The corresponding complexes without the attached azobenzene were also prepared, characterized, and catalytically tested for comparison, and have rates of 30 s -1. Computational studies were undertaken to evaluate the difference in rate between the cis and trans isomers for the β-Ala bound Rh complex, and revealed major structural changes between all cis and trans structures, but only minor structural changes that would be unique to the β-Ala bound Rh complex. We postulate that the slower rate of the azobenzene-containing β-Ala bound Rh complex is due to subtle changes in the bite angle arising from steric strain due to the trans-spanning azobenzene, altering hydricity and consequently rate. This work was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory (PNNL) is a multiprogram national laboratory operated for the DOE by Battelle. A portion of this research was performed using EMSL, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.« less

Computer simulations of the interaction of human immunodeficiency virus (HIV) aspartic protease with spherical gold nanoparticles: implications in acquired immunodeficiency syndrome (AIDS)

NASA Astrophysics Data System (ADS)

Whiteley, Chris G.; Lee, Duu-Jong

2016-09-01

The interaction of gold nanoparticles (AuNP) with human immune-deficiency virus aspartic protease (HIVPR) is modelled using a regime of molecular dynamics simulations. The simulations of the ‘docking’, first as a rigid-body complex, and eventually through flexible-fit analysis, creates 36 different complexes from four initial orientations of the nanoparticle strategically positioned around the surface of the enzyme. The structural deviations of the enzymes from the initial x-ray crystal structure during each docking simulation are assessed by comparative analysis of secondary structural elements, root mean square deviations, B-factors, interactive bonding energies, dihedral angles, radius of gyration (R g), circular dichroism (CD), volume occupied by C α , electrostatic potentials, solvation energies and hydrophobicities. Normalisation of the data narrows the selection from the initial 36 to one ‘final’ probable structure. It is concluded that, after computer simulations on each of the 36 initial complexes incorporating the 12 different biophysical techniques, the top five complexes are the same no matter which technique is explored. The significance of the present work is an expansion of an earlier study on the molecular dynamic simulation for the interaction of HIVPR with silver nanoparticles. This work is supported by experimental evidence since the initial ‘orientation’ of the AgNP with the enzyme is the same as the ‘final’ AuNP-HIVPR complex generated in the present study. The findings will provide insight into the forces of the binding of the HIVPR to AuNP. It is anticipated that the protocol developed in this study will act as a standard process for the interaction of any nanoparticle with any biomedical target.

Computer simulations of the interaction of human immunodeficiency virus (HIV) aspartic protease with spherical gold nanoparticles: implications in acquired immunodeficiency syndrome (AIDS).

PubMed

Whiteley, Chris G; Lee, Duu-Jong

2016-09-09

The interaction of gold nanoparticles (AuNP) with human immune-deficiency virus aspartic protease (HIVPR) is modelled using a regime of molecular dynamics simulations. The simulations of the 'docking', first as a rigid-body complex, and eventually through flexible-fit analysis, creates 36 different complexes from four initial orientations of the nanoparticle strategically positioned around the surface of the enzyme. The structural deviations of the enzymes from the initial x-ray crystal structure during each docking simulation are assessed by comparative analysis of secondary structural elements, root mean square deviations, B-factors, interactive bonding energies, dihedral angles, radius of gyration (R g), circular dichroism (CD), volume occupied by C α , electrostatic potentials, solvation energies and hydrophobicities. Normalisation of the data narrows the selection from the initial 36 to one 'final' probable structure. It is concluded that, after computer simulations on each of the 36 initial complexes incorporating the 12 different biophysical techniques, the top five complexes are the same no matter which technique is explored. The significance of the present work is an expansion of an earlier study on the molecular dynamic simulation for the interaction of HIVPR with silver nanoparticles. This work is supported by experimental evidence since the initial 'orientation' of the AgNP with the enzyme is the same as the 'final' AuNP-HIVPR complex generated in the present study. The findings will provide insight into the forces of the binding of the HIVPR to AuNP. It is anticipated that the protocol developed in this study will act as a standard process for the interaction of any nanoparticle with any biomedical target.

Antigenic peptides containing large PEG loops designed to extend out of the HLA-A2 binding site form stable complexes with class I major histocompatibility complex molecules.

PubMed Central

Bouvier, M; Wiley, D C

1996-01-01

Recognition of peptides bound to class I major histocompatibility complex (MHC) molecules by specific receptors on T cells regulates the development and activity of the cellular immune system. We have designed and synthesized de novo cyclic peptides that incorporate PEG in the ring structure for binding to class I MHC molecules. The large PEG loops are positioned to extend out of the peptide binding site, thus creating steric effects aimed at preventing the recognition of class I MHC complexes by T-cell receptors. Peptides were synthesized and cyclized on polymer support using high molecular weight symmetrical PEG dicarboxylic acids to link the side chains of lysine residues substituted at positions 4 and 8 in the sequence of the HLA-A2-restricted human T-lymphotrophic virus type I Tax peptide. Cyclic peptides promoted the in vitro folding and assembly of HLA-A2 complexes. Thermal denaturation studies using circular dichroism spectroscopy showed that these complexes are as stable as complexes formed with antigenic peptides. Images Fig. 2 Fig. 4 PMID:8643447

Templated Formation of Luminescent Virus-like Particles by Tailor-Made Pt(II) Amphiphiles

PubMed Central

2018-01-01

Virus-like particles (VLPs) have been created from luminescent Pt(II) complex amphiphiles, able to form supramolecular structures in water solutions, that can be encapsulated or act as templates of cowpea chlorotic mottle virus capsid proteins. By virtue of a bottom-up molecular design, icosahedral and nonicosahedral (rod-like) VLPs have been constructed through diverse pathways, and a relationship between the molecular structure of the complexes and the shape and size of the VLPs has been observed. A deep insight into the mechanism for the templated formation of the differently shaped VLPs was achieved, by electron microscopy measurements (TEM and STEM) and bulk analysis (FPLC, DLS, photophysical investigations). Interestingly, the obtained VLPs can be visualized by their intense emission at room temperature, generated by the self-assembly of the Pt(II) complexes. The encapsulation of the luminescent species is further verified by their higher emission quantum yields inside the VLPs, which is due to the confinement effect of the protein cage. These hybrid materials demonstrate the potential of tailor-made supramolecular systems able to control the assembly of biological building blocks. PMID:29357236

Templated Formation of Luminescent Virus-like Particles by Tailor-Made Pt(II) Amphiphiles.

PubMed

Sinn, Stephan; Yang, Liulin; Biedermann, Frank; Wang, Di; Kübel, Christian; Cornelissen, Jeroen J L M; De Cola, Luisa

2018-02-14

Virus-like particles (VLPs) have been created from luminescent Pt(II) complex amphiphiles, able to form supramolecular structures in water solutions, that can be encapsulated or act as templates of cowpea chlorotic mottle virus capsid proteins. By virtue of a bottom-up molecular design, icosahedral and nonicosahedral (rod-like) VLPs have been constructed through diverse pathways, and a relationship between the molecular structure of the complexes and the shape and size of the VLPs has been observed. A deep insight into the mechanism for the templated formation of the differently shaped VLPs was achieved, by electron microscopy measurements (TEM and STEM) and bulk analysis (FPLC, DLS, photophysical investigations). Interestingly, the obtained VLPs can be visualized by their intense emission at room temperature, generated by the self-assembly of the Pt(II) complexes. The encapsulation of the luminescent species is further verified by their higher emission quantum yields inside the VLPs, which is due to the confinement effect of the protein cage. These hybrid materials demonstrate the potential of tailor-made supramolecular systems able to control the assembly of biological building blocks.

The complex ion structure of warm dense carbon measured by spectrally resolved x-ray scattering

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

Kraus, D.; Barbrel, B.; Falcone, R. W.

2015-05-15

We present measurements of the complex ion structure of warm dense carbon close to the melting line at pressures around 100 GPa. High-pressure samples were created by laser-driven shock compression of graphite and probed by intense laser-generated x-ray sources with photon energies of 4.75 keV and 4.95 keV. High-efficiency crystal spectrometers allow for spectrally resolving the scattered radiation. Comparing the ratio of elastically and inelastically scattered radiation, we find evidence for a complex bonded liquid that is predicted by ab-initio quantum simulations showing the influence of chemical bonds under these conditions. Using graphite samples of different initial densities we demonstrate the capability ofmore » spectrally resolved x-ray scattering to monitor the carbon solid-liquid transition at relatively constant pressure of 150 GPa. Showing first single-pulse scattering spectra from cold graphite of unprecedented quality recorded at the Linac Coherent Light Source, we demonstrate the outstanding possibilities for future high-precision measurements at 4th Generation Light Sources.« less

Textile-reinforced concrete using composite binder based on new types of mineral raw materials

NASA Astrophysics Data System (ADS)

Lesovik, V. S.; Glagolev, E. S.; Popov, D. Y.; Lesovik, G. A.; Ageeva, M. S.

2018-03-01

To determine the level of development of science, it is necessary to start with a particular stage in the development of society. At present, the purpose of building materials science is to create composites, which ensure safety of buildings and structures, including their protection against certain natural and man-made impacts. A new stage in construction materials science envisages the development of a technology for creating composites comfortable for a particular person. To implement this, a new paradigm for designing and synthesizing building materials with a new raw material base is needed. The optimization of the “human-material-habitat” system is a complex task, for the solution of which transdisciplinary approaches are required.

Structure of Leishmania major Methionyl-tRNA Synthetase in Complex with Intermediate Products Methionyladenylate and Pyrophosphate

PubMed Central

Larson, Eric T.; Kim, Jessica E.; Zucker, Frank H.; Kelley, Angela; Mueller, Natascha; Napuli, Alberto J.; Verlinde, Christophe L.M.J.; Fan, Erkang; Buckner, Frederick S.; Van Voorhis, Wesley C.; Merritt, Ethan A.; Hol, Wim G.J.

2011-01-01

Leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions people at risk. Due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from Leishmania major in hopes of creating a platform for the rational design of new therapeutics. Crystals of the catalytic core of methionyl-tRNA synthetase from L. major (LmMetRS) were obtained with the substrates MgATP and methionine present in the crystallization medium. These crystals yielded the 2.0 Å resolution structure of LmMetRS in complex with two products, methionyladenylate and pyrophosphate, along with a Mg2+ ion that bridges them. This is the first class I aminoacyl-tRNA synthetase (aaRS) structure with pyrophosphate bound. The residues of the class I aaRS signature sequence motifs, KISKS and HIGH, make numerous contacts with the pyrophosphate. Substantial differences between the LmMetRS structure and previously reported complexes of E. coli MetRS (EcMetRS) with analogs of the methionyladenylate intermediate product are observed, even though one of these analogs only differs by one atom from the intermediate. The source of these structural differences is attributed to the presence of the product pyrophosphate in LmMetRS. Analysis of the LmMetRS structure in light of the Aquifex aeolicus MetRS-tRNAMet complex shows that major rearrangements of multiple structural elements of enzyme and/or tRNA are required to allow the CCA acceptor triplet to reach the methionyladenylate intermediate in the active site. Comparison with sequences of human cytosolic and mitochondrial MetRS reveals interesting differences near the ATP- and methionine-binding regions of LmMetRS, suggesting that it should be possible to obtain compounds that selectively inhibit the parasite enzyme. PMID:21144880

Ligand complex structures of l-amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 and its conformational change.

PubMed

Im, Dohyun; Matsui, Daisuke; Arakawa, Takatoshi; Isobe, Kimiyasu; Asano, Yasuhisa; Fushinobu, Shinya

2018-03-01

l-Amino acid oxidase/monooxygenase from Pseudomonas sp. AIU 813 (l-AAO/MOG) catalyzes both the oxidative deamination and oxidative decarboxylation of the α-group of l-Lys to produce a keto acid and amide, respectively. l-AAO/MOG exhibits limited specificity for l-amino acid substrates with a basic side chain. We previously determined its ligand-free crystal structure and identified a key residue for maintaining the dual activities. Here, we determined the structures of l-AAO/MOG complexed with l-Lys, l-ornithine, and l-Arg and revealed its substrate recognition. Asp238 is located at the ceiling of a long hydrophobic pocket and forms a strong interaction with the terminal, positively charged group of the substrates. A mutational analysis on the D238A mutant indicated that the interaction is critical for substrate binding but not for catalytic control between the oxidase/monooxygenase activities. The catalytic activities of the D238E mutant unexpectedly increased, while the D238F mutant exhibited altered substrate specificity to long hydrophobic substrates. In the ligand-free structure, there are two channels connecting the active site and solvent, and a short region located at the dimer interface is disordered. In the l-Lys complex structure, a loop region is displaced to plug the channels. Moreover, the disordered region in the ligand-free structure forms a short helix in the substrate complex structures and creates the second binding site for the substrate. It is assumed that the amino acid substrate enters the active site of l-AAO/MOG through this route. The atomic coordinates and structure factors (codes 5YB6, 5YB7, and 5YB8) have been deposited in the Protein Data Bank (http://wwpdb.org/). 1.4.3.2 (l-amino acid oxidase), 1.13.12.2 (lysine 2-monooxygenase).

Aerial Survey of Ames Research Center - Flight Simulation Complex' Flight simulators create an

NASA Technical Reports Server (NTRS)

1967-01-01

Aerial Survey of Ames Research Center - Flight Simulation Complex' Flight simulators create an authentic aircraft environment by generating the appropriate physical cues that provide the sensations of flight.

Effect of the crown design and interface lute parameters on the stress-state of a machined crown-tooth system: a finite element analysis.

PubMed

Shahrbaf, Shirin; vanNoort, Richard; Mirzakouchaki, Behnam; Ghassemieh, Elaheh; Martin, Nicolas

2013-08-01

The effect of preparation design and the physical properties of the interface lute on the restored machined ceramic crown-tooth complex are poorly understood. The aim of this work was to determine, by means of three-dimensional finite element analysis (3D FEA) the effect of the tooth preparation design and the elastic modulus of the cement on the stress state of the cemented machined ceramic crown-tooth complex. The three-dimensional structure of human premolar teeth, restored with adhesively cemented machined ceramic crowns, was digitized with a micro-CT scanner. An accurate, high resolution, digital replica model of a restored tooth was created. Two preparation designs, with different occlusal morphologies, were modeled with cements of 3 different elastic moduli. Interactive medical image processing software (mimics and professional CAD modeling software) was used to create sophisticated digital models that included the supporting structures; periodontal ligament and alveolar bone. The generated models were imported into an FEA software program (hypermesh version 10.0, Altair Engineering Inc.) with all degrees of freedom constrained at the outer surface of the supporting cortical bone of the crown-tooth complex. Five different elastic moduli values were given to the adhesive cement interface 1.8GPa, 4GPa, 8GPa, 18.3GPa and 40GPa; the four lower values are representative of currently used cementing lutes and 40GPa is set as an extreme high value. The stress distribution under simulated applied loads was determined. The preparation design demonstrated an effect on the stress state of the restored tooth system. The cement elastic modulus affected the stress state in the cement and dentin structures but not in the crown, the pulp, the periodontal ligament or the cancellous and cortical bone. The results of this study suggest that both the choice of the preparation design and the cement elastic modulus can affect the stress state within the restored crown-tooth complex. Copyright © 2013 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Enhancing implementation science by applying best principles of systems science.

PubMed

Northridge, Mary E; Metcalf, Sara S

2016-10-04

Implementation science holds promise for better ensuring that research is translated into evidence-based policy and practice, but interventions often fail or even worsen the problems they are intended to solve due to a lack of understanding of real world structures and dynamic complexity. While systems science alone cannot possibly solve the major challenges in public health, systems-based approaches may contribute to changing the language and methods for conceptualising and acting within complex systems. The overarching goal of this paper is to improve the modelling used in dissemination and implementation research by applying best principles of systems science. Best principles, as distinct from the more customary term 'best practices', are used to underscore the need to extract the core issues from the context in which they are embedded in order to better ensure that they are transferable across settings. Toward meaningfully grappling with the complex and challenging problems faced in adopting and integrating evidence-based health interventions and changing practice patterns within specific settings, we propose and illustrate four best principles derived from our systems science experience: (1) model the problem, not the system; (2) pay attention to what is important, not just what is quantifiable; (3) leverage the utility of models as boundary objects; and (4) adopt a portfolio approach to model building. To improve our mental models of the real world, system scientists have created methodologies such as system dynamics, agent-based modelling, geographic information science and social network simulation. To understand dynamic complexity, we need the ability to simulate. Otherwise, our understanding will be limited. The practice of dynamic systems modelling, as discussed herein, is the art and science of linking system structure to behaviour for the purpose of changing structure to improve behaviour. A useful computer model creates a knowledge repository and a virtual library for internally consistent exploration of alternative assumptions. Among the benefits of systems modelling are iterative practice, participatory potential and possibility thinking. We trust that the best principles proposed here will resonate with implementation scientists; applying them to the modelling process may abet the translation of research into effective policy and practice.

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.

Dirac electron in a chiral space-time crystal created by counterpropagating circularly polarized plane electromagnetic waves

NASA Astrophysics Data System (ADS)

Borzdov, G. N.

2017-10-01

The family of solutions to the Dirac equation for an electron moving in an electromagnetic lattice with the chiral structure created by counterpropagating circularly polarized plane electromagnetic waves is obtained. At any nonzero quasimomentum, the dispersion equation has two solutions which specify bispinor wave functions describing electron states with different energies and mean values of momentum and spin operators. The inversion of the quasimomentum results in two other linearly independent solutions. These four basic wave functions are uniquely defined by eight complex scalar functions (structural functions), which serve as convenient building blocks of the relations describing the electron properties. These properties are illustrated in graphical form over a wide range of quasimomenta. The superpositions of two basic wave functions describing different spin states and corresponding to (i) the same quasimomentum (unidirectional electron states with the spin precession) and (ii) the two equal-in-magnitude but oppositely directed quasimomenta (bidirectional electron states) are also treated.

Utilizing laser interference lithography to fabricate hierarchical optical active nanostructures inspired by the blue Morpho butterfly

NASA Astrophysics Data System (ADS)

Siddique, Radwanul H.; Faisal, Abrar; Hünig, Ruben; Bartels, Carolin; Wacker, Irene; Lemmer, Uli; Hoelscher, Hendrik

2014-09-01

The famous non-iridescent blue of the Morpho butter by is caused by a `Christmas tree' like nanostructure which is a challenge for common fabrication techniques. Here, we introduce a method to fabricate this complex morphology utilizing dual beam interference lithography. We add a reflective coating below the photoresist to create a second interference pattern in vertical direction by exploiting the back reflection from the substrate. This vertical pattern exposes the lamella structure into the photosensitive polymer while the horizontal interference pattern determines the distance of the ridges. The photosensitive polymer is chosen accordingly to create the Christmas tree' like tapered shape. The resulting artificial Morpho replica shows brilliant non-iridescent blue up to an incident angle of 40. Its optical properties are close to the original Morpho structure because the refractive index of the polymer is close to chitin. Moreover, the biomimetic surface is water repellent with a contact angle of 110.

Influence of using challenging tasks in biology classrooms on students' cognitive knowledge structure: an empirical video study

NASA Astrophysics Data System (ADS)

Nawani, Jigna; Rixius, Julia; Neuhaus, Birgit J.

2016-08-01

Empirical analysis of secondary biology classrooms revealed that, on average, 68% of teaching time in Germany revolved around processing tasks. Quality of instruction can thus be assessed by analyzing the quality of tasks used in classroom discourse. This quasi-experimental study analyzed how teachers used tasks in 38 videotaped biology lessons pertaining to the topic 'blood and circulatory system'. Two fundamental characteristics used to analyze tasks include: (1) required cognitive level of processing (e.g. low level information processing: repetiition, summary, define, classify and high level information processing: interpret-analyze data, formulate hypothesis, etc.) and (2) complexity of task content (e.g. if tasks require use of factual, linking or concept level content). Additionally, students' cognitive knowledge structure about the topic 'blood and circulatory system' was measured using student-drawn concept maps (N = 970 students). Finally, linear multilevel models were created with high-level cognitive processing tasks and higher content complexity tasks as class-level predictors and students' prior knowledge, students' interest in biology, and students' interest in biology activities as control covariates. Results showed a positive influence of high-level cognitive processing tasks (β = 0.07; p < .01) on students' cognitive knowledge structure. However, there was no observed effect of higher content complexity tasks on students' cognitive knowledge structure. Presented findings encourage the use of high-level cognitive processing tasks in biology instruction.

A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure.

PubMed

Steckelberg, Anna-Lena; Akiyama, Benjamin M; Costantino, David A; Sit, Tim L; Nix, Jay C; Kieft, Jeffrey S

2018-06-19

Folded RNA elements that block processive 5' → 3' cellular exoribonucleases (xrRNAs) to produce biologically active viral noncoding RNAs have been discovered in flaviviruses, potentially revealing a new mode of RNA maturation. However, whether this RNA structure-dependent mechanism exists elsewhere and, if so, whether a singular RNA fold is required, have been unclear. Here we demonstrate the existence of authentic RNA structure-dependent xrRNAs in dianthoviruses, plant-infecting viruses unrelated to animal-infecting flaviviruses. These xrRNAs have no sequence similarity to known xrRNAs; thus, we used a combination of biochemistry and virology to characterize their sequence requirements and mechanism of stopping exoribonucleases. By solving the structure of a dianthovirus xrRNA by X-ray crystallography, we reveal a complex fold that is very different from that of the flavivirus xrRNAs. However, both versions of xrRNAs contain a unique topological feature, a pseudoknot that creates a protective ring around the 5' end of the RNA structure; this may be a defining structural feature of xrRNAs. Single-molecule FRET experiments reveal that the dianthovirus xrRNAs undergo conformational changes and can use "codegradational remodeling," exploiting the exoribonucleases' degradation-linked helicase activity to help form their resistant structure; such a mechanism has not previously been reported. Convergent evolution has created RNA structure-dependent exoribonuclease resistance in different contexts, which establishes it as a general RNA maturation mechanism and defines xrRNAs as an authentic functional class of RNAs.

Photonic-magnonic crystals: Multifunctional periodic structures for magnonic and photonic applications

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

Kłos, J. W., E-mail: klos@amu.edu.pl; Krawczyk, M.; Dadoenkova, Yu. S.

2014-05-07

We investigate the properties of a photonic-magnonic crystal, a complex multifunctional one-dimensional structure with magnonic and photonic band gaps in the GHz and PHz frequency ranges for spin waves and light, respectively. The system consists of periodically distributed dielectric magnetic slabs of yttrium iron garnet and nonmagnetic spacers with an internal structure of alternating TiO{sub 2} and SiO{sub 2} layers which form finite-size dielectric photonic crystals. We show that the spin-wave coupling between the magnetic layers, and thus the formation of the magnonic band structure, necessitates a nonzero in-plane component of the spin-wave wave vector. A more complex structure perceivedmore » by light is evidenced by the photonic miniband structure and the transmission spectra in which we have observed transmission peaks related to the repetition of the magnetic slabs in the frequency ranges corresponding to the photonic band gaps of the TiO{sub 2}/SiO{sub 2} stack. Moreover, we show that these modes split to very high sharp (a few THz wide) subpeaks in the transmittance spectra. The proposed novel multifunctional artificial crystals can have interesting applications and be used for creating common resonant cavities for spin waves and light to enhance the mutual influence between them.« less

Genetic approach to reconstruct complex regional geological setting of the Baltic basin in 3D geological model

NASA Astrophysics Data System (ADS)

Popovs, K.; Saks, T.; Ukass, J.; Jatnieks, J.

2012-04-01

Interpretation of geological structures in 3D geological models is a relatively new research topic that is already standardized in many geological branches. Due to its wide practical application, these models are indispensable and become one of the dominant interpretation methods in reducing geological uncertainties in many geology fields. Traditionally, geological concepts complement quantitative as much as qualitative data to obtain a model deemed acceptable, however, available data very often is insufficient and modeling methods primarily focus on spatial data but geological history usually is mostly neglected for the modeling of large sedimentary basins. A need to better integrate the long and often complex geological history and geological knowledge into modeling procedure is very acute to gain geological insight and improve the quality of geological models. During this research, 3D geological model of the Baltic basin (BB) was created. Because of its complex regional geological setting - wide range of the data sources with multiple scales, resolution and density as well as its various source formats, the study area provides a challenge for the 3D geological modeling. In order to create 3D regional geometrical model for the study area algorithmic genetic approach for model geometry reconstruction was applied. The genetic approach is based on the assumption that post-depositional deformation produce no significant change in sedimentary strata volume, assuming that the strata thickness and its length in a cross sectional plane remains unchanged except as a result of erosion. Assuming that the tectonic deformation occurred in sequential cycles and subsequent tectonic stage strata is separated by regional unconformity as is the case of the BB, there is an opportunity for algorithmic approach in reconstructing these conditions by sequentially reconstructing the layer original thickness. Layer thicknesses were sliced along fault lines, where applicable layer thickness was adjusted by taking into account amount of erosion by the presence of the regional unconformities. Borehole data and structural maps of some surfaces were used in creating geological model of the BB. Used approach allowed creating geologically sound geometric model. At first borehole logs were used to reconstruct initial thicknesses of different strata in every tectonic stage, where topography of each strata was obtained sequentially summing thickness to the initial reference surface from structural maps. Thereby each layer reflects the topography and amount of slip along the fault of the overlying layer. Overlying tectonic cycle sequence is implemented into the model structure by using unconformity surface as an initial reference surface. Applied techniques made possible reliably reconstructing and predicting in areas of sparse data layer surface geometry, its thickness distribution and evaluating displacements along the fault planes. Overall results indicate that the used approach has a good potential in development of regional geological models for the sedimentary basins and is valid for spatial interpretation of geological structures, subordinating this process to geological evolution prerequisites. This study is supported by the European Social Fund project No. 2009/0212/1DP/1.1.1.2.0/09/APIA/VIAA/060.

MFIB: a repository of protein complexes with mutual folding induced by binding.

PubMed

Fichó, Erzsébet; Reményi, István; Simon, István; Mészáros, Bálint

2017-11-15

It is commonplace that intrinsically disordered proteins (IDPs) are involved in crucial interactions in the living cell. However, the study of protein complexes formed exclusively by IDPs is hindered by the lack of data and such analyses remain sporadic. Systematic studies benefited other types of protein-protein interactions paving a way from basic science to therapeutics; yet these efforts require reliable datasets that are currently lacking for synergistically folding complexes of IDPs. Here we present the Mutual Folding Induced by Binding (MFIB) database, the first systematic collection of complexes formed exclusively by IDPs. MFIB contains an order of magnitude more data than any dataset used in corresponding studies and offers a wide coverage of known IDP complexes in terms of flexibility, oligomeric composition and protein function from all domains of life. The included complexes are grouped using a hierarchical classification and are complemented with structural and functional annotations. MFIB is backed by a firm development team and infrastructure, and together with possible future community collaboration it will provide the cornerstone for structural and functional studies of IDP complexes. MFIB is freely accessible at http://mfib.enzim.ttk.mta.hu/. The MFIB application is hosted by Apache web server and was implemented in PHP. To enrich querying features and to enhance backend performance a MySQL database was also created. simon.istvan@ttk.mta.hu, meszaros.balint@ttk.mta.hu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Measurement of physical characteristics of materials by ultrasonic methods

DOEpatents

Lu, Wei-yang; Min, Shermann

1998-01-01

A method is described for determining and evaluating physical characteristics of a material. In particular, the present invention provides for determining and evaluating the anisotropic characteristics of materials, especially those resulting from such manufacturing processes as rolling, forming, extruding, drawing, forging, etc. In operation, a complex ultrasonic wave is created in the material of interest by any method. The wave form may be any combination of wave types and modes and is not limited to fundamental plate modes. The velocity of propagation of selected components which make up the complex ultrasonic wave are measured and evaluated to determine the physical characteristics of the material including, texture, strain/stress, grain size, crystal structure, etc.

Measurement of physical characteristics of materials by ultrasonic methods

DOEpatents

Lu, W.Y.; Min, S.

1998-09-08

A method is described for determining and evaluating physical characteristics of a material. In particular, the present invention provides for determining and evaluating the anisotropic characteristics of materials, especially those resulting from such manufacturing processes as rolling, forming, extruding, drawing, forging, etc. In operation, a complex ultrasonic wave is created in the material of interest by any method. The wave form may be any combination of wave types and modes and is not limited to fundamental plate modes. The velocity of propagation of selected components which make up the complex ultrasonic wave are measured and evaluated to determine the physical characteristics of the material including, texture, strain/stress, grain size, crystal structure, etc. 14 figs.

The structural basis for function in diamond-like carbon binding peptides.

PubMed

Gabryelczyk, Bartosz; Szilvay, Géza R; Linder, Markus B

2014-07-29

The molecular structural basis for the function of specific peptides that bind to diamond-like carbon (DLC) surfaces was investigated. For this, a competition assay that provided a robust way of comparing relative affinities of peptide variants was set up. Point mutations of specific residues resulted in significant effects, but it was shown that the chemical composition of the peptide was not sufficient to explain peptide affinity. More significantly, rearrangements in the sequence indicated that the binding is a complex recognition event that is dependent on the overall structure of the peptide. The work demonstrates the unique properties of peptides for creating functionality at interfaces via noncovalent binding for potential applications in, for example, nanomaterials, biomedical materials, and sensors.

Music acquisition: effects of enculturation and formal training on development.

