PL-PatchSurfer: A Novel Molecular Local Surface-Based Method for Exploring Protein-Ligand Interactions

PubMed Central

Hu, Bingjie; Zhu, Xiaolei; Monroe, Lyman; Bures, Mark G.; Kihara, Daisuke

2014-01-01

Structure-based computational methods have been widely used in exploring protein-ligand interactions, including predicting the binding ligands of a given protein based on their structural complementarity. Compared to other protein and ligand representations, the advantages of a surface representation include reduced sensitivity to subtle changes in the pocket and ligand conformation and fast search speed. Here we developed a novel method named PL-PatchSurfer (Protein-Ligand PatchSurfer). PL-PatchSurfer represents the protein binding pocket and the ligand molecular surface as a combination of segmented surface patches. Each patch is characterized by its geometrical shape and the electrostatic potential, which are represented using the 3D Zernike descriptor (3DZD). We first tested PL-PatchSurfer on binding ligand prediction and found it outperformed the pocket-similarity based ligand prediction program. We then optimized the search algorithm of PL-PatchSurfer using the PDBbind dataset. Finally, we explored the utility of applying PL-PatchSurfer to a larger and more diverse dataset and showed that PL-PatchSurfer was able to provide a high early enrichment for most of the targets. To the best of our knowledge, PL-PatchSurfer is the first surface patch-based method that treats ligand complementarity at protein binding sites. We believe that using a surface patch approach to better understand protein-ligand interactions has the potential to significantly enhance the design of new ligands for a wide array of drug-targets. PMID:25167137

Crystal structure of an antibody bound to an immunodominant peptide epitope: novel features in peptide-antibody recognition.

PubMed

Nair, D T; Singh, K; Sahu, N; Rao, K V; Salunke, D M

2000-12-15

The crystal structure of Fab of an Ab PC283 complexed with its corresponding peptide Ag, PS1 (HQLDPAFGANSTNPD), derived from the hepatitis B virus surface Ag was determined. The PS1 stretch Gln2P to Phe7P is present in the Ag binding site of the Ab, while the next three residues of the peptide are raised above the binding groove. The residues Ser11P, Thr12P, and Asn13P then loop back onto the Ag-binding site of the Ab. The last two residues, Pro14P and Asp15P, extend outside the binding site without forming any contacts with the Ab. The PC283-PS1 complex is among the few examples where the light chain complementarity-determining regions show more interactions than the heavy chain complementarity-determining regions, and a distal framework residue is involved in Ag binding. As seen from the crystal structure, most of the contacts between peptide and Ab are through the five residues, Leu3-Asp4-Pro5-Ala6-Phe7, of PS1. The paratope is predominantly hydrophobic with aromatic residues lining the binding pocket, although a salt bridge also contributes to stabilizing the Ag-Ab interaction. The molecular surface area buried upon PS1 binding is 756 A(2) for the peptide and 625 A(2) for the Fab, which is higher than what has been seen to date for Ab-peptide complexes. A comparison between PC283 structure and a homology model of its germline ancestor suggests that paratope optimization for PS1 occurs by improving both charge and shape complementarity.

Structure-Guided Insights into the Function of Merlin in Neurofibromatosis 2 (NF2)

DTIC Science & Technology

2011-08-01

laboratory of Dr. Lars Pederson (NIEHS-NIH, Research Triangle Park, North Carolina) that harbor entropy mutations on the surface of MBP, and which... mutations . Am J Hum Genet 66: 873–891. 37. Lawrence MC, Colman PM (1993) Shape complementar - ity at protein/protein interfaces. J Mol Biol 234:946–950. 38...Appendices…………………………………………………………………………… 10 3 INTRODUCTION: Neurofibromatosis type 2 (NF2) is caused by inherited or sporadic mutations

DARC 2.0: Improved Docking and Virtual Screening at Protein Interaction Sites

PubMed Central

Gowthaman, Ragul; Lyskov, Sergey; Karanicolas, John

2015-01-01

Over the past decade, protein-protein interactions have emerged as attractive but challenging targets for therapeutic intervention using small molecules. Due to the relatively flat surfaces that typify protein interaction sites, modern virtual screening tools developed for optimal performance against “traditional” protein targets perform less well when applied instead at protein interaction sites. Previously, we described a docking method specifically catered to the shallow binding modes characteristic of small-molecule inhibitors of protein interaction sites. This method, called DARC (Docking Approach using Ray Casting), operates by comparing the topography of the protein surface when “viewed” from a vantage point inside the protein against the topography of a bound ligand when “viewed” from the same vantage point. Here, we present five key enhancements to DARC. First, we use multiple vantage points to more accurately determine protein-ligand surface complementarity. Second, we describe a new scheme for rapidly determining optimal weights in the DARC scoring function. Third, we incorporate sampling of ligand conformers “on-the-fly” during docking. Fourth, we move beyond simple shape complementarity and introduce a term in the scoring function to capture electrostatic complementarity. Finally, we adjust the control flow in our GPU implementation of DARC to achieve greater speedup of these calculations. At each step of this study, we evaluate the performance of DARC in a “pose recapitulation” experiment: predicting the binding mode of 25 inhibitors each solved in complex with its distinct target protein (a protein interaction site). Whereas the previous version of DARC docked only one of these inhibitors to within 2 Å RMSD of its position in the crystal structure, the newer version achieves this level of accuracy for 12 of the 25 complexes, corresponding to a statistically significant performance improvement (p < 0.001). Collectively then, we find that the five enhancements described here – which together make up DARC 2.0 – lead to dramatically improved speed and performance relative to the original DARC method. PMID:26181386

Exploring the Roles of Nucleobase Desolvation and Shape Complementarity during the Misreplication of O6-Methylguanine

PubMed Central

Chavarria, Delia; Ramos-Serrano, Andrea; Hirao, Ichiro; Berdis, Anthony J.

2011-01-01

O6-methylguanine is a miscoding DNA lesion arising from the alkylation of guanine. This report uses the bacteriophage T4 DNA polymerase as a model to probe the roles hydrogen-bonding interactions, shape/size, and nucleobase desolvation during the replication of this miscoding lesion. This was accomplished by using transient kinetic techniques to monitor the kinetic parameters for incorporating and extending natural and non-natural nucleotides. In general, the efficiency of nucleotide incorporation does not depend on the hydrogen-bonding potential of the incoming nucleotide. Instead, nucleobase hydrophobicity and shape complementarity appear to be the preeminent factors controlling nucleotide incorporation. In addition, shape complementarity plays a large role in controlling the extension of various mispairs containing O6-methylguanine. This is evident as the rate constants for extension correlate with proper interglycosyl distances and symmetry between the base angles of the formed mispair. Base pairs not conforming to an acceptable geometry within the polymerase’s active site are refractory to elongation and are processed via exonuclease proofreading. The collective data set encompassing nucleotide incorporation, extension, and excision is used to generate a model accounting for the mutagenic potential of O6-methylguanine observed in vivo. In addition, kinetic studies monitoring the incorporation and extension of non-natural nucleotides identified an analog that displays high selectivity for incorporation opposite O6-methylguanine compared to unmodified purines. The unusual selectivity of this analog for replicating damaged DNA provides a novel biochemical tool to study translesion DNA synthesis. PMID:21819995

Integration of molecular dynamics simulation and hotspot residues grafting for de novo scFv design against Salmonella Typhi TolC protein.

PubMed

Leong, Siew Wen; Lim, Theam Soon; Ismail, Asma; Choong, Yee Siew

2018-05-01

With the development of de novo binders for protein targets from non-related scaffolds, many possibilities for therapeutics and diagnostics have been created. In this study, we described the use of de novo design approach to create single-chain fragment variable (scFv) for Salmonella enterica subspecies enterica serovar Typhi TolC protein. Typhoid fever is a global health concern in developing and underdeveloped countries. Rapid typhoid diagnostics will improve disease management and therapy. In this work, molecular dynamics simulation was first performed on a homology model of TolC protein in POPE membrane bilayer to obtain the central structure that was subsequently used as the target for scFv design. Potential hotspot residues capable of anchoring the binders to the target were identified by docking "disembodied" amino acid residues against TolC surface. Next, scFv scaffolds were selected from Protein Data Bank to harbor the computed hotspot residues. The hotspot residues were then incorporated into the scFv scaffold complementarity determining regions. The designs recapitulated binding energy, shape complementarity, and interface surface area of natural protein-antibody interfaces. This approach has yielded 5 designs with high binding affinity against TolC that may be beneficial for the future development of antigen-based detection agents for typhoid diagnostics. Copyright © 2017 John Wiley & Sons, Ltd.

Small-Molecule-Based Self-Assembled Ligands for G-Quadruplex DNA Surface Recognition.

PubMed

Rivera-Sánchez, María Del C; García-Arriaga, Marilyn; Hobley, Gerard; Morales-de-Echegaray, Ana V; Rivera, José M

2017-10-31

Most drugs are small molecules because of their attractive pharmacokinetics, manageable development and manufacturing, and effective binding into the concave crevices of bio-macromolecules. Despite these features, they often fall short when it comes to effectively recognizing the surfaces of bio-macromolecules. One way to overcome the challenge of biomolecular surface recognition is to develop small molecules that become self-assembled ligands (SALs) prior to binding. Herein, we report SALs made from 8-aryl-2'-deoxyguanosine derivatives forming precise hydrophilic supramolecular G-quadruplexes (SGQs) with excellent size, shape, and charge complementarity to G-quadruplex DNA (QDNA). We show that only those compounds forming SGQs act as SALs, which in turn differentially stabilize QDNAs from selected oncogene promoters and the human telomeric regions. Fluorescence resonance energy-transfer melting assays are consistent with spectroscopic, calorimetric, and light scattering studies, showing the formation of a "sandwichlike" complex QDNA·SGQ·QDNA. These results open the door for the advent of SALs that recognize QDNAs and potentially the surfaces of other bio-macromolecules such as proteins.

Testing Electrostatic Complementarity in Enzyme Catalysis: Hydrogen Bonding in the Ketosteroid Isomerase Oxyanion Hole

PubMed Central

Kraut, Daniel A; Sigala, Paul A; Pybus, Brandon; Liu, Corey W; Ringe, Dagmar; Petsko, Gregory A

2006-01-01

A longstanding proposal in enzymology is that enzymes are electrostatically and geometrically complementary to the transition states of the reactions they catalyze and that this complementarity contributes to catalysis. Experimental evaluation of this contribution, however, has been difficult. We have systematically dissected the potential contribution to catalysis from electrostatic complementarity in ketosteroid isomerase. Phenolates, analogs of the transition state and reaction intermediate, bind and accept two hydrogen bonds in an active site oxyanion hole. The binding of substituted phenolates of constant molecular shape but increasing p K a models the charge accumulation in the oxyanion hole during the enzymatic reaction. As charge localization increases, the NMR chemical shifts of protons involved in oxyanion hole hydrogen bonds increase by 0.50–0.76 ppm/p K a unit, suggesting a bond shortening of ˜0.02 Å/p K a unit. Nevertheless, there is little change in binding affinity across a series of substituted phenolates (ΔΔG = −0.2 kcal/mol/p K a unit). The small effect of increased charge localization on affinity occurs despite the shortening of the hydrogen bonds and a large favorable change in binding enthalpy (ΔΔH = −2.0 kcal/mol/p K a unit). This shallow dependence of binding affinity suggests that electrostatic complementarity in the oxyanion hole makes at most a modest contribution to catalysis of ˜300-fold. We propose that geometrical complementarity between the oxyanion hole hydrogen-bond donors and the transition state oxyanion provides a significant catalytic contribution, and suggest that KSI, like other enzymes, achieves its catalytic prowess through a combination of modest contributions from several mechanisms rather than from a single dominant contribution. PMID:16602823

Antiandrogenic steroidal sulfonyl heterocycles. Utility of electrostatic complementarity in defining bioisosteric sulfonyl heterocycles.

PubMed

Mallamo, J P; Pilling, G M; Wetzel, J R; Kowalczyk, P J; Bell, M R; Kullnig, R K; Batzold, F H; Juniewicz, P E; Winneker, R C; Luss, H R

1992-05-15

Complementarity of electrostatic potential surface maps was utilized in defining bioisosteric steroidal androgen receptor antagonists. Semiempirical and ab initio level calculations performed on a series of methanesulfonyl heterocycles indicated the requirement for a partial negative charge at the heteroatom attached to C-3 of the steroid nucleus to attain androgen receptor affinity. Synthesis and testing of six heterocycle A-ring-fused dihydroethisterone derivatives support this hypothesis, and we have identified two new androgen receptor antagonists of this class.

C60 Recognition from Extended Tetrathiafulvalene Bis-acetylide Platinum(II) Complexes.

PubMed

Bastien, Guillaume; Dron, Paul I; Vincent, Manon; Canevet, David; Allain, Magali; Goeb, Sébastien; Sallé, Marc

2016-11-18

The favorable spatial organization imposed by the square planar 4,4'-di(tert-butyl)-2,2'-bipyridine (dbbpy) platinum(II) complex associated with the electronic and shape complementarity of π-extended tetrathiafulvalene derivatives (exTTF) toward fullerenes is usefully exploited to construct molecular tweezers, which display good affinities for C 60 .

Photovoltaic Universal Joints: Ball-and-Socket Interfaces in Molecular Photovoltaic Cells

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

Tremblay, Noah J.; Gorodetsky, Alon A.; Cox, Marshall P.

2010-02-15

A new approach toward higher efficiency organic photovoltaic devices (OPVs) is described. Complementarity in shape between the donor (contorted hexabenzocoronene, see picture) and acceptor (buckminsterfullerene) molecules results in OPVs that perform surprisingly well. This exploitation of host-guest chemistry at the organic/organic interface demonstrates a new direction for OPV device design.

Exploring the Future of Lifelong Learning: Advocacy, Research and Footprinting

ERIC Educational Resources Information Center

Chisholm, Lynne

2013-01-01

This reflective think-tank contribution begins by comparing advocacy and research as distinct modalities of professional and social action. In practice they frequently elide and merge into one another. While alliance and complementarity between the two modalities is constructive for shaping policy and practice, it poses risks when governments and…

Seeing & Feeling How Enzymes Work Using Tangible Models

ERIC Educational Resources Information Center

Lau, Kwok-chi

2013-01-01

This article presents a tangible model used to help students tackle some misconceptions about enzyme actions, particularly the induced-fit model, enzyme-substrate complementarity, and enzyme inhibition. The model can simulate how substrates induce a change in the shape of the active site and the role of attraction force during enzyme-substrate…

FitEM2EM—Tools for Low Resolution Study of Macromolecular Assembly and Dynamics

PubMed Central

Frankenstein, Ziv; Sperling, Joseph; Sperling, Ruth; Eisenstein, Miriam

2008-01-01

Studies of the structure and dynamics of macromolecular assemblies often involve comparison of low resolution models obtained using different techniques such as electron microscopy or atomic force microscopy. We present new computational tools for comparing (matching) and docking of low resolution structures, based on shape complementarity. The matched or docked objects are represented by three dimensional grids where the value of each grid point depends on its position with regard to the interior, surface or exterior of the object. The grids are correlated using fast Fourier transformations producing either matches of related objects or docking models depending on the details of the grid representations. The procedures incorporate thickening and smoothing of the surfaces of the objects which effectively compensates for differences in the resolution of the matched/docked objects, circumventing the need for resolution modification. The presented matching tool FitEM2EMin successfully fitted electron microscopy structures obtained at different resolutions, different conformers of the same structure and partial structures, ranking correct matches at the top in every case. The differences between the grid representations of the matched objects can be used to study conformation differences or to characterize the size and shape of substructures. The presented low-to-low docking tool FitEM2EMout ranked the expected models at the top. PMID:18974836

Individual-based analyses reveal limited functional overlap in a coral reef fish community.

PubMed

Brandl, Simon J; Bellwood, David R

2014-05-01

Detailed knowledge of a species' functional niche is crucial for the study of ecological communities and processes. The extent of niche overlap, functional redundancy and functional complementarity is of particular importance if we are to understand ecosystem processes and their vulnerability to disturbances. Coral reefs are among the most threatened marine systems, and anthropogenic activity is changing the functional composition of reefs. The loss of herbivorous fishes is particularly concerning as the removal of algae is crucial for the growth and survival of corals. Yet, the foraging patterns of the various herbivorous fish species are poorly understood. Using a multidimensional framework, we present novel individual-based analyses of species' realized functional niches, which we apply to a herbivorous coral reef fish community. In calculating niche volumes for 21 species, based on their microhabitat utilization patterns during foraging, and computing functional overlaps, we provide a measurement of functional redundancy or complementarity. Complementarity is the inverse of redundancy and is defined as less than 50% overlap in niche volumes. The analyses reveal extensive complementarity with an average functional overlap of just 15.2%. Furthermore, the analyses divide herbivorous reef fishes into two broad groups. The first group (predominantly surgeonfishes and parrotfishes) comprises species feeding on exposed surfaces and predominantly open reef matrix or sandy substrata, resulting in small niche volumes and extensive complementarity. In contrast, the second group consists of species (predominantly rabbitfishes) that feed over a wider range of microhabitats, penetrating the reef matrix to exploit concealed surfaces of various substratum types. These species show high variation among individuals, leading to large niche volumes, more overlap and less complementarity. These results may have crucial consequences for our understanding of herbivorous processes on coral reefs, as algal removal appears to depend strongly on species-specific microhabitat utilization patterns of herbivores. Furthermore, the results emphasize the capacity of the individual-based analyses to reveal variation in the functional niches of species, even in high-diversity systems such as coral reefs, demonstrating its potential applicability to other high-diversity ecosystems. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

A discriminatory function for prediction of protein-DNA interactions based on alpha shape modeling.

PubMed

Zhou, Weiqiang; Yan, Hong

2010-10-15

Protein-DNA interaction has significant importance in many biological processes. However, the underlying principle of the molecular recognition process is still largely unknown. As more high-resolution 3D structures of protein-DNA complex are becoming available, the surface characteristics of the complex become an important research topic. In our work, we apply an alpha shape model to represent the surface structure of the protein-DNA complex and developed an interface-atom curvature-dependent conditional probability discriminatory function for the prediction of protein-DNA interaction. The interface-atom curvature-dependent formalism captures atomic interaction details better than the atomic distance-based method. The proposed method provides good performance in discriminating the native structures from the docking decoy sets, and outperforms the distance-dependent formalism in terms of the z-score. Computer experiment results show that the curvature-dependent formalism with the optimal parameters can achieve a native z-score of -8.17 in discriminating the native structure from the highest surface-complementarity scored decoy set and a native z-score of -7.38 in discriminating the native structure from the lowest RMSD decoy set. The interface-atom curvature-dependent formalism can also be used to predict apo version of DNA-binding proteins. These results suggest that the interface-atom curvature-dependent formalism has a good prediction capability for protein-DNA interactions. The code and data sets are available for download on http://www.hy8.com/bioinformatics.htm kenandzhou@hotmail.com.

Epitope mapping of anti-interleukin-13 neutralizing antibody CNTO607.

PubMed

Teplyakov, Alexey; Obmolova, Galina; Wu, Sheng-Jiun; Luo, Jinquan; Kang, James; O'Neil, Karyn; Gilliland, Gary L

2009-05-29

CNTO607 is a neutralizing anti-interleukin-13 (IL-13) human monoclonal antibody obtained from a phage display library. To determine how this antibody inhibits the biological effect of IL-13, we determined the binding epitope by X-ray crystallography. The crystal structure of the complex between CNTO607 Fab and IL-13 reveals the antibody epitope at the surface formed by helices A and D of IL-13. This epitope overlaps with the IL-4Ralpha/IL-13Ralpha1 receptor-binding site, which explains the neutralizing effect of CNTO607. The extensive antibody interface covers an area of 1000 A(2), which is consistent with the high binding affinity. The key features of the interface are the charge and shape complementarity of the molecules that include two hydrophobic pockets on IL-13 that accommodate Phe32 [complementarity-determining region (CDR) L2] and Trp100a (CDR H3) and a number of salt bridges between basic residues of IL-13 and acidic residues of the antibody. Comparison with the structure of the free Fab shows that the CDR residues do not change their conformation upon complex formation, with the exception of two residues in CDR H3, Trp100a and Asp100b, which change rotamer conformations. To evaluate the relative contribution of the epitope residues to CNTO607 binding, we performed alanine-scanning mutagenesis of the A-D region of IL-13. This study confirmed the primary role of electrostatic interactions for antigen recognition.

Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires.

PubMed

DeKosky, Brandon J; Lungu, Oana I; Park, Daechan; Johnson, Erik L; Charab, Wissam; Chrysostomou, Constantine; Kuroda, Daisuke; Ellington, Andrew D; Ippolito, Gregory C; Gray, Jeffrey J; Georgiou, George

2016-05-10

Elucidating how antigen exposure and selection shape the human antibody repertoire is fundamental to our understanding of B-cell immunity. We sequenced the paired heavy- and light-chain variable regions (VH and VL, respectively) from large populations of single B cells combined with computational modeling of antibody structures to evaluate sequence and structural features of human antibody repertoires at unprecedented depth. Analysis of a dataset comprising 55,000 antibody clusters from CD19(+)CD20(+)CD27(-) IgM-naive B cells, >120,000 antibody clusters from CD19(+)CD20(+)CD27(+) antigen-experienced B cells, and >2,000 RosettaAntibody-predicted structural models across three healthy donors led to a number of key findings: (i) VH and VL gene sequences pair in a combinatorial fashion without detectable pairing restrictions at the population level; (ii) certain VH:VL gene pairs were significantly enriched or depleted in the antigen-experienced repertoire relative to the naive repertoire; (iii) antigen selection increased antibody paratope net charge and solvent-accessible surface area; and (iv) public heavy-chain third complementarity-determining region (CDR-H3) antibodies in the antigen-experienced repertoire showed signs of convergent paired light-chain genetic signatures, including shared light-chain third complementarity-determining region (CDR-L3) amino acid sequences and/or Vκ,λ-Jκ,λ genes. The data reported here address several longstanding questions regarding antibody repertoire selection and development and provide a benchmark for future repertoire-scale analyses of antibody responses to vaccination and disease.

CPdock: the complementarity plot for docking of proteins: implementing multi-dielectric continuum electrostatics.

PubMed

Basu, Sankar

2017-12-07

The complementarity plot (CP) is an established validation tool for protein structures, applicable to both globular proteins (folding) as well as protein-protein complexes (binding). It computes the shape and electrostatic complementarities (S m , E m ) for amino acid side-chains buried within the protein interior or interface and plots them in a two-dimensional plot having knowledge-based probabilistic quality estimates for the residues as well as for the whole structure. The current report essentially presents an upgraded version of the plot with the implementation of the advanced multi-dielectric functionality (as in Delphi version 6.2 or higher) in the computation of electrostatic complementarity to make the validation tool physico-chemically more realistic. The two methods (single- and multi-dielectric) agree decently in their resultant E m values, and hence, provisions for both methods have been kept in the software suite. So to speak, the global electrostatic balance within a well-folded protein and/or a well-packed interface seems only marginally perturbed by the choice of different internal dielectric values. However, both from theoretical as well as practical grounds, the more advanced multi-dielectric version of the plot is certainly recommended for potentially producing more reliable results. The report also presents a new methodology and a variant plot, namely CP dock , based on the same principles of complementarity specifically designed to be used in the docking of proteins. The efficacy of the method to discriminate between good and bad docked protein complexes has been tested on a recent state-of-the-art docking benchmark. The results unambiguously indicate that CP dock can indeed be effective in the initial screening phase of a docking scoring pipeline before going into more sophisticated and computationally expensive scoring functions. CP dock has been made available at https://github.com/nemo8130/CPdock . Graphical Abstract An example showing the efficacy of CP dock to be used in the initial screening phase of a protein-protein docking scoring pipeline.

From chemical metabolism to life: the origin of the genetic coding process

PubMed Central

2017-01-01

Looking for origins is so much rooted in ideology that most studies reflect opinions that fail to explore the first realistic scenarios. To be sure, trying to understand the origins of life should be based on what we know of current chemistry in the solar system and beyond. There, amino acids and very small compounds such as carbon dioxide, dihydrogen or dinitrogen and their immediate derivatives are ubiquitous. Surface-based chemical metabolism using these basic chemicals is the most likely beginning in which amino acids, coenzymes and phosphate-based small carbon molecules were built up. Nucleotides, and of course RNAs, must have come to being much later. As a consequence, the key question to account for life is to understand how chemical metabolism that began with amino acids progressively shaped into a coding process involving RNAs. Here I explore the role of building up complementarity rules as the first information-based process that allowed for the genetic code to emerge, after RNAs were substituted to surfaces to carry over the basic metabolic pathways that drive the pursuit of life. PMID:28684991

Localized Surface Plasmon Resonance Biosensing: Current Challenges and Approaches

PubMed Central

Unser, Sarah; Bruzas, Ian; He, Jie; Sagle, Laura

2015-01-01

Localized surface plasmon resonance (LSPR) has emerged as a leader among label-free biosensing techniques in that it offers sensitive, robust, and facile detection. Traditional LSPR-based biosensing utilizes the sensitivity of the plasmon frequency to changes in local index of refraction at the nanoparticle surface. Although surface plasmon resonance technologies are now widely used to measure biomolecular interactions, several challenges remain. In this article, we have categorized these challenges into four categories: improving sensitivity and limit of detection, selectivity in complex biological solutions, sensitive detection of membrane-associated species, and the adaptation of sensing elements for point-of-care diagnostic devices. The first section of this article will involve a conceptual discussion of surface plasmon resonance and the factors affecting changes in optical signal detected. The following sections will discuss applications of LSPR biosensing with an emphasis on recent advances and approaches to overcome the four limitations mentioned above. First, improvements in limit of detection through various amplification strategies will be highlighted. The second section will involve advances to improve selectivity in complex media through self-assembled monolayers, “plasmon ruler” devices involving plasmonic coupling, and shape complementarity on the nanoparticle surface. The following section will describe various LSPR platforms designed for the sensitive detection of membrane-associated species. Finally, recent advances towards multiplexed and microfluidic LSPR-based devices for inexpensive, rapid, point-of-care diagnostics will be discussed. PMID:26147727

Programmable molecular recognition based on the geometry of DNA nanostructures.

PubMed

Woo, Sungwook; Rothemund, Paul W K

2011-07-10

From ligand-receptor binding to DNA hybridization, molecular recognition plays a central role in biology. Over the past several decades, chemists have successfully reproduced the exquisite specificity of biomolecular interactions. However, engineering multiple specific interactions in synthetic systems remains difficult. DNA retains its position as the best medium with which to create orthogonal, isoenergetic interactions, based on the complementarity of Watson-Crick binding. Here we show that DNA can be used to create diverse bonds using an entirely different principle: the geometric arrangement of blunt-end stacking interactions. We show that both binary codes and shape complementarity can serve as a basis for such stacking bonds, and explore their specificity, thermodynamics and binding rules. Orthogonal stacking bonds were used to connect five distinct DNA origami. This work, which demonstrates how a single attractive interaction can be developed to create diverse bonds, may guide strategies for molecular recognition in systems beyond DNA nanostructures.

Real-Time Ligand Binding Pocket Database Search Using Local Surface Descriptors

PubMed Central

Chikhi, Rayan; Sael, Lee; Kihara, Daisuke

2010-01-01

Due to the increasing number of structures of unknown function accumulated by ongoing structural genomics projects, there is an urgent need for computational methods for characterizing protein tertiary structures. As functions of many of these proteins are not easily predicted by conventional sequence database searches, a legitimate strategy is to utilize structure information in function characterization. Of a particular interest is prediction of ligand binding to a protein, as ligand molecule recognition is a major part of molecular function of proteins. Predicting whether a ligand molecule binds a protein is a complex problem due to the physical nature of protein-ligand interactions and the flexibility of both binding sites and ligand molecules. However, geometric and physicochemical complementarity is observed between the ligand and its binding site in many cases. Therefore, ligand molecules which bind to a local surface site in a protein can be predicted by finding similar local pockets of known binding ligands in the structure database. Here, we present two representations of ligand binding pockets and utilize them for ligand binding prediction by pocket shape comparison. These representations are based on mapping of surface properties of binding pockets, which are compactly described either by the two dimensional pseudo-Zernike moments or the 3D Zernike descriptors. These compact representations allow a fast real-time pocket searching against a database. Thorough benchmark study employing two different datasets show that our representations are competitive with the other existing methods. Limitations and potentials of the shape-based methods as well as possible improvements are discussed. PMID:20455259

Real-time ligand binding pocket database search using local surface descriptors.

PubMed

Chikhi, Rayan; Sael, Lee; Kihara, Daisuke

2010-07-01

Because of the increasing number of structures of unknown function accumulated by ongoing structural genomics projects, there is an urgent need for computational methods for characterizing protein tertiary structures. As functions of many of these proteins are not easily predicted by conventional sequence database searches, a legitimate strategy is to utilize structure information in function characterization. Of particular interest is prediction of ligand binding to a protein, as ligand molecule recognition is a major part of molecular function of proteins. Predicting whether a ligand molecule binds a protein is a complex problem due to the physical nature of protein-ligand interactions and the flexibility of both binding sites and ligand molecules. However, geometric and physicochemical complementarity is observed between the ligand and its binding site in many cases. Therefore, ligand molecules which bind to a local surface site in a protein can be predicted by finding similar local pockets of known binding ligands in the structure database. Here, we present two representations of ligand binding pockets and utilize them for ligand binding prediction by pocket shape comparison. These representations are based on mapping of surface properties of binding pockets, which are compactly described either by the two-dimensional pseudo-Zernike moments or the three-dimensional Zernike descriptors. These compact representations allow a fast real-time pocket searching against a database. Thorough benchmark studies employing two different datasets show that our representations are competitive with the other existing methods. Limitations and potentials of the shape-based methods as well as possible improvements are discussed.

Tumor-Triggered Geometrical Shape Switch of Chimeric Peptide for Enhanced in Vivo Tumor Internalization and Photodynamic Therapy.

PubMed

Han, Kai; Zhang, Jin; Zhang, Weiyun; Wang, Shibo; Xu, Luming; Zhang, Chi; Zhang, Xianzheng; Han, Heyou

2017-03-28

Geometrical shape of nanoparticles plays an important role in cellular internalization. However, the applicability in tumor selective therapeutics is still scarcely reported. In this article, we designed a tumor extracellular acidity-responsive chimeric peptide with geometrical shape switch for enhanced tumor internalization and photodynamic therapy. This chimeric peptide could self-assemble into spherical nanoparticles at physiological condition. While at tumor extracellular acidic microenvironment, chimeric peptide underwent detachment of acidity-sensitive 2,3-dimethylmaleic anhydride groups. The subsequent recovery of ionic complementarity between chimeric peptides resulted in formation of rod-like nanoparticles. Both in vitro and in vivo studies demonstrated that this acidity-triggered geometrical shape switch endowed chimeric peptide with accelerated internalization in tumor cells, prolonged accumulation in tumor tissue, enhanced photodynamic therapy, and minimal side effects. Our results suggested that fusing tumor microenvironment with geometrical shape switch should be a promising strategy for targeted drug delivery.

Modeling the Alzheimer Abeta17-42 fibril architecture: tight intermolecular sheet-sheet association and intramolecular hydrated cavities.

PubMed

Zheng, Jie; Jang, Hyunbum; Ma, Buyong; Tsai, Chung-Jun; Nussinov, Ruth

2007-11-01

We investigate Abeta(17-42) protofibril structures in solution using molecular dynamics simulations. Recently, NMR and computations modeled the Abeta protofibril as a longitudinal stack of U-shaped molecules, creating an in-parallel beta-sheet and loop spine. Here we study the molecular architecture of the fibril formed by spine-spine association. We model in-register intermolecular beta-sheet-beta-sheet associations and study the consequences of Alzheimer's mutations (E22G, E22Q, E22K, and M35A) on the organization. We assess the structural stability and association force of Abeta oligomers with different sheet-sheet interfaces. Double-layered oligomers associating through the C-terminal-C-terminal interface are energetically more favorable than those with the N-terminal-N-terminal interface, although both interfaces exhibit high structural stability. The C-terminal-C-terminal interface is essentially stabilized by hydrophobic and van der Waals (shape complementarity via M35-M35 contacts) intermolecular interactions, whereas the N-terminal-N-terminal interface is stabilized by hydrophobic and electrostatic interactions. Hence, shape complementarity, or the "steric zipper" motif plays an important role in amyloid formation. On the other hand, the intramolecular Abeta beta-strand-loop-beta-strand U-shaped motif creates a hydrophobic cavity with a diameter of 6-7 A, allowing water molecules and ions to conduct through. The hydrated hydrophobic cavities may allow optimization of the sheet association and constitute a typical feature of fibrils, in addition to the tight sheet-sheet association. Thus, we propose that Abeta fiber architecture consists of alternating layers of tight packing and hydrated cavities running along the fibrillar axis, which might be possibly detected by high-resolution imaging.

Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces

PubMed Central

Chen, Ching-Tai; Peng, Hung-Pin; Jian, Jhih-Wei; Tsai, Keng-Chang; Chang, Jeng-Yih; Yang, Ei-Wen; Chen, Jun-Bo; Ho, Shinn-Ying; Hsu, Wen-Lian; Yang, An-Suei

2012-01-01

Protein-protein interactions are key to many biological processes. Computational methodologies devised to predict protein-protein interaction (PPI) sites on protein surfaces are important tools in providing insights into the biological functions of proteins and in developing therapeutics targeting the protein-protein interaction sites. One of the general features of PPI sites is that the core regions from the two interacting protein surfaces are complementary to each other, similar to the interior of proteins in packing density and in the physicochemical nature of the amino acid composition. In this work, we simulated the physicochemical complementarities by constructing three-dimensional probability density maps of non-covalent interacting atoms on the protein surfaces. The interacting probabilities were derived from the interior of known structures. Machine learning algorithms were applied to learn the characteristic patterns of the probability density maps specific to the PPI sites. The trained predictors for PPI sites were cross-validated with the training cases (consisting of 432 proteins) and were tested on an independent dataset (consisting of 142 proteins). The residue-based Matthews correlation coefficient for the independent test set was 0.423; the accuracy, precision, sensitivity, specificity were 0.753, 0.519, 0.677, and 0.779 respectively. The benchmark results indicate that the optimized machine learning models are among the best predictors in identifying PPI sites on protein surfaces. In particular, the PPI site prediction accuracy increases with increasing size of the PPI site and with increasing hydrophobicity in amino acid composition of the PPI interface; the core interface regions are more likely to be recognized with high prediction confidence. The results indicate that the physicochemical complementarity patterns on protein surfaces are important determinants in PPIs, and a substantial portion of the PPI sites can be predicted correctly with the physicochemical complementarity features based on the non-covalent interaction data derived from protein interiors. PMID:22701576

Structural Analysis of HMGD-DNA Complexes Reveal Influence of Intercalation on Sequence Selectivity and DNA Bending

PubMed Central

Churchill, Mair E.A.; Klass, Janet; Zoetewey, David L.

2010-01-01

The ubiquitous eukaryotic High-Mobility-Group-Box (HMGB) chromosomal proteins promote many chromatin-mediated cellular activities through their non-sequence-specific binding and bending of DNA. Minor groove DNA binding by the HMG box results in substantial DNA bending toward the major groove owing to electrostatic interactions, shape complementarity and DNA intercalation that occurs at two sites. Here, the structures of the complexes formed with DNA by a partially DNA intercalation-deficient mutant of Drosophila melanogaster HMGD have been determined by X-ray crystallography at a resolution of 2.85 Å. The six proteins and fifty base pairs of DNA in the crystal structure revealed a variety of bound conformations. All of the proteins bound in the minor groove, bridging DNA molecules, presumably because these DNA regions are easily deformed. The loss of the primary site of DNA intercalation decreased overall DNA bending and shape complementarity. However, DNA bending at the secondary site of intercalation was retained and most protein-DNA contacts were preserved. The mode of binding resembles the HMGB1-boxA-cisplatin-DNA complex, which also lacks a primary intercalating residue. This study provides new insights into the binding mechanisms used by HMG boxes to recognize varied DNA structures and sequences as well as modulate DNA structure and DNA bending. PMID:20800069

Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires

PubMed Central

DeKosky, Brandon J.; Lungu, Oana I.; Park, Daechan; Johnson, Erik L.; Charab, Wissam; Chrysostomou, Constantine; Kuroda, Daisuke; Ellington, Andrew D.; Ippolito, Gregory C.; Gray, Jeffrey J.; Georgiou, George

2016-01-01

Elucidating how antigen exposure and selection shape the human antibody repertoire is fundamental to our understanding of B-cell immunity. We sequenced the paired heavy- and light-chain variable regions (VH and VL, respectively) from large populations of single B cells combined with computational modeling of antibody structures to evaluate sequence and structural features of human antibody repertoires at unprecedented depth. Analysis of a dataset comprising 55,000 antibody clusters from CD19+CD20+CD27− IgM-naive B cells, >120,000 antibody clusters from CD19+CD20+CD27+ antigen–experienced B cells, and >2,000 RosettaAntibody-predicted structural models across three healthy donors led to a number of key findings: (i) VH and VL gene sequences pair in a combinatorial fashion without detectable pairing restrictions at the population level; (ii) certain VH:VL gene pairs were significantly enriched or depleted in the antigen-experienced repertoire relative to the naive repertoire; (iii) antigen selection increased antibody paratope net charge and solvent-accessible surface area; and (iv) public heavy-chain third complementarity-determining region (CDR-H3) antibodies in the antigen-experienced repertoire showed signs of convergent paired light-chain genetic signatures, including shared light-chain third complementarity-determining region (CDR-L3) amino acid sequences and/or Vκ,λ–Jκ,λ genes. The data reported here address several longstanding questions regarding antibody repertoire selection and development and provide a benchmark for future repertoire-scale analyses of antibody responses to vaccination and disease. PMID:27114511

New Existence Conditions for Order Complementarity Problems

NASA Astrophysics Data System (ADS)

Németh, S. Z.

2009-09-01

Complementarity problems are mathematical models of problems in economics, engineering and physics. A special class of complementarity problems are the order complementarity problems [2]. Order complementarity problems can be applied in lubrication theory [6] and economics [1]. The notion of exceptional family of elements for general order complementarity problems in Banach spaces will be introduced. It will be shown that for general order complementarity problems defined by completely continuous fields the problem has either a solution or an exceptional family of elements (for other notions of exceptional family of elements see [1, 2, 3, 4] and the related references therein). This solves a conjecture of [2] about the existence of exceptional family of elements for order complementarity problems. The proof can be done by using the Leray-Schauder alternative [5]. An application to integral operators will be given.

Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking

PubMed Central

Madaoui, Hocine; Guerois, Raphaël

2008-01-01

Protein surfaces are under significant selection pressure to maintain interactions with their partners throughout evolution. Capturing how selection pressure acts at the interfaces of protein–protein complexes is a fundamental issue with high interest for the structural prediction of macromolecular assemblies. We tackled this issue under the assumption that, throughout evolution, mutations should minimally disrupt the physicochemical compatibility between specific clusters of interacting residues. This constraint drove the development of the so-called Surface COmplementarity Trace in Complex History score (SCOTCH), which was found to discriminate with high efficiency the structure of biological complexes. SCOTCH performances were assessed not only with respect to other evolution-based approaches, such as conservation and coevolution analyses, but also with respect to statistically based scoring methods. Validated on a set of 129 complexes of known structure exhibiting both permanent and transient intermolecular interactions, SCOTCH appears as a robust strategy to guide the prediction of protein–protein complex structures. Of particular interest, it also provides a basic framework to efficiently track how protein surfaces could evolve while keeping their partners in contact. PMID:18511568

Very Strong Binding for a Neutral Calix[4]pyrrole Receptor Displaying Positive Allosteric Binding.

PubMed

Duedal, Troels; Nielsen, Kent A; Olsen, Gunnar; Rasmussen, Charlotte B G; Kongsted, Jacob; Levillain, Eric; Breton, Tony; Miyazaki, Eigo; Takimiya, Kazuo; Bähring, Steffen; Jeppesen, Jan O

2017-02-17

The dual-analyte responsive behavior of tetraTTF-calix[4]pyrrole receptor 1 has been shown to complex electron-deficient planar guests in a 2:1 fashion by adopting a so-called 1,3-alternate conformation. However, stronger 1:1 complexes have been demonstrated with tetraalkylammonium halide salts that defer receptor 1 to its cone conformation. Herein, we report the complexation of an electron-deficient planar guest, 1,4,5,8-naphthalenetetracarboxylic dianhydride (NTCDA, 2) that champions the complexation with 1, resulting in a high association constant K a = 3 × 10 10 M -2 . The tetrathiafulvalene (TTF) subunits in the tetraTTF-calix[4]pyrrole receptor 1 present a near perfect shape and electronic complementarity to the NTCDA guest, which was confirmed by X-ray crystal structure analysis, DFT calculations, and electron density surface mapping. Moreover, the complexation of these species results in the formation of a charge transfer complex (2 2 ⊂1) as visualized by a readily apparent color change from yellow to brown.

Structural basis for highly effective HIV-1 neutralization by CD4-mimetic miniproteins revealed by 1.5 Å co-crystal structure of gp120 and M48U1

PubMed Central

Acharya, Priyamvada; Luongo, Timothy; Louder, Mark K.; McKee, Krisha; Yang, Yongping; Kwon, Young Do; Mascola, John R.; Kessler, Pascal; Martin, Loïc; Kwong, Peter D.

2014-01-01

The interface between HIV-1 gp120 envelope glycoprotein and CD4 receptor contains an unusual interfacial cavity, the “Phe43 cavity”, which miniprotein mimetics of CD4 with non-natural extensions can potentially utilize to enhance their neutralization of HIV-1. Here we report co-crystal structures of HIV-1 gp120 with miniproteins M48U1 and M48U7, which insert cyclohexylmethoxy and 5-hydroxypentylmethoxy extensions, respectively, into the Phe43 cavity. Both inserts displayed flexibility and hydrophobic interactions, but the M48U1 insert showed better shape complementarity with the Phe43 cavity than the M48U7 insert. Subtle alteration in gp120 conformation played a substantial role in optimizing fit. With M48U1, these translated into a YU2-gp120 affinity of 0.015 nM and neutralization of all 180-circulating HIV-1 strains tested, except clade-A/E isolates with non-canonical Phe43 cavities. Ligand chemistry, shape complementary, surface burial, and gp120 conformation act in concert to modulate binding of ligands to the gp120-Phe43 cavity and, when optimized, can effect near pan-neutralization of HIV-1. PMID:23707685

Bioethical pluralism and complementarity.

PubMed

Grinnell, Frederick; Bishop, Jeffrey P; McCullough, Laurence B

2002-01-01

This essay presents complementarity as a novel feature of bioethical pluralism. First introduced by Neils Bohr in conjunction with quantum physics, complementarity in bioethics occurs when different perspectives account for equally important features of a situation but are mutually exclusive. Unlike conventional approaches to bioethical pluralism, which attempt in one fashion or another to isolate and choose between different perspectives, complementarity accepts all perspectives. As a result, complementarity results in a state of holistic, dynamic tension, rather than one that yields singular or final moral judgments.

Decorin Core Protein (Decoron) Shape Complements Collagen Fibril Surface Structure and Mediates Its Binding

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

Orgel, Joseph P.R.O.; Eid, Aya; Antipova, Olga

Decorin is the archetypal small leucine rich repeat proteoglycan of the vertebrate extracellular matrix (ECM). With its glycosaminoglycuronan chain, it is responsible for stabilizing inter-fibrillar organization. Type I collagen is the predominant member of the fibrillar collagen family, fulfilling both organizational and structural roles in animal ECMs. In this study, interactions between decoron (the decorin core protein) and binding sites in the d and e1 bands of the type I collagen fibril were investigated through molecular modeling of their respective X-ray diffraction structures. Previously, it was proposed that a model-based, highly curved concave decoron interacts with a single collagen molecule,more » which would form extensive van der Waals contacts and give rise to strong non-specific binding. However, the large well-ordered aggregate that is the collagen fibril places significant restraints on modes of ligand binding and necessitates multi-collagen molecular contacts. We present here a relatively high-resolution model of the decoron-fibril collagen complex. We find that the respective crystal structures complement each other well, although it is the monomeric form of decoron that shows the most appropriate shape complementarity with the fibril surface and favorable calculated energies of interaction. One molecule of decoron interacts with four to six collagen molecules, and the binding specificity relies on a large number of hydrogen bonds and electrostatic interactions, primarily with the collagen motifs KXGDRGE and AKGDRGE (d and e{sub 1} bands). This work helps us to understand collagen-decorin interactions and the molecular architecture of the fibrillar ECM in health and disease.« less

Decorin core protein (decoron) shape complements collagen fibril surface structure and mediates its binding.

PubMed

Orgel, Joseph P R O; Eid, Aya; Antipova, Olga; Bella, Jordi; Scott, John E

2009-09-15

Decorin is the archetypal small leucine rich repeat proteoglycan of the vertebrate extracellular matrix (ECM). With its glycosaminoglycuronan chain, it is responsible for stabilizing inter-fibrillar organization. Type I collagen is the predominant member of the fibrillar collagen family, fulfilling both organizational and structural roles in animal ECMs. In this study, interactions between decoron (the decorin core protein) and binding sites in the d and e(1) bands of the type I collagen fibril were investigated through molecular modeling of their respective X-ray diffraction structures. Previously, it was proposed that a model-based, highly curved concave decoron interacts with a single collagen molecule, which would form extensive van der Waals contacts and give rise to strong non-specific binding. However, the large well-ordered aggregate that is the collagen fibril places significant restraints on modes of ligand binding and necessitates multi-collagen molecular contacts. We present here a relatively high-resolution model of the decoron-fibril collagen complex. We find that the respective crystal structures complement each other well, although it is the monomeric form of decoron that shows the most appropriate shape complementarity with the fibril surface and favorable calculated energies of interaction. One molecule of decoron interacts with four to six collagen molecules, and the binding specificity relies on a large number of hydrogen bonds and electrostatic interactions, primarily with the collagen motifs KXGDRGE and AKGDRGE (d and e(1) bands). This work helps us to understand collagen-decorin interactions and the molecular architecture of the fibrillar ECM in health and disease.

SDU: A Semidefinite Programming-Based Underestimation Method for Stochastic Global Optimization in Protein Docking

DTIC Science & Technology

2007-04-01

optimization methodology we introduce. State-of-the-art protein - protein docking approaches start by identifying conformations with good surface /chemical com...side-chains on the interface ). The protein - protein docking literature (e.g., [8] and the references therein) is predominantly treating the docking...mations by various measures of surface complementarity which can be efficiently computed using fast Fourier correlation tech- niques (FFTs). However, when

Multifunctional hybrid networks based on self assembling peptide sequences

NASA Astrophysics Data System (ADS)

Sathaye, Sameer

The overall aim of this dissertation is to achieve a comprehensive correlation between the molecular level changes in primary amino acid sequences of amphiphilic beta-hairpin peptides and their consequent solution-assembly properties and bulk network hydrogel behavior. This has been accomplished using two broad approaches. In the first approach, amino acid substitutions were made to peptide sequence MAX1 such that the hydrophobic surfaces of the folded beta-hairpins from the peptides demonstrate shape specificity in hydrophobic interactions with other beta-hairpins during the assembly process, thereby causing changes to the peptide nanostructure and bulk rheological properties of hydrogels formed from the peptides. Steric lock and key complementary hydrophobic interactions were designed to occur between two beta-hairpin molecules of a single molecule, LNK1 during beta-sheet fibrillar assembly of LNK1. Experimental results from circular dichroism, transmission electron microscopy and oscillatory rheology collectively indicate that the molecular design of the LNK1 peptide can be assigned the cause of the drastically different behavior of the networks relative to MAX1. The results indicate elimination or significant reduction of fibrillar branching due to steric complementarity in LNK1 that does not exist in MAX1, thus supporting the original hypothesis. As an extension of the designed steric lock and key complementarity between two beta-hairpin molecules of the same peptide molecule. LNK1, three new pairs of peptide molecules LP1-KP1, LP2-KP2 and LP3-KP3 that resemble complementary 'wedge' and 'trough' shapes when folded into beta-hairpins were designed and studied. All six peptides individually and when blended with their corresponding shape complement formed fibrillar nanostructures with non-uniform thickness values. Loose packing in the assembled structures was observed in all the new peptides as compared to the uniform tight packing in MAX1 by SANS analysis. This loose packing can be attributed to the designed wedge and trough shapes of the peptides disturbing formation of a uniform bilayer type structure proposed in the case of MAX1 with each hairpin having a flat hydrophobic surface. Although designed changes in hydrophobic shape of the peptide nanofibril core in the new peptides were found to significantly influence the self-assembled nanostructure and network rheological behavior, a lack of direct morphological and rheological evidence to prove shape specific hydrophobic interactions between wedge and trough shaped beta-hairpins was encountered. In the second approach, peptides with established differences in assembly kinetics and bulk mechanical properties of assembled peptide hydrogels were used to develop composite materials with diverse morphological and mechanical properties by blending with the biopolymer hyaluronic acid. The diverse properties of the composites have been correlated to the specific peptide hydrogels used to develop the composite and the different stages of peptide assembly at which blending with hyaluronic acid was carried out. Finally along with overall conclusions, the new area of co-assembly of peptides in solution has been explored and discussed as potential future work following the research discussed in this dissertation. Strategies such as construction of composite hydrogels from blends of MAX1/MAX8 peptide hydrogels and biologically important anionic species such as heparin biopolymer and DNA have been discussed. Another area of future work discussed is the design and study of peptides that can incorporate chemically crosslinkable functional groups in their hydrophobic amino acid side chains that can be covalently crosslinked after peptide assembly into fibrils. Such covalent crosslinking can potentially lead to stiffer individual peptide fibrils due to additional bond formation at the fibrillar core and therefore much stiffer hydrogels due to a synergistic effect. These enhanced stiffness values can render these new hydrogels excellent candidates for applications like development of extracellular mimetic materials and substrates with easily tunable stiffness values for stem cell differentiation studies.

Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation

PubMed Central

Serganov, Alexander; Keiper, Sonja; Malinina, Lucy; Tereshko, Valentina; Skripkin, Eugene; Höbartner, Claudia; Polonskaia, Anna; Phan, Anh Tuân; Wombacher, Richard; Micura, Ronald; Dauter, Zbigniew; Jäschke, Andres; Patel, Dinshaw J

2015-01-01

The majority of structural efforts addressing RNA’s catalytic function have focused on natural ribozymes, which catalyze phosphodiester transfer reactions. By contrast, little is known about how RNA catalyzes other types of chemical reactions. We report here the crystal structures of a ribozyme that catalyzes enantioselective carbon-carbon bond formation by the Diels-Alder reaction in the unbound state and in complex with a reaction product. The RNA adopts a λ-shaped nested pseudoknot architecture whose preformed hydrophobic pocket is precisely complementary in shape to the reaction product. RNA folding and product binding are dictated by extensive stacking and hydrogen bonding, whereas stereoselection is governed by the shape of the catalytic pocket. Catalysis is apparently achieved by a combination of proximity, complementarity and electronic effects. We observe structural parallels in the independently evolved catalytic pocket architectures for ribozyme- and antibody-catalyzed Diels-Alder carbon-carbon bond-forming reactions. PMID:15723077

MEGADOCK: An All-to-All Protein-Protein Interaction Prediction System Using Tertiary Structure Data

PubMed Central

Ohue, Masahito; Matsuzaki, Yuri; Uchikoga, Nobuyuki; Ishida, Takashi; Akiyama, Yutaka

2014-01-01

The elucidation of protein-protein interaction (PPI) networks is important for understanding cellular structure and function and structure-based drug design. However, the development of an effective method to conduct exhaustive PPI screening represents a computational challenge. We have been investigating a protein docking approach based on shape complementarity and physicochemical properties. We describe here the development of the protein-protein docking software package “MEGADOCK” that samples an extremely large number of protein dockings at high speed. MEGADOCK reduces the calculation time required for docking by using several techniques such as a novel scoring function called the real Pairwise Shape Complementarity (rPSC) score. We showed that MEGADOCK is capable of exhaustive PPI screening by completing docking calculations 7.5 times faster than the conventional docking software, ZDOCK, while maintaining an acceptable level of accuracy. When MEGADOCK was applied to a subset of a general benchmark dataset to predict 120 relevant interacting pairs from 120 x 120 = 14,400 combinations of proteins, an F-measure value of 0.231 was obtained. Further, we showed that MEGADOCK can be applied to a large-scale protein-protein interaction-screening problem with accuracy better than random. When our approach is combined with parallel high-performance computing systems, it is now feasible to search and analyze protein-protein interactions while taking into account three-dimensional structures at the interactome scale. MEGADOCK is freely available at http://www.bi.cs.titech.ac.jp/megadock. PMID:23855673

Birth-Order Complementarity and Marital Adjustment.

ERIC Educational Resources Information Center

Vos, Cornelia J. Vanderkooy; Hayden, Delbert J.

1985-01-01

Tested the influence of birth-order complementarity on marital adjustment among 327 married women using the Spanier Dyadic Adjustment Scale (1976). Birth-order complementarity was found to be unassociated with marital adjustment. (Author/BL)

New Approaches Towards Recognition of Nucleic Acid Triple Helices

PubMed Central

Arya, Dev P.

2012-01-01

We show that groove recognition of nucleic acid triple helices can be achieved with aminosugars. Among these aminosugars, neomycin is the most effective aminoglycoside (groove binder) for stabilizing a DNA triple helix. It stabilizes both the T·A·T triplex and mixed-base DNA triplexes better than known DNA minor groove binders (which usually destabilize the triplex) and polyamines. Neomycin selectively stabilizes the triplex (T·A·T and mixed base) without any effect on the DNA duplex. The selectivity of neomycin likely originates from its potential and shape complementarity to the triplex Watson–Hoogsteen groove, making it the first molecule that selectively recognizes a triplex groove over a duplex groove. The groove recognition of aminoglycosides is not limited to DNA triplexes, but also extends to RNA and hybrid triple helical structures. Intercalator–neomycin conjugates are shown to simultaneously probe the base stacking and groove surface in the DNA triplex. Calorimetric and spectrosocopic studies allow the quantification of the effect of surface area of the intercalating moiety on binding to the triplex. These studies outline a novel approach to the recognition of DNA triplexes that incorporates the use of non-competing binding sites. These principles of dual recognition should be applicable to the design of ligands that can bind any given nucleic acid target with nanomolar affinities and with high selectivity. PMID:21073199

Amphipathic peptide affects the lateral domain organization of lipid bilayers.

PubMed

Polozov, I V; Polozova, A I; Molotkovsky, J G; Epand, R M

1997-09-04

Using lipid-specific fluorescent probes, we studied the effects of amphipathic helical, membrane active peptides of the A- and L-type on membrane domain organization. In zwitterionic binary systems composed of mixtures of phosphatidylcholine and phosphatidylethanolamine, both types of peptides associated with the fluid phase. While binding with high affinity to fluid membranes, peptides were unable to penetrate into the lipid membrane in the gel state. If trapped kinetically by cooling from the fluid phase, peptides dissociated from the gel membrane on the time scale of several hours. While the geometrical shape of the alpha-helical peptides determines their interactions with membranes with non-bilayer phase propensity, the shape complementarity mechanism by itself is unable to induce lateral phase separation in a fluid membrane. Charge-charge interactions are capable of inducing lateral domain formation in fluid membranes. Both peptides had affinity for anionic lipids which resulted in about 30% enrichment of acidic lipids within several nanometers of the peptide's tryptophan, but there was no long-range order in peptide-induced lipid demixing. Peptide insertion in fluid acidic membranes was accompanied by only a small increase in bilayer surface and a decrease in polarity in the membrane core. Peptide-lipid charge-charge interactions were also capable of modulating existing domain composition in the course of the main phase transition in mixtures of anionic phosphatidylglycerol with zwitterionic phosphatidylcholine.

Investigating functional redundancy versus complementarity in Hawaiian herbivorous coral reef fishes.

PubMed

Kelly, Emily L A; Eynaud, Yoan; Clements, Samantha M; Gleason, Molly; Sparks, Russell T; Williams, Ivor D; Smith, Jennifer E

2016-12-01

Patterns of species resource use provide insight into the functional roles of species and thus their ecological significance within a community. The functional role of herbivorous fishes on coral reefs has been defined through a variety of methods, but from a grazing perspective, less is known about the species-specific preferences of herbivores on different groups of reef algae and the extent of dietary overlap across an herbivore community. Here, we quantified patterns of redundancy and complementarity in a highly diverse community of herbivores at a reef on Maui, Hawaii, USA. First, we tracked fish foraging behavior in situ to record bite rate and type of substrate bitten. Second, we examined gut contents of select herbivorous fishes to determine consumption at a finer scale. Finally, we placed foraging behavior in the context of resource availability to determine how fish selected substrate type. All species predominantly (73-100 %) foraged on turf algae, though there were differences among the types of macroalgae and other substrates bitten. Increased resolution via gut content analysis showed the composition of turf algae consumed by fishes differed across herbivore species. Consideration of foraging behavior by substrate availability revealed 50 % of herbivores selected for turf as opposed to other substrate types, but overall, there were variable foraging portfolios across all species. Through these three methods of investigation, we found higher complementarity among herbivorous fishes than would be revealed using a single metric. These results suggest differences across species in the herbivore "rain of bites" that graze and shape benthic community composition.

Structure determination of an Fab fragment that neutralizes human rhinovirus 14 and analysis of the Fab-virus complex.

PubMed

Liu, H; Smith, T J; Lee, W M; Mosser, A G; Rueckert, R R; Olson, N H; Cheng, R H; Baker, T S

1994-07-08

The crystal structure of Fab17-IA, an antigen-binding fragment from a murine immunoglobulin that neutralizes human rhinovirus 14 (HRV14), has been solved to 2.7 A resolution. Fab17-IA crystallized into three different space groups depending upon the method used to purify the intact antibody. The structure was determined by use of molecular and isomorphous replacement methods. The current model has a crystallographic R-factor of approximately 19% for 10,192 independent reflections between 8 and 2.7 A. Correlation coefficient calculations showed that the Fab17-IA structure can be fit into the Fab17-IA/HRV14 image reconstruction density to within 5 A positional accuracy and to within a few degrees of rotation. The resulting interface of the docked antibody was examined and showed extensive charge and shape complementarity with the virus surface that was supported by site-directed mutagenesis experiments. The success of this approach validates the utility of combining X-ray crystallography with cryo-electron microscopy of complex macromolecular assemblies.

Extra-domain B in oncofetal fibronectin structurally promotes fibrillar head-to-tail dimerization of extracellular matrix protein.

PubMed

Schiefner, André; Gebauer, Michaela; Skerra, Arne

2012-05-18

The type III extra-domain B (ED-B) is specifically spliced into fibronectin (Fn) during embryogenesis and neoangiogenesis, including many cancers. The x-ray structure of the recombinant four-domain fragment Fn(III)7B89 reveals a tightly associated, extended head-to-tail dimer, which is stabilized via pair-wise shape and charge complementarity. A tendency toward ED-B-dependent dimer formation in solution was supported by size exclusion chromatography and analytical ultracentrifugation. When amending the model with the known three-dimensional structure of the Fn(III)10 domain, its RGD loop as well as the adhesion synergy region in Fn(III)9-10 become displayed on the same face of the dimer; this should allow simultaneous binding of at least two integrins and, thus, receptor clustering on the cell surface and intracellular signaling. Insertion of ED-B appears to stabilize overall head-to-tail dimerization of two separate Fn chains, which, together with alternating homodimer formation via disulfide bridges at the C-terminal Fn tail, should lead to the known macromolecular fibril formation.

Spin-echo small-angle neutron scattering (SESANS) measurements of needle-like crystallites of gelator compounds

NASA Astrophysics Data System (ADS)

Coumou, Pieter-Jan C. J. J.; Brizard, Aurelie M. A.; van Esch, Jan H.; de Schepper, Ignatz M.; Bouwman, Wim G.

2010-11-01

From dibenzoyl cystine, a low molecular weight gelator, we have prepared needle shaped crystals at relatively high concentrations. For the first time SESANS measurements are performed on objects with this geometry. From the measurements the average diameter can be seen directly. From a more careful analysis the width distribution is determined. The gel phase itself prepared at lower concentrations did not show any signal, in contrast to what one observes with conventional SANS. This shows the complementarity of SESANS and SANS.

Light-scattering studies of protein solutions: role of hydration in weak protein-protein interactions.

PubMed

Paliwal, A; Asthagiri, D; Abras, D; Lenhoff, A M; Paulaitis, M E

2005-09-01

We model the hydration contribution to short-range electrostatic/dispersion protein interactions embodied in the osmotic second virial coefficient, B(2), by adopting a quasi-chemical description in which water molecules associated with the protein are identified through explicit molecular dynamics simulations. These water molecules reduce the surface complementarity of highly favorable short-range interactions, and therefore can play an important role in mediating protein-protein interactions. Here we examine this quasi-chemical view of hydration by predicting the interaction part of B(2) and comparing our results with those derived from light-scattering measurements of B(2) for staphylococcal nuclease, lysozyme, and chymotrypsinogen at 25 degrees C as a function of solution pH and ionic strength. We find that short-range protein interactions are influenced by water molecules strongly associated with a relatively small fraction of the protein surface. However, the effect of these strongly associated water molecules on the surface complementarity of short-range protein interactions is significant, and must be taken into account for an accurate description of B(2). We also observe remarkably similar hydration behavior for these proteins despite substantial differences in their three-dimensional structures and spatial charge distributions, suggesting a general characterization of protein hydration.

Interpersonal complementarity in the mental health intake: a mixed-methods study.

PubMed

Rosen, Daniel C; Miller, Alisa B; Nakash, Ora; Halpern, Lucila; Halperin, Lucila; Alegría, Margarita

2012-04-01

The study examined which socio-demographic differences between clients and providers influenced interpersonal complementarity during an initial intake session; that is, behaviors that facilitate harmonious interactions between client and provider. Complementarity was assessed using blinded ratings of 114 videotaped intake sessions by trained observers. Hierarchical linear models were used to examine how match between client and provider in race/ethnicity, sex, and age were associated with levels of complementarity. A qualitative analysis investigated potential mechanisms that accounted for overall complementarity beyond match by examining client-provider dyads in the top and bottom quartiles of the complementarity measure. Results indicated significant interactions between client's race/ethnicity (Black) and provider's race/ethnicity (Latino) (p = .036) and client's age and provider's age (p = .044) on the Affiliation axis. The qualitative investigation revealed that client-provider interactions in the upper quartile of complementarity were characterized by consistent descriptions between the client and provider of concerns and expectations as well as depictions of what was important during the meeting. Results suggest that differences in social identities, although important, may be overcome by interpersonal variables early in the therapeutic relationship. Implications for both clinical practice and future research are discussed, as are factors relevant to working across cultures.

Complementarity and Area-Efficiency in the Prioritization of the Global Protected Area Network.

PubMed

Kullberg, Peter; Toivonen, Tuuli; Montesino Pouzols, Federico; Lehtomäki, Joona; Di Minin, Enrico; Moilanen, Atte

2015-01-01

Complementarity and cost-efficiency are widely used principles for protected area network design. Despite the wide use and robust theoretical underpinnings, their effects on the performance and patterns of priority areas are rarely studied in detail. Here we compare two approaches for identifying the management priority areas inside the global protected area network: 1) a scoring-based approach, used in recently published analysis and 2) a spatial prioritization method, which accounts for complementarity and area-efficiency. Using the same IUCN species distribution data the complementarity method found an equal-area set of priority areas with double the mean species ranges covered compared to the scoring-based approach. The complementarity set also had 72% more species with full ranges covered, and lacked any coverage only for half of the species compared to the scoring approach. Protected areas in our complementarity-based solution were on average smaller and geographically more scattered. The large difference between the two solutions highlights the need for critical thinking about the selected prioritization method. According to our analysis, accounting for complementarity and area-efficiency can lead to considerable improvements when setting management priorities for the global protected area network.

Affiliation and control in marital interaction: interpersonal complementarity is present but is not associated with affect or relationship quality.

PubMed

Cundiff, Jenny M; Smith, Timothy W; Butner, Jonathan; Critchfield, Kenneth L; Nealey-Moore, Jill

2015-01-01

The principle of complementarity in interpersonal theory states that an actor's behavior tends to "pull, elicit, invite, or evoke" responses from interaction partners who are similar in affiliation (i.e., warmth vs. hostility) and opposite in control (i.e., dominance vs. submissiveness). Furthermore, complementary interactions are proposed to evoke less negative affect and promote greater relationship satisfaction. These predictions were examined in two studies of married couples. Results suggest that complementarity in affiliation describes a robust general pattern of marital interaction, but complementarity in control varies across contexts. Consistent with behavioral models of marital interaction, greater levels of affiliation and lower control by partners-not complementarity in affiliation or control-were associated with less anger and anxiety and greater relationship quality. Partners' levels of affiliation and control combined in ways other than complementarity-mostly additively, but sometimes synergistically-to predict negative affect and relationship satisfaction. © 2014 by the Society for Personality and Social Psychology, Inc.

Interpersonal Complementarity in the Mental Health Intake: A Mixed-Methods Study

ERIC Educational Resources Information Center

Rosen, Daniel C.; Miller, Alisa B.; Nakash, Ora; Halperin, Lucila; Alegria, Margarita

2012-01-01

The study examined which socio-demographic differences between clients and providers influenced interpersonal complementarity during an initial intake session; that is, behaviors that facilitate harmonious interactions between client and provider. Complementarity was assessed using blinded ratings of 114 videotaped intake sessions by trained…

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.

PubMed

Levy, Roie; Carr, Rogan; Kreimer, Anat; Freilich, Shiri; Borenstein, Elhanan

2015-05-17

Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their host and in the assembly of complex microbial communities. Recently, several studies have demonstrated how such interactions are reflected in the organization of the metabolic networks of the interacting species, and introduced various graph theory-based methods to predict host-microbe and microbe-microbe interactions directly from network topology. Using these methods, such studies have revealed evolutionary and ecological processes that shape species interactions and community assembly, highlighting the potential of this reverse-ecology research paradigm. NetCooperate is a web-based tool and a software package for determining host-microbe and microbe-microbe cooperative potential. It specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score which quantifies the ability of a host species to supply the nutritional requirements of a parasitic or a commensal species, and the Metabolic Complementarity Index which quantifies the complementarity of a pair of microbial organisms' niches. NetCooperate takes as input a pair of metabolic networks, and returns the pairwise metrics as well as a list of potential syntrophic metabolic compounds. The Biosynthetic Support Score and Metabolic Complementarity Index provide insight into host-microbe and microbe-microbe metabolic interactions. NetCooperate determines these interaction indices from metabolic network topology, and can be used for small- or large-scale analyses. NetCooperate is provided as both a web-based tool and an open-source Python module; both are freely available online at http://elbo.gs.washington.edu/software_netcooperate.html.

Biochemistry students' ideas about shape and charge in enzyme-substrate interactions.

PubMed

Linenberger, Kimberly J; Bretz, Stacey Lowery

2014-01-01

Biochemistry is a visual discipline that requires students to develop an understanding of numerous representations. However, there is very little known about what students actually understand about the representations that are used to communicate ideas in biochemistry. This study investigated biochemistry students' understanding of multiple representations of enzyme-substrate interactions through both student interviews (N = 25) and responses by a national sample (N = 707) to the Enzyme-Substrate Interactions Concept Inventory. This manuscript reports the findings regarding one category of misconceptions measured by the concept inventory, namely, students' understandings of shape and charge in the context of enzyme-substrate interactions. Students interpret molecular representations depicting such interactions by determining the complementarity between enzyme and substrate by focusing upon charge and hydrogen bonding, but with a disregard for stereochemistry. Copyright © 2014 by The International Union of Biochemistry and Molecular Biology.

Computational sequence analysis of predicted long dsRNA transcriptomes of major crops reveals sequence complementarity with human genes.

PubMed

Jensen, Peter D; Zhang, Yuanji; Wiggins, B Elizabeth; Petrick, Jay S; Zhu, Jin; Kerstetter, Randall A; Heck, Gregory R; Ivashuta, Sergey I

2013-01-01

Long double-stranded RNAs (long dsRNAs) are precursors for the effector molecules of sequence-specific RNA-based gene silencing in eukaryotes. Plant cells can contain numerous endogenous long dsRNAs. This study demonstrates that such endogenous long dsRNAs in plants have sequence complementarity to human genes. Many of these complementary long dsRNAs have perfect sequence complementarity of at least 21 nucleotides to human genes; enough complementarity to potentially trigger gene silencing in targeted human cells if delivered in functional form. However, the number and diversity of long dsRNA molecules in plant tissue from crops such as lettuce, tomato, corn, soy and rice with complementarity to human genes that have a long history of safe consumption supports a conclusion that long dsRNAs do not present a significant dietary risk.

In vivo encapsulation of nucleic acids using an engineered nonviral protein capsid.

PubMed

Lilavivat, Seth; Sardar, Debosmita; Jana, Subrata; Thomas, Geoffrey C; Woycechowsky, Kenneth J

2012-08-15

In Nature, protein capsids function as molecular containers for a wide variety of molecular cargoes. Such containers have great potential for applications in nanotechnology, which often require encapsulation of non-native guest molecules. Charge complementarity represents a potentially powerful strategy for engineering novel encapsulation systems. In an effort to explore the generality of this approach, we engineered a nonviral, 60-subunit capsid, lumazine synthase from Aquifex aeolicus (AaLS), to act as a container for nucleic acid. Four mutations were introduced per subunit to increase the positive charge at the inner surface of the capsid. Characterization of the mutant (AaLS-pos) revealed that the positive charges lead to the uptake of cellular RNA during production and assembly of the capsid in vivo. Surprisingly, AaLS-pos capsids were found to be enriched with RNA molecules approximately 200-350 bases in length, suggesting that this simple charge complementarity approach to RNA encapsulation leads to both high affinity and a degree of selectivity. The ability to control loading of RNA by tuning the charge at the inner surface of a protein capsid could illuminate aspects of genome recognition by viruses and pave the way for the development of improved RNA delivery systems.

Structure-function analysis of rotavirus NSP2 octamer by using a novel complementation system.

