Integrability and Poisson Structures of Three Dimensional Dynamical Systems and Equations of Hydrodynamic Type

NASA Astrophysics Data System (ADS)

Gumral, Hasan

Poisson structure of completely integrable 3 dimensional dynamical systems can be defined in terms of an integrable 1-form. We take advantage of this fact and use the theory of foliations in discussing the geometrical structure underlying complete and partial integrability. We show that the Halphen system can be formulated in terms of a flat SL(2,R)-valued connection and belongs to a non-trivial Godbillon-Vey class. On the other hand, for the Euler top and a special case of 3-species Lotka-Volterra equations which are contained in the Halphen system as limiting cases, this structure degenerates into the form of globally integrable bi-Hamiltonian structures. The globally integrable bi-Hamiltonian case is a linear and the sl_2 structure is a quadratic unfolding of an integrable 1-form in 3 + 1 dimensions. We complete the discussion of the Hamiltonian structure of 2-component equations of hydrodynamic type by presenting the Hamiltonian operators for Euler's equation and a continuum limit of Toda lattice. We present further infinite sequences of conserved quantities for shallow water equations and show that their generalizations by Kodama admit bi-Hamiltonian structure. We present a simple way of constructing the second Hamiltonian operators for N-component equations admitting some scaling properties. The Kodama reduction of the dispersionless-Boussinesq equations and the Lax reduction of the Benney moment equations are shown to be equivalent by a symmetry transformation. They can be cast into the form of a triplet of conservation laws which enable us to recognize a non-trivial scaling symmetry. The resulting bi-Hamiltonian structure generates three infinite sequences of conserved densities.

In silico modeling of the Moniliophthora perniciosa Atg8 protein.

PubMed

Pereira, A C F; Cardoso, T H S; Brendel, M; Pungartnik, C

2013-12-11

Autophagy is defined as an intracellular system of lysosomal degradation in eukaryotic cells, and the genes involved in this process are conserved from yeast to humans. Among these genes, ATG8 encodes a ubiquitin-like protein that is conjugated to a phosphatidylethanolamine (PE) membrane by the ubiquitination system. The Atg8p-PE complex is important in initiating the formation of the autophagosome and thus plays a critical role in autophagy. In silico modeling of Atg8p of Moniliophthora perniciosa revealed its three-dimensional structure and enabled comparison with its Saccharomyces cerevisiae homologue ScAtg8p. Some common and distinct features were observed between these two proteins, including the conservation of residues required to allow the interaction of α-helix1 with the ubiquitin core. However, the electrostatic potential surfaces of these helices differ, implying particular roles in selecting specific binding partners. The proposed structure was validated by the programs PROCHECK 3.4, ANOLEA, and QMEAN, which demonstrated 100% of amino acids located in favorable regions with low total energy. Our results showed that MpAtg8p contains the same functional domains (3 α-helices and 4 β-sheets) and is similar in structure as the ScAtg8p yeast. Both proteins have many conserved sequences in common, and therefore, their proposed three-dimensional models show similar configuration.

Feedback-Based, System-Level Properties of Vertebrate-Microbial Interactions

PubMed Central

Rivas, Ariel L.; Jankowski, Mark D.; Piccinini, Renata; Leitner, Gabriel; Schwarz, Daniel; Anderson, Kevin L.; Fair, Jeanne M.; Hoogesteijn, Almira L.; Wolter, Wilfried; Chaffer, Marcelo; Blum, Shlomo; Were, Tom; Konah, Stephen N.; Kempaiah, Prakash; Ong’echa, John M.; Diesterbeck, Ulrike S.; Pilla, Rachel; Czerny, Claus-Peter; Hittner, James B.; Hyman, James M.; Perkins, Douglas J.

2013-01-01

Background Improved characterization of infectious disease dynamics is required. To that end, three-dimensional (3D) data analysis of feedback-like processes may be considered. Methods To detect infectious disease data patterns, a systems biology (SB) and evolutionary biology (EB) approach was evaluated, which utilizes leukocyte data structures designed to diminish data variability and enhance discrimination. Using data collected from one avian and two mammalian (human and bovine) species infected with viral, parasite, or bacterial agents (both sensitive and resistant to antimicrobials), four data structures were explored: (i) counts or percentages of a single leukocyte type, such as lymphocytes, neutrophils, or macrophages (the classic approach), and three levels of the SB/EB approach, which assessed (ii) 2D, (iii) 3D, and (iv) multi-dimensional (rotating 3D) host-microbial interactions. Results In all studies, no classic data structure discriminated disease-positive (D+, or observations in which a microbe was isolated) from disease-negative (D–, or microbial-negative) groups: D+ and D– data distributions overlapped. In contrast, multi-dimensional analysis of indicators designed to possess desirable features, such as a single line of observations, displayed a continuous, circular data structure, whose abrupt inflections facilitated partitioning into subsets statistically significantly different from one another. In all studies, the 3D, SB/EB approach distinguished three (steady, positive, and negative) feedback phases, in which D– data characterized the steady state phase, and D+ data were found in the positive and negative phases. In humans, spatial patterns revealed false-negative observations and three malaria-positive data classes. In both humans and bovines, methicillin-resistant Staphylococcus aureus (MRSA) infections were discriminated from non-MRSA infections. Conclusions More information can be extracted, from the same data, provided that data are structured, their 3D relationships are considered, and well-conserved (feedback-like) functions are estimated. Patterns emerging from such structures may distinguish well-conserved from recently developed host-microbial interactions. Applications include diagnosis, error detection, and modeling. PMID:23437039

Feedback-based, system-level properties of vertebrate-microbial interactions.

PubMed

Rivas, Ariel L; Jankowski, Mark D; Piccinini, Renata; Leitner, Gabriel; Schwarz, Daniel; Anderson, Kevin L; Fair, Jeanne M; Hoogesteijn, Almira L; Wolter, Wilfried; Chaffer, Marcelo; Blum, Shlomo; Were, Tom; Konah, Stephen N; Kempaiah, Prakash; Ong'echa, John M; Diesterbeck, Ulrike S; Pilla, Rachel; Czerny, Claus-Peter; Hittner, James B; Hyman, James M; Perkins, Douglas J

2013-01-01

Improved characterization of infectious disease dynamics is required. To that end, three-dimensional (3D) data analysis of feedback-like processes may be considered. To detect infectious disease data patterns, a systems biology (SB) and evolutionary biology (EB) approach was evaluated, which utilizes leukocyte data structures designed to diminish data variability and enhance discrimination. Using data collected from one avian and two mammalian (human and bovine) species infected with viral, parasite, or bacterial agents (both sensitive and resistant to antimicrobials), four data structures were explored: (i) counts or percentages of a single leukocyte type, such as lymphocytes, neutrophils, or macrophages (the classic approach), and three levels of the SB/EB approach, which assessed (ii) 2D, (iii) 3D, and (iv) multi-dimensional (rotating 3D) host-microbial interactions. In all studies, no classic data structure discriminated disease-positive (D+, or observations in which a microbe was isolated) from disease-negative (D-, or microbial-negative) groups: D+ and D- data distributions overlapped. In contrast, multi-dimensional analysis of indicators designed to possess desirable features, such as a single line of observations, displayed a continuous, circular data structure, whose abrupt inflections facilitated partitioning into subsets statistically significantly different from one another. In all studies, the 3D, SB/EB approach distinguished three (steady, positive, and negative) feedback phases, in which D- data characterized the steady state phase, and D+ data were found in the positive and negative phases. In humans, spatial patterns revealed false-negative observations and three malaria-positive data classes. In both humans and bovines, methicillin-resistant Staphylococcus aureus (MRSA) infections were discriminated from non-MRSA infections. More information can be extracted, from the same data, provided that data are structured, their 3D relationships are considered, and well-conserved (feedback-like) functions are estimated. Patterns emerging from such structures may distinguish well-conserved from recently developed host-microbial interactions. Applications include diagnosis, error detection, and modeling.

Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV

NASA Technical Reports Server (NTRS)

Lim, Kap; Ho, Joseph X.; Keeling, Kim; Gilliland, Gary L.; Ji, Xinhua; Rueker, Florian; Carter, Daniel C.

1994-01-01

The 3-dimensional crystal structure of glutathione S-transferase (GST) of Schistosoma japonicum (Sj) fused with a conserved neutralizing epitope on gp41 (glycoprotein, 41 kDa) of human immunodeficiency virus type 1 (HIV-1) was determined at 2.5 A resolution. The structure of the 3-3 isozyme rat GST of the mu gene class was used as a molecular replacement model. The structure consists of a 4-stranded beta-sheet and 3 alpha-helices in domain 1 and 5 alpha-helices in domain 2. The space group of the Sj GST crystal is P4(sub 3)2(sub 1)2 with unit cell dimensions of a = b = 94.7 A, and c = 58.1 A. The crystal has 1 GST monomer per asymmetric unit, and 2 monomers that form an active dimer are related by crystallographic 2-fold symmetry. In the binding site, the ordered structure of reduced glutathione is observed. The gp41 peptide (Glu-Leu-Asp-Lys-Trp-Ala) fused to the C-terminus of Sj GST forms a loop stabilized by symmetry-related GSTs. The Sj GST structure is compared with previously determined GST structures of mammalian gene classes mu, alpha, and pi. Conserved amino acid residues among the 4 GSTs that are important for hydrophobic and hydrophilic interactions for dimer association and glutathione binding are discussed.

Conserved thioredoxin fold is present in Pisum sativum L. sieve element occlusion-1 protein

PubMed Central

Umate, Pavan; Tuteja, Renu

2010-01-01

Homology-based three-dimensional model for Pisum sativum sieve element occlusion 1 (Ps.SEO1) (forisomes) protein was constructed. A stretch of amino acids (residues 320 to 456) which is well conserved in all known members of forisomes proteins was used to model the 3D structure of Ps.SEO1. The structural prediction was done using Protein Homology/analogY Recognition Engine (PHYRE) web server. Based on studies of local sequence alignment, the thioredoxin-fold containing protein [Structural Classification of Proteins (SCOP) code d1o73a_], a member of the glutathione peroxidase family was selected as a template for modeling the spatial structure of Ps.SEO1. Selection was based on comparison of primary sequence, higher match quality and alignment accuracy. Motif 1 (EVF) is conserved in Ps.SEO1, Vicia faba (Vf.For1) and Medicago truncatula (MT.SEO3); motif 2 (KKED) is well conserved across all forisomes proteins and motif 3 (IGYIGNP) is conserved in Ps.SEO1 and Vf.For1. PMID:20404566

Quantifying forest vertical structure to determine bird habitat quality in the Greenbelt Corridor, Denton, TX

NASA Astrophysics Data System (ADS)

Matsubayashi, Shiho

This study presents the integration of light detection and range (LiDAR) and hyperspectral remote sensing to create a three-dimensional bird habitat map in the Greenbelt Corridor of the Elm Fork of the Trinity River. This map permits to examine the relationship between forest stand structure, landscape heterogeneity, and bird community composition. A biannual bird census was conducted at this site during the breeding seasons of 2009 and 2010. Census data combined with the three-dimensional map suggest that local breeding bird abundance, community structure, and spatial distribution patterns are highly influenced by vertical heterogeneity of vegetation surface. For local breeding birds, vertical heterogeneity of canopy surface within stands, connectivity to adjacent forest patches, largest forest patch index, and habitat (vegetation) types proved to be the most influential factors to determine bird community assemblages. Results also highlight the critical role of secondary forests to increase functional connectivity of forest patches. Overall, three-dimensional habitat descriptions derived from integrated LiDAR and hyperspectral data serve as a powerful bird conservation tool that shows how the distribution of bird species relates to forest composition and structure at various scales.

An initial investigation into methods of computing transonic aerodynamic sensitivity coefficients

NASA Technical Reports Server (NTRS)

Carlson, Leland A.

1994-01-01

The primary accomplishments of the project are as follows: (1) Using the transonic small perturbation equation as a flowfield model, the project demonstrated that the quasi-analytical method could be used to obtain aerodynamic sensitivity coefficients for airfoils at subsonic, transonic, and supersonic conditions for design variables such as Mach number, airfoil thickness, maximum camber, angle of attack, and location of maximum camber. It was established that the quasi-analytical approach was an accurate method for obtaining aerodynamic sensitivity derivatives for airfoils at transonic conditions and usually more efficient than the finite difference approach. (2) The usage of symbolic manipulation software to determine the appropriate expressions and computer coding associated with the quasi-analytical method for sensitivity derivatives was investigated. Using the three dimensional fully conservative full potential flowfield model, it was determined that symbolic manipulation along with a chain rule approach was extremely useful in developing a combined flowfield and quasi-analytical sensitivity derivative code capable of considering a large number of realistic design variables. (3) Using the three dimensional fully conservative full potential flowfield model, the quasi-analytical method was applied to swept wings (i.e. three dimensional) at transonic flow conditions. (4) The incremental iterative technique has been applied to the three dimensional transonic nonlinear small perturbation flowfield formulation, an equivalent plate deflection model, and the associated aerodynamic and structural discipline sensitivity equations; and coupled aeroelastic results for an aspect ratio three wing in transonic flow have been obtained.

The Universally Conserved Prokaryotic GTPases

PubMed Central

Verstraeten, Natalie; Fauvart, Maarten; Versées, Wim; Michiels, Jan

2011-01-01

Summary: Members of the large superclass of P-loop GTPases share a core domain with a conserved three-dimensional structure. In eukaryotes, these proteins are implicated in various crucial cellular processes, including translation, membrane trafficking, cell cycle progression, and membrane signaling. As targets of mutation and toxins, GTPases are involved in the pathogenesis of cancer and infectious diseases. In prokaryotes also, it is hard to overestimate the importance of GTPases in cell physiology. Numerous papers have shed new light on the role of bacterial GTPases in cell cycle regulation, ribosome assembly, the stress response, and other cellular processes. Moreover, bacterial GTPases have been identified as high-potential drug targets. A key paper published over 2 decades ago stated that, “It may never again be possible to capture [GTPases] in a family portrait” (H. R. Bourne, D. A. Sanders, and F. McCormick, Nature 348:125-132, 1990) and indeed, the last 20 years have seen a tremendous increase in publications on the subject. Sequence analysis identified 13 bacterial GTPases that are conserved in at least 75% of all bacterial species. We here provide an overview of these 13 protein subfamilies, covering their cellular functions as well as cellular localization and expression levels, three-dimensional structures, biochemical properties, and gene organization. Conserved roles in eukaryotic homologs will be discussed as well. A comprehensive overview summarizing current knowledge on prokaryotic GTPases will aid in further elucidating the function of these important proteins. PMID:21885683

Three Dimensional Flow and Pressure Patterns in a Single Pocket of a Hydrostatic Journal Bearing

NASA Technical Reports Server (NTRS)

Braun, M. Jack; Dzodzo, Milorad B.

1996-01-01

The flow in a hydrostatic pocket is described by a mathematical model that uses the three dimensional Navier-Stokes equations written in terms of the primary variables, u, v, w, and p. Using a conservative formulation, a finite volume multi-block method is applied through a collocated, body fitted grid. The flow is simulated in a shallow pocket with a depth/length ratio of 0.02. The flow structures obtained and described by the authors in their previous two dimensional models are made visible in their three dimensional aspect for the Couette flow. It has been found that the flow regimes formed central and secondary vortical cells with three dimensional corkscrew-like structures that lead the fluid on an outward bound path in the axial direction of the pocket. The position of the central vortical cell center is at the exit region of the capillary restrictor feedline. It has also been determined that a fluid turn around zone occupies all the upstream space between the floor of the pocket and the runner, thus preventing any flow exit through the upstream port. The corresponding pressure distribution under the shaft presented as well. It was clearly established that for the Couette dominated case the pressure varies significantly in the pocket in the circumferential direction, while its variation is less pronounced axially.

On mass and momentum conservation in the variable-parameter Muskingum method

NASA Astrophysics Data System (ADS)

Reggiani, Paolo; Todini, Ezio; Meißner, Dennis

2016-12-01

In this paper we investigate mass and momentum conservation in one-dimensional routing models. To this end we formulate the conservation equations for a finite-dimensional reach and compute individual terms using three standard Saint-Venant (SV) solvers: SOBEK, HEC-RAS and MIKE11. We also employ two different variable-parameter Muskingum (VPM) formulations: the classical Muskingum-Cunge (MC) and the revised, mass-conservative Muskingum-Cunge-Todini (MCT) approach, whereby geometrical cross sections are treated analytically in both cases. We initially compare the three SV solvers for a straight mild-sloping prismatic channel with geometric cross sections and a synthetic hydrograph as boundary conditions against the analytical MC and MCT solutions. The comparison is substantiated by the fact that in this flow regime the conditions for the parabolic equation model solved by MC and MCT are met. Through this intercomparison we show that all approaches have comparable mass and momentum conservation properties, except the MC. Then we extend the MCT to use natural cross sections for a real irregular river channel forced by an observed triple-peak event and compare the results with SOBEK. The model intercomparison demonstrates that the VPM in the form of MCT can be a computationally efficient, fully mass and momentum conservative approach and therefore constitutes a valid alternative to Saint-Venant based flood wave routing for a wide variety of rivers and channels in the world when downstream boundary conditions or hydraulic structures are non-influential.

DRAGON Grid: A Three-Dimensional Hybrid Grid Generation Code Developed

NASA Technical Reports Server (NTRS)

Liou, Meng-Sing

2000-01-01

Because grid generation can consume 70 percent of the total analysis time for a typical three-dimensional viscous flow simulation for a practical engineering device, payoffs from research and development could reduce costs and increase throughputs considerably. In this study, researchers at the NASA Glenn Research Center at Lewis Field developed a new hybrid grid approach with the advantages of flexibility, high-quality grids suitable for an accurate resolution of viscous regions, and a low memory requirement. These advantages will, in turn, reduce analysis time and increase accuracy. They result from an innovative combination of structured and unstructured grids to represent the geometry and the computation domain. The present approach makes use of the respective strengths of both the structured and unstructured grid methods, while minimizing their weaknesses. First, the Chimera grid generates high-quality, mostly orthogonal meshes around individual components. This process is flexible and can be done easily. Normally, these individual grids are required overlap each other so that the solution on one grid can communicate with another. However, when this communication is carried out via a nonconservative interpolation procedure, a spurious solution can result. Current research is aimed at entirely eliminating this undesired interpolation by directly replacing arbitrary grid overlapping with a nonstructured grid called a DRAGON grid, which uses the same set of conservation laws over the entire region, thus ensuring conservation everywhere. The DRAGON grid is shown for a typical film-cooled turbine vane with 33 holes and 3 plenum compartments. There are structured grids around each geometrical entity and unstructured grids connecting them. In fiscal year 1999, Glenn researchers developed and tested the three-dimensional DRAGON grid-generation tools. A flow solver suitable for the DRAGON grid has been developed, and a series of validation tests are underway.

Evolutionary conservativeness of electric field in the Cu,Zn superoxide dismutase active site. Evidence for co-ordinated mutation of charged amino acid residues.

PubMed

Desideri, A; Falconi, M; Polticelli, F; Bolognesi, M; Djinovic, K; Rotilio, G

1992-01-05

Equipotential lines were calculated, using the Poisson-Boltzmann equation, for six Cu,Zn superoxide dismutases with different protein electric charge and various degrees of sequence homology, namely those from ox, pig, sheep, yeast, and the isoenzymes A and B from the amphibian Xenopus laevis. The three-dimensional structures of the porcine and ovine superoxide dismutases were obtained by molecular modelling reconstruction using the structure of the highly homologous bovine enzyme as a template. The three-dimensional structure of the evolutionary distant yeast Cu,Zn superoxide dismutase was recently resolved by us, while computer-modelled structures are available for X. laevis isoenzymes. The six proteins display large differences in the net protein charge and distribution of electrically charged surface residues but the trend of the equipotential lines in the proximity of the active sites was found to be constant in all cases. These results are in line with the very similar catlytic rate constants experimentally measured for the corresponding enzyme activities. This analysis shows that electrostatic guidance for the enzyme-substrate interaction in Cu,Zn superoxide dismutases is related to a spatial distribution of charges, arranged so as to maintain, in the area surrounding the active sites, an identical electrostatic potential distribution, which is conserved in the evolution of this protein family.

Three-dimensional habitat structure and landscape genetics: a step forward in estimating functional connectivity.

PubMed

Milanesi, P; Holderegger, R; Bollmann, K; Gugerli, F; Zellweger, F

2017-02-01

Estimating connectivity among fragmented habitat patches is crucial for evaluating the functionality of ecological networks. However, current estimates of landscape resistance to animal movement and dispersal lack landscape-level data on local habitat structure. Here, we used a landscape genetics approach to show that high-fidelity habitat structure maps derived from Light Detection and Ranging (LiDAR) data critically improve functional connectivity estimates compared to conventional land cover data. We related pairwise genetic distances of 128 Capercaillie (Tetrao urogallus) genotypes to least-cost path distances at multiple scales derived from land cover data. Resulting β values of linear mixed effects models ranged from 0.372 to 0.495, while those derived from LiDAR ranged from 0.558 to 0.758. The identification and conservation of functional ecological networks suffering from habitat fragmentation and homogenization will thus benefit from the growing availability of detailed and contiguous data on three-dimensional habitat structure and associated habitat quality. © 2016 by the Ecological Society of America.

Crystal Structure of VC0702 at 2.0 angstrom: A Conserved Hypothetical Protein from Vibrio Cholerae

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

Ni, Shuisong; Forouhar, Farhad; Bussiere, Dirksen E.

2006-06-01

VC0702, a conserved hypothetical protein of unknown function from Vibrio cholerae, resides in a putative three-gene operon containing the MbaA gene, which is involved in regulating formation of the extracellular matrix of biofilms in Vibrio cholerae. The VC0702 crystal structure has been determined at 2.0? and refined to Rwork=22.8% and Rfree=26.3%. VC0702 crystallized in an orthorhombic crystal lattice in the C2221 space group with dimensions of a=66.61 ?, b=88.118 ?, and c=118.35 ? with a homodimer in the asymmetric unit. VC0702 belongs to the Pfam DUF84 and COG1986 family of proteins. Sequence conservation within the DUF84 and COG1986 families wasmore » used to identify a conserved patch of surface residues that define a cleft and potential substrate-binding site in VC0702. The three-dimensional structure of VC0702 is similar to that of Mj0226 from Methanococcus janeshii, which has been identified as a novel NTPase. The NTP-binding site in Mj0226 is similarly located in comparison to the conserved patch of surface residues in VC0702. Furthermore, the NTP binds to MJ0226 in a cleft and deep cavity, features that are present in the VC0702 structure as well, suggesting that VC0702 may have a biochemical function involving NTP binding that is associated with a cellular function of regulating biofilm formation in Vibrio cholerae.« less

A 3-dimensional mass conserving element for compressible flows

NASA Technical Reports Server (NTRS)

Fix, G.; Suri, M.

1985-01-01

A variety of finite element schemes has been used in the numerical approximation of compressible flows particularly in underwater acoustics. In many instances instabilities have been generated due to the lack of mass conservation. Two- and three-dimensional elements are developed which avoid these problems.

Three-Dimensional Molecular Modeling of a Diverse Range of SC Clan Serine Proteases

PubMed Central

Laskar, Aparna; Chatterjee, Aniruddha; Chatterjee, Somnath; Rodger, Euan J.

2012-01-01

Serine proteases are involved in a variety of biological processes and are classified into clans sharing structural homology. Although various three-dimensional structures of SC clan proteases have been experimentally determined, they are mostly bacterial and animal proteases, with some from archaea, plants, and fungi, and as yet no structures have been determined for protozoa. To bridge this gap, we have used molecular modeling techniques to investigate the structural properties of different SC clan serine proteases from a diverse range of taxa. Either SWISS-MODEL was used for homology-based structure prediction or the LOOPP server was used for threading-based structure prediction. The predicted models were refined using Insight II and SCRWL and validated against experimental structures. Investigation of secondary structures and electrostatic surface potential was performed using MOLMOL. The structural geometry of the catalytic core shows clear deviations between taxa, but the relative positions of the catalytic triad residues were conserved. Evolutionary divergence was also exhibited by large variation in secondary structure features outside the core, differences in overall amino acid distribution, and unique surface electrostatic potential patterns between species. Encompassing a wide range of taxa, our structural analysis provides an evolutionary perspective on SC clan serine proteases. PMID:23213528

Crystal structure of yeast allantoicase reveals a repeated jelly roll motif.

PubMed

Leulliot, Nicolas; Quevillon-Cheruel, Sophie; Sorel, Isabelle; Graille, Marc; Meyer, Philippe; Liger, Dominique; Blondeau, Karine; Janin, Joël; van Tilbeurgh, Herman

2004-05-28

Allantoicase (EC 3.5.3.4) catalyzes the conversion of allantoate into ureidoglycolate and urea, one of the final steps in the degradation of purines to urea. The mechanism of most enzymes involved in this pathway, which has been known for a long time, is unknown. In this paper we describe the three-dimensional crystal structure of the yeast allantoicase determined at a resolution of 2.6 A by single anomalous diffraction. This constitutes the first structure for an enzyme of this pathway. The structure reveals a repeated jelly roll beta-sheet motif, also present in proteins of unrelated biochemical function. Allantoicase has a hexameric arrangement in the crystal (dimer of trimers). Analysis of the protein sequence against the structural data reveals the presence of two totally conserved surface patches, one on each jelly roll motif. The hexameric packing concentrates these patches into conserved pockets that probably constitute the active site.

Three-dimensional structure of Schistosoma japonicum glutathione S-transferase fused with a six-amino acid conserved neutralizing epitope of gp41 from HIV

NASA Technical Reports Server (NTRS)

Lim, K.; Ho, J. X.; Keeling, K.; Gilliland, G. L.; Ji, X.; Ruker, F.; Carter, D. C.

1994-01-01

The 3-dimensional crystal structure of glutathione S-transferase (GST) of Schistosoma japonicum (Sj) fused with a conserved neutralizing epitope on gp41 (glycoprotein, 41 kDa) of human immunodeficiency virus type 1 (HIV-1) (Muster T et al., 1993, J Virol 67:6642-6647) was determined at 2.5 A resolution. The structure of the 3-3 isozyme rat GST of the mu gene class (Ji X, Zhang P, Armstrong RN, Gilliland GL, 1992, Biochemistry 31:10169-10184) was used as a molecular replacement model. The structure consists of a 4-stranded beta-sheet and 3 alpha-helices in domain 1 and 5 alpha-helices in domain 2. The space group of the Sj GST crystal is P4(3)2(1)2, with unit cell dimensions of a = b = 94.7 A, and c = 58.1 A. The crystal has 1 GST monomer per asymmetric unit, and 2 monomers that form an active dimer are related by crystallographic 2-fold symmetry. In the binding site, the ordered structure of reduced glutathione is observed. The gp41 peptide (Glu-Leu-Asp-Lys-Trp-Ala) fused to the C-terminus of Sj GST forms a loop stabilized by symmetry-related GSTs. The Sj GST structure is compared with previously determined GST structures of mammalian gene classes mu, alpha, and pi. Conserved amino acid residues among the 4 GSTs that are important for hydrophobic and hydrophilic interactions for dimer association and glutathione binding are discussed.

Scop3D: three-dimensional visualization of sequence conservation.

PubMed

Vermeire, Tessa; Vermaere, Stijn; Schepens, Bert; Saelens, Xavier; Van Gucht, Steven; Martens, Lennart; Vandermarliere, Elien

2015-04-01

The integration of a protein's structure with its known sequence variation provides insight on how that protein evolves, for instance in terms of (changing) function or immunogenicity. Yet, collating the corresponding sequence variants into a multiple sequence alignment, calculating each position's conservation, and mapping this information back onto a relevant structure is not straightforward. We therefore built the Sequence Conservation on Protein 3D structure (scop3D) tool to perform these tasks automatically. The output consists of two modified PDB files in which the B-values for each position are replaced by the percentage sequence conservation, or the information entropy for each position, respectively. Furthermore, text files with absolute and relative amino acid occurrences for each position are also provided, along with snapshots of the protein from six distinct directions in space. The visualization provided by scop3D can for instance be used as an aid in vaccine development or to identify antigenic hotspots, which we here demonstrate based on an analysis of the fusion proteins of human respiratory syncytial virus and mumps virus. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Helicity conservation under quantum reconnection of vortex rings.

PubMed

Zuccher, Simone; Ricca, Renzo L

2015-12-01

Here we show that under quantum reconnection, simulated by using the three-dimensional Gross-Pitaevskii equation, self-helicity of a system of two interacting vortex rings remains conserved. By resolving the fine structure of the vortex cores, we demonstrate that the total length of the vortex system reaches a maximum at the reconnection time, while both writhe helicity and twist helicity remain separately unchanged throughout the process. Self-helicity is computed by two independent methods, and topological information is based on the extraction and analysis of geometric quantities such as writhe, total torsion, and intrinsic twist of the reconnecting vortex rings.

Invasive plants transform the three-dimensional structure of rain forests

PubMed Central

Asner, Gregory P.; Hughes, R. Flint; Vitousek, Peter M.; Knapp, David E.; Kennedy-Bowdoin, Ty; Boardman, Joseph; Martin, Roberta E.; Eastwood, Michael; Green, Robert O.

2008-01-01

Biological invasions contribute to global environmental change, but the dynamics and consequences of most invasions are difficult to assess at regional scales. We deployed an airborne remote sensing system that mapped the location and impacts of five highly invasive plant species across 221,875 ha of Hawaiian ecosystems, identifying four distinct ways that these species transform the three-dimensional (3D) structure of native rain forests. In lowland to montane forests, three invasive tree species replace native midcanopy and understory plants, whereas one understory invader excludes native species at the ground level. A fifth invasive nitrogen-fixing tree, in combination with a midcanopy alien tree, replaces native plants at all canopy levels in lowland forests. We conclude that this diverse array of alien plant species, each representing a different growth form or functional type, is changing the fundamental 3D structure of native Hawaiian rain forests. Our work also demonstrates how an airborne mapping strategy can identify and track the spread of certain invasive plant species, determine ecological consequences of their proliferation, and provide detailed geographic information to conservation and management efforts. PMID:18316720

[Three-dimensional genome organization: a lesson from the Polycomb-Group proteins].

PubMed

Bantignies, Frédéric

2013-01-01

As more and more genomes are being explored and annotated, important features of three-dimensional (3D) genome organization are just being uncovered. In the light of what we know about Polycomb group (PcG) proteins, we will present the latest findings on this topic. The PcG proteins are well-conserved chromatin factors that repress transcription of numerous target genes. They bind the genome at specific sites, forming chromatin domains of associated histone modifications as well as higher-order chromatin structures. These 3D chromatin structures involve the interactions between PcG-bound regulatory regions at short- and long-range distances, and may significantly contribute to PcG function. Recent high throughput "Chromosome Conformation Capture" (3C) analyses have revealed many other higher order structures along the chromatin fiber, partitioning the genomes into well demarcated topological domains. This revealed an unprecedented link between linear epigenetic domains and chromosome architecture, which might be intimately connected to genome function. © Société de Biologie, 2013.

Generation of a three-dimensional ultrastructural model of human respiratory cilia.

PubMed

Burgoyne, Thomas; Dixon, Mellisa; Luther, Pradeep; Hogg, Claire; Shoemark, Amelia

2012-12-01

The ultrastructures of cilia and flagella are highly similar and well conserved through evolution. Consequently, Chlamydomonas is commonly used as a model organism for the study of human respiratory cilia. Since detailed models of Chlamydomonas axonemes were generated using cryoelectron tomography, disparities among some of the ultrastructural features have become apparent when compared with human cilia. Extrapolating information on human disease from the Chlamydomonas model may lead to discrepancies in translational research. This study aimed to establish the first three-dimensional ultrastructural model of human cilia. Tomograms of transverse sections (n = 6) and longitudinal sections (n = 9) of human nasal respiratory cilia were generated from three healthy volunteers. Key features of the cilium were resolved using subatomic averaging, and were measured. For validation of the method, a model of the well characterized structure of Chlamydomonas reinhardtii was simultaneously generated. Data were combined to create a fully quantified three-dimensional reconstruction of human nasal respiratory cilia. We highlight key differences in the axonemal sheath, microtubular doublets, radial spokes, and dynein arms between the two structures. We show a decreased axial periodicity of the radial spokes, inner dynein arms, and central pair protrusions in the human model. We propose that this first human model will provide a basis for research into the function and structure of human respiratory cilia in health and in disease.

Multiparticle collision simulations of two-dimensional one-component plasmas: Anomalous transport and dimensional crossovers

NASA Astrophysics Data System (ADS)

Di Cintio, Pierfrancesco; Livi, Roberto; Lepri, Stefano; Ciraolo, Guido

2017-04-01

By means of hybrid multiparticle collsion-particle-in-cell (MPC-PIC) simulations we study the dynamical scaling of energy and density correlations at equilibrium in moderately coupled two-dimensional (2D) and quasi-one-dimensional (1D) plasmas. We find that the predictions of nonlinear fluctuating hydrodynamics for the structure factors of density and energy fluctuations in 1D systems with three global conservation laws hold true also for 2D systems that are more extended along one of the two spatial dimensions. Moreover, from the analysis of the equilibrium energy correlators and density structure factors of both 1D and 2D neutral plasmas, we find that neglecting the contribution of the fluctuations of the vanishing self-consistent electrostatic fields overestimates the interval of frequencies over which the anomalous transport is observed. Such violations of the expected scaling in the currents correlation are found in different regimes, hindering the observation of the asymptotic scaling predicted by the theory.

Conformational analysis of processivity clamps in solution demonstrates that tertiary structure does not correlate with protein dynamics.

PubMed

Fang, Jing; Nevin, Philip; Kairys, Visvaldas; Venclovas, Česlovas; Engen, John R; Beuning, Penny J

2014-04-08

The relationship between protein sequence, structure, and dynamics has been elusive. Here, we report a comprehensive analysis using an in-solution experimental approach to study how the conservation of tertiary structure correlates with protein dynamics. Hydrogen exchange measurements of eight processivity clamp proteins from different species revealed that, despite highly similar three-dimensional structures, clamp proteins display a wide range of dynamic behavior. Differences were apparent both for structurally similar domains within proteins and for corresponding domains of different proteins. Several of the clamps contained regions that underwent local unfolding with different half-lives. We also observed a conserved pattern of alternating dynamics of the α helices lining the inner pore of the clamps as well as a correlation between dynamics and the number of salt bridges in these α helices. Our observations reveal that tertiary structure and dynamics are not directly correlated and that primary structure plays an important role in dynamics. Copyright © 2014 Elsevier Ltd. All rights reserved.

Development of Three-Dimensional DRAGON Grid Technology

NASA Technical Reports Server (NTRS)

Zheng, Yao; Kiou, Meng-Sing; Civinskas, Kestutis C.

1999-01-01

For a typical three dimensional flow in a practical engineering device, the time spent in grid generation can take 70 percent of the total analysis effort, resulting in a serious bottleneck in the design/analysis cycle. The present research attempts to develop a procedure that can considerably reduce the grid generation effort. The DRAGON grid, as a hybrid grid, is created by means of a Direct Replacement of Arbitrary Grid Overlapping by Nonstructured grid. The DRAGON grid scheme is an adaptation to the Chimera thinking. The Chimera grid is a composite structured grid, composing a set of overlapped structured grids, which are independently generated and body-fitted. The grid is of high quality and amenable for efficient solution schemes. However, the interpolation used in the overlapped region between grids introduces error, especially when a sharp-gradient region is encountered. The DRAGON grid scheme is capable of completely eliminating the interpolation and preserving the conservation property. It maximizes the advantages of the Chimera scheme and adapts the strengths of the unstructured and while at the same time keeping its weaknesses minimal. In the present paper, we describe the progress towards extending the DRAGON grid technology into three dimensions. Essential and programming aspects of the extension, and new challenges for the three-dimensional cases, are addressed.

Conserving and gapless Hartree-Fock-Bogoliubov theory for the three-dimensional dilute Bose gas

NASA Astrophysics Data System (ADS)

Zhang, Ya-Hui; Li, Dingping

2013-11-01

The excitation spectrum for the three-dimensional Bose gas in the Bose-Einstein condensation phase is calculated nonperturbatively with the modified Hartree-Fock-Bogoliubov theory, which is both conserving and gapless. From improved Φ-derivable theory, the diagrams needed to preserve the Ward-Takahashi identity are re-summed in a systematic and nonperturbative way. It is valid up to the critical temperature where the dispersion relation of the low-energy excitation spectrum changes from linear to quadratic. Because including the higher-order fluctuation, the results show significant improvement on the calculation of the shift of critical temperature with other conserving and gapless theories.

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

DOEpatents

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

2014-03-11

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

On the statistical mechanics of the 2D stochastic Euler equation

NASA Astrophysics Data System (ADS)

Bouchet, Freddy; Laurie, Jason; Zaboronski, Oleg

2011-12-01

The dynamics of vortices and large scale structures is qualitatively very different in two dimensional flows compared to its three dimensional counterparts, due to the presence of multiple integrals of motion. These are believed to be responsible for a variety of phenomena observed in Euler flow such as the formation of large scale coherent structures, the existence of meta-stable states and random abrupt changes in the topology of the flow. In this paper we study stochastic dynamics of the finite dimensional approximation of the 2D Euler flow based on Lie algebra su(N) which preserves all integrals of motion. In particular, we exploit rich algebraic structure responsible for the existence of Euler's conservation laws to calculate the invariant measures and explore their properties and also study the approach to equilibrium. Unexpectedly, we find deep connections between equilibrium measures of finite dimensional su(N) truncations of the stochastic Euler equations and random matrix models. Our work can be regarded as a preparation for addressing the questions of large scale structures, meta-stability and the dynamics of random transitions between different flow topologies in stochastic 2D Euler flows.

Numerical Modeling of Three-Dimensional Confined Flows

NASA Technical Reports Server (NTRS)

Greywall, M. S.

1981-01-01

A three dimensional confined flow model is presented. The flow field is computed by calculating velocity and enthalpy along a set of streamlines. The finite difference equations are obtained by applying conservation principles to streamtubes constructed around the chosen streamlines. With appropriate substitutions for the body force terms, the approach computes three dimensional magnetohydrodynamic channel flows. A listing of a computer code, based on this approach is presented in FORTRAN IV language. The code computes three dimensional compressible viscous flow through a rectangular duct, with the duct cross section specified along the axis.

Weak solutions of the three-dimensional vorticity equation with vortex singularities

NASA Technical Reports Server (NTRS)

Winckelmans, G.; Leonard, A.

1988-01-01

The extension of the concept of vortex singularities, developed by Saffman and Meiron (1986) for the case of two-dimensional point vortices in an incompressible vortical flow, to the three-dimensional case of vortex sticks (vortons) is investigated analytically. The derivation of the governing equations is explained, and it is demonstrated that the formulation obtained conserves total vorticity and is a weak solution of the vorticity equation, making it an appropriate means for representing three-dimensional vortical flows with limited numbers of vortex singularities.

Statistical conservation law in two- and three-dimensional turbulent flows.

PubMed

Frishman, Anna; Boffetta, Guido; De Lillo, Filippo; Liberzon, Alex

2015-03-01

Particles in turbulence live complicated lives. It is nonetheless sometimes possible to find order in this complexity. It was proposed in Falkovich et al. [Phys. Rev. Lett. 110, 214502 (2013)] that pairs of Lagrangian tracers at small scales, in an incompressible isotropic turbulent flow, have a statistical conservation law. More specifically, in a d-dimensional flow the distance R(t) between two neutrally buoyant particles, raised to the power -d and averaged over velocity realizations, remains at all times equal to the initial, fixed, separation raised to the same power. In this work we present evidence from direct numerical simulations of two- and three-dimensional turbulence for this conservation. In both cases the conservation is lost when particles exit the linear flow regime. In two dimensions we show that, as an extension of the conservation law, an Evans-Cohen-Morriss or Gallavotti-Cohen type fluctuation relation exists. We also analyze data from a 3D laboratory experiment [Liberzon et al., Physica D 241, 208 (2012)], finding that although it probes small scales they are not in the smooth regime. Thus instead of 〈R-3〉, we look for a similar, power-law-in-separation conservation law. We show that the existence of an initially slowly varying function of this form can be predicted but that it does not turn into a conservation law. We suggest that the conservation of 〈R-d〉, demonstrated here, can be used as a check of isotropy, incompressibility, and flow dimensionality in numerical and laboratory experiments that focus on small scales.

Toxin structures as evolutionary tools: Using conserved 3D folds to study the evolution of rapidly evolving peptides.

PubMed

Undheim, Eivind A B; Mobli, Mehdi; King, Glenn F

2016-06-01

Three-dimensional (3D) structures have been used to explore the evolution of proteins for decades, yet they have rarely been utilized to study the molecular evolution of peptides. Here, we highlight areas in which 3D structures can be particularly useful for studying the molecular evolution of peptide toxins. Although we focus our discussion on animal toxins, including one of the most widespread disulfide-rich peptide folds known, the inhibitor cystine knot, our conclusions should be widely applicable to studies of the evolution of disulfide-constrained peptides. We show that conserved 3D folds can be used to identify evolutionary links and test hypotheses regarding the evolutionary origin of peptides with extremely low sequence identity; construct accurate multiple sequence alignments; and better understand the evolutionary forces that drive the molecular evolution of peptides. Also watch the video abstract. © 2016 WILEY Periodicals, Inc.

Probing the Donor and Acceptor Substrate Specificity of the Gamma-Glutamyl Transpeptidase

DTIC Science & Technology

2012-01-17

glutathione can function as a source of cysteine. Mutant strains of F. tularensis that lack functional GGT have been shown to have impaired intracellular...conservation of structure and function between human and bacterial GGT homologues, significant differences in acceptor substrate and inhibitor preferences are...with the lowest value of MODELER objective function . The three-dimensional (3D) fold of the generated models was verified with PROSA II,40 and

ePlant and the 3D data display initiative: integrative systems biology on the world wide web.

PubMed

Fucile, Geoffrey; Di Biase, David; Nahal, Hardeep; La, Garon; Khodabandeh, Shokoufeh; Chen, Yani; Easley, Kante; Christendat, Dinesh; Kelley, Lawrence; Provart, Nicholas J

2011-01-10

Visualization tools for biological data are often limited in their ability to interactively integrate data at multiple scales. These computational tools are also typically limited by two-dimensional displays and programmatic implementations that require separate configurations for each of the user's computing devices and recompilation for functional expansion. Towards overcoming these limitations we have developed "ePlant" (http://bar.utoronto.ca/eplant) - a suite of open-source world wide web-based tools for the visualization of large-scale data sets from the model organism Arabidopsis thaliana. These tools display data spanning multiple biological scales on interactive three-dimensional models. Currently, ePlant consists of the following modules: a sequence conservation explorer that includes homology relationships and single nucleotide polymorphism data, a protein structure model explorer, a molecular interaction network explorer, a gene product subcellular localization explorer, and a gene expression pattern explorer. The ePlant's protein structure explorer module represents experimentally determined and theoretical structures covering >70% of the Arabidopsis proteome. The ePlant framework is accessed entirely through a web browser, and is therefore platform-independent. It can be applied to any model organism. To facilitate the development of three-dimensional displays of biological data on the world wide web we have established the "3D Data Display Initiative" (http://3ddi.org).

Variation analysis of the severe acute respiratory syndrome coronavirus putative non-structural protein 2 gene and construction of three-dimensional model.

PubMed

Lu, Jia-hai; Zhang, Ding-mei; Wang, Guo-ling; Guo, Zhong-min; Zhang, Chuan-hai; Tan, Bing-yan; Ouyang, Li-ping; Lin, Li; Liu, Yi-min; Chen, Wei-qing; Ling, Wen-hua; Yu, Xin-bing; Zhong, Nan-shan

2005-05-05

The rapid transmission and high mortality rate made severe acute respiratory syndrome (SARS) a global threat for which no efficacious therapy is available now. Without sufficient knowledge about the SARS coronavirus (SARS-CoV), it is impossible to define the candidate for the anti-SARS targets. The putative non-structural protein 2 (nsp2) (3CL(pro), following the nomenclature by Gao et al, also known as nsp5 in Snidjer et al) of SARS-CoV plays an important role in viral transcription and replication, and is an attractive target for anti-SARS drug development, so we carried on this study to have an insight into putative polymerase nsp2 of SARS-CoV Guangdong (GD) strain. The SARS-CoV strain was isolated from a SARS patient in Guangdong, China, and cultured in Vero E6 cells. The nsp2 gene was amplified by reverse transcription-polymerase chain reaction (RT-PCR) and cloned into eukaryotic expression vector pCI-neo (pCI-neo/nsp2). Then the recombinant eukaryotic expression vector pCI-neo/nsp2 was transfected into COS-7 cells using lipofectin reagent to express the nsp2 protein. The expressive protein of SARS-CoV nsp2 was analyzed by 7% sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE). The nucleotide sequence and protein sequence of GD nsp2 were compared with that of other SARS-CoV strains by nucleotide-nucleotide basic local alignment search tool (BLASTN) and protein-protein basic local alignment search tool (BLASTP) to investigate its variance trend during the transmission. The secondary structure of GD strain and that of other strains were predicted by Garnier-Osguthorpe-Robson (GOR) Secondary Structure Prediction. Three-dimensional-PSSM Protein Fold Recognition (Threading) Server was employed to construct the three-dimensional model of the nsp2 protein. The putative polymerase nsp2 gene of GD strain was amplified by RT-PCR. The eukaryotic expression vector (pCI-neo/nsp2) was constructed and expressed the protein in COS-7 cells successfully. The result of sequencing and sequence comparison with other SARS-CoV strains showed that nsp2 gene was relatively conservative during the transmission and total five base sites mutated in about 100 strains investigated, three of which in the early and middle phases caused synonymous mutation, and another two base sites variation in the late phase resulted in the amino acid substitutions and secondary structure changes. The three-dimensional structure of the nsp2 protein was successfully constructed. The results suggest that polymerase nsp2 is relatively stable during the phase of epidemic. The amino acid and secondary structure change may be important for viral infection. The fact that majority of single nucleotide variations (SNVs) are predicted to cause synonymous, as well as the result of low mutation rate of nsp2 gene in the epidemic variations, indicates that the nsp2 is conservative and could be a target for anti-SARS drugs. The three-dimensional structure result indicates that the nsp2 protein of GD strain is high homologous with 3CL(pro) of SARS-CoV urbani strain, 3CL(pro) of transmissible gastroenteritis virus and 3CL(pro) of human coronavirus 229E strain, which further suggests that nsp2 protein of GD strain possesses the activity of 3CL(pro).

Three-dimensional reconstructions of the bacteriophage CUS-3 virion reveal a conserved coat protein I-domain but a distinct tailspike receptor-binding domain

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

Parent, Kristin N., E-mail: kparent@msu.edu; Tang, Jinghua; Cardone, Giovanni

CUS-3 is a short-tailed, dsDNA bacteriophage that infects serotype K1 Escherichia coli. We report icosahedrally averaged and asymmetric, three-dimensional, cryo-electron microscopic reconstructions of the CUS-3 virion. Its coat protein structure adopts the “HK97-fold” shared by other tailed phages and is quite similar to that in phages P22 and Sf6 despite only weak amino acid sequence similarity. In addition, these coat proteins share a unique extra external domain (“I-domain”), suggesting that the group of P22-like phages has evolved over a very long time period without acquiring a new coat protein gene from another phage group. On the other hand, the morphologymore » of the CUS-3 tailspike differs significantly from that of P22 or Sf6, but is similar to the tailspike of phage K1F, a member of the extremely distantly related T7 group of phages. We conclude that CUS-3 obtained its tailspike gene from a distantly related phage quite recently. - Highlights: • Asymmetric and symmetric three-dimensional reconstructions of phage CUS-3 are presented. • CUS-3 major capsid protein has a conserved I-domain, which is found in all three categories of “P22-like phage”. • CUS-3 has very different tailspike receptor binding domain from those of P22 and Sf6. • The CUS-3 tailspike likely was acquired by horizontal gene transfer.« less

Use of conserved key amino acid positions to morph protein folds.

PubMed

Reddy, Boojala V B; Li, Wilfred W; Bourne, Philip E

2002-07-15

By using three-dimensional (3D) structure alignments and a previously published method to determine Conserved Key Amino Acid Positions (CKAAPs) we propose a theoretical method to design mutations that can be used to morph the protein folds. The original Paracelsus challenge, met by several groups, called for the engineering of a stable but different structure by modifying less than 50% of the amino acid residues. We have used the sequences from the Protein Data Bank (PDB) identifiers 1ROP, and 2CRO, which were previously used in the Paracelsus challenge by those groups, and suggest mutation to CKAAPs to morph the protein fold. The total number of mutations suggested is less than 40% of the starting sequence theoretically improving the challenge results. From secondary structure prediction experiments of the proposed mutant sequence structures, we observe that each of the suggested mutant protein sequences likely folds to a different, non-native potentially stable target structure. These results are an early indicator that analyses using structure alignments leading to CKAAPs of a given structure are of value in protein engineering experiments. Copyright 2002 Wiley Periodicals, Inc.

Three-dimensional finite element analysis for high velocity impact. [of projectiles from space debris

NASA Technical Reports Server (NTRS)

Chan, S. T. K.; Lee, C. H.; Brashears, M. R.

1975-01-01

A finite element algorithm for solving unsteady, three-dimensional high velocity impact problems is presented. A computer program was developed based on the Eulerian hydroelasto-viscoplastic formulation and the utilization of the theorem of weak solutions. The equations solved consist of conservation of mass, momentum, and energy, equation of state, and appropriate constitutive equations. The solution technique is a time-dependent finite element analysis utilizing three-dimensional isoparametric elements, in conjunction with a generalized two-step time integration scheme. The developed code was demonstrated by solving one-dimensional as well as three-dimensional impact problems for both the inviscid hydrodynamic model and the hydroelasto-viscoplastic model.

Preliminary crystallographic studies of four crystal forms of serum albumin

NASA Technical Reports Server (NTRS)

Carter, D. C.; Chang, B.; Ho, J. X.; Keeling, K.; Krishnasami, Z.

1994-01-01

Several crystal forms of serum albumin suitable for three-dimensional structure determination have been grown. These forms include crystals of recombinant and wild-type human serum albumin, baboon serum albumin, and canine serum albumin. The intrinsic limits of X-ray diffraction for these crystals are in the range 0.28-0.22 nm. Two of the crystal forms produced from human and canine albumin include incorporated long-chain fatty acids. Molecular replacement experiments have been successfully conducted on each crystal form using the previously determined atomic coordinates of human serum albumin illustrating the conserved tertiary structure.

Data-driven Modeling of the Solar Corona by a New Three-dimensional Path-conservative Osher-Solomon MHD Model

NASA Astrophysics Data System (ADS)

Feng, Xueshang; Li, Caixia; Xiang, Changqing; Zhang, Man; Li, HuiChao; Wei, Fengsi

2017-11-01

A second-order path-conservative scheme with a Godunov-type finite-volume method has been implemented to advance the equations of single-fluid solar wind plasma magnetohydrodynamics (MHD) in time. This code operates on the six-component composite grid system in three-dimensional spherical coordinates with hexahedral cells of quadrilateral frustum type. The generalized Osher-Solomon Riemann solver is employed based on a numerical integration of the path-dependent dissipation matrix. For simplicity, the straight line segment path is used, and the path integral is evaluated in a fully numerical way by a high-order numerical Gauss-Legendre quadrature. Besides its very close similarity to Godunov type, the resulting scheme retains the attractive features of the original solver: it is nonlinear, free of entropy-fix, differentiable, and complete, in that each characteristic field results in a different numerical viscosity, due to the full use of the MHD eigenstructure. By using a minmod limiter for spatial oscillation control, the path-conservative scheme is realized for the generalized Lagrange multiplier and the extended generalized Lagrange multiplier formulation of solar wind MHD systems. This new model that is second order in space and time is written in the FORTRAN language with Message Passing Interface parallelization and validated in modeling the time-dependent large-scale structure of the solar corona, driven continuously by Global Oscillation Network Group data. To demonstrate the suitability of our code for the simulation of solar wind, we present selected results from 2009 October 9 to 2009 December 29 show its capability of producing a structured solar corona in agreement with solar coronal observations.

Flexwall Hydraulic Hose Replacement in the NASA Glenn 10- by 10-Foot Supersonic Propulsion Wind Tunnel

NASA Technical Reports Server (NTRS)

Smith, Larry E.; Roeder, James W.; Linne, Alan A.; Klann, Gary A.

2003-01-01

The space-time conservation-element and solution-element method is employed to numerically study the near-field screech-tone noise of a typical underexpanded circular jet issuing from a sonic nozzle. Both axisymmetric and fully three-dimensional computations are carried out. The self-sustained feedback loop is properly simulated. The computed shock-cell structure, acoustic wave length, screech-tone frequency, and sound-pressure levels are in good agreement with existing experimental results.

Lax pair, conservation laws and solitons for a (2 + 1)-dimensional fourth-order nonlinear Schrödinger equation governing an α-helical protein

NASA Astrophysics Data System (ADS)

Chai, Jun; Tian, Bo; Zhen, Hui-Ling; Sun, Wen-Rong

2015-11-01

Energy transfer through a (2+1)-dimensional α-helical protein can be described by a (2+1)-dimensional fourth-order nonlinear Schrödinger equation. For such an equation, a Lax pair and the infinitely-many conservation laws are derived. Using an auxiliary function and a bilinear formulation, we get the one-, two-, three- and N-soliton solutions via the Hirota method. The soliton velocity is linearly related to the lattice parameter γ, while the soliton' direction and amplitude do not depend on γ. Interactions between the two solitons are elastic, while those among the three solitons are pairwise elastic. Oblique, head-on and overtaking interactions between the two solitons are displayed. Oblique interaction among the three solitons and interactions among the two parallel solitons and a single one are presented as well.

High-order central ENO finite-volume scheme for hyperbolic conservation laws on three-dimensional cubed-sphere grids

NASA Astrophysics Data System (ADS)

Ivan, L.; De Sterck, H.; Susanto, A.; Groth, C. P. T.

2015-02-01

A fourth-order accurate finite-volume scheme for hyperbolic conservation laws on three-dimensional (3D) cubed-sphere grids is described. The approach is based on a central essentially non-oscillatory (CENO) finite-volume method that was recently introduced for two-dimensional compressible flows and is extended to 3D geometries with structured hexahedral grids. Cubed-sphere grids feature hexahedral cells with nonplanar cell surfaces, which are handled with high-order accuracy using trilinear geometry representations in the proposed approach. Varying stencil sizes and slope discontinuities in grid lines occur at the boundaries and corners of the six sectors of the cubed-sphere grid where the grid topology is unstructured, and these difficulties are handled naturally with high-order accuracy by the multidimensional least-squares based 3D CENO reconstruction with overdetermined stencils. A rotation-based mechanism is introduced to automatically select appropriate smaller stencils at degenerate block boundaries, where fewer ghost cells are available and the grid topology changes, requiring stencils to be modified. Combining these building blocks results in a finite-volume discretization for conservation laws on 3D cubed-sphere grids that is uniformly high-order accurate in all three grid directions. While solution-adaptivity is natural in the multi-block setting of our code, high-order accurate adaptive refinement on cubed-sphere grids is not pursued in this paper. The 3D CENO scheme is an accurate and robust solution method for hyperbolic conservation laws on general hexahedral grids that is attractive because it is inherently multidimensional by employing a K-exact overdetermined reconstruction scheme, and it avoids the complexity of considering multiple non-central stencil configurations that characterizes traditional ENO schemes. Extensive numerical tests demonstrate fourth-order convergence for stationary and time-dependent Euler and magnetohydrodynamic flows on cubed-sphere grids, and robustness against spurious oscillations at 3D shocks. Performance tests illustrate efficiency gains that can be potentially achieved using fourth-order schemes as compared to second-order methods for the same error level. Applications on extended cubed-sphere grids incorporating a seventh root block that discretizes the interior of the inner sphere demonstrate the versatility of the spatial discretization method.

Modeling smoke plume patterns in drainage flows

Treesearch

M.A. Fosberg

1985-01-01

A three-dimensional diagnostic wind model for use in complex terrain has been combined with a three-dimensional trajectory and puff air quality model. The wind model utilizes a terrain following coordinate system and conserves both mass and momentum. The wind model provides the winds required by the predictive trajectory and puff dispersion model. Both the wind model...

Method for making a bio-compatible scaffold

DOEpatents

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

2006-01-31

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

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

PubMed

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

2015-03-01

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

Identification and characterization of gamma-glutamylamine cyclotransferase, an enzyme responsible for gamma-glutamyl-epsilon-lysine catabolism.

PubMed

Oakley, Aaron J; Coggan, Marjorie; Board, Philip G

2010-03-26

Gamma-glutamylamine cyclotransferase (GGACT) is an enzyme that converts gamma-glutamylamines to free amines and 5-oxoproline. GGACT shows high activity toward gamma-glutamyl-epsilon-lysine, derived from the breakdown of fibrin and other proteins cross-linked by transglutaminases. The enzyme adopts the newly identified cyclotransferase fold, observed in gamma-glutamylcyclotransferase (GGCT), an enzyme with activity toward gamma-glutamyl-alpha-amino acids (Oakley, A. J., Yamada, T., Liu, D., Coggan, M., Clark, A. G., and Board, P. G. (2008) J. Biol. Chem. 283, 22031-22042). Despite the absence of significant sequence identity, several residues are conserved in the active sites of GGCT and GGACT, including a putative catalytic acid/base residue (GGACT Glu(82)). The structure of GGACT in complex with the reaction product 5-oxoproline provides evidence for a common catalytic mechanism in both enzymes. The proposed mechanism, combined with the three-dimensional structures, also explains the different substrate specificities of these enzymes. Despite significant sequence divergence, there are at least three subfamilies in prokaryotes and eukaryotes that have conserved the GGCT fold and GGCT enzymatic activity.

Identification and Characterization of γ-Glutamylamine Cyclotransferase, an Enzyme Responsible for γ-Glutamyl-ϵ-lysine Catabolism*

PubMed Central

Oakley, Aaron J.; Coggan, Marjorie; Board, Philip G.

2010-01-01

γ-Glutamylamine cyclotransferase (GGACT) is an enzyme that converts γ-glutamylamines to free amines and 5-oxoproline. GGACT shows high activity toward γ-glutamyl-ϵ-lysine, derived from the breakdown of fibrin and other proteins cross-linked by transglutaminases. The enzyme adopts the newly identified cyclotransferase fold, observed in γ-glutamylcyclotransferase (GGCT), an enzyme with activity toward γ-glutamyl-α-amino acids (Oakley, A. J., Yamada, T., Liu, D., Coggan, M., Clark, A. G., and Board, P. G. (2008) J. Biol. Chem. 283, 22031–22042). Despite the absence of significant sequence identity, several residues are conserved in the active sites of GGCT and GGACT, including a putative catalytic acid/base residue (GGACT Glu82). The structure of GGACT in complex with the reaction product 5-oxoproline provides evidence for a common catalytic mechanism in both enzymes. The proposed mechanism, combined with the three-dimensional structures, also explains the different substrate specificities of these enzymes. Despite significant sequence divergence, there are at least three subfamilies in prokaryotes and eukaryotes that have conserved the GGCT fold and GGCT enzymatic activity. PMID:20110353

Increasing the structural coverage of tuberculosis drug targets.

PubMed

Baugh, Loren; Phan, Isabelle; Begley, Darren W; Clifton, Matthew C; Armour, Brianna; Dranow, David M; Taylor, Brandy M; Muruthi, Marvin M; Abendroth, Jan; Fairman, James W; Fox, David; Dieterich, Shellie H; Staker, Bart L; Gardberg, Anna S; Choi, Ryan; Hewitt, Stephen N; Napuli, Alberto J; Myers, Janette; Barrett, Lynn K; Zhang, Yang; Ferrell, Micah; Mundt, Elizabeth; Thompkins, Katie; Tran, Ngoc; Lyons-Abbott, Sally; Abramov, Ariel; Sekar, Aarthi; Serbzhinskiy, Dmitri; Lorimer, Don; Buchko, Garry W; Stacy, Robin; Stewart, Lance J; Edwards, Thomas E; Van Voorhis, Wesley C; Myler, Peter J

2015-03-01

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases. Copyright © 2014 Elsevier Ltd. All rights reserved.

Increasing the Structural Coverage of Tuberculosis Drug Targets

PubMed Central

Baugh, Loren; Phan, Isabelle; Begley, Darren W.; Clifton, Matthew C.; Armour, Brianna; Dranow, David M.; Taylor, Brandy M.; Muruthi, Marvin M.; Abendroth, Jan; Fairman, James W.; Fox, David; Dieterich, Shellie H.; Staker, Bart L.; Gardberg, Anna S.; Choi, Ryan; Hewitt, Stephen N.; Napuli, Alberto J.; Myers, Janette; Barrett, Lynn K.; Zhang, Yang; Ferrell, Micah; Mundt, Elizabeth; Thompkins, Katie; Tran, Ngoc; Lyons-Abbott, Sally; Abramov, Ariel; Sekar, Aarthi; Serbzhinskiy, Dmitri; Lorimer, Don; Buchko, Garry W.; Stacy, Robin; Stewart, Lance J.; Edwards, Thomas E.; Van Voorhis, Wesley C.; Myler, Peter J.

2015-01-01

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases. PMID:25613812

Three Dimensional Flow and Pressure Patterns in a Hydrostatic Journal Bearing

NASA Technical Reports Server (NTRS)

Braun, M. Jack; Dzodzo, Milorad B.

1996-01-01

The flow in a hydrostatic journal bearing (HJB) is described by a mathematical model that uses the three dimensional non-orthogonal form of the Navier-Stokes equations. Using the u, v, w, and p, as primary variables, a conservative formulation, finite volume multi-block method is applied through a collocated, body fitted grid. The HJB has four shallow pockets with a depth/length ratio of 0.067. This paper represents a natural extension to the two and three dimensional studies undertaken prior to this project.

Dynamically Intuitive and Potentially Predicatable Three-Dimensional Structures in the Low Frequency Flow Variability of the Extratropical Northern Hemisphere

NASA Astrophysics Data System (ADS)

Wettstein, J. J.; Li, C.; Bradshaw, S.

2016-12-01

Canonical tropospheric climate variability patterns and their corresponding indices are ubiquitous, yet a firm dynamical interpretation has remained elusive for many of even the leading extratropical patterns. Part of the lingering difficulty in understanding and predicting atmospheric low frequency variability is the fact that the identification itself of the different patterns is indistinct. This study characterizes three-dimensional structures in the low frequency variability of the extratropical zonal wind field within the entire period of record of the ERA-Interim reanalysis and suggests the foundations for a new paradigm in identifying and predicting extratropical atmospheric low-frequency variability. In concert with previous results, there is a surprisingly rich three-dimensional structure to the variance of the zonal wind field that is not (cannot be) captured by traditional identification protocols that explore covariance of pressure in the lower troposphere, flow variability in the zonal mean or, for that matter, in any variable on any planar surface. Correspondingly, many of the pressure-based canonical indices of low frequency atmospheric variability exhibit inconsistent relationships to physically intuitive reorganizations of the subtropical and polar front jets and with other forcing mechanisms. Different patterns exhibit these inconsistencies to a greater or lesser extent. The three-dimensional variance of the zonal wind field is, by contrast, naturally organized around dynamically intuitive atmospheric redistributions that have a surprisingly large amount of physically intuitive information in the vertical. These conclusions are robust in a variety of seasons and also in intra-seasonal and inter-annual explorations. Similar results and conclusions are also derived using detrended data, other reanalyses, and state-of-the-art coupled climate model output. In addition to providing a clearer perspective on the distinct three-dimensional patterns of atmospheric low frequency variability, the time evolution and potential predictability of the resultant patterns can be explored with much greater clarity because of an intrinsic link between the patterns and the requisite conservation of momentum (i.e. to the primitive equations and candidate forcing mechanisms).