PubMed

Hannon, Erin E; Trainor, Laurel J

2007-11-01

Musical structure is complex, consisting of a small set of elements that combine to form hierarchical levels of pitch and temporal structure according to grammatical rules. As with language, different systems use different elements and rules for combination. Drawing on recent findings, we propose that music acquisition begins with basic features, such as peripheral frequency-coding mechanisms and multisensory timing connections, and proceeds through enculturation, whereby everyday exposure to a particular music system creates, in a systematic order of acquisition, culture-specific brain structures and representations. Finally, we propose that formal musical training invokes domain-specific processes that affect salience of musical input and the amount of cortical tissue devoted to its processing, as well as domain-general processes of attention and executive functioning.

Structural DNA Nanotechnology: State of the Art and Future Perspective

PubMed Central

2015-01-01

Over the past three decades DNA has emerged as an exceptional molecular building block for nanoconstruction due to its predictable conformation and programmable intra- and intermolecular Watson–Crick base-pairing interactions. A variety of convenient design rules and reliable assembly methods have been developed to engineer DNA nanostructures of increasing complexity. The ability to create designer DNA architectures with accurate spatial control has allowed researchers to explore novel applications in many directions, such as directed material assembly, structural biology, biocatalysis, DNA computing, nanorobotics, disease diagnosis, and drug delivery. This Perspective discusses the state of the art in the field of structural DNA nanotechnology and presents some of the challenges and opportunities that exist in DNA-based molecular design and programming. PMID:25029570

The Processing of Extraposed Structures in English

PubMed Central

Levy, Roger; Fedorenko, Evelina; Breen, Mara; Gibson, Ted

2012-01-01

In most languages, most of the syntactic dependency relations found in any given sentence are PROJECTIVE: the word-word dependencies in the sentence do not cross each other. Some syntactic dependency relations, however, are NON-PROJECTIVE: some of their word-word dependencies cross each other. Non-projective dependencies are both rarer and more computationally complex than projective dependencies; hence, it is of natural interest to investigate whether there are any processing costs specific to non-projective dependencies, and whether factors known to influence processing of projective dependencies also affect non-projective dependency processing. We report three self-paced reading studies, together with corpus and sentence completion studies, investigating the comprehension difficulty associated with the non-projective dependencies created by the extraposition of relative clauses in English. We find that extraposition over either verbs or prepositional phrases creates comprehension difficulty, and that this difficulty is consistent with probabilistic syntactic expectations estimated from corpora. Furthermore, we find that manipulating the expectation that a given noun will have a postmodifying relative clause can modulate and even neutralize the difficulty associated with extraposition. Our experiments rule out accounts based purely on derivational complexity and/or dependency locality in terms of linear positioning. Our results demonstrate that comprehenders maintain probabilistic syntactic expectations that persist beyond projective-dependency structures, and suggest that it may be possible to explain observed patterns of comprehension difficulty associated with extraposition entirely through probabilistic expectations. PMID:22035959

Being a webcam.

PubMed

Schmid-Siegel, B; Stompe, T; Ortwein-Swoboda, G

2004-01-01

Searching through studies of schizophrenic delusions with a view to the new media, we came across the case of a young woman who integrated the Internet in her delusional system. Analysing the story she told, we recognised a psychotic symptom, which we preliminarily called 'perception broadcast'. Perception broadcast shows a more complex structure than the related first rank symptom 'thought broadcast' described by Kurt Schneider. In our view the existence of a structure like perception broadcast depends on the existence of new technologies, such as the World Wide Web and 'virtual reality', creating new cultural patterns which themselves are associated with collective perceptions of derealisation. Copyright 2004 S. Karger AG, Basel

A guide to the visual analysis and communication of biomolecular structural data.

PubMed

Johnson, Graham T; Hertig, Samuel

2014-10-01

Biologists regularly face an increasingly difficult task - to effectively communicate bigger and more complex structural data using an ever-expanding suite of visualization tools. Whether presenting results to peers or educating an outreach audience, a scientist can achieve maximal impact with minimal production time by systematically identifying an audience's needs, planning solutions from a variety of visual communication techniques and then applying the most appropriate software tools. A guide to available resources that range from software tools to professional illustrators can help researchers to generate better figures and presentations tailored to any audience's needs, and enable artistically inclined scientists to create captivating outreach imagery.

Drawbacks of mangrove rehabilitation schemes: Lessons learned from the large-scale mangrove plantations

NASA Astrophysics Data System (ADS)

Barnuevo, Abner; Asaeda, Takashi; Sanjaya, Kelum; Kanesaka, Yoshikazu; Fortes, Miguel

2017-11-01

Mangrove rehabilitation programs received much attention in the past decades as a response to widespread global degradation. While the documented successes and failures of mangrove rehabilitation accomplishments were varied, the objective and scheme is common, mainly focused on planting and creating monospecific plantations. This study assessed the structural development and complexity of the large-scale plantations in the central part of Philippines and compared it with the adjacent natural stand as reference. Our study showed that planted forest in both sites had lower structural complexity than the reference natural forest. Between sites, secondary succession in the monospecific plantation in Banacon Island was inhibited as reflected by low regeneration potential, whereas recruitment and colonization of non-planted species was promoted in Olango Island. Even 60 years after the forest was created in Banacon Island, it still lacked the understory of young cohorts which together comprise the regeneration potential that can supposedly add to the structural complexity. Although a potential seed source from adjacent natural forest is available, recruitment and colonization of non-planted species did not progress. MDS analysis of tree density data showed clustering of planted forest from the natural stand. The average SIMPER dissimilarity was 79.9% and the species with highest contributions were R. stylosa (74.6%), S. alba (11.1%) and A. marina (10.6%). Within the natural forest, the same species had the highest dissimilarity contribution, whereas in the planted forest, only R. stylosa contributed the highest dissimilarity. The same trend was also revealed in the MDS ordination analysis of diameter at breast height (DBH). A one-way ANOSIM permutation test of the density and DBH showed a significant difference between the planted and natural forests. Thus, as part of silviculture management intervention, the current practices of mangrove reforestation needs to be reviewed and evaluated to determine the trajectories of its conservation objectives to achieve the best outcome and functionality of the restored habitat.

Spectral characterization, thermal and biological activity studies of Schiff base complexes derived from 4,4‧-Methylenedianiline, ethanol amine and benzil

NASA Astrophysics Data System (ADS)

Emam, Sanaa Moustafa

2017-04-01

Some new metal(II) complexes of asymmetric Schiff base ligand were prepared by template technique. The shaped complexes are in binuclear structures and were explained through elemental analysis, molar conductivity, various spectroscopic methods (IR, U.V-Vis, XRD, ESR), thermal (TG) and magnetic moment measurements. The IR spectra were done demonstrating that the Schiff base ligand acts as neutral tetradentate moiety in all metal complexes. The electronic absorption spectra represented octahedral geometry for all complexes, while, the ESR spectra for Cu(II) complex showed axially symmetric g-tensor parameter with g׀׀ > g⊥ > 2.0023 indicating to 2B1g ground state with (dx2-y2)1 configuration. The nature of the solid residue created from TG estimations was affirmed utilizing IR and XRD spectra. The biological activity of the prepared complexes was studied against Land Snails. Additionally, the in vitro antitumor activity of the synthesized complexes with Hepatocellular Carcinoma cell (Hep-G2) was examined. It was observed that Zn(II) complex (5), exhibits a high inhibition of growth of the cell line with IC50 of 7.09 μg/mL.

Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O -Methyltransferases.

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

Bernard, Steffen M.; Akey, David L.; Tripathi, Ashootosh

Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates,more » show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homolog, active site residues were identified that correlate with the 3'- or 4'- specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. Lastly, this classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.« less

Structural Basis of Substrate Specificity and Regiochemistry in the MycF/TylF Family of Sugar O -Methyltransferases.

DOE PAGES

Bernard, Steffen M.; Akey, David L.; Tripathi, Ashootosh; ...

2015-02-18

Sugar moieties in natural products are frequently modified by O-methylation. In the biosynthesis of the macrolide antibiotic mycinamicin, methylation of a 6'-deoxyallose substituent occurs in a stepwise manner first at the 2'- and then the 3'-hydroxyl groups to produce the mycinose moiety in the final product. The timing and placement of the O-methylations impact final stage C-H functionalization reactions mediated by the P450 monooxygenase MycG. The structural basis of pathway ordering and substrate specificity is unknown. A series of crystal structures of MycF, the 3'-O-methyltransferase, including the free enzyme and complexes with S-adenosyl homocysteine (SAH), substrate, product, and unnatural substrates,more » show that SAM binding induces substantial ordering that creates the binding site for the natural substrate, and a bound metal ion positions the substrate for catalysis. A single amino acid substitution relaxed the 2'-methoxy specificity but retained regiospecificity. The engineered variant produced a new mycinamicin analog, demonstrating the utility of structural information to facilitate bioengineering approaches for the chemoenzymatic synthesis of complex small molecules containing modified sugars. Using the MycF substrate complex and the modeled substrate complex of a 4'-specific homolog, active site residues were identified that correlate with the 3'- or 4'- specificity of MycF family members and define the protein and substrate features that direct the regiochemistry of methyltransfer. Lastly, this classification scheme will be useful in the annotation of new secondary metabolite pathways that utilize this family of enzymes.« less

3D-Printing Technologies for Craniofacial Rehabilitation, Reconstruction, and Regeneration.

PubMed

Nyberg, Ethan L; Farris, Ashley L; Hung, Ben P; Dias, Miguel; Garcia, Juan R; Dorafshar, Amir H; Grayson, Warren L

2017-01-01

The treatment of craniofacial defects can present many challenges due to the variety of tissue-specific requirements and the complexity of anatomical structures in that region. 3D-printing technologies provide clinicians, engineers and scientists with the ability to create patient-specific solutions for craniofacial defects. Currently, there are three key strategies that utilize these technologies to restore both appearance and function to patients: rehabilitation, reconstruction and regeneration. In rehabilitation, 3D-printing can be used to create prostheses to replace or cover damaged tissues. Reconstruction, through plastic surgery, can also leverage 3D-printing technologies to create custom cutting guides, fixation devices, practice models and implanted medical devices to improve patient outcomes. Regeneration of tissue attempts to replace defects with biological materials. 3D-printing can be used to create either scaffolds or living, cellular constructs to signal tissue-forming cells to regenerate defect regions. By integrating these three approaches, 3D-printing technologies afford the opportunity to develop personalized treatment plans and design-driven manufacturing solutions to improve aesthetic and functional outcomes for patients with craniofacial defects.

3D-Printing Technologies for Craniofacial Rehabilitation, Reconstruction, and Regeneration

PubMed Central

Nyberg, Ethan L.; Farris, Ashley L.; Hung, Ben P.; Dias, Miguel; Garcia, Juan R.; Dorafshar, Amir H.; Grayson, Warren L.

2016-01-01

The treatment of craniofacial defects can present many challenges due to the variety of tissue-specific requirements and the complexity of anatomical structures in that region. 3D-printing technologies provide clinicians, engineers and scientists with the ability to create patient-specific solutions for craniofacial defects. Currently, there are 3 key strategies that utilize these technologies to restore both appearance and function to patients: rehabilitation, reconstruction and regeneration. In rehabilitation, 3D-printing can be used to create prostheses to replace or cover damaged tissues. Reconstruction, through plastic surgery, can also leverage 3D-printing technologies to create custom cutting guides, fixation devices, practice models and implanted medical devices to improve patient outcomes. Regeneration of tissue attempts to replace defects with biological materials. 3D-printing can be used to create either scaffolds or living, cellular constructs to signal tissue-forming cells to regenerate defect regions. By integrating these three approaches, 3D-printing technologies afford the opportunity to develop personalized treatment plans and design-driven manufacturing solutions to improve aesthetic and functional outcomes for patients with craniofacial defects. PMID:27295184

Programmable assembly of nanoarchitectures using genetically engineered viruses.

PubMed

Huang, Yu; Chiang, Chung-Yi; Lee, Soo Kwan; Gao, Yan; Hu, Evelyn L; De Yoreo, James; Belcher, Angela M

2005-07-01

Biological systems possess inherent molecular recognition and self-assembly capabilities and are attractive templates for constructing complex material structures with molecular precision. Here we report the assembly of various nanoachitectures including nanoparticle arrays, hetero-nanoparticle architectures, and nanowires utilizing highly engineered M13 bacteriophage as templates. The genome of M13 phage can be rationally engineered to produce viral particles with distinct substrate-specific peptides expressed on the filamentous capsid and the ends, providing a generic template for programmable assembly of complex nanostructures. Phage clones with gold-binding motifs on the capsid and streptavidin-binding motifs at one end are created and used to assemble Au and CdSe nanocrytals into ordered one-dimensional arrays and more complex geometries. Initial studies show such nanoparticle arrays can further function as templates to nucleate highly conductive nanowires that are important for addressing/interconnecting individual nanostructures.

Ternary complexes of Zn(II) and Cu(II) with 1-((2-hydroxynaphthalen-1-yl)methylene)-4-phenylthiosemicarbazide in the presence of heterocyclic bases as auxiliary ligands: Synthesis, spectroscopic and structural characterization and antibacterial activity

NASA Astrophysics Data System (ADS)

Azarkish, Mohammad; Akbari, Alireza; Sedaghat, Tahereh; Simpson, Jim

2018-03-01

The new ternary complexes, ZnLL‧ [L = 1-((2-hydroxynaphthalen-1-yl)methylene)-4-phenylthiosemicarbazide and L‧ = imidazole (1), 2, 2‧-bipyridine (2) and 2-methyimidazole (3)], Zn2L2L‧ [L‧ = 4, 4‧-bipy (4)] and CuLL‧ [L‧ = 2, 2‧-bipy (5)] have been synthesized by the reaction of a metal(II) acetate salt with the thiosemicarbazone and in presence of heterocyclic bases as auxiliary ligands. The synthesized compounds were investigated by elemental analysis and IR, 1H NMR, and 13C NMR spectroscopy and complex 5 was structurally characterized by X-ray crystallography. The results indicate the thiosemicarbazone doubly deprotonated and coordinates to metal through the thiolate sulfur, imine nitrogen and phenolic oxygen atoms. The nitrogen atom(s) of the auxiliary ligand complete the coordination sphere. Complex 4 is binuclear with 4, 4‧-bipy acting as a bridging ligand. The structure of 5 is a distorted square pyramid with one of the bipyridine nitrogen atoms in the apical position. This compound creates an inversion dimer in solid state by intermolecular hydrogen bonds of Nsbnd H⋯S type. The in vitro antibacterial activity of the synthesized compounds were evaluated against Gram-positive (B. subtilis and S. aureus) and Gram-negative (P. aeruginosa) bacteria and is compared to that of standard antibacterial drugs. All complexes exhibit good inhibitory effects and are significantly more effective than the parent ligand.

Crystal structures of the free and inhibited forms of plasmepsin I (PMI) from Plasmodium falciparum

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

Bhaumik, Prasenjit; Horimoto, Yasumi; Xiao, Huogen

2011-09-06

Plasmepsin I (PMI) is one of the four vacuolar pepsin-like proteases responsible for hemoglobin degradation by the malarial parasite Plasmodium falciparum, and the only one with no crystal structure reported to date. Due to substantial functional redundancy of these enzymes, lack of inhibition of even a single plasmepsin can defeat efforts in creating effective antiparasitic agents. We have now solved crystal structures of the recombinant PMI as apoenzyme and in complex with the potent peptidic inhibitor, KNI-10006, at the resolution of 2.4 and 3.1 {angstrom}, respectively. The apoenzyme crystallized in the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} with twomore » molecules in the asymmetric unit and the structure has been refined to the final R-factor of 20.7%. The KNI-10006 bound enzyme crystallized in the tetragonal space group P4{sub 3} with four molecules in the asymmetric unit and the structure has been refined to the final R-factor of 21.1%. In the PMI-KNI-10006 complex, the inhibitors were bound identically to all four enzyme molecules, with the opposite directionality of the main chain of KNI-10006 relative to the direction of the enzyme substrates. Such a mode of binding of inhibitors containing an allophenylnorstatine-dimethylthioproline insert in the P1-P1' positions, previously reported in a complex with PMIV, demonstrates the importance of satisfying the requirements for the proper positioning of the functional groups in the mechanism-based inhibitors towards the catalytic machinery of aspartic proteases, as opposed to binding driven solely by the specificity of the individual enzymes. A comparison of the structure of the PMI-KNI-10006 complex with the structures of other vacuolar plasmepsins identified the important differences between them and may help in the design of specific inhibitors targeting the individual enzymes.« less

Fourth-order structural steganalysis and analysis of cover assumptions

NASA Astrophysics Data System (ADS)

Ker, Andrew D.

2006-02-01

We extend our previous work on structural steganalysis of LSB replacement in digital images, building detectors which analyse the effect of LSB operations on pixel groups as large as four. Some of the method previously applied to triplets of pixels carries over straightforwardly. However we discover new complexities in the specification of a cover image model, a key component of the detector. There are many reasonable symmetry assumptions which we can make about parity and structure in natural images, only some of which provide detection of steganography, and the challenge is to identify the symmetries a) completely, and b) concisely. We give a list of possible symmetries and then reduce them to a complete, non-redundant, and approximately independent set. Some experimental results suggest that all useful symmetries are thus described. A weighting is proposed and its approximate variance stabilisation verified empirically. Finally, we apply symmetries to create a novel quadruples detector for LSB replacement steganography. Experimental results show some improvement, in most cases, over other detectors. However the gain in performance is moderate compared with the increased complexity in the detection algorithm, and we suggest that, without new insight, further extension of structural steganalysis may provide diminishing returns.

Experimental Evaluation of Processing Time for the Synchronization of XML-Based Business Objects

NASA Astrophysics Data System (ADS)

Ameling, Michael; Wolf, Bernhard; Springer, Thomas; Schill, Alexander

Business objects (BOs) are data containers for complex data structures used in business applications such as Supply Chain Management and Customer Relationship Management. Due to the replication of application logic, multiple copies of BOs are created which have to be synchronized and updated. This is a complex and time consuming task because BOs rigorously vary in their structure according to the distribution, number and size of elements. Since BOs are internally represented as XML documents, the parsing of XML is one major cost factor which has to be considered for minimizing the processing time during synchronization. The prediction of the parsing time for BOs is an significant property for the selection of an efficient synchronization mechanism. In this paper, we present a method to evaluate the influence of the structure of BOs on their parsing time. The results of our experimental evaluation incorporating four different XML parsers examine the dependencies between the distribution of elements and the parsing time. Finally, a general cost model will be validated and simplified according to the results of the experimental setup.

Rational growth of branched nanowire heterostructures with synthetically encoded properties and function

PubMed Central

Jiang, Xiaocheng; Tian, Bozhi; Xiang, Jie; Qian, Fang; Zheng, Gengfeng; Wang, Hongtao; Mai, Liqiang; Lieber, Charles M.

2011-01-01

Branched nanostructures represent unique, 3D building blocks for the “bottom-up” paradigm of nanoscale science and technology. Here, we report a rational, multistep approach toward the general synthesis of 3D branched nanowire (NW) heterostructures. Single-crystalline semiconductor, including groups IV, III–V, and II–VI, and metal branches have been selectively grown on core or core/shell NW backbones, with the composition, morphology, and doping of core (core/shell) NWs and branch NWs well controlled during synthesis. Measurements made on the different composition branched NW structures demonstrate encoding of functional p-type/n-type diodes and light-emitting diodes (LEDs) as well as field effect transistors with device function localized at the branch/backbone NW junctions. In addition, multibranch/backbone NW structures were synthesized and used to demonstrate capability to create addressable nanoscale LED arrays, logic circuits, and biological sensors. Our work demonstrates a previously undescribed level of structural and functional complexity in NW materials, and more generally, highlights the potential of bottom-up synthesis to yield increasingly complex functional systems in the future. PMID:21730174

A Cut-and-Paste Approach to 3D Graphene-Oxide-Based Architectures.

PubMed

Luo, Chong; Yeh, Che-Ning; Baltazar, Jesus M Lopez; Tsai, Chao-Lin; Huang, Jiaxing

2018-04-01

Properly cut sheets can be converted into complex 3D structures by three basic operations including folding, bending, and pasting to render new functions. Folding and bending are extensively employed in crumpling, origami, and pop-up fabrications for 3D structures. Pasting joins different parts of a material together, and can create new geometries that are fundamentally unattainable by folding and bending. However, it has been much less explored, likely due to limited choice of weldable thin film materials and residue-free glues. Here it is shown that graphene oxide (GO) paper is one such suitable material. Stacked GO sheets can be readily loosened up and even redispersed in water, which upon drying, restack to form solid structures. Therefore, water can be utilized to heal local damage, glue separated pieces, and release internal stress in bent GO papers to fix their shapes. Complex and dynamic 3D GO architectures can thus be fabricated by a cut-and-paste approach, which is also applicable to GO-based hybrid with carbon nanotubes or clay sheets. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Physical experiments and analysis on the generation and evolution of tsunami-induced turbulent coherent structures

NASA Astrophysics Data System (ADS)

Kalligeris, Nikos; Lynett, Patrick

2017-11-01

Numerous historical accounts describe the formation of ``whirpools'' inside ports and harbors during tsunami events, causing port operation disruptions. Videos from the Japan 2011 tsunami revealed complex nearshore flow patters, resulting from the interaction of tsunami-induced currents with the man-made coastline, and the generation of large eddies (or turbulent coherent structures) in numerous ports and harbors near the earthquake epicenter. The aim of this work is to study the generation and evolution of tsunami-induced turbulent coherent structures (TCS) in a well-controlled environment using realistic scaling. A physical configuration is created in the image of a port entrance at a scale of 1:27 and a small-amplitude, long period wave creates a transient flow through the asymmetric harbor channel. A separated region forms, which coupled with the transient flow, leads to the formation of a stable monopolar TCS. The surface flow is examined through mono- and stereo-PTV techniques to extract surface velocity vectors. Surface velocity maps and vortex flow profiles are used to study the experimental TCS generation and evolution, and characterize the TCS structure. Analytical tools are used to describe the TCS growth rate and kinetic energy decay. This work was funded by the National Science Foundation NEES Research program, with Award Number 1135026.

Controlling Propagation Properties of Surface Plasmon Polariton at Terahertz Frequency

NASA Astrophysics Data System (ADS)

Gupta, Barun

Despite great scientific exploration since the 1900s, the terahertz range is one of the least explored regions of electromagnetic spectrum today. In the field of plasmonics, texturing and patterning allows for control over electromagnetic waves bound to the interface between a metal and the adjacent dielectric medium. The surface plasmon-polaritons (SPPs) display unique dispersion characteristics that depend upon the plasma frequency of the medium. In the long wavelength regime, where metals are highly conductive, such texturing can create an effective medium that can be characterized by an effective plasma frequency that is determined by the geometrical parameters of the surface structure. The terahertz (THz) spectral range offers unique opportunities to utilize such materials. This thesis describes a number of terahertz plasmonic devices, both passive and active, fabricated using different techniques. As an example, inkjet printing is exploited for fabricating two-dimensional plasmonic devices. In this case, we demonstrated the terahertz plasmonic structures in which the conductivity of the metallic film is varied spatially in order to further control the plasmonic response. Using a commercially available inkjet printers, in which one cartridge is filled with conductive silver ink and a second cartridge is filled with resistive carbon ink, computer generated drawings of plasmonic structures are printed in which the individual printed dots can have differing amounts of the two inks, thereby creating a spatial variation in the conductivity. The inkjet printing technique is limited to the two-dimensional structurers. In order to expand the capability of printing complex terahertz devices, which cannot otherwise be fabricated using standard fabricating techniques, we employed 3D printing techniques. 3D printing techniques using polymers to print out the complex structures. In the realm of active plasmonic devices, a wide range of innovative approaches have been developed utilizing a variety of materials. We discuss the use of SMAs for terahertz (THz) plasmonics that allows for switching between different physical geometries corresponding to different electromagnetic responses.

Ecoengineering with Ecohydrology: Successes and failures in estuarine restoration

NASA Astrophysics Data System (ADS)

Elliott, Michael; Mander, Lucas; Mazik, Krysia; Simenstad, Charles; Valesini, Fiona; Whitfield, Alan; Wolanski, Eric

2016-07-01

Ecological Engineering (or Ecoengineering) is increasingly used in estuaries to re-create and restore ecosystems degraded by human activities, including reduced water flow or land poldered for agricultural use. Here we focus on ecosystem recolonization by the biota and their functioning and we separate Type A Ecoengineering where the physico-chemical structure is modified on the basis that ecological structure and functioning will then follow, and Type B Ecoengineering where the biota are engineered directly such as through restocking or replanting. Modifying the physical system to create and restore natural processes and habitats relies on successfully applying Ecohydrology, where suitable physical conditions, especially hydrography and sedimentology, are created to recover estuarine ecology by natural or human-mediated colonisation of primary producers and consumers, or habitat creation. This successional process then allows wading birds and fish to reoccupy the rehabilitated areas, thus restoring the natural food web and recreating nursery areas for aquatic biota. We describe Ecohydrology principles applied during Ecoengineering restoration projects in Europe, Australia, Asia, South Africa and North America. These show some successful and sustainable approaches but also others that were less than successful and not sustainable despite the best of intentions (and which may even have harmed the ecology). Some schemes may be 'good for the ecologists', as conservationists consider it successful that at least some habitat was created, albeit in the short-term, but arguably did little for the overall ecology of the area in space or time. We indicate the trade-offs between the short- and long-term value of restored and created ecosystems, the success at developing natural structure and functioning in disturbed estuaries, the role of this in estuarine and wetland management, and the costs and benefits of Ecoengineering to the socio-ecological system. These global case studies provide important lessons for both the science and management of estuaries, including that successful estuarine restoration is a complex and often difficult process, and that Ecoengineering with Ecohydrology aims to control and/or simulate natural ecosystem processes.

Geologic evolution of the Kastel trough and its implications on the Adiyaman oil fields, SE Turkey

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

Coskun, Bu.

1990-05-01

Oil field developments of the Adiyaman area one of the main oil producing zones in southeast Turkey, have been highly influenced by geologic evolution of the Kastel trough which is situated in front of the suture zone between the Arabian and Anatolian plates. The Upper Cretaceous movements created many paleostructural trends in the Kastel trough where important dolomitic and porous reservoirs exist. The most important tectonic event, which appeared during the Upper Cretaceous movements, is the accumulation of the Kocali-Karadut ophiolitic complex, advancing from the north to the south in the Kastel trough, where heavy materials caused formation of amore » structural model favoring generation and migration and entrapment of oil in the reservoir rocks. Due to the presence of the Kocali-Karadut complex in the Kastel trough the following zones have been distinguished. (1) North Uplift Area. Situated under the allochthonous units, many thrust and reverse faults characterize this zone. The presence of paleohighs, where primary dolomites develop, allows the appearance of some oil fields in the region. This is the main future exploration zone in southeast Turkey. (2) Accumulation Area. Advancing from the north to the south, the allochthonous Kocali-Karadut complex filled the Kastel trough creating a deep graben whose flanks present generally normal faults. (3) Structural Belt. Important paleohighs constitute an exploration trend in this zone where dolomitic and porous carbonates contain actual oil fields. (4) South Accumulation Area. Distant from the Arabian-Anatolian suture zone, regional tectonics and sedimentology show this zone remained deeply buried during geologic time; good source rocks were deposited during the Cretaceous. (5) South Uplift Area. This area corresponds to the northern flank of the huge regional Mardin high in southeast Turkey where new oil fields have been discovered.« less

Columbia River Estuary ecosystem classification—Concept and application

USGS Publications Warehouse

Simenstad, Charles A.; Burke, Jennifer L.; O'Connor, Jim E.; Cannon, Charles; Heatwole, Danelle W.; Ramirez, Mary F.; Waite, Ian R.; Counihan, Timothy D.; Jones, Krista L.

2011-01-01

This document describes the concept, organization, and application of a hierarchical ecosystem classification that integrates saline and tidal freshwater reaches of estuaries in order to characterize the ecosystems of large flood plain rivers that are strongly influenced by riverine and estuarine hydrology. We illustrate the classification by applying it to the Columbia River estuary (Oregon-Washington, USA), a system that extends about 233 river kilometers (rkm) inland from the Pacific Ocean. More than three-quarters of this length is tidal freshwater. The Columbia River Estuary Ecosystem Classification ("Classification") is based on six hierarchical levels, progressing from the coarsest, regional scale to the finest, localized scale: (1) Ecosystem Province; (2) Ecoregion; (3) Hydrogeomorphic Reach; (4) Ecosystem Complex; (5) Geomorphic Catena; and (6) Primary Cover Class. We define and map Levels 1-3 for the entire Columbia River estuary with existing geospatial datasets, and provide examples of Levels 4-6 for one hydrogeomorphic reach. In particular, three levels of the Classification capture the scales and categories of ecosystem structure and processes that are most tractable to estuarine research, monitoring, and management. These three levels are the (1) eight hydrogeomorphic reaches that embody the formative geologic and tectonic processes that created the existing estuarine landscape and encompass the influence of the resulting physiography on interactions between fluvial and tidal hydrology and geomorphology across 230 kilometers (km) of estuary, (2) more than 15 ecosystem complexes composed of broad landforms created predominantly by geologic processes during the Holocene, and (3) more than 25 geomorphic catenae embedded within ecosystem complexes that represent distinct geomorphic landforms, structures, ecosystems, and habitats, and components of the estuarine landscape most likely to change over short time periods.