PubMed

Taraporewala, Zenobia F; Jiang, Xiaofang; Vasquez-Del Carpio, Rodrigo; Jayaram, Hariharan; Prasad, B V Venkataram; Patton, John T

2006-08-01

Viral inclusion bodies, or viroplasms, that form in rotavirus-infected cells direct replication and packaging of the segmented double-stranded RNA (dsRNA) genome. NSP2, one of two rotavirus proteins needed for viroplasm assembly, possesses NTPase, RNA-binding, and helix-unwinding activities. NSP2 of the rotavirus group causing endemic infantile diarrhea (group A) was shown to self-assemble into large doughnut-shaped octamers with circumferential grooves and deep clefts containing nucleotide-binding histidine triad (HIT)-like motifs. Here, we demonstrate that NSP2 of group C rotavirus, a group that fails to reassort with group A viruses, retains the unique architecture of the group A octamer but differs in surface charge distribution. By using an NSP2-dependent complementation system, we show that the HIT-dependent NTPase activity of NSP2 is necessary for dsRNA synthesis, but not for viroplasm formation. The complementation system also showed that despite the retention of the octamer structure and the HIT-like fold, group C NSP2 failed to rescue replication and viroplasm formation in NSP2-deficient cells infected with group A rotavirus. The distinct differences in the surface charges on the Bristol and SA11 NSP2 octamers suggest that charge complementarity of the viroplasm-forming proteins guides the specificity of viroplasm formation and, possibly, reassortment restriction between rotavirus groups.

The illusion of specific capture: surface and solution studies of suboptimal oligonucleotide hybridization

PubMed Central

2013-01-01

Background Hybridization based assays and capture systems depend on the specificity of hybridization between a probe and its intended target. A common guideline in the construction of DNA microarrays, for instance, is that avoiding complementary stretches of more than 15 nucleic acids in a 50 or 60-mer probe will eliminate sequence specific cross-hybridization reactions. Here we present a study of the behavior of partially matched oligonucleotide pairs with complementary stretches starting well below this threshold complementarity length – in silico, in solution, and at the microarray surface. The modeled behavior of pairs of oligonucleotide probes and their targets suggests that even a complementary stretch of sequence 12 nt in length would give rise to specific cross-hybridization. We designed a set of binding partners to a 50-mer oligonucleotide containing complementary stretches from 6 nt to 21 nt in length. Results Solution melting experiments demonstrate that stable partial duplexes can form when only 12 bp of complementary sequence are present; surface hybridization experiments confirm that a signal close in magnitude to full-strength signal can be obtained from hybridization of a 12 bp duplex within a 50mer oligonucleotide. Conclusions Microarray and other molecular capture strategies that rely on a 15 nt lower complementarity bound for eliminating specific cross-hybridization may not be sufficiently conservative. PMID:23445545

The fully actuated traffic control problem solved by global optimization and complementarity

NASA Astrophysics Data System (ADS)

Ribeiro, Isabel M.; de Lurdes de Oliveira Simões, Maria

2016-02-01

Global optimization and complementarity are used to determine the signal timing for fully actuated traffic control, regarding effective green and red times on each cycle. The average values of these parameters can be used to estimate the control delay of vehicles. In this article, a two-phase queuing system for a signalized intersection is outlined, based on the principle of minimization of the total waiting time for the vehicles. The underlying model results in a linear program with linear complementarity constraints, solved by a sequential complementarity algorithm. Departure rates of vehicles during green and yellow periods were treated as deterministic, while arrival rates of vehicles were assumed to follow a Poisson distribution. Several traffic scenarios were created and solved. The numerical results reveal that it is possible to use global optimization and complementarity over a reasonable number of cycles and determine with efficiency effective green and red times for a signalized intersection.

Let's get specific: the relationship between specificity and affinity.

PubMed

Eaton, B E; Gold, L; Zichi, D A

1995-10-01

The factors that lead to high-affinity binding are a good fit between the surfaces of the two molecules in their ground state and charge complementarity. Exactly the same factors give high specificity for a target. We argue that selection for high-affinity binding automatically leads to highly specific binding. This principle can be used to simplify screening approaches aimed at generating useful drugs.

Analysis of Structural Features Contributing to Weak Affinities of Ubiquitin/Protein Interactions.

PubMed

Cohen, Ariel; Rosenthal, Eran; Shifman, Julia M

2017-11-10

Ubiquitin is a small protein that enables one of the most common post-translational modifications, where the whole ubiquitin molecule is attached to various target proteins, forming mono- or polyubiquitin conjugations. As a prototypical multispecific protein, ubiquitin interacts non-covalently with a variety of proteins in the cell, including ubiquitin-modifying enzymes and ubiquitin receptors that recognize signals from ubiquitin-conjugated substrates. To enable recognition of multiple targets and to support fast dissociation from the ubiquitin modifying enzymes, ubiquitin/protein interactions are characterized with low affinities, frequently in the higher μM and lower mM range. To determine how structure encodes low binding affinity of ubiquitin/protein complexes, we analyzed structures of more than a hundred such complexes compiled in the Ubiquitin Structural Relational Database. We calculated various structure-based features of ubiquitin/protein binding interfaces and compared them to the same features of general protein-protein interactions (PPIs) with various functions and generally higher affinities. Our analysis shows that ubiquitin/protein binding interfaces on average do not differ in size and shape complementarity from interfaces of higher-affinity PPIs. However, they contain fewer favorable hydrogen bonds and more unfavorable hydrophobic/charge interactions. We further analyzed how binding interfaces change upon affinity maturation of ubiquitin toward its target proteins. We demonstrate that while different features are improved in different experiments, the majority of the evolved complexes exhibit better shape complementarity and hydrogen bond pattern compared to wild-type complexes. Our analysis helps to understand how low-affinity PPIs have evolved and how they could be converted into high-affinity PPIs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components

NASA Astrophysics Data System (ADS)

Gerling, Thomas; Wagenbauer, Klaus F.; Neuner, Andrea M.; Dietz, Hendrik

2015-03-01

We demonstrate that discrete three-dimensional (3D) DNA components can specifically self-assemble in solution on the basis of shape-complementarity and without base pairing. Using this principle, we produced homo- and heteromultimeric objects, including micrometer-scale one- and two-stranded filaments and lattices, as well as reconfigurable devices, including an actuator, a switchable gear, an unfoldable nanobook, and a nanorobot. These multidomain assemblies were stabilized via short-ranged nucleobase stacking bonds that compete against electrostatic repulsion between the components’ interfaces. Using imaging by electron microscopy, ensemble and single-molecule fluorescence resonance energy transfer spectroscopy, and electrophoretic mobility analysis, we show that the balance between attractive and repulsive interactions, and thus the conformation of the assemblies, may be finely controlled by global parameters such as cation concentration or temperature and by an allosteric mechanism based on strand-displacement reactions.

Solution structure of the phosphoryl transfer complex between the cytoplasmic A domain of the mannitol transporter IIMannitol and HPr of the Escherichia coli phosphotransferase system.

PubMed

Cornilescu, Gabriel; Lee, Byeong Ryong; Cornilescu, Claudia C; Wang, Guangshun; Peterkofsky, Alan; Clore, G Marius

2002-11-01

The solution structure of the complex between the cytoplasmic A domain (IIA(Mtl)) of the mannitol transporter II(Mannitol) and the histidine-containing phosphocarrier protein (HPr) of the Escherichia coli phosphotransferase system has been solved by NMR, including the use of conjoined rigid body/torsion angle dynamics, and residual dipolar couplings, coupled with cross-validation, to permit accurate orientation of the two proteins. A convex surface on HPr, formed by helices 1 and 2, interacts with a complementary concave depression on the surface of IIA(Mtl) formed by helix 3, portions of helices 2 and 4, and beta-strands 2 and 3. The majority of intermolecular contacts are hydrophobic, with a small number of electrostatic interactions at the periphery of the interface. The active site histidines, His-15 of HPr and His-65 of IIA(Mtl), are in close spatial proximity, and a pentacoordinate phosphoryl transition state can be readily accommodated with no change in protein-protein orientation and only minimal perturbations of the backbone immediately adjacent to the histidines. Comparison with two previously solved structures of complexes of HPr with partner proteins of the phosphotransferase system, the N-terminal domain of enzyme I (EIN) and enzyme IIA(Glucose) (IIA(Glc)), reveals a number of common features despite the fact that EIN, IIA(Glc), and IIA(Mtl) bear no structural resemblance to one another. Thus, entirely different underlying structural elements can form binding surfaces for HPr that are similar in terms of both shape and residue composition. These structural comparisons illustrate the roles of surface and residue complementarity, redundancy, incremental build-up of specificity and conformational side chain plasticity in the formation of transient specific protein-protein complexes in signal transduction pathways.

Analysis of the binding loops configuration and surface adaptation of different crystallized single-domain antibodies in response to various antigens.

PubMed

Al Qaraghuli, Mohammed M; Ferro, Valerie A

2017-04-01

Monoclonal antibodies have revolutionized the biomedical field through their ubiquitous utilization in different diagnostics and therapeutic applications. Despite this widespread use, their large size and structural complexity have limited their versatility in specific applications. The antibody variable region that is responsible for binding antigen is embodied within domains that can be rescued individually as single-domain antibody (sdAb) fragments. Because of the unique characteristics of sdAbs, such as low molecular weight, high physicochemical stability, and the ability to bind antigens inaccessible to conventional antibodies, they represent a viable alternative to full-length antibodies. Consequently, 149 crystal structures of sdAbs, originating from human (VH), camelids (VHH), or sharks (VNAR), were retrieved from the Protein Data Bank, and their structures were compared. The 3 types of sdAbs displayed complementarity determining regions (CDRs) with different lengths and configurations. CDR3 of the VHH and VNAR domains were dominated by pleated and extended orientations, respectively. Although VNAR showed the smallest average molecular weight and molecular surface area compared with VHH and VH antibodies. However, the solvent accessible surface area measurements of the 3 tested sdAbs types were very similar. All the antihapten VHH antibodies showed pleated CDR3, which were sufficient to create a binding pocket to accommodate haptens (methotrexate and azo dyes) in terms of shape and electrostatic potential. The sdAbs that recognized lysozyme showed more diversity in their CDR3 orientation to enable them to recognize various topographies of lysozyme. Subsequently, the three sdAb classes were different in size and surface area and have shown distinguishable ability to optimize their CDR length and orientation to recognize different antigen classes. Copyright © 2016 John Wiley & Sons, Ltd.

Structure and stability of the ankyrin domain of the Drosophila Notch receptor.

PubMed

Zweifel, Mark E; Leahy, Daniel J; Hughson, Frederick M; Barrick, Doug

2003-11-01

The Notch receptor contains a conserved ankyrin repeat domain that is required for Notch-mediated signal transduction. The ankyrin domain of Drosophila Notch contains six ankyrin sequence repeats previously identified as closely matching the ankyrin repeat consensus sequence, and a putative seventh C-terminal sequence repeat that exhibits lower similarity to the consensus sequence. To better understand the role of the Notch ankyrin domain in Notch-mediated signaling and to examine how structure is distributed among the seven ankyrin sequence repeats, we have determined the crystal structure of this domain to 2.0 angstroms resolution. The seventh, C-terminal, ankyrin sequence repeat adopts a regular ankyrin fold, but the first, N-terminal ankyrin repeat, which contains a 15-residue insertion, appears to be largely disordered. The structure reveals a substantial interface between ankyrin polypeptides, showing a high degree of shape and charge complementarity, which may be related to homotypic interactions suggested from indirect studies. However, the Notch ankyrin domain remains largely monomeric in solution, demonstrating that this interface alone is not sufficient to promote tight association. Using the structure, we have classified reported mutations within the Notch ankyrin domain that are known to disrupt signaling into those that affect buried residues and those restricted to surface residues. We show that the buried substitutions greatly decrease protein stability, whereas the surface substitutions have only a marginal affect on stability. The surface substitutions are thus likely to interfere with Notch signaling by disrupting specific Notch-effector interactions and map the sites of these interactions.

Structure, thermodynamics, and solubility in tetromino fluids.

PubMed

Barnes, Brian C; Siderius, Daniel W; Gelb, Lev D

2009-06-16

To better understand the self-assembly of small molecules and nanoparticles adsorbed at interfaces, we have performed extensive Monte Carlo simulations of a simple lattice model based on the seven hard "tetrominoes", connected shapes that occupy four lattice sites. The equations of state of the pure fluids and all of the binary mixtures are determined over a wide range of density, and a large selection of multicomponent mixtures are also studied at selected conditions. Calculations are performed in the grand canonical ensemble and are analogous to real systems in which molecules or nanoparticles reversibly adsorb to a surface or interface from a bulk reservoir. The model studied is athermal; objects in these simulations avoid overlap but otherwise do not interact. As a result, all of the behavior observed is entropically driven. The one-component fluids all exhibit marked self-ordering tendencies at higher densities, with quite complex structures formed in some cases. Significant clustering of objects with the same rotational state (orientation) is also observed in some of the pure fluids. In all of the binary mixtures, the two species are fully miscible at large scales, but exhibit strong species-specific clustering (segregation) at small scales. This behavior persists in multicomponent mixtures; even in seven-component mixtures of all the shapes there is significant association between objects of the same shape. To better understand these phenomena, we calculate the second virial coefficients of the tetrominoes and related quantities, extract thermodynamic volume of mixing data from the simulations of binary mixtures, and determine Henry's law solubilities for each shape in a variety of solvents. The overall picture obtained is one in which complementarity of both the shapes of individual objects and the characteristic structures of different fluids are important in determining the overall behavior of a fluid of a given composition, with sometimes counterintuitive results. Finally, we note that no sharp phase transitions are observed but that this appears to be due to the small size of the objects considered. It is likely that complex phase behavior may be found in systems of larger polyominoes.

Complementarity effects on tree growth are contingent on tree size and climatic conditions across Europe

PubMed Central

Madrigal-González, Jaime; Ruiz-Benito, Paloma; Ratcliffe, Sophia; Calatayud, Joaquín; Kändler, Gerald; Lehtonen, Aleksi; Dahlgren, Jonas; Wirth, Christian; Zavala, Miguel A.

2016-01-01

Neglecting tree size and stand structure dynamics might bias the interpretation of the diversity-productivity relationship in forests. Here we show evidence that complementarity is contingent on tree size across large-scale climatic gradients in Europe. We compiled growth data of the 14 most dominant tree species in 32,628 permanent plots covering boreal, temperate and Mediterranean forest biomes. Niche complementarity is expected to result in significant growth increments of trees surrounded by a larger proportion of functionally dissimilar neighbours. Functional dissimilarity at the tree level was assessed using four functional types: i.e. broad-leaved deciduous, broad-leaved evergreen, needle-leaved deciduous and needle-leaved evergreen. Using Linear Mixed Models we show that, complementarity effects depend on tree size along an energy availability gradient across Europe. Specifically: (i) complementarity effects at low and intermediate positions of the gradient (coldest-temperate areas) were stronger for small than for large trees; (ii) in contrast, at the upper end of the gradient (warmer regions), complementarity is more widespread in larger than smaller trees, which in turn showed negative growth responses to increased functional dissimilarity. Our findings suggest that the outcome of species mixing on stand productivity might critically depend on individual size distribution structure along gradients of environmental variation. PMID:27571971

ClusPro: an automated docking and discrimination method for the prediction of protein complexes.

PubMed

Comeau, Stephen R; Gatchell, David W; Vajda, Sandor; Camacho, Carlos J

2004-01-01

Predicting protein interactions is one of the most challenging problems in functional genomics. Given two proteins known to interact, current docking methods evaluate billions of docked conformations by simple scoring functions, and in addition to near-native structures yield many false positives, i.e. structures with good surface complementarity but far from the native. We have developed a fast algorithm for filtering docked conformations with good surface complementarity, and ranking them based on their clustering properties. The free energy filters select complexes with lowest desolvation and electrostatic energies. Clustering is then used to smooth the local minima and to select the ones with the broadest energy wells-a property associated with the free energy at the binding site. The robustness of the method was tested on sets of 2000 docked conformations generated for 48 pairs of interacting proteins. In 31 of these cases, the top 10 predictions include at least one near-native complex, with an average RMSD of 5 A from the native structure. The docking and discrimination method also provides good results for a number of complexes that were used as targets in the Critical Assessment of PRedictions of Interactions experiment. The fully automated docking and discrimination server ClusPro can be found at http://structure.bu.edu

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

PubMed

Xavier, P Lourdu; Chandrasekaran, Arun Richard

2018-02-09

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

Humanization of Antibodies Using Heavy Chain Complementarity-determining Region 3 Grafting Coupled with in Vitro Somatic Hypermutation*

PubMed Central

Bowers, Peter M.; Neben, Tamlyn Y.; Tomlinson, Geoffery L.; Dalton, Jennifer L.; Altobell, Larry; Zhang, Xue; Macomber, John L.; Wu, Betty F.; Toobian, Rachelle M.; McConnell, Audrey D.; Verdino, Petra; Chau, Betty; Horlick, Robert A.; King, David J.

2013-01-01

A method for simultaneous humanization and affinity maturation of monoclonal antibodies has been developed using heavy chain complementarity-determining region (CDR) 3 grafting combined with somatic hypermutation in vitro. To minimize the amount of murine antibody-derived antibody sequence used during humanization, only the CDR3 region from a murine antibody that recognizes the cytokine hβNGF was grafted into a nonhomologous human germ line V region. The resulting CDR3-grafted HC was paired with a CDR-grafted light chain, displayed on the surface of HEK293 cells, and matured using in vitro somatic hypermutation. A high affinity humanized antibody was derived that was considerably more potent than the parental antibody, possessed a low pm dissociation constant, and demonstrated potent inhibition of hβNGF activity in vitro. The resulting antibody contained half the heavy chain murine donor sequence compared with the same antibody humanized using traditional methods. PMID:23355464

Complementarity of genuine multipartite Bell nonlocality

NASA Astrophysics Data System (ADS)

Sami, Sasha; Chakrabarty, Indranil; Chaturvedi, Anubhav

2017-08-01

We introduce a feature of no-signaling (Bell) nonlocal theories: namely, when a system of multiple parties manifests genuine nonlocal correlation, then there cannot be arbitrarily high nonlocal correlation among any subset of the parties. We call this feature complementarity of genuine multipartite nonlocality. We use Svetlichny's criterion for genuine multipartite nonlocality and nonlocal games to derive the complementarity relations under no-signaling constraints. We find that the complementarity relations are tightened for the much stricter quantum constraints. We compare this notion with the well-known notion of monogamy of nonlocality. As a consequence, we obtain tighter nontrivial monogamy relations that take into account genuine multipartite nonlocality. Furthermore, we provide numerical evidence showcasing this feature using a bipartite measure and several other well-known tripartite measures of nonlocality.

Host-Guest Chemistry in Integrated Porous Space Formed by Molecular Self-Assembly at Liquid-Solid Interfaces.

PubMed

Iritani, Kohei; Tahara, Kazukuni; De Feyter, Steven; Tobe, Yoshito

2017-05-16

Host-guest chemistry in two-dimensional (2D) space, that is, physisorbed monolayers of a single atom or a single molecular thickness on surfaces, has become a subject of intense current interest because of perspectives for various applications in molecular-scale electronics, selective sensors, and tailored catalysis. Scanning tunneling microscopy has been used as a powerful tool for the visualization of molecules in real space on a conducting substrate surface. For more than a decade, we have been investigating the self-assembly of a series of triangle-shaped phenylene-ethynylene macrocycles called dehydrobenzo[12]annulenes (DBAs). These molecules are substituted with six alkyl chains and are capable of forming hexagonal porous 2D molecular networks via van der Waals interactions between interdigitated alkyl chains at the interface of organic solvents and graphite. The dimension of the nanoporous space or nanowell formed by the self-assembly of DBAs can be controlled from 1.6 to 4.7 nm by simply changing the alkyl chain length from C 6 to C 20 . Single molecules as well as homoclusters and heteroclusters are capable of coadsorbing within the host matrix using shape- and size-complementarity principles. Moreover, on the basis of the versatility of the DBA molecules that allows chemical modification of the alkyl chain terminals, we were able to decorate the interior space of the nanoporous networks with functional groups such as azobenzenedicarboxylic acid for photoresponsive guest adsorption/desorption or fluoroalkanes and tetraethylene glycol groups for selective guest binding by electrostatic interactions and zinc-porphyrin units for complexation with a guest by charge-transfer interactions. In this Feature Article, we describe the general aspects of molecular self-assembly at liquid/solid interfaces, followed by the formation of programmed porous molecular networks using rationally designed molecular building blocks. We focus on our own work involving host-guest chemistry in integrated nanoporous space that is modified for specific purposes.

Private algebras in quantum information and infinite-dimensional complementarity

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

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

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

Generalized uncertainty principle: implications for black hole complementarity

NASA Astrophysics Data System (ADS)

Chen, Pisin; Ong, Yen Chin; Yeom, Dong-han

2014-12-01

At the heart of the black hole information loss paradox and the firewall controversy lies the conflict between quantum mechanics and general relativity. Much has been said about quantum corrections to general relativity, but much less in the opposite direction. It is therefore crucial to examine possible corrections to quantum mechanics due to gravity. Indeed, the Heisenberg Uncertainty Principle is one profound feature of quantum mechanics, which nevertheless may receive correction when gravitational effects become important. Such generalized uncertainty principle [GUP] has been motivated from not only quite general considerations of quantum mechanics and gravity, but also string theoretic arguments. We examine the role of GUP in the context of black hole complementarity. We find that while complementarity can be violated by large N rescaling if one assumes only the Heisenberg's Uncertainty Principle, the application of GUP may save complementarity, but only if certain N -dependence is also assumed. This raises two important questions beyond the scope of this work, i.e., whether GUP really has the proposed form of N -dependence, and whether black hole complementarity is indeed correct.

Anatomy of the β-branching enzyme of polyketide biosynthesis and its interaction with an acyl-ACP substrate.

PubMed

Maloney, Finn P; Gerwick, Lena; Gerwick, William H; Sherman, David H; Smith, Janet L

2016-09-13

Alkyl branching at the β position of a polyketide intermediate is an important variation on canonical polyketide natural product biosynthesis. The branching enzyme, 3-hydroxy-3-methylglutaryl synthase (HMGS), catalyzes the aldol addition of an acyl donor to a β-keto-polyketide intermediate acceptor. HMGS is highly selective for two specialized acyl carrier proteins (ACPs) that deliver the donor and acceptor substrates. The HMGS from the curacin A biosynthetic pathway (CurD) was examined to establish the basis for ACP selectivity. The donor ACP (CurB) had high affinity for the enzyme (Kd = 0.5 μM) and could not be substituted by the acceptor ACP. High-resolution crystal structures of HMGS alone and in complex with its donor ACP reveal a tight interaction that depends on exquisite surface shape and charge complementarity between the proteins. Selectivity is explained by HMGS binding to an unusual surface cleft on the donor ACP, in a manner that would exclude the acceptor ACP. Within the active site, HMGS discriminates between pre- and postreaction states of the donor ACP. The free phosphopantetheine (Ppant) cofactor of ACP occupies a conserved pocket that excludes the acetyl-Ppant substrate. In comparison with HMG-CoA (CoA) synthase, the homologous enzyme from primary metabolism, HMGS has several differences at the active site entrance, including a flexible-loop insertion, which may account for the specificity of one enzyme for substrates delivered by ACP and the other by CoA.

Reducing Insecurity in Africa: Roles and Responsibilities of the U.S. Military, U.S. Government and Non-Governmental Communities

DTIC Science & Technology

2012-04-01

government, how to create programs that build on the complementarities between various actors (within and outside the government), and what...the participants aired their opinions and listened to each others’ perspectives. Even when they disagreed, learning why disagreements surfaced helped...many African countries the security sector itself—those actors and institutions with the central charge of providing defense and security—have too

Presence of Trifolium repens Promotes Complementarity of Water Use and N Facilitation in Diverse Grass Mixtures.

PubMed

Hernandez, Pauline; Picon-Cochard, Catherine

2016-01-01

Legume species promote productivity and increase the digestibility of herbage in grasslands. Considerable experimental data also indicate that communities with legumes produce more above-ground biomass than is expected from monocultures. While it has been attributed to N facilitation, evidence to identify the mechanisms involved is still lacking and the role of complementarity in soil water acquisition by vertical root differentiation remains unclear. We used a 20-months mesocosm experiment to investigate the effects of species richness (single species, two- and five-species mixtures) and functional diversity (presence of the legume Trifolium repens) on a set of traits related to light, N and water use and measured at community level. We found a positive effect of Trifolium presence and abundance on biomass production and complementarity effects in the two-species mixtures from the second year. In addition the community traits related to water and N acquisition and use (leaf area, N, water-use efficiency, and deep root growth) were higher in the presence of Trifolium. With a multiple regression approach, we showed that the traits related to water acquisition and use were with N the main determinants of biomass production and complementarity effects in diverse mixtures. At shallow soil layers, lower root mass of Trifolium and higher soil moisture should increase soil water availability for the associated grass species. Conversely at deep soil layer, higher root growth and lower soil moisture mirror soil resource use increase of mixtures. Altogether, these results highlight N facilitation but almost soil vertical differentiation and thus complementarity for water acquisition and use in mixtures with Trifolium. Contrary to grass-Trifolium mixtures, no significant over-yielding was measured for grass mixtures even those having complementary traits (short and shallow vs. tall and deep). Thus, vertical complementarity for soil resources uptake in mixtures was not only dependant on the inherent root system architecture but also on root plasticity. We also observed a time-dependence for positive complementarity effects due to the slow development of Trifolium in mixtures, possibly induced by competition with grasses. Overall, our data underlined that soil water resource was an important driver of over-yielding and complementarity effects in Trifolium-grass mixtures.

Complementarity in false memory illusions.

PubMed

Brainerd, C J; Reyna, V F

2018-03-01

For some years, the DRM illusion has been the most widely studied form of false memory. The consensus theoretical interpretation is that the illusion is a reality reversal, in which certain new words (critical distractors) are remembered as though they are old list words rather than as what they are-new words that are similar to old ones. This reality-reversal interpretation is supported by compelling lines of evidence, but prior experiments are limited by the fact that their memory tests only asked whether test items were old. We removed that limitation by also asking whether test items were new-similar. This more comprehensive methodology revealed that list words and critical distractors are remembered quite differently. Memory for list words is compensatory: They are remembered as old at high rates and remembered as new-similar at very low rates. In contrast, memory for critical distractors is complementary: They are remembered as both old and new-similar at high rates, which means that the DRM procedure induces a complementarity illusion rather than a reality reversal. The conjoint recognition model explains complementarity as a function of three retrieval processes (semantic familiarity, target recollection, and context recollection), and it predicts that complementarity can be driven up or down by varying the mix of those processes. Our experiments generated data on that prediction and introduced a convenient statistic, the complementarity ratio, which measures (a) the level of complementarity in memory performance and (b) whether its direction is reality-consistent or reality-reversed. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Assembling oppositely charged lock and key responsive colloids: A mesoscale analog of adaptive chemistry

PubMed Central

Mihut, Adriana M.; Stenqvist, Björn; Lund, Mikael; Schurtenberger, Peter; Crassous, Jérôme J.

2017-01-01

We have seen a considerable effort in colloid sciences to copy Nature’s successful strategies to fabricate complex functional structures through self-assembly. This includes attempts to design colloidal building blocks and their intermolecular interactions, such as creating the colloidal analogs of directional molecular interactions, molecular recognition, host-guest systems, and specific binding. We show that we can use oppositely charged thermoresponsive particles with complementary shapes, such as spherical and bowl-shaped particles, to implement an externally controllable lock-and-key self-assembly mechanism. The use of tunable electrostatic interactions combined with the temperature-dependent size and shape and van der Waals interactions of these building blocks provides an exquisite control over the selectivity and specificity of the interactions and self-assembly process. The dynamic nature of the mechanism allows for reversibly cycling through various structures that range from weakly structured dense liquids to well-defined molecule-shaped clusters with different configurations through variations in temperature and ionic strength. We link this complex and dynamic self-assembly behavior to the relevant molecular interactions, such as screened Coulomb and van der Waals forces and the geometrical complementarity of the two building blocks, and discuss our findings in the context of the concepts of adaptive chemistry recently introduced to molecular systems. PMID:28929133

Protein-protein recognition: crystal structural analysis of a barnase-barstar complex at 2.0-A resolution.

PubMed

Buckle, A M; Schreiber, G; Fersht, A R

1994-08-02

We have solved, refined, and analyzed the 2.0-å resolution crystal structure of a 1:1 complex between the bacterial ribonuclease, barnase, and a Cys-->Ala(40,82) double mutant of its intracellular polypeptide inhibitor, barstar. Barstar inhibits barnase by sterically blocking the active site with a helix and adjacent loop segment. Almost half of the 14 hydrogen bonds between barnase and barstar involve two charged residues, and a third involve one charged partner. The electrostatic contribution to the overall binding energy is considerably greater than for other protein-protein interactions. Consequently, the very high rate constant for the barnase-barstar association (10(8) s-1 M-1) is most likely due to electrostatic steering effects. The barnase active-site residue His102 is located in a pocket on the surface of barstar, and its hydrogen bonds with Asp39 and Gly31 residues of barstar are directly responsible for the pH dependence of barnase-barstar binding. There is a high degree of complementarity both of the shape and of the charge of the interacting surfaces, but neither is perfect. The surface complementarity is slightly poorer than in protease-inhibitor complexes but a little better than in antibody-antigen interactions. However, since the burial of solvent in the barnase-barstar interface improves the fit significantly by filling in the majority of gaps, as well as stabilizing unfavorable electrostatic interactions, its role seems to be more important than in other protein-protein complexes. The electrostatic interactions between barnase and barstar are very similar to those between barnase and the tetranucleotide d(CGAC). In the barnase-barstar complex, the two phosphate-binding sites in the barnase active site are occupied by Asp39 and Gly43 of barstar. However, barstar has no equivalent for a guanine base of an RNA substrate, resulting in the occupation of the guanine recognition site in the barnase-barstar complex by nine ordered water molecules. Upon barnase-barstar binding, entropy losses resulting from the immobilization of segments of the protein chain and the energetic costs of conformational changes are minimized due to the essentially preformed active site of barnase. However, a certain degree of flexibility within the barnase active site is required to allow for the structural differences between barnase-barstar binding and barnase-RNA binding. A comparison between the bound and the free barstar structure shows that the overall structural response to barnase-binding is significant. This response can be best described as outwardly oriented, rigid-body movements of the four alpha-helices of barstar, resulting in the structure of bound barstar being somewhat expanded.

Complementarity in radiochemical and infrared spectroscopic characterization of electrode adsorption

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

Wieckowski, A.

1994-03-01

Radioactive labelling and infrared spectroscopy are frequently used as direct, in situ probes into the structure of the electrochemical solid/liquid interface. These techniques are compared, in a polemical fashion, in the context of a recent publication by Parry et al. (Langmuir 1993, 9, 1878) where the research potential of the former technique was not adequately depicted. It is shown that radiotracers can clearly differentiate between the surface and solution species, both neutrals and anions. In addition to the surface specificity, the radiotracers offer a quantitative determination of adsorbate surface concentrations, a feature not yet demonstrated with surface infrared spectroscopy inmore » electrochemistry. Therefore, these two techniques are complementary. Examples of the combined radiochemical and spectroscopic measurements of adsorption with equivalent (smooth) electrode surfaces are quoted. 11 refs., 2 figs.« less

PatchSurfers: Two methods for local molecular property-based binding ligand prediction.

PubMed

Shin, Woong-Hee; Bures, Mark Gregory; Kihara, Daisuke

2016-01-15

Protein function prediction is an active area of research in computational biology. Function prediction can help biologists make hypotheses for characterization of genes and help interpret biological assays, and thus is a productive area for collaboration between experimental and computational biologists. Among various function prediction methods, predicting binding ligand molecules for a target protein is an important class because ligand binding events for a protein are usually closely intertwined with the proteins' biological function, and also because predicted binding ligands can often be directly tested by biochemical assays. Binding ligand prediction methods can be classified into two types: those which are based on protein-protein (or pocket-pocket) comparison, and those that compare a target pocket directly to ligands. Recently, our group proposed two computational binding ligand prediction methods, Patch-Surfer, which is a pocket-pocket comparison method, and PL-PatchSurfer, which compares a pocket to ligand molecules. The two programs apply surface patch-based descriptions to calculate similarity or complementarity between molecules. A surface patch is characterized by physicochemical properties such as shape, hydrophobicity, and electrostatic potentials. These properties on the surface are represented using three-dimensional Zernike descriptors (3DZD), which are based on a series expansion of a 3 dimensional function. Utilizing 3DZD for describing the physicochemical properties has two main advantages: (1) rotational invariance and (2) fast comparison. Here, we introduce Patch-Surfer and PL-PatchSurfer with an emphasis on PL-PatchSurfer, which is more recently developed. Illustrative examples of PL-PatchSurfer performance on binding ligand prediction as well as virtual drug screening are also provided. Copyright © 2015 Elsevier Inc. All rights reserved.

Unraveling the molecular mechanisms of nitrogenase conformational protection against oxygen in diazotrophic bacteria.

PubMed

Lery, Letícia M S; Bitar, Mainá; Costa, Mauricio G S; Rössle, Shaila C S; Bisch, Paulo M

2010-12-22

G. diazotrophicus and A. vinelandii are aerobic nitrogen-fixing bacteria. Although oxygen is essential for the survival of these organisms, it irreversibly inhibits nitrogenase, the complex responsible for nitrogen fixation. Both microorganisms deal with this paradox through compensatory mechanisms. In A. vinelandii a conformational protection mechanism occurs through the interaction between the nitrogenase complex and the FeSII protein. Previous studies suggested the existence of a similar system in G. diazotrophicus, but the putative protein involved was not yet described. This study intends to identify the protein coding gene in the recently sequenced genome of G. diazotrophicus and also provide detailed structural information of nitrogenase conformational protection in both organisms. Genomic analysis of G. diazotrophicus sequences revealed a protein coding ORF (Gdia0615) enclosing a conserved "fer2" domain, typical of the ferredoxin family and found in A. vinelandii FeSII. Comparative models of both FeSII and Gdia0615 disclosed a conserved beta-grasp fold. Cysteine residues that coordinate the 2[Fe-S] cluster are in conserved positions towards the metallocluster. Analysis of solvent accessible residues and electrostatic surfaces unveiled an hydrophobic dimerization interface. Dimers assembled by molecular docking presented a stable behaviour and a proper accommodation of regions possibly involved in binding of FeSII to nitrogenase throughout molecular dynamics simulations in aqueous solution. Molecular modeling of the nitrogenase complex of G. diazotrophicus was performed and models were compared to the crystal structure of A. vinelandii nitrogenase. Docking experiments of FeSII and Gdia0615 with its corresponding nitrogenase complex pointed out in both systems a putative binding site presenting shape and charge complementarities at the Fe-protein/MoFe-protein complex interface. The identification of the putative FeSII coding gene in G. diazotrophicus genome represents a large step towards the understanding of the conformational protection mechanism of nitrogenase against oxygen. In addition, this is the first study regarding the structural complementarities of FeSII-nitrogenase interactions in diazotrophic bacteria. The combination of bioinformatic tools for genome analysis, comparative protein modeling, docking calculations and molecular dynamics provided a powerful strategy for the elucidation of molecular mechanisms and structural features of FeSII-nitrogenase interaction.

Model of early self-replication based on covalent complementarity for a copolymer of glycerate-3-phosphate and glycerol-3-phosphate

NASA Technical Reports Server (NTRS)

Weber, Arthur L.

1989-01-01

Glyceraldehyde-3-phosphate acts as the substrate in a model of early self-replication of a phosphodiester copolymer of glycerate-3-phosphate and glycerol-3-phosphate. This model of self-replication is based on covalent complementarity in which information transfer is mediated by a single covalent bond, in contrast to multiple weak interactions that establish complementarity in nucleic acid replication. This replication model is connected to contemporary biochemistry through its use of glyceraldehyde-3-phosphate, a central metabolite of glycolysis and photosynthesis.

Modeling and simulation of dynamics of a planar-motion rigid body with friction and surface contact

NASA Astrophysics Data System (ADS)

Wang, Xiaojun; Lv, Jing

2017-07-01

The modeling and numerical method for the dynamics of a planar-motion rigid body with frictional contact between plane surfaces were presented based on the theory of contact mechanics and the algorithm of linear complementarity problem (LCP). The Coulomb’s dry friction model is adopted as the friction law, and the normal contact forces are expressed as functions of the local deformations and their speeds in contact bodies. The dynamic equations of the rigid body are obtained by the Lagrange equation. The transition problem of stick-slip motions between contact surfaces is formulated and solved as LCP through establishing the complementary conditions of the friction law. Finally, a numerical example is presented as an example to show the application.

Phytoplankton Assemblage Characteristics in Recurrently Fluctuating Environments

PubMed Central

Roelke, Daniel L.; Spatharis, Sofie

2015-01-01

Annual variations in biogeochemical and physical processes can lead to nutrient variability and seasonal patterns in phytoplankton productivity and assemblage structure. In many coastal systems river inflow and water exchange with the ocean varies seasonally, and alternating periods can arise where the nutrient most limiting to phytoplankton growth switches. Transitions between these alternating periods can be sudden or gradual and this depends on human activities, such as reservoir construction and interbasin water transfers. How such activities might influence phytoplankton assemblages is largely unknown. Here, we employed a multispecies, multi-nutrient model to explore how nutrient loading switching mode might affect characteristics of phytoplankton assemblages. The model is based on the Monod-relationship, predicting an instantaneous growth rate from ambient inorganic nutrient concentrations whereas the limiting nutrient at any given time was determined by Liebig’s Law of the Minimum. Our simulated phytoplankton assemblages self-organized from species rich pools over a 15-year period, and only the surviving species were considered as assemblage members. Using the model, we explored the interactive effects of complementarity level in trait trade-offs within phytoplankton assemblages and the amount of noise in the resource supply concentrations. We found that the effect of shift from a sudden resource supply transition to a gradual one, as observed in systems impacted by watershed development, was dependent on the level of complementarity. In the extremes, phytoplankton species richness and relative overyielding increased when complementarity was lowest, and phytoplankton biomass increased greatly when complementarity was highest. For low-complementarity simulations, the persistence of poorer-performing phytoplankton species of intermediate R*s led to higher richness and relative overyielding. For high-complementarity simulations, the formation of phytoplankton species clusters and niche compression enabled higher biomass accumulation. Our findings suggest that an understanding of factors influencing the emergence of life history traits important to complementarity is necessary to predict the impact of watershed development on phytoplankton productivity and assemblage structure. PMID:25799563

Black hole complementarity with the generalized uncertainty principle in Gravity's Rainbow

NASA Astrophysics Data System (ADS)

Gim, Yongwan; Um, Hwajin; Kim, Wontae

2018-02-01

When gravitation is combined with quantum theory, the Heisenberg uncertainty principle could be extended to the generalized uncertainty principle accompanying a minimal length. To see how the generalized uncertainty principle works in the context of black hole complementarity, we calculate the required energy to duplicate information for the Schwarzschild black hole. It shows that the duplication of information is not allowed and black hole complementarity is still valid even assuming the generalized uncertainty principle. On the other hand, the generalized uncertainty principle with the minimal length could lead to a modification of the conventional dispersion relation in light of Gravity's Rainbow, where the minimal length is also invariant as well as the speed of light. Revisiting the gedanken experiment, we show that the no-cloning theorem for black hole complementarity can be made valid in the regime of Gravity's Rainbow on a certain combination of parameters.

Complementarity and Compensation: Bridging the Gap between Writing and Design.

ERIC Educational Resources Information Center

Killingsworth, M. Jimmie; Sanders, Scott P.

1990-01-01

Outlines two rhetorical principles for producing iconic-mosaic texts--the principle of complementarity and the principle of compensation. Shows how these principles can be applied to practical problems in coordinating the writing and design processes in student projects. (RS)

Educational Finance Policy: A Search for Complementarities.

ERIC Educational Resources Information Center

Geske, Terry G.

1983-01-01

An overview of recent state level policy developments and policy analysis research as related to equity and efficiency objectives in public school finance is presented. Emphasis is placed on identifying complementarities, rather than the tradeoffs, between equity and efficiency criteria. (Author/LC)

Is the firewall consistent? Gedanken experiments on black hole complementarity and firewall proposal

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

Hwang, Dong-il; Lee, Bum-Hoon; Yeom, Dong-han, E-mail: dongil.j.hwang@gmail.com, E-mail: bhl@sogang.ac.kr, E-mail: innocent.yeom@gmail.com

2013-01-01

In this paper, we discuss the black hole complementarity and the firewall proposal at length. Black hole complementarity is inevitable if we assume the following five things: unitarity, entropy-area formula, existence of an information observer, semi-classical quantum field theory for an asymptotic observer, and the general relativity for an in-falling observer. However, large N rescaling and the AMPS argument show that black hole complementarity is inconsistent. To salvage the basic philosophy of the black hole complementarity, AMPS introduced a firewall around the horizon. According to large N rescaling, the firewall should be located close to the apparent horizon. We investigatemore » the consistency of the firewall with the two critical conditions: the firewall should be near the time-like apparent horizon and it should not affect the future infinity. Concerning this, we have introduced a gravitational collapse with a false vacuum lump which can generate a spacetime structure with disconnected apparent horizons. This reveals a situation that there is a firewall outside of the event horizon, while the apparent horizon is absent. Therefore, the firewall, if it exists, not only does modify the general relativity for an in-falling observer, but also modify the semi-classical quantum field theory for an asymptotic observer.« less

Is the firewall consistent? Gedanken experiments on black hole complementarity and firewall proposal

NASA Astrophysics Data System (ADS)

Hwang, Dong-il; Lee, Bum-Hoon; Yeom, Dong-han

2013-01-01

In this paper, we discuss the black hole complementarity and the firewall proposal at length. Black hole complementarity is inevitable if we assume the following five things: unitarity, entropy-area formula, existence of an information observer, semi-classical quantum field theory for an asymptotic observer, and the general relativity for an in-falling observer. However, large N rescaling and the AMPS argument show that black hole complementarity is inconsistent. To salvage the basic philosophy of the black hole complementarity, AMPS introduced a firewall around the horizon. According to large N rescaling, the firewall should be located close to the apparent horizon. We investigate the consistency of the firewall with the two critical conditions: the firewall should be near the time-like apparent horizon and it should not affect the future infinity. Concerning this, we have introduced a gravitational collapse with a false vacuum lump which can generate a spacetime structure with disconnected apparent horizons. This reveals a situation that there is a firewall outside of the event horizon, while the apparent horizon is absent. Therefore, the firewall, if it exists, not only does modify the general relativity for an in-falling observer, but also modify the semi-classical quantum field theory for an asymptotic observer.

Intron self-complementarity enforces exon inclusion in a yeast pre-mRNA

PubMed Central

Howe, Kenneth James; Ares, Manuel

1997-01-01

Skipping of internal exons during removal of introns from pre-mRNA must be avoided for proper expression of most eukaryotic genes. Despite significant understanding of the mechanics of intron removal, mechanisms that ensure inclusion of internal exons in multi-intron pre-mRNAs remain mysterious. Using a natural two-intron yeast gene, we have identified distinct RNA–RNA complementarities within each intron that prevent exon skipping and ensure inclusion of internal exons. We show that these complementarities are positioned to act as intron identity elements, bringing together only the appropriate 5′ splice sites and branchpoints. Destroying either intron self-complementarity allows exon skipping to occur, and restoring the complementarity using compensatory mutations rescues exon inclusion, indicating that the elements act through formation of RNA secondary structure. Introducing new pairing potential between regions near the 5′ splice site of intron 1 and the branchpoint of intron 2 dramatically enhances exon skipping. Similar elements identified in single intron yeast genes contribute to splicing efficiency. Our results illustrate how intron secondary structure serves to coordinate splice site pairing and enforce exon inclusion. We suggest that similar elements in vertebrate genes could assist in the splicing of very large introns and in the evolution of alternative splicing. PMID:9356473

Deciphering fine molecular details of proteins' structure and function with a Protein Surface Topography (PST) method.

PubMed

Koromyslova, Anna D; Chugunov, Anton O; Efremov, Roman G

2014-04-28

Molecular surfaces are the key players in biomolecular recognition and interactions. Nowadays, it is trivial to visualize a molecular surface and surface-distributed properties in three-dimensional space. However, such a representation trends to be biased and ambiguous in case of thorough analysis. We present a new method to create 2D spherical projection maps of entire protein surfaces and manipulate with them--protein surface topography (PST). It permits visualization and thoughtful analysis of surface properties. PST helps to easily portray conformational transitions, analyze proteins' properties and their dynamic behavior, improve docking performance, and reveal common patterns and dissimilarities in molecular surfaces of related bioactive peptides. This paper describes basic usage of PST with an example of small G-proteins conformational transitions, mapping of caspase-1 intersubunit interface, and intrinsic "complementarity" in the conotoxin-acetylcholine binding protein complex. We suggest that PST is a beneficial approach for structure-function studies of bioactive peptides and small proteins.

Functional traits explain ecosystem function through opposing mechanisms.

PubMed

Cadotte, Marc W

2017-08-01

The ability to explain why multispecies assemblages produce greater biomass compared to monocultures, has been a central goal in the quest to understand biodiversity effects on ecosystem function. Species contributions to ecosystem function can be driven by two processes: niche complementarity and a selection effect that is influenced by fitness (competitive) differences, and both can be approximated with measures of species' traits. It has been hypothesised that fitness differences are associated with few, singular traits while complementarity requires multidimensional trait measures. Here, using experimental data from plant assemblages, I show that the selection effect was strongest when trait dissimilarity was low, while complementarity was greatest with high trait dissimilarity. Selection effects were best explained by a single trait, plant height. Complementarity was correlated with dissimilarity across multiple traits, representing above and below ground processes. By identifying the relevant traits linked to ecosystem function, we obtain the ability to predict combinations of species that will maximise ecosystem function. © 2017 John Wiley & Sons Ltd/CNRS.

Highly viscous antibody solutions are a consequence of network formation caused by domain-domain electrostatic complementarities: insights from coarse-grained simulations.

PubMed

Buck, Patrick M; Chaudhri, Anuj; Kumar, Sandeep; Singh, Satish K

2015-01-05

Therapeutic monoclonal antibody (mAb) candidates that form highly viscous solutions at concentrations above 100 mg/mL can lead to challenges in bioprocessing, formulation development, and subcutaneous drug delivery. Earlier studies of mAbs with concentration-dependent high viscosity have indicated that mAbs with negatively charged Fv regions have a dipole-like quality that increases the likelihood of reversible self-association. This suggests that weak electrostatic intermolecular interactions can form transient antibody networks that participate in resistance to solution deformation under shear stress. Here this hypothesis is explored by parametrizing a coarse-grained (CG) model of an antibody using the domain charges from four different mAbs that have had their concentration-dependent viscosity behaviors previously determined. Multicopy molecular dynamics simulations were performed for these four CG mAbs at several concentrations to understand the effect of surface charge on mass diffusivity, pairwise interactions, and electrostatic network formation. Diffusion coefficients computed from simulations were in qualitative agreement with experimentally determined viscosities for all four mAbs. Contact analysis revealed an overall greater number of pairwise interactions for the two mAbs in this study with high concentration viscosity issues. Further, using equilibrated solution trajectories, the two mAbs with high concentration viscosity issues quantitatively formed more features of an electrostatic network than the other mAbs. The change in the number of these network features as a function of concentration is related to the number of pairwise interactions formed by electrostatic complementarities between antibody domains. Thus, transient antibody network formation caused by domain-domain electrostatic complementarities is the most probable origin of high concentration viscosity for mAbs in this study.

Getting the full picture: Assessing the complementarity of citizen science and agency monitoring data.

PubMed

Hadj-Hammou, Jeneen; Loiselle, Steven; Ophof, Daniel; Thornhill, Ian

2017-01-01

While the role of citizen science in engaging the public and providing large-scale datasets has been demonstrated, the nature of and potential for this science to supplement environmental monitoring efforts by government agencies has not yet been fully explored. To this end, the present study investigates the complementarity of a citizen science programme to agency monitoring of water quality. The Environment Agency (EA) is the governmental public body responsible for, among other duties, managing and monitoring water quality and water resources in England. FreshWater Watch (FWW) is a global citizen science project that supports community monitoring of freshwater quality. FWW and EA data were assessed for their spatio-temporal complementarity by comparing the geographical and seasonal coverage of nitrate (N-NO3) sampling across the River Thames catchment by the respective campaigns between spring 2013 and winter 2015. The analysis reveals that FWW citizen science-collected data complements EA data by filling in both gaps in the spatial and temporal coverage as well as gaps in waterbody type and size. In addition, partial spatio-temporal overlap in sampling efforts by the two actors is discovered, but EA sampling is found to be more consistent than FWW sampling. Statistical analyses indicate that regardless of broader geographical overlap in sampling effort, FWW sampling sites are associated with a lower stream order and water bodies of smaller surface areas than EA sampling sites. FWW also samples more still-water body sites than the EA. As a possible result of such differences in sampling tendencies, nitrate concentrations, a measure of water quality, are lower for FWW sites than EA sites. These findings strongly indicate that citizen science has clear potential to complement agency monitoring efforts by generating information on freshwater ecosystems that would otherwise be under reported.

Getting the full picture: Assessing the complementarity of citizen science and agency monitoring data

PubMed Central

Loiselle, Steven; Ophof, Daniel; Thornhill, Ian

2017-01-01

While the role of citizen science in engaging the public and providing large-scale datasets has been demonstrated, the nature of and potential for this science to supplement environmental monitoring efforts by government agencies has not yet been fully explored. To this end, the present study investigates the complementarity of a citizen science programme to agency monitoring of water quality. The Environment Agency (EA) is the governmental public body responsible for, among other duties, managing and monitoring water quality and water resources in England. FreshWater Watch (FWW) is a global citizen science project that supports community monitoring of freshwater quality. FWW and EA data were assessed for their spatio-temporal complementarity by comparing the geographical and seasonal coverage of nitrate (N-NO3) sampling across the River Thames catchment by the respective campaigns between spring 2013 and winter 2015. The analysis reveals that FWW citizen science-collected data complements EA data by filling in both gaps in the spatial and temporal coverage as well as gaps in waterbody type and size. In addition, partial spatio-temporal overlap in sampling efforts by the two actors is discovered, but EA sampling is found to be more consistent than FWW sampling. Statistical analyses indicate that regardless of broader geographical overlap in sampling effort, FWW sampling sites are associated with a lower stream order and water bodies of smaller surface areas than EA sampling sites. FWW also samples more still-water body sites than the EA. As a possible result of such differences in sampling tendencies, nitrate concentrations, a measure of water quality, are lower for FWW sites than EA sites. These findings strongly indicate that citizen science has clear potential to complement agency monitoring efforts by generating information on freshwater ecosystems that would otherwise be under reported. PMID:29211752

Asymmetrical flow field-flow fractionation with multi-angle light scattering and quasi-elastic light scattering for characterization of polymersomes: comparison with classical techniques.

PubMed

Till, Ugo; Gaucher-Delmas, Mireille; Saint-Aguet, Pascale; Hamon, Glenn; Marty, Jean-Daniel; Chassenieux, Christophe; Payré, Bruno; Goudounèche, Dominique; Mingotaud, Anne-Françoise; Violleau, Frédéric

2014-12-01

Polymersomes formed from amphiphilic block copolymers, such as poly(ethyleneoxide-b-ε-caprolactone) (PEO-b-PCL) or poly(ethyleneoxide-b-methylmethacrylate), were characterized by asymmetrical flow field-flow fractionation coupled with quasi-elastic light scattering (QELS), multi-angle light scattering (MALS), and refractive index detection, leading to the determination of their size, shape, and molecular weight. The method was cross-examined with more classical ones, like batch dynamic and static light scattering, electron microscopy, and atomic force microscopy. The results show good complementarities between all the techniques; asymmetrical flow field-flow fractionation being the most pertinent one when the sample exhibits several different types of population.

Experimental investigation of halogen-bond hard-soft acid-base complementarity.

PubMed

Riel, Asia Marie S; Jessop, Morly J; Decato, Daniel A; Massena, Casey J; Nascimento, Vinicius R; Berryman, Orion B

2017-04-01

The halogen bond (XB) is a topical noncovalent interaction of rapidly increasing importance. The XB employs a `soft' donor atom in comparison to the `hard' proton of the hydrogen bond (HB). This difference has led to the hypothesis that XBs can form more favorable interactions with `soft' bases than HBs. While computational studies have supported this suggestion, solution and solid-state data are lacking. Here, XB soft-soft complementarity is investigated with a bidentate receptor that shows similar associations with neutral carbonyls and heavy chalcogen analogs. The solution speciation and XB soft-soft complementarity is supported by four crystal structures containing neutral and anionic soft Lewis bases.

Climate change mitigation and adaptation in the land use sector: from complementarity to synergy.

PubMed

Duguma, Lalisa A; Minang, Peter A; van Noordwijk, Meine

2014-09-01

Currently, mitigation and adaptation measures are handled separately, due to differences in priorities for the measures and segregated planning and implementation policies at international and national levels. There is a growing argument that synergistic approaches to adaptation and mitigation could bring substantial benefits at multiple scales in the land use sector. Nonetheless, efforts to implement synergies between adaptation and mitigation measures are rare due to the weak conceptual framing of the approach and constraining policy issues. In this paper, we explore the attributes of synergy and the necessary enabling conditions and discuss, as an example, experience with the Ngitili system in Tanzania that serves both adaptation and mitigation functions. An in-depth look into the current practices suggests that more emphasis is laid on complementarity-i.e., mitigation projects providing adaptation co-benefits and vice versa rather than on synergy. Unlike complementarity, synergy should emphasize functionally sustainable landscape systems in which adaptation and mitigation are optimized as part of multiple functions. We argue that the current practice of seeking co-benefits (complementarity) is a necessary but insufficient step toward addressing synergy. Moving forward from complementarity will require a paradigm shift from current compartmentalization between mitigation and adaptation to systems thinking at landscape scale. However, enabling policy, institutional, and investment conditions need to be developed at global, national, and local levels to achieve synergistic goals.

DISTINCT ANTIBODY SPECIES: STRUCTURAL DIFFERENCES CREATING THERAPEUTIC OPPORTUNITIES

PubMed Central

Muyldermans, Serge; Smider, Vaughn V.

2016-01-01

Antibodies have been a remarkably successful class of molecules for binding a large number of antigens in therapeutic, diagnostic, and research applications. Typical antibodies derived from mouse or human sources use the surface formed by complementarity determining regions (CDRs) on the variable regions of the heavy chain/light chain heterodimer, which typically forms a relatively flat binding surface. Alternative species, particularly camelids and bovines, provide a unique paradigm for antigen recognition through novel domains which form the antigen binding paratope. For camelids, heavy chain antibodies bind antigen with only a single heavy chain variable region, in the absence of light chains. In bovines, ultralong CDR-H3 regions form an independently folding minidomain, which protrudes from the surface of the antibody and is diverse in both its sequence and disulfide patterns. The atypical paratopes of camelids and bovines potentially provide the ability to interact with different epitopes, particularly recessed or concave surfaces, compared to traditional antibodies. PMID:26922135

Structural Model for the Interaction of a Designed Ankyrin Repeat Protein with the Human Epidermal Growth Factor Receptor 2

PubMed Central

Epa, V. Chandana; Dolezal, Olan; Doughty, Larissa; Xiao, Xiaowen; Jost, Christian; Plückthun, Andreas; Adams, Timothy E.

2013-01-01

Designed Ankyrin Repeat Proteins are a class of novel binding proteins that can be selected and evolved to bind to targets with high affinity and specificity. We are interested in the DARPin H10-2-G3, which has been evolved to bind with very high affinity to the human epidermal growth factor receptor 2 (HER2). HER2 is found to be over-expressed in 30% of breast cancers, and is the target for the FDA-approved therapeutic monoclonal antibodies trastuzumab and pertuzumab and small molecule tyrosine kinase inhibitors. Here, we use computational macromolecular docking, coupled with several interface metrics such as shape complementarity, interaction energy, and electrostatic complementarity, to model the structure of the complex between the DARPin H10-2-G3 and HER2. We analyzed the interface between the two proteins and then validated the structural model by showing that selected HER2 point mutations at the putative interface with H10-2-G3 reduce the affinity of binding up to 100-fold without affecting the binding of trastuzumab. Comparisons made with a subsequently solved X-ray crystal structure of the complex yielded a backbone atom root mean square deviation of 0.84–1.14 Ångstroms. The study presented here demonstrates the capability of the computational techniques of structural bioinformatics in generating useful structural models of protein-protein interactions. PMID:23527120

The eukaryotic cell originated in the integration and redistribution of hyperstructures from communities of prokaryotic cells based on molecular complementarity.

PubMed

Norris, Vic; Root-Bernstein, Robert

2009-06-04

In the "ecosystems-first" approach to the origins of life, networks of non-covalent assemblies of molecules (composomes), rather than individual protocells, evolved under the constraints of molecular complementarity. Composomes evolved into the hyperstructures of modern bacteria. We extend the ecosystems-first approach to explain the origin of eukaryotic cells through the integration of mixed populations of bacteria. We suggest that mutualism and symbiosis resulted in cellular mergers entailing the loss of redundant hyperstructures, the uncoupling of transcription and translation, and the emergence of introns and multiple chromosomes. Molecular complementarity also facilitated integration of bacterial hyperstructures to perform cytoskeletal and movement functions.

Computational studies of new potential antimalarial compounds Stereoelectronic complementarity with the receptor

NASA Astrophysics Data System (ADS)

Portela, César; Afonso, Carlos M. M.; Pinto, Madalena M. M.; João Ramos, Maria

2003-09-01

One of the most important pharmacological mechanisms of antimalarial action is the inhibition of the aggregation of hematin into hemozoin. We present a group of new potential antimalarial molecules for which we have performed a DFT study of their stereoelectronic properties. Additionally, the same calculations were carried out for the two putative drug receptors involved in the referred activity, i.e., hematin μ-oxo dimer and hemozoin. A complementarity between the structural and electronic profiles of the planned molecules and the receptors can be observed. A docking study of the new compounds in relation to the two putative receptors is also presented, providing a correlation with the defined electrostatic complementarity.

Molecular origins of osmotic second virial coefficients of proteins.

PubMed Central

Neal, B L; Asthagiri, D; Lenhoff, A M

1998-01-01

The thermodynamic properties of protein solutions are determined by the molecular interactions involving both solvent and solute molecules. A quantitative understanding of the relationship would facilitate more systematic procedures for manipulating the properties in a process environment. In this work the molecular basis for the osmotic second virial coefficient, B22, is studied; osmotic effects are critical in membrane transport, and the value of B22 has also been shown to correlate with protein crystallization behavior. The calculations here account for steric, electrostatic, and short-range interactions, with the structural and functional anisotropy of the protein molecules explicitly accounted for. The orientational dependence of the protein interactions is seen to have a pronounced effect on the calculations; in particular, the relatively few protein-protein configurations in which the apposing surfaces display geometric complementarity contribute disproportionately strongly to B22. The importance of electrostatic interactions is also amplified in these high-complementarity configurations. The significance of molecular recognition in determining B22 can explain the correlation with crystallization behavior, and it suggests that alteration of local molecular geometry can help in manipulating protein solution behavior. The results also have implications for the role of protein interactions in biological self-organization. PMID:9788942

Compatibility and Complementarity of Classroom Ecology and Didactique Research Perspectives in Physical Education

ERIC Educational Resources Information Center

Leriche, Jérôme; Desbiens, Jean-François; Amade-Escot, Chantal; Tinning, Richard

2016-01-01

A large diversity of theoretical frameworks exists in the physical education literature. This article focuses on two of those frameworks to examine their compatibility and their complementarity. The classroom ecology paradigm concentrates on the balance between three task systems, two vectors, and programs of actions proposed by the physical…

A Portfolio for Optimal Collaboration of Human and Cyber Physical Production Systems in Problem-Solving

ERIC Educational Resources Information Center

Ansari, Fazel; Seidenberg, Ulrich

2016-01-01

This paper discusses the complementarity of human and cyber physical production systems (CPPS). The discourse of complementarity is elaborated by defining five criteria for comparing the characteristics of human and CPPS. Finally, a management portfolio matrix is proposed for examining the feasibility of optimal collaboration between them. The…

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

NASA Astrophysics Data System (ADS)

Lourdu Xavier, P.; Chandrasekaran, Arun Richard

2018-02-01

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

Protein social behavior makes a stronger signal for partner identification than surface geometry

PubMed Central

Laine, Elodie

2016-01-01

ABSTRACT Cells are interactive living systems where proteins movements, interactions and regulation are substantially free from centralized management. How protein physico‐chemical and geometrical properties determine who interact with whom remains far from fully understood. We show that characterizing how a protein behaves with many potential interactors in a complete cross‐docking study leads to a sharp identification of its cellular/true/native partner(s). We define a sociability index, or S‐index, reflecting whether a protein likes or not to pair with other proteins. Formally, we propose a suitable normalization function that accounts for protein sociability and we combine it with a simple interface‐based (ranking) score to discriminate partners from non‐interactors. We show that sociability is an important factor and that the normalization permits to reach a much higher discriminative power than shape complementarity docking scores. The social effect is also observed with more sophisticated docking algorithms. Docking conformations are evaluated using experimental binding sites. These latter approximate in the best possible way binding sites predictions, which have reached high accuracy in recent years. This makes our analysis helpful for a global understanding of partner identification and for suggesting discriminating strategies. These results contradict previous findings claiming the partner identification problem being solvable solely with geometrical docking. Proteins 2016; 85:137–154. © 2016 Wiley Periodicals, Inc. PMID:27802579

Structural asymmetry in the Thermus thermophilus RuvC dimer suggests a basis for sequential strand cleavages during Holliday junction resolution.

PubMed

Chen, Luan; Shi, Ke; Yin, Zhiqi; Aihara, Hideki

2013-01-07

Holliday junction (HJ) resolvases are structure-specific endonucleases that cleave four-way DNA junctions (HJs) generated during DNA recombination and repair. Bacterial RuvC, a prototypical HJ resolvase, functions as homodimer and nicks DNA strands precisely across the junction point. To gain insights into the mechanisms underlying symmetrical strand cleavages by RuvC, we performed crystallographic and biochemical analyses of RuvC from Thermus thermophilus (T.th. RuvC). The crystal structure of T.th. RuvC shows an overall protein fold similar to that of Escherichia coli RuvC, but T.th. RuvC has a more tightly associated dimer interface possibly reflecting its thermostability. The binding mode of a HJ-DNA substrate can be inferred from the shape/charge complementarity between the T.th. RuvC dimer and HJ-DNA, as well as positions of sulfate ions bound on the protein surface. Unexpectedly, the structure of T.th. RuvC homodimer refined at 1.28 Å resolution shows distinct asymmetry near the dimer interface, in the region harboring catalytically important aromatic residues. The observation suggests that the T.th. RuvC homodimer interconverts between two asymmetric conformations, with alternating subunits switched on for DNA strand cleavage. This model provides a structural basis for the 'nick-counter-nick' mechanism in HJ resolution, a mode of HJ processing shared by prokaryotic and eukaryotic HJ resolvases.

Protein social behavior makes a stronger signal for partner identification than surface geometry.

PubMed

Laine, Elodie; Carbone, Alessandra

2017-01-01

Cells are interactive living systems where proteins movements, interactions and regulation are substantially free from centralized management. How protein physico-chemical and geometrical properties determine who interact with whom remains far from fully understood. We show that characterizing how a protein behaves with many potential interactors in a complete cross-docking study leads to a sharp identification of its cellular/true/native partner(s). We define a sociability index, or S-index, reflecting whether a protein likes or not to pair with other proteins. Formally, we propose a suitable normalization function that accounts for protein sociability and we combine it with a simple interface-based (ranking) score to discriminate partners from non-interactors. We show that sociability is an important factor and that the normalization permits to reach a much higher discriminative power than shape complementarity docking scores. The social effect is also observed with more sophisticated docking algorithms. Docking conformations are evaluated using experimental binding sites. These latter approximate in the best possible way binding sites predictions, which have reached high accuracy in recent years. This makes our analysis helpful for a global understanding of partner identification and for suggesting discriminating strategies. These results contradict previous findings claiming the partner identification problem being solvable solely with geometrical docking. Proteins 2016; 85:137-154. © 2016 Wiley Periodicals, Inc. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

A computational analysis of the binding model of MDM2 with inhibitors

NASA Astrophysics Data System (ADS)

Hu, Guodong; Wang, Dunyou; Liu, Xinguo; Zhang, Qinggang

2010-08-01

It is a new and promising strategy for anticancer drug design to block the MDM2-p53 interaction using a non-peptide small-molecule inhibitor. We carry out molecular dynamics simulations to study the binding of a set of six non-peptide small-molecule inhibitors with the MDM2. The relative binding free energies calculated using molecular mechanics Poisson-Boltzmann surface area method produce a good correlation with experimentally determined results. The study shows that the van der Waals energies are the largest component of the binding free energy for each complex, which indicates that the affinities of these inhibitors for MDM2 are dominated by shape complementarity. The A-ligands and the B-ligands are the same except for the conformation of 2,2-dimethylbutane group. The quantum mechanics and the binding free energies calculation also show the B-ligands are the more possible conformation of ligands. Detailed binding free energies between inhibitors and individual protein residues are calculated to provide insights into the inhibitor-protein binding model through interpretation of the structural and energetic results from the simulations. The study shows that G1, G2 and G3 group mimic the Phe19, Trp23 and Leu26 residues in p53 and their interactions with MDM2, but the binding model of G4 group differs from the original design strategy to mimic Leu22 residue in p53.

Evaluating complementary networks of restoration plantings for landscape-scale occurrence of temporally dynamic species.

PubMed

Ikin, Karen; Tulloch, Ayesha; Gibbons, Philip; Ansell, Dean; Seddon, Julian; Lindenmayer, David

2016-10-01

Multibillion dollar investments in land restoration make it critical that conservation goals are achieved cost-effectively. Approaches developed for systematic conservation planning offer opportunities to evaluate landscape-scale, temporally dynamic biodiversity outcomes from restoration and improve on traditional approaches that focus on the most species-rich plantings. We investigated whether it is possible to apply a complementarity-based approach to evaluate the extent to which an existing network of restoration plantings meets representation targets. Using a case study of woodland birds of conservation concern in southeastern Australia, we compared complementarity-based selections of plantings based on temporally dynamic species occurrences with selections based on static species occurrences and selections based on ranking plantings by species richness. The dynamic complementarity approach, which incorporated species occurrences over 5 years, resulted in higher species occurrences and proportion of targets met compared with the static complementarity approach, in which species occurrences were taken at a single point in time. For equivalent cost, the dynamic complementarity approach also always resulted in higher average minimum percent occurrence of species maintained through time and a higher proportion of the bird community meeting representation targets compared with the species-richness approach. Plantings selected under the complementarity approaches represented the full range of planting attributes, whereas those selected under the species-richness approach were larger in size. Our results suggest that future restoration policy should not attempt to achieve all conservation goals within individual plantings, but should instead capitalize on restoration opportunities as they arise to achieve collective value of multiple plantings across the landscape. Networks of restoration plantings with complementary attributes of age, size, vegetation structure, and landscape context lead to considerably better outcomes than conventional restoration objectives of site-scale species richness and are crucial for allocating restoration investment wisely to reach desired conservation goals. © 2016 Society for Conservation Biology.

The Impact of Electronic Commerce on the Publishing Industry: Towards a Business Value Complementarity Framework of Electronic Publishing.

ERIC Educational Resources Information Center

Scupola, Ada

1999-01-01

Discussion of the publishing industry and its use of information and communication technologies focuses on the way in which electronic-commerce technologies are changing and could change the publishing processes, and develops a business complementarity model of electronic publishing to maximize profitability and improve the competitive position.…

Architecture of the bacteriophage T4 activator MotA/promoter DNA interaction during sigma appropriation.

PubMed

Hsieh, Meng-Lun; James, Tamara D; Knipling, Leslie; Waddell, M Brett; White, Stephen; Hinton, Deborah M

2013-09-20

Gene expression can be regulated through factors that direct RNA polymerase to the correct promoter sequence at the correct time. Bacteriophage T4 controls its development in this way using phage proteins that interact with host RNA polymerase. Using a process called σ appropriation, the T4 co-activator AsiA structurally remodels the σ(70) subunit of host RNA polymerase, while a T4 activator, MotA, engages the C terminus of σ(70) and binds to a DNA promoter element, the MotA box. Structures for the N-terminal (NTD) and C-terminal (CTD) domains of MotA are available, but no structure exists for MotA with or without DNA. We report the first molecular map of the MotA/DNA interaction within the σ-appropriated complex, which we obtained by using the cleaving reagent, iron bromoacetamidobenzyl-EDTA (FeBABE). We conjugated surface-exposed, single cysteines in MotA with FeBABE and performed cleavage reactions in the context of stable transcription complexes. The DNA cleavage sites were analyzed using ICM Molsoft software and three-dimensional physical models of MotA(NTD), MotA(CTD), and the DNA to investigate shape complementarity between the protein and the DNA and to position MotA on the DNA. We found that the unusual "double wing" motif present within MotA(CTD) resides in the major groove of the MotA box. In addition, we have used surface plasmon resonance to show that MotA alone is in a very dynamic equilibrium with the MotA element. Our results demonstrate the utility of fine resolution FeBABE mapping to determine the architecture of protein-DNA complexes that have been recalcitrant to traditional structure analyses.

Complementarity among four highly productive grassland species depends on resource availability.

PubMed

Roscher, Christiane; Schmid, Bernhard; Kolle, Olaf; Schulze, Ernst-Detlef

2016-06-01

Positive species richness-productivity relationships are common in biodiversity experiments, but how resource availability modifies biodiversity effects in grass-legume mixtures composed of highly productive species is yet to be explicitly tested. We addressed this question by choosing two grasses (Arrhenatherum elatius and Dactylis glomerata) and two legumes (Medicago × varia and Onobrychis viciifolia) which are highly productive in monocultures and dominant in mixtures (the Jena Experiment). We established monocultures, all possible two- and three-species mixtures, and the four-species mixture under three different resource supply conditions (control, fertilization, and shading). Compared to the control, community biomass production decreased under shading (-56 %) and increased under fertilization (+12 %). Net diversity effects (i.e., mixture minus mean monoculture biomass) were positive in the control and under shading (on average +15 and +72 %, respectively) and negative under fertilization (-10 %). Positive complementarity effects in the control suggested resource partitioning and facilitation of growth through symbiotic N2 fixation by legumes. Positive complementarity effects under shading indicated that resource partitioning is also possible when growth is carbon-limited. Negative complementarity effects under fertilization suggested that external nutrient supply depressed facilitative grass-legume interactions due to increased competition for light. Selection effects, which quantify the dominance of species with particularly high monoculture biomasses in the mixture, were generally small compared to complementarity effects, and indicated that these species had comparable competitive strengths in the mixture. Our study shows that resource availability has a strong impact on the occurrence of positive diversity effects among tall and highly productive grass and legume species.