A conservative finite difference algorithm for the unsteady transonic potential equation in generalized coordinates

NASA Technical Reports Server (NTRS)

Bridgeman, J. O.; Steger, J. L.; Caradonna, F. X.

1982-01-01

An implicit, approximate-factorization, finite-difference algorithm has been developed for the computation of unsteady, inviscid transonic flows in two and three dimensions. The computer program solves the full-potential equation in generalized coordinates in conservation-law form in order to properly capture shock-wave position and speed. A body-fitted coordinate system is employed for the simple and accurate treatment of boundary conditions on the body surface. The time-accurate algorithm is modified to a conventional ADI relaxation scheme for steady-state computations. Results from two- and three-dimensional steady and two-dimensional unsteady calculations are compared with existing methods.

Increasing the structural coverage of tuberculosis drug targets

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

Baugh, Loren; Phan, Isabelle; Begley, Darren W.

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. We found that of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structuresmore » would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PS APF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.« less

Increasing the structural coverage of tuberculosis drug targets

DOE PAGES

Baugh, Loren; Phan, Isabelle; Begley, Darren W.; ...

2014-12-19

High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. We found that of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structuresmore » would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PS APF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.« less

Three-dimensional modeling of the plasma arc in arc welding

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

Xu, G.; Tsai, H. L.; Hu, J.

2008-11-15

Most previous three-dimensional modeling on gas tungsten arc welding (GTAW) and gas metal arc welding (GMAW) focuses on the weld pool dynamics and assumes the two-dimensional axisymmetric Gaussian distributions for plasma arc pressure and heat flux. In this article, a three-dimensional plasma arc model is developed, and the distributions of velocity, pressure, temperature, current density, and magnetic field of the plasma arc are calculated by solving the conservation equations of mass, momentum, and energy, as well as part of the Maxwell's equations. This three-dimensional model can be used to study the nonaxisymmetric plasma arc caused by external perturbations such asmore » an external magnetic field. It also provides more accurate boundary conditions when modeling the weld pool dynamics. The present work lays a foundation for true three-dimensional comprehensive modeling of GTAW and GMAW including the plasma arc, weld pool, and/or electrode.« less

Gardenia jasminoides Encodes an Inhibitor-2 Protein for Protein Phosphatase Type 1

NASA Astrophysics Data System (ADS)

Gao, Lan; Li, Hao-Ming

2017-08-01

Protein phosphatase-1 (PP1) regulates diverse, essential cellular processes such as cell cycle progression, protein synthesis, muscle contraction, carbohydrate metabolism, transcription and neuronal signaling. Inhibitor-2 (I-2) can inhibit the activity of PP1 and has been found in diverse organisms. In this work, a Gardenia jasminoides fruit cDNA library was constructed, and the GjI-2 cDNA was isolated from the cDNA library by sequencing method. The GjI-2 cDNA contains a predicted 543 bp open reading frame that encodes 180 amino acids. The bioinformatics analysis suggested that the GjI-2 has conserved PP1c binding motif, and contains a conserved phosphorylation site, which is important in regulation of its activity. The three-dimensional model structure of GjI-2 was buite, its similar with the structure of I-2 from mouse. The results suggest that GjI-2 has relatively conserved RVxF, FxxR/KxR/K and HYNE motif, and these motifs are involved in interaction with PP1.

A dimensionally split Cartesian cut cell method for hyperbolic conservation laws

NASA Astrophysics Data System (ADS)

Gokhale, Nandan; Nikiforakis, Nikos; Klein, Rupert

2018-07-01

We present a dimensionally split method for solving hyperbolic conservation laws on Cartesian cut cell meshes. The approach combines local geometric and wave speed information to determine a novel stabilised cut cell flux, and we provide a full description of its three-dimensional implementation in the dimensionally split framework of Klein et al. [1]. The convergence and stability of the method are proved for the one-dimensional linear advection equation, while its multi-dimensional numerical performance is investigated through the computation of solutions to a number of test problems for the linear advection and Euler equations. When compared to the cut cell flux of Klein et al., it was found that the new flux alleviates the problem of oscillatory boundary solutions produced by the former at higher Courant numbers, and also enables the computation of more accurate solutions near stagnation points. Being dimensionally split, the method is simple to implement and extends readily to multiple dimensions.

A three-dimensional movie of structural changes in bacteriorhodopsin.

PubMed

Nango, Eriko; Royant, Antoine; Kubo, Minoru; Nakane, Takanori; Wickstrand, Cecilia; Kimura, Tetsunari; Tanaka, Tomoyuki; Tono, Kensuke; Song, Changyong; Tanaka, Rie; Arima, Toshi; Yamashita, Ayumi; Kobayashi, Jun; Hosaka, Toshiaki; Mizohata, Eiichi; Nogly, Przemyslaw; Sugahara, Michihiro; Nam, Daewoong; Nomura, Takashi; Shimamura, Tatsuro; Im, Dohyun; Fujiwara, Takaaki; Yamanaka, Yasuaki; Jeon, Byeonghyun; Nishizawa, Tomohiro; Oda, Kazumasa; Fukuda, Masahiro; Andersson, Rebecka; Båth, Petra; Dods, Robert; Davidsson, Jan; Matsuoka, Shigeru; Kawatake, Satoshi; Murata, Michio; Nureki, Osamu; Owada, Shigeki; Kameshima, Takashi; Hatsui, Takaki; Joti, Yasumasa; Schertler, Gebhard; Yabashi, Makina; Bondar, Ana-Nicoleta; Standfuss, Jörg; Neutze, Richard; Iwata, So

2016-12-23

Bacteriorhodopsin (bR) is a light-driven proton pump and a model membrane transport protein. We used time-resolved serial femtosecond crystallography at an x-ray free electron laser to visualize conformational changes in bR from nanoseconds to milliseconds following photoactivation. An initially twisted retinal chromophore displaces a conserved tryptophan residue of transmembrane helix F on the cytoplasmic side of the protein while dislodging a key water molecule on the extracellular side. The resulting cascade of structural changes throughout the protein shows how motions are choreographed as bR transports protons uphill against a transmembrane concentration gradient. Copyright © 2016, American Association for the Advancement of Science.

Application of the ideas and techniques of classical fluid mechanics to some problems in physical oceanography.

PubMed

Johnson, R S

2018-01-28

This review makes a case for describing many of the flows observed in our oceans, simply based on the Euler equation, with (piecewise) constant density and with suitable boundary conditions. The analyses start from the Euler and mass conservation equations, expressed in a rotating, spherical coordinate system (but the f -plane and β -plane approximations are also mentioned); five examples are discussed. For three of them, a suitable non-dimensionalization is introduced, and a single small parameter is identified in each case. These three examples lead straightforwardly and directly to new results for: waves on the Pacific Equatorial Undercurrent (EUC) with a thermocline (in the f -plane); a nonlinear, three-dimensional model for EUC-type flows (in the β -plane); and a detailed model for large gyres. The other two examples are exact solutions of the complete system: a flow which corresponds to the underlying structure of the Pacific EUC; and a flow based on the necessary requirement to use a non-conservative body force, which produces the type of flow observed in the Antarctic Circumpolar Current. (All these examples have been discussed in detail in the references cited.) This review concludes with a few comments on how these solutions can be extended and expanded.This article is part of the theme issue 'Nonlinear water waves'. © 2017 The Author(s).

Two-dimensional solitons in conservative and parity-time-symmetric triple-core waveguides with cubic-quintic nonlinearity

NASA Astrophysics Data System (ADS)

Feijoo, David; Zezyulin, Dmitry A.; Konotop, Vladimir V.

2015-12-01

We analyze a system of three two-dimensional nonlinear Schrödinger equations coupled by linear terms and with the cubic-quintic (focusing-defocusing) nonlinearity. We consider two versions of the model: conservative and parity-time (PT ) symmetric. These models describe triple-core nonlinear optical waveguides, with balanced gain and losses in the PT -symmetric case. We obtain families of soliton solutions and discuss their stability. The latter study is performed using a linear stability analysis and checked with direct numerical simulations of the evolutional system of equations. Stable solitons are found in the conservative and PT -symmetric cases. Interactions and collisions between the conservative and PT -symmetric solitons are briefly investigated, as well.

One-dimensional nonlinear elastodynamic models and their local conservation laws with applications to biological membranes.

PubMed

Cheviakov, A F; Ganghoffer, J-F

2016-05-01

The framework of incompressible nonlinear hyperelasticity and viscoelasticity is applied to the derivation of one-dimensional models of nonlinear wave propagation in fiber-reinforced elastic solids. Equivalence transformations are used to simplify the resulting wave equations and to reduce the number of parameters. Local conservation laws and global conserved quantities of the models are systematically computed and discussed, along with other related mathematical properties. Sample numerical solutions are presented. The models considered in the paper are appropriate for the mathematical description of certain aspects of the behavior of biological membranes and similar structures. Copyright © 2015 Elsevier Ltd. All rights reserved.

Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii

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

Soriano, Erika V.; McCloskey, Diane E.; Kinsland, Cynthia

2008-04-01

The crystal structures of two arginine decarboxylase mutant proteins provide insights into the mechanisms of pyruvoyl-group formation and the decarboxylation reaction. Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) catalyzes the first step of the polyamine-biosynthetic pathway in plants and some archaebacteria. The pyruvoyl group of PvlArgDC is generated by an internal autoserinolysis reaction at an absolutely conserved serine residue in the proenzyme, resulting in two polypeptide chains. Based on the native structure of PvlArgDC from Methanococcus jannaschii, the conserved residues Asn47 and Glu109 were proposed to be involved in the decarboxylation and autoprocessing reactions. N47A and E109Q mutant proteins were prepared and themore » three-dimensional structure of each protein was determined at 2.0 Å resolution. The N47A and E109Q mutant proteins showed reduced decarboxylation activity compared with the wild-type PvlArgDC. These residues may also be important for the autoprocessing reaction, which utilizes a mechanism similar to that of the decarboxylation reaction.« less

Scale separation for multi-scale modeling of free-surface and two-phase flows with the conservative sharp interface method

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

Han, L.H., E-mail: Luhui.Han@tum.de; Hu, X.Y., E-mail: Xiangyu.Hu@tum.de; Adams, N.A., E-mail: Nikolaus.Adams@tum.de

In this paper we present a scale separation approach for multi-scale modeling of free-surface and two-phase flows with complex interface evolution. By performing a stimulus-response operation on the level-set function representing the interface, separation of resolvable and non-resolvable interface scales is achieved efficiently. Uniform positive and negative shifts of the level-set function are used to determine non-resolvable interface structures. Non-resolved interface structures are separated from the resolved ones and can be treated by a mixing model or a Lagrangian-particle model in order to preserve mass. Resolved interface structures are treated by the conservative sharp-interface model. Since the proposed scale separationmore » approach does not rely on topological information, unlike in previous work, it can be implemented in a straightforward fashion into a given level set based interface model. A number of two- and three-dimensional numerical tests demonstrate that the proposed method is able to cope with complex interface variations accurately and significantly increases robustness against underresolved interface structures.« less

Research in computational fluid dynamics

NASA Technical Reports Server (NTRS)

Murman, Earll M.

1987-01-01

The numerical integration of quasi-one-dimensional unsteady flow problems which involve finite rate chemistry are discussed, and are expressed in terms of conservative form Euler and species conservation equations. Hypersonic viscous calculations for delta wing geometries is also examined. The conical Navier-Stokes equations model was selected in order to investigate the effects of viscous-inviscid interations. The more complete three-dimensional model is beyond the available computing resources. The flux vector splitting method with van Leer's MUSCL differencing is being used. Preliminary results were computed for several conditions.

A combinatorial code for pattern formation in Drosophila oogenesis.

PubMed

Yakoby, Nir; Bristow, Christopher A; Gong, Danielle; Schafer, Xenia; Lembong, Jessica; Zartman, Jeremiah J; Halfon, Marc S; Schüpbach, Trudi; Shvartsman, Stanislav Y

2008-11-01

Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggests that they follow a simple combinatorial code based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of inductive signals, provided by the highly conserved epidermal growth factor receptor and bone morphogenetic protein signaling pathways. We demonstrate the validity of the code by testing it against a set of patterns obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguish 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterize their joint dynamics over four stages of oogenesis. The proposed combinatorial framework allows systematic analysis of the diversity and dynamics of two-dimensional transcriptional patterns and guides future studies of gene regulation.

Numerical simulation of steady supersonic flow. [spatial marching

NASA Technical Reports Server (NTRS)

Schiff, L. B.; Steger, J. L.

1981-01-01

A noniterative, implicit, space-marching, finite-difference algorithm was developed for the steady thin-layer Navier-Stokes equations in conservation-law form. The numerical algorithm is applicable to steady supersonic viscous flow over bodies of arbitrary shape. In addition, the same code can be used to compute supersonic inviscid flow or three-dimensional boundary layers. Computed results from two-dimensional and three-dimensional versions of the numerical algorithm are in good agreement with those obtained from more costly time-marching techniques.

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

PubMed Central

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

2010-01-01

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

A Novel Multi-scale Simulation Strategy for Turbulent Reacting Flows

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

James, Sutherland C.

In this project, a new methodology was proposed to bridge the gap between Direct Numerical Simulation (DNS) and Large Eddy Simulation (LES). This novel methodology, titled Lattice-Based Multiscale Simulation (LBMS), creates a lattice structure of One-Dimensional Turbulence (ODT) models. This model has been shown to capture turbulent combustion with high fidelity by fully resolving interactions between turbulence and diffusion. By creating a lattice of ODT models, which are then coupled, LBMS overcomes the shortcomings of ODT, which are its inability to capture large scale three dimensional flow structures. However, by spacing these lattices significantly apart, LBMS can avoid the cursemore » of dimensionality that creates untenable computational costs associated with DNS. This project has shown that LBMS is capable of reproducing statistics of isotropic turbulent flows while coarsening the spacing between lines significantly. It also investigates and resolves issues that arise when coupling ODT lines, such as flux reconstruction perpendicular to a given ODT line, preservation of conserved quantities when eddies cross a course cell volume and boundary condition application. Robust parallelization is also investigated.« less

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

Treesearch

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

1998-01-01

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

A semi-implicit finite difference model for three-dimensional tidal circulation,

USGS Publications Warehouse

Casulli, V.; Cheng, R.T.

1992-01-01

A semi-implicit finite difference formulation for the numerical solution of three-dimensional tidal circulation is presented. The governing equations are the three-dimensional Reynolds equations in which the pressure is assumed to be hydrostatic. A minimal degree of implicitness has been introduced in the finite difference formula so that in the absence of horizontal viscosity the resulting algorithm is unconditionally stable at a minimal computational cost. When only one vertical layer is specified this method reduces, as a particular case, to a semi-implicit scheme for the solutions of the corresponding two-dimensional shallow water equations. The resulting two- and three-dimensional algorithm is fast, accurate and mass conservative. This formulation includes the simulation of flooding and drying of tidal flats, and is fully vectorizable for an efficient implementation on modern vector computers.

Dynamics of magnetic shells and information loss problem

NASA Astrophysics Data System (ADS)

Lee, Bum-Hoon; Lee, Wonwoo; Yeom, Dong-han

2015-07-01

We investigate dynamics of magnetic thin-shells in three dimensional anti-de Sitter background. Because of the magnetic field, an oscillatory solution is possible. This oscillating shell can tunnel to a collapsing shell or a bouncing shell, where both tunnelings induce an event horizon and a singularity. In the entire path integral, via the oscillating solution, there is a nonzero probability to maintain a trivial causal structure without a singularity. Therefore, due to the path integral, the entire wave function can conserve information. Since an oscillating shell can tunnel after a number of oscillations, in the end, it will allow an infinite number of different branchings to classical histories. This system can be a good model of the effective loss of information, where information is conserved by a solution that is originated from gauge fields.

Processing of Cholinesterase-like α/β-Hydrolase Fold Proteins: Alterations Associated with Congenital Disorders

PubMed Central

De Jaco, Antonella; Comoletti, Davide; Dubi, Noga; Camp, Shelley; Taylor, Palmer

2016-01-01

The α/β hydrolase fold family is perhaps the largest group of proteins presenting significant structural homology with divergent functions, ranging from catalytic hydrolysis to heterophilic cell adhesive interactions to chaperones in hormone production. All the proteins of the family share a common three-dimensional core structure containing the α/β-hydrolase fold domain that is crucial for proper protein function. Several mutations associated with congenital diseases or disorders have been reported in conserved residues within the α/β-hydrolase fold domain of cholinesterase-like proteins, neuroligins, butyrylcholinesterase and thyroglobulin. These mutations are known to disrupt the architecture of the common structural domain either globally or locally. Characterization of the natural mutations affecting the α/β-hydrolase fold domain in these proteins has shown that they mainly impair processing and trafficking along the secretory pathway causing retention of the mutant protein in the endoplasmic reticulum. Studying the processing of α/β-hydrolase fold mutant proteins should uncover new functions for this domain, that in some cases require structural integrity for both export of the protein from the ER and for facilitating subunit dimerization. A comparative study of homologous mutations in proteins that are closely related family members, along with the definition of new three-dimensional crystal structures, will identify critical residues for the assembly of the α/β-hydrolase fold. PMID:21933121

Genome-Wide Analysis of Oleosin Gene Family in 22 Tree Species: An Accelerator for Metabolic Engineering of BioFuel Crops and Agrigenomics Industrial Applications?

PubMed Central

2015-01-01

Abstract Trees contribute to enormous plant oil reserves because many trees contain 50%–80% of oil (triacylglycerols, TAGs) in the fruits and kernels. TAGs accumulate in subcellular structures called oil bodies/droplets, in which TAGs are covered by low-molecular-mass hydrophobic proteins called oleosins (OLEs). The OLEs/TAGs ratio determines the size and shape of intracellular oil bodies. There is a lack of comprehensive sequence analysis and structural information of OLEs among diverse trees. The objectives of this study were to identify OLEs from 22 tree species (e.g., tung tree, tea-oil tree, castor bean), perform genome-wide analysis of OLEs, classify OLEs, identify conserved sequence motifs and amino acid residues, and predict secondary and three-dimensional structures in tree OLEs and OLE subfamilies. Data mining identified 65 OLEs with perfect conservation of the “proline knot” motif (PX5SPX3P) from 19 trees. These OLEs contained >40% hydrophobic amino acid residues. They displayed similar properties and amino acid composition. Genome-wide phylogenetic analysis and multiple sequence alignment demonstrated that these proteins could be classified into five OLE subfamilies. There were distinct patterns of sequence conservation among the OLE subfamilies and within individual tree species. Computational modeling indicated that OLEs were composed of at least three α-helixes connected with short coils without any β-strand and that they exhibited distinct 3D structures and ligand binding sites. These analyses provide fundamental information in the similarity and specificity of diverse OLE isoforms within the same subfamily and among the different species, which should facilitate studying the structure-function relationship and identify critical amino acid residues in OLEs for metabolic engineering of tree TAGs. PMID:26258573

Genome-Wide Analysis of Oleosin Gene Family in 22 Tree Species: An Accelerator for Metabolic Engineering of BioFuel Crops and Agrigenomics Industrial Applications?

PubMed

Cao, Heping

2015-09-01

Trees contribute to enormous plant oil reserves because many trees contain 50%-80% of oil (triacylglycerols, TAGs) in the fruits and kernels. TAGs accumulate in subcellular structures called oil bodies/droplets, in which TAGs are covered by low-molecular-mass hydrophobic proteins called oleosins (OLEs). The OLEs/TAGs ratio determines the size and shape of intracellular oil bodies. There is a lack of comprehensive sequence analysis and structural information of OLEs among diverse trees. The objectives of this study were to identify OLEs from 22 tree species (e.g., tung tree, tea-oil tree, castor bean), perform genome-wide analysis of OLEs, classify OLEs, identify conserved sequence motifs and amino acid residues, and predict secondary and three-dimensional structures in tree OLEs and OLE subfamilies. Data mining identified 65 OLEs with perfect conservation of the "proline knot" motif (PX5SPX3P) from 19 trees. These OLEs contained >40% hydrophobic amino acid residues. They displayed similar properties and amino acid composition. Genome-wide phylogenetic analysis and multiple sequence alignment demonstrated that these proteins could be classified into five OLE subfamilies. There were distinct patterns of sequence conservation among the OLE subfamilies and within individual tree species. Computational modeling indicated that OLEs were composed of at least three α-helixes connected with short coils without any β-strand and that they exhibited distinct 3D structures and ligand binding sites. These analyses provide fundamental information in the similarity and specificity of diverse OLE isoforms within the same subfamily and among the different species, which should facilitate studying the structure-function relationship and identify critical amino acid residues in OLEs for metabolic engineering of tree TAGs.

Protein structure based prediction of catalytic residues.

PubMed

Fajardo, J Eduardo; Fiser, Andras

2013-02-22

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

Austerity and geometric structure of field theories

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

Kheyfets, A.

The relation between the austerity idea and the geometric structure of the three basic field theories - electrodynamics, Yang-Mills theory, and general relativity - is studied. One of the most significant manifestations of the austerity idea in field theories is thought to be expressed by the boundary of a boundary principle (BBP). The BBP says that almost all content of the field theories can be deduced from the topological identity of delta dot produced with delta = 0 used twice, at the 1-2-3-dimensional level (providing the homogeneous field equations), and at the 2-3-4-dimensional level (providing the conservation laws for themore » source currents). There are some difficulties in this line of thought due to the apparent lack of universality in application of the BBP to the three basic modern field theories above. This dissertation: (a) analyzes the difficulties by means of algebraic topology, integration theory, and modern differential geometry based on the concepts of principal bundles and Ehresmann connections: (b) extends the BBP to the unified Kaluza-Klein theory; (c) reformulates the inhomogeneous field equations and the BBP in terms of E. Cartan moment of rotation, in the way universal for the three theories and compatible with the original austerity idea; and (d) underlines the important role of the soldering structure on spacetime, and indicates that the future development of the austerity idea would involve the generalized theories.« less

SCORE-EVET: a computer code for the multidimensional transient thermal-hydraulic analysis of nuclear fuel rod arrays. [BWR; PWR

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

Benedetti, R. L.; Lords, L. V.; Kiser, D. M.

1978-02-01

The SCORE-EVET code was developed to study multidimensional transient fluid flow in nuclear reactor fuel rod arrays. The conservation equations used were derived by volume averaging the transient compressible three-dimensional local continuum equations in Cartesian coordinates. No assumptions associated with subchannel flow have been incorporated into the derivation of the conservation equations. In addition to the three-dimensional fluid flow equations, the SCORE-EVET code ocntains: (a) a one-dimensional steady state solution scheme to initialize the flow field, (b) steady state and transient fuel rod conduction models, and (c) comprehensive correlation packages to describe fluid-to-fuel rod interfacial energy and momentum exchange. Velocitymore » and pressure boundary conditions can be specified as a function of time and space to model reactor transient conditions such as a hypothesized loss-of-coolant accident (LOCA) or flow blockage.« less

Origin and structures of solar eruptions II: Magnetic modeling

NASA Astrophysics Data System (ADS)

Guo, Yang; Cheng, Xin; Ding, MingDe

2017-07-01

The topology and dynamics of the three-dimensional magnetic field in the solar atmosphere govern various solar eruptive phenomena and activities, such as flares, coronal mass ejections, and filaments/prominences. We have to observe and model the vector magnetic field to understand the structures and physical mechanisms of these solar activities. Vector magnetic fields on the photosphere are routinely observed via the polarized light, and inferred with the inversion of Stokes profiles. To analyze these vector magnetic fields, we need first to remove the 180° ambiguity of the transverse components and correct the projection effect. Then, the vector magnetic field can be served as the boundary conditions for a force-free field modeling after a proper preprocessing. The photospheric velocity field can also be derived from a time sequence of vector magnetic fields. Three-dimensional magnetic field could be derived and studied with theoretical force-free field models, numerical nonlinear force-free field models, magnetohydrostatic models, and magnetohydrodynamic models. Magnetic energy can be computed with three-dimensional magnetic field models or a time series of vector magnetic field. The magnetic topology is analyzed by pinpointing the positions of magnetic null points, bald patches, and quasi-separatrix layers. As a well conserved physical quantity, magnetic helicity can be computed with various methods, such as the finite volume method, discrete flux tube method, and helicity flux integration method. This quantity serves as a promising parameter characterizing the activity level of solar active regions.

Solution structure of an ATP-binding RNA aptamer reveals a novel fold.

PubMed Central

Dieckmann, T; Suzuki, E; Nakamura, G K; Feigon, J

1996-01-01

In vitro selection has been used to isolate several RNA aptamers that bind specifically to biological cofactors. A well-characterized example in the ATP-binding RNA aptamer family, which contains a conserved 11-base loop opposite a bulged G and flanked by regions of double-stranded RNA. The nucleotides in the consensus sequence provide a binding pocket for ATP (or AMP), which binds with a Kd in the micromolar range. Here we present the three-dimensional solution structure of a 36-nucleotide ATP-binding RNA aptamer complexed with AMP, determined from NMR-derived distance and dihedral angle restraints. The conserved loop and bulged G form a novel compact, folded structure around the AMP. The backbone tracing of the loop nucleotides can be described by a Greek zeta (zeta). Consecutive loop nucleotides G, A, A form a U-turn at the bottom of the zeta, and interact with the AMP to form a structure similar to a GNRA tetraloop, with AMP standing in for the final A. Two asymmetric G. G base pairs close the stems flanking the internal loop. Mutated aptamers support the existence of the tertiary interactions within the consensus nucleotides and with the AMP found in the calculated structures. PMID:8756406

Colony geometry and structural complexity of the endangered species Acropora cervicornis partly explains the structure of their associated fish assemblage.

PubMed

Agudo-Adriani, Esteban A; Cappelletto, Jose; Cavada-Blanco, Francoise; Croquer, Aldo

2016-01-01

In the past decade, significant efforts have been made to describe fish-habitat associations. However, most studies have oversimplified actual connections between fish assemblages and their habitats by using univariate correlations. The purpose of this study was to identify the features of habitat forming corals that facilitate and influences assemblages of associated species such as fishes. For this we developed three-dimensional models of colonies of Acropora cervicornis to estimate geometry (length and height), structural complexity (i.e., volume, density of branches, etc.) and biological features of the colonies (i.e., live coral tissue, algae). We then correlated these colony characteristics with the associated fish assemblage using multivariate analyses. We found that geometry and complexity were better predictors of the structure of fish community, compared to other variables such as percentage of live coral tissue or algae. Combined, the geometry of each colony explained 40% of the variability of the fish assemblage structure associated with this coral species; 61% of the abundance and 69% of fish richness, respectively. Our study shows that three-dimensional reconstructions of discrete colonies of Acropora cervicornis provides a useful description of the colonial structural complexity and may explain a great deal of the variance in the structure of the associated coral reef fish community. This demonstration of the strongly trait-dependent ecosystem role of this threatened species has important implications for restoration and conservation efforts.

Colony geometry and structural complexity of the endangered species Acropora cervicornis partly explains the structure of their associated fish assemblage

PubMed Central

Cappelletto, Jose; Cavada-Blanco, Francoise; Croquer, Aldo

2016-01-01

In the past decade, significant efforts have been made to describe fish-habitat associations. However, most studies have oversimplified actual connections between fish assemblages and their habitats by using univariate correlations. The purpose of this study was to identify the features of habitat forming corals that facilitate and influences assemblages of associated species such as fishes. For this we developed three-dimensional models of colonies of Acropora cervicornis to estimate geometry (length and height), structural complexity (i.e., volume, density of branches, etc.) and biological features of the colonies (i.e., live coral tissue, algae). We then correlated these colony characteristics with the associated fish assemblage using multivariate analyses. We found that geometry and complexity were better predictors of the structure of fish community, compared to other variables such as percentage of live coral tissue or algae. Combined, the geometry of each colony explained 40% of the variability of the fish assemblage structure associated with this coral species; 61% of the abundance and 69% of fish richness, respectively. Our study shows that three-dimensional reconstructions of discrete colonies of Acropora cervicornis provides a useful description of the colonial structural complexity and may explain a great deal of the variance in the structure of the associated coral reef fish community. This demonstration of the strongly trait-dependent ecosystem role of this threatened species has important implications for restoration and conservation efforts. PMID:27069801

Fractonic line excitations: An inroad from three-dimensional elasticity theory

NASA Astrophysics Data System (ADS)

Pai, Shriya; Pretko, Michael

2018-06-01

We demonstrate the existence of a fundamentally new type of excitation, fractonic lines, which are linelike excitations with the restricted mobility properties of fractons. These excitations, described using an amalgamation of higher-form gauge theories with symmetric tensor gauge theories, see direct physical realization as the topological lattice defects of ordinary three-dimensional quantum crystals. Starting with the more familiar elasticity theory, we show how theory maps onto a rank-4 tensor gauge theory, with phonons corresponding to gapless gauge modes and disclination defects corresponding to linelike charges. We derive flux conservation laws which lock these linelike excitations in place, analogous to the higher moment charge conservation laws of fracton theories. This way of encoding mobility restrictions of lattice defects could shed light on melting transitions in three dimensions. This new type of extended object may also be a useful tool in the search for improved quantum error-correcting codes in three dimensions.

Integrative Approach for Computationally Inferring Interactions between the Alpha and Beta Subunits of the Calcium-Activated Potassium Channel (BK): a Docking Study

PubMed Central

González, Janneth; Gálvez, Angela; Morales, Ludis; Barreto, George E.; Capani, Francisco; Sierra, Omar; Torres, Yolima

2013-01-01

Three-dimensional models of the alpha- and beta-1 subunits of the calcium-activated potassium channel (BK) were predicted by threading modeling. A recursive approach comprising of sequence alignment and model building based on three templates was used to build these models, with the refinement of non-conserved regions carried out using threading techniques. The complex formed by the subunits was studied by means of docking techniques, using 3D models of the two subunits, and an approach based on rigid-body structures. Structural effects of the complex were analyzed with respect to hydrogen-bond interactions and binding-energy calculations. Potential interaction sites of the complex were determined by referencing a study of the difference accessible surface area (DASA) of the protein subunits in the complex. PMID:23492851

Progress Report on SAM Reduced-Order Model Development for Thermal Stratification and Mixing during Reactor Transients

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

Hu, R.

This report documents the initial progress on the reduced-order flow model developments in SAM for thermal stratification and mixing modeling. Two different modeling approaches are pursued. The first one is based on one-dimensional fluid equations with additional terms accounting for the thermal mixing from both flow circulations and turbulent mixing. The second approach is based on three-dimensional coarse-grid CFD approach, in which the full three-dimensional fluid conservation equations are modeled with closure models to account for the effects of turbulence.

Conservation of Fold and Topology of Functional Elements in Thiamin Pyrophosphate Enzymes

NASA Technical Reports Server (NTRS)

Dominiak, P.; Ciszak, E. M.

2005-01-01

Thiamin pyrophosphate (TPP)-dependent enzymes are a highly divergent family of proteins binding both TPP and metal ions. They perform decarboxylation-hydroxyaldehydes. Prior -ketoacids and of a common - (O=)C-C(OH)- fragment of to knowledge of three-dimensional structures of these enzmes, the GDGY25-30NN sequence was used to identify these enzymes. Subsequently, a number of structural studies on those enzymes revealed multi-subunit organization and the features of the two duplicate cofactor binding sites. Analyzing the structures of 44 structurally known enzymes, we found that the common structure of these enzymes is reduced to 180-220 amino acid long fragments of two PP and two PYR domains that form the [PP:PYR]2 binding center of two cofactor molecules. The structures of PP and PYR are arranged in a similar fold-sheet with triplets of helices on both sides.Dconsisting of a six-stranded Residues surrounding the cofactors are not strictly conserved, but they provide the same interatomic contacts required for the catalytic functions that these enzymes perform while maintaining interactive structural integrity. These structural and functional amino acids are topological counterparts located in the same positions of the conserved fold of sets of PP and PYR domains. Additional parallels include short fragments of sequences that link these amino acids to the fold and function. This report on the structural commonalities amongst TPP dependent enzymes is thought to contribute new approaches to annotation that may assist in advancing the functional proteomics of TPP dependent enzymes, and trace their complexity within evolutionary context.

Sequence and structural characterization of great salt lake bacteriophage CW02, a member of the T7-like supergroup.

PubMed

Shen, Peter S; Domek, Matthew J; Sanz-García, Eduardo; Makaju, Aman; Taylor, Ryan M; Hoggan, Ryan; Culumber, Michele D; Oberg, Craig J; Breakwell, Donald P; Prince, John T; Belnap, David M

2012-08-01

Halophage CW02 infects a Salinivibrio costicola-like bacterium, SA50, isolated from the Great Salt Lake. Following isolation, cultivation, and purification, CW02 was characterized by DNA sequencing, mass spectrometry, and electron microscopy. A conserved module of structural genes places CW02 in the T7 supergroup, members of which are found in diverse aquatic environments, including marine and freshwater ecosystems. CW02 has morphological similarities to viruses of the Podoviridae family. The structure of CW02, solved by cryogenic electron microscopy and three-dimensional reconstruction, enabled the fitting of a portion of the bacteriophage HK97 capsid protein into CW02 capsid density, thereby providing additional evidence that capsid proteins of tailed double-stranded DNA phages have a conserved fold. The CW02 capsid consists of bacteriophage lambda gpD-like densities that likely contribute to particle stability. Turret-like densities were found on icosahedral vertices and may represent a unique adaptation similar to what has been seen in other extremophilic viruses that infect archaea, such as Sulfolobus turreted icosahedral virus and halophage SH1.

Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases.

PubMed

Zarafeta, Dimitra; Moschidi, Danai; Ladoukakis, Efthymios; Gavrilov, Sergey; Chrysina, Evangelia D; Chatziioannou, Aristotelis; Kublanov, Ilya; Skretas, Georgios; Kolisis, Fragiskos N

2016-12-19

Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Here, we have identified a new esterolytic enzyme by screening a metagenomic sample collected from a hot spring in Kamchatka, Russia. Biochemical characterization of the new esterase, termed EstDZ2, revealed that it is highly active against medium chain fatty acid esters at temperatures between 25 and 60 °C and at pH values 7-8. The new enzyme is moderately thermostable with a half-life of more than six hours at 60 °C, but exhibits exquisite stability against high concentrations of organic solvents. Phylogenetic analysis indicated that EstDZ2 is likely an Acetothermia enzyme that belongs to a new family of bacterial esterases, for which we propose the index XV. One distinctive feature of this new family, is the presence of a conserved GHSAG catalytic motif. Multiple sequence alignment, coupled with computational modelling of the three-dimensional structure of EstDZ2, revealed that the enzyme lacks the largest part of the "cap" domain, whose extended structure is characteristic for the closely related Family IV esterases. Thus, EstDZ2 appears to be distinct from known related esterolytic enzymes, both in terms of sequence characteristics, as well as in terms of three-dimensional structure.

A mixed finite difference/Galerkin method for three-dimensional Rayleigh-Benard convection

NASA Technical Reports Server (NTRS)

Buell, Jeffrey C.

1988-01-01

A fast and accurate numerical method, for nonlinear conservation equation systems whose solutions are periodic in two of the three spatial dimensions, is presently implemented for the case of Rayleigh-Benard convection between two rigid parallel plates in the parameter region where steady, three-dimensional convection is known to be stable. High-order streamfunctions secure the reduction of the system of five partial differential equations to a system of only three. Numerical experiments are presented which verify both the expected convergence rates and the absolute accuracy of the method.

Integrated Aeromechanics with Three-Dimensional Solid-Multibody Structures

NASA Technical Reports Server (NTRS)

Datta, Anubhav; Johnson, Wayne

2014-01-01

A full three-dimensional finite element-multibody structural dynamic solver is coupled to a three-dimensional Reynolds-averaged Navier-Stokes solver for the prediction of integrated aeromechanical stresses and strains on a rotor blade in forward flight. The objective is to lay the foundations of all major pieces of an integrated three-dimensional rotor dynamic analysis - from model construction to aeromechanical solution to stress/strain calculation. The primary focus is on the aeromechanical solution. Two types of three-dimensional CFD/CSD interfaces are constructed for this purpose with an emphasis on resolving errors from geometry mis-match so that initial-stage approximate structural geometries can also be effectively analyzed. A three-dimensional structural model is constructed as an approximation to a UH-60A-like fully articulated rotor. The aerodynamic model is identical to the UH-60A rotor. For preliminary validation measurements from a UH-60A high speed flight is used where CFD coupling is essential to capture the advancing side tip transonic effects. The key conclusion is that an integrated aeromechanical analysis is indeed possible with three-dimensional structural dynamics but requires a careful description of its geometry and discretization of its parts.

A new Lagrangian method for three-dimensional steady supersonic flows

NASA Technical Reports Server (NTRS)

Loh, Ching-Yuen; Liou, Meng-Sing

1993-01-01

In this report, the new Lagrangian method introduced by Loh and Hui is extended for three-dimensional, steady supersonic flow computation. The derivation of the conservation form and the solution of the local Riemann solver using the Godunov and the high-resolution TVD (total variation diminished) scheme is presented. This new approach is accurate and robust, capable of handling complicated geometry and interactions between discontinuous waves. Test problems show that the extended Lagrangian method retains all the advantages of the two-dimensional method (e.g., crisp resolution of a slip-surface (contact discontinuity) and automatic grid generation). In this report, we also suggest a novel three dimensional Riemann problem in which interesting and intricate flow features are present.

A Three-Dimensional RNA Motif in Potato spindle tuber viroid Mediates Trafficking from Palisade Mesophyll to Spongy Mesophyll in Nicotiana benthamiana[W

PubMed Central

Takeda, Ryuta; Petrov, Anton I.; Leontis, Neocles B.; Ding, Biao

2011-01-01

Cell-to-cell trafficking of RNA is an emerging biological principle that integrates systemic gene regulation, viral infection, antiviral response, and cell-to-cell communication. A key mechanistic question is how an RNA is specifically selected for trafficking from one type of cell into another type. Here, we report the identification of an RNA motif in Potato spindle tuber viroid (PSTVd) required for trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana leaves. This motif, called loop 6, has the sequence 5′-CGA-3′...5′-GAC-3′ flanked on both sides by cis Watson-Crick G/C and G/U wobble base pairs. We present a three-dimensional (3D) structural model of loop 6 that specifies all non-Watson-Crick base pair interactions, derived by isostericity-based sequence comparisons with 3D RNA motifs from the RNA x-ray crystal structure database. The model is supported by available chemical modification patterns, natural sequence conservation/variations in PSTVd isolates and related species, and functional characterization of all possible mutants for each of the loop 6 base pairs. Our findings and approaches have broad implications for studying the 3D RNA structural motifs mediating trafficking of diverse RNA species across specific cellular boundaries and for studying the structure-function relationships of RNA motifs in other biological processes. PMID:21258006

A three-dimensional RNA motif in Potato spindle tuber viroid mediates trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana.

PubMed

Takeda, Ryuta; Petrov, Anton I; Leontis, Neocles B; Ding, Biao

2011-01-01

Cell-to-cell trafficking of RNA is an emerging biological principle that integrates systemic gene regulation, viral infection, antiviral response, and cell-to-cell communication. A key mechanistic question is how an RNA is specifically selected for trafficking from one type of cell into another type. Here, we report the identification of an RNA motif in Potato spindle tuber viroid (PSTVd) required for trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana leaves. This motif, called loop 6, has the sequence 5'-CGA-3'...5'-GAC-3' flanked on both sides by cis Watson-Crick G/C and G/U wobble base pairs. We present a three-dimensional (3D) structural model of loop 6 that specifies all non-Watson-Crick base pair interactions, derived by isostericity-based sequence comparisons with 3D RNA motifs from the RNA x-ray crystal structure database. The model is supported by available chemical modification patterns, natural sequence conservation/variations in PSTVd isolates and related species, and functional characterization of all possible mutants for each of the loop 6 base pairs. Our findings and approaches have broad implications for studying the 3D RNA structural motifs mediating trafficking of diverse RNA species across specific cellular boundaries and for studying the structure-function relationships of RNA motifs in other biological processes.

Evolutionary history of versatile-lipases from Agaricales through reconstruction of ancestral structures.

PubMed

Barriuso, Jorge; Martínez, María Jesús

2017-01-03

Fungal "Versatile carboxylic ester hydrolases" are enzymes with great biotechnological interest. Here we carried out a bioinformatic screening to find these proteins in genomes from Agaricales, by means of searching for conserved motifs, sequence and phylogenetic analysis, and three-dimensional modeling. Moreover, we reconstructed the molecular evolution of these enzymes along the time by inferring and analyzing the sequence of ancestral intermediate forms. The properties of the ancestral candidates are discussed on the basis of their three-dimensional structural models, the hydrophobicity of the lid, and the substrate binding intramolecular tunnel, revealing all of them featured properties of these enzymes. The evolutionary history of the putative lipases revealed an increase on the length and hydrophobicity of the lid region, as well as in the size of the substrate binding pocket, during evolution time. These facts suggest the enzymes' specialization towards certain substrates and their subsequent loss of promiscuity. These results bring to light the presence of different pools of lipases in fungi with different habitats and life styles. Despite the consistency of the data gathered from reconstruction of ancestral sequences, the heterologous expression of some of these candidates would be essential to corroborate enzymes' activities.

Three-dimensional rotating flow of MHD single wall carbon nanotubes over a stretching sheet in presence of thermal radiation

NASA Astrophysics Data System (ADS)

Nasir, Saleem; Islam, Saeed; Gul, Taza; Shah, Zahir; Khan, Muhammad Altaf; Khan, Waris; Khan, Aurang Zeb; Khan, Saima

2018-05-01

In this article the modeling and computations are exposed to introduce the new idea of MHD three-dimensional rotating flow of nanofluid through a stretching sheet. Single wall carbon nanotubes (SWCNTs) are utilized as a nano-sized materials while water is used as a base liquid. Single-wall carbon nanotubes (SWNTs) parade sole assets due to their rare structure. Such structure has significant optical and electronics features, wonderful strength and elasticity, and high thermal and chemical permanence. The heat exchange phenomena are deliberated subject to thermal radiation and moreover the impact of nanoparticles Brownian motion and thermophoresis are involved in the present investigation. For the nanofluid transport mechanism, we implemented the Xue model (Xue, Phys B Condens Matter 368:302-307, 2005). The governing nonlinear formulation based upon the law of conservation of mass, quantity of motion, thermal field and nanoparticles concentrations is first modeled and then solved by homotopy analysis method (HAM). Moreover, the graphical result has been exposed to investigate that in what manner the velocities, heat and nanomaterial concentration distributions effected through influential parameters. The mathematical facts of skin friction, Nusselt number and Sherwood number are presented through numerical data for SWCNTs.

Multidimensional Riemann problem with self-similar internal structure - part III - a multidimensional analogue of the HLLI Riemann solver for conservative hyperbolic systems

NASA Astrophysics Data System (ADS)

Balsara, Dinshaw S.; Nkonga, Boniface

2017-10-01

Just as the quality of a one-dimensional approximate Riemann solver is improved by the inclusion of internal sub-structure, the quality of a multidimensional Riemann solver is also similarly improved. Such multidimensional Riemann problems arise when multiple states come together at the vertex of a mesh. The interaction of the resulting one-dimensional Riemann problems gives rise to a strongly-interacting state. We wish to endow this strongly-interacting state with physically-motivated sub-structure. The fastest way of endowing such sub-structure consists of making a multidimensional extension of the HLLI Riemann solver for hyperbolic conservation laws. Presenting such a multidimensional analogue of the HLLI Riemann solver with linear sub-structure for use on structured meshes is the goal of this work. The multidimensional MuSIC Riemann solver documented here is universal in the sense that it can be applied to any hyperbolic conservation law. The multidimensional Riemann solver is made to be consistent with constraints that emerge naturally from the Galerkin projection of the self-similar states within the wave model. When the full eigenstructure in both directions is used in the present Riemann solver, it becomes a complete Riemann solver in a multidimensional sense. I.e., all the intermediate waves are represented in the multidimensional wave model. The work also presents, for the very first time, an important analysis of the dissipation characteristics of multidimensional Riemann solvers. The present Riemann solver results in the most efficient implementation of a multidimensional Riemann solver with sub-structure. Because it preserves stationary linearly degenerate waves, it might also help with well-balancing. Implementation-related details are presented in pointwise fashion for the one-dimensional HLLI Riemann solver as well as the multidimensional MuSIC Riemann solver.

Virtual gap element approach for the treatment of non-matching interface using three-dimensional solid elements

NASA Astrophysics Data System (ADS)

Song, Yeo-Ul; Youn, Sung-Kie; Park, K. C.

2017-10-01

A method for three-dimensional non-matching interface treatment with a virtual gap element is developed. When partitioned structures contain curved interfaces and have different brick meshes, the discretized models have gaps along the interfaces. As these gaps bring unexpected errors, special treatments are required to handle the gaps. In the present work, a virtual gap element is introduced to link the frame and surface domain nodes in the frame work of the mortar method. Since the surface of the hexahedron element is quadrilateral, the gap element is pyramidal. The pyramidal gap element consists of four domain nodes and one frame node. Zero-strain condition in the gap element is utilized for the interpolation of frame nodes in terms of the domain nodes. This approach is taken to satisfy the momentum and energy conservation. The present method is applicable not only to curved interfaces with gaps, but also to flat interfaces in three dimensions. Several numerical examples are given to describe the effectiveness and accuracy of the proposed method.

The X-ray Crystallographic Structure and Activity Analysis of a Pseudomonas-Specific Subfamily of the HAD Enzyme Superfamily Evidences a Novel Biochemical Function

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

Peisach,E.; Wang, L.; Burroughs, A.

2008-01-01

The haloacid dehalogenase (HAD) superfamily is a large family of proteins dominated by phosphotransferases. Thirty-three sequence families within the HAD superfamily (HADSF) have been identified to assist in function assignment. One such family includes the enzyme phosphoacetaldehyde hydrolase (phosphonatase). Phosphonatase possesses the conserved Rossmanniod core domain and a C1-type cap domain. Other members of this family do not possess a cap domain and because the cap domain of phosphonatase plays an important role in active site desolvation and catalysis, the function of the capless family members must be unique. A representative of the capless subfamily, PSPTO{_}2114, from the plant pathogenmore » Pseudomonas syringae, was targeted for catalytic activity and structure analyses. The X-ray structure of PSPTO{_}2114 reveals a capless homodimer that conserves some but not all of the intersubunit contacts contributed by the core domains of the phosphonatase homodimer. The region of the PSPTO{_}2114 that corresponds to the catalytic scaffold of phosphonatase (and other HAD phosphotransfereases) positions amino acid residues that are ill suited for Mg+2 cofactor binding and mediation of phosphoryl group transfer between donor and acceptor substrates. The absence of phosphotransferase activity in PSPTO{_}2114 was confirmed by kinetic assays. To explore PSPTO{_}2114 function, the conservation of sequence motifs extending outside of the HADSF catalytic scaffold was examined. The stringently conserved residues among PSPTO{_}2114 homologs were mapped onto the PSPTO{_}2114 three-dimensional structure to identify a surface region unique to the family members that do not possess a cap domain. The hypothesis that this region is used in protein-protein recognition is explored to define, for the first time, HADSF proteins which have acquired a function other than that of a catalyst. Proteins 2008.« less

Protein Modeling and Molecular Dynamics Simulation of Cloned Regucalcin (RGN) Gene from Bubalus bubalis.

PubMed

Pillai, Harikrishna; Yadav, Brijesh Singh; Chaturvedi, Navaneet; Jan, Arif Tasleem; Gupta, Girish Kumar; Baig, Mohammad Hassan; Bhure, Sanjeev Kumar

2017-01-01

Regucalcin (RGN), a calcium regulating protein having anti-prolific, antiapoptotic functions, plays important part in the biosynthesis of ascorbic acid. It is a highly conserved protein that has been reported from many tissue types of various vertebrate species. Employing its effect of regulating enzyme activities through reaction with sulfhydryl group (-SH) and calcium, structural level study believed to offer a better understanding of binding properties and regulatory mechanisms of RGN, was performed. Using sample from testis of Bubalus bubalis, amplification of regucalcin (RGN) gene was subjected to characterization by performing digestion using different restriction endonucleases (RE). Alongside, cDNA was cloned into pPICZαC vector and transformed in DH5α host for custom sequencing. To get a better insight of its structural characteristics, three dimensional (3D) structure of protein sequence was generated using in silico molecular modelling approach. The full trajectory analysis of structure was achieved by the Molecular Dynamics (MD) that explains the stability, flexibility and robustness of protein during simulation in a time of 50ns. Molecular docking against 1,5-anhydrosorbitol was performed for functional characterization of RGN. Preliminary screening of amplified products on Agarose gel showed expected size of ~893 bp of PCR product corresponding to RGN. Following sequencing, BLASTp search of the target sequence revealed that it shares 91% similarity score with human senescence marker protein-30 (pdb id: 3G4E). Molecular docking of 1,5-anhydrosorbitol reveals information regarding important binding site residues of RGN. 1,5-anhydrosorbitol was found to interact with binding free energy of - 6.01 Kcal/mol. RMSD calculation of subunits A, B and D-F might be responsible for functional and conserved regions of modeled protein. Three dimensional structure of RGN was generated and its interactions with 1,5- anhydrosorbitol, demonstrates the role of key binding residues. Until now, no structural details were available for buffalo RGN proteins, hence this study will broaden the horizon towards understanding the structural and functional aspects of different proteins in cattle. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Flux Jacobian matrices and generaled Roe average for an equilibrium real gas

NASA Technical Reports Server (NTRS)

Vinokur, Marcel

1988-01-01

Inviscid flux Jacobian matrices and their properties used in numerical solutions of conservation laws are extended to general, equilibrium gas laws. Exact and approximate generalizations of the Roe average are presented. Results are given for one-dimensional flow, and then extended to three-dimensional flow with time-varying grids.

Seafarers, Great Circles, and a Tad of Rhumb: Understanding the Mercator Misconception

ERIC Educational Resources Information Center

DiSpezio, Michael A.

2010-01-01

Being flat, Mercator maps inherently misrepresent some aspects of Earth's geography. That's because there is absolutely no way to simultaneously conserve all of the elements of three-dimensional space in a two-dimensional model. To dispel misconceptions, check out the Activity Worksheet and the website resources included in this article. Along…

Structural attributes of individual trees for identifying homogeneous patches in a tropical rainforest

NASA Astrophysics Data System (ADS)

Alexander, Cici; Korstjens, Amanda H.; Hill, Ross A.

2017-03-01

Mapping and monitoring tropical rainforests and quantifying their carbon stocks are important, both for devising strategies for their conservation and mitigating the effects of climate change. Airborne Laser Scanning (ALS) has advantages over other remote sensing techniques for describing the three-dimensional structure of forests. This study identifies forest patches using ALS-based structural attributes in a tropical rainforest in Sumatra, Indonesia. A method to group trees with similar attributes into forest patches based on Thiessen polygons and k-medoids clustering is developed, combining the advantages of both raster and individual tree-based methods. The structural composition of the patches could be an indicator of habitat type and quality. The patches could also be a basis for developing allometric models for more accurate estimation of carbon stock than is currently possible with generalised models.

Structure of the cytoplasmic domain of Yersinia pestis YscD, an essential component of the type III secretion system

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

Lountos, George T.; Tropea, Joseph E.; Waugh, David S.

2012-09-17

The Yersinia pestis YscD protein is an essential component of the type III secretion system. YscD consists of an N-terminal cytoplasmic domain (residues 1-121), a transmembrane linker (122-142) and a large periplasmic domain (143-419). Both the cytoplasmic and the periplasmic domains are required for the assembly of the type III secretion system. Here, the structure of the YscD cytoplasmic domain solved by SAD phasing is presented. Although the three-dimensional structure is similar to those of forkhead-associated (FHA) domains, comparison with the structures of canonical FHA domains revealed that the cytoplasmic domain of YscD lacks the conserved residues that are requiredmore » for binding phosphothreonine and is therefore unlikely to function as a true FHA domain.« less

Hybrid-dimensional modelling of two-phase flow through fractured porous media with enhanced matrix fracture transmission conditions

NASA Astrophysics Data System (ADS)

Brenner, Konstantin; Hennicker, Julian; Masson, Roland; Samier, Pierre

2018-03-01

In this work, we extend, to two-phase flow, the single-phase Darcy flow model proposed in [26], [12] in which the (d - 1)-dimensional flow in the fractures is coupled with the d-dimensional flow in the matrix. Three types of so called hybrid-dimensional two-phase Darcy flow models are proposed. They all account for fractures acting either as drains or as barriers, since they allow pressure jumps at the matrix-fracture interfaces. The models also permit to treat gravity dominated flow as well as discontinuous capillary pressure at the material interfaces. The three models differ by their transmission conditions at matrix fracture interfaces: while the first model accounts for the nonlinear two-phase Darcy flux conservations, the second and third ones are based on the linear single phase Darcy flux conservations combined with different approximations of the mobilities. We adapt the Vertex Approximate Gradient (VAG) scheme to this problem, in order to account for anisotropy and heterogeneity aspects as well as for applicability on general meshes. Several test cases are presented to compare our hybrid-dimensional models to the generic equi-dimensional model, in which fractures have the same dimension as the matrix, leading to deep insight about the quality of the proposed reduced models.

Continuum modeling of three-dimensional truss-like space structures

NASA Technical Reports Server (NTRS)

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

1978-01-01

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

Functional analysis of propeptide as an intramolecular chaperone for in vivo folding of subtilisin nattokinase.

PubMed

Jia, Yan; Liu, Hui; Bao, Wei; Weng, Meizhi; Chen, Wei; Cai, Yongjun; Zheng, Zhongliang; Zou, Guolin

2010-12-01

Here, we show that during in vivo folding of the precursor, the propeptide of subtilisin nattokinase functions as an intramolecular chaperone (IMC) that organises the in vivo folding of the subtilisin domain. Two residues belonging to β-strands formed by conserved regions of the IMC are crucial for the folding of the subtilisin domain through direct interactions. An identical protease can fold into different conformations in vivo due to the action of a mutated IMC, resulting in different kinetic parameters. Some interfacial changes involving conserved regions, even those induced by the subtilisin domain, blocked subtilisin folding and altered its conformation. Insight into the interaction between the subtilisin and IMC domains is provided by a three-dimensional structural model. Copyright © 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Pseudo-invariants contributing to inverse energy cascades in three-dimensional turbulence

NASA Astrophysics Data System (ADS)

Rathmann, Nicholas M.; Ditlevsen, Peter D.

2017-05-01

Three-dimensional (3D) turbulence is characterized by a dual forward cascade of both kinetic energy and helicity, a second inviscid flow invariant besides energy, from the integral scale of motion to the viscous dissipative scale. In helical flows, however, such as strongly rotating flows with broken mirror symmetry, an inverse (reversed) energy cascade can be observed analogous to that of two-dimensional turbulence (2D) where enstrophy, a second positive-definite flow invariant, unlike helicity in 3D, effectively blocks the forward cascade of energy. In the spectral-helical decomposition of the Navier-Stokes equation, it has previously been shown that a subset of three-wave (triad) interactions conserve helicity in 3D in a fashion similar to enstrophy in 2D, thus leading to a 2D-like inverse energy cascade in 3D. In this work, we show, both theoretically and numerically, that an additional subset of interactions exist, conserving a new pseudo-invariant in addition to energy and helicity, which contributes either to a forward or an inverse energy cascade depending on the specific triad interaction geometry.

The Effect of Three-Dimensional Simulations on the Understanding of Chemical Structures and Their Properties

ERIC Educational Resources Information Center

Urhahne, Detlef; Nick, Sabine; Schanze, Sascha

2009-01-01

In a series of three experimental studies, the effectiveness of three-dimensional computer simulations to aid the understanding of chemical structures and their properties was investigated. Arguments for the usefulness of three-dimensional simulations were derived from Mayer's generative theory of multimedia learning. Simulations might lead to a…

[Conservative anal fistula treatment with collagenic plug and human fibrin sealant. Preliminary results].

PubMed

Gubitosi, A; Moccia, G; Malinconico, F A; Docimo, G; Ruggiero, R; Iside, G; Avenia, N; Docimo, L; Foroni, F; Gilio, F; Sparavigna, L; Agresti, M

2009-01-01

The authors, on the basis of a long clinical experience with human fibrin glue in general surgery, compared two different extracellular matrix (collagen), Surgisis and TissueDura, with human fibrin glue, applied during the operation, and sometimes in postoperative, to obtain the healing of perianal fistulas. The collagenic extracellular matrix provides, according to the rationale suggested, an optimal three-dimensional structure for the fibroblastic implant and neoangiogenesis, hence for the fistula "fibrotizzation" and closure. The encouraging results for transphincteric fistulas and a simple and easy technique push to researchers on samples statistically significant.

Second order symmetry-preserving conservative Lagrangian scheme for compressible Euler equations in two-dimensional cylindrical coordinates

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

Cheng, Juan, E-mail: cheng_juan@iapcm.ac.cn; Shu, Chi-Wang, E-mail: shu@dam.brown.edu

In applications such as astrophysics and inertial confinement fusion, there are many three-dimensional cylindrical-symmetric multi-material problems which are usually simulated by Lagrangian schemes in the two-dimensional cylindrical coordinates. For this type of simulation, a critical issue for the schemes is to keep spherical symmetry in the cylindrical coordinate system if the original physical problem has this symmetry. In the past decades, several Lagrangian schemes with such symmetry property have been developed, but all of them are only first order accurate. In this paper, we develop a second order cell-centered Lagrangian scheme for solving compressible Euler equations in cylindrical coordinates, basedmore » on the control volume discretizations, which is designed to have uniformly second order accuracy and capability to preserve one-dimensional spherical symmetry in a two-dimensional cylindrical geometry when computed on an equal-angle-zoned initial grid. The scheme maintains several good properties such as conservation for mass, momentum and total energy, and the geometric conservation law. Several two-dimensional numerical examples in cylindrical coordinates are presented to demonstrate the good performance of the scheme in terms of accuracy, symmetry, non-oscillation and robustness. The advantage of higher order accuracy is demonstrated in these examples.« less

Infinite Conservation Laws, Continuous Symmetries and Invariant Solutions of Some Discrete Integrable Equations

NASA Astrophysics Data System (ADS)

Zhang, Yu-Feng; Zhang, Xiang-Zhi; Dong, Huan-He

2017-12-01

Two new shift operators are introduced for which a few differential-difference equations are generated by applying the R-matrix method. These equations can be reduced to the standard Toda lattice equation and (1+1)-dimensional and (2+1)-dimensional Toda-type equations which have important applications in hydrodynamics, plasma physics, and so on. Based on these consequences, we deduce the Hamiltonian structures of two discrete systems. Finally, we obtain some new infinite conservation laws of two discrete equations and employ Lie-point transformation group to obtain some continuous symmetries and part of invariant solutions for the (1+1) and (2+1)-dimensional Toda-type equations. Supported by the Fundamental Research Funds for the Central University under Grant No. 2017XKZD11

From Two- to Three-Dimensional Structures of a Supertetrahedral Boran Using Density Functional Calculations.

PubMed

Getmanskii, Iliya V; Minyaev, Ruslan M; Steglenko, Dmitrii V; Koval, Vitaliy V; Zaitsev, Stanislav A; Minkin, Vladimir I

2017-08-14

With help of the DFT calculations and imposing of periodic boundary conditions the geometrical and electronic structures were investigated of two- and three-dimensional boron systems designed on the basis of graphane and diamond lattices in which carbons were replaced with boron tetrahedrons. The consequent studies of two- and three-layer systems resulted in the construction of a three-dimensional supertetrahedral borane crystal structure. The two-dimensional supertetrahedral borane structures with less than seven layers are dynamically unstable. At the same time the three-dimensional superborane systems were found to be dynamically stable. Lack of the forbidden electronic zone for the studied boron systems testifies that these structures can behave as good conductors. The low density of the supertetrahedral borane crystal structures (0.9 g cm -3 ) is close to that of water, which offers the perspective for their application as aerospace and cosmic materials. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Geomfinder: a multi-feature identifier of similar three-dimensional protein patterns: a ligand-independent approach.

PubMed

Núñez-Vivanco, Gabriel; Valdés-Jiménez, Alejandro; Besoaín, Felipe; Reyes-Parada, Miguel

2016-01-01

Since the structure of proteins is more conserved than the sequence, the identification of conserved three-dimensional (3D) patterns among a set of proteins, can be important for protein function prediction, protein clustering, drug discovery and the establishment of evolutionary relationships. Thus, several computational applications to identify, describe and compare 3D patterns (or motifs) have been developed. Often, these tools consider a 3D pattern as that described by the residues surrounding co-crystallized/docked ligands available from X-ray crystal structures or homology models. Nevertheless, many of the protein structures stored in public databases do not provide information about the location and characteristics of ligand binding sites and/or other important 3D patterns such as allosteric sites, enzyme-cofactor interaction motifs, etc. This makes necessary the development of new ligand-independent methods to search and compare 3D patterns in all available protein structures. Here we introduce Geomfinder, an intuitive, flexible, alignment-free and ligand-independent web server for detailed estimation of similarities between all pairs of 3D patterns detected in any two given protein structures. We used around 1100 protein structures to form pairs of proteins which were assessed with Geomfinder. In these analyses each protein was considered in only one pair (e.g. in a subset of 100 different proteins, 50 pairs of proteins can be defined). Thus: (a) Geomfinder detected identical pairs of 3D patterns in a series of monoamine oxidase-B structures, which corresponded to the effectively similar ligand binding sites at these proteins; (b) we identified structural similarities among pairs of protein structures which are targets of compounds such as acarbose, benzamidine, adenosine triphosphate and pyridoxal phosphate; these similar 3D patterns are not detected using sequence-based methods; (c) the detailed evaluation of three specific cases showed the versatility of Geomfinder, which was able to discriminate between similar and different 3D patterns related to binding sites of common substrates in a range of diverse proteins. Geomfinder allows detecting similar 3D patterns between any two pair of protein structures, regardless of the divergency among their amino acids sequences. Although the software is not intended for simultaneous multiple comparisons in a large number of proteins, it can be particularly useful in cases such as the structure-based design of multitarget drugs, where a detailed analysis of 3D patterns similarities between a few selected protein targets is essential.