Experimental validation of a numerical 3-D finite model applied to wind turbines design under vibration constraints: TREVISE platform

NASA Astrophysics Data System (ADS)

Sellami, Takwa; Jelassi, Sana; Darcherif, Abdel Moumen; Berriri, Hanen; Mimouni, Med Faouzi

2018-04-01

With the advancement of wind turbines towards complex structures, the requirement of trusty structural models has become more apparent. Hence, the vibration characteristics of the wind turbine components, like the blades and the tower, have to be extracted under vibration constraints. Although extracting the modal properties of blades is a simple task, calculating precise modal data for the whole wind turbine coupled to its tower/foundation is still a perplexing task. In this framework, this paper focuses on the investigation of the structural modeling approach of modern commercial micro-turbines. Thus, the structural model a complex designed wind turbine, which is Rutland 504, is established based on both experimental and numerical methods. A three-dimensional (3-D) numerical model of the structure was set up based on the finite volume method (FVM) using the academic finite element analysis software ANSYS. To validate the created model, experimental vibration tests were carried out using the vibration test system of TREVISE platform at ECAM-EPMI. The tests were based on the experimental modal analysis (EMA) technique, which is one of the most efficient techniques for identifying structures parameters. Indeed, the poles and residues of the frequency response functions (FRF), between input and output spectra, were calculated to extract the mode shapes and the natural frequencies of the structure. Based on the obtained modal parameters, the numerical designed model was up-dated.

Effect of surface treatment on stress distribution in immediately loaded dental implants--a 3D finite element analysis.

PubMed

Bahrami, Babak; Shahrbaf, Shirin; Mirzakouchaki, Behnam; Ghalichi, Farzan; Ashtiani, Mohammed; Martin, Nicolas

2014-04-01

To investigate, by means of FE analysis, the effect of surface roughness treatments on the distribution of stresses at the bone-implant interface in immediately loaded mandibular implants. An accurate, high resolution, digital replica model of bone structure (cortical and trabecular components) supporting an implant was created using CT scan data and image processing software (Mimics 13.1; Materialize, Leuven, Belgium). An anatomically accurate 3D model of a mandibular-implant complex was created using a professional 3D-CAD modeller (SolidWorks, DassaultSystèmes Solid Works Corp; 2011). Finite element models were created with one of the four roughness treatments on the implant fixture surface. Of these, three were surface treated to create a uniform coating determined by the coefficient of friction (μ); these were either (1) plasma sprayed or porous-beaded (μ=1.0), (2) sandblasted (μ=0.68) or (3) polished (μ=0.4). The fourth implant had a novel two-part surface roughness consisting of a coronal polished component (μ=0.4) interfacing with the cortical bone, and a body plasma treated surface component (μ=1) interfacing with the trabecular bone. Finite element stress analysis was carried out under vertical and lateral forces. This investigation showed that the type of surface treatment on the implant fixture affects the stress at the bone-implant interface of an immediately loaded implant complex. Von Mises stress data showed that the two-part surface treatment created the better stress distribution at the implant-bone interface. The results from this FE computational analysis suggest that the proposed two-part surface treatment for IL implants creates lower stresses than single uniform treatments at the bone-implant interface, which might decrease peri-implant bone loss. Future investigations should focus on mechanical and clinical validation of these FE results. Copyright © 2014 Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

From Structural Complexity to Structure-Property Relationships in Intermetallics: Development of Density Functional Theory-Chemical Pressure Analysis

NASA Astrophysics Data System (ADS)

Engelkemier, Joshua

The unparalleled structural diversity of intermetallic compounds provides nearly unlimited potential for the discovery and optimization of materials with useful properties, such as thermoelectricity, superconductivity, magnetism, hydrogen storage, superelasticity, and catalysis. This same diversity, however, creates challenges for understanding and controlling the unpredictable structure of intermetallic phases. Moreover, the fundamental design principles that have proven so powerful in molecular chemistry do not have simple analogues for metallic, solid state materials. One of these basic principles is the concept of atomic size effects. Especially in densely packed crystal structures where the need to fill space is in competition with the atoms' preferences for ideal interatomic distances, substitution of one element in a compound for another with similar chemical properties yet different atomic size can have dramatic effects on the ordering of the atoms (which in turn affects the electronic structure, vibrational properties, and materials properties). But because the forces that hold metallic phases together are less easily understood from a local perspective than covalent or ionic interactions in other kinds of materials, it is usually unclear whether the atoms are organized to optimize stabilizing, bonding interactions or rather forced to be close together despite repulsive, steric interactions. This dissertation details the development of a theoretical method, called Density Functional Theory-Chemical Pressure (DFT-CP) analysis, to address this issue. It works by converting the distribution of total energy density from a DFT calculation into a map of chemical pressure through a numerical approximation of the first derivative of energy with respect to voxel volume. The CP distribution is then carefully divided into contact volumes between neighboring atoms, from which it is possible to determine whether atoms are too close together (positive CP) or too far away from each other (negative CP). This technique is used in combination with the concept of structural plasticity (Berns, 2014) to demonstrate how complex intermetallic phases can be understood as a response of simpler structure types to the destabilizing buildup of CP. From this point of view, interfaces created in complex structures relieve the CP manifest in the more basic, parent structures. This is shown specifically for Ca36Sn23 relative to a hypothetical W5Si3-type Ca5Sn3 phase, LnMn xGa3 (Ln = Ho-Tm, x < 0.15) compared to unstuffed AuCu3-type LnGa3 structures, and structural derivatives of CaCu5- and HoCoGa5-type compounds. As a direct result of the technical developments necessitated by these analyses on structural complexity in intermetallics, a further connection is made in this thesis between the calculated CP schemes and the frequencies of vibrational modes in MgCu2-type CaPd2, the Cr 3Si-type superconductor Nb3Ge, and CaCu5-type CaPd5. Local chemical interactions revealed by DFT-CP analysis are used to identify structure-property relationships for the pseudogap in the phonon density of states (DOS) of CaPd2, the higher critical temperature of Nb3Ge vs. Nb3Sn, and the wide diversity of structures based on the CaCu5 type.

Effect of fish gelatin-gum arabic interactions on structural and functional properties of concentrated emulsions.

PubMed

Anvari, Mohammad; Joyner Melito, Helen S

2017-12-01

Concentrated emulsions containing both proteins and polysaccharides are the basis for many commercial products; however, the effects of protein-polysaccharide interactions on the functional properties of these complex systems are often poorly understood from a fundamental standpoint. Hence, the objective of this study was to determine the effects of fish gelatin (FG)-gum arabic (GA) complexation at different aqueous phase pH (3.6, 5.0, and 9.0) on concentrated emulsion structure-function relationships. Concentrated emulsions were prepared using FG-GA mixtures and characterized by rheometry and confocal scanning laser microscopy (CSLM). CSLM images showed that all samples were O/W emulsions; emulsions with lower pH showed smaller oil droplets, greater homogeneity in size distribution, and higher stability. This was attributed to an increased number of FG-GA complexes in the emulsification. Electrostatic attractive interactions and charge neutralization created biopolymer associations with increased emulsification capacity. Samples with FG-GA mixtures at lower pH showed higher elastic moduli under small deformation and exhibited greater deviation between apparent and complex viscosities under the Cox-Merz rule, indicating increased gel network extension and greater intermolecular connectivity between adsorbed layers of adjacent oil droplets. These results can be used to incorporate protein-polysaccharide complexes as a suitable emulsifier in materials comprising concentrated emulsions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Self-organization of multifunctional surfaces--the fingerprints of light on a complex system.

PubMed

Reinhardt, Hendrik; Kim, Hee-Cheol; Pietzonka, Clemens; Kruempelmann, Julia; Harbrecht, Bernd; Roling, Bernhard; Hampp, Norbert

2013-06-25

Nanocomposite patterns and nanotemplates are generated by a single-step bottom-up concept that introduces laser-induced periodic surface structures (LIPSS) as a tool for site-specific reaction control in multicomponent systems. Periodic intensity fluctuations of this photothermal stimulus inflict spatial-selective reorganizations, dewetting scenarios and phase segregations, thus creating regular patterns of anisotropic physicochemical properties that feature attractive optical, electrical, magnetic, and catalytic properties. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Silent Canyon caldera complex: a three-dimensional model based on drill-hole stratigraphy and gravity inversion

USGS Publications Warehouse

McKee, Edwin H.; Hildenbrand, Thomas G.; Anderson, Megan L.; Rowley, Peter D.; Sawyer, David A.

1999-01-01

The structural framework of Pahute Mesa, Nevada, is dominated by the Silent Canyon caldera complex, a buried, multiple collapse caldera complex. Using the boundary surface between low density Tertiary volcanogenic rocks and denser granitic and weakly metamorphosed sedimentary rocks (basement) as the outer fault surfaces for the modeled collapse caldera complex, it is postulated that the caldera complex collapsed on steeply- dipping arcuate faults two, possibly three, times following eruption of at least two major ash-flow tuffs. The caldera and most of its eruptive products are now deeply buried below the surface of Pahute Mesa. Relatively low-density rocks in the caldera complex produce one of the largest gravity lows in the western conterminous United States. Gravity modeling defines a steep sided, cup-shaped depression as much as 6,000 meters (19,800 feet) deep that is surrounded and floored by denser rocks. The steeply dipping surface located between the low-density basin fill and the higher density external rocks is considered to be the surface of the ring faults of the multiple calderas. Extrapolation of this surface upward to the outer, or topographic rim, of the Silent Canyon caldera complex defines the upper part of the caldera collapse structure. Rock units within and outside the Silent Canyon caldera complex are combined into seven hydrostratigraphic units based on their predominant hydrologic characteristics. The caldera structures and other faults on Pahute Mesa are used with the seven hydrostratigraphic units to make a three-dimensional geologic model of Pahute Mesa using the "EarthVision" (Dynamic Graphics, Inc.) modeling computer program. This method allows graphic representation of the geometry of the rocks and produces computer generated cross sections, isopach maps, and three-dimensional oriented diagrams. These products have been created to aid in visualizing and modeling the ground-water flow system beneath Pahute Mesa.

Construction of a 3D structural model based on balanced cross sections and borehole data to create a fundament for further geolocial and hydrological simulations

NASA Astrophysics Data System (ADS)

Donndorf, St.; Malz, A.; Kley, J.

2012-04-01

Cross section balancing is a generally accepted method for studying fault zone geometries. We show a method for the construction of structural 3D models of complex fault zones using a combination of gOcad modelling and balanced cross sections. In this work a 3D model of the Schlotheim graben in the Thuringian basin was created from serial, parallel cross sections and existing borehole data. The Thuringian Basin is originally a part of the North German Basin, which was separated from it by the Harz uplift in the Late Cretaceous. It comprises several parallel NW-trending inversion structures. The Schlotheim graben is one example of these inverted graben zones, whose structure poses special challenges to 3D modelling. The fault zone extends 30 km in NW-SE direction and 1 km in NE-SW direction. This project was split into two parts: data management and model building. To manage the fundamental data a central database was created in ESRI's ArcGIS. The development of a scripting interface handles the data exchange between the different steps of modelling. The first step is the pre-processing of the base data in ArcGIS, followed by cross section balancing with Midland Valley's Move software and finally the construction of the 3D model in Paradigm's gOcad. With the specific aim of constructing a 3D model based on cross sections, the functionality of the gOcad software had to be extended. These extensions include pre-processing functions to create a simplified and usable data base for gOcad as well as construction functions to create surfaces based on linearly distributed data and processing functions to create the 3D model from different surfaces. In order to use the model for further geological and hydrological simulations, special requirements apply to the surface properties. The first characteristic of the surfaces should be a quality mesh, which contains triangles with maximized internal angles. To achieve that, an external meshing tool was included in gOcad. The second characteristic is that intersecting lines between two surfaces must be included in both surfaces and share nodes with them. To finish the modelling process 3D balancing was performed to further improve the model quality.

Rational design and dynamics of self-propelled colloidal bead chains: from rotators to flagella.

PubMed

Vutukuri, Hanumantha Rao; Bet, Bram; van Roij, René; Dijkstra, Marjolein; Huck, Wilhelm T S

2017-12-01

The quest for designing new self-propelled colloids is fuelled by the demand for simple experimental models to study the collective behaviour of their more complex natural counterparts. Most synthetic self-propelled particles move by converting the input energy into translational motion. In this work we address the question if simple self-propelled spheres can assemble into more complex structures that exhibit rotational motion, possibly coupled with translational motion as in flagella. We exploit a combination of induced dipolar interactions and a bonding step to create permanent linear bead chains, composed of self-propelled Janus spheres, with a well-controlled internal structure. Next, we study how flexibility between individual swimmers in a chain can affect its swimming behaviour. Permanent rigid chains showed only active rotational or spinning motion, whereas longer semi-flexible chains showed both translational and rotational motion resembling flagella like-motion, in the presence of the fuel. Moreover, we are able to reproduce our experimental results using numerical calculations with a minimal model, which includes full hydrodynamic interactions with the fluid. Our method is general and opens a new way to design novel self-propelled colloids with complex swimming behaviours, using different complex starting building blocks in combination with the flexibility between them.

Building a virtual simulation platform for quasistatic breast ultrasound elastography using open source software: A preliminary investigation

PubMed Central

Wang, Yu; Helminen, Emily; Jiang, Jingfeng

2015-01-01

Purpose: Quasistatic ultrasound elastography (QUE) is being used to augment in vivo characterization of breast lesions. Results from early clinical trials indicated that there was a lack of confidence in image interpretation. Such confidence can only be gained through rigorous imaging tests using complex, heterogeneous but known media. The objective of this study is to build a virtual breast QUE simulation platform in the public domain that can be used not only for innovative QUE research but also for rigorous imaging tests. Methods: The main thrust of this work is to streamline biomedical ultrasound simulations by leveraging existing open source software packages including Field II (ultrasound simulator), VTK (geometrical visualization and processing), FEBio [finite element (FE) analysis], and Tetgen (mesh generator). However, integration of these open source packages is nontrivial and requires interdisciplinary knowledge. In the first step, a virtual breast model containing complex anatomical geometries was created through a novel combination of image-based landmark structures and randomly distributed (small) structures. Image-based landmark structures were based on data from the NIH Visible Human Project. Subsequently, an unstructured FE-mesh was created by Tetgen. In the second step, randomly positioned point scatterers were placed within the meshed breast model through an octree-based algorithm to make a virtual breast ultrasound phantom. In the third step, an ultrasound simulator (Field II) was used to interrogate the virtual breast phantom to obtain simulated ultrasound echo data. Of note, tissue deformation generated using a FE-simulator (FEBio) was the basis of deforming the original virtual breast phantom in order to obtain the postdeformation breast phantom for subsequent ultrasound simulations. Using the procedures described above, a full cycle of QUE simulations involving complex and highly heterogeneous virtual breast phantoms can be accomplished for the first time. Results: Representative examples were used to demonstrate capabilities of this virtual simulation platform. In the first set of three ultrasound simulation examples, three heterogeneous volumes of interest were selected from a virtual breast ultrasound phantom to perform sophisticated ultrasound simulations. These resultant B-mode images realistically represented the underlying complex but known media. In the second set of three QUE examples, advanced applications in QUE were simulated. The first QUE example was to show breast tumors with complex shapes and/or compositions. The resultant strain images showed complex patterns that were normally seen in freehand clinical ultrasound data. The second and third QUE examples demonstrated (deformation-dependent) nonlinear strain imaging and time-dependent strain imaging, respectively. Conclusions: The proposed virtual QUE platform was implemented and successfully tested in this study. Through show-case examples, the proposed work has demonstrated its capabilities of creating sophisticated QUE data in a way that cannot be done through the manufacture of physical tissue-mimicking phantoms and other software. This open software architecture will soon be made available in the public domain and can be readily adapted to meet specific needs of different research groups to drive innovations in QUE. PMID:26328994

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

NASA Astrophysics Data System (ADS)

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

2015-11-01

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

Artistic forms and complexity.

PubMed

Boon, J-P; Casti, J; Taylor, R P

2011-04-01

We discuss the inter-relationship between various concepts of complexity by introducing a complexity 'triangle' featuring objective complexity, subjective complexity and social complexity. Their connections are explored using visual and musical compositions of art. As examples, we quantify the complexity embedded within the paintings of the Jackson Pollock and the musical works of Johann Sebastian Bach. We discuss the challenges inherent in comparisons of the spatial patterns created by Pollock and the sonic patterns created by Bach, including the differing roles that time plays in these investigations. Our results draw attention to some common intriguing characteristics suggesting 'universality' and conjecturing that the fractal nature of art might have an intrinsic value of more general significance.

Creating Access Points to Instrument-Based Atmospheric Data: Perspectives from the ARM Metadata Manager

NASA Astrophysics Data System (ADS)

Troyan, D.

2016-12-01

The Atmospheric Radiation Measurement (ARM) program has been collecting data from instruments in diverse climate regions for nearly twenty-five years. These data are made available to all interested parties at no cost via specially designed tools found on the ARM website (www.arm.gov). Metadata is created and applied to the various datastreams to facilitate information retrieval using the ARM website, the ARM Data Discovery Tool, and data quality reporting tools. Over the last year, the Metadata Manager - a relatively new position within the ARM program - created two documents that summarize the state of ARM metadata processes: ARM Metadata Workflow, and ARM Metadata Standards. These documents serve as guides to the creation and management of ARM metadata. With many of ARM's data functions spread around the Department of Energy national laboratory complex and with many of the original architects of the metadata structure no longer working for ARM, there is increased importance on using these documents to resolve issues from data flow bottlenecks and inaccurate metadata to improving data discovery and organizing web pages. This presentation will provide some examples from the workflow and standards documents. The examples will illustrate the complexity of the ARM metadata processes and the efficiency by which the metadata team works towards achieving the goal of providing access to data collected under the auspices of the ARM program.

Expanding the functionality of speech recognition in radiology: creating a real-time methodology for measurement and analysis of occupational stress and fatigue.

PubMed

Reiner, Bruce I

2013-02-01

While occupational stress and fatigue have been well described throughout medicine, the radiology community is particularly susceptible due to declining reimbursements, heightened demands for service deliverables, and increasing exam volume and complexity. The resulting occupational stress can be variable in nature and dependent upon a number of intrinsic and extrinsic stressors. Intrinsic stressors largely account for inter-radiologist stress variability and relate to unique attributes of the radiologist such as personality, emotional state, education/training, and experience. Extrinsic stressors may account for intra-radiologist stress variability and include cumulative workload and task complexity. The creation of personalized stress profiles creates a mechanism for accounting for both inter- and intra-radiologist stress variability, which is essential in creating customizable stress intervention strategies. One viable option for real-time occupational stress measurement is voice stress analysis, which can be directly implemented through existing speech recognition technology and has been proven to be effective in stress measurement and analysis outside of medicine. This technology operates by detecting stress in the acoustic properties of speech through a number of different variables including duration, glottis source factors, pitch distribution, spectral structure, and intensity. The correlation of these speech derived stress measures with outcomes data can be used to determine the user-specific inflection point at which stress becomes detrimental to clinical performance.

Communities of solution: partnerships for population health.

PubMed

Griswold, Kim S; Lesko, Sarah E; Westfall, John M

2013-01-01

Communities of solution (COSs) are the key principle for improving population health. The 1967 Folsom Report explains that the COS concept arose from the recognition that complex political and administrative structures often hinder problem solving by creating barriers to communication and compromise. A 2012 reexamination of the Folsom Report resurrects the idea of the COS and presents 13 grand challenges that define the critical links among community, public health, and primary care and call for ongoing demonstrations of COSs grounded in patient-centered care. In this issue, examples of COSs from around the country demonstrate core principles and propose visions of the future. Essential themes of each COS are the crossing of "jurisdictional boundaries," community-led or -oriented initiatives, measurement of outcomes, and creating durable connections with public health.

Digitally tunable physicochemical coding of material composition and topography in continuous microfibres.

PubMed

Kang, Edward; Jeong, Gi Seok; Choi, Yoon Young; Lee, Kwang Ho; Khademhosseini, Ali; Lee, Sang-Hoon

2011-09-04

Heterotypic functional materials with compositional and topographical properties that vary spatiotemporally on the micro- or nanoscale are common in nature. However, fabricating such complex materials in the laboratory remains challenging. Here we describe a method to continuously create microfibres with tunable morphological, structural and chemical features using a microfluidic system consisting of a digital, programmable flow control that mimics the silk-spinning process of spiders. With this method we fabricated hydrogel microfibres coded with varying chemical composition and topography along the fibre, including gas micro-bubbles as well as nanoporous spindle-knots and joints that enabled directional water collection. We also explored the potential use of the coded microfibres for tissue engineering applications by creating multifunctional microfibres with a spatially controlled co-culture of encapsulated cells.

A senior manager with a knowledge management portfolio: the Santa Clara County experience.

PubMed

Lindberg, Arley

2012-01-01

The agency director sought to create a systematically coordinated department that utilizes knowledge management strategies to promote evidence-informed practice. In his view, the organization was not providing needed information or organizational supports for practitioners to use knowledge effectively. To address this issue, he created a Director of Development and Operational Planning (DDOP) position with the responsibility to build structures and facilitate processes that support knowledge management. The DDOP oversees research and planning, government relations, legislative development and support, Board of Supervisors communications, staff development and training, community contracts, public information and in-house communication. The DDOP is reorganizing units under her supervision to create a knowledge management matrix that will implement new knowledge sharing strategies related to evaluation, contracts, legislation, organizational development, policy and planning, and staff development. The case study describes challenges and strategies related to: government regulations, size and complexity of the agency, staff resistance, and the developmental nature of the process. Copyright © Taylor & Francis Group, LLC

UbSRD: The Ubiquitin Structural Relational Database.

PubMed

Harrison, Joseph S; Jacobs, Tim M; Houlihan, Kevin; Van Doorslaer, Koenraad; Kuhlman, Brian

2016-02-22

The structurally defined ubiquitin-like homology fold (UBL) can engage in several unique protein-protein interactions and many of these complexes have been characterized with high-resolution techniques. Using Rosetta's structural classification tools, we have created the Ubiquitin Structural Relational Database (UbSRD), an SQL database of features for all 509 UBL-containing structures in the PDB, allowing users to browse these structures by protein-protein interaction and providing a platform for quantitative analysis of structural features. We used UbSRD to define the recognition features of ubiquitin (UBQ) and SUMO observed in the PDB and the orientation of the UBQ tail while interacting with certain types of proteins. While some of the interaction surfaces on UBQ and SUMO overlap, each molecule has distinct features that aid in molecular discrimination. Additionally, we find that the UBQ tail is malleable and can adopt a variety of conformations upon binding. UbSRD is accessible as an online resource at rosettadesign.med.unc.edu/ubsrd. Copyright © 2015 Elsevier Ltd. All rights reserved.

A highly printable and biocompatible hydrogel composite for direct printing of soft and perfusable vasculature-like structures.

PubMed

Suntornnond, Ratima; Tan, Edgar Yong Sheng; An, Jia; Chua, Chee Kai

2017-12-04

Vascularization is one major obstacle in bioprinting and tissue engineering. In order to create thick tissues or organs that can function like original body parts, the presence of a perfusable vascular system is essential. However, it is challenging to bioprint a hydrogel-based three-dimensional vasculature-like structure in a single step. In this paper, we report a new hydrogel-based composite that offers impressive printability, shape integrity, and biocompatibility for 3D bioprinting of a perfusable complex vasculature-like structure. The hydrogel composite can be used on a non-liquid platform and is printable at human body temperature. Moreover, the hydrogel composite supports both cell proliferation and cell differentiation. Our results represent a potentially new vascularization strategy for 3D bioprinting and tissue engineering.

Orthogonal labeling of M13 minor capsid proteins with DNA to self-assemble end-to-end multiphage structures.

PubMed

Hess, Gaelen T; Guimaraes, Carla P; Spooner, Eric; Ploegh, Hidde L; Belcher, Angela M

2013-09-20

M13 bacteriophage has been used as a scaffold to organize materials for various applications. Building more complex multiphage devices requires precise control of interactions between the M13 capsid proteins. Toward this end, we engineered a loop structure onto the pIII capsid protein of M13 bacteriophage to enable sortase-mediated labeling reactions for C-terminal display. Combining this with N-terminal sortase-mediated labeling, we thus created a phage scaffold that can be labeled orthogonally on three capsid proteins: the body and both ends. We show that covalent attachment of different DNA oligonucleotides at the ends of the new phage structure enables formation of multiphage particles oriented in a specific order. These have potential as nanoscale scaffolds for multi-material devices.

An organelle-specific protein landscape identifies novel diseases and molecular mechanisms

PubMed Central

Boldt, Karsten; van Reeuwijk, Jeroen; Lu, Qianhao; Koutroumpas, Konstantinos; Nguyen, Thanh-Minh T.; Texier, Yves; van Beersum, Sylvia E. C.; Horn, Nicola; Willer, Jason R.; Mans, Dorus A.; Dougherty, Gerard; Lamers, Ideke J. C.; Coene, Karlien L. M.; Arts, Heleen H.; Betts, Matthew J.; Beyer, Tina; Bolat, Emine; Gloeckner, Christian Johannes; Haidari, Khatera; Hetterschijt, Lisette; Iaconis, Daniela; Jenkins, Dagan; Klose, Franziska; Knapp, Barbara; Latour, Brooke; Letteboer, Stef J. F.; Marcelis, Carlo L.; Mitic, Dragana; Morleo, Manuela; Oud, Machteld M.; Riemersma, Moniek; Rix, Susan; Terhal, Paulien A.; Toedt, Grischa; van Dam, Teunis J. P.; de Vrieze, Erik; Wissinger, Yasmin; Wu, Ka Man; Apic, Gordana; Beales, Philip L.; Blacque, Oliver E.; Gibson, Toby J.; Huynen, Martijn A.; Katsanis, Nicholas; Kremer, Hannie; Omran, Heymut; van Wijk, Erwin; Wolfrum, Uwe; Kepes, François; Davis, Erica E.; Franco, Brunella; Giles, Rachel H.; Ueffing, Marius; Russell, Robert B.; Roepman, Ronald; Al-Turki, Saeed; Anderson, Carl; Antony, Dinu; Barroso, Inês; Bentham, Jamie; Bhattacharya, Shoumo; Carss, Keren; Chatterjee, Krishna; Cirak, Sebahattin; Cosgrove, Catherine; Danecek, Petr; Durbin, Richard; Fitzpatrick, David; Floyd, Jamie; Reghan Foley, A.; Franklin, Chris; Futema, Marta; Humphries, Steve E.; Hurles, Matt; Joyce, Chris; McCarthy, Shane; Mitchison, Hannah M.; Muddyman, Dawn; Muntoni, Francesco; O'Rahilly, Stephen; Onoufriadis, Alexandros; Payne, Felicity; Plagnol, Vincent; Raymond, Lucy; Savage, David B.; Scambler, Peter; Schmidts, Miriam; Schoenmakers, Nadia; Semple, Robert; Serra, Eva; Stalker, Jim; van Kogelenberg, Margriet; Vijayarangakannan, Parthiban; Walter, Klaudia; Whittall, Ros; Williamson, Kathy

2016-01-01

Cellular organelles provide opportunities to relate biological mechanisms to disease. Here we use affinity proteomics, genetics and cell biology to interrogate cilia: poorly understood organelles, where defects cause genetic diseases. Two hundred and seventeen tagged human ciliary proteins create a final landscape of 1,319 proteins, 4,905 interactions and 52 complexes. Reverse tagging, repetition of purifications and statistical analyses, produce a high-resolution network that reveals organelle-specific interactions and complexes not apparent in larger studies, and links vesicle transport, the cytoskeleton, signalling and ubiquitination to ciliary signalling and proteostasis. We observe sub-complexes in exocyst and intraflagellar transport complexes, which we validate biochemically, and by probing structurally predicted, disruptive, genetic variants from ciliary disease patients. The landscape suggests other genetic diseases could be ciliary including 3M syndrome. We show that 3M genes are involved in ciliogenesis, and that patient fibroblasts lack cilia. Overall, this organelle-specific targeting strategy shows considerable promise for Systems Medicine. PMID:27173435

Reactivity of uranium(iii) with H2E (E = S, Se, Te): synthesis of a series of mononuclear and dinuclear uranium(iv) hydrochalcogenido complexes.

PubMed

Franke, Sebastian M; Rosenzweig, Michael W; Heinemann, Frank W; Meyer, Karsten

2015-01-01

We report the syntheses, electronic properties, and molecular structures of a series of mono- and dinuclear uranium(iv) hydrochalcogenido complexes supported by the sterically demanding but very flexible, single N-anchored tris(aryloxide) ligand ( Ad ArO) 3 N) 3- . The mononuclear complexes [(( Ad ArO) 3 N)U(DME)(EH)] (E = S, Se, Te) can be obtained from the reaction of the uranium(iii) starting material [(( Ad ArO) 3 N)U III (DME)] in DME via reduction of H 2 E and the elimination of 0.5 equivalents of H 2 . The dinuclear complexes [{(( Ad ArO) 3 N)U} 2 (μ-EH) 2 ] can be obtained by dissolving their mononuclear counterparts in non-coordinating solvents such as benzene. In order to facilitate the work with the highly toxic gases, we created concentrated THF solutions that can be handled using simple glovebox techniques and can be stored at -35 °C for several weeks.

Emergence of Scale-Free Syntax Networks

NASA Astrophysics Data System (ADS)

Corominas-Murtra, Bernat; Valverde, Sergi; Solé, Ricard V.