On the Embedded Complementarity of Agent-Based and Aggregate Reasoning in Students' Developing Understanding of Dynamic Systems

ERIC Educational Resources Information Center

Stroup, Walter M.; Wilensky, Uri

2014-01-01

Placed in the larger context of broadening the engagement with systems dynamics and complexity theory in school-aged learning and teaching, this paper is intended to introduce, situate, and illustrate--with results from the use of network supported participatory simulations in classrooms--a stance we call "embedded complementarity" as an…

Has Complementarity between Employer-Sponsored Training and Education in the U.S. Changed during the 2000s?

ERIC Educational Resources Information Center

Waddoups, C. Jeffrey

2018-01-01

The study reveals that the positive correlation between formal education and job training (complementarity) has weakened during the 2000s. Using U.S. Census Bureau data from the Survey of Income and Program Participation, the study finds that although workers in all categories of educational attainment felt the decline, the effects were strongest…

Multiple-algorithm parallel fusion of infrared polarization and intensity images based on algorithmic complementarity and synergy

NASA Astrophysics Data System (ADS)

Zhang, Lei; Yang, Fengbao; Ji, Linna; Lv, Sheng

2018-01-01

Diverse image fusion methods perform differently. Each method has advantages and disadvantages compared with others. One notion is that the advantages of different image methods can be effectively combined. A multiple-algorithm parallel fusion method based on algorithmic complementarity and synergy is proposed. First, in view of the characteristics of the different algorithms and difference-features among images, an index vector-based feature-similarity is proposed to define the degree of complementarity and synergy. This proposed index vector is a reliable evidence indicator for algorithm selection. Second, the algorithms with a high degree of complementarity and synergy are selected. Then, the different degrees of various features and infrared intensity images are used as the initial weights for the nonnegative matrix factorization (NMF). This avoids randomness of the NMF initialization parameter. Finally, the fused images of different algorithms are integrated using the NMF because of its excellent data fusing performance on independent features. Experimental results demonstrate that the visual effect and objective evaluation index of the fused images obtained using the proposed method are better than those obtained using traditional methods. The proposed method retains all the advantages that individual fusion algorithms have.

Leveraging genome-wide datasets to quantify the functional role of the anti-Shine-Dalgarno sequence in regulating translation efficiency.

PubMed

Hockenberry, Adam J; Pah, Adam R; Jewett, Michael C; Amaral, Luís A N

2017-01-01

Studies dating back to the 1970s established that sequence complementarity between the anti-Shine-Dalgarno (aSD) sequence on prokaryotic ribosomes and the 5' untranslated region of mRNAs helps to facilitate translation initiation. The optimal location of aSD sequence binding relative to the start codon, the full extents of the aSD sequence and the functional form of the relationship between aSD sequence complementarity and translation efficiency have not been fully resolved. Here, we investigate these relationships by leveraging the sequence diversity of endogenous genes and recently available genome-wide estimates of translation efficiency. We show that-after accounting for predicted mRNA structure-aSD sequence complementarity increases the translation of endogenous mRNAs by roughly 50%. Further, we observe that this relationship is nonlinear, with translation efficiency maximized for mRNAs with intermediate levels of aSD sequence complementarity. The mechanistic insights that we observe are highly robust: we find nearly identical results in multiple datasets spanning three distantly related bacteria. Further, we verify our main conclusions by re-analysing a controlled experimental dataset. © 2017 The Authors.

Plant diversity effects on grassland productivity are robust to both nutrient enrichment and drought

PubMed Central

Isbell, Forest; Manning, Pete; Connolly, John; Bruelheide, Helge; Ebeling, Anne; Roscher, Christiane; van Ruijven, Jasper; Weigelt, Alexandra; Wilsey, Brian; Beierkuhnlein, Carl; de Luca, Enrica; Griffin, John N.; Hautier, Yann; Hector, Andy; Jentsch, Anke; Kreyling, Jürgen; Lanta, Vojtech; Loreau, Michel; Meyer, Sebastian T.; Mori, Akira S.; Naeem, Shahid; Palmborg, Cecilia; Polley, H. Wayne; Reich, Peter B.; Schmid, Bernhard; Siebenkäs, Alrun; Seabloom, Eric; Thakur, Madhav P.; Tilman, David; Vogel, Anja; Eisenhauer, Nico

2016-01-01

Global change drivers are rapidly altering resource availability and biodiversity. While there is consensus that greater biodiversity increases the functioning of ecosystems, the extent to which biodiversity buffers ecosystem productivity in response to changes in resource availability remains unclear. We use data from 16 grassland experiments across North America and Europe that manipulated plant species richness and one of two essential resources—soil nutrients or water—to assess the direction and strength of the interaction between plant diversity and resource alteration on above-ground productivity and net biodiversity, complementarity, and selection effects. Despite strong increases in productivity with nutrient addition and decreases in productivity with drought, we found that resource alterations did not alter biodiversity–ecosystem functioning relationships. Our results suggest that these relationships are largely determined by increases in complementarity effects along plant species richness gradients. Although nutrient addition reduced complementarity effects at high diversity, this appears to be due to high biomass in monocultures under nutrient enrichment. Our results indicate that diversity and the complementarity of species are important regulators of grassland ecosystem productivity, regardless of changes in other drivers of ecosystem function. PMID:27114579

By-product mutualism with evolving common enemies.

PubMed

De Jaegher, Kris

2017-05-07

The common-enemy hypothesis of by-product mutualism states that organisms cooperate when it is in their individual interests to do so, with benefits for other organisms arising as a by-product; in particular, such cooperation is hypothesized to arise when organisms face the common enemy of a sufficiently adverse environment. In an evolutionary game where two defenders can cooperate to defend a common resource, this paper analyzes the common-enemy hypothesis when adversity is endogenous, in that an attacker sets the number of attacks. As a benchmark, we first consider exogenous adversity, where adversity is not subject to evolution. In this case, the common-enemy hypothesis is predicted when the degree of complementarity between defenders' defensive efforts is sufficiently low. When the degree of complementarity is high, the hypothesis is predicted only when cooperation costs are high; when cooperation costs are instead low, a competing hypothesis is predicted, where adversity discourages cooperation. Second, we consider the case of endogenous adversity. In this case, we continue to predict the competing hypothesis for a high degree of complementarity and low cooperation costs. The common-enemy hypothesis, however, only continues to be predicted for the lowest degrees of complementarity. Copyright © 2017 Elsevier Ltd. All rights reserved.

Generalized Models for Rock Joint Surface Shapes

PubMed Central

Du, Shigui; Hu, Yunjin; Hu, Xiaofei

2014-01-01

Generalized models of joint surface shapes are the foundation for mechanism studies on the mechanical effects of rock joint surface shapes. Based on extensive field investigations of rock joint surface shapes, generalized models for three level shapes named macroscopic outline, surface undulating shape, and microcosmic roughness were established through statistical analyses of 20,078 rock joint surface profiles. The relative amplitude of profile curves was used as a borderline for the division of different level shapes. The study results show that the macroscopic outline has three basic features such as planar, arc-shaped, and stepped; the surface undulating shape has three basic features such as planar, undulating, and stepped; and the microcosmic roughness has two basic features such as smooth and rough. PMID:25152901

Structure and mechanism of the T-box riboswitches

PubMed Central

Zhang, Jinwei

2015-01-01

In most Gram-positive bacteria, including many clinically devastating pathogens from genera such as Bacillus, Clostridium, Listeria and Staphylococcus, T-box riboswitches sense and regulate intracellular availability of amino acids through a multipartite mRNA-tRNA interaction. The T-box mRNA leaders respond to nutrient starvation by specifically binding cognate tRNAs and sensing whether the bound tRNA is aminoacylated, as a proxy for amino acid availability. Based on this readout, T-boxes direct a transcriptional or translational switch to control the expression of downstream genes involved in various aspects of amino acid metabolism: biosynthesis, transport, aminoacylation, transamidation, etc. Two decades after its discovery, the structural and mechanistic underpinnings of the T-box riboswitch were recently elucidated, producing a wealth of insights into how two structured RNAs can recognize each other with robust affinity and exquisite selectivity. The T-box paradigm exemplifies how natural non-coding RNAs can interact not just through sequence complementarity, but can add molecular specificity by precisely juxtaposing RNA structural motifs, exploiting inherently flexible elements and the biophysical properties of post-transcriptional modifications, ultimately achieving a high degree of shape complementarity through mutually induced fit. The T-box also provides a proof-of-principle that compact RNA domains can recognize minute chemical changes (such as tRNA aminoacylation) on another RNA. The unveiling of the structure and mechanism of the T-box system thus expands our appreciation of the range of capabilities and modes of action of structured non-coding RNAs, and hints at the existence of networks of non-coding RNAs that communicate through both, structural and sequence specificity. PMID:25959893

A Metasynthesis of the Complementarity of Culturally Responsive and Inquiry-Based Science Education in K-12 Settings: Implications for Advancing Equitable Science Teaching and Learning

ERIC Educational Resources Information Center

Brown, Julie C.

2017-01-01

Employing metasynthesis as a method, this study examined 52 empirical articles on culturally relevant and responsive science education in K-12 settings to determine the nature and scope of complementarity between culturally responsive and inquiry-based science practices (i.e., science and engineering practices identified in the National Research…

Convergence analysis of modulus-based matrix splitting iterative methods for implicit complementarity problems.

PubMed

Wang, An; Cao, Yang; Shi, Quan

2018-01-01

In this paper, we demonstrate a complete version of the convergence theory of the modulus-based matrix splitting iteration methods for solving a class of implicit complementarity problems proposed by Hong and Li (Numer. Linear Algebra Appl. 23:629-641, 2016). New convergence conditions are presented when the system matrix is a positive-definite matrix and an [Formula: see text]-matrix, respectively.

Horizons of description: Black holes and complementarity

NASA Astrophysics Data System (ADS)

Bokulich, Peter Joshua Martin

Niels Bohr famously argued that a consistent understanding of quantum mechanics requires a new epistemic framework, which he named complementarity . This position asserts that even in the context of quantum theory, classical concepts must be used to understand and communicate measurement results. The apparent conflict between certain classical descriptions is avoided by recognizing that their application now crucially depends on the measurement context. Recently it has been argued that a new form of complementarity can provide a solution to the so-called information loss paradox. Stephen Hawking argues that the evolution of black holes cannot be described by standard unitary quantum evolution, because such evolution always preserves information, while the evaporation of a black hole will imply that any information that fell into it is irrevocably lost---hence a "paradox." Some researchers in quantum gravity have argued that this paradox can be resolved if one interprets certain seemingly incompatible descriptions of events around black holes as instead being complementary. In this dissertation I assess the extent to which this black hole complementarity can be undergirded by Bohr's account of the limitations of classical concepts. I begin by offering an interpretation of Bohr's complementarity and the role that it plays in his philosophy of quantum theory. After clarifying the nature of classical concepts, I offer an account of the limitations these concepts face, and argue that Bohr's appeal to disturbance is best understood as referring to these conceptual limits. Following preparatory chapters on issues in quantum field theory and black hole mechanics, I offer an analysis of the information loss paradox and various responses to it. I consider the three most prominent accounts of black hole complementarity and argue that they fail to offer sufficient justification for the proposed incompatibility between descriptions. The lesson that emerges from this dissertation is that we have as much to learn from the limitations facing our scientific descriptions as we do from the successes they enjoy. Because all of our scientific theories offer at best limited, effective accounts of the world, an important part of our interpretive efforts will be assessing the borders of these domains of description.

Modelling charge interactions in the prion protein: predictions for pathogenesis.

PubMed

Warwicker, J

1999-04-30

Calculations are presented for the pH-dependence of stability and membrane charge complementarity of prion protein fragments. The theoretical results are compared with reported characterisations of prion protein folding in vitro. Discussion of models for conformational change and pathogenesis in vivo leads to the prediction of amino acids that could mediate sensitivity to the endosomal pH and to a design strategy for recombinant prion proteins with an increased susceptibility to prion proteinSc-like properties in vitro. In this model, the protective effect of certain basic polymorphisms can be interpreted in terms of oligomerisation on a negatively-charged surface.

Molecular evidence of stereo-specific lactoferrin dimers in solution.

PubMed

Persson, Björn A; Lund, Mikael; Forsman, Jan; Chatterton, Dereck E W; Akesson, Torbjörn

2010-10-01

Gathering experimental evidence suggests that bovine as well as human lactoferrin self-associate in aqueous solution. Still, a molecular level explanation is unavailable. Using force field based molecular modeling of the protein-protein interaction free energy we demonstrate (1) that lactoferrin forms highly stereo-specific dimers at neutral pH and (2) that the self-association is driven by a high charge complementarity across the contact surface of the proteins. Our theoretical predictions of dimer formation are verified by electrophoretic mobility and N-terminal sequence analysis on bovine lactoferrin. 2010 Elsevier B.V. All rights reserved.

Complementary structure for designer localized surface plasmons

NASA Astrophysics Data System (ADS)

Gao, Zhen; Gao, Fei; Zhang, Youming; Zhang, Baile

2015-11-01

Magnetic localized surface plasmons (LSPs) supported on metallic structures corrugated by very long and curved grooves have been recently proposed and demonstrated on an extremely thin metallic spiral structure (MSS) in the microwave regime. However, the mode profile for the magnetic LSPs was demonstrated by measuring only the electric field, not the magnetic field. Here, based on Babinet's principle, we propose a Babinet-inverted, or complementary MSS whose electric/magnetic mode profiles match the magnetic/electric mode profiles of MSS. This complementarity of mode profiles allows mapping the magnetic field distribution of magnetic LSP mode profile on MSS by measuring the electric field distribution of the corresponding mode on complementary MSS. Experiment at microwave frequencies also demonstrate the use of complementary MSS in sensing refractive-index change in the environment.

Invasive carnivores alter ecological function and enhance complementarity in scavenger assemblages on ocean beaches.

PubMed

Brown, Marion B; Schlacher, Thomas A; Schoeman, David S; Weston, Michael A; Huijbers, Chantal M; Olds, Andrew D; Connolly, Rod M

2015-10-01

Species composition is expected to alter ecological function in assemblages if species traits differ strongly. Such effects are often large and persistent for nonnative carnivores invading islands. Alternatively, high similarity in traits within assemblages creates a degree of functional redundancy in ecosystems. Here we tested whether species turnover results in functional ecological equivalence or complementarity, and whether invasive carnivores on islands significantly alter such ecological function. The model system consisted of vertebrate scavengers (dominated by raptors) foraging on animal carcasses on ocean beaches on two Australian islands, one with and one without invasive red foxes (Vulpes vulpes). Partitioning of scavenging events among species, carcass removal rates, and detection speeds were quantified using camera traps baited with fish carcasses at the dune-beach interface. Complete segregation of temporal foraging niches between mammals (nocturnal) and birds (diurnal) reflects complementarity in carrion utilization. Conversely, functional redundancy exists within the bird guild where several species of raptors dominate carrion removal in a broadly similar way. As predicted, effects of red foxes were large. They substantially changed the nature and rate of the scavenging process in the system: (1) foxes consumed over half (55%) of all carrion available at night, compared with negligible mammalian foraging at night on the fox-free island, and (2) significant shifts in the composition of the scavenger assemblages consuming beach-cast carrion are the consequence of fox invasion at one island. Arguably, in the absence of other mammalian apex predators, the addition of red foxes creates a new dimension of functional complementarity in beach food webs. However, this functional complementarity added by foxes is neither benign nor neutral, as marine carrion subsidies to coastal red fox populations are likely to facilitate their persistence as exotic carnivores.

Design and synthesis of inositolphosphoglycan putative insulin mediators.

PubMed

López-Prados, Javier; Cuevas, Félix; Reichardt, Niels-Christian; de Paz, José-Luis; Morales, Ezequiel Q; Martín-Lomas, Manuel

2005-03-07

The binding modes of a series of molecules, containing the glucosamine (1-->6) myo-inositol structural motif, into the ATP binding site of the catalytic subunit of cAMP-dependent protein kinase (PKA) have been analysed using molecular docking. These calculations predict that the presence of a phosphate group at the non-reducing end in pseudodisaccharide and pseudotrisaccharide structures properly orientate the molecule into the binding site and that pseudotrisaccharide structures present the best shape complementarity. Therefore, pseudodisaccharides and pseudotrisaccharides have been synthesised from common intermediates using effective synthetic strategies. On the basis of this synthetic chemistry, the feasibility of constructing small pseudotrisaccharide libraries on solid-phase using the same intermediates has been explored. The results from the biological evaluation of these molecules provide additional support to an insulin-mediated signalling system which involves the intermediacy of inositolphosphoglycans as putative insulin mediators.

Crystal structure of a cocaine-binding antibody.

PubMed

Larsen, N A; Zhou, B; Heine, A; Wirsching, P; Janda, K D; Wilson, I A

2001-08-03

Murine monoclonal antibody GNC92H2 was elicited by active immunization with a cocaine immunoconjugate and binds free cocaine with excellent specificity and moderate affinity. Improvement of affinity, as well as humanization of GNC92H2, would be advantageous in immunopharmacotherapy for cocaine addiction, and for emergency cases of drug overdose. Toward this end, the crystal structure of an engineered murine-human chimeric Fab of GNC92H2 complexed with cocaine was determined at 2.3 A resolution. Structural analysis reveals a binding pocket with high shape and charge complementarity to the cocaine framework, which explains the specificity for cocaine, as opposed to the pharmacologically inactive cocaine metabolites. Importantly, the structure provides a foundation for mutagenesis to enhance the binding affinity for cocaine and potent cocaine derivatives, such as cocaethylene, and for additional humanization of the antibody. Copyright 2001 Academic Press.

In search of new lead compounds for trypanosomiasis drug design: A protein structure-based linked-fragment approach

NASA Astrophysics Data System (ADS)

Verlinde, Christophe L. M. J.; Rudenko, Gabrielle; Hol, Wim G. J.

1992-04-01

A modular method for pursuing structure-based inhibitor design in the framework of a design cycle is presented. The approach entails four stages: (1) a design pathway is defined in the three-dimensional structure of a target protein; (2) this pathway is divided into subregions; (3) complementary building blocks, also called fragments, are designed in each subregion; complementarity is defined in terms of shape, hydrophobicity, hydrogen bond properties and electrostatics; and (4) fragments from different subregions are linked into potential lead compounds. Stages (3) and (4) are qualitatively guided by force-field calculations. In addition, the designed fragments serve as entries for retrieving existing compounds from chemical databases. This linked-fragment approach has been applied in the design of potentially selective inhibitors of triosephosphate isomerase from Trypanosoma brucei, the causative agent of sleeping sickness.

Shape information from a critical point analysis of calculated electron density maps: application to DNA-drug systems

NASA Astrophysics Data System (ADS)

Leherte, L.; Allen, F. H.; Vercauteren, D. P.

1995-04-01

A computational method is described for mapping the volume within the DNA double helix accessible to a groove-binding antibiotic, netropsin. Topological critical point analysis is used to locate maxima in electron density maps reconstructed from crystallographically determined atomic coordinates. The peaks obtained in this way are represented as ellipsoids with axes related to local curvature of the electron density function. Combining the ellipsoids produces a single electron density function which can be probed to estimate effective volumes of the interacting species. Close complementarity between host and ligand in this example shows the method to be a good representation of the electron density function at various resolutions; while at the atomic level the ellipsoid method gives results which are in close agreement with those from the conventional, spherical, van der Waals approach.

Shape information from a critical point analysis of calculated electron density maps: Application to DNA-drug systems

NASA Astrophysics Data System (ADS)

Leherte, Laurence; Allen, Frank H.

1994-06-01

A computational method is described for mapping the volume within the DNA double helix accessible to the groove-binding antibiotic netropsin. Topological critical point analysis is used to locate maxima in electron density maps reconstructed from crystallographically determined atomic coordinates. The peaks obtained in this way are represented as ellipsoids with axes related to local curvature of the electron density function. Combining the ellipsoids produces a single electron density function which can be probed to estimate effective volumes of the interacting species. Close complementarity between host and ligand in this example shows the method to give a good representation of the electron density function at various resolutions. At the atomic level, the ellipsoid method gives results which are in close agreement with those from the conventional spherical van der Waals approach.

Branchpoint expansion in a fully complementary three-way DNA junction.

PubMed

Sabir, Tara; Toulmin, Anita; Ma, Long; Jones, Anita C; McGlynn, Peter; Schröder, Gunnar F; Magennis, Steven W

2012-04-11

Branched nucleic acid molecules serve as key intermediates in DNA replication, recombination, and repair; architectural elements in RNA; and building blocks and functional components for nanoscience applications. Using a combination of high-resolution single-molecule FRET, time-resolved spectroscopy, and molecular modeling, we have probed the local and global structure of a DNA three-way junction (3WJ) in solution. We found that it adopts a Y-shaped, pyramidal structure, in which the bases adjacent to the branchpoint are unpaired, despite the full Watson-Crick complementarity of the molecule. The unpairing allows a nanoscale cavity to form at the junction center. Our structure accounts for earlier observations made of the structure, flexibility, and reactivity of 3WJs. We anticipate that these results will guide the development of new DNA-based supramolecular receptors and nanosystems. © 2012 American Chemical Society

An augmented Lagrangian trust region method for inclusion boundary reconstruction using ultrasound/electrical dual-modality tomography

NASA Astrophysics Data System (ADS)

Liang, Guanghui; Ren, Shangjie; Dong, Feng

2018-07-01

The ultrasound/electrical dual-modality tomography utilizes the complementarity of ultrasound reflection tomography (URT) and electrical impedance tomography (EIT) to improve the speed and accuracy of image reconstruction. Due to its advantages of no-invasive, no-radiation and low-cost, ultrasound/electrical dual-modality tomography has attracted much attention in the field of dual-modality imaging and has many potential applications in industrial and biomedical imaging. However, the data fusion of URT and EIT is difficult due to their different theoretical foundations and measurement principles. The most commonly used data fusion strategy in ultrasound/electrical dual-modality tomography is incorporating the structured information extracted from the URT into the EIT image reconstruction process through a pixel-based constraint. Due to the inherent non-linearity and ill-posedness of EIT, the reconstructed images from the strategy suffer from the low resolution, especially at the boundary of the observed inclusions. To improve this condition, an augmented Lagrangian trust region method is proposed to directly reconstruct the shapes of the inclusions from the ultrasound/electrical dual-modality measurements. In the proposed method, the shape of the target inclusion is parameterized by a radial shape model whose coefficients are used as the shape parameters. Then, the dual-modality shape inversion problem is formulated by an energy minimization problem in which the energy function derived from EIT is constrained by an ultrasound measurements model through an equality constraint equation. Finally, the optimal shape parameters associated with the optimal inclusion shape guesses are determined by minimizing the constrained cost function using the augmented Lagrangian trust region method. To evaluate the proposed method, numerical tests are carried out. Compared with single modality EIT, the proposed dual-modality inclusion boundary reconstruction method has a higher accuracy and is more robust to the measurement noise.

Skill complementarity enhances heterophily in collaboration networks

PubMed Central

Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Tan, Qun-Zhao; Podobnik, Boris; Zhou, Wei-Xing; Stanley, H. Eugene

2016-01-01

Much empirical evidence shows that individuals usually exhibit significant homophily in social networks. We demonstrate, however, skill complementarity enhances heterophily in the formation of collaboration networks, where people prefer to forge social ties with people who have professions different from their own. We construct a model to quantify the heterophily by assuming that individuals choose collaborators to maximize utility. Using a huge database of online societies, we find evidence of heterophily in collaboration networks. The results of model calibration confirm the presence of heterophily. Both empirical analysis and model calibration show that the heterophilous feature is persistent along the evolution of online societies. Furthermore, the degree of skill complementarity is positively correlated with their production output. Our work sheds new light on the scientific research utility of virtual worlds for studying human behaviors in complex socioeconomic systems. PMID:26743687

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

Hart, William E.; Siirola, John Daniel

We describe new capabilities for modeling MPEC problems within the Pyomo modeling software. These capabilities include new modeling components that represent complementar- ity conditions, modeling transformations for re-expressing models with complementarity con- ditions in other forms, and meta-solvers that apply transformations and numeric optimization solvers to optimize MPEC problems. We illustrate the breadth of Pyomo's modeling capabil- ities for MPEC problems, and we describe how Pyomo's meta-solvers can perform local and global optimization of MPEC problems.

Functional divergence in nitrogen uptake rates explains diversity-productivity relationship in microalgal communities

DOE PAGES

Mandal, Shovon; Shurin, Jonathan B.; Efroymson, Rebecca A.; ...

2018-05-23

The relationship between biodiversity and productivity has emerged as a central theme in ecology. Mechanistic explanations for this relationship suggest that the role organisms play in the ecosystem (i.e., niches or functional traits) is a better predictor of ecosystem stability and productivity than taxonomic richness. Here, we tested the capacity of functional diversity in nitrogen uptake in experimental microalgal communities to predict the complementarity effect (CE) and selection effect (SE) of biodiversity on productivity. We grew five algal species as monocultures and as polycultures in pairwise combinations in homogeneous (ammonium, nitrate, or urea alone) and heterogeneous nitrogen (mixed nitrogen) environmentsmore » to determine whether complementarity between species may be enhanced in heterogeneous environments. We show that the positive diversity effects on productivity in heterogeneous environments resulted from complementarity effects with no positive contribution by species–specific SEs. Positive biodiversity effects in homogeneous environments, when present (nitrate and urea treatments but not ammonium), were driven both by CE and SE. Our results suggest that functional diversity increases species complementarity and productivity mainly in heterogeneous resource environments. Furthermore, these results provide evidence that the positive effect of functional diversity on community productivity depends on the diversity of resources present in the environment.« less

Functional divergence in nitrogen uptake rates explains diversity-productivity relationship in microalgal communities

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

Mandal, Shovon; Shurin, Jonathan B.; Efroymson, Rebecca A.

The relationship between biodiversity and productivity has emerged as a central theme in ecology. Mechanistic explanations for this relationship suggest that the role organisms play in the ecosystem (i.e., niches or functional traits) is a better predictor of ecosystem stability and productivity than taxonomic richness. Here, we tested the capacity of functional diversity in nitrogen uptake in experimental microalgal communities to predict the complementarity effect (CE) and selection effect (SE) of biodiversity on productivity. We grew five algal species as monocultures and as polycultures in pairwise combinations in homogeneous (ammonium, nitrate, or urea alone) and heterogeneous nitrogen (mixed nitrogen) environmentsmore » to determine whether complementarity between species may be enhanced in heterogeneous environments. We show that the positive diversity effects on productivity in heterogeneous environments resulted from complementarity effects with no positive contribution by species–specific SEs. Positive biodiversity effects in homogeneous environments, when present (nitrate and urea treatments but not ammonium), were driven both by CE and SE. Our results suggest that functional diversity increases species complementarity and productivity mainly in heterogeneous resource environments. Furthermore, these results provide evidence that the positive effect of functional diversity on community productivity depends on the diversity of resources present in the environment.« less

Functional group diversity of bee pollinators increases crop yield

PubMed Central

Hoehn, Patrick; Tscharntke, Teja; Tylianakis, Jason M; Steffan-Dewenter, Ingolf

2008-01-01

Niche complementarity is a commonly invoked mechanism underlying the positive relationship between biodiversity and ecosystem functioning, but little empirical evidence exists for complementarity among pollinator species. This study related differences in three functional traits of pollinating bees (flower height preference, daily time of flower visitation and within-flower behaviour) to the seed set of the obligate cross-pollinated pumpkin Cucurbita moschata Duch. ex Poir. across a land-use intensity gradient from tropical rainforest and agroforests to grassland in Indonesia. Bee richness and abundance changed with habitat variables and we used this natural variation to test whether complementary resource use by the diverse pollinator community enhanced final yield. We found that pollinator diversity, but not abundance, was positively related to seed set of pumpkins. Bees showed species-specific spatial and temporal variation in flower visitation traits and within-flower behaviour, allowing for classification into functional guilds. Diversity of functional groups explained even more of the variance in seed set (r2=45%) than did species richness (r2=32%) highlighting the role of functional complementarity. Even though we do not provide experimental, but rather correlative evidence, we can link spatial and temporal complementarity in highly diverse pollinator communities to pollination success in the field, leading to enhanced crop yield without any managed honeybees. PMID:18595841

Low energy electron catalyst: the electronic origin of catalytic strategies.

PubMed

Davis, Daly; Sajeev, Y

2016-10-12

Using a low energy electron (LEE) as a catalyst, the electronic origin of the catalytic strategies corresponding to substrate selectivity, reaction specificity and reaction rate enhancement is investigated for a reversible unimolecular elementary reaction. An electronic energy complementarity between the catalyst and the substrate molecule is the origin of substrate selectivity and reaction specificity. The electronic energy complementarity is induced by tuning the electronic energy of the catalyst. The energy complementarity maximizes the binding forces between the catalyst and the molecule. Consequently, a new electronically metastable high-energy reactant state and a corresponding new low barrier reaction path are resonantly created for a specific reaction of the substrate through the formation of a catalyst-substrate transient adduct. The LEE catalysis also reveals a fundamental structure-energy correspondence in the formation of the catalyst-substrate transient adduct. Since the energy complementarities corresponding to the substrate molecules of the forward and the backward steps of the reversible reactions are not the same due to their structural differences, the LEE catalyst exhibits a unique one-way catalytic strategy, i.e., the LEE catalyst favors the reversible reaction more effectively in one direction. A characteristic stronger binding of the catalyst to the transition state of the reaction than in the initial reactant state and the final product state is the molecular origin of barrier lowering.

Aging and the haptic perception of 3D surface shape.

PubMed

Norman, J Farley; Kappers, Astrid M L; Beers, Amanda M; Scott, A Kate; Norman, Hideko F; Koenderink, Jan J

2011-04-01

Two experiments evaluated the ability of older and younger adults to perceive the three-dimensional (3D) shape of object surfaces from active touch (haptics). The ages of the older adults ranged from 64 to 84 years, while those of the younger adults ranged from 18 to 27 years. In Experiment 1, the participants haptically judged the shape of large (20 cm diameter) surfaces with an entire hand. In contrast, in Experiment 2, the participants explored the shape of small (5 cm diameter) surfaces with a single finger. The haptic surfaces varied in shape index (Koenderink, Solid shape, 1990; Koenderink, Image and Vision Computing, 10, 557-564, 1992) from -1.0 to +1.0 in steps of 0.25. For both types of surfaces (large and small), the participants were able to judge surface shape reliably. The older participants' judgments of surface shape were just as accurate and precise as those of the younger participants. The results of the current study demonstrate that while older adults do possess reductions in tactile sensitivity and acuity, they nevertheless can effectively perceive 3D surface shape from haptic exploration.

Intuitive, but not simple: including explicit water molecules in protein-protein docking simulations improves model quality.

PubMed

Parikh, Hardik I; Kellogg, Glen E

2014-06-01

Characterizing the nature of interaction between proteins that have not been experimentally cocrystallized requires a computational docking approach that can successfully predict the spatial conformation adopted in the complex. In this work, the Hydropathic INTeractions (HINT) force field model was used for scoring docked models in a data set of 30 high-resolution crystallographically characterized "dry" protein-protein complexes and was shown to reliably identify native-like models. However, most current protein-protein docking algorithms fail to explicitly account for water molecules involved in bridging interactions that mediate and stabilize the association of the protein partners, so we used HINT to illuminate the physical and chemical properties of bridging waters and account for their energetic stabilizing contributions. The HINT water Relevance metric identified the "truly" bridging waters at the 30 protein-protein interfaces and we utilized them in "solvated" docking by manually inserting them into the input files for the rigid body ZDOCK program. By accounting for these interfacial waters, a statistically significant improvement of ∼24% in the average hit-count within the top-10 predictions the protein-protein dataset was seen, compared to standard "dry" docking. The results also show scoring improvement, with medium and high accuracy models ranking much better than incorrect ones. These improvements can be attributed to the physical presence of water molecules that alter surface properties and better represent native shape and hydropathic complementarity between interacting partners, with concomitantly more accurate native-like structure predictions. © 2013 Wiley Periodicals, Inc.

Marine Diterpenes: Molecular Modeling of Thrombin Inhibitors with Potential Biotechnological Application as an Antithrombotic

PubMed Central

Pereira, Rebeca Cristina Costa; Lourenço, André Luiz; Terra, Luciana; Abreu, Paula Alvarez; Laneuville Teixeira, Valéria; Castro, Helena Carla

2017-01-01

Thrombosis related diseases are among the main causes of death and incapacity in the world. Despite the existence of antithrombotic agents available for therapy, they still present adverse effects like hemorrhagic risks which justify the search for new options. Recently, pachydictyol A, isopachydictyol A, and dichotomanol, three diterpenes isolated from Brazilian marine brown alga Dictyota menstrualis were identified as potent antithrombotic molecules through inhibition of thrombin, a key enzyme of coagulation cascade and a platelet agonist. Due to the biotechnological potential of these marine metabolites, in this work we evaluated their binding mode to thrombin in silico and identified structural features related to the activity in order to characterize their molecular mechanism. According to our theoretical studies including structure-activity relationship and molecular docking analysis, the highest dipole moment, polar surface area, and lowest electronic density of dichotomanol are probably involved in its higher inhibition percentage towards thrombin catalytic activity compared to pachydictyol A and isopachydictyol A. Interestingly, the molecular docking studies also revealed a good shape complementarity of pachydictyol A and isopachydictyol A and interactions with important residues and regions (e.g., H57, S195, W215, G216, and loop-60), which probably justify their thrombin inhibitor effects demonstrated in vitro. Finally, this study explored the structural features and binding mode of these three diterpenes in thrombin which reinforced their potential to be further explored and may help in the design of new antithrombotic agents. PMID:28335516

Marine Diterpenes: Molecular Modeling of Thrombin Inhibitors with Potential Biotechnological Application as an Antithrombotic.

PubMed

Pereira, Rebeca Cristina Costa; Lourenço, André Luiz; Terra, Luciana; Abreu, Paula Alvarez; Laneuville Teixeira, Valéria; Castro, Helena Carla

2017-03-20

Thrombosis related diseases are among the main causes of death and incapacity in the world. Despite the existence of antithrombotic agents available for therapy, they still present adverse effects like hemorrhagic risks which justify the search for new options. Recently, pachydictyol A, isopachydictyol A, and dichotomanol, three diterpenes isolated from Brazilian marine brown alga Dictyota menstrualis were identified as potent antithrombotic molecules through inhibition of thrombin, a key enzyme of coagulation cascade and a platelet agonist. Due to the biotechnological potential of these marine metabolites, in this work we evaluated their binding mode to thrombin in silico and identified structural features related to the activity in order to characterize their molecular mechanism. According to our theoretical studies including structure-activity relationship and molecular docking analysis, the highest dipole moment, polar surface area, and lowest electronic density of dichotomanol are probably involved in its higher inhibition percentage towards thrombin catalytic activity compared to pachydictyol A and isopachydictyol A. Interestingly, the molecular docking studies also revealed a good shape complementarity of pachydictyol A and isopachydictyol A and interactions with important residues and regions (e.g., H57, S195, W215, G216, and loop-60), which probably justify their thrombin inhibitor effects demonstrated in vitro. Finally, this study explored the structural features and binding mode of these three diterpenes in thrombin which reinforced their potential to be further explored and may help in the design of new antithrombotic agents.

An improved error bound for linear complementarity problems for B-matrices.

PubMed

Gao, Lei; Li, Chaoqian

2017-01-01

A new error bound for the linear complementarity problem when the matrix involved is a B -matrix is presented, which improves the corresponding result in (Li et al. in Electron. J. Linear Algebra 31(1):476-484, 2016). In addition some sufficient conditions such that the new bound is sharper than that in (García-Esnaola and Peña in Appl. Math. Lett. 22(7):1071-1075, 2009) are provided.

Correlation complementarity yields bell monogamy relations.

PubMed

Kurzyński, P; Paterek, T; Ramanathan, R; Laskowski, W; Kaszlikowski, D

2011-05-06

We present a method to derive Bell monogamy relations by connecting the complementarity principle with quantum nonlocality. The resulting monogamy relations are stronger than those obtained from the no-signaling principle alone. In many cases, they yield tight quantum bounds on the amount of violation of single and multiple qubit correlation Bell inequalities. In contrast with the two-qubit case, a rich structure of possible violation patterns is shown to exist in the multipartite scenario.

Reviving Complementarity: John Wheeler's efforts to apply complementarity toward a quantum description of gravitation

NASA Astrophysics Data System (ADS)

Halpern, Paul

2017-01-01

In 1978, John Wheeler proposed the delayed-choice thought experiment as a generalization of the classic double slit experiment intended to help elucidate the nature of decision making in quantum measurement. In particular, he wished to illustrate how a decision made after a quantum system was prepared might retrospectively affect the outcome. He extended his methods to the universe itself, raising the question of whether the universe is a ``self-excited circuit'' in which scientific measurements in the present affect the quantum dynamics in the past. In this talk we'll show how Wheeler's approach revived the notion of Bohr's complementarity, which had by then faded from the prevailing discourse of quantum measurement theory. Wheeler's advocacy reflected, in part, his wish to eliminate the divide in quantum theory between measurer and what was being measured, bringing greater consistency to the ideas of Bohr, a mentor whom he deeply respected.

Bohrian Complementarity in the Light of Kantian Teleology

NASA Astrophysics Data System (ADS)

Pringe, Hernán

2014-03-01

The Kantian influences on Bohr's thought and the relationship between the perspective of complementarity in physics and in biology seem at first sight completely unrelated issues. However, the goal of this work is to show their intimate connection. We shall see that Bohr's views on biology shed light on Kantian elements of his thought, which enables a better understanding of his complementary interpretation of quantum theory. For this purpose, we shall begin by discussing Bohr's views on the analogies concerning the epistemological situation in biology and in physics. Later, we shall compare the Bohrian and the Kantian approaches to the science of life in order to show their close connection. On this basis, we shall finally turn to the issue of complementarity in quantum theory in order to assess what we can learn about the epistemological problems in the quantum realm from a consideration of Kant's views on teleology.

Bohr, Heisenberg and the divergent views of complementarity

NASA Astrophysics Data System (ADS)

Camilleri, Kristian

The fractious discussions between Bohr and Heisenberg in Copenhagen in 1927 have been the subject of much historical scholarship. However, little attention has been given to Heisenberg's understanding of the notion of complementary space-time and causal descriptions, which was presented for the first time in Bohr's lecture at the 1927 Como conference. In this paper, I argue that Heisenberg's own interpretation of this notion differed substantially from Bohr's. Whereas Bohr had intended this form of complementarity to entail a choice between a space-time description of the electron in an atom, and defining the energy of a stationary state, Heisenberg interpreted the 'causal' description in terms of ψ -function in configuration space. In disentangling the two views of complementarity, this paper sheds new light on the hidden philosophical disagreements between the proponents of these two founders of the so-called 'Copenhagen interpretation' of quantum mechanics.

Quasi-static shape adjustment of a 15 meter diameter space antenna

NASA Technical Reports Server (NTRS)

Belvin, W. Keith; Herstrom, Catherine L.; Edighoffer, Harold H.

1987-01-01

A 15 meter diameter Hoop-Column antenna has been analyzed and tested to study shape adjustment of the reflector surface. The Hoop-Column antenna concept employs pretensioned cables and mesh to produce a paraboloidal reflector surface. Fabrication errors and thermal distortions may significantly reduce surface accuracy and consequently degrade electromagnetic performance. Thus, the ability to adjust the surface shape is desirable. The shape adjustment algorithm consisted of finite element and least squares error analyses to minimize the surface distortions. Experimental results verified the analysis. Application of the procedure resulted in a reduction of surface error by 38 percent. Quasi-static shape adjustment has the potential for on-orbit compensation for a variety of surface shape distortions.

Vegetative and Atmospheric Controls on the Bouchet-Morton Complementary Relationship Hypothesis

NASA Astrophysics Data System (ADS)

Pettijohn, J. C.; Salvucci, G. D.; Phillips, N. G.; Daley, M. J.

2006-12-01

The Bouchet-Morton Complementary Relationship (CR) hypothesis is a potentially-powerful analytic tool to help understand the feedback between evapotranspiring land surfaces and the atmospheric boundary layer (ABL), and how potential evaporation reflects this coupling on multiple time and length scales. In spite of advances in our ability to measure and model these processes, the heuristic CR hypothesis remains an unsolved, first-order problem. The leading theoretical models, i.e., Morton, Granger, and Szilagyi, of the coupled land surface atmosphere mechanisms responsible for CR focus primarily on vertical humidity (vapor pressure) profiles while assuming that vegetative and/or atmospheric diffusivities play an insignificant role in regulating CR. Further, whereas Granger and Szilagyi assume almost opposite vertical temperature profile boundary conditions, both derivations appear to validate CR. Contrary to these multiple working hypotheses' assumptions, our recent CR evaluation of 147 days (1987-1989) at the FIFE temperate grassland discovered that canopy conductance was an essential forcing variable in complementarity, and thus improved CR in application when included in the definition of potential evaporation. To isolate the exact forcing mechanisms of canopy and ABL conductances to complementarity, we evaluated CR in a mixed-deciduous forest at Harvard Forest (summers 2005-2006) by comparing daily averaged water-stressed (non-irrigated, regionally stressed soil moisture) and water-unstressed (irrigated, `potential') transpiration. Root-zone soil moisture of a red maple (Acer rubrum L.) sample set was elevated using a pulse-irrigation system. Whole-tree transpiration of the `potential` (water-unstressed) and a reference (water-stressed) set of maples was monitored at high frequency using heat-dissipation Granier-type sap flux sensors. To isolate physiological and/or atmospheric forcing of CR, we estimated isothermal Penman-Monteith transpiration models of both irrigated and non-irrigated time series using a Jarvis type multiplicative stress model of scaled canopy conductance to water vapor transport. Poorly-constrained model parameters (e.g., environmental stress boundary conditions) were estimated using a grid search routine; further, parameter confidence limits were inferred using bootstrap replacement sampling. Preliminary results suggest the following: (1) the absence of an unstressed canopy conductance in the Penman equation results in violation of fundamental CR assumptions (similar to FIFE); and (2) unlimited root-zone water availability does not reduce the leaf-level stomatal resistance enough to yield complementarity, i.e., the typical CR potential signal is also a function of other environmental stresses, e.g., vapor pressure deficit. In summary, our results yield valuable insight into the role of vertical atmospheric and vegetative conductances in CR.

COMplementary Primer ASymmetric PCR (COMPAS-PCR) Applied to the Identification of Salmo salar, Salmo trutta and Their Hybrids

PubMed Central

2016-01-01

Avoiding complementarity between primers when designing a PCR assay constitutes a central rule strongly anchored in the mind of the molecular scientist. 3’-complementarity will extend the primers during PCR elongation using one another as template, consequently disabling further possible involvement in traditional target amplification. However, a 5’-complementarity will leave the primers unchanged during PCR cycles, albeit sequestered to one another, therefore also suppressing target amplification. We show that 5’-complementarity between primers may be exploited in a new PCR method called COMplementary-Primer-Asymmetric (COMPAS)-PCR, using asymmetric primer concentrations to achieve target PCR amplification. Moreover, such a design may paradoxically reduce spurious non-target amplification by actively sequestering the limiting primer. The general principles were demonstrated using 5S rDNA direct repeats as target sequences to design a species-specific assay for identifying Salmo salar and Salmo trutta using almost fully complementary primers overlapping the same target sequence. Specificity was enhanced by using 3’-penultimate point mutations and the assay was further developed to enable identification of S. salar x S. trutta hybrids by High Resolution Melt analysis in a 35 min one-tube assay. This small paradigm shift, using highly complementary primers for PCR, should help develop robust assays that previously would not be considered. PMID:27783658

Optimization of binding electrostatics: Charge complementarity in the barnase-barstar protein complex

PubMed Central

lee, Lee-Peng; Tidor, Bruce

2001-01-01

Theoretical and experimental studies have shown that the large desolvation penalty required for polar and charged groups frequently precludes their involvement in electrostatic interactions that contribute strongly to net stability in the folding or binding of proteins in aqueous solution near room temperature. We have previously developed a theoretical framework for computing optimized electrostatic interactions and illustrated use of the algorithm with simplified geometries. Given a receptor and model assumptions, the method computes the ligand-charge distribution that provides the most favorable balance of desolvation and interaction effects on binding. In this paper the method has been extended to treat complexes using actual molecular shapes. The barnase-barstar protein complex was investigated with barnase treated as a target receptor. The atomic point charges of barstar were varied to optimize the electrostatic binding free energy. Barnase and natural barstar form a tight complex (Kd ∼ 10−14 M) with many charged and polar groups near the interface that make this a particularly relevant system for investigating the role of electrostatic effects on binding. The results show that sets of barstar charges (resulting from optimization with different constraints) can be found that give rise to relatively large predicted improvements in electrostatic binding free energy. Principles for enhancing the effect of electrostatic interactions in molecular binding in aqueous environments are discussed in light of the optima. Our findings suggest that, in general, the enhancements in electrostatic binding free energy resulting from modification of polar and charged groups can be substantial. Moreover, a recently proposed definition of electrostatic complementarity is shown to be a useful tool for examining binding interfaces. Finally, calculational results suggest that wild-type barstar is closer to being affinity optimized than is barnase for their mutual binding, consistent with the known roles of these proteins. PMID:11266622

Harsh environments and the evolution of multi-player cooperation.

PubMed

De Jaegher, Kris

2017-02-01

The game-theoretic model in this paper provides micro-foundations for the effect a harsher environment on the probability of cooperation among multiple players. The harshness of the environment is alternatively measured by the degree of complementarity between the players' cooperative efforts in producing a public good, and by the number of attacks on an existing public good that the players can collectively defend, where it is shown that these two measures of the degree of adversity facing the players operate in a similar fashion. We show that the effect of the degree of adversity on the probability of cooperation is monotonous, and has an opposite sign for smaller and for larger cooperation costs. For intermediate cooperation costs, we show that the effect of a harsher environment on the probability of cooperation is hill-shaped. Copyright © 2016 Elsevier Inc. All rights reserved.

Quantum interference experiments with large molecules

NASA Astrophysics Data System (ADS)

Nairz, Olaf; Arndt, Markus; Zeilinger, Anton

2003-04-01

Wave-particle duality is frequently the first topic students encounter in elementary quantum physics. Although this phenomenon has been demonstrated with photons, electrons, neutrons, and atoms, the dual quantum character of the famous double-slit experiment can be best explained with the largest and most classical objects, which are currently the fullerene molecules. The soccer-ball-shaped carbon cages C60 are large, massive, and appealing objects for which it is clear that they must behave like particles under ordinary circumstances. We present the results of a multislit diffraction experiment with such objects to demonstrate their wave nature. The experiment serves as the basis for a discussion of several quantum concepts such as coherence, randomness, complementarity, and wave-particle duality. In particular, the effect of longitudinal (spectral) coherence can be demonstrated by a direct comparison of interferograms obtained with a thermal beam and a velocity selected beam in close analogy to the usual two-slit experiments using light.

Selective binding of choline by a phosphate-coordination-based triple helicate featuring an aromatic box

DOE PAGES

Jia, Chuandong; Zuo, Wei; Yang, Dong; ...

2017-10-16

In nature, proteins have evolved sophisticated cavities tailored for capturing target guests selectively among competitors of similar size, shape, and charge. The fundamental principles guiding the molecular recognition, such as self-assembly and complementarity, have inspired the development of biomimetic receptors. In the current work, we report a self-assembled triple anion helicate (host 2) featuring a cavity resembling that of the choline-binding protein ChoX, as revealed by crystal and density functional theory (DFT)-optimized structures, which binds choline in a unique dual-site-binding mode. Here, this similarity in structure leads to a similarly high selectivity of host 2 for choline over its derivatives,more » as demonstrated by the NMR and fluorescence competition experiments. Furthermore, host 2 is able to act as a fluorescence displacement sensor for discriminating choline, acetylcholine, l-carnitine, and glycine betaine effectively.« less

Shape-based diffeomorphic registration on hippocampal surfaces using Beltrami holomorphic flow.

PubMed

Lui, Lok Ming; Wong, Tsz Wai; Thompson, Paul; Chan, Tony; Gu, Xianfeng; Yau, Shing-Tung

2010-01-01

We develop a new algorithm to automatically register hippocampal (HP) surfaces with complete geometric matching, avoiding the need to manually label landmark features. A good registration depends on a reasonable choice of shape energy that measures the dissimilarity between surfaces. In our work, we first propose a complete shape index using the Beltrami coefficient and curvatures, which measures subtle local differences. The proposed shape energy is zero if and only if two shapes are identical up to a rigid motion. We then seek the best surface registration by minimizing the shape energy. We propose a simple representation of surface diffeomorphisms using Beltrami coefficients, which simplifies the optimization process. We then iteratively minimize the shape energy using the proposed Beltrami Holomorphic flow (BHF) method. Experimental results on 212 HP of normal and diseased (Alzheimer's disease) subjects show our proposed algorithm is effective in registering HP surfaces with complete geometric matching. The proposed shape energy can also capture local shape differences between HP for disease analysis.

The relative contributions of facial shape and surface information to perceptions of attractiveness and dominance.

PubMed

Torrance, Jaimie S; Wincenciak, Joanna; Hahn, Amanda C; DeBruine, Lisa M; Jones, Benedict C

2014-01-01

Although many studies have investigated the facial characteristics that influence perceptions of others' attractiveness and dominance, the majority of these studies have focused on either the effects of shape information or surface information alone. Consequently, the relative contributions of facial shape and surface characteristics to attractiveness and dominance perceptions are unclear. To address this issue, we investigated the relationships between ratings of original versions of faces and ratings of versions in which either surface information had been standardized (i.e., shape-only versions) or shape information had been standardized (i.e., surface-only versions). For attractiveness and dominance judgments of both male and female faces, ratings of shape-only and surface-only versions independently predicted ratings of the original versions of faces. The correlations between ratings of original and shape-only versions and between ratings of original and surface-only versions differed only in two instances. For male attractiveness, ratings of original versions were more strongly related to ratings of surface-only than shape-only versions, suggesting that surface information is particularly important for men's facial attractiveness. The opposite was true for female physical dominance, suggesting that shape information is particularly important for women's facial physical dominance. In summary, our results indicate that both facial shape and surface information contribute to judgments of others' attractiveness and dominance, suggesting that it may be important to consider both sources of information in research on these topics.

Investigating protein-protein interaction surfaces using a reduced stereochemical and electrostatic model.

PubMed

Warwicker, J

1989-03-20

A method of calculating the electrostatic potential energy between two molecules, using finite difference potential, is presented. A reduced charge set is used so that the interaction energy can be calculated as the two static molecules explore their full six-dimensional configurational space. The energies are contoured over surfaces fixed to each molecule with an interactive computer graphics program. For two crystal structures (trypsin-trypsin inhibitor and anti-lysozyme Fab-lysozyme), it is found that the complex corresponds to highly favourable interacting regions in the contour plots. These matches arise from a small number of protruding basic residues interacting with enhanced negative potential in each case. The redox pair cytochrome c peroxidase-cytochrome c exhibits an extensive favourably interacting surface within which a possible electron transfer complex may be defined by an increased electrostatic complementarity, but a decreased electrostatic energy. A possible substrate transfer configuration for the glycolytic enzyme pair glyceraldehyde phosphate dehydrogenase-phosphoglycerate kinase is presented.

Crystal structure of human proteasome assembly chaperone PAC4 involved in proteasome formation.

PubMed

Kurimoto, Eiji; Satoh, Tadashi; Ito, Yuri; Ishihara, Eri; Okamoto, Kenta; Yagi-Utsumi, Maho; Tanaka, Keiji; Kato, Koichi

2017-05-01

The 26S proteasome is a large protein complex, responsible for degradation of ubiquinated proteins in eukaryotic cells. Eukaryotic proteasome formation is a highly ordered process that is assisted by several assembly chaperones. The assembly of its catalytic 20S core particle depends on at least five proteasome-specific chaperones, i.e., proteasome-assembling chaperons 1-4 (PAC1-4) and proteasome maturation protein (POMP). The orthologues of yeast assembly chaperones have been structurally characterized, whereas most mammalian assembly chaperones are not. In the present study, we determined a crystal structure of human PAC4 at 1.90-Å resolution. Our crystallographic data identify a hydrophobic surface that is surrounded by charged residues. The hydrophobic surface is complementary to that of its binding partner, PAC3. The surface also exhibits charge complementarity with the proteasomal α4-5 subunits. This will provide insights into human proteasome-assembling chaperones as potential anticancer drug targets. © 2017 The Protein Society.

Contributions of feature shapes and surface cues to the recognition of facial expressions.

PubMed

Sormaz, Mladen; Young, Andrew W; Andrews, Timothy J

2016-10-01

Theoretical accounts of face processing often emphasise feature shapes as the primary visual cue to the recognition of facial expressions. However, changes in facial expression also affect the surface properties of the face. In this study, we investigated whether this surface information can also be used in the recognition of facial expression. First, participants identified facial expressions (fear, anger, disgust, sadness, happiness) from images that were manipulated such that they varied mainly in shape or mainly in surface properties. We found that the categorization of facial expression is possible in either type of image, but that different expressions are relatively dependent on surface or shape properties. Next, we investigated the relative contributions of shape and surface information to the categorization of facial expressions. This employed a complementary method that involved combining the surface properties of one expression with the shape properties from a different expression. Our results showed that the categorization of facial expressions in these hybrid images was equally dependent on the surface and shape properties of the image. Together, these findings provide a direct demonstration that both feature shape and surface information make significant contributions to the recognition of facial expressions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Design and simulation of the surface shape control system for membrane mirror

NASA Astrophysics Data System (ADS)

Zhang, Gengsheng; Tang, Minxue

2009-11-01

The surface shape control is one of the key technologies for the manufacture of membrane mirror. This paper presents a design of membrane mirror's surface shape control system on the basis of fuzzy logic control. The system contains such function modules as surface shape design, surface shape control, surface shape analysis, and etc. The system functions are realized by using hybrid programming technology of Visual C# and MATLAB. The finite element method is adopted to simulate the surface shape control of membrane mirror. The finite element analysis model is established through ANSYS Parametric Design Language (APDL). ANSYS software kernel is called by the system in background running mode when doing the simulation. The controller is designed by means of controlling the sag of the mirror's central crosssection. The surface shape of the membrane mirror and its optical aberration are obtained by applying Zernike polynomial fitting. The analysis of surface shape control and the simulation of disturbance response are performed for a membrane mirror with 300mm aperture and F/2.7. The result of the simulation shows that by using the designed control system, the RMS wavefront error of the mirror can reach to 142λ (λ=632.8nm), which is consistent to the surface accuracy of the membrane mirror obtained by the large deformation theory of membrane under the same condition.

Hybrid ququart-encoded quantum cryptography protected by Kochen-Specker contextuality

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

Cabello, Adan; Department of Physics, Stockholm University, S-10691 Stockholm; D'Ambrosio, Vincenzo

2011-09-15

Quantum cryptographic protocols based on complementarity are not secure against attacks in which complementarity is imitated with classical resources. The Kochen-Specker (KS) theorem provides protection against these attacks, without requiring entanglement or spatially separated composite systems. We analyze the maximum tolerated noise to guarantee the security of a KS-protected cryptographic scheme against these attacks and describe a photonic realization of this scheme using hybrid ququarts defined by the polarization and orbital angular momentum of single photons.

The perception of 3-D shape from shadows cast onto curved surfaces.

PubMed

Norman, J Farley; Lee, Young-lim; Phillips, Flip; Norman, Hideko F; Jennings, L RaShae; McBride, T Ryan

2009-05-01

In a natural environment, cast shadows abound. Objects cast shadows both upon themselves and upon background surfaces. Previous research on the perception of 3-D shape from cast shadows has only examined the informativeness of shadows cast upon flat background surfaces. In outdoor environments, however, background surfaces often possess significant curvature (large rocks, trees, hills, etc.), and this background curvature distorts the shape of cast shadows. The purpose of this study was to determine the extent to which observers can "discount" the distorting effects of curved background surfaces. In our experiments, observers viewed deforming or static shadows of naturally shaped objects, which were cast upon flat and curved background surfaces. The results showed that the discrimination of 3-D object shape from cast shadows was generally invariant over the distortions produced by hemispherical background surfaces. The observers often had difficulty, however, in identifying the shadows cast onto saddle-shaped background surfaces. The variations in curvature which occur in different directions on saddle-shaped background surfaces cause shadow distortions that lead to difficulties in object recognition and discrimination.

Virtual Ligand Screening Using PL-PatchSurfer2, a Molecular Surface-Based Protein-Ligand Docking Method.

PubMed

Shin, Woong-Hee; Kihara, Daisuke

2018-01-01

Virtual screening is a computational technique for predicting a potent binding compound for a receptor protein from a ligand library. It has been a widely used in the drug discovery field to reduce the efforts of medicinal chemists to find hit compounds by experiments.Here, we introduce our novel structure-based virtual screening program, PL-PatchSurfer, which uses molecular surface representation with the three-dimensional Zernike descriptors, which is an effective mathematical representation for identifying physicochemical complementarities between local surfaces of a target protein and a ligand. The advantage of the surface-patch description is its tolerance on a receptor and compound structure variation. PL-PatchSurfer2 achieves higher accuracy on apo form and computationally modeled receptor structures than conventional structure-based virtual screening programs. Thus, PL-PatchSurfer2 opens up an opportunity for targets that do not have their crystal structures. The program is provided as a stand-alone program at http://kiharalab.org/plps2 . We also provide files for two ligand libraries, ChEMBL and ZINC Drug-like.

The role of side chain conformational flexibility in surface recognition by Tenebrio molitor antifreeze protein

PubMed Central

Daley, Margaret E.; Sykes, Brian D.

2003-01-01

Two-dimensional nuclear magnetic resonance spectroscopy was used to investigate the flexibility of the threonine side chains in the β-helical Tenebrio molitor antifreeze protein (TmAFP) at low temperatures. From measurement of the 3Jαβ 1H-1H scalar coupling constants, the χ1 angles and preferred rotamer populations can be calculated. It was determined that the threonines on the ice-binding face of the protein adopt a preferred rotameric conformation at near freezing temperatures, whereas the threonines not on the ice-binding face sample many rotameric states. This suggests that TmAFP maintains a preformed ice-binding conformation in solution, wherein the rigid array of threonines that form the AFP-ice interface matches the ice crystal lattice. A key factor in binding to the ice surface and inhibition of ice crystal growth appears to be the close surface-to-surface complementarity between the AFP and crystalline ice, and the lack of an entropic penalty associated with freezing out motions in a flexible ligand. PMID:12824479

Enhanced lines and box-shaped features in the gamma-ray spectrum from annihilating dark matter in the NMSSM

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

Cerdeño, D.G.; Peiró, M.; Robles, S., E-mail: davidg.cerdeno@gmail.com, E-mail: miguel.peiro@uam.es, E-mail: sandra.robles@uam.es

2016-04-01

We study spectral features in the gamma-ray emission from dark matter (DM) annihilation in the Next-to-Minimal Supersymmetric Standard Model (NMSSM), with either neutralino or right-handed (RH) sneutrino DM . We perform a series of scans over the NMSSM parameter space, compute the DM annihilation cross section into two photons and the contribution of box-shaped features, and compare them with the limits derived from the Fermi-LAT search for gamma-ray lines using the latest Pass 8 data. We implement the LHC bounds on the Higgs sector and on the masses of supersymmetric particles as well as the constraints on low-energy observables. Wemore » also consider the recent upper limits from the Fermi-LAT satellite on the continuum gamma-ray emission from dwarf spheroidal galaxies (dSphs). We show that in the case of the RH sneutrino the constraint on gamma-ray spectral features can be more stringent than the dSph bounds. This is due to the Breit-Wigner enhancement near the ubiquitous resonances with a CP even Higgs and the contribution of scalar and pseudoscalar Higgs final states to box-shaped features. By contrast, for neutralino DM, the di-photon final state is only enhanced in the resonance with a Z boson and box-shaped features are even more suppressed. Therefore, the observation of spectral features could constitute a discriminating factor between both models. In addition, we compare our results with direct DM searches, including the SuperCDMS and LUX limits on the elastic DM-nucleus scattering cross section and show that some of these scenarios would be accessible to next generation experiments. Thus, our findings strengthen the idea of complementarity among distinct DM search strategies.« less

Wave-particle dualism and complementarity unraveled by a different mode

PubMed Central

Menzel, Ralf; Puhlmann, Dirk; Heuer, Axel; Schleich, Wolfgang P.

2012-01-01

The precise knowledge of one of two complementary experimental outcomes prevents us from obtaining complete information about the other one. This formulation of Niels Bohr’s principle of complementarity when applied to the paradigm of wave-particle dualism—that is, to Young’s double-slit experiment—implies that the information about the slit through which a quantum particle has passed erases interference. In the present paper we report a double-slit experiment using two photons created by spontaneous parametric down-conversion where we observe interference in the signal photon despite the fact that we have located it in one of the slits due to its entanglement with the idler photon. This surprising aspect of complementarity comes to light by our special choice of the TEM01 pump mode. According to quantum field theory the signal photon is then in a coherent superposition of two distinct wave vectors giving rise to interference fringes analogous to two mechanical slits. PMID:22628561

Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions

PubMed Central

Deschout, Hendrik; Lukes, Tomas; Sharipov, Azat; Szlag, Daniel; Feletti, Lely; Vandenberg, Wim; Dedecker, Peter; Hofkens, Johan; Leutenegger, Marcel; Lasser, Theo; Radenovic, Aleksandra

2016-01-01

Live-cell imaging of focal adhesions requires a sufficiently high temporal resolution, which remains a challenge for super-resolution microscopy. Here we address this important issue by combining photoactivated localization microscopy (PALM) with super-resolution optical fluctuation imaging (SOFI). Using simulations and fixed-cell focal adhesion images, we investigate the complementarity between PALM and SOFI in terms of spatial and temporal resolution. This PALM-SOFI framework is used to image focal adhesions in living cells, while obtaining a temporal resolution below 10 s. We visualize the dynamics of focal adhesions, and reveal local mean velocities around 190 nm min−1. The complementarity of PALM and SOFI is assessed in detail with a methodology that integrates a resolution and signal-to-noise metric. This PALM and SOFI concept provides an enlarged quantitative imaging framework, allowing unprecedented functional exploration of focal adhesions through the estimation of molecular parameters such as fluorophore densities and photoactivation or photoswitching kinetics. PMID:27991512

Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions

NASA Astrophysics Data System (ADS)

Deschout, Hendrik; Lukes, Tomas; Sharipov, Azat; Szlag, Daniel; Feletti, Lely; Vandenberg, Wim; Dedecker, Peter; Hofkens, Johan; Leutenegger, Marcel; Lasser, Theo; Radenovic, Aleksandra

2016-12-01

Live-cell imaging of focal adhesions requires a sufficiently high temporal resolution, which remains a challenge for super-resolution microscopy. Here we address this important issue by combining photoactivated localization microscopy (PALM) with super-resolution optical fluctuation imaging (SOFI). Using simulations and fixed-cell focal adhesion images, we investigate the complementarity between PALM and SOFI in terms of spatial and temporal resolution. This PALM-SOFI framework is used to image focal adhesions in living cells, while obtaining a temporal resolution below 10 s. We visualize the dynamics of focal adhesions, and reveal local mean velocities around 190 nm min-1. The complementarity of PALM and SOFI is assessed in detail with a methodology that integrates a resolution and signal-to-noise metric. This PALM and SOFI concept provides an enlarged quantitative imaging framework, allowing unprecedented functional exploration of focal adhesions through the estimation of molecular parameters such as fluorophore densities and photoactivation or photoswitching kinetics.

Complementarity of PALM and SOFI for super-resolution live-cell imaging of focal adhesions.

PubMed

Deschout, Hendrik; Lukes, Tomas; Sharipov, Azat; Szlag, Daniel; Feletti, Lely; Vandenberg, Wim; Dedecker, Peter; Hofkens, Johan; Leutenegger, Marcel; Lasser, Theo; Radenovic, Aleksandra

2016-12-19

Live-cell imaging of focal adhesions requires a sufficiently high temporal resolution, which remains a challenge for super-resolution microscopy. Here we address this important issue by combining photoactivated localization microscopy (PALM) with super-resolution optical fluctuation imaging (SOFI). Using simulations and fixed-cell focal adhesion images, we investigate the complementarity between PALM and SOFI in terms of spatial and temporal resolution. This PALM-SOFI framework is used to image focal adhesions in living cells, while obtaining a temporal resolution below 10 s. We visualize the dynamics of focal adhesions, and reveal local mean velocities around 190 nm min -1 . The complementarity of PALM and SOFI is assessed in detail with a methodology that integrates a resolution and signal-to-noise metric. This PALM and SOFI concept provides an enlarged quantitative imaging framework, allowing unprecedented functional exploration of focal adhesions through the estimation of molecular parameters such as fluorophore densities and photoactivation or photoswitching kinetics.

Reproductive glycogenetics--a critical factor in pregnancy success and species hybridisation.

PubMed

Jones, C J P; Aplin, J D

2009-03-01

Hybridisation occurs rarely in nature and experiments using interspecific transfer of embryos generally result in implantation failure. Here we show that appropriate glycosylation of the apposing surfaces of endometrium and trophoblast probably is an important factor and may play a critical role in pregnancy success. Examination of closely related species shows that each has its own specific pattern of glycosylation, or glycotype, at the fetomaternal interface and that interacting surfaces appear to show complementarity, suggesting the existence of a glycocode. Studies on a camel/llama hybrid show that for successful implantation to occur, a hybrid must have a placental glycosylation pattern similar to that of the host species, suggesting that the glycocode and appropriate glycosylation may be critical factors in the establishment and maintenance of pregnancy. This new field of reproductive glycogenetics is not only relevant to the development of new species but may also have important implications in the area of human fertility.

Multiple wavelength interferometry for distance measurements of moving objects with nanometer uncertainty

NASA Astrophysics Data System (ADS)

Kuschmierz, R.; Czarske, J.; Fischer, A.

2014-08-01

Optical measurement techniques offer great opportunities in diverse applications, such as lathe monitoring and microfluidics. Doppler-based interferometric techniques enable simultaneous measurement of the lateral velocity and axial distance of a moving object. However, there is a complementarity between the unambiguous axial measurement range and the uncertainty of the distance. Therefore, we present an extended sensor setup, which provides an unambiguous axial measurement range of 1 mm while achieving uncertainties below 100 nm. Measurements at a calibration system are performed. When using a pinhole for emulating a single scattering particle, the tumbling motion of the rotating object is resolved with a distance uncertainty of 50 nm. For measurements at the rough surface, the distance uncertainty amounts to 280 nm due to a lower signal-to-noise ratio. Both experimental results are close to the respective Cramér-Rao bound, which is derived analytically for both surface and single particle measurements.

Coevolutionary constraints in the sequence-space of macromolecular complexes reflect their self-assembly pathways.

PubMed

Mallik, Saurav; Kundu, Sudip

2017-07-01

Is the order in which biomolecular subunits self-assemble into functional macromolecular complexes imprinted in their sequence-space? Here, we demonstrate that the temporal order of macromolecular complex self-assembly can be efficiently captured using the landscape of residue-level coevolutionary constraints. This predictive power of coevolutionary constraints is irrespective of the structural, functional, and phylogenetic classification of the complex and of the stoichiometry and quaternary arrangement of the constituent monomers. Combining this result with a number of structural attributes estimated from the crystal structure data, we find indications that stronger coevolutionary constraints at interfaces formed early in the assembly hierarchy probably promotes coordinated fixation of mutations that leads to high-affinity binding with higher surface area, increased surface complementarity and elevated number of molecular contacts, compared to those that form late in the assembly. Proteins 2017; 85:1183-1189. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Evidence for Context-Dependent Complementarity of Non-Shine-Dalgarno Ribosome Binding Sites to Escherichia coli rRNA

PubMed Central

Barendt, Pamela A.; Shah, Najaf A.; Barendt, Gregory A.; Kothari, Parth A.; Sarkar, Casim A.

2013-01-01

While the ribosome has evolved to function in complex intracellular environments, these contexts do not easily allow for the study of its inherent capabilities. We have used a synthetic, well-defined, Escherichia coli (E. coli)-based translation system in conjunction with ribosome display, a powerful in vitro selection method, to identify ribosome binding sites (RBSs) that can promote the efficient translation of messenger RNAs (mRNAs) with a leader length representative of natural E. coli mRNAs. In previous work, we used a longer leader sequence and unexpectedly recovered highly efficient cytosine-rich sequences with complementarity to the 16S ribosomal RNA (rRNA) and similarity to eukaryotic RBSs. In the current study, Shine-Dalgarno (SD) sequences were prevalent but non-SD sequences were also heavily enriched and were dominated by novel guanine- and uracil-rich motifs which showed statistically significant complementarity to the 16S rRNA. Additionally, only SD motifs exhibited position-dependent decreases in sequence entropy, indicating that non-SD motifs likely operate by increasing the local concentration of ribosomes in the vicinity of the start codon, rather than by a position-dependent mechanism. These results further support the putative generality of mRNA-rRNA complementarity in facilitating mRNA translation, but also suggest that context (e.g., leader length and composition) dictates the specific subset of possible RBSs that are used for efficient translation of a given transcript. PMID:23427812

A FRAMEWORK FOR INTERPRETING FAST RADIO TRANSIENTS SEARCH EXPERIMENTS: APPLICATION TO THE V-FASTR EXPERIMENT

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

Trott, Cathryn M.; Tingay, Steven J.; Wayth, Randall B.