A Space-Time Conservation Element and Solution Element Method for Solving the Two- and Three-Dimensional Unsteady Euler Equations Using Quadrilateral and Hexahedral Meshes

NASA Technical Reports Server (NTRS)

Zhang, Zeng-Chan; Yu, S. T. John; Chang, Sin-Chung; Jorgenson, Philip (Technical Monitor)

2001-01-01

In this paper, we report a version of the Space-Time Conservation Element and Solution Element (CE/SE) Method in which the 2D and 3D unsteady Euler equations are simulated using structured or unstructured quadrilateral and hexahedral meshes, respectively. In the present method, mesh values of flow variables and their spatial derivatives are treated as independent unknowns to be solved for. At each mesh point, the value of a flow variable is obtained by imposing a flux conservation condition. On the other hand, the spatial derivatives are evaluated using a finite-difference/weighted-average procedure. Note that the present extension retains many key advantages of the original CE/SE method which uses triangular and tetrahedral meshes, respectively, for its 2D and 3D applications. These advantages include efficient parallel computing ease of implementing non-reflecting boundary conditions, high-fidelity resolution of shocks and waves, and a genuinely multidimensional formulation without using a dimensional-splitting approach. In particular, because Riemann solvers, the cornerstones of the Godunov-type upwind schemes, are not needed to capture shocks, the computational logic of the present method is considerably simpler. To demonstrate the capability of the present method, numerical results are presented for several benchmark problems including oblique shock reflection, supersonic flow over a wedge, and a 3D detonation flow.

Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola

NASA Astrophysics Data System (ADS)

Dhakshnamoorthy, Balasundaresan; Rohaim, Ahmed; Rui, Huan; Blachowicz, Lydia; Roux, Benoît

2016-09-01

The selectivity filter is an essential functional element of K+ channels that is highly conserved both in terms of its primary sequence and its three-dimensional structure. Here, we investigate the properties of an ion channel from the Gram-positive bacterium Tsukamurella paurometabola with a selectivity filter formed by an uncommon proline-rich sequence. Electrophysiological recordings show that it is a non-selective cation channel and that its activity depends on Ca2+ concentration. In the crystal structure, the selectivity filter adopts a novel conformation with Ca2+ ions bound within the filter near the pore helix where they are coordinated by backbone oxygen atoms, a recurrent motif found in multiple proteins. The binding of Ca2+ ion in the selectivity filter controls the widening of the pore as shown in crystal structures and in molecular dynamics simulations. The structural, functional and computational data provide a characterization of this calcium-gated cationic channel.

Ab Initio Structural Modeling of and Experimental Validation for Chlamydia trachomatis Protein CT296 Reveal Structural Similarity to Fe(II) 2-Oxoglutarate-Dependent Enzymes▿

PubMed Central

Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott

2011-01-01

Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-Å Cα root mean square deviation [RMSD]) the high-resolution (1.8-Å) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur. PMID:21965559

Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes

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

Kemege, Kyle E.; Hickey, John M.; Lovell, Scott

2012-02-13

Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF)more » CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-{angstrom} C{alpha} root mean square deviation [RMSD]) the high-resolution (1.8-{angstrom}) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur.« less

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

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

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

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

Guiding principles for peptide nanotechnology through directed discovery.

PubMed

Lampel, A; Ulijn, R V; Tuttle, T

2018-05-21

Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks - the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design.

BMS3 invariant fluid dynamics at null infinity

NASA Astrophysics Data System (ADS)

Penna, Robert F.

2018-02-01

We revisit the boundary dynamics of asymptotically flat, three dimensional gravity. The boundary is governed by a momentum conservation equation and an energy conservation equation, which we interpret as fluid equations, following the membrane paradigm. We reformulate the boundary’s equations of motion as Hamiltonian flow on the dual of an infinite-dimensional, semi-direct product Lie algebra equipped with a Lie–Poisson bracket. This gives the analogue for boundary fluid dynamics of the Marsden–Ratiu–Weinstein formulation of the compressible Euler equations on a manifold, M, as Hamiltonian flow on the dual of the Lie algebra of \

Three-dimensional simulation of vortex breakdown

NASA Technical Reports Server (NTRS)

Kuruvila, G.; Salas, M. D.

1990-01-01

The integral form of the complete, unsteady, compressible, three-dimensional Navier-Stokes equations in the conservation form, cast in generalized coordinate system, are solved, numerically, to simulate the vortex breakdown phenomenon. The inviscid fluxes are discretized using Roe's upwind-biased flux-difference splitting scheme and the viscous fluxes are discretized using central differencing. Time integration is performed using a backward Euler ADI (alternating direction implicit) scheme. A full approximation multigrid is used to accelerate the convergence to steady state.

Catalytic Subunit 1 of Protein Phosphatase 2A Is a Subunit of the STRIPAK Complex and Governs Fungal Sexual Development.

PubMed

Beier, Anna; Teichert, Ines; Krisp, Christoph; Wolters, Dirk A; Kück, Ulrich

2016-06-21

The generation of complex three-dimensional structures is a key developmental step for most eukaryotic organisms. The details of the molecular machinery controlling this step remain to be determined. An excellent model system to study this general process is the generation of three-dimensional fruiting bodies in filamentous fungi like Sordaria macrospora Fruiting body development is controlled by subunits of the highly conserved striatin-interacting phosphatase and kinase (STRIPAK) complex, which has been described in organisms ranging from yeasts to humans. The highly conserved heterotrimeric protein phosphatase PP2A is a subunit of STRIPAK. Here, catalytic subunit 1 of PP2A was functionally characterized. The Δpp2Ac1 strain is sterile, unable to undergo hyphal fusion, and devoid of ascogonial septation. Further, PP2Ac1, together with STRIPAK subunit PRO22, governs vegetative and stress-related growth. We revealed in vitro catalytic activity of wild-type PP2Ac1, and our in vivo analysis showed that inactive PP2Ac1 blocks the complementation of the sterile deletion strain. Tandem affinity purification, followed by mass spectrometry and yeast two-hybrid analysis, verified that PP2Ac1 is a subunit of STRIPAK. Further, these data indicate links between the STRIPAK complex and other developmental signaling pathways, implying the presence of a large interconnected signaling network that controls eukaryotic developmental processes. The insights gained in our study can be transferred to higher eukaryotes and will be important for understanding eukaryotic cellular development in general. The striatin-interacting phosphatase and kinase (STRIPAK) complex is highly conserved from yeasts to humans and is an important regulator of numerous eukaryotic developmental processes, such as cellular signaling and cell development. Although functional insights into the STRIPAK complex are accumulating, the detailed molecular mechanisms of single subunits are only partially understood. The first fungal STRIPAK was described in Sordaria macrospora, which is a well-established model organism used to study the formation of fungal fruiting bodies, three-dimensional organ-like structures. We analyzed STRIPAK subunit PP2Ac1, catalytic subunit 1 of protein phosphatase PP2A, to study the importance of the catalytic activity of this protein during sexual development. The results of our yeast two-hybrid analysis and tandem affinity purification, followed by mass spectrometry, indicate that PP2Ac1 activity connects STRIPAK with other signaling pathways and thus forms a large interconnected signaling network. Copyright © 2016 Beier et al.

Design of three-dimensional nonimaging concentrators with inhomogeneous media

NASA Astrophysics Data System (ADS)

Minano, J. C.

1986-09-01

A three-dimensional nonimaging concentrator is an optical system that transforms a given four-parametric manifold of rays reaching a surface (entry aperture) into another four-parametric manifold of rays reaching the receiver. A procedure of design of such concentrators is developed. In general, the concentrators use mirrors and inhomogeneous media (i.e., gradient-index media). The concentrator has the maximum concentration allowed by the theorem of conservation of phase-space volume. This is the first known concentrator with such properties. The Welford-Winston edge-ray principle in three-dimensional geometry is proven under several assumptions. The linear compound parabolic concentrator is derived as a particular case of the procedure of design.

Softly-confined water cluster between freestanding graphene sheets

NASA Astrophysics Data System (ADS)

Agustian, Rifan; Akaishi, Akira; Nakamura, Jun

2018-01-01

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

Trimeric Structure of (+)-Pinoresinol-forming Dirigent Protein at 1.95 Å Resolution with Three Isolated Active Sites

DOE PAGES

Kim, Kye-Won; Smith, Clyde A.; Daily, Michael D.; ...

2014-11-19

Control over phenoxy radical-radical coupling reactions in vivo in vascular plants was enigmatic until our discovery of dirigent proteins (DPs, from the Latin dirigere, to guide or align). The first three-dimensional structure of a DP ((+)-pinoresinol-forming DP, 1.95 Å resolution, rhombohedral space group H32)) is reported herein. It has a tightly packed trimeric structure with an eight-stranded β-barrel topology for each DP monomer. Each putative substrate binding and orientation coupling site is located on the trimer surface but too far apart for intermolecular coupling between sites. It is proposed that each site enables stereoselective coupling (using either two coniferyl alcoholmore » radicals or a radical and a monolignol). Interestingly, there are six differentially conserved residues in DPs affording either the (+)- or (₋)-antipodes in the vicinity of the putative binding site and region known to control stereoselectivity. We find DPs are involved in lignan biosynthesis, whereas dirigent domains/sites have been implicated in lignin deposition.« less

Experiments on an unsteady, three-dimensional separation

NASA Technical Reports Server (NTRS)

Henk, R. W.; Reynolds, W. C.; Reed, H. L.

1992-01-01

Unsteady, three-dimensional flow separation occurs in a variety of technical situations including turbomachinery and low-speed aircraft. An experimental program at Stanford in unsteady, three-dimensional, pressure-driven laminar separation has investigated the structure and time-scaling of these flows; of particular interest is the development, washout, and control of flow separation. Results reveal that a two-dimensional, laminar boundary layer passes through several stages on its way to a quasi-steady three-dimensional separation. The quasi-steady state of the separation embodies a complex, unsteady, vortical structure.

NMR structure and conformational dynamics of AtPDFL2.1, a defensin-like peptide from Arabidopsis thaliana.

PubMed

Omidvar, Reza; Xia, Youlin; Porcelli, Fernando; Bohlmann, Holger; Veglia, Gianluigi

2016-12-01

Plant defensins constitute the innate immune response against pathogens such as fungi and bacteria. Typical plant defensins are small, basic peptides that possess a characteristic three-dimensional fold stabilized by three or four disulfide bridges. In addition to known defensin genes, the Arabidopsis genome comprises >300 defensin-like genes coding for small cysteine-rich peptides. One of such genes encodes for AtPDFL2.1, a putative antifungal peptide of 55 amino acids, with six cysteine residues in its primary sequence. To understand the functional role of AtPDFL2.1, we carried out antifungal activity assays and determined its high-resolution three-dimensional structure using multidimensional solution NMR spectroscopy. We found that AtPDFL2.1 displays a strong inhibitory effect against Fusarium graminearum (IC 50 ≈4μM). This peptide folds in the canonical cysteine-stabilized αβ (CSαβ) motif, consisting of one α-helix and one triple-stranded antiparallel β-sheet stabilized by three disulfide bridges and a hydrophobic cluster of residues within its core where the α-helix packs tightly against the β-sheets. Nuclear spin relaxation measurements show that the structure of AtPDFL2.1 is essentially rigid, with the L3 loop located between β-strands 2 and 3 being more flexible and displaying conformational exchange. Interestingly, the dynamic features of loop L3 are conserved among defensins and are probably correlated to the antifungal and receptor binding activities. Copyright © 2016 Elsevier B.V. All rights reserved.

Motion of gas in highly rarefied space

NASA Astrophysics Data System (ADS)

Chirkunov, Yu A.

2017-10-01

A model describing a motion of gas in a highly rarefied space received an unlucky number 13 in the list of the basic models of the motion of gas in the three-dimensional space obtained by L.V. Ovsyannikov. For a given initial pressure distribution, a special choice of mass Lagrangian variables leads to the system describing this motion for which the number of independent variables is less by one. Hence, there is a foliation of a highly rarefied gas with respect to pressure. In a strongly rarefied space for each given initial pressure distribution, all gas particles are localized on a two-dimensional surface that moves with time in this space We found some exact solutions of the obtained system that describe the processes taking place inside of the tornado. For this system we found all nontrivial conservation laws of the first order. In addition to the classical conservation laws the system has another conservation law, which generalizes the energy conservation law. With the additional condition we found another one generalized energy conservation law.

Multi-Hamiltonian structure of the Born-Infeld equation

NASA Astrophysics Data System (ADS)

Arik, Metin; Neyzi, Fahrünisa; Nutku, Yavuz; Olver, Peter J.; Verosky, John M.

1989-06-01

The multi-Hamiltonian structure, conservation laws, and higher order symmetries for the Born-Infeld equation are exhibited. A new transformation of the Born-Infeld equation to the equations of a Chaplygin gas is presented and explored. The Born-Infeld equation is distinguished among two-dimensional hyperbolic systems by its wealth of such multi-Hamiltonian structures.

A proposed architecture for lecithin cholesterol acyl transferase (LCAT): identification of the catalytic triad and molecular modeling.

PubMed Central

Peelman, F.; Vinaimont, N.; Verhee, A.; Vanloo, B.; Verschelde, J. L.; Labeur, C.; Seguret-Mace, S.; Duverger, N.; Hutchinson, G.; Vandekerckhove, J.; Tavernier, J.; Rosseneu, M.

1998-01-01

The enzyme cholesterol lecithin acyl transferase (LCAT) shares the Ser/Asp-Glu/His triad with lipases, esterases and proteases, but the low level of sequence homology between LCAT and these enzymes did not allow for the LCAT fold to be identified yet. We, therefore, relied upon structural homology calculations using threading methods based on alignment of the sequence against a library of solved three-dimensional protein structures, for prediction of the LCAT fold. We propose that LCAT, like lipases, belongs to the alpha/beta hydrolase fold family, and that the central domain of LCAT consists of seven conserved parallel beta-strands connected by four alpha-helices and separated by loops. We used the conserved features of this protein fold for the prediction of functional domains in LCAT, and carried out site-directed mutagenesis for the localization of the active site residues. The wild-type enzyme and mutants were expressed in Cos-1 cells. LCAT mass was measured by ELISA, and enzymatic activity was measured on recombinant HDL, on LDL and on a monomeric substrate. We identified D345 and H377 as the catalytic residues of LCAT, together with F103 and L182 as the oxyanion hole residues. In analogy with lipases, we further propose that a potential "lid" domain at residues 50-74 of LCAT might be involved in the enzyme-substrate interaction. Molecular modeling of human LCAT was carried out using human pancreatic and Candida antarctica lipases as templates. The three-dimensional model proposed here is compatible with the position of natural mutants for either LCAT deficiency or Fish-eye disease. It enables moreover prediction of the LCAT domains involved in the interaction with the phospholipid and cholesterol substrates. PMID:9541390

Mass-corrections for the conservative coupling of flow and transport on collocated meshes

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

Waluga, Christian, E-mail: waluga@ma.tum.de; Wohlmuth, Barbara; Rüde, Ulrich

2016-01-15

Buoyancy-driven flow models demand a careful treatment of the mass-balance equation to avoid spurious source and sink terms in the non-linear coupling between flow and transport. In the context of finite-elements, it is therefore commonly proposed to employ sufficiently rich pressure spaces, containing piecewise constant shape functions to obtain local or even strong mass-conservation. In three-dimensional computations, this usually requires nonconforming approaches, special meshes or higher order velocities, which make these schemes prohibitively expensive for some applications and complicate the implementation into legacy code. In this paper, we therefore propose a lean and conservatively coupled scheme based on standard stabilizedmore » linear equal-order finite elements for the Stokes part and vertex-centered finite volumes for the energy equation. We show that in a weak mass-balance it is possible to recover exact conservation properties by a local flux-correction which can be computed efficiently on the control volume boundaries of the transport mesh. We discuss implementation aspects and demonstrate the effectiveness of the flux-correction by different two- and three-dimensional examples which are motivated by geophysical applications.« less

Parallel computation of three-dimensional aeroelastic fluid-structure interaction

NASA Astrophysics Data System (ADS)

Sadeghi, Mani

This dissertation presents a numerical method for the parallel computation of aeroelasticity (ParCAE). A flow solver is coupled to a structural solver by use of a fluid-structure interface method. The integration of the three-dimensional unsteady Navier-Stokes equations is performed in the time domain, simultaneously to the integration of a modal three-dimensional structural model. The flow solution is accelerated by using a multigrid method and a parallel multiblock approach. Fluid-structure coupling is achieved by subiteration. A grid-deformation algorithm is developed to interpolate the deformation of the structural boundaries onto the flow grid. The code is formulated to allow application to general, three-dimensional, complex configurations with multiple independent structures. Computational results are presented for various configurations, such as turbomachinery blade rows and aircraft wings. Investigations are performed on vortex-induced vibrations, effects of cascade mistuning on flutter, and cases of nonlinear cascade and wing flutter.

Three dimensional electron microscopy and in silico tools for macromolecular structure determination

PubMed Central

Borkotoky, Subhomoi; Meena, Chetan Kumar; Khan, Mohammad Wahab; Murali, Ayaluru

2013-01-01

Recently, structural biology witnessed a major tool - electron microscopy - in solving the structures of macromolecules in addition to the conventional techniques, X-ray crystallography and nuclear magnetic resonance (NMR). Three dimensional transmission electron microscopy (3DTEM) is one of the most sophisticated techniques for structure determination of molecular machines. Known to give the 3-dimensional structures in its native form with literally no upper limit on size of the macromolecule, this tool does not need the crystallization of the protein. Combining the 3DTEM data with in silico tools, one can have better refined structure of a desired complex. In this review we are discussing about the recent advancements in three dimensional electron microscopy and tools associated with it. PMID:27092033

Crystal structure of YHI9, the yeast member of the phenazine biosynthesis PhzF enzyme superfamily.

PubMed

Liger, Dominique; Quevillon-Cheruel, Sophie; Sorel, Isabelle; Bremang, Michael; Blondeau, Karine; Aboulfath, Ilham; Janin, Joël; van Tilbeurgh, Herman; Leulliot, Nicolas

2005-09-01

In the Pseudomonas bacterial genomes, the PhzF proteins are involved in the production of phenazine derivative antibiotic and antifungal compounds. The PhzF superfamily however also encompasses proteins in all genomes from bacteria to eukaryotes, for which no function has been assigned. We have determined the three dimensional crystal structure at 2.05 A resolution of YHI9, the yeast member of the PhzF family. YHI9 has a fold similar to bacterial diaminopimelate epimerase, revealing a bimodular structure with an internal symmetry. Residue conservation identifies a putative active site at the interface between the two domains. Evolution of this protein by gene duplication, gene fusion and domain swapping from an ancestral gene containing the "hot dog" fold, identifies the protein as a "kinked double hot dog" fold. Copyright 2005 Wiley-Liss, Inc.

Learning the Cell Structures with Three-Dimensional Models: Students' Achievement by Methods, Type of School and Questions' Cognitive Level

ERIC Educational Resources Information Center

Lazarowitz, Reuven; Naim, Raphael

2014-01-01

The cell topic was taught to 9th-grade students in three modes of instruction: (a) students "hands-on," who constructed three-dimensional cell organelles and macromolecules during the learning process; (b) teacher demonstration of the three-dimensional model of the cell structures; and (c) teaching the cell topic with the regular…

Three Dimensional Immobilization of Beta-Galactosidase on a Silicon Surface (Preprint)

DTIC Science & Technology

2006-12-01

initial activity after 10 days at 24°C. The ability to generate three- dimensional structures with enhanced loading capacity for biosensing molecules...dimensional structures for biosensors (Charles et al. 2004). Silicon samples that had been washed but not activated with APTS did not retain any enzyme...preparation. The use of silica particles to build a 3-dimensional structure not only provides an increased capacity for the immobilization of β

Direct Numerical Simulation of a Temporally Evolving Incompressible Plane Wake: Effect of Initial Conditions on Evolution and Topology

NASA Technical Reports Server (NTRS)

Sondergaard, R.; Cantwell, B.; Mansour, N.

1997-01-01

Direct numerical simulations have been used to examine the effect of the initial disturbance field on the development of three-dimensionality and the transition to turbulence in the incompressible plane wake. The simulations were performed using a new numerical method for solving the time-dependent, three-dimensional, incompressible Navier-Stokes equations in flows with one infinite and two periodic directions. The method uses standard Fast Fourier Transforms and is applicable to cases where the vorticity field is compact in the infinite direction. Initial disturbances fields examined were combinations of two-dimensional waves and symmetric pairs of 60 deg oblique waves at the fundamental, subharmonic, and sub-subharmonic wavelengths. The results of these simulations indicate that the presence of 60 deg disturbances at the subharmonic streamwise wavelength results in the development of strong coherent three-dimensional structures. The resulting strong three-dimensional rate-of-strain triggers the growth of intense fine scale motions. Wakes initiated with 60 deg disturbances at the fundamental streamwise wavelength develop weak coherent streamwise structures, and do not develop significant fine scale motions, even at high Reynolds numbers. The wakes which develop strong three-dimensional structures exhibit growth rates on par with experimentally observed turbulent plane wakes. Wakes which develop only weak three-dimensional structures exhibit significantly lower late time growth rates. Preliminary studies of wakes initiated with an oblique fundamental and a two-dimensional subharmonic, which develop asymmetric coherent oblique structures at the subharmonic wavelength, indicate that significant fine scale motions only develop if the resulting oblique structures are above an angle of approximately 45 deg.

Protein structure based prediction of catalytic residues

PubMed Central

2013-01-01

Background Worldwide structural genomics projects continue to release new protein structures at an unprecedented pace, so far nearly 6000, but only about 60% of these proteins have any sort of functional annotation. Results We explored a range of features that can be used for the prediction of functional residues given a known three-dimensional structure. These features include various centrality measures of nodes in graphs of interacting residues: closeness, betweenness and page-rank centrality. We also analyzed the distance of functional amino acids to the general center of mass (GCM) of the structure, relative solvent accessibility (RSA), and the use of relative entropy as a measure of sequence conservation. From the selected features, neural networks were trained to identify catalytic residues. We found that using distance to the GCM together with amino acid type provide a good discriminant function, when combined independently with sequence conservation. Using an independent test set of 29 annotated protein structures, the method returned 411 of the initial 9262 residues as the most likely to be involved in function. The output 411 residues contain 70 of the annotated 111 catalytic residues. This represents an approximately 14-fold enrichment of catalytic residues on the entire input set (corresponding to a sensitivity of 63% and a precision of 17%), a performance competitive with that of other state-of-the-art methods. Conclusions We found that several of the graph based measures utilize the same underlying feature of protein structures, which can be simply and more effectively captured with the distance to GCM definition. This also has the added the advantage of simplicity and easy implementation. Meanwhile sequence conservation remains by far the most influential feature in identifying functional residues. We also found that due the rapid changes in size and composition of sequence databases, conservation calculations must be recalibrated for specific reference databases. PMID:23433045

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

Three-dimensional computer simulation of non-reacting jet-gas flow mixing in an MHD second stage combustor

NASA Astrophysics Data System (ADS)

Chang, S. L.; Lottes, S. A.; Berry, G. F.

Argonne National Laboratory is investigating the non-reacting jet-gas mixing patterns in a magnetohydrodynamics (MHD) second stage combustor by using a three-dimensional single-phase hydrodynamics computer program. The computer simulation is intended to enhance the understanding of flow and mixing patterns in the combustor, which in turn may improve downstream MHD channel performance. The code is used to examine the three-dimensional effects of the side walls and the distributed jet flows on the non-reacting jet-gas mixing patterns. The code solves the conservation equations of mass, momentum, and energy, and a transport equation of a turbulence parameter and allows permeable surfaces to be specified for any computational cell.

Shock-jump conditions in a general medium: weak-solution approach

NASA Astrophysics Data System (ADS)

Forbes, L. K.; Krzysik, O. A.

2017-05-01

General conservation laws are considered, and the concept of a weak solution is extended to the case of an equation involving three space variables and time. Four-dimensional vector calculus is used to develop general jump conditions at a shock wave in the material. To illustrate the use of this result, jump conditions at a shock in unsteady three-dimensional compressible gas flow are presented. It is then proved rigorously that these reduce to the commonly assumed conditions in coordinates normal and tangential to the shock face. A similar calculation is also outlined for an unsteady three-dimensional shock in magnetohydrodynamics, and in a chemically reactive fluid. The technique is available for determining shock-jump conditions in quite general continuous media.

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

PubMed

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

2014-01-01

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

Framework to model neutral particle flux in convex high aspect ratio structures using one-dimensional radiosity

NASA Astrophysics Data System (ADS)

Manstetten, Paul; Filipovic, Lado; Hössinger, Andreas; Weinbub, Josef; Selberherr, Siegfried

2017-02-01

We present a computationally efficient framework to compute the neutral flux in high aspect ratio structures during three-dimensional plasma etching simulations. The framework is based on a one-dimensional radiosity approach and is applicable to simulations of convex rotationally symmetric holes and convex symmetric trenches with a constant cross-section. The framework is intended to replace the full three-dimensional simulation step required to calculate the neutral flux during plasma etching simulations. Especially for high aspect ratio structures, the computational effort, required to perform the full three-dimensional simulation of the neutral flux at the desired spatial resolution, conflicts with practical simulation time constraints. Our results are in agreement with those obtained by three-dimensional Monte Carlo based ray tracing simulations for various aspect ratios and convex geometries. With this framework we present a comprehensive analysis of the influence of the geometrical properties of high aspect ratio structures as well as of the particle sticking probability on the neutral particle flux.

Crystal Structures of Aedes Aegypt Alanine Glyoxylate Aminotransferase

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

Han,Q.; Robinson, H.; Gao, Y.

Mosquitoes are unique in having evolved two alanine glyoxylate aminotransferases (AGTs). One is 3-hydroxykynurenine transaminase (HKT), which is primarily responsible for catalyzing the transamination of 3-hydroxykynurenine (3-HK) to xanthurenic acid (XA). Interestingly, XA is used by malaria parasites as a chemical trigger for their development within the mosquito. This 3-HK to XA conversion is considered the major mechanism mosquitoes use to detoxify the chemically reactive and potentially toxic 3-HK. The other AGT is a typical dipteran insect AGT and is specific for converting glyoxylic acid to glycine. Here we report the 1.75{angstrom} high-resolution three-dimensional crystal structure of AGT from themore » mosquito Aedes aegypti (AeAGT) and structures of its complexes with reactants glyoxylic acid and alanine at 1.75 and 2.1{angstrom} resolution, respectively. This is the first time that the three-dimensional crystal structures of an AGT with its amino acceptor, glyoxylic acid, and amino donor, alanine, have been determined. The protein is dimeric and adopts the type I-fold of pyridoxal 5-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure, and its binding site is similar to those of other AGTs. The comparison of the AeAGT-glyoxylic acid structure with other AGT structures revealed that these glyoxylic acid binding residues are conserved in most AGTs. Comparison of the AeAGT-alanine structure with that of the Anopheles HKT-inhibitor complex suggests that a Ser-Asn-Phe motif in the latter may be responsible for the substrate specificity of HKT enzymes for 3-HK.« less

Helicity transformation under the collision and merging of two magnetic flux ropes

NASA Astrophysics Data System (ADS)

DeHaas, Timothy; Gekelman, Walter

2017-07-01

Magnetic helicity has become a useful tool in the analysis of astrophysical plasmas. Its conservation in the magnetohydrodynamic limit (and other fluid approaches) constrains the global behavior of large plasma structures. One such astrophysical structure is a magnetic flux rope: a tube-like, current-carrying plasma embedded in an external magnetic field. Bundles of these ropes are commonly observed in the near-earth environment and solar atmosphere. In this well-diagnosed experiment (three-dimensional measurements of ne, Te, Vp, B, J, E, and uflow), two magnetic flux ropes are generated in the Large Plasma Device at UCLA. These ropes are driven kink-unstable to trigger complex motion. As they interact, helicity conservation is examined in regions of reconnection. We examine (1) the transport of helicity and (2) the dissipation of the helicity. As the ropes move and the topology of the field lines diverge, a quasi-separatrix layer (QSL) is formed. As the QSL forms, magnetic helicity is dissipated within this region. At the same time, there is an influx of canonical helicity into the region such that the temporal derivative of magnetic helicity is zero.

Terrestrial laser scanning for heritage conservation: the Cologne Cathedral documentation project

NASA Astrophysics Data System (ADS)

Pritchard, D.; Sperner, J.; Hoepner, S.; Tenschert, R.

2017-08-01

Contemporary terrestrial laser scanners and photogrammetric imaging systems are an invaluable tool in providing objectively precise, as-built records of existing architectural, engineering and industrial sites. The comprehensive three-dimensional (3D) recording of culturally important sites such as heritage buildings, monuments, and sites can serve a variety of invaluable purposes; the data can assist in the conservation, management, and repair of a structure, as well as provide a visually engaging educational resource for both the public and scholars. The acquired data acts as a form of digital preservation, a timeless virtual representation of the as-built structure. The technical capability of these systems is particularly suited for the documentation of a richly articulated and detailed building such as the high Gothic Cologne Cathedral. The 3D documentation of the Cologne Cathedral UNESCO World Heritage Site is a multiphase project developed by Heriot-Watt University, Edinburgh in partnership with the Fresenius University of Applied Sciences, Cologne, and the Metropolitankapitel der Hohen Domkirche Köln Dombauhütte. The project has also received generous support from Zoller + Fröhlich (Z+F) and the City of Cologne.

Advection of Potential Temperature in the Atmosphere of Irradiated Exoplanets: A Robust Mechanism to Explain Radius Inflation

NASA Technical Reports Server (NTRS)

Tremblin, P.; Chabrier, G.; Mayne, N. J.; Amundsen, D. S.; Baraffe, I.; Debras, F.; Drummond, B.; Manners, J.; Fromang, S.

2017-01-01

The anomalously large radii of strongly irradiated exoplanets have remained a major puzzle in astronomy. Based on a two-dimensional steady-state atmospheric circulation model, the validity of which is assessed by comparison to three-dimensional calculations, we reveal a new mechanism, namely the advection of the potential temperature due to mass and longitudinal momentum conservation, a process occurring in the Earth's atmosphere or oceans. In the deep atmosphere, the vanishing heating flux forces the atmospheric structure to converge to a hotter adiabat than the one obtained with 1D calculations, implying a larger radius for the planet. Not only do the calculations reproduce the observed radius of HD 209458b, but also reproduce the observed correlation between radius inflation and irradiation for transiting planets. Vertical advection of potential temperature induced by non-uniform atmospheric heating thus provides a robust mechanism to explain the inflated radii of irradiated hot Jupiters.

Equivalent D = 3 supergravity amplitudes from double copies of three-algebra and two-algebra gauge theories.

PubMed

Huang, Yu-tin; Johansson, Henrik

2013-04-26

We show that three-dimensional supergravity amplitudes can be obtained as double copies of either three-algebra super-Chern-Simons matter theory or two-algebra super-Yang-Mills theory when either theory is organized to display the color-kinematics duality. We prove that only helicity-conserving four-dimensional gravity amplitudes have nonvanishing descendants when reduced to three dimensions, implying the vanishing of odd-multiplicity S-matrix elements, in agreement with Chern-Simons matter theory. We explicitly verify the double-copy correspondence at four and six points for N = 12,10,8 supergravity theories and discuss its validity for all multiplicity.

Functionally Graded Metal-Metal Composite Structures

NASA Technical Reports Server (NTRS)

Brice, Craig A. (Inventor)

2017-01-01

Methods and devices are disclosed for creating a multiple alloy composite structure by forming a three-dimensional arrangement of a first alloy composition in which the three-dimensional arrangement has a substantially open and continuous porosity. The three-dimensional arrangement of the first alloy composition is infused with at least a second alloy composition, where the second alloy composition comprises a shape memory alloy. The three-dimensional arrangement is consolidated into a fully dense solid structure, and the original shape of the second alloy composition is set for reversible transformation. Strain is applied to the fully dense solid structure, which is treated with heat so that the shape memory alloy composition becomes memory activated to recover the original shape. An interwoven composite of the first alloy composition and the memory-activated second alloy composition is thereby formed in the multiple alloy composite structure.

Three-dimensional biofilm structure quantification.

PubMed

Beyenal, Haluk; Donovan, Conrad; Lewandowski, Zbigniew; Harkin, Gary

2004-12-01

Quantitative parameters describing biofilm physical structure have been extracted from three-dimensional confocal laser scanning microscopy images and used to compare biofilm structures, monitor biofilm development, and quantify environmental factors affecting biofilm structure. Researchers have previously used biovolume, volume to surface ratio, roughness coefficient, and mean and maximum thicknesses to compare biofilm structures. The selection of these parameters is dependent on the availability of software to perform calculations. We believe it is necessary to develop more comprehensive parameters to describe heterogeneous biofilm morphology in three dimensions. This research presents parameters describing three-dimensional biofilm heterogeneity, size, and morphology of biomass calculated from confocal laser scanning microscopy images. This study extends previous work which extracted quantitative parameters regarding morphological features from two-dimensional biofilm images to three-dimensional biofilm images. We describe two types of parameters: (1) textural parameters showing microscale heterogeneity of biofilms and (2) volumetric parameters describing size and morphology of biomass. The three-dimensional features presented are average (ADD) and maximum diffusion distances (MDD), fractal dimension, average run lengths (in X, Y and Z directions), aspect ratio, textural entropy, energy and homogeneity. We discuss the meaning of each parameter and present the calculations in detail. The developed algorithms, including automatic thresholding, are implemented in software as MATLAB programs which will be available at site prior to publication of the paper.

Computation of an Underexpanded 3-D Rectangular Jet by the CE/SE Method

NASA Technical Reports Server (NTRS)

Loh, Ching Y.; Himansu, Ananda; Wang, Xiao Y.; Jorgenson, Philip C. E.

2000-01-01

Recently, an unstructured three-dimensional space-time conservation element and solution element (CE/SE) Euler solver was developed. Now it is also developed for parallel computation using METIS for domain decomposition and MPI (message passing interface). The method is employed here to numerically study the near-field of a typical 3-D rectangular under-expanded jet. For the computed case-a jet with Mach number Mj = 1.6. with a very modest grid of 1.7 million tetrahedrons, the flow features such as the shock-cell structures and the axis switching, are in good qualitative agreement with experimental results.

Closedness of orbits in a space with SU(2) Poisson structure

NASA Astrophysics Data System (ADS)

Fatollahi, Amir H.; Shariati, Ahmad; Khorrami, Mohammad

2014-06-01

The closedness of orbits of central forces is addressed in a three-dimensional space in which the Poisson bracket among the coordinates is that of the SU(2) Lie algebra. In particular it is shown that among problems with spherically symmetric potential energies, it is only the Kepler problem for which all bounded orbits are closed. In analogy with the case of the ordinary space, a conserved vector (apart from the angular momentum) is explicitly constructed, which is responsible for the orbits being closed. This is the analog of the Laplace-Runge-Lenz vector. The algebra of the constants of the motion is also worked out.

One-dimensional, two-dimensional, and three-dimensional photonic crystals fabricated with interferometric techniques on ultrafine-grain silver halide emulsions

NASA Astrophysics Data System (ADS)

Ulibarrena, Manuel; Carretero, Luis; Acebal, Pablo; Madrigal, Roque; Blaya, Salvador; Fimia, Antonio

2004-09-01

Holographic techniques have been used for manufacturing multiple band one-dimensional, two-dimensional, and three-dimensional photonic crystals with different configurations, by multiplexing reflection and transmission setups on a single layer of holographic material. The recording material used for storage is an ultra fine grain silver halide emulsion, with an average grain size around 20 nm. The results are a set of photonic crystals with the one-dimensional, two-dimensional, and three-dimensional index modulation structure consisting of silver halide particles embedded in the gelatin layer of the emulsion. The characterisation of the fabricated photonic crystals by measuring their transmission band structures has been done and compared with theoretical calculations.

Fabrication of 3D nano-structures using reverse imprint lithography

NASA Astrophysics Data System (ADS)

Han, Kang-Soo; Hong, Sung-Hoon; Kim, Kang-In; Cho, Joong-Yeon; Choi, Kyung-woo; Lee, Heon

2013-02-01

In spite of the fact that the fabrication process of three-dimensional nano-structures is complicated and expensive, it can be applied to a range of devices to increase their efficiency and sensitivity. Simple and inexpensive fabrication of three-dimensional nano-structures is necessary. In this study, reverse imprint lithography (RIL) with UV-curable benzylmethacrylate, methacryloxypropyl terminated poly-dimethylsiloxane (M-PDMS) resin and ZnO-nano-particle-dispersed resin was used to fabricate three-dimensional nano-structures. UV-curable resins were placed between a silicon stamp and a PVA transfer template, followed by a UV curing process. Then, the silicon stamp was detached and a 2D pattern layer was transferred to the substrate using diluted UV-curable glue. Consequently, three-dimensional nano-structures were formed by stacking the two-dimensional nano-patterned layers. RIL was applied to a light-emitting diode (LED) to evaluate the optical effects of a nano-patterned layer. As a result, the light extraction of the patterned LED was increased by about 12% compared to an unpatterned LED.

Fabrication of 3D nano-structures using reverse imprint lithography.

PubMed

Han, Kang-Soo; Hong, Sung-Hoon; Kim, Kang-In; Cho, Joong-Yeon; Choi, Kyung-Woo; Lee, Heon

2013-02-01

In spite of the fact that the fabrication process of three-dimensional nano-structures is complicated and expensive, it can be applied to a range of devices to increase their efficiency and sensitivity. Simple and inexpensive fabrication of three-dimensional nano-structures is necessary. In this study, reverse imprint lithography (RIL) with UV-curable benzylmethacrylate, methacryloxypropyl terminated poly-dimethylsiloxane (M-PDMS) resin and ZnO-nano-particle-dispersed resin was used to fabricate three-dimensional nano-structures.UV-curable resins were placed between a silicon stamp and a PVA transfer template, followed by a UV curing process. Then, the silicon stamp was detached and a 2D pattern layer was transferred to the substrate using diluted UV-curable glue. Consequently, three-dimensional nano-structures were formed by stacking the two-dimensional nano-patterned layers. RIL was applied to a light-emitting diode (LED) to evaluate the optical effects of a nano-patterned layer. As a result, the light extraction of the patterned LED was increased by about 12% compared to an unpatterned LED.

Homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. AMS8

PubMed Central

Garba, Lawal; Mohamad Yussoff, Mohamad Ariff; Abd Halim, Khairul Bariyyah; Ishak, Siti Nor Hasmah; Mohamad Ali, Mohd Shukuri; Oslan, Siti Nurbaya

2018-01-01

Membrane-bound fatty acid desaturases perform oxygenated desaturation reactions to insert double bonds within fatty acyl chains in regioselective and stereoselective manners. The Δ9-fatty acid desaturase strictly creates the first double bond between C9 and 10 positions of most saturated substrates. As the three-dimensional structures of the bacterial membrane fatty acid desaturases are not available, relevant information about the enzymes are derived from their amino acid sequences, site-directed mutagenesis and domain swapping in similar membrane-bound desaturases. The cold-tolerant Pseudomonas sp. AMS8 was found to produce high amount of monounsaturated fatty acids at low temperature. Subsequently, an active Δ9-fatty acid desaturase was isolated and functionally expressed in Escherichia coli. In this paper we report homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. AMS8 for the first time to the best of our knowledge. Three dimensional structure of the enzyme was built using MODELLER version 9.18 using a suitable template. The protein model contained the three conserved-histidine residues typical for all membrane-bound desaturase catalytic activity. The structure was subjected to energy minimization and checked for correctness using Ramachandran plots and ERRAT, which showed a good quality model of 91.6 and 65.0%, respectively. The protein model was used to preform MD simulation and docking of palmitic acid using CHARMM36 force field in GROMACS Version 5 and Autodock tool Version 4.2, respectively. The docking simulation with the lowest binding energy, −6.8 kcal/mol had a number of residues in close contact with the docked palmitic acid namely, Ile26, Tyr95, Val179, Gly180, Pro64, Glu203, His34, His206, His71, Arg182, Thr85, Lys98 and His177. Interestingly, among the binding residues are His34, His71 and His206 from the first, second, and third conserved histidine motif, respectively, which constitute the active site of the enzyme. The results obtained are in compliance with the in vivo activity of the Δ9-fatty acid desaturase on the membrane phospholipids. PMID:29576935

Proteus three-dimensional Navier-Stokes computer code, version 1.0. Volume 3: Programmer's reference

NASA Technical Reports Server (NTRS)

Towne, Charles E.; Schwab, John R.; Bui, Trong T.

1993-01-01

A computer code called Proteus 3D was developed to solve the three-dimensional, Reynolds-averaged, unsteady compressible Navier-Stokes equations in strong conservation law form. The objective in this effort was to develop a code for aerospace propulsion applications that is easy to use and easy to modify. Code readability, modularity, and documentation were emphasized. The governing equations are solved in generalized nonorthogonal body fitted coordinates, by marching in time using a fully-coupled ADI solution procedure. The boundary conditions are treated implicitly. All terms, including the diffusion terms, are linearized using second-order Taylor series expansions. Turbulence is modeled using either an algebraic or two-equation eddy viscosity model. The thin-layer or Euler equations may also be solved. The energy equation may be eliminated by the assumption of constant total enthalpy. Explicit and implicit artificial viscosity may be used. Several time step options are available for convergence acceleration. The documentation is divided into three volumes. The Programmer's Reference contains detailed information useful when modifying the program. The program structure, the Fortran variables stored in common blocks, and the details of each subprogram are described.

More About The Farley Three-Dimensional Braider

NASA Technical Reports Server (NTRS)

Farley, Gary L.

1993-01-01

Farley three-dimensional braider, undergoing development, is machine for automatic fabrication of three-dimensional braided structures. Incorporates yarns into structure at arbitrary braid angles to produce complicated shape. Braiding surface includes movable braiding segments containing pivot points, along which yarn carriers travel during braiding process. Yarn carrier travels along sequence of pivot points as braiding segments move. Combined motions position yarns for braiding onto preform. Intended for use in making fiber preforms for fiber/matrix composite parts, such as multiblade propellers. Machine also described in "Farley Three-Dimensional Braiding Machine" (LAR-13911).

Seismic response of 3D steel buildings considering the effect of PR connections and gravity frames.

PubMed

Reyes-Salazar, Alfredo; Bojórquez, Edén; Haldar, Achintya; López-Barraza, Arturo; Rivera-Salas, J Luz

2014-01-01

The nonlinear seismic responses of 3D steel buildings with perimeter moment resisting frames (PMRF) and interior gravity frames (IGF) are studied explicitly considering the contribution of the IGF. The effect on the structural response of the stiffness of the beam-to-column connections of the IGF, which is usually neglected, is also studied. It is commonly believed that the flexibility of shear connections is negligible and that 2D models can be used to properly represent 3D real structures. The results of the study indicate, however, that the moments developed on columns of IGF can be considerable and that modeling buildings as plane frames may result in very conservative designs. The contribution of IGF to the lateral structural resistance may be significant. The contribution increases when their connections are assumed to be partially restrained (PR). The incremented participation of IGF when the stiffness of their connections is considered helps to counteract the no conservative effect that results in practice when lateral seismic loads are not considered in IGF while designing steel buildings with PMRF. Thus, if the structural system under consideration is used, the three-dimensional model should be used in seismic analysis and the IGF and the stiffness of their connections should be considered as part of the lateral resistance system.

Computational unsteady aerodynamics for lifting surfaces

NASA Technical Reports Server (NTRS)

Edwards, John W.

1988-01-01

Two dimensional problems are solved using numerical techniques. Navier-Stokes equations are studied both in the vorticity-stream function formulation which appears to be the optimal choice for two dimensional problems, using a storage approach, and in the velocity pressure formulation which minimizes the number of unknowns in three dimensional problems. Analysis shows that compact centered conservative second order schemes for the vorticity equation are the most robust for high Reynolds number flows. Serious difficulties remain in the choice of turbulent models, to keep reasonable CPU efficiency.

Structural analysis of key gap junction domains--Lessons from genome data and disease-linked mutants.

PubMed

Bai, Donglin

2016-02-01

A gap junction (GJ) channel is formed by docking of two GJ hemichannels and each of these hemichannels is a hexamer of connexins. All connexin genes have been identified in human, mouse, and rat genomes and their homologous genes in many other vertebrates are available in public databases. The protein sequences of these connexins align well with high sequence identity in the same connexin across different species. Domains in closely related connexins and several residues in all known connexins are also well-conserved. These conserved residues form signatures (also known as sequence logos) in these domains and are likely to play important biological functions. In this review, the sequence logos of individual connexins, groups of connexins with common ancestors, and all connexins are analyzed to visualize natural evolutionary variations and the hot spots for human disease-linked mutations. Several gap junction domains are homologous, likely forming similar structures essential for their function. The availability of a high resolution Cx26 GJ structure and the subsequently-derived homology structure models for other connexin GJ channels elevated our understanding of sequence logos at the three-dimensional GJ structure level, thus facilitating the understanding of how disease-linked connexin mutants might impair GJ structure and function. This knowledge will enable the design of complementary variants to rescue disease-linked mutants. Copyright © 2015 Elsevier Ltd. All rights reserved.

COMMIX-PPC: A three-dimensional transient multicomponent computer program for analyzing performance of power plant condensers

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

Chien, T.H.; Domanus, H.M.; Sha, W.T.

1993-02-01

The COMMIX-PPC computer pregrain is an extended and improved version of earlier COMMIX codes and is specifically designed for evaluating the thermal performance of power plant condensers. The COMMIX codes are general-purpose computer programs for the analysis of fluid flow and heat transfer in complex Industrial systems. In COMMIX-PPC, two major features have been added to previously published COMMIX codes. One feature is the incorporation of one-dimensional equations of conservation of mass, momentum, and energy on the tube stile and the proper accounting for the thermal interaction between shell and tube side through the porous-medium approach. The other added featuremore » is the extension of the three-dimensional conservation equations for shell-side flow to treat the flow of a multicomponent medium. COMMIX-PPC is designed to perform steady-state and transient. Three-dimensional analysis of fluid flow with heat transfer tn a power plant condenser. However, the code is designed in a generalized fashion so that, with some modification, it can be used to analyze processes in any heat exchanger or other single-phase engineering applications. Volume I (Equations and Numerics) of this report describes in detail the basic equations, formulation, solution procedures, and models for a phenomena. Volume II (User's Guide and Manual) contains the input instruction, flow charts, sample problems, and descriptions of available options and boundary conditions.« less

Density and pressure variability in the mesosphere and thermosphere

NASA Technical Reports Server (NTRS)

Davis, T. M.

1986-01-01

In an effort to isolate the essential physics of the mesosphere and the thermosphere, a steady one-dimensional density and pressure model has been developed in support of related NASA activities, i.e., projects such as the AOTV and the Space Station. The model incorporates a zeroth order basic state including both the three-dimensional wind field and its associated shear structure, etc. A first order wave field is also incorporated in period bands ranging from about one second to one day. Both basic state and perturbation quantities satsify the combined constraints of mass, linear momentum and energy conservation on the midlatitude beta plane. A numerical (iterative) technique is used to solve for the vertical wind which is coupled to the density and pressure fields. The temperature structure from 1 to 1000 km and the lower boundary conditions are specified using the U.S. Standard Atmosphere 1976. Vertical winds are initialized at the top of the Planetary Boundary Layer using Ekman pumping values over flat terrain. The model also allows for the generation of waves during the geostrophic adjustment process and incorporates wave nonlinearity effects.

ADER schemes for scalar non-linear hyperbolic conservation laws with source terms in three-space dimensions

NASA Astrophysics Data System (ADS)

Toro, E. F.; Titarev, V. A.

2005-01-01

In this paper we develop non-linear ADER schemes for time-dependent scalar linear and non-linear conservation laws in one-, two- and three-space dimensions. Numerical results of schemes of up to fifth order of accuracy in both time and space illustrate that the designed order of accuracy is achieved in all space dimensions for a fixed Courant number and essentially non-oscillatory results are obtained for solutions with discontinuities. We also present preliminary results for two-dimensional non-linear systems.

Structural basis of Bloom syndrome (BS) causing mutations in the BLM helicase domain.

PubMed Central

Rong, S. B.; Väliaho, J.; Vihinen, M.

2000-01-01

BACKGROUND: Bloom syndrome (BS) is characterized by mutations within the BLM gene. The Bloom syndrome protein (BLM) has similarity to the RecQ subfamily of DNA helicases, which contain seven conserved helicase domains and share significant sequence and structural similarity with the Rep and PcrA DNA helicases. We modeled the three-dimensional structure of the BLM helicase domain to analyze the structural basis of BS-causing mutations. MATERIALS AND METHODS: The sequence alignment was performed for RecQ DNA helicases and Rep and PcrA helicases. The crystal structure of PcrA helicase (PDB entry 3PJR) was used as the template for modeling the BLM helicase domain. The model was used to infer the function of BLM and to analyze the effect of the mutations. RESULTS: The structural model with good stereochemistry of the BLM helicase domain contains two subdomains, 1A and 2A. The electrostatic potential of the model is highly negative over most of the surface, except for the cleft between subdomains 1A and 2A which is similar to the template protein. The ATP-binding site is located inside the model between subdomains 1A and 2A; whereas, the DNA-binding region is situated at the surface cleft, with positive potential between 1A and 2A. CONCLUSIONS: The three-dimensional structure of the BLM helicase domain was modeled and applied to interpret BS-causing mutations. The mutation I841T is likely to weaken DNA binding, while the mutations C891R, C901Y, and Q672R presumably disturb the ATP binding. In addition, other critical positions are discussed. PMID:10965492

On the continuity of mean total normal stress in geometrical multiscale cardiovascular problems

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

Blanco, Pablo J., E-mail: pjblanco@lncc.br; INCT-MACC, Instituto Nacional de Ciência e Tecnologia em Medicina Assistida por Computação Científica, Petrópolis; Deparis, Simone, E-mail: simone.deparis@epfl.ch

2013-10-15

In this work an iterative strategy to implicitly couple dimensionally-heterogeneous blood flow models accounting for the continuity of mean total normal stress at interface boundaries is developed. Conservation of mean total normal stress in the coupling of heterogeneous models is mandatory to satisfy energetic consistency between them. Nevertheless, existing methodologies are based on modifications of the Navier–Stokes variational formulation, which are undesired when dealing with fluid–structure interaction or black box codes. The proposed methodology makes possible to couple one-dimensional and three-dimensional fluid–structure interaction models, enforcing the continuity of mean total normal stress while just imposing flow rate data or evenmore » the classical Neumann boundary data to the models. This is accomplished by modifying an existing iterative algorithm, which is also able to account for the continuity of the vessel area, when required. Comparisons are performed to assess differences in the convergence properties of the algorithms when considering the continuity of mean normal stress and the continuity of mean total normal stress for a wide range of flow regimes. Finally, examples in the physiological regime are shown to evaluate the importance, or not, of considering the continuity of mean total normal stress in hemodynamics simulations.« less

Three-dimensional structural analysis using interactive graphics

NASA Technical Reports Server (NTRS)

Biffle, J.; Sumlin, H. A.

1975-01-01

The application of computer interactive graphics to three-dimensional structural analysis was described, with emphasis on the following aspects: (1) structural analysis, and (2) generation and checking of input data and examination of the large volume of output data (stresses, displacements, velocities, accelerations). Handling of three-dimensional input processing with a special MESH3D computer program was explained. Similarly, a special code PLTZ may be used to perform all the needed tasks for output processing from a finite element code. Examples were illustrated.

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

McHugh, P.R.; Ramshaw, J.D.

MAGMA is a FORTRAN computer code designed to viscous flow in in situ vitrification melt pools. It models three-dimensional, incompressible, viscous flow and heat transfer. The momentum equation is coupled to the temperature field through the buoyancy force terms arising from the Boussinesq approximation. All fluid properties, except density, are assumed variable. Density is assumed constant except in the buoyancy force terms in the momentum equation. A simple melting model based on the enthalpy method allows the study of the melt front progression and latent heat effects. An indirect addressing scheme used in the numerical solution of the momentum equationmore » voids unnecessary calculations in cells devoid of liquid. Two-dimensional calculations can be performed using either rectangular or cylindrical coordinates, while three-dimensional calculations use rectangular coordinates. All derivatives are approximated by finite differences. The incompressible Navier-Stokes equations are solved using a new fully implicit iterative technique, while the energy equation is differenced explicitly in time. Spatial derivatives are written in conservative form using a uniform, rectangular, staggered mesh based on the marker and cell placement of variables. Convective terms are differenced using a weighted average of centered and donor cell differencing to ensure numerical stability. Complete descriptions of MAGMA governing equations, numerics, code structure, and code verification are provided. 14 refs.« less

Highly cytocompatible and flexible three-dimensional graphene/polydimethylsiloxane composite for culture and electrochemical detection of L929 fibroblast cells.

PubMed

Waiwijit, Uraiwan; Maturos, Thitima; Pakapongpan, Saithip; Phokharatkul, Ditsayut; Wisitsoraat, Anurat; Tuantranont, Adisorn

2016-08-01

Recently, three-dimensional graphene interconnected network has attracted great interest as a scaffold structure for tissue engineering due to its high biocompatibility, high electrical conductivity, high specific surface area and high porosity. However, free-standing three-dimensional graphene exhibits poor flexibility and stability due to ease of disintegration during processing. In this work, three-dimensional graphene is composited with polydimethylsiloxane to improve the structural flexibility and stability by a new simple two-step process comprising dip coating of polydimethylsiloxane on chemical vapor deposited graphene/Ni foam and wet etching of nickel foam. Structural characterizations confirmed an interconnected three-dimensional multi-layer graphene structure with thin polydimethylsiloxane scaffold. The composite was employed as a substrate for culture of L929 fibroblast cells and its cytocompatibility was evaluated by cell viability (Alamar blue assay), reactive oxygen species production and vinculin immunofluorescence imaging. The result revealed that cell viability on three-dimensional graphene/polydimethylsiloxane composite increased with increasing culture time and was slightly different from a polystyrene substrate (control). Moreover, cells cultured on three-dimensional graphene/polydimethylsiloxane composite generated less ROS than the control at culture times of 3-6 h. The results of immunofluorescence staining demonstrated that fibroblast cells expressed adhesion protein (vinculin) and adhered well on three-dimensional graphene/polydimethylsiloxane surface. Good cell adhesion could be attributed to suitable surface properties of three-dimensional graphene/polydimethylsiloxane with moderate contact angle and small negative zeta potential in culture solution. The results of electrochemical study by cyclic voltammetry showed that an oxidation current signal with no apparent peak was induced by fibroblast cells and the oxidation current at an oxidation potential of +0.9 V increased linearly with increasing cell number. Therefore, the three-dimensional graphene/polydimethylsiloxane composite exhibits high cytocompatibility and can potentially be used as a conductive substrate for cell-based electrochemical sensing. © The Author(s) 2016.

An implicit solution of the three-dimensional Navier-Stokes equations for an airfoil spanning a wind tunnel. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Moitra, A.

1982-01-01

An implicit finite-difference algorithm is developed for the numerical solution of the incompressible three dimensional Navier-Stokes equations in the non-conservative primitive-variable formulation. The flow field about an airfoil spanning a wind-tunnel is computed. The coordinate system is generated by an extension of the two dimensional body-fitted coordinate generation techniques of Thompson, as well as that of Sorenson, into three dimensions. Two dimensional grids are stacked along a spanwise coordinate defined by a simple analytical function. A Poisson pressure equation for advancing the pressure in time is arrived at by performing a divergence operation on the momentum equations. The pressure at each time-step is calculated on the assumption that continuity be unconditionally satisfied. An eddy viscosity coefficient, computed according to the algebraic turbulence formulation of Baldwin and Lomax, simulates the effects of turbulence.

Austerity and Geometric Structure of Field Theories

NASA Astrophysics Data System (ADS)

Kheyfets, Arkady

The relation between the austerity idea and the geometric structure of the three basic field theories- -electrodynamics, Yang-Mills theory, and general relativity --is studied. The idea of austerity was originally suggested by J. A. Wheeler in an attempt to formulate the laws of physics in such a way that they would come into being only within "the gates of time" extending from big bang to big crunch, rather than exist from everlasting to everlasting. One of the most significant manifestations of the austerity idea in field theories is thought to be expressed by the boundary of a boundary principle (BBP). The BBP says that almost all content of the field theories can be deduced from the topological identity (PAR-DIFF)(CCIRC)(PAR -DIFF) = 0 used twice, at the 1-2-3-dimensional level (providing the homgeneous field equations), and at the 2-3-4-dimensional level (providing the conservation laws for the source currents). There are some difficulties in this line of thought due to the apparent lack of universality in application of the BBP to the three basic modern field theories--electrodynamics, Yang-Mills theory, and general relativity. This dissertation: (a) analyses the difficulties by means of algebraic topology, integration theory and modern differential geometry based on the concepts of principal bundles and Ehresmann connections; (b) extends the BBP to the unified Kaluza-Klein theory; (c) reformulates the inhomogeneous field equations and the BBP in terms of E. Cartan moment of rotation, in the way universal for all the three theories and compatible with the original austerity idea; (d) underlines the important role of the soldering structure on spacetime, and indicates that the future development of the austerity idea would involve the generalized theories, including the soldering form as a dynamical variable rather than as a background structure.

In silico ligand binding studies of cyanogenic β-glucosidase, dhurrinase-2 from Sorghum bicolor.

PubMed

Mahajan, Chavi; Patel, Krunal; Khan, Bashir M; Rawal, Shuban S

2015-07-01

Dhurrinase, a cyanogenic β-glucosidase from Sorghum bicolor is the key enzyme responsible for the hydrolysis of dhurrin to produce toxic hydrogen cyanide, as a part of plant defence mechanism. Dhurrinase 1 (SbDhr1) and dhurrinase 2 (SbDhr2), two isozymes have been isolated and characterized from S. bicolor. However, there is no information in the literature about the three dimensional (3D) structure of SbDhr2 and molecular interactions involved between the protein and ligand. In this study, the three dimensional structure of SbDhr2 was built based on homology modeling by using the X-ray crystallographic structure of its close homologue SbDhr1 as the template. The generated 3D model was energy minimized and the quality was validated by Ramachndran plot, various bioinformatic tools and their relevant parameters. Stability, folding-unfolding and flexibility of the modeled SbDhr2 was evaluated on the basis of RMSD, radius of gyration (Rg) and RMSF values respectively, obtained through molecular dynamic (MD) simulation. Further, molecular docking was performed with its natural substrate dhurrin, one substrate analogue, three un-natural substrates, and one inhibitor. Analysis of molecular interactions in the SbDhr2-ligand complexes revealed the key amino acid residues responsible to stabilize the ligands within the binding pocket through non-bonded interactions and some of them were found to be conserved (Glu239, Tyr381, Trp426, Glu454, Trp511). Reasonably broader substrate specificity of SbDhr2 was explained through the wider entrance passage observed in comparison to SbDhr1.

A New Runge-Kutta Discontinuous Galerkin Method with Conservation Constraint to Improve CFL Condition for Solving Conservation Laws

PubMed Central

Xu, Zhiliang; Chen, Xu-Yan; Liu, Yingjie

2014-01-01

We present a new formulation of the Runge-Kutta discontinuous Galerkin (RKDG) method [9, 8, 7, 6] for solving conservation Laws with increased CFL numbers. The new formulation requires the computed RKDG solution in a cell to satisfy additional conservation constraint in adjacent cells and does not increase the complexity or change the compactness of the RKDG method. Numerical computations for solving one-dimensional and two-dimensional scalar and systems of nonlinear hyperbolic conservation laws are performed with approximate solutions represented by piecewise quadratic and cubic polynomials, respectively. The hierarchical reconstruction [17, 33] is applied as a limiter to eliminate spurious oscillations in discontinuous solutions. From both numerical experiments and the analytic estimate of the CFL number of the newly formulated method, we find that: 1) this new formulation improves the CFL number over the original RKDG formulation by at least three times or more and thus reduces the overall computational cost; and 2) the new formulation essentially does not compromise the resolution of the numerical solutions of shock wave problems compared with ones computed by the RKDG method. PMID:25414520

Semi-implicit finite difference methods for three-dimensional shallow water flow

USGS Publications Warehouse

Casulli, Vincenzo; Cheng, Ralph T.

1992-01-01

A semi-implicit finite difference method for the numerical solution of three-dimensional shallow water flows is presented and discussed. The governing equations are the primitive three-dimensional turbulent mean flow equations where the pressure distribution in the vertical has been assumed to be hydrostatic. In the method of solution a minimal degree of implicitness has been adopted in such a fashion that the resulting algorithm is stable and gives a maximal computational efficiency at a minimal computational cost. At each time step the numerical method requires the solution of one large linear system which can be formally decomposed into a set of small three-diagonal systems coupled with one five-diagonal system. All these linear systems are symmetric and positive definite. Thus the existence and uniquencess of the numerical solution are assured. When only one vertical layer is specified, this method reduces as a special case to a semi-implicit scheme for solving the corresponding two-dimensional shallow water equations. The resulting two- and three-dimensional algorithm has been shown to be fast, accurate and mass-conservative and can also be applied to simulate flooding and drying of tidal mud-flats in conjunction with three-dimensional flows. Furthermore, the resulting algorithm is fully vectorizable for an efficient implementation on modern vector computers.

The Two-Dimensional Gabor Function Adapted to Natural Image Statistics: A Model of Simple-Cell Receptive Fields and Sparse Structure in Images.

PubMed

Loxley, P N

2017-10-01

The two-dimensional Gabor function is adapted to natural image statistics, leading to a tractable probabilistic generative model that can be used to model simple cell receptive field profiles, or generate basis functions for sparse coding applications. Learning is found to be most pronounced in three Gabor function parameters representing the size and spatial frequency of the two-dimensional Gabor function and characterized by a nonuniform probability distribution with heavy tails. All three parameters are found to be strongly correlated, resulting in a basis of multiscale Gabor functions with similar aspect ratios and size-dependent spatial frequencies. A key finding is that the distribution of receptive-field sizes is scale invariant over a wide range of values, so there is no characteristic receptive field size selected by natural image statistics. The Gabor function aspect ratio is found to be approximately conserved by the learning rules and is therefore not well determined by natural image statistics. This allows for three distinct solutions: a basis of Gabor functions with sharp orientation resolution at the expense of spatial-frequency resolution, a basis of Gabor functions with sharp spatial-frequency resolution at the expense of orientation resolution, or a basis with unit aspect ratio. Arbitrary mixtures of all three cases are also possible. Two parameters controlling the shape of the marginal distributions in a probabilistic generative model fully account for all three solutions. The best-performing probabilistic generative model for sparse coding applications is found to be a gaussian copula with Pareto marginal probability density functions.

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

NASA Astrophysics Data System (ADS)

Yamauchi, Toyohiko; Iwai, Hidenao; Yamashita, Yutaka

2013-03-01

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

HYDRA-II: A hydrothermal analysis computer code: Volume 2, User's manual

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

McCann, R.A.; Lowery, P.S.; Lessor, D.L.