The evolution of human language allowed the efficient propagation of nongenetic information, thus creating a new form of evolutionary change. Language development in children offers the opportunity of exploring the emergence of such complex communication system and provides a window to understanding the transition from protolanguage to language. Here we present the first analysis of the emergence of syntax in terms of complex networks. A previously unreported, sharp transition is shown to occur around two years of age from a (pre-syntactic) tree-like structure to a scale-free, small world syntax network. The observed combinatorial patterns provide valuable data to understand the nature of the cognitive processes involved in the acquisition of syntax, introducing a new ingredient to understand the possible biological endowment of human beings which results in the emergence of complex language. We explore this problem by using a minimal, data-driven model that is able to capture several statistical traits, but some key features related to the emergence of syntactic complexity display important divergences.

The evolutionary pathway from anoxygenic to oxygenic photosynthesis examined by comparison of the properties of photosystem II and bacterial reaction centers.

PubMed

Allen, J P; Williams, J C

2011-01-01

In photosynthetic organisms, such as purple bacteria, cyanobacteria, and plants, light is captured and converted into energy to create energy-rich compounds. The primary process of energy conversion involves the transfer of electrons from an excited donor molecule to a series of electron acceptors in pigment-protein complexes. Two of these complexes, the bacterial reaction center and photosystem II, are evolutionarily related and structurally similar. However, only photosystem II is capable of performing the unique reaction of water oxidation. An understanding of the evolutionary process that lead to the development of oxygenic photosynthesis can be found by comparison of these two complexes. In this review, we summarize how insight is being gained by examination of the differences in critical functional properties of these complexes and by experimental efforts to alter pigment-protein interactions of the bacterial reaction center in order to enable it to perform reactions, such as amino acid and metal oxidation, observable in photosystem II.

Tailoring Thermodynamics and Kinetics for Hydrogen Storage in Complex Hydrides towards Applications.

PubMed

Liu, Yongfeng; Yang, Yaxiong; Gao, Mingxia; Pan, Hongge

2016-02-01

Solid-state hydrogen storage using various materials is expected to provide the ultimate solution for safe and efficient on-board storage. Complex hydrides have attracted increasing attention over the past two decades due to their high gravimetric and volumetric hydrogen densities. In this account, we review studies from our lab on tailoring the thermodynamics and kinetics for hydrogen storage in complex hydrides, including metal alanates, borohydrides and amides. By changing the material composition and structure, developing feasible preparation methods, doping high-performance catalysts, optimizing multifunctional additives, creating nanostructures and understanding the interaction mechanisms with hydrogen, the operating temperatures for hydrogen storage in metal amides, alanates and borohydrides are remarkably reduced. This temperature reduction is associated with enhanced reaction kinetics and improved reversibility. The examples discussed in this review are expected to provide new inspiration for the development of complex hydrides with high hydrogen capacity and appropriate thermodynamics and kinetics for hydrogen storage. © 2015 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Coevolutionary diversification creates nested-modular structure in phage–bacteria interaction networks

PubMed Central

Beckett, Stephen J.; Williams, Hywel T. P.

2013-01-01

Phage and their bacterial hosts are the most diverse and abundant biological entities in the oceans, where their interactions have a major impact on marine ecology and ecosystem function. The structure of interaction networks for natural phage–bacteria communities offers insight into their coevolutionary origin. At small phylogenetic scales, observed communities typically show a nested structure, in which both hosts and phages can be ranked by their range of resistance and infectivity, respectively. A qualitatively different multi-scale structure is seen at larger phylogenetic scales; a natural assemblage sampled from the Atlantic Ocean displays large-scale modularity and local nestedness within each module. Here, we show that such ‘nested-modular’ interaction networks can be produced by a simple model of host–phage coevolution in which infection depends on genetic matching. Negative frequency-dependent selection causes diversification of hosts (to escape phages) and phages (to track their evolving hosts). This creates a diverse community of bacteria and phage, maintained by kill-the-winner ecological dynamics. When the resulting communities are visualized as bipartite networks of who infects whom, they show the nested-modular structure characteristic of the Atlantic sample. The statistical significance and strength of this observation varies depending on whether the interaction networks take into account the density of the interacting strains, with implications for interpretation of interaction networks constructed by different methods. Our results suggest that the apparently complex community structures associated with marine bacteria and phage may arise from relatively simple coevolutionary origins. PMID:24516719

Breakdown of the balanced lethals in Rhoeo: the structure of the Alethal Renner complex of the homozygotic stock of Rhoeo.

PubMed

Golczyk, H

2011-01-01

Fluorescence in situ hybridization, base-specific fluorescence, C-banding and silver-staining were performed to reveal the cyto-molecular constitution of the karyotype in the bivalent-forming Rhoeo spathacea concolor. It was shown that the genome of this form is almost identical to the β-complex of the ring-forming rhoeos. In spite of some modifications in the arrangement of a few distal rDNA sites and in the amount of pericentromeric AT-rich heterochromatin, the alethal genome of the bivalent-forming Rhoeo seems segmentally unaltered. Thus, the breakdown of balanced lethals in Rhoeo is most likely uncoupled from creating new chromosome arm combinations. Copyright © 2011 S. Karger AG, Basel.

Thermodynamics of complexity and pattern manipulation.

PubMed

Garner, Andrew J P; Thompson, Jayne; Vedral, Vlatko; Gu, Mile

2017-04-01

Many organisms capitalize on their ability to predict the environment to maximize available free energy and reinvest this energy to create new complex structures. This functionality relies on the manipulation of patterns-temporally ordered sequences of data. Here, we propose a framework to describe pattern manipulators-devices that convert thermodynamic work to patterns or vice versa-and use them to build a "pattern engine" that facilitates a thermodynamic cycle of pattern creation and consumption. We show that the least heat dissipation is achieved by the provably simplest devices, the ones that exhibit desired operational behavior while maintaining the least internal memory. We derive the ultimate limits of this heat dissipation and show that it is generally nonzero and connected with the pattern's intrinsic crypticity-a complexity theoretic quantity that captures the puzzling difference between the amount of information the pattern's past behavior reveals about its future and the amount one needs to communicate about this past to optimally predict the future.

Supramolecular guests in solvent driven block copolymer assembly: From internally structured nanoparticles to micelles

PubMed Central

Klinger, Daniel; Robb, Maxwell J.; Spruell, Jason M.; Lynd, Nathaniel A.; Hawker, Craig J.

2014-01-01

Supramolecular interactions between different hydrogen-bonding guests and poly(2-vinyl pyridine)-block-poly (styrene) can be exploited to prepare remarkably diverse self-assembled nanostructures in dispersion from a single block copolymer (BCP). The characteristics of the BCP can be efficiently controlled by tailoring the properties of a guest which preferentially binds to the P2VP block. For example, the incorporation of a hydrophobic guest creates a hydrophobic BCP complex that forms phase separated nanoparticles upon self-assembly. Conversely, the incorporation of a hydrophilic guest results in an amphiphilic BCP complex that forms spherical micelles in water. The ability to tune the self-assembly behavior and access dramatically different nanostructures from a single BCP substrate demonstrates the exceptional versatility of the self-assembly of BCPs driven by supramolecular interactions. This approach represents a new methodology that will enable the further design of complex, responsive self-assembled nanostructures. PMID:25525473

Thermodynamics of complexity and pattern manipulation

NASA Astrophysics Data System (ADS)

Garner, Andrew J. P.; Thompson, Jayne; Vedral, Vlatko; Gu, Mile

2017-04-01

Many organisms capitalize on their ability to predict the environment to maximize available free energy and reinvest this energy to create new complex structures. This functionality relies on the manipulation of patterns—temporally ordered sequences of data. Here, we propose a framework to describe pattern manipulators—devices that convert thermodynamic work to patterns or vice versa—and use them to build a "pattern engine" that facilitates a thermodynamic cycle of pattern creation and consumption. We show that the least heat dissipation is achieved by the provably simplest devices, the ones that exhibit desired operational behavior while maintaining the least internal memory. We derive the ultimate limits of this heat dissipation and show that it is generally nonzero and connected with the pattern's intrinsic crypticity—a complexity theoretic quantity that captures the puzzling difference between the amount of information the pattern's past behavior reveals about its future and the amount one needs to communicate about this past to optimally predict the future.

Mobility and Position Error Analysis of a Complex Planar Mechanism with Redundant Constraints

NASA Astrophysics Data System (ADS)

Sun, Qipeng; Li, Gangyan

2018-03-01

Nowadays mechanisms with redundant constraints have been created and attracted much attention for their merits. The mechanism of the redundant constraints in a mechanical system is analyzed in this paper. A analysis method of Planar Linkage with a repetitive structure is proposed to get the number and type of constraints. According to the difference of applications and constraint characteristics, the redundant constraints are divided into the theoretical planar redundant constraints and the space-planar redundant constraints. And the calculation formula for the number of redundant constraints and type of judging method are carried out. And a complex mechanism with redundant constraints is analyzed of the influence about redundant constraints on mechanical performance. With the combination of theoretical derivation and simulation research, a mechanism analysis method is put forward about the position error of complex mechanism with redundant constraints. It points out the direction on how to eliminate or reduce the influence of redundant constraints.

Telephone calls postdischarge from hospital to home: a literature review.

PubMed

Hand, Kristin E; Cunningham, Regina S

2014-02-01

The oncology population is particularly affected by hospital readmissions because hospitalized patients with cancer often have complex needs. The complexity and diversity of care requirements create substantial challenges in planning for appropriate postdischarge support. Implementing postdischarge telephone calls in the population of patients with cancer could offer a low-cost intervention to address the complex needs of patients during the transition from hospital to home. The goal of the current literature review is to provide an understanding about postdischarge telephone calls in patients with cancer. Findings from this review support the notion that discharge phone calls could improve care continuity for patients transitioning from hospital to home. The literature review outlines information related to telephone call content, timing, and structure for healthcare systems that want to use a postdischarge telephone intervention for patients with cancer. However, additional research is needed to develop and test cancer-specific protocols.

How to Select the most Relevant Roughness Parameters of a Surface: Methodology Research Strategy

NASA Astrophysics Data System (ADS)

Bobrovskij, I. N.

2018-01-01

In this paper, the foundations for new methodology creation which provides solving problem of surfaces structure new standards parameters huge amount conflicted with necessary actual floors quantity of surfaces structure parameters which is related to measurement complexity decreasing are considered. At the moment, there is no single assessment of the importance of a parameters. The approval of presented methodology for aerospace cluster components surfaces allows to create necessary foundation, to develop scientific estimation of surfaces texture parameters, to obtain material for investigators of chosen technological procedure. The methods necessary for further work, the creation of a fundamental reserve and development as a scientific direction for assessing the significance of microgeometry parameters are selected.

State of the dam at the Zeya hydroelectric station with consideration of the geodynamic effect

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

Marchuk, A.N.; Dudchenko, L.N.; Bolgov, V.V.

1995-11-01

The buttress dam of the Zeya hydroelectric station has already been operating successfully for 20 years under complex climatic, geological, and seismological conditions. Additional difficulties are created by some uncertainty of the interaction of the structure with the geological environment subjected to tectonic movements. The seismotectonic conditions of the region of the Zeya reservoir are determined by proximity to the boundary of two large structural zones with a different character of tectonic movements: regions of the uplift of the Tukuringra-Soktokhan Range and the downwarping Amur-Zeya Plateau. This boundary is represented by the Pkan fault located about 1 km from themore » dam on the downstream side.« less

Improving Grasp Skills Using Schema Structured Learning

NASA Technical Reports Server (NTRS)

Platt, Robert; Grupen, ROderic A.; Fagg, Andrew H.

2006-01-01

Abstract In the control-based approach to robotics, complex behavior is created by sequencing and combining control primitives. While it is desirable for the robot to autonomously learn the correct control sequence, searching through the large number of potential solutions can be time consuming. This paper constrains this search to variations of a generalized solution encoded in a framework known as an action schema. A new algorithm, SCHEMA STRUCTURED LEARNING, is proposed that repeatedly executes variations of the generalized solution in search of instantiations that satisfy action schema objectives. This approach is tested in a grasping task where Dexter, the UMass humanoid robot, learns which reaching and grasping controllers maximize the probability of grasp success.

Harlequin-Inspired Story-Based Learning: An Educational Innovation for Pediatric Nursing Communication.

PubMed

Shaw, Alison; Lind, Candace; Ewashen, Carol

2017-05-01

Effective communication with patients and families is essential for quality care in the pediatric environment. Despite this, the current structure and content of undergraduate nursing education often contributes to novice RNs feeling unprepared to manage complex pediatric communication situations. By merging the characteristics of the Harlequin persona with the structure of story-based learning, undergraduate students can be introduced to increasingly advanced pediatric communication scenarios in the classroom. Although story-based learning encourages students to identify and address the contextual and emotional elements of a story, the Harlequin encourages educators to challenge assumptions and upset the status quo. Nursing students can develop advanced communication abilities and learn to identify and cope with the emotions and complexities inherent in pediatric practice and communication. Harlequin-inspired story-based learning can enable nurse educators to create interesting, realistic, and challenging pediatric nursing stories designed to push students outside their comfort zones and enhance their advanced pediatric communication abilities. [J Nurs Educ. 2017;56(5):300-303.]. Copyright 2017, SLACK Incorporated.

Split green fluorescent protein as a modular binding partner for protein crystallization.

PubMed

Nguyen, Hau B; Hung, Li-Wei; Yeates, Todd O; Terwilliger, Thomas C; Waldo, Geoffrey S

2013-12-01

A modular strategy for protein crystallization using split green fluorescent protein (GFP) as a crystallization partner is demonstrated. Insertion of a hairpin containing GFP β-strands 10 and 11 into a surface loop of a target protein provides two chain crossings between the target and the reconstituted GFP compared with the single connection afforded by terminal GFP fusions. This strategy was tested by inserting this hairpin into a loop of another fluorescent protein, sfCherry. The crystal structure of the sfCherry-GFP(10-11) hairpin in complex with GFP(1-9) was determined at a resolution of 2.6 Å. Analysis of the complex shows that the reconstituted GFP is attached to the target protein (sfCherry) in a structurally ordered way. This work opens the way to rapidly creating crystallization variants by reconstituting a target protein bearing the GFP(10-11) hairpin with a variety of GFP(1-9) mutants engineered for favorable crystallization.

Design and 4D Printing of Cross-Folded Origami Structures: A Preliminary Investigation.

PubMed

Teoh, Joanne Ee Mei; An, Jia; Feng, Xiaofan; Zhao, Yue; Chua, Chee Kai; Liu, Yong

2018-03-03

In 4D printing research, different types of complex structure folding and unfolding have been investigated. However, research on cross-folding of origami structures (defined as a folding structure with at least two overlapping folds) has not been reported. This research focuses on the investigation of cross-folding structures using multi-material components along different axes and different horizontal hinge thickness with single homogeneous material. Tensile tests were conducted to determine the impact of multi-material components and horizontal hinge thickness. In the case of multi-material structures, the hybrid material composition has a significant impact on the overall maximum strain and Young's modulus properties. In the case of single material structures, the shape recovery speed is inversely proportional to the horizontal hinge thickness, while the flexural or bending strength is proportional to the horizontal hinge thickness. A hinge with a thickness of 0.5 mm could be folded three times prior to fracture whilst a hinge with a thickness of 0.3 mm could be folded only once prior to fracture. A hinge with a thickness of 0.1 mm could not even be folded without cracking. The introduction of a physical hole in the center of the folding/unfolding line provided stress relief and prevented fracture. A complex flower petal shape was used to successfully demonstrate the implementation of overlapping and non-overlapping folding lines using both single material segments and multi-material segments. Design guidelines for establishing cross-folding structures using multi-material components along different axes and different horizontal hinge thicknesses with single or homogeneous material were established. These guidelines can be used to design and implement complex origami structures with overlapping and non-overlapping folding lines. Combined overlapping folding structures could be implemented and allocating specific hole locations in the overall designs could be further explored. In addition, creating a more precise prediction by investigating sets of in between hinge thicknesses and comparing the folding times before fracture, will be the subject of future work.

A multimodal parallel architecture: A cognitive framework for multimodal interactions.

PubMed

Cohn, Neil

2016-01-01

Human communication is naturally multimodal, and substantial focus has examined the semantic correspondences in speech-gesture and text-image relationships. However, visual narratives, like those in comics, provide an interesting challenge to multimodal communication because the words and/or images can guide the overall meaning, and both modalities can appear in complicated "grammatical" sequences: sentences use a syntactic structure and sequential images use a narrative structure. These dual structures create complexity beyond those typically addressed by theories of multimodality where only a single form uses combinatorial structure, and also poses challenges for models of the linguistic system that focus on single modalities. This paper outlines a broad theoretical framework for multimodal interactions by expanding on Jackendoff's (2002) parallel architecture for language. Multimodal interactions are characterized in terms of their component cognitive structures: whether a particular modality (verbal, bodily, visual) is present, whether it uses a grammatical structure (syntax, narrative), and whether it "dominates" the semantics of the overall expression. Altogether, this approach integrates multimodal interactions into an existing framework of language and cognition, and characterizes interactions between varying complexity in the verbal, bodily, and graphic domains. The resulting theoretical model presents an expanded consideration of the boundaries of the "linguistic" system and its involvement in multimodal interactions, with a framework that can benefit research on corpus analyses, experimentation, and the educational benefits of multimodality. Copyright © 2015.

Structure and biophysics of type III secretion in bacteria.

PubMed

Chatterjee, Srirupa; Chaudhury, Sukanya; McShan, Andrew C; Kaur, Kawaljit; De Guzman, Roberto N

2013-04-16

Many plant and animal bacterial pathogens assemble a needle-like nanomachine, the type III secretion system (T3SS), to inject virulence proteins directly into eukaryotic cells to initiate infection. The ability of bacteria to inject effectors into host cells is essential for infection, survival, and pathogenesis for many Gram-negative bacteria, including Salmonella, Escherichia, Shigella, Yersinia, Pseudomonas, and Chlamydia spp. These pathogens are responsible for a wide variety of diseases, such as typhoid fever, large-scale food-borne illnesses, dysentery, bubonic plague, secondary hospital infections, and sexually transmitted diseases. The T3SS consists of structural and nonstructural proteins. The structural proteins assemble the needle apparatus, which consists of a membrane-embedded basal structure, an external needle that protrudes from the bacterial surface, and a tip complex that caps the needle. Upon host cell contact, a translocon is assembled between the needle tip complex and the host cell, serving as a gateway for translocation of effector proteins by creating a pore in the host cell membrane. Following delivery into the host cytoplasm, effectors initiate and maintain infection by manipulating host cell biology, such as cell signaling, secretory trafficking, cytoskeletal dynamics, and the inflammatory response. Finally, chaperones serve as regulators of secretion by sequestering effectors and some structural proteins within the bacterial cytoplasm. This review will focus on the latest developments and future challenges concerning the structure and biophysics of the needle apparatus.

Probing into hybrid organic-molecule and InAs quantum-dots nanosystem with multistacked dots-in-a-well units

NASA Astrophysics Data System (ADS)

Chen, Miaoxiang; Kobashi, Kazufumi

2012-09-01

Hybridizing air-stable organic-molecules with advanced III-V semiconductor quantum-dots (QDs) structures can be utilized to create a new generation of biochemical sensing devices. In order to enhance their optical performances, the active regions in these QDs structures commonly consist of multistacked dots-in-a-well (DWELL) units. The effects of grafted molecules on the performances of the QDs structures with multistacked DWELLs, however, still remain unclear. Here, we show the significant improvements in the optical properties of InAs QDs in a hybrid nanosystem obtained by grafting biocompatible diazonium salt compound (amine donor) atop InAs QDs structure. Since its interface between the QDs structure and molecular monolayer retains an uncontaminated and non-oxidized condition, the nanosystem is an ideal platform to study the intrinsic properties of charge-carrier transport inside the system. Because of the complexity of the energy-levels in the QDs structure due to the existing surface QDs and DWELLs, selective excitation wavelengths (400, 633, and 885 nm, respectively) with different photo-energies are used to exactly analyze the complete charging mechanism in these QDs. A clear view of charge-carrier transfer inside the nanosystem is revealed by employing photoluminescence technique under selective-wavelength excitations. The present work provides new quantitative evidences for exploiting inorganic QDs applications in complex biological systems.

Revealing pathologies in the liquid crystalline structures of the brain by polarimetric studies (Presentation Recording)

NASA Astrophysics Data System (ADS)

Bakhshetyan, Karen; Melkonyan, Gurgen G.; Galstian, Tigran V.; Saghatelyan, Armen

2015-10-01

Natural or "self" alignment of molecular complexes in living tissue represents many similarities with liquid crystals (LC), which are anisotropic liquids. The orientational characteristics of those complexes may be related to many important functional parameters and their study may reveal important pathologies. The know-how, accumulated thanks to the study of LC materials, may thus be used to this end. One of the traditionally used methods, to characterize those materials, is the polarized light imaging (PLI) that allows for label-free analysis of anisotropic structures in the brain tissue and can be used, for example, for the analysis of myelinated fiber bundles. In the current work, we first attempted to apply the PLI on the mouse histological brain sections to create a map of anisotropic structures using cross-polarizer transmission light. Then we implemented the PLI for comparative study of histological sections of human postmortem brain samples under normal and pathological conditions, such as Parkinson's disease (PD). Imaging the coronal, sagittal and horizontal sections of mouse brain allowed us to create a false color-coded fiber orientation map under polarized light. In human brain datasets for both control and PD groups we measured the pixel intensities in myelin-rich subregions of internal capsule and normalized these to non-myelinated background signal from putamen and caudate nucleus. Quantification of intensities revealed a statistically significant reduction of fiber intensity of PD compared to control subjects (2.801 +/- 0.303 and 3.724 +/- 0.07 respectively; *p < 0.05). Our study confirms the validity of PLI method for visualizing myelinated axonal fibers. This relatively simple technique can become a promising tool for study of neurodegenerative diseases where labeling-free imaging is an important benefit.

Azole Functionalized Polyoxo-Titanium Clusters with Sunlight-Driven Dye Degradation Applications: Synthesis, Structure, and Photocatalytic Studies.

PubMed

Narayanam, Nagaraju; Chintakrinda, Kalpana; Fang, Wei-Hui; Kang, Yao; Zhang, Lei; Zhang, Jian

2016-10-06

Six polyoxo-titanium clusters (PTCs) with varying nuclearities containing Ti-N bonds and heteronuclearity, namely, [Ti 6 (μ 3 -O) 2 (μ 2 -O) 2 (O 3 P-Phen) 2 (OiPr) 10 (1-hbta) 2 ] (PTC-37), Ti 8 (μ 3 -O) 2 (μ 2 -O) 2 (O 3 P-Phen) 2 (OiPr) 16 (adn) 2 (NO 3 ) 2 ] (PTC-38), [Ti 4 (μ 3 -O)(μ 2 -O)(μ 2 -OiPr) 2 (OiPr) 4 (O 3 P-Phen) 3 (1,10-phn)](HOiPr) (PTC-39), [Ti 4 (μ 3 -O)(μ 2 -OiPr) 3 (OiPr) 5 (O 3 P-Phen) 3 (Im)] (PTC-40), [Ti 4 (μ 3 -O)(μ 2 -OiPr) 3 (OiPr) 5 (O 3 P-Phen) 3 (Im)][Ti 3 M(μ 3 -O)(μ 2 -OiPr) 3 (OiPr) 3 (O 3 P-Phen) 3 (Im)] (M = Co for PTC-41 and M = Zn for PTC-42; O 3 P-Phen = phenyl phosphonate, 1-hbta = 1-hydroxy benzotriazolate, adn = adenine, 1,10-phn = 1,10-phenanthroline, Im = imidazolate, and OiPr = isopropoxide) were prepared as crystalline samples and structurally characterized. Simultaneous doping of nitrogen and transition metal heteroatoms into the Ti-O clusters created complex chemical environments in the resulting hybrid materials. Thus, photocatalytic methylene blue degradation studies were performed to understand structure-property relationships in these Ti cluster-based materials. The complex chemical environment created in these novel molecular clusters had proved to exhibit ligand-dependent photocatalytic activities under normal sunlight. Adenine-functionalized PTC-38 presented moderate activities, while other PTCs all show rapid dye degradation.

Substrate Recognition and Hydrolysis by a Family 50 exo-β-Agarase, Aga50D, from the Marine Bacterium Saccharophagus degradans*

PubMed Central

Pluvinage, Benjamin; Hehemann, Jan-Hendrik; Boraston, Alisdair B.

2013-01-01

The bacteria that metabolize agarose use multiple enzymes of complementary specificities to hydrolyze the glycosidic linkages in agarose, a linear polymer comprising the repeating disaccharide subunit of neoagarobiose (3,6-anhydro-l-galactose-α-(1,3)-d-galactose) that are β-(1,4)-linked. Here we present the crystal structure of a glycoside hydrolase family 50 exo-β-agarase, Aga50D, from the marine microbe Saccharophagus degradans. This enzyme catalyzes a critical step in the metabolism of agarose by S. degradans through cleaving agarose oligomers into neoagarobiose products that can be further processed into monomers. The crystal structure of Aga50D to 1.9 Å resolution reveals a (β/α)8-barrel fold that is elaborated with a β-sandwich domain and extensive loops. The structures of catalytically inactivated Aga50D in complex with non-hydrolyzed neoagarotetraose (2.05 Å resolution) and neoagarooctaose (2.30 Å resolution) provide views of Michaelis complexes for a β-agarase. In these structures, the d-galactose residue in the −1 subsite is distorted into a 1S3 skew boat conformation. The relative positioning of the putative catalytic residues are most consistent with a retaining catalytic mechanism. Additionally, the neoagarooctaose complex showed that this extended substrate made substantial interactions with the β-sandwich domain, which resembles a carbohydrate-binding module, thus creating additional plus (+) subsites and funneling the polymeric substrate through the tunnel-shaped active site. A synthesis of these results in combination with an additional neoagarobiose product complex suggests a potential exo-processive mode of action of Aga50D on the agarose double helix. PMID:23921382

Process Approach for Modeling of Machine and Tractor Fleet Structure

NASA Astrophysics Data System (ADS)

Dokin, B. D.; Aletdinova, A. A.; Kravchenko, M. S.; Tsybina, Y. S.

2018-05-01

The existing software complexes on modelling of the machine and tractor fleet structure are mostly aimed at solving the task of optimization. However, the creators, choosing only one optimization criterion and incorporating it in their software, provide grounds on why it is the best without giving a decision maker the opportunity to choose it for their enterprise. To analyze “bottlenecks” of machine and tractor fleet modelling, the authors of this article created a process model, in which they included adjustment to the plan of using machinery based on searching through alternative technologies. As a result, the following recommendations for software complex development have been worked out: the introduction of a database of alternative technologies; the possibility for a user to change the timing of the operations even beyond the allowable limits and in that case the calculation of the incurred loss; the possibility to rule out the solution of an optimization task, and if there is a necessity in it - the possibility to choose an optimization criterion; introducing graphical display of an annual complex of works, which could be enough for the development and adjustment of a business strategy.

Molecular Dynamics of the ZIKA Virus NS3 Helicase

NASA Astrophysics Data System (ADS)

Raubenolt, Bryan; Rick, Steven; The Rick Group Team

The recent outbreaks of the ZIKA virus (ZIKV) and its connection to microcephaly in newborns has raised its awareness as a global threat and many scientific research efforts are currently underway in attempt to create a vaccine. Molecular Dynamics is a powerful method of investigating the physical behavior of protein complexes. ZIKV is comprised of 3 structural and 7 nonstructural proteins. The NS3 helicase protein appears to play a significant role in the replication complex and its inhibition could be a crucial source of antiviral drug design. This research primarily focuses on studying the structural dynamics, over the course of few hundred nanoseconds, of NS3 helicase in the free state, as well as in complex form with human ssRNA, ATP, and an analogue of GTP. RMSD and RMSF plots of each simulation will provide details on the forces involved in the overall stability of the active and inactive states. Furthermore, free energy calculations on a per residue level will reveal the most interactive residues between states and ultimately the primary driving force behind these interactions. Together these analyses will provide highly relevant information on the binding surface chemistry and thus serve as the basis for potential drug design.

Structural, spectroscopic and theoretical studies on 3,4,7,8-tetramethyl-1,10-phenantroline complex with picric acid

NASA Astrophysics Data System (ADS)

Bator, G.; Sobczyk, L.; Sawka-Dobrowolska, W.; Wuttke, J.; Pawlukojć, A.; Grech, E.; Nowicka-Scheibe, J.

2013-01-01

The almost planar molecular complex, formed by 3,4,7,8-tetramethyl-phenantroline (Me4phen) and picric acid (2,4,6-trinitrophenol, PA), has been investigated by using X-ray diffraction, vibrational spectroscopy, tunnel splitting and theoretical analysis. In the crystal of Me4phen·PA two short bifurcated hydrogen bonds N+-H···O- [2.6238(14) Å] and N+-H···N [2.6898(15) Å] are created. Infra-red spectra show the hydrogen bonds are short. The neutron backscattering spectrum of Me4phenṡPA at 3 K shows two tunneling peaks at ca. 1 and 3 μeV. The number of the peaks is consistent with X-ray diffraction studies, which disclosed the inequivalence of methyl groups in the crystal structure. The comparison of the tunnel splitting for neat Me4phen and for its complex with picric acid indicates that in the latter case the methyl groups are more strongly engaged in the intermolecular interactions, particularly with nitro group oxygen atoms of picric acid, leading to an increase of the CH3 rotational barrier height.