2013-04-10

We define a framework for determining constraints on the detection rate of fast transient events from a population of underlying sources, with a view to incorporate beam shape, frequency effects, scattering effects, and detection efficiency into the metric. We then demonstrate a method for combining independent data sets into a single event rate constraint diagram, using a probabilistic approach to the limits on parameter space. We apply this new framework to present the latest results from the V-FASTR experiment, a commensal fast transients search using the Very Long Baseline Array (VLBA). In the 20 cm band, V-FASTR now has themore » ability to probe the regions of parameter space of importance for the observed Lorimer and Keane fast radio transient candidates by combining the information from observations with differing bandwidths, and properly accounting for the source dispersion measure, VLBA antenna beam shape, experiment time sampling, and stochastic nature of events. We then apply the framework to combine the results of the V-FASTR and Allen Telescope Array Fly's Eye experiments, demonstrating their complementarity. Expectations for fast transients experiments for the SKA Phase I dish array are then computed, and the impact of large differential bandwidths is discussed.« less

Compositional Analysis of Martian Soil: Synergism of APEX and MECA Experiments on MPS 2001

NASA Technical Reports Server (NTRS)

Arvidson, R.; Marshall, J.

1999-01-01

The APEX (ATHENA Precursor Experiment) payload for the Mars 2001 mission will analyze soil and dust with a multispectral panoramic imager and an emission spectrometer on a mast on the lander, a Moessbauer spectrometer on the lander robotic arm (RA), and APXS measurements on the Marie Curie rover. These analytical methods will provide data on elemental abundances and mineralogy. The MECA payload on the lander will apply microscopy, AFM, wet chemistry, adhesive substrates, and electrometry to determine the shape and size of particles in the soil and dust, the presence of toxic substances, and electrostatic, magnetic, and hardness qualities of particles. The two experiments will complement one another through several interactions: (1) The panoramic imager provides the geological setting in which both APEX and MECA samples are acquired, (2) The RA provides samples to MECA from the surface and subsurface and will permit APEX analytical tools access to materials below the immediate surface, (3) Comparisons can be made between elemental analyses of the Moessbauer, IR, APXS on APEX and the wet chemistry of MECA which will define trace elements (ionic species in solution) and soil redox potential and conductivity. (4) APEX bulk compositional measurements will place MECA trace measurements in context, and similarly, MECA microscopy will provide particle size data that may correlate with compositional differences determined by the APEX instruments. Additionally, lithic fragments viewed by the MECA microscope station should correlate with mineral/rock species inferred by APEX data, (5) If APEX instruments detect quartz for example, the scratch plates of the MECA microscope stage will define if a mineral of this hardness is registered during abrasion tests. This is by no means an exhaustive list of potential interactions, but it is clear that both the sheer number of analytical techniques and their complementarity should provide an analytically powerful capability for both planetary and HEDS communities.

Compositional Analysis of Martian Soil: Synergism of APEX and MECA Experiments on MPS 2001

NASA Technical Reports Server (NTRS)

Arvidson, R.; Marshall, J.

1999-01-01

The APEX (ATHENA Precursor Experiment) payload for the Mars 2001 mission will analyze soil and dust with a multispectral panoramic imager and an emission spectrometer on a mast on the lander, a Moessbauer spectrometer on the lander robotic arm (RA), and APXS measurements on the Marie Curie rover. These analytical methods will provide data on elemental abundances and mineralogy. The MECA payload on the lander will apply microscopy, AFM, wet chemistry, adhesive substrates, and electrometry to determine the shape and size of particles in the soil and dust, the presence of toxic substances, and electrostatic, magnetic, and hardness qualities of particles. The two experiments will complement one another through several interactions: (1) The panoramic imager provides the geological setting in which both APEX and MECA samples are acquired, (2) The RA provides samples to MECA from the surface and subsurface and will permit APEX analytical tools access to materials below the inunediate surface, (3) Comparisons can be made between elemental analyses of the Moessbauer, IR, APXS on APEX and the wet chemistry of MECA which will define trace elements (ionic species in solution) and soil redox potential and conductivity. (4) APEX bulk compositional measurements will place MECA trace measurements in context, and similarly, MECA microscopy will provide particle size data that may correlate with compositional differences determined by the APEX instruments. Additionally, lithic fragments viewed by the NMCA microscope station should correlate with mineral/rock species inferred by APEX data, (5) If APEX instruments detect quartz for example, the scratch plates of the N4ECA microscope stage will define if a mineral of this hardness is registered during abrasion tests. This is by no means an exhaustive list of potential interactions, but it is clear that both the sheer number of analytical techniques and their complementarity should provide an analytically powerful capability for both planetary and BEDS communities.

Molecular architecture of protein-RNA recognition sites.

PubMed

Barik, Amita; C, Nithin; Pilla, Smita P; Bahadur, Ranjit Prasad

2015-01-01

The molecular architecture of protein-RNA interfaces are analyzed using a non-redundant dataset of 152 protein-RNA complexes. We find that an average protein-RNA interface is smaller than an average protein-DNA interface but larger than an average protein-protein interface. Among the different classes of protein-RNA complexes, interfaces with tRNA are the largest, while the interfaces with the single-stranded RNA are the smallest. Significantly, RNA contributes more to the interface area than its partner protein. Moreover, unlike protein-protein interfaces where the side chain contributes less to the interface area compared to the main chain, the main chain and side chain contributions flipped in protein-RNA interfaces. We find that the protein surface in contact with the RNA in protein-RNA complexes is better packed than that in contact with the DNA in protein-DNA complexes, but loosely packed than that in contact with the protein in protein-protein complexes. Shape complementarity and electrostatic potential are the two major factors that determine the specificity of the protein-RNA interaction. We find that the H-bond density at the protein-RNA interfaces is similar with that of protein-DNA interfaces but higher than the protein-protein interfaces. Unlike protein-DNA interfaces where the deoxyribose has little role in intermolecular H-bonds, due to the presence of an oxygen atom at the 2' position, the ribose in RNA plays significant role in protein-RNA H-bonds. We find that besides H-bonds, salt bridges and stacking interactions also play significant role in stabilizing protein-nucleic acids interfaces; however, their contribution at the protein-protein interfaces is insignificant.

BiGGER: a new (soft) docking algorithm for predicting protein interactions.

PubMed

Palma, P N; Krippahl, L; Wampler, J E; Moura, J J

2000-06-01

A new computationally efficient and automated "soft docking" algorithm is described to assist the prediction of the mode of binding between two proteins, using the three-dimensional structures of the unbound molecules. The method is implemented in a software package called BiGGER (Bimolecular Complex Generation with Global Evaluation and Ranking) and works in two sequential steps: first, the complete 6-dimensional binding spaces of both molecules is systematically searched. A population of candidate protein-protein docked geometries is thus generated and selected on the basis of the geometric complementarity and amino acid pairwise affinities between the two molecular surfaces. Most of the conformational changes observed during protein association are treated in an implicit way and test results are equally satisfactory, regardless of starting from the bound or the unbound forms of known structures of the interacting proteins. In contrast to other methods, the entire molecular surfaces are searched during the simulation, using absolutely no additional information regarding the binding sites. In a second step, an interaction scoring function is used to rank the putative docked structures. The function incorporates interaction terms that are thought to be relevant to the stabilization of protein complexes. These include: geometric complementarity of the surfaces, explicit electrostatic interactions, desolvation energy, and pairwise propensities of the amino acid side chains to contact across the molecular interface. The relative functional contribution of each of these interaction terms to the global scoring function has been empirically adjusted through a neural network optimizer using a learning set of 25 protein-protein complexes of known crystallographic structures. In 22 out of 25 protein-protein complexes tested, near-native docked geometries were found with C(alpha) RMS deviations < or =4.0 A from the experimental structures, of which 14 were found within the 20 top ranking solutions. The program works on widely available personal computers and takes 2 to 8 hours of CPU time to run any of the docking tests herein presented. Finally, the value and limitations of the method for the study of macromolecular interactions, not yet revealed by experimental techniques, are discussed.

General monogamy equalities of complementarity relation and distributive entanglement for multi-qubit pure states

NASA Astrophysics Data System (ADS)

Zha, Xinwei; Da, Zhang; Ahmed, Irfan; Zhang, Dan; Zhang, Yanpeng

2018-02-01

In this paper, we determine the complementarity relations for pure quantum states of N qubits by presenting the definition of local and non-local forms. By comparing the entanglement monogamy equality proposed by Coffman, Kundu, and Wootters, we prove that there exist strict monogamy laws for quantum correlations in all many-qubit systems. Further, the proper form of general entanglement monogamy equality for arbitrary quantum states is found with the characterization of total quantum correlation of qubits. These results may open a new window for multi-qubit entanglement.

Shaping off-axis metallic membrane reflectors using optimal boundary shapes and inelastic strains

NASA Technical Reports Server (NTRS)

White, C. V.; Dragovan, M.

2004-01-01

This paper will describe a novel concept for constructing off-axis membrane reflector surfaces. Membrane reflectors have been extensively studied, including investigations into inflated lenticular architectures, shaping by spin casting, shaping using electrostatic forces, and shaping by evacuating behind a membrane surface stretched between circular or annular-shaped supports.

Determining the mechanism by which fish diversity influences production.

PubMed

Carey, Michael P; Wahl, David H

2011-09-01

Understanding the ability of biodiversity to govern ecosystem function is essential with current pressures on natural communities from species invasions and extirpations. Changes in fish communities can be a major determinant of food web dynamics, and even small shifts in species composition or richness can translate into large effects on ecosystems. In addition, there is a large information gap in extrapolating results of small-scale biodiversity-ecosystem function experiments to natural systems with realistic environmental complexity. Thus, we tested the key mechanisms (resource complementarity and selection effect) for biodiversity to influence fish production in mesocosms and ponds. Fish diversity treatments were created by replicating species richness and species composition within each richness level. In mesocosms, increasing richness had a positive effect on fish biomass with an overyielding pattern indicating species mixtures were more productive than any individual species. Additive partitioning confirmed a positive net effect of biodiversity driven by a complementarity effect. Productivity was less affected by species diversity when species were more similar. Thus, the primary mechanism driving fish production in the mesocosms was resource complementarity. In the ponds, the mechanism driving fish production changed through time. The key mechanism was initially resource complementarity until production was influenced by the selection effect. Varying strength of intraspecific interactions resulting from differences in resource levels and heterogeneity likely caused differences in mechanisms between the mesocosm and pond experiments, as well as changes through time in the ponds. Understanding the mechanisms by which fish diversity governs ecosystem function and how environmental complexity and resource levels alter these relationships can be used to improve predictions for natural systems.

[Action of hormones at the molecular level].

PubMed

Korolkovas, A

1973-03-01

A review of the literature (the list of citations is available from the author on request) is given on the molecular pharmacology of steroid hormones and on efforts to isolate androgen, estrogen, and progestogen receptors with the object of understanding the mechanism of action at the cellular and molecular levels. Complementarity is the necessary factor for interaction between drug and chemoreceptor or the tension induced by proximity, as in the case of enzyme-substrate interaction. In reacting with a receptor, the drug molecule is seen as being, in general, in a state of least energy. Binding forces are the same as those operating in the interior of simple molecules. 2 factors are of special importance to the complex action of drug-receptor: the distribution of the electron charge in each and the molecular conformation of each. A number of examples illustrates this structure-activity relationship. For steroid hormones, 3 stereochemical aspects are significant for their molecular action: 1) binding sites (equatorial or axial), 2) the position of substituents, and 3) the form of cyclohexane (bound and most stable or free and thermodynamically less stable). The mode of action of steroid hormones is outlined, including a diagram of gene regulation and the function of operons and messenger RNA. Androgens, estrogens, and progestogens each owe their specific biological activity to interaction with a macromolecular receptor, such interaction presumably being due to complementarity between receptor and hormone surfaces. Several theories to account for this interaction are discussed and diagrammed.

Photogrammetry research for FAST eleven-meter reflector panel surface shape measurement

NASA Astrophysics Data System (ADS)

Zhou, Rongwei; Zhu, Lichun; Li, Weimin; Hu, Jingwen; Zhai, Xuebing

2010-10-01

In order to design and manufacture the Five-hundred-meter Aperture Spherical Radio Telescope (FAST) active reflector measuring equipment, measurement on each reflector panel surface shape was presented, static measurement of the whole neutral spherical network of nodes was performed, real-time dynamic measurement at the cable network dynamic deformation was undertaken. In the implementation process of the FAST, reflector panel surface shape detection was completed before eleven-meter reflector panel installation. Binocular vision system was constructed based on the method of binocular stereo vision in machine vision, eleven-meter reflector panel surface shape was measured with photogrammetry method. Cameras were calibrated with the feature points. Under the linearity camera model, the lighting spot array was used as calibration standard pattern, and the intrinsic and extrinsic parameters were acquired. The images were collected for digital image processing and analyzing with two cameras, feature points were extracted with the detection algorithm of characteristic points, and those characteristic points were matched based on epipolar constraint method. Three-dimensional reconstruction coordinates of feature points were analyzed and reflective panel surface shape structure was established by curve and surface fitting method. The error of reflector panel surface shape was calculated to realize automatic measurement on reflector panel surface shape. The results show that unit reflector panel surface inspection accuracy was 2.30mm, within the standard deviation error of 5.00mm. Compared with the requirement of reflector panel machining precision, photogrammetry has fine precision and operation feasibility on eleven-meter reflector panel surface shape measurement for FAST.

I-HEDGE: determining the optimum complementary sets of taxa for conservation using evolutionary isolation

PubMed Central

Mooers, Arne Ø.; Caccone, Adalgisa; Russello, Michael A.

2016-01-01

In the midst of the current biodiversity crisis, conservation efforts might profitably be directed towards ensuring that extinctions do not result in inordinate losses of evolutionary history. Numerous methods have been developed to evaluate the importance of species based on their contribution to total phylogenetic diversity on trees and networks, but existing methods fail to take complementarity into account, and thus cannot identify the best order or subset of taxa to protect. Here, we develop a novel iterative calculation of the heightened evolutionary distinctiveness and globally endangered metric (I-HEDGE) that produces the optimal ranked list for conservation prioritization, taking into account complementarity and based on both phylogenetic diversity and extinction probability. We applied this metric to a phylogenetic network based on mitochondrial control region data from extant and recently extinct giant Galápagos tortoises, a highly endangered group of closely related species. We found that the restoration of two extinct species (a project currently underway) will contribute the greatest gain in phylogenetic diversity, and present an ordered list of rankings that is the optimum complementarity set for conservation prioritization. PMID:27635324

I-HEDGE: determining the optimum complementary sets of taxa for conservation using evolutionary isolation.

PubMed

Jensen, Evelyn L; Mooers, Arne Ø; Caccone, Adalgisa; Russello, Michael A

2016-01-01

In the midst of the current biodiversity crisis, conservation efforts might profitably be directed towards ensuring that extinctions do not result in inordinate losses of evolutionary history. Numerous methods have been developed to evaluate the importance of species based on their contribution to total phylogenetic diversity on trees and networks, but existing methods fail to take complementarity into account, and thus cannot identify the best order or subset of taxa to protect. Here, we develop a novel iterative calculation of the heightened evolutionary distinctiveness and globally endangered metric (I-HEDGE) that produces the optimal ranked list for conservation prioritization, taking into account complementarity and based on both phylogenetic diversity and extinction probability. We applied this metric to a phylogenetic network based on mitochondrial control region data from extant and recently extinct giant Galápagos tortoises, a highly endangered group of closely related species. We found that the restoration of two extinct species (a project currently underway) will contribute the greatest gain in phylogenetic diversity, and present an ordered list of rankings that is the optimum complementarity set for conservation prioritization.

Somatic Hypermutation-Induced Changes in the Structure and Dynamics of HIV-1 Broadly Neutralizing Antibodies.

PubMed

Davenport, Thaddeus M; Gorman, Jason; Joyce, M Gordon; Zhou, Tongqing; Soto, Cinque; Guttman, Miklos; Moquin, Stephanie; Yang, Yongping; Zhang, Baoshan; Doria-Rose, Nicole A; Hu, Shiu-Lok; Mascola, John R; Kwong, Peter D; Lee, Kelly K

2016-08-02

Antibody somatic hypermutation (SHM) and affinity maturation enhance antigen recognition by modifying antibody paratope structure to improve its complementarity with the target epitope. SHM-induced changes in paratope dynamics may also contribute to antibody maturation, but direct evidence of this is limited. Here, we examine two classes of HIV-1 broadly neutralizing antibodies (bNAbs) for SHM-induced changes in structure and dynamics, and delineate the effects of these changes on interactions with the HIV-1 envelope glycoprotein (Env). In combination with new and existing structures of unmutated and affinity matured antibody Fab fragments, we used hydrogen/deuterium exchange with mass spectrometry to directly measure Fab structural dynamics. Changes in antibody structure and dynamics were positioned to improve complementarity with Env, with changes in dynamics primarily observed at the paratope peripheries. We conclude that SHM optimizes paratope complementarity to conserved HIV-1 epitopes and restricts the mobility of paratope-peripheral residues to minimize clashes with variable features on HIV-1 Env. Copyright © 2016 Elsevier Ltd. All rights reserved.

Intraspecific genetic diversity and composition modify species-level diversity-productivity relationships.

PubMed

Schöb, Christian; Kerle, Sarah; Karley, Alison J; Morcillo, Luna; Pakeman, Robin J; Newton, Adrian C; Brooker, Rob W

2015-01-01

Biodiversity regulates ecosystem functions such as productivity, and experimental studies of species mixtures have revealed selection and complementarity effects driving these responses. However, the impacts of intraspecific genotypic diversity in these studies are unknown, despite it forming a substantial part of the biodiversity. In a glasshouse experiment we constructed plant communities with different levels of barley (Hordeum vulgare) genotype and weed species diversity and assessed their relative biodiversity effects through additive partitioning into selection and complementarity effects. Barley genotype diversity had weak positive effects on aboveground biomass through complementarity effects, whereas weed species diversity increased biomass predominantly through selection effects. When combined, increasing genotype diversity of barley tended to dilute the selection effect of weeds. We interpret these different effects of barley genotype and weed species diversity as the consequence of small vs large trait variation associated with intraspecific barley diversity and interspecific weed diversity, respectively. The different effects of intra- vs interspecific diversity highlight the underestimated and overlooked role of genetic diversity for ecosystem functioning. © 2014 The Authors New Phytologist © 2014 New Phytologist Trust.

Homology modelling of Drosophila cytochrome P450 enzymes associated with insecticide resistance.

PubMed

Jones, Robert T; Bakker, Saskia E; Stone, Deborah; Shuttleworth, Sally N; Boundy, Sam; McCart, Caroline; Daborn, Phillip J; ffrench-Constant, Richard H; van den Elsen, Jean M H

2010-10-01

Overexpression of the cytochrome P450 gene Cyp6g1 confers resistance against DDT and a broad range of other insecticides in Drosophila melanogaster Meig. In the absence of crystal structures of CYP6G1 or complexes with its substrates, structural studies rely on homology modelling and ligand docking to understand P450-substrate interactions. Homology models are presented for CYP6G1, a P450 associated with resistance to DDT and neonicotinoids, and two other enzymes associated with insecticide resistance in D. melanogaster, CYP12D1 and CYP6A2. The models are based on a template of the X-ray structure of the phylogenetically related human CYP3A4, which is known for its broad substrate specificity. The model of CYP6G1 has a much smaller active site cavity than the template. The cavity is also 'V'-shaped and is lined with hydrophobic residues, showing high shape and chemical complementarity with the molecular characteristics of DDT. Comparison of the DDT-CYP6G1 complex and a non-resistant CYP6A2 homology model implies that tight-fit recognition of this insecticide is important in CYP6G1. The active site can accommodate differently shaped substrates ranging from imidacloprid to malathion but not the pyrethroids permethrin and cyfluthrin. The CYP6G1, CYP12D1 and CYP6A2 homology models can provide a structural insight into insecticide resistance in flies overexpressing P450 enzymes with broad substrate specificities.

Geometry- and Length Scale-Dependent Deformation and Recovery on Micro- and Nanopatterned Shape Memory Polymer Surfaces

PubMed Central

Lee, Wei Li; Low, Hong Yee

2016-01-01

Micro- and nanoscale surface textures, when optimally designed, present a unique approach to improve surface functionalities. Coupling surface texture with shape memory polymers may generate reversibly tuneable surface properties. A shape memory polyetherurethane is used to prepare various surface textures including 2 μm- and 200 nm-gratings, 250 nm-pillars and 200 nm-holes. The mechanical deformation via stretching and recovery of the surface texture are investigated as a function of length scales and shapes. Results show the 200 nm-grating exhibiting more deformation than 2 μm-grating. Grating imparts anisotropic and surface area-to-volume effects, causing different degree of deformation between gratings and pillars under the same applied macroscopic strain. Full distribution of stress within the film causes the holes to deform more substantially than the pillars. In the recovery study, unlike a nearly complete recovery for the gratings after 10 transformation cycles, the high contribution of surface energy impedes the recovery of holes and pillars. The surface textures are shown to perform a switchable wetting function. This study provides insights into how geometric features of shape memory surface patterns can be designed to modulate the shape programming and recovery, and how the control of reversibly deformable surface textures can be applied to transfer microdroplets. PMID:27026290

Effects of surface characteristics on the plantar shape of feet and subjects' perceived sensations.

PubMed

Witana, Channa P; Goonetilleke, Ravindra S; Xiong, Shuping; Au, Emily Y L

2009-03-01

Orthotics and other types of shoe inserts are primarily designed to reduce injury and improve comfort. The interaction between the plantar surface of the foot and the load-bearing surface contributes to foot and surface deformations and hence to perceived comfort, discomfort or pain. The plantar shapes of 16 participants' feet were captured when standing on three support surfaces that had different cushioning properties in the mid-foot region. Foot shape deformations were quantified using 3D laser scans. A questionnaire was used to evaluate the participant's perceptions of perceived shape and perceived feeling. The results showed that the structure in the mid-foot could change shape, independent of the rear-foot and forefoot regions. Participants were capable of identifying the shape changes with distinct preferences towards certain shapes. The cushioning properties of the mid-foot materials also have a direct influence on perceived feelings. This research has strong implications for the design and material selection of orthotics, insoles and footwear.

Contributions of feature shapes and surface cues to the recognition and neural representation of facial identity.

PubMed

Andrews, Timothy J; Baseler, Heidi; Jenkins, Rob; Burton, A Mike; Young, Andrew W

2016-10-01

A full understanding of face recognition will involve identifying the visual information that is used to discriminate different identities and how this is represented in the brain. The aim of this study was to explore the importance of shape and surface properties in the recognition and neural representation of familiar faces. We used image morphing techniques to generate hybrid faces that mixed shape properties (more specifically, second order spatial configural information as defined by feature positions in the 2D-image) from one identity and surface properties from a different identity. Behavioural responses showed that recognition and matching of these hybrid faces was primarily based on their surface properties. These behavioural findings contrasted with neural responses recorded using a block design fMRI adaptation paradigm to test the sensitivity of Haxby et al.'s (2000) core face-selective regions in the human brain to the shape or surface properties of the face. The fusiform face area (FFA) and occipital face area (OFA) showed a lower response (adaptation) to repeated images of the same face (same shape, same surface) compared to different faces (different shapes, different surfaces). From the behavioural data indicating the critical contribution of surface properties to the recognition of identity, we predicted that brain regions responsible for familiar face recognition should continue to adapt to faces that vary in shape but not surface properties, but show a release from adaptation to faces that vary in surface properties but not shape. However, we found that the FFA and OFA showed an equivalent release from adaptation to changes in both shape and surface properties. The dissociation between the neural and perceptual responses suggests that, although they may play a role in the process, these core face regions are not solely responsible for the recognition of facial identity. Copyright © 2016 Elsevier Ltd. All rights reserved.

Solution structure of Apaf-1 CARD and its interaction with caspase-9 CARD: a structural basis for specific adaptor/caspase interaction.

PubMed

Zhou, P; Chou, J; Olea, R S; Yuan, J; Wagner, G

1999-09-28

Direct recruitment and activation of caspase-9 by Apaf-1 through the homophilic CARD/CARD (Caspase Recruitment Domain) interaction is critical for the activation of caspases downstream of mitochondrial damage in apoptosis. Here we report the solution structure of the Apaf-1 CARD domain and its surface of interaction with caspase-9 CARD. Apaf-1 CARD consists of six tightly packed amphipathic alpha-helices and is topologically similar to the RAIDD CARD, with the exception of a kink observed in the middle of the N-terminal helix. By using chemical shift perturbation data, the homophilic interaction was mapped to the acidic surface of Apaf-1 CARD centered around helices 2 and 3. Interestingly, a significant portion of the chemically perturbed residues are hydrophobic, indicating that in addition to the electrostatic interactions predicted previously, hydrophobic interaction is also an important driving force underlying the CARD/CARD interaction. On the basis of the identified functional residues of Apaf-1 CARD and the surface charge complementarity, we propose a model of CARD/CARD interaction between Apaf-1 and caspase-9.

Rational Design of Peptide-Functionalized Surface Plasmon Resonance Sensor for Specific Detection of TNT Explosive.

PubMed

Wang, Jin; Muto, Masaki; Yatabe, Rui; Onodera, Takeshi; Tanaka, Masayoshi; Okochi, Mina; Toko, Kiyoshi

2017-09-30

In this study, a rationally-designed 2,4,6-trinitrotoluene (TNT) binding peptide derived from an amino acid sequence of the complementarity-determining region (CDR) of an anti-TNT monoclonal antibody was used for TNT detection based on a maleimide-functionalized surface plasmon resonance (SPR) sensor. By antigen-docking simulation and screening, the TNT binding candidate peptides were obtained as TNTHCDR1 derived from the heavy chain of CDR1, TNTHCDR2 derived from CDR2, and TNTHCDR3 from CDR3 of an anti-TNT antibody. The binding events between candidate peptides and TNT were evaluated using the SPR sensor by direct determination based on the 3-aminopropyltriethoxysilane (APTES) surface. The TNT binding peptide was directly immobilized on the maleimide-functionalized sensor chip surface from N-γ-maleimidobutyryl-oxysuccinimide ester (GMBS). The results demonstrated that peptide TNTHCDR3 was identified and selected as a TNT binding peptide among the other two candidate peptides. Five kinds of TNT analogues were also investigated to testify the selectivity of TNT binding peptide TNTHCDR3. Furthermore, the results indicated that the APTES-GMBS-based SPR sensor chip procedure featured a great potential application for the direct detection of TNT.

Rational Design of Peptide-Functionalized Surface Plasmon Resonance Sensor for Specific Detection of TNT Explosive

PubMed Central

Wang, Jin; Muto, Masaki; Yatabe, Rui; Onodera, Takeshi; Okochi, Mina; Toko, Kiyoshi

2017-01-01

In this study, a rationally-designed 2,4,6-trinitrotoluene (TNT) binding peptide derived from an amino acid sequence of the complementarity-determining region (CDR) of an anti-TNT monoclonal antibody was used for TNT detection based on a maleimide-functionalized surface plasmon resonance (SPR) sensor. By antigen-docking simulation and screening, the TNT binding candidate peptides were obtained as TNTHCDR1 derived from the heavy chain of CDR1, TNTHCDR2 derived from CDR2, and TNTHCDR3 from CDR3 of an anti-TNT antibody. The binding events between candidate peptides and TNT were evaluated using the SPR sensor by direct determination based on the 3-aminopropyltriethoxysilane (APTES) surface. The TNT binding peptide was directly immobilized on the maleimide-functionalized sensor chip surface from N-γ-maleimidobutyryl-oxysuccinimide ester (GMBS). The results demonstrated that peptide TNTHCDR3 was identified and selected as a TNT binding peptide among the other two candidate peptides. Five kinds of TNT analogues were also investigated to testify the selectivity of TNT binding peptide TNTHCDR3. Furthermore, the results indicated that the APTES-GMBS-based SPR sensor chip procedure featured a great potential application for the direct detection of TNT. PMID:28973962

Dependence of the quark-lepton complementarity on parametrizations of the Cabibbo-Kobayashi-Maskawa and Pontecorvo-Maki-Nakagawa-Sakata matrices

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

Zheng Yajuan

2010-04-01

The quark-lepton complementarity (QLC) is very suggestive in understanding possible relations between quark and lepton mixing matrices. We explore the QLC relations in all the possible angle-phase parametrizations and point out that they can approximately hold in five parametrizations. Furthermore, the vanishing of the smallest mixing angles in the Cabibbo-Kobayashi-Maskawa and Pontecorvo-Maki-Nakagawa-Sakata matrices can make sure that the QLC relations exactly hold in those five parametrizations. Finally, the sensitivity of the QLC relations to radiative corrections is also discussed.

Dark-matter decay as a complementary probe of multicomponent dark sectors.

PubMed

Dienes, Keith R; Kumar, Jason; Thomas, Brooks; Yaylali, David

2015-02-06

In single-component theories of dark matter, the 2→2 amplitudes for dark-matter production, annihilation, and scattering can be related to each other through various crossing symmetries. The detection techniques based on these processes are thus complementary. However, multicomponent theories exhibit an additional direction for dark-matter complementarity: the possibility of dark-matter decay from heavier to lighter components. We discuss how this new detection channel may be correlated with the others, and demonstrate that the enhanced complementarity which emerges can be an important ingredient in probing and constraining the parameter spaces of such models.

Health, Enterprise, and Labor Complementarity in the Household*

PubMed Central

Adhvaryu, Achyuta; Nyshadham, Anant

2017-01-01

We study the role of household enterprise as a coping mechanism after health shocks. Using variation in the cost of traveling to formal sector health facilities to predict recovery from acute illness in Tanzania, we show that individuals with prolonged illness switch from farm labor to enterprise activity. This response occurs along both the extensive (entry) and intensive (capital stock and labor supply) margins. Family members who are not ill exhibit exactly the same pattern of responses. Deriving a simple extension to the canonical agricultural household model, we show that our results suggest complementarities in household labor. PMID:28943705

Analysis of X-ray structures of matrix metalloproteinases via chaotic map clustering.

PubMed

Giangreco, Ilenia; Nicolotti, Orazio; Carotti, Angelo; De Carlo, Francesco; Gargano, Gianfranco; Bellotti, Roberto

2010-10-08

Matrix metalloproteinases (MMPs) are well-known biological targets implicated in tumour progression, homeostatic regulation, innate immunity, impaired delivery of pro-apoptotic ligands, and the release and cleavage of cell-surface receptors. With this in mind, the perception of the intimate relationships among diverse MMPs could be a solid basis for accelerated learning in designing new selective MMP inhibitors. In this regard, decrypting the latent molecular reasons in order to elucidate similarity among MMPs is a key challenge. We describe a pairwise variant of the non-parametric chaotic map clustering (CMC) algorithm and its application to 104 X-ray MMP structures. In this analysis electrostatic potentials are computed and used as input for the CMC algorithm. It was shown that differences between proteins reflect genuine variation of their electrostatic potentials. In addition, the analysis has been also extended to analyze the protein primary structures and the molecular shapes of the MMP co-crystallised ligands. The CMC algorithm was shown to be a valuable tool in knowledge acquisition and transfer from MMP structures. Based on the variation of electrostatic potentials, CMC was successful in analysing the MMP target family landscape and different subsites. The first investigation resulted in rational figure interpretation of both domain organization as well as of substrate specificity classifications. The second made it possible to distinguish the MMP classes, demonstrating the high specificity of the S1' pocket, to detect both the occurrence of punctual mutations of ionisable residues and different side-chain conformations that likely account for induced-fit phenomena. In addition, CMC demonstrated a potential comparable to the most popular UPGMA (Unweighted Pair Group Method with Arithmetic mean) method that, at present, represents a standard clustering bioinformatics approach. Interestingly, CMC and UPGMA resulted in closely comparable outcomes, but often CMC produced more informative and more easy interpretable dendrograms. Finally, CMC was successful for standard pairwise analysis (i.e., Smith-Waterman algorithm) of protein sequences and was used to convincingly explain the complementarity existing between the molecular shapes of the co-crystallised ligand molecules and the accessible MMP void volumes.

Automatic forest-fire measuring using ground stations and Unmanned Aerial Systems.

PubMed

Martínez-de Dios, José Ramiro; Merino, Luis; Caballero, Fernando; Ollero, Anibal

2011-01-01

This paper presents a novel system for automatic forest-fire measurement using cameras distributed at ground stations and mounted on Unmanned Aerial Systems (UAS). It can obtain geometrical measurements of forest fires in real-time such as the location and shape of the fire front, flame height and rate of spread, among others. Measurement of forest fires is a challenging problem that is affected by numerous potential sources of error. The proposed system addresses them by exploiting the complementarities between infrared and visual cameras located at different ground locations together with others onboard Unmanned Aerial Systems (UAS). The system applies image processing and geo-location techniques to obtain forest-fire measurements individually from each camera and then integrates the results from all the cameras using statistical data fusion techniques. The proposed system has been extensively tested and validated in close-to-operational conditions in field fire experiments with controlled safety conditions carried out in Portugal and Spain from 2001 to 2006.

Structures of Adnectin/Protein Complexes Reveal an Expanded Binding Footprint

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

Ramamurthy, Vidhyashankar; Krystek, Jr., Stanley R.; Bush, Alexander

2014-10-02

Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin ({sup 10}Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three {sup 10}Fn3 loops that are analogous to the complementarity determining regions of antibodies. The crystal structures of two Adnectins were determined, each in complex with its therapeutic target, EGFR or IL-23. Both Adnectins bind different epitopes than those bound by known monoclonal antibodies. Molecular modeling suggests that some of these epitopes might not be accessible to antibodies because of the size and concave shape of the antibodymore » combining site. In addition to interactions from the Adnectin diversified loops, residues from the N terminus and/or the {beta} strands interact with the target proteins in both complexes. Alanine-scanning mutagenesis confirmed the calculated binding energies of these {beta} strand interactions, indicating that these nonloop residues can expand the available binding footprint.« less

Automatic Forest-Fire Measuring Using Ground Stations and Unmanned Aerial Systems

PubMed Central

Martínez-de Dios, José Ramiro; Merino, Luis; Caballero, Fernando; Ollero, Anibal

2011-01-01

This paper presents a novel system for automatic forest-fire measurement using cameras distributed at ground stations and mounted on Unmanned Aerial Systems (UAS). It can obtain geometrical measurements of forest fires in real-time such as the location and shape of the fire front, flame height and rate of spread, among others. Measurement of forest fires is a challenging problem that is affected by numerous potential sources of error. The proposed system addresses them by exploiting the complementarities between infrared and visual cameras located at different ground locations together with others onboard Unmanned Aerial Systems (UAS). The system applies image processing and geo-location techniques to obtain forest-fire measurements individually from each camera and then integrates the results from all the cameras using statistical data fusion techniques. The proposed system has been extensively tested and validated in close-to-operational conditions in field fire experiments with controlled safety conditions carried out in Portugal and Spain from 2001 to 2006. PMID:22163958

Tethered lives: A couple-based perspective on the consequences of parenthood for time use, occupation, and wages.

PubMed

Killewald, Alexandra; García-Manglano, Javier

2016-11-01

Prior research on parenthood effects has typically used single-sex models and estimated average effects. By contrast, we estimate population-level variability in partners' changes in housework hours, paid work hours, occupation traits, and wages after becoming parents, and we explore whether one partner's adjustment offsets or supplements the other's. We find tradeoffs between spouses on paid work adjustments to parenthood, but complementarity in adjustments to housework hours, occupation traits, and wages. The effect of parenthood on wives' behaviors is larger and more variable than on husbands' behaviors in every domain. The modest variation between husbands in work responses to parenthood explains little of the variation in the motherhood penalty, while variation in wives' own behaviors plays a larger role. We refer to this pattern as tethered autonomy: variation across American couples in work responses to parenthood is shaped primarily by variation in wives' adjustments, while husbands' work acts largely as a fixed point. Copyright © 2016 Elsevier Inc. All rights reserved.

Multi-Scale Surface Descriptors

PubMed Central

Cipriano, Gregory; Phillips, George N.; Gleicher, Michael

2010-01-01

Local shape descriptors compactly characterize regions of a surface, and have been applied to tasks in visualization, shape matching, and analysis. Classically, curvature has be used as a shape descriptor; however, this differential property characterizes only an infinitesimal neighborhood. In this paper, we provide shape descriptors for surface meshes designed to be multi-scale, that is, capable of characterizing regions of varying size. These descriptors capture statistically the shape of a neighborhood around a central point by fitting a quadratic surface. They therefore mimic differential curvature, are efficient to compute, and encode anisotropy. We show how simple variants of mesh operations can be used to compute the descriptors without resorting to expensive parameterizations, and additionally provide a statistical approximation for reduced computational cost. We show how these descriptors apply to a number of uses in visualization, analysis, and matching of surfaces, particularly to tasks in protein surface analysis. PMID:19834190

Shaped platinum nanoparticles directly synthesized inside mesoporous silica supports

NASA Astrophysics Data System (ADS)

Kim, Jiwhan; Bae, Youn-Sang; Lee, Hyunjoo

2014-10-01

It is difficult to deposit shape-controlled nanoparticles into a mesoporous framework while preserving the shape. For shaped platinum nanoparticles, which are typically 5-10 nm in size, capillary inclusion by sonication or the formation of a mesoporous framework around the shaped platinum nanoparticles has been attempted, but the nanoparticles aggregated or their shapes were degraded easily. In this work, we directly nucleated platinum on the surface inside a mesoporous silica support and controlled the overgrowth step, producing cubic shaped nanoparticles. Mercaptopropyltrimethoxysilane was used as an anchoring agent causing nucleation at the silica surface, and it also helped to shape the nanoparticles. Platinum nanocubes, which were synthesized with polymeric capping agents separately, were deposited inside the mesoporous silica by sonication, but most of the nanoparticles were clogged at the entrance to the pores, and the surface of the platinum had very few sites that were catalytically active, as evidenced by the small H2 uptake. Unshaped platinum nanoparticles, which were prepared by conventional wet impregnation, showed a similar amount of H2 uptake as the in situ shaped platinum cubes, but the selectivity for pyrrole hydrogenation was poorer towards the production of pyrrolidine. The mesoporosity and the residual thiol groups on the surface of the in situ shaped Pt nanocubes might cause a high selectivity for pyrrolidine.It is difficult to deposit shape-controlled nanoparticles into a mesoporous framework while preserving the shape. For shaped platinum nanoparticles, which are typically 5-10 nm in size, capillary inclusion by sonication or the formation of a mesoporous framework around the shaped platinum nanoparticles has been attempted, but the nanoparticles aggregated or their shapes were degraded easily. In this work, we directly nucleated platinum on the surface inside a mesoporous silica support and controlled the overgrowth step, producing cubic shaped nanoparticles. Mercaptopropyltrimethoxysilane was used as an anchoring agent causing nucleation at the silica surface, and it also helped to shape the nanoparticles. Platinum nanocubes, which were synthesized with polymeric capping agents separately, were deposited inside the mesoporous silica by sonication, but most of the nanoparticles were clogged at the entrance to the pores, and the surface of the platinum had very few sites that were catalytically active, as evidenced by the small H2 uptake. Unshaped platinum nanoparticles, which were prepared by conventional wet impregnation, showed a similar amount of H2 uptake as the in situ shaped platinum cubes, but the selectivity for pyrrole hydrogenation was poorer towards the production of pyrrolidine. The mesoporosity and the residual thiol groups on the surface of the in situ shaped Pt nanocubes might cause a high selectivity for pyrrolidine. Electronic supplementary information (ESI) available: Fig. S1-S9. See DOI: 10.1039/c4nr03951c

Predicting infant cortical surface development using a 4D varifold-based learning framework and local topography-based shape morphing.

PubMed

Rekik, Islem; Li, Gang; Lin, Weili; Shen, Dinggang

2016-02-01

Longitudinal neuroimaging analysis methods have remarkably advanced our understanding of early postnatal brain development. However, learning predictive models to trace forth the evolution trajectories of both normal and abnormal cortical shapes remains broadly absent. To fill this critical gap, we pioneered the first prediction model for longitudinal developing cortical surfaces in infants using a spatiotemporal current-based learning framework solely from the baseline cortical surface. In this paper, we detail this prediction model and even further improve its performance by introducing two key variants. First, we use the varifold metric to overcome the limitations of the current metric for surface registration that was used in our preliminary study. We also extend the conventional varifold-based surface registration model for pairwise registration to a spatiotemporal surface regression model. Second, we propose a morphing process of the baseline surface using its topographic attributes such as normal direction and principal curvature sign. Specifically, our method learns from longitudinal data both the geometric (vertices positions) and dynamic (temporal evolution trajectories) features of the infant cortical surface, comprising a training stage and a prediction stage. In the training stage, we use the proposed varifold-based shape regression model to estimate geodesic cortical shape evolution trajectories for each training subject. We then build an empirical mean spatiotemporal surface atlas. In the prediction stage, given an infant, we select the best learnt features from training subjects to simultaneously predict the cortical surface shapes at all later timepoints, based on similarity metrics between this baseline surface and the learnt baseline population average surface atlas. We used a leave-one-out cross validation method to predict the inner cortical surface shape at 3, 6, 9 and 12 months of age from the baseline cortical surface shape at birth. Our method attained a higher prediction accuracy and better captured the spatiotemporal dynamic change of the highly folded cortical surface than the previous proposed prediction method. Copyright © 2015 Elsevier B.V. All rights reserved.

Investigation of the Influence of Shapes-Texture on Surface Deformation of UHMWPE as a Bearing Material in Static Normal Load and Rolling Contact

NASA Astrophysics Data System (ADS)

Lestari, W. D.; Ismail, R.; Jamari, J.; Bayuseno, A. P.

2017-05-01

Surface texture is a common method for improving wear properties of a tribo-pair of soft and hard bearing material. The reduction of wear rates on the contacting surface material is becoming important issues. In the present study, analysis of the contact pressure on the flat surface of UHMWPE (Ultra High Molecular Weight Polyethylene) under the static- and rolling motion with the surface of steel ball used the 3D finite element method (FEM) (the ABAQUS software version 6.12). Five shaped-texture models (square, circle, ellipse, triangle, and chevron) were presented on the flat surface for analysis. The normal load of 17, 30 and 50 N was deliberately set-up for static and rolling contact analysis. The contact pressure was determined to predict the wear behavior of the shaped-texture on the flat surface of UHMWPE. The results have shown that the static normal load yielded the lowest von-Mises stress distribution on the shaped-texture of the ellipse for all values applied a load, while the square shape experienced the highest stress distribution. Under rolling contact, however, the increasing load yielded the increasing von Mises stress distribution for the texture with a triangle shape. Moreover, the texture shapes for circle, ellipse, and chevron respectively, may undergo the lowest stress distribution for all load. The wear calculation provided that the circle and square shape may undergo the highest wear rates. Obviously, the surface texture of circle, ellipse, and chevron may experience the lowest wear rates and is potential for use in the surface engineering of bearing materials.

Effect of planar cuts' orientation on the perceived surface layout and object's shape.

PubMed

Bocheva, Nadejda

2009-07-01

The effect of the orientation of the cutting planes producing planar curves over the surface of an object on its perceived pose and shape was investigated for line drawings representing three-dimensional objects. The results suggest that the orientational flow produced by the surface curves introduces an apparent object rotation in depth and in the image plane and changes in its perceived elongation. The apparent location of the nearest points is determined by the points of maximal view-dependent unsigned curvature of the surface curves. The data are discussed in relation to the interaction of the shape-from-silhouette system and shape-from-contour system and its effect on the interpretation of the surface contours with respect to the surface geometry.

Size- and shape-dependent surface thermodynamic properties of nanocrystals

NASA Astrophysics Data System (ADS)

Fu, Qingshan; Xue, Yongqiang; Cui, Zixiang

2018-05-01

As the fundamental properties, the surface thermodynamic properties of nanocrystals play a key role in the physical and chemical changes. However, it remains ambiguous about the quantitative influence regularities of size and shape on the surface thermodynamic properties of nanocrystals. Thus by introducing interface variables into the Gibbs energy and combining Young-Laplace equation, relations between the surface thermodynamic properties (surface Gibbs energy, surface enthalpy, surface entropy, surface energy and surface heat capacity), respectively, and size of nanocrystals with different shapes were derived. Theoretical estimations of the orders of the surface thermodynamic properties of nanocrystals agree with available experimental values. Calculated results of the surface thermodynamic properties of Au, Bi and Al nanocrystals suggest that when r > 10 nm, the surface thermodynamic properties linearly vary with the reciprocal of particle size, and when r < 10 nm, the effect of particle size on the surface thermodynamic properties becomes greater and deviates from linear variation. For nanocrystals with identical equivalent diameter, the more the shape deviates from sphere, the larger the surface thermodynamic properties (absolute value) are.

The Impact Of Surface Shape Of Chip-Breaker On Machined Surface

NASA Astrophysics Data System (ADS)

Šajgalík, Michal; Czán, Andrej; Martinček, Juraj; Varga, Daniel; Hemžský, Pavel; Pitela, David

2015-12-01

Machined surface is one of the most used indicators of workpiece quality. But machined surface is influenced by several factors such as cutting parameters, cutting material, shape of cutting tool or cutting insert, micro-structure of machined material and other known as technological parameters. By improving of these parameters, we can improve machined surface. In the machining, there is important to identify the characteristics of main product of these processes - workpiece, but also the byproduct - the chip. Size and shape of chip has impact on lifetime of cutting tools and its inappropriate form can influence the machine functionality and lifetime, too. This article deals with elimination of long chip created when machining of shaft in automotive industry and with impact of shape of chip-breaker on shape of chip in various cutting conditions based on production requirements.

Watching adsorption and electron beam induced decomposition on the model system Mo(CO)6/Cu(1 1 1) by X-ray absorption and photoemission spectroscopies

NASA Astrophysics Data System (ADS)

Paufert, Pierre; Fonda, Emiliano; Li, Zheshen; Domenichini, Bruno; Bourgeois, Sylvie

2013-11-01

An in-depth study of the first steps of electron beam assisted growth of Mo from molybdenum hexacarbonyl on Cu(1 1 1) has been carried out exploiting the complementarity of X-ray photoemission and X-ray absorption spectroscopies. Frank van der Merwe (2D) growth mode has been observed for the completion of the two first monolayers of adsorbed molecules through a simple physisorption process. Irradiation of the Mo(CO)6 deposit by 1 keV electron beam induces a modification of molybdenum coordination, the average number of C-neighbors decreasing from 6 to 3. Decomposed molecules remain on the surface after annealing at 520 K and organize themselves, the molybdenum atoms moving in Cu(1 1 1) surface fcc hollow sites. After annealing at 670 K, metallic molybdenum growth begins, if the total amount of adsorbed Mo atoms exceeds 1.2 monolayers.

Superhydrophobic Surface With Shape Memory Micro/Nanostructure and Its Application in Rewritable Chip for Droplet Storage.

PubMed

Lv, Tong; Cheng, Zhongjun; Zhang, Dongjie; Zhang, Enshuang; Zhao, Qianlong; Liu, Yuyan; Jiang, Lei

2016-09-21

Recently, superhydrophobic surfaces with tunable wettability have aroused much attention. Noticeably, almost all present smart performances rely on the variation of surface chemistry on static micro/nanostructure, to obtain a surface with dynamically tunable micro/nanostructure, especially that can memorize and keep different micro/nanostructures and related wettabilities, is still a challenge. Herein, by creating micro/nanostructured arrays on shape memory polymer, a superhydrophobic surface that has shape memory ability in changing and recovering its hierarchical structures and related wettabilities was reported. Meanwhile, the surface was successfully used in the rewritable functional chip for droplet storage by designing microstructure-dependent patterns, which breaks through current research that structure patterns cannot be reprogrammed. This article advances a superhydrophobic surface with shape memory hierarchical structure and the application in rewritable functional chip, which could start some fresh ideas for the development of smart superhydrophobic surface.

Method for deploying and recovering a wave energy converter

DOEpatents

Mundon, Timothy R

2017-05-23

A system for transporting a buoy and a heave plate. The system includes a buoy and a heave plate. An outer surface of the buoy has a first geometrical shape. A surface of the heave plate has a geometrical shape complementary to the first geometrical shape of the buoy. The complementary shapes of the buoy and the heave plate facilitate coupling of the heave plate to the outer surface of the buoy in a transport mode.

Investigations into the development of catalytic activity in anti-acetylcholinesterase idiotypic and anti-idiotypic antibodies.

PubMed

Johnson, Glynis; Moore, Samuel W

2009-01-01

We have previously described anti-acetylcholinesterase antibodies that display acetylcholinesterase-like catalytic activity. No evidence of contaminating enzymes was found, and the antibodies are kinetically and apparently structurally distinct from both acetylcholinesterase (AChE) and butyrylcholinesterase. We have also mimicked the antibody catalytic sites in anti-anti-idiotypic (Ab3) antibodies. Independently from us, similar acetylcholinesterase-like antibodies have been raised as anti-idiotypic (Ab2) antibodies against a non-catalytic anti-acetylcholinesterase antibody, AE-2. In this paper, we describe an epitope analysis, using synthetic peptides in ELISA and competition ELISA, and a peptide array, of five catalytic anti-acetylcholinesterase antibodies (Ab1s), three catalytic Ab3s, as well as antibody AE-2 and a non-catalytic Ab2. The catalytic Ab1s and Ab3s recognized three Pro- and Gly-containing sequences ((40)PPMGPRRFL, (78)PGFEGTE, and (258)PPGGTGGNDTELVAC) on the AChE surface. As these sequences do not adjoin in the AChE structure, recognition would appear to be due to cross-reaction. This was confirmed by the observation that the sequences superimpose structurally. The non-catalytic antibodies, AE-2 and the Ab2, recognized AChE's peripheral anionic site (PAS), in particular, the sequence (70)YQYVD, which contains two of the site's residues. The crystal structure of the AChE tetramer (Bourne et al., 1999) shows direct interaction and high complementarity between the (257)CPPGGTGGNDTELVAC sequence and the PAS. Antibodies recognizing the sequence and the PAS may, in turn, be complementary; this may account for the apparent paradox of catalytic development in both Ab1s and Ab2s. The PAS binds, but does not hydrolyze, substrate. The catalytic Ab1s, therefore, recognize a site that may function as a substrate analog, and this, together with the presence of an Arg-Glu salt bridge in the epitope, suggests mechanisms whereby catalytic activity may have developed. In conclusion, the development of AChE-like catalytic activity in anti-AChE Ab1s and Ab2s appears to be the result of a combination of structural complementarity to a substrate-binding site, charge complementarity to a salt bridge, and specific structural peculiarities of the AChE molecule. Copyright 2008 John Wiley & Sons, Ltd.

Reinforcement learning in complementarity game and population dynamics

NASA Astrophysics Data System (ADS)

Jost, Jürgen; Li, Wei

2014-02-01

We systematically test and compare different reinforcement learning schemes in a complementarity game [J. Jost and W. Li, Physica A 345, 245 (2005), 10.1016/j.physa.2004.07.005] played between members of two populations. More precisely, we study the Roth-Erev, Bush-Mosteller, and SoftMax reinforcement learning schemes. A modified version of Roth-Erev with a power exponent of 1.5, as opposed to 1 in the standard version, performs best. We also compare these reinforcement learning strategies with evolutionary schemes. This gives insight into aspects like the issue of quick adaptation as opposed to systematic exploration or the role of learning rates.

Genetic programming over context-free languages with linear constraints for the knapsack problem: first results.

PubMed

Bruhn, Peter; Geyer-Schulz, Andreas

2002-01-01

In this paper, we introduce genetic programming over context-free languages with linear constraints for combinatorial optimization, apply this method to several variants of the multidimensional knapsack problem, and discuss its performance relative to Michalewicz's genetic algorithm with penalty functions. With respect to Michalewicz's approach, we demonstrate that genetic programming over context-free languages with linear constraints improves convergence. A final result is that genetic programming over context-free languages with linear constraints is ideally suited to modeling complementarities between items in a knapsack problem: The more complementarities in the problem, the stronger the performance in comparison to its competitors.

Structure—activity relationships for insecticidal carbamates*

PubMed Central

Metcalf, Robert L.

1971-01-01

Carbamate insecticides are biologically active because of their structural complementarity to the active site of acetylcholinesterase (AChE) and their consequent action as substrates with very low turnover numbers. Carbamates behave as synthetic neurohormones that produce their toxic action by interrupting the normal action of AChE so that acetylcholine accumulates at synaptic junctions. The necessary properties for a suitable insecticidal carbamate are lipid solubility, suitable structural complementarity to AChE, and sufficient stability to multifunction-oxidase detoxification. The relationships between the structure and the activity of a large number of synthetic carbamates are analysed in detail, with particular attention to the second of these properties. PMID:5315358

Open-quantum-systems approach to complementarity in neutral-kaon interferometry

NASA Astrophysics Data System (ADS)

de Souza, Gustavo; de Oliveira, J. G. G.; Varizi, Adalberto D.; Nogueira, Edson C.; Sampaio, Marcos D.

2016-12-01

In bipartite quantum systems, entanglement correlations between the parties exerts direct influence in the phenomenon of wave-particle duality. This effect has been quantitatively analyzed in the context of two qubits by Jakob and Bergou [Opt. Commun. 283, 827 (2010), 10.1016/j.optcom.2009.10.044]. Employing a description of the K -meson propagation in free space where its weak decay states are included as a second party, we study here this effect in the kaon-antikaon oscillations. We show that a new quantitative "triality" relation holds, similar to the one considered by Jakob and Bergou. In our case, it relates the distinguishability between the decay-product states corresponding to the distinct kaon propagation modes KS, KL, the amount of wave-like path interference between these states, and the amount of entanglement given by the reduced von Neumann entropy. The inequality can account for the complementarity between strangeness oscillations and lifetime information previously considered in the literature, therefore allowing one to see how it is affected by entanglement correlations. As we will discuss, it allows one to visualize clearly through the K0-K ¯0 oscillations the fundamental role of entanglement in quantum complementarity.

Plant genotypic diversity reduces the rate of consumer resource utilization

PubMed Central

McArt, Scott H.; Thaler, Jennifer S.

2013-01-01

While plant species diversity can reduce herbivore densities and herbivory, little is known regarding how plant genotypic diversity alters resource utilization by herbivores. Here, we show that an invasive folivore—the Japanese beetle (Popillia japonica)—increases 28 per cent in abundance, but consumes 24 per cent less foliage in genotypic polycultures compared with monocultures of the common evening primrose (Oenothera biennis). We found strong complementarity for reduced herbivore damage among plant genotypes growing in polycultures and a weak dominance effect of particularly resistant genotypes. Sequential feeding by P. japonica on different genotypes from polycultures resulted in reduced consumption compared with feeding on different plants of the same genotype from monocultures. Thus, diet mixing among plant genotypes reduced herbivore consumption efficiency. Despite positive complementarity driving an increase in fruit production in polycultures, we observed a trade-off between complementarity for increased plant productivity and resistance to herbivory, suggesting costs in the complementary use of resources by plant genotypes may manifest across trophic levels. These results elucidate mechanisms for how plant genotypic diversity simultaneously alters resource utilization by both producers and consumers, and show that population genotypic diversity can increase the resistance of a native plant to an invasive herbivore. PMID:23658201

Plant genotypic diversity reduces the rate of consumer resource utilization.

PubMed

McArt, Scott H; Thaler, Jennifer S

2013-07-07

While plant species diversity can reduce herbivore densities and herbivory, little is known regarding how plant genotypic diversity alters resource utilization by herbivores. Here, we show that an invasive folivore--the Japanese beetle (Popillia japonica)--increases 28 per cent in abundance, but consumes 24 per cent less foliage in genotypic polycultures compared with monocultures of the common evening primrose (Oenothera biennis). We found strong complementarity for reduced herbivore damage among plant genotypes growing in polycultures and a weak dominance effect of particularly resistant genotypes. Sequential feeding by P. japonica on different genotypes from polycultures resulted in reduced consumption compared with feeding on different plants of the same genotype from monocultures. Thus, diet mixing among plant genotypes reduced herbivore consumption efficiency. Despite positive complementarity driving an increase in fruit production in polycultures, we observed a trade-off between complementarity for increased plant productivity and resistance to herbivory, suggesting costs in the complementary use of resources by plant genotypes may manifest across trophic levels. These results elucidate mechanisms for how plant genotypic diversity simultaneously alters resource utilization by both producers and consumers, and show that population genotypic diversity can increase the resistance of a native plant to an invasive herbivore.

Climate conditions of the “El Niño” phenomenon for a hydro-eolic complementarity project in peru

NASA Astrophysics Data System (ADS)

Castillo N, Leonardo; Ortega M, Arturo; Luyo, Jaime E.

2018-05-01

Northern Peru is threatened by the consequences of a natural phenomenon called “El Niño”, mainly during the months of December to April. In the summer of 2017, this event reported strong climatic variations with intense rains, increasing the water levels of the Chira and Piura rivers, filling the Poechos reservoir, together with flooding and mudding. However, from an energetic perspective, these climatic alterations have a strong potential to increase the availability of the wind and hydro renewable energies in northern Peru. This work performs an evaluation of the hydro-eolic complementarity as part of the sustainability of energy systems. The study includes evaluation of historical records of wind velocity and water flow rates. It then evaluates correlation, analysis, and estimates the hydro and wind energy potentials generated by this phenomenon. The implications of the "El Niño" phenomenon are mostly negative. Nonetheless, it is possible to take advantage of higher wind and water flow rates with a hybrid energy system. The results obtained show a high degree of complementarity both normal and "El Niño" phenomenon condition in northern Peru.

Reconstructing liver shape and position from MR image slices using an active shape model

NASA Astrophysics Data System (ADS)

Fenchel, Matthias; Thesen, Stefan; Schilling, Andreas

2008-03-01

We present an algorithm for fully automatic reconstruction of 3D position, orientation and shape of the human liver from a sparsely covering set of n 2D MR slice images. Reconstructing the shape of an organ from slice images can be used for scan planning, for surgical planning or other purposes where 3D anatomical knowledge has to be inferred from sparse slices. The algorithm is based on adapting an active shape model of the liver surface to a given set of slice images. The active shape model is created from a training set of liver segmentations from a group of volunteers. The training set is set up with semi-manual segmentations of T1-weighted volumetric MR images. Searching for the optimal shape model that best fits to the image data is done by maximizing a similarity measure based on local appearance at the surface. Two different algorithms for the active shape model search are proposed and compared: both algorithms seek to maximize the a-posteriori probability of the grey level appearance around the surface while constraining the surface to the space of valid shapes. The first algorithm works by using grey value profile statistics in normal direction. The second algorithm uses average and variance images to calculate the local surface appearance on the fly. Both algorithms are validated by fitting the active shape model to abdominal 2D slice images and comparing the shapes, which have been reconstructed, to the manual segmentations and to the results of active shape model searches from 3D image data. The results turn out to be promising and competitive to active shape model segmentations from 3D data.

The design research of the test support structure for a large-diameter main mirror

NASA Astrophysics Data System (ADS)

Shi, Jiao-hong; Luo, Shi-kui; Ren, Hai-pei; Tang, Lu; Luo, Ting-yun; Mao, Yi-feng

2018-01-01

The accuracy of the main mirror surface shape measurement on ground is vital because of the importance of the main mirror in a optical remote sensor. Generally speaking, the main effects of the mirror surface shape measurement accuracy are due to the optical measurement system and support structure. The aim of this thesis is researching the design of the mirror shape measurement support structure. The main mirror discussed in this paper equipped with 650mm diameter. The requirements of PV and RMS for surface shape are no more than 0.136λ and 0.017λ respectively while λ is determined as 632.8nm. At present, the on ground adjustment methods of camera lens are optical axis horizontal and gravity discharging. In order to make the same condition between camera lens adjustment and main mirror operating, the surface shape measurement of main mirror should keep optical axis horizontal condition for mirror either. The support structure of the mirror introduced in this paper is able to extremely reduce the surface shape distortion caused by the effects of support structure mostly. According to the simulating calculation, the variation of main mirror surface shape is no more than 0.001λ. The result is acceptable for camera adjustment. Based on the measurement support structure mentioned before, the main mirror could rotate 360-degree under the condition of optical axis horizontal; the four-direction measurement for mirror is achieved. Eliminate the effects of ground gravity for surface shape measurement data, the four-direction mirror shape error is controlled no more than 0.001λ on this support structure which calculated by simulation.

Optimal Multiple Surface Segmentation With Shape and Context Priors

PubMed Central

Bai, Junjie; Garvin, Mona K.; Sonka, Milan; Buatti, John M.; Wu, Xiaodong

2014-01-01

Segmentation of multiple surfaces in medical images is a challenging problem, further complicated by the frequent presence of weak boundary evidence, large object deformations, and mutual influence between adjacent objects. This paper reports a novel approach to multi-object segmentation that incorporates both shape and context prior knowledge in a 3-D graph-theoretic framework to help overcome the stated challenges. We employ an arc-based graph representation to incorporate a wide spectrum of prior information through pair-wise energy terms. In particular, a shape-prior term is used to penalize local shape changes and a context-prior term is used to penalize local surface-distance changes from a model of the expected shape and surface distances, respectively. The globally optimal solution for multiple surfaces is obtained by computing a maximum flow in a low-order polynomial time. The proposed method was validated on intraretinal layer segmentation of optical coherence tomography images and demonstrated statistically significant improvement of segmentation accuracy compared to our earlier graph-search method that was not utilizing shape and context priors. The mean unsigned surface positioning errors obtained by the conventional graph-search approach (6.30 ± 1.58 μm) was improved to 5.14 ± 0.99 μm when employing our new method with shape and context priors. PMID:23193309

3D shape decomposition and comparison for gallbladder modeling

NASA Astrophysics Data System (ADS)

Huang, Weimin; Zhou, Jiayin; Liu, Jiang; Zhang, Jing; Yang, Tao; Su, Yi; Law, Gim Han; Chui, Chee Kong; Chang, Stephen

2011-03-01

This paper presents an approach to gallbladder shape comparison by using 3D shape modeling and decomposition. The gallbladder models can be used for shape anomaly analysis and model comparison and selection in image guided robotic surgical training, especially for laparoscopic cholecystectomy simulation. The 3D shape of a gallbladder is first represented as a surface model, reconstructed from the contours segmented in CT data by a scheme of propagation based voxel learning and classification. To better extract the shape feature, the surface mesh is further down-sampled by a decimation filter and smoothed by a Taubin algorithm, followed by applying an advancing front algorithm to further enhance the regularity of the mesh. Multi-scale curvatures are then computed on the regularized mesh for the robust saliency landmark localization on the surface. The shape decomposition is proposed based on the saliency landmarks and the concavity, measured by the distance from the surface point to the convex hull. With a given tolerance the 3D shape can be decomposed and represented as 3D ellipsoids, which reveal the shape topology and anomaly of a gallbladder. The features based on the decomposed shape model are proposed for gallbladder shape comparison, which can be used for new model selection. We have collected 19 sets of abdominal CT scan data with gallbladders, some shown in normal shape and some in abnormal shapes. The experiments have shown that the decomposed shapes reveal important topology features.

Contribution of the hydrostatic pressure to the shape of silver island particles

NASA Astrophysics Data System (ADS)

Anno, E.; Hoshino, R.

1984-09-01

We have investigated the shape change of silver island particles caused by the surface energy reduction. When the surface energy was reduced by the reaction with hydrogen sulfide, the flattening of the particles was observed. As is well known, the similar shape change takes place when the particle size increases. Therefore, the particle shape is considered to depend both on the surface energy and the particle size. From this consideration, we predict the contribution of the hydrostatic pressure P to the particle shape. As evidence of this contribution, we consider the existence of the critical size below which P is larger than the adhesive force FA between deposit and substrate surface. Investigating the influence of the flattening due to the surface energy reduction on the size distribution, the critical size is found and estimated to be about 80 Å in diameter. This value is comparable with that estimated from the condition P = FA.

Programming 2D/3D shape-shifting with hobbyist 3D printers† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7mh00269f

PubMed Central

van Manen, Teunis; Janbaz, Shahram

2017-01-01

Materials and devices with advanced functionalities often need to combine complex 3D shapes with functionality-inducing surface features. Precisely controlled bio-nanopatterns, printed electronic components, and sensors/actuators are all examples of such surface features. However, the vast majority of the refined technologies that are currently available for creating functional surface features work only on flat surfaces. Here we present initially flat constructs that upon triggering by high temperatures change their shape to a pre-programmed 3D shape, thereby enabling the combination of surface-related functionalities with complex 3D shapes. A number of shape-shifting materials have been proposed during the last few years based on various types of advanced technologies. The proposed techniques often require multiple fabrication steps and special materials, while being limited in terms of the 3D shapes they could achieve. The approach presented here is a single-step printing process that requires only a hobbyist 3D printer and inexpensive off-the-shelf materials. It also lends itself to a host of design strategies based on self-folding origami, instability-driven pop-up, and ‘sequential’ shape-shifting to unprecedentedly expand the space of achievable 3D shapes. This combination of simplicity and versatility is a key to widespread applications. PMID:29308207

Complementarity of ResourceSat-1 AWiFS and Landsat TM/ETM+ sensors

USGS Publications Warehouse

Goward, S.N.; Chander, G.; Pagnutti, M.; Marx, A.; Ryan, R.; Thomas, N.; Tetrault, R.

2012-01-01

Considerable interest has been given to forming an international collaboration to develop a virtual moderate spatial resolution land observation constellation through aggregation of data sets from comparable national observatories such as the US Landsat, the Indian ResourceSat and related systems. This study explores the complementarity of India's ResourceSat-1 Advanced Wide Field Sensor (AWiFS) with the Landsat 5 Thematic Mapper (TM) and Landsat 7 Enhanced Thematic Mapper Plus (ETM+). The analysis focuses on the comparative radiometry, geometry, and spectral properties of the two sensors. Two applied assessments of these data are also explored to examine the strengths and limitations of these alternate sources of moderate resolution land imagery with specific application domains. There are significant technical differences in these imaging systems including spectral band response, pixel dimensions, swath width, and radiometric resolution which produce differences in observation data sets. None of these differences was found to strongly limit comparable analyses in agricultural and forestry applications. Overall, we found that the AWiFS and Landsat TM/ETM+ imagery are comparable and in some ways complementary, particularly with respect to temporal repeat frequency. We have found that there are limits to our understanding of the AWiFS performance, for example, multi-camera design and stability of radiometric calibration over time, that leave some uncertainty that has been better addressed for Landsat through the Image Assessment System and related cross-sensor calibration studies. Such work still needs to be undertaken for AWiFS and similar observatories that may play roles in the Global Earth Observation System of Systems Land Surface Imaging Constellation.

Differential surface models for tactile perception of shape and on-line tracking of features

NASA Technical Reports Server (NTRS)

Hemami, H.

1987-01-01

Tactile perception of shape involves an on-line controller and a shape perceptor. The purpose of the on-line controller is to maintain gliding or rolling contact with the surface, and collect information, or track specific features of the surface such as edges of a certain sharpness. The shape perceptor uses the information to perceive, estimate the parameters of, or recognize the shape. The differential surface model depends on the information collected and on the a priori information known about the robot and its physical parameters. These differential models are certain functionals that are projections of the dynamics of the robot onto the surface gradient or onto the tangent plane. A number of differential properties may be directly measured from present day tactile sensors. Others may have to be indirectly computed from measurements. Others may constitute design objectives for distributed tactile sensors of the future. A parameterization of the surface leads to linear and nonlinear sequential parameter estimation techniques for identification of the surface. Many interesting compromises between measurement and computation are possible.

Prospective virtual screening for novel p53-MDM2 inhibitors using ultrafast shape recognition

NASA Astrophysics Data System (ADS)

Patil, Sachin P.; Ballester, Pedro J.; Kerezsi, Cassidy R.

2014-02-01

The p53 protein, known as the guardian of genome, is mutated or deleted in approximately 50 % of human tumors. In the rest of the cancers, p53 is expressed in its wild-type form, but its function is inhibited by direct binding with the murine double minute 2 (MDM2) protein. Therefore, inhibition of the p53-MDM2 interaction, leading to the activation of tumor suppressor p53 protein presents a fundamentally novel therapeutic strategy against several types of cancers. The present study utilized ultrafast shape recognition (USR), a virtual screening technique based on ligand-receptor 3D shape complementarity, to screen DrugBank database for novel p53-MDM2 inhibitors. Specifically, using 3D shape of one of the most potent crystal ligands of MDM2, MI-63, as the query molecule, six compounds were identified as potential p53-MDM2 inhibitors. These six USR hits were then subjected to molecular modeling investigations through flexible receptor docking followed by comparative binding energy analysis. These studies suggested a potential role of the USR-selected molecules as p53-MDM2 inhibitors. This was further supported by experimental tests showing that the treatment of human colon tumor cells with the top USR hit, telmisartan, led to a dose-dependent cell growth inhibition in a p53-dependent manner. It is noteworthy that telmisartan has a long history of safe human use as an approved anti-hypertension drug and thus may present an immediate clinical potential as a cancer therapeutic. Furthermore, it could also serve as a structurally-novel lead molecule for the development of more potent, small-molecule p53-MDM2 inhibitors against variety of cancers. Importantly, the present study demonstrates that the adopted USR-based virtual screening protocol is a useful tool for hit identification in the domain of small molecule p53-MDM2 inhibitors.

Investigation of Liquid Surface Rheology of Surfactant Solutions by Droplet Shape Oscillations: Experiments

PubMed

Tian; Holt; Apfel

1997-03-01

The experimental results of droplet shape oscillations are reported and applied to the analysis of surface rheological properties of surfactant solutions. An acoustic levitation technique is used to suspend the test drop in air and excite it into quadrupole shape oscillations. The equilibrium surface tension, Gibbs elasticity, and surface dilatational viscosity are determined from the measurements of droplet static shape under different levitation sound pressure, oscillation frequency, and free damping constant. Aqueous solutions of sodium dodecyl sulfate, dodecyltrimethylammonium bromide, and n-octyl beta-d-glucopyranoside are tested with this system. The concentrations of the solutions are below the critical micelle concentration. For these solutions it is found that the surface Gibbs elasticity approaches a maximum at a moderate concentration, and its value is less than that directly calculated from the state equation of a static liquid surface. The surface dilatational viscosity is found to be in a range around 0.1 cps.