1987-09-01

HYDRA-II is a hydrothermal computer code capable of three-dimensional analysis of coupled conduction, convection, and thermal radiation problems. This code is especially appropriate for simulating the steady-state performance of spent fuel storage systems. The code has been evaluated for this application for the US Department of Energy's Commercial Spent Fuel Management Program. HYDRA-II provides a finite-difference solution in cartesian coordinates to the equations governing the conservation of mass, momentum, and energy. A cylindrical coordinate system may also be used to enclose the cartesian coordinate system. This exterior coordinate system is useful for modeling cylindrical cask bodies. The difference equations formore » conservation of momentum incorporate directional porosities and permeabilities that are available to model solid structures whose dimensions may be smaller than the computational mesh. The equation for conservation of energy permits modeling of orthotropic physical properties and film resistances. Several automated methods are available to model radiation transfer within enclosures and from fuel rod to fuel rod. The documentation of HYDRA-II is presented in three separate volumes. Volume 1 - Equations and Numerics describes the basic differential equations, illustrates how the difference equations are formulated, and gives the solution procedures employed. This volume, Volume 2 - User's Manual, contains code flow charts, discusses the code structure, provides detailed instructions for preparing an input file, and illustrates the operation of the code by means of a sample problem. The final volume, Volume 3 - Verification/Validation Assessments, provides a comparison between the analytical solution and the numerical simulation for problems with a known solution. 6 refs.« less

Bacterial Transcription as a Target for Antibacterial Drug Development

PubMed Central

Ma, Cong; Yang, Xiao

2016-01-01

SUMMARY Transcription, the first step of gene expression, is carried out by the enzyme RNA polymerase (RNAP) and is regulated through interaction with a series of protein transcription factors. RNAP and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. Despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. The determination of the three-dimensional structures of RNAP and transcription complexes at high resolution over the last 15 years has led to renewed interest in targeting this essential process for antibiotic development by utilizing rational structure-based approaches. In this review, we describe the inhibition of the bacterial transcription process with respect to structural studies of RNAP, highlight recent progress toward the discovery of novel transcription inhibitors, and suggest additional potential antibacterial targets for rational drug design. PMID:26764017

Transonic Navier-Stokes solutions of three-dimensional afterbody flows

NASA Technical Reports Server (NTRS)

Compton, William B., III; Thomas, James L.; Abeyounis, William K.; Mason, Mary L.

1989-01-01

The performance of a three-dimensional Navier-Stokes solution technique in predicting the transonic flow past a nonaxisymmetric nozzle was investigated. The investigation was conducted at free-stream Mach numbers ranging from 0.60 to 0.94 and an angle of attack of 0 degrees. The numerical solution procedure employs the three-dimensional, unsteady, Reynolds-averaged Navier-Stokes equations written in strong conservation form, a thin layer assumption, and the Baldwin-Lomax turbulence model. The equations are solved by using the finite-volume principle in conjunction with an approximately factored upwind-biased numerical algorithm. In the numerical procedure, the jet exhaust is represented by a solid sting. Wind-tunnel data with the jet exhaust simulated by high pressure air were also obtained to compare with the numerical calculations.

Three-Dimensional Navier-Stokes Calculations Using the Modified Space-Time CESE Method

NASA Technical Reports Server (NTRS)

Chang, Chau-lyan

2007-01-01

The space-time conservation element solution element (CESE) method is modified to address the robustness issues of high-aspect-ratio, viscous, near-wall meshes. In this new approach, the dependent variable gradients are evaluated using element edges and the corresponding neighboring solution elements while keeping the original flux integration procedure intact. As such, the excellent flux conservation property is retained and the new edge-based gradients evaluation significantly improves the robustness for high-aspect ratio meshes frequently encountered in three-dimensional, Navier-Stokes calculations. The order of accuracy of the proposed method is demonstrated for oblique acoustic wave propagation, shock-wave interaction, and hypersonic flows over a blunt body. The confirmed second-order convergence along with the enhanced robustness in handling hypersonic blunt body flow calculations makes the proposed approach a very competitive CFD framework for 3D Navier-Stokes simulations.

A three-dimensional, time-dependent model of Mobile Bay

NASA Technical Reports Server (NTRS)

Pitts, F. H.; Farmer, R. C.

1976-01-01

A three-dimensional, time-variant mathematical model for momentum and mass transport in estuaries was developed and its solution implemented on a digital computer. The mathematical model is based on state and conservation equations applied to turbulent flow of a two-component, incompressible fluid having a free surface. Thus, bouyancy effects caused by density differences between the fresh and salt water, inertia from thare river and tidal currents, and differences in hydrostatic head are taken into account. The conservation equations, which are partial differential equations, are solved numerically by an explicit, one-step finite difference scheme and the solutions displayed numerically and graphically. To test the validity of the model, a specific estuary for which scaled model and experimental field data are available, Mobile Bay, was simulated. Comparisons of velocity, salinity and water level data show that the model is valid and a viable means of simulating the hydrodynamics and mass transport in non-idealized estuaries.

Gain in three-dimensional metamaterials utilizing semiconductor quantum structures

NASA Astrophysics Data System (ADS)

Schwaiger, Stephan; Klingbeil, Matthias; Kerbst, Jochen; Rottler, Andreas; Costa, Ricardo; Koitmäe, Aune; Bröll, Markus; Heyn, Christian; Stark, Yuliya; Heitmann, Detlef; Mendach, Stefan

2011-10-01

We demonstrate gain in a three-dimensional metal/semiconductor metamaterial by the integration of optically active semiconductor quantum structures. The rolling-up of a metallic structure on top of strained semiconductor layers containing a quantum well allows us to achieve a tightly bent superlattice consisting of alternating layers of lossy metallic and amplifying gain material. We show that the transmission through the superlattice can be enhanced by exciting the quantum well optically under both pulsed or continuous wave excitation. This points out that our structures can be used as a starting point for arbitrary three-dimensional metamaterials including gain.

The Structure Lacuna

PubMed Central

Boeyens, Jan C.A.; Levendis, Demetrius C.

2012-01-01

Molecular symmetry is intimately connected with the classical concept of three-dimensional molecular structure. In a non-classical theory of wave-like interaction in four-dimensional space-time, both of these concepts and traditional quantum mechanics lose their operational meaning, unless suitably modified. A required reformulation should emphasize the importance of four-dimensional effects like spin and the symmetry effects of space-time curvature that could lead to a fundamentally different understanding of molecular symmetry and structure in terms of elementary number theory. Isolated single molecules have no characteristic shape and macro-biomolecules only develop robust three-dimensional structure in hydrophobic response to aqueous cellular media. PMID:22942753

Recent developments in structural proteomics for protein structure determination.

PubMed

Liu, Hsuan-Liang; Hsu, Jyh-Ping

2005-05-01

The major challenges in structural proteomics include identifying all the proteins on the genome-wide scale, determining their structure-function relationships, and outlining the precise three-dimensional structures of the proteins. Protein structures are typically determined by experimental approaches such as X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. However, the knowledge of three-dimensional space by these techniques is still limited. Thus, computational methods such as comparative and de novo approaches and molecular dynamic simulations are intensively used as alternative tools to predict the three-dimensional structures and dynamic behavior of proteins. This review summarizes recent developments in structural proteomics for protein structure determination; including instrumental methods such as X-ray crystallography and NMR spectroscopy, and computational methods such as comparative and de novo structure prediction and molecular dynamics simulations.

An adaptive mesh-moving and refinement procedure for one-dimensional conservation laws

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Flaherty, Joseph E.; Arney, David C.

1993-01-01

We examine the performance of an adaptive mesh-moving and /or local mesh refinement procedure for the finite difference solution of one-dimensional hyperbolic systems of conservation laws. Adaptive motion of a base mesh is designed to isolate spatially distinct phenomena, and recursive local refinement of the time step and cells of the stationary or moving base mesh is performed in regions where a refinement indicator exceeds a prescribed tolerance. These adaptive procedures are incorporated into a computer code that includes a MacCormack finite difference scheme wih Davis' artificial viscosity model and a discretization error estimate based on Richardson's extrapolation. Experiments are conducted on three problems in order to qualify the advantages of adaptive techniques relative to uniform mesh computations and the relative benefits of mesh moving and refinement. Key results indicate that local mesh refinement, with and without mesh moving, can provide reliable solutions at much lower computational cost than possible on uniform meshes; that mesh motion can be used to improve the results of uniform mesh solutions for a modest computational effort; that the cost of managing the tree data structure associated with refinement is small; and that a combination of mesh motion and refinement reliably produces solutions for the least cost per unit accuracy.

Three-Dimensional High-Order Spectral Volume Method for Solving Maxwell's Equations on Unstructured Grids

NASA Technical Reports Server (NTRS)

Liu, Yen; Vinokur, Marcel; Wang, Z. J.

2004-01-01

A three-dimensional, high-order, conservative, and efficient discontinuous spectral volume (SV) method for the solutions of Maxwell's equations on unstructured grids is presented. The concept of discontinuous 2nd high-order loca1 representations to achieve conservation and high accuracy is utilized in a manner similar to the Discontinuous Galerkin (DG) method, but instead of using a Galerkin finite-element formulation, the SV method is based on a finite-volume approach to attain a simpler formulation. Conventional unstructured finite-volume methods require data reconstruction based on the least-squares formulation using neighboring cell data. Since each unknown employs a different stencil, one must repeat the least-squares inversion for every cell at each time step, or to store the inversion coefficients. In a high-order, three-dimensional computation, the former would involve impractically large CPU time, while for the latter the memory requirement becomes prohibitive. In the SV method, one starts with a relatively coarse grid of triangles or tetrahedra, called spectral volumes (SVs), and partition each SV into a number of structured subcells, called control volumes (CVs), that support a polynomial expansion of a desired degree of precision. The unknowns are cell averages over CVs. If all the SVs are partitioned in a geometrically similar manner, the reconstruction becomes universal as a weighted sum of unknowns, and only a few universal coefficients need to be stored for the surface integrals over CV faces. Since the solution is discontinuous across the SV boundaries, a Riemann solver is thus necessary to maintain conservation. In the paper, multi-parameter and symmetric SV partitions, up to quartic for triangle and cubic for tetrahedron, are first presented. The corresponding weight coefficients for CV face integrals in terms of CV cell averages for each partition are analytically determined. These discretization formulas are then applied to the integral form of the Maxwell equations. All numerical procedures for outer boundary, material interface, zonal interface, and interior SV face are unified with a single characteristic formulation. The load balancing in a massive parallel computing environment is therefore easier to achieve. A parameter is introduced in the Riemann solver to control the strength of the smoothing term. Important aspects of the data structure and its effects to communication and the optimum use of cache memory are discussed. Results will be presented for plane TE and TM waves incident on a perfectly conducting cylinder for up to fifth order of accuracy, and a plane wave incident on a perfectly conducting sphere for up to fourth order of accuracy. Comparisons are made with exact solutions for these cases.

Trimeric structure of (+)-pinoresinol-forming dirigent protein at 1.95 Å resolution with three isolated active sites.

PubMed

Kim, Kye-Won; Smith, Clyde A; Daily, Michael D; Cort, John R; Davin, Laurence B; Lewis, Norman G

2015-01-16

Control over phenoxy radical-radical coupling reactions in vivo in vascular plants was enigmatic until our discovery of dirigent proteins (DPs, from the Latin dirigere, to guide or align). The first three-dimensional structure of a DP ((+)-pinoresinol-forming DP, 1.95 Å resolution, rhombohedral space group H32)) is reported herein. It has a tightly packed trimeric structure with an eight-stranded β-barrel topology for each DP monomer. Each putative substrate binding and orientation coupling site is located on the trimer surface but too far apart for intermolecular coupling between sites. It is proposed that each site enables stereoselective coupling (using either two coniferyl alcohol radicals or a radical and a monolignol). Interestingly, there are six differentially conserved residues in DPs affording either the (+)- or (-)-antipodes in the vicinity of the putative binding site and region known to control stereoselectivity. DPs are involved in lignan biosynthesis, whereas dirigent domains/sites have been implicated in lignin deposition. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Geometry of Conservation Laws for a Class of Parabolic Partial Differential Equations

NASA Astrophysics Data System (ADS)

Clelland, Jeanne Nielsen

1996-08-01

I consider the problem of computing the space of conservation laws for a second-order, parabolic partial differential equation for one function of three independent variables. The PDE is formulated as an exterior differential system {cal I} on a 12 -manifold M, and its conservation laws are identified with the vector space of closed 3-forms in the infinite prolongation of {cal I} modulo the so -called "trivial" conservation laws. I use the tools of exterior differential systems and Cartan's method of equivalence to study the structure of the space of conservation laws. My main result is:. Theorem. Any conservation law for a second-order, parabolic PDE for one function of three independent variables can be represented by a closed 3-form in the differential ideal {cal I} on the original 12-manifold M. I show that if a nontrivial conservation law exists, then {cal I} has a deprolongation to an equivalent system {cal J} on a 7-manifold N, and any conservation law for {cal I} can be expressed as a closed 3-form on N which lies in {cal J}. Furthermore, any such system in the real analytic category is locally equivalent to a system generated by a (parabolic) equation of the formA(u _{xx}u_{yy}-u_sp {xy}{2}) + B_1u_{xx }+2B_2u_{xy} +B_3u_ {yy}+C=0crwhere A, B_{i}, C are functions of x, y, t, u, u_{x}, u _{y}, u_{t}. I compute the space of conservation laws for several examples, and I begin the process of analyzing the general case using Cartan's method of equivalence. I show that the non-linearizable equation u_{t} = {1over2}e ^{-u}(u_{xx}+u_ {yy})has an infinite-dimensional space of conservation laws. This stands in contrast to the two-variable case, for which Bryant and Griffiths showed that any equation whose space of conservation laws has dimension 4 or more is locally equivalent to a linear equation, i.e., is linearizable.

Flux-vector splitting algorithm for chain-rule conservation-law form

NASA Technical Reports Server (NTRS)

Shih, T. I.-P.; Nguyen, H. L.; Willis, E. A.; Steinthorsson, E.; Li, Z.

1991-01-01

A flux-vector splitting algorithm with Newton-Raphson iteration was developed for the 'full compressible' Navier-Stokes equations cast in chain-rule conservation-law form. The algorithm is intended for problems with deforming spatial domains and for problems whose governing equations cannot be cast in strong conservation-law form. The usefulness of the algorithm for such problems was demonstrated by applying it to analyze the unsteady, two- and three-dimensional flows inside one combustion chamber of a Wankel engine under nonfiring conditions. Solutions were obtained to examine the algorithm in terms of conservation error, robustness, and ability to handle complex flows on time-dependent grid systems.

Suitability of a three-dimensional model to measure empathy and its relationship with social and normative adjustment in Spanish adolescents: a cross-sectional study

PubMed Central

Gómez-Ortiz, Olga; Ortega-Ruiz, Rosario; Jolliffe, Darrick; Romera, Eva M.

2017-01-01

Objectives (1) To examine the psychometric properties of the Basic Empathy Scale (BES) with Spanish adolescents, comparing a two and a three-dimensional structure;(2) To analyse the relationship between the three-dimensional empathy and social and normative adjustment in school. Design Transversal and ex post facto retrospective study. Confirmatory factorial analysis, multifactorial invariance analysis and structural equations models were used. Participants 747 students (51.3% girls) from Cordoba, Spain, aged 12–17 years (M=13.8; SD=1.21). Results The original two-dimensional structure was confirmed (cognitive empathy, affective empathy), but a three-dimensional structure showed better psychometric properties, highlighting the good fit found in confirmatory factorial analysis and adequate internal consistent valued, measured with Cronbach’s alpha and McDonald’s omega. Composite reliability and average variance extracted showed better indices for a three-factor model. The research also showed evidence of measurement invariance across gender. All the factors of the final three-dimensional BES model were direct and significantly associated with social and normative adjustment, being most strongly related to cognitive empathy. Conclusions This research supports the advances in neuroscience, developmental psychology and psychopathology through a three-dimensional version of the BES, which represents an improvement in the original two-factorial model. The organisation of empathy in three factors benefits the understanding of social and normative adjustment in adolescents, in which emotional disengagement favours adjusted peer relationships. Psychoeducational interventions aimed at improving the quality of social life in schools should target these components of empathy. PMID:28951400

A polyhedron made of tRNAs.

PubMed

Severcan, Isil; Geary, Cody; Chworos, Arkadiusz; Voss, Neil; Jacovetty, Erica; Jaeger, Luc

2010-09-01

Supramolecular assembly is a powerful strategy used by nature to build nanoscale architectures with predefined sizes and shapes. With synthetic systems, however, numerous challenges remain to be solved before precise control over the synthesis, folding and assembly of rationally designed three-dimensional nano-objects made of RNA can be achieved. Here, using the transfer RNA molecule as a structural building block, we report the design, efficient synthesis and structural characterization of stable, modular three-dimensional particles adopting the polyhedral geometry of a non-uniform square antiprism. The spatial control within the final architecture allows the precise positioning and encapsulation of proteins. This work demonstrates that a remarkable degree of structural control can be achieved with RNA structural motifs for the construction of thermostable three-dimensional nano-architectures that do not rely on helix bundles or tensegrity. RNA three-dimensional particles could potentially be used as carriers or scaffolds in nanomedicine and synthetic biology.

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

NASA Astrophysics Data System (ADS)

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

2012-11-01

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

Characterization of the structure and cross-shore transport properties of a coastal upwelling filament using three-dimensional finite-size Lyapunov exponents

NASA Astrophysics Data System (ADS)

Bettencourt, João. H.; Rossi, Vincent; Hernández-García, Emilio; Marta-Almeida, Martinho; López, Cristóbal

2017-09-01

The three-dimensional structure, dynamics, and dispersion characteristics of a simulated upwelling filament in the Iberian upwelling system are analyzed using Lagrangian tools. We used a realistic regional simulation of the western Iberian shelf which is concomitant with an in situ oceanographic campaign that surveyed the area. We compute 3-D fields of finite-size Lyapunov exponents (FSLE) from 3-D velocity fields and extract the field's ridges to study the spatial distribution and temporal evolution of the Lagrangian Coherent Structures (LCSs) evolving around the filament. We find that the most intense curtain-like LCSs delimit the boundaries of the whole filamentary structure whose general properties match well the observations. The filament interior is characterized by small dispersion of fluid elements. Furthermore, we identify a weak LCS separating the filament into a warmer vein and a colder filament associated with the interaction of a mesoscale eddy with the upwelling front. The cold upwelled water parcels move along the filament conserving their density. The filament itself is characterized by small dispersion of fluid elements in its interior. The comparison of LCSs with potential temperature and salinity gradient fields shows that the outer limits of the filament coincide with regions of large hydrographic gradients, similar to those observed, explaining the isolation of the interior of the filament with the surrounding waters. We conclude that the Lagrangian analysis used in this work is useful in explaining the dynamics of cross-shore exchanges of materials between coastal regions and the open ocean due to mesoscale processes.

WebCSD: the online portal to the Cambridge Structural Database

PubMed Central

Thomas, Ian R.; Bruno, Ian J.; Cole, Jason C.; Macrae, Clare F.; Pidcock, Elna; Wood, Peter A.

2010-01-01

WebCSD, a new web-based application developed by the Cambridge Crystallographic Data Centre, offers fast searching of the Cambridge Structural Database using only a standard internet browser. Search facilities include two-dimensional substructure, molecular similarity, text/numeric and reduced cell searching. Text, chemical diagrams and three-dimensional structural information can all be studied in the results browser using the efficient entry summaries and embedded three-dimensional viewer. PMID:22477776

Smoothed Particle Hydrodynamics Simulations of Ultrarelativistic Shocks with Artificial Viscosity

NASA Astrophysics Data System (ADS)

Siegler, S.; Riffert, H.

2000-03-01

We present a fully Lagrangian conservation form of the general relativistic hydrodynamic equations for perfect fluids with artificial viscosity in a given arbitrary background spacetime. This conservation formulation is achieved by choosing suitable Lagrangian time evolution variables, from which the generic fluid variables of rest-mass density, 3-velocity, and thermodynamic pressure have to be determined. We present the corresponding equations for an ideal gas and show the existence and uniqueness of the solution. On the basis of the Lagrangian formulation we have developed a three-dimensional general relativistic smoothed particle hydrodynamics (SPH) code using the standard SPH formalism as known from nonrelativistic fluid dynamics. One-dimensional simulations of a shock tube and a wall shock are presented together with a two-dimensional test calculation of an inclined shock tube. With our method we can model ultrarelativistic fluid flows including shocks with Lorentz factors of even 1000.

Helical structures in vertically aligned dust particle chains in a complex plasma

NASA Astrophysics Data System (ADS)

Hyde, Truell W.; Kong, Jie; Matthews, Lorin S.

2013-05-01

Self-assembly of structures from vertically aligned, charged dust particle bundles within a glass box placed on the lower, powered electrode of a Gaseous Electronics Conference rf reference cell were produced and examined experimentally. Self-organized formation of one-dimensional vertical chains, two-dimensional zigzag structures, and three-dimensional helical structures of triangular, quadrangular, pentagonal, hexagonal, and heptagonal symmetries are shown to occur. System evolution is shown to progress from a one-dimensional chain structure, through a zigzag transition to a two-dimensional, spindlelike structure, and then to various three-dimensional, helical structures exhibiting multiple symmetries. Stable configurations are found to be dependent upon the system confinement, γ2=ω0h/ω0v2 (where ω0h,v are the horizontal and vertical dust resonance frequencies), the total number of particles within a bundle, and the rf power. For clusters having fixed numbers of particles, the rf power at which structural phase transitions occur is repeatable and exhibits no observable hysteresis. The critical conditions for these structural phase transitions as well as the basic symmetry exhibited by the one-, two-, and three-dimensional structures that subsequently develop are in good agreement with the theoretically predicted configurations of minimum energy determined employing molecular dynamics simulations for charged dust particles confined in a prolate, spheroidal potential as presented theoretically by Kamimura and Ishihara [Kamimura and Ishihara, Phys. Rev. EPLEEE81063-651X10.1103/PhysRevE.85.016406 85, 016406 (2012)].

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

PubMed

Tegze, Miklós; Bortel, Gábor

2016-07-01

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

Mathematical modeling of transformation process of structurally unstable magnetic configurations into structurally stable ones in two-dimensional and three-dimensional geometry

NASA Astrophysics Data System (ADS)

Inovenkov, Igor; Echkina, Eugenia; Ponomarenko, Loubov

Magnetic reconnection is a fundamental process in astrophysical, space and laboratory plasma. In essence, it represents a change of topology of the magnetic field caused by readjustment of the structure of the magnetic field lines. This change leads to release of energy accumulated in the field. We consider transformation process of structurally unstable magnetic configurations into the structurally steady ones from the point of view of the Catastrophe theory. Special attention is paid to modeling of evolution of the structurally unstable three-dimensional magnetic fields.

System for generating two-dimensional masks from a three-dimensional model using topological analysis

DOEpatents

Schiek, Richard [Albuquerque, NM

2006-06-20

A method of generating two-dimensional masks from a three-dimensional model comprises providing a three-dimensional model representing a micro-electro-mechanical structure for manufacture and a description of process mask requirements, reducing the three-dimensional model to a topological description of unique cross sections, and selecting candidate masks from the unique cross sections and the cross section topology. The method further can comprise reconciling the candidate masks based on the process mask requirements description to produce two-dimensional process masks.

Ray tracing a three-dimensional scene using a hierarchical data structure

DOEpatents

Wald, Ingo; Boulos, Solomon; Shirley, Peter

2012-09-04

Ray tracing a three-dimensional scene made up of geometric primitives that are spatially partitioned into a hierarchical data structure. One example embodiment is a method for ray tracing a three-dimensional scene made up of geometric primitives that are spatially partitioned into a hierarchical data structure. In this example embodiment, the hierarchical data structure includes at least a parent node and a corresponding plurality of child nodes. The method includes a first act of determining that a first active ray in the packet hits the parent node and a second act of descending to each of the plurality of child nodes.

COMMIX-PPC: A three-dimensional transient multicomponent computer program for analyzing performance of power plant condensers. Volume 1, Equations and numerics

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

Chien, T.H.; Domanus, H.M.; Sha, W.T.

1993-02-01

The COMMIX-PPC computer pregrain is an extended and improved version of earlier COMMIX codes and is specifically designed for evaluating the thermal performance of power plant condensers. The COMMIX codes are general-purpose computer programs for the analysis of fluid flow and heat transfer in complex Industrial systems. In COMMIX-PPC, two major features have been added to previously published COMMIX codes. One feature is the incorporation of one-dimensional equations of conservation of mass, momentum, and energy on the tube stile and the proper accounting for the thermal interaction between shell and tube side through the porous-medium approach. The other added featuremore » is the extension of the three-dimensional conservation equations for shell-side flow to treat the flow of a multicomponent medium. COMMIX-PPC is designed to perform steady-state and transient. Three-dimensional analysis of fluid flow with heat transfer tn a power plant condenser. However, the code is designed in a generalized fashion so that, with some modification, it can be used to analyze processes in any heat exchanger or other single-phase engineering applications. Volume I (Equations and Numerics) of this report describes in detail the basic equations, formulation, solution procedures, and models for a phenomena. Volume II (User`s Guide and Manual) contains the input instruction, flow charts, sample problems, and descriptions of available options and boundary conditions.« less

Crystallized N-terminal domain of influenza virus matrix protein M1 and method of determining and using same

NASA Technical Reports Server (NTRS)

Luo, Ming (Inventor); Sha, Bingdong (Inventor)

2000-01-01

The matrix protein, M1, of influenza virus strain A/PR/8/34 has been purified from virions and crystallized. The crystals consist of a stable fragment (18 Kd) of the M1 protein. X-ray diffraction studies indicated that the crystals have a space group of P3.sub.t 21 or P3.sub.2 21. Vm calculations showed that there are two monomers in an asymmetric unit. A crystallized N-terminal domain of M1, wherein the N-terminal domain of M1 is crystallized such that the three dimensional structure of the crystallized N-terminal domain of M1 can be determined to a resolution of about 2.1 .ANG. or better, and wherein the three dimensional structure of the uncrystallized N-terminal domain of M1 cannot be determined to a resolution of about 2.1 .ANG. or better. A method of purifying M1 and a method of crystallizing M1. A method of using the three-dimensional crystal structure of M1 to screen for antiviral, influenza virus treating or preventing compounds. A method of using the three-dimensional crystal structure of M1 to screen for improved binding to or inhibition of influenza virus M1. The use of the three-dimensional crystal structure of the M1 protein of influenza virus in the manufacture of an inhibitor of influenza virus M1. The use of the three-dimensional crystal structure of the M1 protein of influenza virus in the screening of candidates for inhibition of influenza virus M1.

Microreplication of laser-fabricated surface and three-dimensional structures

NASA Astrophysics Data System (ADS)

Koroleva, Anastasia; Schlie, Sabrina; Fadeeva, Elena; Gittard, Shaun D.; Miller, Philip; Ovsianikov, Aleksandr; Koch, Jürgen; Narayan, Roger J.; Chichkov, Boris N.

2010-12-01

The fabrication of defined surface topographies and three-dimensional structures is a challenging process for various applications, e.g. in photonics and biomedicine. Laser-based technologies provide a promising approach for the production of such structures. The advantages of femtosecond laser ablation and two-photon polymerization for microstructuring are well known. However, these methods cannot be applied to all materials and are limited by their high cost and long production time. In this study, biomedical applications of an indirect rapid prototyping, molding microreplication of laser-fabricated two- and three-dimensional structures are examined. We demonstrate that by this method any laser-generated surface topography as well as three-dimensional structures can be replicated in various materials without losing the original geometry. The replication into multiple copies enables fast and perfect reproducibility of original microstructures for investigations of cell-surface interactions. Compared to unstructured materials, we observe that microstructures have strong influence on morphology and localization of fibroblasts, whereas neuroblastoma cells are not negatively affected.

Inverse statistical physics of protein sequences: a key issues review.

PubMed

Cocco, Simona; Feinauer, Christoph; Figliuzzi, Matteo; Monasson, Rémi; Weigt, Martin

2018-03-01

In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques, sequence data accumulate at unprecedented pace. This provides large sets of so-called homologous, i.e. evolutionarily related protein sequences, to which methods of inverse statistical physics can be applied. Using sequence data as the basis for the inference of Boltzmann distributions from samples of microscopic configurations or observables, it is possible to extract information about evolutionary constraints and thus protein function and structure. Here we give an overview over some biologically important questions, and how statistical-mechanics inspired modeling approaches can help to answer them. Finally, we discuss some open questions, which we expect to be addressed over the next years.

Inverse statistical physics of protein sequences: a key issues review

NASA Astrophysics Data System (ADS)

Cocco, Simona; Feinauer, Christoph; Figliuzzi, Matteo; Monasson, Rémi; Weigt, Martin

2018-03-01

In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques, sequence data accumulate at unprecedented pace. This provides large sets of so-called homologous, i.e. evolutionarily related protein sequences, to which methods of inverse statistical physics can be applied. Using sequence data as the basis for the inference of Boltzmann distributions from samples of microscopic configurations or observables, it is possible to extract information about evolutionary constraints and thus protein function and structure. Here we give an overview over some biologically important questions, and how statistical-mechanics inspired modeling approaches can help to answer them. Finally, we discuss some open questions, which we expect to be addressed over the next years.

MULTISHOCKED,THREE-DIMENSIONAL SUPERSONIC FLOWFIELDS WITH REAL GAS EFFECTS

NASA Technical Reports Server (NTRS)

Kutler, P.

1994-01-01

This program determines the supersonic flowfield surrounding three-dimensional wing-body configurations of a delta wing. It was designed to provide the numerical computation of three dimensional inviscid, flowfields of either perfect or real gases about supersonic or hypersonic airplanes. The governing equations in conservation law form are solved by a finite difference method using a second order noncentered algorithm between the body and the outermost shock wave, which is treated as a sharp discontinuity. Secondary shocks which form between these boundaries are captured automatically. The flowfield between the body and outermost shock is treated in a shock capturing fashion and therefore allows for the correct formation of secondary internal shocks . The program operates in batch mode, is in CDC update format, has been implemented on the CDC 7600, and requires more than 140K (octal) word locations.

An efficient semi-implicit method for three-dimensional non-hydrostatic flows in compliant arterial vessels.

PubMed

Fambri, Francesco; Dumbser, Michael; Casulli, Vincenzo

2014-11-01

Blood flow in arterial systems can be described by the three-dimensional Navier-Stokes equations within a time-dependent spatial domain that accounts for the elasticity of the arterial walls. In this article, blood is treated as an incompressible Newtonian fluid that flows through compliant vessels of general cross section. A three-dimensional semi-implicit finite difference and finite volume model is derived so that numerical stability is obtained at a low computational cost on a staggered grid. The key idea of the method consists in a splitting of the pressure into a hydrostatic and a non-hydrostatic part, where first a small quasi-one-dimensional nonlinear system is solved for the hydrostatic pressure and only in a second step the fully three-dimensional non-hydrostatic pressure is computed from a three-dimensional nonlinear system as a correction to the hydrostatic one. The resulting algorithm is robust, efficient, locally and globally mass conservative, and applies to hydrostatic and non-hydrostatic flows in one, two and three space dimensions. These features are illustrated on nontrivial test cases for flows in tubes with circular or elliptical cross section where the exact analytical solution is known. Test cases of steady and pulsatile flows in uniformly curved rigid and elastic tubes are presented. Wherever possible, axial velocity development and secondary flows are shown and compared with previously published results. Copyright © 2014 John Wiley & Sons, Ltd.

An energy and potential enstrophy conserving scheme for the shallow water equations. [orography effects on atmospheric circulation

NASA Technical Reports Server (NTRS)

Arakawa, A.; Lamb, V. R.

1979-01-01

A three-dimensional finite difference scheme for the solution of the shallow water momentum equations which accounts for the conservation of potential enstrophy in the flow of a homogeneous incompressible shallow atmosphere over steep topography as well as for total energy conservation is presented. The scheme is derived to be consistent with a reasonable scheme for potential vorticity advection in a long-term integration for a general flow with divergent mass flux. Numerical comparisons of the characteristics of the present potential enstrophy-conserving scheme with those of a scheme that conserves potential enstrophy only for purely horizontal nondivergent flow are presented which demonstrate the reduction of computational noise in the wind field with the enstrophy-conserving scheme and its convergence even in relatively coarse grids.

A Numerical Model of Exchange Chromatography Through 3D Lattice Structures

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

Salloum, Maher; Robinson, David B.

Rapid progress in the development of additive manufacturing technologies is opening new opportunities to fabricate structures that control mass transport in three dimensions across a broad range of length scales. We describe a structure that can be fabricated by newly available commercial 3D printers. It contains an array of regular three-dimensional flow paths that are in intimate contact with a solid phase, and thoroughly shuffle material among the paths. We implement a chemically reacting flow model to study its behavior as an exchange chromatography column, and compare it to an array of one-dimensional flow paths that resemble more traditional honeycombmore » monoliths. A reaction front moves through the columns and then elutes. Here, the front is sharper at all flow rates for the structure with three-dimensional flow paths, and this structure is more robust to channel width defects than the one-dimensional array.« less

A Numerical Model of Exchange Chromatography Through 3D Lattice Structures

DOE PAGES

Salloum, Maher; Robinson, David B.

2018-01-30

Rapid progress in the development of additive manufacturing technologies is opening new opportunities to fabricate structures that control mass transport in three dimensions across a broad range of length scales. We describe a structure that can be fabricated by newly available commercial 3D printers. It contains an array of regular three-dimensional flow paths that are in intimate contact with a solid phase, and thoroughly shuffle material among the paths. We implement a chemically reacting flow model to study its behavior as an exchange chromatography column, and compare it to an array of one-dimensional flow paths that resemble more traditional honeycombmore » monoliths. A reaction front moves through the columns and then elutes. Here, the front is sharper at all flow rates for the structure with three-dimensional flow paths, and this structure is more robust to channel width defects than the one-dimensional array.« less

Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli

PubMed Central

Singh, S.; Folkers, G.E.; Bonvin, A.M.J.J.; Boelens, R.; Wechselberger, R.; Niztayev, A.; Kaptein, R.

2002-01-01

The C-terminal domain of the UvrC protein (UvrC CTD) is essential for 5′ incision in the prokaryotic nucleotide excision repair process. We have determined the three-dimensional structure of the UvrC CTD using heteronuclear NMR techniques. The structure shows two helix–hairpin–helix (HhH) motifs connected by a small connector helix. The UvrC CTD is shown to mediate structure-specific DNA binding. The domain binds to a single-stranded–double-stranded junction DNA, with a strong specificity towards looped duplex DNA that contains at least six unpaired bases per loop (‘bubble DNA’). Using chemical shift perturbation experiments, the DNA-binding surface is mapped to the first hairpin region encompassing the conserved glycine–valine–glycine residues followed by lysine–arginine–arginine, a positively charged surface patch and the second hairpin region consisting of glycine–isoleucine–serine. A model for the protein– DNA complex is proposed that accounts for this specificity. PMID:12426397

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

Cavalier, Michael C.; Yim, Young-Sun; Asamizu, Shumpei

The pseudo-glycosyltransferase VldE catalyzes non-glycosidic C-N coupling between an unsaturated cyclitol and a saturated aminocyclitol with the conservation of the stereochemical configuration of the substrates to form validoxylamine A 7'-phosphate, the biosynthetic precursor of the antibiotic validamycin A. To study the molecular basis of its mechanism, the three-dimensional structures of VldE from Streptomyces hygroscopicus subsp. limoneus was determined in apo form, in complex with GDP, in complex with GDP and validoxylamine A 7'-phosphate, and in complex with GDP and trehalose. The structure of VldE with the catalytic site in both an “open” and “closed” conformation is also described. With thesemore » structures, the preferred binding of the guanine moiety by VldE, rather than the uracil moiety as seen in OtsA could be explained. The elucidation of the VldE structure in complex with the entirety of its products provides insight into the internal return mechanism by which catalysis occurs with a net retention of the stereochemical configuration of the donated cyclitol.« less

The structure of partially-premixed methane/air flames under varying premixing

NASA Astrophysics Data System (ADS)

Kluzek, Celine; Karpetis, Adonios

2008-11-01

The present work examines the spatial and scalar structure of laminar, partially premixed methane/air flames with the objective of developing flamelet mappings that capture the effect of varying premixture strength (air addition in fuel.) Experimental databases containing full thermochemistry measurements within laminar axisymmetric flames were obtained at Sandia National Laboratories, and the measurements of all major species and temperature are compared to opposed-jet one-dimensional flow simulation using Cantera and the full chemical kinetic mechanism of GRI 3.0. Particular emphasis is placed on the scalar structure of the laminar flames, and the formation of flamelet mappings that capture all of the salient features of thermochemistry in a conserved scalar representation. Three different premixture strengths were examined in detail: equivalence ratios of 1.8, 2.2, and 3.17 resulted in clear differences in the flame scalar structure, particularly in the position of the rich premixed flame zone and the attendant levels of major and intermediate species (carbon monoxide and hydrogen).

A Rich Man, Poor Man Story of S-Adenosylmethionine and Cobalamin Revisited.

PubMed

Bridwell-Rabb, Jennifer; Grell, Tsehai A J; Drennan, Catherine L

2018-06-20

S-adenosylmethionine (AdoMet) has been referred to as both "a poor man's adenosylcobalamin (AdoCbl)" and "a rich man's AdoCbl," but today, with the ever-increasing number of functions attributed to each cofactor, both appear equally rich and surprising. The recent characterization of an organometallic species in an AdoMet radical enzyme suggests that the line that differentiates them in nature will be constantly challenged. Here, we compare and contrast AdoMet and cobalamin (Cbl) and consider why Cbl-dependent AdoMet radical enzymes require two cofactors that are so similar in their reactivity. We further carry out structural comparisons employing the recently determined crystal structure of oxetanocin-A biosynthetic enzyme OxsB, the first three-dimensional structural data on a Cbl-dependent AdoMet radical enzyme. We find that the structural motifs responsible for housing the AdoMet radical machinery are largely conserved, whereas the motifs responsible for binding additional cofactors are much more varied.

Eco-evo-devo in the Study of Adaptive Divergence: Examples from Threespine Stickleback (Gasterosteus aculeatus).

PubMed

Jamniczky, Heather A; Barry, Tegan N; Rogers, Sean M

2015-07-01

The tight fit between form and function in organisms suggests the influence of adaptive evolution in biomechanics; however, the prevalence of adaptive traits, the mechanisms by which they arise and the corresponding responses to selection are subjects of extensive debate. We used three-dimensional microcomputed tomography and geometric morphometrics to characterize the structure of phenotypic covariance within the G. aculeatus trophic apparatus and its supporting structures in wild and controlled crosses of fish from two different localities. Our results reveal that while the structure of phenotypic covariance is conserved in marine and freshwater forms, it may be disrupted in the progeny of artificial crosses or during rapid adaptive divergence events. We discuss these results within the context of integrating covariance structure with quantitative genetics, toward establishing predictive links between genes, development, biomechanics, and the environment. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 2. Teaching Units that Utilize an Interactive Web-Accessible Subset of the Cambridge Structural Database

ERIC Educational Resources Information Center

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

2010-01-01

A series of online interactive teaching units have been developed that illustrate the use of experimentally measured three-dimensional (3D) structures to teach fundamental chemistry concepts. The units integrate a 500-structure subset of the Cambridge Structural Database specially chosen for their pedagogical value. The units span a number of key…

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 4. Examples of Discovery-Based Learning Using the Complete Cambridge Structural Database

ERIC Educational Resources Information Center

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

2011-01-01

Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 3. The Cambridge Structural Database System: Information Content and Access Software in Educational Applications

ERIC Educational Resources Information Center

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

2011-01-01

Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

Computer program for calculating full potential transonic, quasi-three-dimensional flow through a rotating turbomachinery blade row

NASA Technical Reports Server (NTRS)

Farrell, C. A.

1982-01-01

A fast, reliable computer code is described for calculating the flow field about a cascade of arbitrary two dimensional airfoils. The method approximates the three dimensional flow in a turbomachinery blade row by correcting for stream tube convergence and radius change in the throughflow direction. A fully conservative solution of the full potential equation is combined with the finite volume technique on a body-fitted periodic mesh, with an artificial density imposed in the transonic region to insure stability and the capture of shock waves. The instructions required to set up and use the code are included. The name of the code is QSONIC. A numerical example is also given to illustrate the output of the program.

A 3-D turbulent flow analysis using finite elements with k-ɛ model

NASA Astrophysics Data System (ADS)

Okuda, H.; Yagawa, G.; Eguchi, Y.

1989-03-01

This paper describes the finite element turbulent flow analysis, which is suitable for three-dimensional large scale problems. The k-ɛ turbulence model as well as the conservation equations of mass and momentum are discretized in space using rather low order elements. Resulting coefficient matrices are evaluated by one-point quadrature in order to reduce the computational storage and the CPU cost. The time integration scheme based on the velocity correction method is employed to obtain steady state solutions. For the verification of this FEM program, two-dimensional plenum flow is simulated and compared with experiment. As the application to three-dimensional practical problems, the turbulent flows in the upper plenum of the fast breeder reactor are calculated for various boundary conditions.

A combined direct/inverse three-dimensional transonic wing design method for vector computers

NASA Technical Reports Server (NTRS)

Weed, R. A.; Carlson, L. A.; Anderson, W. K.

1984-01-01

A three-dimensional transonic-wing design algorithm for vector computers is developed, and the results of sample computations are presented graphically. The method incorporates the direct/inverse scheme of Carlson (1975), a Cartesian grid system with boundary conditions applied at a mean plane, and a potential-flow solver based on the conservative form of the full potential equation and using the ZEBRA II vectorizable solution algorithm of South et al. (1980). The accuracy and consistency of the method with regard to direct and inverse analysis and trailing-edge closure are verified in the test computations.

Confinement and Structural Changes in Vertically Aligned Dust Structures

NASA Astrophysics Data System (ADS)

Hyde, Truell

2013-10-01

In physics, confinement is known to influence collective system behavior. Examples include coulomb crystal variants such as those formed from ions or dust particles (classical), electrons in quantum dots (quantum) and the structural changes observed in vertically aligned dust particle systems formed within a glass box placed on the lower electrode of a Gaseous Electronics Conference (GEC) rf reference cell. Recent experimental studies have expanded the above to include the biological domain by showing that the stability and dynamics of proteins confined through encapsulation and enzyme molecules placed in inorganic cavities such as those found in biosensors are also directly influenced by their confinement. In this paper, the self-assembly and subsequent collective behavior of structures formed from n, charged dust particles interacting with one another and located within a glass box placed on the lower, powered electrode of a GEC rf reference cell is discussed. Self-organized formation of vertically aligned one-dimensional chains, two-dimensional zigzag structures, and three-dimensional helical structures of triangular, quadrangular, pentagonal, hexagonal, and heptagonal symmetries are shown to occur. System evolution is shown to progress from one-dimensional chain structures, through a zigzag transition to a two-dimensional, spindle like structures, and then to various three-dimensional, helical structures exhibiting various symmetries. Stable configurations are shown to be strongly dependent upon system confinement. The critical conditions for structural transitions as well as the basic symmetry exhibited by the one-, two-, and three-dimensional structures that subsequently develop will be shown to be in good agreement with molecular dynamics simulations.

Model of lightning strike to a steel reinforce structure using PSpice

NASA Astrophysics Data System (ADS)

Koone, Neil; Condren, Brian

2003-03-01

Surges and arcs from lightning can pose hazards to personnel and sensitive equipment and processes. Steel reinforcement in structures can act as a Faraday cage mitigating lightning effects. Knowing a structure's response to a lightning strike allows hazards associated with lightning to be analyzed. A model of lightning's response in a steel reinforced structure has been developed using PSpice (a commercial circuit simulation). Segments of rebar are modeled as inductors and resistors in series. A program has been written to take architectural information of a steel reinforced structure and "build" a circuit network that is analogous to the network of reinforcement in a facility. A severe current waveform (simulating a 99th percentile lightning strike), modeled as a current source, is introduced in the circuit network, and potential differences within the structure are determined using PSpice. A visual three-dimensional model of the facility displays the voltage distribution across the structure using color to indicate the potential difference relative to the floor. Clear air arcing distances can be calculated from the voltage distribution using a conservative value for the dielectric breakdown strength of air.

Metriplectic integrators for the Landau collision operator

DOE PAGES

Kraus, Michael; Hirvijoki, Eero

2017-10-02

Here, we present a novel framework for addressing the nonlinear Landau collision integral in terms of finite element and other subspace projection methods. We employ the underlying metriplectic structure of the Landau collision integral and, using a Galerkin discretization for the velocity space, we transform the infinite-dimensional system into a finite-dimensional, time-continuous metriplectic system. Temporal discretization is accomplished using the concept of discrete gradients. The conservation of energy, momentum, and particle densities, as well as the production of entropy is demonstrated algebraically for the fully discrete system. Due to the generality of our approach, the conservation properties and the monotonicmore » behavior of entropy are guaranteed for finite element discretizations, in general, independently of the mesh configuration.« less

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

PubMed

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

2017-07-31

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

Molecular cloning, sequence analysis and homology modeling of the first caudata amphibian antifreeze-like protein in axolotl (Ambystoma mexicanum).

PubMed

Zhang, Songyan; Gao, Jiuxiang; Lu, Yiling; Cai, Shasha; Qiao, Xue; Wang, Yipeng; Yu, Haining

2013-08-01

Antifreeze proteins (AFPs) refer to a class of polypeptides that are produced by certain vertebrates, plants, fungi, and bacteria and which permit their survival in subzero environments. In this study, we report the molecular cloning, sequence analysis and three-dimensional structure of the axolotl antifreeze-like protein (AFLP) by homology modeling of the first caudate amphibian AFLP. We constructed a full-length spleen cDNA library of axolotl (Ambystoma mexicanum). An EST having highest similarity (∼42%) with freeze-responsive liver protein Li16 from Rana sylvatica was identified, and the full-length cDNA was subsequently obtained by RACE-PCR. The axolotl antifreeze-like protein sequence represents an open reading frame for a putative signal peptide and the mature protein composed of 93 amino acids. The calculated molecular mass and the theoretical isoelectric point (pl) of this mature protein were 10128.6 Da and 8.97, respectively. The molecular characterization of this gene and its deduced protein were further performed by detailed bioinformatics analysis. The three-dimensional structure of current AFLP was predicted by homology modeling, and the conserved residues required for functionality were identified. The homology model constructed could be of use for effective drug design. This is the first report of an antifreeze-like protein identified from a caudate amphibian.

Investigation of deformation of elements of three-dimensional reinforced concrete structures located in the soil, interacting with each other through rubber gaskets

NASA Astrophysics Data System (ADS)

Berezhnoi, D. V.; Balafendieva, I. S.; Sachenkov, A. A.; Sekaeva, L. R.

2017-06-01

In work the technique of calculation of elements of three-dimensional reinforced concrete substructures located in a soil, interacting with each other through rubber linings is realized. To describe the interaction of deformable structures with the ground, special “semi-infinite” finite elements are used. A technique has been implemented that allows one to describe the contact interaction of three-dimensional structures by means of a special contact finite element with specific properties. The obtained numerical results are compared with the experimental data, their good agreement is noted.

The caveolin-cavin system plays a conserved and critical role in mechanoprotection of skeletal muscle.

PubMed

Lo, Harriet P; Nixon, Susan J; Hall, Thomas E; Cowling, Belinda S; Ferguson, Charles; Morgan, Garry P; Schieber, Nicole L; Fernandez-Rojo, Manuel A; Bastiani, Michele; Floetenmeyer, Matthias; Martel, Nick; Laporte, Jocelyn; Pilch, Paul F; Parton, Robert G

2015-08-31

Dysfunction of caveolae is involved in human muscle disease, although the underlying molecular mechanisms remain unclear. In this paper, we have functionally characterized mouse and zebrafish models of caveolae-associated muscle disease. Using electron tomography, we quantitatively defined the unique three-dimensional membrane architecture of the mature muscle surface. Caveolae occupied around 50% of the sarcolemmal area predominantly assembled into multilobed rosettes. These rosettes were preferentially disassembled in response to increased membrane tension. Caveola-deficient cavin-1(-/-) muscle fibers showed a striking loss of sarcolemmal organization, aberrant T-tubule structures, and increased sensitivity to membrane tension, which was rescued by muscle-specific Cavin-1 reexpression. In vivo imaging of live zebrafish embryos revealed that loss of muscle-specific Cavin-1 or expression of a dystrophy-associated Caveolin-3 mutant both led to sarcolemmal damage but only in response to vigorous muscle activity. Our findings define a conserved and critical role in mechanoprotection for the unique membrane architecture generated by the caveolin-cavin system. © 2015 Lo et al.

The caveolin–cavin system plays a conserved and critical role in mechanoprotection of skeletal muscle

PubMed Central

Lo, Harriet P.; Nixon, Susan J.; Hall, Thomas E.; Cowling, Belinda S.; Ferguson, Charles; Morgan, Garry P.; Schieber, Nicole L.; Fernandez-Rojo, Manuel A.; Bastiani, Michele; Floetenmeyer, Matthias; Martel, Nick; Laporte, Jocelyn; Pilch, Paul F.

2015-01-01

Dysfunction of caveolae is involved in human muscle disease, although the underlying molecular mechanisms remain unclear. In this paper, we have functionally characterized mouse and zebrafish models of caveolae-associated muscle disease. Using electron tomography, we quantitatively defined the unique three-dimensional membrane architecture of the mature muscle surface. Caveolae occupied around 50% of the sarcolemmal area predominantly assembled into multilobed rosettes. These rosettes were preferentially disassembled in response to increased membrane tension. Caveola-deficient cavin-1−/− muscle fibers showed a striking loss of sarcolemmal organization, aberrant T-tubule structures, and increased sensitivity to membrane tension, which was rescued by muscle-specific Cavin-1 reexpression. In vivo imaging of live zebrafish embryos revealed that loss of muscle-specific Cavin-1 or expression of a dystrophy-associated Caveolin-3 mutant both led to sarcolemmal damage but only in response to vigorous muscle activity. Our findings define a conserved and critical role in mechanoprotection for the unique membrane architecture generated by the caveolin–cavin system. PMID:26323694

Seismic Response of 3D Steel Buildings considering the Effect of PR Connections and Gravity Frames

PubMed Central

Haldar, Achintya; López-Barraza, Arturo; Rivera-Salas, J. Luz

2014-01-01

The nonlinear seismic responses of 3D steel buildings with perimeter moment resisting frames (PMRF) and interior gravity frames (IGF) are studied explicitly considering the contribution of the IGF. The effect on the structural response of the stiffness of the beam-to-column connections of the IGF, which is usually neglected, is also studied. It is commonly believed that the flexibility of shear connections is negligible and that 2D models can be used to properly represent 3D real structures. The results of the study indicate, however, that the moments developed on columns of IGF can be considerable and that modeling buildings as plane frames may result in very conservative designs. The contribution of IGF to the lateral structural resistance may be significant. The contribution increases when their connections are assumed to be partially restrained (PR). The incremented participation of IGF when the stiffness of their connections is considered helps to counteract the no conservative effect that results in practice when lateral seismic loads are not considered in IGF while designing steel buildings with PMRF. Thus, if the structural system under consideration is used, the three-dimensional model should be used in seismic analysis and the IGF and the stiffness of their connections should be considered as part of the lateral resistance system. PMID:24995357

Structural adaptation of extreme halophilic proteins through decrease of conserved hydrophobic contact surface

PubMed Central

2011-01-01

Background Halophiles are extremophilic microorganisms growing optimally at high salt concentrations. There are two strategies used by halophiles to maintain proper osmotic pressure in their cytoplasm: accumulation of molar concentrations of potassium and chloride with extensive adaptation of the intracellular macromolecules ("salt-in" strategy) or biosynthesis and/or accumulation of organic osmotic solutes ("osmolyte" strategy). Our work was aimed at contributing to the understanding of the shared molecular mechanisms of protein haloadaptation through a detailed and systematic comparison of a sample of several three-dimensional structures of halophilic and non-halophilic proteins. Structural differences observed between the "salt-in" and the mesophilic homologous proteins were contrasted to those observed between the "osmolyte" and mesophilic pairs. Results The results suggest that haloadaptation strategy in the presence of molar salt concentration, but not of osmolytes, necessitates a weakening of the hydrophobic interactions, in particular at the level of conserved hydrophobic contacts. Weakening of these interactions counterbalances their strengthening by the presence of salts in solution and may help the structure preventing aggregation and/or loss of function in hypersaline environments. Conclusions Considering the significant increase of biotechnology applications of halophiles, the understanding of halophilicity can provide the theoretical basis for the engineering of proteins of great interest because stable at concentrations of salts that cause the denaturation or aggregation of the majority of macromolecules. PMID:22192175

iDBPs: a web server for the identification of DNA binding proteins.

PubMed

Nimrod, Guy; Schushan, Maya; Szilágyi, András; Leslie, Christina; Ben-Tal, Nir

2010-03-01

The iDBPs server uses the three-dimensional (3D) structure of a query protein to predict whether it binds DNA. First, the algorithm predicts the functional region of the protein based on its evolutionary profile; the assumption is that large clusters of conserved residues are good markers of functional regions. Next, various characteristics of the predicted functional region as well as global features of the protein are calculated, such as the average surface electrostatic potential, the dipole moment and cluster-based amino acid conservation patterns. Finally, a random forests classifier is used to predict whether the query protein is likely to bind DNA and to estimate the prediction confidence. We have trained and tested the classifier on various datasets and shown that it outperformed related methods. On a dataset that reflects the fraction of DNA binding proteins (DBPs) in a proteome, the area under the ROC curve was 0.90. The application of the server to an updated version of the N-Func database, which contains proteins of unknown function with solved 3D-structure, suggested new putative DBPs for experimental studies. http://idbps.tau.ac.il/

Experimental Investigation of the Unsteady Flow Structures of Two Interacting Pitching Wings

NASA Astrophysics Data System (ADS)

Kurt, Melike; Moored, Keith

2015-11-01

Birds, insects and fish propel themselves with unsteady motions of their wings and fins. Many of these animals are also found to fly or swim in three-dimensional flocks and schools. Numerous studies have explored the three-dimensional steady flow interactions and the two-dimensional unsteady flow interactions in collectives. Yet, the characterization of the three-dimensional unsteady interactions remains relatively unexplored. This study aims to characterize the flow structures and interactions between two sinusoidally pitching finite-span wings. The arrangement of the wings varies from a tandem to a bi-plane configuration. The vortex structures for these various arrangements are quantified by using particle image velocimetry. The vortex-wing interactions are also characterized as the synchrony between the wings is modified.

Suitability of a three-dimensional model to measure empathy and its relationship with social and normative adjustment in Spanish adolescents: a cross-sectional study.

PubMed

Herrera-López, Mauricio; Gómez-Ortiz, Olga; Ortega-Ruiz, Rosario; Jolliffe, Darrick; Romera, Eva M

2017-09-25

(1) To examine the psychometric properties of the Basic Empathy Scale (BES) with Spanish adolescents, comparing a two and a three-dimensional structure;(2) To analyse the relationship between the three-dimensional empathy and social and normative adjustment in school. Transversal and ex post facto retrospective study. Confirmatory factorial analysis, multifactorial invariance analysis and structural equations models were used. 747 students (51.3% girls) from Cordoba, Spain, aged 12-17 years (M=13.8; SD=1.21). The original two-dimensional structure was confirmed (cognitive empathy, affective empathy), but a three-dimensional structure showed better psychometric properties, highlighting the good fit found in confirmatory factorial analysis and adequate internal consistent valued, measured with Cronbach's alpha and McDonald's omega. Composite reliability and average variance extracted showed better indices for a three-factor model. The research also showed evidence of measurement invariance across gender. All the factors of the final three-dimensional BES model were direct and significantly associated with social and normative adjustment, being most strongly related to cognitive empathy. This research supports the advances in neuroscience, developmental psychology and psychopathology through a three-dimensional version of the BES, which represents an improvement in the original two-factorial model. The organisation of empathy in three factors benefits the understanding of social and normative adjustment in adolescents, in which emotional disengagement favours adjusted peer relationships. Psychoeducational interventions aimed at improving the quality of social life in schools should target these components of empathy. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Three-dimensional effects on pure tone fan noise due to inflow distortion. [rotor blade noise prediction

NASA Technical Reports Server (NTRS)

Kobayashi, H.

1978-01-01

Two dimensional, quasi three dimensional and three dimensional theories for the prediction of pure tone fan noise due to the interaction of inflow distortion with a subsonic annular blade row were studied with the aid of an unsteady three dimensional lifting surface theory. The effects of compact and noncompact source distributions on pure tone fan noise in an annular cascade were investigated. Numerical results show that the strip theory and quasi three-dimensional theory are reasonably adequate for fan noise prediction. The quasi three-dimensional method is more accurate for acoustic power and model structure prediction with an acoustic power estimation error of about plus or minus 2db.

A higher-order conservation element solution element method for solving hyperbolic differential equations on unstructured meshes

NASA Astrophysics Data System (ADS)

Bilyeu, David

This dissertation presents an extension of the Conservation Element Solution Element (CESE) method from second- to higher-order accuracy. The new method retains the favorable characteristics of the original second-order CESE scheme, including (i) the use of the space-time integral equation for conservation laws, (ii) a compact mesh stencil, (iii) the scheme will remain stable up to a CFL number of unity, (iv) a fully explicit, time-marching integration scheme, (v) true multidimensionality without using directional splitting, and (vi) the ability to handle two- and three-dimensional geometries by using unstructured meshes. This algorithm has been thoroughly tested in one, two and three spatial dimensions and has been shown to obtain the desired order of accuracy for solving both linear and non-linear hyperbolic partial differential equations. The scheme has also shown its ability to accurately resolve discontinuities in the solutions. Higher order unstructured methods such as the Discontinuous Galerkin (DG) method and the Spectral Volume (SV) methods have been developed for one-, two- and three-dimensional application. Although these schemes have seen extensive development and use, certain drawbacks of these methods have been well documented. For example, the explicit versions of these two methods have very stringent stability criteria. This stability criteria requires that the time step be reduced as the order of the solver increases, for a given simulation on a given mesh. The research presented in this dissertation builds upon the work of Chang, who developed a fourth-order CESE scheme to solve a scalar one-dimensional hyperbolic partial differential equation. The completed research has resulted in two key deliverables. The first is a detailed derivation of a high-order CESE methods on unstructured meshes for solving the conservation laws in two- and three-dimensional spaces. The second is the code implementation of these numerical methods in a computer code. For code development, a one-dimensional solver for the Euler equations was developed. This work is an extension of Chang's work on the fourth-order CESE method for solving a one-dimensional scalar convection equation. A generic formulation for the nth-order CESE method, where n ≥ 4, was derived. Indeed, numerical implementation of the scheme confirmed that the order of convergence was consistent with the order of the scheme. For the two- and three-dimensional solvers, SOLVCON was used as the basic framework for code implementation. A new solver kernel for the fourth-order CESE method has been developed and integrated into the framework provided by SOLVCON. The main part of SOLVCON, which deals with unstructured meshes and parallel computing, remains intact. The SOLVCON code for data transmission between computer nodes for High Performance Computing (HPC). To validate and verify the newly developed high-order CESE algorithms, several one-, two- and three-dimensional simulations where conducted. For the arbitrary order, one-dimensional, CESE solver, three sets of governing equations were selected for simulation: (i) the linear convection equation, (ii) the linear acoustic equations, (iii) the nonlinear Euler equations. All three systems of equations were used to verify the order of convergence through mesh refinement. In addition the Euler equations were used to solve the Shu-Osher and Blastwave problems. These two simulations demonstrated that the new high-order CESE methods can accurately resolve discontinuities in the flow field.For the two-dimensional, fourth-order CESE solver, the Euler equation was employed in four different test cases. The first case was used to verify the order of convergence through mesh refinement. The next three cases demonstrated the ability of the new solver to accurately resolve discontinuities in the flows. This was demonstrated through: (i) the interaction between acoustic waves and an entropy pulse, (ii) supersonic flow over a circular blunt body, (iii) supersonic flow over a guttered wedge. To validate and verify the three-dimensional, fourth-order CESE solver, two different simulations where selected. The first used the linear convection equations to demonstrate fourth-order convergence. The second used the Euler equations to simulate supersonic flow over a spherical body to demonstrate the scheme's ability to accurately resolve shocks. All test cases used are well known benchmark problems and as such, there are multiple sources available to validate the numerical results. Furthermore, the simulations showed that the high-order CESE solver was stable at a CFL number near unity.

Three species one-dimensional kinetic model for weakly ionized plasmas

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

Gonzalez, J., E-mail: jorge.gonzalez@upm.es; Donoso, J. M.; Tierno, S. P.

2016-06-15

A three species one-dimensional kinetic model is presented for a spatially homogeneous weakly ionized plasma subjected to the action of a time varying electric field. Planar geometry is assumed, which means that the plasma evolves in the privileged direction of the field. The energy transmitted to the electric charges is channelized to the neutrals thanks to collisions, a mechanism that influences the plasma dynamics. Charge-charge interactions have been designed as a one-dimensional collision term equivalent to the Landau operator used for fully ionized plasmas. Charge-neutral collisions are modelled by a conservative drift-diffusion operator in the Dougherty's form. The resulting setmore » of coupled integro-differential equations is solved with the stable and robust propagator integral method. This semi–analytical method feasibility accounts for non–linear effects without appealing to linearisation or simplifications, providing conservative physically meaningful solutions even for initial or emerging sharp velocity distribution function profiles. It is found that charge-neutral collisions exert a significant effect since a quite different plasma evolution arises if compared to the collisionless limit. In addition, substantial differences in the system motion are found for constant and temperature dependent collision frequencies cases.« less

Structural study of Bombyx mori silk fibroin during processing for regeneration

NASA Astrophysics Data System (ADS)

Ha, Sung-Won

Bombyx mori silk fibroin has excellent mechanical properties combined with flexibility, tissue compatibility, and high oxygen permeability in the wet condition. This important material should be dissolved and regenerated to be utilized as useful forms such as gel, film, fiber, powder, or non-woven. However, it has long been a problem that the regenerated fibroin materials show poor mechanical properties and brittleness. These problems were technically solved by improving a fiber processing method reported here. The regenerated fibroin fibers showed much better mechanical properties compared to the original silk fibers. This improved technique for the fiber processing of Bombyx mori silk fibroin may be used as a model system for other semi-crystalline fiber forming proteins, becoming available through biotechnology. The physical and chemical properties of the regenerated fibers were characterized by SinTechRTM tensile testing, X-ray diffraction, solid state 13C NMR spectroscopy, and SEM. Unlike synthetic polymers, the molecular weight distribution of Bombyx mori silk fibroin is mono-disperse because silk fibroin is synthesized from DNA template. Genetic studies have revealed the entire amino acid sequence of Bombyx mori silk fibroin. It is known that the crystalline silk II structure is composed of hexa-amino acid sequences, GAGAGS. However, in the amino acid sequence of Bombyx mori silk fibroin heavy chain, there are present 11 chemically irregular but evolutionarily conserved sequences with about 31 amino acid residues (irregular GT˜GT sequences). The structure and role of these irregular sequences have remained unknown. One of the most frequently appearing irregular sequences was synthesized by a peptide synthesizer. The three-dimensional structure of this irregular silk peptide was studied by the high resolution two-dimensional NMR technique. The three-dimensional structure of this peptide shows that it makes a turn or loop structure (distorted O shape), which means the proceeding backbone direction is changed 180° by this sequence. This may facilitate the beta-sheet formation of the crystal forming building blocks, GAGAGS/GY˜GY sequences, in fibroin heavy chain. It may also facilitate the solubilization of the fibroin heavy chain within the silk gland.