User Manual for the PROTEUS Mesh Tools

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

Smith, Micheal A.; Shemon, Emily R

2016-09-19

PROTEUS is built around a finite element representation of the geometry for visualization. In addition, the PROTEUS-SN solver was built to solve the even-parity transport equation on a finite element mesh provided as input. Similarly, PROTEUS-MOC and PROTEUS-NEMO were built to apply the method of characteristics on unstructured finite element meshes. Given the complexity of real world problems, experience has shown that using commercial mesh generator to create rather simple input geometries is overly complex and slow. As a consequence, significant effort has been put into place to create multiple codes that help assist in the mesh generation and manipulation.more » There are three input means to create a mesh in PROTEUS: UFMESH, GRID, and NEMESH. At present, the UFMESH is a simple way to generate two-dimensional Cartesian and hexagonal fuel assembly geometries. The UFmesh input allows for simple assembly mesh generation while the GRID input allows the generation of Cartesian, hexagonal, and regular triangular structured grid geometry options. The NEMESH is a way for the user to create their own mesh or convert another mesh file format into a PROTEUS input format. Given that one has an input mesh format acceptable for PROTEUS, we have constructed several tools which allow further mesh and geometry construction (i.e. mesh extrusion and merging). This report describes the various mesh tools that are provided with the PROTEUS code giving both descriptions of the input and output. In many cases the examples are provided with a regression test of the mesh tools. The most important mesh tools for any user to consider using are the MT_MeshToMesh.x and the MT_RadialLattice.x codes. The former allows the conversion between most mesh types handled by PROTEUS while the second allows the merging of multiple (assembly) meshes into a radial structured grid. Note that the mesh generation process is recursive in nature and that each input specific for a given mesh tool (such as .axial or .merge) can be used as “mesh” input for any of the mesh tools discussed in this manual.« less

Exploiting CELLULOSE SYNTHASE (CESA) Class Specificity to Probe Cellulose Microfibril Biosynthesis.

PubMed

Kumar, Manoj; Mishra, Laxmi; Carr, Paul; Pilling, Michael; Gardner, Peter; Mansfield, Shawn D; Turner, Simon

2018-05-01

Cellulose microfibrils are the basic units of cellulose in plants. The structure of these microfibrils is at least partly determined by the structure of the cellulose synthase complex. In higher plants, this complex is composed of 18 to 24 catalytic subunits known as CELLULOSE SYNTHASE A (CESA) proteins. Three different classes of CESA proteins are required for cellulose synthesis and for secondary cell wall cellulose biosynthesis these classes are represented by CESA4, CESA7, and CESA8. To probe the relationship between CESA proteins and microfibril structure, we created mutant cesa proteins that lack catalytic activity but retain sufficient structural integrity to allow assembly of the cellulose synthase complex. Using a series of Arabidopsis ( Arabidopsis thaliana ) mutants and genetic backgrounds, we found consistent differences in the ability of these mutant cesa proteins to complement the cellulose-deficient phenotype of the cesa null mutants. The best complementation was observed with catalytically inactive cesa4, while the equivalent mutation in cesa8 exhibited significantly lower levels of complementation. Using a variety of biophysical techniques, including solid-state nuclear magnetic resonance and Fourier transform infrared microscopy, to study these mutant plants, we found evidence for changes in cellulose microfibril structure, but these changes largely correlated with cellulose content and reflected differences in the relative proportions of primary and secondary cell walls. Our results suggest that individual CESA classes have similar roles in determining cellulose microfibril structure, and it is likely that the different effects of mutating members of different CESA classes are the consequence of their different catalytic activity and their influence on the overall rate of cellulose synthesis. © 2018 American Society of Plant Biologists. All Rights Reserved.

Comparison of roll-to-roll replication approaches for microfluidic and optical functions in lab-on-a-chip diagnostic devices

NASA Astrophysics Data System (ADS)

Brecher, Christian; Baum, Christoph; Bastuck, Thomas

2015-03-01

Economically advantageous microfabrication technologies for lab-on-a-chip diagnostic devices substituting commonly used glass etching or injection molding processes are one of the key enablers for the emerging market of microfluidic devices. On-site detection in fields of life sciences, point of care diagnostics and environmental analysis requires compact, disposable and highly functionalized systems. Roll-to-roll production as a high volume process has become the emerging fabrication technology for integrated, complex high technology products within recent years (e.g. fuel cells). Differently functionalized polymer films enable researchers to create a new generation of lab-on-a-chip devices by combining electronic, microfluidic and optical functions in multilayer architecture. For replication of microfluidic and optical functions via roll-to-roll production process competitive approaches are available. One of them is to imprint fluidic channels and optical structures of micro- or nanometer scale from embossing rollers into ultraviolet (UV) curable lacquers on polymer substrates. Depending on dimension, shape and quantity of those structures there are alternative manufacturing technologies for the embossing roller. Ultra-precise diamond turning, electroforming or casting polymer materials are used either for direct structuring or manufacturing of roller sleeves. Mastering methods are selected for application considering replication quality required and structure complexity. Criteria for the replication quality are surface roughness and contour accuracy. Structure complexity is evaluated by shapes producible (e.g. linear, circular) and aspect ratio. Costs for the mastering process and structure lifetime are major cost factors. The alternative replication approaches are introduced and analyzed corresponding to the criteria presented. Advantages and drawbacks of each technology are discussed and exemplary applications are presented.

Exploiting CELLULOSE SYNTHASE (CESA) Class Specificity to Probe Cellulose Microfibril Biosynthesis1[OPEN

PubMed Central

Mishra, Laxmi; Carr, Paul; Gardner, Peter

2018-01-01

Cellulose microfibrils are the basic units of cellulose in plants. The structure of these microfibrils is at least partly determined by the structure of the cellulose synthase complex. In higher plants, this complex is composed of 18 to 24 catalytic subunits known as CELLULOSE SYNTHASE A (CESA) proteins. Three different classes of CESA proteins are required for cellulose synthesis and for secondary cell wall cellulose biosynthesis these classes are represented by CESA4, CESA7, and CESA8. To probe the relationship between CESA proteins and microfibril structure, we created mutant cesa proteins that lack catalytic activity but retain sufficient structural integrity to allow assembly of the cellulose synthase complex. Using a series of Arabidopsis (Arabidopsis thaliana) mutants and genetic backgrounds, we found consistent differences in the ability of these mutant cesa proteins to complement the cellulose-deficient phenotype of the cesa null mutants. The best complementation was observed with catalytically inactive cesa4, while the equivalent mutation in cesa8 exhibited significantly lower levels of complementation. Using a variety of biophysical techniques, including solid-state nuclear magnetic resonance and Fourier transform infrared microscopy, to study these mutant plants, we found evidence for changes in cellulose microfibril structure, but these changes largely correlated with cellulose content and reflected differences in the relative proportions of primary and secondary cell walls. Our results suggest that individual CESA classes have similar roles in determining cellulose microfibril structure, and it is likely that the different effects of mutating members of different CESA classes are the consequence of their different catalytic activity and their influence on the overall rate of cellulose synthesis. PMID:29523715

Investigation of bio polymer electrolyte based on cellulose acetate-ammonium nitrate for potential use in electrochemical devices.

PubMed

Monisha, S; Mathavan, T; Selvasekarapandian, S; Milton Franklin Benial, A; Aristatil, G; Mani, N; Premalatha, M; Vinoth Pandi, D

2017-02-10

Proton conducting materials create prime interest in electro chemical device development. Present work has been carried out to design environment friendly new biopolymer electrolytes (BPEs) using cellulose acetate (CA) complex with different concentrations of ammonium nitrate (NH 4 NO 3 ), which have been prepared as film and characterized. The 50mol% CA and 50mol% NH 4 NO 3 complex has highest ionic conductivity (1.02×10 -3 Scm -1 ). Differential scanning calorimetry shows the changes in glass transition temperature depends on salt concentration. Structural analysis indicates that the highest ionic conductivity complex exhibits more amorphous nature. Vibrational analysis confirms the complex formation, which has been validated theoretically by Gaussian 09 software. Conducting element in the BPEs has been predicted. Primary proton battery and proton exchange membrane fuel cell have been developed for highest ionic conductivity complex. Output voltage and power performance has been compared for single fuel cell application, which manifests the present BPE holds promise application in electrochemical devices. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structural and mechanistic insights into Mcm2-7 double-hexamer assembly and function

DOE PAGES

Sun, Jingchuan; Li, Huilin; Fernandez-Cid, Alejandra; ...

2014-10-15

Eukaryotic cells license each DNA replication origin during G1 phase by assembling a prereplication complex that contains a Mcm2–7 (minichromosome maintenance proteins 2–7) double hexamer. During S phase, each Mcm2–7 hexamer forms the core of a replicative DNA helicase. However, the mechanisms of origin licensing and helicase activation are poorly understood. The helicase loaders ORC–Cdc6 function to recruit a single Cdt1–Mcm2–7 heptamer to replication origins prior to Cdt1 release and ORC–Cdc6–Mcm2–7 complex formation, but how the second Mcm2–7 hexamer is recruited to promote double-hexamer formation is not well understood. Here, structural evidence for intermediates consisting of an ORC–Cdc6–Mcm2–7 complex andmore » an ORC–Cdc6–Mcm2–7–Mcm2–7 complex are reported, which together provide new insights into DNA licensing. Detailed structural analysis of the loaded Mcm2–7 double-hexamer complex demonstrates that the two hexamers are interlocked and misaligned along the DNA axis and lack ATP hydrolysis activity that is essential for DNA helicase activity. Moreover, we show that the head-to-head juxtaposition of the Mcm2–7 double hexamer generates a new protein interaction surface that creates a multisubunit-binding site for an S-phase protein kinase that is known to activate DNA replication. The data suggest how the double hexamer is assembled and how helicase activity is regulated during DNA licensing, with implications for cell cycle control of DNA replication and genome stability.« less

Synchrotron Radiation Circular Dichroism (SRCD) Spectroscopy - An Enhanced Method for Examining Protein Conformations and Protein Interactions

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

B Wallace; R Janes

CD (circular dichroism) spectroscopy is a well-established technique in structural biology. SRCD (synchrotron radiation circular dichroism) spectroscopy extends the utility and applications of conventional CD spectroscopy (using laboratory-based instruments) because the high flux of a synchrotron enables collection of data at lower wavelengths (resulting in higher information content), detection of spectra with higher signal-to-noise levels and measurements in the presence of absorbing components (buffers, salts, lipids and detergents). SRCD spectroscopy can provide important static and dynamic structural information on proteins in solution, including secondary structures of intact proteins and their domains, protein stability, the differences between wild-type and mutant proteins,more » the identification of natively disordered regions in proteins, and the dynamic processes of protein folding and membrane insertion and the kinetics of enzyme reactions. It has also been used to effectively study protein interactions, including protein-protein complex formation involving either induced-fit or rigid-body mechanisms, and protein-lipid complexes. A new web-based bioinformatics resource, the Protein Circular Dichroism Data Bank (PCDDB), has been created which enables archiving, access and analyses of CD and SRCD spectra and supporting metadata, now making this information publicly available. To summarize, the developing method of SRCD spectroscopy has the potential for playing an important role in new types of studies of protein conformations and their complexes.« less

Impact of aldosterone antagonists on the substrate for atrial fibrillation: Aldosterone promotes oxidative stress and atrial structural/electrical remodeling

PubMed Central

Mayyas, Fadia; Alzoubi, Karem H.; Van Wagoner, David R.

2014-01-01

Atrial fibrillation (AF), the most common cardiac arrhythmia, is an electrocardiographic description of a condition with multiple and complex underlying mechanisms. Oxidative stress is an important driver of structural remodeling that creates a substrate for AF. Oxidant radicals may promote increase of atrial oxidative damage, electrical and structural remodeling, and atrial inflammation. AF and other cardiovascular morbidities activate angiotensin (Ang-II)-dependent and independent cascades. A key component of the renin–angiotensin-aldosterone system (RAAS) is the mineralocorticoid aldosterone. Recent studies provide evidence of myocardial aldosterone synthesis. Aldosterone promotes cardiac oxidative stress, inflammation and structural/electrical remodeling via multiple mechanisms. In HF patients, aldosterone production is enhanced. In patients and in experimental HF and AF models, aldosterone receptor antagonists have favorable influences on cardiac remodeling and oxidative stress. Therapeutic approaches that seek to reduce AF burden by modulating the aldosterone system are likely beneficial but underutilized. PMID:23993726

Parametric Workflow (BIM) for the Repair Construction of Traditional Historic Architecture in Taiwan

NASA Astrophysics Data System (ADS)

Ma, Y.-P.; Hsu, C. C.; Lin, M.-C.; Tsai, Z.-W.; Chen, J.-Y.

2015-08-01

In Taiwan, numerous existing traditional buildings are constructed with wooden structures, brick structures, and stone structures. This paper will focus on the Taiwan traditional historic architecture and target the traditional wooden structure buildings as the design proposition and process the BIM workflow for modeling complex wooden combination geometry, integrating with more traditional 2D documents and for visualizing repair construction assumptions within the 3D model representation. The goal of this article is to explore the current problems to overcome in wooden historic building conservation, and introduce the BIM technology in the case of conserving, documenting, managing, and creating full engineering drawings and information for effectively support historic conservation. Although BIM is mostly oriented to current construction praxis, there have been some attempts to investigate its applicability in historic conservation projects. This article also illustrates the importance and advantages of using BIM workflow in repair construction process, when comparing with generic workflow.

Shrink-induced superhydrophobic and antibacterial surfaces in consumer plastics.

PubMed

Freschauf, Lauren R; McLane, Jolie; Sharma, Himanshu; Khine, Michelle

2012-01-01

Structurally modified superhydrophobic surfaces have become particularly desirable as stable antibacterial surfaces. Because their self-cleaning and water resistant properties prohibit bacteria growth, structurally modified superhydrophobic surfaces obviate bacterial resistance common with chemical agents, and therefore a robust and stable means to prevent bacteria growth is possible. In this study, we present a rapid fabrication method for creating such superhydrophobic surfaces in consumer hard plastic materials with resulting antibacterial effects. To replace complex fabrication materials and techniques, the initial mold is made with commodity shrink-wrap film and is compatible with large plastic roll-to-roll manufacturing and scale-up techniques. This method involves a purely structural modification free of chemical additives leading to its inherent consistency over time and successive recasting from the same molds. Finally, antibacterial properties are demonstrated in polystyrene (PS), polycarbonate (PC), and polyethylene (PE) by demonstrating the prevention of gram-negative Escherichia coli (E. coli) bacteria growth on our structured plastic surfaces.

Dynamic multifactor clustering of financial networks

NASA Astrophysics Data System (ADS)

Ross, Gordon J.

2014-02-01

We investigate the tendency for financial instruments to form clusters when there are multiple factors influencing the correlation structure. Specifically, we consider a stock portfolio which contains companies from different industrial sectors, located in several different countries. Both sector membership and geography combine to create a complex clustering structure where companies seem to first be divided based on sector, with geographical subclusters emerging within each industrial sector. We argue that standard techniques for detecting overlapping clusters and communities are not able to capture this type of structure and show how robust regression techniques can instead be used to remove the influence of both sector and geography from the correlation matrix separately. Our analysis reveals that prior to the 2008 financial crisis, companies did not tend to form clusters based on geography. This changed immediately following the crisis, with geography becoming a more important determinant of clustering structure.

XML schemas for common bioinformatic data types and their application in workflow systems

PubMed Central

Seibel, Philipp N; Krüger, Jan; Hartmeier, Sven; Schwarzer, Knut; Löwenthal, Kai; Mersch, Henning; Dandekar, Thomas; Giegerich, Robert

2006-01-01

Background Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats. Results Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at , the BioDOM library can be obtained at . Conclusion The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios. PMID:17087823

Asymmetric triplex metallohelices with high and selective activity against cancer cells

NASA Astrophysics Data System (ADS)

Faulkner, Alan D.; Kaner, Rebecca A.; Abdallah, Qasem M. A.; Clarkson, Guy; Fox, David J.; Gurnani, Pratik; Howson, Suzanne E.; Phillips, Roger M.; Roper, David I.; Simpson, Daniel H.; Scott, Peter

2014-09-01

Small cationic amphiphilic α-helical peptides are emerging as agents for the treatment of cancer and infection, but they are costly and display unfavourable pharmacokinetics. Helical coordination complexes may offer a three-dimensional scaffold for the synthesis of mimetic architectures. However, the high symmetry and modest functionality of current systems offer little scope to tailor the structure to interact with specific biomolecular targets, or to create libraries for phenotypic screens. Here, we report the highly stereoselective asymmetric self-assembly of very stable, functionalized metallohelices. Their anti-parallel head-to-head-to-tail ‘triplex’ strand arrangement creates an amphipathic functional topology akin to that of the active sub-units of, for example, host-defence peptides and p53. The metallohelices display high, structure-dependent toxicity to the human colon carcinoma cell-line HCT116 p53++, causing dramatic changes in the cell cycle without DNA damage. They have lower toxicity to human breast adenocarcinoma cells (MDA-MB-468) and, most remarkably, they show no significant toxicity to the bacteria methicillin-resistant Staphylococcus aureus and Escherichia coli.

Markets on Networks

NASA Astrophysics Data System (ADS)

Toroczkai, Zoltan; Anghel, Marian; Bassler, Kevin; Korniss, Gyorgy

2003-03-01

The dynamics of human, and most biological populations is characterized by competition for resources. By its own nature, this dynamics creates the group of "elites", formed by those agents who have strategies that are the most successful in the given situation, and therefore the rest of the agents will tend to follow, imitate, or interact with them, creating a social structure of leadership in the agent society. These inter-agent communications generate a complex social network with small-world character which itself forms the substrate for a second network, the action network. The latter is a highly dynamic, adaptive, directed network, defined by those inter-agent communication links on the substrate along which the passed information /prediction is acted upon by the other agents. By using the minority game for competition dynamics, here we show that when the substrate network is highly connected, the action network spontaneously develops hubs with a broad distribution of out-degrees, defining a robust leadership structure that is scale-free. Furthermore, in certain, realistic parameter ranges, facilitated by information passing on the action network, agents can spontaneously generate a high degree of cooperation making the collective almost maximally efficient.

Evolution of a protein folding nucleus.

PubMed

Xia, Xue; Longo, Liam M; Sutherland, Mason A; Blaber, Michael

2016-07-01

The folding nucleus (FN) is a cryptic element within protein primary structure that enables an efficient folding pathway and is the postulated heritable element in the evolution of protein architecture; however, almost nothing is known regarding how the FN structurally changes as complex protein architecture evolves from simpler peptide motifs. We report characterization of the FN of a designed purely symmetric β-trefoil protein by ϕ-value analysis. We compare the structure and folding properties of key foldable intermediates along the evolutionary trajectory of the β-trefoil. The results show structural acquisition of the FN during gene fusion events, incorporating novel turn structure created by gene fusion. Furthermore, the FN is adjusted by circular permutation in response to destabilizing functional mutation. FN plasticity by way of circular permutation is made possible by the intrinsic C3 cyclic symmetry of the β-trefoil architecture, identifying a possible selective advantage that helps explain the prevalence of cyclic structural symmetry in the proteome. © 2015 The Protein Society.

Intuitive web-based experimental design for high-throughput biomedical data.

PubMed

Friedrich, Andreas; Kenar, Erhan; Kohlbacher, Oliver; Nahnsen, Sven

2015-01-01

Big data bioinformatics aims at drawing biological conclusions from huge and complex biological datasets. Added value from the analysis of big data, however, is only possible if the data is accompanied by accurate metadata annotation. Particularly in high-throughput experiments intelligent approaches are needed to keep track of the experimental design, including the conditions that are studied as well as information that might be interesting for failure analysis or further experiments in the future. In addition to the management of this information, means for an integrated design and interfaces for structured data annotation are urgently needed by researchers. Here, we propose a factor-based experimental design approach that enables scientists to easily create large-scale experiments with the help of a web-based system. We present a novel implementation of a web-based interface allowing the collection of arbitrary metadata. To exchange and edit information we provide a spreadsheet-based, humanly readable format. Subsequently, sample sheets with identifiers and metainformation for data generation facilities can be created. Data files created after measurement of the samples can be uploaded to a datastore, where they are automatically linked to the previously created experimental design model.

Implications of network structure on public health collaboratives.

PubMed

Retrum, Jessica H; Chapman, Carrie L; Varda, Danielle M

2013-10-01

Interorganizational collaboration is an essential function of public health agencies. These partnerships form social networks that involve diverse types of partners and varying levels of interaction. Such collaborations are widely accepted and encouraged, yet very little comparative research exists on how public health partnerships develop and evolve, specifically in terms of how subsequent network structures are linked to outcomes. A systems science approach, that is, one that considers the interdependencies and nested features of networks, provides the appropriate methods to examine the complex nature of these networks. Applying Mays and Scutchfields's categorization of "structural signatures" (breadth, density, and centralization), this research examines how network structure influences the outcomes of public health collaboratives. Secondary data from the Program to Analyze, Record, and Track Networks to Enhance Relationships (www.partnertool.net) data set are analyzed. This data set consists of dyadic (N = 12,355), organizational (N = 2,486), and whole network (N = 99) data from public health collaborations around the United States. Network data are used to calculate structural signatures and weighted least squares regression is used to examine how network structures can predict selected intermediary outcomes (resource contributions, overall value and trust rankings, and outcomes) in public health collaboratives. Our findings suggest that network structure may have an influence on collaborative-related outcomes. The structural signature that had the most significant relationship to outcomes was density, with higher density indicating more positive outcomes. Also significant was the finding that more breadth creates new challenges such as difficulty in reaching consensus and creating ties with other members. However, assumptions that these structural components lead to improved outcomes for public health collaboratives may be slightly premature. Implications of these findings for research and practice are discussed.

NMR study of xenotropic murine leukemia virus-related virus protease in a complex with amprenavir

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

Furukawa, Ayako; Okamura, Hideyasu; Morishita, Ryo

2012-08-24

Highlights: Black-Right-Pointing-Pointer Protease (PR) of XMR virus (XMRV) was successfully synthesized with cell-free system. Black-Right-Pointing-Pointer Interface of XMRV PR with an inhibitor, amprenavir (APV), was identified with NMR. Black-Right-Pointing-Pointer Structural heterogeneity is induced for two PR protomers in the APV:PR = 1:2 complex. Black-Right-Pointing-Pointer Structural heterogeneity is transmitted even to distant regions from the interface. Black-Right-Pointing-Pointer Long-range transmission of structural change may be utilized for drug discovery. -- Abstract: Xenotropic murine leukemia virus-related virus (XMRV) is a virus created through recombination of two murine leukemia proviruses under artificial conditions during the passage of human prostate cancer cells in athymic nudemore » mice. The homodimeric protease (PR) of XMRV plays a critical role in the production of functional viral proteins and is a prerequisite for viral replication. We synthesized XMRV PR using the wheat germ cell-free expression system and carried out structural analysis of XMRV PR in a complex with an inhibitor, amprenavir (APV), by means of NMR. Five different combinatorially {sup 15}N-labeled samples were prepared and backbone resonance assignments were made by applying Otting's method, with which the amino acid types of the [{sup 1}H, {sup 15}N] HSQC resonances were automatically identified using the five samples (Wu et al., 2006) . A titration experiment involving APV revealed that one APV molecule binds to one XMRV PR dimer. For many residues, two distinct resonances were observed, which is thought to be due to the structural heterogeneity between the two protomers in the APV:XMRV PR = 1:2 complex. PR residues at the interface with APV have been identified on the basis of chemical shift perturbation and identification of the intermolecular NOEs by means of filtered NOE experiments. Interestingly, chemical shift heterogeneity between the two protomers of XMRV PR has been observed not only at the interface with APV but also in regions apart from the interface. This indicates that the structural heterogeneity induced by the asymmetry of the binding of APV to the XMRV PR dimer is transmitted to distant regions. This is in contrast to the case of the APV:HIV-1 PR complex, in which the structural heterogeneity is only localized at the interface. Long-range transmission of the structural change identified for the XMRV PR complex might be utilized for the discovery of a new type of drug.« less

The Aegean/Cycladic and the Basin and Range Extensional Provinces - A Tectonic and Geochronologic Perspective

NASA Astrophysics Data System (ADS)

Stockli, D. F.

2017-12-01

The Aegean/Cycladic region (AC) and the Basin and Range Province (B&R) are two of the most famous Cenozoic extensional provinces and have greatly influenced our thinking about syn-convergent back-arc extension, core complex formation, syn-extensional magmatism, and kinematic transitions. They share numerous tectonic and structural similarities, such as a syn-convergent setting, previous contractional deformation, and core complex formation, but fundamental geological ambiguities remain, mainly centering around timing. The B&R affected a previously contractional belt (Sevier) and voluminous continental magmatic arc that created a pre-extensional orogenic highland. Extension was long-lived and complex, driven by both gravitational collapse and temporally distinct kinematic boundary condition changes. The B&R was also affected by massive, largely pre-extensional regional magmatic flare-ups that modified both the thermal and crustal composition. As the B&R occupies an elevated interior plateau, syn-extensional basin deposits are exclusively continental in character. In contrast, the AC is a classic marine back-arc extensional province that affected an active subduction margin with numerous accreted oceanic and continental ribbons, exhuming an early Cenozoic HP-LT subduction complex. Exhumation of the HP-LT complex, however, was accommodated both by vertical extrusion and crustal extension. Late Cenozoic extensional faulting was contemporaneous with S-ward sweeping arc magmatism and affected by little to no kinematic changes. As both the AC and B&R experienced contractional deformation during K-Cz subduction and J-K shortening, respectively, it is critical to differentiate between contractional and extensional structures and fabrics. The lack of temporal constraints hampers the reconstructions of pre-extensional structural anatomies and extensional strain magnitudes or even the attribution of structures to specific geodynamic settings. Novel methodologies in petrochronology, detrital geochronology, and high- and low-T thermochronometry allow us to elucidate pre-extensional crustal geometries, differentiate contractional from extensional fabrics, and understand the thermal and rheological evolution of these extensional provinces in a more holistic fashion.

Knowledge-based fragment binding prediction.

PubMed

Tang, Grace W; Altman, Russ B

2014-04-01

Target-based drug discovery must assess many drug-like compounds for potential activity. Focusing on low-molecular-weight compounds (fragments) can dramatically reduce the chemical search space. However, approaches for determining protein-fragment interactions have limitations. Experimental assays are time-consuming, expensive, and not always applicable. At the same time, computational approaches using physics-based methods have limited accuracy. With increasing high-resolution structural data for protein-ligand complexes, there is now an opportunity for data-driven approaches to fragment binding prediction. We present FragFEATURE, a machine learning approach to predict small molecule fragments preferred by a target protein structure. We first create a knowledge base of protein structural environments annotated with the small molecule substructures they bind. These substructures have low-molecular weight and serve as a proxy for fragments. FragFEATURE then compares the structural environments within a target protein to those in the knowledge base to retrieve statistically preferred fragments. It merges information across diverse ligands with shared substructures to generate predictions. Our results demonstrate FragFEATURE's ability to rediscover fragments corresponding to the ligand bound with 74% precision and 82% recall on average. For many protein targets, it identifies high scoring fragments that are substructures of known inhibitors. FragFEATURE thus predicts fragments that can serve as inputs to fragment-based drug design or serve as refinement criteria for creating target-specific compound libraries for experimental or computational screening.

Knowledge-based Fragment Binding Prediction

PubMed Central

Tang, Grace W.; Altman, Russ B.

2014-01-01

Target-based drug discovery must assess many drug-like compounds for potential activity. Focusing on low-molecular-weight compounds (fragments) can dramatically reduce the chemical search space. However, approaches for determining protein-fragment interactions have limitations. Experimental assays are time-consuming, expensive, and not always applicable. At the same time, computational approaches using physics-based methods have limited accuracy. With increasing high-resolution structural data for protein-ligand complexes, there is now an opportunity for data-driven approaches to fragment binding prediction. We present FragFEATURE, a machine learning approach to predict small molecule fragments preferred by a target protein structure. We first create a knowledge base of protein structural environments annotated with the small molecule substructures they bind. These substructures have low-molecular weight and serve as a proxy for fragments. FragFEATURE then compares the structural environments within a target protein to those in the knowledge base to retrieve statistically preferred fragments. It merges information across diverse ligands with shared substructures to generate predictions. Our results demonstrate FragFEATURE's ability to rediscover fragments corresponding to the ligand bound with 74% precision and 82% recall on average. For many protein targets, it identifies high scoring fragments that are substructures of known inhibitors. FragFEATURE thus predicts fragments that can serve as inputs to fragment-based drug design or serve as refinement criteria for creating target-specific compound libraries for experimental or computational screening. PMID:24762971

The museum of unnatural form: a visual and tactile experience of fractals.

PubMed

Della-Bosca, D; Taylor, R P

2009-01-01

A remarkable computer technology is revolutionizing the world of design, allowing intricate patterns to be created with mathematical precision and then 'printed' as physical objects. Contour crafting is a fabrication process capable of assembling physical structures the sizes of houses, firing the imagination of a new generation of architects and artists (Khoshnevisat, 2008). Daniel Della-Bosca has jumped at this opportunity to create the 'Museum of Unnatural Form' at Griffith University. Della-Bosca's museum is populated with fractals sculptures - his own versions of nature's complex objects - that have been printed with the new technology. His sculptures bridge the historical divide in fractal studies between the abstract images of mathematics and the physical objects of Nature (Mandelbrot, 1982). Four of his fractal images will be featured on the cover of NDPLS in 2009.

Silica biomineralization via the self-assembly of helical biomolecules.