A Finger-Shaped Tactile Sensor for Fabric Surfaces Evaluation by 2-Dimensional Active Sliding Touch

PubMed Central

Hu, Haihua; Han, Yezhen; Song, Aiguo; Chen, Shanguang; Wang, Chunhui; Wang, Zheng

2014-01-01

Sliding tactile perception is a basic function for human beings to determine the mechanical properties of object surfaces and recognize materials. Imitating this process, this paper proposes a novel finger-shaped tactile sensor based on a thin piezoelectric polyvinylidene fluoride (PVDF) film for surface texture measurement. A parallelogram mechanism is designed to ensure that the sensor applies a constant contact force perpendicular to the object surface, and a 2-dimensional movable mechanical structure is utilized to generate the relative motion at a certain speed between the sensor and the object surface. By controlling the 2-dimensional motion of the finger-shaped sensor along the object surface, small height/depth variation of surface texture changes the output charge of PVDF film then surface texture can be measured. In this paper, the finger-shaped tactile sensor is used to evaluate and classify five different kinds of linen. Fast Fourier Transformation (FFT) is utilized to get original attribute data of surface in the frequency domain, and principal component analysis (PCA) is used to compress the attribute data and extract feature information. Finally, low dimensional features are classified by Support Vector Machine (SVM). The experimental results show that this finger-shaped tactile sensor is effective and high accurate for discriminating the five textures. PMID:24618775

A finger-shaped tactile sensor for fabric surfaces evaluation by 2-dimensional active sliding touch.

PubMed

Hu, Haihua; Han, Yezhen; Song, Aiguo; Chen, Shanguang; Wang, Chunhui; Wang, Zheng

2014-03-11

Sliding tactile perception is a basic function for human beings to determine the mechanical properties of object surfaces and recognize materials. Imitating this process, this paper proposes a novel finger-shaped tactile sensor based on a thin piezoelectric polyvinylidene fluoride (PVDF) film for surface texture measurement. A parallelogram mechanism is designed to ensure that the sensor applies a constant contact force perpendicular to the object surface, and a 2-dimensional movable mechanical structure is utilized to generate the relative motion at a certain speed between the sensor and the object surface. By controlling the 2-dimensional motion of the finger-shaped sensor along the object surface, small height/depth variation of surface texture changes the output charge of PVDF film then surface texture can be measured. In this paper, the finger-shaped tactile sensor is used to evaluate and classify five different kinds of linen. Fast Fourier Transformation (FFT) is utilized to get original attribute data of surface in the frequency domain, and principal component analysis (PCA) is used to compress the attribute data and extract feature information. Finally, low dimensional features are classified by Support Vector Machine (SVM). The experimental results show that this finger-shaped tactile sensor is effective and high accurate for discriminating the five textures.

The Role of Interface Shape on the Impact Characteristics and Cranial Fracture Patterns Using the Immature Porcine Head Model,.

PubMed

Vaughan, Patrick E; Vogelsberg, Caitlin C M; Vollner, Jennifer M; Fenton, Todd W; Haut, Roger C

2016-09-01

The forensic literature suggests that when adolescents fall onto edged and pointed surfaces, depressed fractures can occur at low energy levels. This study documents impact biomechanics and fracture characteristics of infant porcine skulls dropped onto flat, curved, edged, and focal surfaces. Results showed that the energy needed for fracture initiation was nearly four times higher against a flat surface than against the other surfaces. While characteristic measures of fracture such as number and length of fractures did not vary with impact surface shape, the fracture patterns did depend on impact surface shape. While experimental impacts against the flat surface produced linear fractures initiating at sutural boundaries peripheral to the point of impact (POI), more focal impacts produced depressed fractures initiating at the POI. The study supported case-based forensic literature suggesting cranial fracture patterns depend on impact surface shape and that fracture initiation energy is lower for more focal impacts. © 2016 American Academy of Forensic Sciences.

Pressure sensitive microparticle adhesion through biomimicry of the pollen-stigma interaction.

PubMed

Lin, Haisheng; Qu, Zihao; Meredith, J Carson

2016-03-21

Many soft biomimetic synthetic adhesives, optimized to support macroscopic masses (∼kg), have been inspired by geckos, insects and other animals. Far less work has investigated bioinspired adhesion that is tuned to micro- and nano-scale sizes and forces. However, such adhesive forces are extremely important in the adhesion of micro- and nanoparticles to surfaces, relevant to a wide range of industrial and biological systems. Pollens, whose adhesion is critical to plant reproduction, are an evolutionary-optimized system for biomimicry to engineer tunable adhesion between particles and micro-patterned soft matter surfaces. In addition, the adhesion of pollen particles is relevant to topics as varied as pollinator ecology, transport of allergens, and atmospheric phenomena. We report the first observation of structurally-derived pressure-sensitive adhesion of a microparticle by using the sunflower pollen and stigma surfaces as a model. This strong, pressure-sensitive adhesion results from interlocking between the pollen's conical spines and the stigma's receptive papillae. Inspired by this behavior, we fabricated synthetic polymeric patterned surfaces that mimic the stigma surface's receptivity to pollen. These soft mimics allow the magnitude of the pressure-sensitive response to be tuned by adjusting the size and spacing of surface features. These results provide an important new insight for soft material adhesion based on bio-inspired principles, namely that ornamented microparticles and micro-patterned surfaces can be designed with complementarity that enable a tunable, pressure-sensitive adhesion on the microparticle size and length scale.

Three-dimensional structure of an antibody-antigen complex.

PubMed

Sheriff, S; Silverton, E W; Padlan, E A; Cohen, G H; Smith-Gill, S J; Finzel, B C; Davies, D R

1987-11-01

We have determined the three-dimensional structure of two crystal forms of an antilysozyme Fab-lysozyme complex by x-ray crystallography. The epitope on lysozyme consists of three sequentially separated subsites, including one long, nearly continuous, site from Gln-41 through Tyr-53 and one from Gly-67 through Pro-70. Antibody residues interacting with lysozyme occur in each of the six complementarity-determining regions and also include one framework residue. Arg-45 and Arg-68 form a ridge on the surface of lysozyme, which binds in a groove on the antibody surface. Otherwise the surface of interaction between the two proteins is relatively flat, although it curls at the edges. The surface of interaction is approximately 26 X 19 A. No water molecules are found in the interface. The positive charge on the two arginines is complemented by the negative charge of Glu-35 and Glu-50 from the heavy chain of the antibody. The backbone structure of the antigen, lysozyme, is mostly unperturbed, although there are some changes in the epitope region, most notably Pro-70. One side chain not in the epitope, Trp-63, undergoes a rotation of approximately 180 degrees about the C beta--C gamma bond. The Fab elbow bends in the two crystal forms differ by 7 degrees.

AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein–Protein Interaction Interfaces

PubMed Central

2016-01-01

Inhibition of protein–protein interactions (PPIs) is emerging as a promising therapeutic strategy despite the difficulty in targeting such interfaces with drug-like small molecules. PPIs generally feature large and flat binding surfaces as compared to typical drug targets. These features pose a challenge for structural characterization of the surface using geometry-based pocket-detection methods. An attractive mapping strategy—that builds on the principles of fragment-based drug discovery (FBDD)—is to detect the fragment-centric modularity at the protein surface and then characterize the large PPI interface as a set of localized, fragment-targetable interaction regions. Here, we introduce AlphaSpace, a computational analysis tool designed for fragment-centric topographical mapping (FCTM) of PPI interfaces. Our approach uses the alpha sphere construct, a geometric feature of a protein’s Voronoi diagram, to map out concave interaction space at the protein surface. We introduce two new features—alpha-atom and alpha-space—and the concept of the alpha-atom/alpha-space pair to rank pockets for fragment-targetability and to facilitate the evaluation of pocket/fragment complementarity. The resulting high-resolution interfacial map of targetable pocket space can be used to guide the rational design and optimization of small molecule or biomimetic PPI inhibitors. PMID:26225450

Amorphous silica as a versatile supermolecular ligand for Ni(II) amine complexes: toward interfacial molecular recognition.

PubMed

Boujday, Souhir; Lambert, Jean-François; Che, Michel

2004-07-19

Selective adsorption of Ni(II) amine complexes used as precursors for supported catalysts was studied on amorphous silica surfaces. The nature of the adsorption sites was probed by [Ni(en)(dien) (H2O)]2+, [Ni(en)2(H2O)2]2+, and [Ni(dien)(H2O)3]2+ (en = ethylenediamine, dien = diethylenetriamine), which respectively contain one, two, and three labile aqua ligands. The silica surface acts as a mono- or polydentate ligand that can substitute the aqua ligands of the Ni(II) complexes in an inner-sphere adsorption mechanism. Room-temperature adsorption isotherms indicate that each nickel complex selects a limited number of adsorption sites; different sites are recognised by the three complexes, even though they have the same charge and comparable sizes. Several spectroscopic techniques (UV/Vis/NIR, EXAFS, and 29Si NMR) were used to confirm the selective character of the interaction of Ni(II) amine complexes with the silica surface. The specific sites include both silanol/silanolate groups in the same number as the original labile ligands and other surface groups that probably act as hydrogen-bond acceptors. These two types of groups cooperate to result in interfacial molecular-recognition phenomena with interactional complementarity.

Role of protein surface charge in monellin sweetness.

PubMed

Xue, Wei-Feng; Szczepankiewicz, Olga; Thulin, Eva; Linse, Sara; Carey, Jannette

2009-03-01

A small number of proteins have the unusual property of tasting intensely sweet. Despite many studies aimed at identifying their sweet taste determinants, the molecular basis of protein sweetness is not fully understood. Recent mutational studies of monellin have implicated positively charged residues in sweetness. In the present work, the effect of overall net charge was investigated using the complementary approach of negative charge alterations. Multiple substitutions of Asp/Asn and Glu/Gln residues radically altered the surface charge of single-chain monellin by removing six negative charges or adding four negative charges. Biophysical characterization using circular dichroism, fluorescence, and two-dimensional NMR demonstrates that the native fold of monellin is preserved in the variant proteins under physiological solution conditions although their stability toward chemical denaturation is altered. A human taste test was employed to determine the sweetness detection threshold of the variants. Removal of negative charges preserves monellin sweetness, whereas added negative charge has a large negative impact on sweetness. Meta-analysis of published charge variants of monellin and other sweet proteins reveals a general trend toward increasing sweetness with increasing positive net charge. Structural mapping of monellin variants identifies a hydrophobic surface predicted to face the receptor where introduced positive or negative charge reduces sweetness, and a polar surface where charges modulate long-range electrostatic complementarity.

Resolution-independent surface rendering using programmable graphics hardware

DOEpatents

Loop, Charles T.; Blinn, James Frederick

2008-12-16

Surfaces defined by a Bezier tetrahedron, and in particular quadric surfaces, are rendered on programmable graphics hardware. Pixels are rendered through triangular sides of the tetrahedra and locations on the shapes, as well as surface normals for lighting evaluations, are computed using pixel shader computations. Additionally, vertex shaders are used to aid interpolation over a small number of values as input to the pixel shaders. Through this, rendering of the surfaces is performed independently of viewing resolution, allowing for advanced level-of-detail management. By individually rendering tetrahedrally-defined surfaces which together form complex shapes, the complex shapes can be rendered in their entirety.

Oxidation in the complementarity-determining regions differentially influences the properties of therapeutic antibodies

PubMed Central

Dashivets, Tetyana; Stracke, Jan; Dengl, Stefan; Knaupp, Alexander; Pollmann, Jan; Buchner, Johannes; Schlothauer, Tilman

2016-01-01

ABSTRACT Therapeutic antibodies can undergo a variety of chemical modification reactions in vitro. Depending on the site of modification, either antigen binding or Fc-mediated functions can be affected. Oxidation of tryptophan residues is one of the post-translational modifications leading to altered antibody functionality. In this study, we examined the structural and functional properties of a therapeutic antibody construct and 2 affinity matured variants thereof. Two of the 3 antibodies carry an oxidation-prone tryptophan residue in the complementarity-determining region of the VL domain. We demonstrate the differences in the stability and bioactivity of the 3 antibodies, and reveal differential degradation pathways for the antibodies susceptible to oxidation. PMID:27612038

Structural stability of posterior retainer design for resin-bonded prostheses: a 3D finite element study.

PubMed

Lin, Jie; Zheng, Zhiqiang; Shinya, Akikazu; Matinlinna, Jukka Pekka; Botelho, Michael George; Shinya, Akiyoshi

2015-09-01

The purpose of this in vitro study was to compare the stress distribution and natural frequency of different shape and thickness retainer designs for maxillary posterior resin-bonded prostheses using finite element (FE) method. A 3D FE model of a three unit posterior resin-bonded prosthesis analysis model was generated. Three different shaped retainer designs, viz. C-shaped (three axial surface wraparounds), D-shaped (three axial surface wraparounds with central groove) and O-shaped (360° wraparounds), and three different thicknesses, viz., 0.4, 0.8, and 1.2 mm, resin-bonded prostheses were used in this study. The resin-bonded prosthesis analysis model was imported into an FE analysis software (ANSYS 10.0, ANSYS, USA) and attribution of material properties. The nodes at the bottom surface of the roots were assigned fixed zero displacement in the three spatial dimensions. A simulated angle of 45° loading of a 100 N force was applied to the node of the pontic lingual cusp surface. The stress distributions and corresponding natural frequencies were analyzed and resolved. The C-shaped retainer for 0.4 mm thickness recorded the greatest von Mises stresses of 71.4 MPa for all three groups. C-shaped, D-shaped and O-shaped retainer presented natural frequencies 3,988, 7,754, and 10,494 Hz, respectively. D-shaped retainer and O-shaped retainer increased natural frequencies and structural rigidity over the traditional C-shaped retainer. The maximum von Mises stresses values of the remaining tooth and prosthesis decreased with greater retainer thickness. D-shaped retainer and O-shaped retainer increased natural frequencies and structural rigidity over the traditional C-shaped retainer.

Memory color of natural familiar objects: effects of surface texture and 3-D shape.

PubMed

Vurro, Milena; Ling, Yazhu; Hurlbert, Anya C

2013-06-28

Natural objects typically possess characteristic contours, chromatic surface textures, and three-dimensional shapes. These diagnostic features aid object recognition, as does memory color, the color most associated in memory with a particular object. Here we aim to determine whether polychromatic surface texture, 3-D shape, and contour diagnosticity improve memory color for familiar objects, separately and in combination. We use solid three-dimensional familiar objects rendered with their natural texture, which participants adjust in real time to match their memory color for the object. We analyze mean, accuracy, and precision of the memory color settings relative to the natural color of the objects under the same conditions. We find that in all conditions, memory colors deviate slightly but significantly in the same direction from the natural color. Surface polychromaticity, shape diagnosticity, and three dimensionality each improve memory color accuracy, relative to uniformly colored, generic, or two-dimensional shapes, respectively. Shape diagnosticity improves the precision of memory color also, and there is a trend for polychromaticity to do so as well. Differently from other studies, we find that the object contour alone also improves memory color. Thus, enhancing the naturalness of the stimulus, in terms of either surface or shape properties, enhances the accuracy and precision of memory color. The results support the hypothesis that memory color representations are polychromatic and are synergistically linked with diagnostic shape representations.

An Unified Multiscale Framework for Planar, Surface, and Curve Skeletonization.

PubMed

Jalba, Andrei C; Sobiecki, Andre; Telea, Alexandru C

2016-01-01

Computing skeletons of 2D shapes, and medial surface and curve skeletons of 3D shapes, is a challenging task. In particular, there is no unified framework that detects all types of skeletons using a single model, and also produces a multiscale representation which allows to progressively simplify, or regularize, all skeleton types. In this paper, we present such a framework. We model skeleton detection and regularization by a conservative mass transport process from a shape's boundary to its surface skeleton, next to its curve skeleton, and finally to the shape center. The resulting density field can be thresholded to obtain a multiscale representation of progressively simplified surface, or curve, skeletons. We detail a numerical implementation of our framework which is demonstrably stable and has high computational efficiency. We demonstrate our framework on several complex 2D and 3D shapes.

Rational Design of Multilayer Collagen Nanosheets with Compositional and Structural Control.

PubMed

Jiang, Tao; Vail, Owen A; Jiang, Zhigang; Zuo, Xiaobing; Conticello, Vincent P

2015-06-24

Two collagen-mimetic peptides, CP(+) and CP(-), are reported in which the sequences comprise a multiblock architecture having positively charged N-terminal (Pro-Arg-Gly)3 and negatively charged C-terminal (Glu-Hyp-Gly)3 triad extensions, respectively. CP(+) rapidly self-associates into positively charged nanosheets based on a monolayer structure. In contrast, CP(-) self-assembles to form negatively charged monolayer nanosheets at a much slower rate, which can be accelerated in the presence of calcium(II) ion. A 2:1 mixture of unassociated CP(-) peptide with preformed CP(+) nanosheets generates structurally defined triple-layer nanosheets in which two CP(-) monolayers have formed on the identical surfaces of the CP(+) nanosheet template. Experimental data from electrostatic force microscopy (EFM) image analysis, zeta potential measurements, and charged nanoparticle binding assays support a negative surface charge state for the triple-layer nanosheets, which is the reverse of the positive surface charge state observed for the CP(+) monolayer nanosheets. The electrostatic complementarity between the CP(+) and CP(-) triple helical cohesive ends at the layer interfaces promotes a (CP(-)/CP(+)/CP(-)) compositional gradient along the z-direction of the nanosheet. This structurally informed approach represents an attractive strategy for the fabrication of two-dimensional nanostructures with compositional control.

The Unfolding MD Simulations of Cyclophilin: Analyzed by Surface Contact Networks and Their Associated Metrics

PubMed Central

Roy, Sourav; Basu, Sankar; Dasgupta, Dipak; Bhattacharyya, Dhananjay; Banerjee, Rahul

2015-01-01

Currently, considerable interest exists with regard to the dissociation of close packed aminoacids within proteins, in the course of unfolding, which could result in either wet or dry moltenglobules. The progressive disjuncture of residues constituting the hydrophobic core ofcyclophilin from L. donovani (LdCyp) has been studied during the thermal unfolding of the molecule, by molecular dynamics simulations. LdCyp has been represented as a surface contactnetwork (SCN) based on the surface complementarity (Sm) of interacting residues within themolecular interior. The application of Sm to side chain packing within proteins make it a very sensitive indicator of subtle perturbations in packing, in the thermal unfolding of the protein. Network based metrics have been defined to track the sequential changes in the disintegration ofthe SCN spanning the hydrophobic core of LdCyp and these metrics prove to be highly sensitive compared to traditional metrics in indicating the increased conformational (and dynamical) flexibility in the network. These metrics have been applied to suggest criteria distinguishing DMG, WMG and transition state ensembles and to identify key residues involved in crucial conformational/topological events during the unfolding process. PMID:26545107

Method for a Leading Edge Slat on a Wing of an Aircraft

NASA Technical Reports Server (NTRS)

Pitt, Dale M. (Inventor); Eckstein, Nicholas Stephen (Inventor)

2016-01-01

A method for managing a flight control surface system. A leading edge device is moved on a leading edge from an undeployed position to a deployed position. The leading edge device has an outer surface, an inner surface, and a deformable fairing attached to the leading edge device such that the deformable fairing covers at least a portion of the inner surface. The deformable fairing changes from a deformed shape to an original shape when the leading edge device is moved to the deployed position. The leading edge device is then moved from the deployed position to the undeployed position, wherein the deformable fairing changes from the original shape to the deformed shape.

Surface shape analysis with an application to brain surface asymmetry in schizophrenia.

PubMed

Brignell, Christopher J; Dryden, Ian L; Gattone, S Antonio; Park, Bert; Leask, Stuart; Browne, William J; Flynn, Sean

2010-10-01

Some methods for the statistical analysis of surface shapes and asymmetry are introduced. We focus on a case study where magnetic resonance images of the brain are available from groups of 30 schizophrenia patients and 38 controls, and we investigate large-scale brain surface shape differences. Key aspects of shape analysis are to remove nuisance transformations by registration and to identify which parts of one object correspond with the parts of another object. We introduce maximum likelihood and Bayesian methods for registering brain images and providing large-scale correspondences of the brain surfaces. Brain surface size-and-shape analysis is considered using random field theory, and also dimension reduction is carried out using principal and independent components analysis. Some small but significant differences are observed between the the patient and control groups. We then investigate a particular type of asymmetry called torque. Differences in asymmetry are observed between the control and patient groups, which add strength to other observations in the literature. Further investigations of the midline plane location in the 2 groups and the fitting of nonplanar curved midlines are also considered.

3D numerical simulation of free surface shape during the crystal growth of floating zone (FZ) silicon

NASA Astrophysics Data System (ADS)

Han, Xue-Feng; Liu, Xin; Nakano, Satoshi; Harada, Hirofumi; Miyamura, Yoshiji; Kakimoto, Koichi

2018-02-01

In FZ growth processes, the stability of the free surface is important in the production of single crystal silicon with high quality. To investigate the shape of the free surface in the FZ silicon crystal growth, a 3D numerical model that included gas and liquid phases was developed. In this present study, 3D Young-Laplacian equations have been solved using the Volume of Fluid (VOF) Model. Using this new model, we predicted the 3D shape of the free surface in FZ silicon crystal growth. The effect of magnetic pressure on shape of free surface has been considered. In particular, the free surface of the eccentric growth model, which could not be previously solved using the 2D Young-Laplacian equations, was solved using the VOF model. The calculation results are validated by the experimental results.

Proximal metatarsal articular surface shape and the evolution of a rigid lateral foot in hominins.

PubMed

Proctor, Daniel J

2013-12-01

This study quantifies the proximal articular surface shape of metatarsal (MT) 4 and MT 5 using three-dimensional morphometrics. Humans and apes are compared to test whether they have significantly different shapes that are skeletal correlates to comparative lateral foot function. In addition, shod and unshod humans are compared to test for significant differences in surface shape. The MT 4 fossils OH 8, Stw 628, and AL 333-160, and the MT 5 fossils AL 333-13, AL 333-78, OH 8, and Stw 114/115 are compared with humans and apes to assess whether they bear greater similarities to humans, which would imply a relatively stable lateral foot, or to apes, which would imply a flexible foot with a midfoot break. Apes have a convex curved MT 4 surface, and humans have a flat surface. The MT 4 fossils show greater similarity to unshod humans, suggesting a stable lateral foot. Unshod humans have a relatively flatter MT 4 surface compared with shod humans. There is much overlap in MT 5 shape between humans and apes, with more similarity between humans and Gorilla. The fossil MT 5 surfaces are generally flat, most similar to humans and Gorilla. Because of the high degree of shape overlap between humans and apes, one must use caution in interpreting lateral foot function from the proximal MT 5 surface alone. Copyright © 2013 Elsevier Ltd. All rights reserved.

The von Mises stress distribution on the surface of UHMWPE with texture-shaped variation in the presence of normal load and dry sliding contact

NASA Astrophysics Data System (ADS)

Lestari, W. D.; Jamari, J.; Bayuseno, A. P.

2017-04-01

The texture shapes play a key role in the tribological performance of the surface material. This paper presents a study on the use of the 3D finite element method for surface stress analysis on the different texture shape under load and dry sliding contact. The five texture-shaped model was investigated in this work, namely square, circle, ellipse, triangle, and chevron. The result shown that the square shape has the highest value of von Mises resultant stress under static load. In contrast, the dry sliding contact on the triangle shape provided the highest von Mises stress distribution. The lowest value of von Mises stress can be found in the texture pattern of circle, square, and chevron under influence of load for 17 N, 30 N, and 50 N, respectively. Those texture patterns applied to surface of Ultra High Molecular Weight Polyethylene (UHMWPE) may have a strong effect on the reduction of wear rate and enhance tribological performance.

Gliding locomotion of manta rays, killer whales and swordfish near the water surface.

PubMed

Zhan, Jie-Min; Gong, Ye-Jun; Li, Tian-Zeng

2017-03-24

The hydrodynamic performance of the locomotive near the water surface is impacted by its geometrical shape. For marine animals, their geometrical shape is naturally selective; thus, investigating gliding locomotion of marine animal under the water surface may be able to elucidate the influence of the geometrical shape. We investigate three marine animals with specific geometries: the killer whale is fusiform shaped; the manta ray is flat and broad-winged; and the swordfish is best streamlined. The numerical results are validated by the measured drag coefficients of the manta ray model in a towing tank. The friction drag of the three target models are very similar; the body shape affected form drag coefficient is order as swordfish < killer whale < manta ray; the induced wave breaking upon the body of the manta ray performs different to killer whale and swordfish. These bio-inspired observations provide a new and in-depth understanding of the shape effects on the hydrodynamic performances near the free surface.

Local shape of pictorial relief

PubMed Central

Koenderink, Jan; van Doorn, Andrea; Wagemans, Johan

2014-01-01

How is pictorial relief represented in visual awareness? Certainly not as a “depth map,” but perhaps as a map of local surface attitudes (Koenderink & van Doorn, 1995). Here we consider the possibility that observers might instead, or concurrently, represent local surface shape, a geometrical invariant with respect to motions. Observers judge local surface shape, in a picture of a piece of sculpture, on a five-point categorical scale. Categories are cap–ridge–saddle–rut–cup–flat, where “flat” denotes the absence of shape. We find that observers readily perform such a task, with full resolution of a shape index scale (cap–ridge–saddle–rut–cup), and with excellent self-consistency over days. There exist remarkable inter-observer differences. Over a group of 10 naive observers we find that the dispersion of judgments peaks at the saddle category. There may be a relation of this finding to the history of the topic—Alberti's (1827) omission of the saddle category in his purportedly exhaustive catalog of local surface shapes. PMID:25469225

Local Solid Shape

PubMed Central

Koenderink, Jan; van Doorn, Andrea

2015-01-01

Local solid shape applies to the surface curvature of small surface patches—essentially regions of approximately constant curvatures—of volumetric objects that are smooth volumetric regions in Euclidean 3-space. This should be distinguished from local shape in pictorial space. The difference is categorical. Although local solid shape has naturally been explored in haptics, results in vision are not forthcoming. We describe a simple experiment in which observers judge shape quality and magnitude of cinematographic presentations. Without prior training, observers readily use continuous shape index and Casorati curvature scales with reasonable resolution. PMID:27648217

Drop shape visualization and contact angle measurement on curved surfaces.

PubMed

Guilizzoni, Manfredo

2011-12-01

The shape and contact angles of drops on curved surfaces is experimentally investigated. Image processing, spline fitting and numerical integration are used to extract the drop contour in a number of cross-sections. The three-dimensional surfaces which describe the surface-air and drop-air interfaces can be visualized and a simple procedure to determine the equilibrium contact angle starting from measurements on curved surfaces is proposed. Contact angles on flat surfaces serve as a reference term and a procedure to measure them is proposed. Such procedure is not as accurate as the axisymmetric drop shape analysis algorithms, but it has the advantage of requiring only a side view of the drop-surface couple and no further information. It can therefore be used also for fluids with unknown surface tension and there is no need to measure the drop volume. Examples of application of the proposed techniques for distilled water drops on gemstones confirm that they can be useful for drop shape analysis and contact angle measurement on three-dimensional sculptured surfaces. Copyright © 2011 Elsevier Inc. All rights reserved.

Aging and the discrimination of 3-D shape from motion and binocular disparity.

PubMed

Norman, J Farley; Holmin, Jessica S; Beers, Amanda M; Cheeseman, Jacob R; Ronning, Cecilia; Stethen, Angela G; Frost, Adam L

2012-10-01

Two experiments evaluated the ability of younger and older adults to visually discriminate 3-D shape as a function of surface coherence. The coherence was manipulated by embedding the 3-D surfaces in volumetric noise (e.g., for a 55 % coherent surface, 55 % of the stimulus points fell on a 3-D surface, while 45 % of the points occupied random locations within the same volume of space). The 3-D surfaces were defined by static binocular disparity, dynamic binocular disparity, and motion. The results of both experiments demonstrated significant effects of age: Older adults required more coherence (tolerated volumetric noise less) for reliable shape discrimination than did younger adults. Motion-defined and static-binocular-disparity-defined surfaces resulted in similar coherence thresholds. However, performance for dynamic-binocular-disparity-defined surfaces was superior (i.e., the observers' surface coherence thresholds were lowest for these stimuli). The results of both experiments showed that younger and older adults possess considerable tolerance to the disrupting effects of volumetric noise; the observers could reliably discriminate 3-D surface shape even when 45 % of the stimulus points (or more) constituted noise.

Surface characteristics of isopod digestive gland epithelium studied by SEM.

PubMed

Millaku, Agron; Leser, Vladka; Drobne, Damjana; Godec, Matjaz; Torkar, Matjaz; Jenko, Monika; Milani, Marziale; Tatti, Francesco

2010-05-01

The structure of the digestive gland epithelium of a terrestrial isopod Porcellio scaber has been investigated by conventional scanning electron microscopy (SEM), focused ion beam-scanning electron microscopy (FIB/SEM), and light microscopy in order to provide evidence on morphology of the gland epithelial surface in animals from a stock culture. We investigated the shape of cells, extrusion of lipid droplets, shape and distribution of microvilli, and the presence of bacteria on the cell surface. A total of 22 animals were investigated and we found some variability in the appearance of the gland epithelial surface. Seventeen of the animals had dome-shaped digestive gland "normal" epithelial cells, which were densely and homogeneously covered by microvilli and varying proportions of which extruded lipid droplets. On the surface of microvilli we routinely observed sparsely distributed bacteria of different shapes. Five of the 22 animals had "abnormal" epithelial cells with a significantly altered shape. In three of these animals, the cells were much smaller, partly or completely flat or sometimes pyramid-like. A thick layer of bacteria was detected on the microvillous border, and in places, the shape and size of microvilli were altered. In two animals, hypertrophic cells containing large vacuoles were observed indicating a characteristic intracellular infection. The potential of SEM in morphological investigations of epithelial surfaces is discussed.

Active shape models incorporating isolated landmarks for medical image annotation

NASA Astrophysics Data System (ADS)

Norajitra, Tobias; Meinzer, Hans-Peter; Stieltjes, Bram; Maier-Hein, Klaus H.

2014-03-01

Apart from their robustness in anatomic surface segmentation, purely surface based 3D Active Shape Models lack the ability to automatically detect and annotate non-surface key points of interest. However, annotation of anatomic landmarks is desirable, as it yields additional anatomic and functional information. Moreover, landmark detection might help to further improve accuracy during ASM segmentation. We present an extension of surface-based 3D Active Shape Models incorporating isolated non-surface landmarks. Positions of isolated and surface landmarks are modeled conjoint within a point distribution model (PDM). Isolated landmark appearance is described by a set of haar-like features, supporting local landmark detection on the PDM estimates using a kNN-Classi er. Landmark detection was evaluated in a leave-one-out cross validation on a reference dataset comprising 45 CT volumes of the human liver after shape space projection. Depending on the anatomical landmark to be detected, our experiments have shown in about 1/4 up to more than 1/2 of all test cases a signi cant improvement in detection accuracy compared to the position estimates delivered by the PDM. Our results encourage further research with regard to the combination of shape priors and machine learning for landmark detection within the Active Shape Model Framework.

Regional difference of the vertical structure of seasonal thermocline and its impact on sea surface temperature in the North Pacific

NASA Astrophysics Data System (ADS)

Yamaguchi, R.; Suga, T.

2016-12-01

Recent observational studies show that, during the warming season, a large amount of heat flux is penetrated through the base of thin mixed layer by vertical eddy diffusion, in addition to penetration of solar radiation [1]. In order to understand this heat penetration process due to vertical eddy diffusivity and its contribution to seasonal variation of sea surface temperature, we investigated the evolution of thermal stratification below the summertime thin mixed layer (i.e. evolution of seasonal thermocline) and its vertical structure in the North Pacific using high vertical resolution temperature profile observed by Argo floats. We quantified the vertical structure of seasonal thermocline as deviations from the linear structure where the vertical gradient of temperature is constant, that is, "shape anomaly". The shape anomaly is variable representing the extent of the bend of temperature profiles. We found that there are larger values of shape anomaly in the region where the seasonal sea surface temperature warming is relatively faster. To understand the regional difference of shape anomalies, we investigated the relationship between time changes in shape anomalies and net surface heat flux and surface kinetic energy flux. From May to July, the analysis indicated that, in a large part of North Pacific, there's a tendency for shape anomalies to develop strongly (weakly) under the conditions of large (small) downward net surface heat flux and small (large) downward surface kinetic energy flux. Since weak (strong) development of shape anomalies means efficient (inefficient) downward heat transport from the surface, these results suggest that the regional difference of the downward heat penetration below mixed layer is explained reasonably well by differences in surface heat forcing and surface wind forcing in a vertical one dimensional framework. [1] Hosoda et al. (2015), J. Oceanogr., 71, 541-556.

What is complementarity?: Niels Bohr and the architecture of quantum theory

NASA Astrophysics Data System (ADS)

Plotnitsky, Arkady

2014-12-01

This article explores Bohr’s argument, advanced under the heading of ‘complementarity,’ concerning quantum phenomena and quantum mechanics, and its physical and philosophical implications. In Bohr, the term complementarity designates both a particular concept and an overall interpretation of quantum phenomena and quantum mechanics, in part grounded in this concept. While the argument of this article is primarily philosophical, it will also address, historically, the development and transformations of Bohr’s thinking, under the impact of the development of quantum theory and Bohr’s confrontation with Einstein, especially their exchange concerning the EPR experiment, proposed by Einstein, Podolsky and Rosen in 1935. Bohr’s interpretation was progressively characterized by a more radical epistemology, in its ultimate form, which was developed in the 1930s and with which I shall be especially concerned here, defined by his new concepts of phenomenon and atomicity. According to this epistemology, quantum objects are seen as indescribable and possibly even as inconceivable, and as manifesting their existence only in the effects of their interactions with measuring instruments upon those instruments, effects that define phenomena in Bohr’s sense. The absence of causality is an automatic consequence of this epistemology. I shall also consider how probability and statistics work under these epistemological conditions.

Indivisibility, Complementarity and Ontology: A Bohrian Interpretation of Quantum Mechanics

NASA Astrophysics Data System (ADS)

Roldán-Charria, Jairo

2014-12-01

The interpretation of quantum mechanics presented in this paper is inspired by two ideas that are fundamental in Bohr's writings: indivisibility and complementarity. Further basic assumptions of the proposed interpretation are completeness, universality and conceptual economy. In the interpretation, decoherence plays a fundamental role for the understanding of measurement. A general and precise conception of complementarity is proposed. It is fundamental in this interpretation to make a distinction between ontological reality, constituted by everything that does not depend at all on the collectivity of human beings, nor on their decisions or limitations, nor on their existence, and empirical reality constituted by everything that not being ontological is, however, intersubjective. According to the proposed interpretation, neither the dynamical properties, nor the constitutive properties of microsystems like mass, charge and spin, are ontological. The properties of macroscopic systems and space-time are also considered to belong to empirical reality. The acceptance of the above mentioned conclusion does not imply a total rejection of the notion of ontological reality. In the paper, utilizing the Aristotelian ideas of general cause and potentiality, a relation between ontological reality and empirical reality is proposed. Some glimpses of ontological reality, in the form of what can be said about it, are finally presented.

A linear complementarity method for the solution of vertical vehicle-track interaction

NASA Astrophysics Data System (ADS)

Zhang, Jian; Gao, Qiang; Wu, Feng; Zhong, Wan-Xie

2018-02-01

A new method is proposed for the solution of the vertical vehicle-track interaction including a separation between wheel and rail. The vehicle is modelled as a multi-body system using rigid bodies, and the track is treated as a three-layer beam model in which the rail is considered as an Euler-Bernoulli beam and both the sleepers and the ballast are represented by lumped masses. A linear complementarity formulation is directly established using a combination of the wheel-rail normal contact condition and the generalised-α method. This linear complementarity problem is solved using the Lemke algorithm, and the wheel-rail contact force can be obtained. Then the dynamic responses of the vehicle and the track are solved without iteration based on the generalised-α method. The same equations of motion for the vehicle and track are adopted at the different wheel-rail contact situations. This method can remove some restrictions, that is, time-dependent mass, damping and stiffness matrices of the coupled system, multiple equations of motion for the different contact situations and the effect of the contact stiffness. Numerical results demonstrate that the proposed method is effective for simulating the vehicle-track interaction including a separation between wheel and rail.

Emergence of complementarity and the Baconian roots of Niels Bohr's method

NASA Astrophysics Data System (ADS)

Perovic, Slobodan

2013-08-01

I argue that instead of a rather narrow focus on N. Bohr's account of complementarity as a particular and perhaps obscure metaphysical or epistemological concept (or as being motivated by such a concept), we should consider it to result from pursuing a particular method of studying physical phenomena. More precisely, I identify a strong undercurrent of Baconian method of induction in Bohr's work that likely emerged during his experimental training and practice. When its development is analyzed in light of Baconian induction, complementarity emerges as a levelheaded rather than a controversial account, carefully elicited from a comprehensive grasp of the available experimental basis, shunning hasty metaphysically motivated generalizations based on partial experimental evidence. In fact, Bohr's insistence on the "classical" nature of observations in experiments, as well as the counterintuitive synthesis of wave and particle concepts that have puzzled scholars, seem a natural outcome (an updated instance) of the inductive method. Such analysis clarifies the intricacies of early Schrödinger's critique of the account as well as Bohr's response, which have been misinterpreted in the literature. If adequate, the analysis may lend considerable support to the view that Bacon explicated the general terms of an experimentally minded strand of the scientific method, developed and refined by scientists in the following three centuries.

Reciprocal and Complementary Sibling Interactions: Relations with Socialization Outcomes in the Kindergarten Classroom

PubMed Central

Harrist, Amanda W.; Achacoso, Joseph A.; John, Aesha; Pettit, Gregory S.; Bates, John E.; Dodge, Kenneth A.

2013-01-01

Research Findings To examine associations between sibling interaction patterns and later social outcomes in single- and two-parent families, 113 kindergarteners took part in naturalistic observations at home with siblings, classmates participated in sociometric interviews, and teachers completed behavior ratings. Sibling interactions were coded using a newly-developed 39-item checklist, and proportions of complementary and reciprocal sibling interactions computed. Complementarity occurred more among dyads where kindergartners were with toddler or infant siblings than among kindergartners with older or near-age younger siblings. Higher levels of complementarity predicted lower levels of internalizing but were not related to externalizing problems. Kindergartners’ sociometric status in the classroom differed as a function of sibling interaction patterns, with neglected and controversial children experiencing less complementarity/more reciprocity than popular, average, and rejected children. Finally, there was some evidence for differential associations of sibling interaction patterns with social outcomes for children in single- versus two-parent families: regressions testing interaction effects show sibling reciprocity positively associated with kindergartners’ social skills only in single-parent families, and complementary sibling interactions positively related to internalizing problems only in two-parent families. Implications for Practice Those working with divorcing or other single-parent families might consider sibling interactions as a potential target for social skill building. PMID:26005311

Target mimicry provides a new mechanism for regulation of microRNA activity.

PubMed

Franco-Zorrilla, José Manuel; Valli, Adrián; Todesco, Marco; Mateos, Isabel; Puga, María Isabel; Rubio-Somoza, Ignacio; Leyva, Antonio; Weigel, Detlef; García, Juan Antonio; Paz-Ares, Javier

2007-08-01

MicroRNAs (miRNA) regulate key aspects of development and physiology in animals and plants. These regulatory RNAs act as guides of effector complexes to recognize specific mRNA sequences based on sequence complementarity, resulting in translational repression or site-specific cleavage. In plants, most miRNA targets are cleaved and show almost perfect complementarity with the miRNAs around the cleavage site. Here, we examined the non-protein coding gene IPS1 (INDUCED BY PHOSPHATE STARVATION 1) from Arabidopsis thaliana. IPS1 contains a motif with sequence complementarity to the phosphate (Pi) starvation-induced miRNA miR-399, but the pairing is interrupted by a mismatched loop at the expected miRNA cleavage site. We show that IPS1 RNA is not cleaved but instead sequesters miR-399. Thus, IPS1 overexpression results in increased accumulation of the miR-399 target PHO2 mRNA and, concomitantly, in reduced shoot Pi content. Engineering of IPS1 to be cleavable abolishes its inhibitory activity on miR-399. We coin the term 'target mimicry' to define this mechanism of inhibition of miRNA activity. Target mimicry can be generalized beyond the control of Pi homeostasis, as demonstrated using artificial target mimics.

Accuracy in breast shape alignment with 3D surface fitting algorithms.

PubMed

Riboldi, Marco; Gierga, David P; Chen, George T Y; Baroni, Guido

2009-04-01

Surface imaging is in use in radiotherapy clinical practice for patient setup optimization and monitoring. Breast alignment is accomplished by searching for a tentative spatial correspondence between the reference and daily surface shape models. In this study, the authors quantify whole breast shape alignment by relying on texture features digitized on 3D surface models. Texture feature localization was validated through repeated measurements in a silicone breast phantom, mounted on a high precision mechanical stage. Clinical investigations on breast shape alignment included 133 fractions in 18 patients treated with accelerated partial breast irradiation. The breast shape was detected with a 3D video based surface imaging system so that breathing was compensated. An in-house algorithm for breast alignment, based on surface fitting constrained by nipple matching (constrained surface fitting), was applied. Results were compared with a commercial software where no constraints are utilized (unconstrained surface fitting). Texture feature localization was validated within 2 mm in each anatomical direction. Clinical data show that unconstrained surface fitting achieves adequate accuracy in most cases, though nipple mismatch is considerably higher than residual surface distances (3.9 mm vs 0.6 mm on average). Outliers beyond 1 cm can be experienced as the result of a degenerate surface fit, where unconstrained surface fitting is not sufficient to establish spatial correspondence. In the constrained surface fitting algorithm, average surface mismatch within 1 mm was obtained when nipple position was forced to match in the [1.5; 5] mm range. In conclusion, optimal results can be obtained by trading off the desired overall surface congruence vs matching of selected landmarks (constraint). Constrained surface fitting is put forward to represent an improvement in setup accuracy for those applications where whole breast positional reproducibility is an issue.

Conveying 3D shape with texture: recent advances and experimental findings

NASA Astrophysics Data System (ADS)

Interrante, Victoria; Kim, Sunghee; Hagh-Shenas, Haleh

2002-06-01

If we could design the perfect texture pattern to apply to any smooth surface in order to enable observers to more accurately perceive the surface's shape in a static monocular image taken from an arbitrary generic viewpoint under standard lighting conditions, what would the characteristics of that texture pattern be? In order to gain insight into this question, our group has developed an efficient algorithm for synthesizing a high resolution texture pattern, derived from a provided 2D sample, over an arbitrary doubly curved surface in such a way that the orientation of the texture is constrained to follow a specified underlying vector field over the surface, at a per-pixel level, without evidence of seams or projective distortion artifacts. In this paper, we report the findings of a recent experiment in which we attempt to use this new texture synthesis method to assess the shape information carrying capacity of two different types of directional texture patterns (unidirectional and bi-directional) under three different orientation conditions (following the first principal direction, following a constant uniform direction, or swirling sinusoidally in the surface). In a four alternative forced choice task, we asked participants to identify the quadrant in which two B-spline surfaces, illuminated from different random directions and simultaneously and persistently displayed, differed in their shapes. We found, after all subjects had gained sufficient training in the task, that accuracy increased fairly consistently with increasing magnitude of surface shape disparity, but that the characteristics of this increase differed under the different texture orientation conditions. Subjects were able to more reliably perceive smaller shape differences when the surfaces were textured with a pattern whose orientation followed one of the principal directions than when the surfaces were textured with a pattern that either gradually swirled in the surface or followed a constant uniform direction in the tangent plane regardless of the surface shape characteristics. These findings appear to support our hypothesis that anisotropic textures aligned with the first principal direction may facilitate shape perception, for a generic view, by making more, reliable information about the extent of the surface curvature explicitly available to the observer than would be available if the texture pattern were oriented in any other way.

Photogrammetric Verification of Fiber Optic Shape Sensors on Flexible Aerospace Structures

NASA Technical Reports Server (NTRS)

Moore, Jason P.; Rogge, Matthew D.; Jones, Thomas W.

2012-01-01

Multi-core fiber (MCF) optic shape sensing offers the possibility of providing in-flight shape measurements of highly flexible aerospace structures and control surfaces for such purposes as gust load alleviation, flutter suppression, general flight control and structural health monitoring. Photogrammetric measurements of surface mounted MCF shape sensing cable can be used to quantify the MCF installation path and verify measurement methods.

Complementarity As Generative Principle: A Thought Pattern for Aesthetic Appreciations and Cognitive Appraisals in General

PubMed Central

Bao, Yan; von Stosch, Alexandra; Park, Mona; Pöppel, Ernst

2017-01-01

In experimental aesthetics the relationship between the arts and cognitive neuroscience has gained particular interest in recent years. But has cognitive neuroscience indeed something to offer when studying the arts? Here we present a theoretical frame within which the concept of complementarity as a generative or creative principle is proposed; neurocognitive processes are characterized by the duality of complementary activities like bottom-up and top-down control, or logistical functions like temporal control and content functions like perceptions in the neural machinery. On that basis a thought pattern is suggested for aesthetic appreciations and cognitive appraisals in general. This thought pattern is deeply rooted in the history of philosophy and art theory since antiquity; and complementarity also characterizes neural operations as basis for cognitive processes. We then discuss some challenges one is confronted with in experimental aesthetics; in our opinion, one serious problem is the lack of a taxonomy of functions in psychology and neuroscience which is generally accepted. This deficit makes it next to impossible to develop acceptable models which are similar to what has to be modeled. Another problem is the severe language bias in this field of research as knowledge gained in many languages over the ages remains inaccessible to most scientists. Thus, an inspection of research results or theoretical concepts is necessarily too narrow. In spite of these limitations we provide a selective summary of some results and viewpoints with a focus on visual art and its appreciation. It is described how questions of art and aesthetic appreciations using behavioral methods and in particular brain-imaging techniques are analyzed and evaluated focusing on such issues like the representation of artwork or affective experiences. Finally, we emphasize complementarity as a generative principle on a practical level when artists and scientists work directly together which can lead to new insights and broader perspectives on both sides. PMID:28536548

Complementarity As Generative Principle: A Thought Pattern for Aesthetic Appreciations and Cognitive Appraisals in General.

PubMed

Bao, Yan; von Stosch, Alexandra; Park, Mona; Pöppel, Ernst

2017-01-01

In experimental aesthetics the relationship between the arts and cognitive neuroscience has gained particular interest in recent years. But has cognitive neuroscience indeed something to offer when studying the arts? Here we present a theoretical frame within which the concept of complementarity as a generative or creative principle is proposed; neurocognitive processes are characterized by the duality of complementary activities like bottom-up and top-down control, or logistical functions like temporal control and content functions like perceptions in the neural machinery. On that basis a thought pattern is suggested for aesthetic appreciations and cognitive appraisals in general. This thought pattern is deeply rooted in the history of philosophy and art theory since antiquity; and complementarity also characterizes neural operations as basis for cognitive processes. We then discuss some challenges one is confronted with in experimental aesthetics; in our opinion, one serious problem is the lack of a taxonomy of functions in psychology and neuroscience which is generally accepted. This deficit makes it next to impossible to develop acceptable models which are similar to what has to be modeled. Another problem is the severe language bias in this field of research as knowledge gained in many languages over the ages remains inaccessible to most scientists. Thus, an inspection of research results or theoretical concepts is necessarily too narrow. In spite of these limitations we provide a selective summary of some results and viewpoints with a focus on visual art and its appreciation. It is described how questions of art and aesthetic appreciations using behavioral methods and in particular brain-imaging techniques are analyzed and evaluated focusing on such issues like the representation of artwork or affective experiences. Finally, we emphasize complementarity as a generative principle on a practical level when artists and scientists work directly together which can lead to new insights and broader perspectives on both sides.

Detecting the role of individual species for overyielding in experimental grassland communities composed of potentially dominant species.

PubMed

Roscher, Christiane; Schumacher, Jens; Weisser, Wolfgang W; Schmid, Bernhard; Schulze, Ernst-Detlef

2007-12-01

Several studies have shown that the contribution of individual species to the positive relationship between species richness and community biomass production cannot be easily predicted from species monocultures. Here, we used a biodiversity experiment with a pool of nine potentially dominant grassland species to relate the species richness-productivity relationship to responses in density, size and aboveground allocation patterns of individual species. Aboveground community biomass increased strongly with the transition from monocultures to two-species mixtures but only slightly with the transition from two- to nine-species mixtures. Tripartite partitioning showed that the strong increase shown by the former was due to trait-independent complementarity effects, while the slight increase shown by the latter was due to dominance effects. Trait-dependent complementarity effects depended on species composition. Relative yield total (RYT) was greater than 1 (RYT>1) in mixtures but did not increase with species richness, which is consistent with the constant complementarity effect. The relative yield (RY) of only one species, Arrhenatherum elatius, continually increased with species richness, while those of the other species studied decreased with species richness or varied among different species compositions within richness levels. High observed/expected RYs (RYo/RYe>1) of individual species were mainly due to increased module densities, whereas low observed/expected RYs (RYo/RYe<1) were due to more pronounced decreases in module density (species with stoloniferous or creeping growth) or module size (species with clearly-defined plant individuals). The trade-off between module density and size, typical for plant populations under the law of constant final yield, was compensated among species. The positive trait-independent complementarity effect could be explained by an increase in community module density, which reached a maximum at low species richness. In contrast, the increasing dominance effect was attributable to the species-specific ability, in particular that of A. elatius, to increase module size, while intrinsic growth limitations led to a suppression of the remaining species in many mixtures.

Ge growth on vicinal si(001) surfaces: island's shape and pair interaction versus miscut angle.

PubMed

Persichetti, L; Sgarlata, A; Fanfoni, M; Balzarotti, A

2011-10-01

A complete description of Ge growth on vicinal Si(001) surfaces is provided. The distinctive mechanisms of the epitaxial growth process on vicinal surfaces are clarified from the very early stages of Ge deposition to the nucleation of 3D islands. By interpolating high-resolution scanning tunneling microscopy measurements with continuum elasticity modeling, we assess the dependence of island's shape and elastic interaction on the substrate misorientation. Our results confirm that vicinal surfaces offer an additional degree of control over the shape and symmetry of self-assembled nanostructures.

Profile shape optimization in multi-jet impingement cooling of dimpled topologies for local heat transfer enhancement

NASA Astrophysics Data System (ADS)

Negi, Deepchand Singh; Pattamatta, Arvind

2015-04-01

The present study deals with shape optimization of dimples on the target surface in multi-jet impingement heat transfer. Bezier polynomial formulation is incorporated to generate profile shapes for the dimple profile generation and a multi-objective optimization is performed. The optimized dimple shape exhibits higher local Nusselt number values compared to the reference hemispherical dimpled plate optimized shape which can be used to alleviate local temperature hot spots on target surface.

High-resolution liquid patterns via three-dimensional droplet shape control.

PubMed

Raj, Rishi; Adera, Solomon; Enright, Ryan; Wang, Evelyn N

2014-09-25

Understanding liquid dynamics on surfaces can provide insight into nature's design and enable fine manipulation capability in biological, manufacturing, microfluidic and thermal management applications. Of particular interest is the ability to control the shape of the droplet contact area on the surface, which is typically circular on a smooth homogeneous surface. Here, we show the ability to tailor various droplet contact area shapes ranging from squares, rectangles, hexagons, octagons, to dodecagons via the design of the structure or chemical heterogeneity on the surface. We simultaneously obtain the necessary physical insights to develop a universal model for the three-dimensional droplet shape by characterizing the droplet side and top profiles. Furthermore, arrays of droplets with controlled shapes and high spatial resolution can be achieved using this approach. This liquid-based patterning strategy promises low-cost fabrication of integrated circuits, conductive patterns and bio-microarrays for high-density information storage and miniaturized biochips and biosensors, among others.

Optimal Mass Transport for Shape Matching and Comparison

PubMed Central

Su, Zhengyu; Wang, Yalin; Shi, Rui; Zeng, Wei; Sun, Jian; Luo, Feng; Gu, Xianfeng

2015-01-01

Surface based 3D shape analysis plays a fundamental role in computer vision and medical imaging. This work proposes to use optimal mass transport map for shape matching and comparison, focusing on two important applications including surface registration and shape space. The computation of the optimal mass transport map is based on Monge-Brenier theory, in comparison to the conventional method based on Monge-Kantorovich theory, this method significantly improves the efficiency by reducing computational complexity from O(n2) to O(n). For surface registration problem, one commonly used approach is to use conformal map to convert the shapes into some canonical space. Although conformal mappings have small angle distortions, they may introduce large area distortions which are likely to cause numerical instability thus resulting failures of shape analysis. This work proposes to compose the conformal map with the optimal mass transport map to get the unique area-preserving map, which is intrinsic to the Riemannian metric, unique, and diffeomorphic. For shape space study, this work introduces a novel Riemannian framework, Conformal Wasserstein Shape Space, by combing conformal geometry and optimal mass transport theory. In our work, all metric surfaces with the disk topology are mapped to the unit planar disk by a conformal mapping, which pushes the area element on the surface to a probability measure on the disk. The optimal mass transport provides a map from the shape space of all topological disks with metrics to the Wasserstein space of the disk and the pullback Wasserstein metric equips the shape space with a Riemannian metric. We validate our work by numerous experiments and comparisons with prior approaches and the experimental results demonstrate the efficiency and efficacy of our proposed approach. PMID:26440265

Reconstructing surface wave profiles from reflected acoustic pulses using multiple receivers.

PubMed

Walstead, Sean P; Deane, Grant B

2014-08-01

Surface wave shapes are determined by analyzing underwater reflected acoustic signals collected at multiple receivers. The transmitted signals are of nominal frequency 300 kHz and are reflected off surface gravity waves that are paddle-generated in a wave tank. An inverse processing algorithm reconstructs 50 surface wave shapes over a length span of 2.10 m. The inverse scheme uses a broadband forward scattering model based on Kirchhoff's diffraction formula to determine wave shapes. The surface reconstruction algorithm is self-starting in that source and receiver geometry and initial estimates of wave shape are determined from the same acoustic signals used in the inverse processing. A high speed camera provides ground-truth measurements of the surface wave field for comparison with the acoustically derived surface waves. Within Fresnel zone regions the statistical confidence of the inversely optimized surface profile exceeds that of the camera profile. Reconstructed surfaces are accurate to a resolution of about a quarter-wavelength of the acoustic pulse only within Fresnel zones associated with each source and receiver pair. Multiple isolated Fresnel zones from multiple receivers extend the spatial extent of accurate surface reconstruction while overlapping Fresnel zones increase confidence in the optimized profiles there.

Method and Apparatus for a Leading Edge Slat on a Wing of an Aircraft

NASA Technical Reports Server (NTRS)

Pitt, Dale M. (Inventor); Eckstein, Nicholas Stephen (Inventor)

2013-01-01

A method and apparatus for managing a flight control surface system. A leading edge device is moved on a leading edge from an undeployed position to a deployed position. The leading edge device has an outer surface, an inner surface, and a deformable fairing attached to the leading edge device such that the deformable fairing covers at least a portion of the inner surface. The deformable fairing changes from a deformed shape to an original shape when the leading edge device is moved to the deployed position. The leading edge device is then moved from the deployed position to the undeployed position, wherein the deformable fairing changes from the original shape to the deformed shape.

Equilibrium shape of 4He crystal under zero gravity below 200 mK

PubMed Central

Takahashi, Takuya; Ohuchi, Haruka; Nomura, Ryuji; Okuda, Yuichi

2015-01-01

Equilibrium crystal shape is the lowest energy crystal shape that is hardly realized in ordinary crystals because of their slow relaxation. 4He quantum crystals in a superfluid have been expected as unique exceptions that grow extremely fast at very low temperatures. However, on the ground, gravity considerably deforms the crystals and conceals the equilibrium crystal shape, and thus, gravity-free environment is needed to observe the equilibrium shape of 4He. We report the relaxation processes of macroscopic 4He crystals in a superfluid below 200 mK under zero gravity using a parabolic flight of a jet plane. When gravity was removed from a gravity-flattened 4He crystal, the crystal rapidly transformed into a shape with flat surfaces. Although the relaxation processes were highly dependent on the initial condition, the crystals relaxed to a nearly homothetic shape in the end, indicating that they were truly in an equilibrium shape minimizing the interfacial free energy. Thanks to the equilibrium shape, we were able to determine the Wulff’s origin and the size of the c-facet together with the vicinal surface profile next to the c-facet. The c-facet size was extremely small in the quantum crystals, and the facet-like flat surfaces were found to be the vicinal surfaces. At the same time, the interfacial free energy of the a-facet and s-facet was also obtained. PMID:26601315

Assessment of the accuracy of plasma shape reconstruction by the Cauchy condition surface method in JT-60SA

NASA Astrophysics Data System (ADS)

Miyata, Y.; Suzuki, T.; Takechi, M.; Urano, H.; Ide, S.

2015-07-01

For the purpose of stable plasma equilibrium control and detailed analysis, it is essential to reconstruct an accurate plasma boundary on the poloidal cross section in tokamak devices. The Cauchy condition surface (CCS) method is a numerical approach for calculating the spatial distribution of the magnetic flux outside a hypothetical surface and reconstructing the plasma boundary from the magnetic measurements located outside the plasma. The accuracy of the plasma shape reconstruction has been assessed by comparing the CCS method and an equilibrium calculation in JT-60SA with a high elongation and triangularity of plasma shape. The CCS, on which both Dirichlet and Neumann conditions are unknown, is defined as a hypothetical surface located inside the real plasma region. The accuracy of the plasma shape reconstruction is sensitive to the CCS free parameters such as the number of unknown parameters and the shape in JT-60SA. It is found that the optimum number of unknown parameters and the size of the CCS that minimizes errors in the reconstructed plasma shape are in proportion to the plasma size. Furthermore, it is shown that the accuracy of the plasma shape reconstruction is greatly improved using the optimum number of unknown parameters and shape of the CCS, and the reachable reconstruction errors in plasma shape and locations of strike points are within the target ranges in JT-60SA.

Assessing breathing motion by shape matching of lung and diaphragm surfaces

NASA Astrophysics Data System (ADS)

Urschler, Martin; Bischof, Horst

2005-04-01

Studying complex thorax breating motion is an important research topic for accurate fusion of functional and anatomical data, radiotherapy planning or reduction of breathing motion artifacts. We investigate segmented CT lung, airway and diaphragm surfaces at several different breathing states between Functional Residual and Total Lung Capacity. In general, it is hard to robustly derive corresponding shape features like curvature maxima from lung and diaphragm surfaces since diaphragm and rib cage muscles tend to deform the elastic lung tissue such that e.g. ridges might disappear. A novel registration method based on the shape context approach for shape matching is presented where we extend shape context to 3D surfaces. The shape context approach was reported as a promising method for matching 2D shapes without relying on extracted shape features. We use the point correspondences for a non-rigid thin-plate-spline registration to get deformation fields that describe the movement of lung and diaphragm. Our validation consists of experiments on phantom and real sheep thorax data sets. Phantom experiments make use of shapes that are manipulated with known transformations that simulate breathing behaviour. Real thorax data experiments use a data set showing lungs and diaphragm at 5 distinct breathing states, where we compare subsets of the data sets and qualitatively and quantitatively asses the registration performance by using manually identified corresponding landmarks.

Equilibrium shape of (4)He crystal under zero gravity below 200 mK.

PubMed

Takahashi, Takuya; Ohuchi, Haruka; Nomura, Ryuji; Okuda, Yuichi

2015-10-01

Equilibrium crystal shape is the lowest energy crystal shape that is hardly realized in ordinary crystals because of their slow relaxation. (4)He quantum crystals in a superfluid have been expected as unique exceptions that grow extremely fast at very low temperatures. However, on the ground, gravity considerably deforms the crystals and conceals the equilibrium crystal shape, and thus, gravity-free environment is needed to observe the equilibrium shape of (4)He. We report the relaxation processes of macroscopic (4)He crystals in a superfluid below 200 mK under zero gravity using a parabolic flight of a jet plane. When gravity was removed from a gravity-flattened (4)He crystal, the crystal rapidly transformed into a shape with flat surfaces. Although the relaxation processes were highly dependent on the initial condition, the crystals relaxed to a nearly homothetic shape in the end, indicating that they were truly in an equilibrium shape minimizing the interfacial free energy. Thanks to the equilibrium shape, we were able to determine the Wulff's origin and the size of the c-facet together with the vicinal surface profile next to the c-facet. The c-facet size was extremely small in the quantum crystals, and the facet-like flat surfaces were found to be the vicinal surfaces. At the same time, the interfacial free energy of the a-facet and s-facet was also obtained.

Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code

PubMed Central

Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

2016-01-01

Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNALysUUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine–pyrimidine mismatches. We show that mnm5s2U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism. PMID:26791911

Electrophilic Triterpenoid Enones: A Comparative Thiol-Trapping and Bioactivity Study.

PubMed

Del Prete, Danilo; Taglialatela-Scafati, Orazio; Minassi, Alberto; Sirignano, Carmina; Cruz, Cristina; Bellido, Maria L; Muñoz, Eduardo; Appendino, Giovanni

2017-08-25

Bardoxolone methyl (1) is the quintessential member of triterpenoid cyanoacrylates, an emerging class of bioactive compounds capable of transient covalent binding to thiols. The mechanistic basis for this unusual "pulsed reactivity" profile and the mode of its biological translation are unknown. To provide clues on these issues, a series of Δ 1 -dehydrooleanolates bearing an electron-withdrawing group at C-2 (7a-m) were prepared from oleanolic acid (3a) and comparatively investigated in terms of reactivity with thiols and bioactivity against a series of electrophile-sensitive transcription factors (Nrf2, NF-κB, STAT3). The emerging picture suggests that the triterpenoid scaffold sharply decreases the reactivity of the enone system by steric encumbrance and that only strongly electrophilic and sterically undemanding substituents such as a cyanide or a carboxylate group can re-establish Michael reactivity, albeit in a transient way for the cyanide group. In general, a substantial dissection between the thiol-trapping ability and the modulation of biological end-points sensitive to thiol alkylation was observed, highlighting the role of shape complementarity for the activity of triterpenoid thia-Michael acceptors.

F2Dock: Fast Fourier Protein-Protein Docking

PubMed Central

Bajaj, Chandrajit; Chowdhury, Rezaul; Siddavanahalli, Vinay

2009-01-01

The functions of proteins is often realized through their mutual interactions. Determining a relative transformation for a pair of proteins and their conformations which form a stable complex, reproducible in nature, is known as docking. It is an important step in drug design, structure determination and understanding function and structure relationships. In this paper we extend our non-uniform fast Fourier transform docking algorithm to include an adaptive search phase (both translational and rotational) and thereby speed up its execution. We have also implemented a multithreaded version of the adaptive docking algorithm for even faster execution on multicore machines. We call this protein-protein docking code F2Dock (F2 = Fast Fourier). We have calibrated F2Dock based on an extensive experimental study on a list of benchmark complexes and conclude that F2Dock works very well in practice. Though all docking results reported in this paper use shape complementarity and Coulombic potential based scores only, F2Dock is structured to incorporate Lennard-Jones potential and re-ranking docking solutions based on desolvation energy. PMID:21071796

Crystal structure of the human natural killer cell inhibitory receptor KIR2DL1-HLA-Cw4 complex.

PubMed

Fan, Q R; Long, E O; Wiley, D C

2001-05-01

Inhibitory natural killer (NK) cell receptors down-regulate the cytotoxicity of NK cells upon recognition of specific class I major histocompatibility complex (MHC) molecules on target cells. We report here the crystal structure of the inhibitory human killer cell immunoglobulin-like receptor 2DL1 (KIR2DL1) bound to its class I MHC ligand, HLA-Cw4. The KIR2DL1-HLA-Cw4 interface exhibits charge and shape complementarity. Specificity is mediated by a pocket in KIR2DL1 that hosts the Lys80 residue of HLA-Cw4. Many residues conserved in HLA-C and in KIR2DL receptors make different interactions in KIR2DL1-HLA-Cw4 and in a previously reported KIR2DL2-HLA-Cw3 complex. A dimeric aggregate of KIR-HLA-C complexes was observed in one KIR2DL1-HLA-Cw4 crystal. Most of the amino acids that differ between human and chimpanzee KIRs with HLA-C specificities form solvent-accessible clusters outside the KIR-HLA interface, which suggests undiscovered interactions by KIRs.

Structural basis of toxicity and immunity in contact-dependent growth inhibition (CDI) systems.

PubMed

Morse, Robert P; Nikolakakis, Kiel C; Willett, Julia L E; Gerrick, Elias; Low, David A; Hayes, Christopher S; Goulding, Celia W

2012-12-26

Contact-dependent growth inhibition (CDI) systems encode polymorphic toxin/immunity proteins that mediate competition between neighboring bacterial cells. We present crystal structures of CDI toxin/immunity complexes from Escherichia coli EC869 and Burkholderia pseudomallei 1026b. Despite sharing little sequence identity, the toxin domains are structurally similar and have homology to endonucleases. The EC869 toxin is a Zn(2+)-dependent DNase capable of completely degrading the genomes of target cells, whereas the Bp1026b toxin cleaves the aminoacyl acceptor stems of tRNA molecules. Each immunity protein binds and inactivates its cognate toxin in a unique manner. The EC869 toxin/immunity complex is stabilized through an unusual β-augmentation interaction. In contrast, the Bp1026b immunity protein exploits shape and charge complementarity to occlude the toxin active site. These structures represent the initial glimpse into the CDI toxin/immunity network, illustrating how sequence-diverse toxins adopt convergent folds yet retain distinct binding interactions with cognate immunity proteins. Moreover, we present visual demonstration of CDI toxin delivery into a target cell.

Selective binding of choline by a phosphate-coordination-based triple helicate featuring an aromatic box.

PubMed

Jia, Chuandong; Zuo, Wei; Yang, Dong; Chen, Yanming; Cao, Liping; Custelcean, Radu; Hostaš, Jiří; Hobza, Pavel; Glaser, Robert; Wang, Yao-Yu; Yang, Xiao-Juan; Wu, Biao

2017-10-16

In nature, proteins have evolved sophisticated cavities tailored for capturing target guests selectively among competitors of similar size, shape, and charge. The fundamental principles guiding the molecular recognition, such as self-assembly and complementarity, have inspired the development of biomimetic receptors. In the current work, we report a self-assembled triple anion helicate (host 2) featuring a cavity resembling that of the choline-binding protein ChoX, as revealed by crystal and density functional theory (DFT)-optimized structures, which binds choline in a unique dual-site-binding mode. This similarity in structure leads to a similarly high selectivity of host 2 for choline over its derivatives, as demonstrated by the NMR and fluorescence competition experiments. Furthermore, host 2 is able to act as a fluorescence displacement sensor for discriminating choline, acetylcholine, L-carnitine, and glycine betaine effectively.The choline-binding protein ChoX exhibits a synergistic dual-site binding mode that allows it to discriminate choline over structural analogues. Here, the authors design a biomimetic triple anion helicate receptor whose selectivity for choline arises from a similar binding mechanism.

Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism

DOE PAGES

Ren, Aiming; Rajashankar, Kanagalaghatta R.; Patel, Dinshaw J.

2015-06-25

ZTP, the pyrophosphorylated analog of ZMP (5- amino-4-imidazole carboxamide ribose-5'-monophosphate), was identified as an alarmone that senses 10-formyl-tetrahydroflate deficiency in bacteria. Recently, a pfl riboswitch was identified that selectively binds ZMP and regulates genes associated with purine biosynthesis and one-carbon metabolism. Here we report on the structure of the ZMP-bound Thermosinus carboxydivorans pfl riboswitch sensing domain, thereby defining the pseudoknot-based tertiary RNA fold, the binding-pocket architecture, and principles underlying ligand recognition specificity. Molecular recognition involves shape complementarity, with the ZMP 5-amino and carboxamide groups paired with the Watson-Crick edge of an invariant uracil, and the imidazole ring sandwiched between guanines,more » while the sugar hydroxyls form intermolecular hydrogen bond contacts. The burial of the ZMP base and ribose moieties, together with unanticipated coordination of the carboxamide by Mg 2+, contrasts with exposure of the 5'-phosphate to solvent. Lastly, our studies highlight the principles underlying RNA-based recognition of ZMP, a master regulator of one-carbon metabolism.« less

Quantum jump from singularity to outside of black hole

NASA Astrophysics Data System (ADS)

Dündar, Furkan Semih; Hajian, Kamal

2016-02-01

Considering the role of black hole singularity in quantum evolution, a resolution to the firewall paradox is presented. It is emphasized that if an observer has the singularity as a part of his spacetime, then the semi-classical evolution would be non-unitary as viewed by him. Specifically, a free-falling observer inside the black hole would have a Hilbert space with non-unitary evolution; a quantum jump for particles encountering the singularity to outside of the horizon as late Hawking radiations. The non-unitarity in the jump resembles the one in collapse of wave function, but preserves entanglements. Accordingly, we elaborate the first postulate of black hole complementarity: freely falling observers who pass through the event horizon would have non-unitary evolution, while it does not have physically measurable effects for them. Besides, no information would be lost in the singularity. Taking the modified picture into account, the firewall paradox can be resolved, respecting No Drama. A by-product of our modification is that roughly half of the entropy of the black hole is released close to the end of evaporation in the shape of very hot Hawking radiation.

The Crystal Structure of Coxsackievirus A21 and Its Interaction with ICAM-1

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

Xiao, Chuan; Bator-Kelly, Carol M.; Rieder, Elizabeth

2010-11-30

CVA21 and polioviruses both belong to the Enterovirus genus in the family of Picornaviridae, whereas rhinoviruses form a distinct picornavirus genus. Nevertheless, CVA21 and the major group of human rhinoviruses recognize intercellular adhesion molecule-1 (ICAM-1) as their cellular receptor, whereas polioviruses use poliovirus receptor. The crystal structure of CVA21 has been determined to 3.2 {angstrom} resolution. Its structure has greater similarity to poliovirus structures than to other known picornavirus structures. Cryo-electron microscopy (cryo-EM) was used to determine an 8.0 {angstrom} resolution structure of CVA21 complexed with an ICAM-1 variant, ICAM-1{sup Kilifi}. The cryo-EM map was fitted with the crystal structuresmore » of ICAM-1 and CVA21. Significant differences in the structure of CVA21 with respect to the poliovirus structures account for the inability of ICAM-1 to bind polioviruses. The interface between CVA21 and ICAM-1 has shape and electrostatic complementarity with many residues being conserved among those CVAs that bind ICAM-1.« less

Global RNA Fold and Molecular Recognition for a pfl Riboswitch Bound to ZMP, a Master Regulator of One-Carbon Metabolism

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

Ren, Aiming; Rajashankar, Kanagalaghatta R.; Patel, Dinshaw J.