Power-scaling performance of a three-dimensional tritium betavoltaic diode

NASA Astrophysics Data System (ADS)

Liu, Baojun; Chen, Kevin P.; Kherani, Nazir P.; Zukotynski, Stefan

2009-12-01

Three-dimensional diodes fabricated by electrochemical etching are exposed to tritium gas at pressures from 0.05 to 33 atm at room temperature to examine its power scaling performance. It is shown that the three-dimensional microporous structure overcomes the self-absorption limited saturation of beta flux at high tritium pressures. These results are contrasted against the three-dimensional device powered in one instance by tritium absorbed in the near surface region of the three-dimensional microporous network, and in another by a planar scandium tritide foil. These findings suggest that direct tritium occlusion in the near surface of three-dimensional diode can improve the specific power production.

The Reconstruction of Three-Dimensional Morphological and Electrical Paraneters from Two-Dimensional Sections of Neurones

NASA Astrophysics Data System (ADS)

Brawn, A. D.; Wheal, H. V.

1986-07-01

A system is described which can be used to create a three-dimensional model of a neurone from the central nervous system. This model can then be used to obtain quantitative data on the physical and electrical pro, perties of the neurone. Living neurones are either raised in culture, or taken from in vitro preparations of brain tissue and optically sectioned. These two-dimensional sections are digitised, and input to a 68008-based microcomputer. The system reconstructs the three-dimensional structure of the neurone, both geanetrically and electrically. The user can a) View the structure fran any point at any angle b) "Move through" the structure along any given vector c) Nave through" the structure following a neurone process d) Fire the neurone at any point, and "watch" the action potentials propagate e) Vary the parameters of the electrical model of a process element. The system is targeted to a research programme on epilepsy, which makes frequent use of both geometric and electrical neurone modelling. Current techniques which may involve crude histology and two-dimensional drawings have considerable short camings.

Finite element analysis of steady and transiently moving/rolling nonlinear viscoelastic structure. II - Shell and three-dimensional simulations

NASA Technical Reports Server (NTRS)

Kennedy, Ronald; Padovan, Joe

1987-01-01

In a three-part series of papers, a generalized finite element solution strategy is developed to handle traveling load problems in rolling, moving and rotating structure. The main thrust of this section consists of the development of three-dimensional and shell type moving elements. In conjunction with this work, a compatible three-dimensional contact strategy is also developed. Based on these modeling capabilities, extensive analytical and experimental benchmarking is presented. Such testing includes traveling loads in rotating structure as well as low- and high-speed rolling contact involving standing wave-type response behavior. These point to the excellent modeling capabilities of moving element strategies.

A 2D nonlinear multiring model for blood flow in large elastic arteries

NASA Astrophysics Data System (ADS)

Ghigo, Arthur R.; Fullana, Jose-Maria; Lagrée, Pierre-Yves

2017-12-01

In this paper, we propose a two-dimensional nonlinear ;multiring; model to compute blood flow in axisymmetric elastic arteries. This model is designed to overcome the numerical difficulties of three-dimensional fluid-structure interaction simulations of blood flow without using the over-simplifications necessary to obtain one-dimensional blood flow models. This multiring model is derived by integrating over concentric rings of fluid the simplified long-wave Navier-Stokes equations coupled to an elastic model of the arterial wall. The resulting system of balance laws provides a unified framework in which both the motion of the fluid and the displacement of the wall are dealt with simultaneously. The mathematical structure of the multiring model allows us to use a finite volume method that guarantees the conservation of mass and the positivity of the numerical solution and can deal with nonlinear flows and large deformations of the arterial wall. We show that the finite volume numerical solution of the multiring model provides at a reasonable computational cost an asymptotically valid description of blood flow velocity profiles and other averaged quantities (wall shear stress, flow rate, ...) in large elastic and quasi-rigid arteries. In particular, we validate the multiring model against well-known solutions such as the Womersley or the Poiseuille solutions as well as against steady boundary layer solutions in quasi-rigid constricted and expanded tubes.

HYDRA-II: A hydrothermal analysis computer code: Volume 3, Verification/validation assessments

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

McCann, R.A.; Lowery, P.S.

1987-10-01

HYDRA-II is a hydrothermal computer code capable of three-dimensional analysis of coupled conduction, convection, and thermal radiation problems. This code is especially appropriate for simulating the steady-state performance of spent fuel storage systems. The code has been evaluated for this application for the US Department of Energy's Commercial Spent Fuel Management Program. HYDRA-II provides a finite difference solution in cartesian coordinates to the equations governing the conservation of mass, momentum, and energy. A cylindrical coordinate system may also be used to enclose the cartesian coordinate system. This exterior coordinate system is useful for modeling cylindrical cask bodies. The difference equationsmore » for conservation of momentum are enhanced by the incorporation of directional porosities and permeabilities that aid in modeling solid structures whose dimensions may be smaller than the computational mesh. The equation for conservation of energy permits modeling of orthotropic physical properties and film resistances. Several automated procedures are available to model radiation transfer within enclosures and from fuel rod to fuel rod. The documentation of HYDRA-II is presented in three separate volumes. Volume I - Equations and Numerics describes the basic differential equations, illustrates how the difference equations are formulated, and gives the solution procedures employed. Volume II - User's Manual contains code flow charts, discusses the code structure, provides detailed instructions for preparing an input file, and illustrates the operation of the code by means of a model problem. This volume, Volume III - Verification/Validation Assessments, provides a comparison between the analytical solution and the numerical simulation for problems with a known solution. This volume also documents comparisons between the results of simulations of single- and multiassembly storage systems and actual experimental data. 11 refs., 55 figs., 13 tabs.« less

Three-Dimensional Printing of a Scalable Molecular Model and Orbital Kit for Organic Chemistry Teaching and Learning

ERIC Educational Resources Information Center

Penny, Matthew R.; Cao, Zi Jing; Patel, Bhaven; dos Santos, Bruno Sil; Asquith, Christopher R. M.; Szulc, Blanka R.; Rao, Zenobia X.; Muwaffak, Zaid; Malkinson, John P.; Hilton, Stephen T.

2017-01-01

Three-dimensional (3D) chemical models are a well-established learning tool used to enhance the understanding of chemical structures by converting two-dimensional paper or screen outputs into realistic three-dimensional objects. While commercial atom model kits are readily available, there is a surprising lack of large molecular and orbital models…

Structure and topology of three-dimensional hydrocarbon polymers.

PubMed

Kondrin, Mikhail V; Lebed, Yulia B; Brazhkin, Vadim V

2016-08-01

A new family of three-dimensional hydrocarbon polymers which are more energetically favorable than benzene is proposed. Although structurally these polymers are closely related to well known diamond and lonsdaleite carbon structures, using topological arguments we demonstrate that they have no known structural analogs. Topological considerations also give some indication of possible methods of synthesis. Taking into account their exceptional optical, structural and mechanical properties these polymers might have interesting applications.

Localization of yeast RNA polymerase I core subunits by immunoelectron microscopy.

PubMed Central

Klinger, C; Huet, J; Song, D; Petersen, G; Riva, M; Bautz, E K; Sentenac, A; Oudet, P; Schultz, P

1996-01-01

Immunoelectron microscopy was used to determine the spatial organization of the yeast RNA polymerase I core subunits on a three-dimensional model of the enzyme. Images of antibody-labeled enzymes were compared with the native enzyme to determine the localization of the antibody binding site on the surface of the model. Monoclonal antibodies were used as probes to identify the two largest subunits homologous to the bacterial beta and beta' subunits. The epitopes for the two monoclonal antibodies were mapped using subunit-specific phage display libraries, thus allowing a direct correlation of the structural data with functional information on conserved sequence elements. An epitope close to conserved region C of the beta-like subunit is located at the base of the finger-like domain, whereas a sequence between conserved regions C and D of the beta'-like subunit is located in the apical region of the enzyme. Polyclonal antibodies outlined the alpha-like subunit AC40 and subunit AC19 which were found co-localized also in the apical region of the enzyme. The spatial location of the subunits is correlated with their biological activity and the inhibitory effect of the antibodies. Images PMID:8887555

Density functional study of molecular interactions in secondary structures of proteins.

PubMed

Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki

2016-01-01

Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

Advection of Potential Temperature in the Atmosphere of Irradiated Exoplanets: A Robust Mechanism to Explain Radius Inflation

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

Tremblin, P.; Chabrier, G.; Mayne, N. J.

The anomalously large radii of strongly irradiated exoplanets have remained a major puzzle in astronomy. Based on a two-dimensional steady-state atmospheric circulation model, the validity of which is assessed by comparison to three-dimensional calculations, we reveal a new mechanism, namely the advection of the potential temperature due to mass and longitudinal momentum conservation, a process occurring in the Earth’s atmosphere or oceans. In the deep atmosphere, the vanishing heating flux forces the atmospheric structure to converge to a hotter adiabat than the one obtained with 1D calculations, implying a larger radius for the planet. Not only do the calculations reproducemore » the observed radius of HD 209458b, but also reproduce the observed correlation between radius inflation and irradiation for transiting planets. Vertical advection of potential temperature induced by non-uniform atmospheric heating thus provides a robust mechanism to explain the inflated radii of irradiated hot Jupiters.« less

Analysis of micro computed tomography images; a look inside historic enamelled metal objects

NASA Astrophysics Data System (ADS)

van der Linden, Veerle; van de Casteele, Elke; Thomas, Mienke Simon; de Vos, Annemie; Janssen, Elsje; Janssens, Koen

2010-02-01

In this study the usefulness of micro-Computed Tomography (µ-CT) for the in-depth analysis of enamelled metal objects was tested. Usually investigations of enamelled metal artefacts are restricted to non-destructive surface analysis or analysis of cross sections after destructive sampling. Radiography, a commonly used technique in the field of cultural heritage studies, is limited to providing two-dimensional information about a three-dimensional object (Lang and Middleton, Radiography of Cultural Material, pp. 60-61, Elsevier-Butterworth-Heinemann, Amsterdam-Stoneham-London, 2005). Obtaining virtual slices and information about the internal structure of these objects was made possible by CT analysis. With this technique the underlying metal work was studied without removing the decorative enamel layer. Moreover visible defects such as cracks were measured in both width and depth and as of yet invisible defects and weaker areas are visualised. All these features are of great interest to restorers and conservators as they allow a view inside these objects without so much as touching them.

Reduced Dynamics of the Non-holonomic Whipple Bicycle

NASA Astrophysics Data System (ADS)

Boyer, Frédéric; Porez, Mathieu; Mauny, Johan

2018-06-01

Though the bicycle is a familiar object of everyday life, modeling its full nonlinear three-dimensional dynamics in a closed symbolic form is a difficult issue for classical mechanics. In this article, we address this issue without resorting to the usual simplifications on the bicycle kinematics nor its dynamics. To derive this model, we use a general reduction-based approach in the principal fiber bundle of configurations of the three-dimensional bicycle. This includes a geometrically exact model of the contacts between the wheels and the ground, the explicit calculation of the kernel of constraints, along with the dynamics of the system free of any external forces, and its projection onto the kernel of admissible velocities. The approach takes benefits of the intrinsic formulation of geometric mechanics. Along the path toward the final equations, we show that the exact model of the bicycle dynamics requires to cope with a set of non-symmetric constraints with respect to the structural group of its configuration fiber bundle. The final reduced dynamics are simulated on several examples representative of the bicycle. As expected the constraints imposed by the ground contacts, as well as the energy conservation, are satisfied, while the dynamics can be numerically integrated in real time.

Three-Dimensional Model of Holographic Formation of Inhomogeneous PPLC Diffraction Structures

NASA Astrophysics Data System (ADS)

Semkin, A. O.; Sharangovich, S. N.

2018-05-01

A three-dimensional theoretical model of holographic formation of inhomogeneous diffraction structures in composite photopolymer - liquid crystal materials is presented considering both the nonlinearity of recording and the amplitude-phase inhomogeneity of the recording light field. Based on the results of numerical simulation, the kinematics of formations of such structures and their spatial profile are investigated.

Three-dimensional shape transformations of hydrogel sheets induced by small-scale modulation of internal stresses

NASA Astrophysics Data System (ADS)

Wu, Zi Liang; Moshe, Michael; Greener, Jesse; Therien-Aubin, Heloise; Nie, Zhihong; Sharon, Eran; Kumacheva, Eugenia

2013-03-01

Although Nature has always been a common source of inspiration in the development of artificial materials, only recently has the ability of man-made materials to produce complex three-dimensional (3D) structures from two-dimensional sheets been explored. Here we present a new approach to the self-shaping of soft matter that mimics fibrous plant tissues by exploiting small-scale variations in the internal stresses to form three-dimensional morphologies. We design single-layer hydrogel sheets with chemically distinct, fibre-like regions that exhibit differential shrinkage and elastic moduli under the application of external stimulus. Using a planar-to-helical three-dimensional shape transformation as an example, we explore the relation between the internal architecture of the sheets and their transition to cylindrical and conical helices with specific structural characteristics. The ability to engineer multiple three-dimensional shape transformations determined by small-scale patterns in a hydrogel sheet represents a promising step in the development of programmable soft matter.

Multilocality and fusion rules on the generalized structure functions in two-dimensional and three-dimensional Navier-Stokes turbulence.

PubMed

Gkioulekas, Eleftherios

2016-09-01

Using the fusion-rules hypothesis for three-dimensional and two-dimensional Navier-Stokes turbulence, we generalize a previous nonperturbative locality proof to multiple applications of the nonlinear interactions operator on generalized structure functions of velocity differences. We call this generalization of nonperturbative locality to multiple applications of the nonlinear interactions operator "multilocality." The resulting cross terms pose a new challenge requiring a new argument and the introduction of a new fusion rule that takes advantage of rotational symmetry. Our main result is that the fusion-rules hypothesis implies both locality and multilocality in both the IR and UV limits for the downscale energy cascade of three-dimensional Navier-Stokes turbulence and the downscale enstrophy cascade and inverse energy cascade of two-dimensional Navier-Stokes turbulence. We stress that these claims relate to nonperturbative locality of generalized structure functions on all orders and not the term-by-term perturbative locality of diagrammatic theories or closure models that involve only two-point correlation and response functions.

Exact solutions and conservation laws of the system of two-dimensional viscous Burgers equations

NASA Astrophysics Data System (ADS)

Abdulwahhab, Muhammad Alim

2016-10-01

Fluid turbulence is one of the phenomena that has been studied extensively for many decades. Due to its huge practical importance in fluid dynamics, various models have been developed to capture both the indispensable physical quality and the mathematical structure of turbulent fluid flow. Among the prominent equations used for gaining in-depth insight of fluid turbulence is the two-dimensional Burgers equations. Its solutions have been studied by researchers through various methods, most of which are numerical. Being a simplified form of the two-dimensional Navier-Stokes equations and its wide range of applicability in various fields of science and engineering, development of computationally efficient methods for the solution of the two-dimensional Burgers equations is still an active field of research. In this study, Lie symmetry method is used to perform detailed analysis on the system of two-dimensional Burgers equations. Optimal system of one-dimensional subalgebras up to conjugacy is derived and used to obtain distinct exact solutions. These solutions not only help in understanding the physical effects of the model problem but also, can serve as benchmarks for constructing algorithms and validation of numerical solutions of the system of Burgers equations under consideration at finite Reynolds numbers. Independent and nontrivial conserved vectors are also constructed.

Validating two-dimensional leadership models on three-dimensionally structured fish schools

PubMed Central

Nagy, Máté; Holbrook, Robert I.; Biro, Dora; Burt de Perera, Theresa

2017-01-01

Identifying leader–follower interactions is crucial for understanding how a group decides where or when to move, and how this information is transferred between members. Although many animal groups have a three-dimensional structure, previous studies investigating leader–follower interactions have often ignored vertical information. This raises the question of whether commonly used two-dimensional leader–follower analyses can be used justifiably on groups that interact in three dimensions. To address this, we quantified the individual movements of banded tetra fish (Astyanax mexicanus) within shoals by computing the three-dimensional trajectories of all individuals using a stereo-camera technique. We used these data firstly to identify and compare leader–follower interactions in two and three dimensions, and secondly to analyse leadership with respect to an individual's spatial position in three dimensions. We show that for 95% of all pairwise interactions leadership identified through two-dimensional analysis matches that identified through three-dimensional analysis, and we reveal that fish attend to the same shoalmates for vertical information as they do for horizontal information. Our results therefore highlight that three-dimensional analyses are not always required to identify leader–follower relationships in species that move freely in three dimensions. We discuss our results in terms of the importance of taking species' sensory capacities into account when studying interaction networks within groups. PMID:28280582

Bifurcations and degenerate periodic points in a three dimensional chaotic fluid flow

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

Smith, L. D., E-mail: lachlan.smith@monash.edu; CSIRO Mineral Resources, Clayton, Victoria 3800; Rudman, M.

2016-05-15

Analysis of the periodic points of a conservative periodic dynamical system uncovers the basic kinematic structure of the transport dynamics and identifies regions of local stability or chaos. While elliptic and hyperbolic points typically govern such behaviour in 3D systems, degenerate (parabolic) points also play an important role. These points represent a bifurcation in local stability and Lagrangian topology. In this study, we consider the ramifications of the two types of degenerate periodic points that occur in a model 3D fluid flow. (1) Period-tripling bifurcations occur when the local rotation angle associated with elliptic points is reversed, creating a reversalmore » in the orientation of associated Lagrangian structures. Even though a single unstable point is created, the bifurcation in local stability has a large influence on local transport and the global arrangement of manifolds as the unstable degenerate point has three stable and three unstable directions, similar to hyperbolic points, and occurs at the intersection of three hyperbolic periodic lines. The presence of period-tripling bifurcation points indicates regions of both chaos and confinement, with the extent of each depending on the nature of the associated manifold intersections. (2) The second type of bifurcation occurs when periodic lines become tangent to local or global invariant surfaces. This bifurcation creates both saddle–centre bifurcations which can create both chaotic and stable regions, and period-doubling bifurcations which are a common route to chaos in 2D systems. We provide conditions for the occurrence of these tangent bifurcations in 3D conservative systems, as well as constraints on the possible types of tangent bifurcation that can occur based on topological considerations.« less

WIND: Computer program for calculation of three dimensional potential compressible flow about wind turbine rotor blades

NASA Technical Reports Server (NTRS)

Dulikravich, D. S.

1980-01-01

A computer program is presented which numerically solves an exact, full potential equation (FPE) for three dimensional, steady, inviscid flow through an isolated wind turbine rotor. The program automatically generates a three dimensional, boundary conforming grid and iteratively solves the FPE while fully accounting for both the rotating cascade and Coriolis effects. The numerical techniques incorporated involve rotated, type dependent finite differencing, a finite volume method, artificial viscosity in conservative form, and a successive line overrelaxation combined with the sequential grid refinement procedure to accelerate the iterative convergence rate. Consequently, the WIND program is capable of accurately analyzing incompressible and compressible flows, including those that are locally transonic and terminated by weak shocks. The program can also be used to analyze the flow around isolated aircraft propellers and helicopter rotors in hover as long as the total relative Mach number of the oncoming flow is subsonic.

Identification of DNA-Binding Proteins Using Structural, Electrostatic and Evolutionary Features

PubMed Central

Nimrod, Guy; Szilágyi, András; Leslie, Christina; Ben-Tal, Nir

2009-01-01

Summary DNA binding proteins (DBPs) often take part in various crucial processes of the cell's life cycle. Therefore, the identification and characterization of these proteins are of great importance. We present here a random forests classifier for identifying DBPs among proteins with known three-dimensional structures. First, clusters of evolutionarily conserved regions (patches) on the protein's surface are detected using the PatchFinder algorithm; previous studies showed that these regions are typically the proteins' functionally important regions. Next, we train a classifier using features like the electrostatic potential, cluster-based amino acid conservation patterns and the secondary structure content of the patches, as well as features of the whole protein including its dipole moment. Using 10-fold cross validation on a dataset of 138 DNA-binding proteins and 110 proteins which do not bind DNA, the classifier achieved a sensitivity and a specificity of 0.90, which is overall better than the performance of previously published methods. Furthermore, when we tested 5 different methods on 11 new DBPs which did not appear in the original dataset, only our method annotated all correctly. The resulting classifier was applied to a collection of 757 proteins of known structure and unknown function. Of these proteins, 218 were predicted to bind DNA, and we anticipate that some of them interact with DNA using new structural motifs. The use of complementary computational tools supports the notion that at least some of them do bind DNA. PMID:19233205

Engineering the internal surfaces of three-dimensional nanoporous catalysts by surfactant-modified dealloying.

PubMed

Wang, Zhili; Liu, Pan; Han, Jiuhui; Cheng, Chun; Ning, Shoucong; Hirata, Akihiko; Fujita, Takeshi; Chen, Mingwei

2017-10-20

Tuning surface structures by bottom-up synthesis has been demonstrated as an effective strategy to improve the catalytic performances of nanoparticle catalysts. Nevertheless, the surface modification of three-dimensional nanoporous metals, fabricated by a top-down dealloying approach, has not been achieved despite great efforts devoted to improving the catalytic performance of three-dimensional nanoporous catalysts. Here we report a surfactant-modified dealloying method to tailor the surface structure of nanoporous gold for amplified electrocatalysis toward methanol oxidation and oxygen reduction reactions. With the assistance of surfactants, {111} or {100} faceted internal surfaces of nanoporous gold can be realized in a controllable manner by optimizing dealloying conditions. The surface modified nanoporous gold exhibits significantly enhanced electrocatalytic activities in comparison with conventional nanoporous gold. This study paves the way to develop high-performance three-dimensional nanoporous catalysts with a tunable surface structure by top-down dealloying for efficient chemical and electrochemical reactions.

X-ray diffraction study of Penicillium Vitale catalase in the complex with aminotriazole

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

Borovik, A. A.; Grebenko, A. I.; Melik-Adamyan, V. R., E-mail: mawr@ns.crys.ras.ru

2011-07-15

The three-dimensional structure of the enzyme catalase from Penicillium vitale in a complex with the inhibitor aminotriazole was solved and refined by protein X-ray crystallography methods. An analysis of the three-dimensional structure of the complex showed that the inhibition of the enzyme occurs as a result of the covalent binding of aminotriazole to the amino-acid residue His64 in the active site of the enzyme. An investigation of the three-dimensional structure of the complex resulted in the amino-acid residues being more precisely identified. The binding sites of saccharide residues and calcium ions in the protein molecule were found.

Modelling the drying of three-dimensional pulp moulded structures. Part II, Drying data obtained from flat panels using virgin and recycled paper fibre

Treesearch

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

1999-01-01

A three-dimensional structural panel, called FPL Spaceboard, was developed at the USDA Forest Products Laboratory. Spaceboard panels have been formed using a variety of fibrous materials using either a wet- or dry-forming process. Geometrically, the panel departs from the traditional two-dimensional flat panel by integrally forming an array of perpendicular ribs and...

Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement.

PubMed

Butler, J B; Vaillancourt, R E; Potts, B M; Lee, D J; King, G J; Baten, A; Shepherd, M; Freeman, J S

2017-05-22

Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomic information between these important taxa and provide further insights into the rate of structural change in tree genomes. We constructed three high density linkage maps for two Corymbia species (Corymbia citriodora subsp. variegata and Corymbia torelliana) which were used to compare genome structure between both species and Eucalyptus grandis. Genome structure was highly conserved between the Corymbia species. However, the comparison of Corymbia and E. grandis suggests large (from 1-13 MB) intra-chromosomal rearrangements have occurred on seven of the 11 chromosomes. Most rearrangements were supported through comparisons of the three independent Corymbia maps to the E. grandis genome sequence, and to other independently constructed Eucalyptus linkage maps. These are the first large scale chromosomal rearrangements discovered between eucalypts. Nonetheless, in the general context of plants, the genomic structure of the two genera was remarkably conserved; adding to a growing body of evidence that conservation of genome structure is common amongst woody angiosperms.

Balancing Newtonian gravity and spin to create localized structures

NASA Astrophysics Data System (ADS)

Bush, Michael; Lindner, John

2015-03-01

Using geometry and Newtonian physics, we design localized structures that do not require electromagnetic or other forces to resist implosion or explosion. In two-dimensional Euclidean space, we find an equilibrium configuration of a rotating ring of massive dust whose inward gravity is the centripetal force that spins it. We find similar solutions in three-dimensional Euclidean and hyperbolic spaces, but only in the limit of vanishing mass. Finally, in three-dimensional Euclidean space, we generalize the two-dimensional result by finding an equilibrium configuration of a spherical shell of massive dust that supports itself against gravitational collapse by spinning isoclinically in four dimensions so its three-dimensional acceleration is everywhere inward. These Newtonian ``atoms'' illuminate classical physics and geometry.

Gold nanocrystals with DNA-directed morphologies.

PubMed

Ma, Xingyi; Huh, June; Park, Wounjhang; Lee, Luke P; Kwon, Young Jik; Sim, Sang Jun

2016-09-16

Precise control over the structure of metal nanomaterials is important for developing advanced nanobiotechnology. Assembly methods of nanoparticles into structured blocks have been widely demonstrated recently. However, synthesis of nanocrystals with controlled, three-dimensional structures remains challenging. Here we show a directed crystallization of gold by a single DNA molecular regulator in a sequence-independent manner and its applications in three-dimensional topological controls of crystalline nanostructures. We anchor DNA onto gold nanoseed with various alignments to form gold nanocrystals with defined topologies. Some topologies are asymmetric including pushpin-, star- and biconcave disk-like structures, as well as more complex jellyfish- and flower-like structures. The approach of employing DNA enables the solution-based synthesis of nanocrystals with controlled, three-dimensional structures in a desired direction, and expands the current tools available for designing and synthesizing feature-rich nanomaterials for future translational biotechnology.

Gold nanocrystals with DNA-directed morphologies

NASA Astrophysics Data System (ADS)

Ma, Xingyi; Huh, June; Park, Wounjhang; Lee, Luke P.; Kwon, Young Jik; Sim, Sang Jun

2016-09-01

Precise control over the structure of metal nanomaterials is important for developing advanced nanobiotechnology. Assembly methods of nanoparticles into structured blocks have been widely demonstrated recently. However, synthesis of nanocrystals with controlled, three-dimensional structures remains challenging. Here we show a directed crystallization of gold by a single DNA molecular regulator in a sequence-independent manner and its applications in three-dimensional topological controls of crystalline nanostructures. We anchor DNA onto gold nanoseed with various alignments to form gold nanocrystals with defined topologies. Some topologies are asymmetric including pushpin-, star- and biconcave disk-like structures, as well as more complex jellyfish- and flower-like structures. The approach of employing DNA enables the solution-based synthesis of nanocrystals with controlled, three-dimensional structures in a desired direction, and expands the current tools available for designing and synthesizing feature-rich nanomaterials for future translational biotechnology.

Aspects of Higher Spin Symmetry and its Breaking

NASA Astrophysics Data System (ADS)

Zhiboedov, Alexander

This thesis explores different aspects of higher spin symmetry and its breaking in the context of Quantum Field Theory, AdS/CFT and String Theory. In chapter 2, we study the constraints imposed by the existence of a single higher spin conserved current on a three-dimensional conformal field theory (CFT). A single higher spin conserved current implies the existence of an infinite number of higher spin conserved currents. The correlation functions of the stress tensor and the conserved currents are then shown to be equal to those of a free field theory. Namely a theory of N free bosons or free fermions. This is an extension of the Coleman-Mandula theorem to CFT's, which do not have a conventional S-matrix. In chapter 3, we consider three-dimensional conformal field theories that have a higher spin symmetry that is slightly broken. The theories have a large N limit, in the sense that the operators separate into single-trace and multi-trace and obey the usual large N factorization properties. We assume that the only single trace operators are the higher spin currents plus an additional scalar. Using the slightly broken higher spin symmetry we constrain the three-point functions of the theories to leading order in N. We show that there are two families of solutions. One family can be realized as a theory of N fermions with an O( N) Chern-Simons gauge field, the other as a N bosons plus the Chern-Simons gauge field. In chapter 4, we consider several aspects of unitary higher-dimensional conformal field theories. We investigate the dimensions of spinning operators via the crossing equations in the light-cone limit. We find that, in a sense, CFTs become free at large spin and 1/s is a weak coupling parameter. The spectrum of CFTs enjoys additivity: if two twists tau 1, tau2 appear in the spectrum, there are operators whose twists are arbitrarily close to tau1 + tau2. We characterize how tau1 + tau2 is approached at large spin by solving the crossing equations analytically. Applications include the 3d Ising model, theories with a gravity dual, SCFTs, and patterns of higher spin symmetry breaking. In chapter 5, we consider higher derivative corrections to the graviton three-point coupling within a weakly coupled theory of gravity. We devise a thought experiment involving a high energy scattering process which leads to causality violation if the graviton three-point vertex contains the additional structures. This violation cannot be fixed by adding conventional particles with spins J ≤ 2. But, it can be fixed by adding an infinite tower of extra massive particles with higher spins, J > 2. In AdS theories this implies a constraint on the conformal anomaly coefficients (a-c)/c lesssim 1/Delta gap2 in terms of Deltagap, the dimension of the lightest single particle operator with spin J > 2. For inflation, or de Sitter-like solutions, it indicates the existence of massive higher spin particles if the gravity wave non-gaussianity deviates significantly from the one computed in the Einstein theory.

Three-dimensional confocal microscopy of the living cornea and ocular lens

NASA Astrophysics Data System (ADS)

Masters, Barry R.

1991-07-01

The three-dimensional reconstruction of the optic zone of the cornea and the ocular crystalline lens has been accomplished using confocal microscopy and volume rendering computer techniques. A laser scanning confocal microscope was used in the reflected light mode to obtain the two-dimensional images from the cornea and the ocular lens of a freshly enucleated rabbit eye. The light source was an argon ion laser with a 488 nm wavelength. The microscope objective was a Leitz X25, NA 0.6 water immersion lens. The 400 micron thick cornea was optically sectioned into 133 three micron sections. The semi-transparent cornea and the in-situ ocular lens was visualized as high resolution, high contrast two-dimensional images. The structures observed in the cornea include: superficial epithelial cells and their nuclei, basal epithelial cells and their 'beaded' cell borders, basal lamina, nerve plexus, nerve fibers, nuclei of stromal keratocytes, and endothelial cells. The structures observed in the in- situ ocular lens include: lens capsule, lens epithelial cells, and individual lens fibers. The three-dimensional data sets of the cornea and the ocular lens were reconstructed in the computer using volume rendering techniques. Stereo pairs were also created of the two- dimensional ocular images for visualization. The stack of two-dimensional images was reconstructed into a three-dimensional object using volume rendering techniques. This demonstration of the three-dimensional visualization of the intact, enucleated eye provides an important step toward quantitative three-dimensional morphometry of the eye. The important aspects of three-dimensional reconstruction are discussed.

Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

PubMed Central

Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

2013-01-01

The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

Quasi-three-dimensional particle imaging with digital holography.

PubMed

Kemppinen, Osku; Heinson, Yuli; Berg, Matthew

2017-05-01

In this work, approximate three-dimensional structures of microparticles are generated with digital holography using an automated focus method. This is done by stacking a collection of silhouette-like images of a particle reconstructed from a single in-line hologram. The method enables estimation of the particle size in the longitudinal and transverse dimensions. Using the discrete dipole approximation, the method is tested computationally by simulating holograms for a variety of particles and attempting to reconstruct the known three-dimensional structure. It is found that poor longitudinal resolution strongly perturbs the reconstructed structure, yet the method does provide an approximate sense for the structure's longitudinal dimension. The method is then applied to laboratory measurements of holograms of single microparticles and their scattering patterns.

Solar dynamic modules for Space Station Freedom: The relationship between fine-pointing control and thermal loading of the aperture plate

NASA Technical Reports Server (NTRS)

Quinn, Roger D.; Kerslake, Thomas W.

1992-01-01

Dynamic simulations of Space Station Freedom (SSF) configured with solar dynamic (SD) power modules were performed. The structure was subjected to Space Shuttle docking disturbances, while being controlled with a 'natural' vibration and tracking control approach. Three control cases were investigated for the purpose of investigating the relationship between actuator effort, SD pointing, and thermal loading on the receiver aperture plate. Transient, one-dimensional heat transfer analyses were performed to conservatively predict temperatures of the multi-layered receiver aperture plate assembly and thermal stresses in its shield layer. Results indicate that the proposed aperture plate is tolerant of concentrated flux impingement during short-lived structural disturbances. Pointing requirements may be loosened and the requirement control torques lessened from that previously specified. Downsizing and simplifying the joint drive system should result in a considerable savings mass.

Three-Dimensional, Inelastic Response of Single-Edge Notch Bend Specimens Subjected to Impact Loading

DTIC Science & Technology

1993-08-01

measure the inherent fracture toughness of a material. A thor- ough understanding of the test specimen behavior is a prerequisite to the application of...measured material properties in structural applications . Three- dimensional dynamic analyses are performed for three different specimen configurations...derstanding of the test specimen behavior is a prerequisite to the application of measured ma- terial properties in structural applications . Three

Automated integration of lidar into the LANDFIRE product suite

Treesearch

Birgit Peterson; Kurtis J. Nelson; Carl Seielstad; Jason Stoker; W. Matt Jolly; Russell Parsons

2015-01-01

Accurate information about three-dimensional canopy structure and wildland fuel across the landscape is necessary for fire behaviour modelling system predictions. Remotely sensed data are invaluable for assessing these canopy characteristics over large areas; lidar data, in particular, are uniquely suited for quantifying three-dimensional canopy structure. Although...

Two-photon polymerization of a three dimensional structure using beams with orbital angular momentum

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

Zhang, Shi-Jie; Li, Yan, E-mail: li@pku.edu.cn; Liu, Zhao-Pei

The focus of a beam with orbital angular momentum exhibits internal structure instead of an elliptical intensity distribution of a Gaussian beam, and the superposition of Gauss-Laguerre beams realized by two-dimensional phase modulation can generate a complex three-dimensional (3D) focus. By taking advantage of the flexibility of this 3D focus tailoring, we have fabricated a 3D microstructure with high resolution by two-photon polymerization with a single exposure. Furthermore, we have polymerized an array of double-helix structures that demonstrates optical chirality.

Three-dimensional nanomagnetism

DOE PAGES

Fernandez-Pacheco, Amalio; Streubel, Robert; Fruchart, Olivier; ...

2017-06-09

Magnetic nanostructures are being developed for use in many aspects of our daily life, spanning areas such as data storage, sensing and biomedicine. Whereas patterned nanomagnets are traditionally two-dimensional planar structures, recent work is expanding nanomagnetism into three dimensions; a move triggered by the advance of unconventional synthesis methods and the discovery of new magnetic effects. In three-dimensional nanomagnets more complex magnetic configurations become possible, many with unprecedented properties. Here we review the creation of these structures and their implications for the emergence of new physics, the development of instrumentation and computational methods, and exploitation in numerous applications.

Application of a novel design paradigm to generate general nonpeptide combinatorial templates mimicking beta-turns: synthesis of ligands for melanocortin receptors.

PubMed

Webb, Thomas R; Jiang, Luyong; Sviridov, Sergey; Venegas, Ruben E; Vlaskina, Anna V; McGrath, Douglas; Tucker, John; Wang, Jian; Deschenes, Alain; Li, Rongshi

2007-01-01

We report the further application of a novel approach to template and ligand design by the synthesis of agonists of the melanocortin receptor. This design method uses the conserved structural data from the three-dimensional conformations of beta-turn peptides to design rigid nonpeptide templates that mimic the orientation of the main chain C-alpha atoms in a peptide beta-turn. We report details on a new synthesis of derivatives of template 1 that are useful for the synthesis of exploratory libraries. The utility of this technique is further exemplified by several iterative rounds of high-throughput synthesis and screening, which result in new partially optimized nonpeptide agonists for several melanocortin receptors.

NLF technology is ready to go

NASA Technical Reports Server (NTRS)

Holmes, Bruce J.

1988-01-01

Natural laminar flow (NLF) can reduce drag on aircraft developed using modern structural design methods. Modern metal and composite construction methods can meet NLF requirements for subsonic commuter and business airframes. NLF research at NASA concentrates on expanding the practical application of NLF drag reduction technology; payoffs include progress with liquid-crystal flow visualization, NLF on three-dimensional bodies, and the effects of acoustics on laminar stability. Fuel savings from 2 to 4 percent are expected if laminar flow could be achieved over the forward 50 percent of engine nacelles on large transports depending on the configuration. It is concluded that the skill required to use NLF for drag reduction depends on understanding the conservative design corridors within which laminar flow is durable and reliable.

Topology of large-scale structure. IV - Topology in two dimensions

NASA Technical Reports Server (NTRS)

Melott, Adrian L.; Cohen, Alexander P.; Hamilton, Andrew J. S.; Gott, J. Richard, III; Weinberg, David H.

1989-01-01

In a recent series of papers, an algorithm was developed for quantitatively measuring the topology of the large-scale structure of the universe and this algorithm was applied to numerical models and to three-dimensional observational data sets. In this paper, it is shown that topological information can be derived from a two-dimensional cross section of a density field, and analytic expressions are given for a Gaussian random field. The application of a two-dimensional numerical algorithm for measuring topology to cross sections of three-dimensional models is demonstrated.

Prediction of a common beta-propeller catalytic domain for fructosyltransferases of different origin and substrate specificity.

PubMed

Pons, T; Hernández, L; Batista, F R; Chinea, G

2000-11-01

The three-dimensional (3D) structure of fructan biosynthetic enzymes is still unknown. Here, we have explored folding similarities between reported microbial and plant enzymes that catalyze transfructosylation reactions. A sequence-structure compatibility search using TOPITS, SDP, 3D-PSSM, and SAM-T98 programs identified a beta-propeller fold with scores above the confidence threshold that indicate a structurally conserved catalytic domain in fructosyltransferases (FTFs) of diverse origin and substrate specificity. The predicted fold appeared related to that of neuraminidase and sialidase, of glycoside hydrolase families 33 and 34, respectively. The most reliable structural model was obtained using the crystal structure of neuraminidase (Protein Data Bank file: 5nn9) as template, and it is consistent with the location of previously identified functional residues of bacterial levansucrases (Batista et al., 1999; Song & Jacques, 1999). The sequence-sequence analysis presented here reinforces the recent inclusion of fungal and plant FTFs into glycoside hydrolase family 32, and suggests a modified sequence pattern H-x (2)-[PTV]-x (4)-[LIVMA]-[NSCAYG]-[DE]-P-[NDSC][GA]3 for this family.

Prediction of a common beta-propeller catalytic domain for fructosyltransferases of different origin and substrate specificity.

PubMed Central

Pons, T.; Hernández, L.; Batista, F. R.; Chinea, G.

2000-01-01

The three-dimensional (3D) structure of fructan biosynthetic enzymes is still unknown. Here, we have explored folding similarities between reported microbial and plant enzymes that catalyze transfructosylation reactions. A sequence-structure compatibility search using TOPITS, SDP, 3D-PSSM, and SAM-T98 programs identified a beta-propeller fold with scores above the confidence threshold that indicate a structurally conserved catalytic domain in fructosyltransferases (FTFs) of diverse origin and substrate specificity. The predicted fold appeared related to that of neuraminidase and sialidase, of glycoside hydrolase families 33 and 34, respectively. The most reliable structural model was obtained using the crystal structure of neuraminidase (Protein Data Bank file: 5nn9) as template, and it is consistent with the location of previously identified functional residues of bacterial levansucrases (Batista et al., 1999; Song & Jacques, 1999). The sequence-sequence analysis presented here reinforces the recent inclusion of fungal and plant FTFs into glycoside hydrolase family 32, and suggests a modified sequence pattern H-x (2)-[PTV]-x (4)-[LIVMA]-[NSCAYG]-[DE]-P-[NDSC][GA]3 for this family. PMID:11305239

Hydroelastic behaviour of a structure exposed to an underwater explosion

PubMed Central

Colicchio, G.; Greco, M.; Brocchini, M.; Faltinsen, O. M.

2015-01-01

The hydroelastic interaction between an underwater explosion and an elastic plate is investigated num- erically through a domain-decomposition strategy. The three-dimensional features of the problem require a large computational effort, which is reduced through a weak coupling between a one-dimensional radial blast solver, which resolves the blast evolution far from the boundaries, and a three-dimensional compressible flow solver used where the interactions between the compression wave and the boundaries take place and the flow becomes three-dimensional. The three-dimensional flow solver at the boundaries is directly coupled with a modal structural solver that models the response of the solid boundaries like elastic plates. This enables one to simulate the fluid–structure interaction as a strong coupling, in order to capture hydroelastic effects. The method has been applied to the experimental case of Hung et al. (2005 Int. J. Impact Eng. 31, 151–168 (doi:10.1016/j.ijimpeng.2003.10.039)) with explosion and structure sufficiently far from other boundaries and successfully validated in terms of the evolution of the acceleration induced on the plate. It was also used to investigate the interaction of an underwater explosion with the bottom of a close-by ship modelled as an orthotropic plate. In the application, the acoustic phase of the fluid–structure interaction is examined, highlighting the need of the fluid–structure coupling to capture correctly the possible inception of cavitation. PMID:25512585

The secondary structure of the ets domain of human Fli-1 resembles that of the helix-turn-helix DNA-binding motif of the Escherichia coli catabolite gene activator protein.

PubMed Central

Liang, H; Olejniczak, E T; Mao, X; Nettesheim, D G; Yu, L; Thompson, C B; Fesik, S W

1994-01-01

The ets family of eukaryotic transcription factors is characterized by a conserved DNA-binding domain of approximately 85 amino acids for which the three-dimensional structure is not known. By using multidimensional NMR spectroscopy, we have determined the secondary structure of the ets domain of one member of this gene family, human Fli-1, both in the free form and in a complex with a 16-bp cognate DNA site. The secondary structure of the Fli-1 ets domain consists of three alpha-helices and a short four-stranded antiparallel beta-sheet. This secondary structure arrangement resembles that of the DNA-binding domain of the catabolite gene activator protein of Escherichia coli, as well as those of several eukaryotic DNA-binding proteins including histone H5, HNF-3/fork head, and the heat shock transcription factor. Differences in chemical shifts of backbone resonances and amide exchange rates between the DNA-bound and free forms of the Fli-1 ets domain suggest that the third helix is the DNA recognition helix, as in the catabolite gene activator protein and other structurally related proteins. These results suggest that the ets domain is structurally similar to the catabolite gene activator protein family of helix-turn-helix DNA-binding proteins. Images PMID:7972119

Dark State Optical Lattice with a Subwavelength Spatial Structure

NASA Astrophysics Data System (ADS)

Wang, Y.; Subhankar, S.; Bienias, P.; ŁÄ cki, M.; Tsui, T.-C.; Baranov, M. A.; Gorshkov, A. V.; Zoller, P.; Porto, J. V.; Rolston, S. L.

2018-02-01

We report on the experimental realization of a conservative optical lattice for cold atoms with a subwavelength spatial structure. The potential is based on the nonlinear optical response of three-level atoms in laser-dressed dark states, which is not constrained by the diffraction limit of the light generating the potential. The lattice consists of a one-dimensional array of ultranarrow barriers with widths less than 10 nm, well below the wavelength of the lattice light, physically realizing a Kronig-Penney potential. We study the band structure and dissipation of this lattice and find good agreement with theoretical predictions. Even on resonance, the observed lifetimes of atoms trapped in the lattice are as long as 44 ms, nearly 1 05 times the excited state lifetime, and could be further improved with more laser intensity. The potential is readily generalizable to higher dimensions and different geometries, allowing, for example, nearly perfect box traps, narrow tunnel junctions for atomtronics applications, and dynamically generated lattices with subwavelength spacings.

Solution structure of the strawberry allergen Fra a 1

PubMed Central

Seutter von Loetzen, Christian; Schweimer, Kristian; Schwab, Wilfried; Rösch, Paul; Hartl-Spiegelhauer, Olivia

2012-01-01

The PR10 family protein Fra a 1E from strawberry (Fragaria x ananassa) is down-regulated in white strawberry mutants, and transient RNAi (RNA interference)-mediated silencing experiments confirmed that Fra a 1 is involved in fruit pigment synthesis. In the present study, we determined the solution structure of Fra a 1E. The protein fold is identical with that of other members of the PR10 protein family and consists of a seven-stranded antiparallel β-sheet, two short V-shaped α-helices and a long C-terminal α-helix that encompass a hydrophobic pocket. Whereas Fra a 1E contains the glycine-rich loop that is highly conserved throughout the protein family, the volume of the hydrophobic pocket and the size of its entrance are much larger than expected. The three-dimensional structure may shed some light on its physiological function and may help to further understand the role of PR10 proteins in plants. PMID:22913709

Intrinsic disorder mediates the diverse regulatory functions of the Cdk inhibitor p21

PubMed Central

Wang, Yuefeng; Fisher, John C.; Mathew, Rose; Ou, Li; Otieno, Steve; Sublett, Jack; Xiao, Limin; Chen, Jianhan; Roussel, Martine F.; Kriwacki, Richard W.

2011-01-01

Traditionally, well-defined three-dimensional structure was thought to be essential for protein function. However, myriad biological functions are performed by highly dynamic, intrinsically disordered proteins (IDPs). IDPs often fold upon binding their biological targets and frequently exhibit “binding diversity” by targeting multiple ligands. We sought to understand the physical basis of IDP binding diversity and herein report that the cyclin-dependent kinase (Cdk) inhibitor, p21Cip1, adaptively binds to and inhibits the various Cdk/cyclin complexes that regulate eukaryotic cell division. Based on results from NMR spectroscopy, and biochemical and cellular assays, we show that structural adaptability of a helical sub-domain within p21 termed LH enables two other sub-domains termed D1 and D2 to specifically bind conserved surface features of the cyclin and Cdk subunits, respectively, within otherwise structurally distinct Cdk/cyclin complexes. Adaptive folding upon binding is likely to mediate the diverse biological functions of the thousands of IDPs present in eukaryotes. PMID:21358637

Structured Overlapping Grid Simulations of Contra-rotating Open Rotor Noise

NASA Technical Reports Server (NTRS)

Housman, Jeffrey A.; Kiris, Cetin C.

2015-01-01

Computational simulations using structured overlapping grids with the Launch Ascent and Vehicle Aerodynamics (LAVA) solver framework are presented for predicting tonal noise generated by a contra-rotating open rotor (CROR) propulsion system. A coupled Computational Fluid Dynamics (CFD) and Computational AeroAcoustics (CAA) numerical approach is applied. Three-dimensional time-accurate hybrid Reynolds Averaged Navier-Stokes/Large Eddy Simulation (RANS/LES) CFD simulations are performed in the inertial frame, including dynamic moving grids, using a higher-order accurate finite difference discretization on structured overlapping grids. A higher-order accurate free-stream preserving metric discretization with discrete enforcement of the Geometric Conservation Law (GCL) on moving curvilinear grids is used to create an accurate, efficient, and stable numerical scheme. The aeroacoustic analysis is based on a permeable surface Ffowcs Williams-Hawkings (FW-H) approach, evaluated in the frequency domain. A time-step sensitivity study was performed using only the forward row of blades to determine an adequate time-step. The numerical approach is validated against existing wind tunnel measurements.

Candidate Cell and Matrix Interaction Domains on the Collagen Fibril, the Predominant Protein of Vertebrates*S⃞

PubMed Central

Sweeney, Shawn M.; Orgel, Joseph P.; Fertala, Andrzej; McAuliffe, Jon D.; Turner, Kevin R.; Di Lullo, Gloria A.; Chen, Steven; Antipova, Olga; Perumal, Shiamalee; Ala-Kokko, Leena; Forlino, Antonella; Cabral, Wayne A.; Barnes, Aileen M.; Marini, Joan C.; Antonio, James D. San

2008-01-01

Type I collagen, the predominant protein of vertebrates, polymerizes with type III and V collagens and non-collagenous molecules into large cable-like fibrils, yet how the fibril interacts with cells and other binding partners remains poorly understood. To help reveal insights into the collagen structure-function relationship, a data base was assembled including hundreds of type I collagen ligand binding sites and mutations on a two-dimensional model of the fibril. Visual examination of the distribution of functional sites, and statistical analysis of mutation distributions on the fibril suggest it is organized into two domains. The “cell interaction domain” is proposed to regulate dynamic aspects of collagen biology, including integrin-mediated cell interactions and fibril remodeling. The “matrix interaction domain” may assume a structural role, mediating collagen cross-linking, proteoglycan interactions, and tissue mineralization. Molecular modeling was used to superimpose the positions of functional sites and mutations from the two-dimensional fibril map onto a three-dimensional x-ray diffraction structure of the collagen microfibril in situ, indicating the existence of domains in the native fibril. Sequence searches revealed that major fibril domain elements are conserved in type I collagens through evolution and in the type II/XI collagen fibril predominant in cartilage. Moreover, the fibril domain model provides potential insights into the genotype-phenotype relationship for several classes of human connective tissue diseases, mechanisms of integrin clustering by fibrils, the polarity of fibril assembly, heterotypic fibril function, and connective tissue pathology in diabetes and aging. PMID:18487200

Candidate Cell and Matrix Interaction Domains on the Collagen Fibril, the Predominant Protein of Vertebrates

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

Sweeney, Shawn M.; Orgel, Joseph P.; Fertala, Andrzej

Type I collagen, the predominant protein of vertebrates, polymerizes with type III and V collagens and non-collagenous molecules into large cable-like fibrils, yet how the fibril interacts with cells and other binding partners remains poorly understood. To help reveal insights into the collagen structure-function relationship, a data base was assembled including hundreds of type I collagen ligand binding sites and mutations on a two-dimensional model of the fibril. Visual examination of the distribution of functional sites, and statistical analysis of mutation distributions on the fibril suggest it is organized into two domains. The 'cell interaction domain' is proposed to regulatemore » dynamic aspects of collagen biology, including integrin-mediated cell interactions and fibril remodeling. The 'matrix interaction domain' may assume a structural role, mediating collagen cross-linking, proteoglycan interactions, and tissue mineralization. Molecular modeling was used to superimpose the positions of functional sites and mutations from the two-dimensional fibril map onto a three-dimensional x-ray diffraction structure of the collagen microfibril in situ, indicating the existence of domains in the native fibril. Sequence searches revealed that major fibril domain elements are conserved in type I collagens through evolution and in the type II/XI collagen fibril predominant in cartilage. Moreover, the fibril domain model provides potential insights into the genotype-phenotype relationship for several classes of human connective tissue diseases, mechanisms of integrin clustering by fibrils, the polarity of fibril assembly, heterotypic fibril function, and connective tissue pathology in diabetes and aging.« less

A coupled sharp-interface immersed boundary-finite-element method for flow-structure interaction with application to human phonation.

PubMed

Zheng, X; Xue, Q; Mittal, R; Beilamowicz, S

2010-11-01

A new flow-structure interaction method is presented, which couples a sharp-interface immersed boundary method flow solver with a finite-element method based solid dynamics solver. The coupled method provides robust and high-fidelity solution for complex flow-structure interaction (FSI) problems such as those involving three-dimensional flow and viscoelastic solids. The FSI solver is used to simulate flow-induced vibrations of the vocal folds during phonation. Both two- and three-dimensional models have been examined and qualitative, as well as quantitative comparisons, have been made with established results in order to validate the solver. The solver is used to study the onset of phonation in a two-dimensional laryngeal model and the dynamics of the glottal jet in a three-dimensional model and results from these studies are also presented.

Molecular cloning and characterization of sea bass (Dicentrarchus labrax, L.) Tapasin.

PubMed

Pinto, Rute D; da Silva, Diogo V; Pereira, Pedro J B; dos Santos, Nuno M S

2012-01-01

Mammalian tapasin (TPN) is a key member of the major histocompatibility complex (MHC) class I antigen presentation pathway, being part of the multi-protein complex called the peptide loading complex (PLC). Several studies describe its important roles in stabilizing empty MHC class I complexes, facilitating peptide loading and editing the repertoire of bound peptides, with impact on CD8(+) T cell immune responses. In this work, the gene and cDNA of the sea bass (Dicentrarchus labrax) glycoprotein TPN have been isolated and characterized. The coding sequence has a 1329 bp ORF encoding a 442-residue precursor protein with a predicted 24-amino acid leader peptide, generating a 418-amino acid mature form that retains a conserved N-glycosylation site, three conserved mammalian tapasin motifs, two Ig superfamily domains, a transmembrane domain and an ER-retention di-lysine motif at the C-terminus, suggestive of a function similar to mammalian tapasins. Similar to the human counterpart, the sea bass TPN gene comprises 8 exons, some of which correspond to separate functional domains of the protein. A three-dimensional homology model of sea bass tapasin was calculated and is consistent with the structural features described for the human molecule. Together, these results support the concept that the basic structure of TPN has been maintained through evolution. Moreover, the present data provides information that will allow further studies on cell-mediated immunity and class I antigen presentation pathway in particular, in this important fish species. Copyright © 2011 Elsevier Ltd. All rights reserved.

Development of a locally mass flux conservative computer code for calculating 3-D viscous flow in turbomachines

NASA Technical Reports Server (NTRS)

Walitt, L.

1982-01-01

The VANS successive approximation numerical method was extended to the computation of three dimensional, viscous, transonic flows in turbomachines. A cross-sectional computer code, which conserves mass flux at each point of the cross-sectional surface of computation was developed. In the VANS numerical method, the cross-sectional computation follows a blade-to-blade calculation. Numerical calculations were made for an axial annular turbine cascade and a transonic, centrifugal impeller with splitter vanes. The subsonic turbine cascade computation was generated in blade-to-blade surface to evaluate the accuracy of the blade-to-blade mode of marching. Calculated blade pressures at the hub, mid, and tip radii of the cascade agreed with corresponding measurements. The transonic impeller computation was conducted to test the newly developed locally mass flux conservative cross-sectional computer code. Both blade-to-blade and cross sectional modes of calculation were implemented for this problem. A triplet point shock structure was computed in the inducer region of the impeller. In addition, time-averaged shroud static pressures generally agreed with measured shroud pressures. It is concluded that the blade-to-blade computation produces a useful engineering flow field in regions of subsonic relative flow; and cross-sectional computation, with a locally mass flux conservative continuity equation, is required to compute the shock waves in regions of supersonic relative flow.

Three dimensional contact/impact methodology

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

Kulak, R.F.

1987-01-01

The simulation of three-dimensional interface mechanics between reactor components and structures during static contact or dynamic impact is necessary to realistically evaluate their structural integrity to off-normal loads. In our studies of postulated core energy release events, we have found that significant structure-structure interactions occur in some reactor vessel head closure designs and that fluid-structure interactions occur within the reactor vessel. Other examples in which three-dimensional interface mechanics play an important role are: (1) impact response of shipping casks containing spent fuel, (2) whipping pipe impact on reinforced concrete panels or pipe-to-pipe impact after a pipe break, (3) aircraft crashmore » on secondary containment structures, (4) missiles generated by turbine failures or tornados, and (5) drops of heavy components due to lifting accidents. The above is a partial list of reactor safety problems that require adequate treatment of interface mechanics and are discussed in this paper.« less

Visualization of molecular structures using HoloLens-based augmented reality

PubMed Central

Hoffman, MA; Provance, JB

2017-01-01

Biological molecules and biologically active small molecules are complex three dimensional structures. Current flat screen monitors are limited in their ability to convey the full three dimensional characteristics of these molecules. Augmented reality devices, including the Microsoft HoloLens, offer an immersive platform to change how we interact with molecular visualizations. We describe a process to incorporate the three dimensional structures of small molecules and complex proteins into the Microsoft HoloLens using aspirin and the human leukocyte antigen (HLA) as examples. Small molecular structures can be introduced into the HoloStudio application, which provides native support for rotating, resizing and performing other interactions with these molecules. Larger molecules can be imported through the Unity gaming development platform and then Microsoft Visual Developer. The processes described here can be modified to import a wide variety of molecular structures into augmented reality systems and improve our comprehension of complex structural features. PMID:28815109

Three-Dimensional Temperature Field Simulation for the Rotor of an Asynchronous Motor

ERIC Educational Resources Information Center

Wang, Yanwu; Fan, Chunli; Yang, Li; Sun, Fengrui

2010-01-01

A three-dimensional heat transfer model is built according to the rotor structure of an asynchronous motor, and three-dimensional temperature fields of the rotor under different working conditions, such as the unloaded, rated loaded and that with broken rotor bars, are studied based on the finite element numerical method and experiments. The…

Fabrication of three-dimensional collagen scaffold using an inverse mould-leaching process.

PubMed

Ahn, SeungHyun; Lee, SuYeon; Cho, Youngseok; Chun, Wook; Kim, GeunHyung

2011-09-01

Natural biopolymers, such as collagen or chitosan, are considered ideal for biomedical scaffolds. However, low processability of the materials has hindered the fabrication of designed pore structures controlled by various solid freeform-fabrication methods. A new technique to fabricate a biomedical three-dimensional collagen scaffold, supplemented with a sacrificial poly(ethylene oxide) mould is proposed. The fabricated collagen scaffold shows a highly porous surface and a three-dimensional structure with high porosity as well as mechanically stable structure. To show its feasibility for biomedical applications, fibroblasts/keratinocytes were co-cultured on the scaffold, and the cell proliferation and cell migration of the scaffold was more favorable than that obtained with a spongy-type collagen scaffold.

Self-Organization of Zonal Jets in Outer Planet Atmospheres: Uranus and Neptune

NASA Technical Reports Server (NTRS)

Friedson, A. James

1997-01-01

The statistical mechnical theory of a two-dimensional Euler fluid is appleid for the first time to explore the spontaneous self-oganization of zonal jets in outer planet atmospheres. Globally conserved integralls of motion are found to play a central role in defining jet structure.

Three-Dimensional Gene Map of Cancer Cell Types: Structural Entropy Minimisation Principle for Defining Tumour Subtypes

PubMed Central

Li, Angsheng; Yin, Xianchen; Pan, Yicheng

2016-01-01

In this study, we propose a method for constructing cell sample networks from gene expression profiles, and a structural entropy minimisation principle for detecting natural structure of networks and for identifying cancer cell subtypes. Our method establishes a three-dimensional gene map of cancer cell types and subtypes. The identified subtypes are defined by a unique gene expression pattern, and a three-dimensional gene map is established by defining the unique gene expression pattern for each identified subtype for cancers, including acute leukaemia, lymphoma, multi-tissue, lung cancer and healthy tissue. Our three-dimensional gene map demonstrates that a true tumour type may be divided into subtypes, each defined by a unique gene expression pattern. Clinical data analyses demonstrate that most cell samples of an identified subtype share similar survival times, survival indicators and International Prognostic Index (IPI) scores and indicate that distinct subtypes identified by our algorithms exhibit different overall survival times, survival ratios and IPI scores. Our three-dimensional gene map establishes a high-definition, one-to-one map between the biologically and medically meaningful tumour subtypes and the gene expression patterns, and identifies remarkable cells that form singleton submodules. PMID:26842724

Three-dimensional water impact at normal incidence to a blunt structure

PubMed Central

Cooker, M. J.; Korobkin, A. A.

2016-01-01

The three-dimensional water impact onto a blunt structure with a spreading rectangular contact region is studied. The structure is mounted on a flat rigid plane with the impermeable curved surface of the structure perpendicular to the plane. Before impact, the water region is a rectangular domain of finite thickness bounded from below by the rigid plane and above by the flat free surface. The front free surface of the water region is vertical, representing the front of an advancing steep wave. The water region is initially advancing towards the structure at a constant uniform speed. We are concerned with the slamming loads acting on the surface of the structure during the initial stage of water impact. Air, gravity and surface tension are neglected. The problem is analysed by using some ideas of pressure-impulse theory, but including the time-dependence of the wetted area of the structure. The flow caused by the impact is three-dimensional and incompressible. The distribution of the pressure-impulse (the time-integral of pressure) over the surface of the structure is analysed and compared with the distributions provided by strip theories. The total impulse exerted on the structure during the impact stage is evaluated and compared with numerical and experimental predictions. An example calculation is presented of water impact onto a vertical rigid cylinder. Three-dimensional effects on the slamming loads are the main concern in this study. PMID:27616912

A new idea for broad band reflector and tunable multichannel filter of one dimensional symmetric photonic crystal with magnetized cold plasma defects

NASA Astrophysics Data System (ADS)

Kumar, Asish; Singh, Prabal P.; Thapa, Khem B.

2018-05-01

The optical properties of one-dimensional periodic structure composed by SiO2 and dielectric (air) layers with asymmetric and symmetric forms studied. The transmittance for symmetric periodic defective structure analyzed by introducing one, two, three layers of magnetized cold plasma (MCP) in one-dimensional periodic structure. We found better result for symmetric defect of three layer of the MCP compare to the other defective structures. On the basis of our calculated results, we proposed a new idea for broadband reflector at lower frequency range as well as the multichannel filter at higher frequency range.

[Family of ribosomal proteins S1 contains unique conservative domain].

PubMed

Deriusheva, E I; Machulin, A V; Selivanova, O M; Serdiuk, I N

2010-01-01

Different representatives of bacteria have different number of amino acid residues in the ribosomal proteins S1. This number varies from 111 (Spiroplasma kunkelii) to 863 a.a. (Treponema pallidum). Traditionally and for lack of this protein three-dimensional structure, its architecture is represented as repeating S1 domains. Number of these domains depends on the protein's length. Domain's quantity and its boundaries data are contained in the specialized databases, such as SMART, Pfam and PROSITE. However, for the same object these data may be very different. For search of domain's quantity and its boundaries, new approach, based on the analysis of dicted secondary structure (PsiPred), was used. This approach allowed us to reveal structural domains in amino acid sequences of S1 proteins and at that number varied from one to six. Alignment of S1 proteins, containing different domain's number, with the S1 RNAbinding domain of Escherichia coli PNPase elicited a fact that in family of ribosomal proteins SI one domain has maximal homology with S1 domain from PNPase. This conservative domain migrates along polypeptide chain and locates in proteins, containing different domain's number, according to specified pattern. In this domain as well in the S1 domain from PNPase, residues Phe-19, Phe-22, His-34, Asp-64 and Arg-68 are clustered on the surface and formed RNA binding site.

M553 sphere forming experiment: Pure nickel specimen evaluation

NASA Technical Reports Server (NTRS)

Johnson, P. C.; Peters, E. T.

1973-01-01

A region or cap of very fine two-dimensional surface growth structure was observed at the top of three of the six pure nickel flight specimens. Such two-dimensional surface growth structures have been observed both on the ground-based specimens and on other surface areas of the flight specimens. However, the fine structures observed on the three flight samples are at least an order of magnitude finer than those previously observed, and resemble similar localized, fine, two-dimensional surface structures observed in both ground and flight specimens for the nickel alloys. The two-dimensional growth areas consist primarily of fine equiaxed grains, specimen SL-2.6, fine dendrites, specimen SL-2.5, or a core of fine equiaxed grains surrounded by a ring of fine dendrites, specimen SL-1.9.