PubMed

Liu, Ben; Cao, Yuanyuan; Huang, Zhehao; Duan, Yingying; Che, Shunai

2015-01-21

The biomimetic synthesis of relevant silica materials using biological macromolecules as templates via silica biomineralization processes attract rapidly rising attention toward natural and artificial materials. Biomimetic synthesis studies are useful for improving the understanding of the formation mechanism of the hierarchical structures found in living organisms (such as diatoms and sponges) and for promoting significant developments in the biotechnology, nanotechnology and materials chemistry fields. Chirality is a ubiquitous phenomenon in nature and is an inherent feature of biomolecular components in organisms. Helical biomolecules, one of the most important types of chiral macromolecules, can self-assemble into multiple liquid-crystal structures and be used as biotemplates for silica biomineralization, which renders them particularly useful for fabricating complex silica materials under ambient conditions. Over the past two decades, many new silica materials with hierarchical structures and complex morphologies have been created using helical biomolecules. In this review, the developments in this field are described and the recent progress in silica biomineralization templating using several classes of helical biomolecules, including DNA, polypeptides, cellulose and rod-like viruses is summarized. Particular focus is placed on the formation mechanism of biomolecule-silica materials (BSMs) with hierarchical structures. Finally, current research challenges and future developments are discussed in the conclusion. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Composite Development and Applications for RLV Tankage

NASA Technical Reports Server (NTRS)

Wright, Richard J.; Achary, David C.; McBain, Michael C.

2003-01-01

The development of polymer composite cryogenic tanks is a critical step in creating the next generation of launch vehicles. Future launch vehicles need to minimize the gross liftoff weight (GLOW), which is possible due to the 28%-41% reduction in weight that composite materials can provide over current aluminum technology. The development of composite cryogenic tanks, feedlines, and unpressurized structures are key enabling technologies for performance and cost enhancements for Reusable Launch Vehicles (RLVs). The technology development of composite tanks has provided direct and applicable data for feedlines, unpressurized structures, material compatibility, and cryogenic fluid containment for highly loaded complex structures and interfaces. All three types of structure have similar material systems, processing parameters, scaling issues, analysis methodologies, NDE development, damage tolerance, and repair scenarios. Composite cryogenic tankage is the most complex of the 3 areas and provides the largest breakthrough in technology. A building block approach has been employed to bring this family of difficult technologies to maturity. This approach has built up composite materials, processes, design, analysis and test methods technology through a series of composite test programs beginning with the NASP program to meet aggressive performance goals for reusable launch vehicles. In this paper, the development and application of advanced composites for RLV use is described.

Complex, multi-scale small intestinal topography replicated in cellular growth substrates fabricated via chemical vapor deposition of Parylene C.

PubMed

Koppes, Abigail N; Kamath, Megha; Pfluger, Courtney A; Burkey, Daniel D; Dokmeci, Mehmet; Wang, Lin; Carrier, Rebecca L

2016-08-22

Native small intestine possesses distinct multi-scale structures (e.g., crypts, villi) not included in traditional 2D intestinal culture models for drug delivery and regenerative medicine. The known impact of structure on cell function motivates exploration of the influence of intestinal topography on the phenotype of cultured epithelial cells, but the irregular, macro- to submicron-scale features of native intestine are challenging to precisely replicate in cellular growth substrates. Herein, we utilized chemical vapor deposition of Parylene C on decellularized porcine small intestine to create polymeric intestinal replicas containing biomimetic irregular, multi-scale structures. These replicas were used as molds for polydimethylsiloxane (PDMS) growth substrates with macro to submicron intestinal topographical features. Resultant PDMS replicas exhibit multiscale resolution including macro- to micro-scale folds, crypt and villus structures, and submicron-scale features of the underlying basement membrane. After 10 d of human epithelial colorectal cell culture on PDMS substrates, the inclusion of biomimetic topographical features enhanced alkaline phosphatase expression 2.3-fold compared to flat controls, suggesting biomimetic topography is important in induced epithelial differentiation. This work presents a facile, inexpensive method for precisely replicating complex hierarchal features of native tissue, towards a new model for regenerative medicine and drug delivery for intestinal disorders and diseases.

Complexity and the Limits of Revolution: What Will Happen to the Arab Spring?

NASA Astrophysics Data System (ADS)

Gard-Murray, Alexander S.; Bar-Yam, Yaneer

The recent social unrest across the Middle East and North Africa has deposed dictators who had ruled for decades. While the events have been hailed as an "Arab Spring" by those who hope that repressive autocracies will be replaced by democracies, what sort of regimes will eventually emerge from the crisis remains far from certain. Here we provide a complex systems framework, validated by historical precedent, to help answer this question. We describe the dynamics of governmental change as an evolutionary process similar to biological evolution, in which complex organizations gradually arise by replication, variation, and competitive selection. Different kinds of governments, however, have differing levels of complexity. Democracies must be more systemically complex than autocracies because of their need to incorporate large numbers of people in decision-making. This difference has important implications for the relative robustness of democratic and autocratic governments after revolutions. Revolutions may disrupt existing evolved complexity, limiting the potential for building more complex structures quickly. Insofar as systemic complexity is reduced by revolution, democracy is harder to create in the wake of unrest than autocracy. Applying this analysis to the Middle East and North Africa, we infer that in the absence of stable institutions or external assistance, new governments are in danger of facing increasingly insurmountable challenges and reverting to autocracy.

The influence of different cucumariosides on immunogenicity of OmpF porin from Yersinia pseudotuberulosis as a model protein antigen of tubular immunostimulating complex

NASA Astrophysics Data System (ADS)

Sanina, N. M.; Chopenko, N. S.; Davydova, L. A.; Mazeika, A. N.; Portnyagina, O. Yu.; Kim, N. Yu.; Golotin, V. A.; Kostetsky, E. Y.; Shnyrov, V. L.

2017-09-01

Nanoparticulate tubular immunostimulating complex (TI-complex) is a novel promising adjuvant carrier of antigens allowing to create safe and effective vaccines of new generation. The adjuvant activity of TI-complexes based on monogalactosyldyacylglycerol (MGDG) from the sea alga Ulva lactuca and different triterpene glycosides cucumariosides (CDs) from marine invertebrate Cucumaria japonica and their fractions was studied to assess effects of different CDs on the immunogenicity of porin OmpF from Yersinia pseudotuberculosis (YOmpF). TI-complexes with cucumarioside A2-2 (CDA2-2) maximally stimulated anti-porin antibody production. Studies of protein intrinsic fluorescence showed that all CDs had a relaxing effect on the conformation of YOmpF, loosening peripheral region of protein and promoting exposure of the protein antigenic determinants to the water environment. The greatest immunostimulating effect of TI-complexes comprising CDA2-2 was accompanied by mild effect of this CD on the tertiary structure of protein antigen YOmpF, whereas cucumarioside E (CDE) and cucumarioside A2-4 (CDA2-4) caused especially sharp redistribution of spectral form of the YOmpF corresponding to the emission of an intrinsic protein fluorophore tryptophan.

High Resolution Stratigraphic Mapping in Complex Terrain: A Comparison of Traditional Remote Sensing Techniques with Unmanned Aerial Vehicle - Structure from Motion Photogrammetry

NASA Astrophysics Data System (ADS)

Nesbit, P. R.; Hugenholtz, C.; Durkin, P.; Hubbard, S. M.; Kucharczyk, M.; Barchyn, T.

2016-12-01

Remote sensing and digital mapping have started to revolutionize geologic mapping in recent years as a result of their realized potential to provide high resolution 3D models of outcrops to assist with interpretation, visualization, and obtaining accurate measurements of inaccessible areas. However, in stratigraphic mapping applications in complex terrain, it is difficult to acquire information with sufficient detail at a wide spatial coverage with conventional techniques. We demonstrate the potential of a UAV and Structure from Motion (SfM) photogrammetric approach for improving 3D stratigraphic mapping applications within a complex badland topography. Our case study is performed in Dinosaur Provincial Park (Alberta, Canada), mapping late Cretaceous fluvial meander belt deposits of the Dinosaur Park formation amidst a succession of steeply sloping hills and abundant drainages - creating a challenge for stratigraphic mapping. The UAV-SfM dataset (2 cm spatial resolution) is compared directly with a combined satellite and aerial LiDAR dataset (30 cm spatial resolution) to reveal advantages and limitations of each dataset before presenting a unique workflow that utilizes the dense point cloud from the UAV-SfM dataset for analysis. The UAV-SfM dense point cloud minimizes distortion, preserves 3D structure, and records an RGB attribute - adding potential value in future studies. The proposed UAV-SfM workflow allows for high spatial resolution remote sensing of stratigraphy in complex topographic environments. This extended capability can add value to field observations and has the potential to be integrated with subsurface petroleum models.

The impacts of mobile fishing gear on seafloor habitats in the Gulf of Maine (Northwest Atlantic): implications for conservation of fish populations

USGS Publications Warehouse

Auster, Peter J.; Malatesta, Richard J.; Langton, Richard W.; Watting, Les; Valentine, Page C.; Donaldson, Carol Lee S.; Langton, Elizabeth W.; Shepard, Andrew N.; Babb, War G.

1997-01-01

Fishing gear alters seafloor habitats, but the extent of these alterations, and their effects, have not been quantified extensively in the northwest Atlantic. Understanding the extent of these impacts, and their effects on populations of living marine resources, is needed to properly manage current and future levels of fishing effort and fishing power. For example, the entire U.S. side of the Gulf of Maine was impacted annually by mobile fishing gear between 1984 and 1990, based on calculations of area swept by trawl and dredge gear. Georges Bank was imparted three to nearly four times annually during the same period. Studies at three sites in the Gulf of Maine (off Swans Island, Jeffreys Bank, and Stellwagen Bank) showed that mobile fishing gear altered the physical structure (=complexity) of benthic habitats. Complexity was reduced by direct removal of biogenic (e.g., sponges, hydrozoans, bryozoans, amphipod tubes, holothurians, shell aggregates) and‐ sedimentary (e.g., sand waves, depressions) structures. Also, removal of organisms that create.structures (e.g., crabs, scallops) indirectly reduced complexity. Reductions in habitat complexity may lead to increased predation on juveniles of harvested species and ultimately recruitment to the harvestable stock. Because of a lack of reference sites, where use of mobile fishing is prohibited, no empirical studies have yet been conducted on a scale that could demonstrate population level effects of habitat‐management options. If marine fisheries management is to evolve toward an ecosystem or habitat management approach, experiments are required on the effects of habitat change, both anthropogenic and natural.

The impacts of mobile fishing gear on seafloor habitats in the gulf of maine (Northwest Atlantic): Implications for conservation of fish populations

USGS Publications Warehouse

Auster, P.J.; Malatesta, R.J.; Langton, R.W.; Watling, Les; Valentine, P.C.; Donaldson, C.L.S.; Langton, E.W.; Shepard, A.N.; Babb, Ivar G.

1996-01-01

Fishing gear alters seafloor habitats, but the extent of these alterations, and their effects, have not been quantified extensively in the northwest Atlantic. Understanding the extent of these impacts, and their effects on populations of living marine resources, is needed to properly manage current and future levels of fishing effort and fishing power. For example, the entire U.S. side of the Gulf of Maine was impacted annually by mobile fishing gear between 1984 and 1990, based on calculations of area swept by trawl and dredge gear. Georges Bank was impacted three to nearly four times annually during the same period. Studies at three sites in the Gulf of Maine (off Swans Island, Jeffreys Bank, and Stellwagen Bank) showed that mobile fishing gear altered the physical structure (=complexity) of benthic habitats. Complexity was reduced by direct removal of biogenic (e.g., sponges, hydrozoans, bryozoans, amphipod tubes, holothurians, shell aggregates) and sedimentary (e.g., sand waves, depressions) structures. Also, removal of organisms that create structures (e.g., crabs, scallops) indirectly reduced complexity. Reductions in habitat complexity may lead to increased predation on juveniles of harvested species and ultimately recruitment to the harvestable stock. Because of a lack of reference sites, where use of mobile fishing is prohibited, no empirical studies have yet been conducted on a scale that could demonstrate population level effects of habitat-management options. If marine fisheries management is to evolve toward an ecosystem or habitat management approach, experiments are required on the effects of habitat change, both anthropogenic and natural.

Narrative Skill in Children with Early Unilateral Brain Injury: A Possible Limit to Functional Plasticity

PubMed Central

Demir, Özlem Ece; Levine, Susan C.; Goldin-Meadow, Susan

2009-01-01

Children with pre- or perinatal brain injury (PL) exhibit marked plasticity for language learning. Previous work mostly focused on the emergence of earlier developing skills, such as vocabulary and syntax. Here we ask whether this plasticity for earlier developing aspects of language extends to more complex, later-developing language functions by examining the narrative production of children with PL. Using an elicitation technique that involves asking children to create stories de novo in response to a story stem, we collected narratives from 11 children with PL and 20 typically-developing (TD) children. Narratives were analyzed for length, diversity of the vocabulary used, use of complex syntax, complexity of the macro-level narrative structure and use of narrative evaluation. Children’s language performance on vocabulary and syntax tasks outside of the narrative context was also measured. Findings show that children with PL produced shorter stories, used less diverse vocabulary, produced structurally less complex stories at the macro-level, and made fewer inferences regarding the cognitive states of the story characters. These differences in the narrative task emerged even though children with PL did not differ from TD children on vocabulary and syntax tasks outside of the narrative context. Thus, findings suggest that there may be limitations to the plasticity for language functions displayed by children with PL, and that these limitations may be most apparent in complex, decontextualized language tasks such as narrative production. PMID:20590727

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.

PubMed

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2014-01-01

pyOpenMS is an open-source, Python-based interface to the C++ OpenMS library, providing facile access to a feature-rich, open-source algorithm library for MS-based proteomics analysis. It contains Python bindings that allow raw access to the data structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping, and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ, and SWATH analysis tools). pyOpenMS thus allows fast prototyping and efficient workflow development in a fully interactive manner (using the interactive Python interpreter) and is also ideally suited for researchers not proficient in C++. In addition, our code to wrap a complex C++ library is completely open-source, allowing other projects to create similar bindings with ease. The pyOpenMS framework is freely available at https://pypi.python.org/pypi/pyopenms while the autowrap tool to create Cython code automatically is available at https://pypi.python.org/pypi/autowrap (both released under the 3-clause BSD licence). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

From complexity to reality: providing useful frameworks for defining systems of care.

PubMed

Levison-Johnson, Jody; Wenz-Gross, Melodie

2010-02-01

Because systems of care are not uniform across communities, there is a need to better document the process of system development, define the complexity, and describe the development of the structures, processes, and relationships within communities engaged in system transformation. By doing so, we begin to identify the necessary and sufficient components that, at minimum, move us from usual care within a naturally occurring system to a true system of care. Further, by documenting and measuring the degree to which key components are operating, we may be able to identify the most successful strategies in creating system reform. The theory of change and logic model offer a useful framework for communities to begin the adaptive work necessary to effect true transformation. Using the experience of two system of care communities, this new definition and the utility of a theory of change and logic model framework for defining local system transformation efforts will be discussed. Implications for the field, including the need to further examine the natural progression of systems change and to create quantifiable measures of transformation, will be raised as new challenges for the evolving system of care movement.

Lassoing saddle splay and the geometrical control of topological defects

NASA Astrophysics Data System (ADS)

Tran, Lisa; Lavrentovich, Maxim O.; Beller, Daniel A.; Li, Ningwei; Stebe, Kathleen J.; Kamien, Randall D.

2016-06-01

Systems with holes, such as colloidal handlebodies and toroidal droplets, have been studied in the nematic liquid crystal (NLC) 4-cyano-4'-pentylbiphenyl (5CB): Both point and ring topological defects can occur within each hole and around the system while conserving the system's overall topological charge. However, what has not been fully appreciated is the ability to manipulate the hole geometry with homeotropic (perpendicular) anchoring conditions to induce complex, saddle-like deformations. We exploit this by creating an array of holes suspended in an NLC cell with oriented planar (parallel) anchoring at the cell boundaries. We study both 5CB and a binary mixture of bicyclohexane derivatives (CCN-47 and CCN-55). Through simulations and experiments, we study how the bulk saddle deformations of each hole interact to create defect structures, including an array of disclination lines, reminiscent of those found in liquid-crystal blue phases. The line locations are tunable via the NLC elastic constants, the cell geometry, and the size and spacing of holes in the array. This research lays the groundwork for the control of complex elastic deformations of varying length scales via geometrical cues in materials that are renowned in the display industry for their stability and easy manipulability.

3D and 4D echo--applications in EP laboratory procedures.

PubMed

Kautzner, Josef; Peichl, Petr

2008-08-01

3D echocardiography allows imaging and analysis of cardiovascular structures as they move in time and space, thus creating possibility for creation of 4D datasets (3D + time). Intracardiac echocardiography (ICE) further broadens the spectrum of echocardiographic techniques by allowing detailed imaging of intracardiac anatomy with 3D reconstructions. The paper reviews the current status of development of 3D and 4D echocardiography in electrophysiology. In ablation area, 3D echocardiography can enhance the performance of catheter ablation for complex arrhythmias such as atrial fibrillation. Currently, several strategies to obtain 3D reconstructions from ICE are available. One involves combination with electroanatomical mapping system; others create reconstruction from standard phased-array or single-element ICE catheter using special rotational or pull-back devices. Secondly, 3D echocardiography may be used for precise assessment of cardiac dyssynchrony before cardiac resynchronization therapy. Its reliable detection is expected to minimize number of non-responders to this treatment and optimize left ventricular lead positioning to get maximum hemodynamic benefit. The main potential benefit of 3D and 4D echocardiography in electrophysiology lie in real-time guidance of complex ablation procedures and precise assessment of cardiac dyssynchrony.

A Computational Workflow for the Automated Generation of Models of Genetic Designs.

PubMed

Misirli, Göksel; Nguyen, Tramy; McLaughlin, James Alastair; Vaidyanathan, Prashant; Jones, Timothy S; Densmore, Douglas; Myers, Chris; Wipat, Anil

2018-06-05

Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modeling often requires expert knowledge and data to build models. Clearly, manual creation of models is not scalable for large designs. Despite several automated model construction approaches, computational methodologies to bridge knowledge in design repositories and the process of creating computational models have still not been established. This paper describes a workflow for automatic generation of computational models of genetic circuits from data stored in design repositories using existing standards. This workflow leverages the software tool SBOLDesigner to build structural models that are then enriched by the Virtual Parts Repository API using Systems Biology Open Language (SBOL) data fetched from the SynBioHub design repository. The iBioSim software tool is then utilized to convert this SBOL description into a computational model encoded using the Systems Biology Markup Language (SBML). Finally, this SBML model can be simulated using a variety of methods. This workflow provides synthetic biologists with easy to use tools to create predictable biological systems, hiding away the complexity of building computational models. This approach can further be incorporated into other computational workflows for design automation.

Spatio-Temporal Cellular Imaging of Polymer-pDNA Nanocomplexes Affords In Situ Morphology and Trafficking Trends

PubMed Central

Ingle, Nilesh P.; Lian, Xue; Reineke, Theresa M.

2013-01-01

Synthetic polymers are ubiquitous in the development of drug and polynucleotide delivery vehicles, offering promise for personalized medicine. However, the polymer structure plays a central yet elusive role in dictating the efficacy, safety, mechanisms, and kinetics of therapeutic transport in a spatial and temporal manner. Here, we decipher the intracellular evolutionary pathways pertaining to shape, size, location, and mechanism of four structurally-divergent polymer vehicles (Tr455, Tr477, jetPEI™ and Glycofect™) that create colloidal nanoparticles (polyplexes) when complexed with fluorescently-labeled plasmid DNA (pDNA). Multiple high resolution tomographic images of whole HeLa (human cervical adenocarcinoma) cells were captured via confocal microscopy at 4, 8, 12 and 24 hours. The images were reconstructed to visualize and quantify trends in situ in a four-dimensional spatio-temporal manner. The data revealed heretofore-unseen images of polyplexes in situ and structure-function relationships, i.e., Glycofect™ polyplexes are trafficked as the smallest polyplex complexes and Tr455 polyplexes have expedited translocation to the perinuclear region. Also, all of the polyplex types appeared to be preferentially internalized and trafficked via early endosomes affiliated with caveolae, a Rab-5-dependent pathway, actin, and microtubules. PMID:24007201

The tertiary structures of porcine AhR and ARNT proteins and molecular interactions within the TCDD/AhR/ARNT complex.

PubMed

Orlowska, Karina; Molcan, Tomasz; Swigonska, Sylwia; Sadowska, Agnieszka; Jablonska, Monika; Nynca, Anna; Jastrzebski, Jan P; Ciereszko, Renata E

2016-06-01

The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that can be activated by structurally diverse synthetic and natural chemicals, including toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). In the present study, homology models of the porcine AhR-ligand binding domain (LBD) and the porcine aryl hydrocarbon receptor nuclear translocator-ligand binding domain (ARNT-LBD) were created on the basis of structures of closely related respective proteins i.e., human Hif-2α and ARNT. Molecular docking of TCDD to the porcine AhR-LBD model revealed high binding affinity (-8.8kcal/mol) between TCDD and the receptor. Moreover, formation of the TCDD/AhR-LBD complex was confirmed experimentally with the use of electrophoretic mobility shift assay (EMSA). It was found that TCDD (10nM, 2h of incubation) not only bound to the AhR in the porcine granulosa cells but also activated the receptor. The current study provides a framework for examining the key events involved in the ligand-dependent activation of the AhR. Copyright © 2016 Elsevier Inc. All rights reserved.

Topological study of diverse hydrogen-bonded patterns found in a system of a nickel(II) complex and the sulfate anion.

PubMed

Harvey, Miguel Angel; Suarez, Sebastián; Zolotarev, Pavel N; Proserpio, Davide M; Baggio, Ricardo

2018-03-01

A nickel(II) coordination complex, bis[2,6-bis(1H-benzimidazol-2-yl-κN 3 )pyridine-κN]nickel(II) sulfate, [Ni(C 19 H 13 N 5 ) 2 ]SO 4 or [Ni(H 2 L) 2 ]SO 4 , having four peripheral tetrahedrally oriented N-H donor units, combines with sulfate bridges to create hydrogen-bonded structures of varied dimensionality. The three crystal structures reported herein in the space groups P2 1 2 1 2 1 , I-4 and Pccn are defined solely by strong charge-assisted N-H...O hydrogen bonds and contain disordered guests (water and dimethylformamide) that vary in size, shape and degree of hydrophilicity. Two of the compounds are channelled solids with three-dimensional structures, while the third is one-dimensional in nature. In spite of their differences, all three present a striking resemblance to the previously reported anhydrous relative [Guo et al. (2011). Chin. J. Inorg. Chem. 27, 1517-1520], which is considered as the reference framework from which all three title compounds are derived. The hydrogen-bonded frameworks are described and compared using crystallographic and topological approaches.

Compliance and High Reliability in a Complex Healthcare Organization.

PubMed

Simon, Maxine dellaBadia

2018-01-01

When considering the impact of regulation on healthcare, visualize a spider's web. The spider weaves sections together to create the whole, with each fiber adding to the structure to support its success or lead to its failure. Each section is dependent on the others, and all must be aligned to maintain the structure. Outside forces can cause a shift in the web's fragile equilibrium.The interdependence of the sections of the spider's web is similar to the way hospital departments and services work together. An organization's structure must be shaped to support its mission and vision. At the same time, the business of healthcare requires the development and achievement of operational objectives and financial performance goals. Establishing a culture that is flexible enough to permit creativity, provide resiliency, and manage complexity as the organization grows is fundamental to success. An organization must address each of these factors while maintaining stability, carrying out its mission, and fostering improvement.Nature's order maintains the spider's web. Likewise, regulation can strengthen healthcare organizations by initiating disruptive changes that can support efforts to achieve and sustain high reliability in the delivery of care. To that end, leadership must be willing to provide the necessary vision and resources.

Slovenia’s Construction Act and Implementation Plans: A Case Study of Izola IPA-8

NASA Astrophysics Data System (ADS)

Ažman Momirski, Lucija

2017-10-01

The guidelines for urban design in Izola’s IPA-8 planning area, which is earmarked for hotels, apartment complexes, and sports, specify diverse forms of leisure living space required by modern society. The new tourist complex is not a large monotonous hotel complex, but rather a spatial arrangement in which guests experience an authentic local environment and city residents enjoy the new high-quality ambience. The hotel area is defined by three major communication axes from north to south, linking the countryside to the coastal area and opening up attractive sea views in the new complex. Internal east-west links connect buildings and public spaces. Because of the terraced terrain, a large number of paved ramps and internal public gardens have been designed between the structures. The extensions of the communication axes are laid out as squares, named based on the function of the public spaces. Hotel Street is the central axis and main connecting street, with public hotel services and restaurants. The west axis extends into Culture Square, where activities related to Izola’s culture and history are presented; here there is an opportunity to create new galleries, a small local museum, and an exhibition room. Apartment Square is located on the east communication axis, along which only a limited number of trade, catering, and service activities are planned. The plan received first prize in a public competition, and it later developed into detailed municipal spatial plan. In this process, it became clear that Slovenia’s Construction Act (ZGO-1) does not support plans to create terraced buildings.

The Various Applications of 3D Printing in Cardiovascular Diseases.

PubMed

El Sabbagh, Abdallah; Eleid, Mackram F; Al-Hijji, Mohammed; Anavekar, Nandan S; Holmes, David R; Nkomo, Vuyisile T; Oderich, Gustavo S; Cassivi, Stephen D; Said, Sameh M; Rihal, Charanjit S; Matsumoto, Jane M; Foley, Thomas A

2018-05-10

To highlight the various applications of 3D printing in cardiovascular disease and discuss its limitations and future direction. Use of handheld 3D printed models of cardiovascular structures has emerged as a facile modality in procedural and surgical planning as well as education and communication. Three-dimensional (3D) printing is a novel imaging modality which involves creating patient-specific models of cardiovascular structures. As percutaneous and surgical therapies evolve, spatial recognition of complex cardiovascular anatomic relationships by cardiologists and cardiovascular surgeons is imperative. Handheld 3D printed models of cardiovascular structures provide a facile and intuitive road map for procedural and surgical planning, complementing conventional imaging modalities. Moreover, 3D printed models are efficacious educational and communication tools. This review highlights the various applications of 3D printing in cardiovascular diseases and discusses its limitations and future directions.

Enhancing AFLOW Visualization using Jmol

NASA Astrophysics Data System (ADS)

Lanasa, Jacob; New, Elizabeth; Stefek, Patrik; Honaker, Brigette; Hanson, Robert; Aflow Collaboration

The AFLOW library is a database of theoretical solid-state structures and calculated properties created using high-throughput ab initio calculations. Jmol is a Java-based program capable of visualizing and analyzing complex molecular structures and energy landscapes. In collaboration with the AFLOW consortium, our goal is the enhancement of the AFLOWLIB database through the extension of Jmol's capabilities in the area of materials science. Modifications made to Jmol include the ability to read and visualize AFLOW binary alloy data files, the ability to extract from these files information using Jmol scripting macros that can be utilized in the creation of interactive web-based convex hull graphs, the capability to identify and classify local atomic environments by symmetry, and the ability to search one or more related crystal structures for atomic environments using a novel extension of inorganic polyhedron-based SMILES strings

Do organizational and political-legal arrangements explain financial wrongdoing?

PubMed

Prechel, Harland; Zheng, Lu

2016-12-01

The 2008 financial crisis was a systemic problem with deep-rooted structural causes that created opportunities to engage in financial malfeasance, a form of corporate wrongdoing. However, few quantitative studies exist on the effects of organizational and political-legal arrangements on financial malfeasance. In this paper, we examine the effects of organizational and political-legal arrangements that emerged in the 1990s in the FIRE sector (i.e., financial, insurance, and real estate) on financial malfeasance. Our historical contextualization demonstrates how changes in the political-legal arrangements facilitate the emergence of new corporate structures and opportunities for financial malfeasance. Our longitudinal quantitative analysis demonstrates that US FIRE sector corporations with a more complex organizational structure, larger size, lower dividend payment, and higher executive compensation are more prone to commit financial malfeasance. © London School of Economics and Political Science 2016.

Optically resilient 3D micro-optics on the tips of optical fibers

NASA Astrophysics Data System (ADS)

Jonušauskas, Linas

2017-05-01

In this paper we present a study aimed at investigating an optical resiliency of polymers that could be applied in 3D femtosecond laser lithography. These include popular in lithography SU8 and OrmoClear as well as hybrid organic-inorganic zirconium containing SZ2080. We show that latter material in its pure (non-photosensitized) form has the best optical resiliency out of all tested materials. Furthermore, its 3D structurability is investigated. Despite threshold-like quality degradation outside fabrication window, we show that this material is suitable for creating complex 3D structures on the tips of optical fibers. Overall it is demonstrated, that unique capability of 3DLL to structure pure materials can lead to very compact functional fiber-based devices that could withstand high (GW/cm2) light intensities.

Butterfly effects: novel functional materials inspired from the wings scales.

PubMed

Zhang, Wang; Gu, Jiajun; Liu, Qinglei; Su, Huilan; Fan, Tongxiang; Zhang, Di

2014-10-07

Through millions of years of evolutionary selection, nature has created biological materials with various functional properties for survival. Many complex natural architectures, such as shells, bones, and honeycombs, have been studied and imitated in the design and fabrication of materials with enhanced hardness and stiffness. Recently, more and more researchers have started to research the wings of butterflies, mostly because of their dazzling colors. It was found that most of these iridescent colors are caused by periodic photonic structures on the scales that make up the surfaces of these wings. These materials have recently become a focus of multidiscipline research because of their promising applications in the display of structural colors, and in advanced sensors, photonic crystals, and solar cells. This paper review aims to provide a perspective overview of the research inspired by these wing structures in recent years.