ZTP, the pyrophosphorylated analog of ZMP (5- amino-4-imidazole carboxamide ribose-5'-monophosphate), was identified as an alarmone that senses 10-formyl-tetrahydroflate deficiency in bacteria. Recently, a pfl riboswitch was identified that selectively binds ZMP and regulates genes associated with purine biosynthesis and one-carbon metabolism. Here we report on the structure of the ZMP-bound Thermosinus carboxydivorans pfl riboswitch sensing domain, thereby defining the pseudoknot-based tertiary RNA fold, the binding-pocket architecture, and principles underlying ligand recognition specificity. Molecular recognition involves shape complementarity, with the ZMP 5-amino and carboxamide groups paired with the Watson-Crick edge of an invariant uracil, and the imidazole ring sandwiched between guanines,more » while the sugar hydroxyls form intermolecular hydrogen bond contacts. The burial of the ZMP base and ribose moieties, together with unanticipated coordination of the carboxamide by Mg 2+, contrasts with exposure of the 5'-phosphate to solvent. Lastly, our studies highlight the principles underlying RNA-based recognition of ZMP, a master regulator of one-carbon metabolism.« less

Novel endohedral derivatives of Sc3N C2n (n = 34, 40) and unique tether controlled bis-functionalization of fullerenes

NASA Astrophysics Data System (ADS)

Ceron Hernandez, Maira Raquel

Since the discovery of fullerenes in 1985, their exohedral functionalization has been necessary to increase their solubility and explore their properties and potential applications in materials science and medicinal chemistry. This thesis provides a short overview of the importance of electronic, size and shape complementarity in determining the structures of specific endohedral fullerene compounds. This is followed by a description of a new method for the separation of scandium nitride endohedral fullerenes Sc3N C2n (n = 34, 39 and 40), and their monofunctionalization. We also present the regioselective synthesis of easily isolable bis-derivatives of C60, C70, and M3N Ih-C80 (M = Sc, Lu) using 1,3-dipolar, addition/elimination (Bingel reaction) and diazo cycloadditions. The following sections are composed of a brief introduction and a pre-peer reviewed version of the published article, each section follows its own nomenclature and numerical order. The experimental section in each section includes methods, synthesis and characterization of the most relevant compounds.

Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code.

PubMed

Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

2016-01-21

Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNA(Lys)(UUU) with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm(5)s(2)U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.

Novel base-pairing interactions at the tRNA wobble position crucial for accurate reading of the genetic code

NASA Astrophysics Data System (ADS)

Rozov, Alexey; Demeshkina, Natalia; Khusainov, Iskander; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

2016-01-01

Posttranscriptional modifications at the wobble position of transfer RNAs play a substantial role in deciphering the degenerate genetic code on the ribosome. The number and variety of modifications suggest different mechanisms of action during messenger RNA decoding, of which only a few were described so far. Here, on the basis of several 70S ribosome complex X-ray structures, we demonstrate how Escherichia coli tRNALysUUU with hypermodified 5-methylaminomethyl-2-thiouridine (mnm5s2U) at the wobble position discriminates between cognate codons AAA and AAG, and near-cognate stop codon UAA or isoleucine codon AUA, with which it forms pyrimidine-pyrimidine mismatches. We show that mnm5s2U forms an unusual pair with guanosine at the wobble position that expands general knowledge on the degeneracy of the genetic code and specifies a powerful role of tRNA modifications in translation. Our models consolidate the translational fidelity mechanism proposed previously where the steric complementarity and shape acceptance dominate the decoding mechanism.

Working Group Report: Dark Matter Complementarity (Dark Matter in the Coming Decade: Complementary Paths to Discovery and Beyond)

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

Arrenberg, Sebastian; et al.,

2013-10-31

In this Report we discuss the four complementary searches for the identity of dark matter: direct detection experiments that look for dark matter interacting in the lab, indirect detection experiments that connect lab signals to dark matter in our own and other galaxies, collider experiments that elucidate the particle properties of dark matter, and astrophysical probes sensitive to non-gravitational interactions of dark matter. The complementarity among the different dark matter searches is discussed qualitatively and illustrated quantitatively in several theoretical scenarios. Our primary conclusion is that the diversity of possible dark matter candidates requires a balanced program based on allmore » four of those approaches.« less

Insights to primitive replication derived from structures of small oligonucleotides

NASA Technical Reports Server (NTRS)

Smith, G. K.; Fox, G. E.

1995-01-01

Available information on the structure of small oligonucleotides is surveyed. It is observed that even small oligomers typically exhibit defined structures over a wide range of pH and temperature. These structures rely on a plethora of non-standard base-base interactions in addition to the traditional Watson-Crick pairings. Stable duplexes, though typically antiparallel, can be parallel or staggered and perfect complementarity is not essential. These results imply that primitive template directed reactions do not require high fidelity. Hence, the extensive use of Watson-Crick complementarity in genes rather than being a direct consequence of the primitive condensation process, may instead reflect subsequent selection based on the advantage of accuracy in maintaining the primitive genetic machinery once it arose.

Quantification of surface tension and internal pressure generated by single mitotic cells

NASA Astrophysics Data System (ADS)

Fischer-Friedrich, Elisabeth; Hyman, Anthony A.; Jülicher, Frank; Müller, Daniel J.; Helenius, Jonne

2014-08-01

During mitosis, adherent cells round up, by increasing the tension of the contractile actomyosin cortex while increasing the internal hydrostatic pressure. In the simple scenario of a liquid cell interior, the surface tension is related to the local curvature and the hydrostatic pressure difference by Laplace's law. However, verification of this scenario for cells requires accurate measurements of cell shape. Here, we use wedged micro-cantilevers to uniaxially confine single cells and determine confinement forces while concurrently determining cell shape using confocal microscopy. We fit experimentally measured confined cell shapes to shapes obeying Laplace's law with uniform surface tension and find quantitative agreement. Geometrical parameters derived from fitting the cell shape, and the measured force were used to calculate hydrostatic pressure excess and surface tension of cells. We find that HeLa cells increase their internal hydrostatic pressure excess and surface tension from ~ 40 Pa and 0.2 mNm-1 during interphase to ~ 400 Pa and 1.6 mNm-1 during metaphase. The method introduced provides a means to determine internal pressure excess and surface tension of rounded cells accurately and with minimal cellular perturbation, and should be applicable to characterize the mechanical properties of various cellular systems.

Variable-Domain Displacement Transfer Functions for Converting Surface Strains into Deflections for Structural Deformed Shape Predictions

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2015-01-01

Variable-Domain Displacement Transfer Functions were formulated for shape predictions of complex wing structures, for which surface strain-sensing stations must be properly distributed to avoid jointed junctures, and must be increased in the high strain gradient region. Each embedded beam (depth-wise cross section of structure along a surface strain-sensing line) was discretized into small variable domains. Thus, the surface strain distribution can be described with a piecewise linear or a piecewise nonlinear function. Through discretization, the embedded beam curvature equation can be piece-wisely integrated to obtain the Variable-Domain Displacement Transfer Functions (for each embedded beam), which are expressed in terms of geometrical parameters of the embedded beam and the surface strains along the strain-sensing line. By inputting the surface strain data into the Displacement Transfer Functions, slopes and deflections along each embedded beam can be calculated for mapping out overall structural deformed shapes. A long tapered cantilever tubular beam was chosen for shape prediction analysis. The input surface strains were analytically generated from finite-element analysis. The shape prediction accuracies of the Variable- Domain Displacement Transfer Functions were then determined in light of the finite-element generated slopes and deflections, and were fofound to be comparable to the accuracies of the constant-domain Displacement Transfer Functions

Changes in complementarity-determining regions significantly alter IgG binding to the neonatal Fc receptor (FcRn) and pharmacokinetics

PubMed Central

King, Amy C.; Kavosi, Mania; Wang, Mengmeng; O'Hara, Denise M.; Tchistiakova, Lioudmila; Katragadda, Madan

2018-01-01

ABSTRACT A large body of data exists demonstrating that neonatal Fc receptor (FcRn) binding of an IgG via its Fc CH2-CH3 interface trends with the pharmacokinetics (PK) of IgG. We have observed that PK of IgG molecules vary widely, even when they share identical Fc domains. This led us to hypothesize that domains distal from the Fc could contribute to FcRn binding and affect PK. In this study, we explored the role of these IgG domains in altering the affinity between IgG and FcRn. Using a surface plasmon resonance-based assay developed to examine the steady-state binding affinity (KD) of IgG molecules to FcRn, we dissected the contributions of IgG domains in modulating the affinity between FcRn and IgG. Through analysis of a broad collection of therapeutic antibodies containing more than 50 unique IgG molecules, we demonstrated that variable domains, and in particular complementarity-determining regions (CDRs), significantly alter binding affinity to FcRn in vitro. Furthermore, a panel of IgG molecules differing only by 1–5 mutations in CDRs altered binding affinity to FcRn in vitro, by up to 79-fold, and the affinity values correlated with calculated isoelectric point values of both variable domains and CDR-L3. In addition, tighter affinity values trend with faster in vivo clearance of a set of IgG molecules differing only by 1–3 mutations in human FcRn transgenic mice. Understanding the role of CDRs in modulation of IgG affinity to FcRn in vitro and their effect on PK of IgG may have far-reaching implications in the optimization of IgG therapeutics. PMID:28991504

The role of nanopore shape in surface-induced crystallization

NASA Astrophysics Data System (ADS)

Diao, Ying; Harada, Takuya; Myerson, Allan S.; Alan Hatton, T.; Trout, Bernhardt L.

2011-11-01

Crystallization of a molecular liquid from solution often initiates at solid-liquid interfaces, and nucleation rates are generally believed to be enhanced by surface roughness. Here we show that, on a rough surface, the shape of surface nanopores can also alter nucleation kinetics. Using lithographic methods, we patterned polymer films with nanopores of various shapes and found that spherical nanopores 15-120 nm in diameter hindered nucleation of aspirin crystals, whereas angular nanopores of the same size promoted it. We also show that favourable surface-solute interactions are required for angular nanopores to promote nucleation, and propose that pore shape affects nucleation kinetics through the alteration of the orientational order of the crystallizing molecule near the angles of the pores. Our findings have clear technological implications, for instance in the control of pharmaceutical polymorphism and in the design of ‘seed’ particles for the regulation of crystallization of fine chemicals.

Influence of boundary conditions on the existence and stability of minimal surfaces of revolution made of soap films

NASA Astrophysics Data System (ADS)

Salkin, Louis; Schmit, Alexandre; Panizza, Pascal; Courbin, Laurent

2014-09-01

Because of surface tension, soap films seek the shape that minimizes their surface energy and thus their surface area. This mathematical postulate allows one to predict the existence and stability of simple minimal surfaces. After briefly recalling classical results obtained in the case of symmetric catenoids that span two circular rings with the same radius, we discuss the role of boundary conditions on such shapes, working with two rings having different radii. We then investigate the conditions of existence and stability of other shapes that include two portions of catenoids connected by a planar soap film and half-symmetric catenoids for which we introduce a method of observation. We report a variety of experimental results including metastability—an hysteretic evolution of the shape taken by a soap film—explained using simple physical arguments. Working by analogy with the theory of phase transitions, we conclude by discussing universal behaviors of the studied minimal surfaces in the vicinity of their existence thresholds.

Fabrication of high quality aspheric microlens array by dose-modulated lithography and surface thermal reflow

NASA Astrophysics Data System (ADS)

Huang, Shengzhou; Li, Mujun; Shen, Lianguan; Qiu, Jinfeng; Zhou, Youquan

2018-03-01

A novel fabrication method for high quality aspheric microlens array (MLA) was developed by combining the dose-modulated DMD-based lithography and surface thermal reflow process. In this method, the complex shape of aspheric microlens is pre-modeled via dose modulation in a digital micromirror device (DMD) based maskless projection lithography. And the dose modulation mainly depends on the distribution of exposure dose of photoresist. Then the pre-shaped aspheric microlens is polished by a following non-contact thermal reflow (NCTR) process. Different from the normal process, the reflow process here is investigated to improve the surface quality while keeping the pre-modeled shape unchanged, and thus will avoid the difficulties in generating the aspheric surface during reflow. Fabrication of a designed aspheric MLA with this method was demonstrated in experiments. Results showed that the obtained aspheric MLA was good in both shape accuracy and surface quality. The presented method may be a promising approach in rapidly fabricating high quality aspheric microlens with complex surface.

Programmable thermal emissivity structures based on bioinspired self-shape materials

NASA Astrophysics Data System (ADS)

Athanasopoulos, N.; Siakavellas, N. J.

2015-12-01

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

Programmable thermal emissivity structures based on bioinspired self-shape materials

PubMed Central

Athanasopoulos, N.; Siakavellas, N. J.

2015-01-01

Programmable thermal emissivity structures based on the bioinspired self-shape anisotropic materials were developed at macro-scale, and further studied theoretically at smaller scale. We study a novel concept, incorporating materials that are capable of transforming their shape via microstructural rearrangements under temperature stimuli, while avoiding the use of exotic shape memory materials or complex micro-mechanisms. Thus, programmed thermal emissivity behaviour of a surface is achievable. The self-shape structure reacts according to the temperature of the surrounding environment or the radiative heat flux. A surface which incorporates self-shape structures can be designed to quickly absorb radiative heat energy at low temperature levels, but is simultaneously capable of passively controlling its maximum temperature in order to prevent overheating. It resembles a “game” of colours, where two or more materials coexist with different values of thermal emissivity/ absorptivity/ reflectivity. The transformation of the structure conceals or reveals one of the materials, creating a surface with programmable – and therefore, variable- effective thermal emissivity. Variable thermal emissivity surfaces may be developed with a total hemispherical emissivity ratio (εEff_H/εEff_L) equal to 28. PMID:26635316

Developmental prosopagnosia and super-recognition: no special role for surface reflectance processing

PubMed Central

Russell, Richard; Chatterjee, Garga; Nakayama, Ken

2011-01-01

Face recognition by normal subjects depends in roughly equal proportions on shape and surface reflectance cues, while object recognition depends predominantly on shape cues. It is possible that developmental prosopagnosics are deficient not in their ability to recognize faces per se, but rather in their ability to use reflectance cues. Similarly, super-recognizers’ exceptional ability with face recognition may be a result of superior surface reflectance perception and memory. We tested this possibility by administering tests of face perception and face recognition in which only shape or reflectance cues are available to developmental prosopagnosics, super-recognizers, and control subjects. Face recognition ability and the relative use of shape and pigmentation were unrelated in all the tests. Subjects who were better at using shape or reflectance cues were also better at using the other type of cue. These results do not support the proposal that variation in surface reflectance perception ability is the underlying cause of variation in face recognition ability. Instead, these findings support the idea that face recognition ability is related to neural circuits using representations that integrate shape and pigmentation information. PMID:22192636

Shape-Controllable Gold Nanoparticle-MoS2 Hybrids Prepared by Tuning Edge-Active Sites and Surface Structures of MoS2 via Temporally Shaped Femtosecond Pulses.

PubMed

Zuo, Pei; Jiang, Lan; Li, Xin; Li, Bo; Xu, Yongda; Shi, Xuesong; Ran, Peng; Ma, Tianbao; Li, Dawei; Qu, Liangti; Lu, Yongfeng; Grigoropoulos, Costas P

2017-03-01

Edge-active site control of MoS 2 is crucial for applications such as chemical catalysis, synthesis of functional composites, and biochemical sensing. This work presents a novel nonthermal method to simultaneously tune surface chemical (edge-active sites) and physical (surface periodic micro/nano structures) properties of MoS 2 using temporally shaped femtosecond pulses, through which shape-controlled gold nanoparticles are in situ and self-assembly grown on MoS 2 surfaces to form Au-MoS 2 hybrids. The edge-active sites with unbound sulfurs of laser-treated MoS 2 drive the reduction of gold nanoparticles, while the surface periodic structures of laser-treated MoS 2 assist the shape-controllable growth of gold nanoparticles. The proposed novel method highlights the broad application potential of MoS 2 ; for example, these Au-MoS 2 hybrids exhibit tunable and highly sensitive SERS activity with an enhancement factor up to 1.2 × 10 7 , indicating the marked potential of MoS 2 in future chemical and biological sensing applications.

Effect of shape and size of lung and chest wall on stresses in the lung

NASA Technical Reports Server (NTRS)

Vawter, D. L.; Matthews, F. L.; West, J. B.

1975-01-01

To understand better the effect of shape and size of lung and chest wall on the distribution of stresses, strains, and surface pressures, we analyzed a theoretical model using the technique of finite elements. First we investigated the effects of changing the chest wall shape during expansion, and second we studied lungs of a variety of inherent shapes and sizes. We found that, in general, the distributions of alveolar size, mechanical stresses, and surface pressures in the lungs were dominated by the weight of the lung and that changing the shape of the lung or chest wall had relatively little effect. Only at high states of expansion where the lung was very stiff did changing the shape of the chest wall cause substantial changes. Altering the inherent shape of the lung generally had little effect but the topographical differences in stresses and surface pressures were approximately proportional to lung height. The results are generally consistent with those found in the dog by Hoppin et al (1969).

Shaping of parabolic cylindrical membrane reflectors for the Dart Precision Test Bed

NASA Technical Reports Server (NTRS)

Morgan, R.; Agnes, Gregory S.; Dragovan, M.; Barber, D.; Marcin, M.; White, C.; Dooley, J.; Hatheway, A.

2004-01-01

The DART is a new telescope architecture consisting of a single aperture formed from two cylindrical parabolic reflectors. The system is ideally suited to using tensioned membranes for the reflective surfaces, owing to the zero Gaussian curvature of a cylindrical parabola. In this paper, we present experimental measurements for shaping the membranes by using curved boundary elements to achieve coarse shaping, and a pair of precision rails shaped by moments and forces at the ends, and lightly pushed into the surface, to provide fine shape control.

A hypothetical complex between crystalline flavocytochrome b2 and cytochrome c.

PubMed

Tegoni, M; White, S A; Roussel, A; Mathews, F S; Cambillau, C

1993-08-01

Flavocytochrome b2 and cytochrome c are physiological electron transfer partners in yeast mitochondria. The formation of a stable complex between them has been demonstrated both in solution and in the crystalline state. On the basis of the three-dimensional structures, using molecular modeling and energy minimization, we have generated a hypothetical model for the interaction of these redox partners in the crystal lattice. General criteria such as good charge and surface complementarity, plausible orientation, and separation distance of the prosthetic groups, as well as more specific criteria such as the stoichiometry determined in the crystal, and the involvement of both domains and of more than one subunit of flavocytochrome b2 led us to discriminate between several possible interaction sites. In the hypothetical model we present, four cytochrome c molecules interact with a tetramer of flavocytochrome b2. The b2 and c hemes are coplanar, with an edge-to-edge distance of 14 A. The contact surface area is ca. 800 A2. Several electrostatic interactions involving the flavin and the heme domains of flavocytochrome b2 stabilize the binding of cytochrome c.

Structural basis for the specific recognition of IL-18 by its alpha receptor.

PubMed

Wei, Hui; Wang, Dongli; Qian, Yun; Liu, Xi; Fan, Shilong; Yin, Hsien-Sheng; Wang, Xinquan

2014-11-03

Interleukin 18 (IL-18), a member of the IL-1 family of cytokines, is an important regulator of innate and acquired immune responses. It signals through its ligand-binding primary receptor IL-18Rα and accessory receptor IL-18Rβ. Here we report the crystal structure of IL-18 with the ectodomain of IL-18Rα, which reveals the structural basis for their specific recognition. It confirms that surface charge complementarity determines the ligand-binding specificity of primary receptors in the IL-1 receptor family. We suggest that IL-18 signaling complex adopts an architecture similar to other agonistic cytokines and propose a general ligand-receptor assembly and activation model for the IL-1 family. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Improved Displacement Transfer Functions for Structure Deformed Shape Predictions Using Discretely Distributed Surface Strains

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2012-01-01

In the formulations of earlier Displacement Transfer Functions for structure shape predictions, the surface strain distributions, along a strain-sensing line, were represented with piecewise linear functions. To improve the shape-prediction accuracies, Improved Displacement Transfer Functions were formulated using piecewise nonlinear strain representations. Through discretization of an embedded beam (depth-wise cross section of a structure along a strain-sensing line) into multiple small domains, piecewise nonlinear functions were used to describe the surface strain distributions along the discretized embedded beam. Such piecewise approach enabled the piecewise integrations of the embedded beam curvature equations to yield slope and deflection equations in recursive forms. The resulting Improved Displacement Transfer Functions, written in summation forms, were expressed in terms of beam geometrical parameters and surface strains along the strain-sensing line. By feeding the surface strains into the Improved Displacement Transfer Functions, structural deflections could be calculated at multiple points for mapping out the overall structural deformed shapes for visual display. The shape-prediction accuracies of the Improved Displacement Transfer Functions were then examined in view of finite-element-calculated deflections using different tapered cantilever tubular beams. It was found that by using the piecewise nonlinear strain representations, the shape-prediction accuracies could be greatly improved, especially for highly-tapered cantilever tubular beams.

Shape-driven 3D segmentation using spherical wavelets.

PubMed

Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, Allen

2006-01-01

This paper presents a novel active surface segmentation algorithm using a multiscale shape representation and prior. We define a parametric model of a surface using spherical wavelet functions and learn a prior probability distribution over the wavelet coefficients to model shape variations at different scales and spatial locations in a training set. Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior in the segmentation framework. Additionally, the optimization method can be applied in a coarse-to-fine manner. We apply our algorithm to the segmentation of brain caudate nucleus, of interest in the study of schizophrenia. Our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model algorithm by capturing finer shape details.

Finite element solution of low bond number sloshing

NASA Technical Reports Server (NTRS)

Wohlen, R. L.; Park, A. C.; Warner, D. M.

1975-01-01

The dynamics of liquid propellant in a low Bond number environment which are critical to the design of spacecraft systems with respect to orbital propellant transfer and attitude control system were investigated. Digital computer programs were developed for the determination of liquid free surface equilibrium shape, lateral slosh natural vibration mode shapes, and frequencies for a liquid in a container of arbitrary axisymmetric shape with surface tension forces the same order of magnitude as acceleration forces. A finite volume element representation of the liquid was used for the vibration analysis. The liquid free surface equilibrium shapes were computed for several tanks at various contact angles and ullage volumes. A configuration was selected for vibration analysis and lateral slosh mode shapes and natural frequencies were obtained. Results are documented.

The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks

PubMed Central

Patil, Ashwini; Nakamura, Haruki

2007-01-01

Hubs are highly connected proteins in a protein-protein interaction network. Previous work has implicated disordered domains and high surface charge as the properties significant in the ability of hubs to bind multiple proteins. While conformational flexibility of disordered domains plays an important role in the binding ability of large hubs, high surface charge is the dominant property in small hubs. In this study, we further investigate the role of the high surface charge in the binding ability of small hubs in the absence of disordered domains. Using multipole expansion, we find that the charges are highly distributed over the hub surfaces. Residue enrichment studies show that the charged residues in hubs are more prevalent on the exposed surface, with the exception of Arg, which is predominantly found at the interface, as compared to non-hubs. This suggests that the charged residues act primarily from the exposed surface rather than the interface to affect the binding ability of small hubs. They do this through (i) enhanced intra-molecular electrostatic interactions to lower the desolvation penalty, (ii) indirect long – range intermolecular interactions with charged residues on the partner proteins for better complementarity and electrostatic steering, and (iii) increased solubility for enhanced diffusion-controlled rate of binding. Along with Arg, we also find a high prevalence of polar residues Tyr, Gln and His and the hydrophobic residue Met at the interfaces of hubs, all of which have the ability to form multiple types of interactions, indicating that the interfaces of hubs are optimized to participate in multiple interactions. PMID:27857564

The role of charged surface residues in the binding ability of small hubs in protein-protein interaction networks.

PubMed

Patil, Ashwini; Nakamura, Haruki

2007-01-01

Hubs are highly connected proteins in a protein-protein interaction network. Previous work has implicated disordered domains and high surface charge as the properties significant in the ability of hubs to bind multiple proteins. While conformational flexibility of disordered domains plays an important role in the binding ability of large hubs, high surface charge is the dominant property in small hubs. In this study, we further investigate the role of the high surface charge in the binding ability of small hubs in the absence of disordered domains. Using multipole expansion, we find that the charges are highly distributed over the hub surfaces. Residue enrichment studies show that the charged residues in hubs are more prevalent on the exposed surface, with the exception of Arg, which is predominantly found at the interface, as compared to non-hubs. This suggests that the charged residues act primarily from the exposed surface rather than the interface to affect the binding ability of small hubs. They do this through (i) enhanced intra-molecular electrostatic interactions to lower the desolvation penalty, (ii) indirect long - range intermolecular interactions with charged residues on the partner proteins for better complementarity and electrostatic steering, and (iii) increased solubility for enhanced diffusion-controlled rate of binding. Along with Arg, we also find a high prevalence of polar residues Tyr, Gln and His and the hydrophobic residue Met at the interfaces of hubs, all of which have the ability to form multiple types of interactions, indicating that the interfaces of hubs are optimized to participate in multiple interactions.

Impact of cell shape in hierarchically structured plant surfaces on the attachment of male Colorado potato beetles (Leptinotarsa decemlineata)

PubMed Central

Seidel, Robin; Bohn, Holger Florian; Speck, Thomas

2012-01-01

Summary Plant surfaces showing hierarchical structuring are frequently found in plant organs such as leaves, petals, fruits and stems. In our study we focus on the level of cell shape and on the level of superimposed microstructuring, leading to hierarchical surfaces if both levels are present. While it has been shown that epicuticular wax crystals and cuticular folds strongly reduce insect attachment, and that smooth papillate epidermal cells in petals improve the grip of pollinators, the impact of hierarchical surface structuring of plant surfaces possessing convex or papillate cells on insect attachment remains unclear. We performed traction experiments with male Colorado potato beetles on nine different plant surfaces with different structures. The selected plant surfaces showed epidermal cells with either tabular, convex or papillate cell shape, covered either with flat films of wax, epicuticular wax crystals or with cuticular folds. On surfaces possessing either superimposed wax crystals or cuticular folds we found traction forces to be almost one order of magnitude lower than on surfaces covered only with flat films of wax. Independent of superimposed microstructures we found that convex and papillate epidermal cell shapes slightly enhance the attachment ability of the beetles. Thus, in plant surfaces, cell shape and superimposed microstructuring yield contrary effects on the attachment of the Colorado potato beetle, with convex or papillate cells enhancing attachment and both wax crystals or cuticular folds reducing attachment. However, the overall magnitude of traction force mainly depends on the presence or absence of superimposed microstructuring. PMID:22428097

Statistical Analyses of Brain Surfaces Using Gaussian Random Fields on 2-D Manifolds

PubMed Central

Staib, Lawrence H.; Xu, Dongrong; Zhu, Hongtu; Peterson, Bradley S.

2008-01-01

Interest in the morphometric analysis of the brain and its subregions has recently intensified because growth or degeneration of the brain in health or illness affects not only the volume but also the shape of cortical and subcortical brain regions, and new image processing techniques permit detection of small and highly localized perturbations in shape or localized volume, with remarkable precision. An appropriate statistical representation of the shape of a brain region is essential, however, for detecting, localizing, and interpreting variability in its surface contour and for identifying differences in volume of the underlying tissue that produce that variability across individuals and groups of individuals. Our statistical representation of the shape of a brain region is defined by a reference region for that region and by a Gaussian random field (GRF) that is defined across the entire surface of the region. We first select a reference region from a set of segmented brain images of healthy individuals. The GRF is then estimated as the signed Euclidean distances between points on the surface of the reference region and the corresponding points on the corresponding region in images of brains that have been coregistered to the reference. Correspondences between points on these surfaces are defined through deformations of each region of a brain into the coordinate space of the reference region using the principles of fluid dynamics. The warped, coregistered region of each subject is then unwarped into its native space, simultaneously bringing into that space the map of corresponding points that was established when the surfaces of the subject and reference regions were tightly coregistered. The proposed statistical description of the shape of surface contours makes no assumptions, other than smoothness, about the shape of the region or its GRF. The description also allows for the detection and localization of statistically significant differences in the shapes of the surfaces across groups of subjects at both a fine and coarse scale. We demonstrate the effectiveness of these statistical methods by applying them to study differences in shape of the amygdala and hippocampus in a large sample of normal subjects and in subjects with attention deficit/hyperactivity disorder (ADHD). PMID:17243583

The Design of Case Products’ Shape Form Information Database Based on NURBS Surface

NASA Astrophysics Data System (ADS)

Liu, Xing; Liu, Guo-zhong; Xu, Nuo-qi; Zhang, Wei-she

2017-07-01

In order to improve the computer design of product shape design,applying the Non-uniform Rational B-splines(NURBS) of curves and surfaces surface to the representation of the product shape helps designers to design the product effectively.On the basis of the typical product image contour extraction and using Pro/Engineer(Pro/E) to extract the geometric feature of scanning mold,in order to structure the information data base system of value point,control point and node vector parameter information,this paper put forward a unified expression method of using NURBS curves and surfaces to describe products’ geometric shape and using matrix laboratory(MATLAB) to simulate when products have the same or similar function.A case study of electric vehicle’s front cover illustrates the access process of geometric shape information of case product in this paper.This method can not only greatly reduce the capacity of information debate,but also improve the effectiveness of computer aided geometric innovation modeling.

Assessment of the accuracy of plasma shape reconstruction by the Cauchy condition surface method in JT-60SA

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

Miyata, Y.; Suzuki, T.; Takechi, M.

2015-07-15

For the purpose of stable plasma equilibrium control and detailed analysis, it is essential to reconstruct an accurate plasma boundary on the poloidal cross section in tokamak devices. The Cauchy condition surface (CCS) method is a numerical approach for calculating the spatial distribution of the magnetic flux outside a hypothetical surface and reconstructing the plasma boundary from the magnetic measurements located outside the plasma. The accuracy of the plasma shape reconstruction has been assessed by comparing the CCS method and an equilibrium calculation in JT-60SA with a high elongation and triangularity of plasma shape. The CCS, on which both Dirichletmore » and Neumann conditions are unknown, is defined as a hypothetical surface located inside the real plasma region. The accuracy of the plasma shape reconstruction is sensitive to the CCS free parameters such as the number of unknown parameters and the shape in JT-60SA. It is found that the optimum number of unknown parameters and the size of the CCS that minimizes errors in the reconstructed plasma shape are in proportion to the plasma size. Furthermore, it is shown that the accuracy of the plasma shape reconstruction is greatly improved using the optimum number of unknown parameters and shape of the CCS, and the reachable reconstruction errors in plasma shape and locations of strike points are within the target ranges in JT-60SA.« less

Electromagnetic properties of material coated surfaces

NASA Technical Reports Server (NTRS)

Beard, L.; Berrie, J.; Burkholder, R.; Dominek, A.; Walton, E.; Wang, N.

1989-01-01

The electromagnetic properties of material coated conducting surfaces were investigated. The coating geometries consist of uniform layers over a planar surface, irregularly shaped formations near edges and randomly positioned, electrically small, irregularly shaped formations over a surface. Techniques to measure the scattered field and constitutive parameters from these geometries were studied. The significance of the scattered field from these geometries warrants further study.

Computation of stress on the surface of a soft homogeneous arbitrarily shaped particle.

PubMed

Yang, Minglin; Ren, Kuan Fang; Wu, Yueqian; Sheng, Xinqing

2014-04-01

Prediction of the stress on the surface of an arbitrarily shaped particle of soft material is essential in the study of elastic properties of the particles with optical force. It is also necessary in the manipulation and sorting of small particles with optical tweezers, since a regular-shaped particle, such as a sphere, may be deformed under the nonuniform optical stress on its surface. The stress profile on a spherical or small spheroidal soft particle trapped by shaped beams has been studied, however little work on computing the surface stress of an irregular-shaped particle has been reported. We apply in this paper the surface integral equation with multilevel fast multipole algorithm to compute the surface stress on soft homogeneous arbitrarily shaped particles. The comparison of the computed stress profile with that predicted by the generalized Lorenz-Mie theory for a water droplet of diameter equal to 51 wavelengths in a focused Gaussian beam show that the precision of our method is very good. Then stress profiles on spheroids with different aspect ratios are computed. The particles are illuminated by a Gaussian beam of different waist radius at different incidences. Physical analysis on the mechanism of optical stress is given with help of our recently developed vectorial complex ray model. It is found that the maximum of the stress profile on the surface of prolate spheroids is not only determined by the reflected and refracted rays (orders p=0,1) but also the rays undergoing one or two internal reflections where they focus. Computational study of stress on surface of a biconcave cell-like particle, which is a typical application in life science, is also undertaken.

Airfoil-shaped micro-mixers for reducing fouling on membrane surfaces

DOEpatents

Ho, Clifford K; Altman, Susan J; Clem, Paul G; Hibbs, Michael; Cook, Adam W

2012-10-23

An array of airfoil-shaped micro-mixers that enhances fluid mixing within permeable membrane channels, such as used in reverse-osmosis filtration units, while minimizing additional pressure drop. The enhanced mixing reduces fouling of the membrane surfaces. The airfoil-shaped micro-mixer can also be coated with or comprised of biofouling-resistant (biocidal/germicidal) ingredients.

Shape from Shading in Pigeons

ERIC Educational Resources Information Center

Cook, Robert G.; Qadri, Muhammad A. J.; Kieres, Art; Commons-Miller, Nicholas

2012-01-01

Light is the origin of vision. The pattern of shading reflected from object surfaces is one of several optical features that provide fundamental information about shape and surface orientation. To understand how surface and object shading is processed by birds, six pigeons were tested with differentially illuminated convex and concave curved…

Optical Estimation of the 3D Shape of a Solar Illuminated, Reflecting Satellite Surface

NASA Astrophysics Data System (ADS)

Antolin, J.; Yu, Z.; Prasad, S.

2016-09-01

The spatial distribution of the polarized component of the power reflected by a macroscopically smooth but microscopically roughened curved surface under highly directional illumination, as characterized by an appropriate bi-directional reflectance distribution function (BRDF), carries information about the three-dimensional (3D) shape of the surface. This information can be exploited to recover the surface shape locally under rather general conditions whenever power reflectance data for at least two different illumination or observation directions can be obtained. We present here two different parametric approaches for surface reconstruction, amounting to the recovery of the surface parameters that are either the global parameters of the family to which the surface is known a priori to belong or the coefficients of a low-order polynomial that can be employed to characterize a smoothly varying surface locally over the observed patch.

Substitution and Complementarity of Alcohol and Cannabis: A Review of the Literature.

PubMed

Subbaraman, Meenakshi Sabina

2016-09-18

Whether alcohol and cannabis are used as substitutes or complements remains debated, and findings across various disciplines have not been synthesized to date. This article is a first step towards organizing the interdisciplinary literature on alcohol and cannabis substitution and complementarity. Electronic searches were performed using PubMed and ISI Web of Knowledge. Behavioral studies of humans with "alcohol" (or "ethanol") and "cannabis" (or "marijuana") and "complement(*)" (or "substitut(*)") in the title or as a keyword were considered. Studies were organized according to sample characteristics (youth, general population, clinical and community-based). These groups were not set a priori, but were informed by the literature review process. Of the 39 studies reviewed, 16 support substitution, ten support complementarity, 12 support neither and one supports both. Results from studies of youth suggest that youth may reduce alcohol in more liberal cannabis environments (substitute), but reduce cannabis in more stringent alcohol environments (complement). Results from the general population suggest that substitution of cannabis for alcohol may occur under more lenient cannabis policies, though cannabis-related laws may affect alcohol use differently across genders and racial groups. Alcohol and cannabis act as both substitutes and complements. Policies aimed at one substance may inadvertently affect consumption of other substances. Future studies should collect fine-grained longitudinal, prospective data from the general population and subgroups of interest, especially in locations likely to legalize cannabis.

Separation of Atmospheric and Surface Spectral Features in Mars Global Surveyor Thermal Emission Spectrometer (TES) Spectra

NASA Technical Reports Server (NTRS)

Smith, Michael D.; Bandfield, Joshua L.; Christensen, Philip R.

2000-01-01

We present two algorithms for the separation of spectral features caused by atmospheric and surface components in Thermal Emission Spectrometer (TES) data. One algorithm uses radiative transfer and successive least squares fitting to find spectral shapes first for atmospheric dust, then for water-ice aerosols, and then, finally, for surface emissivity. A second independent algorithm uses a combination of factor analysis, target transformation, and deconvolution to simultaneously find dust, water ice, and surface emissivity spectral shapes. Both algorithms have been applied to TES spectra, and both find very similar atmospheric and surface spectral shapes. For TES spectra taken during aerobraking and science phasing periods in nadir-geometry these two algorithms give meaningful and usable surface emissivity spectra that can be used for mineralogical identification.

Modified Displacement Transfer Functions for Deformed Shape Predictions of Slender Curved Structures with Varying Curvatives

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2014-01-01

To eliminate the need to use finite-element modeling for structure shape predictions, a new method was invented. This method is to use the Displacement Transfer Functions to transform the measured surface strains into deflections for mapping out overall structural deformed shapes. The Displacement Transfer Functions are expressed in terms of rectilinearly distributed surface strains, and contain no material properties. This report is to apply the patented method to the shape predictions of non-symmetrically loaded slender curved structures with different curvatures up to a full circle. Because the measured surface strains are not available, finite-element analysis had to be used to analytically generate the surface strains. Previously formulated straight-beam Displacement Transfer Functions were modified by introducing the curvature-effect correction terms. Through single-point or dual-point collocations with finite-elementgenerated deflection curves, functional forms of the curvature-effect correction terms were empirically established. The resulting modified Displacement Transfer Functions can then provide quite accurate shape predictions. Also, the uniform straight-beam Displacement Transfer Function was applied to the shape predictions of a section-cut of a generic capsule (GC) outer curved sandwich wall. The resulting GC shape predictions are quite accurate in partial regions where the radius of curvature does not change sharply.

Role of nanoparticle size, shape and surface chemistry in oral drug delivery.

PubMed

Banerjee, Amrita; Qi, Jianping; Gogoi, Rohan; Wong, Jessica; Mitragotri, Samir

2016-09-28

Nanoparticles find intriguing applications in oral drug delivery since they present a large surface area for interactions with the gastrointestinal tract and can be modified in various ways to address the barriers associated with oral delivery. The size, shape and surface chemistry of nanoparticles can greatly impact cellular uptake and efficacy of the treatment. However, the interplay between particle size, shape and surface chemistry has not been well investigated especially for oral drug delivery. To this end, we prepared sphere-, rod- and disc-shaped nanoparticles and conjugated them with targeting ligands to study the influence of size, shape and surface chemistry on their uptake and transport across intestinal cells. A triple co-culture model of intestinal cells was utilized to more closely mimic the intestinal epithelium. Results demonstrated higher cellular uptake of rod-shaped nanoparticles in the co-culture compared to spheres regardless of the presence of active targeting moieties. Transport of nanorods across the intestinal co-culture was also significantly higher than spheres. The findings indicate that nanoparticle-mediated oral drug delivery can be potentially improved with departure from spherical shape which has been traditionally utilized for the design of nanoparticles. We believe that understanding the role of nanoparticle geometry in intestinal uptake and transport will bring forth a paradigm shift in nanoparticle engineering for oral delivery and non-spherical nanoparticles should be further investigated and considered for oral delivery of therapeutic drugs and diagnostic materials. Copyright © 2016 Elsevier B.V. All rights reserved.

Quantitative Outline-based Shape Analysis and Classification of Planetary Craterforms using Supervised Learning Models

NASA Astrophysics Data System (ADS)

Slezak, Thomas Joseph; Radebaugh, Jani; Christiansen, Eric

2017-10-01

The shapes of craterform morphology on planetary surfaces provides rich information about their origins and evolution. While morphologic information provides rich visual clues to geologic processes and properties, the ability to quantitatively communicate this information is less easily accomplished. This study examines the morphology of craterforms using the quantitative outline-based shape methods of geometric morphometrics, commonly used in biology and paleontology. We examine and compare landforms on planetary surfaces using shape, a property of morphology that is invariant to translation, rotation, and size. We quantify the shapes of paterae on Io, martian calderas, terrestrial basaltic shield calderas, terrestrial ash-flow calderas, and lunar impact craters using elliptic Fourier analysis (EFA) and the Zahn and Roskies (Z-R) shape function, or tangent angle approach to produce multivariate shape descriptors. These shape descriptors are subjected to multivariate statistical analysis including canonical variate analysis (CVA), a multiple-comparison variant of discriminant analysis, to investigate the link between craterform shape and classification. Paterae on Io are most similar in shape to terrestrial ash-flow calderas and the shapes of terrestrial basaltic shield volcanoes are most similar to martian calderas. The shapes of lunar impact craters, including simple, transitional, and complex morphology, are classified with a 100% rate of success in all models. Multiple CVA models effectively predict and classify different craterforms using shape-based identification and demonstrate significant potential for use in the analysis of planetary surfaces.

Fermi Surface as a Driver for the Shape-Memory Effect in AuZn

NASA Astrophysics Data System (ADS)

Lashley, Jason

2005-03-01

Martensites are materials that undergo diffusionless, solid-state transitions. The martensitic transition yields properties that depend on the history of the material and if reversible can allow it to recover its previous shape after plastic deformation. This is known as the shape-memory effect (SME). We have succeeded in identifying the operative electronic mechanism responsible for the martensitic transition in the shape-memory alloy AuZn by using Fermi-surface measurements (de Haas-van Alphen oscillations) and band-structure calculations. Our findings suggest that electronic band structure gives rise to special features on the Fermi surface that is important to consider in the design of SME alloys.

Vector vortex beam generation with dolphin-shaped cell meta-surface.

PubMed

Yang, Zhuo; Kuang, Deng-Feng; Cheng, Fang

2017-09-18

We present a dolphin-shaped cell meta-surface, which is a combination of dolphin-shaped metallic cells and dielectric substrate, for vector vortex beam generation with the illumination of linearly polarized light. Surface plasmon polaritons are excited at the boundary of the metallic cells, then guided by the metallic structures, and finally squeezed to the tips to form highly localized strong electromagnetic fields, which generate the intensity of vector vortex beams at z component. Synchronously, the abrupt phase change produced by the meta-surface is utilized to explain the vortex phase generated by elements. The new kind of structure can be utilized for communication, bioscience, and materiality.

Shape dependence of slip length on patterned hydrophobic surfaces

NASA Astrophysics Data System (ADS)

Gu, Xiaokun; Chen, Min

2011-08-01

The effects of solid-liquid interfacial shape on the boundary velocity slip of patterned hydrophobic surfaces are investigated. The scaling law in literature is extended to demonstrate the role of such shape, indicating a decrease of the effective slip length with increasing interfacial roughness. A patterned surface with horizontally aligned carbon nanotube arrays reaches an effective slip length of 83 nm, by utilizing large intrinsic slippage of carbon nanotube while keeping away from the negative effects of interfacial curvature through the flow direction. The results emphasize the importance of avoiding the solid-liquid interfacial roughness in low-friction patterned surface design and manufacture.

Complementarity in Spontaneous Emission: Quantum Jumps, Staggers and Slides

NASA Astrophysics Data System (ADS)

Wiseman, H.

Dan Walls is rightly famous for his part in many of the outstanding developments in quantum optics in the last 30 years. Two of these are most relevant to this paper. The first is the prediction of nonclassical properties of the fluorescence of a two-level atom, such as antibunching [1] and squeezing [2]. Both of these predictions have now been verified experimentally [3,4]. The second is the investigation of fundamental issues such as complementarity and the uncertainty principle [5,6]. This latter area is one which has generated a lively theoretical discussion [7], and, more importantly, suggested new experiments [8]. It was also an area in which I had the honour of working with Dan [9], and of gaining the benefit of his instinct for picking a fruitful line of investigation.

Black hole complementarity in gravity's rainbow

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

Gim, Yongwan; Kim, Wontae, E-mail: yongwan89@sogang.ac.kr, E-mail: wtkim@sogang.ac.kr

2015-05-01

To see how the gravity's rainbow works for black hole complementary, we evaluate the required energy for duplication of information in the context of black hole complementarity by calculating the critical value of the rainbow parameter in the certain class of the rainbow Schwarzschild black hole. The resultant energy can be written as the well-defined limit for the vanishing rainbow parameter which characterizes the deformation of the relativistic dispersion relation in the freely falling frame. It shows that the duplication of information in quantum mechanics could not be allowed below a certain critical value of the rainbow parameter; however, itmore » might be possible above the critical value of the rainbow parameter, so that the consistent formulation in our model requires additional constraints or any other resolutions for the latter case.« less

Linear complementarity formulation for 3D frictional sliding problems

USGS Publications Warehouse

Kaven, Joern; Hickman, Stephen H.; Davatzes, Nicholas C.; Mutlu, Ovunc

2012-01-01

Frictional sliding on quasi-statically deforming faults and fractures can be modeled efficiently using a linear complementarity formulation. We review the formulation in two dimensions and expand the formulation to three-dimensional problems including problems of orthotropic friction. This formulation accurately reproduces analytical solutions to static Coulomb friction sliding problems. The formulation accounts for opening displacements that can occur near regions of non-planarity even under large confining pressures. Such problems are difficult to solve owing to the coupling of relative displacements and tractions; thus, many geomechanical problems tend to neglect these effects. Simple test cases highlight the importance of including friction and allowing for opening when solving quasi-static fault mechanics models. These results also underscore the importance of considering the effects of non-planarity in modeling processes associated with crustal faulting.

Shape-Driven 3D Segmentation Using Spherical Wavelets

PubMed Central

Nain, Delphine; Haker, Steven; Bobick, Aaron; Tannenbaum, Allen

2013-01-01

This paper presents a novel active surface segmentation algorithm using a multiscale shape representation and prior. We define a parametric model of a surface using spherical wavelet functions and learn a prior probability distribution over the wavelet coefficients to model shape variations at different scales and spatial locations in a training set. Based on this representation, we derive a parametric active surface evolution using the multiscale prior coefficients as parameters for our optimization procedure to naturally include the prior in the segmentation framework. Additionally, the optimization method can be applied in a coarse-to-fine manner. We apply our algorithm to the segmentation of brain caudate nucleus, of interest in the study of schizophrenia. Our validation shows our algorithm is computationally efficient and outperforms the Active Shape Model algorithm by capturing finer shape details. PMID:17354875

Direct recognition of superparamagnetic nanocrystals by macrophage scavenger receptor SR-AI.

PubMed

Chao, Ying; Karmali, Priya P; Mukthavaram, Rajesh; Kesari, Santosh; Kouznetsova, Valentina L; Tsigelny, Igor F; Simberg, Dmitri

2013-05-28

Scavenger receptors (SRs) are molecular pattern recognition receptors that have been shown to mediate opsonin-independent uptake of therapeutic and imaging nanoparticles, underlying the importance of SRs in nanomedicine. Unlike pathogens, engineered nanomaterials offer great flexibility in control of surface properties, allowing addressing specific questions regarding the molecular mechanisms of nanoparticle recognition. Recently, we showed that SR-type AI/II mediates opsonin-independent internalization of dextran superparamagnetic iron oxide (SPIO) nanoparticles via positively charged extracellular collagen-like domain. To understand the mechanism of opsonin-independent SPIO recognition, we tested the binding and uptake of nanoparticles with different surface coatings by SR-AI. SPIO coated with 10 kDa dextran was efficiently recognized and taken up by SR-AI transfected cells and J774 macrophages, while SPIO with 20 kDa dextran coating or cross-linked dextran hydrogel avoided the binding and uptake. Nanoparticle negative charge density and zeta-potential did not correlate with SR-AI binding/uptake efficiency. Additional experiments and computer modeling revealed that recognition of the iron oxide crystalline core by the positively charged collagen-like domain of SR-AI is sterically hindered by surface polymer coating. Importantly, the modeling revealed a strong complementarity between the surface Fe-OH groups of the magnetite crystal and the charged lysines of the collagen-like domain of SR-AI, suggesting a specific recognition of SPIO crystalline surface. These data provide an insight into the molecular recognition of nanocrystals by innate immunity receptors and the mechanisms whereby polymer coatings promote immune evasion.

System for closure of a physical anomaly

DOEpatents

Bearinger, Jane P; Maitland, Duncan J; Schumann, Daniel L; Wilson, Thomas S

2014-11-11

Systems for closure of a physical anomaly. Closure is accomplished by a closure body with an exterior surface. The exterior surface contacts the opening of the anomaly and closes the anomaly. The closure body has a primary shape for closing the anomaly and a secondary shape for being positioned in the physical anomaly. The closure body preferably comprises a shape memory polymer.

The shape of a hole and that of the surface-with-hole cannot be analyzed separately.

PubMed

Bertamini, Marco; Helmy, Mai Salah

2012-08-01

Figure-ground organization has a central role in visual perception, since it creates the regions to which properties, such as shape descriptions, are then assigned. However, there is disagreement on how much shape analysis is independent of figure-ground. The reversal of figure-ground of a single closed region is the purest form of figure-ground organization, and the two resulting percepts are that of an object and that of a hole. Both object and hole are nonaccidental regions and can share an identical outline. We devised a test of how figure-ground and contour ownership dramatically affect how shape is processed. Observers judged the shape of a contour that could be either the same as or different from an irrelevant surrounding contour. We report that different (incongruent) inside and outside contours produce a stronger interference effect when they form a single object-with-hole, as compared with a hierarchical set of surfaces or a single hole separating different surfaces (a trench). We conclude that (1) which surface owns the contour constrains the interference between shapes and that (2) despite some recent claims, holes do not display objectlike properties.

Developmental prosopagnosia and super-recognition: no special role for surface reflectance processing.

PubMed

Russell, Richard; Chatterjee, Garga; Nakayama, Ken

2012-01-01

Face recognition by normal subjects depends in roughly equal proportions on shape and surface reflectance cues, while object recognition depends predominantly on shape cues. It is possible that developmental prosopagnosics are deficient not in their ability to recognize faces per se, but rather in their ability to use reflectance cues. Similarly, super-recognizers' exceptional ability with face recognition may be a result of superior surface reflectance perception and memory. We tested this possibility by administering tests of face perception and face recognition in which only shape or reflectance cues are available to developmental prosopagnosics, super-recognizers, and control subjects. Face recognition ability and the relative use of shape and pigmentation were unrelated in all the tests. Subjects who were better at using shape or reflectance cues were also better at using the other type of cue. These results do not support the proposal that variation in surface reflectance perception ability is the underlying cause of variation in face recognition ability. Instead, these findings support the idea that face recognition ability is related to neural circuits using representations that integrate shape and pigmentation information. Copyright © 2011 Elsevier Ltd. All rights reserved.

Automatic casting surface defect recognition and classification

NASA Astrophysics Data System (ADS)

Wong, Boon K.; Elliot, M. P.; Rapley, C. W.

1995-03-01

High integrity castings require surfaces free from defects to reduce, if not eliminate, vulnerability to component failure from such as physical or thermal fatigue or corrosion attack. Previous studies have shown that defects on casting surfaces can be optically enhanced from the surrounding randomly textured surface by liquid penetrants, magnetic particle and other methods. However, very little has been reported on recognition and classification of the defects. The basic problem is one of shape recognition and classification, where the shape can vary in size and orientation as well as in actual shape generally within an envelope that classifies it as a particular defect. The initial work done towards this has focused on recognizing and classifying standard shapes such as the circle, square, rectangle and triangle. Various approaches were tried and this led eventually to a series of fuzzy logic based algorithms from which very good results were obtained. From this work fuzzy logic memberships were generated for the detection of defects found on casting surfaces. Simulated model shapes of such as the quench crack, mechanical crack and hole have been used to test the generated algorithm and the results for recognition and classification are very encouraging.

Approach to solution of coupled heat transfer problem on the surface of hypersonic vehicle of arbitrary shape

NASA Astrophysics Data System (ADS)

Bocharov, A. N.; Bityurin, V. A.; Golovin, N. N.; Evstigneev, N. M.; Petrovskiy, V. P.; Ryabkov, O. I.; Teplyakov, I. O.; Shustov, A. A.; Solomonov, Yu S.; Fortov, V. E.

2016-11-01

In this paper, an approach to solve conjugate heat- and mass-transfer problems is considered to be applied to hypersonic vehicle surface of arbitrary shape. The approach under developing should satisfy the following demands. (i) The surface of the body of interest may have arbitrary geometrical shape. (ii) The shape of the body can change during calculation. (iii) The flight characteristics may vary in a wide range, specifically flight altitude, free-stream Mach number, angle-of-attack, etc. (iv) The approach should be realized with using the high-performance-computing (HPC) technologies. The approach is based on coupled solution of 3D unsteady hypersonic flow equations and 3D unsteady heat conductance problem for the thick wall. Iterative process is applied to account for ablation of wall material and, consequently, mass injection from the surface and changes in the surface shape. While iterations, unstructured computational grids both in the flow region and within the wall interior are adapted to the current geometry and flow conditions. The flow computations are done on HPC platform and are most time-consuming part of the whole problem, while heat conductance problem can be solved on many kinds of computers.

The acid-base titration of montmorillonite

NASA Astrophysics Data System (ADS)

Bourg, I. C.; Sposito, G.; Bourg, A. C.

2003-12-01

Proton binding to clay minerals plays an important role in the chemical reactivity of soils (e.g., acidification, retention of nutrients or pollutants). If should also affect the performance of clay barriers for waste disposal. The surface acidity of clay minerals is commonly modelled empirically by assuming generic amphoteric surface sites (>SOH) on a flat surface, with fitted site densities and acidity constant. Current advances in experimental methods (notably spectroscopy) are rapidly improving our understanding of the structure and reactivity of the surface of clay minerals (arrangement of the particles, nature of the reactive surface sites, adsorption mechanisms). These developments are motivated by the difficulty of modelling the surface chemistry of mineral surfaces at the macro-scale (e.g., adsorption or titration) without a detailed (molecular-scale) picture of the mechanisms, and should be progressively incorporated into surface complexation models. In this view, we have combined recent estimates of montmorillonite surface properties (surface site density and structure, edge surface area, surface electrostatic potential) with surface site acidities obtained from the titration of alpha-Al2O3 and SiO2, and a novel method of accounting for the unknown initial net proton surface charge of the solid. The model predictions were compared to experimental titrations of SWy-1 montmorillonite and purified MX-80 bentonite in 0.1-0.5 mol/L NaClO4 and 0.005-0.5 mol/L NaNO3 background electrolytes, respectively. Most of the experimental data were appropriately described by the model after we adjusted a single parameter (silanol sites on the surface of montmorillonite were made to be slightly more acidic than those of silica). At low ionic strength and acidic pH the model underestimated the buffering capacity of the montmorillonite, perhaps due to clay swelling or to the interlayer adsorption of dissolved aluminum. The agreement between our model and the experimental data illustrates the complementarity of molecular and macro-scale descriptions of the clay reactivity.

A parametric study of cut-off corrugated surface properties

NASA Technical Reports Server (NTRS)

Mentzer, C. A.; Peters, L., Jr.

1973-01-01

Corrugated horns involve a junction between the corrugated surface and a conducting groundplane. Proper horn design requires an understanding of the electromagnetic properties of the corrugated surface and this junction. Therefore, an integral equation solution has been used to study the influence of corrugation density and shape on the power loss. Surface current, and the scattering from a groundplane-corrugated surface junction. Both square and vee shape corrugations have been considered over the range of corrugation depths where the surface acts as a cut-off corrugated surface.

Asymptotic behavior of curvature of surface elements in isotropic turbulence

NASA Technical Reports Server (NTRS)

Girimaji, S. S.

1991-01-01

The asymptotic behavior of the curvature of material elements in turbulence is investigated using Lagrangian velocity-gradient time series obtained from direct numerical simulations of isotropic turbulence. Several material-element ensembles of different initial curvatures and shapes are studied. It is found that, at long times, the (first five) moments of the logarithm of characteristic curvature and shape factor asymptote to values that are independent of the initial curvature or shape. This evidence strongly suggests that the asymptotic pdf's of the curvature and shape of material elements are stationary and independent of initial conditions. Irrespective of initial curvature or shape, the asymptotic shape of a material surface is cylindrical with a high probability.

Diffeomorphic Sulcal Shape Analysis on the Cortex

PubMed Central

Joshi, Shantanu H.; Cabeen, Ryan P.; Joshi, Anand A.; Sun, Bo; Dinov, Ivo; Narr, Katherine L.; Toga, Arthur W.; Woods, Roger P.

2014-01-01

We present a diffeomorphic approach for constructing intrinsic shape atlases of sulci on the human cortex. Sulci are represented as square-root velocity functions of continuous open curves in ℝ3, and their shapes are studied as functional representations of an infinite-dimensional sphere. This spherical manifold has some advantageous properties – it is equipped with a Riemannian metric on the tangent space and facilitates computational analyses and correspondences between sulcal shapes. Sulcal shape mapping is achieved by computing geodesics in the quotient space of shapes modulo scales, translations, rigid rotations and reparameterizations. The resulting sulcal shape atlas preserves important local geometry inherently present in the sample population. The sulcal shape atlas is integrated in a cortical registration framework and exhibits better geometric matching compared to the conventional euclidean method. We demonstrate experimental results for sulcal shape mapping, cortical surface registration, and sulcal classification for two different surface extraction protocols for separate subject populations. PMID:22328177

UV laser-ablated surface textures as potential regulator of cellular response.

PubMed

Chandra, Prafulla; Lai, Karen; Sung, Hak-Joon; Murthy, N Sanjeeva; Kohn, Joachim

2010-06-01

Textured surfaces obtained by UV laser ablation of poly(ethylene terephthalate) films were used to study the effect of shape and spacing of surface features on cellular response. Two distinct patterns, cones and ripples with spacing from 2 to 25 μm, were produced. Surface features with different shapes and spacings were produced by varying pulse repetition rate, laser fluence, and exposure time. The effects of the surface texture parameters, i.e., shape and spacing, on cell attachment, proliferation, and morphology of neonatal human dermal fibroblasts and mouse fibroblasts were studied. Cell attachment was the highest in the regions with cones at ∼4 μm spacing. As feature spacing increased, cell spreading decreased, and the fibroblasts became more circular, indicating a stress-mediated cell shrinkage. This study shows that UV laser ablation is a useful alternative to lithographic techniques to produce surface patterns for controlling cell attachment and growth on biomaterial surfaces.

The Effects of Size, Shape, and Surface Functional Group of Gold Nanostructures on Their Adsorption and Internalization by Cells

PubMed Central

Cho, Eun Chul; Au, Leslie; Zhang, Qiang; Xia, Younan

2010-01-01

In this study, we examined the effects of size, shape, and surface chemistry of gold nanostructures on their uptake (including both adsorption and internalization) by SK-BR-3 breast cancer cells. We used both spherical and cubic Au nanostructures (nanospheres and nanocages, respectively) of two different sizes, and their surface was modified with poly(ethylene glycol) (PEG), antibody anti-HER2, or poly(allyamine hydrochloride) (PAA). Our results showed that the size of the Au nanostructures influenced their uptake by the cells in a similar way regardless of the surface chemistry, while the shape dependency could vary depending on the surface functional group. In addition, the cells preferred to take up the Au nanostructures covered by different surface groups in the following order: PAA>> anti-HER2> PEG. The fraction of Au nanostructures attached to the cell surface was also dependent on the aforementioned parameters. PMID:20029850

Recognizing an individual face: 3D shape contributes earlier than 2D surface reflectance information.

PubMed

Caharel, Stéphanie; Jiang, Fang; Blanz, Volker; Rossion, Bruno

2009-10-01

The human brain recognizes faces by means of two main diagnostic sources of information: three-dimensional (3D) shape and two-dimensional (2D) surface reflectance. Here we used event-related potentials (ERPs) in a face adaptation paradigm to examine the time-course of processing for these two types of information. With a 3D morphable model, we generated pairs of faces that were either identical, varied in 3D shape only, in 2D surface reflectance only, or in both. Sixteen human observers discriminated individual faces in these 4 types of pairs, in which a first (adapting) face was followed shortly by a second (test) face. Behaviorally, observers were as accurate and as fast for discriminating individual faces based on either 3D shape or 2D surface reflectance alone, but were faster when both sources of information were present. As early as the face-sensitive N170 component (approximately 160 ms following the test face), there was larger amplitude for changes in 3D shape relative to the repetition of the same face, especially over the right occipito-temporal electrodes. However, changes in 2D reflectance between the adapter and target face did not increase the N170 amplitude. At about 250 ms, both 3D shape and 2D reflectance contributed equally, and the largest difference in amplitude compared to the repetition of the same face was found when both 3D shape and 2D reflectance were combined, in line with observers' behavior. These observations indicate that evidence to recognize individual faces accumulate faster in the right hemisphere human visual cortex from diagnostic 3D shape information than from 2D surface reflectance information.

Shape recognition of microbial cells by colloidal cell imprints

NASA Astrophysics Data System (ADS)

Borovička, Josef; Stoyanov, Simeon D.; Paunov, Vesselin N.

2013-08-01

We have engineered a class of colloids which can recognize the shape and size of targeted microbial cells and selectively bind to their surfaces. These imprinted colloid particles, which we called ``colloid antibodies'', were fabricated by partial fragmentation of silica shells obtained by templating the targeted microbial cells. We successfully demonstrated the shape and size recognition between such colloidal imprints and matching microbial cells. High percentage of binding events of colloidal imprints with the size matching target particles was achieved. We demonstrated selective binding of colloidal imprints to target microbial cells in a binary mixture of cells of different shapes and sizes, which also resulted in high binding selectivity. We explored the role of the electrostatic interactions between the target cells and their colloid imprints by pre-coating both of them with polyelectrolytes. Selective binding occurred predominantly in the case of opposite surface charges of the colloid cell imprint and the targeted cells. The mechanism of the recognition is based on the amplification of the surface adhesion in the case of shape and size match due to the increased contact area between the target cell and the colloidal imprint. We also tested the selective binding for colloid imprints of particles of fixed shape and varying sizes. The concept of cell recognition by colloid imprints could be used for development of colloid antibodies for shape-selective binding of microbes. Such colloid antibodies could be additionally functionalized with surface groups to enhance their binding efficiency to cells of specific shape and deliver a drug payload directly to their surface or allow them to be manipulated using external fields. They could benefit the pharmaceutical industry in developing selective antimicrobial therapies and formulations.

The effect of age upon the perception of 3-D shape from motion.

PubMed

Norman, J Farley; Cheeseman, Jacob R; Pyles, Jessica; Baxter, Michael W; Thomason, Kelsey E; Calloway, Autum B

2013-12-18

Two experiments evaluated the ability of 50 older, middle-aged, and younger adults to discriminate the 3-dimensional (3-D) shape of curved surfaces defined by optical motion. In Experiment 1, temporal correspondence was disrupted by limiting the lifetimes of the moving surface points. In order to discriminate 3-D surface shape reliably, the younger and middle-aged adults needed a surface point lifetime of approximately 4 views (in the apparent motion sequences). In contrast, the older adults needed a much longer surface point lifetime of approximately 9 views in order to reliably perform the same task. In Experiment 2, the negative effect of age upon 3-D shape discrimination from motion was replicated. In this experiment, however, the participants' abilities to discriminate grating orientation and speed were also assessed. Edden et al. (2009) have recently demonstrated that behavioral grating orientation discrimination correlates with GABA (gamma aminobutyric acid) concentration in human visual cortex. Our results demonstrate that the negative effect of age upon 3-D shape perception from motion is not caused by impairments in the ability to perceive motion per se, but does correlate significantly with grating orientation discrimination. This result suggests that the age-related decline in 3-D shape discrimination from motion is related to decline in GABA concentration in visual cortex. Copyright © 2013 Elsevier B.V. All rights reserved.

Full area covered 3D profile measurement of special-shaped optics based on a new prototype non-contact profiler

NASA Astrophysics Data System (ADS)

Du, Hui-Lin; Zhou, Zhao-Zhong; Sun, Ze-Qing; Ju, Bing-Feng; Xu, Shaoning; Sun, Anyu

2017-06-01

A new prototype non-contact profiler based on surface tracking has been specially developed. Surface tracking is carried out by a specially designed dual stage probe system with the aid of a four-Degree Of Freedom high-precision motion platform. The dual stage probe system keeps a short-range optical probe constantly tracking the surface by a self-developed voice coil motor servo, by which a wide measuring range of up to 10 mm is realized. The system performance evaluation including resolution, repeatability, and scanning speed proved the good capability of the new prototype non-contact profiler. To realize a full area covered 3D profile measurement of special-shaped optics within one scanning procedure, a signal intensity monitor integrated in the surface tracking controller is specially developed. In the experiment, a snip-single-corner-rectangular-shaped freeform surface was successfully measured over full area by the new non-contact profiler. This work provides an effective solution for 3D profile measurement of special-shaped optical surfaces over full reflecting area. Experimental results demonstrate that the proposed measuring system is of great significance in quality evaluation of optical surfaces.

Full area covered 3D profile measurement of special-shaped optics based on a new prototype non-contact profiler.

PubMed

Du, Hui-Lin; Zhou, Zhao-Zhong; Sun, Ze-Qing; Ju, Bing-Feng; Xu, Shaoning; Sun, Anyu

2017-06-01

A new prototype non-contact profiler based on surface tracking has been specially developed. Surface tracking is carried out by a specially designed dual stage probe system with the aid of a four-Degree Of Freedom high-precision motion platform. The dual stage probe system keeps a short-range optical probe constantly tracking the surface by a self-developed voice coil motor servo, by which a wide measuring range of up to 10 mm is realized. The system performance evaluation including resolution, repeatability, and scanning speed proved the good capability of the new prototype non-contact profiler. To realize a full area covered 3D profile measurement of special-shaped optics within one scanning procedure, a signal intensity monitor integrated in the surface tracking controller is specially developed. In the experiment, a snip-single-corner-rectangular-shaped freeform surface was successfully measured over full area by the new non-contact profiler. This work provides an effective solution for 3D profile measurement of special-shaped optical surfaces over full reflecting area. Experimental results demonstrate that the proposed measuring system is of great significance in quality evaluation of optical surfaces.

Doughnut-shaped soap bubbles.

PubMed

Préve, Deison; Saa, Alberto

2015-10-01

Soap bubbles are thin liquid films enclosing a fixed volume of air. Since the surface tension is typically assumed to be the only factor responsible for conforming the soap bubble shape, the realized bubble surfaces are always minimal area ones. Here, we consider the problem of finding the axisymmetric minimal area surface enclosing a fixed volume V and with a fixed equatorial perimeter L. It is well known that the sphere is the solution for V=L(3)/6π(2), and this is indeed the case of a free soap bubble, for instance. Surprisingly, we show that for V<αL(3)/6π(2), with α≈0.21, such a surface cannot be the usual lens-shaped surface formed by the juxtaposition of two spherical caps, but is rather a toroidal surface. Practically, a doughnut-shaped bubble is known to be ultimately unstable and, hence, it will eventually lose its axisymmetry by breaking apart in smaller bubbles. Indisputably, however, the topological transition from spherical to toroidal surfaces is mandatory here for obtaining the global solution for this axisymmetric isoperimetric problem. Our result suggests that deformed bubbles with V<αL(3)/6π(2) cannot be stable and should not exist in foams, for instance.

Doughnut-shaped soap bubbles

NASA Astrophysics Data System (ADS)

Préve, Deison; Saa, Alberto

2015-10-01

Soap bubbles are thin liquid films enclosing a fixed volume of air. Since the surface tension is typically assumed to be the only factor responsible for conforming the soap bubble shape, the realized bubble surfaces are always minimal area ones. Here, we consider the problem of finding the axisymmetric minimal area surface enclosing a fixed volume V and with a fixed equatorial perimeter L . It is well known that the sphere is the solution for V =L3/6 π2 , and this is indeed the case of a free soap bubble, for instance. Surprisingly, we show that for V <α L3/6 π2 , with α ≈0.21 , such a surface cannot be the usual lens-shaped surface formed by the juxtaposition of two spherical caps, but is rather a toroidal surface. Practically, a doughnut-shaped bubble is known to be ultimately unstable and, hence, it will eventually lose its axisymmetry by breaking apart in smaller bubbles. Indisputably, however, the topological transition from spherical to toroidal surfaces is mandatory here for obtaining the global solution for this axisymmetric isoperimetric problem. Our result suggests that deformed bubbles with V <α L3/6 π2 cannot be stable and should not exist in foams, for instance.

Patterned gradient surface for spontaneous droplet transportation and water collection: simulation and experiment

NASA Astrophysics Data System (ADS)

Tan, Xianhua; Zhu, Yiying; Shi, Tielin; Tang, Zirong; Liao, Guanglan

2016-11-01

We demonstrate spontaneous droplet transportation and water collection on wedge-shaped gradient surfaces consisting of alternating hydrophilic and hydrophobic regions. Droplets on the surfaces are modeled and simulated to analyze the Gibbs free energy and free energy gradient distributions. Big half-apex angle and great wettability difference result in considerable free energy gradient, corresponding to large driving force for spontaneous droplet transportation, thus causing the droplets to move towards the open end of the wedge-shaped hydrophilic regions, where the Gibbs free energy is low. Gradient surfaces are then fabricated and tested. Filmwise condensation begins on the hydrophilic regions, forming wedge-shaped tracks for water collection. Dropwise condensation occurs on the hydrophobic regions, where the droplet size distribution and departure diameters are controlled by the width of the regions. Condensate water from both the hydrophilic and hydrophobic regions are collected directionally to the open end of the wedge-shaped hydrophilic regions, agreeing with the simulations. Directional droplet transport and controllable departure diameters make the branched gradient surfaces more efficient than smooth surfaces for water collection, which proves that gradient surfaces are potential in water collection, microfluidic devices, anti-fogging and self-cleaning.