Three-dimensionally modulated anisotropic structure for diffractive optical elements created by one-step three-beam polarization holographic photoalignment

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

Kawai, Kotaro, E-mail: s135016@stn.nagaokaut.ac.jp; Sakamoto, Moritsugu; Noda, Kohei

2016-03-28

A diffractive optical element with a three-dimensional liquid crystal (LC) alignment structure for advanced control of polarized beams was fabricated by a highly efficient one-step photoalignment method. This study is of great significance because different two-dimensional continuous and complex alignment patterns can be produced on two alignment films by simultaneously irradiating an empty glass cell composed of two unaligned photocrosslinkable polymer LC films with three-beam polarized interference beam. The polarization azimuth, ellipticity, and rotation direction of the diffracted beams from the resultant LC grating widely varied depending on the two-dimensional diffracted position and the polarization states of the incident beams.more » These polarization diffraction properties are well explained by theoretical analysis based on Jones calculus.« less

Multifunctionality and diversity of GDSL esterase/lipase gene family in rice (Oryza sativa L. japonica) genome: new insights from bioinformatics analysis

PubMed Central

2012-01-01

Background GDSL esterases/lipases are a newly discovered subclass of lipolytic enzymes that are very important and attractive research subjects because of their multifunctional properties, such as broad substrate specificity and regiospecificity. Compared with the current knowledge regarding these enzymes in bacteria, our understanding of the plant GDSL enzymes is very limited, although the GDSL gene family in plant species include numerous members in many fully sequenced plant genomes. Only two genes from a large rice GDSL esterase/lipase gene family were previously characterised, and the majority of the members remain unknown. In the present study, we describe the rice OsGELP (Oryza sativa GDSL esterase/lipase protein) gene family at the genomic and proteomic levels, and use this knowledge to provide insights into the multifunctionality of the rice OsGELP enzymes. Results In this study, an extensive bioinformatics analysis identified 114 genes in the rice OsGELP gene family. A complete overview of this family in rice is presented, including the chromosome locations, gene structures, phylogeny, and protein motifs. Among the OsGELPs and the plant GDSL esterase/lipase proteins of known functions, 41 motifs were found that represent the core secondary structure elements or appear specifically in different phylogenetic subclades. The specification and distribution of identified putative conserved clade-common and -specific peptide motifs, and their location on the predicted protein three dimensional structure may possibly signify their functional roles. Potentially important regions for substrate specificity are highlighted, in accordance with protein three-dimensional model and location of the phylogenetic specific conserved motifs. The differential expression of some representative genes were confirmed by quantitative real-time PCR. The phylogenetic analysis, together with protein motif architectures, and the expression profiling were analysed to predict the possible biological functions of the rice OsGELP genes. Conclusions Our current genomic analysis, for the first time, presents fundamental information on the organization of the rice OsGELP gene family. With combination of the genomic, phylogenetic, microarray expression, protein motif distribution, and protein structure analyses, we were able to create supported basis for the functional prediction of many members in the rice GDSL esterase/lipase family. The present study provides a platform for the selection of candidate genes for further detailed functional study. PMID:22793791

The Impact of Stereoscopic Imagery and Motion on Anatomical Structure Recognition and Visual Attention Performance

ERIC Educational Resources Information Center

Remmele, Martin; Schmidt, Elena; Lingenfelder, Melissa; Martens, Andreas

2018-01-01

Gross anatomy is located in a three-dimensional space. Visualizing aspects of structures in gross anatomy education should aim to provide information that best resembles their original spatial proportions. Stereoscopic three-dimensional imagery might offer possibilities to implement this aim, though some research has revealed potential impairments…

Polyimide Aerogels with Three-Dimensional Cross-Linked Structure

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B. (Inventor)

2016-01-01

A method for creating a three dimensional cross-linked polyimide structure includes dissolving a diamine, a dianhydride, and a triamine in a solvent, imidizing a polyamic acid gel by heating the gel, extracting the gel in a second solvent, supercritically drying the gel, and removing the solvent to create a polyimide aerogel.

A light-trapping strategy for nanocrystalline silicon thin-film solar cells using three-dimensionally assembled nanoparticle structures.

PubMed

Ha, Kyungyeon; Jang, Eunseok; Jang, Segeun; Lee, Jong-Kwon; Jang, Min Seok; Choi, Hoseop; Cho, Jun-Sik; Choi, Mansoo

2016-02-05

We report three-dimensionally assembled nanoparticle structures inducing multiple plasmon resonances for broadband light harvesting in nanocrystalline silicon (nc-Si:H) thin-film solar cells. A three-dimensional multiscale (3DM) assembly of nanoparticles generated using a multi-pin spark discharge method has been accomplished over a large area under atmospheric conditions via ion-assisted aerosol lithography. The multiscale features of the sophisticated 3DM structures exhibit surface plasmon resonances at multiple frequencies, which increase light scattering and absorption efficiency over a wide spectral range from 350-1100 nm. The multiple plasmon resonances, together with the antireflection functionality arising from the conformally deposited top surface of the 3D solar cell, lead to a 22% and an 11% improvement in power conversion efficiency of the nc-Si:H thin-film solar cells compared to flat cells and cells employing nanoparticle clusters, respectively. Finite-difference time-domain simulations were also carried out to confirm that the improved device performance mainly originates from the multiple plasmon resonances generated from three-dimensionally assembled nanoparticle structures.

Three-Dimensional Navier-Stokes Method with Two-Equation Turbulence Models for Efficient Numerical Simulation of Hypersonic Flows

NASA Technical Reports Server (NTRS)

Bardina, J. E.

1994-01-01

A new computational efficient 3-D compressible Reynolds-averaged implicit Navier-Stokes method with advanced two equation turbulence models for high speed flows is presented. All convective terms are modeled using an entropy satisfying higher-order Total Variation Diminishing (TVD) scheme based on implicit upwind flux-difference split approximations and arithmetic averaging procedure of primitive variables. This method combines the best features of data management and computational efficiency of space marching procedures with the generality and stability of time dependent Navier-Stokes procedures to solve flows with mixed supersonic and subsonic zones, including streamwise separated flows. Its robust stability derives from a combination of conservative implicit upwind flux-difference splitting with Roe's property U to provide accurate shock capturing capability that non-conservative schemes do not guarantee, alternating symmetric Gauss-Seidel 'method of planes' relaxation procedure coupled with a three-dimensional two-factor diagonal-dominant approximate factorization scheme, TVD flux limiters of higher-order flux differences satisfying realizability, and well-posed characteristic-based implicit boundary-point a'pproximations consistent with the local characteristics domain of dependence. The efficiency of the method is highly increased with Newton Raphson acceleration which allows convergence in essentially one forward sweep for supersonic flows. The method is verified by comparing with experiment and other Navier-Stokes methods. Here, results of adiabatic and cooled flat plate flows, compression corner flow, and 3-D hypersonic shock-wave/turbulent boundary layer interaction flows are presented. The robust 3-D method achieves a better computational efficiency of at least one order of magnitude over the CNS Navier-Stokes code. It provides cost-effective aerodynamic predictions in agreement with experiment, and the capability of predicting complex flow structures in complex geometries with good accuracy.

Comparison of different hip prosthesis shapes considering micro-level bone remodeling and stress-shielding criteria using three-dimensional design space topology optimization.

PubMed

Boyle, Christopher; Kim, Il Yong

2011-06-03

Since the late 1980s, computational analysis of total hip arthroplasty (THA) prosthesis components has been completed using macro-level bone remodeling algorithms. The utilization of macro-sized elements requires apparent bone densities to predict cancellous bone strength, thereby, preventing visualization and analysis of realistic trabecular architecture. In this study, we utilized a recently developed structural optimization algorithm, design space optimization (DSO), to perform a micro-level three-dimensional finite element bone remodeling simulation on the human proximal femur pre- and post-THA. The computational simulation facilitated direct performance comparison between two commercially available prosthetic implant stems from Zimmer Inc.: the Alloclassic and the Mayo conservative. The novel micro-level approach allowed the unique ability to visualize the trabecular bone adaption post-operation and to quantify the changes in bone mineral content by region. Stress-shielding and strain energy distribution were also quantified for the immediate post-operation and the stably fixated, post-remodeling conditions. Stress-shielding was highest in the proximal region and remained unchanged post-remodeling; conversely, the mid and distal portions show large increases in stress, suggesting a distal shift in the loadpath. The Mayo design conserves bone mass, while simultaneously reducing the incidence of stress-shielding compared to the Alloclassic, revealing a key benefit of the distinctive geometry. Several important factors for stable fixation, determined in clinical evaluations from the literature, were evident in both designs: high levels of proximal bone loss and distal bone densification. The results suggest this novel computational framework can be utilized for comparative hip prosthesis shape, uniquely considering the post-operation bone remodeling as a design criterion. Copyright © 2011 Elsevier Ltd. All rights reserved.

The geometry of structural equilibrium

PubMed Central

2017-01-01

Building on a long tradition from Maxwell, Rankine, Klein and others, this paper puts forward a geometrical description of structural equilibrium which contains a procedure for the graphic analysis of stress resultants within general three-dimensional frames. The method is a natural generalization of Rankine’s reciprocal diagrams for three-dimensional trusses. The vertices and edges of dual abstract 4-polytopes are embedded within dual four-dimensional vector spaces, wherein the oriented area of generalized polygons give all six components (axial and shear forces with torsion and bending moments) of the stress resultants. The relevant quantities may be readily calculated using four-dimensional Clifford algebra. As well as giving access to frame analysis and design, the description resolves a number of long-standing problems with the incompleteness of Rankine’s description of three-dimensional trusses. Examples are given of how the procedure may be applied to structures of engineering interest, including an outline of a two-stage procedure for addressing the equilibrium of loaded gridshell rooves. PMID:28405361

Obtaining an equivalent beam

NASA Technical Reports Server (NTRS)

Butler, Thomas G.

1990-01-01

In modeling a complex structure the researcher was faced with a component that would have logical appeal if it were modeled as a beam. The structure was a mast of a robot controlled gantry crane. The structure up to this point already had a large number of degrees of freedom, so the idea of conserving grid points by modeling the mast as a beam was attractive. The researcher decided to make a separate problem of of the mast and model it in three dimensions with plates, then extract the equivalent beam properties by setting up the loading to simulate beam-like deformation and constraints. The results could then be used to represent the mast as a beam in the full model. A comparison was made of properties derived from models of different constraints versus manual calculations. The researcher shows that the three-dimensional model is ineffective in trying to conform to the requirements of an equivalent beam representation. If a full 3-D plate model were used in the complete representation of the crane structure, good results would be obtained. Since the attempt is to economize on the size of the model, a better way to achieve the same results is to use substructuring and condense the mast to equivalent end boundary and intermediate mass points.

Learning the Cell Structures with Three-Dimensional Models: Students' Achievement by Methods, Type of School and Questions' Cognitive Level

NASA Astrophysics Data System (ADS)

Lazarowitz, Reuven; Naim, Raphael

2013-08-01

The cell topic was taught to 9th-grade students in three modes of instruction: (a) students "hands-on," who constructed three-dimensional cell organelles and macromolecules during the learning process; (b) teacher demonstration of the three-dimensional model of the cell structures; and (c) teaching the cell topic with the regular learning material in an expository mode (which use one- or two-dimensional cell structures as are presented in charts, textbooks and microscopic slides). The sample included 669, 9th-grade students from 25 classes who were taught by 22 Biology teachers. Students were randomly assigned to the three modes of instruction, and two tests in content knowledge in Biology were used. Data were treated with multiple analyses of variance. The results indicate that entry behavior in Biology was equal for all the study groups and types of schools. The "hands-on" learning group who build three-dimensional models through the learning process achieved significantly higher on academic achievements and on the high and low cognitive questions' levels than the other two groups. The study indicates the advantages students may have being actively engaged in the learning process through the "hands-on" mode of instruction/learning.

Bimetallic 3D nanostar dimers in ring cavities: recyclable and robust surface-enhanced Raman scattering substrates for signal detection from few molecules.

PubMed

Gopalakrishnan, Anisha; Chirumamilla, Manohar; De Angelis, Francesco; Toma, Andrea; Zaccaria, Remo Proietti; Krahne, Roman

2014-08-26

Top-down fabrication of electron-beam lithography (EBL)-defined metallic nanostructures is a successful route to obtain extremely high electromagnetic field enhancement via plasmonic effects in well-defined regions. To this aim, various geometries have been introduced such as disks, triangles, dimers, rings, self-similar lenses, and more. In particular, metallic dimers are highly efficient for surface-enhanced Raman spectroscopy (SERS), and their decoupling from the substrate in a three-dimensional design has proven to further improve their performance. However, the large fabrication time and cost has hindered EBL-defined structures from playing a role in practical applications. Here we present three-dimensional nanostar dimer devices that can be recycled via maskless metal etching and deposition processes, due to conservation of the nanostructure pattern in the 3D geometry of the underlying Si substrate. Furthermore, our 3D-nanostar-dimer-in-ring structures (3D-NSDiRs) incorporate several advantageous aspects for SERS by enhancing the performance of plasmonic dimers via an external ring cavity, by efficient decoupling from the substrate through an elevated 3D design, and by bimetallic AuAg layers that exploit the increased performance of Ag while maintaining the biocompatibility of Au. We demonstrate SERS detection on rhodamine and adenine at extremely low density up to the limit of few molecules and analyze the field enhancement of the 3D-NSDiRs with respect to the exciting wavelength and metal composition.

Quasilocal energy for three-dimensional massive gravity solutions with chiral deformations of AdS{sub 3} boundary conditions

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

Garbarz, Alan, E-mail: alan-at@df.uba.ar; Giribet, Gaston, E-mail: gaston-at@df.uba.ar, E-mail: af.goya-at@df.uba.ar; Goya, Andrés, E-mail: gaston-at@df.uba.ar, E-mail: af.goya-at@df.uba.ar

2015-03-26

We consider critical gravity in three dimensions; that is, the New Massive Gravity theory formulated about Anti-de Sitter (AdS) space with the specific value of the graviton mass for which it results dual to a two-dimensional conformai field theory with vanishing central charge. As it happens with Kerr black holes in four-dimensional critical gravity, in three-dimensional critical gravity the Bañados-Teitelboim-Zanelli black holes have vanishing mass and vanishing angular momentum. However, provided suitable asymptotic conditions are chosen, the theory may also admit solutions carrying non-vanishing charges. Here, we give simple examples of exact solutions that exhibit falling-off conditions that are evenmore » weaker than those of the so-called Log-gravity. For such solutions, we define the quasilocal stress-tensor and use it to compute conserved charges. Despite the drastic deformation of AdS{sub 3} asymptotic, these solutions have finite mass and angular momentum, which are shown to be non-zero.« less

Healthy coral reefs may assure coastal protection in face of climate change related sea level rise

NASA Astrophysics Data System (ADS)

Harris, D. L.; Rovere, A.; Parravicini, V.; Casella, E.; Canavesio, R.; Collin, A.

2016-12-01

Coral reefs are diverse ecosystems that support millions of people worldwide providing crucial services, of which, coastal protection is one of the most relevant. The efficiency of coral reefs in protecting coastlines and dissipating waves is directly linked to the cover of living corals and three dimensional reef structural complexity. Climate change and human impacts are leading to severe global reductions in live coral cover, posing serious concerns regarding the capacity of degraded reef systems in protecting tropical coastal regions. Although it is known that the loss of structurally complex reefs may lead to greater erosion of coastlines, this process has rarely been quantified and it is still unknown whether the maintenance of healthy reefs through conservation will be enough to guarantee coastal protection during rising sea levels. We show that a significant loss of wave dissipation and a subsequent increase in back-reef wave height (up to 5 times present wave height) could occur even at present sea level if living corals are lost and reef structural complexity is reduced. Yet we also show that healthy reefs, measured by structural complexity and efficiency of vertical reef accretion, may maintain their present capacity of wave dissipation even under rising sea levels. Our results indicate that the health of coral reefs and not sea level rise will be the major determinant of the coastal protection services provided by coral reefs and calls for investments into coral reef conservation to ensure the future protection of tropical coastal communities.

An analysis of finite-difference and finite-volume formulations of conservation laws

NASA Technical Reports Server (NTRS)

Vinokur, Marcel

1986-01-01

Finite-difference and finite-volume formulations are analyzed in order to clear up the confusion concerning their application to the numerical solution of conservation laws. A new coordinate-free formulation of systems of conservation laws is developed, which clearly distinguishes the role of physical vectors from that of algebraic vectors which characterize the system. The analysis considers general types of equations--potential, Euler, and Navier-Stokes. Three-dimensional unsteady flows with time-varying grids are described using a single, consistent nomeclature for both formulations. Grid motion due to a non-inertial reference frame as well as flow adaptation is covered. In comparing the two formulations, it is found useful to distinguish between differences in numerical methods and differences in grid definition. The former plays a role for non-Cartesian grids, and results in only cosmetic differences in the manner in which geometric terms are handled. The differences in grid definition for the two formulations is found to be more important, since it affects the manner in which boundary conditions, zonal procedures, and grid singularities are handled at computational boundaries. The proper interpretation of strong and weak conservation-law forms for quasi-one-dimensional and axisymmetric flows is brought out.

An analysis of finite-difference and finite-volume formulations of conservation laws

NASA Technical Reports Server (NTRS)

Vinokur, Marcel

1989-01-01

Finite-difference and finite-volume formulations are analyzed in order to clear up the confusion concerning their application to the numerical solution of conservation laws. A new coordinate-free formulation of systems of conservation laws is developed, which clearly distinguishes the role of physical vectors from that of algebraic vectors which characterize the system. The analysis considers general types of equations: potential, Euler, and Navier-Stokes. Three-dimensional unsteady flows with time-varying grids are described using a single, consistent nomenclature for both formulations. Grid motion due to a non-inertial reference frame as well as flow adaptation is covered. In comparing the two formulations, it is found useful to distinguish between differences in numerical methods and differences in grid definition. The former plays a role for non-Cartesian grids, and results in only cosmetic differences in the manner in which geometric terms are handled. The differences in grid definition for the two formulations is found to be more important, since it affects the manner in which boundary conditions, zonal procedures, and grid singularities are handled at computational boundaries. The proper interpretation of strong and weak conservation-law forms for quasi-one-dimensional and axisymmetric flows is brought out.

Comparative mtDNA analyses of three sympatric macropodids from a conservation area on the Huon Peninsula, Papua New Guinea.

PubMed

McGreevy, Thomas J; Dabek, Lisa; Husband, Thomas P

2016-07-01

Matschie's tree kangaroo (Dendrolagus matschiei), New Guinea pademelon (Thylogale browni), and small dorcopsis (Dorcopsulus vanheurni) are sympatric macropodid taxa, of conservation concern, that inhabit the Yopno-Urawa-Som (YUS) Conservation Area on the Huon Peninsula, Papua New Guinea. We sequenced three partial mitochondrial DNA (mtDNA) genes from the three taxa to (i) investigate network structure; and (ii) identify conservation units within the YUS Conservation Area. All three taxa displayed a similar pattern in the spatial distribution of their mtDNA haplotypes and the Urawa and Som rivers on the Huon may have acted as a barrier to maternal gene flow. Matschie's tree kangaroo and New Guinea pademelon within the YUS Conservation Area should be managed as single conservation units because mtDNA nucleotides were not fixed for a given geographic area. However, two distinct conservation units were identified for small dorcopsis from the two different mountain ranges within the YUS Conservation Area.

Three-dimensional metamaterials

DOEpatents

Burckel, David Bruce [Albuquerque, NM

2012-06-12

A fabrication method is capable of creating canonical metamaterial structures arrayed in a three-dimensional geometry. The method uses a membrane suspended over a cavity with predefined pattern as a directional evaporation mask. Metallic and/or dielectric material can be evaporated at high vacuum through the patterned membrane to deposit resonator structures on the interior walls of the cavity, thereby providing a unit cell of micron-scale dimension. The method can produce volumetric metamaterial structures comprising layers of such unit cells of resonator structures.

Application of ground-penetrating radar imagery for three-dimensional visualisation of near-surface structures in ice-rich permafrost, Barrow, Alaska

USGS Publications Warehouse

Munroe, Jeffrey S.; Doolittle, James A.; Kanevskiy, Mikhail; Hinkel, Kenneth M.; Nelson, Frederick E.; Jones, Benjamin M.; Shur, Yuri; Kimble, John M.

2007-01-01

Three-dimensional ground-penetrating radar (3D GPR) was used to investigate the subsurface structure of ice-wedge polygons and other features of the frozen active layer and near-surface permafrost near Barrow, Alaska. Surveys were conducted at three sites located on landscapes of different geomorphic age. At each site, sediment cores were collected and characterised to aid interpretation of GPR data. At two sites, 3D GPR was able to delineate subsurface ice-wedge networks with high fidelity. Three-dimensional GPR data also revealed a fundamental difference in ice-wedge morphology between these two sites that is consistent with differences in landscape age. At a third site, the combination of two-dimensional and 3D GPR revealed the location of an active frost boil with ataxitic cryostructure. When supplemented by analysis of soil cores, 3D GPR offers considerable potential for imaging, interpreting and 3D mapping of near-surface soil and ice structures in permafrost environments.

PSpice Model of Lightning Strike to a Steel Reinforced Structure

NASA Astrophysics Data System (ADS)

Koone, Neil; Condren, Brian

2003-12-01

Surges and arcs from lightning can pose hazards to personnel and sensitive equipment, and processes. Steel reinforcement in structures can act as a Faraday cage mitigating lightning effects. Knowing a structure's response to a lightning strike allows hazards associated with lightning to be analyzed. A model of lightning's response in a steel reinforced structure has been developed using PSpice (a commercial circuit simulation). Segments of rebar are modeled as inductors and resistors in series. A program has been written to take architectural information of a steel reinforced structure and "build" a circuit network that is analogous to the network of reinforcement in a facility. A severe current waveform (simulating a 99th percentile lightning strike), modeled as a current source, is introduced in the circuit network, and potential differences within the structure are determined using PSpice. A visual three-dimensional model of the facility displays the voltage distribution across the structure using color to indicate the potential difference relative to the floor. Clear air arcing distances can be calculated from the voltage distribution using a conservative value for the dielectric breakdown strength of air. Potential validation tests for the model will be presented.

De novo discovery of structural motifs in RNA 3D structures through clustering.

PubMed

Ge, Ping; Islam, Shahidul; Zhong, Cuncong; Zhang, Shaojie

2018-05-18

As functional components in three-dimensional (3D) conformation of an RNA, the RNA structural motifs provide an easy way to associate the molecular architectures with their biological mechanisms. In the past years, many computational tools have been developed to search motif instances by using the existing knowledge of well-studied families. Recently, with the rapidly increasing number of resolved RNA 3D structures, there is an urgent need to discover novel motifs with the newly presented information. In this work, we classify all the loops in non-redundant RNA 3D structures to detect plausible RNA structural motif families by using a clustering pipeline. Compared with other clustering approaches, our method has two benefits: first, the underlying alignment algorithm is tolerant to the variations in 3D structures. Second, sophisticated downstream analysis has been performed to ensure the clusters are valid and easily applied to further research. The final clustering results contain many interesting new variants of known motif families, such as GNAA tetraloop, kink-turn, sarcin-ricin and T-loop. We have also discovered potential novel functional motifs conserved in ribosomal RNA, sgRNA, SRP RNA, riboswitch and ribozyme.

Solution structure of the tandem acyl carrier protein domains from a polyunsaturated fatty acid synthase reveals beads-on-a-string configuration.

PubMed

Trujillo, Uldaeliz; Vázquez-Rosa, Edwin; Oyola-Robles, Delise; Stagg, Loren J; Vassallo, David A; Vega, Irving E; Arold, Stefan T; Baerga-Ortiz, Abel

2013-01-01

The polyunsaturated fatty acid (PUFA) synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP) domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect) and in structural stabilization of the multidomain protein (synergistic effect). While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS) revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of multiple ACP domains for increasing the yield of fatty acids in bacterial cultures.

Solution Structure of the Tandem Acyl Carrier Protein Domains from a Polyunsaturated Fatty Acid Synthase Reveals Beads-on-a-String Configuration

PubMed Central

Trujillo, Uldaeliz; Vázquez-Rosa, Edwin; Oyola-Robles, Delise; Stagg, Loren J.; Vassallo, David A.; Vega, Irving E.; Arold, Stefan T.; Baerga-Ortiz, Abel

2013-01-01

The polyunsaturated fatty acid (PUFA) synthases from deep-sea bacteria invariably contain multiple acyl carrier protein (ACP) domains in tandem. This conserved tandem arrangement has been implicated in both amplification of fatty acid production (additive effect) and in structural stabilization of the multidomain protein (synergistic effect). While the more accepted model is one in which domains act independently, recent reports suggest that ACP domains may form higher oligomers. Elucidating the three-dimensional structure of tandem arrangements may therefore give important insights into the functional relevance of these structures, and hence guide bioengineering strategies. In an effort to elucidate the three-dimensional structure of tandem repeats from deep-sea anaerobic bacteria, we have expressed and purified a fragment consisting of five tandem ACP domains from the PUFA synthase from Photobacterium profundum. Analysis of the tandem ACP fragment by analytical gel filtration chromatography showed a retention time suggestive of a multimeric protein. However, small angle X-ray scattering (SAXS) revealed that the multi-ACP fragment is an elongated monomer which does not form a globular unit. Stokes radii calculated from atomic monomeric SAXS models were comparable to those measured by analytical gel filtration chromatography, showing that in the gel filtration experiment, the molecular weight was overestimated due to the elongated protein shape. Thermal denaturation monitored by circular dichroism showed that unfolding of the tandem construct was not cooperative, and that the tandem arrangement did not stabilize the protein. Taken together, these data are consistent with an elongated beads-on-a-string arrangement of the tandem ACP domains in PUFA synthases, and speak against synergistic biocatalytic effects promoted by quaternary structuring. Thus, it is possible to envision bioengineering strategies which simply involve the artificial linking of multiple ACP domains for increasing the yield of fatty acids in bacterial cultures. PMID:23469090

Cornea and ocular lens visualized with three-dimensional confocal microscopy

NASA Astrophysics Data System (ADS)

Masters, Barry R.

1992-08-01

This paper demonstrates the advantages of three-dimensional reconstruction of the cornea and the ocular crystalline lens by confocal microscopy and volume rendering computer techniques. The advantages of noninvasive observation of ocular structures in living, unstained, unfixed tissue include the following: the tissue is in a natural living state without the artifacts of fixation, mechanical sectioning, and staining; the three-dimensional structure can be observed from any view point and quantitatively analyzed; the dynamics of morphological changes can be studied; and the use of confocal microscopic observation results in a reduction of the number of animals required for ocular morphometric studies. The main advantage is that the dynamic morphology of ocular structures can be investigated in living ocular tissue. A laser scanning confocal microscope was used in the reflected light mode to obtain the two- dimensional images from the cornea and the ocular lens of a freshly enucleated rabbit eye. The light source was an argon ion laser with 488 nm wavelength. The microscope objective was a Leitz 25X, NA 0.6 water immersion lens. The 400 micron thick cornea was optically sectioned into 133, three micron sections. The semi-transparent cornea and the in-situ ocular lens was visualized as high resolution, high contrast two-dimensional images. The under sampling resulted in a three-dimensional visualization rendering in which the corneal thickness (z-axis) is compressed. The structures observed in the cornea include: superficial epithelial cells and their nuclei, basal epithelial cells and their `beaded' cell borders, basal lamina, nerve plexus, nerve fibers, free nerve endings in the basal epithelial cells, nuclei of stromal keratocytes, and endothelial cells. The structures observed in the in-situ ocular lens include: lens capsule, lens epithelial cells, and individual lens fibers.

Hydroelastic behaviour of a structure exposed to an underwater explosion.

PubMed

Colicchio, G; Greco, M; Brocchini, M; Faltinsen, O M

2015-01-28

The hydroelastic interaction between an underwater explosion and an elastic plate is investigated num- erically through a domain-decomposition strategy. The three-dimensional features of the problem require a large computational effort, which is reduced through a weak coupling between a one-dimensional radial blast solver, which resolves the blast evolution far from the boundaries, and a three-dimensional compressible flow solver used where the interactions between the compression wave and the boundaries take place and the flow becomes three-dimensional. The three-dimensional flow solver at the boundaries is directly coupled with a modal structural solver that models the response of the solid boundaries like elastic plates. This enables one to simulate the fluid-structure interaction as a strong coupling, in order to capture hydroelastic effects. The method has been applied to the experimental case of Hung et al. (2005 Int. J. Impact Eng. 31, 151-168 (doi:10.1016/j.ijimpeng.2003.10.039)) with explosion and structure sufficiently far from other boundaries and successfully validated in terms of the evolution of the acceleration induced on the plate. It was also used to investigate the interaction of an underwater explosion with the bottom of a close-by ship modelled as an orthotropic plate. In the application, the acoustic phase of the fluid-structure interaction is examined, highlighting the need of the fluid-structure coupling to capture correctly the possible inception of cavitation. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Three-dimensional boron particle loaded thermal neutron detector

DOEpatents

Nikolic, Rebecca J.; Conway, Adam M.; Graff, Robert T.; Kuntz, Joshua D.; Reinhardt, Catherine; Voss, Lars F.; Cheung, Chin Li; Heineck, Daniel

2014-09-09

Three-dimensional boron particle loaded thermal neutron detectors utilize neutron sensitive conversion materials in the form of nano-powders and micro-sized particles, as opposed to thin films, suspensions, paraffin, etc. More specifically, methods to infiltrate, intersperse and embed the neutron nano-powders to form two-dimensional and/or three-dimensional charge sensitive platforms are specified. The use of nano-powders enables conformal contact with the entire charge-collecting structure regardless of its shape or configuration.

iDBPs: a web server for the identification of DNA binding proteins

PubMed Central

Nimrod, Guy; Schushan, Maya; Szilágyi, András; Leslie, Christina; Ben-Tal, Nir

2010-01-01

Summary: The iDBPs server uses the three-dimensional (3D) structure of a query protein to predict whether it binds DNA. First, the algorithm predicts the functional region of the protein based on its evolutionary profile; the assumption is that large clusters of conserved residues are good markers of functional regions. Next, various characteristics of the predicted functional region as well as global features of the protein are calculated, such as the average surface electrostatic potential, the dipole moment and cluster-based amino acid conservation patterns. Finally, a random forests classifier is used to predict whether the query protein is likely to bind DNA and to estimate the prediction confidence. We have trained and tested the classifier on various datasets and shown that it outperformed related methods. On a dataset that reflects the fraction of DNA binding proteins (DBPs) in a proteome, the area under the ROC curve was 0.90. The application of the server to an updated version of the N-Func database, which contains proteins of unknown function with solved 3D-structure, suggested new putative DBPs for experimental studies. Availability: http://idbps.tau.ac.il/ Contact: NirB@tauex.tau.ac.il Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20089514

Three-dimensional cardiac architecture determined by two-photon microtomy

NASA Astrophysics Data System (ADS)

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

2009-07-01

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

Three-dimensional coherent X-ray diffractive imaging of whole frozen-hydrated cells

PubMed Central

Rodriguez, Jose A.; Xu, Rui; Chen, Chien-Chun; Huang, Zhifeng; Jiang, Huaidong; Chen, Allan L.; Raines, Kevin S.; Pryor Jr, Alan; Nam, Daewoong; Wiegart, Lutz; Song, Changyong; Madsen, Anders; Chushkin, Yuriy; Zontone, Federico; Bradley, Peter J.; Miao, Jianwei

2015-01-01

A structural understanding of whole cells in three dimensions at high spatial resolution remains a significant challenge and, in the case of X-rays, has been limited by radiation damage. By alleviating this limitation, cryogenic coherent diffractive imaging (cryo-CDI) can in principle be used to bridge the important resolution gap between optical and electron microscopy in bio-imaging. Here, the first experimental demonstration of cryo-CDI for quantitative three-dimensional imaging of whole frozen-hydrated cells using 8 keV X-rays is reported. As a proof of principle, a tilt series of 72 diffraction patterns was collected from a frozen-hydrated Neospora caninum cell and the three-dimensional mass density of the cell was reconstructed and quantified based on its natural contrast. This three-dimensional reconstruction reveals the surface and internal morphology of the cell, including its complex polarized sub-cellular structure. It is believed that this work represents an experimental milestone towards routine quantitative three-dimensional imaging of whole cells in their natural state with spatial resolutions in the tens of nanometres. PMID:26306199

Face and content validation of a novel three-dimensional printed temporal bone for surgical skills development.

PubMed

Da Cruz, M J; Francis, H W

2015-07-01

To assess the face and content validity of a novel synthetic, three-dimensional printed temporal bone for surgical skills development and training. A synthetic temporal bone was printed using composite materials and three-dimensional printing technology. Surgical trainees were asked to complete three structured temporal bone dissection exercises. Attitudes and impressions were then assessed using a semi-structured questionnaire. Previous cadaver and real operating experiences were used as a reference. Trainees' experiences of the synthetic temporal bone were analysed in terms of four domains: anatomical realism, usefulness as a training tool, task-based usefulness and overall reactions. Responses across all domains indicated a high degree of acceptance, suggesting that the three-dimensional printed temporal bone was a useful tool in skills development. A sophisticated three-dimensional printed temporal bone that demonstrates face and content validity was developed. The efficiency in cost savings coupled with low associated biohazards make it likely that the printed temporal bone will be incorporated into traditional temporal bone skills development programmes in the near future.

Three-dimensional coherent X-ray diffractive imaging of whole frozen-hydrated cells

DOE PAGES

Rodriguez, Jose A.; Xu, Rui; Chen, Chien -Chun; ...

2015-09-01

Here, a structural understanding of whole cells in three dimensions at high spatial resolution remains a significant challenge and, in the case of X-rays, has been limited by radiation damage. By alleviating this limitation, cryogenic coherent diffractive imaging (cryo-CDI) can in principle be used to bridge the important resolution gap between optical and electron microscopy in bio-imaging. Here, the first experimental demonstration of cryo-CDI for quantitative three-dimensional imaging of whole frozen-hydrated cells using 8 Kev X-rays is reported. As a proof of principle, a tilt series of 72 diffraction patterns was collected from a frozen-hydrated Neospora caninum cell and themore » three-dimensional mass density of the cell was reconstructed and quantified based on its natural contrast. This three-dimensional reconstruction reveals the surface and internal morphology of the cell, including its complex polarized sub-cellular structure. Finally, it is believed that this work represents an experimental milestone towards routine quantitative three-dimensional imaging of whole cells in their natural state with spatial resolutions in the tens of nanometres.« less

Three-dimensional coherent X-ray diffractive imaging of whole frozen-hydrated cells.

PubMed

Rodriguez, Jose A; Xu, Rui; Chen, Chien-Chun; Huang, Zhifeng; Jiang, Huaidong; Chen, Allan L; Raines, Kevin S; Pryor, Alan; Nam, Daewoong; Wiegart, Lutz; Song, Changyong; Madsen, Anders; Chushkin, Yuriy; Zontone, Federico; Bradley, Peter J; Miao, Jianwei

2015-09-01

A structural understanding of whole cells in three dimensions at high spatial resolution remains a significant challenge and, in the case of X-rays, has been limited by radiation damage. By alleviating this limitation, cryogenic coherent diffractive imaging (cryo-CDI) can in principle be used to bridge the important resolution gap between optical and electron microscopy in bio-imaging. Here, the first experimental demonstration of cryo-CDI for quantitative three-dimensional imaging of whole frozen-hydrated cells using 8 keV X-rays is reported. As a proof of principle, a tilt series of 72 diffraction patterns was collected from a frozen-hydrated Neospora caninum cell and the three-dimensional mass density of the cell was reconstructed and quantified based on its natural contrast. This three-dimensional reconstruction reveals the surface and internal morphology of the cell, including its complex polarized sub-cellular structure. It is believed that this work represents an experimental milestone towards routine quantitative three-dimensional imaging of whole cells in their natural state with spatial resolutions in the tens of nanometres.

An interpolation-free ALE scheme for unsteady inviscid flows computations with large boundary displacements over three-dimensional adaptive grids

NASA Astrophysics Data System (ADS)

Re, B.; Dobrzynski, C.; Guardone, A.

2017-07-01

A novel strategy to solve the finite volume discretization of the unsteady Euler equations within the Arbitrary Lagrangian-Eulerian framework over tetrahedral adaptive grids is proposed. The volume changes due to local mesh adaptation are treated as continuous deformations of the finite volumes and they are taken into account by adding fictitious numerical fluxes to the governing equation. This peculiar interpretation enables to avoid any explicit interpolation of the solution between different grids and to compute grid velocities so that the Geometric Conservation Law is automatically fulfilled also for connectivity changes. The solution on the new grid is obtained through standard ALE techniques, thus preserving the underlying scheme properties, such as conservativeness, stability and monotonicity. The adaptation procedure includes node insertion, node deletion, edge swapping and points relocation and it is exploited both to enhance grid quality after the boundary movement and to modify the grid spacing to increase solution accuracy. The presented approach is assessed by three-dimensional simulations of steady and unsteady flow fields. The capability of dealing with large boundary displacements is demonstrated by computing the flow around the translating infinite- and finite-span NACA 0012 wing moving through the domain at the flight speed. The proposed adaptive scheme is applied also to the simulation of a pitching infinite-span wing, where the bi-dimensional character of the flow is well reproduced despite the three-dimensional unstructured grid. Finally, the scheme is exploited in a piston-induced shock-tube problem to take into account simultaneously the large deformation of the domain and the shock wave. In all tests, mesh adaptation plays a crucial role.

Magnetic helicity conservation and inverse energy cascade in electron magnetohydrodynamic wave packets.

PubMed

Cho, Jungyeon

2011-05-13

Electron magnetohydrodynamics (EMHD) provides a fluidlike description of small-scale magnetized plasmas. An EMHD wave propagates along magnetic field lines. The direction of propagation can be either parallel or antiparallel to the magnetic field lines. We numerically study propagation of three-dimensional (3D) EMHD wave packets moving in one direction. We obtain two major results. (1) Unlike its magnetohydrodynamic (MHD) counterpart, an EMHD wave packet is dispersive. Because of this, EMHD wave packets traveling in one direction create opposite-traveling wave packets via self-interaction and cascade energy to smaller scales. (2) EMHD wave packets traveling in one direction clearly exhibit inverse energy cascade. We find that the latter is due to conservation of magnetic helicity. We compare inverse energy cascade in 3D EMHD turbulence and two-dimensional (2D) hydrodynamic turbulence.

Nonlinear Conservation Laws and Finite Volume Methods

NASA Astrophysics Data System (ADS)

Leveque, Randall J.

Introduction Software Notation Classification of Differential Equations Derivation of Conservation Laws The Euler Equations of Gas Dynamics Dissipative Fluxes Source Terms Radiative Transfer and Isothermal Equations Multi-dimensional Conservation Laws The Shock Tube Problem Mathematical Theory of Hyperbolic Systems Scalar Equations Linear Hyperbolic Systems Nonlinear Systems The Riemann Problem for the Euler Equations Numerical Methods in One Dimension Finite Difference Theory Finite Volume Methods Importance of Conservation Form - Incorrect Shock Speeds Numerical Flux Functions Godunov's Method Approximate Riemann Solvers High-Resolution Methods Other Approaches Boundary Conditions Source Terms and Fractional Steps Unsplit Methods Fractional Step Methods General Formulation of Fractional Step Methods Stiff Source Terms Quasi-stationary Flow and Gravity Multi-dimensional Problems Dimensional Splitting Multi-dimensional Finite Volume Methods Grids and Adaptive Refinement Computational Difficulties Low-Density Flows Discrete Shocks and Viscous Profiles Start-Up Errors Wall Heating Slow-Moving Shocks Grid Orientation Effects Grid-Aligned Shocks Magnetohydrodynamics The MHD Equations One-Dimensional MHD Solving the Riemann Problem Nonstrict Hyperbolicity Stiffness The Divergence of B Riemann Problems in Multi-dimensional MHD Staggered Grids The 8-Wave Riemann Solver Relativistic Hydrodynamics Conservation Laws in Spacetime The Continuity Equation The 4-Momentum of a Particle The Stress-Energy Tensor Finite Volume Methods Multi-dimensional Relativistic Flow Gravitation and General Relativity References

Photodeposition Method For Fabricating A Three-Dimensional, Patterned Polymer Microstructure

DOEpatents

Walt, David R.; Healey, Brian G.

2001-03-13

The present invention is a photodeposition methodology for fabricating a three-dimensional patterned polymer microstructure. A variety of polymeric structures can be fabricated on solid substrates using unitary fiber optic arrays for light delivery. The methodology allows micrometer-scale photopatterning for the fabricated structures using masks substantially larger than the desired dimensions of the microstructure.

Electron tomography and computer visualisation of a three-dimensional 'photonic' crystal in a butterfly wing-scale.

PubMed

Argyros, A; Manos, S; Large, M C J; McKenzie, D R; Cox, G C; Dwarte, D M

2002-01-01

A combination of transmission electron tomography and computer modelling has been used to determine the three-dimensional structure of the photonic crystals found in the wing-scales of the Kaiser-I-Hind butterfly (Teinopalpus imperialis). These scales presented challenges for electron microscopy because the periodicity of the structure was comparable to the thickness of a section and because of the complex connectivity of the object. The structure obtained has been confirmed by taking slices of the three-dimensional computer model constructed from the tomography and comparing these with transmission electron microscope (TEM) images of microtomed sections of the actual scale. The crystal was found to have chiral tetrahedral repeating units packed in a triclinic lattice.

Crystal structure of product-bound complex of UDP-N-acetyl-D-mannosamine dehydrogenase from Pyrococcus horikoshii OT3

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

Pampa, K.J., E-mail: sagarikakj@gmail.com; Lokanath, N.K.; Girish, T.U.

Highlights: • Determined the structure of UDP-D-ManNAcADH to a resolution of 1.55 Å. • First complex structure of PhUDP-D-ManNAcADH with UDP-D-ManMAcA. • The monomeric structure consists of three distinct domains. • Cys258 acting as catalytic nucleophilic and Lys204 acts as acid/base catalyst. • Oligomeric state plays an important role for the catalytic function. - Abstract: UDP-N-acetyl-D-mannosamine dehydrogenase (UDP-D-ManNAcDH) belongs to UDP-glucose/GDP-mannose dehydrogenase family and catalyzes Uridine-diphospho-N-acetyl-D-mannosamine (UDP-D-ManNAc) to Uridine-diphospho-N-acetyl-D-mannosaminuronic acid (UDP-D-ManNAcA) through twofold oxidation of NAD{sup +}. In order to reveal the structural features of the Pyrococcus horikoshii UDP-D-ManNAcADH, we have determined the crystal structure of the product-bound enzyme bymore » X-ray diffraction to resolution of 1.55 Å. The protomer folds into three distinct domains; nucleotide binding domain (NBD), substrate binding domain (SBD) and oligomerization domain (OD, involved in the dimerization). The clear electron density of the UDP-D-ManNAcA is observed and the residues binding are identified for the first time. Crystal structures reveal a tight dimeric polymer chains with product-bound in all the structures. The catalytic residues Cys258 and Lys204 are conserved. The Cys258 acts as catalytic nucleophile and Lys204 as acid/base catalyst. The product is directly interacts with residues Arg211, Thr249, Arg244, Gly255, Arg289, Lys319 and Arg398. In addition, the structural parameters responsible for thermostability and oligomerization of the three dimensional structure are analyzed.« less

Exploration of the relationship between topology and designability of conformations

NASA Astrophysics Data System (ADS)

Leelananda, Sumudu P.; Towfic, Fadi; Jernigan, Robert L.; Kloczkowski, Andrzej

2011-06-01

Protein structures are evolutionarily more conserved than sequences, and sequences with very low sequence identity frequently share the same fold. This leads to the concept of protein designability. Some folds are more designable and lots of sequences can assume that fold. Elucidating the relationship between protein sequence and the three-dimensional (3D) structure that the sequence folds into is an important problem in computational structural biology. Lattice models have been utilized in numerous studies to model protein folds and predict the designability of certain folds. In this study, all possible compact conformations within a set of two-dimensional and 3D lattice spaces are explored. Complementary interaction graphs are then generated for each conformation and are described using a set of graph features. The full HP sequence space for each lattice model is generated and contact energies are calculated by threading each sequence onto all the possible conformations. Unique conformation giving minimum energy is identified for each sequence and the number of sequences folding to each conformation (designability) is obtained. Machine learning algorithms are used to predict the designability of each conformation. We find that the highly designable structures can be distinguished from other non-designable conformations based on certain graphical geometric features of the interactions. This finding confirms the fact that the topology of a conformation is an important determinant of the extent of its designability and suggests that the interactions themselves are important for determining the designability.

3D model for Cancerous Inhibitor of Protein Phosphatase 2A armadillo domain unveils highly conserved protein-protein interaction characteristics.

PubMed

Dahlström, Käthe M; Salminen, Tiina A

2015-12-07

Cancerous Inhibitor of Protein Phosphatase 2A (CIP2A) is a human oncoprotein, which exerts its cancer-promoting function through interaction with other proteins, for example Protein Phosphatase 2A (PP2A) and MYC. The lack of structural information for CIP2A significantly prevents the design of anti-cancer therapeutics targeting this protein. In an attempt to counteract this fact, we modeled the three-dimensional structure of the N-terminal domain (CIP2A-ArmRP), analyzed key areas and amino acids, and coupled the results to the existing literature. The model reliably shows a stable armadillo repeat fold with a positively charged groove. The fact that this conserved groove highly likely binds peptides is corroborated by the presence of a conserved polar ladder, which is essential for the proper peptide-binding mode of armadillo repeat proteins and, according to our results, several known CIP2A interaction partners appropriately possess an ArmRP-binding consensus motif. Moreover, we show that Arg229Gln, which has been linked to the development of cancer, causes a significant change in charge and surface properties of CIP2A-ArmRP. In conclusion, our results reveal that CIP2A-ArmRP shares the typical fold, protein-protein interaction site and interaction patterns with other natural armadillo proteins and that, presumably, several interaction partners bind into the central groove of the modeled CIP2A-ArmRP. By providing essential structural characteristics of CIP2A, the present study significantly increases our knowledge on how CIP2A interacts with other proteins in cancer progression and how to develop new therapeutics targeting CIP2A. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Microbial Relatives of the Seed Storage Proteins of Higher Plants: Conservation of Structure and Diversification of Function during Evolution of the Cupin Superfamily

PubMed Central

Dunwell, Jim M.; Khuri, Sawsan; Gane, Paul J.

2000-01-01

This review summarizes the recent discovery of the cupin superfamily (from the Latin term “cupa,” a small barrel) of functionally diverse proteins that initially were limited to several higher plant proteins such as seed storage proteins, germin (an oxalate oxidase), germin-like proteins, and auxin-binding protein. Knowledge of the three-dimensional structure of two vicilins, seed proteins with a characteristic β-barrel core, led to the identification of a small number of conserved residues and thence to the discovery of several microbial proteins which share these key amino acids. In particular, there is a highly conserved pattern of two histidine-containing motifs with a varied intermotif spacing. This cupin signature is found as a central component of many microbial proteins including certain types of phosphomannose isomerase, polyketide synthase, epimerase, and dioxygenase. In addition, the signature has been identified within the N-terminal effector domain in a subgroup of bacterial AraC transcription factors. As well as these single-domain cupins, this survey has identified other classes of two-domain bicupins including bacterial gentisate 1,2-dioxygenases and 1-hydroxy-2-naphthoate dioxygenases, fungal oxalate decarboxylases, and legume sucrose-binding proteins. Cupin evolution is discussed from the perspective of the structure-function relationships, using data from the genomes of several prokaryotes, especially Bacillus subtilis. Many of these functions involve aspects of sugar metabolism and cell wall synthesis and are concerned with responses to abiotic stress such as heat, desiccation, or starvation. Particular emphasis is also given to the oxalate-degrading enzymes from microbes, their biological significance, and their value in a range of medical and other applications. PMID:10704478

Structure of turbulence in three-dimensional boundary layers

NASA Technical Reports Server (NTRS)

Subramanian, Chelakara S.

1993-01-01

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

Microfabrication and Test of a Three-Dimensional Polymer Hydro-focusing Unit for Flow Cytometry Applications

NASA Technical Reports Server (NTRS)

Yang, Ren; Feeback, Daniel L.; Wang, Wan-Jun

2005-01-01

This paper details a novel three-dimensional (3D) hydro-focusing micro cell sorter for micro flow cytometry applications. The unit was microfabricated by means of SU-8 3D lithography. The 3D microstructure for coaxial sheathing was designed, microfabricated, and tested. Three-dimensional hydrofocusing capability was demonstrated with an experiment to sort labeled tanned sheep erythrocytes (red blood cells). This polymer hydro-focusing microstructure is easily microfabricated and integrated with other polymer microfluidic structures. Keywords: SU-8, three-dimensional hydro-focusing, microfluidic, microchannel, cytometer

CONTRAIS: CONservative TReatment for Adolescent Idiopathic Scoliosis: a randomised controlled trial protocol

PubMed Central

2013-01-01

Background Idiopathic scoliosis is a three-dimensional structural deformity of the spine that occurs in children and adolescents. Recent reviews on bracing and exercise treatment have provided some evidence for effect of these interventions. The purpose of this study is to improve the evidence base regarding the effectiveness of conservative treatments for preventing curve progression in idiopathic scoliosis. Methods/design Patients: Previously untreated girls and boys with idiopathic scoliosis, 9 to 17 years of age with at least one year of remaining growth and a curve Cobb angle of 25–40 degrees will be included. A total of 135 participants will be randomly allocated in groups of 45 patients each to receive one of the three interventions. Interventions: All three groups will receive a physical activity prescription according to the World Health Organisation recommendations. One group will additionally wear a hyper-corrective night-time brace. One group will additionally perform postural scoliosis-specific exercises. Outcome: Participation in the study will last until the curve has progressed, or until cessation of skeletal growth. Outcome variables will be measured every 6 months. The primary outcome variable, failure of treatment, is defined as progression of the Cobb angle more than 6 degrees, compared to the primary x-ray, seen on two consecutive spinal standing x-rays taken with 6 months interval. Secondary outcome measures include the SRS-22r and EQ5D-Y quality of life questionnaires, the International Physical Activity Questionnaire (IPAQ) short form, and Cobb angle at end of the study. Discussion This trial will evaluate which of the tested conservative treatment approaches that is the most effective for patients with adolescent idiopathic scoliosis. Trial registration NCT01761305 PMID:24007599

CONTRAIS: CONservative TReatment for Adolescent Idiopathic Scoliosis: a randomised controlled trial protocol.

PubMed

Abbott, Allan; Möller, Hans; Gerdhem, Paul

2013-09-05

Idiopathic scoliosis is a three-dimensional structural deformity of the spine that occurs in children and adolescents. Recent reviews on bracing and exercise treatment have provided some evidence for effect of these interventions. The purpose of this study is to improve the evidence base regarding the effectiveness of conservative treatments for preventing curve progression in idiopathic scoliosis. Previously untreated girls and boys with idiopathic scoliosis, 9 to 17 years of age with at least one year of remaining growth and a curve Cobb angle of 25-40 degrees will be included. A total of 135 participants will be randomly allocated in groups of 45 patients each to receive one of the three interventions. All three groups will receive a physical activity prescription according to the World Health Organisation recommendations. One group will additionally wear a hyper-corrective night-time brace. One group will additionally perform postural scoliosis-specific exercises. Participation in the study will last until the curve has progressed, or until cessation of skeletal growth. OUTCOME variables will be measured every 6 months. The primary outcome variable, failure of treatment, is defined as progression of the Cobb angle more than 6 degrees, compared to the primary x-ray, seen on two consecutive spinal standing x-rays taken with 6 months interval. Secondary outcome measures include the SRS-22r and EQ5D-Y quality of life questionnaires, the International Physical Activity Questionnaire (IPAQ) short form, and Cobb angle at end of the study. This trial will evaluate which of the tested conservative treatment approaches that is the most effective for patients with adolescent idiopathic scoliosis. NCT01761305.

Three-dimensional macro-structures of two-dimensional nanomaterials.

PubMed

Shehzad, Khurram; Xu, Yang; Gao, Chao; Duan, Xiangfeng

2016-10-21

If two-dimensional (2D) nanomaterials are ever to be utilized as components of practical, macroscopic devices on a large scale, there is a complementary need to controllably assemble these 2D building blocks into more sophisticated and hierarchical three-dimensional (3D) architectures. Such a capability is key to design and build complex, functional devices with tailored properties. This review provides a comprehensive overview of the various experimental strategies currently used to fabricate the 3D macro-structures of 2D nanomaterials. Additionally, various approaches for the decoration of the 3D macro-structures with organic molecules, polymers, and inorganic materials are reviewed. Finally, we discuss the applications of 3D macro-structures, especially in the areas of energy, environment, sensing, and electronics, and describe the existing challenges and the outlook for this fast emerging field.

Applications to car bodies - Generalized layout design of three-dimensional shells

NASA Technical Reports Server (NTRS)

Fukushima, Junichi; Suzuki, Katsuyuki; Kikuchi, Noboru

1993-01-01

We shall describe applications of the homogenization method, formulated in Part 1, to design layout of car bodies represented by three-dimensional shell structures based on a multi-loading optimization.

Three-dimensional simulation of beam propagation and heat transfer in static gas Cs DPALs using wave optics and fluid dynamics models

NASA Astrophysics Data System (ADS)

Waichman, Karol; Barmashenko, Boris D.; Rosenwaks, Salman

2017-10-01

Analysis of beam propagation, kinetic and fluid dynamic processes in Cs diode pumped alkali lasers (DPALs), using wave optics model and gasdynamic code, is reported. The analysis is based on a three-dimensional, time-dependent computational fluid dynamics (3D CFD) model. The Navier-Stokes equations for momentum, heat and mass transfer are solved by a commercial Ansys FLUENT solver based on the finite volume discretization technique. The CFD code which solves the gas conservation equations includes effects of natural convection and temperature diffusion of the species in the DPAL mixture. The DPAL kinetic processes in the Cs/He/C2H6 gas mixture dealt with in this paper involve the three lowest energy levels of Cs, (1) 62S1/2, (2) 62P1/2 and (3) 62P3/2. The kinetic processes include absorption due to the 1->3 D2 transition followed by relaxation the 3 to 2 fine structure levels and stimulated emission due to the 2->1 D1 transition. Collisional quenching of levels 2 and 3 and spontaneous emission from these levels are also considered. The gas flow conservation equations are coupled to fast-Fourier-transform algorithm for transverse mode propagation to obtain a solution of the scalar paraxial propagation equation for the laser beam. The wave propagation equation is solved by the split-step beam propagation method where the gain and refractive index in the DPAL medium affect the wave amplitude and phase. Using the CFD and beam propagation models, the gas flow pattern and spatial distributions of the pump and laser intensities in the resonator were calculated for end-pumped Cs DPAL. The laser power, DPAL medium temperature and the laser beam quality were calculated as a function of pump power. The results of the theoretical model for laser power were compared to experimental results of Cs DPAL.

Multiple object, three-dimensional motion tracking using the Xbox Kinect sensor

NASA Astrophysics Data System (ADS)

Rosi, T.; Onorato, P.; Oss, S.

2017-11-01

In this article we discuss the capability of the Xbox Kinect sensor to acquire three-dimensional motion data of multiple objects. Two experiments regarding fundamental features of Newtonian mechanics are performed to test the tracking abilities of our setup. Particular attention is paid to check and visualise the conservation of linear momentum, angular momentum and energy. In both experiments, two objects are tracked while falling in the gravitational field. The obtained data is visualised in a 3D virtual environment to help students understand the physics behind the performed experiments. The proposed experiments were analysed with a group of university students who are aspirant physics and mathematics teachers. Their comments are presented in this paper.

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

PubMed

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

2013-04-01

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

On the three dimensional structure of stratospheric material transport associated with various types of waves

NASA Astrophysics Data System (ADS)

Kinoshita, T.; Sato, K.

2016-12-01

The Transformed Eulerian-Mean (TEM) equations were derived by Andrews and McIntyre (1976, 1978) and have been widely used to examine wave-mean flow interaction in the meridional cross section. According to previous studies, the Brewer-Dobson circulation in the stratosphere is driven by planetary waves, baroclinic waves, and inertia-gravity waves, and that the meridional circulation from the summer hemisphere to the winter hemisphere in the mesosphere is mainly driven by gravity waves (e.g., Garcia and Boville 1994; Plumb and Semeniuk 2003; Watanabe et al. 2008; Okamoto et al. 2011). However, the TEM equations do not provide the three-dimensional view of the transport, so that the three dimensional TEM equations have been formulated (Hoskins et al. 1983, Trenberth 1986, Plumb 1985, 1986, Takaya and Nakamura 1997, 2001, Miyahara 2006, Kinoshita et al. 2010, Noda 2010, Kinoshita and Sato 2013a, b, and Noda 2014). On the other hand, the TEM equations cannot properly treat the lower boundary and unstable waves. The Mass-weighted Isentropic Mean (MIM) equations derived by Iwasaki (1989, 1990) are the equations that overcome those problems and the formulation of three-dimensional MIM equations have been studied. The present study applies the three-dimensional TEM and MIM equations to the ERA-Interim reanalysis data and examines the climatological character of three-dimensional structure of Stratospheric Brewer-Dobson circulation. Next, we will discuss how to treat the flow associated with spatial structure of stationary waves.

A stretch of 11 amino acids in the betaB-betaC loop of the coat protein of grapevine fanleaf virus is essential for transmission by the nematode Xiphinema index.

PubMed

Schellenberger, Pascale; Andret-Link, Peggy; Schmitt-Keichinger, Corinne; Bergdoll, Marc; Marmonier, Aurélie; Vigne, Emmanuelle; Lemaire, Olivier; Fuchs, Marc; Demangeat, Gérard; Ritzenthaler, Christophe

2010-08-01

Grapevine fanleaf virus (GFLV) and Arabis mosaic virus (ArMV) from the genus Nepovirus, family Secoviridae, cause a severe degeneration of grapevines. GFLV and ArMV have a bipartite RNA genome and are transmitted specifically by the ectoparasitic nematodes Xiphinema index and Xiphinema diversicaudatum, respectively. The transmission specificity of both viruses maps to their respective RNA2-encoded coat protein (CP). To further delineate the GFLV CP determinants of transmission specificity, three-dimensional (3D) homology structure models of virions and CP subunits were constructed based on the crystal structure of Tobacco ringspot virus, the type member of the genus Nepovirus. The 3D models were examined to predict amino acids that are exposed at the external virion surface, highly conserved among GFLV isolates but divergent between GFLV and ArMV. Five short amino acid stretches that matched these topographical and sequence conservation criteria were selected and substituted in single and multiple combinations by their ArMV counterparts in a GFLV RNA2 cDNA clone. Among the 21 chimeric RNA2 molecules engineered, transcripts of only three of them induced systemic plant infection in the presence of GFLV RNA1. Nematode transmission assays of the three viable recombinant viruses showed that swapping a stretch of (i) 11 residues in the betaB-betaC loop near the icosahedral 3-fold axis abolished transmission by X. index but was insufficient to restore transmission by X. diversicaudatum and (ii) 7 residues in the betaE-alphaB loop did not interfere with transmission by the two Xiphinema species. This study provides new insights into GFLV CP determinants of nematode transmission.

An Intramolecular Salt Bridge in Bacillus thuringiensis Cry4Ba Toxin Is Involved in the Stability of Helix α-3, Which Is Needed for Oligomerization and Insecticidal Activity.

PubMed

Pacheco, Sabino; Gómez, Isabel; Sánchez, Jorge; García-Gómez, Blanca-Ines; Soberón, Mario; Bravo, Alejandra

2017-10-15

Bacillus thuringiensis three-domain Cry toxins kill insects by forming pores in the apical membrane of larval midgut cells. Oligomerization of the toxin is an important step for pore formation. Domain I helix α-3 participates in toxin oligomerization. Here we identify an intramolecular salt bridge within helix α-3 of Cry4Ba (D111-K115) that is conserved in many members of the family of three-domain Cry toxins. Single point mutations such as D111K or K115D resulted in proteins severely affected in toxicity. These mutants were also altered in oligomerization, and the mutant K115D was more sensitive to protease digestion. The double point mutant with reversed charges, D111K-K115D, recovered both oligomerization and toxicity, suggesting that this salt bridge is highly important for conservation of the structure of helix α-3 and necessary to promote the correct oligomerization of the toxin. IMPORTANCE Domain I has been shown to be involved in oligomerization through helix α-3 in different Cry toxins, and mutations affecting oligomerization also elicit changes in toxicity. The three-dimensional structure of the Cry4Ba toxin reveals an intramolecular salt bridge in helix α-3 of domain I. Mutations that disrupt this salt bridge resulted in changes in Cry4Ba oligomerization and toxicity, while a double point reciprocal mutation that restored the salt bridge resulted in recovery of toxin oligomerization and toxicity. These data highlight the role of oligomer formation as a key step in Cry4Ba toxicity. Copyright © 2017 American Society for Microbiology.

Three-dimensional periodic dielectric structures having photonic Dirac points

DOEpatents

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

2015-06-02

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

Studies of the structure-activity relationships of peptides and proteins involved in growth and development based on their three-dimensional structures.

PubMed

Nagata, Koji

2010-01-01

Peptides and proteins with similar amino acid sequences can have different biological functions. Knowledge of their three-dimensional molecular structures is critically important in identifying their functional determinants. In this review, I describe the results of our and other groups' structure-based functional characterization of insect insulin-like peptides, a crustacean hyperglycemic hormone-family peptide, a mammalian epidermal growth factor-family protein, and an intracellular signaling domain that recognizes proline-rich sequence.

Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots.

PubMed

Hirata, Yoshito; Oda, Arisa; Ohta, Kunihiro; Aihara, Kazuyuki

2016-10-11

Single-cell analysis of the three-dimensional (3D) chromosome structure can reveal cell-to-cell variability in genome activities. Here, we propose to apply recurrence plots, a mathematical method of nonlinear time series analysis, to reconstruct the 3D chromosome structure of a single cell based on information of chromosomal contacts from genome-wide chromosome conformation capture (Hi-C) data. This recurrence plot-based reconstruction (RPR) method enables rapid reconstruction of a unique structure in single cells, even from incomplete Hi-C information.

Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots

NASA Astrophysics Data System (ADS)

Hirata, Yoshito; Oda, Arisa; Ohta, Kunihiro; Aihara, Kazuyuki

2016-10-01

Single-cell analysis of the three-dimensional (3D) chromosome structure can reveal cell-to-cell variability in genome activities. Here, we propose to apply recurrence plots, a mathematical method of nonlinear time series analysis, to reconstruct the 3D chromosome structure of a single cell based on information of chromosomal contacts from genome-wide chromosome conformation capture (Hi-C) data. This recurrence plot-based reconstruction (RPR) method enables rapid reconstruction of a unique structure in single cells, even from incomplete Hi-C information.

Dorello's Canal for Laymen: A Lego-Like Presentation.

PubMed

Ezer, Haim; Banerjee, Anirban Deep; Thakur, Jai Deep; Nanda, Anil

2012-06-01

Objective Dorello's canal was first described by Gruber in 1859, and later by Dorello. Vail also described the anatomy of Dorello's canal. In the preceding century, Dorello's canal was clinically important, in understanding sixth nerve palsy and nowadays it is mostly important for skull base surgery. The understanding of the three dimensional anatomy, of this canal is very difficult to understand, and there is no simple explanation for its anatomy and its relationship with adjacent structures. We present a simple, Lego-like, presentation of Dorello's canal, in a stepwise manner. Materials and Methods Dorello's canal was dissected in five formalin-fixed cadaver specimens (10 sides). The craniotomy was performed, while preserving the neural and vascular structures associated with the canal. A 3D model was created, to explain the canal's anatomy. Results Using the petrous pyramid, the sixth nerve, the cavernous sinus, the trigeminal ganglion, the petorclival ligament and the posterior clinoid, the three-dimensional structure of Dorello's canal was defined. This simple representation aids in understanding the three dimensional relationship of Dorello's canal to its neighboring structures. Conclusion Dorello's canal with its three dimensional structure and relationship to its neighboring anatomical structures could be reconstructed using a few anatomical building blocks. This method simplifies the understanding of this complex anatomical structure, and could be used for teaching purposes for aspiring neurosurgeons, and anatomy students.