Challenges and solutions for high-volume testing of silicon photonics

NASA Astrophysics Data System (ADS)

Polster, Robert; Dai, Liang Yuan; Oikonomou, Michail; Cheng, Qixiang; Rumley, Sebastien; Bergman, Keren

2018-02-01

The first generation of silicon photonic products is now commercially available. While silicon photonics possesses key economic advantages over classical photonic platforms, it has yet to become a commercial success because these advantages can be fully realized only when high-volume testing of silicon photonic devices is made possible. We discuss the costs, challenges, and solutions of photonic chip testing as reported in the recent research literature. We define and propose three underlying paradigms that should be considered when creating photonic test structures: Design for Fast Coupling, Design for Minimal Taps, and Design for Parallel Testing. We underline that a coherent test methodology must be established prior to the design of test structures, and demonstrate how an optimized methodology dramatically reduces the burden when designing for test, by reducing the needed complexity of test structures.

The role of pre-oedipal and oedipal factors in psychic life.

PubMed

Kancyper, Luis

2006-02-01

The Oedipus complex, a basic concept in Freudian theory, is an essential factor in the constitution of the human subject. It plays a key role in the structuring of the personality and in the orientation of desire. It is the oedipal triangular structure that precedes the pre-oedipal situation (in a logical, not chronological, order), and not vice versa. The oedipal structure exists before the infant's biological birth. It is present in the parents' desires and identifications, which inexorably fall upon each subject. That is why the author believes that it is necessary to leave behind a solipsistic reading of the nuclear complex of neuroses--a reading that is based solely on Oedipus's drive nucleus--and take a joint and comprehensive view of Laius's and Jocasta's histories and traumatic experiences, which were invested in their son. Among these three vertices, a dynamic set of forces emerges whereby a basic, original unconscious field phantasy is created that bears a unique narrative and an invisible and hermetic web made of passions and beliefs, scandals and secrets. This phantasy gives shape to an unrepeatable oedipal structure in each subject, a structure that articulates with the effects of the narcissistic and fraternal dynamic and may determine the subject's fate. This paper develops the following issues: 1) Oedipus, victimizer or victim?; 2) the generational confrontation as dynamic field; and 3) neuroses with a preponderance of dualistic relationships.

A Novel Cofactor-binding Mode in Bacterial IMP Dehydrogenases Explains Inhibitor Selectivity*

PubMed Central

Makowska-Grzyska, Magdalena; Kim, Youngchang; Maltseva, Natalia; Osipiuk, Jerzy; Gu, Minyi; Zhang, Minjia; Mandapati, Kavitha; Gollapalli, Deviprasad R.; Gorla, Suresh Kumar; Hedstrom, Lizbeth; Joachimiak, Andrzej

2015-01-01

The steadily rising frequency of emerging diseases and antibiotic resistance creates an urgent need for new drugs and targets. Inosine 5′-monophosphate dehydrogenase (IMP dehydrogenase or IMPDH) is a promising target for the development of new antimicrobial agents. IMPDH catalyzes the oxidation of IMP to XMP with the concomitant reduction of NAD+, which is the pivotal step in the biosynthesis of guanine nucleotides. Potent inhibitors of bacterial IMPDHs have been identified that bind in a structurally distinct pocket that is absent in eukaryotic IMPDHs. The physiological role of this pocket was not understood. Here, we report the structures of complexes with different classes of inhibitors of Bacillus anthracis, Campylobacter jejuni, and Clostridium perfringens IMPDHs. These structures in combination with inhibition studies provide important insights into the interactions that modulate selectivity and potency. We also present two structures of the Vibrio cholerae IMPDH in complex with IMP/NAD+ and XMP/NAD+. In both structures, the cofactor assumes a dramatically different conformation than reported previously for eukaryotic IMPDHs and other dehydrogenases, with the major change observed for the position of the NAD+ adenosine moiety. More importantly, this new NAD+-binding site involves the same pocket that is utilized by the inhibitors. Thus, the bacterial IMPDH-specific NAD+-binding mode helps to rationalize the conformation adopted by several classes of prokaryotic IMPDH inhibitors. These findings offer a potential strategy for further ligand optimization. PMID:25572472

Creating realistic models and resolution assessment in tomographic inversion of wide-angle active seismic profiling data

NASA Astrophysics Data System (ADS)

Stupina, T.; Koulakov, I.; Kopp, H.

2009-04-01

We consider questions of creating structural models and resolution assessment in tomographic inversion of wide-angle active seismic profiling data. For our investigations, we use the PROFIT (Profile Forward and Inverse Tomographic modeling) algorithm which was tested earlier with different datasets. Here we consider offshore seismic profiling data from three areas (Chile, Java and Central Pacific). Two of the study areas are characterized by subduction zones whereas the third data set covers a seamount province. We have explored different algorithmic issues concerning the quality of the solution, such as (1) resolution assessment using different sizes and complexity of synthetic anomalies; (2) grid spacing effects; (3) amplitude damping and smoothing; (4) criteria for rejection of outliers; (5) quantitative criteria for comparing models. Having determined optimal algorithmic parameters for the observed seismic profiling data we have created structural synthetic models which reproduce the results of the observed data inversion. For the Chilean and Java subduction zones our results show similar patterns: a relatively thin sediment layer on the oceanic plate, thicker inhomogeneous sediments in the overlying plate and a large area of very strong low velocity anomalies in the accretionary wedge. For two seamounts in the Pacific we observe high velocity anomalies in the crust which can be interpreted as frozen channels inside the dormant volcano cones. Along both profiles we obtain considerable crustal thickening beneath the seamounts.

Grassroots Engagement: Securing Support for Science Communication Training Programs Created by Graduate Students for Graduate Students

NASA Astrophysics Data System (ADS)

Rohde, J. A.

2016-12-01

The need for science communication and outreach is widely recognized throughout the scientific community. Yet, at present, graduate students and early career scientists have, at best, widely variable access to opportunities to train in science communication techniques and to hone their outreach skills. In 2010, a small group of graduate students at the University of Washington led a grassroots effort to increase their own access to communication and outreach training by creating "The Engage Program." They developed a novel, interdisciplinary curriculum focused on storytelling, public speaking and improvisation, design, and the distillation of complex topics to clear and accessible forms. These entrepreneurial students faced (real or perceived) barriers to building this program, including the pressure to hide or dampen their enthusiasm from advisors and mentors, ignorance of university structures, and lack of institutional support. They overcame these barriers and secured institutional champions and funding, partnered with Town Hall Seattle to create a science speaker series, and developed a student leadership structure to ensure long-term sustainability of the program. Additionally, they crowdfunded an evaluation of the program's effectiveness in order demonstrate the benefits of such training to the scientific careers of the students. Here we present our key strategies for overcoming barriers to support, and compare them with several similar grassroots graduate-student led public communication programs from other institutions.

Named Entity Recognition in a Hungarian NL Based QA System

NASA Astrophysics Data System (ADS)

Tikkl, Domonkos; Szidarovszky, P. Ferenc; Kardkovacs, Zsolt T.; Magyar, Gábor

In WoW project our purpose is to create a complex search interface with the following features: search in the deep web content of contracted partners' databases, processing Hungarian natural language (NL) questions and transforming them to SQL queries for database access, image search supported by a visual thesaurus that describes in a structural form the visual content of images (also in Hungarian). This paper primarily focuses on a particular problem of question processing task: the entity recognition. Before going into details we give a short overview of the project's aims.

Wear of carbide inserts with complex surface treatment when milling nickel alloy

NASA Astrophysics Data System (ADS)

Fedorov, Sergey; Swe, Min Htet; Kapitanov, Alexey; Egorov, Sergey

2018-03-01

One of the effective ways of strengthening hard alloys is the creating structure layers on their surface with the gradient distribution of physical and mechanical properties between the wear-resistant coating and the base material. The article discusses the influence of the near-surface layer which is modified by low-energy high-current electron-beam alloying and the upper anti-friction layer in a multi-component coating on the wear mechanism of the replaceable multifaceted plates in the dry milling of the difficult to machine nickel alloys.

3D DNA Crystals and Nanotechnology

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

Paukstelis, Paul; Seeman, Nadrian

DNA's molecular recognition properties have made it one of the most widely used biomacromolecular construction materials. The programmed assembly of DNA oligonucleotides has been used to create complex 2D and 3D self-assembled architectures and to guide the assembly of other molecules. The origins of DNA nanotechnology are rooted in the goal of assembling DNA molecules into designed periodic arrays, i.e., crystals. Here, we highlight several DNA crystal structures, the progress made in designing DNA crystals, and look at the current prospects and future directions of DNA crystals in nanotechnology.

The room-temperature synthesis of anisotropic CdHgTe quantum dot alloys: a "molecular welding" effect.

PubMed

Taniguchi, Shohei; Green, Mark; Lim, Teck

2011-03-16

The room-temperature chemical transformation of spherical CdTe nanoparticles into anisotropic alloyed CdHgTe particles using mercury bromide in a toluene/methanol system at room temperature has been investigated. The resulting materials readily dissolved in toluene and exhibited a significant red-shift in the optical properties toward the infrared region. Structural transformations were observed, with electron microscopy showing that the CdTe nanoparticles were chemically attached ('welded') to other CdTe nanoparticles, creating highly complex anisotropic heterostructures which also incorporated mercury.

3D DNA Crystals and Nanotechnology

DOE PAGES

Paukstelis, Paul; Seeman, Nadrian

2016-08-18

DNA's molecular recognition properties have made it one of the most widely used biomacromolecular construction materials. The programmed assembly of DNA oligonucleotides has been used to create complex 2D and 3D self-assembled architectures and to guide the assembly of other molecules. The origins of DNA nanotechnology are rooted in the goal of assembling DNA molecules into designed periodic arrays, i.e., crystals. Here, we highlight several DNA crystal structures, the progress made in designing DNA crystals, and look at the current prospects and future directions of DNA crystals in nanotechnology.

Crustal Seismic Structure beneath Portugal (Western Iberia) and the role of Variscan Inheritance

NASA Astrophysics Data System (ADS)

Veludo, Idalina; Afonso Dias, Nuno; Fonseca, Paulo; Matias, Luís; Carrilho, Fernando; Haberland, Christian; Villaseñor, Antonio

2017-04-01

Mainland Portugal comprises most of the Western portion of the Iberian Peninsula, in a geodynamic setting associated with the Africa-Eurasia plate boundary. The crustal structure in Portugal is the result of a complex assemblage history of continental collision and extension with most of the surface is covered by rocks dating to the Variscan orogeny, the coastal ranges dominated by Mesozoic structures and Mesocenozoic basins covering partially the mainland. The impact and extension of this complex tectonic in the structure of the Iberian Lithosphere is still a matter of discussion, especially in its western part beneath Portugal. The existing knowledge relating the observed surface geology and lithospheric structures is sparse and sometimes incoherent, the relation between shallow and deep structures and their lateral extension still widely undetermined. Some questions still pertinent are the role and influence of the several tectonic units and their contacts in the present tectonic regime and in the stress field observed today, and the relation between the anomalous seismicity and associated crustal deformation rates with the inherited structure from past orogenies. In this study we present the results of a local earthquake tomographic study, performed to image this complex crustal structure down to 20 km depth. The relocation of the onshore seismicity recorded in the period 2000-2014 with the new 3D model allows cleansing some of the alignments and their correlation with some of the main active structures in Portugal enabling for the first time to correlate a large number of tectonic features to the small magnitude seismicity pattern. The seismicity distribution also displays a complex pattern, mainly reflecting the interaction between inherited Variscan structures with more recent fault systems created during the rifting stages of the Atlantic and diapir magmatic intrusions. The complex history of the assemblage of the crust beneath Western Iberia is well-marked in the final models. The arcuate shape of the Ibero-Armorican Arc can be perceived over the general pattern of the Vp and Vp/Vs anomalies and the heterogeneity observed on the surface geology are clearly marked in the tomograms. Other significant features are the low Vp values associated with the Mesocenozoic rocks outcropping in the Lusitanian and Algarve basins, and the low Vp and high Vp/Vs values of the sedimentary cover of the Lower-Tagus and Sado Basin. Publication supported by FCT- project UID/GEO/50019/2013 - Instituto Dom Luiz.

Confirming the key role of Ar+ ion bombardment in the growth feature of nanostructured carbon materials by PECVD

NASA Astrophysics Data System (ADS)

Liu, Yulin; Lin, Jinghuang; Jia, Henan; Chen, Shulin; Qi, Junlei; Qu, Chaoqun; Cao, Jian; Feng, Jicai; Fei, Weidong

2017-11-01

In order to confirm the key role of Ar+ ion bombardment in the growth feature of nanostructured carbon materials (NCMs), here we report a novel strategy to create different Ar+ ion states in situ in plasma enhanced chemical vapor deposition (PECVD) by separating catalyst film from the substrate. Different bombardment environments on either side of the catalyst film were created simultaneously to achieve multi-layered structural NCMs. Results showed that Ar+ ion bombardment is crucial and complex for the growth of NCMs. Firstly, Ar+ ion bombardment has both positive and negative effects on carbon nanotubes (CNTs). On one hand, Ar+ ions can break up the graphic structure of CNTs and suppress thin CNT nucleation and growth. On the other hand, Ar+ ion bombardment can remove redundant carbon layers on the surface of large catalyst particles which is essential for thick CNTs. As a result, the diameter of the CNTs depends on the Ar+ ion state. As for vertically oriented few-layer graphene (VFG), Ar+ ions are essential and can even convert the CNTs into VFG. Therefore, by combining with the catalyst separation method, specific or multi-layered structural NCMs can be obtained by PECVD only by changing the intensity of Ar+ ion bombardment, and these special NCMs are promising in many fields.

Confirming the key role of Ar+ ion bombardment in the growth feature of nanostructured carbon materials by PECVD.

PubMed

Liu, Yulin; Lin, Jinghuang; Jia, Henan; Chen, Shulin; Qi, Junlei; Qu, Chaoqun; Cao, Jian; Feng, Jicai; Fei, Weidong

2017-11-24

In order to confirm the key role of Ar + ion bombardment in the growth feature of nanostructured carbon materials (NCMs), here we report a novel strategy to create different Ar + ion states in situ in plasma enhanced chemical vapor deposition (PECVD) by separating catalyst film from the substrate. Different bombardment environments on either side of the catalyst film were created simultaneously to achieve multi-layered structural NCMs. Results showed that Ar + ion bombardment is crucial and complex for the growth of NCMs. Firstly, Ar + ion bombardment has both positive and negative effects on carbon nanotubes (CNTs). On one hand, Ar + ions can break up the graphic structure of CNTs and suppress thin CNT nucleation and growth. On the other hand, Ar + ion bombardment can remove redundant carbon layers on the surface of large catalyst particles which is essential for thick CNTs. As a result, the diameter of the CNTs depends on the Ar + ion state. As for vertically oriented few-layer graphene (VFG), Ar + ions are essential and can even convert the CNTs into VFG. Therefore, by combining with the catalyst separation method, specific or multi-layered structural NCMs can be obtained by PECVD only by changing the intensity of Ar + ion bombardment, and these special NCMs are promising in many fields.

Structure of FcRY, an avian immunoglobulin receptor related to mammalian mannose receptors, and its complex with IgY

PubMed Central

He, Yongning; Bjorkman, Pamela J.

2011-01-01

Fc receptors transport maternal antibodies across epithelial cell barriers to passively immunize newborns. FcRY, the functional counterpart of mammalian FcRn (a major histocompatibility complex homolog), transfers IgY across the avian yolk sac, and represents a new class of Fc receptor related to the mammalian mannose receptor family. FcRY and FcRn bind immunoglobulins at pH ≤6.5, but not pH ≥7, allowing receptor–ligand association inside intracellular vesicles and release at the pH of blood. We obtained structures of monomeric and dimeric FcRY and an FcRY–IgY complex and explored FcRY's pH-dependent binding mechanism using electron cryomicroscopy (cryoEM) and small-angle X-ray scattering. The cryoEM structure of FcRY at pH 6 revealed a compact double-ring “head,” in which the N-terminal cysteine-rich and fibronectin II domains were folded back to contact C-type lectin-like domains 1–6, and a “tail” comprising C-type lectin-like domains 7–8. Conformational changes at pH 8 created a more elongated structure that cannot bind IgY. CryoEM reconstruction of FcRY dimers at pH 6 and small-angle X-ray scattering analysis at both pH values confirmed both structures. The cryoEM structure of the FcRY–IgY revealed symmetric binding of two FcRY heads to the dimeric FcY, each head contacting the CH4 domain of one FcY chain. FcRY shares structural properties with mannose receptor family members, including a head and tail domain organization, multimerization that may regulate ligand binding, and pH-dependent conformational changes. Our results facilitate understanding of immune recognition by the structurally related mannose receptor family and comparison of diverse methods of Ig transport across evolution. PMID:21746914

A model based bayesian solution for characterization of complex damage scenarios in aerospace composite structures.

PubMed

Reed, H; Leckey, Cara A C; Dick, A; Harvey, G; Dobson, J

2018-01-01

Ultrasonic damage detection and characterization is commonly used in nondestructive evaluation (NDE) of aerospace composite components. In recent years there has been an increased development of guided wave based methods. In real materials and structures, these dispersive waves result in complicated behavior in the presence of complex damage scenarios. Model-based characterization methods utilize accurate three dimensional finite element models (FEMs) of guided wave interaction with realistic damage scenarios to aid in defect identification and classification. This work describes an inverse solution for realistic composite damage characterization by comparing the wavenumber-frequency spectra of experimental and simulated ultrasonic inspections. The composite laminate material properties are first verified through a Bayesian solution (Markov chain Monte Carlo), enabling uncertainty quantification surrounding the characterization. A study is undertaken to assess the efficacy of the proposed damage model and comparative metrics between the experimental and simulated output. The FEM is then parameterized with a damage model capable of describing the typical complex damage created by impact events in composites. The damage is characterized through a transdimensional Markov chain Monte Carlo solution, enabling a flexible damage model capable of adapting to the complex damage geometry investigated here. The posterior probability distributions of the individual delamination petals as well as the overall envelope of the damage site are determined. Copyright © 2017 Elsevier B.V. All rights reserved.

Tips on Creating Complex Geometry Using Solid Modeling Software

ERIC Educational Resources Information Center

Gow, George

2008-01-01

Three-dimensional computer-aided drafting (CAD) software, sometimes referred to as "solid modeling" software, is easy to learn, fun to use, and becoming the standard in industry. However, many users have difficulty creating complex geometry with the solid modeling software. And the problem is not entirely a student problem. Even some teachers and…

Biofilm three-dimensional architecture influences in situ pH distribution pattern on the human enamel surface

PubMed Central

Xiao, Jin; Hara, Anderson T; Kim, Dongyeop; Zero, Domenick T; Koo, Hyun; Hwang, Geelsu

2017-01-01

To investigate how the biofilm three-dimensional (3D) architecture influences in situ pH distribution patterns on the enamel surface. Biofilms were formed on human tooth enamel in the presence of 1% sucrose or 0.5% glucose plus 0.5% fructose. At specific time points, biofilms were exposed to a neutral pH buffer to mimic the buffering of saliva and subsequently pulsed with 1% glucose to induce re-acidification. Simultaneous 3D pH mapping and architecture of intact biofilms was performed using two-photon confocal microscopy. The enamel surface and mineral content characteristics were examined successively via optical profilometry and microradiography analyses. Sucrose-mediated biofilm formation created spatial heterogeneities manifested by complex networks of bacterial clusters (microcolonies). Acidic regions (pH<5.5) were found only in the interior of microcolonies, which impedes rapid neutralization (taking more than 120 min for neutralization). Glucose exposure rapidly re-created the acidic niches, indicating formation of diffusion barriers associated with microcolonies structure. Enamel demineralization (white spots), rougher surface, deeper lesion and more mineral loss appeared to be associated with the localization of these bacterial clusters at the biofilm-enamel interface. Similar 3D architecture was observed in plaque-biofilms formed in vivo in the presence of sucrose. The formation of complex 3D architectures creates spatially heterogeneous acidic microenvironments in close proximity of enamel surface, which might correlate with the localized pattern of the onset of carious lesions (white spot like) on teeth. PMID:28452377

Motorizing fibres with geometric zero-energy modes

NASA Astrophysics Data System (ADS)

Baumann, Arthur; Sánchez-Ferrer, Antoni; Jacomine, Leandro; Martinoty, Philippe; Le Houerou, Vincent; Ziebert, Falko; Kulić, Igor M.

2018-06-01

Responsive materials1-3 have been used to generate structures with built-in complex geometries4-6, linear actuators7-9 and microswimmers10-12. These results suggest that complex, fully functional machines composed solely from shape-changing materials might be possible13. Nonetheless, to accomplish rotary motion in these materials still relies on the classical wheel and axle motifs. Here we explore geometric zero-energy modes to elicit rotary motion in elastic materials in the absence of a rigid wheel travelling around an axle. We show that prestrained polymer fibres closed into rings exhibit self-actuation and continuous motion when placed between two heat baths due to elastic deformations that arise from rotational-symmetry breaking around the rod's axis. Our findings illustrate a simple but robust model to create active motion in mechanically prestrained objects.

Ta-Nb-Mo-W refractory high-entropy alloys: Anomalous ordering behavior and its intriguing electronic origin

DOE PAGES

Singh, Prashant; Smirnov, A. V.; Johnson, Duane D.

2018-05-31

From electronic-structure-based thermodynamic linear response, we establish chemical ordering behavior in complex solid solutions versus how Gibbs' space is traversed—applying it on prototype refractory A2 Ta-Nb-Mo-W high-entropy alloys. Near ideal stoichiometry, this alloy has anomalous, intricate chemical ordering tendencies, with long-ranged chemical interactions that produce competing short-range order (SRO) with a crossover to spinodal segregation. This atypical SRO arises from canonical band behavior that, with alloying, creates features near the Fermi surface (well defined even with disorder) that change to simple commensurate SRO with (un)filling of these states. In conclusion, our results reveal how complexity and competing electronic effects controlmore » ordering in these alloys.« less

Materials Manufactured from 3D Printed Synthetic Biology Arrays

NASA Technical Reports Server (NTRS)

Gentry, Diana; Micks, Ashley

2013-01-01

Many complex, biologically-derived materials have extremely useful properties (think wood or silk), but are unsuitable for space-related applications due to production, manufacturing, or processing limitations. Large-scale ecosystem-based production, such as raising and harvesting trees for wood, is impractical in a self-contained habitat such as a space station or potential Mars colony. Manufacturing requirements, such as the specialized equipment needed to harvest and process cotton, add too much upmass for current launch technology. Cells in nature are already highly specialized for making complex biological materials on a micro scale. We envision combining these strengths with the recently emergent technologies of synthetic biology and 3D printing to create 3D-structured arrays of cells that are bioengineered to secrete different materials in a specified three-dimensional pattern.

Ta-Nb-Mo-W refractory high-entropy alloys: Anomalous ordering behavior and its intriguing electronic origin

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

Singh, Prashant; Smirnov, A. V.; Johnson, Duane D.

From electronic-structure-based thermodynamic linear response, we establish chemical ordering behavior in complex solid solutions versus how Gibbs' space is traversed—applying it on prototype refractory A2 Ta-Nb-Mo-W high-entropy alloys. Near ideal stoichiometry, this alloy has anomalous, intricate chemical ordering tendencies, with long-ranged chemical interactions that produce competing short-range order (SRO) with a crossover to spinodal segregation. This atypical SRO arises from canonical band behavior that, with alloying, creates features near the Fermi surface (well defined even with disorder) that change to simple commensurate SRO with (un)filling of these states. In conclusion, our results reveal how complexity and competing electronic effects controlmore » ordering in these alloys.« less

Fish-derived nutrient hotspots shape coral reef benthic communities.

PubMed

Shantz, Andrew A; Ladd, Mark C; Schrack, Elizabeth; Burkepile, Deron E

2015-12-01

Animal-derived nutrients play an important role in structuring nutrient regimes within and between ecosystems. When animals undergo repetitive, aggregating behavior through time, they can create nutrient hotspots where rates of biogeochemical activity are higher than those found in the surrounding environment. In turn, these hotspots can influence ecosystem processes and community structure. We examined the potential for reef fishes from the family Haemulidae (grunts) to create nutrient hotspots and the potential impact of these hotspots on reef communities. To do so, we tracked the schooling locations of diurnally migrating grunts, which shelter at reef sites during the day but forage off reef each night, and measured the impact of these fish schools on benthic communities. We found that grunt schools showed a high degree of site fidelity, repeatedly returning to the same coral heads. These aggregations created nutrient hotspots around coral heads where nitrogen and phosphorus delivery was roughly 10 and 7 times the respective rates of delivery to structurally similar sites that lacked schools of these fishes. In turn, grazing rates of herbivorous fishes at grunt-derived hotspots were approximately 3 times those of sites where grunts were rare. These differences in nutrient delivery and grazing led to distinct benthic communities with higher cover of crustose coralline algae and less total algal abundance at grunt aggregation sites. Importantly, coral growth was roughly 1.5 times greater at grunt hotspots, likely due to the important nutrient subsidy. Our results suggest that schooling reef fish and their nutrient subsidies play an important role in mediating community structure on coral reefs and that overfishing may have important negative consequences on ecosystem functions. As such, management strategies must consider mesopredatory fishes in addition to current protection often offered to herbivores and top-tier predators. Furthermore, our results suggest that restoration strategies may benefit from focusing on providing structure for aggregating fishes on reefs with low topographic complexity or focusing the restoration of nursery raised corals around existing nutrient hotspots.

Velocity Structure Determination Through Seismic Waveform Modeling and Time Deviations

NASA Astrophysics Data System (ADS)

Savage, B.; Zhu, L.; Tan, Y.; Helmberger, D. V.

2001-12-01

Through the use of seismic waveforms recorded by TriNet, a dataset of earthquake focal mechanisms and deviations (time shifts) relative to a standard model facilitates the investigation of the crust and uppermost mantle of southern California. The CAP method of focal mechanism determination, in use by TriNet on a routine basis, provides time shifts for surface waves and Pnl arrivals independently relative to the reference model. These shifts serve as initial data for calibration of local and regional seismic paths. Time shifts from the CAP method are derived by splitting the Pnl section of the waveform, the first arriving Pn to just before the arrival of the S wave, from the much slower surface waves then cross-correlating the data with synthetic waveforms computed from a standard model. Surface waves interact with the entire crust, but the upper crust causes the greatest effect. Whereas, Pnl arrivals sample the deeper crust, upper mantle, and source region. This natural division separates the upper from lower crust for regional calibration and structural modeling and allows 3-D velocity maps to be created using the resulting time shifts. Further examination of Pnl and other arrivals which interact with the Moho illuminate the complex nature of this boundary. Initial attempts at using the first 10 seconds of the Pnl section to determine upper most mantle structure have proven insightful. Two large earthquakes north of southern California in Nevada and Mammoth Lakes, CA allow the creation of record sections from 200 to 600 km. As the paths swing from east to west across southern California, simple 1-D models turn into complex structure, dramatically changing the waveform character. Using finite difference models to explain the structure, we determine that a low velocity zone is present at the base of the crust and extends to 100 km in depth. Velocity variations of 5 percent of the mantle in combination with steeply sloping edges produces complex waveform variations. Characteristics of this complex propagation appear from the southern Sierra Nevada Mountains, in the west, to Death Valley in the east. The structure does not cross the Garlock fault to the south, but we are unsure of the structures northern extent.

An electrostatic Particle-In-Cell code on multi-block structured meshes

NASA Astrophysics Data System (ADS)

Meierbachtol, Collin S.; Svyatskiy, Daniil; Delzanno, Gian Luca; Vernon, Louis J.; Moulton, J. David

2017-12-01

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. Despite the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where an arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma-material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. Compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.

An electrostatic Particle-In-Cell code on multi-block structured meshes

DOE PAGES

Meierbachtol, Collin S.; Svyatskiy, Daniil; Delzanno, Gian Luca; ...

2017-09-14

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. In spite of the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where anmore » arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma–material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. And compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.« less

Applications of nuclear magnetic resonance spectroscopy for the understanding of enantiomer separation mechanisms in capillary electrophoresis.

PubMed

Salgado, Antonio; Chankvetadze, Bezhan

2016-10-07

This review deals with the applications of nuclear magnetic resonance (NMR) spectroscopy to understand the mechanisms of chiral separation in capillary electrophoresis (CE). It is accepted that changes observed in the separation process, including the reversal of enantiomer migration order (EMO), can be caused by subtle modifications in the molecular recognition mechanisms between enantiomer and chiral selector. These modifications may imply minor structural differences in those selector-selectand complexes that arise from the above mentioned interactions. Therefore, it is mandatory to understand the fine intermolecular interactions between analytes and chiral selectors. In other words, it is necessary to know in detail the structures of the complexes formed by the enantiomer (selectand) and the selector. Any differences in the structures of these complexes arising from either enantiomer should be detected, so that enantiomeric bias in the separation process could be explained. As to the nature of these interactions, those have been extensively reviewed, and it is not intended to be discussed here. These interactions contemplate ionic, ion-dipole and dipole-dipole interactions, hydrogen bonding, van der Waals forces, π-π stacking, steric and hydrophobic interactions. The main subject of this review is to describe how NMR spectroscopy helps to gain insight into the non-covalent intermolecular interactions between selector and selectand that lead to enantiomer separation by CE. Examples in which diastereomeric species are created by covalent (irreversible) derivatization will not be considered here. This review is structured upon the different structural classes of chiral selectors employed in CE, in which NMR spectroscopy has made substantial contributions to rationalize the observed enantioseparations. Cases in which other techniques complement NMR spectroscopic data are also mentioned. Copyright © 2016 Elsevier B.V. All rights reserved.