TU-CD-207-09: Analysis of the 3-D Shape of Patients’ Breast for Breast Imaging and Surgery Planning

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

Agasthya, G; Sechopoulos, I

2015-06-15

Purpose: Develop a method to accurately capture the 3-D shape of patients’ external breast surface before and during breast compression for mammography/tomosynthesis. Methods: During this IRB-approved, HIPAA-compliant study, 50 women were recruited to undergo 3-D breast surface imaging during breast compression and imaging for the cranio-caudal (CC) view on a digital mammography/breast tomosynthesis system. Digital projectors and cameras mounted on tripods were used to acquire 3-D surface images of the breast, in three conditions: (a) positioned on the support paddle before compression, (b) during compression by the compression paddle and (c) the anterior-posterior view with the breast in its natural,more » unsupported position. The breast was compressed to standard full compression with the compression paddle and a tomosynthesis image was acquired simultaneously with the 3-D surface. The 3-D surface curvature and deformation with respect to the uncompressed surface was analyzed using contours. The 3-D surfaces were voxelized to capture breast shape in a format that can be manipulated for further analysis. Results: A protocol was developed to accurately capture the 3-D shape of patients’ breast before and during compression for mammography. Using a pair of 3-D scanners, the 50 patient breasts were scanned in three conditions, resulting in accurate representations of the breast surfaces. The surfaces were post processed, analyzed using contours and voxelized, with 1 mm{sup 3} voxels, converting the breast shape into a format that can be easily modified as required. Conclusion: Accurate characterization of the breast curvature and shape for the generation of 3-D models is possible. These models can be used for various applications such as improving breast dosimetry, accurate scatter estimation, conducting virtual clinical trials and validating compression algorithms. Ioannis Sechopoulos is consultant for Fuji Medical Systems USA.« less

Particle compositions with a pre-selected cell internalization mode

NASA Technical Reports Server (NTRS)

Ferrari, Mauro (Inventor); Decuzzi, Paolo (Inventor)

2012-01-01

A method of formulating a particle composition having a pre-selected cell internalization mode involves selecting a target cell having surface receptors and obtaining particles that have i) surface moieties, that have an affinity for or are capable of binding to the surface receptors of the cell and ii) a preselected shape, where a surface distribution of the surface moieties on the particles and the shape of the particles are effective for the pre-selected cell internalization mode.

Study on Dynamic Development of Three-dimensional Weld Pool Surface in Stationary GTAW

NASA Astrophysics Data System (ADS)

Huang, Jiankang; He, Jing; He, Xiaoying; Shi, Yu; Fan, Ding

2018-04-01

The weld pool contains abundant information about the welding process. In particular, the type of the weld pool surface shape, i. e., convex or concave, is determined by the weld penetration. To detect it, an innovative laser-vision-based sensing method is employed to observe the weld pool surface of the gas tungsten arc welding (GTAW). A low-power laser dots pattern is projected onto the entire weld pool surface. Its reflection is intercepted by a screen and captured by a camera. Then the dynamic development process of the weld pool surface can be detected. By observing and analyzing, the change of the reflected laser dots reflection pattern, for shape of the weld pool surface shape, was found to closely correlate to the penetration of weld pool in the welding process. A mathematical model was proposed to correlate the incident ray, reflected ray, screen and surface of weld pool based on structured laser specular reflection. The dynamic variation of the weld pool surface and its corresponding dots laser pattern were simulated and analyzed. By combining the experimental data and the mathematical analysis, the results show that the pattern of the reflected laser dots pattern is closely correlated to the development of weld pool, such as the weld penetration. The concavity of the pool surface was found to increase rapidly after the surface shape was changed from convex to concave during the stationary GTAW process.

Effect of surface charge convection and shape deformation on the dielectrophoretic motion of a liquid drop

NASA Astrophysics Data System (ADS)

Mandal, Shubhadeep; Bandopadhyay, Aditya; Chakraborty, Suman

2016-04-01

The dielectrophoretic motion and shape deformation of a Newtonian liquid drop in an otherwise quiescent Newtonian liquid medium in the presence of an axisymmetric nonuniform dc electric field consisting of uniform and quadrupole components is investigated. The theory put forward by Feng [J. Q. Feng, Phys. Rev. E 54, 4438 (1996), 10.1103/PhysRevE.54.4438] is generalized by incorporating the following two nonlinear effects—surface charge convection and shape deformation—towards determining the drop velocity. This two-way coupled moving boundary problem is solved analytically by considering small values of electric Reynolds number (ratio of charge relaxation time scale to the convection time scale) and electric capillary number (ratio of electrical stress to the surface tension) under the framework of the leaky dielectric model. We focus on investigating the effects of charge convection and shape deformation for different drop-medium combinations. A perfectly conducting drop suspended in a leaky (or perfectly) dielectric medium always deforms to a prolate shape and this kind of shape deformation always augments the dielectrophoretic drop velocity. For a perfectly dielectric drop suspended in a perfectly dielectric medium, the shape deformation leads to either increase (for prolate shape) or decrease (for oblate shape) in the dielectrophoretic drop velocity. Both surface charge convection and shape deformation affect the drop motion for leaky dielectric drops. The combined effect of these can significantly increase or decrease the dielectrophoretic drop velocity depending on the electrohydrodynamic properties of both the liquids and the relative strength of the electric Reynolds number and electric capillary number. Finally, comparison with the existing experiments reveals better agreement with the present theory.

Toroidal cell and battery. [storage battery for high amp-hour load applications

NASA Technical Reports Server (NTRS)

Nagle, W. J. (Inventor)

1981-01-01

A toroidal storage battery designed to handle relatively high amp-hour loads is described. The cell includes a wound core disposed within a pair of toroidal channel shaped electrodes spaced apart by nylon insulator. The shape of the case electrodes of this toroidal cell allows a first planar doughnut shaped surface and the inner cylindrical case wall to be used as a first electrode and a second planar doughnut shaped surface and the outer cylindrical case wall to be used as a second electrode. Connectors may be used to stack two or more toroidal cells together by connecting substantially the entire surface area of the first electrode of a first cell to substantially the entire surface area of the second electrode of a second cell. The central cavity of each toroidal cell may be used as a conduit for pumping a fluid through the toroidal cell to thereby cool the cell.

Dendritic growth shapes in kinetic Monte Carlo models

NASA Astrophysics Data System (ADS)

Krumwiede, Tim R.; Schulze, Tim P.

2017-02-01

For the most part, the study of dendritic crystal growth has focused on continuum models featuring surface energies that yield six pointed dendrites. In such models, the growth shape is a function of the surface energy anisotropy, and recent work has shown that considering a broader class of anisotropies yields a correspondingly richer set of growth morphologies. Motivated by this work, we generalize nanoscale models of dendritic growth based on kinetic Monte Carlo simulation. In particular, we examine the effects of extending the truncation radius for atomic interactions in a bond-counting model. This is done by calculating the model’s corresponding surface energy and equilibrium shape, as well as by running KMC simulations to obtain nanodendritic growth shapes. Additionally, we compare the effects of extending the interaction radius in bond-counting models to that of extending the number of terms retained in the cubic harmonic expansion of surface energy anisotropy in the context of continuum models.

Rapid Parameterization Schemes for Aircraft Shape Optimization

NASA Technical Reports Server (NTRS)

Li, Wu

2012-01-01

A rapid shape parameterization tool called PROTEUS is developed for aircraft shape optimization. This tool can be applied directly to any aircraft geometry that has been defined in PLOT3D format, with the restriction that each aircraft component must be defined by only one data block. PROTEUS has eight types of parameterization schemes: planform, wing surface, twist, body surface, body scaling, body camber line, shifting/scaling, and linear morphing. These parametric schemes can be applied to two types of components: wing-type surfaces (e.g., wing, canard, horizontal tail, vertical tail, and pylon) and body-type surfaces (e.g., fuselage, pod, and nacelle). These schemes permit the easy setup of commonly used shape modification methods, and each customized parametric scheme can be applied to the same type of component for any configuration. This paper explains the mathematics for these parametric schemes and uses two supersonic configurations to demonstrate the application of these schemes.

Can niche plasticity promote biodiversity-productivity relationships through increased complementarity?

PubMed

Niklaus, Pascal A; Baruffol, Martin; He, Jin-Sheng; Ma, Keping; Schmid, Bernhard

2017-04-01

Most experimental biodiversity-ecosystem functioning research to date has addressed herbaceous plant communities. Comparably little is known about how forest communities will respond to species losses, despite their importance for global biogeochemical cycling. We studied tree species interactions in experimental subtropical tree communities with 33 distinct tree species mixtures and one, two, or four species. Plots were either exposed to natural light levels or shaded. Trees grew rapidly and were intensely competing above ground after 1.5 growing seasons when plots were thinned and the vertical distribution of leaves and wood determined by separating the biomass of harvested trees into 50 cm height increments. Our aim was to analyze effects of species richness in relation to the vertical allocation of leaf biomass and wood, with an emphasis on bipartite competitive interactions among species. Aboveground productivity increased with species richness. The community-level vertical leaf and wood distribution depended on the species composition of communities. Mean height and breadth of species-level vertical leaf and wood distributions did not change with species richness. However, the extra biomass produced by mixtures compared to monocultures of the component species increased when vertical leaf distributions of monocultures were more different. Decomposition of biodiversity effects with the additive partitioning scheme indicated positive complementarity effects that were higher in light than in shade. Selection effects did not deviate from zero, irrespective of light levels. Vertical leaf distributions shifted apart in mixed stands as consequence of competition-driven phenotypic plasticity, promoting realized complementarity. Structural equation models showed that this effect was larger for species that differed more in growth strategies that were characterized by functional traits. In 13 of the 18 investigated two-species mixtures, both species benefitted relative to intraspecific competition in monoculture. In the remaining five pairwise mixtures, the relative yield gain of one species exceeded the relative yield loss of the other species, resulting in a relative yield total (RYT) exceeding 1. Overall, our analysis indicates that richness-productivity relationships are promoted by interspecific niche complementarity at early stages of stand development, and that this effect is enhanced by architectural plasticity. © 2017 by the Ecological Society of America.

Rebounding of a shaped-charge jet

NASA Astrophysics Data System (ADS)

Proskuryakov, E. V.; Sorokin, M. V.; Fomin, V. M.

2007-09-01

The phenomenon of rebounding of a shaped-charge jet from the armour surface with small angles between the jet axis and the target surface is considered. Rebounding angles as a function of jet velocity are obtained in experiments for a copper shaped-charge jet. An engineering calculation technique is developed. The results calculated with the use of this technique are in reasonable agreement with experimental data.

Fabrication of small complex-shaped optics by plasma chemical vaporization machining with a microelectrode

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

Takino, Hideo; Shibata, Norio; Itoh, Hiroshi

2006-08-10

We have developed plasma chemical vaporization machining by using a microelectrode for the fabrication of small complex-shaped optical surfaces. In this method, a0.5 mm diameter pipe microelectrode, from which processing gas is drawn in, generates a small localized plasma that is scanned over a work piece under numerical computer control to shape a desired surface. A12 mmx12 mm nonaxisymmetric mirror with a maximum depth of approximately 3 {mu}m was successfully fabricated with a peak-to-valley shape accuracy of 0.04 {mu}m in an area excluding the edges of the mirror. The average surface roughness was 0.58 nm, which is smooth enough formore » optical use.« less

First-and Second-Order Displacement Transfer Functions for Structural Shape Calculations Using Analytically Predicted Surface Strains

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2012-01-01

New first- and second-order displacement transfer functions have been developed for deformed shape calculations of nonuniform cross-sectional beam structures such as aircraft wings. The displacement transfer functions are expressed explicitly in terms of beam geometrical parameters and surface strains (uniaxial bending strains) obtained at equally spaced strain stations along the surface of the beam structure. By inputting the measured or analytically calculated surface strains into the displacement transfer functions, one could calculate local slopes, deflections, and cross-sectional twist angles of the nonuniform beam structure for mapping the overall structural deformed shapes for visual display. The accuracy of deformed shape calculations by the first- and second-order displacement transfer functions are determined by comparing these values to the analytically predicted values obtained from finite element analyses. This comparison shows that the new displacement transfer functions could quite accurately calculate the deformed shapes of tapered cantilever tubular beams with different tapered angles. The accuracy of the present displacement transfer functions also are compared to those of the previously developed displacement transfer functions.

Design and development of LED-based irregular leather area measuring machine

NASA Astrophysics Data System (ADS)

Adil, Rehan; Khan, Sarah Jamal

2012-01-01

Using optical sensor array, a precision motion control system in a conveyer follows the irregular shaped leather sheet to measure its surface area. In operation, irregular shaped leather sheet passes on conveyer belt and optical sensor array detects the leather sheet edge. In this way outside curvature of the leather sheet is detected and is then feed to the controller to measure its approximate area. Such system can measure irregular shapes, by neglecting rounded corners, ellipses etc. To minimize the error in calculating surface area of irregular curve to the above mentioned system, the motion control system only requires the footprint of the optical sensor to be small and the distance between the sensors is to be minimized. In the proposed technique surface area measurement of irregular shaped leather sheet is done by defining velocity and detecting position of the move. The motion controller takes the information and creates the necessary edge profile on point-to-point bases. As a result irregular shape of leather sheet is mapped and is then feed to the controller to calculate surface area.

Shape analysis of corpus callosum in autism subtype using planar conformal mapping

NASA Astrophysics Data System (ADS)

He, Qing; Duan, Ye; Yin, Xiaotian; Gu, Xianfeng; Karsch, Kevin; Miles, Judith

2009-02-01

A number of studies have documented that autism has a neurobiological basis, but the anatomical extent of these neurobiological abnormalities is largely unknown. In this study, we aimed at analyzing highly localized shape abnormalities of the corpus callosum in a homogeneous group of autism children. Thirty patients with essential autism and twenty-four controls participated in this study. 2D contours of the corpus callosum were extracted from MR images by a semiautomatic segmentation method, and the 3D model was constructed by stacking the contours. The resulting 3D model had two openings at the ends, thus a new conformal parameterization for high genus surfaces was applied in our shape analysis work, which mapped each surface onto a planar domain. Surface matching among different individual meshes was achieved by re-triangulating each mesh according to a template surface. Statistical shape analysis was used to compare the 3D shapes point by point between patients with autism and their controls. The results revealed significant abnormalities in the anterior most and anterior body in essential autism group.

Production of atmospheric pressure microwave plasma with dielectric half-mirror resonator and its application to polymer surface treatment

NASA Astrophysics Data System (ADS)

Sasai, Kensuke; Keyamura, Kazuki; Suzuki, Haruka; Toyoda, Hirotaka

2018-06-01

For the surface treatment of a polymer tube, a ring-shaped atmospheric pressure microwave plasma (APMP) using a coaxial waveguide is studied. In this APMP, a dielectric plate is used not only as a partial mirror for cavity resonation but also for the precise alignment of the discharge gap for ring-shaped plasma production. The optimum position of the dielectric plate is investigated by electromagnetic wave simulation. On the basis of simulation results, a ring-shaped plasma with good uniformity along the ring is produced. The coaxial APMP is applied to the surface treatment of ethylene tetrafluoroethylene. A very fast surface modification within 3 s is observed.

Shape design sensitivity analysis and optimization of three dimensional elastic solids using geometric modeling and automatic regridding. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Yao, Tse-Min; Choi, Kyung K.

1987-01-01

An automatic regridding method and a three dimensional shape design parameterization technique were constructed and integrated into a unified theory of shape design sensitivity analysis. An algorithm was developed for general shape design sensitivity analysis of three dimensional eleastic solids. Numerical implementation of this shape design sensitivity analysis method was carried out using the finite element code ANSYS. The unified theory of shape design sensitivity analysis uses the material derivative of continuum mechanics with a design velocity field that represents shape change effects over the structural design. Automatic regridding methods were developed by generating a domain velocity field with boundary displacement method. Shape design parameterization for three dimensional surface design problems was illustrated using a Bezier surface with boundary perturbations that depend linearly on the perturbation of design parameters. A linearization method of optimization, LINRM, was used to obtain optimum shapes. Three examples from different engineering disciplines were investigated to demonstrate the accuracy and versatility of this shape design sensitivity analysis method.

Mixing in Sessile Drops Merging on a Surface

NASA Astrophysics Data System (ADS)

Anna, Shelley; Zhang, Ying; Oberdick, Samuel; Garoff, Stephen

2011-11-01

We investigate the mixing of two sessile drops that merge on a surface. The drops consist of low viscosity glycerol-water mixtures deposited on a silicone elastomer surface with contact angle near 90°. We observe the shape of the drops and the location of their intersection by placing a fluorescent dye in one drop and using a laser light sheet to image a plane perpendicular to the surface. The initial healing of the meniscus bridge between the merging drops, and the damping of capillary waves appearing on their surfaces occur on timescales comparable to the inertio-capillary relaxation time. However, the interface between the two fluids remains sharp, broadening diffusively over several minutes. The shape of the merged drops and the boundary between them also continues to evolve on a timescale of minutes. This later motion is controlled by gravity, capillary pressure, and viscous stresses. Images of the 3D drop shape indicate that small contact line motions are correlated to the slow relaxation. Although the two drops contain identical liquids except for the presence of the dye, the shape of the interface consistently evolves asymmetrically, assuming a characteristic crescent shape. We note that very tiny surface tension gradients can produce an asymmetric flow like the one observed here. We characterize the long timescale flow as a function of the drop sizes, and we use numerical simulations to aid in elucidating the essential physics.

Subject-specific longitudinal shape analysis by coupling spatiotemporal shape modeling with medial analysis

NASA Astrophysics Data System (ADS)

Hong, Sungmin; Fishbaugh, James; Rezanejad, Morteza; Siddiqi, Kaleem; Johnson, Hans; Paulsen, Jane; Kim, Eun Young; Gerig, Guido

2017-02-01

Modeling subject-specific shape change is one of the most important challenges in longitudinal shape analysis of disease progression. Whereas anatomical change over time can be a function of normal aging, anatomy can also be impacted by disease related degeneration. Anatomical shape change may also be affected by structural changes from neighboring shapes, which may cause non-linear variations in pose. In this paper, we propose a framework to analyze disease related shape changes by coupling extrinsic modeling of the ambient anatomical space via spatiotemporal deformations with intrinsic shape properties from medial surface analysis. We compare intrinsic shape properties of a subject-specific shape trajectory to a normative 4D shape atlas representing normal aging to isolate shape changes related to disease. The spatiotemporal shape modeling establishes inter/intra subject anatomical correspondence, which in turn enables comparisons between subjects and the 4D shape atlas, and also quantitative analysis of disease related shape change. The medial surface analysis captures intrinsic shape properties related to local patterns of deformation. The proposed framework jointly models extrinsic longitudinal shape changes in the ambient anatomical space, as well as intrinsic shape properties to give localized measurements of degeneration. Six high risk subjects and six controls are randomly sampled from a Huntington's disease image database for qualitative and quantitative comparison.

Multiwavelength digital holography for polishing tool shape measurement

NASA Astrophysics Data System (ADS)

Lédl, Vít.; Psota, Pavel; Václavík, Jan; Doleček, Roman; Vojtíšek, Petr

2013-09-01

Classical mechano-chemical polishing is still a valuable technique, which gives unbeatable results for some types of optical surfaces. For example, optics for high power lasers requires minimized subsurface damage, very high cosmetic quality, and low mid spatial frequency error. One can hardly achieve this with use of subaperture polishing. The shape of the polishing tool plays a crucial role in achieving the required form of the optical surface. Often the shape of the polishing tool or pad is not known precisely enough during the manufacturing process. The tool shape is usually premachined and later is changed during the polishing procedure. An experienced worker could estimate the shape of the tool indirectly from the shape of the polished element, and that is why he can achieve the required shape in few reasonably long iterative steps. Therefore the lack of the exact tool shape knowledge is tolerated. Sometimes, this indirect method is not feasible even if small parts are considered. Moreover, if processes on machines like planetary (continuous) polishers are considered, the incorrect shape of the polishing pad could extend the polishing times extremely. Every iteration step takes hours. Even worse, polished piece could be wasted if the pad has a poor shape. The ability of the tool shape determination would be very valuable in those types of lengthy processes. It was our primary motivation to develop a contactless measurement method for large diffusive surfaces and demonstrate its usability. The proposed method is based on application of multiwavelength digital holographic interferometry with phase shift.

3D shape measurement of automotive glass by using a fringe reflection technique

NASA Astrophysics Data System (ADS)

Skydan, O. A.; Lalor, M. J.; Burton, D. R.

2007-01-01

In automotive and glass making industries, there is a need for accurately measuring the 3D shapes of reflective surfaces to speed up and ensure product development and manufacturing quality by using non-contact techniques. This paper describes a technique for the measurement of non-full-field reflective surfaces of automotive glass by using a fringe reflection technique. Physical properties of the measurement surfaces do not allow us to apply optical geometries used in existing techniques for surface measurement based upon direct fringe pattern illumination. However, this property of surface reflectivity can be used to implement similar ideas from existing techniques in a new improved method. In other words, the reflective surface can be used as a mirror to reflect illuminated fringe patterns onto a screen behind. It has been found that in the case of implementing the reflective fringe technique, the phase-shift distribution depends not only on the height of the object but also on the slope at each measurement point. This requires the solving of differential equations to find the surface slope and height distributions in the x and y directions and development of the additional height reconstruction algorithms. The main focus has been made on developing a mathematical model of the optical sub-system and discussing ways for its practical implementation including calibration procedures. A number of implemented image processing algorithms for system calibration and data analysis are discussed and two experimental results are given for automotive glass surfaces with different shapes and defects. The proposed technique showed the ability to provide accurate non-destructive measurement of 3D shapes of the reflective automotive glass surfaces and can be used as a key element for a glass shape quality control system on-line or in a laboratory environment.

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

Fulkerson, Edward; Lanning, Rodney K.; Telford, Steven

A device includes a u-channel shaped member and a printed circuit board including a plurality of capacitors. Each of the plurality of capacitors has a mounting surface mounted to the printed circuit board and an opposing heat transfer surface thermally coupled to the u-channel shaped member. The device also includes an output cable coupled to the printed circuit board and a return cable coupled to the printed circuit board. The device further includes a control transistor disposed inside the u-channel shaped member and a current sensing resistor disposed inside the u-channel shaped member.

Perfect mixing of immiscible macromolecules at fluid interfaces

NASA Astrophysics Data System (ADS)

Sheiko, Sergei S.; Zhou, Jing; Arnold, Jamie; Neugebauer, Dorota; Matyjaszewski, Krzysztof; Tsitsilianis, Constantinos; Tsukruk, Vladimir V.; Carrillo, Jan-Michael Y.; Dobrynin, Andrey V.; Rubinstein, Michael

2013-08-01

The difficulty of mixing chemically incompatible substances—in particular macromolecules and colloidal particles—is a canonical problem limiting advances in fields ranging from health care to materials engineering. Although the self-assembly of chemically different moieties has been demonstrated in coordination complexes, supramolecular structures, and colloidal lattices among other systems, the mechanisms of mixing largely rely on specific interfacing of chemically, physically or geometrically complementary objects. Here, by taking advantage of the steric repulsion between brush-like polymers tethered to surface-active species, we obtained long-range arrays of perfectly mixed macromolecules with a variety of polymer architectures and a wide range of chemistries without the need of encoding specific complementarity. The net repulsion arises from the significant increase in the conformational entropy of the brush-like polymers with increasing distance between adjacent macromolecules at fluid interfaces. This entropic-templating assembly strategy enables long-range patterning of thin films on sub-100 nm length scales.

Improving Docking Performance Using Negative Image-Based Rescoring.

PubMed

Kurkinen, Sami T; Niinivehmas, Sanna; Ahinko, Mira; Lätti, Sakari; Pentikäinen, Olli T; Postila, Pekka A

2018-01-01

Despite the large computational costs of molecular docking, the default scoring functions are often unable to recognize the active hits from the inactive molecules in large-scale virtual screening experiments. Thus, even though a correct binding pose might be sampled during the docking, the active compound or its biologically relevant pose is not necessarily given high enough score to arouse the attention. Various rescoring and post-processing approaches have emerged for improving the docking performance. Here, it is shown that the very early enrichment (number of actives scored higher than 1% of the highest ranked decoys) can be improved on average 2.5-fold or even 8.7-fold by comparing the docking-based ligand conformers directly against the target protein's cavity shape and electrostatics. The similarity comparison of the conformers is performed without geometry optimization against the negative image of the target protein's ligand-binding cavity using the negative image-based (NIB) screening protocol. The viability of the NIB rescoring or the R-NiB, pioneered in this study, was tested with 11 target proteins using benchmark libraries. By focusing on the shape/electrostatics complementarity of the ligand-receptor association, the R-NiB is able to improve the early enrichment of docking essentially without adding to the computing cost. By implementing consensus scoring, in which the R-NiB and the original docking scoring are weighted for optimal outcome, the early enrichment is improved to a level that facilitates effective drug discovery. Moreover, the use of equal weight from the original docking scoring and the R-NiB scoring improves the yield in most cases.

Scaled SFS method for Lambertian surface 3D measurement under point source lighting.

PubMed

Ma, Long; Lyu, Yi; Pei, Xin; Hu, Yan Min; Sun, Feng Ming

2018-05-28

A Lambertian surface is a kind of very important assumption in shape from shading (SFS), which is widely used in many measurement cases. In this paper, a novel scaled SFS method is developed to measure the shape of a Lambertian surface with dimensions. In which, a more accurate light source model is investigated under the illumination of a simple point light source, the relationship between surface depth map and the recorded image grayscale is established by introducing the camera matrix into the model. Together with the constraints of brightness, smoothness and integrability, the surface shape with dimensions can be obtained by analyzing only one image using the scaled SFS method. The algorithm simulations show a perfect matching between the simulated structures and the results, the rebuilding root mean square error (RMSE) is below 0.6mm. Further experiment is performed by measuring a PVC tube internal surface, the overall measurement error lies below 2%.

Human Anti-V3 HIV-1 Monoclonal Antibodies Encoded by the VH5-51/VL Lambda Genes Define a Conserved Antigenic Structure

PubMed Central

Gorny, Miroslaw K.; Sampson, Jared; Li, Huiguang; Jiang, Xunqing; Totrov, Maxim; Wang, Xiao-Hong; Williams, Constance; O'Neal, Timothy; Volsky, Barbara; Li, Liuzhe; Cardozo, Timothy; Nyambi, Phillipe; Zolla-Pazner, Susan; Kong, Xiang-Peng

2011-01-01

Preferential usage of immunoglobulin (Ig) genes that encode antibodies (Abs) against various pathogens is rarely observed and the nature of their dominance is unclear in the context of stochastic recombination of Ig genes. The hypothesis that restricted usage of Ig genes predetermines the antibody specificity was tested in this study of 18 human anti-V3 monoclonal Abs (mAbs) generated from unrelated individuals infected with various subtypes of HIV-1, all of which preferentially used pairing of the VH5-51 and VL lambda genes. Crystallographic analysis of five VH5-51/VL lambda-encoded Fabs complexed with various V3 peptides revealed a common three dimensional (3D) shape of the antigen-binding sites primarily determined by the four complementarity determining regions (CDR) for the heavy (H) and light (L) chains: specifically, the H1, H2, L1 and L2 domains. The CDR H3 domain did not contribute to the shape of the binding pocket, as it had different lengths, sequences and conformations for each mAb. The same shape of the binding site was further confirmed by the identical backbone conformation exhibited by V3 peptides in complex with Fabs which fully adapted to the binding pocket and the same key contact residues, mainly germline-encoded in the heavy and light chains of five Fabs. Finally, the VH5-51 anti-V3 mAbs recognized an epitope with an identical 3D structure which is mimicked by a single mimotope recognized by the majority of VH5-51-derived mAbs but not by other V3 mAbs. These data suggest that the identification of preferentially used Ig genes by neutralizing mAbs may define conserved epitopes in the diverse virus envelopes. This will be useful information for designing vaccine immunogen inducing cross-neutralizing Abs. PMID:22164215

Amplitude spectrum distance: measuring the global shape divergence of protein fragments.

PubMed

Galiez, Clovis; Coste, François

2015-08-14

In structural bioinformatics, there is an increasing interest in identifying and understanding the evolution of local protein structures regarded as key structural or functional protein building blocks. A central need is then to compare these, possibly short, fragments by measuring efficiently and accurately their (dis)similarity. Progress towards this goal has given rise to scores enabling to assess the strong similarity of fragments. Yet, there is still a lack of more progressive scores, with meaningful intermediate values, for the comparison, retrieval or clustering of distantly related fragments. We introduce here the Amplitude Spectrum Distance (ASD), a novel way of comparing protein fragments based on the discrete Fourier transform of their C(α) distance matrix. Defined as the distance between their amplitude spectra, ASD can be computed efficiently and provides a parameter-free measure of the global shape dissimilarity of two fragments. ASD inherits from nice theoretical properties, making it tolerant to shifts, insertions, deletions, circular permutations or sequence reversals while satisfying the triangle inequality. The practical interest of ASD with respect to RMSD, RMSDd, BC and TM scores is illustrated through zinc finger retrieval experiments and concrete structure examples. The benefits of ASD are also illustrated by two additional clustering experiments: domain linkers fragments and complementarity-determining regions of antibodies. Taking advantage of the Fourier transform to compare fragments at a global shape level, ASD is an objective and progressive measure taking into account the whole fragments. Its practical computation time and its properties make ASD particularly relevant for applications requiring meaningful measures on distantly related protein fragments, such as similar fragments retrieval asking for high recalls as shown in the experiments, or for any application taking also advantage of triangle inequality, such as fragments clustering. ASD program and source code are freely available at: http://www.irisa.fr/dyliss/public/ASD/.

Quantification of in vivo site-specific Asp isomerization and Asn deamidation of mAbs in animal serum using IP-LC-MS.

PubMed

Mehl, John T; Sleczka, Bogdan G; Ciccimaro, Eugene F; Kozhich, Alexander T; Gilbertson, Deb G; Vuppugalla, Ragini; Huang, Christine S; Stevens, Brenda; Mo, Jingjie; Deyanova, Ekaterina G; Wang, Yun; Huang, Richard Yc; Chen, Guodong; Olah, Timothy V

2016-08-01

Isomerization of aspartic acid and deamidation of asparagine are two common amino acid modifications that are of particular concern if located within the complementarity-determining region of therapeutic antibodies. Questions arise as to the extent of modification occurring in circulation due to potential exposure of the therapeutic antibody to different pH regimes. To enable evaluation of site-specific isomerization and deamidation of human mAbs in vivo, immunoprecipitation (IP) has been combined with LC-MS providing selective enrichment, separation and detection of naive and modified forms of tryptic peptides comprising complementarity-determining region sequences. IP-LC-MS can be applied to simultaneously quantify in vivo drug concentrations and measure the extent of isomerization or deamidation in PK studies conducted during the drug discovery stage.

Household adoption of energy and water-efficient appliances: An analysis of attitudes, labelling and complementary green behaviours in selected OECD countries.

PubMed

Dieu-Hang, To; Grafton, R Quentin; Martínez-Espiñeira, Roberto; Garcia-Valiñas, Maria

2017-07-15

Using a household-based data set of more than 12,000 households from 11 OECD countries, we analyse the factors underlying the decision by households to adopt energy-efficient and water-efficient equipment. We evaluate the roles of both attitudes and labelling schemes on the adoption of energy and water-efficient equipment, and also the interaction and complementarity between energy and water conservation behaviours. Our findings show: one, 'green' social norms and favourable attitudes towards the environment are associated with an increased likelihood of households' adoption of energy and water-efficient appliances; two, households' purchase decisions are positively affected by their awareness, understanding, and trust of labelling schemes; and three, there is evidence of complementarity between energy conservation and water conservation behaviours. Copyright © 2017 Elsevier Ltd. All rights reserved.

A wave function for stock market returns

NASA Astrophysics Data System (ADS)

Ataullah, Ali; Davidson, Ian; Tippett, Mark

2009-02-01

The instantaneous return on the Financial Times-Stock Exchange (FTSE) All Share Index is viewed as a frictionless particle moving in a one-dimensional square well but where there is a non-trivial probability of the particle tunneling into the well’s retaining walls. Our analysis demonstrates how the complementarity principle from quantum mechanics applies to stock market prices and of how the wave function presented by it leads to a probability density which exhibits strong compatibility with returns earned on the FTSE All Share Index. In particular, our analysis shows that the probability density for stock market returns is highly leptokurtic with slight (though not significant) negative skewness. Moreover, the moments of the probability density determined under the complementarity principle employed here are all convergent - in contrast to many of the probability density functions on which the received theory of finance is based.

"It's best not to think about it at all-like the new taxes": Reality, observer, and complementarity in Bohr and Pauli

NASA Astrophysics Data System (ADS)

Plotnitsky, Arkady

2012-12-01

This article considers the concepts of reality, observer, and complementarity in Pauli and Bohr, and the similarities and, especially, differences in their understanding of these concepts, differences defined most essentially by their respective views of the role of the human observer in quantum measurement. These differences are significant even in the case of their respective interpretations of quantum phenomena and quantum mechanics, where the influence of Bohr's ideas on Pauli's understanding of quantum physics is particularly strong. They become especially strong and even radical in the case of their overall philosophical visions, where the impact of Jungean psychology, coupled to that of the earlier archetypal thinking of such figures as Kepler and Fludd, drives Pauli's thinking ever further away from that of Bohr.

Accelerator and reactor complementarity in coherent neutrino-nucleus scattering

NASA Astrophysics Data System (ADS)

Dent, James B.; Dutta, Bhaskar; Liao, Shu; Newstead, Jayden L.; Strigari, Louis E.; Walker, Joel W.

2018-02-01

We study the complementarity between accelerator and reactor coherent elastic neutrino-nucleus elastic scattering (CE ν NS ) experiments for constraining new physics in the form of nonstandard neutrino interactions (NSI). First, considering just data from the recent observation by the Coherent experiment, we explore interpretive degeneracies that emerge when activating either two or four unknown NSI parameters. Next, we demonstrate that simultaneous treatment of reactor and accelerator experiments, each employing at least two distinct target materials, can break a degeneracy between up and down flavor-diagonal NSI terms that survives analysis of neutrino oscillation experiments. Considering four flavor-diagonal (e e /μ μ ) up- and down-type NSI parameters, we find that all terms can be measured with high local precision (to a width as small as ˜5 % in Fermi units) by next-generation experiments, although discrete reflection ambiguities persist.

An evolutionary conserved pattern of 18S rRNA sequence complementarity to mRNA 5′ UTRs and its implications for eukaryotic gene translation regulation

PubMed Central

Pánek, Josef; Kolář, Michal; Vohradský, Jiří; Shivaya Valášek, Leoš

2013-01-01

There are several key mechanisms regulating eukaryotic gene expression at the level of protein synthesis. Interestingly, the least explored mechanisms of translational control are those that involve the translating ribosome per se, mediated for example via predicted interactions between the ribosomal RNAs (rRNAs) and mRNAs. Here, we took advantage of robustly growing large-scale data sets of mRNA sequences for numerous organisms, solved ribosomal structures and computational power to computationally explore the mRNA–rRNA complementarity that is statistically significant across the species. Our predictions reveal highly specific sequence complementarity of 18S rRNA sequences with mRNA 5′ untranslated regions (UTRs) forming a well-defined 3D pattern on the rRNA sequence of the 40S subunit. Broader evolutionary conservation of this pattern may imply that 5′ UTRs of eukaryotic mRNAs, which have already emerged from the mRNA-binding channel, may contact several complementary spots on 18S rRNA situated near the exit of the mRNA binding channel and on the middle-to-lower body of the solvent-exposed 40S ribosome including its left foot. We discuss physiological significance of this structurally conserved pattern and, in the context of previously published experimental results, propose that it modulates scanning of the 40S subunit through 5′ UTRs of mRNAs. PMID:23804757

Rescuing complementarity with little drama

NASA Astrophysics Data System (ADS)

Bao, Ning; Bouland, Adam; Chatwin-Davies, Aidan; Pollack, Jason; Yuen, Henry

2016-12-01

The AMPS paradox challenges black hole complementarity by apparently constructing a way for an observer to bring information from the outside of the black hole into its interior if there is no drama at its horizon, making manifest a violation of monogamy of entanglement. We propose a new resolution to the paradox: this violation cannot be explicitly checked by an infalling observer in the finite proper time they have to live after crossing the horizon. Our resolution depends on a weak relaxation of the no-drama condition (we call it "little-drama") which is the "complementarity dual" of scrambling of information on the stretched horizon. When translated to the description of the black hole interior, this implies that the fine-grained quantum information of infalling matter is rapidly diffused across the entire interior while classical observables and coarse-grained geometry remain unaffected. Under the assumption that information has diffused throughout the interior, we consider the difficulty of the information-theoretic task that an observer must perform after crossing the event horizon of a Schwarzschild black hole in order to verify a violation of monogamy of entanglement. We find that the time required to complete a necessary subroutine of this task, namely the decoding of Bell pairs from the interior and the late radiation, takes longer than the maximum amount of time that an observer can spend inside the black hole before hitting the singularity. Therefore, an infalling observer cannot observe monogamy violation before encountering the singularity.

AVC: Selecting discriminative features on basis of AUC by maximizing variable complementarity.

PubMed

Sun, Lei; Wang, Jun; Wei, Jinmao

2017-03-14

The Receiver Operator Characteristic (ROC) curve is well-known in evaluating classification performance in biomedical field. Owing to its superiority in dealing with imbalanced and cost-sensitive data, the ROC curve has been exploited as a popular metric to evaluate and find out disease-related genes (features). The existing ROC-based feature selection approaches are simple and effective in evaluating individual features. However, these approaches may fail to find real target feature subset due to their lack of effective means to reduce the redundancy between features, which is essential in machine learning. In this paper, we propose to assess feature complementarity by a trick of measuring the distances between the misclassified instances and their nearest misses on the dimensions of pairwise features. If a misclassified instance and its nearest miss on one feature dimension are far apart on another feature dimension, the two features are regarded as complementary to each other. Subsequently, we propose a novel filter feature selection approach on the basis of the ROC analysis. The new approach employs an efficient heuristic search strategy to select optimal features with highest complementarities. The experimental results on a broad range of microarray data sets validate that the classifiers built on the feature subset selected by our approach can get the minimal balanced error rate with a small amount of significant features. Compared with other ROC-based feature selection approaches, our new approach can select fewer features and effectively improve the classification performance.

Rescuing complementarity with little drama

DOE PAGES

Bao, Ning; Bouland, Adam; Chatwin-Davies, Aidan; ...

2016-12-07

The AMPS paradox challenges black hole complementarity by apparently constructing a way for an observer to bring information from the outside of the black hole into its interior if there is no drama at its horizon, making manifest a violation of monogamy of entanglement. We propose a new resolution to the paradox: this violation cannot be explicitly checked by an infalling observer in the finite proper time they have to live after crossing the horizon. Our resolution depends on a weak relaxation of the no-drama condition (we call it “little-drama”) which is the “complementarity dual” of scrambling of information onmore » the stretched horizon. When translated to the description of the black hole interior, this implies that the fine-grained quantum information of infalling matter is rapidly diffused across the entire interior while classical observables and coarse-grained geometry remain unaffected. Under the assumption that information has diffused throughout the interior, we consider the difficulty of the information-theoretic task that an observer must perform after crossing the event horizon of a Schwarzschild black hole in order to verify a violation of monogamy of entanglement. We find that the time required to complete a necessary subroutine of this task, namely the decoding of Bell pairs from the interior and the late radiation, takes longer than the maximum amount of time that an observer can spend inside the black hole before hitting the singularity. Furthermore, an infalling observer cannot observe monogamy violation before encountering the singularity.« less

Categorizing the telehealth policy response of countries and their implications for complementarity of telehealth policy.

PubMed

Varghese, Sunil; Scott, Richard E

2004-01-01

Developing countries are exploring the role of telehealth to overcome the challenges of providing adequate health care services. However, this process faces disparities, and no complementarity in telehealth policy development. Telehealth has the potential to transcend geopolitical boundaries, yet telehealth policy developed in one jurisdiction may hamper applications in another. Understanding such policy complexities is essential for telehealth to realize its full global potential. This study investigated 12 East Asian countries that may represent a microcosm of the world, to determine if the telehealth policy response of countries could be categorized, and whether any implications could be identified for the development of complementary telehealth policy. The countries were Cambodia, China, Hong Kong, Indonesia, Japan, Malaysia, Myanmar, Singapore, South Korea, Taiwan, Thailand, and Vietnam. Three categories of country response were identified in regard to national policy support and development. The first category was "None" (Cambodia, Myanmar, and Vietnam) where international partners, driven by humanitarian concerns, lead telehealth activity. The second category was "Proactive" (China, Indonesia, Malaysia, Singapore, South Korea, Taiwan, and Thailand) where national policies were designed with the view that telehealth initiatives are a component of larger development objectives. The third was "Reactive" (Hong Kong and Japan), where policies were only proffered after telehealth activities were sustainable. It is concluded that although complementarity of telehealth policy development is not occurring, increased interjurisdictional telehealth activity, regional clusters, and concerted and coordinated effort amongst researchers, practitioners, and policy makers may alter this trend.

Substitution and complementarity of alcohol and cannabis: A review of the literature

PubMed Central

2016-01-01

Background Whether alcohol and cannabis are used as substitutes or complements remains debated, and findings across various disciplines have not been synthesized to date. Objective This paper is a first step towards organizing the interdisciplinary literature on alcohol and cannabis substitution and complementarity. Method Electronic searches were performed using PubMed and ISI Web of Knowledge. Behavioral studies of humans with ‘alcohol’ (or ‘ethanol’) and ‘cannabis’ (or ‘marijuana”) and ‘complement*’ (or ‘substitut*’) in the title or as a keyword were considered. Studies were organized according to sample characteristics (youth, general population, clinical and community-based). These groups were not set a priori, but were informed by the literature review process. Results Of the 39 studies reviewed, 16 support substitution, ten support complementarity, 12 support neither and one supports both. Results from studies of youth suggest that youth may reduce alcohol in more liberal cannabis environments (substitute), but reduce cannabis in more stringent alcohol environments (complement). Results from the general population suggest that substitution of cannabis for alcohol may occur under more lenient cannabis policies, though cannabis-related laws may affect alcohol use differently across genders and racial groups. Conclusions Alcohol and cannabis act as both substitutes and complements. Policies aimed at one substance may inadvertently affect consumption of other substances. Future studies should collect fine-grained longitudinal, prospective data from the general population and subgroups of interest, especially in locations likely to legalize cannabis. PMID:27249324

Study of silicon crystal surface formation based on molecular dynamics simulation results

NASA Astrophysics Data System (ADS)

Barinovs, G.; Sabanskis, A.; Muiznieks, A.

2014-04-01

The equilibrium shape of <110>-oriented single crystal silicon nanowire, 8 nm in cross-section, was found from molecular dynamics simulations using LAMMPS molecular dynamics package. The calculated shape agrees well to the shape predicted from experimental observations of nanocavities in silicon crystals. By parametrization of the shape and scaling to a known value of {111} surface energy, Wulff form for solid-vapor interface was obtained. The Wulff form for solid-liquid interface was constructed using the same model of the shape as for the solid-vapor interface. The parameters describing solid-liquid interface shape were found using values of surface energies in low-index directions known from published molecular dynamics simulations. Using an experimental value of the liquid-vapor interface energy for silicon and graphical solution of Herring's equation, we constructed angular diagram showing relative equilibrium orientation of solid-liquid, liquid-vapor and solid-vapor interfaces at the triple phase line. The diagram gives quantitative predictions about growth angles for different growth directions and formation of facets on the solid-liquid and solid-vapor interfaces. The diagram can be used to describe growth ridges appearing on the crystal surface grown from a melt. Qualitative comparison to the ridges of a Float zone silicon crystal cone is given.

Quantification of Shape, Angularity, and Surface texture of Base Course Materials

DOT National Transportation Integrated Search

1998-01-01

A state-of-the-art review was conducted to determine existing test methods for characterizing the shape, angularity, and surface texture of coarse aggregates. The review found direct methods used by geologists to determine these characteristics. Thes...

Shape abnormalities of the striatum in Alzheimer's disease.

PubMed

de Jong, Laura W; Ferrarini, Luca; van der Grond, Jeroen; Milles, Julien R; Reiber, Johan H C; Westendorp, Rudi G J; Bollen, Edward L E M; Middelkoop, Huub A M; van Buchem, Mark A

2011-01-01

Postmortem studies show pathological changes in the striatum in Alzheimer's disease (AD). Here, we examine the surface of the striatum in AD and assess whether changes of the surface are associated with impaired cognitive functioning. The shape of the striatum (n. accumbens, caudate nucleus, and putamen) was compared between 35 AD patients and 35 individuals without cognitive impairment. The striatum was automatically segmented from 3D T1 magnetic resonance images and automatic shape modeling tools (Growing Adaptive Meshes) were applied for morphometrical analysis. Repeated permutation tests were used to identify locations of consistent shape deformities of the striatal surface in AD. Linear regression models, corrected for age, gender, educational level, head size, and total brain parenchymal volume were used to assess the relation between cognitive performance and local surface deformities. In AD patients, differences of shape were observed on the medial head of the caudate nucleus and on the ventral lateral putamen, but not on the accumbens. The head of the caudate nucleus and ventral lateral putamen are characterized by extensive connections with the orbitofrontal and medial temporal cortices. Severity of cognitive impairment was associated with the degree of deformity of the surfaces of the accumbens, rostral medial caudate nucleus, and ventral lateral putamen. These findings provide evidence for the hypothesis that in AD primarily associative and limbic cerebral networks are affected.

Curved Displacement Transfer Functions for Geometric Nonlinear Large Deformation Structure Shape Predictions

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran; Lung, Shun-Fat

2017-01-01

For shape predictions of structures under large geometrically nonlinear deformations, Curved Displacement Transfer Functions were formulated based on a curved displacement, traced by a material point from the undeformed position to deformed position. The embedded beam (depth-wise cross section of a structure along a surface strain-sensing line) was discretized into multiple small domains, with domain junctures matching the strain-sensing stations. Thus, the surface strain distribution could be described with a piecewise linear or a piecewise nonlinear function. The discretization approach enabled piecewise integrations of the embedded-beam curvature equations to yield the Curved Displacement Transfer Functions, expressed in terms of embedded beam geometrical parameters and surface strains. By entering the surface strain data into the Displacement Transfer Functions, deflections along each embedded beam can be calculated at multiple points for mapping the overall structural deformed shapes. Finite-element linear and nonlinear analyses of a tapered cantilever tubular beam were performed to generate linear and nonlinear surface strains and the associated deflections to be used for validation. The shape prediction accuracies were then determined by comparing the theoretical deflections with the finiteelement- generated deflections. The results show that the newly developed Curved Displacement Transfer Functions are very accurate for shape predictions of structures under large geometrically nonlinear deformations.

Surface shape affects the three-dimensional exploratory movements of nocturnal arboreal snakes.

PubMed

Jayne, Bruce C; Olberding, Jeffrey P; Athreya, Dilip; Riley, Michael A

2012-12-01

Movement and searching behaviors at diverse spatial scales are important for understanding how animals interact with their environment. Although the shapes of branches and the voids in arboreal habitats seem likely to affect searching behaviors, their influence is poorly understood. To gain insights into how both environmental structure and the attributes of an animal may affect movement and searching, we compared the three-dimensional exploratory movements of snakes in the dark on two simulated arboreal surfaces (disc and horizontal cylinder). Most of the exploratory movements of snakes in the dark were a small fraction of the distances they could reach while bridging gaps in the light. The snakes extended farther away from the edge of the supporting surface at the ends of the cylinder than from the sides of the cylinder or from any direction from the surface of the disc. The exploratory movements were not random, and the surface shape and three-dimensional directions had significant interactive effects on how the movements were structured in time. Thus, the physical capacity for reaching did not limit the area that was explored, but the shape of the supporting surface and the orientation relative to gravity did create biased searching patterns.

Laplace-Beltrami Eigenvalues and Topological Features of Eigenfunctions for Statistical Shape Analysis

PubMed Central

Reuter, Martin; Wolter, Franz-Erich; Shenton, Martha; Niethammer, Marc

2009-01-01

This paper proposes the use of the surface based Laplace-Beltrami and the volumetric Laplace eigenvalues and -functions as shape descriptors for the comparison and analysis of shapes. These spectral measures are isometry invariant and therefore allow for shape comparisons with minimal shape pre-processing. In particular, no registration, mapping, or remeshing is necessary. The discriminatory power of the 2D surface and 3D solid methods is demonstrated on a population of female caudate nuclei (a subcortical gray matter structure of the brain, involved in memory function, emotion processing, and learning) of normal control subjects and of subjects with schizotypal personality disorder. The behavior and properties of the Laplace-Beltrami eigenvalues and -functions are discussed extensively for both the Dirichlet and Neumann boundary condition showing advantages of the Neumann vs. the Dirichlet spectra in 3D. Furthermore, topological analyses employing the Morse-Smale complex (on the surfaces) and the Reeb graph (in the solids) are performed on selected eigenfunctions, yielding shape descriptors, that are capable of localizing geometric properties and detecting shape differences by indirectly registering topological features such as critical points, level sets and integral lines of the gradient field across subjects. The use of these topological features of the Laplace-Beltrami eigenfunctions in 2D and 3D for statistical shape analysis is novel. PMID:20161035

Finger-Shaped GelForce: Sensor for Measuring Surface Traction Fields for Robotic Hand.

PubMed

Sato, K; Kamiyama, K; Kawakami, N; Tachi, S

2010-01-01

It is believed that the use of haptic sensors to measure the magnitude, direction, and distribution of a force will enable a robotic hand to perform dexterous operations. Therefore, we develop a new type of finger-shaped haptic sensor using GelForce technology. GelForce is a vision-based sensor that can be used to measure the distribution of force vectors, or surface traction fields. The simple structure of the GelForce enables us to develop a compact finger-shaped GelForce for the robotic hand. GelForce that is developed on the basis of an elastic theory can be used to calculate surface traction fields using a conversion equation. However, this conversion equation cannot be analytically solved when the elastic body of the sensor has a complicated shape such as the shape of a finger. Therefore, we propose an observational method and construct a prototype of the finger-shaped GelForce. By using this prototype, we evaluate the basic performance of the finger-shaped GelForce. Then, we conduct a field test by performing grasping operations using a robotic hand. The results of this test show that using the observational method, the finger-shaped GelForce can be successfully used in a robotic hand.

Shape-memory surfaces for cell mechanobiology

PubMed Central

Ebara, Mitsuhiro

2015-01-01

Shape-memory polymers (SMPs) are a new class of smart materials, which have the capability to change from a temporary shape ‘A’ to a memorized permanent shape ‘B’ upon application of an external stimulus. In recent years, SMPs have attracted much attention from basic and fundamental research to industrial and practical applications due to the cheap and efficient alternative to well-known metallic shape-memory alloys. Since the shape-memory effect in SMPs is not related to a specific material property of single polymers, the control of nanoarchitecture of polymer networks is particularly important for the smart functions of SMPs. Such nanoarchitectonic approaches have enabled us to further create shape-memory surfaces (SMSs) with tunable surface topography at nano scale. The present review aims to bring together the exciting design of SMSs and the ever-expanding range of their uses as tools to control cell functions. The goal for these endeavors is to mimic the surrounding mechanical cues of extracellular environments which have been considered as critical parameters in cell fate determination. The untapped potential of SMSs makes them one of the most exciting interfaces of materials science and cell mechanobiology. PMID:27877747

Restoring warped document images through 3D shape modeling.

PubMed

Tan, Chew Lim; Zhang, Li; Zhang, Zheng; Xia, Tao

2006-02-01

Scanning a document page from a thick bound volume often results in two kinds of distortions in the scanned image, i.e., shade along the "spine" of the book and warping in the shade area. In this paper, we propose an efficient restoration method based on the discovery of the 3D shape of a book surface from the shading information in a scanned document image. From a technical point of view, this shape from shading (SFS) problem in real-world environments is characterized by 1) a proximal and moving light source, 2) Lambertian reflection, 3) nonuniform albedo distribution, and 4) document skew. Taking all these factors into account, we first build practical models (consisting of a 3D geometric model and a 3D optical model) for the practical scanning conditions to reconstruct the 3D shape of the book surface. We next restore the scanned document image using this shape based on deshading and dewarping models. Finally, we evaluate the restoration results by comparing our estimated surface shape with the real shape as well as the OCR performance on original and restored document images. The results show that the geometric and photometric distortions are mostly removed and the OCR results are improved markedly.

The Information Available to a Moving Observer on Shape with Unknown, Isotropic BRDFs.

PubMed

Chandraker, Manmohan

2016-07-01

Psychophysical studies show motion cues inform about shape even with unknown reflectance. Recent works in computer vision have considered shape recovery for an object of unknown BRDF using light source or object motions. This paper proposes a theory that addresses the remaining problem of determining shape from the (small or differential) motion of the camera, for unknown isotropic BRDFs. Our theory derives a differential stereo relation that relates camera motion to surface depth, which generalizes traditional Lambertian assumptions. Under orthographic projection, we show differential stereo may not determine shape for general BRDFs, but suffices to yield an invariant for several restricted (still unknown) BRDFs exhibited by common materials. For the perspective case, we show that differential stereo yields the surface depth for unknown isotropic BRDF and unknown directional lighting, while additional constraints are obtained with restrictions on the BRDF or lighting. The limits imposed by our theory are intrinsic to the shape recovery problem and independent of choice of reconstruction method. We also illustrate trends shared by theories on shape from differential motion of light source, object or camera, to relate the hardness of surface reconstruction to the complexity of imaging setup.

A theoretical prediction of the paradoxical surface free energy for FCC metallic nanosolids

NASA Astrophysics Data System (ADS)

Abdul-Hafidh, Esam H.; Aïssa, Brahim

2016-08-01

We report on the development of an efficient and simple method to calculate the surface free energy (surface tension) of a general-shaped metallic nanosolid. Both nanoparticles and nanostructures that account for the crystal structure and size were considered. The surface free energy of a face-centered cubic structure of a metallic nanoparticles was found to decrease as the size decreases, for a shape factor equal to 1.0 (i.e., spherical). However, when the shape factor exceeds this value, which includes disk-like, regular tetrahedral, regular hexahedral, regular octahedral, nanorod, and regular quadrangular structures, the behavior of the surface free energy was found to reverse, especially for small nanoparticles and then increases as the size decreases. Moreover, this behavior was systematically recorded for large nanoparticles when the mechanical distortion was appreciable. As a matter of fact, this model was also applied to the noble transition metals, including gold and silver nanoparticles. This work is a clear step forward establishing a systematic mechanism for controlling the mechanical properties of nanoscale particles by controlling the shape, size and structure.

The effect of texture on the shaft surface on the sealing performance of radial lip seals

NASA Astrophysics Data System (ADS)

Guo, Fei; Jia, XiaoHong; Gao, Zhi; Wang, YuMing

2014-07-01

On the basis of elastohydrodynamic model, the present study numerically analyzes the effect of various microdimple texture shapes, namely, circular, square, oriented isosceles triangular, on the pumping rate and the friction torque of radial lip seals, and determines the microdimple texture shape that can produce positive pumping rate. The area ratio, depth and shape dimension of a single texture are the most important geometric parameters which influence the tribological performance. According to the selected texture shape, parameter analysis is conducted to determine the optimal combination for the above three parameters. Simultaneously, the simulated performances of radial lip seal with texture on the shaft surface are compared with those of the conventional lip seal without any texture on the shaft surface.

Charged drop dynamics experiment using an electrostatic-acoustic hybrid system

NASA Technical Reports Server (NTRS)

Rhim, W. K.; Chung, S. K.; Trinh, E. H.; Elleman, D. D.

1987-01-01

The design and the performance of an electrostatic-acoustic hybrid system and its application to a charge drop rotation experiment are presented. This system can levitate a charged drop electrostatically and induce drop rotation or oscillation by imposing an acoustic torque or an oscillating acoustic pressure. Using this system, the equilibrium shapes and stability of a rotating charged drop were experimentally investigated. A 3 mm size water drop was rotated as a rigid body and its gyrostatic equilibrium shapes were observed. Families of axisymmetric shapes, two-lobed shapes, and eventual fissioning have been observed. With the assumption of 'effective surface tension' in which the surface charge simply modified the surface tension of neutral liquid, the results agree exceptionally well with the Brown and Scriven's (1980) prediction for uncharged drops.

Experimental evaluation of a new morphological approximation of the articular surfaces of the ankle joint.

PubMed

Belvedere, Claudio; Siegler, Sorin; Ensini, Andrea; Toy, Jason; Caravaggi, Paolo; Namani, Ramya; Giannini, Giulia; Durante, Stefano; Leardini, Alberto

2017-02-28

The mechanical characteristics of the ankle such as its kinematics and load transfer properties are influenced by the geometry of the articulating surfaces. A recent, image-based study found that these surfaces can be approximated by a saddle-shaped, skewed, truncated cone with its apex oriented laterally. The goal of this study was to establish a reliable experimental technique to study the relationship between the geometry of the articular surfaces of the ankle and its mobility and stability characteristics and to use this technique to determine if morphological approximations of the ankle surfaces based on recent discoveries, produce close to normal behavior. The study was performed on ten cadavers. For each specimen, a process based on medical imaging, modeling and 3D printing was used to produce two subject specific artificial implantable sets of the ankle surfaces. One set was a replica of the natural surfaces. The second approximated the ankle surfaces as an original saddle-shaped truncated cone with apex oriented laterally. Testing under cyclic loading conditions was then performed on each specimen following a previously established technique to determine its mobility and stability characteristics under three different conditions: natural surfaces; artificial surfaces replicating the natural surface morphology; and artificial approximation based on the saddle-shaped truncated cone concept. A repeated measure analysis of variance was then used to compare between the three conditions. The results show that (1): the artificial surfaces replicating natural morphology produce close to natural mobility and stability behavior thus establishing the reliability of the technique; and (2): the approximated surfaces based on saddle-shaped truncated cone concept produce mobility and stability behavior close to the ankle with natural surfaces. Copyright © 2017 Elsevier Ltd. All rights reserved.

OBSERVED ASTEROID SURFACE AREA IN THE THERMAL INFRARED

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

Nugent, C. R.; Mainzer, A.; Masiero, J.

The rapid accumulation of thermal infrared observations and shape models of asteroids has led to increased interest in thermophysical modeling. Most of these infrared observations are unresolved. We consider what fraction of an asteroid’s surface area contributes the bulk of the emitted thermal flux for two model asteroids of different shapes over a range of thermal parameters. The resulting observed surface in the infrared is generally more fragmented than the area observed in visible wavelengths, indicating high sensitivity to shape. For objects with low values of the thermal parameter, small fractions of the surface contribute the majority of thermally emittedmore » flux. Calculating observed areas could enable the production of spatially resolved thermal inertia maps from non-resolved observations of asteroids.« less

Aging and visual 3-D shape recognition from motion.

PubMed

Norman, J Farley; Adkins, Olivia C; Dowell, Catherine J; Hoyng, Stevie C; Shain, Lindsey M; Pedersen, Lauren E; Kinnard, Jonathan D; Higginbotham, Alexia J; Gilliam, Ashley N

2017-11-01

Two experiments were conducted to evaluate the ability of younger and older adults to recognize 3-D object shape from patterns of optical motion. In Experiment 1, participants were required to identify dotted surfaces that rotated in depth (i.e., surface structure portrayed using the kinetic depth effect). The task difficulty was manipulated by limiting the surface point lifetimes within the stimulus apparent motion sequences. In Experiment 2, the participants identified solid, naturally shaped objects (replicas of bell peppers, Capsicum annuum) that were defined by occlusion boundary contours, patterns of specular highlights, or combined optical patterns containing both boundary contours and specular highlights. Significant and adverse effects of increased age were found in both experiments. Despite the fact that previous research has found that increases in age do not reduce solid shape discrimination, our current results indicated that the same conclusion does not hold for shape identification. We demonstrated that aging results in a reduction in the ability to visually recognize 3-D shape independent of how the 3-D structure is defined (motions of isolated points, deformations of smooth optical fields containing specular highlights, etc.).

Classification of mathematics deficiency using shape and scale analysis of 3D brain structures

NASA Astrophysics Data System (ADS)

Kurtek, Sebastian; Klassen, Eric; Gore, John C.; Ding, Zhaohua; Srivastava, Anuj

2011-03-01

We investigate the use of a recent technique for shape analysis of brain substructures in identifying learning disabilities in third-grade children. This Riemannian technique provides a quantification of differences in shapes of parameterized surfaces, using a distance that is invariant to rigid motions and re-parameterizations. Additionally, it provides an optimal registration across surfaces for improved matching and comparisons. We utilize an efficient gradient based method to obtain the optimal re-parameterizations of surfaces. In this study we consider 20 different substructures in the human brain and correlate the differences in their shapes with abnormalities manifested in deficiency of mathematical skills in 106 subjects. The selection of these structures is motivated in part by the past links between their shapes and cognitive skills, albeit in broader contexts. We have studied the use of both individual substructures and multiple structures jointly for disease classification. Using a leave-one-out nearest neighbor classifier, we obtained a 62.3% classification rate based on the shape of the left hippocampus. The use of multiple structures resulted in an improved classification rate of 71.4%.

A shape-based account for holistic face processing.

PubMed

Zhao, Mintao; Bülthoff, Heinrich H; Bülthoff, Isabelle

2016-04-01

Faces are processed holistically, so selective attention to 1 face part without any influence of the others often fails. In this study, 3 experiments investigated what type of facial information (shape or surface) underlies holistic face processing and whether generalization of holistic processing to nonexperienced faces requires extensive discrimination experience. Results show that facial shape information alone is sufficient to elicit the composite face effect (CFE), 1 of the most convincing demonstrations of holistic processing, whereas facial surface information is unnecessary (Experiment 1). The CFE is eliminated when faces differ only in surface but not shape information, suggesting that variation of facial shape information is necessary to observe holistic face processing (Experiment 2). Removing 3-dimensional (3D) facial shape information also eliminates the CFE, indicating the necessity of 3D shape information for holistic face processing (Experiment 3). Moreover, participants show similar holistic processing for faces with and without extensive discrimination experience (i.e., own- and other-race faces), suggesting that generalization of holistic processing to nonexperienced faces requires facial shape information, but does not necessarily require further individuation experience. These results provide compelling evidence that facial shape information underlies holistic face processing. This shape-based account not only offers a consistent explanation for previous studies of holistic face processing, but also suggests a new ground-in addition to expertise-for the generalization of holistic processing to different types of faces and to nonface objects. (c) 2016 APA, all rights reserved).

The physics of water droplets on surfaces: exploring the effects of roughness and surface chemistry

NASA Astrophysics Data System (ADS)

Eid, K. F.; Panth, M.; Sommers, A. D.

2018-03-01

This paper explores the fluid property commonly called surface tension, its effect on droplet shape and contact angle, and the major influences of contact angle behaviour (i.e. surface roughness and surface chemistry). Images of water droplets placed on treated copper surfaces are used to measure the contact angles between the droplets and the surface. The surface wettability is manipulated either by growing a self-assembled monolayer on the surface to make it hydrophobic or by changing the surface roughness. The main activities in this experiment, then, are (1) preparing and studying surfaces with different surface wettability and roughness; (2) determining the shape and contact angles of water droplets on these surfaces; and (3) demonstrating the spontaneous motion of water droplets using surface tension gradients.

Radar-derived asteroid shapes point to a 'zone of stability' for topography slopes and surface erosion rates

NASA Astrophysics Data System (ADS)

Richardson, J.; Graves, K.; Bowling, T.

2014-07-01

Previous studies of the combined effects of asteroid shape, spin, and self-gravity have focused primarily upon the failure limits for bodies with a variety of standard shapes, friction, and cohesion values [1,2,3]. In this study, we look in the opposite direction and utilize 22 asteroid shape-models derived from radar inversion [4] and 7 small body shape-models derived from spacecraft observations [5] to investigate the region in shape/spin space [1,2] wherein self-gravity and rotation combine to produce a stable minimum state with respect to surface potential differences, dynamic topography, slope magnitudes, and erosion rates. This erosional minimum state is self-correcting, such that changes in the body's rotation rate, either up or down, will increase slope magnitudes across the body, thereby driving up erosion rates non-linearly until the body has once again reached a stable, minimized surface state [5]. We investigated this phenomenon in a systematic fashion using a series of synthesized, increasingly prolate spheroid shape models. Adjusting the rotation rate of each synthetic shape to minimize surface potential differences, dynamic topography, and slope magnitudes results in the magenta curve of the figure (right side), defining the zone of maximum surface stability (MSS). This MSS zone is invariant both with respect to body size (gravitational potential and rotational potential scale together with radius), and density when the scaled-spin of [2] is used. Within our sample of observationally derived small-body shape models, slow rotators (Group A: blue points), that are not in the maximum surface stability (MSS) zone and where gravity dominates the slopes, will generally experience moderate erosion rates (left plot) and will tend to move up and to the right in shape/spin space as the body evolves (right plot). Fast rotators (Group C: red points), that are not in the MSS zone and where spin dominates the slopes, will generally experience high erosion rates (left plot) and will tend to move down and to the left in shape/spin space as the body evolves (right plot), barring other influences such as YORP spin-up [6]. Moderate rotators (Group B: green points) have slopes that are influenced equally by gravity and spin, lie in or near the self-correcting MSS zone (right plot), and will generally experience the lowest erosion rates (left plot). These objects comprise 12 (43%) of the 28 bodies studied, perhaps indicating some prevalence for the MSS zone. On the other hand, a sample of 1300 asteroid shape and spin parameters (small grey points), derived from asteroid lightcurve data [7], do not show this same degree of correlation, perhaps indicating the relative weakness of erosion-driven shape modification as compared to other influences. We will continue to investigate this phenomenon as the number of detailed shape models from ground-based radar and other observations continues to increase.

Effect of crystal habits on the surface energy and cohesion of crystalline powders.

PubMed

Shah, Umang V; Olusanmi, Dolapo; Narang, Ajit S; Hussain, Munir A; Gamble, John F; Tobyn, Michael J; Heng, Jerry Y Y

2014-09-10

The role of surface properties, influenced by particle processing, in particle-particle interactions (powder cohesion) is investigated in this study. Wetting behaviour of mefenamic acid was found to be anisotropic by sessile drop contact angle measurements on macroscopic (>1cm) single crystals, with variations in contact angle of water from 56.3° to 92.0°. This is attributed to variations in surface chemical functionality at specific facets, and confirmed using X-ray photoelectron spectroscopy (XPS). Using a finite dilution inverse gas chromatography (FD-IGC) approach, the surface energy heterogeneity of powders was determined. The surface energy profile of different mefenamic acid crystal habits was directly related to the relative exposure of different crystal facets. Cohesion, determined by a uniaxial compression test, was also found to relate to surface energy of the powders. By employing a surface modification (silanisation) approach, the contribution from crystal shape from surface area and surface energy was decoupled. By "normalising" contribution from surface energy and surface area, needle shaped crystals were found to be ∼2.5× more cohesive compared to elongated plates or hexagonal cuboid shapes crystals. Copyright © 2014. Published by Elsevier B.V.

Shape Oscillations of Gas Bubbles With Newtonian Interfacial Rheological Properties

NASA Technical Reports Server (NTRS)

Nadim, Ali

1996-01-01

The oscillation frequency and damping rate for small-amplitude axisymmetric shape modes of a gas bubble in an ideal liquid are obtained, in the limit when the bubble interface possesses Newtonian interfacial rheology with constant surface shear and dilatational viscosities. Such results permit the latter surface properties to be measured by analyzing experimental data on frequency shift and damping rate of specific shape modes of suspended bubbles in the presence of surfactants.

Trans-Membrane Area Asymmetry Controls the Shape of Cellular Organelles

PubMed Central

Beznoussenko, Galina V.; Pilyugin, Sergei S.; Geerts, Willie J. C.; Kozlov, Michael M.; Burger, Koert N. J.; Luini, Alberto; Derganc, Jure; Mironov, Alexander A.

2015-01-01

Membrane organelles often have complicated shapes and differ in their volume, surface area and membrane curvature. The ratio between the surface area of the cytosolic and luminal leaflets (trans-membrane area asymmetry (TAA)) determines the membrane curvature within different sites of the organelle. Thus, the shape of the organelle could be critically dependent on TAA. Here, using mathematical modeling and stereological measurements of TAA during fast transformation of organelle shapes, we present evidence that suggests that when organelle volume and surface area are constant, TAA can regulate transformation of the shape of the Golgi apparatus, endosomal multivesicular bodies, and microvilli of brush borders of kidney epithelial cells. Extraction of membrane curvature by small spheres, such as COPI-dependent vesicles within the Golgi (extraction of positive curvature), or by intraluminal vesicles within endosomes (extraction of negative curvature) controls the shape of these organelles. For instance, Golgi tubulation is critically dependent on the fusion of COPI vesicles with Golgi cisternae, and vice versa, for the extraction of membrane curvature into 50–60 nm vesicles, to induce transformation of Golgi tubules into cisternae. Also, formation of intraluminal ultra-small vesicles after fusion of endosomes allows equilibration of their TAA, volume and surface area. Finally, when microvilli of the brush border are broken into vesicles and microvilli fragments, TAA of these membranes remains the same as TAA of the microvilli. Thus, TAA has a significant role in transformation of organelle shape when other factors remain constant. PMID:25761238

The Contribution of Object Shape and Surface Properties to Object Ensemble Representation in Anterior-medial Ventral Visual Cortex.

PubMed

Cant, Jonathan S; Xu, Yaoda

2017-02-01

Our visual system can extract summary statistics from large collections of objects without forming detailed representations of the individual objects in the ensemble. In a region in ventral visual cortex encompassing the collateral sulcus and the parahippocampal gyrus and overlapping extensively with the scene-selective parahippocampal place area (PPA), we have previously reported fMRI adaptation to object ensembles when ensemble statistics repeated, even when local image features differed across images (e.g., two different images of the same strawberry pile). We additionally showed that this ensemble representation is similar to (but still distinct from) how visual texture patterns are processed in this region and is not explained by appealing to differences in the color of the elements that make up the ensemble. To further explore the nature of ensemble representation in this brain region, here we used PPA as our ROI and investigated in detail how the shape and surface properties (i.e., both texture and color) of the individual objects constituting an ensemble affect the ensemble representation in anterior-medial ventral visual cortex. We photographed object ensembles of stone beads that varied in shape and surface properties. A given ensemble always contained beads of the same shape and surface properties (e.g., an ensemble of star-shaped rose quartz beads). A change to the shape and/or surface properties of all the beads in an ensemble resulted in a significant release from adaptation in PPA compared with conditions in which no ensemble feature changed. In contrast, in the object-sensitive lateral occipital area (LO), we only observed a significant release from adaptation when the shape of the ensemble elements varied, and found no significant results in additional scene-sensitive regions, namely, the retrosplenial complex and occipital place area. Together, these results demonstrate that the shape and surface properties of the individual objects comprising an ensemble both contribute significantly to object ensemble representation in anterior-medial ventral visual cortex and further demonstrate a functional dissociation between object- (LO) and scene-selective (PPA) visual cortical regions and within the broader scene-processing network itself.