Dorello's Canal for Laymen: A Lego-Like Presentation

PubMed Central

Ezer, Haim; Banerjee, Anirban Deep; Thakur, Jai Deep; Nanda, Anil

2012-01-01

Objective Dorello's canal was first described by Gruber in 1859, and later by Dorello. Vail also described the anatomy of Dorello's canal. In the preceding century, Dorello's canal was clinically important, in understanding sixth nerve palsy and nowadays it is mostly important for skull base surgery. The understanding of the three dimensional anatomy, of this canal is very difficult to understand, and there is no simple explanation for its anatomy and its relationship with adjacent structures. We present a simple, Lego-like, presentation of Dorello's canal, in a stepwise manner. Materials and Methods Dorello's canal was dissected in five formalin-fixed cadaver specimens (10 sides). The craniotomy was performed, while preserving the neural and vascular structures associated with the canal. A 3D model was created, to explain the canal's anatomy. Results Using the petrous pyramid, the sixth nerve, the cavernous sinus, the trigeminal ganglion, the petorclival ligament and the posterior clinoid, the three-dimensional structure of Dorello's canal was defined. This simple representation aids in understanding the three dimensional relationship of Dorello's canal to its neighboring structures. Conclusion Dorello's canal with its three dimensional structure and relationship to its neighboring anatomical structures could be reconstructed using a few anatomical building blocks. This method simplifies the understanding of this complex anatomical structure, and could be used for teaching purposes for aspiring neurosurgeons, and anatomy students. PMID:23730547

RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

PubMed Central

Cruz, José Almeida; Blanchet, Marc-Frédérick; Boniecki, Michal; Bujnicki, Janusz M.; Chen, Shi-Jie; Cao, Song; Das, Rhiju; Ding, Feng; Dokholyan, Nikolay V.; Flores, Samuel Coulbourn; Huang, Lili; Lavender, Christopher A.; Lisi, Véronique; Major, François; Mikolajczak, Katarzyna; Patel, Dinshaw J.; Philips, Anna; Puton, Tomasz; Santalucia, John; Sijenyi, Fredrick; Hermann, Thomas; Rother, Kristian; Rother, Magdalena; Serganov, Alexander; Skorupski, Marcin; Soltysinski, Tomasz; Sripakdeevong, Parin; Tuszynska, Irina; Weeks, Kevin M.; Waldsich, Christina; Wildauer, Michael; Leontis, Neocles B.; Westhof, Eric

2012-01-01

We report the results of a first, collective, blind experiment in RNA three-dimensional (3D) structure prediction, encompassing three prediction puzzles. The goals are to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations in terms of sequence length and structural complexity. The results should give potential users insight into the suitability of available methods for different applications and facilitate efforts in the RNA structure prediction community in ongoing efforts to improve prediction tools. We also report the creation of an automated evaluation pipeline to facilitate the analysis of future RNA structure prediction exercises. PMID:22361291

Computational mining for hypothetical patterns of amino acid side chains in protein data bank (PDB)

NASA Astrophysics Data System (ADS)

Ghani, Nur Syatila Ab; Firdaus-Raih, Mohd

2018-04-01

The three-dimensional structure of a protein can provide insights regarding its function. Functional relationship between proteins can be inferred from fold and sequence similarities. In certain cases, sequence or fold comparison fails to conclude homology between proteins with similar mechanism. Since the structure is more conserved than the sequence, a constellation of functional residues can be similarly arranged among proteins of similar mechanism. Local structural similarity searches are able to detect such constellation of amino acids among distinct proteins, which can be useful to annotate proteins of unknown function. Detection of such patterns of amino acids on a large scale can increase the repertoire of important 3D motifs since available known 3D motifs currently, could not compensate the ever-increasing numbers of uncharacterized proteins to be annotated. Here, a computational platform for an automated detection of 3D motifs is described. A fuzzy-pattern searching algorithm derived from IMagine an Amino Acid 3D Arrangement search EnGINE (IMAAAGINE) was implemented to develop an automated method for searching of hypothetical patterns of amino acid side chains in Protein Data Bank (PDB), without the need for prior knowledge on related sequence or structure of pattern of interest. We present an example of the searches, which is the detection of a hypothetical pattern derived from known structural motif of C2H2 structural pattern from zinc fingers. The conservation of particular patterns of amino acid side chains in unrelated proteins is highlighted. This approach can act as a complementary method for available structure- and sequence-based platforms and may contribute in improving functional association between proteins.

Traveling wave solutions and conservation laws for nonlinear evolution equation

NASA Astrophysics Data System (ADS)

Baleanu, Dumitru; Inc, Mustafa; Yusuf, Abdullahi; Aliyu, Aliyu Isa

2018-02-01

In this work, the Riccati-Bernoulli sub-ordinary differential equation and modified tanh-coth methods are used to reach soliton solutions of the nonlinear evolution equation. We acquire new types of traveling wave solutions for the governing equation. We show that the equation is nonlinear self-adjoint by obtaining suitable substitution. Therefore, we construct conservation laws for the equation using new conservation theorem. The obtained solutions in this work may be used to explain and understand the physical nature of the wave spreads in the most dispersive medium. The constraint condition for the existence of solitons is stated. Some three dimensional figures for some of the acquired results are illustrated.

Three-dimensional spiral CT during arterial portography: comparison of three rendering techniques.

PubMed

Heath, D G; Soyer, P A; Kuszyk, B S; Bliss, D F; Calhoun, P S; Bluemke, D A; Choti, M A; Fishman, E K

1995-07-01

The three most common techniques for three-dimensional reconstruction are surface rendering, maximum-intensity projection (MIP), and volume rendering. Surface-rendering algorithms model objects as collections of geometric primitives that are displayed with surface shading. The MIP algorithm renders an image by selecting the voxel with the maximum intensity signal along a line extended from the viewer's eye through the data volume. Volume-rendering algorithms sum the weighted contributions of all voxels along the line. Each technique has advantages and shortcomings that must be considered during selection of one for a specific clinical problem and during interpretation of the resulting images. With surface rendering, sharp-edged, clear three-dimensional reconstruction can be completed on modest computer systems; however, overlapping structures cannot be visualized and artifacts are a problem. MIP is computationally a fast technique, but it does not allow depiction of overlapping structures, and its images are three-dimensionally ambiguous unless depth cues are provided. Both surface rendering and MIP use less than 10% of the image data. In contrast, volume rendering uses nearly all of the data, allows demonstration of overlapping structures, and engenders few artifacts, but it requires substantially more computer power than the other techniques.

Structural Insights into the Transport Mechanism of the Human Sodium-dependent Lysophosphatidylcholine Transporter MFSD2A*♦

PubMed Central

Quek, Debra Q. Y.; Nguyen, Long N.; Fan, Hao; Silver, David L.

2016-01-01

Major facilitator superfamily domain containing 2A (MFSD2A) was recently characterized as a sodium-dependent lysophosphatidylcholine transporter expressed at the blood-brain barrier endothelium. It is the primary route for importation of docosohexaenoic acid and other long-chain fatty acids into fetal and adult brain and is essential for mouse and human brain growth and function. Remarkably, MFSD2A is the first identified major facilitator superfamily member that uniquely transports lipids, implying that MFSD2A harbors unique structural features and transport mechanism. Here, we present three three-dimensional structural models of human MFSD2A derived by homology modeling using MelB- and LacY-based crystal structures and refined by biochemical analysis. All models revealed 12 transmembrane helices and connecting loops and represented the partially outward-open, outward-partially occluded, and inward-open states of the transport cycle. In addition to a conserved sodium-binding site, three unique structural features were identified as follows: a phosphate headgroup binding site, a hydrophobic cleft to accommodate a hydrophobic hydrocarbon tail, and three sets of ionic locks that stabilize the outward-open conformation. Ligand docking studies and biochemical assays identified Lys-436 as a key residue for transport. It is seen forming a salt bridge with the negative charge on the phosphate headgroup. Importantly, MFSD2A transported structurally related acylcarnitines but not a lysolipid without a negative charge, demonstrating the necessity of a negatively charged headgroup interaction with Lys-436 for transport. These findings support a novel transport mechanism by which lysophosphatidylcholines are “flipped” within the transporter cavity by pivoting about Lys-436 leading to net transport from the outer to the inner leaflet of the plasma membrane. PMID:26945070

Embryonic stem cells growing in 3-dimensions shift from reliance on the substrate to each other for mechanical support.

PubMed

Teo, Ailing; Lim, Mayasari; Weihs, Daphne

2015-07-16

Embryonic stem cells (ESCs) grow into three-dimensional (3D) spheroid structures en-route to tissue growth. In vitro spheroids can be controllably induced on a two-dimensional (2D) substrate with high viability. Here we use a method for inducing pluripotent embryoid body (EB) formation on flat polyacrylamide gels while simultaneously evaluating the dynamic changes in the mechano-biology of the growing 3D spheroids. During colony growth in 3D, pluripotency is conserved while the spheroid-substrate interactions change significantly. We correlate colony-size, cell-applied traction-forces, and expressions of cell-surface molecules indicating cell-cell and cell-substrate interactions, while verifying pluripotency. We show that as the colony size increases with time, the stresses applied by the spheroid to the gel decrease in the 3D growing EBs; control cells growing in 2D-monolayers maintain unvarying forces. Concurrently, focal-adhesion mediated cell-substrate interactions give way to E-cadherin cell-cell connections, while pluripotency. The mechano-biological changes occurring in the growing embryoid body are required for stabilization of the growing pluripotent 3D-structure, and can affect its potential uses including differentiation. This could enable development of more effective expansion, differentiation, and separation approaches for clinical purposes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Crystal structures of trypanosomal histidyl-tRNA synthetase illuminate differences between eukaryotic and prokaryotic homologs

PubMed Central

Merritt, Ethan A; Arakaki, Tracy L; Gillespie, J Robert; Larson, Eric T; Kelley, Angela; Mueller, Natascha; Napuli, Alberto J; Kim, Jessica; Zhang, Li; Verlinde, Christophe L M J; Fan, Erkang; Zucker, Frank; Buckner, Frederick S; Van Voorhis, Wesley C; Hol, Wim G J

2010-01-01

Crystal structures of histidyl-tRNA synthetase from the eukaryotic parasites Trypanosoma brucei and Trypanosoma cruzi provide a first structural view of a eukaryotic form of this enzyme, and reveal differences from bacterial homologs. Histidyl-tRNA synthetases in general contain an extra domain inserted between conserved motifs 2 and 3 of the Class II aminoacyl-tRNA synthetase catalytic core. The current structures show that the three dimensional topology of this domain is very different in bacterial and archaeal/eukaryotic forms of the enzyme. Comparison of apo and histidine-bound trypanosomal structures indicates substantial active site rearrangement upon histidine binding, but relatively little subsequent rearrangement after reaction of histidine with ATP to form the enzyme’s first reaction product, histidyladenylate. The specific residues involved in forming the binding pocket for the adenine moiety differ substantially both from the previously characterized binding site in bacterial structures and from the homologous residues in human histidyl-tRNA synthetases. The essentiality of the single histidyl-tRNA synthetase gene in T. brucei is shown by a severe depression of parasite growth rate that results from even partial suppression of expression by RNA interference. PMID:20132829

A purely Lagrangian method for computing linearly-perturbed flows in spherical geometry

NASA Astrophysics Data System (ADS)

Jaouen, Stéphane

2007-07-01

In many physical applications, one wishes to control the development of multi-dimensional instabilities around a one-dimensional (1D) complex flow. For predicting the growth rates of these perturbations, a general numerical approach is viable which consists in solving simultaneously the one-dimensional equations and their linearized form for three-dimensional perturbations. In Clarisse et al. [J.-M. Clarisse, S. Jaouen, P.-A. Raviart, A Godunov-type method in Lagrangian coordinates for computing linearly-perturbed planar-symmetric flows of gas dynamics, J. Comp. Phys. 198 (2004) 80-105], a class of Godunov-type schemes for planar-symmetric flows of gas dynamics has been proposed. Pursuing this effort, we extend these results to spherically symmetric flows. A new method to derive the Lagrangian perturbation equations, based on the canonical form of systems of conservation laws with zero entropy flux [B. Després, Lagrangian systems of conservation laws. Invariance properties of Lagrangian systems of conservation laws, approximate Riemann solvers and the entropy condition, Numer. Math. 89 (2001) 99-134; B. Després, C. Mazeran, Lagrangian gas dynamics in two dimensions and Lagrangian systems, Arch. Rational Mech. Anal. 178 (2005) 327-372] is also described. It leads to many advantages. First of all, many physical problems we are interested in enter this formalism (gas dynamics, two-temperature plasma equations, ideal magnetohydrodynamics, etc.) whatever is the geometry. Secondly, a class of numerical entropic schemes is available for the basic flow [11]. Last, linearizing and devising numerical schemes for the perturbed flow is straightforward. The numerical capabilities of these methods are illustrated on three test cases of increasing difficulties and we show that - due to its simplicity and its low computational cost - the Linear Perturbations Code (LPC) is a powerful tool to understand and predict the development of hydrodynamic instabilities in the linear regime.

Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

PubMed

Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

2010-01-01

The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by <25% in sequence identity fold into very similar structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

Nonlinear geometric scaling of coercivity in a three-dimensional nanoscale analog of spin ice

NASA Astrophysics Data System (ADS)

Shishkin, I. S.; Mistonov, A. A.; Dubitskiy, I. S.; Grigoryeva, N. A.; Menzel, D.; Grigoriev, S. V.

2016-08-01

Magnetization hysteresis loops of a three-dimensional nanoscale analog of spin ice based on the nickel inverse opal-like structure (IOLS) have been studied at room temperature. The samples are produced by filling nickel into the voids of artificial opal-like films. The spin ice behavior is induced by tetrahedral elements within the IOLS, which have the same arrangement of magnetic moments as a spin ice. The thickness of the films vary from a two-dimensional, i.e., single-layered, antidot array to a three-dimensional, i.e., multilayered, structure. The coercive force, the saturation, and the irreversibility field have been measured in dependence of the thickness of the IOLS for in-plane and out-of-plane applied fields. The irreversibility and saturation fields change abruptly from the antidot array to the three-dimensional IOLS and remain constant upon further increase of the number of layers n . The coercive force Hc seems to increase logarithmically with increasing n as Hc=Hc 0+α ln(n +1 ) . The logarithmic law implies the avalanchelike remagnetization of anisotropic structural elements connecting tetrahedral and cubic nodes in the IOLS. We conclude that the "ice rule" is the base of mechanism regulating this process.

Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package

PubMed Central

Kumar, Yadhu; Westram, Ralf; Kipfer, Peter; Meier, Harald; Ludwig, Wolfgang

2006-01-01

Background Availability of high-resolution RNA crystal structures for the 30S and 50S ribosomal subunits and the subsequent validation of comparative secondary structure models have prompted the biologists to use three-dimensional structure of ribosomal RNA (rRNA) for evaluating sequence alignments of rRNA genes. Furthermore, the secondary and tertiary structural features of rRNA are highly useful and successfully employed in designing rRNA targeted oligonucleotide probes intended for in situ hybridization experiments. RNA3D, a program to combine sequence alignment information with three-dimensional structure of rRNA was developed. Integration into ARB software package, which is used extensively by the scientific community for phylogenetic analysis and molecular probe designing, has substantially extended the functionality of ARB software suite with 3D environment. Results Three-dimensional structure of rRNA is visualized in OpenGL 3D environment with the abilities to change the display and overlay information onto the molecule, dynamically. Phylogenetic information derived from the multiple sequence alignments can be overlaid onto the molecule structure in a real time. Superimposition of both statistical and non-statistical sequence associated information onto the rRNA 3D structure can be done using customizable color scheme, which is also applied to a textual sequence alignment for reference. Oligonucleotide probes designed by ARB probe design tools can be mapped onto the 3D structure along with the probe accessibility models for evaluation with respect to secondary and tertiary structural conformations of rRNA. Conclusion Visualization of three-dimensional structure of rRNA in an intuitive display provides the biologists with the greater possibilities to carry out structure based phylogenetic analysis. Coupled with secondary structure models of rRNA, RNA3D program aids in validating the sequence alignments of rRNA genes and evaluating probe target sites. Superimposition of the information derived from the multiple sequence alignment onto the molecule dynamically allows the researchers to observe any sequence inherited characteristics (phylogenetic information) in real-time environment. The extended ARB software package is made freely available for the scientific community via . PMID:16672074

Impedance Eduction in Sound Fields With Peripherally Varying Liners and Flow

NASA Technical Reports Server (NTRS)

Watson, W. R.; Jones, M. G.

2015-01-01

A two-dimensional impedance eduction theory is extended to three-dimensional sound fields and peripherally varying duct liners. The approach is to first measure the acoustic pressure field at a series of flush-mounted wall microphones located around the periphery of the flow duct. The numerical solution for the acoustic pressure field at these microphones is also obtained by solving the three-dimensional convected Helmholtz equation using the finite element method. A quadratic objective function based on the difference between the measured and finite element solution is constructed and the unknown impedance function is obtained by minimizing this objective function. Impedance spectra educed for two uniform-structure liners (a wire-mesh and a conventional liner) and a hard-soft-hard peripherally varying liner (for which the soft segment is that of the conventional liner) are presented. Results are presented at three mean flow Mach numbers and fourteen sound source frequencies. The impedance spectra of the uniform-structure liners are also computed using a two-dimensional impedance eduction theory. The primary conclusions of the study are: 1) when measured data is used with the uniform-structure liners, the three-dimensional theory reproduces the same impedance spectra as the two-dimensional theory except for frequencies corresponding to very low or very high liner attenuation; and 2) good agreement between the educed impedance spectra of the uniform structure conventional liner and the soft segment of the peripherally varying liner is obtained.

Predictive Computational Modeling of Chromatin Folding

NASA Astrophysics Data System (ADS)

di Pierro, Miichele; Zhang, Bin; Wolynes, Peter J.; Onuchic, Jose N.

In vivo, the human genome folds into well-determined and conserved three-dimensional structures. The mechanism driving the folding process remains unknown. We report a theoretical model (MiChroM) for chromatin derived by using the maximum entropy principle. The proposed model allows Molecular Dynamics simulations of the genome using as input the classification of loci into chromatin types and the presence of binding sites of loop forming protein CTCF. The model was trained to reproduce the Hi-C map of chromosome 10 of human lymphoblastoid cells. With no additional tuning the model was able to predict accurately the Hi-C maps of chromosomes 1-22 for the same cell line. Simulations show unknotted chromosomes, phase separation of chromatin types and a preference of chromatin of type A to sit at the periphery of the chromosomes.

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

NASA Astrophysics Data System (ADS)

Shobeiri, Vahid; Ahmadi-Nedushan, Behrouz

2017-12-01

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

Depth-enhanced three-dimensional-two-dimensional convertible display based on modified integral imaging.

PubMed

Park, Jae-Hyeung; Kim, Hak-Rin; Kim, Yunhee; Kim, Joohwan; Hong, Jisoo; Lee, Sin-Doo; Lee, Byoungho

2004-12-01

A depth-enhanced three-dimensional-two-dimensional convertible display that uses a polymer-dispersed liquid crystal based on the principle of integral imaging is proposed. In the proposed method, a lens array is located behind a transmission-type display panel to form an array of point-light sources, and a polymer-dispersed liquid crystal is electrically controlled to pass or to scatter light coming from these point-light sources. Therefore, three-dimensional-two-dimensional conversion is accomplished electrically without any mechanical movement. Moreover, the nonimaging structure of the proposed method increases the expressible depth range considerably. We explain the method of operation and present experimental results.

Google Earth Mapping Exercises for Structural Geology Students--A Promising Intervention for Improving Penetrative Visualization Ability

ERIC Educational Resources Information Center

Giorgis, Scott

2015-01-01

Three-dimensional thinking skills are extremely useful for geoscientists, and at the undergraduate level, these skills are often emphasized in structural geology courses. Google Earth is a powerful tool for visualizing the three-dimensional nature of data collected on the surface of Earth. The results of a 5 y pre- and posttest study of the…

Computer program determines vibration in three-dimensional space of hydraulic lines excited by forced displacements

NASA Technical Reports Server (NTRS)

Dodge, W. G.

1968-01-01

Computer program determines the forced vibration in three dimensional space of a multiple degree of freedom beam type structural system. Provision is made for the longitudinal axis of the analytical model to change orientation at any point along its length. This program is used by industries in which structural design dynamic analyses are performed.

Three-dimensional flow visualization and vorticity dynamics in revolving wings

NASA Astrophysics Data System (ADS)

Cheng, Bo; Sane, Sanjay P.; Barbera, Giovanni; Troolin, Daniel R.; Strand, Tyson; Deng, Xinyan

2013-01-01

We investigated the three-dimensional vorticity dynamics of the flows generated by revolving wings using a volumetric 3-component velocimetry system. The three-dimensional velocity and vorticity fields were represented with respect to the base axes of rotating Cartesian reference frames, and the second invariant of the velocity gradient was evaluated and used as a criterion to identify two core vortex structures. The first structure was a composite of leading, trailing, and tip-edge vortices attached to the wing edges, whereas the second structure was a strong tip vortex tilted from leading-edge vortices and shed into the wake together with the vorticity generated at the tip edge. Using the fundamental vorticity equation, we evaluated the convection, stretching, and tilting of vorticity in the rotating wing frame to understand the generation and evolution of vorticity. Based on these data, we propose that the vorticity generated at the leading edge is carried away by strong tangential flow into the wake and travels downwards with the induced downwash. The convection by spanwise flow is comparatively negligible. The three-dimensional flow in the wake also exhibits considerable vortex tilting and stretching. Together these data underscore the complex and interconnected vortical structures and dynamics generated by revolving wings.

Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Duckhoe; Sahin, Ozgur

2015-03-01

Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip-sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin-streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2 Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.

Three-dimensional cross-linking composite of graphene, carbon nanotubes and Si nanoparticles for lithium ion battery anode

NASA Astrophysics Data System (ADS)

Tian, Suyun; Zhu, Guannan; Tang, Yanping; Xie, Xiaohua; Wang, Qian; Ma, Yufei; Ding, Guqiao; Xie, Xiaoming

2018-03-01

Various graphene-based Si nanocomposites have been reported to improve the performance of active materials in Li-ion batteries. However, these candidates still yield severe capacity fading due to the electrical disconnection and fractures caused by the huge volume changes over extended cycles. Therefore, we have designed a novel three-dimensional cross-linked graphene and single-wall carbon nanotube structure to encapsulate the Si nanoparticles. The synthesized three-dimensional structure is attributed to the excellent self-assembly of carbon nanotubes with graphene oxide as well as a thermal treatment process at 900 °C. This special structure provides sufficient void spaces for the volume expansion of Si nanoparticles and channels for the diffusion of ions and electrons. In addition, the cross-linking of the graphene and single-wall carbon nanotubes also strengthens the stability of the structure. As a result, the volume expansion of the Si nanoparticles is restrained. The specific capacity remains at 1450 mAh g-1 after 100 cycles at 200 mA g-1. This well-defined three-dimensional structure facilitates superior capacity and cycling stability in comparison with bare Si and a mechanically mixed composite electrode of graphene, single-wall carbon nanotubes and silicon nanoparticles.

Method of using triaxial magnetic fields for making particle structures

DOEpatents

Martin, James E.; Anderson, Robert A.; Williamson, Rodney L.

2005-01-18

A method of producing three-dimensional particle structures with enhanced magnetic susceptibility in three dimensions by applying a triaxial energetic field to a magnetic particle suspension and subsequently stabilizing said particle structure. Combinations of direct current and alternating current fields in three dimensions produce particle gel structures, honeycomb structures, and foam-like structures.

Boundary Conditions for Infinite Conservation Laws

NASA Astrophysics Data System (ADS)

Rosenhaus, V.; Bruzón, M. S.; Gandarias, M. L.

2016-12-01

Regular soliton equations (KdV, sine-Gordon, NLS) are known to possess infinite sets of local conservation laws. Some other classes of nonlinear PDE possess infinite-dimensional symmetries parametrized by arbitrary functions of independent or dependent variables; among them are Zabolotskaya-Khokhlov, Kadomtsev-Petviashvili, Davey-Stewartson equations and Born-Infeld equation. Boundary conditions were shown to play an important role for the existence of local conservation laws associated with infinite-dimensional symmetries. In this paper, we analyze boundary conditions for the infinite conserved densities of regular soliton equations: KdV, potential KdV, Sine-Gordon equation, and nonlinear Schrödinger equation, and compare them with boundary conditions for the conserved densities obtained from infinite-dimensional symmetries with arbitrary functions of independent and dependent variables.

Mutational epitope analysis of Pru av 1 and Api g 1, the major allergens of cherry (Prunus avium) and celery (Apium graveolens): correlating IgE reactivity with three-dimensional structure.

PubMed Central

Neudecker, Philipp; Lehmann, Katrin; Nerkamp, Jörg; Haase, Tanja; Wangorsch, Andrea; Fötisch, Kay; Hoffmann, Silke; Rösch, Paul; Vieths, Stefan; Scheurer, Stephan

2003-01-01

Birch pollinosis is often accompanied by adverse reactions to food due to pollen-allergen specific IgE cross-reacting with homologous food allergens. The tertiary structure of Pru av 1, the major cherry (Prunus avium) allergen, for example, is nearly identical with Bet v 1, the major birch (Betula verrucosa) pollen allergen. In order to define cross-reactive IgE epitopes, we generated and analysed mutants of Pru av 1 and Api g 1.0101, the major celery (Apium graveolens) allergen, by immunoblotting, EAST (enzyme allergosorbent test), CD and NMR spectroscopy. The mutation of Glu45 to Trp45 in the P-loop region, a known IgE epitope of Bet v 1, significantly reduced IgE binding to Pru av 1 in a subgroup of cherry-allergic patients. The backbone conformation of Pru av 1 wild-type is conserved in the three-dimensional structure of Pru av 1 Trp45, demonstrating that the side chain of Glu45 is involved in a cross-reactive IgE epitope. Accordingly, for a subgroup of celery-allergic patients, IgE binding to the homologous celery allergen Api g 1.0101 was enhanced by the mutation of Lys44 to Glu. The almost complete loss of IgE reactivity to the Pru av 1 Pro112 mutant is due to disruption of its tertiary structure. Neither the mutation Ala112 nor deletion of the C-terminal residues 155-159 influenced IgE binding to Pru av 1. In conclusion, the structure of the P-loop partially explains the cross-reactivity pattern, and modulation of IgE-binding by site-directed mutagenesis is a promising approach to develop hypo-allergenic variants for patient-tailored specific immunotherapy. PMID:12943529

Graphic kinematics, visual virtual work and elastographics

PubMed Central

Konstantatou, Marina; Athanasopoulos, Georgios; Hannigan, Laura

2017-01-01

In this paper, recent progress in graphic statics is combined with Williot displacement diagrams to create a graphical description of both statics and kinematics for two- and three-dimensional pin-jointed trusses. We begin with reciprocal form and force diagrams. The force diagram is dissected into its component cells which are then translated relative to each other. This defines a displacement diagram which is topologically equivalent to the form diagram (the structure). The various contributions to the overall Virtual Work appear as parallelograms (for two-dimensional trusses) or parallelopipeds (for three-dimensional trusses) that separate the force and the displacement pieces. Structural mechanisms can be identified by translating the force cells such that their shared faces slide across each other without separating. Elastic solutions can be obtained by choosing parallelograms or parallelopipeds of the appropriate aspect ratio. Finally, a new type of ‘elastographic’ diagram—termed a deformed Maxwell–Williot diagram (two-dimensional) or a deformed Rankine–Williot diagram (three-dimensional)—is presented which combines the deflected structure with the forces carried by its members. PMID:28573030

Particle tracking approach for transport in three-dimensional discrete fracture networks: Particle tracking in 3-D DFNs

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

Makedonska, Nataliia; Painter, Scott L.; Bui, Quan M.

The discrete fracture network (DFN) model is a method to mimic discrete pathways for fluid flow through a fractured low-permeable rock mass, and may be combined with particle tracking simulations to address solute transport. However, experience has shown that it is challenging to obtain accurate transport results in three-dimensional DFNs because of the high computational burden and difficulty in constructing a high-quality unstructured computational mesh on simulated fractures. We present a new particle tracking capability, which is adapted to control volume (Voronoi polygons) flow solutions on unstructured grids (Delaunay triangulations) on three-dimensional DFNs. The locally mass-conserving finite-volume approach eliminates massmore » balance-related problems during particle tracking. The scalar fluxes calculated for each control volume face by the flow solver are used to reconstruct a Darcy velocity at each control volume centroid. The groundwater velocities can then be continuously interpolated to any point in the domain of interest. The control volumes at fracture intersections are split into four pieces, and the velocity is reconstructed independently on each piece, which results in multiple groundwater velocities at the intersection, one for each fracture on each side of the intersection line. This technique enables detailed particle transport representation through a complex DFN structure. Verified for small DFNs, the new simulation capability enables numerical experiments on advective transport in large DFNs to be performed. As a result, we demonstrate this particle transport approach on a DFN model using parameters similar to those of crystalline rock at a proposed geologic repository for spent nuclear fuel in Forsmark, Sweden.« less

Particle tracking approach for transport in three-dimensional discrete fracture networks: Particle tracking in 3-D DFNs

DOE PAGES

Makedonska, Nataliia; Painter, Scott L.; Bui, Quan M.; ...

2015-09-16

The discrete fracture network (DFN) model is a method to mimic discrete pathways for fluid flow through a fractured low-permeable rock mass, and may be combined with particle tracking simulations to address solute transport. However, experience has shown that it is challenging to obtain accurate transport results in three-dimensional DFNs because of the high computational burden and difficulty in constructing a high-quality unstructured computational mesh on simulated fractures. We present a new particle tracking capability, which is adapted to control volume (Voronoi polygons) flow solutions on unstructured grids (Delaunay triangulations) on three-dimensional DFNs. The locally mass-conserving finite-volume approach eliminates massmore » balance-related problems during particle tracking. The scalar fluxes calculated for each control volume face by the flow solver are used to reconstruct a Darcy velocity at each control volume centroid. The groundwater velocities can then be continuously interpolated to any point in the domain of interest. The control volumes at fracture intersections are split into four pieces, and the velocity is reconstructed independently on each piece, which results in multiple groundwater velocities at the intersection, one for each fracture on each side of the intersection line. This technique enables detailed particle transport representation through a complex DFN structure. Verified for small DFNs, the new simulation capability enables numerical experiments on advective transport in large DFNs to be performed. As a result, we demonstrate this particle transport approach on a DFN model using parameters similar to those of crystalline rock at a proposed geologic repository for spent nuclear fuel in Forsmark, Sweden.« less

Maxwell Strata and Cut Locus in the Sub-Riemannian Problem on the Engel Group

NASA Astrophysics Data System (ADS)

Ardentov, Andrei A.; Sachkov, Yuri L.

2017-12-01

We consider the nilpotent left-invariant sub-Riemannian structure on the Engel group. This structure gives a fundamental local approximation of a generic rank 2 sub-Riemannian structure on a 4-manifold near a generic point (in particular, of the kinematic models of a car with a trailer). On the other hand, this is the simplest sub-Riemannian structure of step three. We describe the global structure of the cut locus (the set of points where geodesics lose their global optimality), the Maxwell set (the set of points that admit more than one minimizer), and the intersection of the cut locus with the caustic (the set of conjugate points along all geodesics). The group of symmetries of the cut locus is described: it is generated by a one-parameter group of dilations R+ and a discrete group of reflections Z2 × Z2 × Z2. The cut locus admits a stratification with 6 three-dimensional strata, 12 two-dimensional strata, and 2 one-dimensional strata. Three-dimensional strata of the cut locus are Maxwell strata of multiplicity 2 (for each point there are 2 minimizers). Two-dimensional strata of the cut locus consist of conjugate points. Finally, one-dimensional strata are Maxwell strata of infinite multiplicity, they consist of conjugate points as well. Projections of sub-Riemannian geodesics to the 2-dimensional plane of the distribution are Euler elasticae. For each point of the cut locus, we describe the Euler elasticae corresponding to minimizers coming to this point. Finally, we describe the structure of the optimal synthesis, i. e., the set of minimizers for each terminal point in the Engel group.

A three-dimensional wide-angle BPM for optical waveguide structures.

PubMed

Ma, Changbao; Van Keuren, Edward

2007-01-22

Algorithms for effective modeling of optical propagation in three- dimensional waveguide structures are critical for the design of photonic devices. We present a three-dimensional (3-D) wide-angle beam propagation method (WA-BPM) using Hoekstra's scheme. A sparse matrix algebraic equation is formed and solved using iterative methods. The applicability, accuracy and effectiveness of our method are demonstrated by applying it to simulations of wide-angle beam propagation, along with a technique for shifting the simulation window to reduce the dimension of the numerical equation and a threshold technique to further ensure its convergence. These techniques can ensure the implementation of iterative methods for waveguide structures by relaxing the convergence problem, which will further enable us to develop higher-order 3-D WA-BPMs based on Padé approximant operators.

A three-dimensional wide-angle BPM for optical waveguide structures

NASA Astrophysics Data System (ADS)

Ma, Changbao; van Keuren, Edward

2007-01-01

Algorithms for effective modeling of optical propagation in three- dimensional waveguide structures are critical for the design of photonic devices. We present a three-dimensional (3-D) wide-angle beam propagation method (WA-BPM) using Hoekstra’s scheme. A sparse matrix algebraic equation is formed and solved using iterative methods. The applicability, accuracy and effectiveness of our method are demonstrated by applying it to simulations of wide-angle beam propagation, along with a technique for shifting the simulation window to reduce the dimension of the numerical equation and a threshold technique to further ensure its convergence. These techniques can ensure the implementation of iterative methods for waveguide structures by relaxing the convergence problem, which will further enable us to develop higher-order 3-D WA-BPMs based on Padé approximant operators.

Electromagnetic momentum and the energy–momentum tensor in a linear medium with magnetic and dielectric properties

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

Crenshaw, Michael E., E-mail: michael.e.crenshaw4.civ@mail.mil

2014-04-15

In a continuum setting, the energy–momentum tensor embodies the relations between conservation of energy, conservation of linear momentum, and conservation of angular momentum. The well-defined total energy and the well-defined total momentum in a thermodynamically closed system with complete equations of motion are used to construct the total energy–momentum tensor for a stationary simple linear material with both magnetic and dielectric properties illuminated by a quasimonochromatic pulse of light through a gradient-index antireflection coating. The perplexing issues surrounding the Abraham and Minkowski momentums are bypassed by working entirely with conservation principles, the total energy, and the total momentum. We derivemore » electromagnetic continuity equations and equations of motion for the macroscopic fields based on the material four-divergence of the traceless, symmetric total energy–momentum tensor. We identify contradictions between the macroscopic Maxwell equations and the continuum form of the conservation principles. We resolve the contradictions, which are the actual fundamental issues underlying the Abraham–Minkowski controversy, by constructing a unified version of continuum electrodynamics that is based on establishing consistency between the three-dimensional Maxwell equations for macroscopic fields, the electromagnetic continuity equations, the four-divergence of the total energy–momentum tensor, and a four-dimensional tensor formulation of electrodynamics for macroscopic fields in a simple linear medium.« less

Quantitative molecular characterization of bovine vitreous and lens with non-invasive dynamic light scattering

NASA Technical Reports Server (NTRS)

Ansari, R. R.; Suh, K. I.; Dunker, S.; Kitaya, N.; Sebag, J.

2001-01-01

The non-invasive technique of dynamic light scattering (DLS) was used to quantitatively characterize vitreous and lens structure on a molecular level by measuring the sizes of the predominant particles and mapping the three-dimensional topographic distribution of these structural macromolecules in three spatial dimensions. The results of DLS measurements in five fresh adult bovine eyes were compared to DLS measurements in model solutions of hyaluronan (HA) and collagen (Coll). In the bovine eyes DLS measurements were obtained from excised samples of gel and liquid vitreous and compared to the model solutions. Measurements in whole vitreous were obtained at multiple points posterior to the lens to generate a three-dimensional 'map' of molecular structure. The macromolecule distribution in bovine lens was similarly characterized.In each bovine vitreous (Bo Vit) specimen, DLS predominantly detected two distinct particles, which differed in diffusion properties and hence size. Comparisons with model vitreous solutions demonstrated that these most likely corresponded to the Coll and HA components of vitreous. Three-dimensional mapping of Bo Vit found heterogeneity throughout the vitreous body, with different particle size distributions for Coll and HA at different loci. In contrast, the three-dimensional distribution of lens macromolecules was more homogeneous. Thus, the non-invasive DLS technique can quantitate the average sizes of vitreous and lens macromolecules and map their three-dimensional distribution. This method to assess quantitatively the macromolecular structure of vitreous and lens should be useful for clinical as well as experimental applications in health and disease. Copyright 2001 Academic Press.

Topology of three-dimensional separated flows

NASA Technical Reports Server (NTRS)

Tobak, M.; Peake, D. J.

1981-01-01

Based on the hypothesis that patterns of skin-friction lines and external streamlines reflect the properties of continuous vector fields, topology rules define a small number of singular points (nodes, saddle points, and foci) that characterize the patterns on the surface and on particular projections of the flow (e.g., the crossflow plane). The restricted number of singular points and the rules that they obey are considered as an organizing principle whose finite number of elements can be combined in various ways to connect together the properties common to all steady three dimensional viscous flows. Introduction of a distinction between local and global properties of the flow resolves an ambiguity in the proper definition of a three dimensional separated flow. Adoption of the notions of topological structure, structural stability, and bifurcation provides a framework to describe how three dimensional separated flows originate and succeed each other as the relevant parameters of the problem are varied.

System and method for representing and manipulating three-dimensional objects on massively parallel architectures

DOEpatents

Karasick, Michael S.; Strip, David R.

1996-01-01

A parallel computing system is described that comprises a plurality of uniquely labeled, parallel processors, each processor capable of modelling a three-dimensional object that includes a plurality of vertices, faces and edges. The system comprises a front-end processor for issuing a modelling command to the parallel processors, relating to a three-dimensional object. Each parallel processor, in response to the command and through the use of its own unique label, creates a directed-edge (d-edge) data structure that uniquely relates an edge of the three-dimensional object to one face of the object. Each d-edge data structure at least includes vertex descriptions of the edge and a description of the one face. As a result, each processor, in response to the modelling command, operates upon a small component of the model and generates results, in parallel with all other processors, without the need for processor-to-processor intercommunication.

Observation of three-dimensional internal structure of steel materials by means of serial sectioning with ultrasonic elliptical vibration cutting.

PubMed

Fujisaki, K; Yokota, H; Nakatsuchi, H; Yamagata, Y; Nishikawa, T; Udagawa, T; Makinouchi, A

2010-01-01

A three-dimensional (3D) internal structure observation system based on serial sectioning was developed from an ultrasonic elliptical vibration cutting device and an optical microscope combined with a high-precision positioning device. For bearing steel samples, the cutting device created mirrored surfaces suitable for optical metallography, even for long-cutting distances during serial sectioning of these ferrous materials. Serial sectioning progressed automatically by means of numerical control. The system was used to observe inclusions in steel materials on a scale of several tens of micrometers. Three specimens containing inclusions were prepared from bearing steels. These inclusions could be detected as two-dimensional (2D) sectional images with resolution better than 1 mum. A three-dimensional (3D) model of each inclusion was reconstructed from the 2D serial images. The microscopic 3D models had sharp edges and complicated surfaces.

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

NASA Astrophysics Data System (ADS)

Sauls, Barbara Lynn

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

Formation of bulk refractive index structures

DOEpatents

Potter, Jr., Barrett George; Potter, Kelly Simmons; Wheeler, David R.; Jamison, Gregory M.

2003-07-15

A method of making a stacked three-dimensional refractive index structure in photosensitive materials using photo-patterning where first determined is the wavelength at which a photosensitive material film exhibits a change in refractive index upon exposure to optical radiation, a portion of the surfaces of the photosensitive material film is optically irradiated, the film is marked to produce a registry mark. Multiple films are produced and aligned using the registry marks to form a stacked three-dimensional refractive index structure.

Compact 3D photonic crystals sensing platform with 45 degree angle polished fibers

NASA Astrophysics Data System (ADS)

Guo, Yuqing; Chen, Lu; Zhu, Jiali; Ni, Haibin; Xia, Wei; Wang, Ming

2017-07-01

Three dimensional photonic crystals are a kind of promising sensing materials in biology and chemistry. A compact structure, consists of planner colloidal crystals and 45 degree angle polished fiber, is proposed as a platform for accurate, fast, reliable three dimensional photonic crystals sensing in practice. This structure show advantages in compact size for integration and it is ease for large scale manufacture. Reflectivity of the 45 degree angle polished surface with and without a layer of Ag film are simulated by FDTD simulation. Refractive index sensing properties as well as mode distribution of this structure consists of both polystyrene opal and silica inverse opal film is investigated, and an experimental demonstration of silica inverse opal film is performed, which shows a sensitivity of 733 nm/RIU. Different kinds of three dimensional photonic crystals can also be applied in this structure for particular purpose.

[Research progress of three-dimensional digital model for repair and reconstruction of knee joint].

PubMed

Tong, Lu; Li, Yanlin; Hu, Meng

2013-01-01

To review recent advance in the application and research of three-dimensional digital knee model. The recent original articles about three-dimensional digital knee model were extensively reviewed and analyzed. The digital three-dimensional knee model can simulate the knee complex anatomical structure very well. Based on this, there are some developments of new software and techniques, and good clinical results are achieved. With the development of computer techniques and software, the knee repair and reconstruction procedure has been improved, the operation will be more simple and its accuracy will be further improved.

[Advances in the research of application of hydrogels in three-dimensional bioprinting].

PubMed

Yang, J; Zhao, Y; Li, H H; Zhu, S H

2016-08-20

Hydrogels are three-dimensional networks made of hydrophilic polymer crosslinked through covalent bonds or physical intermolecular attractions, which can contain growth media and growth factors to support cell growth. In bioprinting, hydrogels are used to provide accurate control over cellular microenvironment and to dramatically reduce experimental repetition times, meanwhile we can obtain three-dimensional cell images of high quality. Hydrogels in three-dimensional bioprinting have received a considerable interest due to their structural similarities to the natural extracellular matrix and polyporous frameworks which can support the cellular proliferation and survival. Meanwhile, they are accompanied by many challenges.

BAYESIAN PROTEIN STRUCTURE ALIGNMENT.

PubMed

Rodriguez, Abel; Schmidler, Scott C

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

Three-dimensional behavior of ice crystals and biological cells during freezing of cell suspensions.

PubMed

Ishiguro, H; Koike, K

1998-09-11

Behavior of ice crystals and human red blood cells during extracellular-freezing was investigated in three-dimensions using a confocal laser scanning microscope(CLSM), which noninvasively produces tomograms of biological materials. Physiological saline and physiological saline with 2.4 M glycerol were used for suspension. Various cooling rates for directional solidification were used for distinctive morphology of the ice crystals. Addition of acridine orange as a fluorescent dye into the cell suspension enabled ice crystal, cells and unfrozen solution to be distinguished by different colors. The results indicate that the microscopic structure is three-dimensional for flat, cellular, and dendritic solid-liquid interfaces and that a CLSM is very effective in studying three-dimensional structure during the freezing of cell suspensions.

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

Toward atomic-scale bright-field electron tomography for the study of fullerene-like nanostructures.

PubMed

Bar Sadan, Maya; Houben, Lothar; Wolf, Sharon G; Enyashin, Andrey; Seifert, Gotthard; Tenne, Reshef; Urban, Knut

2008-03-01

We present the advancement of electron tomography for three-dimensional structure reconstruction of fullerene-like particles toward atomic-scale resolution. The three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is achieved by the combination of low voltage operation of the electron microscope with aberration-corrected phase contrast imaging. The method enables the study of defects and irregularities in the three-dimensional structure of individual fullerene-like particles on the scale of 2-3 A. Control over shape, size, and atomic architecture is a key issue in synthesis and design of functional nanoparticles. Transmission electron microscopy (TEM) is the primary technique to characterize materials down to the atomic level, albeit the images are two-dimensional projections of the studied objects. Recent advancements in aberration-corrected TEM have demonstrated single atom sensitivity for light elements at subångström resolution. Yet, the resolution of tomographic schemes for three-dimensional structure reconstruction has not surpassed 1 nm3, preventing it from becoming a powerful tool for characterization in the physical sciences on the atomic scale. Here we demonstrate that negative spherical aberration imaging at low acceleration voltage enables tomography down to the atomic scale at reduced radiation damage. First experimental data on the three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is presented. The method is applicable to the analysis of the atomic architecture of a wide range of nanostructures where strong electron channeling is absent, in particular to carbon fullerenes and inorganic fullerenes.

Two- and three-dimensional ultrasound imaging to facilitate detection and targeting of taut bands in myofascial pain syndrome.

PubMed

Shankar, Hariharan; Reddy, Sapna

2012-07-01

Ultrasound imaging has gained acceptance in pain management interventions. Features of myofascial pain syndrome have been explored using ultrasound imaging and elastography. There is a paucity of reports showing the benefit clinically. This report provides three-dimensional features of taut bands and highlights the advantages of using two-dimensional ultrasound imaging to improve targeting of taut bands in deeper locations. Fifty-eight-year-old man with pain and decreased range of motion of the right shoulder was referred for further management of pain above the scapula after having failed conservative management for myofascial pain syndrome. Three-dimensional ultrasound images provided evidence of aberrancy in the architecture of the muscle fascicles around the taut bands compared to the adjacent normal muscle tissue during serial sectioning of the accrued image. On two-dimensional ultrasound imaging over the palpated taut band, areas of hyperechogenicity were visualized in the trapezius and supraspinatus muscles. Subsequently, the patient received ultrasound-guided real-time lidocaine injections to the trigger points with successful resolution of symptoms. This is a successful demonstration of utility of ultrasound imaging of taut bands in the management of myofascial pain syndrome. Utility of this imaging modality in myofascial pain syndrome requires further clinical validation. Wiley Periodicals, Inc.

Tonal Interface to MacroMolecules (TIMMol): A Textual and Tonal Tool for Molecular Visualization

ERIC Educational Resources Information Center

Cordes, Timothy J.; Carlson, C. Britt; Forest, Katrina T.

2008-01-01

We developed the three-dimensional visualization software, Tonal Interface to MacroMolecules or TIMMol, for studying atomic coordinates of protein structures. Key features include audio tones indicating x, y, z location, identification of the cursor location in one-dimensional and three-dimensional space, textual output that can be easily linked…

A model of tripeptidyl-peptidase I (CLN2), a ubiquitous and highly conserved member of the sedolisin family of serine-carboxyl peptidases

PubMed Central

Wlodawer, Alexander; Durell, Stewart R; Li, Mi; Oyama, Hiroshi; Oda, Kohei; Dunn, Ben M

2003-01-01

Background Tripeptidyl-peptidase I, also known as CLN2, is a member of the family of sedolisins (serine-carboxyl peptidases). In humans, defects in expression of this enzyme lead to a fatal neurodegenerative disease, classical late-infantile neuronal ceroid lipofuscinosis. Similar enzymes have been found in the genomic sequences of several species, but neither systematic analyses of their distribution nor modeling of their structures have been previously attempted. Results We have analyzed the presence of orthologs of human CLN2 in the genomic sequences of a number of eukaryotic species. Enzymes with sequences sharing over 80% identity have been found in the genomes of macaque, mouse, rat, dog, and cow. Closely related, although clearly distinct, enzymes are present in fish (fugu and zebra), as well as in frogs (Xenopus tropicalis). A three-dimensional model of human CLN2 was built based mainly on the homology with Pseudomonas sp. 101 sedolisin. Conclusion CLN2 is very highly conserved and widely distributed among higher organisms and may play an important role in their life cycles. The model presented here indicates a very open and accessible active site that is almost completely conserved among all known CLN2 enzymes. This result is somehow surprising for a tripeptidase where the presence of a more constrained binding pocket was anticipated. This structural model should be useful in the search for the physiological substrates of these enzymes and in the design of more specific inhibitors of CLN2. PMID:14609438

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…

Three-Dimensional Magnetic Resonance Imaging of Velopharyngeal Structures

ERIC Educational Resources Information Center

Bae, Youkyung; Kuehn, David P.; Sutton, Bradley P.; Conway, Charles A.; Perry, Jamie L.

2011-01-01

Purpose: To report the feasibility of using a 3-dimensional (3D) magnetic resonance imaging (MRI) protocol for examining velopharyngeal structures. Using collected 3D MRI data, the authors investigated the effect of sex on the midsagittal velopharyngeal structures and the levator veli palatini (levator) muscle configurations. Method: Ten Caucasian…

Unified field theory from the classical wave equation: Preliminary application to atomic and nuclear structure

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

Múnera, Héctor A., E-mail: hmunera@hotmail.com; Retired professor, Department of Physics, Universidad Nacional de Colombia, Bogotá, Colombia, South America

2016-07-07

It is postulated that there exists a fundamental energy-like fluid, which occupies the flat three-dimensional Euclidean space that contains our universe, and obeys the two basic laws of classical physics: conservation of linear momentum, and conservation of total energy; the fluid is described by the classical wave equation (CWE), which was Schrödinger’s first candidate to develop his quantum theory. Novel solutions for the CWE discovered twenty years ago are nonharmonic, inherently quantized, and universal in the sense of scale invariance, thus leading to quantization at all scales of the universe, from galactic clusters to the sub-quark world, and yielding amore » unified Lorentz-invariant quantum theory ab initio. Quingal solutions are isomorphic under both neo-Galilean and Lorentz transformations, and exhibit nother remarkable property: intrinsic unstability for large values of ℓ (a quantum number), thus limiting the size of each system at a given scale. Unstability and scale-invariance together lead to nested structures observed in our solar system; unstability may explain the small number of rows in the chemical periodic table, and nuclear unstability of nuclides beyond lead and bismuth. Quingal functions lend mathematical basis for Boscovich’s unified force (which is compatible with many pieces of evidence collected over the past century), and also yield a simple geometrical solution for the classical three-body problem, which is a useful model for electronic orbits in simple diatomic molecules. A testable prediction for the helicoidal-type force is suggested.« less

Development and test results of a flight management algorithm for fuel conservative descents in a time-based metered traffic environment

NASA Technical Reports Server (NTRS)

Knox, C. E.; Cannon, D. G.

1980-01-01

A simple flight management descent algorithm designed to improve the accuracy of delivering an airplane in a fuel-conservative manner to a metering fix at a time designated by air traffic control was developed and flight tested. This algorithm provides a three dimensional path with terminal area time constraints (four dimensional) for an airplane to make an idle thrust, clean configured (landing gear up, flaps zero, and speed brakes retracted) descent to arrive at the metering fix at a predetermined time, altitude, and airspeed. The descent path was calculated for a constant Mach/airspeed schedule from linear approximations of airplane performance with considerations given for gross weight, wind, and nonstandard pressure and temperature effects. The flight management descent algorithm is described. The results of the flight tests flown with the Terminal Configured Vehicle airplane are presented.

Analysis of high-rise constructions with the using of three-dimensional models of rods in the finite element program PRINS

NASA Astrophysics Data System (ADS)

Agapov, Vladimir

2018-03-01

The necessity of new approaches to the modeling of rods in the analysis of high-rise constructions is justified. The possibility of the application of the three-dimensional superelements of rods with rectangular cross section for the static and dynamic calculation of the bar and combined structures is considered. The results of the eighteen-story spatial frame free vibrations analysis using both one-dimensional and three-dimensional models of rods are presented. A comparative analysis of the obtained results is carried out and the conclusions on the possibility of three-dimensional superelements application in static and dynamic analysis of high-rise constructions are given on its basis.

The Factor Structure of Some Piagetian Tasks

ERIC Educational Resources Information Center

Lawson, Anton E.; Nordland, Floyd H.

1976-01-01

Investigated was the hypothesis that conservation tasks are unifactor by administering eight different conservation tasks to 96 seventh-grade science students and performing a principal component analysis on the data. Results indicated that conservation tasks may measure up to three different components of cognitive thought. (SL)

Sculpting Cells with Play Doh.

ERIC Educational Resources Information Center

Way, Virginia A.

1982-01-01

Suggests using Play Doh to mold models of the nucleus, mitochondria, and inner cellular structures. Students can conceptualize the cell's structures as three-dimensional even though they appear two-dimensional under a microscope. Includes instructions for preparing homemade dough. (Author/JN)

Research in Seismology

DTIC Science & Technology

1978-12-31

Koyanagi, Three-dimensional crust and mantle structure of Kilauea Volcano , Hawaii , J. Geophys. Res., 82, 5379-5394, 1977. Engdahl, E.R., J.G. Sindorf, and...Johnson, 1967), in Japan (Zandt, 1975; Hirahara, 1977), at NORSAR (Aki, 1977), in Yellowstone National Park (1yer, 1975; Zandt, 1978), in Hawaii ...1962. Ellsworth, W.L., Three-dimensional structure of the crust and mantle beneath the island of Hawaii , unpublished Ph.D. thesis, Massachusetts

Multi-symplectic integrators: numerical schemes for Hamiltonian PDEs that conserve symplecticity

NASA Astrophysics Data System (ADS)

Bridges, Thomas J.; Reich, Sebastian

2001-06-01

The symplectic numerical integration of finite-dimensional Hamiltonian systems is a well established subject and has led to a deeper understanding of existing methods as well as to the development of new very efficient and accurate schemes, e.g., for rigid body, constrained, and molecular dynamics. The numerical integration of infinite-dimensional Hamiltonian systems or Hamiltonian PDEs is much less explored. In this Letter, we suggest a new theoretical framework for generalizing symplectic numerical integrators for ODEs to Hamiltonian PDEs in R2: time plus one space dimension. The central idea is that symplecticity for Hamiltonian PDEs is directional: the symplectic structure of the PDE is decomposed into distinct components representing space and time independently. In this setting PDE integrators can be constructed by concatenating uni-directional ODE symplectic integrators. This suggests a natural definition of multi-symplectic integrator as a discretization that conserves a discrete version of the conservation of symplecticity for Hamiltonian PDEs. We show that this approach leads to a general framework for geometric numerical schemes for Hamiltonian PDEs, which have remarkable energy and momentum conservation properties. Generalizations, including development of higher-order methods, application to the Euler equations in fluid mechanics, application to perturbed systems, and extension to more than one space dimension are also discussed.

Synthesis, structure and photoluminescence properties of amine-templated open-framework bismuth sulfates

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

Marri, Subba R.; Behera, J.N., E-mail: jnbehera@niser.ac.in

2014-02-15

Two organically-templated bismuth sulfates of the compositions, [C{sub 6}N{sub 2}H{sub 14}] [Bi(SO{sub 4}){sub 2}(NO{sub 3})], (1) and [C{sub 4}N{sub 2}H{sub 12}]{sub 4}[Bi{sub 4}(SO{sub 4}){sub 10}(H{sub 2}O){sub 4}], (2), with open architecture have been synthesized and their structures determined by single crystal X-ray diffraction. 1 has a corrugated layered structure with 8-membered aperture wherein the SO{sub 4} tetrahedra and the BiO{sub 8} polyhedra join together to form (4, 4) net sheets of the metal centers while 2 has a three-dimensional structure possessing 8- and 12-membered channels. Both the compounds show good fluorescence properties exhibiting blue luminescence. Time-resolved fluorescence behavior of 1more » and 2 shows mean fluorescence life time of 0.9 and 1.0 ns, respectively. - Graphical abstract: Two open-framework bismuth sulfates with the layered and three-dimensional structures have been synthesized and characterized. Both the compounds show good fluorescence properties exhibiting blue luminescence. Display Omitted - Highlights: • Two organically-templated bismuth sulfates with open architecture have been synthesized and characterized. • One has a corrugated layered structure while the other one has a three-dimensional structure possessing channels. • They are novel in that open-framework three-dimensional main group metal sulfates are first to be reported. • They show good fluorescence properties exhibiting blue luminescence.« less

A plasma source driven predator-prey like mechanism as a potential cause of spiraling intermittencies in linear plasma devices

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

Reiser, D.; Ohno, N.; Tanaka, H.

2014-03-15

Three-dimensional global drift fluid simulations are carried out to analyze coherent plasma structures appearing in the NAGDIS-II linear device (nagoya divertor plasma Simulator-II). The numerical simulations reproduce several features of the intermittent spiraling structures observed, for instance, statistical properties, rotation frequency, and the frequency of plasma expulsion. The detailed inspection of the three-dimensional plasma dynamics allows to identify the key mechanism behind the formation of these intermittent events. The resistive coupling between electron pressure and parallel electric field in the plasma source region gives rise to a quasilinear predator-prey like dynamics where the axisymmetric mode represents the prey and themore » spiraling structure with low azimuthal mode number represents the predator. This interpretation is confirmed by a reduced one-dimensional quasilinear model derived on the basis of the findings in the full three-dimensional simulations. The dominant dynamics reveals certain similarities to the classical Lotka-Volterra cycle.« less

Aromatic carboxylate effect on dimensionality of three bis(benzimidazole)-based cobalt(II) coordination polymers: Syntheses, structures and properties

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

Zhang, Ju-Wen; Gong, Chun-Hua; Hou, Li-Li

2013-09-15

Three new metal-organic coordination polymers [Co(4-bbc){sub 2}(bbbm)] (1), [Co(3,5-pdc)(bbbm)]·2H{sub 2}O (2) and [Co(1,4-ndc)(bbbm)] (3) (4-Hbbc=4-bromobenzoic acid, 3,5-H{sub 2}pdc=3,5-pyridinedicarboxylic acid, 1,4-H{sub 2}ndc=1,4-naphthalenedicarboxylic acid and bbbm=1,1-(1,4-butanediyl)bis-1H-benzimidazole) were hydrothermally synthesized and structurally characterized. Polymer 1 is a 1D chain formed by the bbbm ligands and Co{sup II} ions. Polymer 2 exhibits a 2D network with a (3·4·5)(3{sup 2}·4·5·6{sup 2}·7{sup 4}) topology. Polymer 3 possesses a 3D three-fold interpenetrating framework. The versatile structures of title polymers indicate that the aromatic carboxylates have an important influence on the dimensionality of 1–3. Moreover, the thermal stability, electrochemical and luminescent properties of 1–3 were investigated. - graphicalmore » abstract: Three bis(benzimidazole)-based cobalt(II) coordination polymers tuned by aromatic carboxylates were hydrothermally synthesized and structurally characterized. The aromatic carboxylates play a key role in the dimensionality of three polymers. The electrochemical and luminescent properties of three polymers were investigated. Display Omitted - Highlights: • Three bis(benzimidazole)-based cobalt(II) coordination polymers tuned by aromatic carboxylates were obtained. • The aromatic carboxylates have an important influence on the dimensionality of three polymers. • The electrochemical and luminescent properties of three polymers were investigated.« less

Combined sequence and structure analysis of the fungal laccase family.

PubMed

Kumar, S V Suresh; Phale, Prashant S; Durani, S; Wangikar, Pramod P

2003-08-20

Plant and fungal laccases belong to the family of multi-copper oxidases and show much broader substrate specificity than other members of the family. Laccases have consequently been of interest for potential industrial applications. We have analyzed the essential sequence features of fungal laccases based on multiple sequence alignments of more than 100 laccases. This has resulted in identification of a set of four ungapped sequence regions, L1-L4, as the overall signature sequences that can be used to identify the laccases, distinguishing them within the broader class of multi-copper oxidases. The 12 amino acid residues in the enzymes serving as the copper ligands are housed within these four identified conserved regions, of which L2 and L4 conform to the earlier reported copper signature sequences of multi-copper oxidases while L1 and L3 are distinctive to the laccases. The mapping of regions L1-L4 on to the three-dimensional structure of the Coprinus cinerius laccase indicates that many of the non-copper-ligating residues of the conserved regions could be critical in maintaining a specific, more or less C-2 symmetric, protein conformational motif characterizing the active site apparatus of the enzymes. The observed intraprotein homologies between L1 and L3 and between L2 and L4 at both the structure and the sequence levels suggest that the quasi C-2 symmetric active site conformational motif may have arisen from a structural duplication event that neither the sequence homology analysis nor the structure homology analysis alone would have unraveled. Although the sequence and structure homology is not detectable in the rest of the protein, the relative orientation of region L1 with L2 is similar to that of L3 with L4. The structure duplication of first-shell and second-shell residues has become cryptic because the intraprotein sequence homology noticeable for a given laccase becomes significant only after comparing the conservation pattern in several fungal laccases. The identified motifs, L1-L4, can be useful in searching the newly sequenced genomes for putative laccase enzymes. Copyright 2003 Wiley Periodicals, Inc. Biotechnol Bioeng 83: 386-394, 2003.

X-Ray Crystallography as a Tool to Determine Three-Dimensional Structures of Commercial Enzymes Subjected to Treatment in Pressurized Fluids.

PubMed

Feiten, Mirian Cristina; Di Luccio, Marco; Santos, Karine F; de Oliveira, Débora; Oliveira, J Vladimir

2017-06-01

The study of enzyme function often involves a multi-disciplinary approach. Several techniques are documented in the literature towards determining secondary and tertiary structures of enzymes, and X-ray crystallography is the most explored technique for obtaining three-dimensional structures of proteins. Knowledge of three-dimensional structures is essential to understand reaction mechanisms at the atomic level. Additionally, structures can be used to modulate or improve functional activity of enzymes by the production of small molecules that act as substrates/cofactors or by engineering selected mutants with enhanced biological activity. This paper presentes a short overview on how to streamline sample preparation for crystallographic studies of treated enzymes. We additionally revise recent developments on the effects of pressurized fluid treatment on activity and stability of commercial enzymes. Future directions and perspectives on the the role of crystallography as a tool to access the molecular mechanisms underlying enzymatic activity modulation upon treatment in pressurized fluids are also addressed.

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

Laboratory-size three-dimensional water-window x-ray microscope with Wolter type I mirror optics

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

Ohsuka, Shinji; The Graduate School for the Creation of New Photonics Industries, 1955-1 Kurematsu-cho, Nishi-ku, Hamamatsu-City, 431-1202; Ohba, Akira

2016-01-28

We constructed a laboratory-size three-dimensional water-window x-ray microscope that combines wide-field transmission x-ray microscopy with tomographic reconstruction techniques. It consists of an electron-impact x-ray source emitting oxygen Kα x-rays, Wolter type I grazing incidence mirror optics, and a back-illuminated CCD for x-ray imaging. A spatial resolution limit better than 1.0 line pairs per micrometer was obtained for two-dimensional transmission images, and 1-μm-scale three-dimensional fine structures were resolved.

Self-assembly of three-dimensional open structures using patchy colloidal particles.