An electrostatic Particle-In-Cell code on multi-block structured meshes

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

Meierbachtol, Collin S.; Svyatskiy, Daniil; Delzanno, Gian Luca

We present an electrostatic Particle-In-Cell (PIC) code on multi-block, locally structured, curvilinear meshes called Curvilinear PIC (CPIC). Multi-block meshes are essential to capture complex geometries accurately and with good mesh quality, something that would not be possible with single-block structured meshes that are often used in PIC and for which CPIC was initially developed. In spite of the structured nature of the individual blocks, multi-block meshes resemble unstructured meshes in a global sense and introduce several new challenges, such as the presence of discontinuities in the mesh properties and coordinate orientation changes across adjacent blocks, and polyjunction points where anmore » arbitrary number of blocks meet. In CPIC, these challenges have been met by an approach that features: (1) a curvilinear formulation of the PIC method: each mesh block is mapped from the physical space, where the mesh is curvilinear and arbitrarily distorted, to the logical space, where the mesh is uniform and Cartesian on the unit cube; (2) a mimetic discretization of Poisson's equation suitable for multi-block meshes; and (3) a hybrid (logical-space position/physical-space velocity), asynchronous particle mover that mitigates the performance degradation created by the necessity to track particles as they move across blocks. The numerical accuracy of CPIC was verified using two standard plasma–material interaction tests, which demonstrate good agreement with the corresponding analytic solutions. And compared to PIC codes on unstructured meshes, which have also been used for their flexibility in handling complex geometries but whose performance suffers from issues associated with data locality and indirect data access patterns, PIC codes on multi-block structured meshes may offer the best compromise for capturing complex geometries while also maintaining solution accuracy and computational efficiency.« less

Sequence-Dependent Structure/Function Relationships of Catalytic Peptide-Enabled Gold Nanoparticles Generated under Ambient Synthetic Conditions.

PubMed

Bedford, Nicholas M; Hughes, Zak E; Tang, Zhenghua; Li, Yue; Briggs, Beverly D; Ren, Yang; Swihart, Mark T; Petkov, Valeri G; Naik, Rajesh R; Knecht, Marc R; Walsh, Tiffany R

2016-01-20

Peptide-enabled nanoparticle (NP) synthesis routes can create and/or assemble functional nanomaterials under environmentally friendly conditions, with properties dictated by complex interactions at the biotic/abiotic interface. Manipulation of this interface through sequence modification can provide the capability for material properties to be tailored to create enhanced materials for energy, catalysis, and sensing applications. Fully realizing the potential of these materials requires a comprehensive understanding of sequence-dependent structure/function relationships that is presently lacking. In this work, the atomic-scale structures of a series of peptide-capped Au NPs are determined using a combination of atomic pair distribution function analysis of high-energy X-ray diffraction data and advanced molecular dynamics (MD) simulations. The Au NPs produced with different peptide sequences exhibit varying degrees of catalytic activity for the exemplar reaction 4-nitrophenol reduction. The experimentally derived atomic-scale NP configurations reveal sequence-dependent differences in structural order at the NP surface. Replica exchange with solute-tempering MD simulations are then used to predict the morphology of the peptide overlayer on these Au NPs and identify factors determining the structure/catalytic properties relationship. We show that the amount of exposed Au surface, the underlying surface structural disorder, and the interaction strength of the peptide with the Au surface all influence catalytic performance. A simplified computational prediction of catalytic performance is developed that can potentially serve as a screening tool for future studies. Our approach provides a platform for broadening the analysis of catalytic peptide-enabled metallic NP systems, potentially allowing for the development of rational design rules for property enhancement.

Using Powder Cored Tubular Wire Technology to Enhance Electron Beam Freeform Fabricated Structures

NASA Technical Reports Server (NTRS)

Gonzales, Devon; Liu, Stephen; Domack, Marcia; Hafley, Robert

2016-01-01

Electron Beam Freeform Fabrication (EBF3) is an additive manufacturing technique, developed at NASA Langley Research Center, capable of fabricating large scale aerospace parts. Advantages of using EBF3 as opposed to conventional manufacturing methods include, decreased design-to-product time, decreased wasted material, and the ability to adapt controls to produce geometrically complex parts with properties comparable to wrought products. However, to fully exploit the potential of the EBF3 process development of materials tailored for the process is required. Powder cored tubular wire (PCTW) technology was used to modify Ti-6Al-4V and Al 6061 feedstock to enhance alloy content, refine grain size, and create a metal matrix composite in the as-solidified structures, respectively.

Operational use of Landsat data for timber inventory

NASA Technical Reports Server (NTRS)

Price, Curtis V.; Bowlin, Harry L.

1987-01-01

Landsat TM data, digital elevation model (DEM) data, and field observations were used to generate a timber type/structure and land-cover strata map of the Sequoia National Forest in California, U.S. and to create a classification data set. The spectral classes were identified as 32 information classes of land cover or timber type and structure. DEM data were used for the determination of major timber specie types by topographic regions of natural occurrence. The results suggest that, for inventories over large areas, traditional per-pixel classifiers are not appropriate for TM-resolution data sets over spatially complex regions such as forest lands; either resolution must be degraded, or more context-dependent classifiers, such as the ECHO classifier described by Landgrebe (1979), must be used.

DROPWISE CONDENSATION ON MICRO- AND NANOSTRUCTURED SURFACES

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

Enright, R; Miljkovic, N; Alvarado, JL

In this review we cover recent developments in the area of surface-enhanced dropwise condensation against the background of earlier work. The development of fabrication techniques to create surface structures at the micro-and nanoscale using both bottom-up and top-down approaches has led to increased study of complex interfacial phenomena. In the heat transfer community, researchers have been extensively exploring the use of advanced surface structuring techniques to enhance phase-change heat transfer processes. In particular, the field of vapor-to-liquid condensation and especially that of water condensation has experienced a renaissance due to the promise of further optimizing this process at the micro-andmore » nanoscale by exploiting advances in surface engineering developed over the last several decades.« less

Conifer ovulate cones accumulate pollen principally by simple impaction.

PubMed

Cresswell, James E; Henning, Kevin; Pennel, Christophe; Lahoubi, Mohamed; Patrick, Michael A; Young, Phillipe G; Tabor, Gavin R

2007-11-13

In many pine species (Family Pinaceae), ovulate cones structurally resemble a turbine, which has been widely interpreted as an adaptation for improving pollination by producing complex aerodynamic effects. We tested the turbine interpretation by quantifying patterns of pollen accumulation on ovulate cones in a wind tunnel and by using simulation models based on computational fluid dynamics. We used computer-aided design and computed tomography to create computational fluid dynamics model cones. We studied three species: Pinus radiata, Pinus sylvestris, and Cedrus libani. Irrespective of the approach or species studied, we found no evidence that turbine-like aerodynamics made a significant contribution to pollen accumulation, which instead occurred primarily by simple impaction. Consequently, we suggest alternative adaptive interpretations for the structure of ovulate cones.

Conifer ovulate cones accumulate pollen principally by simple impaction

PubMed Central

Cresswell, James E.; Henning, Kevin; Pennel, Christophe; Lahoubi, Mohamed; Patrick, Michael A.; Young, Phillipe G.; Tabor, Gavin R.

2007-01-01

In many pine species (Family Pinaceae), ovulate cones structurally resemble a turbine, which has been widely interpreted as an adaptation for improving pollination by producing complex aerodynamic effects. We tested the turbine interpretation by quantifying patterns of pollen accumulation on ovulate cones in a wind tunnel and by using simulation models based on computational fluid dynamics. We used computer-aided design and computed tomography to create computational fluid dynamics model cones. We studied three species: Pinus radiata, Pinus sylvestris, and Cedrus libani. Irrespective of the approach or species studied, we found no evidence that turbine-like aerodynamics made a significant contribution to pollen accumulation, which instead occurred primarily by simple impaction. Consequently, we suggest alternative adaptive interpretations for the structure of ovulate cones. PMID:17986613

DNA rendering of polyhedral meshes at the nanoscale

NASA Astrophysics Data System (ADS)

Benson, Erik; Mohammed, Abdulmelik; Gardell, Johan; Masich, Sergej; Czeizler, Eugen; Orponen, Pekka; Högberg, Björn

2015-07-01

It was suggested more than thirty years ago that Watson-Crick base pairing might be used for the rational design of nanometre-scale structures from nucleic acids. Since then, and especially since the introduction of the origami technique, DNA nanotechnology has enabled increasingly more complex structures. But although general approaches for creating DNA origami polygonal meshes and design software are available, there are still important constraints arising from DNA geometry and sense/antisense pairing, necessitating some manual adjustment during the design process. Here we present a general method of folding arbitrary polygonal digital meshes in DNA that readily produces structures that would be very difficult to realize using previous approaches. The design process is highly automated, using a routeing algorithm based on graph theory and a relaxation simulation that traces scaffold strands through the target structures. Moreover, unlike conventional origami designs built from close-packed helices, our structures have a more open conformation with one helix per edge and are therefore stable under the ionic conditions usually used in biological assays.

DNA rendering of polyhedral meshes at the nanoscale.

PubMed

Benson, Erik; Mohammed, Abdulmelik; Gardell, Johan; Masich, Sergej; Czeizler, Eugen; Orponen, Pekka; Högberg, Björn

2015-07-23

It was suggested more than thirty years ago that Watson-Crick base pairing might be used for the rational design of nanometre-scale structures from nucleic acids. Since then, and especially since the introduction of the origami technique, DNA nanotechnology has enabled increasingly more complex structures. But although general approaches for creating DNA origami polygonal meshes and design software are available, there are still important constraints arising from DNA geometry and sense/antisense pairing, necessitating some manual adjustment during the design process. Here we present a general method of folding arbitrary polygonal digital meshes in DNA that readily produces structures that would be very difficult to realize using previous approaches. The design process is highly automated, using a routeing algorithm based on graph theory and a relaxation simulation that traces scaffold strands through the target structures. Moreover, unlike conventional origami designs built from close-packed helices, our structures have a more open conformation with one helix per edge and are therefore stable under the ionic conditions usually used in biological assays.

Color from hierarchy: Diverse optical properties of micron-sized spherical colloidal assemblies.

PubMed

Vogel, Nicolas; Utech, Stefanie; England, Grant T; Shirman, Tanya; Phillips, Katherine R; Koay, Natalie; Burgess, Ian B; Kolle, Mathias; Weitz, David A; Aizenberg, Joanna

2015-09-01

Materials in nature are characterized by structural order over multiple length scales have evolved for maximum performance and multifunctionality, and are often produced by self-assembly processes. A striking example of this design principle is structural coloration, where interference, diffraction, and absorption effects result in vivid colors. Mimicking this emergence of complex effects from simple building blocks is a key challenge for man-made materials. Here, we show that a simple confined self-assembly process leads to a complex hierarchical geometry that displays a variety of optical effects. Colloidal crystallization in an emulsion droplet creates micron-sized superstructures, termed photonic balls. The curvature imposed by the emulsion droplet leads to frustrated crystallization. We observe spherical colloidal crystals with ordered, crystalline layers and a disordered core. This geometry produces multiple optical effects. The ordered layers give rise to structural color from Bragg diffraction with limited angular dependence and unusual transmission due to the curved nature of the individual crystals. The disordered core contributes nonresonant scattering that induces a macroscopically whitish appearance, which we mitigate by incorporating absorbing gold nanoparticles that suppress scattering and macroscopically purify the color. With increasing size of the constituent colloidal particles, grating diffraction effects dominate, which result from order along the crystal's curved surface and induce a vivid polychromatic appearance. The control of multiple optical effects induced by the hierarchical morphology in photonic balls paves the way to use them as building blocks for complex optical assemblies--potentially as more efficient mimics of structural color as it occurs in nature.

Deuterium Labeling Together with Contrast Variation Small-angle Neutron Scattering Suggests How Skp Captures and Releases Unfolded Outer Membrane Proteins

PubMed Central

Zaccai, Nathan R.; Sandlin, Clifford W.; Hoopes, James T.; Curtis, Joseph E.; Fleming, Patrick J.; Fleming, Karen G.; Krueger, Susan

2016-01-01

In gram-negative bacteria, the chaperone protein Skp forms specific and stable complexes with membrane proteins while they are transported across the periplasm to the outer membrane. The jellyfish-like architecture of Skp is similar to the eukaryotic and archeal prefoldins and the mitochondrial Tim chaperones, that is α-helical ‘tentacles’ extend from a β-strand ‘body’ to create an internal cavity. Contrast variation small-angle neutron scattering (SANS) experiments on Skp alone in solution and bound in two different complexes to unfolded outer membrane proteins (uOMPs), OmpA and OmpW, demonstrate that the helical tentacles of Skp bind their substrate in a clamp-like mechanism in a conformation similar to that previously observed in the apo crystal structure of Skp. Deuteration of the uOMP component combined with contrast variation analysis allowed the shapes of Skp and uOMP as well as the location of uOMP with respect to Skp to be determined in both complexes. This represents unique information that could not be obtained without deuterium labeling of the uOMPs. The data yield the first direct structural evidence that the α-helical Skp tentacles move closer together on binding its substrate and that the structure of Skp is different when binding different uOMPs. This work presents, by example, a tutorial on performing SANS experiments using both deuterium labeling and contrast variation, including SANS theory, sample preparation, data collection, sample quality validation, data analysis and structure modeling. PMID:26791979

Deuterium Labeling Together with Contrast Variation Small-Angle Neutron Scattering Suggests How Skp Captures and Releases Unfolded Outer Membrane Proteins.

PubMed

Zaccai, Nathan R; Sandlin, Clifford W; Hoopes, James T; Curtis, Joseph E; Fleming, Patrick J; Fleming, Karen G; Krueger, Susan

2016-01-01

In Gram-negative bacteria, the chaperone protein Skp forms specific and stable complexes with membrane proteins while they are transported across the periplasm to the outer membrane. The jellyfish-like architecture of Skp is similar to the eukaryotic and archaeal prefoldins and the mitochondrial Tim chaperones, that is the α-helical "tentacles" extend from a β-strand "body" to create an internal cavity. Contrast variation small-angle neutron scattering (SANS) experiments on Skp alone in solution and bound in two different complexes to unfolded outer membrane proteins (uOMPs), OmpA and OmpW, demonstrate that the helical tentacles of Skp bind their substrate in a clamp-like mechanism in a conformation similar to that previously observed in the apo crystal structure of Skp. Deuteration of the uOMP component combined with contrast variation analysis allowed the shapes of Skp and uOMP as well as the location of uOMP with respect to Skp to be determined in both complexes. This represents unique information that could not be obtained without deuterium labeling of the uOMPs. The data yield the first direct structural evidence that the α-helical Skp tentacles move closer together on binding its substrate and that the structure of Skp is different when binding different uOMPs. This work presents, by example, a tutorial on performing SANS experiments using both deuterium labeling and contrast variation, including SANS theory, sample preparation, data collection, sample quality validation, data analysis, and structure modeling. © 2016 Elsevier Inc. All rights reserved.

Color from hierarchy: Diverse optical properties of micron-sized spherical colloidal assemblies

PubMed Central

Vogel, Nicolas; Utech, Stefanie; England, Grant T.; Shirman, Tanya; Phillips, Katherine R.; Koay, Natalie; Burgess, Ian B.; Kolle, Mathias; Weitz, David A.; Aizenberg, Joanna

2015-01-01

Materials in nature are characterized by structural order over multiple length scales have evolved for maximum performance and multifunctionality, and are often produced by self-assembly processes. A striking example of this design principle is structural coloration, where interference, diffraction, and absorption effects result in vivid colors. Mimicking this emergence of complex effects from simple building blocks is a key challenge for man-made materials. Here, we show that a simple confined self-assembly process leads to a complex hierarchical geometry that displays a variety of optical effects. Colloidal crystallization in an emulsion droplet creates micron-sized superstructures, termed photonic balls. The curvature imposed by the emulsion droplet leads to frustrated crystallization. We observe spherical colloidal crystals with ordered, crystalline layers and a disordered core. This geometry produces multiple optical effects. The ordered layers give rise to structural color from Bragg diffraction with limited angular dependence and unusual transmission due to the curved nature of the individual crystals. The disordered core contributes nonresonant scattering that induces a macroscopically whitish appearance, which we mitigate by incorporating absorbing gold nanoparticles that suppress scattering and macroscopically purify the color. With increasing size of the constituent colloidal particles, grating diffraction effects dominate, which result from order along the crystal’s curved surface and induce a vivid polychromatic appearance. The control of multiple optical effects induced by the hierarchical morphology in photonic balls paves the way to use them as building blocks for complex optical assemblies—potentially as more efficient mimics of structural color as it occurs in nature. PMID:26290583

GRASP/Ada 95: Reverse Engineering Tools for Ada

NASA Technical Reports Server (NTRS)

Cross, James H., II

1996-01-01

The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) has successfully created and prototyped an algorithmic level graphical representation for Ada software, the Control Structure Diagram (CSD), and a new visualization for a fine-grained complexity metric called the Complexity Profile Graph (CPG). By synchronizing the CSD and the CPG, the CSD view of control structure, nesting, and source code is directly linked to the corresponding visualization of statement level complexity in the CPG. GRASP has been integrated with GNAT, the GNU Ada 95 Translator to provide a comprehensive graphical user interface and development environment for Ada 95. The user may view, edit, print, and compile source code as a CSD with no discernible addition to storage or computational overhead. The primary impetus for creation of the CSD was to improve the comprehension efficiency of Ada software and, as a result, improve reliability and reduce costs. The emphasis has been on the automatic generation of the CSD from Ada 95 source code to support reverse engineering and maintenance. The CSD has the potential to replace traditional prettyprinted Ada source code. The current update has focused on the design and implementation of a new Motif compliant user interface, and a new CSD generator consisting of a tagger and renderer. The Complexity Profile Graph (CPG) is based on a set of functions that describes the context, content, and the scaling for complexity on a statement by statement basis. When combined graphicafly, the result is a composite profile of complexity for the program unit. Ongoing research includes the development and refinement of the associated functions, and the development of the CPG generator prototype. The current Version 5.0 prototype provides the capability for the user to generate CSDs and CPGs from Ada 95 source code in a reverse engineering as well as forward engineering mode with a level of flexibility suitable for practical application. This report provides an overview of the GRASP/Ada project with an emphasis on the current update.

Scaffolding Learning from Informational Texts in the Intervention Setting

ERIC Educational Resources Information Center

Bergeson, Kristi Tamte

2016-01-01

The act of creating meaning with texts is complex, and this complexity creates unclear views of instruction in schools and even greater perplexity in knowing how to instruct students who may be struggling in this area of their schoolwork. Comprehension is often measured in schools as a product and an outcome, making it difficult to understand why…

Structured Head and Neck CT Angiography Reporting Reduces Resident Revision Rates.

PubMed

Johnson, Tucker F; Brinjikji, Waleed; Doolittle, Derrick A; Nagelschneider, Alex A; Welch, Brian T; Kotsenas, Amy L

2018-04-12

This resident-driven quality improvement project was undertaken to assess the effectiveness of structured reporting to reduce revision rates for afterhours reports dictated by residents. The first part of the study assessed baseline revision rates for head and neck CT angiography (CTA) examinations dictated by residents during afterhours call. A structured report was subsequently created based on templates on the RSNA informatics reporting website and critical findings that should be assessed for on all CTA examinations. The template was made available to residents through the speech recognition software for all head and neck CTA examinations for a duration of 2 months. Report revision rates were then compared with and without use of the structured template. The structured template was found to reduce revision rates by approximately 50% with 10/41 unstructured reports revised and 2/17 structured reports revised. We believe that structured reporting can help reduce reporting errors, particularly in term of typographical errors, train residents to evaluate complex examinations in a systematic fashion, and assist them in recalling critical findings on these examinations. Copyright © 2018 Elsevier Inc. All rights reserved.

Tectonic context of the penetrative fracture system origin in the Early Paleozoic shale complex (Baltic Basin, Poland/Sweden).

NASA Astrophysics Data System (ADS)

Jarosiński, Marek; Gluszynski, Andrzej; Bobek, Kinga; Dyrka, Ireneusz

2017-04-01

Characterization of natural fracture and fault pattern play significant role for reservoir stimulation design and evaluation of its results. Having structural observations limited to immediate borehole surrounding it is a common need to build up a fracture model of reservoir in a range of stimulation reservoir volume or even beyond. To do this we need both a 3D seismic model and a consistent concept of the regional tectonic evolution. We present the result of integrated tectonic study in several deep boreholes target the Lower Paleozoic shale complex of Baltic Basin (BB), combined with analysis of 3D seismic survey and outcrop screening in Scania (Swedish part of the BB). During deposition of shale complex in the Ordovician and Silurian the research area was located 200-300 km away from the continental margin of Baltica involved in the Caledonian collision with the Eastern Avalonia. This distance allowed the shale complex to avoid significant tectonic deformation. Regional seismic cross section reveals the general pattern of the BB infill characteristic for the foreland basin underwent post-collisional isostatic rebound. Due to stress changes in collisional context the shale complex was cross-cut by steep, mostly inverse faults trending NW-SE and NE-SW. The fault zones oriented NW-SE are associated with an array of en echelon faults characteristic for strike-slip displacement. In our interpretation, these faults of Silurian (Wenlock) age create pattern of the regional pop-up structure, which is simultaneously involved in the plate flexure extension. Seismic attributes (e.g. curvature or ant tracking) highlight lineaments which mostly mimic the faults orientation. However, attributes show also some artefacts that come from regular array of seismic sources and receivers, which mimic the orthogonal joint system. Structural observations on borehole core lead us to conclusion that regular, orthogonal fracture system developed after maximum burial of the complex, triggered by mechanism of natural hydraulic fracturing due to hydrocarbon generation. These fractures create veins filled with calcite that growth was controlled by mechanical layering and the TOC content of the shale complex. The main joint fracture pattern is stable across at least 300 hundred kilometers, from the Polish to Swedish portion of Baltic Basin. Therefore a major tectonic event is expected to govern its origin. The Late Carboniferous thin-skinned compression exerted at the edge of the East European Craton, is preferred tectonic fracture triggering factor. This age of jointing is confirmed by the strike of principal joint set characteristic for Variscan compression. In addition, principal joint system is sensitive (=younger) to a presence of the Caledonian-age faults in Pomerania but insensitive (=older) to the Mesozoic faults in Scania. Above genetic considerations should be taken into account while building the self-consistent discrete fracture network of faults and fractures for the purpose of shale reservoir stimulation.

Active control of complex, multicomponent self-assembly processes

NASA Astrophysics Data System (ADS)

Schulman, Rebecca

The kinetics of many complex biological self-assembly processes such as cytoskeletal assembly are precisely controlled by cells. Spatiotemporal control over rates of filament nucleation, growth and disassembly determine how self-assembly occurs and how the assembled form changes over time. These reaction rates can be manipulated by changing the concentrations of the components needed for assembly by activating or deactivating them. I will describe how we can use these principles to design driven self-assembly processes in which we assemble and disassemble multiple types of components to create micron-scale networks of semiflexible filaments assembled from DNA. The same set of primitive components can be assembled into many different, structures depending on the concentrations of different components and how designed, DNA-based chemical reaction networks manipulate these concentrations over time. These chemical reaction networks can in turn interpret environmental stimuli to direct complex, multistage response. Such a system is a laboratory for understanding complex active material behaviors, such as metamorphosis, self-healing or adaptation to the environment that are ubiquitous in biological systems but difficult to quantitatively characterize or engineer.

Electrostatics Explains the Position-Dependent Effect of G⋅U Wobble Base Pairs on the Affinity of RNA Kissing Complexes.

PubMed

Abi-Ghanem, Josephine; Rabin, Clémence; Porrini, Massimiliano; Dausse, Eric; Toulmé, Jean-Jacques; Gabelica, Valérie

2017-10-06

In the RNA realm, non-Watson-Crick base pairs are abundant and can affect both the RNA 3D structure and its function. Here, we investigated the formation of RNA kissing complexes in which the loop-loop interaction is modulated by non-Watson-Crick pairs. Mass spectrometry, surface plasmon resonance, and UV-melting experiments show that the G⋅U wobble base pair favors kissing complex formation only when placed at specific positions. We tried to rationalize this effect by molecular modeling, including molecular mechanics Poisson-Boltzmann surface area (MMPBSA) thermodynamics calculations and PBSA calculations of the electrostatic potential surfaces. Modeling reveals that the G⋅U stabilization is due to a specific electrostatic environment defined by the base pairs of the entire loop-loop region. The loop is not symmetric, and therefore the identity and position of each base pair matters. Predicting and visualizing the electrostatic environment created by a given sequence can help to design specific kissing complexes with high affinity, for potential therapeutic, nanotechnology or analytical applications. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Orangutan pantomime: elaborating the message

PubMed Central

Russon, Anne; Andrews, Kristin

2011-01-01

We present an exploratory study of forest-living orangutan pantomiming, i.e. gesturing in which they act out their meaning, focusing on its occurrence, communicative functions, and complexities. Studies show that captive great apes may elaborate messages if communication fails, and isolated reports suggest that great apes occasionally pantomime. We predicted forest-living orangutans would pantomime spontaneously to communicate, especially to elaborate after communication failures. Mining existing databases on free-ranging rehabilitant orangutans' behaviour identified 18 salient pantomimes. These pantomimes most often functioned as elaborations of failed requests, but also as deceptions and declaratives. Complexities identified include multimodality, re-enactments of past events and several features of language (productivity, compositionality, systematicity). These findings confirm that free-ranging rehabilitant orangutans pantomime and use pantomime to elaborate on their messages. Further, they use pantomime for multiple functions and create complex pantomimes that can express propositionally structured content. Thus, orangutan pantomime serves as a medium for communication, not a particular function. Mining cases of complex great ape communication originally reported in functional terms may then yield more evidence of pantomime. PMID:20702451

A system for rapid prototyping of hearts with congenital malformations based on the medical imaging interaction toolkit (MITK)

NASA Astrophysics Data System (ADS)

Wolf, Ivo; Böttger, Thomas; Rietdorf, Urte; Maleike, Daniel; Greil, Gerald; Sieverding, Ludger; Miller, Stephan; Mottl-Link, Sibylle; Meinzer, Hans-Peter

2006-03-01

Precise knowledge of the individual cardiac anatomy is essential for diagnosis and treatment of congenital heart disease. Complex malformations of the heart can best be comprehended not from images but from anatomic specimens. Physical models can be created from data using rapid prototyping techniques, e.g., lasersintering or 3D-printing. We have developed a system for obtaining data that show the relevant cardiac anatomy from high-resolution CT/MR images and are suitable for rapid prototyping. The challenge is to preserve all relevant details unaltered in the produced models. The main anatomical structures of interest are the four heart cavities (atria, ventricles), the valves and the septum separating the cavities, and the great vessels. These can be shown either by reproducing the morphology itself or by producing a model of the blood-pool, thus creating a negative of the morphology. Algorithmically the key issue is segmentation. Practically, possibilities allowing the cardiologist or cardiac surgeon to interactively check and correct the segmentation are even more important due to the complex, irregular anatomy and imaging artefacts. The paper presents the algorithmic and interactive processing steps implemented in the system, which is based on the open-source Medical Imaging Interaction Toolkit (MITK, www.mitk.org). It is shown how the principles used in MITK enable to assemble the system from modules (functionalities) developed independently from each other. The system allows to produce models of the heart (and other anatomic structures) of individual patients as well as to reproduce unique specimens from pathology collections for teaching purposes.

Endoscopic skull base training using 3D printed models with pre-existing pathology.

PubMed

Narayanan, Vairavan; Narayanan, Prepageran; Rajagopalan, Raman; Karuppiah, Ravindran; Rahman, Zainal Ariff Abdul; Wormald, Peter-John; Van Hasselt, Charles Andrew; Waran, Vicknes

2015-03-01

Endoscopic base of skull surgery has been growing in acceptance in the recent past due to improvements in visualisation and micro instrumentation as well as the surgical maturing of early endoscopic skull base practitioners. Unfortunately, these demanding procedures have a steep learning curve. A physical simulation that is able to reproduce the complex anatomy of the anterior skull base provides very useful means of learning the necessary skills in a safe and effective environment. This paper aims to assess the ease of learning endoscopic skull base exposure and drilling techniques using an anatomically accurate physical model with a pre-existing pathology (i.e., basilar invagination) created from actual patient data. Five models of a patient with platy-basia and basilar invagination were created from the original MRI and CT imaging data of a patient. The models were used as part of a training workshop for ENT surgeons with varying degrees of experience in endoscopic base of skull surgery, from trainees to experienced consultants. The surgeons were given a list of key steps to achieve in exposing and drilling the skull base using the simulation model. They were then asked to list the level of difficulty of learning these steps using the model. The participants found the models suitable for learning registration, navigation and skull base drilling techniques. All participants also found the deep structures to be accurately represented spatially as confirmed by the navigation system. These models allow structured simulation to be conducted in a workshop environment where surgeons and trainees can practice to perform complex procedures in a controlled fashion under the supervision of experts.