Core@shell@shell structured carbon-based magnetic ternary nanohybrids: Synthesis and their enhanced microwave absorption properties

NASA Astrophysics Data System (ADS)

Yang, Erqi; Qi, Xiaosi; Xie, Ren; Bai, Zhongchen; Jiang, Yang; Qin, Shuijie; Zhong, Wei; Du, Youwei

2018-05-01

High encapsulation efficiency of core@shell@shell structured carbon-based magnetic ternary nanohybrids have been synthesized in high yield by chemical vapor deposition of acetylene directly over octahedral-shaped Fe2O3 nanoparticles. By controlling the pyrolysis temperature, Fe3O4@Fe3C@carbon nanotubes (CNTs) and Fe@Fe3C@CNTs ternary nanohybrids could be selectively produced. The optimal RL values for the as-prepared ternary nanohybrids could reach up to ca. -46.7, -52.7 and -29.5 dB, respectively. The excellent microwave absorption properties of the obtaiend ternary nanohybrids were proved to ascribe to the quarter-wavelength matching model. Moreover, the as-prepared Fe@Fe3C@CNTs ternary nanohybrids displayed remarkably enhanced EM wave absorption capabilities compared to Fe3O4@Fe3C@CNTs due to their excellent dielectric loss abilities, good complementarities between the dielectric loss and the magnetic loss, and high attenuation constant. Generally, this strategy can be extended to explore other categories of core@shell or core@shell@shell structured carbon-based nanohybrids, which is very beneficial to accelerate the advancements of high performance MAMs.

Precision is essential for efficient catalysis in an evolved Kemp eliminase.

PubMed

Blomberg, Rebecca; Kries, Hajo; Pinkas, Daniel M; Mittl, Peer R E; Grütter, Markus G; Privett, Heidi K; Mayo, Stephen L; Hilvert, Donald

2013-11-21

Linus Pauling established the conceptual framework for understanding and mimicking enzymes more than six decades ago. The notion that enzymes selectively stabilize the rate-limiting transition state of the catalysed reaction relative to the bound ground state reduces the problem of design to one of molecular recognition. Nevertheless, past attempts to capitalize on this idea, for example by using transition state analogues to elicit antibodies with catalytic activities, have generally failed to deliver true enzymatic rates. The advent of computational design approaches, combined with directed evolution, has provided an opportunity to revisit this problem. Starting from a computationally designed catalyst for the Kemp elimination--a well-studied model system for proton transfer from carbon--we show that an artificial enzyme can be evolved that accelerates an elementary chemical reaction 6 × 10(8)-fold, approaching the exceptional efficiency of highly optimized natural enzymes such as triosephosphate isomerase. A 1.09 Å resolution crystal structure of the evolved enzyme indicates that familiar catalytic strategies such as shape complementarity and precisely placed catalytic groups can be successfully harnessed to afford such high rate accelerations, making us optimistic about the prospects of designing more sophisticated catalysts.

Deck and Cable Dynamic Testing of a Single-span Bridge Using Radar Interferometry and Videometry Measurements

NASA Astrophysics Data System (ADS)

Piniotis, George; Gikas, Vassilis; Mpimis, Thanassis; Perakis, Harris

2016-03-01

This paper presents the dynamic testing of a roadway, single-span, cable-stayed bridge for a sequence of static load and ambient vibration monitoring scenarios. Deck movements were captured along both sideways of the bridge using a Digital Image Correlation (DIC) and a Ground-based Microwave Interfererometer (GBMI) system. Cable vibrations were measured at a single point location on each of the six cables using the GBMI technique. Dynamic testing involves three types of analyses; firstly, vibration analysis and modal parameter estimation (i. e., natural frequencies and modal shapes) of the deck using the combined DIC and GBMI measurements. Secondly, dynamic testing of the cables is performed through vibration analysis and experimental computation of their tension forces. Thirdly, the mechanism of cable-deck dynamic interaction is studied through their Power Spectra Density (PSD) and the Short Time Fourier Transform (STFT) analyses. Thereby, the global (deck and cable) and local (either deck or cable) bridge modes are identified, serving a concrete benchmark of the current state of the bridge for studying the evolution of its structural performance in the future. The level of synergy and complementarity between the GBMI and DIC techniques for bridge monitoring is also examined and assessed.

A conserved TLR5 binding and activation hot spot on flagellin.

PubMed

Song, Wan Seok; Jeon, Ye Ji; Namgung, Byeol; Hong, Minsun; Yoon, Sung-Il

2017-01-20

Flagellin is a bacterial protein that polymerizes into the flagellar filament and is essential for bacterial motility. When flagellated bacteria invade the host, flagellin is recognized by Toll-like receptor 5 (TLR5) as a pathogen invasion signal and eventually evokes the innate immune response. Here, we provide a conserved structural mechanism by which flagellins from Gram-negative γ-proteobacteria and Gram-positive Firmicutes bacteria bind and activate TLR5. The comparative structural analysis using our crystal structure of a complex between Bacillus subtilis flagellin (bsflagellin) and TLR5 at 2.1 Å resolution, combined with the alanine scanning analysis of the binding interface, reveals a common hot spot in flagellin for TLR5 activation. An arginine residue (bsflagellin R89) of the flagellin D1 domain and its adjacent residues (bsflagellin E114 and L93) constitute a hot spot that provides shape and chemical complementarity to a cavity generated by the loop of leucine-rich repeat 9 in TLR5. In addition to the flagellin D1 domain, the D0 domain also contributes to TLR5 activity through structurally dispersed regions, but not a single focal area. These results establish the groundwork for the future design of flagellin-based therapeutics.

Super-resolution fusion of complementary panoramic images based on cross-selection kernel regression interpolation.

PubMed

Chen, Lidong; Basu, Anup; Zhang, Maojun; Wang, Wei; Liu, Yu

2014-03-20

A complementary catadioptric imaging technique was proposed to solve the problem of low and nonuniform resolution in omnidirectional imaging. To enhance this research, our paper focuses on how to generate a high-resolution panoramic image from the captured omnidirectional image. To avoid the interference between the inner and outer images while fusing the two complementary views, a cross-selection kernel regression method is proposed. First, in view of the complementarity of sampling resolution in the tangential and radial directions between the inner and the outer images, respectively, the horizontal gradients in the expected panoramic image are estimated based on the scattered neighboring pixels mapped from the outer, while the vertical gradients are estimated using the inner image. Then, the size and shape of the regression kernel are adaptively steered based on the local gradients. Furthermore, the neighboring pixels in the next interpolation step of kernel regression are also selected based on the comparison between the horizontal and vertical gradients. In simulation and real-image experiments, the proposed method outperforms existing kernel regression methods and our previous wavelet-based fusion method in terms of both visual quality and objective evaluation.

Topography from shading and stereo

NASA Technical Reports Server (NTRS)

Horn, Berthold K. P.

1994-01-01

Methods exploiting photometric information in images that have been developed in machine vision can be applied to planetary imagery. Integrating shape from shading, binocular stereo, and photometric stereo yields a robust system for recovering detailed surface shape and surface reflectance information. Such a system is useful in producing quantitative information from the vast volume of imagery being received, as well as in helping visualize the underlying surface.

Solute transport by flow yields geometric shocks in shape evolution

NASA Astrophysics Data System (ADS)

Huang, Jinzi (Mac); Davies Wykes, Megan; Hajjar, George; Ristroph, Leif; Shelley, Michael

2017-11-01

Geological processes such as erosion and dissolution of surfaces often lead to striking shapes with strikingly sharp features. We present observations of such features forming in dissolution under gravity. In our experiment, a dissolving body with initially smooth surface evolves into an increasingly sharp needle shape. A mathematical model of its shape dynamics, derived from a boundary layer theory, predicts that a geometric shock forms at the tip of dissolved body, with the tip curvature becoming infinite in finite time. We further discuss the model's application to similar processes, such as flow driven erosion which can yield corners.

Geometries for roughness shapes in laminar flow

NASA Technical Reports Server (NTRS)

Holmes, Bruce J. (Inventor); Martin, Glenn L. (Inventor); Domack, Christopher S. (Inventor); Obara, Clifford J. (Inventor); Hassan, Ahmed A. (Inventor)

1986-01-01

A passive interface mechanism between upper and lower skin structures, and a leading edge structure of a laminar flow airfoil is described. The interface mechanism takes many shapes. All are designed to be different than the sharp orthogonal arrangement prevalent in the prior art. The shapes of the interface structures are generally of two types: steps away from the centerline of the airfoil with a sloping surface directed toward the trailing edge and, the other design has a gap before the sloping surface. By properly shaping the step, the critical step height is increased by more than 50% over the orthogonal edged step.

The integration of a mesh reflector to a 15-foot box truss structure. Task 3: Box truss analysis and technology development

NASA Technical Reports Server (NTRS)

Bachtell, E. E.; Thiemet, W. F.; Morosow, G.

1987-01-01

To demonstrate the design and integration of a reflective mesh surface to a deployable truss structure, a mesh reflector was installed on a 15 foot box truss cube. The specific features demonstrated include: (1) sewing seams in reflective mesh; (2) mesh stretching to desired preload; (3) installation of surface tie cords; (4) installation of reflective surface on truss; (5) setting of reflective surface; (6) verification of surface shape/accuracy; (7) storage and deployment; (8) repeatability of reflector surface; and (9) comparison of surface with predicted shape using analytical methods developed under a previous task.

Fabrication of hexagonal star-shaped and ring-shaped patterns arrays by Mie resonance sphere-lens-lithography

NASA Astrophysics Data System (ADS)

Liu, Xianchao; Wang, Jun; Li, Ling; Gou, Jun; Zheng, Jie; Huang, Zehua; Pan, Rui

2018-05-01

Mie resonance sphere-lens-lithography has proved to be a good candidate for fabrication of large-area tunable surface nanopattern arrays. Different patterns on photoresist surface are obtained theoretically by adjusting optical coupling among neighboring spheres with different gap sizes. The effect of light reflection from the substrate on the pattern produced on the photoresist with a thin thickness is also discussed. Sub-micron hexagonal star-shaped and ring-shaped patterns arrays are achieved with close-packed spheres arrays and spheres arrays with big gaps, respectively. Changing of star-shaped vertices is induced by different polarization of illumination. Experimental results agree well with the simulation. By using smaller resonance spheres, sub-400 nm star-shaped and ring-shaped patterns can be realized. These tunable patterns are different from results of previous reports and have enriched pattern morphology fabricated by sphere-lens-lithography, which can find application in biosensor and optic devices.

Method for shaping sheet thermoplastic and the like

NASA Technical Reports Server (NTRS)

Akilian, Mireille K. (Inventor); Schattenburg, Mark L. (Inventor)

2011-01-01

Processes and apparati for shaping sheet glass or thermoplastic materials use force from a layer of a flowing fluid, such as air, between the sheet and a mandrel at close to the softening temperature of the thermoplastic. The shape is preserved by cooling. The shape of the air bearing mandrel and the pressure distribution of the fluid contribute to the final shape. A process can be conducted on one or two surfaces such that the force from the air layer is on one or two surfaces of the sheet. The gap size between the sheet and mandrel determines the pressure profile in the gap, which also determines the final sheet shape. In general, smaller gaps lead to larger viscous forces. The pressure profile depends on the shape of the mandrel, the size of the fluid gap and the sheet and the fluid supply pressure.

Ternary Polymeric Composites Exhibiting Bulk and Surface Quadruple-Shape Memory Properties.

PubMed

Buffington, Shelby Lois; Posnick, Benjamin M; Paul, Justine Elizabeth; Mather, Patrick T

2018-06-19

We report the design and characterization of a multiphase quadruple shape memory composite capable of switching between 4 programmed shapes, three temporary and one permanent. Our approach combined two previously reported fabrication methods by embedding an electrospun mat of PCL in a miscible blend of epoxy monomers and PMMA as a composite matrix. As epoxy polymerization occurred the matrix underwent phase separation between the epoxy and PMMA materials. This created a multiphase composite with PCL fibers and a two-phase matrix composed of phase-separated epoxy and PMMA. The resulting composite demonstrated three separate thermal transitions and amenability to mechanical programming of three separate temporary shapes in addition to one final, equilibrium shape. In addition, quadruple surface shape memory abilities are successfully demonstrated. The versatility of this approach offers a large degree of design flexibility for multi-shape memory materials. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Surface Control of Cold Hibernated Elastic Memory Self-Deployable Structure

NASA Technical Reports Server (NTRS)

Sokolowski, Witold M.; Ghaffarian, Reza

2006-01-01

A new class of simple, reliable, lightweight, low packaging volume and cost, self-deployable structures has been developed for use in space and commercial applications. This technology called 'cold hibernated elastic memory' (CHEM) utilizes shape memory polymers (SMP)in open cellular (foam) structure or sandwich structures made of shape memory polymer foam cores and polymeric composite skins. Some of many potential CHEM space applications require a high precision deployment and surface accuracy during operation. However, a CHEM structure could be slightly distorted by the thermo-mechanical processing as well as by thermal space environment Therefore, the sensor system is desirable to monitor and correct the potential surface imperfection. During these studies, the surface control of CHEM smart structures was demonstrated using a Macro-Fiber Composite (MFC) actuator developed by the NASA LaRC and US Army ARL. The test results indicate that the MFC actuator performed well before and after processing cycles. It reduced some residue compressive strain that in turn corrected very small shape distortion after each processing cycle. The integrated precision strain gages were detecting only a small flat shape imperfection indicating a good recoverability of original shape of the CHEM test structure.

Complementarity of stability patches at the interfaces of protein complexes: Implication for the structural organization of energetic hot spots.

PubMed

Kuttner, Yosef Y; Engel, Stanislav

2018-02-01

A rational design of protein complexes with defined functionalities and of drugs aimed at disrupting protein-protein interactions requires fundamental understanding of the mechanisms underlying the formation of specific protein complexes. Efforts to develop efficient small-molecule or protein-based binders often exploit energetic hot spots on protein surfaces, namely, the interfacial residues that provide most of the binding free energy in the complex. The molecular basis underlying the unusually high energy contribution of the hot spots remains obscure, and its elucidation would facilitate the design of interface-targeted drugs. To study the nature of the energetic hot spots, we analyzed the backbone dynamic properties of contact surfaces in several protein complexes. We demonstrate that, in most complexes, the backbone dynamic landscapes of interacting surfaces form complementary "stability patches," in which static areas from the opposing surfaces superimpose, and that these areas are predominantly located near the geometric center of the interface. We propose that a diminished enthalpy-entropy compensation effect augments the degree to which residues positioned within the complementary stability patches contribute to complex affinity, thereby giving rise to the energetic hot spots. These findings offer new insights into the nature of energetic hot spots and the role that backbone dynamics play in facilitating intermolecular recognition. Mapping the interfacial stability patches may provide guidance for protein engineering approaches aimed at improving the stability of protein complexes and could facilitate the design of ligands that target complex interfaces. © 2017 Wiley Periodicals, Inc.

Influence of Molecular Shape on the Thermal Stability and Molecular Orientation of Vapor-Deposited Organic Semiconductors

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

Walters, Diane M; Antony, Lucas; de Pablo, Juan

High thermal stability and anisotropic molecular orientation enhance the performance of vapor-deposited organic semiconductors, but controlling these properties is a challenge in amorphous materials. To understand the influence of molecular shape on these properties, vapor-deposited glasses of three disk-shaped molecules were prepared. For all three systems, enhanced thermal stability is observed for glasses prepared over a wide range of substrate temperatures and anisotropic molecular orientation is observed at lower substrate temperatures. For two of the disk-shaped molecules, atomistic simulations of thin films were also performed and anisotropic molecular orientation was observed at the equilibrium liquid surface. We find that themore » structure and thermal stability of these vapor-deposited glasses results from high surface mobility and partial equilibration toward the structure of the equilibrium liquid surface during the deposition process. For the three molecules studied, molecular shape is a dominant factor in determining the anisotropy of vapor-deposited glasses.« less

New oxidation treatment of NiTi shape memory alloys to obtain Ni-free surfaces and to improve biocompatibility.

PubMed

Michiardi, A; Aparicio, C; Planell, J A; Gil, F J

2006-05-01

Various oxidation treatments were applied to nearly equiatomic NiTi alloys so as to form a Ni-free protective oxide on the surface. Sample surfaces were analyzed by X-ray Photoelectron Spectroscopy, and NiTi transformation temperatures were determined by differential scanning calorimetry (DSC) before and after the surface treatment. An ion release experiment was carried out up to one month of immersion in SBF for both oxidized and untreated surfaces. The results show that oxidation treatment in a low-oxygen pressure atmosphere leads to a high surface Ti/Ni ratio, a very low Ni surface concentration and a thick oxide layer. This oxidation treatment does not significantly affect the shape memory properties of the alloy. Moreover, the oxide formed significantly decreases Ni release into exterior medium comparing with untreated surfaces. As a consequence, this new oxidation treatment could be of great interest for biomedical applications, as it could minimize sensitization and allergies and improve biocompatibility and corrosion resistance of NiTi shape memory alloys. (c) 2005 Wiley Periodicals, Inc.

Orthogonal basis with a conicoid first mode for shape specification of optical surfaces.

PubMed

Ferreira, Chelo; López, José L; Navarro, Rafael; Sinusía, Ester Pérez

2016-03-07

A rigorous and powerful theoretical framework is proposed to obtain systems of orthogonal functions (or shape modes) to represent optical surfaces. The method is general so it can be applied to different initial shapes and different polynomials. Here we present results for surfaces with circular apertures when the first basis function (mode) is a conicoid. The system for aspheres with rotational symmetry is obtained applying an appropriate change of variables to Legendre polynomials, whereas the system for general freeform case is obtained applying a similar procedure to spherical harmonics. Numerical comparisons with standard systems, such as Forbes and Zernike polynomials, are performed and discussed.

A statistical shape modelling framework to extract 3D shape biomarkers from medical imaging data: assessing arch morphology of repaired coarctation of the aorta.

PubMed

Bruse, Jan L; McLeod, Kristin; Biglino, Giovanni; Ntsinjana, Hopewell N; Capelli, Claudio; Hsia, Tain-Yen; Sermesant, Maxime; Pennec, Xavier; Taylor, Andrew M; Schievano, Silvia

2016-05-31

Medical image analysis in clinical practice is commonly carried out on 2D image data, without fully exploiting the detailed 3D anatomical information that is provided by modern non-invasive medical imaging techniques. In this paper, a statistical shape analysis method is presented, which enables the extraction of 3D anatomical shape features from cardiovascular magnetic resonance (CMR) image data, with no need for manual landmarking. The method was applied to repaired aortic coarctation arches that present complex shapes, with the aim of capturing shape features as biomarkers of potential functional relevance. The method is presented from the user-perspective and is evaluated by comparing results with traditional morphometric measurements. Steps required to set up the statistical shape modelling analyses, from pre-processing of the CMR images to parameter setting and strategies to account for size differences and outliers, are described in detail. The anatomical mean shape of 20 aortic arches post-aortic coarctation repair (CoA) was computed based on surface models reconstructed from CMR data. By analysing transformations that deform the mean shape towards each of the individual patient's anatomy, shape patterns related to differences in body surface area (BSA) and ejection fraction (EF) were extracted. The resulting shape vectors, describing shape features in 3D, were compared with traditionally measured 2D and 3D morphometric parameters. The computed 3D mean shape was close to population mean values of geometric shape descriptors and visually integrated characteristic shape features associated with our population of CoA shapes. After removing size effects due to differences in body surface area (BSA) between patients, distinct 3D shape features of the aortic arch correlated significantly with EF (r = 0.521, p = .022) and were well in agreement with trends as shown by traditional shape descriptors. The suggested method has the potential to discover previously unknown 3D shape biomarkers from medical imaging data. Thus, it could contribute to improving diagnosis and risk stratification in complex cardiac disease.

Effects of Gear-Shape Fibre on the Transverse Mechanical Properties of Unidirectional Composites: Virtual Material Design by Computational Micromechanics

NASA Astrophysics Data System (ADS)

Yang, Lei; Li, Zhiwei; Sun, Tao; Wu, Zhanjun

2017-10-01

This paper aims to study the effect of fibre cross-section shape on the mechanical properties of unidirectional fibre reinforced composites. First, the specific surface area of different cross-section shape is compared, and the gear-shape fibre is selected for further study, which has the largest specific surface area. The effect of gear-shape fibre with various tooth number on the transverse mechanical properties of unidirectional composites is investigated by computational micromechanics, comparing with the traditional round fibre. It is found that all the gear-shape fibre reinforced composites have higher transverse stiffness and strength than the round fibre reinforced composite, and the gear-shape fibre with fewer tooth number has greater reinforcing effect on the mechanical properties of the composite. The mechanism of this phenomenon is revealed by examine the damage initiation and evolution process of the composite, and suggestion is made on the optimal cross-section shape of the reinforcing fibre for the composites.

Nonflat equilibrium liquid shapes on flat surfaces.

PubMed

Starov, Victor M

2004-01-15

The hydrostatic pressure in thin liquid layers differs from the pressure in the ambient air. This difference is caused by the actions of surface forces and capillary pressure. The manifestation of the surface force action is the disjoining pressure, which has a very special S-shaped form in the case of partial wetting (aqueous thin films and thin films of aqueous electrolyte and surfactant solutions, both free films and films on solid substrates). In thin flat liquid films the disjoining pressure acts alone and determines their thickness. However, if the film surface is curved then both the disjoining and the capillary pressures act simultaneously. In the case of partial wetting their simultaneous action results in the existence of nonflat equilibrium liquid shapes. It is shown that in the case of S-shaped disjoining pressure isotherm microdrops, microdepressions, and equilibrium periodic films exist on flat solid substrates. Criteria are found for both the existence and the stability of these nonflat equilibrium liquid shapes. It is shown that a transition from thick films to thinner films can go via intermediate nonflat states, microdepressions and periodic films, which both can be more stable than flat films within some range of hydrostatic pressure. Experimental investigations of shapes of the predicted nonflat layers can open new possibilities of determination of disjoining pressure in the range of thickness in which flat films are unstable.

Effect of surface oxidation on thermomechanical behavior of NiTi shape memory alloy wire

NASA Astrophysics Data System (ADS)

Ng, Ching Wei; Mahmud, Abdus Samad

2017-12-01

Nickel titanium (NiTi) alloy is a unique alloy that exhibits special behavior that recovers fully its shape after being deformed to beyond elastic region. However, this alloy is sensitive to any changes of its composition and introduction of inclusion in its matrix. Heat treatment of NiTi shape memory alloy to above 600 °C leads to the formation of the titanium oxide (TiO2) layer. Titanium oxide is a ceramic material that does not exhibit shape memory behaviors and possess different mechanical properties than that of NiTi alloy, thus disturbs the shape memory behavior of the alloy. In this work, the effect of formation of TiO2 surface oxide layer towards the thermal phase transformation and stress-induced deformation behaviors of the NiTi alloy were studied. The NiTi wire with composition of Ti-50.6 at% Ni was subjected to thermal oxidation at 600 °C to 900 °C for 30 and 60 minutes. The formation of the surface oxide layers was characterized by using the Scanning Electron Microscope (SEM). The effect of surface oxide layers with different thickness towards the thermal phase transformation behavior was studied by using the Differential Scanning Calorimeter (DSC). The effect of surface oxidation towards the stress-induced deformation behavior was studied through the tensile deformation test. The stress-induced deformation behavior and the shape memory recovery of the NiTi wire under tensile deformation were found to be affected marginally by the formation of thick TiO2 layer.

Advanced flow-polishing and surface metrology of the SO56 X Ray Telescope

NASA Technical Reports Server (NTRS)

1992-01-01

The surface finishing of X ray grazing incidence optics is a most demanding area of optical processing, both in terms of metrology and application of optical finishing techniques. An existing optical mirror was processed using a new removal technique that uses a jet of finely dispersed and extremely small particles that impact a surface, which under the correct conditions, produces an ultrasmooth surface, especially on aspheric curvatures. The surfaces of the SO56 mirror are tapered conical shapes that have a continuously changing radius with the primary mirror having a parabolic shape and the secondary mirror a hyperbolic shape. An optical ray trace that was conducted of a telescope used the measured parameters from the existing substrates to set up the prescription for the optical layout. The optimization indicated a wavefront performance of 0.10 A at 0.633 micron.

Hexagonal bubble formation and nucleation in sodium chloride solution

NASA Astrophysics Data System (ADS)

Wang, Lifen; Liu, Lei; Mohsin, Ali; Wen, Jianguo; Gu, Gong; Miller, Dean

The bubble is formed frequently at a solid-liquid interface when the surface of the solid or liquid has a tendency of accumulating molecular species due to unbalanced surface hydrophobicity attraction. Morphology and shape of the bubble are thought to be associated with the Laplace pressure that spherical-cap-shaped object are commonly observed. Dynamic surface nanobubble formation and nucleation in the controlled system have been not fully investigated due to the direct visualization challenge in liquid systems. Here, utilizing in situ TEM, dynamic formation and collapse of spherical-shaped nanobubbles were observed at the water-graphene interface, while hexagonal nanobubbles grew and merged with each other at water-crystalline sodium chloride interface. Our finding demonstrates that different hydrophobic-hydrophilic interaction systems give rise to the varied morphology of surface nanobubble, leading to the fundamental understanding of the interface-interaction-governed law on the formation of surface nanobubble.

Using tobacco mosaic virus to probe enhanced surface diffusion of molecular glasses.

PubMed

Zhang, Yue; Potter, Richard; Zhang, William; Fakhraai, Zahra

2016-11-09

Recent studies have shown that diffusion on the surface of organic glasses can be many orders of magnitude faster than bulk diffusion. Developing new probes that can readily measure surface diffusion can help study the effect of parameters such as chemical structure, intermolecular interaction, molecules' shape and size on the enhanced surface diffusion. In this study, we develop a novel probe that significantly simplifies these types of studies. Tobacco mosaic virus (TMV) is used as probe particle to measure surface diffusion coefficient of molecular glass N,N'-bis(3-methylphenyl)-N,N'-diphenylbenzidine (TPD). The evolution of the meniscus formed around TMV is probed as a function of time at various temperatures. TMV has a well-defined, mono-dispersed, cylindrical shape, with a large aspect-ratio (average diameter of 16.6 nm, length of 300 nm). As such, the shape of the meniscus around the center of TMV is semi-two dimensional, which compared to using a nanosphere as probe, increases the driving force for meniscus formation and simplifies the analysis of surface diffusion. We show that under these conditions, after a short transient time the shape of the meniscus is self-similar, allowing accurate determination of the surface diffusion coefficient. Measurements at various temperatures are then performed to investigate the temperature dependence of the surface diffusion coefficient. It is found that surface diffusion is greatly enhanced in TPD and has a lower activation barrier compared to the bulk counterpart. These observations are consistent with previous studies of surface diffusion on molecular glasses, demonstrating the accuracy of this method.

Complementarity of information and the emergence of the classical world

NASA Astrophysics Data System (ADS)

Zwolak, Michael; Zurek, Wojciech

2013-03-01

We prove an anti-symmetry property relating accessible information about a system through some auxiliary system F and the quantum discord with respect to a complementary system F'. In Quantum Darwinism, where fragments of the environment relay information to observers - this relation allows us to understand some fundamental properties regarding correlations between a quantum system and its environment. First, it relies on a natural separation of accessible information and quantum information about a system. Under decoherence, this separation shows that accessible information is maximized for the quasi-classical pointer observable. Other observables are accessible only via correlations with the pointer observable. Second, It shows that objective information becomes accessible to many observers only when quantum information is relegated to correlations with the global environment, and, therefore, locally inaccessible. The resulting complementarity explains why, in a quantum Universe, we perceive objective classical reality, and supports Bohr's intuition that quantum phenomena acquire classical reality only when communicated.

de Sitter space as a tensor network: Cosmic no-hair, complementarity, and complexity

NASA Astrophysics Data System (ADS)

Bao, Ning; Cao, ChunJun; Carroll, Sean M.; Chatwin-Davies, Aidan

2017-12-01

We investigate the proposed connection between de Sitter spacetime and the multiscale entanglement renormalization ansatz (MERA) tensor network, and ask what can be learned via such a construction. We show that the quantum state obeys a cosmic no-hair theorem: the reduced density operator describing a causal patch of the MERA asymptotes to a fixed point of a quantum channel, just as spacetimes with a positive cosmological constant asymptote to de Sitter space. The MERA is potentially compatible with a weak form of complementarity (local physics only describes single patches at a time, but the overall Hilbert space is infinite dimensional) or, with certain specific modifications to the tensor structure, a strong form (the entire theory describes only a single patch plus its horizon, in a finite-dimensional Hilbert space). We also suggest that de Sitter evolution has an interpretation in terms of circuit complexity, as has been conjectured for anti-de Sitter space.

Comment on measuring the tt forward-backward asymmetry at ATLAS and CMS

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

Arguin, Jean-Francois; Ligeti, Zoltan; Freytsis, Marat

2011-10-01

We suggest a new possibility for ATLAS and CMS to explore the tt forward-backward asymmetry measured at the Tevatron, by attempting to reconstruct tt events, with one of the tops decaying semileptonically in the central region (|{eta}|<2.5) and the other decaying hadronically in the forward region (|{eta}|>2.5). For several models which give comparable Tevatron signals, we study the charge asymmetry at the LHC as a function of cuts on |{eta}| and on the tt invariant mass, m{sub tt}. We show that there is an interesting complementarity between cuts on |{eta}| and m{sub tt} to suppress the dominant and symmetric gg{yields}ttmore » rate, and different combinations of cuts enhance the distinguishing power between models. This complementarity is likely to hold in other new physics scenarios as well, which affect the tt cross section, so it motivates extending tt reconstruction to higher |{eta}|.« less

Theory of Excitonic Delocalization for Robust Vibronic Dynamics in LH2.

PubMed

Caycedo-Soler, Felipe; Lim, James; Oviedo-Casado, Santiago; van Hulst, Niek F; Huelga, Susana F; Plenio, Martin B

2018-06-11

Nonlinear spectroscopy has revealed long-lasting oscillations in the optical response of a variety of photosynthetic complexes. Different theoretical models that involve the coherent coupling of electronic (excitonic) or electronic-vibrational (vibronic) degrees of freedom have been put forward to explain these observations. The ensuing debate concerning the relevance of either mechanism may have obscured their complementarity. To illustrate this balance, we quantify how the excitonic delocalization in the LH2 unit of Rhodopseudomonas acidophila purple bacterium leads to correlations of excitonic energy fluctuations, relevant coherent vibronic coupling, and importantly, a decrease in the excitonic dephasing rates. Combining these effects, we identify a feasible origin for the long-lasting oscillations observed in fluorescent traces from time-delayed two-pulse single-molecule experiments performed on this photosynthetic complex and use this approach to discuss the role of this complementarity in other photosynthetic systems.

Complementarity of quantum discord and classically accessible information

DOE PAGES

Zwolak, Michael P.; Zurek, Wojciech H.

2013-05-20

The sum of the Holevo quantity (that bounds the capacity of quantum channels to transmit classical information about an observable) and the quantum discord (a measure of the quantumness of correlations of that observable) yields an observable-independent total given by the quantum mutual information. This split naturally delineates information about quantum systems accessible to observers – information that is redundantly transmitted by the environment – while showing that it is maximized for the quasi-classical pointer observable. Other observables are accessible only via correlations with the pointer observable. In addition, we prove an anti-symmetry property relating accessible information and discord. Itmore » shows that information becomes objective – accessible to many observers – only as quantum information is relegated to correlations with the global environment, and, therefore, locally inaccessible. Lastly, the resulting complementarity explains why, in a quantum Universe, we perceive objective classical reality while flagrantly quantum superpositions are out of reach.« less

Power Moves Beyond Complementarity: A Staring Look Elicits Avoidance in Low Power Perceivers and Approach in High Power Perceivers

PubMed Central

Weick, Mario; McCall, Cade; Blascovich, Jim

2017-01-01

Sustained, direct eye-gaze—staring—is a powerful cue that elicits strong responses in many primate and nonprimate species. The present research examined whether fleeting experiences of high and low power alter individuals’ spontaneous responses to the staring gaze of an onlooker. We report two experimental studies showing that sustained, direct gaze elicits spontaneous avoidance tendencies in low power perceivers and spontaneous approach tendencies in high power perceivers. These effects emerged during interactions with different targets and when power was manipulated between-individuals (Study 1) and within-individuals (Study 2), thus attesting to a high degree of flexibility in perceivers’ reactions to gaze cues. Together, the present findings indicate that power can break the cycle of complementarity in individuals’ spontaneous responding: Low power perceivers complement and move away from, and high power perceivers reciprocate and move toward, staring onlookers. PMID:28903712

Extended Minus-Strand DNA as Template for R-U5-Mediated Second-Strand Transfer in Recombinational Rescue of Primer Binding Site-Modified Retroviral Vectors

PubMed Central

Mikkelsen, Jacob Giehm; Lund, Anders H.; Dybkær, Karen; Duch, Mogens; Pedersen, Finn Skou

1998-01-01

We have previously demonstrated recombinational rescue of primer binding site (PBS)-impaired Akv murine leukemia virus-based vectors involving initial priming on endogenous viral sequences and template switching during cDNA synthesis to obtain PBS complementarity in second-strand transfer of reverse transcription (Mikkelsen et al., J. Virol. 70:1439–1447, 1996). By use of the same forced recombination system, we have now found recombinant proviruses of different structures, suggesting that PBS knockout vectors may be rescued through initial priming on endogenous virus RNA, read-through of the mutated PBS during minus-strand synthesis, and subsequent second-strand transfer mediated by the R-U5 complementarity of the plus strand and the extended minus-strand DNA acceptor template. Mechanisms for R-U5-mediated second-strand transfer and its possible role in retrovirus replication and evolution are discussed. PMID:9499117

The extent of sequence complementarity correlates with the potency of cellular miRNA-mediated restriction of HIV-1

PubMed Central

Houzet, Laurent; Klase, Zachary; Yeung, Man Lung; Wu, Annie; Le, Shu-Yun; Quiñones, Mariam; Jeang, Kuan-Teh

2012-01-01

MicroRNAs (miRNAs) are 22-nt non-coding RNAs involved in the regulation of cellular gene expression and potential cellular defense against viral infection. Using in silico analyses, we predicted target sites for 22 human miRNAs in the HIV genome. Transfection experiments using synthetic miRNAs showed that five of these miRNAs capably decreased HIV replication. Using one of these five miRNAs, human miR-326 as an example, we demonstrated that the degree of complementarity between the predicted viral sequence and cellular miR-326 correlates, in a Dicer-dependent manner, with the potency of miRNA-mediated restriction of viral replication. Antagomirs to miR-326 that knocked down this cell endogenous miRNA increased HIV-1 replication in cells, suggesting that miR-326 is physiologically functional in moderating HIV-1 replication in human cells. PMID:23042677

Nonlocality versus complementarity: a conservative approach to the information problem

NASA Astrophysics Data System (ADS)

Giddings, Steven B.

2011-01-01

A proposal for resolution of the information paradox is that 'nice slice' states, which have been viewed as providing a sharp argument for information loss, do not in fact do so as they do not give a fully accurate description of the quantum state of a black hole. This however leaves an information problem, which is to provide a consistent description of how information escapes when a black hole evaporates. While a rather extreme form of nonlocality has been advocated in the form of complementarity, this paper argues that is not necessary, and more modest nonlocality could solve the information problem. One possible distinguishing characteristic of scenarios is the information retention time. The question of whether such nonlocality implies acausality, and particularly inconsistency, is briefly addressed. The need for such nonlocality, and its apparent tension with our empirical observations of local quantum field theory, may be a critical missing piece in understanding the principles of quantum gravity.

Robust surface reconstruction by design-guided SEM photometric stereo

NASA Astrophysics Data System (ADS)

Miyamoto, Atsushi; Matsuse, Hiroki; Koutaki, Gou

2017-04-01

We present a novel approach that addresses the blind reconstruction problem in scanning electron microscope (SEM) photometric stereo for complicated semiconductor patterns to be measured. In our previous work, we developed a bootstrapping de-shadowing and self-calibration (BDS) method, which automatically calibrates the parameter of the gradient measurement formulas and resolves shadowing errors for estimating an accurate three-dimensional (3D) shape and underlying shadowless images. Experimental results on 3D surface reconstruction demonstrated the significance of the BDS method for simple shapes, such as an isolated line pattern. However, we found that complicated shapes, such as line-and-space (L&S) and multilayered patterns, produce deformed and inaccurate measurement results. This problem is due to brightness fluctuations in the SEM images, which are mainly caused by the energy fluctuations of the primary electron beam, variations in the electronic expanse inside a specimen, and electrical charging of specimens. Despite these being essential difficulties encountered in SEM photometric stereo, it is difficult to model accurately all the complicated physical phenomena of electronic behavior. We improved the robustness of the surface reconstruction in order to deal with these practical difficulties with complicated shapes. Here, design data are useful clues as to the pattern layout and layer information of integrated semiconductors. We used the design data as a guide of the measured shape and incorporated a geometrical constraint term to evaluate the difference between the measured and designed shapes into the objective function of the BDS method. Because the true shape does not necessarily correspond to the designed one, we use an iterative scheme to develop proper guide patterns and a 3D surface that provides both a less distorted and more accurate 3D shape after convergence. Extensive experiments on real image data demonstrate the robustness and effectiveness of our method.

Computer Aided Process Planning for Non-Axisymmetric Deep Drawing Products

NASA Astrophysics Data System (ADS)

Park, Dong Hwan; Yarlagadda, Prasad K. D. V.

2004-06-01

In general, deep drawing products have various cross-section shapes such as cylindrical, rectangular and non-axisymmetric shapes. The application of the surface area calculation to non-axisymmetric deep drawing process has not been published yet. In this research, a surface area calculation for non-axisymmetric deep drawing products with elliptical shape was constructed for a design of blank shape of deep drawing products by using an AutoLISP function of AutoCAD software. A computer-aided process planning (CAPP) system for rotationally symmetric deep drawing products has been developed. However, the application of the system to non-axisymmetric components has not been reported yet. Thus, the CAPP system for non-axisymmetric deep drawing products with elliptical shape was constructed by using process sequence design. The system developed in this work consists of four modules. The first is recognition of shape module to recognize non-axisymmetric products. The second is a three-dimensional (3-D) modeling module to calculate the surface area for non-axisymmetric products. The third is a blank design module to create an oval-shaped blank with the identical surface area. The forth is a process planning module based on the production rules that play the best important role in an expert system for manufacturing. The production rules are generated and upgraded by interviewing field engineers. Especially, the drawing coefficient, the punch and die radii for elliptical shape products are considered as main design parameters. The suitability of this system was verified by applying to a real deep drawing product. This CAPP system constructed would be very useful to reduce lead-time for manufacturing and improve an accuracy of products.

Shape Effect Undermined by Surface Reconstruction: Ethanol Dehydrogenation over Shape-Controlled SrTiO 3 Nanocrystals

DOE PAGES

Foo, Guo Shiou; Hood, Zachary D.; Wu, Zili

2017-12-05

For this research, to gain an in-depth understanding of the surface properties relevant for catalysis using ternary oxides, we report the acid–base pair reactivity of shape-controlled SrTiO 3 (STO) nanocrystals for the dehydrogenation of ethanol. Cubes, truncated cubes, dodecahedra, and etched cubes of STO with varying ratios of (001) and (110) crystal facets were synthesized using a hydrothermal method. Low-energy ion scattering (LEIS) analysis revealed that the (001) surface on cubes of STO is enriched with SrO due to surface reconstruction, resulting in a high ratio of strong base sites. Chemical treatment with dilute nitric acid to form etched cubesmore » of STO resulted in a surface enriched with Ti cations and strong acidity. Furthermore, the strength and distribution of surface acidic sites increase with the ratio of (110) facet from cubes to truncated cubes to dodecahedra for STO. Kinetic, isotopic, and spectroscopy methods show that the dehydrogenation of ethanol proceeds through the facile dissociation of the alcohol group, followed by the cleavage of the C α–H bond, which is the rate-determining step. Co-feeding of various probe molecules during catalysis, such as NH 3, 2,6-di-tert-butylpyridine, CO 2, and SO 2, reveals that a pair of Lewis acid site and basic surface oxygen atom is involved in the dehydrogenation reaction. The surface density of acid–base site pairs was measured using acetic acid as a probe molecule, allowing initial acetaldehyde formation turnover rates to be obtained. Comparison among various catalysts reveals no simple correlation between ethanol turnover rate and the percentage of either surface facet ((001) or (110)) of the STO nanocrystals. Instead, the reaction rate is found to increase with the strength of acid sites but reversely with the strength of base sites. The acid–base property is directly related to the surface composition as a result from different surface reconstruction behaviors of the shaped STO nanocrystals. Lastly, the finding in this work underscores the importance of characterizing the top surface compositions and sites properties when assessing the catalytic performance of shape-controlled complex oxides such as perovskites.« less

Shape Effect Undermined by Surface Reconstruction: Ethanol Dehydrogenation over Shape-Controlled SrTiO 3 Nanocrystals

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

Foo, Guo Shiou; Hood, Zachary D.; Wu, Zili

For this research, to gain an in-depth understanding of the surface properties relevant for catalysis using ternary oxides, we report the acid–base pair reactivity of shape-controlled SrTiO 3 (STO) nanocrystals for the dehydrogenation of ethanol. Cubes, truncated cubes, dodecahedra, and etched cubes of STO with varying ratios of (001) and (110) crystal facets were synthesized using a hydrothermal method. Low-energy ion scattering (LEIS) analysis revealed that the (001) surface on cubes of STO is enriched with SrO due to surface reconstruction, resulting in a high ratio of strong base sites. Chemical treatment with dilute nitric acid to form etched cubesmore » of STO resulted in a surface enriched with Ti cations and strong acidity. Furthermore, the strength and distribution of surface acidic sites increase with the ratio of (110) facet from cubes to truncated cubes to dodecahedra for STO. Kinetic, isotopic, and spectroscopy methods show that the dehydrogenation of ethanol proceeds through the facile dissociation of the alcohol group, followed by the cleavage of the C α–H bond, which is the rate-determining step. Co-feeding of various probe molecules during catalysis, such as NH 3, 2,6-di-tert-butylpyridine, CO 2, and SO 2, reveals that a pair of Lewis acid site and basic surface oxygen atom is involved in the dehydrogenation reaction. The surface density of acid–base site pairs was measured using acetic acid as a probe molecule, allowing initial acetaldehyde formation turnover rates to be obtained. Comparison among various catalysts reveals no simple correlation between ethanol turnover rate and the percentage of either surface facet ((001) or (110)) of the STO nanocrystals. Instead, the reaction rate is found to increase with the strength of acid sites but reversely with the strength of base sites. The acid–base property is directly related to the surface composition as a result from different surface reconstruction behaviors of the shaped STO nanocrystals. Lastly, the finding in this work underscores the importance of characterizing the top surface compositions and sites properties when assessing the catalytic performance of shape-controlled complex oxides such as perovskites.« less

An Elliptic PDE Approach for Shape Characterization

PubMed Central

Haidar, Haissam; Bouix, Sylvain; Levitt, James; McCarley, Robert W.; Shenton, Martha E.; Soul, Janet S.

2009-01-01

This paper presents a novel approach to analyze the shape of anatomical structures. Our methodology is rooted in classical physics and in particular Poisson's equation, a fundamental partial differential equation [1]. The solution to this equation and more specifically its equipotential surfaces display properties that are useful for shape analysis. We present a numerical algorithm to calculate the length of streamlines formed by the gradient field of the solution to this equation for 2D and 3D objects. The length of the streamlines along the equipotential surfaces was used to build a new function which can characterize the shape of objects. We illustrate our method on 2D synthetic and natural shapes as well as 3D medical data. PMID:17271986

Laser diode assembly including a cylindrical lens

DOEpatents

Snyder, James J.; Reichert, Patrick

1992-01-01

The present invention provides a diffraction limited, high numerical aperture (fast) cylindrical microlens. The method for making the microlens is adaptable to produce a cylindrical lens that has almost any shape on its optical surfaces. The cylindrical lens may have a shape, such as elliptical or hyperbolic, designed to transform some particular given input light distribution into some desired output light distribution. In the method, the desired shape is first formed in a glass preform. Then, the preform is heated to the minimum drawing temperature and a fiber is drawn from it. The cross-sectional shape of the fiber bears a direct relation to the shape of the preform from which it was drawn. During the drawing process, the surfaces become optically smooth due to fire polishing.

Viability of Using Diamond Field Emitter Array Cathodes in Free Electron Lasers

DTIC Science & Technology

2010-06-01

essential component of a field emitter array is the shape of the electric field lines and equipotential lines at the surface of the array. The...BARRIER AND QUANTUM TUNNELING ...........25 B. FIELD ENHANCEMENT AND SURFACE PROTRUSIONS .........26 C. ELECTRIC FIELDS AND ELECTRON TRAVEL...26 Figure 4. Diagram of a protrusion (triangular in shape) from the surface of a cathode. The protrusion is of height h, with a

A subdivision-based parametric deformable model for surface extraction and statistical shape modeling of the knee cartilages

NASA Astrophysics Data System (ADS)

Fripp, Jurgen; Crozier, Stuart; Warfield, Simon K.; Ourselin, Sébastien

2006-03-01

Subdivision surfaces and parameterization are desirable for many algorithms that are commonly used in Medical Image Analysis. However, extracting an accurate surface and parameterization can be difficult for many anatomical objects of interest, due to noisy segmentations and the inherent variability of the object. The thin cartilages of the knee are an example of this, especially after damage is incurred from injuries or conditions like osteoarthritis. As a result, the cartilages can have different topologies or exist in multiple pieces. In this paper we present a topology preserving (genus 0) subdivision-based parametric deformable model that is used to extract the surfaces of the patella and tibial cartilages in the knee. These surfaces have minimal thickness in areas without cartilage. The algorithm inherently incorporates several desirable properties, including: shape based interpolation, sub-division remeshing and parameterization. To illustrate the usefulness of this approach, the surfaces and parameterizations of the patella cartilage are used to generate a 3D statistical shape model.

Experimental evidence for modifying the current physical model for ice accretion on aircraft surfaces

NASA Technical Reports Server (NTRS)

Olsen, W.; Walker, E.

1986-01-01

Closeup movies, still photographs, and other experimental data suggest that the current physical model for ice accretion needs significant modification. At aircraft airspeeds there was no flow of liquid over the surface of the ice after a short initial flow, even at barely subfreezing temperatures. Instead, there were very large stationary drops on the ice surface that lose water from their bottoms by freezing and replenish their liquid by catching the microscopic cloud droplets. This observation disagrees with the existing physical model, which assumes there is a thin liquid film continuously flowing over the ice surface. With no such flow, the freezing-fraction concept of the model fails when a mass balance is performed on the surface water. Rime ice does, as the model predicts, form when the air temperature is low enough to cause the cloud droplets to freeze almost immediately on impact. However, the characteristic shapes of horn-glaze ice or rime ice are primarily caused by the ice shape affecting the airflow locally and consequently the droplet catch and the resulting ice shape. Ice roughness greatly increases the heat transfer coefficient, stops the movement of drops along the surface, and may also affect the airflow initially and thereby the droplet catch. At high subreezing temperatures the initial flow and shedding of surface drops have a large effect on the ice shape. At the incipient freezing limit, no ice forms.

Investigating Evolutionary Conservation of Dendritic Cell Subset Identity and Functions

PubMed Central

Vu Manh, Thien-Phong; Bertho, Nicolas; Hosmalin, Anne; Schwartz-Cornil, Isabelle; Dalod, Marc

2015-01-01

Dendritic cells (DCs) were initially defined as mononuclear phagocytes with a dendritic morphology and an exquisite efficiency for naïve T-cell activation. DC encompass several subsets initially identified by their expression of specific cell surface molecules and later shown to excel in distinct functions and to develop under the instruction of different transcription factors or cytokines. Very few cell surface molecules are expressed in a specific manner on any immune cell type. Hence, to identify cell types, the sole use of a small number of cell surface markers in classical flow cytometry can be deceiving. Moreover, the markers currently used to define mononuclear phagocyte subsets vary depending on the tissue and animal species studied and even between laboratories. This has led to confusion in the definition of DC subset identity and in their attribution of specific functions. There is a strong need to identify a rigorous and consensus way to define mononuclear phagocyte subsets, with precise guidelines potentially applicable throughout tissues and species. We will discuss the advantages, drawbacks, and complementarities of different methodologies: cell surface phenotyping, ontogeny, functional characterization, and molecular profiling. We will advocate that gene expression profiling is a very rigorous, largely unbiased and accessible method to define the identity of mononuclear phagocyte subsets, which strengthens and refines surface phenotyping. It is uniquely powerful to yield new, experimentally testable, hypotheses on the ontogeny or functions of mononuclear phagocyte subsets, their molecular regulation, and their evolutionary conservation. We propose defining cell populations based on a combination of cell surface phenotyping, expression analysis of hallmark genes, and robust functional assays, in order to reach a consensus and integrate faster the huge but scattered knowledge accumulated by different laboratories on different cell types, organs, and species. PMID:26082777

Quantification of L-band InSAR coherence over volcanic areas using LiDAR and in situ measurements

NASA Astrophysics Data System (ADS)

Arab-Sedze, Melanie; Heggy, Essam; Bretard, Frederic; Berveiller, Daniel; Jacquemoud, Stephane

2014-07-01

Interferometric Synthetic Aperture Radar (InSAR) is a powerful tool to monitor large-scale ground deformation at active volcanoes. However, vegetation and pyroclastic deposits degrade the radar coherence and therefore the measurement of 3-D surface displacements. In this article, we explore the complementarity between ALOS - PALSAR coherence images, airborne LiDAR data and in situ measurements acquired over the Piton de La Fournaise volcano (Reunion Island, France) to determine the sources of errors that may affect repeat-pass InSAR measure- ments. We investigate three types of surfaces: terrains covered with vegetation, lava flows (a'a, pahoehoe or slabby pahoehoe lava flows) and pyroclastic deposits (lapilli). To explain the loss of coherence observed over the Dolomieu crater between 2008 and 2009, we first use laser altimetry data to map topographic variations. The LiDAR intensity, which depends on surface reflectance, also provides ancillary information about the potential sources of coherence loss. In addition, surface roughness and rock dielectric properties of each terrain have been determined in situ to better understand how electromagnetic waves interact with such media: rough and porous surfaces, such as the a'a lava flows, produce a higher coherence loss than smoother surfaces, such as the pahoehoe lava flows. Variations in dielectric properties suggest a higher penetration depth in pyroclasts than in lava flows at L-band frequency. Decorrelation over the lapilli is hence mainly caused by volumetric effects. Finally, a map of LAI (Leaf Area Index) produced using SPOT 5 imagery allows us to quantify the effect of vegeta- tion density: radar coherence is negatively correlated with LAI and is unreliable for values higher than 7.5.

Shape-related characteristics of age-related differences in subcortical structures.

PubMed

Madan, Christopher R

2018-01-11

With an increasing aging population, it is important to understand biological markers of aging. Subcortical volume is known to differ with age; additionally considering shape-related characteristics may provide a better index of age-related differences. Fractal dimensionality is more sensitive to age-related differences, but is borne out of mathematical principles, rather than neurobiological relevance. We considered four distinct measures of shape and how they relate to aging and fractal dimensionality: surface-to-volume ratio, sphericity, long-axis curvature, and surface texture. Structural MRIs from a combined sample of over 600 healthy adults were used to measure age-related differences in the structure of the thalamus, putamen, caudate, and hippocampus. For each, volume and fractal dimensionality were calculated, as well as four distinct shape measures. These measures were examined for their utility in explaining age-related variability in brain structure. The four shape measures were able to account for 80%-90% of the variance in fractal dimensionality. Of the distinct shape measures, surface-to-volume ratio was the most sensitive biomarker. Though volume is often used to characterize inter-individual differences in subcortical structures, our results demonstrate that additional measures can be useful complements. Our results indicate that shape characteristics are useful biological markers of aging.

A comparison of 3 wound measurement techniques: effects of pressure ulcer size and shape.

PubMed

Bilgin, Mehtap; Güneş, Ulkü Yapucu

2013-01-01

The aim of this study was to examine the levels of agreement among 3 techniques used in wound measurement comparing more spherical versus irregularly shaped wounds. The design of this study is evaluative research. Sixty-five consecutive patients with 80 pressure ulcers of various sizes referred from a university hospital in Izmir, Turkey, were evaluated. The 80 pressure ulcers identified on the 65 participants were divided into 2 groups based on pressure ulcer shape and wound surface area. Twenty-four of the 80 ulcers (30%) were characterized as irregularly shaped and greater than 10 cm. Fifty-six were regularly shaped (approximating a circle) and less than 10 cm. Pressure ulcer areas were measured using 3 techniques: measurement with a ruler (wound area was calculated by measuring and multiplying the greatest length by the greatest width perpendicular to the greatest length), wound tracing using graduated acetate paper, and digital planimetry. The level of agreement among the techniques was explored using the intraclass correlation coefficient (ICC). Strong agreement was observed among the techniques when assessing small, more regularly shaped wounds (ICC = 0.95). Modest agreement was achieved when measuring larger, irregularly shaped wounds (ICC = 0.70). Each of these techniques is adequate for measuring surface areas of smaller wounds with an approximately circular shape. Measurement of pressure ulcer area via the ruler method tended to overestimate surface area in larger and more irregularly shaped wounds when compared to acetate and digital planimetry. We recommend digital planimetry or acetate tracing for measurement of larger and more irregularly shaped pressure ulcers in the clinical setting.

Airfoil shape for flight at subsonic speeds

DOEpatents

Whitcomb, Richard T.

1976-01-01

An airfoil having an upper surface shaped to control flow accelerations and pressure distribution over the upper surface and to prevent separation of the boundary layer due to shock wave formulation at high subsonic speeds well above the critical Mach number. A highly cambered trailing edge section improves overall airfoil lifting efficiency.

A THz Tomography System for Arbitrarily Shaped Samples

NASA Astrophysics Data System (ADS)

Stübling, E.; Bauckhage, Y.; Jelli, E.; Fischer, B.; Globisch, B.; Schell, M.; Heinrich, A.; Balzer, J. C.; Koch, M.

2017-10-01

We combine a THz time-domain spectroscopy system with a robotic arm. With this scheme, the THz emitter and receiver can be positioned perpendicular and at defined distance to the sample surface. Our system allows the acquisition of reflection THz tomographic images of samples with an arbitrarily shaped surface.

Investigating the role of particle shape on colloid transport and retention in saturated porous media (Invited)

NASA Astrophysics Data System (ADS)

Li, Y.; Seymour, M.; Chen, G.; Su, C.

2013-12-01

Mechanistic understanding of the transport and retention of nanoparticles in porous media is essential both for environmental applications of nanotechnology and assessing the potential environmental impacts of engineered nanomaterials. Engineered and naturally occurring nanoparticles can be found in various shapes including rod-shape carbon nanotubes that have high aspect ratios. Although it is expected that nonspherical shape could play an important role on their transport and retention behaviors, current theoretical models for particle transport in porous media, however, are mostly based on spherical particle shape. In this work, the effect of particle shape on its transport and retention in porous media was evaluated by stretching carboxylate-modified fluorescent polystyrene spheres into rod shapes with aspect ratios of 2:1 and 4:1. Quartz crystal microbalance with dissipation experiments (QCM-D) were conducted to measure the deposition rates of spherical and rod-shaped nanoparticles to the collector (poly-L-lysine coated silica sensor) surface under favorable conditions. Under unfavorable conditions, the retention of nanoparticles in a microfluidic flow cell packed with glass beads was studied with the use of laser scanning cytometry (LSC). Under favorable conditions, the spherical particles displayed a significantly higher deposition rate compared with that of the rod-shaped particles. Theoretical analysis based on Smoluchowski-Levich approximation indicated that the rod-shaped particles largely counterbalance the attractive energies due to higher hydrodynamic forces and torques experienced during their transport and rotation. Under unfavorable conditions, significantly more attachment was observed for rod-shaped particles than spherical particles, and the attachment rate of the rod-shaped particles showed an increasing trend with the increase in injection volume. Rod-shaped particles were found to be less sensitive to the surface charge heterogeneity change than spherical particles. Increased attachment rate of rod-shaped particles was attributed to surface heterogeneity and possibly enhanced hydrophobicity during the stretching process.

Deconstructing Quinoline-Class Antimalarials to Identify Fundamental Physicochemical Properties of Beta-Hematin Crystal Growth Inhibitors.

PubMed

Olafson, Katy N; Nguyen, Tam Q; Vekilov, Peter G; Rimer, Jeffrey D

2017-10-04

A versatile approach to control crystallization involves the use of modifiers, which are additives that interact with crystal surfaces and alter their growth rates. Elucidating a modifier's binding specificity to anisotropic crystal surfaces is a ubiquitous challenge that is critical to their design. In this study, we select hematin, a byproduct of malaria parasites, as a model system to examine the complementarity of modifiers (i.e., antimalarial drugs) to β-hematin crystal surfaces. We divide two antimalarials, chloroquine and amodiaquine, into segments consisting of a quinoline base, common to both drugs, and side chains that differentiate their modes of action. Using a combination of scanning probe microscopy, bulk crystallization, and analytical techniques, we show that the base and side chain work synergistically to reduce the rate of hematin crystallization. In contrast to general observations that modifiers retain their function upon segmentation, we show that the constituents do not act as modifiers. A systematic study of quinoline isomers and analogues shows how subtle rearrangement and removal of functional moieties can create effective constituents from previously ineffective modifiers, along with tuning their inhibitory modes of action. These findings highlight the importance of specific functional moieties in drug compounds, leading to an improved understanding of modifier-crystal interactions that could prove to be applicable to the design of new antimalarials. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Free energy landscapes of encounter complexes in protein-protein association.

PubMed

Camacho, C J; Weng, Z; Vajda, S; DeLisi, C

1999-03-01

We report the computer generation of a high-density map of the thermodynamic properties of the diffusion-accessible encounter conformations of four receptor-ligand protein pairs, and use it to study the electrostatic and desolvation components of the free energy of association. Encounter complex conformations are generated by sampling the translational/rotational space of the ligand around the receptor, both at 5-A and zero surface-to-surface separations. We find that partial desolvation is always an important effect, and it becomes dominant for complexes in which one of the reactants is neutral or weakly charged. The interaction provides a slowly varying attractive force over a small but significant region of the molecular surface. In complexes with no strong charge complementarity this region surrounds the binding site, and the orientation of the ligand in the encounter conformation with the lowest desolvation free energy is similar to the one observed in the fully formed complex. Complexes with strong opposite charges exhibit two types of behavior. In the first group, represented by barnase/barstar, electrostatics exerts strong orientational steering toward the binding site, and desolvation provides some added adhesion within the local region of low electrostatic energy. In the second group, represented by the complex of kallikrein and pancreatic trypsin inhibitor, the overall stability results from the rather nonspecific electrostatic attraction, whereas the affinity toward the binding region is determined by desolvation interactions.

Plasma immersion ion implantation of polyurethane shape memory polymer: Surface properties and protein immobilization

NASA Astrophysics Data System (ADS)

Cheng, Xinying; Kondyurin, Alexey; Bao, Shisan; Bilek, Marcela M. M.; Ye, Lin

2017-09-01

Polyurethane-type shape memory polymers (SMPU) are promising biomedical implant materials due to their ability to recover to a predetermined shape from a temporary shape induced by thermal activation close to human body temperature and their advantageous mechanical properties including large recovery strains and low recovery stresses. Plasma Immersion Ion Implantation (PIII) is a surface modification process using energetic ions that generates radicals in polymer surfaces leading to carbonisation and oxidation and the ability to covalently immobilise proteins without the need for wet chemistry. Here we show that PIII treatment of SMPU significantly enhances its bioactivity making SMPU suitable for applications in permanent implantable biomedical devices. Scanning Electron Microscopy (SEM), contact angle measurements, surface energy measurements, attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS) were used to characterise the PIII modified surface, including its after treatment aging kinetics and its capability to covalently immobilise protein directly from solution. The results show a substantial improvement in wettability and dramatic changes of surface chemical composition dependent on treatment duration, due to the generation of radicals and subsequent oxidation. The SMPU surface, PIII treated for 200s, achieved a saturated level of covalently immobilized protein indicating that a full monolayer coverage was achieved. We conclude that PIII is a promising and efficient surface modification method to enhance the biocompatibility of SMPU for use in medical applications that demand bioactivity for tissue integration and stability in vivo.

Conveying the 3D Shape of Transparent Surfaces Via Texture

NASA Technical Reports Server (NTRS)

Interrante, Victoria; Fuchs, Henry; Pizer, Stephen

1997-01-01

Transparency can be a useful device for depicting multiple overlapping surfaces in a single image. The challenge is to render the transparent surfaces in such a way that their three-dimensional shape can be readily understood and their depth distance from underlying structures clearly perceived. This paper describes our investigations into the use of sparsely-distributed discrete, opaque texture as an 'artistic device' for more explicitly indicating the relative depth of a transparent surface and for communicating the essential features of its 3D shape in an intuitively meaningful and minimally occluding way. The driving application for this work is the visualization of layered surfaces in radiation therapy treatment planning data, and the technique is illustrated on transparent isointensity surfaces of radiation dose. We describe the perceptual motivation and artistic inspiration for defining a stroke texture that is locally oriented in the direction of greatest normal curvature (and in which individual strokes are of a length proportional to the magnitude of the curvature in the direction they indicate), and discuss several alternative methods for applying this texture to isointensity surfaces defined in a volume. We propose an experimental paradigm for objectively measuring observers' ability to judge the shape and depth of a layered transparent surface, in the course of a task relevant to the needs of radiotherapy treatment planning, and use this paradigm to evaluate the practical effectiveness of our approach through a controlled observer experiment based on images generated from actual clinical data.

Insight of DFT and ab initio atomistic thermodynamics on the surface stability and morphology of In2O3

NASA Astrophysics Data System (ADS)

Zhang, Minhua; Wang, Wenyi; Chen, Yifei

2018-03-01

In2O3 catalysts show remarkable activity and selectivity in methanol synthesis from CO2 hydrogenation. In order to get insight into the surface stability of this catalyst, density functional theory and ab initio atomistic thermodynamics method were used to investigate the surface free energies of various facets as a function of oxygen chemical potential, as well as the influences of temperature, pressure and gas compositions. The results show that the (111) facet presents lowest surface free energy under oxygen-rich condition, while the indium-terminated (100) facet is the most stable one under oxygen-lean condition. Moreover, we applied Wulff construction to determine the equilibrium shape of In2O3 with different oxygen chemical potentials. The equilibrium shape under oxygen-lean condition is cubic, which only expose (100) facet, while, the equilibrium shape under oxygen-rich condition is octahedron, which only expose (111) facet. Meanwhile, the results agree well with what is observed experimentally. It is further predicted that Wulff shape of In2O3 exists in a truncated octahedron morphology in which the (100) surface becomes predominant plane under CO2 hydrogenation reaction conditions.

Method for Molding Planar Billet of Thermally Insulative Material Into Predetermined Non-Planar Shape

NASA Technical Reports Server (NTRS)

Kolodziej, Paul (Inventor); Carroll, Joe A. (Inventor); Smith, Dane (Inventor)

1998-01-01

A method and apparatus is discussed for molding thermal protection system (TPS) tiles for spacecraft. The apparatus and method include a bottom mold member defining a mold surface shaped like a surface of the spacecraft, e.g., the nose cap of wing leading edge, sought to be thermally protected. A flat billet of TPS material is positioned over the periphery of the mold surface, and a hollow weight element that has a periphery configured like the periphery of the mold surface is positioned on the billet. The billet is then heated in accordance with a predetermined heating regime, and during the heating process the weight of the weight element causes the billet to deform to assume the shape of the mold surface. If desired, a TUFI coating is impregnated into the billet prior to heating, and the coating is sintered to the billet during heating. After heating, a composite matrix material, e.g., a graphite or fiberglass cloth which is impregnated with epoxy or polimide, is bonded to the now-shaped tile to support the tile. Silicone can then be impregnated into the now-formed tile to provide flexibility of the tile.

Attempts to locate residues in complementarity-determining regions of antibody combining sites that make contact with antigen.

PubMed

Kabat, E A; Wu, T T; Bilofsky, H

1976-02-01

From collected data on variable region sequences of heavy chains of immunoglobulins, the probability of random associations of any two amino-acid residues in the complementarity-determining segments was computed, and pairs of residues occurring significantly more frequently than expected were selected by computer. Significant associations between Phe 32 and Tyr 33, Phe 32 and Glu 35, and Tyr 33 and Glu 35 were found in six proteins, all of which were mouse myeloma proteins which bound phosphorylcholine (= phosphocholine). From the x-ray structure of McPC603, Tyr 33 and Glu 35 are contacting residues; a seventh phosphorylcholine-binding mouse myeloma protein also contained Phe 32 and Tyr 33 but position 35 had only been determined as Glx and thus this position had not been selected. Met 34 occurred in all seven phosphorylcholine-binding myeoma proteins but was also present at this position in 29 other proteins and thus was not selected; it is seen in the x-ray structure not to be a contacting residue. The role of Phe 32 is not obvious but it could have some conformational influence. A human phosphorylcholine-binding myeloma protien also had Phe, Tyr, and Met at positions 32, 33, and 34, but had Asp instead of Glu at position 35 and showed a lower binding constant. The ability to use sequence data to locate residues in complementarity-determing segments making contact with antigenic determinants and those playing essentially a structural role would contribute substantially to the understanding of antibody specificity.

Phosphorus acquisition by citrate- and phytase-exuding Nicotiana tabacum plant mixtures depends on soil phosphorus availability and root intermingling.

PubMed

Giles, Courtney D; Richardson, Alan E; Cade-Menun, Barbara J; Mezeli, Malika M; Brown, Lawrie K; Menezes-Blackburn, Daniel; Darch, Tegan; Blackwell, Martin Sa; Shand, Charles A; Stutter, Marc I; Wendler, Renate; Cooper, Patricia; Lumsdon, David G; Wearing, Catherine; Zhang, Hao; Haygarth, Philip M; George, Timothy S

2018-03-02

Citrate and phytase root exudates contribute to improved phosphorus (P) acquisition efficiency in Nicotiana tabacum (tobacco) when both exudates are produced in a P deficient soil. To test the importance of root intermingling in the interaction of citrate and phytase exudates, Nicotiana tabacum plant-lines with constitutive expression of heterologous citrate (Cit) or fungal phytase (Phy) exudation traits were grown under two root treatments (roots separated or intermingled) and in two soils with contrasting soil P availability. Complementarity of plant mixtures varying in citrate efflux rate and mobility of the expressed phytase in soil was determined based on plant biomass and P accumulation. Soil P composition was evaluated using solution 31 P NMR spectroscopy. In the soil with limited available P, positive complementarity occurred in Cit+Phy mixtures with roots intermingled. Root separation eliminated positive interactions in mixtures expressing the less mobile phytase (Aspergillus niger PhyA) whereas positive complementarity persisted in mixtures that expressed the more mobile phytase (Peniophora lycii PhyA). Soils from Cit+Phy mixtures contained less inorganic P and more organic P compared to monocultures. Exudate-specific strategies for the acquisition of soil P were most effective in P-limited soil and depended on citrate efflux rate and the relative mobility of the expressed phytase in soil. Plant growth and soil P utilization in plant systems with complementary exudation strategies are expected to be greatest where exudates persist in soil and are expressed synchronously in space and time. This article is protected by copyright. All rights reserved.

Ant-mediated ecosystem processes are driven by trophic community structure but mainly by the environment.

PubMed

Salas-Lopez, Alex; Mickal, Houadria; Menzel, Florian; Orivel, Jérôme

2017-01-01

The diversity and functional identity of organisms are known to be relevant to the maintenance of ecosystem processes but can be variable in different environments. Particularly, it is uncertain whether ecosystem processes are driven by complementary effects or by dominant groups of species. We investigated how community structure (i.e., the diversity and relative abundance of biological entities) explains the community-level contribution of Neotropical ant communities to different ecosystem processes in different environments. Ants were attracted with food resources representing six ant-mediated ecosystem processes in four environments: ground and vegetation strata in cropland and forest habitats. The exploitation frequencies of the baits were used to calculate the taxonomic and trophic structures of ant communities and their contribution to ecosystem processes considered individually or in combination (i.e., multifunctionality). We then investigated whether community structure variables could predict ecosystem processes and whether such relationships were affected by the environment. We found that forests presented a greater biodiversity and trophic complementarity and lower dominance than croplands, but this did not affect ecosystem processes. In contrast, trophic complementarity was greater on the ground than on vegetation and was followed by greater resource exploitation levels. Although ant participation in ecosystem processes can be predicted by means of trophic-based indices, we found that variations in community structure and performance in ecosystem processes were best explained by environment. We conclude that determining the extent to which the dominance and complementarity of communities affect ecosystem processes in different environments requires a better understanding of resource availability to different species.

Improving protein-protein interaction prediction using evolutionary information from low-quality MSAs.

PubMed

Várnai, Csilla; Burkoff, Nikolas S; Wild, David L

2017-01-01

Evolutionary information stored in multiple sequence alignments (MSAs) has been used to identify the interaction interface of protein complexes, by measuring either co-conservation or co-mutation of amino acid residues across the interface. Recently, maximum entropy related correlated mutation measures (CMMs) such as direct information, decoupling direct from indirect interactions, have been developed to identify residue pairs interacting across the protein complex interface. These studies have focussed on carefully selected protein complexes with large, good-quality MSAs. In this work, we study protein complexes with a more typical MSA consisting of fewer than 400 sequences, using a set of 79 intramolecular protein complexes. Using a maximum entropy based CMM at the residue level, we develop an interface level CMM score to be used in re-ranking docking decoys. We demonstrate that our interface level CMM score compares favourably to the complementarity trace score, an evolutionary information-based score measuring co-conservation, when combined with the number of interface residues, a knowledge-based potential and the variability score of individual amino acid sites. We also demonstrate, that, since co-mutation and co-complementarity in the MSA contain orthogonal information, the best prediction performance using evolutionary information can be achieved by combining the co-mutation information of the CMM with co-conservation information of a complementarity trace score, predicting a near-native structure as the top prediction for 41% of the dataset. The method presented is not restricted to small MSAs, and will likely improve interface prediction also for complexes with large and good-quality MSAs.