PubMed

Rocklin, D Zeb; Mao, Xiaoming

2014-10-14

Open structures can display a number of unusual properties, including a negative Poisson's ratio, negative thermal expansion, and holographic elasticity, and have many interesting applications in engineering. However, it is a grand challenge to self-assemble open structures at the colloidal scale, where short-range interactions and low coordination number can leave them mechanically unstable. In this paper we discuss the self-assembly of three-dimensional open structures using triblock Janus particles, which have two large attractive patches that can form multiple bonds, separated by a band with purely hard-sphere repulsion. Such surface patterning leads to open structures that are stabilized by orientational entropy (in an order-by-disorder effect) and selected over close-packed structures by vibrational entropy. For different patch sizes the particles can form into either tetrahedral or octahedral structural motifs which then compose open lattices, including the pyrochlore, the hexagonal tetrastack and the perovskite lattices. Using an analytic theory, we examine the phase diagrams of these possible open and close-packed structures for triblock Janus particles and characterize the mechanical properties of these structures. Our theory leads to rational designs of particles for the self-assembly of three-dimensional colloidal structures that are possible using current experimental techniques.

An Implicit Characteristic Based Method for Electromagnetics

NASA Technical Reports Server (NTRS)

Beggs, John H.; Briley, W. Roger

2001-01-01

An implicit characteristic-based approach for numerical solution of Maxwell's time-dependent curl equations in flux conservative form is introduced. This method combines a characteristic based finite difference spatial approximation with an implicit lower-upper approximate factorization (LU/AF) time integration scheme. This approach is advantageous for three-dimensional applications because the characteristic differencing enables a two-factor approximate factorization that retains its unconditional stability in three space dimensions, and it does not require solution of tridiagonal systems. Results are given both for a Fourier analysis of stability, damping and dispersion properties, and for one-dimensional model problems involving propagation and scattering for free space and dielectric materials using both uniform and nonuniform grids. The explicit Finite Difference Time Domain Method (FDTD) algorithm is used as a convenient reference algorithm for comparison. The one-dimensional results indicate that for low frequency problems on a highly resolved uniform or nonuniform grid, this LU/AF algorithm can produce accurate solutions at Courant numbers significantly greater than one, with a corresponding improvement in efficiency for simulating a given period of time. This approach appears promising for development of dispersion optimized LU/AF schemes for three dimensional applications.

Three-dimensional magnetophotonic crystals based on artificial opals

NASA Astrophysics Data System (ADS)

Baryshev, A. V.; Kodama, T.; Nishimura, K.; Uchida, H.; Inoue, M.

2004-06-01

We fabricated and experimentally investigated three-dimensional magnetophotonic crystals (3D MPCs) based on artificial opals. Opal samples with three-dimensional dielectric lattices were impregnated with different types of magnetic material. Magnetic and structural properties of 3D MPCs were studied by field emission scanning electron microscopy, x-ray diffraction analysis, and vibrating sample magnetometer. We have shown that magnetic materials synthesized in voids of opal lattices and the composites obtained have typical magnetic properties.

Flow transition with 2-D roughness elements in a 3-D channel

NASA Technical Reports Server (NTRS)

Liu, Zhining; Liu, Chaoquin; Mccormick, Stephen F.

1993-01-01

We develop a new numerical approach to study the spatially evolving instability of the streamwise dominant flow in the presence of roughness elements. The difficulty in handling the flow over the boundary surface with general geometry is removed by using a new conservative form of the governing equations and an analytical mapping. The numerical scheme uses second-order backward Euler in time, fourth-order central differences in all three spatial directions, and boundary-fitted staggered grids. A three-dimensional channel with multiple two-dimensional-type roughness elements is employed as the test case. Fourier analysis is used to decompose different Fourier modes of the disturbance. The results show that surface roughness leads to transition at lower Reynolds number than for smooth channels.

Three-dimensional analysis of tokamaks and stellarators

PubMed Central

Garabedian, Paul R.

2008-01-01

The NSTAB equilibrium and stability code and the TRAN Monte Carlo transport code furnish a simple but effective numerical simulation of essential features of present tokamak and stellarator experiments. When the mesh size is comparable to the island width, an accurate radial difference scheme in conservation form captures magnetic islands successfully despite a nested surface hypothesis imposed by the mathematics. Three-dimensional asymmetries in bifurcated numerical solutions of the axially symmetric tokamak problem are relevant to the observation of unstable neoclassical tearing modes and edge localized modes in experiments. Islands in compact stellarators with quasiaxial symmetry are easier to control, so these configurations will become good candidates for magnetic fusion if difficulties with safety and stability are encountered in the International Thermonuclear Experimental Reactor (ITER) project. PMID:18768807

Manipulation of fluids in three-dimensional porous photonic structures with patterned surface properties

DOEpatents

Aizenberg, Joanna; Burgess, Ian B.; Mishchenko, Lidiya; Hatton, Benjamin; Loncar, Marko

2016-03-08

A three-dimensional porous photonic structure, whose internal pore surfaces can be provided with desired surface properties in a spatially selective manner with arbitrary patterns, and methods for making the same are described. When exposed to a fluid (e.g., via immersion or wicking), the fluid can selectively penetrate the regions of the structure with compatible surface properties. Broad applications, for example in security, encryption and document authentication, as well as in areas such as simple microfluidics and diagnostics, are anticipated.

An Essential Protein Repair Enzyme: Investigation of the Molecular Recognition Mechanism of Methionine Sulfoxide Reductase A

DTIC Science & Technology

2008-05-01

4 ). The three-dimensional spatial orientation of the atoms for these resolved solution structures (Protein Data Bank accession codes: 2gt3...Crystal structure of the Escherichia coli peptide methionine sulphoxide reductase at 1.9 Å resolution . Struct. Fold. Des. 8: 1167 – 1178. 2 . Brot...sources (8). There is a 67% sequence identity between the E.coli and human MsrA ( 2 ). N-terminus C-terminus Figure 2 . Three-dimensional structure

Manipulation of fluids in three-dimensional porous photonic structures with patterned surface properties

DOEpatents

Aizenberg, Joanna; Burgess, Ian; Mishchenko, Lidiya; Hatton, Benjamin; Loncar, Marko

2017-12-26

A three-dimensional porous photonic structure, whose internal pore surfaces can be provided with desired surface properties in a spatially selective manner with arbitrary patterns, and methods for making the same are described. When exposed to a fluid (e.g., via immersion or wicking), the fluid can selectively penetrate the regions of the structure with compatible surface properties. Broad applications, for example in security, encryption and document authentication, as well as in areas such as simple microfluidics and diagnostics, are anticipated.

A Semi-Implicit, Three-Dimensional Model for Estuarine Circulation

USGS Publications Warehouse

Smith, Peter E.

2006-01-01

A semi-implicit, finite-difference method for the numerical solution of the three-dimensional equations for circulation in estuaries is presented and tested. The method uses a three-time-level, leapfrog-trapezoidal scheme that is essentially second-order accurate in the spatial and temporal numerical approximations. The three-time-level scheme is shown to be preferred over a two-time-level scheme, especially for problems with strong nonlinearities. The stability of the semi-implicit scheme is free from any time-step limitation related to the terms describing vertical diffusion and the propagation of the surface gravity waves. The scheme does not rely on any form of vertical/horizontal mode-splitting to treat the vertical diffusion implicitly. At each time step, the numerical method uses a double-sweep method to transform a large number of small tridiagonal equation systems and then uses the preconditioned conjugate-gradient method to solve a single, large, five-diagonal equation system for the water surface elevation. The governing equations for the multi-level scheme are prepared in a conservative form by integrating them over the height of each horizontal layer. The layer-integrated volumetric transports replace velocities as the dependent variables so that the depth-integrated continuity equation that is used in the solution for the water surface elevation is linear. Volumetric transports are computed explicitly from the momentum equations. The resulting method is mass conservative, efficient, and numerically accurate.

Structure and Function of the N-Terminal Domain of the Vesicular Stomatitis Virus RNA Polymerase

PubMed Central

Qiu, Shihong; Ogino, Minako; Luo, Ming

2015-01-01

ABSTRACT Viruses have various mechanisms to duplicate their genomes and produce virus-specific mRNAs. Negative-strand RNA viruses encode their own polymerases to perform each of these processes. For the nonsegmented negative-strand RNA viruses, the polymerase is comprised of the large polymerase subunit (L) and the phosphoprotein (P). L proteins from members of the Rhabdoviridae, Paramyxoviridae, and Filoviridae share sequence and predicted secondary structure homology. Here, we present the structure of the N-terminal domain (conserved region I) of the L protein from a rhabdovirus, vesicular stomatitis virus, at 1.8-Å resolution. The strictly and strongly conserved residues in this domain cluster in a single area of the protein. Serial mutation of these residues shows that many of the amino acids are essential for viral transcription but not for mRNA capping. Three-dimensional alignments show that this domain shares structural homology with polymerases from other viral families, including segmented negative-strand RNA and double-stranded RNA (dsRNA) viruses. IMPORTANCE Negative-strand RNA viruses include a diverse set of viral families that infect animals and plants, causing serious illness and economic impact. The members of this group of viruses share a set of functionally conserved proteins that are essential to their replication cycle. Among this set of proteins is the viral polymerase, which performs a unique set of reactions to produce genome- and subgenome-length RNA transcripts. In this article, we study the polymerase of vesicular stomatitis virus, a member of the rhabdoviruses, which has served in the past as a model to study negative-strand RNA virus replication. We have identified a site in the N-terminal domain of the polymerase that is essential to viral transcription and that shares sequence homology with members of the paramyxoviruses and the filoviruses. Newly identified sites such as that described here could prove to be useful targets in the design of new therapeutics against negative-strand RNA viruses. PMID:26512087

DDRprot: a database of DNA damage response-related proteins.

PubMed

Andrés-León, Eduardo; Cases, Ildefonso; Arcas, Aida; Rojas, Ana M

2016-01-01

The DNA Damage Response (DDR) signalling network is an essential system that protects the genome's integrity. The DDRprot database presented here is a resource that integrates manually curated information on the human DDR network and its sub-pathways. For each particular DDR protein, we present detailed information about its function. If involved in post-translational modifications (PTMs) with each other, we depict the position of the modified residue/s in the three-dimensional structures, when resolved structures are available for the proteins. All this information is linked to the original publication from where it was obtained. Phylogenetic information is also shown, including time of emergence and conservation across 47 selected species, family trees and sequence alignments of homologues. The DDRprot database can be queried by different criteria: pathways, species, evolutionary age or involvement in (PTM). Sequence searches using hidden Markov models can be also used.Database URL: http://ddr.cbbio.es. © The Author(s) 2016. Published by Oxford University Press.

Fabrication of dielectric elastomer stack transducers (DEST) by liquid deposition modeling

NASA Astrophysics Data System (ADS)

Klug, Florian; Solano-Arana, Susana; Mößinger, Holger; Förster-Zügel, Florentine; Schlaak, Helmut F.

2017-04-01

Established fabrication methods for dielectric elastomer stack transducers (DEST) are mostly based on twodimensional thin-film technology. Because of this, DEST are based on simple two-dimensionally structured shapes. For certain applications, like valves or Braille displays, these structures are suited well enough. However, a more flexible fabrication method allows for more complex actuator designs, which would otherwise require extra processing steps. Fabrication methods with the possibility of three-dimensional structuring allow e.g. the integration of electrical connections, cavities, channels, sensor and other structural elements during the fabrication. This opens up new applications, as well as the opportunity for faster prototype production of individually designed DEST for a given application. In this work, a manufacturing system allowing three dimensional structuring is described. It enables the production of multilayer and three-dimensional structured DEST by liquid deposition modelling. The system is based on a custom made dual extruder, connected to a commercial threeaxis positioning system. It allows a computer controlled liquid deposition of two materials. After tuning the manufacturing parameters the production of thin layers with at thickness of less than 50 μm, as well as stacking electrode and dielectric materials is feasible. With this setup a first DEST with dielectric layer thickness less than 50 μm is build successfully and its performance is evaluated.

Use of an airborne lidar system to model plant species composition and diversity of Mediterranean oak forests.

PubMed

Simonson, William D; Allen, Harriet D; Coomes, David A

2012-10-01

Airborne lidar is a remote-sensing tool of increasing importance in ecological and conservation research due to its ability to characterize three-dimensional vegetation structure. If different aspects of plant species diversity and composition can be related to vegetation structure, landscape-level assessments of plant communities may be possible. We examined this possibility for Mediterranean oak forests in southern Portugal, which are rich in biological diversity but also threatened. We compared data from a discrete, first-and-last return lidar data set collected for 31 plots of cork oak (Quercus suber) and Algerian oak (Quercus canariensis) forest with field data to test whether lidar can be used to predict the vertical structure of vegetation, diversity of plant species, and community type. Lidar- and field-measured structural data were significantly correlated (up to r= 0.85). Diversity of forest species was significantly associated with lidar-measured vegetation height (R(2) = 0.50, p < 0.001). Clustering and ordination of the species data pointed to the presence of 2 main forest classes that could be discriminated with an accuracy of 89% on the basis of lidar data. Lidar can be applied widely for mapping of habitat and assessments of habitat condition (e.g., in support of the European Species and Habitats Directive [92/43/EEC]). However, particular attention needs to be paid to issues of survey design: density of lidar points and geospatial accuracy of ground-truthing and its timing relative to acquisition of lidar data. ©2012 Society for Conservation Biology.

Non-3D domain swapped crystal structure of truncated zebrafish alphaA crystallin

PubMed Central

Laganowsky, A; Eisenberg, D

2010-01-01

In previous work on truncated alpha crystallins (Laganowsky et al., Protein Sci 2010; 19:1031–1043), we determined crystal structures of the alpha crystallin core, a seven beta-stranded immunoglobulin-like domain, with its conserved C-terminal extension. These extensions swap into neighboring cores forming oligomeric assemblies. The extension is palindromic in sequence, binding in either of two directions. Here, we report the crystal structure of a truncated alphaA crystallin (AAC) from zebrafish (Danio rerio) revealing C-terminal extensions in a non three-dimensional (3D) domain swapped, “closed” state. The extension is quasi-palindromic, bound within its own zebrafish core domain, lying in the opposite direction to that of bovine AAC, which is bound within an adjacent core domain (Laganowsky et al., Protein Sci 2010; 19:1031–1043). Our findings establish that the C-terminal extension of alpha crystallin proteins can be either 3D domain swapped or non-3D domain swapped. This duality provides another molecular mechanism for alpha crystallin proteins to maintain the polydispersity that is crucial for eye lens transparency. PMID:20669149

ORF157 from the Archaeal Virus Acidianus Filamentous Virus 1 Defines a New Class of Nuclease▿

PubMed Central

Goulet, Adeline; Pina, Mery; Redder, Peter; Prangishvili, David; Vera, Laura; Lichière, Julie; Leulliot, Nicolas; van Tilbeurgh, Herman; Ortiz-Lombardia, Miguel; Campanacci, Valérie; Cambillau, Christian

2010-01-01

Acidianus filamentous virus 1 (AFV1) (Lipothrixviridae) is an enveloped filamentous virus that was characterized from a crenarchaeal host. It infects Acidianus species that thrive in the acidic hot springs (>85°C and pH <3) of Yellowstone National Park, WY. The AFV1 20.8-kb, linear, double-stranded DNA genome encodes 40 putative open reading frames whose sequences generally show little similarity to other genes in the sequence databases. Because three-dimensional structures are more conserved than sequences and hence are more effective at revealing function, we set out to determine protein structures from putative AFV1 open reading frames (ORF). The crystal structure of ORF157 reveals an α+β protein with a novel fold that remotely resembles the nucleotidyltransferase topology. In vitro, AFV1-157 displays a nuclease activity on linear double-stranded DNA. Alanine substitution mutations demonstrated that E86 is essential to catalysis. AFV1-157 represents a novel class of nuclease, but its exact role in vivo remains to be determined. PMID:20200253

Life Origination Hydrate Theory (LOH-Theory) and Mitosis and Replication Hydrate Theory (MRH-Theory): three-dimensional PC validation

NASA Astrophysics Data System (ADS)

Kadyshevich, E. A.; Dzyabchenko, A. V.; Ostrovskii, V. E.

2014-04-01

Size compatibility of the CH4-hydrate structure II and multi-component DNA fragments is confirmed by three-dimensional simulation; it is validation of the Life Origination Hydrate Theory (LOH-Theory).

Three dimensional fabrication at small size scales

PubMed Central

Leong, Timothy G.; Zarafshar, Aasiyeh M.; Gracias, David H.

2010-01-01

Despite the fact that we live in a three-dimensional (3D) world and macroscale engineering is 3D, conventional sub-mm scale engineering is inherently two-dimensional (2D). New fabrication and patterning strategies are needed to enable truly three-dimensionally-engineered structures at small size scales. Here, we review strategies that have been developed over the last two decades that seek to enable such millimeter to nanoscale 3D fabrication and patterning. A focus of this review is the strategy of self-assembly, specifically in a biologically inspired, more deterministic form known as self-folding. Self-folding methods can leverage the strengths of lithography to enable the construction of precisely patterned 3D structures and “smart” components. This self-assembling approach is compared with other 3D fabrication paradigms, and its advantages and disadvantages are discussed. PMID:20349446

Three dimensional canonical singularity and five dimensional N = 1 SCFT

NASA Astrophysics Data System (ADS)

Xie, Dan; Yau, Shing-Tung

2017-06-01

We conjecture that every three dimensional canonical singularity defines a five dimensional N = 1 SCFT. Flavor symmetry can be found from singularity structure: non-abelian flavor symmetry is read from the singularity type over one dimensional singular locus. The dimension of Coulomb branch is given by the number of compact crepant divisors from a crepant resolution of singularity. The detailed structure of Coulomb branch is described as follows: a) a chamber of Coulomb branch is described by a crepant resolution, and this chamber is given by its Nef cone and the prepotential is computed from triple intersection numbers; b) Crepant resolution is not unique and different resolutions are related by flops; Nef cones from crepant resolutions form a fan which is claimed to be the full Coulomb branch.

Three-dimensional vortex wake structure of flapping wings in hovering flight.

PubMed

Cheng, Bo; Roll, Jesse; Liu, Yun; Troolin, Daniel R; Deng, Xinyan

2014-02-06

Flapping wings continuously create and send vortices into their wake, while imparting downward momentum into the surrounding fluid. However, experimental studies concerning the details of the three-dimensional vorticity distribution and evolution in the far wake are limited. In this study, the three-dimensional vortex wake structure in both the near and far field of a dynamically scaled flapping wing was investigated experimentally, using volumetric three-component velocimetry. A single wing, with shape and kinematics similar to those of a fruitfly, was examined. The overall result of the wing action is to create an integrated vortex structure consisting of a tip vortex (TV), trailing-edge shear layer (TESL) and leading-edge vortex. The TESL rolls up into a root vortex (RV) as it is shed from the wing, and together with the TV, contracts radially and stretches tangentially in the downstream wake. The downwash is distributed in an arc-shaped region enclosed by the stretched tangential vorticity of the TVs and the RVs. A closed vortex ring structure is not observed in the current study owing to the lack of well-established starting and stopping vortex structures that smoothly connect the TV and RV. An evaluation of the vorticity transport equation shows that both the TV and the RV undergo vortex stretching while convecting downwards: a three-dimensional phenomenon in rotating flows. It also confirms that convection and secondary tilting and stretching effects dominate the evolution of vorticity.

Dual wing, swept forward swept rearward wing, and single wing design optimization for high performance business airplanes

NASA Technical Reports Server (NTRS)

Rhodes, M. D.; Selberg, B. P.

1982-01-01

An investigation was performed to compare closely coupled dual wing and swept forward swept rearward wing aircraft to corresponding single wing 'baseline' designs to judge the advantages offered by aircraft designed with multiple wing systems. The optimum multiple wing geometry used on the multiple wing designs was determined in an analytic study which investigated the two- and three-dimensional aerodynamic behavior of a wide range of multiple wing configurations in order to find the wing geometry that created the minimum cruise drag. This analysis used a multi-element inviscid vortex panel program coupled to a momentum integral boundary layer analysis program to account for the aerodynamic coupling between the wings and to provide the two-dimensional aerodynamic data, which was then used as input for a three-dimensional vortex lattice program, which calculated the three-dimensional aerodynamic data. The low drag of the multiple wing configurations is due to a combination of two dimensional drag reductions, tailoring the three dimensional drag for the swept forward swept rearward design, and the structural advantages of the two wings that because of the structural connections permitted higher aspect ratios.

Decoupling Principle Analysis and Development of a Parallel Three-Dimensional Force Sensor

PubMed Central

Zhao, Yanzhi; Jiao, Leihao; Weng, Dacheng; Zhang, Dan; Zheng, Rencheng

2016-01-01

In the development of the multi-dimensional force sensor, dimension coupling is the ubiquitous factor restricting the improvement of the measurement accuracy. To effectively reduce the influence of dimension coupling on the parallel multi-dimensional force sensor, a novel parallel three-dimensional force sensor is proposed using a mechanical decoupling principle, and the influence of the friction on dimension coupling is effectively reduced by making the friction rolling instead of sliding friction. In this paper, the mathematical model is established by combining with the structure model of the parallel three-dimensional force sensor, and the modeling and analysis of mechanical decoupling are carried out. The coupling degree (ε) of the designed sensor is defined and calculated, and the calculation results show that the mechanical decoupling parallel structure of the sensor possesses good decoupling performance. A prototype of the parallel three-dimensional force sensor was developed, and FEM analysis was carried out. The load calibration and data acquisition experiment system are built, and then calibration experiments were done. According to the calibration experiments, the measurement accuracy is less than 2.86% and the coupling accuracy is less than 3.02%. The experimental results show that the sensor system possesses high measuring accuracy, which provides a basis for the applied research of the parallel multi-dimensional force sensor. PMID:27649194

Technique of semiautomatic surface reconstruction of the visible Korean human data using commercial software.

PubMed

Park, Jin Seo; Shin, Dong Sun; Chung, Min Suk; Hwang, Sung Bae; Chung, Jinoh

2007-11-01

This article describes the technique of semiautomatic surface reconstruction of anatomic structures using widely available commercial software. This technique would enable researchers to promptly and objectively perform surface reconstruction, creating three-dimensional anatomic images without any assistance from computer engineers. To develop the technique, we used data from the Visible Korean Human project, which produced digitalized photographic serial images of an entire cadaver. We selected 114 anatomic structures (skin [1], bones [32], knee joint structures [7], muscles [60], arteries [7], and nerves [7]) from the 976 anatomic images which were generated from the left lower limb of the cadaver. Using Adobe Photoshop, the selected anatomic structures in each serial image were outlined, creating a segmented image. The Photoshop files were then converted into Adobe Illustrator files to prepare isolated segmented images, so that the contours of the structure could be viewed independent of the surrounding anatomy. Using Alias Maya, these isolated segmented images were then stacked to construct a contour image. Gaps between the contour lines were filled with surfaces, and three-dimensional surface reconstruction could be visualized with Rhinoceros. Surface imperfections were then corrected to complete the three-dimensional images in Alias Maya. We believe that the three-dimensional anatomic images created by these methods will have widespread application in both medical education and research. 2007 Wiley-Liss, Inc

Functions of the 3′ and 5′ genome RNA regions of members of the genus Flavivirus

PubMed Central

Brinton, Margo A.; Basu, Mausumi

2015-01-01

The positive sense genomes of members of the genus Flavivirus in the family Flaviviridae are ~11 kb nts in length and have a 5′ type I cap but no 3′ poly A. The 5′ and 3′ terminal regions contain short conserved sequences that are proposed to be repeated remnants of an ancient sequence. However, the functions of most of these conserved sequences have not yet been determined. The terminal regions of the genome also contain multiple conserved RNA structures. Functional data for many of these structures has been obtained. Three sets of complementary 3′ and 5′ terminal region sequences, some of which are located in conserved RNA structures, interact to form a panhandle structure that is required for initiation of minus strand RNA synthesis with the 5′ terminal structure functioning as the promoter. How the switch from the terminal RNA structure base pairing to the long distance RNA-RNA interaction is triggered and regulated is not well understood but evidence suggests involvement of a cell protein binding to three sites on the 3′ terminal RNA structures and a cis-acting metastable 3′ RNA element in the 3′ terminal structure. Cell proteins may also be involved in facilitating exponential replication of nascent genomic RNA within replication vesicles at later times of infection cycle. Other conserved RNA structures and/or sequences in the 5′ and 3′ terminal regions have been proposed to regulate genome translation. Additional functions of the 5′ and 3′ terminal sequences have also been reported. PMID:25683510

Mining protein loops using a structural alphabet and statistical exceptionality

PubMed Central

2010-01-01

Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 Å). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. Conclusions We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/. PMID:20132552

Mining protein loops using a structural alphabet and statistical exceptionality.

PubMed

Regad, Leslie; Martin, Juliette; Nuel, Gregory; Camproux, Anne-Claude

2010-02-04

Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times). Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words). These structural words have low structural variability (mean RMSd of 0.85 A). As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues) and long loops. Moreover, half of recurrent motifs exhibit a significant level of amino-acid conservation with at least four significant positions and 87% of long loops contain at least one such word. We complement our analysis with the detection of statistically over-represented patterns of structural letters as in conventional DNA sequence analysis. About 30% (930) of structural words are over-represented, and cover about 40% of loop lengths. Interestingly, these words exhibit lower structural variability and higher sequential specificity, suggesting structural or functional constraints. We developed a method to systematically decompose and study protein loops using recurrent structural motifs. This method is based on the structural alphabet HMM-SA and not on structural alignment and geometrical parameters. We extracted meaningful structural motifs that are found in both short and long loops. To our knowledge, it is the first time that pattern mining helps to increase the signal-to-noise ratio in protein loops. This finding helps to better describe protein loops and might permit to decrease the complexity of long-loop analysis. Detailed results are available at http://www.mti.univ-paris-diderot.fr/publication/supplementary/2009/ACCLoop/.

[The estimation method of compounds opiate activity based on universal three-dimensional model of the nonselective opiate pharmacophore].

PubMed

Kuz'mina, N E; Iashkir, V A; Merkulov, V A; Osipova, E S

2012-01-01

Created by means alternative strategy of structural similarity search universal three-dimensional model of the nonselective opiate pharmacophore and the estimation method of agonistic and antagonistic properties of opiate receptors ligands based on its were described. The examples of the present method use are given for opiate activity estimation of compounds essentially distinguished on the structure from opiates and traditional opioids.

Temporal focusing microscopy combined with three-dimensional structured illumination

NASA Astrophysics Data System (ADS)

Isobe, Keisuke; Toda, Keisuke; Song, Qiyuan; Kannari, Fumihiko; Kawano, Hiroyuki; Miyawaki, Atsushi; Midorikawa, Katsumi

2017-05-01

Temporal focusing microscopy provides the optical sectioning capability in wide-field two-photon fluorescence imaging. Here, we demonstrate temporal focusing microscopy combined with three-dimensional structured illumination, which enables us to enhance the three-dimensional spatial resolution and reject the background fluorescence. Experimentally, the periodic pattern of the illumination was produced not only in the lateral direction but also in the axial direction by the interference between three temporal focusing pulses, which were easily generated using a digital micromirror device. The lateral resolution and optical sectioning capability were successfully enhanced by factors of 1.6 and 3.6, respectively, compared with those of temporal focusing microscopy. In the two-photon fluorescence imaging of a tissue-like phantom, the out-of-focus background fluorescence and the scattered background fluorescence could also be rejected.

Optimum Particle Size for Gold-Catalyzed CO Oxidation

PubMed Central

2018-01-01

The structure sensitivity of gold-catalyzed CO oxidation is presented by analyzing in detail the dependence of CO oxidation rate on particle size. Clusters with less than 14 gold atoms adopt a planar structure, whereas larger ones adopt a three-dimensional structure. The CO and O2 adsorption properties depend strongly on particle structure and size. All of the reaction barriers relevant to CO oxidation display linear scaling relationships with CO and O2 binding strengths as main reactivity descriptors. Planar and three-dimensional gold clusters exhibit different linear scaling relationship due to different surface topologies and different coordination numbers of the surface atoms. On the basis of these linear scaling relationships, first-principles microkinetics simulations were conducted to determine CO oxidation rates and possible rate-determining step of Au particles. Planar Au9 and three-dimensional Au79 clusters present the highest CO oxidation rates for planar and three-dimensional clusters, respectively. The planar Au9 cluster is much more active than the optimum Au79 cluster. A common feature of optimum CO oxidation performance is the intermediate binding strengths of CO and O2, resulting in intermediate coverages of CO, O2, and O. Both these optimum particles present lower performance than maximum Sabatier performance, indicating that there is sufficient room for improvement of gold catalysts for CO oxidation. PMID:29707098

Real-time Three-dimensional Echocardiography: From Diagnosis to Intervention.

PubMed

Orvalho, João S

2017-09-01

Echocardiography is one of the most important diagnostic tools in veterinary cardiology, and one of the greatest recent developments is real-time three-dimensional imaging. Real-time three-dimensional echocardiography is a new ultrasonography modality that provides comprehensive views of the cardiac valves and congenital heart defects. The main advantages of this technique, particularly real-time three-dimensional transesophageal echocardiography, are the ability to visualize the catheters, and balloons or other devices, and the ability to image the structure that is undergoing intervention with unprecedented quality. This technique may become one of the main choices for the guidance of interventional cardiology procedures. Copyright © 2017 Elsevier Inc. All rights reserved.

Three Dimensional Modeling of the Attenuation Structure in the Part of the Kumaon Himalaya, India Using Strong Motion Data

NASA Astrophysics Data System (ADS)

Joshi, A.; LAL, S.

2017-12-01

Attenuation property of the medium determines the amplitude of seismic waves at different locations during an earthquake. Attenuation can be defined by the inverse of the parameter known as quality factor `Q' (Knopoff, 1964). It has been observed that the peak ground acceleration in the strong motion accelerogram is associated with arrival of S-waves which is controlled mainly by the shear wave attenuation characteristics of the medium. In the present work attenuation structure is obtained using the modified inversion algorithm given by Joshi et al. (2010). The modified inversion algorithm is designed to provide three dimensional attenuation structure of the region at different frequencies. A strong motion network is installed in the Kumaon Himalaya by the Department of Earth Sciences, Indian Institute of Technology Roorkee under a major research project sponsored by the Ministry of Earth Sciences, Government of India. In this work the detailed three dimensional shear wave quality factor has been determined for the Kumaon Himalaya using strong motion data obtained from this network. In the present work 164 records from 26 events recorded at 15 stations located in an area of 129 km x 62 km has been used. The shear wave attenuation structure for the Kumaon Himalaya has been calculated by dividing the study region into 108 three dimensional rectangular blocks of size 22 km x 11 km x 5 km. The input to the inversion algorithm is the acceleration spectra of S wave identified from each record. A total of 164 spectra from equal number of accelerograms with sampling frequency of .024 Hz is used as an input to the algorithms. A total of 2048 three dimensional attenuation structure is obtained upto frequency of 50 Hz. The obtained structure at various frequencies is compared with the existing geological models in the region and it is seen that the obtained model correlated well with the geological model of the region. References: Joshi, A., Mohanty, M., Bansal, A. R., Dimri, V. P. and Chadha, R. K., 2010, Use of spectral acceleration data for determination of three dimensional attenuation structure in the Pithoragarh region of Kumaon Himalaya, J Seismol., 14, 247-272. Knopoff, L., 1964, Q, Reviews of Geophysics, 2, 625-660.

Application of MSCTA combined with VRT in the operation of cervical dumbbell tumors

PubMed Central

Wang, Wan; Lin, Jia; Knosp, Engelbert; Zhao, Yuanzheng; Xiu, Dianhui; Guo, Yongchuan

2015-01-01

Cervical dumbbell tumor poses great difficulties for neurosurgical treatment and incurs remarkable local recurrence rate as the formidable problem for neurosurgery. However, as the routine preoperative evaluation scheme, MRI and CT failed to reveal the mutual three-dimensional relationships between tumor and adjacent structures. Here, we report the clinical application of MSCTA and VRT in three-dimensional reconstruction of cervical dumbbell tumors. From January 2012 to July 2014, 24 patients diagnosed with cervical dumbbell tumor were retrospectively analyzed. All patients enrolled were indicated for preoperative MSCTA/VRT image reconstruction to explore the three-dimensional stereoscopic anatomical relationships among neuroma, spinal cord and vertebral artery to achieve optimal surgical approach from multiple configurations and surgical practice. Three-dimensional mutual anatomical relationships among tumor, adjacent vessels and vertebrae were vividly reconstructed by MSCTA/VRT in all patients in accordance with intraoperative findings. Multiple configurations for optimal surgical approach contribute to total resection of tumor, minimal damage to vessels and nerves, and maximal maintenance of cervical spine stability. Preoperative MSCTA/VRT contributes to reconstruction of three-dimensional stereoscopic anatomical relationships between cervical dumbbell tumor and adjacent structures for optimal surgical approach by multiple configurations and reduction of intraoperative damages and postoperative complications. PMID:26550385

Application of MSCTA combined with VRT in the operation of cervical dumbbell tumors.

PubMed

Wang, Wan; Lin, Jia; Knosp, Engelbert; Zhao, Yuanzheng; Xiu, Dianhui; Guo, Yongchuan

2015-01-01

Cervical dumbbell tumor poses great difficulties for neurosurgical treatment and incurs remarkable local recurrence rate as the formidable problem for neurosurgery. However, as the routine preoperative evaluation scheme, MRI and CT failed to reveal the mutual three-dimensional relationships between tumor and adjacent structures. Here, we report the clinical application of MSCTA and VRT in three-dimensional reconstruction of cervical dumbbell tumors. From January 2012 to July 2014, 24 patients diagnosed with cervical dumbbell tumor were retrospectively analyzed. All patients enrolled were indicated for preoperative MSCTA/VRT image reconstruction to explore the three-dimensional stereoscopic anatomical relationships among neuroma, spinal cord and vertebral artery to achieve optimal surgical approach from multiple configurations and surgical practice. Three-dimensional mutual anatomical relationships among tumor, adjacent vessels and vertebrae were vividly reconstructed by MSCTA/VRT in all patients in accordance with intraoperative findings. Multiple configurations for optimal surgical approach contribute to total resection of tumor, minimal damage to vessels and nerves, and maximal maintenance of cervical spine stability. Preoperative MSCTA/VRT contributes to reconstruction of three-dimensional stereoscopic anatomical relationships between cervical dumbbell tumor and adjacent structures for optimal surgical approach by multiple configurations and reduction of intraoperative damages and postoperative complications.

Three-dimensional structure and ligand interactions of the low molecular weight protein tyrosine phosphatase from Campylobacter jejuni.

PubMed

Tolkatchev, Dmitri; Shaykhutdinov, Rustem; Xu, Ping; Plamondon, Josée; Watson, David C; Young, N Martin; Ni, Feng

2006-10-01

A putative low molecular weight protein tyrosine phosphatase (LMW-PTP) was identified in the genome sequence of the bacterial pathogen, Campylobacter jejuni. This novel gene, cj1258, has sequence homology with a distinctive class of phosphatases widely distributed among prokaryotes and eukaryotes. We report here the solution structure of Cj1258 established by high-resolution NMR spectroscopy using NOE-derived distance restraints, hydrogen bond data, and torsion angle restraints. The three-dimensional structure consists of a central four-stranded parallel beta-sheet flanked by five alpha-helices, revealing an overall structural topology similar to those of the eukaryotic LMW-PTPs, such as human HCPTP-A, bovine BPTP, and Saccharomyces cerevisiae LTP1, and to those of the bacterial LMW-PTPs MPtpA from Mycobacterium tuberculosis and YwlE from Bacillus subtilis. The active site of the enzyme is flexible in solution and readily adapts to the binding of ligands, such as the phosphate ion. An NMR-based screen was carried out against a number of potential inhibitors and activators, including phosphonomethylphenylalanine, derivatives of the cinnamic acid, 2-hydroxy-5-nitrobenzaldehyde, cinnamaldehyde, adenine, and hypoxanthine. Despite its bacterial origin, both the three-dimensional structure and ligand-binding properties of Cj1258 suggest that this novel phosphatase may have functional roles close to those of eukaryotic and mammalian tyrosine phosphatases. The three-dimensional structure along with mapping of small-molecule binding will be discussed in the context of developing high-affinity inhibitors of this novel LMW-PTP.

Forced free-shear layer measurements

NASA Technical Reports Server (NTRS)

Leboeuf, Richard L.

1994-01-01

Detailed three-dimensional three-component phase averaged measurements of the spanwise and streamwise vorticity formation and evolution in acoustically forced plane free-shear flows have been obtained. For the first time, phase-averaged measurements of all three velocity components have been obtained in both a mixing layer and a wake on three-dimensional grids, yielding the spanwise and streamwise vorticity distributions without invoking Taylor's hypothesis. Initially, two-frequency forcing was used to phase-lock the roll-up and first pairing of the spanwise vortical structures in a plane mixing layer. The objective of this study was to measure the near-field vortical structure morphology in a mixing layer with 'natural' laminar initial boundary layers. For the second experiment the second and third subharmonics of the fundamental roll-up frequency were added to the previous two-frequency forcing in order to phase-lock the roll-up and first three pairings of the spanwise rollers in the mixing layer. The objective of this study was to determine the details of spanwise scale changes observed in previous time-averaged measurements and flow visualization of unforced mixing layers. For the final experiment, single-frequency forcing was used to phase-lock the Karman vortex street in a plane wake developing from nominally two-dimensional laminar initial boundary layers. The objective of this study was to compare measurements of the three-dimensional structure in a wake developing from 'natural' initial boundary layers to existing models of wake vortical structure.

Weak form of Stokes-Dirac structures and geometric discretization of port-Hamiltonian systems

NASA Astrophysics Data System (ADS)

Kotyczka, Paul; Maschke, Bernhard; Lefèvre, Laurent

2018-05-01

We present the mixed Galerkin discretization of distributed parameter port-Hamiltonian systems. On the prototypical example of hyperbolic systems of two conservation laws in arbitrary spatial dimension, we derive the main contributions: (i) A weak formulation of the underlying geometric (Stokes-Dirac) structure with a segmented boundary according to the causality of the boundary ports. (ii) The geometric approximation of the Stokes-Dirac structure by a finite-dimensional Dirac structure is realized using a mixed Galerkin approach and power-preserving linear maps, which define minimal discrete power variables. (iii) With a consistent approximation of the Hamiltonian, we obtain finite-dimensional port-Hamiltonian state space models. By the degrees of freedom in the power-preserving maps, the resulting family of structure-preserving schemes allows for trade-offs between centered approximations and upwinding. We illustrate the method on the example of Whitney finite elements on a 2D simplicial triangulation and compare the eigenvalue approximation in 1D with a related approach.

Catalytic zinc site and mechanism of the metalloenzyme PR-AMP cyclohydrolase.

PubMed

D'Ordine, Robert L; Linger, Rebecca S; Thai, Carolyn J; Davisson, V Jo

2012-07-24

The enzyme N(1)-(5'-phosphoribosyl) adenosine-5'-monophosphate cyclohydrolase (PR-AMP cyclohydrolase) is a Zn(2+) metalloprotein encoded by the hisI gene. It catalyzes the third step of histidine biosynthesis, an uncommon ring-opening of a purine heterocycle for use in primary metabolism. A three-dimensional structure of the enzyme from Methanobacterium thermoautotrophicum has revealed that three conserved cysteine residues occur at the dimer interface and likely form the catalytic site. To investigate the functions of these cysteines in the enzyme from Methanococcus vannielii, a series of biochemical studies were pursued to test the basic hypothesis regarding their roles in catalysis. Inactivation of the enzyme activity by methyl methane thiosulfonate (MMTS) or 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB) also compromised the Zn(2+) binding properties of the protein inducing loss of up to 90% of the metal. Overall reaction stoichiometry and the potassium cyanide (KCN) induced cleavage of the protein suggested that all three cysteines were modified in the process. The enzyme was protected from DTNB-induced inactivation by inclusion of the substrate N(1)-(5'-phosphoribosyl)adenosine 5'-monophosphate; (PR-AMP), while Mg(2+), a metal required for catalytic activity, enhanced the rate of inactivation. Site-directed mutations of the conserved C93, C109, C116 and the double mutant C109/C116 were prepared and analyzed for catalytic activity, Zn(2+) content, and reactivity with DTNB. Substitution of alanine for each of the conserved cysteines showed no measurable catalytic activity, and only the C116A was still capable of binding Zn(2+). Reactions of DTNB with the C109A/C116A double mutant showed that C93 is completely modified within 0.5 s. A model consistent with these data involves a DTNB-induced mixed disulfide linkage between C93 and C109 or C116, followed by ejection of the active site Zn(2+) and provides further evidence that the Zn(2+) coordination site involves the three conserved cysteine residues. The C93 reactivity is modulated by the presence of the Zn(2+) and Mg(2+) and substantiates the role of this residue as a metal ligand. In addition, Mg(2+) ligand binding site(s) indicated by the structural analysis were probed by site-directed mutagenesis of three key aspartate residues flanking the conserved C93 which were shown to have a functional impact on catalysis, cysteine activation, and metal (zinc) binding capacity. The unique amino acid sequence, the dynamic properties of the cysteine ligands involved in Zn(2+) coordination, and the requirement for a second metal (Mg(2+)) are discussed in the context of their roles in catalysis. The results are consistent with a Zn(2+)-mediated activation of H(2)O mechanism involving histidine as a general base that has features similar to but distinct from those of previously characterized purine and pyrimidine deaminases.

Surface representations of two- and three-dimensional fluid flow topology

NASA Technical Reports Server (NTRS)

Helman, James L.; Hesselink, Lambertus

1990-01-01

We discuss our work using critical point analysis to generate representations of the vector field topology of numerical flow data sets. Critical points are located and characterized in a two-dimensional domain, which may be either a two-dimensional flow field or the tangential velocity field near a three-dimensional body. Tangent curves are then integrated out along the principal directions of certain classes of critical points. The points and curves are linked to form a skeleton representing the two-dimensional vector field topology. When generated from the tangential velocity field near a body in a three-dimensional flow, the skeleton includes the critical points and curves which provide a basis for analyzing the three-dimensional structure of the flow separation. The points along the separation curves in the skeleton are used to start tangent curve integrations to generate surfaces representing the topology of the associated flow separations.

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.

Dimensional Effects on the Charge Density Waves in Ultrathin Films of TiSe 2

DOE PAGES

Chen, P.; Chan, Y. -H.; Wong, M. -H.; ...

2016-09-20

Charge density wave (CDW) formation in solids is a critical phenomenon involving the collective reorganization of the electrons and atoms in the system into a wave structure, and it is expected to be sensitive to the geometric constraint of the system at the nanoscale. Here, we study the CDW transition in TiSe 2, a quasi-two-dimensional layered material, to determine the effects of quantum confinement and changing dimensions in films ranging from a single layer to multilayers. Of key interest is the characteristic length scale for the transformation from a two-dimensional case to the three-dimensional limit. Angle-resolved photoemission (ARPES) measurements ofmore » films with thicknesses up to six layers reveal substantial variations in the energy structure of discrete quantum well states; however, the temperature-dependent band-gap renormalization converges at just three layers. The results indicate a layer-dependent mixture of two transition temperatures and a very-short-range CDW interaction within a three-dimensional framework.« less

Multigrid finite element method in stress analysis of three-dimensional elastic bodies of heterogeneous structure

NASA Astrophysics Data System (ADS)

Matveev, A. D.

2016-11-01

To calculate the three-dimensional elastic body of heterogeneous structure under static loading, a method of multigrid finite element is provided, when implemented on the basis of algorithms of finite element method (FEM), using homogeneous and composite threedimensional multigrid finite elements (MFE). Peculiarities and differences of MFE from the currently available finite elements (FE) are to develop composite MFE (without increasing their dimensions), arbitrarily small basic partition of composite solids consisting of single-grid homogeneous FE of the first order can be used, i.e. in fact, to use micro approach in finite element form. These small partitions allow one to take into account in MFE, i.e. in the basic discrete models of composite solids, complex heterogeneous and microscopically inhomogeneous structure, shape, the complex nature of the loading and fixation and describe arbitrarily closely the stress and stain state by the equations of three-dimensional elastic theory without any additional simplifying hypotheses. When building the m grid FE, m of nested grids is used. The fine grid is generated by a basic partition of MFE, the other m —1 large grids are applied to reduce MFE dimensionality, when m is increased, MFE dimensionality becomes smaller. The procedures of developing MFE of rectangular parallelepiped, irregular shape, plate and beam types are given. MFE generate the small dimensional discrete models and numerical solutions with a high accuracy. An example of calculating the laminated plate, using three-dimensional 3-grid FE and the reference discrete model is given, with that having 2.2 milliards of FEM nodal unknowns.

The DIMA web resource--exploring the protein domain network.

PubMed

Pagel, Philipp; Oesterheld, Matthias; Stümpflen, Volker; Frishman, Dmitrij

2006-04-15

Conserved domains represent essential building blocks of most known proteins. Owing to their role as modular components carrying out specific functions they form a network based both on functional relations and direct physical interactions. We have previously shown that domain interaction networks provide substantially novel information with respect to networks built on full-length protein chains. In this work we present a comprehensive web resource for exploring the Domain Interaction MAp (DIMA), interactively. The tool aims at integration of multiple data sources and prediction techniques, two of which have been implemented so far: domain phylogenetic profiling and experimentally demonstrated domain contacts from known three-dimensional structures. A powerful yet simple user interface enables the user to compute, visualize, navigate and download domain networks based on specific search criteria. http://mips.gsf.de/genre/proj/dima

The hemoglobins of the trematodes Fasciola hepatica and Paramphistomum epiclitum: A molecular biological, physico-chemical, kinetic, and vaccination study

PubMed Central

Dewilde, Sylvia; Ioanitescu, A. Iulia; Kiger, Laurent; Gilany, Kambiz; Marden, Michael C.; Van Doorslaer, Sabine; Vercruysse, Jozef; Pesce, Alessandra; Nardini, Marco; Bolognesi, Martino; Moens, Luc

2008-01-01

The trematode Fasciola hepatica (Fa.he.) is a common parasite of human and livestock. The hemoglobin (Hb) of Fa.he., a potential immunogen, was chosen for characterization in the search for an effective vaccine. Characterization of trematode Hbs show that they are intracellular single-domain globins with the following remarkable features: (1) Fa.he. expresses two Hb isoforms that differ at two amino acid sites (F1: 119Y/123Q; F2: 119F/123L). Both isoforms are monoacetylated at their N-termini; (2) the genes coding for Fa.he. and Paramphistomum epiclitum (Pa.ep.) Hbs are interrupted by two introns at the conserved positions B12.2 and G7.0.; (3) UV/VIS and resonance Raman spectroscopy identify the recombinant Fa.he. HbF2 as a pentacoordinated high-spin ferrous Hb; (4) electron paramagnetic resonance spectroscopy of cyano-met Fa.he. HbF2 proves that the endogenously bound imidazole has no imidazolate character; (5) the major structural determinants of the globin fold are present, they contain a TyrB10/TyrE7 residue pair on the distal side. Although such distal-site pair is a signature for high oxygen affinity, as shown for Pa.ep. Hb, the oxygen-binding rate parameters for Fa.he. Hb are intermediate between those of myoglobin and those of other trematode Hbs; (6) the three-dimensional structure of recombinant Fa.he. HbF2 from this study closely resembles the three-dimensional structure of Pa.ep. determined earlier. The set of distal-site polar interactions observed in Pa.ep. Hb is matched with small but significant structural adjustments; (7) despite the potential immunogenic character of the fluke Hb, vaccination of calves with recombinant Fa.he. HbF2 failed to promote protection against parasitic infection. PMID:18621914

Three-Dimensional parton structure of light nuclei

NASA Astrophysics Data System (ADS)

Scopetta, Sergio; Del Dotto, Alessio; Kaptari, Leonid; Pace, Emanuele; Rinaldi, Matteo; Salmè, Giovanni

2018-03-01

Two promising directions beyond inclusive deep inelastic scattering experiments, aimed at unveiling the three dimensional structure of the bound nucleon, are reviewed, considering in particular the 3He nuclear target. The 3D structure in coordinate space can be accessed through deep exclusive processes, whose non-perturbative part is encoded in generalized parton distributions. In this way, the distribution of partons in the transverse plane can be obtained. As an example of a deep exclusive process, coherent deeply virtual Compton scattering off 3He nuclei, important to access the neutron generalized parton distributions (GPDs), will be discussed. In Impulse Approximation (IA), the sum of the two leading twist, quark helicity conserving GPDs of 3He, H and E, at low momentum transfer, turns out to be dominated by the neutron contribution. Besides, a technique, able to take into account the nuclear effects included in the Impulse Approximation analysis, has been developed. The spin dependent GPD \\tilde H of 3He is also found to be largely dominated, at low momentum transfer, by the neutron contribution. The knowledge of the GPDs H,E and \\tilde H of 3He is relevant for the planning of coherent DVCS off 3He measurements. Semi-inclusive deep inelastic scattering processes access the momentum space 3D structure parameterized through transverse momentum dependent parton distributions. A distorted spin-dependent spectral function has been recently introduced for 3He, in a non-relativistic framework, to take care of the final state interaction between the observed pion and the remnant in semi-inclusive deep inelastic electron scattering off transversely polarized 3He. The calculation of the Sivers and Collins single spin asymmetries for 3He, and a straightforward procedure to effectively take into account nuclear dynamics and final state interactions, will be reviewed. The Light-front dynamics generalization of the analysis is also addressed.

Algebraic multigrid methods applied to problems in computational structural mechanics

NASA Technical Reports Server (NTRS)

Mccormick, Steve; Ruge, John

1989-01-01

The development of algebraic multigrid (AMG) methods and their application to certain problems in structural mechanics are described with emphasis on two- and three-dimensional linear elasticity equations and the 'jacket problems' (three-dimensional beam structures). Various possible extensions of AMG are also described. The basic idea of AMG is to develop the discretization sequence based on the target matrix and not the differential equation. Therefore, the matrix is analyzed for certain dependencies that permit the proper construction of coarser matrices and attendant transfer operators. In this manner, AMG appears to be adaptable to structural analysis applications.

Three-dimensional study of the vector potential of magnetic structures.

PubMed

Phatak, Charudatta; Petford-Long, Amanda K; De Graef, Marc

2010-06-25

The vector potential is central to a number of areas of condensed matter physics, such as superconductivity and magnetism. We have used a combination of electron wave phase reconstruction and electron tomographic reconstruction to experimentally measure and visualize the three-dimensional vector potential in and around a magnetic Permalloy structure. The method can probe the vector potential of the patterned structures with a resolution of about 13 nm. A transmission electron microscope operated in the Lorentz mode is used to record four tomographic tilt series. Measurements for a square Permalloy structure with an internal closure domain configuration are presented.

Three-dimensional microbubble streaming flows

NASA Astrophysics Data System (ADS)

Rallabandi, Bhargav; Marin, Alvaro; Rossi, Massimiliano; Kaehler, Christian; Hilgenfeldt, Sascha

2014-11-01

Streaming due to acoustically excited bubbles has been used successfully for applications such as size-sorting, trapping and focusing of particles, as well as fluid mixing. Many of these applications involve the precise control of particle trajectories, typically achieved using cylindrical bubbles, which establish planar flows. Using astigmatic particle tracking velocimetry (APTV), we show that, while this two-dimensional picture is a useful description of the flow over short times, a systematic three-dimensional flow structure is evident over long time scales. We demonstrate that this long-time three-dimensional fluid motion can be understood through asymptotic theory, superimposing secondary axial flows (induced by boundary conditions at the device walls) onto the two-dimensional description. This leads to a general framework that describes three-dimensional flows in confined microstreaming systems, guiding the design of applications that profit from minimizing or maximizing these effects.

On a fourth order accurate implicit finite difference scheme for hyperbolic conservation laws. I - Nonstiff strongly dynamic problems

NASA Technical Reports Server (NTRS)

Harten, A.; Tal-Ezer, H.

1981-01-01

An implicit finite difference method of fourth order accuracy in space and time is introduced for the numerical solution of one-dimensional systems of hyperbolic conservation laws. The basic form of the method is a two-level scheme which is unconditionally stable and nondissipative. The scheme uses only three mesh points at level t and three mesh points at level t + delta t. The dissipative version of the basic method given is conditionally stable under the CFL (Courant-Friedrichs-Lewy) condition. This version is particularly useful for the numerical solution of problems with strong but nonstiff dynamic features, where the CFL restriction is reasonable on accuracy grounds. Numerical results are provided to illustrate properties of the proposed method.

Effects of three-dimensional velocity structure on the seismicity of the 1984 Morgan Hill, California, aftershock sequence

USGS Publications Warehouse

Michael, A.J.

1988-01-01

A three-dimensional velocity model for the area surrounding the 24 April 1984 Morgan Hill earthquake has been developed by simultaneously inverting local earthquake and refraction arrival-time data. This velocity model corresponds well to the surface geology of the region, predominantly showing a low-velocity region associated with the sedimentary sequence to the south-west of the Madrone Springs fault. The focal mechanisms were also determined for 946 earthquakes using both the one-dimensional and three-dimensional earth models. Both earth models yield similar focal mechanisms for these earthquakes. -from Author

Modern cosmology and the origin of our three dimensionality.

PubMed

Woodbury, M A; Woodbury, M F

1998-01-01

We are three dimensional egocentric beings existing within a specific space/time continuum and dimensionality which we assume wrongly is the same for all times and places throughout the entire universe. Physicists name Omnipoint the origin of the universe at Dimension zero, which exploded as a Big Bang of energy proceeding at enormous speed along one dimension which eventually curled up into matter: particles, atoms, molecules and Galaxies which exist in two dimensional space. Finally from matter spread throughout the cosmos evolved life generating eventually the DNA molecules which control the construction of brains complex enough to construct our three dimensional Body Representation from which is extrapolated what we perceive as a 3-D universe. The whole interconnected structures which conjure up our three dimensionality are as fragile as Humpty Dumpty, capable of breaking apart with terrifying effects for the individual patient during a psychotic panic, revealing our three dimensionality to be but "maya", an illusion, which we psychiatrists work at putting back together.

Fabrication of 2D and 3D photonic structures using laser lithography

NASA Astrophysics Data System (ADS)

Gaso, P.; Jandura, D.; Pudis, D.

2016-12-01

In this paper we demonstrate possibilities of three-dimensional (3D) printing technology based on two photon polymerization. We used three-dimensional dip-in direct-laser-writing (DLW) optical lithography to fabricate 2D and 3D optical structures for optoelectronics and for optical sensing applications. DLW lithography allows us use a non conventional way how to couple light into the waveguide structure. We prepared ring resonator and we investigated its transmission spectral characteristic. We present 3D inverse opal structure from its design to printing and scanning electron microscope (SEM) imaging. Finally, SEM images of some prepared photonic crystal structures were performed.

Evolution of the three-dimensional collagen structure in vascular walls during deformation: an in situ mechanical testing under multiphoton microscopy observation.

PubMed

Nierenberger, Mathieu; Fargier, Guillaume; Ahzi, Saïd; Rémond, Yves

2015-08-01

The collagen fibers' three-dimensional architecture has a strong influence on the mechanical behavior of biological tissues. To accurately model this behavior, it is necessary to get some knowledge about the structure of the collagen network. In the present paper, we focus on the in situ characterization of the collagenous structure, which is present in porcine jugular vein walls. An observation of the vessel wall is first proposed in an unloaded configuration. The vein is then put into a mechanical tensile testing device. As the vein is stretched, three-dimensional images of its collagenous structure are acquired using multiphoton microscopy. Orientation analyses are provided for the multiple images recorded during the mechanical test. From these analyses, the reorientation of the two families of collagen fibers existing in the vein wall is quantified. We noticed that the reorientation of the fibers stops as the tissue stiffness starts decreasing, corresponding to the onset of damage. Besides, no relevant evolutions of the out of plane collagen orientations were observed. Due to the applied loading, our analysis also allowed for linking the stress relaxation within the tissue to its internal collagenous structure. Finally, this analysis constitutes the first mechanical test performed under a multiphoton microscope with a continuous three-dimensional observation of the tissue structure all along the test. It allows for a quantitative evaluation of microstructural parameters combined with a measure of the global mechanical behavior. Such data are useful for the development of structural mechanical models for living tissues.

System and method for representing and manipulating three-dimensional objects on massively parallel architectures

DOEpatents

Karasick, M.S.; Strip, D.R.

1996-01-30

A parallel computing system is described that comprises a plurality of uniquely labeled, parallel processors, each processor capable of modeling a three-dimensional object that includes a plurality of vertices, faces and edges. The system comprises a front-end processor for issuing a modeling command to the parallel processors, relating to a three-dimensional object. Each parallel processor, in response to the command and through the use of its own unique label, creates a directed-edge (d-edge) data structure that uniquely relates an edge of the three-dimensional object to one face of the object. Each d-edge data structure at least includes vertex descriptions of the edge and a description of the one face. As a result, each processor, in response to the modeling command, operates upon a small component of the model and generates results, in parallel with all other processors, without the need for processor-to-processor intercommunication. 8 figs.

Blue-phase templated fabrication of three-dimensional nanostructures for photonic applications.

PubMed

Castles, F; Day, F V; Morris, S M; Ko, D-H; Gardiner, D J; Qasim, M M; Nosheen, S; Hands, P J W; Choi, S S; Friend, R H; Coles, H J

2012-05-13

A promising approach to the fabrication of materials with nanoscale features is the transfer of liquid-crystalline structure to polymers. However, this has not been achieved in systems with full three-dimensional periodicity. Here we demonstrate the fabrication of self-assembled three-dimensional nanostructures by polymer templating blue phase I, a chiral liquid crystal with cubic symmetry. Blue phase I was photopolymerized and the remaining liquid crystal removed to create a porous free-standing cast, which retains the chiral three-dimensional structure of the blue phase, yet contains no chiral additive molecules. The cast may in turn be used as a hard template for the fabrication of new materials. By refilling the cast with an achiral nematic liquid crystal, we created templated blue phases that have unprecedented thermal stability in the range -125 to 125 °C, and that act as both mirrorless lasers and switchable electro-optic devices. Blue-phase templated materials will facilitate advances in device architectures for photonics applications in particular.

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

PubMed

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

2014-05-01

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

Finite difference methods for the solution of unsteady potential flows

NASA Technical Reports Server (NTRS)

Caradonna, F. X.

1982-01-01

Various problems which are confronted in the development of an unsteady finite difference potential code are reviewed mainly in the context of what is done for a typical small disturbance and full potential method. The issues discussed include choice of equations, linearization and conservation, differencing schemes, and algorithm development. A number of applications, including unsteady three dimensional rotor calculations, are demonstrated.

77 FR 24539 - Virginia Electric and Power Company; Surry Power Station Units 1 and 2; Independent Spent Fuel...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-24

... bounding thermal analysis using ANSYS finite element software to evaluate the misloading events. The ANSYS analysis consists of a half-symmetric, three-dimensional model of a 32PTH DSC with a number of conservative... the maximum fuel cladding temperature presented in the UFSAR analysis dated October 2, 2009, with the...

Novel Structure and Unexpected RNA-Binding Ability of the C-Terminal Domain of Herpes Simplex Virus 1 Tegument Protein UL21

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

Metrick, Claire M.; Heldwein, Ekaterina E.; Sandri-Goldin, R. M.

Proteins forming the tegument layers of herpesviral virions mediate many essential processes in the viral replication cycle, yet few have been characterized in detail. UL21 is one such multifunctional tegument protein and is conserved among alphaherpesviruses. While UL21 has been implicated in many processes in viral replication, ranging from nuclear egress to virion morphogenesis to cell-cell spread, its precise roles remain unclear. Here we report the 2.7-Å crystal structure of the C-terminal domain of herpes simplex virus 1 (HSV-1) UL21 (UL21C), which has a unique α-helical fold resembling a dragonfly. Analysis of evolutionary conservation patterns and surface electrostatics pinpointed fourmore » regions of potential functional importance on the surface of UL21C to be pursued by mutagenesis. In combination with the previously determined structure of the N-terminal domain of UL21, the structure of UL21C provides a 3-dimensional framework for targeted exploration of the multiple roles of UL21 in the replication and pathogenesis of alphaherpesviruses. Additionally, we describe an unanticipated ability of UL21 to bind RNA, which may hint at a yet unexplored function. IMPORTANCEDue to the limited genomic coding capacity of viruses, viral proteins are often multifunctional, which makes them attractive antiviral targets. Such multifunctionality, however, complicates their study, which often involves constructing and characterizing null mutant viruses. Systematic exploration of these multifunctional proteins requires detailed road maps in the form of 3-dimensional structures. In this work, we determined the crystal structure of the C-terminal domain of UL21, a multifunctional tegument protein that is conserved among alphaherpesviruses. Structural analysis pinpointed surface areas of potential functional importance that provide a starting point for mutagenesis. In addition, the unexpected RNA-binding ability of UL21 may expand its functional repertoire. The structure of UL21C and the observation of its RNA-binding ability are the latest additions to the navigational chart that can guide the exploration of the multiple functions of UL21.« less

A novel diagnostic parameter, foraminal stenotic ratio using three-dimensional magnetic resonance imaging, as a discriminator for surgery in symptomatic lumbar foraminal stenosis.

PubMed

Yamada, Kentaro; Abe, Yuichiro; Satoh, Shigenobu; Yanagibashi, Yasushi; Hyakumachi, Takahiko; Masuda, Takeshi

2017-08-01

No previous studies have reported the radiological features of patients requiring surgery in symptomatic lumbar foraminal stenosis (LFS). This study aims to investigate the diagnostic accuracy of a novel technique, foraminal stenotic ratio (FSR), using three-dimensional magnetic resonance imaging for LFS at L5-S by comparing patients requiring surgery, patients with successful conservative treatment, and asymptomatic patients. This is a retrospective radiological comparative study. We assessed the magnetic resonance imaging (MRI) results of 84 patients (168 L5-S foramina) aged ≥40 years without L4-L5 lumbar spinal stenosis. The foramina were divided into three groups following standardized treatment: stenosis requiring surgery (20 foramina), stenosis with successful conservative treatment (26 foramina), and asymptomatic stenotic foramen (122 foramina). Foraminal stenotic ratio was defined as the ratio of the length of the stenosis to the length of the foramen on the reconstructed oblique coronal image, referring to perineural fat obliterations in whole oblique sagittal images. We also evaluated the foraminal nerve angle and the minimum nerve diameter on reconstructed images, and the Lee classification on conventional T1 images. The differences in each MRI parameter between the groups were investigated. To predict which patients require surgery, receiver operating characteristic (ROC) curves were plotted after calculating the area under the ROC curve. The FSR showed a stepwise increase when comparing asymptomatic, conservative, and surgical groups (mean, 8.6%, 38.5%, 54.9%, respectively). Only FSR was significantly different between the surgical and conservative groups (p=.002), whereas all parameters were significantly different comparing the symptomatic and asymptomatic groups. The ROC curve showed that the area under the curve for FSR was 0.742, and the optimal cutoff value for FSR for predicting a surgical requirement in symptomatic patients was 50% (sensitivity, 75%; specificity, 80.7%). The FSR determined LFS requiring surgery among symptomatic patients, with moderate accuracy. Foramina occupied ≥50% by fat obliteration were likely to fail conservative treatment, with a positive predictive value of 75%. Copyright © 2017 Elsevier Inc. All rights reserved.